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Sample records for caracol helix aspersa

  1. Efecto de un suplemento con humus sobre el crecimiento, digestibilidad y eficiencia nutricional en el caracol Helix aspersa juvenil

    OpenAIRE

    García Martínez, Antón Rafael; Acero de la Cruz, Raquel; Perea Muñoz, José Manuel; Peña Blanco, Francisco; Gómez-Castro, A.G.

    2008-01-01

    El humus es importante en la dieta de Helix aspersa y de otras especies de caracoles comestibles aunque su contribución nutricional es poco conocida. En el presente trabajo se evalúa el efecto de un suplemento con humus sobre el crecimiento, eficiencia nutricional y digestibilidad del caracol H. aspersa durante la fase juvenil. El experimento se hizo en laboratorio usando un diseño completamente al azar con dos tratamientos (dietas) con diez repeticiones de veinte caracol...

  2. Lead reduces shell mass in juvenile garden snails (Helix aspersa)

    International Nuclear Information System (INIS)

    A high Pb diet causes differential depression of juvenile shell mass in populations of Helix. - In an earlier paper examining inherited tolerance to Pb, the shell growth of laboratory-bred offspring of Helix aspersa from contaminated sites was compared with that of juveniles from naieve populations on dosed and undosed diets. Eight-week-old snails were fed either 500 μg g-1 Pb or a control food in competitive trials between two populations. In the first series of trials, a parental history of exposure to Pb did not confer any advantage to either of two populations (BI and MI) competing with a naieve population (LE), whether Pb was present in the diet or not. However, in the analysis of their metal concentrations reported here, LE are found to retain higher levels of Pb in the soft tissues than either BI or MI. Compared to their siblings on the unleaded diet, dosed LE and BI juveniles had lower soft tissue concentrations of Ca and Mg. Although the growth in shell height is unaffected by diet, LE and BI juveniles build lighter shells on the Pb-dosed diet, achieving around 75% of the shell mass of their controls. In contrast, the shell weights of dosed MI juveniles are depressed by only 15% and show no change in the essential metal concentrations of their soft tissues. A second experiment using five populations fed only the dosed food show that the shell weight/soft tissue weight ratios are comparable to the dosed snails of the previous experiment. Building a lighter shell thus appears to be the common response of all Helix populations to a high Pb diet, at least amongst juveniles. The reduction in its mass means that less Ca and Mg is added to the shell and, along with the lowered soft tissue concentrations observed in some populations, may be a consequence of an increased effort to excrete Pb. The possibility that the MI population shows a genotypic adaptation, perhaps as some form of modification of its Ca metabolism, is briefly discussed

  3. Trace metallic elements in Helix aspersa terrestrial snails of a semiarid ecosystem

    International Nuclear Information System (INIS)

    The concentration of some major elements and traces in soil samples and of Helix aspersa eatable terrestrial snails were analysed at the Radioactive Wastes Storage Center (CADER) and in other reference sites. The methodology includes the use of an atomic absorption spectrophotometer, an X-ray fluorescence equipment and an Icp-mass spectroscope. The concentrations of some toxic elements (Ba, Cd, Cr, Ni, Pb and V) in the soft tissue of the snails were greater than the toxic levels reported in the literature for such trace elements. The snails compared with another wild eatable foods present transfer coefficients soil-snail high relatively. (Author)

  4. Effect of microclimatic conditions on the reproductive behavior of the Helix aspersa

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    Hugo Ángel Fernández Cabrera

    2013-12-01

    Full Text Available The aim of this study was to evaluate the effect of microclimatic conditions (temperature and relative humidity on the reproduction of land snails (Helix aspersa. For this, incubation’s chambers were conditioned with different four levels of relative humidity and temperature. Posture, length of incubation and hatching rate were evaluated. It was concluded that 81.0 ± 0.63% of relative humidity and 23.9 ± 0.39 °C of temperature the best results are achieved.

  5. Evaluation of the genotoxic potential of soil contaminated with mineral coal tailings on snail Helix aspersa.

    Science.gov (United States)

    de Souza, Melissa Rosa; da Silva, Fernanda Rabaioli; de Souza, Claudia Telles; Niekraszewicz, Liana; Dias, Johnny Ferraz; Premoli, Suziane; Corrêa, Dione Silva; Soares, Mariana do Couto; Marroni, Norma Possa; Morgam-Martins, Maria Isabel; da Silva, Juliana

    2015-11-01

    Coal remains an important source of energy, although the fuel is a greater environmental pollutant. Coal is a mixture of several chemicals, especially inorganic elements and polycyclic aromatic hydrocarbons (PAH). Many of these compounds have mutagenic and carcinogenic effects on organisms exposed to this mineral. In the town of Charqueadas (Brazil), the tailings from mining were used for landfill in the lower areas of the town, and the consequence is the formation of large deposits of this material. The purpose of this study was to evaluate the genotoxic potential of soil samples contaminated by coal waste in different sites at Charqueadas, using the land snail Helix aspersa as a biomonitor organism. Thirty terrestrial snails were exposed to different treatments: 20 were exposed to the soil from two different sites in Charqueadas (site 1 and 2; 10 in each group) and 10 non-exposed (control group). Hemolymph cells were collected after 24h, 5days and 7days of exposure and comet assay, micronucleus test, oxidative stress tests were performed. Furthermore, this study quantified the inorganic elements present in soil samples by the PIXE technique and polycyclic aromatic hydrocarbons (PAH) by HPLC. This evaluation shows that, in general, soils from sites in Charqueadas, demonstrated a genotoxic effect associated with increased oxidative stress, inorganic and PAH content. These results demonstrate that the coal pyrite tailings from Charqueadas are potentially genotoxic and that H. aspersa is confirmed to be a sensitive instrument for risk assessment of environmental pollution. PMID:26295689

  6. In vitro metabolism of androstenedione and identification of endogenous steroids in Helix aspersa

    International Nuclear Information System (INIS)

    In vitro metabolism of androstenedione in gonads of juvenile and adult Helix aspersa has been investigated. The conversion of [3H]androstenedione into testosterone, 5 alpha-dihydrotestosterone, androsterone, and estriol was demonstrated. In juvenile animals testosterone (59.8%) is the major metabolite whereas in adult animals androsterone (18.8%) is. The following endogenous steroids have been identified by gas chromatography-mass spectrometry in adult gonads: androsterone, dehydroepiandrosterone, androstenedione, 3 alpha-androstanediol, estrone, estradiol-17 beta, and estriol. The levels of testosterone, 5 alpha-dihydrotestosterone, androstenedione, and progesterone have been measured by RIAs in gonads and hemolymph. Their levels vary with the physiological stage: the gonadal and circulating levels of testosterone decrease with the sexual maturation whereas the 5 alpha-dihydrotestosterone increases. These differences observed in metabolism and in level of steroids between the juvenile and the adult snails allow us to suppose that these steroids have a biological role

  7. Studies on the Edible Terrestrial Snails Helix aspersa Muller Food Conversion Ratio in a Confined Microclimate System

    OpenAIRE

    Adrian Toader-Williams; Aurel Şara

    2010-01-01

    Terrestrial edible snail breeding is an agricultural activity that finds itself at pioneering stage in Romania. One of the species used in snail farming is Helix aspersa Muller. In order to accelerate their growth, farmers feed the snails with pumpkins as well as concentrated forage consisting of mix of flours to which calcium carbonate is added in order to supplement snails need for shell’s development. In a controlled microclimate environment we measured the average growth of six weeks old ...

  8. Use of the land snail Helix aspersa for monitoring heavy metal soil contamination in Northeast Algeria.

    Science.gov (United States)

    Larba, R; Soltani, N

    2014-08-01

    The objective of this study was to investigate the impact of anthropogenic activities on soil quality using the land snail Helix aspersa as a bioindicator. Soil samples and snails were collected from several sites in Northeast Algeria during the summer and winter of 2010. All of the sites were chosen due to their proximity to industrial factories-a potential source of soil pollution via heavy metal contamination. The concentration of heavy metals (Pb, Cd, Mn, and Fe) in soil samples was analyzed using atomic absorption spectrophotometry. Activity levels of glutathione S-transferase (GST) and acetylcholinesterase (AChE), indicators of oxidative stress and neurotoxicity, respectively, were measured in snails collected from each site. GST and AChE activity were found to vary between sites and by season. The highest levels of GST activity were registered during the summer at sites closest to potential sources of pollution. AChE activity levels also peaked during the summer with the highest values recorded at the site in El Hadjar. These increased levels of bioindicative stress response correlated with increasing metal concentration in soil samples collected at each site. PMID:24687691

  9. Pro-oxidant effects of extremely low frequency electromagnetic fields in the land snail Helix aspersa.

    Science.gov (United States)

    Regoli, Francesco; Gorbi, Stefania; Machella, Nicola; Tedesco, Sara; Benedetti, Maura; Bocchetti, Raffaella; Notti, Alessandra; Fattorini, Daniele; Piva, Francesco; Principato, Giovanni

    2005-12-15

    Pro-oxidant effects of extremely low frequency (ELF) 50-Hz magnetic fields were investigated in the land snail Helix aspersa exposed both in short-term laboratory treatments and under field conditions by maintaining the organisms in the proximity of a power line for up to 2 months. Oxidative perturbations were investigated as individual antioxidants (catalase, glutathione reductase, glutathione S-transferases, and total glutathione) and total scavenging capacity toward peroxyl radicals and hydroxyl radicals. Accumulation of lipid peroxidation products, destabilization of lysosomal membranes, and loss of DNA integrity were also evaluated as markers of cell damage. The overall results indicated an oxidative challenge caused by ELF magnetic fields with particularly prompt and sensitive responses for catalase, glutathione reductase, and the overall capability to neutralize peroxyl radicals. Cell injuries occurred to different extents according to duration and intensity of electromagnetic exposure and confirmed complex cause-effect relationships between pro-oxidant factors, efficiency of antioxidant defenses, and the onset of oxidative toxicity. This study highlights the importance of a multimarker approach for detecting a wide panel of biological responses, the necessity of investigating the long-term effects of early oxidative responses, and the role of ELF in enhancing susceptibility to other forms of pathologies or diseases. PMID:16298687

  10. Genotoxic effect of polycyclic aromatic hydrocarbons in the metropolitan area of Porto Alegre, Brazil, evaluated by Helix aspersa (Mueller, 1774)

    Energy Technology Data Exchange (ETDEWEB)

    Ianistcki, M. [Laboratorio de Genetica Toxicologica, Department of Biology, ULBRA, Av. Farroupilha 8001, Pr. 14/Sala 218, Bairro Sao Jose, CEP 92425-900 Canoas, RS (Brazil); Dallarosa, J. [Laboratorio de Ecologia, UFRGS (Brazil); Sauer, C.; Teixeira, C.E. [Fundacao Estadual de Protecao Ambiental Henrique Luis Roessler, FEPAM, RS (Brazil); Silva, J. da, E-mail: juliana.silva@ulbra.b [Laboratorio de Genetica Toxicologica, Department of Biology, ULBRA, Av. Farroupilha 8001, Pr. 14/Sala 218, Bairro Sao Jose, CEP 92425-900 Canoas, RS (Brazil)

    2009-07-15

    The purpose of this study was to biomonitor metropolitan areas of Porto Alegre (Brazil) for PAHs associated with atmospheric particles and check their effects on the DNA of the land mollusk Helix aspersa. The sampling sites are located in an urban area with heavy traffic: (i) Canoas, (ii) Sapucaia do Sul, and (iii) FIERGS/Porto Alegre. The samples were collected during a continuous period of 24 hours during 15 days using Stacked Filter Units (SFU) on polycarbonate filters (two separated size fractions: PM{sub 10-2.5} and PM{sub <2.5}). The concentrations of 16 major PAHs were determined according to EPA. Comet assay on H. aspersa hemolymph cells was chosen for genotoxicity evaluation. This evaluation shows that, in general, the smaller PM-size fractions (PM{sub <2.5}) have the highest genotoxicity and contain higher concentrations of extractable organic matter. In addition, associations between chemical characteristics and PM carcinogenicity tend to be stronger for the smaller PM-size fractions. - DNA damage in H. aspersa exposed to atmospheric particulate in Metropolitan Area of Porto Alegre demonstrated association with PAHs in the fine filter (PM{sub <2.5}).

  11. Genotoxic effect of polycyclic aromatic hydrocarbons in the metropolitan area of Porto Alegre, Brazil, evaluated by Helix aspersa (Mueller, 1774)

    International Nuclear Information System (INIS)

    The purpose of this study was to biomonitor metropolitan areas of Porto Alegre (Brazil) for PAHs associated with atmospheric particles and check their effects on the DNA of the land mollusk Helix aspersa. The sampling sites are located in an urban area with heavy traffic: (i) Canoas, (ii) Sapucaia do Sul, and (iii) FIERGS/Porto Alegre. The samples were collected during a continuous period of 24 hours during 15 days using Stacked Filter Units (SFU) on polycarbonate filters (two separated size fractions: PM10-2.5 and PM). The concentrations of 16 major PAHs were determined according to EPA. Comet assay on H. aspersa hemolymph cells was chosen for genotoxicity evaluation. This evaluation shows that, in general, the smaller PM-size fractions (PM) have the highest genotoxicity and contain higher concentrations of extractable organic matter. In addition, associations between chemical characteristics and PM carcinogenicity tend to be stronger for the smaller PM-size fractions. - DNA damage in H. aspersa exposed to atmospheric particulate in Metropolitan Area of Porto Alegre demonstrated association with PAHs in the fine filter (PM).

  12. Evaluation of different methods for the experimental infection of the land snail Helix aspersa with Aelurostrongylus abstrusus lungworm.

    Science.gov (United States)

    Napoli, Ettore; Falsone, Luigi; Gaglio, Gabriella; Colella, Vito; Otranto, Domenico; Giannetto, Salvatore; Brianti, Emanuele

    2016-07-30

    The laboratory maintenance of parasitic life cycles is crucial to support research in many fields of parasitology. The land snail Helix aspersa (syn. Cornu aspersum), an intermediate host of feline lungworms Aelurostrongylus abstrusus and Troglostrongylus brevior, is adopted to produce infective stages of those nematodes in laboratory condition. The aim of this study was to compare the most common methods of experimental infection of H. aspersa with first stage larvae (L1) of A. abstrusus (i.e., contact of the snail foot with the L1) with the injection of these larvae in the foot of the snail, instrumental to reduce the infection time and to maximize the output of third-stage larvae (L3). Three groups (i.e., A, B, C) of 15 H. aspersa snails were infected with L1 of A. abstrusus (n=250 for each snail), whereas a fourth group (group D) was not infected (control). Snails were individually placed for 48h on a microfilm containing L1 (group A), on a potato slice previously irrigated with a suspension of L1 (group B), or they were inoculated by injection of L1 in the posterior-ventral portion of the foot (group C). Eighteen days after the infection all snails were analyzed and tissues were digested to recover L3. No difference in mortality rate was recorded among snail groups and the mean number of retrieved L3 was significantly larger in group C (71.5±52.9) compared to group B (38.2±44.9; p=0.0161) and group A (19±23.3; p<0.0001). The injection of A. abstrusus L1 in the foot of H. aspersa proved to be a fast, easy to apply and effective method, resulting in the largest number of infective larvae retrieved. PMID:27369568

  13. Studies on the Edible Terrestrial Snails Helix aspersa Muller Food Conversion Ratio in a Confined Microclimate System

    Directory of Open Access Journals (Sweden)

    Adrian Toader-Williams

    2010-05-01

    Full Text Available Terrestrial edible snail breeding is an agricultural activity that finds itself at pioneering stage in Romania. One of the species used in snail farming is Helix aspersa Muller. In order to accelerate their growth, farmers feed the snails with pumpkins as well as concentrated forage consisting of mix of flours to which calcium carbonate is added in order to supplement snails need for shell’s development. In a controlled microclimate environment we measured the average growth of six weeks old Helix aspersa Muller snails placed in four different plastic enclosures. The consumption of different type of foods within 24 hours period was measured. The wheat (60%, corn flour (20% and calcium carbonate (20% mix had a superior food conversion ratio (FCR of 4.80, whereas the second FCR registered 6.04 in the case of 53% pumpkin and 47% flour mix served in the same time followed by the pure fresh vegetable mix accounting for a FCR of 8.00 and by 19.02 when only the pumpkin has been administrated as meal. During the experiments the snails did not have access to soil, being known that soil is an integral part of their diet.

  14. Exigência de proteína para o escargot francês, Helix aspersa maxima em fase de crescimento Protein requirement for Helix aspersa maxima during the growing phase

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    Claudemir Martins Soares

    2002-04-01

    Full Text Available Com o objetivo de determinar a exigência de proteína bruta (PB em dietas para o "escargot" francês (Helix aspersa maxima, 200 animais com peso inicial médio de 2,00 g foram distribuídos em um experimento inteiramente casualizado com quatro tratamentos [12,00; 15,00; 18,00 e 21,00% de PB] e cinco repetições, com 10 animais por unidade experimental, durante 90 dias. Foi observado efeito quadrático dos teores de PB sobre o peso final médio, a conversão alimentar, taxa de eficiência protéica, porcentagem de concha e rendimento de carcaça com os melhores valores nos teores de 16,23; 16,95; 14,79; 16,07 e 15,87% de PB, respectivamente. A taxa de sobrevivência não foi afetada pelos teores de PB utilizados. Concluiu-se que a exigência de PB em dietas para "escargot" francês é de 16,23%.Aiming to determinate the dietary crude protein (CP requirements for Helix aspersa maxima snail, 200 animals, with average initial weight of 2.00 g were used, and assigned to a completely randomized design with four treatments [12.00, 15.00, 18.00, and 21.00% CP] and five replicates of 10 animals per experimental unit, during a period of 90 days. It was observed a quadratic effect of CP levels on final mean weight, feed conversion, protein efficiency rate, shell percentage and carcass yield with the best values for 16.23, 16.95, 14.79, 16.07, and 15.87% CP, respectively. The CP levels did not affect the survival rate. It may be concluded that the requirement of CP on diets for the Helix aspersa maxima is 16.23%.

  15. Efeito da endogamia sobre a sobrevivência e a longevidade no escargot da espécie Helix aspersa Effect of inbreeding on viability and longevity of edible snail Helix aspersa

    Directory of Open Access Journals (Sweden)

    E.D.R. Soares

    2010-06-01

    Full Text Available Estudou-se o efeito da endogamia sobre as características sobrevivência (intervalos de 0-30; 30-60; 60-90 e 90-120 dias e longevidade do escargot da espécie Helix aspersa em três gerações consecutivas de acasalamentos entre irmãos perfeitos. Os animais foram criados em laboratório com temperatura entre 20 e 25ºC e umidade relativa entre 70 a 90%. O menor percentual de sobrevivência ocorreu no primeiro intervalo, mas, com o aumento da endogamia, observou-se diminuição na sobrevivência nos quatro intervalos testados. A longevidade média foi de 314 e 306 dias para as gerações um e três, respectivamente, não tendo sido observados animais em hibernação. O estudo de simulação para o caráter sobrevivência, em função do coeficiente de endogamia, indicou que se deve iniciar uma criação com, pelo menos, 100 reprodutores não aparentados.The effect of inbreeding on longevity and viability (intervals of 0-30, 30-60, 60-90, and 90-120 days of birth in three consecutive generations of full sibs of escargot Helix aspersa raised under laboratory conditions (20-25ºC temperature; 70-90% relative humidity was studied. Inbreeding effects decreased the viability for all the studied intervals. The longevity means were 314 and 306 days, respectively to the first and third generations. Hibernating animals were not observed. Population size of at least 100 non-related mating escargots replaced after 10 generations to avoid inbreeding effect is recommended.

  16. Teores de cálcio em rações para o escargot francês Helix aspersa máxima em fase de crescimento - DOI: 10.4025/actascibiolsci.v27i1.1361 Calcium levels in escargot Helix aspersa maxima diets in growth phase - DOI: 10.4025/actascibiolsci.v27i1.1361

    Directory of Open Access Journals (Sweden)

    Giovani Sampaio Gonçalves

    2005-03-01

    Full Text Available Com o objetivo de avaliar o efeito de diferentes teores de cálcio em rações para o escargot francês Helix aspersa máxima na fase de crescimento foram utilizados 160 animais, com peso vivo inicial médio de 6,00 g, distribuídos em um delineamento inteiramente casualizado com quatro tratamentos (2,00; 3,00; 4,00 e 5,00 % de cálcio e quatro repetições. Foram observados efeito linear positivo (p Helix aspersa máxima na fase de crescimento, e que dentre as rações estudadas a mais indicada é a com 5% de cálcioThe experiment was carried out to evaluate the effects of different calcium levels in diets for Helix aspersa maxima in growth phase. One hundred and sixty animals were used with initial mean weight of 6.00 g distributed in a completely randomized design with four treatments (2.00, 3.00, 4.00 and 5.00% of calcium and four replicates. Linear improve (p Helix aspersa maxima in growth phase and that the diet with 5.00% of calcium is highly recommended

  17. Variabilidade genética em algumas criações comerciais brasileiras de escargots (Helix aspersa, Müller, 1774 Genetic variation at eight isoenzyme loci in subpopulations of the edible snail (Helix aspersa, Müller, 1774

    Directory of Open Access Journals (Sweden)

    B.F. Vasconcellos

    2006-04-01

    Full Text Available Descreveram-se os marcadores isoenzimáticos e estimou-se a variabilidade genética de 20 subpopulações brasileiras de escargots (Helix aspersa. O estudo dos oito locos foi feito por eletroforese em gel de amido, em amostras com 30 indivíduos cada, obtidas em criatórios dos estados de Santa Catarina, São Paulo e Rio de Janeiro (uma, duas e 17 amostras, respectivamente. Observou-se polimorfismo nos locos das enzimas LAP, 6-PGD, PEP 2, PEP 1 e MDH, com três alelos nos três primeiros locos e dois nos demais. Os locos da ME, da SOD e da PGI apresentaram-se monomórficos. As freqüências gênicas de sete amostras ajustaram-se ao modelo de Hardy-Weinberg (PIn order to assess genetic variability in subpopulations of Helix aspersa, eight isoenzyme loci in 30 individuals in each of 20 subpopulations, obtained from breeders in Santa Catarina (1, São Paulo(2 and Rio de Janeiro (17 states of Brazil, were examined. Polymorphic loci included LAP, 6-PGD, PEP 2, PEP 1 and MDH, with three alelles at each of the first three loci and two at each of the others. The ME, SOD and PGI loci were monomorphic. Gene frequencies in 7 of 20 subpopulations were consistent with the Hardy-Wienberg equilibrium (P<0.05, and 6 were consistent with Wright model, indicating that these subpopulations did not meet requirements for genotypic equilibrium to be achieved. Despite the fact that some F values were high, F IS and F IT were not significantly different from zero (P³0.05. Although small, the F ST value (0.0485 was significant, suggesting small differences among populations. Most of the low genetic variation at isoenzyme loci was observed within subpopulations rather than among subpopulations, suggesting a small genetic basis for these samples. Estimated genetic distances among pairs of subpopulations also were low.

  18. Efeito da endogamia sobre a maturidade sexual e fecundidade do escargot da espécie Helix aspersa

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    Soares E.D.R.

    2003-01-01

    Full Text Available Estudou-se o efeito da endogamia sobre a maturidade sexual e fecundidade de escargot da espécie Helix aspersa, em três gerações consecutivas de irmãos perfeitos. Os animais foram criados em laboratório com temperatura entre 20 e 25ºC e umidade relativa entre 70 e 90%. O efeito da endogamia foi negativo para as duas características. Quando o valor de F aumentou de 0,25 para 0,50, o percentual de animais sexualmente maduros aos 120 dias diminuiu de 59 para 18% e o número de animais nascidos por postura diminuiu de 94 para 53. Para evitar o efeito negativo, recomenda-se o início de uma criação com pelo menos 100 reprodutores não aparentados, introduzindo-se novas matrizes após a 10ª geração.

  19. Hydroxyapatite, a biomaterial: Its chemical synthesis, characterization and study of biocompatibility prepared from shell of garden snail, Helix aspersa

    Indian Academy of Sciences (India)

    Anjuvan Singh

    2012-11-01

    The shell of garden snail (Helix aspersa) is basically made of calcium carbonate. An attempt is made to convert calcium carbonate of garden snail shell to hydroxyapatite. The snail shell was found to decompose within 850°C to all the carbonate phases. The calcined snail shells were then treated with acids followed by different chemicals in ammoniacal media maintaining proper stoichiometry to produce fine hydroxyapatite (HAP) as filter cake with a Ca/P molar ratio of 1.67. The dried HAP powder was extremely pure with a specific surface area of 15 m2/g. The different characterization techniques were adopted both for calcined snail shell and HAP synthesized by X-ray diffraction (XRD), thermal analysis (DTA/TGA), Fourier transform infrared spectroscopy (FTIR) and scanning electron microscopy (SEM). The surface area and particle size of HAP powder prepared by chemical precipitation route, were also determined by BET and Malvern particle size analyser, respectively. The synthesized powder was soaked in stimulated body fluid (SBF) medium for various periods of time in order to evaluate its bioactivity. The changes of pH of SBF medium were measured. High bioactivity of prepared HAP powder due to the formation of apatite on its surface was observed.

  20. The xenobiotic-metabolizing enzymes in Helix aspersa (snail) and Pleurozium schreberi (moss), potential bio-marker of polycyclic aromatic hydrocarbons air pollution; Les enzymes de biotransformation des xenobiotiques chez helix aspersa (escargot) et pleurozium schreberi (mousse), biomarqueurs potentiels de la pollution atmospherique par les hydrocarbures aromatiques polycycliques

    Energy Technology Data Exchange (ETDEWEB)

    Ismert, M.

    2000-12-01

    The aim of this work was to evaluate the potential value of xenobiotic-metabolizing enzymes as bio-marker of air pollution by polycyclic aromatic hydrocarbons (PAH). Using several models of PAH air pollution, we investigated their effects on cytochrome P450 (7-ethoxyresorufin O-deethylase, EROD and 7-ethoxycoumarin O-deethylase, ECOD) and glutathione-dependent enzyme activities (glutathione S-transferases, GST with 1-chloro-2,4-dinitro-benzene and 4-nitro-quinoline-1-oxide as substrates, glutathione reductase and glutathione peroxidases) in three organs of the snail Helix aspersa as well as on glutathione-dependent and antioxidant (ascorbate peroxidase and catalase) enzyme activities in the moss Pleurozium schreberi. In the first model, H. aspersa and P. schreberi were exposed to a naphthalene-saturated atmosphere during three days. While, this treatment did not provoke any variation of the enzyme activities explored in P. schreberi, it modified the level of some snail enzyme activities in an organ-dependent manner. Naphthalene exposure affected none of the tested activities in the mantle cavity-forming tissues (MCFT), but significantly decreased EROD and ECOD activities in the kidney (KD) as opposed to their increase in the digestive gland (DG). In the second model, these organisms were exposed for 8 hours to a work place where the atmosphere was essentially PAH burden. Benzo[a]pyrene was used as the PAH model compound. None of the selected enzyme activities were affected in the moss. Conversely, EROD and ECOD activities were significantly increased in the KD and DG of H. aspersa, whatever the PAH burden. Moreover, GST activities with 1-chloro-2,4-dinitro-benzene as the acceptor substrate were enhanced in the DG. In the third model, the organisms were transplanted in three urban places during one or several weeks. GST activities with both substrates were positively correlated with the level of nitrogen oxides in the digestive gland of H. aspersa. Overall, our work

  1. Desempenho e características de carcaça do escargot francês (Helix aspersa maxima alimentado com rações contendo diferentes óleos vegetais Performance and carcass characteristics of “gros gris” (Helix aspersa maxima fed with different vegetable oils in diets

    Directory of Open Access Journals (Sweden)

    Carmino Hayashi

    2004-02-01

    Full Text Available Objetivando avaliar a utilização de óleos vegetais de diferentes origens em rações no desempenho e características de carcaça do escargot francês “gros gris” (Helix aspersa maxima, 240 animais com peso inicial médio de 0,11g, foram distribuídos em um delineamento inteiramente casualizado com seis tratamentos e quatro repetições com dez animais cada, em aquários de 12L. As rações foram formuladas de forma a diferirem quanto ao emprego (3 % da ração dos óleos de soja, canola, girassol, linhaça, arroz e milho. Os valores médios de peso final, conversão alimentar, taxa de eficiência protéica, rendimento de carcaça, percentagem de concha e taxa de sobrevivência dos animais alimentados com as rações com os diferentes óleos não diferiram (p>0,01 entre si. Os teores de umidade, cinza, proteína bruta e lipídeos totais e a relação ácidos graxos poliinsaturados/ácidos graxos saturados da porção comestível dos animais submetidos as diferentes rações não foram influenciados (p>0,05. Entretanto, os animais que receberam dieta com óleo de linhaça apresentaram o melhor (p0,05 nos teores de umidade e cinza das conchas dos animais submetidos às diferentes rações. Por outro lado, os animais que receberam óleo de linhaça tiveram concha com menor (pAiming to evaluate the use of different vegetable oil sources on performance and carcass characteristics of “gros gris” (Helix aspersa maxima diets, two hundred forty snails with initial average weight of 0.11g samples were distributed in an entirely randomized design with six treatments and four replications in twelve-liter aquaria. The diets were formulated to have differences on soybean, canola, sunflower, linseed, rice and corn oil inclusion at 3% of the diet. The average final weight, feed conversion, protein efficiency rate, carcass yields, percentage of shell and survival rates were not affected (p>0.01 by the use of different oils. The moisture, ash, crud

  2. Composição química e perfil de ácidos graxos em escargot (Helix aspersa maxima alimentados com dietas contendo diferentes fontes protéicas - DOI: 10.4025/actascianimsci.v26i4.1722 Chemical composition and fatty acid profile of snail (Helix aspersa maxima muscle fed with different protein source in diets - DOI: 10.4025/actascianimsci.v26i4.1722

    Directory of Open Access Journals (Sweden)

    Nilson Evelázio de Souza

    2004-04-01

    Full Text Available Foram analisadas composição centesimal e perfil de ácidos graxos no músculo de escargot (Helix aspersa maxima submetidos à dieta contendo diferentes fontes protéicas (farelo de soja; farelo de soja + farelo de canola; farelo de canola; farelo de soja + farelo de girassol; e farelo de girassol. Os ácidos graxos foram identificados em cromatógrafo gasoso equipado com detector de ionização de chama e coluna capilar de sílica fundida. Foram predominantes nas dietas os ácidos graxos: 16:0, 18:0, 18:1 n-9, 18:2 n-6 e 18:3 n-3. Em todos os tratamentos foi observado bom índice para total de ácidos graxos poliinsaturados na porção comestível (músculo do escargot, destacando-se o tratamento contendo farelo de canola, que proporcionou maior nível protéico e melhor razão n-6/n-3.Proximate composition and fatty acid profile of snail (Helix aspersa maxima muscle submitted the diets containing differents protein source (soybean meal; soybean meal + canola meal; canola meal; soybean meal + sunflower meal; and sunflower meal were analyzed. Fatty acid were analyzed using a gas chromatograph fitted with flame ionization detector and fused silica capillary column. The fatty acids predominant in diets were: 16:0, 18:0, 18:1 n-9, 18:2 n-6 and 18:3 n-3. All the treatments presented high fatty acids polyunsaturated in the escargot comestible part (muscle. The treatment using canola meal presented high protein level and the better ratio n-6/n-3.

  3. Treatment of acute radiodermatitis with Cryptomphalus Aspersa Secretion

    International Nuclear Information System (INIS)

    A clinical study with 100 patients with acute radiodermatitis is presented. They received treatment with Cryptomphalus Aspersa secretion (n=50) or its excipients (n=50) for three months. They were evaluated after first week, and at one, two, three and six months after initiation of therapy. In the group treated with Cryptomphalus Aspersa, a statistically significant clinical improvement in erythema, itching and burning pain was noted, both at first week and one month after starling therapy. These results open a new way in the future treatment of acute radiodermatitis. Cryptomphalus Aspersa is an alternative therapy for many patients diagnosed of malignant tumors which require radiotherapy, with specially good results in breast and neck radiodermatitis. (Author) 10 refs

  4. The caracol tower at chichen itza: an ancient astronomical observatory?

    Science.gov (United States)

    Aveni, A F; Gibbs, S L; Hartung, H

    1975-06-01

    Although our investigations reveal a number of significant astronomical events coinciding with many of the measured alignments presented in Table 1, not every alignment appears to have an astronomical match which we can recognize. It may be that only some of the sighting possibilities we have discussed were actually functional. Moreover, our search of significant astronomical events to match the alignments has included only those which seem of obvious functional importance to us: sun, moon, and planetary extremes and the setting positions of the brightest stars. We have emphasized those celestial bodies which are documented in the literature as having been of importance. Perhaps hitherto unrecognized constellations were sighted in the windows, perhaps fainter stars, the heliacal rising and setting times of which could have served to mark important dates in the calendar. While we propose no grand cosmic scheme for the astronomical design of the Caracol it can be inferred that the building, apart from being a monument related to Quetzalcoatl, was erected primarily for the purpose of embodying in its architecture certain significant astronomical event alignments, in the same sense that a modern astronomical ephemeris exhibits information of importance to us in the keeping of the current calendar. There are examples in the Mesoamerican historical literature of deliberate attempts to align buildings with astronomical directions of importance. For example, Maudslay (33) quotes Father Motolinia, who tells us that in Tenochtitlan the festival called Tlacaxipeualistli "took place when the sun stood in the middle of Huicholobos, which was at the equinox, and because it was a little out of the straight, Montezuma wished to pull it down and set it right." According to Maudslay, worshipers were probably facing east to watch the sun rise between the two oratories on the Great Temple of Tenochtitlan at the time of the equinox. The directions of the faces of the Lower and Upper

  5. LAS PREGUNTAS DEL TIEMPO Y LAS CONFESIONES: CARACOL Y OTROS CUENTOS Temporality and Confessions in Caracol y otros cuentos

    Directory of Open Access Journals (Sweden)

    Fernando Burgos

    2005-12-01

    Full Text Available El discurso posmoderno en el que se sostiene la obra del escritor panameño Enrique Jaramillo Levi expone la necesidad de situar la conciencia como la formación receptora de una experiencia plural de tiempos tales como la vivencia de un tiempo psíquico profundo, otro puramente perceptivo, otro de raíces imaginarias, otro de encuentro espiritual, otro de tonos confesionales en el que el impredecible viaje de la memoria busca impetuosamente un punto de universalización en el poder introspectivo del arte. El original enfoque sobre el tiempo en la obra de Jaramillo Levi es inseparable, por otra parte, de las dudas metafísicas de la escritura y del escritor. Nuestro trabajo estudia relacionadamente ambas dimensiones en su obra Caracol y otros cuentos,Postmodern discourse is central to Panamanian writer Enrique Jaramillo Levis´ work. Its usage illustrates the need to regard conscience as the receptive agent of a plural experience of temporality such as that of a deep psychological scope, or one which is purely perceptive, another one rooted in the imaginative process, one other spiritual, as well as a confessional dimension of time guided by the unpredictability of memory in search of universal meaning and the introspective power of art. On the other hand, Jaramillo Levis´ original approach to time is inseparable from the metaphysical questions underlying the intersection of writing and writer emerging from the act of creation. In this essay, I study both dimensions in his work Caracol y otros cuentos.

  6. Helix aspersa gelatin as an emulsifier and emulsion stabilizer: functional properties and effects on pancreatic lipolysis.

    Science.gov (United States)

    Zarai, Zied; Balti, Rafik; Sila, Assaâd; Ben Ali, Yassine; Gargouri, Youssef

    2016-01-20

    Emulsions are widely used in food and pharmaceutical applications for the encapsulation, solubilization, entrapment, and controlled delivery of active ingredients. In order to fulfill the increasing demand for clean label excipients, natural polymers could be used to replace the potentially irritative synthetic surfactants used in emulsion formulation. In the present study, we have studied the properties of oil-in-water emulsions prepared with land snail gelatin (LSG) as the sole emulsifying agent, extracted and described for the first time. LSG was evaluated in terms of proximate composition, oil and water holding capacity, emulsifying and foaming properties, color and amino acid composition. Emulsions of trioctanoylglycerol (TC8) and olive oil were made at different gelatin/oil ratios and changes in droplet-size distribution were determined. The superior emulsifying properties of LSG, the susceptibility of gelatin protein emulsions increasing flocculation on storage, and the coalescence of gelatin emulsions following centrifugation were demonstrated. Furthermore, the effect of LSG on the activity of turkey pancreatic lipase (TPL) was evaluated through the pH-stat methodology with TC8 and olive oil emulsions. The LSG affected the TPL activity in a concentration-dependent way. Our results showed that LSG, comparably to gum arabic, increases the pancreatic lipase activity and improves its stability at the oil-water interface. PMID:26487504

  7. Amino acid, fatty acid, vitamin and mineral contents of the edible garden snail (Helix aspersa)

    OpenAIRE

    Ferhat Çağıltay; (1), Nuray Erkan; Deniz Tosun; Arif Selçuk

    2011-01-01

    The nutritive and market value of meat of edible garden snail from northern Turkey was deter¬mined. Protein, fat, ash, water and carbohydrate value of edible garden snail were found 9.87, 0.58, 1.07, 82.50 and 5.99 % wet weight, respectively. The results of this study have showed that garden snails are good sources of amino acid, fatty acid, vitamins and minerals. The ly¬sine, isoleucine and leucine content from essential amino acids were 721, 467.57 and 611.50 mg/100g, respectively. The m...

  8. Amino acid, fatty acid, vitamin and mineral contents of the edible garden snail (Helix aspersa

    Directory of Open Access Journals (Sweden)

    Ferhat Çağıltay

    2011-10-01

    Full Text Available The nutritive and market value of meat of edible garden snail from northern Turkey was deter¬mined. Protein, fat, ash, water and carbohydrate value of edible garden snail were found 9.87, 0.58, 1.07, 82.50 and 5.99 % wet weight, respectively. The results of this study have showed that garden snails are good sources of amino acid, fatty acid, vitamins and minerals. The ly¬sine, isoleucine and leucine content from essential amino acids were 721, 467.57 and 611.50 mg/100g, respectively. The major amino acids detected were aspartic acid (996.814 mg/100g, glutamic acid (1405.158 mg/100g, alanine (1063.877 mg/100g, serine (1039.248 mg/100g. Total saturated fatty acid, monounsaturated fatty acid and polyunsaturated fatty acid were de¬termined 28, 76, 20.66 and 34.38 %. The vitamin A, vitamin E, vitamin B1, B2, B3 and B6 of vitamins were 5.462, 0.887, 0.154, 0.065, 3.226 and 0.288 mg/100g wet wt, respectively. Min¬eral analysis of garden snails showed that they are rich in calcium and potassium (1357 and 1054 mg/kg and low in iron (5.21 mg/kg.

  9. Effect of low energy X ray on Helix identifiable neuron electrical activity

    International Nuclear Information System (INIS)

    The giant cells of snail brain (Helix pomatia and Helix aspersa) are studied before, during and after low energy X rays irradiation. Electrophysiological data are recorded from 2 intracellular glass micropipettes. During the irradiation, a membrane resistance decrease and a depolarization are recorded, in accordance to dose and dose-rate. Thresholds are respectively 2,000 R and 1 kR.mn-1. Depolarization is partially reversible. The electrical threshold decreases in connection with depolarization: indeed, previous repolarization abolishes this effect. Spontaneous action potentials are often recorded during irradiation especially with a high dose-rate. Action potential shape also changes. Initially, it becomes higher with an increase of its rising-rate (dV/dt). Later, action potential becomes broader and smaller. Results are explained according to ionic theory of membrane potential

  10. Triple Helix going abroad?

    DEFF Research Database (Denmark)

    Sørensen, Olav Jull; Hu, Yimei

    2014-01-01

    The aim of the article is to explore to what extent the Tripple helix is being internationalized. Each of the helixes have their own internationalization rationale but the article show by small example that the helix itself is being internationalized and integrated with the host country tripple h...

  11. IDENTIFICACIÓN MOLECULAR DE POBLACIONES BACTERIANAS ASOCIADAS AL CARACOL PALA (Strombus gigas DEL CARIBE COLOMBIANO

    Directory of Open Access Journals (Sweden)

    ROMERO MAGALLY

    2009-08-01

    Full Text Available RESUMEN

    El caracol Pala, Strombus gigas (Strombidae, es de gran importancia ecológica y socioeconómica en el área caribeña colombiana. Sin embargo, es una especie catalogada como “vulnerable” y existe muy poca información referente a las especies bacterianas asociadas al caracol que puedan ser importantes para el desarrollo, manejo productivo y de seguridad acuícola de estos gastrópodos. En este trabajo, nosotros empleamos un estudio microbiológico y molecular de la región intergénica entre los genes 16S y 23S rDNA, análisis del gen rDNA 16S y secuenciación, para analizar las bacterias asociadas al caracol Pala (S. gigas. La composición de bacterias cultivables asociadas fue evaluada por su capacidad para crecer en agar marino y en medios de cultivos selectivos. De un total de 28 muestras analizadas encontramos que el número de bacterias cultivadas en condiciones aerobias fue de alrededor 106 ufc mL-1 donde las bacterias pertenecientes a la familia Vibrionacea fueron las más abundantes, cerca de >105 ufc mL-1 . El análisis molecular de la región intergénica entre los genes 16S y 23S rDNA de las diferentes muestras, reveló una gran complejidad bacteriana asociada a S. gigas. Las secuencias de los amplificados del gen rDNA 16S identificó Pseudoalteromonas sp., Halomonas sp., Psycrobacter sp., Cobetia sp., Pseudomonas sp. y Vibrios sp. Nuestros resultados podrían sugerir un rol importante de estas bacterias como componentes de la comunidad asociada al S. gigas. Esta información puede complementar los estudios que se están implementando en los procesos para la conservación y repoblamiento de las poblaciones de S. gigas en Colombia.

    Palabras clave: Strombus gigas, Caracol pala, Bacteria, Región intergénica 16S-23S, rDNA 16S.

    ABSTRACT

    The Queen Conch, Strombus gigas (Strombidae, is a species of great ecological and socioeconomic importance in the Caribbean area of Colombia

  12. La empresa 60 de las Empresas Morales de Juan de Borja. Posible origen textual de la imagen del caracol

    OpenAIRE

    Martínez Sobrino, Alejandro

    2013-01-01

    ABSTRACT: The author of this essay argues that the source of the image of the snail from Juan de Borja’s 60th impresa of his Empresas Morales is textual, and that it can be traced back to the Picta Poesis by Aneau Barthèlemy. KEYWORDS: Source, Snail, Impresa, Empresas Morales, Juan de Borja, Picta Poesis, Aneau Barthèlemy.   RESUMEN: El autor defiende, en el presente artículo, que el origen de la imagen del caracol que aparece en la empresa número 60 de las Empresas Morales de Juan de Borja p...

  13. Higher codimensional Euclidean helix submanifolds

    OpenAIRE

    Di Scala, Antonio J.; Ruiz-Hernández, Gabriel

    2010-01-01

    A submanifold of Rn whose tangent space makes constant angle with a fixed direction d is called a helix. Helix submanifolds are related with the eikonal PDE equation. We give a method to find every solution to the eikonal PDE on a Riemannian manifold locally. As a consequence we give a local construction of arbitrary Euclidean helix submanifolds of any dimension and codimension. Also we characterize the ruled helix submanifolds and in particular we describe those which are minimal.

  14. Microbiological and chemical evaluation of Helix spp. snails from local and non-EU markets, utilised as food in Sardinia

    Directory of Open Access Journals (Sweden)

    Arianna Corda

    2014-04-01

    Full Text Available With this study, 28 pools of snails of the genus Helix, respectively Helix aspersa (n=24 and Helix vermiculata (n=4 were analysed. They were taken from snail farming and stores. The snails were from Sardinia, other regions of Italy, and from abroad. All the samples were examined as pool looking for these microbiological target: Salmonella spp., Listeria monocytogenes, Escherichia coli O157, Clostridium perfringens, Norovirus and Hepatitis A Virus (HAV. In the same pools, the concentration of cadmium and lead by inductively coupled plasma mass spectrometry was also determined. The levels of these heavy metals were quite high, especially for cadmium. Two samples were positive for Salmonella spp., while no sample was positive for Escherichia coli O157, HAV and Norovirus. Two samples were positive for Clostridium perfringens and 8 for Listeria monocytogenes. The microrganisms related to Listeria monocytogenes were identified using biochemical techniques, then serotyped and gene sequenced by multiple loci sequence typing technique. Furthermore, antimicrobial restistence was tested on the same samples.

  15. The Effects of HCl and CaCl2 Injections on Intracellular Calcium and pH in Voltage-clamped Snail (Helix aspersa) Neurons

    OpenAIRE

    Thomas, Roger C

    2002-01-01

    To investigate the mechanisms by which low intracellular pH influences calcium signaling, I have injected HCl, and in some experiments CaCl2, into snail neurons while recording intracellular pH (pHi) and calcium concentration ([Ca2+]i) with ion-sensitive microelectrodes. Unlike fluorescent indicators, these do not increase buffering. Slow injections of HCl (changing pHi by 0.1–0.2 pH units min−1) first decreased [Ca2+]i while pHi was still close to normal, but then increased [Ca2+]i when pHi ...

  16. Folding pathways of a helix-turn-helix model protein

    CERN Document Server

    Hoffmann, D

    1997-01-01

    A small model polypeptide represented in atomic detail is folded using Monte Carlo dynamics. The polypeptide is designed to have a native conformation similar to the central part of the helix-turn-helix protein ROP. Starting from a beta-strand conformation or two different loop conformations of the protein glutamine synthetase, six trajectories are generated using the so-called window move in dihedral angle space. This move changes conformations locally and leads to realistic, quasi-continuously evolving trajectories. Four of the six trajectories end in stable native-like conformations. Their folding pathways show a fast initial development of a helix-bend-helix motif, followed by a dynamic behaviour predicted by the diffusion-collision model of Karplus and Weaver. The phenomenology of the pathways is consistent with experimental results.

  17. Acción patogénica de Heterorhabditis bacteriophora (Poinar) sobre el caracol manzana (Pomacea canaliculata Lamarck), plaga de los cultivos de arroz (Oriza sativa) en la cuenca baja del río Daule, Guayas, Ecuador

    OpenAIRE

    G. A. Salcedo

    2013-01-01

    Los cultivos de arroz en la cuenca baja del río Daule, Ecuador, son afectados por el caracol manzana. La pérdida estimada es de 40 al 60% de la producción/ha. El agricultor, para evitar pérdidas considerables, aplica agroquímicos en dosis elevadas, desequilibrando la fauna y microfauna nativa, agravando el problema. Razón por la cual, se evaluó la patogenicidad de H. bacteriophora sobre el caracol manzana, con tres dosis; mediante un diseño completamente al azar (DCA) con cuatro tratamientos ...

  18. Macrocyclis peruvianus (Gastropoda, Acavidae, an endemic land snail from Chile Macrocyclis peruvianus (Gastropoda, Acavidae, um caracol terrestre endêmico do Chile

    Directory of Open Access Journals (Sweden)

    Leticia F. da Silva

    2009-06-01

    Full Text Available Macrocyclis peruvianus (Lamarck, 1822 is a large terrestrial snail which is endemic in Chile. A detailed description of its shell structure, jaw, radula, palial cavity and reproductive system is presented here for the first time.Macrocyclis peruvianus (Lamarck, 1822 é um grande caracol terrestre endêmico do Chile. Uma descrição detalhada da esculturação de sua concha, rádula, mandíbula, cavidade palial e sistema reprodutor são apresentados aqui pela primeira vez.

  19. Experimentación geométrica y constructiva en piedra: algunos casos especiales de escaleras de caracol

    Directory of Open Access Journals (Sweden)

    Sanjurjo, A.

    2013-10-01

    Full Text Available Stonecutting specialized literature often describes, specifically between the 16th and the 18th century, complex spiral staircases that, in many cases, have never been carried out practically. At the same time, hidden inside of towers and turrets or concealed in buttresses, there is a variety of built examples whose arrangements differentiate from those of the written treatises, showing an outstanding technical mastery, clear sign of experimentation and professional training. They are characterized by their complex geometry and complicated construction, which emphasizes their singularity in comparison to their small dimension and their irrelevant location. Both models, those conceived and drawn in the treatises, but not built, and those constructed in churches and cathedrals, but not considered in the treatises, are the objective of this paper. To this end, we will look at some of these stairs, analysing them and trying to find the source of their existence.La literatura técnica de la cantería describió, fundamentalmente entre el siglo XVI y el XVIII, complejos caracoles de piedra que, en algunos casos, no se llevaron nunca a la práctica. Asimismo, escondidos en torreones y disimulados en machones, estribos y contrafuertes encontramos ejemplos construidos, con soluciones distintas a las de los tratados escritos, de un gran virtuosismo técnico, testigos evidentes de procesos de experimentación y capacitación profesional. Su compleja geometría y difícil construcción las caracteriza, y acentúa aún más su singularidad en contraposición con su pequeña dimensión y su secundaria ubicación. Ambos modelos, los pensados y dibujados en los tratados, pero no construidos, y los construidos en iglesias y catedrales, pero no contemplados en los tratados, son el objeto de este artículo. En él, hacemos un recorrido por algunas de esas escaleras especiales, estudiándolas y tratando de encontrar el porqué de su existencia.

  20. Study for design and implementation of marketing in caracol commercial dependencies in turistic activity at the central region of Cuba (I.

    Directory of Open Access Journals (Sweden)

    Naybi Salas Vargas

    2012-03-01

    Full Text Available The proposal is based on the studio of marketing in touristic sector with emphasis in shops as tool in commercial management that allows work team coordination, resources and materials, and the orientation towards the client to afford best earnings, position in market and image. This thematic responds to the conditions of the Tiendas Recaudadoras de Divisas (TRD in Sancti Spiritus Province, solving problems in manipulating and managing of inventories and the marketing of Caracol product, what affects the financial results given by a non fitable activity to the market challenges. The previous said is the result of the estimable practical, financial and economic values of an investigation in order to achieve social satisfaction of the clients needs. The investigation proposed a methodology supported in Sainz (1995 methodological scheme with the necessary adaptations related to the development of commercial activity in TRD, as fitable response to actual context of this enterprise in the touristic activity in Cuba.

  1. Efecto de la depuración en la biomasa del caracol Pomacea patula [Baker, 1922] usando el índice de condición

    Directory of Open Access Journals (Sweden)

    M. García-Ulloa

    2006-01-01

    Full Text Available La depuración de organismos acuáticos en cultivo es una práctica común. El tiempo de exposición de los animales al agua tratada es uno de los factores más importantes para su eficiencia, pudiendo afectar su biomasa. Se evaluó el efecto de la depuración en adultos de Pomacea patula mediante la aplicación del índice de condición (IC, bajo condiciones de laboratorio. Caracoles adultos obtenidos en cultivo se mantuvieron en peceras (Grupo 1 expuestos a un flujo de agua constante, tratada con radiación ultravioleta y limpieza diaria y en condiciones normales de mantenimiento (Grupo 2, con 5 réplicas por grupo. Se obtuvo el peso húmedo y longitud total individualmente, al inicio y después de una depuración de 10 días. El valor promedio del coeficiente de correlación (animales iniciales y de los Grupos 1 y 2 fue mayor a 0.90. El IC entre el valor inicial (771.81 ± 40.41 y los Grupos 1 y 2 (763.527 ± 25.24 y 765.465 ± 38.59, respectivamente, no mostró diferencias significativas (P > 0.05 al final del experimento. Los resultados sugieren que el proceso de depuración usado no afectó la biomasa de adultos de P. patula. El IC se mostró como una herramienta práctica de evaluación sin considerar la diferencia inicial de tallas de caracoles adultos

  2. Recent advances in helix-coil theory.

    Science.gov (United States)

    Doig, Andrew J

    2002-12-10

    Peptide helices in solution form a complex mixture of all helix, all coil or, most frequently, central helices with frayed coil ends. In order to interpret experiments on helical peptides and make theoretical predictions on helices, it is therefore essential to use a helix-coil theory that takes account of this equilibrium. The original Zimm-Bragg and Lifson-Roig helix-coil theories have been greatly extended in the last 10 years to include additional interactions. These include preferences for the N-cap, N1, N2, N3 and C-cap positions, capping motifs, helix dipoles, side chain interactions and 3(10)-helix formation. These have been applied to determine energies for these preferences from experimental data and to predict the helix contents of peptides. This review discusses these newly recognised structural features of helices and how they have been included in helix-coil models. PMID:12488008

  3. Acción patogénica de Heterorhabditis bacteriophora (Poinar sobre el caracol manzana (Pomacea canaliculata Lamarck, plaga de los cultivos de arroz (Oriza sativa en la cuenca baja del río Daule, Guayas, Ecuador

    Directory of Open Access Journals (Sweden)

    G. A. Salcedo

    2013-01-01

    Full Text Available Los cultivos de arroz en la cuenca baja del río Daule, Ecuador, son afectados por el caracol manzana. La pérdida estimada es de 40 al 60% de la producción/ha. El agricultor, para evitar pérdidas considerables, aplica agroquímicos en dosis elevadas, desequilibrando la fauna y microfauna nativa, agravando el problema. Razón por la cual, se evaluó la patogenicidad de H. bacteriophora sobre el caracol manzana, con tres dosis; mediante un diseño completamente al azar (DCA con cuatro tratamientos y cinco repeticiones. Los resultados muestran el 100% de mortalidad por septicemia a las 96 horas de la inoculación, con relación al testigo.

  4. Multiple helix ecosystems for sustainable competitiveness

    CERN Document Server

    Ferreira, João; Farinha, Luís; Fernandes, Nuno

    2016-01-01

    This book discusses the main issues, challenges, opportunities, and trends involving the interactions between academia, industry, government and society. Specifically, it aims to explore how these interactions enhance the ways in which companies deliver products and services in order to achieve sustainable competitiveness in the marketplace. Sustainable competitiveness has been widely discussed by academics and practitioners, considering the importance of protecting the environment while sustaining the economic goals of organizations. The Quintuple Helix innovation model is a framework for facilitating knowledge, innovation and sustainable competitive advantage. It embeds the Triple and the Quadruple Helix models by adding a fifth helix, the “natural environment.” The Triple Helix model focuses on the university-industry-government triad, while the Quadruple adds civil society (the media- and culture-driven public) as a fourth helix. The Quintuple Helix model facilitates research, public policy, and pract...

  5. Actividad molusquicida del Piquerol A aislado de Piqueria trinervia (compositae) sobre ocho especies de caracoles pulmonados The molluscicide activity of Piquerol A isolated from Piqueria trinervia (Compositae) against eight species of pulmonate snails

    OpenAIRE

    Alejandro Cruz-Reys; Carolina Chavarin; Martha P. Campos Arias; Javier Taboada; Manuel Jímenez E.

    1989-01-01

    De las partes aéreas de la planta Piqueria trinervia (Compositae) colectada en diveresas áereas de México, se aisló el Piquerol A. Este compuesto se probó como agente molusquicida contra ocho especies de caracoles pulmonados: Fossaria (Fossaria) humilis, F. (Bakerilymnae) sp., Pseudosuccinea columella, Stagnicola attenuata, de México; F. (B.) cubensis y Physacubensis, de Cuba; P. Columella y Biomphalaria glabrata, de Brasil; B glabrata, de Puerto Rico; S. elodes, de Estados Unidos. Se utiliza...

  6. La escalera de caracol en los tratados de cantería españoles de la Edad Moderna y su presencia en el Patrimonio Construido hispánico: estudio geométrico y constructivo

    OpenAIRE

    Sanjurjo Álvarez, Alberto

    2015-01-01

    La escalera de caracol es uno de los elementos que mejor define la evolución de la construcción pétrea a lo largo de nuestra historia moderna. El movimiento helicoidal de las piezas de una escalera muestra, con frecuencia, el virtuosismo que alcanzaron los maestros del arte de la cantería y la plasticidad, expresividad y ligereza de sus obras. A pesar de su origen exclusivamente utilitario y de su ubicación secundaria, se convertirán en signo de maestría y en elementos protagonistas del espa...

  7. Cylindrical Helix Spline Approximation of Spatial Curves

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    In this paper, we present a new method for approximating spatial curves with a G1 cylindrical helix spline within a prescribed tolerance. We deduce the general formulation of a cylindrical helix,which has 11 freedoms. This means that it needs 11 restrictions to determine a cylindrical helix. Given a spatial parametric curve segment, including the start point and the end point of this segment, the tangent and the principal normal of the start point, we can always find a cylindrical segment to interpolate the given direction and position vectors. In order to approximate the known parametric curve within the prescribed tolerance, we adopt the trial method step by step. First, we must ensure the helix segment to interpolate the given two end points and match the principal normal and tangent of the start point, and then, we can keep the deviation between the cylindrical helix segment and the known curve segment within the prescribed tolerance everywhere. After the first segment had been formed, we can construct the next segment. Circularly, we can construct the G1 cylindrical helix spline to approximate the whole spatial parametric curve within the prescribed tolerance. Several examples are also given to show the efficiency of this method.

  8. A Helix Replacement Mechanism Directs Metavinculin Functions

    Energy Technology Data Exchange (ETDEWEB)

    Rangarajan, Erumbi S.; Lee, Jun Hyuck; Yogesha, S.D.; Izard, Tina (Scripps)

    2010-10-11

    Cells require distinct adhesion complexes to form contacts with their neighbors or the extracellular matrix, and vinculin links these complexes to the actin cytoskeleton. Metavinculin, an isoform of vinculin that harbors a unique 68-residue insert in its tail domain, has distinct actin bundling and oligomerization properties and plays essential roles in muscle development and homeostasis. Moreover, patients with sporadic or familial mutations in the metavinculin-specific insert invariably develop fatal cardiomyopathies. Here we report the high resolution crystal structure of the metavinculin tail domain, as well as the crystal structures of full-length human native metavinculin (1,134 residues) and of the full-length cardiomyopathy-associated {Delta}Leu954 metavinculin deletion mutant. These structures reveal that an {alpha}-helix (H1{prime}) and extended coil of the metavinculin insert replace {alpha}-helix H1 and its preceding extended coil found in the N-terminal region of the vinculin tail domain to form a new five-helix bundle tail domain. Further, biochemical analyses demonstrate that this helix replacement directs the distinct actin bundling and oligomerization properties of metavinculin. Finally, the cardiomyopathy associated {Delta}Leu954 and Arg975Trp metavinculin mutants reside on the replaced extended coil and the H1{prime} {alpha}-helix, respectively. Thus, a helix replacement mechanism directs metavinculin's unique functions.

  9. Into the Eye of the Helix

    Science.gov (United States)

    2009-02-01

    A deep new image of the magnificent Helix planetary nebula has been obtained using the Wide Field Imager at ESO's La Silla Observatory. The image shows a rich background of distant galaxies, usually not seen in other images of this object. ESO PR Photo 07a/09 The Helix Nebula ESO PR Video 06a/09 Helix Nebula Zoom-in ESO PR Video 06b/09 Pan over the Helix Nebula ESO PR Video 06c/09 Zoom and pan over the Helix Nebula The Helix Nebula, NGC 7293, lies about 700 light-years away in the constellation of Aquarius (the Water Bearer). It is one of the closest and most spectacular examples of a planetary nebula. These exotic objects have nothing to do with planets, but are the final blooming of Sun-like stars before their retirement as white dwarfs. Shells of gas are blown off from a star's surface, often in intricate and beautiful patterns, and shine under the harsh ultraviolet radiation from the faint, but very hot, central star. The main ring of the Helix Nebula is about two light-years across or half the distance between the Sun and its closest stellar neighbour. Despite being photographically very spectacular the Helix is hard to see visually as its light is thinly spread over a large area of sky and the history of its discovery is rather obscure. It first appears in a list of new objects compiled by the German astronomer Karl Ludwig Harding in 1824. The name Helix comes from the rough corkscrew shape seen in the earlier photographs. Although the Helix looks very much like a doughnut, studies have shown that it possibly consists of at least two separate discs with outer rings and filaments. The brighter inner disc seems to be expanding at about 100 000 km/h and to have taken about 12 000 years to have formed. Because the Helix is relatively close -- it covers an area of the sky about a quarter of the full Moon -- it can be studied in much greater detail than most other planetary nebulae and has been found to have an unexpected and complex structure. All around the

  10. I. Collagen-like polypeptides. II. Helix-turn-helix peptides and turn mimetics.

    OpenAIRE

    Dai, Nan

    2008-01-01

    Collagen is one of the most important and abundant proteins in mammals. It consists of three left-handed PPII helixes coiled along a common axis to form a very compact right-handed super helix. The primary structure is shown to be (Gly-Xaa-Yaa)n repeats with high content of prolyl residues at both Xaa and Yaa positions. Cis-trans isomerization of the prolyl amide bonds is one of the rate-limiting steps during collagen triple helix folding. The conformationally locked alkene isosteres Fmoc-...

  11. Optimization Design of Helix Pitch for Efficiency Enhancement in the Helix Travelling Wave Tubes

    Institute of Scientific and Technical Information of China (English)

    DUAN Zhao-Yun; GONG Yu-Bin; L(U) Ming-Yi; WEI Yan-Yu; WANG Wen-Xiang

    2008-01-01

    @@ The output section of a helix travelling wave tube usually contains a helix pitch taper for high rf electron efficiency.By keeping the rf field as synchronous as possible with the decelerating electron beam bunches,the rf field can extract much more energy from the beam,and thus the maximum electron efficiency can be realized.Recently,a global simulated annealing algorithm has been employed to design the helix pitch profile so as to improve the electron efficiency as much as possible.From the numerical results,it is concluded that the electron efficiency can be enhanced by about 4%-8%.

  12. Bendix: intuitive helix geometry analysis and abstraction

    OpenAIRE

    Dahl, Anna Caroline E.; Chavent, Matthieu; Sansom, Mark S P

    2012-01-01

    Summary: The flexibility of α-helices is important for membrane protein function and calls for better visualization and analysis. Software is presented that quantifies and projects the helix axis evolution over time, with the choice of uniform or analytic heatmap graphics according to the local geometry. Bendix supports static, molecular dynamics, atomistic and coarse-grained input.

  13. Thermodynamics of helix-coil transitions studied by multicanonical algorithms

    CERN Document Server

    Okamoto, Y; Okamoto, Yuko; Hansmann, Ulrich H.E.

    1995-01-01

    Thermodynamics of helix-coil transitions in amino-acid homo-oligomers are studied by the recently proposed multicanonical algorithms. Homo-oligomers of length 10 are considered for three characteristic amino acids, alanine (helix former), valine (helix indifferent), and glycine (helix breaker). For alanine other lengths (15 and 20) are also considered in order to examine the length dependence. From one multicanonical production run with completely random initial conformations, we have obtained the lowest-energy conformations and various thermodynamic quantities (average helicity, Zimm-Bragg $s$ and $\\sigma$ parameters, free energy differences between helix and coil states, etc.) as functions of temperature. The results confirm the fact that alanine is helix-forming, valine is helix-indifferent, and glycine is helix-breaking.

  14. Role of Helix-Loop-Helix Proteins during Differentiation of Erythroid Cells ▿

    OpenAIRE

    Anantharaman, Archana; Lin, I-Ju; Barrow, Joeva; Liang, Shermi Y; Masannat, Jude; Strouboulis, John; Huang, Suming; Bungert, Jörg

    2011-01-01

    Helix-loop-helix (HLH) proteins play a profound role in the process of development and cellular differentiation. Among the HLH proteins expressed in differentiating erythroid cells are the ubiquitous proteins Myc, USF1, USF2, and TFII-I, as well as the hematopoiesis-specific transcription factor Tal1/SCL. All of these HLH proteins exhibit distinct functions during the differentiation of erythroid cells. For example, Myc stimulates the proliferation of erythroid progenitor cells, while the USF...

  15. The Quintuple Helix innovation model: Global warming as a challenge and driver for innovation

    OpenAIRE

    Elias G. Carayannis; Thorsten D. Barth; Campbell David F. J.

    2012-01-01

    The Triple Helix innovation model focuses on university-industry-government relations. The Quadruple Helix embeds the Triple Helix by adding as a fourth helix the media-based and culture-based public and civil society. The Quintuple Helix innovation model is even broader and more comprehensive by contextualizing the Quadruple Helix and by additionally adding the helix (and perspective) of the natural environments of society. The Triple Helix acknowledges explicitly the importance of higher ed...

  16. Geological and environmental controls on the change of eruptive style (phreatomagmatic to Strombolian-effusive) of Late Pleistocene El Caracol tuff cone and its comparison with adjacent volcanoes around the Zacapu basin (Michoacán, México)

    Science.gov (United States)

    Kshirsagar, Pooja; Siebe, Claus; Guilbaud, Marie Noëlle; Salinas, Sergio

    2016-05-01

    The 28,300 year BP (cal 32,300 BP) El Caracol tuff cone complex is one of the few phreatomagmatic volcanoes in the scoria-cone dominated Plio-Quaternary Michoacán-Guanajuato Volcanic Field (MGVF). It displays a shallow circular crater of ~ 1 km in diameter that is filled with several meter-thick lava flows and is located between two NE-SW trending normal faults dipping NW. It lies directly on top of Pliocene lavas of the San Lorenzo shield volcano that forms part of a tectonic horst (topographic high) separating the Zacapu lake basin (1980 m) in the south from the Río Angulo river valley (1760 m) to the north. Detailed study of the tephra sequence indicates that the eruption occurred in two stages: 1) Weak phreatomagmatic, in which about 0.1-0.5 km3 dense rock equivalent (DRE) of magma was issued within ~ 1 to 3 months at the rate of 4-40 m3/s, and 2) purely magmatic (Strombolian-effusive) during which the vent shifted slightly its position toward the NW, forming a small scoria cone (~ 100 m high) on the crater rim of the tuff cone. From this scoria cone lava flows were issued, first into the tuff cone crater occupying its bottom, and subsequently toward the NW, down the outer flank of the tuff cone and into the plain, where they reached a distance of ~ 3.5 km. During this stage ~ 0.6 km3 DRE of magma was produced at the rate of ~ 4 m3/s in a period of ~ 5 months. Although El Caracol displays many features that are characteristic for a phreatomagmatic vent, its morphology, types of deposits, and its complex process of formation makes it strikingly different from the more typical case of the ~ 21,000 year BP (cal 25,300 BP) Alberca de Guadalupe maar volcano, situated not far at the SE margin of the Zacapu basin. The latter was solely phreatomagmatic during the course of its eruption and is formed in its entirety by surge and fallout breccias consisting largely of xenolithic material. In contrast, at El Caracol the hydrogeological environment (namely the low

  17. CRIANZA ARTIFICIAL DEL CARACOL DE AGUA DULCE Physa venustula Gould PARA ESTUDIOS ECOTOXICOLÓGICOS DE PLAGUICIDAS Artificial rearing of the freshwater snail Physa venustula Gould for ecotoxicological studies of pesticides

    Directory of Open Access Journals (Sweden)

    José Iannacone O.

    2002-04-01

    Full Text Available Se realizó una crianza artificial estandarizada del caracol de agua dulce Physa venustula Gould para estudios ecotoxicológicos de plaguicidas. Los bioensayos se estandarizaron con el protocolo de crianza con cuatro camadas de P. venustula, alimentadas con una solución de Cereal Leaves® y hojuelas de pescado y Chlorella vulgaris en nuestro laboratorio. La oviposición siguió un patrón descendente a través del tiempo. La eclosión de los huevos fue de 7 a 14 d bajo condiciones experimentales. El promedio de huevos por cápsula fue de 12,04 ± 10,66 (rango = 1 a 45 y el porcentaje promedio de fecundidad fue de 65,22%. En los caracoles que produjeron más masas, éstas contuvieron menor número promedio de huevos. El alimento Cereal Leaves® demostró ser una dieta más completa para el caracol dulceacuícola P. venustula comparado con la microalga Chlorella vulgaris. Se describen las características morfológicas de los huevos y el comportamiento de las formas juveniles. El rotífero Philodina acutiformis se comportó como un agente biológico contaminante que no permitió el desarrollo normal de los huevos en los cultivos. El protocolo de ensayo ecotoxicológico empleando P. venustula presenta las siguientes ventajas: amplia distribución en el neotrópico, confiabilidad, repetibilidad, alta sensibilidad en comparación a otros caracoles y corta duración del ensayo.Standard artificial breeding of the freshwater snail Physa venustula for ecotoxicological evaluation of pesticides was realized. The bioassays were standardized with a breeding protocol of four batches of P. venustula fed with a solution of Cereal Leaves™ plus fishmeal and Chlorella vulgaris in our laboratory. The oviposition had a downward trend through the time. The eggs were hatched between 7 and 14 d under experimental conditions. The average of eggs per capsule was 12.04 ± 10.66 (range= 1 to 45 and the average fecundity percentage was 65.22%. The snails which produced

  18. The Triple Helix of the Organizational Knowledge

    OpenAIRE

    Contantin BRĂTIANU

    2013-01-01

    The purpose of this paper is to present the inner triple helix dynamics of the organizationalknowledge. This is a new perspective of the classical view of tacit knowledge– explicit knowledge dyad of the organizational knowledge promoted by Nonaka and hisco-workers. The new perspective is based on the metaphor that organizational knowledge isa "eld rather than a stock, or stocks and flows. It is a complex metaphor using the thermodynamicsprinciples. The organizational knowledge is composed of ...

  19. Investigation of a Short Conical Helix Antenna

    OpenAIRE

    Nakano, Hisamatsu; Mikawa, Takao; Yamauchi, Junji

    1985-01-01

    The input impedance, radiation pattern, axial ratio, and power gain of a conical helix antenna with a short arm are calculated as a function of frequency, using theoretically determined current distributions. It is shown that the antenna radiates a circularly polarized wave over a frequency range ratio of about 1:1.2, having a power gain of about 7.7 dB. The experimental results are also presented.

  20. Damping effect of helix-like pili

    CERN Document Server

    Zakrisson, Johan; Axner, Ove; Andersson, Magnus

    2014-01-01

    Biopolymers are vital structures for many living organisms; for a variety of bacteria, adhesion polymers play a crucial role for the initiation of colonization. Some bacteria express, on their surface, attachment organelles (pili) that comprise subunits formed into stiff helix-like structures that possess unique biomechanical properties. These helix-like structures possess a high degree of flexibility that gives the biopolymers a unique extendibility. This has been considered beneficial for piliated bacteria adhering to host surfaces in the presence of a fluid flow. We show in this work that helix-like pili have the ability to act as efficient dampers of force that can, for a limited time, lower the load on the force-mediating adhesin-receptor bond on the tip of an individual pilus. The model presented is applied to bacteria adhering with a single pilus of either of the two most common types expressed by uropathogenic Escherichia coli, P or type 1 pili, subjected to realistic flows. The results indicate that ...

  1. Charged histidine affects alpha-helix stability at all positions in the helix by interacting with the backbone charges.

    OpenAIRE

    Armstrong, K M; Baldwin, R L

    1993-01-01

    To determine whether a charged histidine side chain affects alpha-helix stability only when histidine is close to one end of the helix or also when it is in the central region, we substitute a single histidine residue at many positions in two reference peptides and measure helix stability and histidine pKa. The position of a charged histidine residue has a major effect on helix stability in 0.01 M NaCl: the helix content of a 17-residue peptide is 24% when histidine is at position 3 compared ...

  2. Positive and negative transcriptional control by the TAL1 helix-loop-helix protein.

    OpenAIRE

    Hsu, H L; Wadman, I; Tsan, J T; Baer, R

    1994-01-01

    Tumor-specific activation of the TAL1 gene is the most common genetic defect associated with T-cell acute lymphoblastic leukemia. The TAL1 gene products possess a basic helix-loop-helix (bHLH) motif, a protein-dimerization and DNA-binding domain found in several transcription factors. TAL1 polypeptides interact, in vitro and in vivo, with class A bHLH proteins (e.g., E47) to form heterodimers with sequence-specific DNA-binding activity. In this study, we show that TAL1 can regulate the transc...

  3. Preferred sequences for DNA recognition by the TAL1 helix-loop-helix proteins.

    OpenAIRE

    Hsu, H L; Huang, L; Tsan, J T; Funk, W.; Wright, W. E.; Hu, J S; Kingston, R E; Baer, R

    1994-01-01

    Tumor-specific activation of the TAL1 gene is the most common genetic alteration seen in patients with T-cell acute lymphoblastic leukemia. The TAL1 gene products contain the basic helix-loop-helix (bHLH) domain, a protein dimerization and DNA-binding motif common to several known transcription factors. A binding-site selection procedure has now been used to evaluate the DNA recognition properties of TAL1. These studies demonstrate that TAL1 polypeptides do not have intrinsic DNA-binding acti...

  4. High power, high frequency helix TWT's

    Science.gov (United States)

    Sloley, H. J.; Willard, J.; Paatz, S. R.; Keat, M. J.

    The design and performance characteristics of a 34-GHz pulse tube capable of 75 W peak power output at 30 percent duty cycle and a broadband CW tube are presented. Particular attention is given to the engineering problems encountered during the development of the tubes, including the suppression of backward wave oscillation, the design of electron guns for small-diameter high-current beams, and the thermal capability of small helix structures. The discussion also covers the effects of various design parameters and choice of engineering materials on the ultimate practical limit of power and gain at the operating frequencies. Measurements are presented for advanced experimental tubes.

  5. [Quaternion-based Characterization of Protein α Helix].

    Science.gov (United States)

    Xu, Yonghong; Chu, Zefei

    2016-02-01

    This paper proposes a method based on quaternion for characterization a helix of proteins. The method defines the parameter called Quaternion Helix Axis Spherical Distance (QHASD) on the basis of mapping protein Cα frames' helical axis onto a unit sphere, and uses QHASD to characterize the a helix of the protein secondary structure. Application of this method has been verified based on the PDBselect database, with an a helix characterization accuracy of 91.7%. This method possesses significant advantages of high detection accuracy, low computation and clear geometric significance. PMID:27382757

  6. Morphology and Composition of the Helix Nebula

    CERN Document Server

    Henry, R B C; Dufour, R J

    1999-01-01

    We present new narrow-band filter imagery in H-alpha and [N II] 6584 along with UV and optical spectrophotometry measurements from 1200 to 9600 Angstroms of NGC 7293, the Helix Nebula, a nearby, photogenic planetary nebula of large diameter and low surface brightness. Detailed models of the observable ionized nebula support the recent claim that the Helix is actually a flattened disk whose thickness is roughly one-third its diameter with an inner region containing hot, highly ionized gas which is generally invisible in narrow-band images. The outer visible ring structure is of lower ionization and temperature and is brighter because of a thickening in the disk. We also confirm a central star effective temperature and luminosity of 120,000K and 100L_sun, and we estimate a lower limit to the nebular mass to be 0.30M_sun. Abundance measurements indicate the following values: He/H=0.12 (+/-0.017), O/H=4.60x10^-4 (+/-0.18), C/O=0.87 (+/-0.12), N/O=0.54 (+/-0.14), Ne/O=0.33 (+/-0.04), S/O=3.22x10^-3 (+/-0.26), and ...

  7. IDENTIFICACIÓN MOLECULAR DE POBLACIONES BACTERIANAS ASOCIADAS AL CARACOL PALA (Strombus gigas DEL CARIBE COLOMBIANO Molecular Identification Of Bacterial Populations Associated To Queen Conch (Strombus gigas From Colombian Caribbe

    Directory of Open Access Journals (Sweden)

    EDINSON ANDRÉS ACOSTA

    Full Text Available El caracol Pala, Strombus gigas (Strombidae, es de gran importancia ecológica y socioeconómica en el área caribeña colombiana. Sin embargo, es una especie catalogada como "vulnerable" y existe muy poca información referente a las especies bacterianas asociadas al caracol que puedan ser importantes para el desarrollo, manejo productivo y de seguridad acuícola de estos gastrópodos. En este trabajo, nosotros empleamos un estudio microbiológico y molecular de la región intergénica entre los genes 16S y 23S rDNA, análisis del gen rDNA 16S y secuenciación, para analizar las bacterias asociadas al caracol Pala (S. gigas. La composición de bacterias cultivables asociadas fue evaluada por su capacidad para crecer en agar marino y en medios de cultivos selectivos. De un total de 28 muestras analizadas encontramos que el número de bacterias cultivadas en condiciones aerobias fue de alrededor 10(6 ufc mL-1 donde las bacterias pertenecientes a la familia Vibrionacea fueron las más abundantes, cerca de >10(5 ufc mL-1. El análisis molecular de la región intergénica entre los genes 16S y 23S rDNA de las diferentes muestras, reveló una gran complejidad bacteriana asociada a S. gigas. Las secuencias de los amplificados del gen rDNA 16S identificó Pseudoalteromonas sp., Halomonas sp., Psycrobacter sp., Cobetia sp., Pseudomonas sp. y Vibrios sp. Nuestros resultados podrían sugerir un rol importante de estas bacterias como componentes de la comunidad asociada al S. gigas. Esta información puede complementar los estudios que se están implementando en los procesos para la conservación y repoblamiento de las poblaciones de S. gigas en Colombia.The Queen Conch, Strombus gigas (Strombidae, is a species of great ecological and socioeconomic importance in the Caribbean area of Colombia. However, it is currently catalogued as "vulnerable"; there is limited information concerning the bacterial species associated with conch and important in the

  8. DNA-like double helix formed by peptide nucleic acid

    DEFF Research Database (Denmark)

    Wittung, P; Nielsen, Peter E.; Buchardt, O; Egholm, M; Nordén, B

    1994-01-01

    Although the importance of the nucleobases in the DNA double helix is well understood, the evolutionary significance of the deoxyribose phosphate backbone and the contribution of this chemical entity to the overall helical structure and stability of the double helix is not so clear. Peptide nucleic...... of double helical DNA-like structures in solution....

  9. Government and Governance of Regional Triple Helix Interactions

    Science.gov (United States)

    Danson, Mike; Todeva, Emanuela

    2016-01-01

    This conceptual paper contributes to the discussion of the role of regional government and regional Triple Helix constellations driving economic development and growth within regional boundaries. The impact of regionalism and subsidiarity on regional Triple Helix constellations, and the questions of governmentality, governance and institutional…

  10. FPGA helix tracking algorithm for PANDA

    International Nuclear Information System (INIS)

    The PANDA detector is a general-purpose detector for physics with high luminosity cooled antiproton beams, planed to operate at the FAIR facility in Darmstadt, Germany. The central detector includes a silicon Micro Vertex Detector (MVD) and a Straw Tube Tracker (STT). Without any hardware trigger, large amounts of raw data are streaming into the data acquisition system. The data reduction task is performed in the online system by reconstruction algorithms programmed in VHDL (Very High Speed Integrated Circuit Hardware Description Language) on FPGAs (Field Programmable Gate Arrays) as first level and on a farm of GPUs or PCs as a second level. One important part in the system is the online track reconstruction. In this presentation, an online tracking finding algorithm for helix track reconstruction in the solenoidal field is shown. A performance study using C++ and the status of the VHDL implementation are presented.

  11. The Triple Helix Perspective of Innovation Systems

    CERN Document Server

    Leydesdorff, Loet

    2010-01-01

    Alongside the neo-institutional model of networked relations among universities, industries, and governments, the Triple Helix can be provided with a neo-evolutionary interpretation as three selection environments operating upon one another: markets, organizations, and technological opportunities. How are technological innovation systems different from national ones? The three selection environments fulfill social functions: wealth creation, organization control, and organized knowledge production. The main carriers of this system-industry, government, and academia-provide the variation both recursively and by interacting among them under the pressure of competition. Empirical case studies enable us to understand how these evolutionary mechanisms can be expected to operate in historical instance. The model is needed for distinguishing, for example, between trajectories and regimes.

  12. FPGA helix tracking algorithm for PANDA

    Energy Technology Data Exchange (ETDEWEB)

    Liang, Yutie; Galuska, Martin; Gessler, Thomas; Hu, Jifeng; Kuehn, Wolfgang; Lange, Jens Soeren; Muenchow, David; Spruck, Bjoern [II. Physikalisches, Giessen University (Germany); Ye, Hua [II. Physikalisches, Giessen University (Germany); Institute of High Energy Physics, Beijing (China); Collaboration: PANDA-Collaboration

    2014-07-01

    The PANDA detector is a general-purpose detector for physics with high luminosity cooled antiproton beams, planed to operate at the FAIR facility in Darmstadt, Germany. The central detector includes a silicon Micro Vertex Detector (MVD) and a Straw Tube Tracker (STT). Without any hardware trigger, large amounts of raw data are streaming into the data acquisition system. The data reduction task is performed in the online system by reconstruction algorithms programmed in VHDL (Very High Speed Integrated Circuit Hardware Description Language) on FPGAs (Field Programmable Gate Arrays) as first level and on a farm of GPUs or PCs as a second level. One important part in the system is the online track reconstruction. In this presentation, an online tracking finding algorithm for helix track reconstruction in the solenoidal field is shown. A performance study using C++ and the status of the VHDL implementation are presented.

  13. Triple helix interactions for eco-innovation

    DEFF Research Database (Denmark)

    Hermann, Roberto Rivas; Riisgaard, Henrik; Remmen, Arne

    . Overall, the research found that the Panamanian national innovation system facilitates eco-innovation by: providing research and development, building competence and financing of innovation processes. The “green maritime route” is an example of institutional eco-innovation promoted by the Panama Canal......Eco-innovation encompasses the “creative destruction” of unsustainable patterns of production and consumption. Research on eco-innovation promotion highlights the role of university in supporting industry and government partnerships to achieve sustainability. However, scant literature analyses the...... role of science parks in promoting eco-innovation. This study uses qualitative data gathered in two units of analysis: Panama Canal Authority and City of Knowledge Science Park. The study examines how Triple Helix interactions have built the regional system of eco-innovation at the Panama Canal...

  14. Folding and Unfolding of Helix-Turn-Helix Motifs in the Gas Phase

    OpenAIRE

    Zilch, Lloyd W.; Kaleta, David T.; Kohtani, Motoya; Krishnan, Ranjani; Jarrold, Martin F.

    2007-01-01

    Ion mobility measurements and molecular dynamic simulations have been performed for a series of peptides designed to have helix-turn-helix motifs. For peptides with two helical sections linked by a short loop region: AcA14KG3A14K+2H+, AcA14KG5A14K+2H+, AcA14KG7A14K+2H+, and AcA14KSar3A14K+2H+ (Ac = acetyl, A = alanine, G = glycine, Sar = sarcosine and K = lysine); a coiled-coil geometry with two anti-parallel helices is the lowest energy conformation. The helices uncouple and the coiled-coil ...

  15. NMR-based approach to measure the free energy of transmembrane helix-helix interactions.

    Science.gov (United States)

    Mineev, Konstantin S; Lesovoy, Dmitry M; Usmanova, Dinara R; Goncharuk, Sergey A; Shulepko, Mikhail A; Lyukmanova, Ekaterina N; Kirpichnikov, Mikhail P; Bocharov, Eduard V; Arseniev, Alexander S

    2014-01-01

    Knowledge of the energetic parameters of transmembrane helix-helix interactions is necessary for the establishment of a structure-energy relationship for α-helical membrane domains. A number of techniques have been developed to measure the free energies of dimerization and oligomerization of transmembrane α-helices, and all of these have their advantages and drawbacks. In this study we propose a methodology to determine the magnitudes of the free energy of interactions between transmembrane helices in detergent micelles. The suggested approach employs solution nuclear magnetic resonance (NMR) spectroscopy to determine the population of the oligomeric states of the transmembrane domains and introduces a new formalism to describe the oligomerization equilibrium, which is based on the assumption that both the dimerization of the transmembrane domains and the dissociation of the dimer can occur only upon the collision of detergent micelles. The technique has three major advantages compared with other existing approaches: it may be used to analyze both weak and relatively strong dimerization/oligomerization processes, it works well for the analysis of complex equilibria, e.g. when monomer, dimer and high-order oligomer populations are simultaneously present in the solution, and it can simultaneously yield both structural and energetic characteristics of the helix-helix interaction under study. The proposed methodology was applied to investigate the oligomerization process of transmembrane domains of fibroblast growth factor receptor 3 (FGFR3) and vascular endothelium growth factor receptor 2 (VEGFR2), and allowed the measurement of the free energy of dimerization of both of these objects. In addition the proposed method was able to describe the multi-state oligomerization process of the VEGFR2 transmembrane domain. PMID:24036227

  16. The Basic Helix-Loop-Helix Transcription Factor PIF5 Acts on Ethylene Biosynthesis and Phytochrome Signaling by Distinct Mechanisms

    Science.gov (United States)

    HYTOCHROME-INTERACTING FACTOR5 (PIF5), a basic helix-loop-helix transcription factor, interacts specifically with the photoactivated form of phytochrome B (phyB). Here, we report that dark-grown Arabidopsis thaliana seedlings overexpressing PIF5 (PIF5-OX) exhibit exaggerated apical hooks and short h...

  17. Exigência de proteína para o caracol gigante (Achatina fulica em fase de crescimento Protein requirements for giant snail (Achatina fulica during the growth phase

    Directory of Open Access Journals (Sweden)

    Giovani Sampaio Gonçalves

    1999-11-01

    Full Text Available Com o objetivo de determinar a exigência de proteína bruta (PB em dietas para o caracol gigante, 480 animais, com peso inicial médio de 4,05±0,04g, foram distribuídos em um delineamento inteiramente casualizado com quatro tratamentos (12,00%, 15,00%, 18,00% e 21,00% de PB e três repetições de 40 animais por unidade experimental, durante um período de 90 dias. Foi observado efeito quadrático (P Achatina fulica é de 18,28%.Aiming to determine the requirements of crude protein (CP in diets for giant snail, 480 animals, with 4.05±0.04g initial mean weight were used, and distributed in a completely randomized design with four treatments (12.00%, 15.00%, 18.00% and 21.00% CP, three replications of 40 animals per experimental unit, during a period of 90 days. A quadratic effect (P Achatina fulica is 18.28%.

  18. Direct folding simulation of a long helix in explicit water

    Science.gov (United States)

    Gao, Ya; Lu, Xiaoliang; Duan, Lili; Zhang, Dawei; Mei, Ye; Zhang, John Z. H.

    2013-05-01

    A recently proposed Polarizable Hydrogen Bond (PHB) method has been employed to simulate the folding of a 53 amino acid helix (PDB ID 2KHK) in explicit water. Under PHB simulation, starting from a fully extended structure, the peptide folds into the native state as confirmed by measured time evolutions of radius of gyration, root mean square deviation (RMSD), and native hydrogen bond. Free energy and cluster analysis show that the folded helix is thermally stable under the PHB model. Comparison of simulation results under, respectively, PHB and standard nonpolarizable force field demonstrates that polarization is critical for stable folding of this long α-helix.

  19. Effect of Hedera helix on lung histopathology in chronic asthma.

    OpenAIRE

    Arzu Babayigit Hocaoglu; Ozkan Karaman; Duygu Olmez Erge; Guven Erbil; Osman Yilmaz; Bijen Kivcak; H Alper Bagriyanik; Nevin Uzuner

    2012-01-01

    Hedera helix  is widely used to treat bronchial asthma for many years. However, effects of this herb on lung histopathology is still far from clear. We aimed to determine the effect of oral administration of Hedera helix on lung histopathology in a murine model of chronic asthma.BALB/c  mice  were  divided  into  four  groups;   I  (Placebo),  II  (Hedera  helix), III (Dexamethasone) and IV (Control). All mice except controls were sensitized and challenged with ovalbumin. Then, mice in group ...

  20. Effects of radiation on DNA's double helix

    Science.gov (United States)

    2003-01-01

    The blueprint of life, DNA's double helix is found in the cells of everything from bacteria to astronauts. Exposure to radiation(depicted at right) such as X-rays (upper) or heavy ion particles (lower), can damage DNA and cause dire consequences both to the organism itself and to future generations. One of NASA's main goals is to develop better radiation shielding materials to protect astronauts from destructive radiation in space. This is particularly important for long space missions. NASA has selected researchers to study materials that provide better shielding. This research is managed by NASA's Office of Biological and Physical Research and is supported by the Microgravity Science and Applications Department at NASA's Marshall Center. During International Space Station Expedition Six, the Extravehicular Activity Radiation Monitoring (EVARM) will continue to measure radiation dosage encountered by the eyes, internal organs and skin during specific spacewalks, and relate it to the type of activity, location and other factors. An analysis of this information may be useful in mitigating potential exposure to space walkers in the future. (Illustration by Dr. Frank Cucinotta, NASA/Johnson Space Center, and Prem Saganti, Lockheed Martin)

  1. A supramolecular helix that disregards chirality

    Science.gov (United States)

    Roche, Cécile; Sun, Hao-Jan; Leowanawat, Pawaret; Araoka, Fumito; Partridge, Benjamin E.; Peterca, Mihai; Wilson, Daniela A.; Prendergast, Margaret E.; Heiney, Paul A.; Graf, Robert; Spiess, Hans W.; Zeng, Xiangbing; Ungar, Goran; Percec, Virgil

    2016-01-01

    The functions of complex crystalline systems derived from supramolecular biological and non-biological assemblies typically emerge from homochiral programmed primary structures via first principles involving secondary, tertiary and quaternary structures. In contrast, heterochiral and racemic compounds yield disordered crystals, amorphous solids or liquids. Here, we report the self-assembly of perylene bisimide derivatives in a supramolecular helix that in turn self-organizes in columnar hexagonal crystalline domains regardless of the enantiomeric purity of the perylene bisimide. We show that both homochiral and racemic perylene bisimide compounds, including a mixture of 21 diastereomers that cannot be deracemized at the molecular level, self-organize to form single-handed helical assemblies with identical single-crystal-like order. We propose that this high crystalline order is generated via a cogwheel mechanism that disregards the chirality of the self-assembling building blocks. We anticipate that this mechanism will facilitate access to previously inaccessible complex crystalline systems from racemic and homochiral building blocks.

  2. Role of hydration and intramolecular interactions in the helix-coil transition and helix-helix assembly in a deca-alanine peptide

    CERN Document Server

    Tomar, Dheeraj S; Pettitt, B M; Asthagiri, D

    2015-01-01

    For a model deca-alanine peptide the cavity (ideal hydrophobic) contribution to hydration favors the helix state in the coil-to-helix transition and the paired helix bundle in the assembly of two helices. The energetic contributions of attractive protein-solvent interactions are separated into a short-range part arising from interactions with solvent in the first hydration shell and the remaining long-range part. In the helix-coil transition, short-range attractive protein-solvent interactions outweigh hydrophobic hydration and favor the unfolded coil states. Analysis of enthalpic effects shows that it is the favorable hydration of the peptide backbone that favors the unfolded state. Protein intramolecular interactions favor the helix state and are decisive in folding. In the pairing of two helices, the cavity contribution outweighs short-range attractive protein-water interactions. However, long-range, protein-solvent attractive interactions can either enhance or reverse this trend depending on the mutual or...

  3. Half wave helix loaded superconducting resonator for heavy ion Linac

    International Nuclear Information System (INIS)

    We report here the main characteristics and performances of the helix superconducting resonators designed and mounted in the new Saclay Booster Linac which is the first european heavy ion superconducting accelerator

  4. Microbiological and chemical analysis of land snails commercialised in Sicily

    Directory of Open Access Journals (Sweden)

    Antonello Cicero

    2015-05-01

    Full Text Available In this study 160 samples of snails belonging to the species Helix aspersa maxima and Helix aspersa muller were examined for chemical and microbiological analysis. Samples came from Greece and Poland. Results showed mean concentration of cadmium (0.35±0.036 mg/kg and lead (0.05±0.013 mg/kg much higher than the limit of detection. Mercury levels in both species were not detected. Microbiological analysis revealed the absence of Salmonella spp. and Clostridium spp. in both examined species. E. coli and K. oxytoca were observed in Helix aspersa maxima and Helix aspersa muller. Furthermore, one case of fungi positivity in samples of Helix aspersa muller was found. The reported investigations highlight the need to create and adopt a reference legislation to protect the health of consumers.

  5. Detection of Listeria monocytogenes by using PCR in Helix pomatia

    OpenAIRE

    KIRKAN, Şükrü; GÖKSOY, Ergün Ö.; KAYA, Osman

    2006-01-01

    The detection of Listeria monocytogenes in Helix pomatia, both raw and cooked is presented here. Polymerase chain reaction (PCR) is a rapid procedure with both sensitivity and specificity for quick detection and identification of Listeria monocytogenes from raw and cooked Helix pomatia. A total of 30 bags (10 g each) of H. pomatia samples were investigated for the Listeria monocytogenes inlB gene with the PCR method. PCR amplification products demonstrated that 18 of the 30 samples showed pos...

  6. Hedera helix L. and damages in Tlos Ancient City

    Directory of Open Access Journals (Sweden)

    Elinç, Z.K.

    2013-03-01

    Full Text Available There are various plant types in Tlos Ancient City of Fethiye district in the Province of Mugla, a city where different residential ruins of Lycia Civilization starting from Classical Age until Byzantine Period. Tlos is an important city in West-Lycia and is situated right on the control point of Lycia Way. Hedera helix L. is one of the plants living in this area, which attracts the attention as it mostly harms the ancient ruins. One of the most important reasons why Hedera helix L. is growing commonly in this region is the perfect ecological circumstances for the growth of this plant of the location where this ancient city is situated in. Additionally the fact that the ruins of the city are left on their fate, is another perfect circumstance for the Hedera helix L. to grow. Climbing or creeping stems of Hedera helix L. stick easily to the objects it touches and encircle them. Due to this characteristic, the walls of the ancient city are covered by this plant. Nevertheless, Hedera helix L. does not only harm the ancient constructions and natural rocks but also woody plants. The harm caused by dried out or cut Hedera helix L. are more than the harm caused by them when they were untouched. The subject of this study is to prove the shape and level of the harm caused by Hedera helix L. on ancient ruins of Tlos. At the same time, this study will underline the fighting methods against Hedera helix L. by comparing similar studies in other countries. Knowledge collected after this study will offer an insight into the excavation and restoration studies undertaken in all Mediterranean countries.

  7. A statistically derived parameterization for the collagen triple-helix

    OpenAIRE

    Rainey, Jan K.; Goh, M. Cynthia

    2002-01-01

    The triple-helix is a unique secondary structural motif found primarily within the collagens. In collagen, it is a homo- or hetero-tripeptide with a repeating primary sequence of (Gly-X-Y)n, displaying characteristic peptide backbone dihedral angles. Studies of bulk collagen fibrils indicate that the triple-helix must be a highly repetitive secondary structure, with very specific constraints. Primary sequence analysis shows that most collagen molecules are primarily triple-helical; however, n...

  8. About the helix structure of the Lund string

    OpenAIRE

    Todorova, Sarka

    2011-01-01

    The helix structure of the Lund string, first derived from studies devoted to the emission of soft gluons at the end of the parton cascade, may be at the origin of certain characteristic discrepancies observed in the low transverse momentum region at LEP and LHC. A study of the relation between different helix implementations and observable effects is presented. The model is extended to cover a multiparton string topology (result of parton shower), and compared with the experimental data. It ...

  9. The basic helix-loop-helix transcription factor, Mist1, induces maturation of mouse fetal hepatoblasts.

    Science.gov (United States)

    Chikada, Hiromi; Ito, Keiichi; Yanagida, Ayaka; Nakauchi, Hiromitsu; Kamiya, Akihide

    2015-01-01

    Hepatic stem/progenitor cells, hepatoblasts, have a high proliferative ability and can differentiate into mature hepatocytes and cholangiocytes. Therefore, these cells are considered to be useful for regenerative medicine and drug screening for liver diseases. However, it is problem that in vitro maturation of hepatoblasts is insufficient in the present culture system. In this study, a novel regulator to induce hepatic differentiation was identified and the molecular function of this factor was examined in embryonic day 13 hepatoblast culture with maturation factor, oncostatin M and extracellular matrices. Overexpression of the basic helix-loop-helix type transcription factor, Mist1, induced expression of mature hepatocytic markers such as carbamoyl-phosphate synthetase1 and several cytochrome P450 (CYP) genes in this culture system. In contrast, Mist1 suppressed expression of cholangiocytic markers such as Sox9, Sox17, Ck19, and Grhl2. CYP3A metabolic activity was significantly induced by Mist1 in this hepatoblast culture. In addition, Mist1 induced liver-enriched transcription factors, CCAAT/enhancer-binding protein α and Hepatocyte nuclear factor 1α, which are known to be involved in liver functions. These results suggest that Mist1 partially induces mature hepatocytic expression and function accompanied by the down-regulation of cholangiocytic markers. PMID:26456005

  10. Macrocyclization and labeling of helix-loop-helix peptide with intramolecular bis-thioether linkage.

    Science.gov (United States)

    Nishihara, Toshio; Kitada, Hidekazu; Fujiwara, Daisuke; Fujii, Ikuo

    2016-11-01

    Conformationally constrained peptides have been developed as an inhibitor for protein-protein interactions (PPIs), and we have de novo designed cyclized helix-loop-helix (cHLH) peptide with a disulfide bond consisting of 40 amino acids to generate molecular-targeting peptides. However, synthesis of long peptides has sometimes resulted in low yield according to the respective amino acid sequences. Here we developed a method for efficient synthesis and labeling for cHLH peptides. First, we synthesized two peptide fragments and connected them by the copper-mediated alkyne and azide cycloaddition (CuAAC) reaction. Cyclization was performed by bis-thioether linkage using 1,3-dibromomethyl-5-propargyloxybenzene, and subsequently, the cHLH peptide was labeled with an azide-labeled probe. Finally, we designed and synthesized a peptide inhibitor for the p53-HDM2 interaction using a structure-guided design and successfully labeled it with a fluorescent probe or a functional peptide, respectively, by click chemistry. This macrocyclization and labeling method for cHLH peptide would facilitate the discovery of de novo bioactive ligands and therapeutic leads. © 2016 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 415-421, 2016. PMID:26917088

  11. Nanoparticle biofabrication using English ivy (Hedera helix

    Directory of Open Access Journals (Sweden)

    Burris Jason N

    2012-10-01

    Full Text Available Abstract Background English ivy (Hedera helix is well known for its adhesive properties and climbing ability. Essential to its ability to adhere to vertical surfaces is the secretion of a nanocomposite adhesive containing spherical nanoparticles, 60–85 nm in diameter, produced exclusively by root hairs present on adventitious roots. These organic nanoparticles have shown promise in biomedical and cosmetic applications, and represent a safer alternative to metal oxide nanoparticles currently available. Results It was discovered that the maximum adventitious root production was achieved by a 4 h application of 1 mg/ml indole-3 butyric acid (IBA to juvenile English ivy shoot segments cultured in custom vessels. After incubation of the shoots under continuous light at 83 μmol/m2 s at 20°C for 2 weeks, the adventitious roots were harvested from the culture system and it was possible to isolate 90 mg of dry weight nanoparticles per 12 g of roots. The nanoparticle morphology was characterized by atomic force microscopy, and found to be similar to previous studies. Conclusions An enhanced system for the production of English ivy adventitious roots and their nanoparticles by modifying GA7 Magenta boxes and identifying the optimal concentration of IBA for adventitious root growth was developed. This system is the first such platform for growing and harvesting organic nanoparticles from plants, and represents an important step in the development of plant-based nanomanufacturing. It is a significant improvement on the exploitation of plant systems for the formation of metallic nanoparticles, and represents a pathway for the generation of bulk ivy nanoparticles for translation into biomedical applications.

  12. A possible family of B-like triple helix structures: comparison with the Arnott A-like triple helix.

    Science.gov (United States)

    Ouali, M; Letellier, R; Adnet, F; Liquier, J; Sun, J S; Lavery, R; Taillandier, E

    1993-03-01

    Recent experimental studies of the structure of triple helices show that their conformation in solution differs from the A-like structure derived from diffraction data on triple helix fibers by Arnott and co-workers. Here we show by means of molecular modeling that a family of triple helix structures may exist with similar conformational energies, but with a variety of sugar puckers. The characteristics of these putative triple helices are analyzed for three different base sequences: (T.AxT)n, (C.GxC+)n, and alternating (C.GxC+/T.AxT)n. In the case of (C.GxC+)n triple helix, infrared and Raman spectra have been obtained and clearly reveal the existence of both N- and S-type sugars in solution. The molecular mechanics calculations allow us to propose a stereochemically reasonable model for this triple helix, in good agreement with the vibrational spectroscopy results. PMID:8448168

  13. Conformational and dynamics simulation study of antimicrobial peptide hedistin-heterogeneity of its helix-turn-helix motif.

    Science.gov (United States)

    Xu, Guohua; Wu, Min; Wang, Lin; Zhang, Xu; Cao, Shufen; Liu, Maili; Cui, Yanfang

    2009-12-01

    Hedistin is an antimicrobial peptide isolated from the coelomocytes of Nereis diversicolor, possessing activity against a large spectrum of bacteria including the methicillin resistant Staphylococcus aureus and Vibrio alginolyticus. The three-dimensional structure of hedistin in both aqueous solution and deuterated dodecylphosphocholine (DPC) micelles was examined using circular dichroism (CD) and nuclear magnetic resonance (NMR) techniques. And, the early events of the antibacterial process of hedistin were simulated using palmitoyl-oleoyl-phophatidylcholine (POPC) lipid bilayers and molecular dynamics (MD) simulation methods. Hedistin lacks secondary structure in aqueous solution, however, in DPC micelles, it features with a heterogeneous helix-turn-helix moiety and exhibits obvious amphipathic nature. The turn region (residues Val9-Thr12) in the moiety is a four-residue hinge, lying in between the first N-terminal alpha-helix (residues Leu5-Lys8) and the second alpha-helix (residues Val13-Ala17) regions and causing an approximately 120 degrees angle between the axes of the two helices. The segmental and nonlinear nature of hedistin structure is referred to as the heterogeneity of its helix-turn-helix motif which was found to be corresponding to a kind of discrete dynamics behavior, herein coined as its dynamical heterogeneity, at the early stage (0-50 ns) of the MD simulations. That is, the first helix segment, prior to (at 310 K) or following (at 363 K) the second helix, binds to the lipid head-group region and subsequently permeates into the hydrophobic lipid tail region, and the hinge is the last portion entering the lipid environment. This result implies that hedistin may adopt a "carpet" model action when disrupting bacterial membrane. PMID:19819221

  14. Aspectos biológicos de los caracoles Plicopurpura pansa y Plicopurpura columellaris mediante observaciones en condiciones de laboratorio (Biological aspects of snails Plicopurpura pansa and Plicopurpura columellaris through observations in laboratory conditions

    Directory of Open Access Journals (Sweden)

    Domínguez-Ojeda, Delia

    2009-02-01

    Full Text Available ResumenPlicopurpura pansa y Plicopurpura columellaris (Familia Thaididae, son gasterópodos dioicos, depredadores de la zona intermareal, comunes sobre sustratos duros en el Pacífico este tropical. Se tuvieron en observación diaria caracoles del género Plicopurpura desde 1999 al 2004 en condiciones de laboratorio. Éstos se encontraban confinados en acuarios de diferentes medidas, con agua marina, equipados con filtros y cabezas de poder con recambio constante y se les suministró alimento. Se observaron cambios en su morfología, en las diferentes etapas reproductivas, en su desarrollo larvario y embrionario y en el proceso de regeneración del órgano copulador. De manera preliminar, se destaca que pueden no existir límites en los hábitos reproductivos entre estas dos especies, o que quizá se trate de subespecies o incluso de la misma con variaciones morfológicas dadas por las condiciones ambientales.SummaryPlicopurpura pansa y Plicopurpura columellaris (Family Thaididae, are gastropods dioecious, predators of the intertidal zone, commons on hard substrates in the tropical eastern Pacific. They were in observation every day from 1999 to 2004 in laboratory conditions. These were confined in aquariums of different measures, with seawater and equipped with filters and replacement with heads of power with continuous change of water and supplied with food. There were changes in their morphology, at different reproductive stages in their embryonic and larval development and in the process of regeneration of their copulative organ. As a primary statement, it is stressed that cannot exist limits on the reproductive habitsbetween these two species, or perhaps might be subspecies or even thesame with morphological variation due to environmental conditions.

  15. Effect of Hedera helix on lung histopathology in chronic asthma.

    Directory of Open Access Journals (Sweden)

    Arzu Babayigit Hocaoglu

    2012-12-01

    Full Text Available Hedera helix  is widely used to treat bronchial asthma for many years. However, effects of this herb on lung histopathology is still far from clear. We aimed to determine the effect of oral administration of Hedera helix on lung histopathology in a murine model of chronic asthma.BALB/c  mice  were  divided  into  four  groups;   I  (Placebo,  II  (Hedera  helix, III (Dexamethasone and IV (Control. All mice except controls were sensitized and challenged with ovalbumin. Then, mice in group I received saline, group II 100 mg/kg Hedera helix and group III 1 mg/kg  dexamethasone via orogastic gavage once daily for one week. Airway histopathology was evaluated by using light and electron microscopy in all groups.Goblet  cell numbers and thicknesses of basement membrane were found  significantly lower in group II, but there was no statistically significant difference in terms of number of mast cells, thicknesses of epithelium and subepithelial smooth muscle layers between group I and II. When Hedera helix and dexamethasone groups were compared with each other, thickness of epithelium, subepithelial muscle layers, number of mast cells and goblet cells of group III were significantly ameliorated when compared with the group II.Although Hedera helix administration reduced only goblet cell counts and the thicknesses of basement membrane  in the  asthmatic airways, dexamethasone ameliorated all histopathologic parameters except thickness of  basement  membrane  better  than  Hedera helix.

  16. Preferred sequences for DNA recognition by the TAL1 helix-loop-helix proteins

    Energy Technology Data Exchange (ETDEWEB)

    Hai-Ling Hsu; Lan Huang; Julia Tsou Tsan [Univ. of Texas Southwestern Medical Center, Dallas, TX (United States)] [and others

    1994-02-01

    Tumor-specific activation of the TAL1 gene is the most common genetic alteration seen in patients with T-cell acute lymphoblastic leukemia. The TAL1 gene products contain the basic helix-loop-helix (bHLH) domain, a protein dimerization and DNA-binding motif common to several known transcription factors. A binding-site selection procedure has now been used to evaluate the DNA recognition properties of TAL1. These studies demonstrate that TAL1 polypeptides do not have intrinsic DNA-binding activity, presumably because of their inability to form bHLH homodimers. However, TAL1 readily interacts with any of the known class A bHLH proteins (E12, E47, E2-2, and HEB) to form heterodimers that bind DNA in a sequence-specific manner. The TAL1 heterodimers preferentially recognize a subset of E-box elements (CANNTG) that can be represented by the consensus sequence AACAGATGGT. This consensus is composed of half-sites for recognition by the participating class A bHLH polypeptide (AACAG) and the TAL1 polypeptide (ATGGT). TAL1 heterodimers with DNA-binding activity are readily detected in nuclear extracts of Jurkat, a leukemic cell line derived from a patient with T-cell acute lymphoblastic leukemia. Hence, TAL1 is likely to bind and regulate the transcription of a unique subset of subordinate target genes, some of which may mediate the malignant function of TAL1 during T-cell leukemogenesis. 48 refs., 10 figs.

  17. Conformation dependent electronic transport in a DNA double-helix

    International Nuclear Information System (INIS)

    We present a tight-binding study of conformation dependent electronic transport properties of DNA double-helix including its helical symmetry. We have studied the changes in the localization properties of DNA as we alter the number of stacked bases within every pitch of the double-helix keeping fixed the total number of nitrogen bases within the DNA molecule. We take three DNA sequences, two of them are periodic and one is random and observe that in all the cases localization length increases as we increase the radius of DNA double-helix i.e., number of nucleobases within a pitch. We have also investigated the effect of backbone energetic on the I-V response of the system and found that in presence of helical symmetry, depending on the interplay of conformal variation and disorder, DNA can be found in either metallic, semiconducting and insulating phases, as observed experimentally

  18. Conformation dependent electronic transport in a DNA double-helix

    Energy Technology Data Exchange (ETDEWEB)

    Kundu, Sourav, E-mail: sourav.kundu@saha.ac.in; Karmakar, S. N., E-mail: sachindranath.karmakar@saha.ac.in [Condensed Matter Physics Division, Saha Institute of Nuclear Physics, 1/AF, Bidhannagar, Kolkata 700 064 (India)

    2015-10-15

    We present a tight-binding study of conformation dependent electronic transport properties of DNA double-helix including its helical symmetry. We have studied the changes in the localization properties of DNA as we alter the number of stacked bases within every pitch of the double-helix keeping fixed the total number of nitrogen bases within the DNA molecule. We take three DNA sequences, two of them are periodic and one is random and observe that in all the cases localization length increases as we increase the radius of DNA double-helix i.e., number of nucleobases within a pitch. We have also investigated the effect of backbone energetic on the I-V response of the system and found that in presence of helical symmetry, depending on the interplay of conformal variation and disorder, DNA can be found in either metallic, semiconducting and insulating phases, as observed experimentally.

  19. The Knowledge-Based Economy and the Triple Helix Model

    CERN Document Server

    Leydesdorff, Loet

    2012-01-01

    1. Introduction - the metaphor of a "knowledge-based economy"; 2. The Triple Helix as a model of the knowledge-based economy; 3. Knowledge as a social coordination mechanism; 4. Neo-evolutionary dynamics in a Triple Helix of coordination mechanism; 5. The operation of the knowledge base; 6. The restructuring of knowledge production in a KBE; 7. The KBE and the systems-of-innovation approach; 8. The KBE and neo-evolutionary theories of innovation; 8.1 The construction of the evolving unit; 8.2 User-producer relations in systems of innovation; 8.3 'Mode-2' and the production of scientific knowledge; 8.4 A Triple Helix model of innovations; 9. Empirical studies and simulations using the TH model; 10. The KBE and the measurement; 10.1 The communication of meaning and information; 10.2 The expectation of social structure; 10.3 Configurations in a knowledge-based economy

  20. Hedera helix L. and damages in Tlos Ancient City

    OpenAIRE

    Elinç, Z.K.; Korkut, T.; Kaya, L.G.

    2013-01-01

    There are various plant types in Tlos Ancient City of Fethiye district in the Province of Mugla, a city where different residential ruins of Lycia Civilization starting from Classical Age until Byzantine Period. Tlos is an important city in West-Lycia and is situated right on the control point of Lycia Way. Hedera helix L. is one of the plants living in this area, which attracts the attention as it mostly harms the ancient ruins. One of the most important reasons why Hedera helix L. is gr...

  1. Dynamics of helix-coil transition and isotope exchange reaction

    International Nuclear Information System (INIS)

    A dynamical theory is presented for the helix-coil transition and the isotope exchange reaction in a short polypeptide chain. In this theory it is assumed that there is always one and only one helical sequence. The boundaries of the helix are assumed to move randomly along the chain. If we assume slow movement of the boundaries, our model theory explains the experimental results, i.e., the very low rate of the isotope exchange in the central portion of the chain and the site dependence of the rate. (author)

  2. Experimental Validation of Chatter Stability for Variable Helix Milling Tools

    International Nuclear Information System (INIS)

    The occurrence of self-excited vibrations during machining is known as regenerative chatter, and this phenomenon can severely limit the machining productivity. By modifying and optimising the tool's pitch and helix geometry, this regenerative chatter can be suppressed to increase material removal rate. In this paper, experimental verification of an optimised variable helix and variable pitch tools is presented. The geometry was optimised using a Differential Evolution (DE) algorithm. Based on stability diagrams of original and optimised milling tools, the experiment was conducted and the results were compared when chatter occurred. The optimised cutter significantly outperformed the original cutter in term of chatter suppression.

  3. Genética poblacional del caracol rosado Strombus gigas en la Península de Yucatán: Implicaciones para su manejo y pesquería

    Directory of Open Access Journals (Sweden)

    2005-01-01

    Full Text Available Se determinó la estructura genética poblacional del caracol rosado Strombus gigas en la Península de Yucatán, México, mediante la expresión de isoenzimas en geles de poliacrilamida. Se utilizaron muestras de músculo de 50 organismos, capturados en cada uno de los cuatro sitios de la Península de Yucatán seleccionados, para caracterizar la expresión genotípica revelada por la expresión de 55 loci en 30 sistemas enzimáticos. Se utilizó el programa TFPGA versión 1.3 para procesar los datos de frecuencias génicas de aloenzimas de las poblaciones en estudio. Los parámetros determinados fueron: estadística descriptiva, estadística F, distancias genéticas, equilibrio de Hardy-Weinberg, UPGMA y el número de migrantes como indicador del flujo de genes. Los valores de heterocigosis, en un rango de 0.3240 para OCTDH 2 hasta 0.0440 para FUM y promedio de 0.0366, los de Fis, con un rango de 0.0835 para OCTDH 2 hasta 0.3600 para la FUM y promedio de –0.0492, y los de Fst, con un rango de 0.0082 para LAP 2 hasta 0.1967 para MDH 2 y promedio de 0.1039, indican una deficiencia de heterocigotos. El número de migrantes derivado de la ecuación de Slatkin resultó de 2.156 por generación, lo que en forma global indica un cierto grado de variabilidad entre las poblaciones y es consistente con los bajos valores de distancia genética de Nei encontrados, particularmente en el nodo que sugiere la separación de la población de Alacranes de las otras poblaciones estudiadas, con un valor obtenido de 0.0053. Por los resultados, se concluye que las poblaciones de S. gigas en el Caribe mexicano presentan niveles de variabilidad genética que no reflejan fragilidad para su subsistencia.

  4. Geometría y traza de escaleras góticas. Las escuadras como ábacos en la construcción de los caracoles de la catedral de Tortosa

    Directory of Open Access Journals (Sweden)

    Lluis i Ginovart, J.

    2016-03-01

    Full Text Available In the Gothic era, spiral staircases were one of the greatest showpieces of the magister operis knowledge. They were the focus of arithmetic and geometric medieval constructor knowledge. Their construction involved the use of templates known as gabarits, which required the polygonal division of the circumference. These regular 11-, 13-, 14-, 17- and 19-sided polygons do not appear in the Euclid’s Elementa or the Tolomeo’s Almagest, or in the few Practica Geometriae of the time. These polygons can be constructed by using a square with two arms, supporting repeatedly the legs on the hypotenuse, a rotation of the instrument. Squares constructed using arithmetic or geometric methods must always be calibrated and can therefore be used as an abacus, which enables the circumference to be divided with sufficient accuracy. San Pedro (1383 and Santa Catalina staircases (1424, of Tortosa’s cathedral, have been drawn by the instruments explained previously.Las escaleras de caracol en el período gótico han sido uno de los mayores exponentes del conocimiento de los magister operis. En él se concentran los saberes aritméticos y geométricos del constructor medieval. Para su construcción se utilizan los gabarits, que necesitan el concurso de la división poligonal de la circunferencia. Los polígonos regulares de 11, 13, 14, 17 y 19 caras no aparecen en los Elementa de Euclides, ni en el Almagesto de Tolomeo, ni en las escasas Practica Geometriae de la época. Estos polígonos pueden ser construidos mediante la utilización de una escuadra de dos brazos, con el apoyo reiterado de los catetos sobre la hipotenusa, creando así una rotación del instrumento. Las escuadras construidas por métodos aritméticos o geométricos pueden ser utilizadas como un ábaco, el cual permite resolver con suficiente exactitud la división de la circunferencia. Las escaleras de San Pedro (1383 y Santa Catalina (1424 de la catedral de Tortosa han sido trazadas mediante

  5. Control of regulatory T cell and Th17 cell differentiation by inhibitory helix-loop-helix protein Id3

    OpenAIRE

    Maruyama, Takashi; Li, Jun; Vaque, Jose P.; Konkel, Joanne E.; Wang, Weifeng; Zhang, Baojun; Zhang, Pin; Zamarron, Brian; Yu, Dongyang; Wu, Yuntao; Zhuang, Yuan; Gutkind, J Silvio; Chen, Wanjun

    2010-01-01

    The molecular mechanisms directing Foxp3 gene transcription in CD4+ T cells remain ill defined. We show that deletion of the inhibitory helix-loop-helix (HLH) protein Id3 results in defective Foxp3+ Treg cell generation. We identified two transforming grothw factor-β1 (TGF-β1)-dependent mechanisms that are vital for activation of Foxp3 gene transcription, and are defective in Id3−/− CD4+ T cells. Enhanced binding of the HLH protein E2A to the Foxp3 promoter promoted Foxp3 gene transcription. ...

  6. A review of fast circle and helix fitting

    CERN Document Server

    Frühwirth, R; Waltenberger, W; Wroldsen, J

    2003-01-01

    Circle and helix fitting is of paramount importance in the data analysis of LHC experiments. We review several approaches to exact but fast fitting, including a recent development based on the projection of the measured points onto a second-order surface in space (a sphere or a paraboloid). We present results of a comparison with global and recursive linearized least-squares estimators.

  7. Talent Development as a University Mission: The Quadruple Helix

    Science.gov (United States)

    Holm-Nielsen, Lauritz B.; Thorn, Kristian; Olesen, Jeppe Dorup; Huey, Tina

    2013-01-01

    In this paper, the authors discuss the rationale behind making talent development at the PhD, post-doctoral and early career levels an equal fourth pillar of the university's mission, alongside the more traditional pillars of the triple helix. Using Denmark and Aarhus University as a case study, the paper describes how increased institutional…

  8. Structural constraints regulating triple helix formation by A-tracts.

    Science.gov (United States)

    Sen, A; Gräslund, A

    2000-12-15

    The study concerns the propensity of triple helix formation by different DNA oligonucleotides containing long A-tracts with and without flanking GxC base pairs in order to probe the role of length of the A-tract and the flanking sequences. From nuclear magnetic resonance (NMR) studies of imino proton spectra and circular dichroism (CD) spectroscopy of samples composed of potential triplex forming strand sequences in correct stoichiometries, we have concluded that 8-mer A-tracts flanked by GxC base pairs exert significant steric hindrance to triple helix formation. When as much as 50 mM Mg2+ was added, no triple helix formation was observed in these samples. In contrast, open-ended 8-mer A-tracts formed triplex with the corresponding two T8 strands under relatively mild ionic conditions (100 mM Na+). Moreover, the shorter the length of the A-tract, the less is the hindrance to form a triple helix. PMID:11152277

  9. Anomalous radio emission from dust in the Helix

    CERN Document Server

    Casassus, S; Pearson, T J; Nyman, L A A; Shepherd, M C; Bronfman, L

    2004-01-01

    A byproduct of experiments designed to map the CMB is the recent detection of a new component of foreground Galactic emission. The anomalous foreground at ~ 10--30 GHz, unexplained by traditional emission mechanisms, correlates with 100um dust emission. We report that in the Helix the emission at 31 GHz and 100um are well correlated, and exhibit similar features on sky images, which are absent in H\\beta. Upper limits on the 250 GHz continuum emission in the Helix rule out cold grains as candidates for the 31 GHz emission, and provide spectroscopic evidence for an excess at 31 GHz over bremsstrahlung. We estimate that the 100um-correlated radio emission, presumably due to dust, accounts for at least 20% of the 31 GHz emission in the Helix. This result strengthens previous tentative interpretations of diffuse ISM spectra involving a new dust emission mechanism at radio frequencies. Very small grains have not been detected in the Helix, which hampers interpreting the new component in terms of spinning dust. The ...

  10. Enhancer of splitD, a dominant mutation of Drosophila, and its use in the study of functional domains of a helix-loop-helix protein.

    OpenAIRE

    Tietze, K.; Oellers, N; Knust, E.

    1992-01-01

    Helix-loop-helix proteins play important roles in developmental processes, such as myogenesis, neurogenesis, and sex determination. The gene Enhancer of split [E(spl)] of Drosophila, a member of a gene complex that is involved in early neurogenesis, encodes a protein with a basic domain and a helix-loop-helix motif. We took advantage of a dominant mutation of this gene, E(spl)D, to define in vivo structural features of this protein for proper function. The mutation renders the otherwise reces...

  11. Enhancer of split^D, a dominant mutation of Drosophila, and its use in the study of functional domains of a helix-loop-helix protein

    OpenAIRE

    Tietze, Kyria; Oellers, Nadja; Knust, Elisabeth

    1992-01-01

    Helix-loop-helix proteins play important roles in developmental processes, such as myogenesis, neurogenesis, and sex determination. The gene Enhancer of split [E(spl)] of Drosophila, a member of a gene complex that is involved in early neurogenesis, encodes a protein with a basic domain and a helix-loop-helix motif. We took advantage of a dominant mutation of this gene, E(spl)^D, to define in vivo structural features of this protein for proper function. The mutation renders the otherwise rece...

  12. Structure of single-wall carbon nanotubes: a graphene helix.

    Science.gov (United States)

    Lee, Jae-Kap; Lee, Sohyung; Kim, Jin-Gyu; Min, Bong-Ki; Kim, Yong-Il; Lee, Kyung-Il; An, Kay Hyeok; John, Phillip

    2014-08-27

    Evidence is presented in this paper that certain single-wall carbon nanotubes are not seamless tubes, but rather adopt a graphene helix resulting from the spiral growth of a nano-graphene ribbon. The residual traces of the helices are confirmed by high-resolution transmission electron microscopy and atomic force microscopy. The analysis also shows that the tubular graphene material may exhibit a unique armchair structure and the chirality is not a necessary condition for the growth of carbon nanotubes. The description of the structure of the helical carbon nanomaterials is generalized using the plane indices of hexagonal space groups instead of using chiral vectors. It is also proposed that the growth model, via a graphene helix, results in a ubiquitous structure of single-wall carbon nanotubes. PMID:24838196

  13. Triple Helix Formation in a Topologically Controlled DNA Nanosystem.

    Science.gov (United States)

    Yamagata, Yutaro; Emura, Tomoko; Hidaka, Kumi; Sugiyama, Hiroshi; Endo, Masayuki

    2016-04-11

    In the present study, we demonstrate single-molecule imaging of triple helix formation in DNA nanostructures. The binding of the single-molecule third strand to double-stranded DNA in a DNA origami frame was examined using two different types of triplet base pairs. The target DNA strand and the third strand were incorporated into the DNA frame, and the binding of the third strand was controlled by the formation of Watson-Crick base pairing. Triple helix formation was monitored by observing the structural changes in the incorporated DNA strands. It was also examined using a photocaged third strand wherein the binding of the third strand was directly observed using high-speed atomic force microscopy during photoirradiation. We found that the binding of the third strand could be controlled by regulating duplex formation and the uncaging of the photocaged strands in the designed nanospace. PMID:26938310

  14. Nonlinear time-dependent simulation of helix traveling wave tubes

    International Nuclear Information System (INIS)

    A one-dimensional nonlinear time-dependent theory for helix traveling wave tubes is studied. A generalized electromagnetic field is applied to the expression of the radio frequency field. To simulate the variations of the high frequency structure, such as the pitch taper and the effect of harmonics, the spatial average over a wavelength is substituted by a time average over a wave period in the equation of the radio frequency field. Under this assumption, the space charge field of the electron beam can be treated by a space charge wave model along with the space charge coefficient. The effects of the radio frequency and the space charge fields on the electrons are presented by the equations of the electron energy and the electron phase. The time-dependent simulation is compared with the frequency-domain simulation for a helix TWT, which validates the availability of this theory. (interdisciplinary physics and related areas of science and technology)

  15. Design and synthesis of DNA four-helix bundles

    Energy Technology Data Exchange (ETDEWEB)

    Rangnekar, Abhijit; Gothelf, Kurt V [Department of Chemistry, Centre for DNA Nanotechnology (CDNA) and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, DK-8000 Aarhus C (Denmark); LaBean, Thomas H, E-mail: kvg@chem.au.dk, E-mail: thl@cs.duke.edu [Department of Chemistry, Duke University, Durham, NC 27708 (United States)

    2011-06-10

    The field of DNA nanotechnology has evolved significantly in the past decade. Researchers have succeeded in synthesizing tile-based structures and using them to form periodic lattices in one, two and three dimensions. Origami-based structures have also been used to create nanoscale structures in two and three dimensions. Design and construction of DNA bundles with fixed circumference has added a new dimension to the field. Here we report the design and synthesis of a DNA four-helix bundle. It was found to be extremely rigid and stable. When several such bundles were assembled using appropriate sticky-ends, they formed micrometre-long filaments. However, when creation of two-dimensional sheet-like arrays of the four-helix bundles was attempted, nanoscale rings were observed instead. The exact reason behind the nanoring formation is yet to be ascertained, but it provides an exciting prospect for making programmable circular nanostructures using DNA.

  16. Chiral transformation: From single nanowire to double helix

    KAUST Repository

    Wang, Yong

    2011-12-21

    We report a new type of water-soluble ultrathin Au-Ag alloy nanowire (NW), which exhibits unprecedented behavior in a colloidal solution. Upon growth of a thin metal (Pd, Pt, or Au) layer, the NW winds around itself to give a metallic double helix. We propose that the winding originates from the chirality within the as-synthesized Au-Ag NWs, which were induced to untwist upon metal deposition. © 2011 American Chemical Society.

  17. Apolipophorin III: lipopolysaccharide binding requires helix bundle opening

    OpenAIRE

    Leon, Leonardo J.; Idangodage, Hasitha; Wan, Chung-Ping L.; Weers, Paul M.M.

    2006-01-01

    Apolipophorin III (apoLp-III) is a prototypical apolipoprotein used for structure-function studies. Besides its crucial role in lipid transport, apoLp-III is able to associate with fungal and bacterial membranes and stimulate cellular immune responses. We recently demonstrated binding interaction of apoLp-III of the greater wax moth, Galleria mellonella, with lipopolysaccharides (LPS). In the present study, the requirement of helix bundle opening for LPS binding interaction was investigated. ...

  18. AND BUSINESS INCUBATORS INTO THE TRIPLE HELIX CONCEPT

    Directory of Open Access Journals (Sweden)

    Sizova, Y.S.

    2016-04-01

    Full Text Available The article’s author endeavors to create a practical model of the Russian economy’s development while integrating such tools of supporting and stimulating entrepreneurship as business incubators and research and technology parks into the Triple Helix concept. The article points out that configurations fusing together the nation-state, business and science/education, possess a greater potential for development.

  19. Periodic modification of the Boerdijk-Coxeter helix (tetrahelix)

    OpenAIRE

    Sadler, Garrett; Fang, Fang; Kovacs, Julio; Irwin, Klee

    2013-01-01

    The Boerdijk-Coxeter helix is a helical structure of tetrahedra which possesses no non-trivial translational or rotational symmetries. In this document, we develop a procedure by which this structure is modified to obtain both translational and rotational (upon projection) symmetries along/about its central axis. We report the finding of several, distinct periodic structures, and focus on two particular forms related to the pentagonal and icosahedral aggregates of tetrahedra as well as Buckmi...

  20. Design of a Broadband Inverted Conical Quadrifilar Helix Antenna

    OpenAIRE

    Jingyan Mo; Wei Liu; Weidong Fang; Haigao Xue; Zhongchao Lin

    2016-01-01

    This paper introduces the design of a broadband inverted conical circularly polarized quadrifilar helix antenna (QHA). The antenna has many good characteristics, including wide beam and broad bandwidth, which are achieved by utilizing inverted conical geometry and adjusting the dimensions of the inverted conical support. The antenna is fed by a wideband network to provide 90° phase difference between the four arms with constant amplitude. The antenna impedance and axial ratio bandwidth values...

  1. Establishing triple helix relationships : The case of PEA

    OpenAIRE

    Svensson, Peter

    2009-01-01

    This case describes the umbrella organization Printed Electronics Arena (PEA) which is situated in the Norrköping region, Sweden. The strategy of the PEA organization is based on the triple helix model, which is an academic model that promotes regional development through the interaction between academy, public bodies, and industry. The main asset is a new technology – printed electronics (PE) - that the research institute Acreo and Linköping University (LiU) are creating, developing and expl...

  2. Unambiguous demonstration of triple-helix-directed gene modification

    OpenAIRE

    Barre, François-Xavier; Ait-Si-Ali, Slimane; Giovannangeli, Carine; Luis, Richard; Robin, Philippe; Pritchard, Linda L; Hélène, Claude; Harel-Bellan, Annick

    2000-01-01

    Triple-helix-forming oligonucleotides (TFOs), which can potentially modify target genes irreversibly, represent promising tools for antiviral therapies. However, their effectiveness on endogenous genes has yet to be unambiguously demonstrated. To monitor endogenous gene modification by TFOs in a yeast model, we inactivated an auxotrophic marker gene by inserting target sequences of interest into its coding region. The genetically engineered yeast cells then were tr...

  3. Demographic Differential Vulnerability to Extreme Climate Change (HELIX)

    OpenAIRE

    Zickgraf, Caroline; Perrin, Nathalie; Gemenne, François

    2014-01-01

    With the target of limiting global warming to 2ºC becoming increasingly difficult to achieve, policymakers, businesses and other decision-makers need to begin to plan ahead for adaptation to changes in climate associated with higher levels of global warming. Alongside this, ongoing international negotiations on limiting global warming require clear information on the demographic consequences of different levels of climate change. The HELIX project (High-End cLimate Impacts and eXtremes), and ...

  4. Chatter Prediction for Variable Pitch and Variable Helix Milling

    OpenAIRE

    Yong Wang; Taiyong Wang; Zhiqiang Yu; Yue Zhang; Yulong Wang; Hengli Liu

    2015-01-01

    Regenerative chatter is a self-excited vibration that can occur during milling, which shortens the lifetime of the tool and results in unacceptable surface quality. In this paper, an improved semidiscretization method for modeling and simulation with variable pitch and variable helix milling is proposed. Because the delay between each flute varies along the axial depth of the tool in milling, the cutting tool is discrete into some axial layers to simplify calculation. A comparison of the pred...

  5. A 20 GHz, 75 watt, helix TWT for space communications

    Science.gov (United States)

    Heney, J. F.; Tamashiro, R. N.

    1983-01-01

    A space-qualified, helix-type traveling wave tube is being developed for satellite communication systems in the frequency band of 17.7 to 21.2 GHz. The design approach stresses very high efficiency operation, but with very low distortion. The tube provides multi-mode operation, permitting CW saturated power output levels of 75, 40, and 7.5 W. Operation is also anticipated at 5 dB below these saturation levels to achieve the required low distortion levels. Advanced construction features include a five-stage depressed collector, a diamond supported helix slow-wave circuit, and a type M dispenser cathode. High reliability and long life (10 yr) are objectives of the tube design. Preliminary test results on early developmental models of this tube are very encouraging. An output power of 75 to 90 W has been achieved over the full bandwidth with about 40 dB of saturated gain. More importantly, the basic electronic efficiency of the interaction process has been increased from about 7.5-11 percent by the use of the diamond helix support compared to earlier tubes using BeO support rods. This effort is supported by NASA Lewis Research Center and is aimed toward application in the NASA Advanced Communications Satellite Technology Program.

  6. Actividad molusquicida del Piquerol A aislado de Piqueria trinervia (compositae sobre ocho especies de caracoles pulmonados The molluscicide activity of Piquerol A isolated from Piqueria trinervia (Compositae against eight species of pulmonate snails

    Directory of Open Access Journals (Sweden)

    Alejandro Cruz-Reys

    1989-03-01

    Full Text Available De las partes aéreas de la planta Piqueria trinervia (Compositae colectada en diveresas áereas de México, se aisló el Piquerol A. Este compuesto se probó como agente molusquicida contra ocho especies de caracoles pulmonados: Fossaria (Fossaria humilis, F. (Bakerilymnae sp., Pseudosuccinea columella, Stagnicola attenuata, de México; F. (B. cubensis y Physacubensis, de Cuba; P. Columella y Biomphalaria glabrata, de Brasil; B glabrata, de Puerto Rico; S. elodes, de Estados Unidos. Se utilizaron tres concentraciones 50, 25 y 5 ppm para cada una de las especies y 2 períodos de exposición, 6 y 24 horas, a 20-22ºC. En 50 ppm, después de 6 horas, y 25 ppm, después de 24 horas los ejemplares de todas las especies murieron. En 5 ppm después de 24 horas, se observaron mortalidades de 60 a 100%. En ningún caso se observó recuperación después de la exposición por 24 horas. El piquerol A es un terpeno biodegradable que presenta otras actividades biológicas. No se han hecho pruebas de toxicidad en otros animales ni pruebas de campo. Sin embargo, es una substacia con alto potencial de uso como molusquicida en zonas de transmisión focal. Es la primera que en México se hacen estudios sistemáticos sobre molusquicidas de origen vegetal.In laboratory trials an aqueous solution of Piquerol A from Piqueria trinervia, collected in several regions of Mexico, showed a molluscicide action on the adults of eight different pulmonates snails species. Fossaria (Fossaria humilis, F. (Bakerilymnaea sp., Pseudosuccinea columella and Stagnicola attenuata from Mexico; F. (B. cubensis and Physa cubensis from Cuba; P. columella and Biomphalaria glabrata from Brazil; B. glabrata from Puerto Rico; and S. elodes from USA. The solution was tested at 50, 25 and 5 ppm concentration, for two periods of 6 and 24 hours, at room temperature (20-22ºC. A 100% mortality was obtained for all species at 50 ppm concentration after 6 hours of exposure; the same percentage at 25

  7. Npas4, a novel helix-loop-helix PAS domain protein, is regulated in response to cerebral ischemia

    DEFF Research Database (Denmark)

    Shamloo, Mehrdad; Soriano, Liza; von Schack, David;

    2006-01-01

    Basic helix-loop-helix PAS domain proteins form a growing family of transcription factors. These proteins are involved in the process of adaptation to cellular stresses and environmental factors such as a change in oxygen concentration. We describe the identification and characterization of a rec...... lead to a decrease in the 200 kDa form and a simultaneous increase in the 100 kDa immunoreactivity. This could indicate a novel regulatory mechanism for activation and/or deactivation of this protein in response to ischemic brain injury....... expression characterized with in situ hybridization and Northern blotting. The Npas4 mRNA is specifically expressed in the brain and is highly up-regulated in ischemic tissues following both focal and global cerebral ischemic insults. Immunohistochemistry revealed a strong expression in the limbic system and...

  8. Evaluation of a high-precision gear measuring machine for helix measurement using helix and wedge artifacts

    Science.gov (United States)

    Taguchi, Tetsuya; Kondo, Yohan

    2016-08-01

    High-precision gears are required for advanced motion and power transmission. The reliability of the measured value becomes important as the gear accuracy increases, and the establishment of a traceability system is needed. Therefore, a high-precision gear measuring machine (GMM) with a smaller uncertainty is expected to improve the gear calibration uncertainty. For this purpose, we developed a prototype of a high-precision GMM that adopts a direct drive mechanism and other features. Then, the high measurement capability of the developed GMM was verified using gear artifacts. Recently, some new measurement methods using simple shapes such as spheres and planes have been proposed as standards. We have verified the tooth profile measurement using a sphere artifact and reported the results that the developed GMM had a high capability in tooth profile measurement. Therefore, we attempted to devise a new evaluation method for helix measurement using a wedge artifact (WA) whose plane was treated as the tooth flank, and the high measurement capability of the developed GMM was verified. The results will provide a part of information to fully assess measurement uncertainty as our future work. This paper describes the evaluation results of the developed GMM for helix measurement using both a helix artifact and the WA, and discusses the effectiveness of the WA as a new artifact to evaluate the GMMs.

  9. A basic helix-loop-helix transcription factor, PhFBH4, regulates flower senescence by modulating ethylene biosynthesis pathway in petunia

    Science.gov (United States)

    The basic helix-loop-helix (bHLH) transcription factors (TFs) play important roles in regulating multiple biological processes in plants. However, there are few reports about the function of bHLHs in flower senescence. In this study, a bHLH TF, PhFBH4, was found to be dramatically upregulated during...

  10. Dermatitis from common ivy (Hedera helix L. subsp. helix) in Europe: past, present, and future

    DEFF Research Database (Denmark)

    Paulsen, Evy; Christensen, Lars P; Andersen, Klaus E

    2010-01-01

    Common ivy (Hedera helix subsp. helix) is a well-known native and ornamental plant in Europe. Reports on contact dermatitis from ivy have regularly appeared since 1899. Recently, it has been suggested that allergic contact dermatitis from the plant may be under-diagnosed, partly due to lack of...

  11. Antinociceptive Effect of Hydroalcoholic Leaf Extract of Hedera helix in Male Rat

    Directory of Open Access Journals (Sweden)

    S. Shahidi

    2013-07-01

    Full Text Available Introduction & Objective: The consumption of chemical compounds and medicinal herbs are different ways to control pain. On the other hand, the complications of chemical drugs and their expensiveness cause people to use herbal medicines The aim of this study was to inves-tigate the antinociceptive effect of hydroalcoholic leaf extract of Hedera helix in male rats. Materials & Methods: In this experimental study, 36 adult male rats were divided into 6 groups: control, morphine (1mg/kg, Hedera helix extract (100, 200, 300mg/kg, i.p. and naloxone (1mg/kg with Hedera helix extract (200 mg/kg. The analgesic effects of Hedera helix ex-tract were assessed with writhing and tail flick tests. Results: The results of this study showed that doses of 200 and 300mg/kg of Hedera helix ex-tract decreased pain significantly. However, dose of 300mg/kg of Hedera helix extract showed more antinociceptive effect of Hedera helix extract. The naloxone and Hedera helix extract combination increased the number of writhing compared with the Hedera helix ex-tract group. Conclusion: In this study analgesic effect of the hydroalcoholic extract of Hedera helix was observed. The antinociceptive effect of extract was probably occurred by activation of opioid system. (Sci J Hamadan Univ Med Sci 2013; 20 (2:119-125

  12. The Norwegian PV manufacturing industry in a Triple Helix perspective

    International Nuclear Information System (INIS)

    For the benefit of our common future, policies aimed at the development and promotion of renewable energy technologies should be based on a Triple Helix approach with a sense of technological agency. This view is supported by a case study on the emergence and development of a Norwegian solar photovoltaic manufacturing industry. The data and analyses demonstrate how this new industry was fostered by interactions between existing companies, public R and D funding programmes and research organisations and policy contexts; illustrating a policy-driven technological agency in accordance with a Triple Helix innovation process. During the last decade, a solar PV manufacturing industry has emerged in Norway and gone on to a 10 to 20 per cent share of various segments of world markets for solar PV feedstock, wafers and related components. The present financial crisis has caused an investment slump in solar PV installations, especially in Europe. Therefore, the future prospects for the Norwegian solar PV industry are at risk despite of its focus on innovation and R and D, and its technological agency. Political action is needed: (1) creation of market incentives in near markets for the deployment of solar PV, (2) international cooperation for boosting deployment of solar PV in developing countries. - Highlights: • We examine the emergence of the Norwegian solar PV manufacturing industry. • A policy-driven technological agency was essential for the Norwegian PV industry. The Triple Helix model explains the emergence of the Norwegian PV industry. • Market incentives in near markets are needed for the deployment of solar PV. • International cooperation is needed for boosting solar PV in developing countries

  13. Some quality parameters of land snail meat - Helix pomatia

    Directory of Open Access Journals (Sweden)

    Tojagić Slobodan N.

    2004-01-01

    Full Text Available Considering the tradition in our regions to collect land snails (Helix pomatia for export, which is "disrupted" by social control resulting in limited possibilities to develop this attractive activity, there is a great interest lately for land snail breeding and fattening at farms. For this reason it is necessary to investigate systematically the possibilities to develop this activity in a longer period and in larger areas. The first investigations, although covering only nutritive and health safety aspects of the edible parts yielded the results presented in this work. Chemical composition, the content of some elements and organochlorine insecticides were followed as unavoidable in human living and environment.

  14. A network of yeast basic helix–loop–helix interactions

    OpenAIRE

    Robinson, Kelly A.; Koepke, Jay I.; Kharodawala, Murtaza; Lopes, John M.

    2000-01-01

    The Ino4 protein belongs to the basic helix–loop–helix (bHLH) family of proteins. It is known to form a dimer with Ino2p, which regulates phospholipid biosynthetic genes. Mammalian bHLH proteins have been shown to form multiple dimer combinations. However, this flexibility in dimerization had not been documented for yeast bHLH proteins. Using the yeast two-hybrid assay and a biochemical assay we show that Ino4p dimerizes with the Pho4p, Rtg1p, Rtg3p and Sgc1p bHLH proteins. Screening a yeast ...

  15. Triple helix structures: sequence dependence, flexibility and mismatch effects.

    Science.gov (United States)

    Sun, J S; Mergny, J L; Lavery, R; Montenay-Garestier, T; Hélène, C

    1991-12-01

    By means of molecular modelling, electrostatic interactions are shown to play an important role in the sequence-dependent structure of triple helices formed by a homopyrimidine oligonucleotide bound to a homopurine. homopyrimidine sequence on DNA. This is caused by the presence of positive charges due to the protonation of cytosines in the Hoogsteen-bonded strand, required in order to form C.GxC+ triplets. Energetic and conformational characteristics of triple helices with different sequences are analyzed and discussed. The effects of duplex mismatches on the triple helix stability are investigated via thermal dissociation using UV absorption. PMID:1815635

  16. Folding Dynamics of an α Helix and a β Hairpin

    Science.gov (United States)

    Hofrichter, James

    1998-03-01

    What processes limit the rate at which proteins fold? In an effort to address this question we have begun to study the dynamics of the formation of loops, α helices and the minimal β structural element, a β hairpin, which must occur on the pathway from random coils to folded proteins. Because these processes occur on time scales of 10-5-10-9 seconds and experimental access to these time scales has been limited, the kinetics of these processes have not been extensively studied. The expectation is that a more complete understanding of the dynamics of these microprocesses will provide constraints on possible mechanisms for the overall folding of more complex structures. We have explored the kinetics of the helix-coil transition of a synthetic, 21-residue peptide: Ac-WAAAH^+(AAARA)_3A-NH2 and of the folding of a 16 residue β hairpin from protein G B1 using the nanosecond temperature jump technique. Both processes were studied by monitoring tryptophan fluorescence. In the helical peptide, the quantum yield of tryptophan decreases as a result of the interaction between tryptophan in position 1 with the protonated histidine in position 5. In the native conformation of the hairpin, it increases because it forms part of a hydrophobic cluster which stabilizes the native conformation (in a peptide in which a dansylated lysine is incorporated at the C-terminus the fluorescence is quenched). At 300 K, the relaxation time for the helix-coil transition is ~ 250 ns and that for the hairpin-coil transition is ~ 2.2 μs, about 10 times slower. The apparent activation energies are 6.8 kcal/mol for the helix and 10 kcal/mol for the hairpin. We have developed simple kinetic models for these processes which incorporate the sequence- and position-dependent properties known from equilibrium studies and the single-sequence approximation. These models provide a remarkably consistent picture of the dynamics, permitting us to extract information on both the microscopic rates for the c

  17. Design of a Broadband Inverted Conical Quadrifilar Helix Antenna

    Directory of Open Access Journals (Sweden)

    Jingyan Mo

    2016-01-01

    Full Text Available This paper introduces the design of a broadband inverted conical circularly polarized quadrifilar helix antenna (QHA. The antenna has many good characteristics, including wide beam and broad bandwidth, which are achieved by utilizing inverted conical geometry and adjusting the dimensions of the inverted conical support. The antenna is fed by a wideband network to provide 90° phase difference between the four arms with constant amplitude. The antenna impedance and axial ratio bandwidth values are more than 39% and 31.5%, respectively. The measured results coincide well with the simulated ones, which verified the effectiveness of the proposed design.

  18. Repair and recombination induced by triple helix DNA.

    Science.gov (United States)

    Chin, Joanna Y; Schleifman, Erica B; Glazer, Peter M

    2007-01-01

    Triple-helix DNA structures can form endogenously at mirror repeat polypurine/polypyrimidine sequences or by introduction of triplex-forming oligonucleotides (TFOs). Recent evidence suggests that triple helices are sources of genetic instability, and are subject to increased rates of mutagenesis and recruitment of repair factors. Indeed, observations using TFOs suggest that triple helices provoke a variety of biological processes which can be harnessed to modulate gene expression and induce heritable changes in targeted genes. This review surveys the biological applications of TFOs, with particular attention to their recombinogenic and mutagenic potential, and summarizes available evidence for the mechanism of triplex and triplex-associated repair. PMID:17485375

  19. DNA triple helix formation: A potential tool for genetic repair

    Directory of Open Access Journals (Sweden)

    Nayak A

    2006-01-01

    Full Text Available DNA triple helices offer new perspectives towards oligonucleotide-directed gene regulation. Triple helix forming oligonucleotides, which bind to double-stranded DNA, are of special interest since they are targeted to the gene itself rather than to its mRNA product (as in the antisense strategy. However, the poor stability of some of these structures might limit their use under physiological conditions. Specific ligands can intercalate into DNA triple helices and stabilize them. This review summarizes recent advances in this field while also highlighting major obstacles that remain to be overcome, before the application of triplex technology to therapeutic gene repair can be achieved.

  20. Broadband circular polarizers constructed using helix-like chiral metamaterials

    Science.gov (United States)

    Ji, Ruonan; Wang, Shao-Wei; Liu, Xingxing; Chen, Xiaoshuang; Lu, Wei

    2016-08-01

    In this paper, one kind of helix-like chiral metamaterial which can be realized by multiple conventional lithography or electron beam lithographic techniques is proposed to have a broadband bianisotropic optical response analogous to helical metamaterials. On the basis of twisted metamaterials, via tailoring the relative orientation within the lattice, the anisotropy of arcs is converted into magneto-electric coupling of closely spaced arc pairs, which leads to a broad bianisotropic optical response. By connecting the adjacent upper and lower arcs, the coupling of metasurface pairs is transformed into the coupling of the three-dimensional inclusions, and provides a much broader and higher bianisotropic optical response. For only a four-layer helix-like metamaterial, the maximum extinction ratio can reach 19.7. The operation band is in the wavelength range of 4.69 μm to 8.98 μm with an average extinction ratio of 6.9. And the transmittance for selective polarization is above 0.8 in the entire operation band. Such a structure is a promising candidate for integratable and scalable broadband circular polarizers, especially it has great potential to act as a broadband circular micropolarizer in the field of the full-Stokes division of focal plane polarimeters.In this paper, one kind of helix-like chiral metamaterial which can be realized by multiple conventional lithography or electron beam lithographic techniques is proposed to have a broadband bianisotropic optical response analogous to helical metamaterials. On the basis of twisted metamaterials, via tailoring the relative orientation within the lattice, the anisotropy of arcs is converted into magneto-electric coupling of closely spaced arc pairs, which leads to a broad bianisotropic optical response. By connecting the adjacent upper and lower arcs, the coupling of metasurface pairs is transformed into the coupling of the three-dimensional inclusions, and provides a much broader and higher bianisotropic optical

  1. Three-dimensional simulation of helix traveling-wave tube cold-test characteristics using MAFIA

    Energy Technology Data Exchange (ETDEWEB)

    Kory, C.L. [ANALEX Corp, Cleveland, OH (United States)

    1996-08-01

    The cold-test parameters including dispersion, impedance, and attenuation have been calculated for a helix traveling-wave tube (TWT) slow-wave circuit using MAFIA, the three-dimensional (3-D) electromagnetic finite-integration computer code. The helix model includes tape thickness, rectangular dielectric supports, and material properties consistent with the actual circuit. Measured cold-test data and computer-derived results for the helix circuit are presented with excellent agreement.

  2. Distributional Characteristics of Lianas: Example of Hedera helix, Drayton Wood, Norwich.

    OpenAIRE

    Mercer, Theresa

    2003-01-01

    The principal objective of this project was to determine whether Hedera helix was distributed randomly or exhibited host preferences within Drayton Wood, Norwich. 200 random tree samples >10cm diameter were studied. Of these, the CBH (circumference breast height), bark texture, abundance of H. helix and growth form were recorded. The percentage of ground covered by H. helix around the base of the sample trees was also recorded. Finally, the distance of the sample trees from the outer reaches ...

  3. On the Helix-coil Transition in Alanine-based Polypeptides in Gas Phase

    CERN Document Server

    Wei, Y; Hansmann, U H E

    2007-01-01

    Using multicanonical simulations, the authors study the effect of charged end groups on helix formation in alanine based polypeptides. They confirm earlier reports that neutral polyalanine exhibits a pronounced helix-coil transition in gas phase simulations. Introducing a charged Lys+ at the C terminal stabilizes the helix and leads to a higher transition temperature. On the other hand, adding the Lys+ at the N terminal inhibits helix formation. Instead, a more globular structure was found. These results are in agreement with recent experiments on alanine based polypeptides in gas phase. They indicate that present force fields describe accurately the intramolecular interactions in proteins.

  4. The close-packed triple helix as a possible new structural motif for collagen

    DEFF Research Database (Denmark)

    Bohr, Jakob; Olsen, Kasper

    2010-01-01

    The one-dimensional problem of selecting the triple helix with the highest volume fraction is solved and hence the condition for a helix to be close-packed is obtained. The close-packed triple helix is shown to have a pitch angle of v CP = 43.3°. Contrary to the conventional notion, we suggest that...... close packing form the underlying principle behind the structure of collagen, and the implications of this suggestion are considered. Further, it is shown that the unique zero-twist structure with no strain-twist coupling is practically identical to the close-packed triple helix. Some of the...

  5. Transmembrane Helix Assembly by Max-Min Ant System Algorithm.

    Science.gov (United States)

    Sujaree, Kanon; Kitjaruwankul, Sunan; Boonamnaj, Panisak; Supunyabut, Chirayut; Sompornpisut, Pornthep

    2015-12-01

    Because of the rapid progress in biochemical and structural studies of membrane proteins, considerable attention has been given on developing efficient computational methods for solving low-to-medium resolution structures using sparse structural data. In this study, we demonstrate a novel algorithm, max-min ant system (MMAS), designed to find an assembly of α-helical transmembrane proteins using a rigid helix arrangement guided by distance constraints. The new algorithm generates a large variety with finite number of orientations of transmembrane helix bundle and finds the solution that is matched with the provided distance constraints based on the behavior of ants to search for the shortest possible path between their nest and the food source. To demonstrate the efficiency of the novel search algorithm, MMAS is applied to determine the transmembrane packing of KcsA and MscL ion channels from a limited distance information extracted from the crystal structures, and the packing of KvAP voltage sensor domain using a set of 10 experimentally determined constraints, and the results are compared with those of two popular used stochastic methods, simulated annealing Monte Carlo method and genetic algorithm. PMID:26058409

  6. Broadband Circular Polarizers Constructed by Helix-like Chiral Metamaterials

    CERN Document Server

    Ji, Ruonan; Liu, Xingxing; Chen, Xiaoshuang; Lu, Wei

    2016-01-01

    In this paper, a kind of helix-like chiral metamaterial, which can be realized with multiple conventional lithography or electron beam lithographic techniques, is proposed to achieve broadband bianisotropic optical response analogous to helical metamaterial. On the basis of twisted metamaterial, via tailoring the relative orientation within the lattice, the anisotropy of arc is converted into magneto-electric coupling of closely spaced arc pairs, which leads to a broad bianisotropic optical response. By connecting the adjacent upper and lower arcs, the coupling of metasurface pairs is transformed to the coupling of the three-dimensional inclusions, and provides a much broader and higher bianisotropic optical response. For only a four-layer helix-like metamaterial, the maximum extinction ratio can reach 19.7. The operation band is in the wavelength range from 4.69 {\\mu}m to 8.98 {\\mu}m with an average extinction ratio of 6.9. And the transmittance for selective polarization is above 0.8 in the entire operation...

  7. Helix probe areas for the utilization of geothermal power. A practical example; Helix-Sondenfelder zur Nutzung von Erdwaerme. Ein Praxisbeispiel

    Energy Technology Data Exchange (ETDEWEB)

    Kuebert, Markus; Walker-Hertkorn, Simone [tewag Technologie - Erdwaermeanlagen - Umweltschutz GmbH, Starzach (Germany); Tietz, Jan [REHAU AG und Co., Erlangen-Eltersdorf (Germany); Riepold, Markus; Gloeckl, Andreas [MR Tiefbau GmbH, Brunnen (Germany)

    2013-02-01

    Thanks to their spiral shape so-called helix probes with a tube length of 40 meter have a height of only three meter: A lot of heat exchange area in a small space. Thus, helix probes are an ideal solution for the utilization of geothermal energy at places at which one cannot drill deeply due to geothermal reasons. Under this aspect, the contribution under consideration reports on the planning of a helix probe area being sustainably adapted to the user requirements for the new construction of a production facility.

  8. DNA recognition for virus assembly through multiple sequence-independent interactions with a helix-turn-helix motif.

    Science.gov (United States)

    Greive, Sandra J; Fung, Herman K H; Chechik, Maria; Jenkins, Huw T; Weitzel, Stephen E; Aguiar, Pedro M; Brentnall, Andrew S; Glousieau, Matthieu; Gladyshev, Grigory V; Potts, Jennifer R; Antson, Alfred A

    2016-01-29

    The helix-turn-helix (HTH) motif features frequently in protein DNA-binding assemblies. Viral pac site-targeting small terminase proteins possess an unusual architecture in which the HTH motifs are displayed in a ring, distinct from the classical HTH dimer. Here we investigate how such a circular array of HTH motifs enables specific recognition of the viral genome for initiation of DNA packaging during virus assembly. We found, by surface plasmon resonance and analytical ultracentrifugation, that individual HTH motifs of the Bacillus phage SF6 small terminase bind the packaging regions of SF6 and related SPP1 genome weakly, with little local sequence specificity. Nuclear magnetic resonance chemical shift perturbation studies with an arbitrary single-site substrate suggest that the HTH motif contacts DNA similarly to how certain HTH proteins contact DNA non-specifically. Our observations support a model where specificity is generated through conformational selection of an intrinsically bent DNA segment by a ring of HTHs which bind weakly but cooperatively. Such a system would enable viral gene regulation and control of the viral life cycle, with a minimal genome, conferring a major evolutionary advantage for SPP1-like viruses. PMID:26673721

  9. Phylogeny, Functional Annotation, and Protein Interaction Network Analyses of the Xenopus tropicalis Basic Helix-Loop-Helix Transcription Factors

    Directory of Open Access Journals (Sweden)

    Wuyi Liu

    2013-01-01

    Full Text Available The previous survey identified 70 basic helix-loop-helix (bHLH proteins, but it was proved to be incomplete, and the functional information and regulatory networks of frog bHLH transcription factors were not fully known. Therefore, we conducted an updated genome-wide survey in the Xenopus tropicalis genome project databases and identified 105 bHLH sequences. Among the retrieved 105 sequences, phylogenetic analyses revealed that 103 bHLH proteins belonged to 43 families or subfamilies with 46, 26, 11, 3, 15, and 4 members in the corresponding supergroups. Next, gene ontology (GO enrichment analyses showed 65 significant GO annotations of biological processes and molecular functions and KEGG pathways counted in frequency. To explore the functional pathways, regulatory gene networks, and/or related gene groups coding for Xenopus tropicalis bHLH proteins, the identified bHLH genes were put into the databases KOBAS and STRING to get the signaling information of pathways and protein interaction networks according to available public databases and known protein interactions. From the genome annotation and pathway analysis using KOBAS, we identified 16 pathways in the Xenopus tropicalis genome. From the STRING interaction analysis, 68 hub proteins were identified, and many hub proteins created a tight network or a functional module within the protein families.

  10. Observation of helix associations for insertion of a retinal molecule and distortions of helix structures in bacteriorhodopsin

    Science.gov (United States)

    Urano, Ryo; Okamoto, Yuko

    2015-12-01

    We applied a newly proposed prediction method for membrane protein structures to bacteriorhodopsin that has distorted transmembrane helices in the native structure. This method uses an implicit membrane model, which restricts sampling space during folding in a membrane region, and includes helix bending. Replica-exchange simulations were performed with seven transmembrane helices only without a retinal molecule. Obtained structures were classified into clusters of similar structures, which correspond to local-minimum free energy states. The two lowest free energy states corresponded to a native-like structure with the correct empty space for retinal and a structure with this empty space filled with a helix. Previous experiments of bacteriorhodopsin suggested that association of transmembrane helices enables them to make a room for insertion of a retinal. Our results are consistent with these results. Moreover, distortions of helices in the native-like structures were successfully reproduced. In the distortions, whereas the locations of kinks for all helices were similar to those of Protein Data Bank's data, the amount of bends was more similar for helices away from the retinal than for those close to the retinal in the native structure. This suggests a hypothesis that the amino-acid sequence specifies the location of kinks in transmembrane helices and that the amount of distortions depends on the interactions with the surrounding molecules such as neighboring helices, lipids, and retinal.

  11. A Dual Mechanism Controls Nuclear Localization in the Atypical Basic-Helix-Loop-Helix Protein PAR1 of Arabidopsis thaliana

    Institute of Scientific and Technical Information of China (English)

    Anahit Galstyan; Jordi Bou-Torrent; Irma Roig-Villanova; Jaime F. Martínez-García

    2012-01-01

    PAR1 is an atypical basic-helix-loop-helix (bHLH) protein that negatively regulates the shade avoidance syndrome in Arabidopsis thaliana acting as a transcriptional cofactor.Consistently with this function,PAR1 has to be in the nucleus to display biological activity.Previous structure-function analyses revealed that the N-terminal region of PAR1 drives the protein to the nucleus.However,truncated forms of PAR1 lacking this region still display biological activity,implying that PAR1 has additional mechanisms to localize into the nucleus.In this work,we compared the primary structure of PAR1 and various related and unrelated plant bHLH proteins,which led us to suggest that PAR1 contains a non-canonical nuclear localization signal (NLS) in the N-terminal region.By overexpressing truncated and mutated derivatives of PAR1,we have also investigated the importance of other regions of PAR1,such as the acidic and the extended HLH dimerization domains,for its nuclear localization.We found that,in the absence of the N-terminal region,a functional HLH domain is required for nuclear localization.Our results suggest the existence of a dual mechanism for PAR1 nuclear localization:(1) one mediated by the N-terminal non-consensus NLS and (2) a second one that involves interaction with other proteins via the dimerization domain.

  12. Proposal of a new hydrogen-bonding form to maintain curdlan triple helix.

    Science.gov (United States)

    Miyoshi, Kentaro; Uezu, Kazuya; Sakurai, Kazuo; Shinkai, Seiji

    2004-06-01

    Curdlan and other beta-1,3-D-glucans form right-handed triple helices, and it has been believed that the intermolecular H-bond is present at the center of the helix to maintain the structure. In this H-bond model, three secondary OH groups form an inequilateral hexagonal shape perpendicular to the helix axis. This hexagonal form seems to be characteristic for beta-1,3-D-glucans and is widely accepted. We carried out MOPAC and ab initio calculations for the curdlan helix, and we propose a new intermolecular H-bonding model. In our model, the H-bonds are formed between the O2-atoms on different x-y planes along the curdlan helix, hence the H-bonds are not perpendicular to the helix axis. The new H-bonds are connected along the helix, traversing three curdlan chains to make a left-handed helix. Therefore, the H-bonding array leads to a reverse helix of the main chain. According to our MOPAC calculation, this model is more stable than the previous one. We believe that the continuous H-bonding array is stabilized by cooperative phenomena in the polymeric system. PMID:17191891

  13. Inactivation of colicin Y by intramembrane helix–helix interaction with its immunity protein

    Czech Academy of Sciences Publication Activity Database

    Šmajs, D.; Doležalová, M.; Macek, Pavel; Žídek, L.

    2008-01-01

    Roč. 275, č. 21 (2008), s. 5325-5331. ISSN 1742-464X Institutional research plan: CEZ:AV0Z50200510 Keywords : colicin immunity * colicin y * helix-helix interaction Subject RIV: CE - Biochemistry Impact factor: 3.139, year: 2008

  14. Ab initio theory of helix <-> coil phase transition

    DEFF Research Database (Denmark)

    Yakubovich, Alexander V.; Solov'yov, Ilia; Solov'yov, Andrey V.;

    2008-01-01

    In this paper, we suggest a theoretical method based on the statistical mechanics for treating the alpha-helix <-> random coil transition in alanine polypeptides. We consider this process as a first-order phase transition and develop a theory which is free of model parameters and is based solely on...... fundamental physical principles. It describes essential thermodynamical properties of the system such as heat capacity, the phase transition temperature and others from the analysis of the polypeptide potential energy surface calculated as a function of two dihedral angles, responsible for the polypeptide...... twisting. The suggested theory is general and with some modification can be applied for the description of phase transitions in other complex molecular systems (e.g. proteins, DNA, nanotubes, atomic clusters, fullerenes)....

  15. Photo-active collagen systems with controlled triple helix architecture

    CERN Document Server

    Tronci, Giuseppe; Wood, David J

    2013-01-01

    The design of photo-active collagen systems is presented as a basis for establishing biomimetic materials with varied network architecture and programmable macroscopic properties. Following in-house isolation of type I collagen, reaction with vinyl-bearing compounds of varied backbone rigidity, i.e. 4-vinylbenzyl chloride (4VBC) and glycidyl methacrylate (GMA), was carried out. TNBS colorimetric assay, 1H-NMR and ATR-FTIR confirmed covalent and tunable functionalization of collagen lysines. Depending on the type and extent of functionalization, controlled stability and thermal denaturation of triple helices were observed via circular dichroism (CD), whereby the hydrogen-bonding capability of introduced moieties was shown to play a major role. Full gel formation was observed following photo-activation of functionalized collagen solutions. The presence of a covalent network only slightly affected collagen triple helix conformation (as observed by WAXS and ATR-FTIR), confirming the structural organization of fun...

  16. RFID Tag Helix Antenna Sensors for Wireless Drug Dosage Monitoring.

    Science.gov (United States)

    Huang, Haiyu; Zhao, Peisen; Chen, Pai-Yen; Ren, Yong; Liu, Xuewu; Ferrari, Mauro; Hu, Ye; Akinwande, Deji

    2014-01-01

    Miniaturized helix antennas are integrated with drug reservoirs to function as RFID wireless tag sensors for real-time drug dosage monitoring. The general design procedure of this type of biomedical antenna sensors is proposed based on electromagnetic theory and finite element simulation. A cost effective fabrication process is utilized to encapsulate the antenna sensor within a biocompatible package layer using PDMS material, and at the same time form a drug storage or drug delivery unit inside the sensor. The in vitro experiment on two prototypes of antenna sensor-drug reservoir assembly have shown the ability to monitor the drug dosage by tracking antenna resonant frequency shift from 2.4-2.5-GHz ISM band with realized sensitivity of 1.27 [Formula: see text] for transdermal drug delivery monitoring and 2.76-[Formula: see text] sensitivity for implanted drug delivery monitoring. PMID:27170865

  17. Connecting two proteins using a fusion alpha helix stabilized by a chemical cross linker

    Science.gov (United States)

    Jeong, Woo Hyeon; Lee, Haerim; Song, Dong Hyun; Eom, Jae-Hoon; Kim, Sun Chang; Lee, Hee-Seung; Lee, Hayyoung; Lee, Jie-Oh

    2016-03-01

    Building a sophisticated protein nano-assembly requires a method for linking protein components in a predictable and stable structure. Most of the cross linkers available have flexible spacers. Because of this, the linked hybrids have significant structural flexibility and the relative structure between their two components is largely unpredictable. Here we describe a method of connecting two proteins via a `fusion α helix' formed by joining two pre-existing helices into a single extended helix. Because simple ligation of two helices does not guarantee the formation of a continuous helix, we used EY-CBS, a synthetic cross linker that has been shown to react selectively with cysteines in α-helices, to stabilize the connecting helix. Formation and stabilization of the fusion helix was confirmed by determining the crystal structures of the fusion proteins with and without bound EY-CBS. Our method should be widely applicable for linking protein building blocks to generate predictable structures.

  18. Folding simulations of gramicidin A into the β-helix conformations: Simulated annealing molecular dynamics study

    Science.gov (United States)

    Mori, Takaharu; Okamoto, Yuko

    2009-10-01

    Gramicidin A is a linear hydrophobic 15-residue peptide which consists of alternating D- and L-amino acids and forms a unique tertiary structure, called the β6.3-helix, to act as a cation-selective ion channel in the natural conditions. In order to investigate the intrinsic ability of the gramicidin A monomer to form secondary structures, we performed the folding simulation of gramicidin A using a simulated annealing molecular dynamics (MD) method in vacuum mimicking the low-dielectric, homogeneous membrane environment. The initial conformation was a fully extended one. From the 200 different MD runs, we obtained a right-handed β4.4-helix as the lowest-potential-energy structure, and left-handed β4.4-helix, right-handed and left-handed β6.3-helix as local-minimum energy states. These results are in accord with those of the experiments of gramicidin A in homogeneous organic solvent. Our simulations showed a slight right-hand sense in the lower-energy conformations and a quite β-sheet-forming tendency throughout almost the entire sequence. In order to examine the stability of the obtained right-handed β6.3-helix and β4.4-helix structures in more realistic membrane environment, we have also performed all-atom MD simulations in explicit water, ion, and lipid molecules, starting from these β-helix structures. The results suggested that β6.3-helix is more stable than β4.4-helix in the inhomogeneous, explicit membrane environment, where the pore water and the hydrogen bonds between Trp side-chains and lipid-head groups have a role to further stabilize the β6.3-helix conformation.

  19. Direct comparison of {sup 111}In-labelled two-helix and three-helix Affibody molecules for in vivo molecular imaging

    Energy Technology Data Exchange (ETDEWEB)

    Rosik, Daniel; Karlstroem, Amelie Eriksson [KTH Royal Institute of Technology, Division of Molecular Biotechnology, School of Biotechnology, Stockholm (Sweden); Orlova, Anna; Malmberg, Jennie; Varasteh, Zohreh [Uppsala University, Preclinical PET Platform, Uppsala (Sweden); Altai, Mohamed; Tolmachev, Vladimir [Uppsala University, Unit of Biomedical Radiation Sciences, Rudbeck Laboratory, Uppsala (Sweden); Sandstroem, Mattias [Uppsala University Hospital, Section of Medical Physics, Department of Oncology, Uppsala (Sweden)

    2012-04-15

    Radiolabelled Affibody molecules have demonstrated a potential for visualization of tumour-associated molecular targets. Affibody molecules (7 kDa) are composed of three alpha-helices. Recently, a smaller two-helix variant of Affibody molecules (5.1 kDa) was developed. The aim of this study was to compare two- and three-helix HER2-targeting Affibody molecules directly in vivo. The three-helix Affibody molecule ABY-002 and the two-helix Affibody molecule PEP09239 were labelled with {sup 111}In at the N-termini via DOTA chelator. Tumour-targeting properties were directly compared at 1 and 4 h after injection in mice bearing SKOV-3 xenografts with high HER2 expression and LS174T xenografts with low HER2 expression. The dissociation constants (K{sub D}) for HER2 binding were 78 pM for the three-helix Affibody molecule and 2.1 nM for the two-helix Affibody molecule. {sup 111}In-PEP09239 cleared more rapidly from the blood. In xenografts with high HER2 expression, the uptake of {sup 111}In-ABY-002 was significantly higher than that of {sup 111}In-PEP09239. The tumour-to-blood ratio was higher for {sup 111}In-PEP09239 at 4 h after injection, while there was no significant difference in other tumour-to-organ ratios. The tumour uptake of {sup 111}In-ABY-002 was eightfold higher than that of {sup 111}In-PEP09239 in xenografts with low expression. Tumour-to-blood ratios were equal in this case, but other tumour-to-organ ratios were appreciably higher for the three-helix variant. For tumours with high HER2 expression, two-helix HER2-targeting Affibody molecules can provide higher tumour-to-blood ratio at the cost of lower tumour uptake. In the case of low expression, both tumour uptake and tumour-to-organ ratios are appreciably higher for three-helix than for two-helix HER2-targeting Affibody molecules. (orig.)

  20. A smallest 6 kda metalloprotease, mini-matrilysin, in living world: a revolutionary conserved zinc-dependent proteolytic domain- helix-loop-helix catalytic zinc binding domain (ZBD

    Directory of Open Access Journals (Sweden)

    Yu Wei-Hsuan

    2012-05-01

    Full Text Available Abstract Background The Aim of this study is to study the minimum zinc dependent metalloprotease catalytic folding motif, helix B Met loop-helix C, with proteolytic catalytic activities in metzincin super family. The metzincin super family share a catalytic domain consisting of a twisted five-stranded β sheet and three long α helices (A, B and C. The catalytic zinc is at the bottom of the cleft and is ligated by three His residues in the consensus sequence motif, HEXXHXXGXXH, which is located in helix B and part of the adjacent Met turn region. An interesting question is - what is the minimum portion of the enzyme that still possesses catalytic and inhibitor recognition?” Methods We have expressed a 60-residue truncated form of matrilysin which retains only the helix B-Met turn-helix C region and deletes helix A and the five-stranded β sheet which form the upper portion of the active cleft. This is only 1/4 of the full catalytic domain. The E. coli derived 6 kDa MMP-7 ZBD fragments were purified and refolded. The proteolytic activities were analyzed by Mca-Pro-Leu-Gly-Leu-Dpa-Ala-Arg-NH2 peptide assay and CM-transferrin zymography analysis. SC44463, BB94 and Phosphoramidon were computationally docked into the 3day structure of the human MMP7 ZBD and TAD and thermolysin using the docking program GOLD. Results This minimal 6 kDa matrilysin has been refolded and shown to have proteolytic activity in the Mca-Pro-Leu-Gly-Leu-Dpa-Ala-Arg-NH2 peptide assay. Triton X-100 and heparin are important factors in the refolding environment for this mini-enzyme matrilysin. This minienzyme has the proteolytic activity towards peptide substrate, but the hexamer and octamer of the mini MMP-7 complex demonstrates the CM-transferrin proteolytic activities in zymographic analysis. Peptide digestion is inhibited by SC44463, specific MMP7 inhibitors, but not phosphorimadon. Interestingly, the mini MMP-7 can be processed by autolysis and producing ~ 6

  1. De novo design of protein-protein interactions through modification of inter-molecular helix-helix interface residues.

    Science.gov (United States)

    Yagi, Sota; Akanuma, Satoshi; Yamagishi, Manami; Uchida, Tatsuya; Yamagishi, Akihiko

    2016-05-01

    For de novo design of protein-protein interactions (PPIs), information on the shape and chemical complementarity of their interfaces is generally required. Recent advances in computational PPI design have allowed for de novo design of protein complexes, and several successful examples have been reported. In addition, a simple and easy-to-use approach has also been reported that arranges leucines on a solvent-accessible region of an α-helix and places charged residues around the leucine patch to induce interactions between the two helical peptides. For this study, we adopted this approach to de novo design a new PPI between the helical bundle proteins sulerythrin and LARFH. A non-polar patch was created on an α-helix of LARFH around which arginine residues were introduced to retain its solubility. The strongest interaction found was for the LARFH variant cysLARFH-IV-3L3R and the sulerythrin mutant 6L6D (KD=0.16 μM). This artificial protein complex is maintained by hydrophobic and ionic interactions formed by the inter-molecular helical bundle structure. Therefore, by the simple and easy-to-use approach to create de novo interfaces on the α-helices, we successfully generated an artificial PPI. We also created a second LARFH variant with the non-polar patch surrounded by positively charged residues at each end. Upon mixing this LARFH variant with 6L6D, mesh-like fibrous nanostructures were observed by atomic force microscopy. Our method may, therefore, also be applicable to the de novo design of protein nanostructures. PMID:26867971

  2. The Antiinflammatory and Antiarthritic Properties of Ethanol Extract of Hedera helix

    Directory of Open Access Journals (Sweden)

    Anuradha Rai

    2013-01-01

    Full Text Available The ethanol Hedera helix plant extract was tested for its antiinflammatory properties. Intraperitoneal injections of 7.5 ml/kg wt ethanol extract showed antiinflammatory activity with 88.89% inhibition as compared to reference drug diclofenac, which showed 94.44% inhibition in formalin-induced paw oedema. As formalin-induced paw oedema closely resembles human arthritis, the antiarthritic property of ethanol extract of Hedera helix was also investigated. The visible reduction in arthritic symptoms by extract of Hedera helix suggests the potential of the plant extract against inflammation and arthritis.

  3. Translocation of Biopolymer Chain Through a Nanopore: Coil-Helix Transition

    Institute of Scientific and Technical Information of China (English)

    GU Fang; WANG Hai-Jun; HONG Xiao-Zhong; BA Xin-Wu

    2008-01-01

    @@ The translocation dynamics of a single biopolymer chain through a nanopore in a membrane is investigated by taking the coil-helix transition into account. Based on the changing of the free energy due to the coil-helix transition, the mean first passage time τ is obtained, and then the corresponding numerical simulations are presented under different conditions. It is shown that the coil helix transition can significantly shorten the translocation time of the biopolymer chain. In addition, we also discuss the scaling behaviour for τ with the chain length N and some related problems.

  4. Accessing commercial cloud resources within the European Helix Nebula cloud marketplace

    Science.gov (United States)

    Cordeiro, C.; De Salvo, A.; Di Girolamo, A.; Field, L.; Giordano, D.; Jones, R.; Villazon, L.

    2015-12-01

    Helix Nebula - the Science Cloud Initiative - is a public-private partnership between Europe's leading scientific research organisations and European IT cloud providers. CERN contributed to this initiative by providing a flagship use case: the workloads from the ATLAS experiment. Aiming to gain experience in managing and monitoring large-scale deployments, as well as in benchmarking the cloud resources, a sizable Monte Carlo production was performed using the Helix Nebula platform. This contribution describes the Helix Nebula initiative and summarizes the experience and the lessons learned from deploying ATLAS experiment application within large cloud setups involving several commercial providers.

  5. Potassium-resistant triple helix formation and improved intracellular gene targeting by oligodeoxyribonucleotides containing 7-deazaxanthine.

    OpenAIRE

    Faruqi, A F; Krawczyk, S H; Matteucci, M D; Glazer, P M

    1997-01-01

    Triple helix formation by purine-rich oligonucleotides in the anti-parallel motif is inhibited by physiological concentrations of potassium. Substitution with 7-deazaxanthine (c7X) has been suggested as a strategy to overcome this effect. We have tested this by examining triple helix formation both in vitro and in vivo by a series of triple helix-forming oligonucleotides (TFOs) containing guanine plus either adenine, thymine, or c7X. The TFOs were conjugated to psoralen at the 5'end and were ...

  6. Inhibition of HIV-1 reverse transcription by triple-helix forming oligonucleotides with viral RNA.

    OpenAIRE

    Volkmann, S; Jendis, J; Frauendorf, A; Moelling, K

    1995-01-01

    Reverse transcription of retroviral RNA into double-stranded DNA is catalyzed by reverse transcriptase (RT). A highly conserved polypurine tract (PPT) on the viral RNA serves as primer for plus-strand DNA synthesis and is a possible target for triple-helix formation. Triple-helix formation during reverse transcription involves either single-stranded RNA or an RNA.DNA hybrid. The effect of triple-helix formation on reverse transcription has been analyzed here in vitro using a three-strand-syst...

  7. Structure-based prediction reveals capping motifs that inhibit β-helix aggregation

    OpenAIRE

    Bryan, Allen W.; Starner-Kreinbrink, Jennifer L.; Hosur, Raghavendra; Clark, Patricia L.; Berger, Bonnie

    2011-01-01

    The parallel β-helix is a geometrically regular fold commonly found in the proteomes of bacteria, viruses, fungi, archaea, and some vertebrates. β-helix structure has been observed in monomeric units of some aggregated amyloid fibers. In contrast, soluble β-helices, both right- and left-handed, are usually “capped” on each end by one or more secondary structures. Here, an in-depth classification of the diverse range of β-helix cap structures reveals subtle commonalities in structural componen...

  8. Translocation of Biopolymer Chain Through a Nanopore: Coil-Helix Transition

    International Nuclear Information System (INIS)

    The translocation dynamics of a single biopolymer chain through a nanopore in a membrane is investigated by taking the coil—helix transition into account. Based on the changing of the free energy due to the coil—helix transition, the mean first passage time τ is obtained, and then the corresponding numerical simulations are presented under different conditions. It is shown that the coil—helix transition can significantly shorten the translocation time of the biopolymer chain. In addition, we also discuss the scaling behaviour for τ with the chain length N and some related problems. (atomic and molecular physics)

  9. A four-helix bundle stores copper for methane oxidation.

    Science.gov (United States)

    Vita, Nicolas; Platsaki, Semeli; Baslé, Arnaud; Allen, Stephen J; Paterson, Neil G; Crombie, Andrew T; Murrell, J Colin; Waldron, Kevin J; Dennison, Christopher

    2015-09-01

    Methane-oxidizing bacteria (methanotrophs) require large quantities of copper for the membrane-bound (particulate) methane monooxygenase. Certain methanotrophs are also able to switch to using the iron-containing soluble methane monooxygenase to catalyse methane oxidation, with this switchover regulated by copper. Methane monooxygenases are nature's primary biological mechanism for suppressing atmospheric levels of methane, a potent greenhouse gas. Furthermore, methanotrophs and methane monooxygenases have enormous potential in bioremediation and for biotransformations producing bulk and fine chemicals, and in bioenergy, particularly considering increased methane availability from renewable sources and hydraulic fracturing of shale rock. Here we discover and characterize a novel copper storage protein (Csp1) from the methanotroph Methylosinus trichosporium OB3b that is exported from the cytosol, and stores copper for particulate methane monooxygenase. Csp1 is a tetramer of four-helix bundles with each monomer binding up to 13 Cu(I) ions in a previously unseen manner via mainly Cys residues that point into the core of the bundle. Csp1 is the first example of a protein that stores a metal within an established protein-folding motif. This work provides a detailed insight into how methanotrophs accumulate copper for the oxidation of methane. Understanding this process is essential if the wide-ranging biotechnological applications of methanotrophs are to be realized. Cytosolic homologues of Csp1 are present in diverse bacteria, thus challenging the dogma that such organisms do not use copper in this location. PMID:26308900

  10. Optical and dielectric properties of double helix DNA thin films

    International Nuclear Information System (INIS)

    In this work, the thin film of wheat DNA was deposited by spin-coating technique onto glass substrate, and the optical and dielectric properties of the double helix DNA thin film were investigated. The optical constants such as refractive index, extinction coefficient, dielectric constant, dissipation factor, relaxation time, and optical conductivity were determined from the measured transmittance spectra in the wavelength range 190-1100 nm. Meanwhile, the dispersion behavior of the refractive index was studied in terms of the single oscillator Wemple-DiDomenico (W-D) model, and the physical parameters of the average oscillator strength, average oscillator wavelength, average oscillator energy, the refractive index dispersion parameter and the dispersion energy were achieved. Furthermore, the optical band gap values were calculated by W-D model and Tauc model, respectively, and the values obtained from W-D model are in agreement with those determined from the Tauc model. The analysis of the optical absorption data indicates that the optical band gap Eg was indirect transitions. These results provide some useful references for the potential application of the DNA thin films in fiber optic, solar cell and optoelectronic devices. Highlights: → The optical constants of DNA in full UV-vis spectrum were determined. → The change in optical and dielectric property demonstrates that this material has potential to be used as a novel technology. → DNA shows promise to be more suitable material than other materials currently being used for photonic devices.

  11. Hydrophobic pulses predict transmembrane helix irregularities and channel transmembrane units

    Directory of Open Access Journals (Sweden)

    Claustres Mireille

    2011-05-01

    Full Text Available Abstract Background Few high-resolution structures of integral membranes proteins are available, as crystallization of such proteins needs yet to overcome too many technical limitations. Nevertheless, prediction of their transmembrane (TM structure by bioinformatics tools provides interesting insights on the topology of these proteins. Methods We describe here how to extract new information from the analysis of hydrophobicity variations or hydrophobic pulses (HPulses in the sequence of integral membrane proteins using the Hydrophobic Pulse Predictor, a new tool we developed for this purpose. To analyze the primary sequence of 70 integral membrane proteins we defined two levels of analysis: G1-HPulses for sliding windows of n = 2 to 6 and G2-HPulses for sliding windows of n = 12 to 16. Results The G2-HPulse analysis of 541 transmembrane helices allowed the definition of the new concept of transmembrane unit (TMU that groups together transmembrane helices and segments with potential adjacent structures. In addition, the G1-HPulse analysis identified helix irregularities that corresponded to kinks, partial helices or unannotated structural events. These irregularities could represent key dynamic elements that are alternatively activated depending on the channel status as illustrated by the crystal structures of the lactose permease in different conformations. Conclusions Our results open a new way in the understanding of transmembrane secondary structures: hydrophobicity through hydrophobic pulses strongly impacts on such embedded structures and is not confined to define the transmembrane status of amino acids.

  12. Assembly of liposomes controlled by triple helix formation.

    Science.gov (United States)

    Jakobsen, Ulla; Vogel, Stefan

    2013-09-18

    Attachment of DNA to the surface of different solid nanoparticles (e.g., gold and silica nanoparticles) is well established, and a number of DNA-modified solid nanoparticle systems have been applied to thermal denaturation analysis of oligonucleotides. We report herein the noncovalent immobilization of oligonucleotides on the surface of soft nanoparticles (i.e., liposomes) and the subsequent controlled assembly by DNA triple helix formation. The noncovalent approach avoids tedious surface chemistry and necessary purification procedures and can simplify and extend the available methodology for the otherwise difficult thermal denaturation analysis of complex triple helical DNA assemblies. The approach is based on lipid modified triplex forming oligonucleotides (TFOs) which control the assembly of liposomes in solution in the presence of single- or double-stranded DNA targets. The thermal denaturation analysis is monitored by ultraviolet spectroscopy at submicromolar concentrations and compared to regular thermal denaturation assays in the absence of liposomes. We report on triplex forming oligonucleotides (TFOs) based on DNA and locked nucleic acid (LNA)/DNA hybrid building blocks and different target sequences (G or C-rich) to explore the applicability of the method for different triple helical assembly modes. We demonstrate advantages and limitations of the approach and show the reversible and reproducible formation of liposome aggregates during thermal denaturation cycles. Nanoparticle tracking analysis (NTA) and dynamic light scattering (DLS) show independently from ultraviolet spectroscopy experiments the formation of liposome aggregates. PMID:23885785

  13. Helix Nebula: sunshine and clouds on the CERN computing horizon

    CERN Multimedia

    Joannah Caborn Wengler

    2012-01-01

    23 petabytes is how much data CERN recorded during 2011, and this number will rise in 2012. In order to respond to the challenge, the IT department is upping its game, amongst other things by participating in the Helix Nebula project, a public-private partnership to create a European cloud-computing platform, as announced in a recent CERN press release.   “We’re not replacing the Grid,” clarifies Bob Jones, responsible for CERN openlab who is also responsible for EC-funded projects in IT, “but looking at three complementary ways of increasing CERN’s computing capacity, so that as demand goes up we can continue to satisfy our users.” “First we are upgrading the electrical and cooling infrastructure of the computer centre in order to increase the availability of critical IT services needed for the Laboratory. This will also provide more floor space in the area called The Barn, allowing for more servers to fit in.”...

  14. Slow alpha helix formation during folding of a membrane protein.

    Science.gov (United States)

    Riley, M L; Wallace, B A; Flitsch, S L; Booth, P J

    1997-01-01

    Very little is known about the folding of proteins within biological membranes. A "two-stage" model has been proposed on thermodynamic grounds for the folding of alpha helical, integral membrane proteins, the first stage of which involves formation of transmembrane alpha helices that are proposed to behave as autonomous folding domains. Here, we investigate alpha helix formation in bacteriorhodopsin and present a time-resolved circular dichroism study of the slow in vitro folding of this protein. We show that, although some of the protein's alpha helices form early, a significant part of the protein's secondary structure appears to form late in the folding process. Over 30 amino acids, equivalent to at least one of bacteriorhodopsin's seven transmembrane segments, slowly fold from disordered structures to alpha helices with an apparent rate constant of about 0.012 s-1 at pH 6 or 0.0077 s-1 at pH 8. This is a rate-limiting step in protein folding, which is dependent on the pH and the composition of the lipid bilayer. PMID:8993333

  15. The Basic/Helix-Loop-Helix Protein Family in Gossypium: Reference Genes and Their Evolution during Tetraploidization.

    Science.gov (United States)

    Yan, Qian; Liu, Hou-Sheng; Yao, Dan; Li, Xin; Chen, Han; Dou, Yang; Wang, Yi; Pei, Yan; Xiao, Yue-Hua

    2015-01-01

    Basic/helix-loop-helix (bHLH) proteins comprise one of the largest transcription factor families and play important roles in diverse cellular and molecular processes. Comprehensive analyses of the composition and evolution of the bHLH family in cotton are essential to elucidate their functions and the molecular basis of cotton development. By searching bHLH homologous genes in sequenced diploid cotton genomes (Gossypium raimondii and G. arboreum), a set of cotton bHLH reference genes containing 289 paralogs were identified and named as GobHLH001-289. Based on their phylogenetic relationships, these cotton bHLH proteins were clustered into 27 subfamilies. Compared to those in Arabidopsis and cacao, cotton bHLH proteins generally increased in number, but unevenly in different subfamilies. To further uncover evolutionary changes of bHLH genes during tetraploidization of cotton, all genes of S5a and S5b subfamilies in upland cotton and its diploid progenitors were cloned and compared, and their transcript profiles were determined in upland cotton. A total of 10 genes of S5a and S5b subfamilies (doubled from A- and D-genome progenitors) maintained in tetraploid cottons. The major sequence changes in upland cotton included a 15-bp in-frame deletion in GhbHLH130D and a long terminal repeat retrotransposon inserted in GhbHLH062A, which eliminated GhbHLH062A expression in various tissues. The S5a and S5b bHLH genes of A and D genomes (except GobHLH062) showed similar transcription patterns in various tissues including roots, stems, leaves, petals, ovules, and fibers, while the A- and D-genome genes of GobHLH110 and GobHLH130 displayed clearly different transcript profiles during fiber development. In total, this study represented a genome-wide analysis of cotton bHLH family, and revealed significant changes in sequence and expression of these genes in tetraploid cottons, which paved the way for further functional analyses of bHLH genes in the cotton genus. PMID:25992947

  16. The Triple Helix, Quadruple Helix, . . ., and an N-tuple of Helices: Explanatory Models for Analyzing the Knowledge-based Economy?

    CERN Document Server

    Leydesdorff, Loet

    2010-01-01

    Using the Triple Helix model of university-industry-government relations, one can measure the extent to which innovation has become systemic instead of assuming the existence of national (or regional) systems of innovations on a priori grounds. Systemness of innovation patterns, however, can be expected to remain in transition because of integrating and differentiating forces. Integration among the functions of wealth creation, knowledge production, and normative control takes place at the interfaces in organizations, while exchanges on the market, scholarly communication in knowledge production, and political discourse tend to differentiate globally. The neo-institutional and the neo-evolutionary versions of the Triple Helix model enable us to capture this tension reflexively. Empirical studies inform us whether more than three helices are needed for the explanation. The Triple Helix indicator can be extended algorithmically, for example, with local-global as a fourth dimension or, more generally, to an N-tu...

  17. Functional Diversity of Human Basic Helix-Loop-Helix Transcription Factor TCF4 Isoforms Generated by Alternative 5′ Exon Usage and Splicing

    OpenAIRE

    Sepp, Mari; Kannike, Kaja; Eesmaa, Ave; Urb, Mari; Timmusk, Tõnis

    2011-01-01

    Background Transcription factor 4 (TCF4 alias ITF2, E2-2, ME2 or SEF2) is a ubiquitous class A basic helix-loop-helix protein that binds to E-box DNA sequences (CANNTG). While involved in the development and functioning of many different cell types, recent studies point to important roles for TCF4 in the nervous system. Specifically, human TCF4 gene is implicated in susceptibility to schizophrenia and TCF4 haploinsufficiency is the cause of the Pitt-Hopkins mental retardation syndrome. Howeve...

  18. The E2A and tal-1 helix-loop-helix proteins associate in vivo and are modulated by Id proteins during interleukin 6-induced myeloid differentiation.

    OpenAIRE

    Voronova, A F; Lee, F.

    1994-01-01

    The immunoglobulin enhancer-binding proteins, E12 and E47, encoded by the E2A gene belong to the basic helix-loop-helix (bHLH) family of regulatory proteins and act as transcriptional activators. In addition to their critical role in B-lymphocyte development, the E12 and E47 proteins have been implicated in the induction of myogenesis as heterodimeric partners of myogenic bHLH proteins, MyoD and myogenin. Here we demonstrate that the E2A proteins form heterodimers with the bHLH oncoprotein ta...

  19. The LIM protein RBTN2 and the basic helix-loop-helix protein TAL1 are present in a complex in erythroid cells.

    OpenAIRE

    Valge-Archer, V E; Osada, H; Warren, A.J.; Forster, A.; Li, J.; Baer, R; Rabbitts, T H

    1994-01-01

    Chromosomal translocations in T-cell acute leukemias can activate genes encoding putative transcription factors such as the LIM proteins RBTN1 and RBTN2 and the DNA-binding basic helix-loop-helix transcription factor TAL1 associated with T-cell acute lymphocytic leukemia. While not expressed in normal T cells, RBTN2 and TAL1 are coexpressed in erythroid cells and are both important for erythroid differentiation. We demonstrate, using anti-RBTN2 and anti-TAL1 antisera, that the LIM protein RBT...

  20. Enhancer-binding activity of the tal-1 oncoprotein in association with the E47/E12 helix-loop-helix proteins.

    OpenAIRE

    Hsu, H L; Cheng, J. T.; Chen, Q; Baer, R

    1991-01-01

    Almost 30% of patients with T-cell acute lymphoblastic leukemia (T-ALL) bear structural alterations of tal-1, a presumptive proto-oncogene that encodes sequences homologous to the helix-loop-helix (HLH) DNA-binding and dimerization domain. Analysis of the tal-1 gene product reveals that its HLH domain mediates protein-protein interactions with either of the ubiquitously expressed HLH proteins E47 and E12. The resultant tal-1/E47 and tal-1/E12 heterodimers specifically recognize the E-box DNA ...

  1. The p48 DNA-binding subunit of transcription factor PTF1 is a new exocrine pancreas-specific basic helix-loop-helix protein.

    OpenAIRE

    Krapp, A; Knöfler, M.; Frutiger, S; Hughes, G. J.; Hagenbüchle, O; Wellauer, P K

    1996-01-01

    We report the isolation of cDNA for the p48 DNA-binding subunit of the heterooligomeric transcription factor PTF1. A sequence analysis of the cDNA demonstrates that p48 is a new member of the family of basic helix-loop-helix (bHLH) transcription factors. The p48 bHLH domain shows striking amino acid sequence similarity with the bHLH domain of proteins that act as developmental regulators, including the twist gene product, myogenic factors and proteins involved in hematopoietic differentiation...

  2. Analysis of ColE1 MbeC unveils an extended ribbon-helix-helix family of nicking accessory proteins

    OpenAIRE

    Varsaki, Athanasia; Moncalián, Gabriel; Garcillán-Barcia, M. Pilar; Drainas, Constantin; Cruz, Fernando de la

    2009-01-01

    MbeC is a 13-kDa ColEl-encoded protein required for efficient mobilization of ColE1, a plasmid widely used in cloning vector technology. MbeC protein was purified and used for in vitro DNA binding, which showed that it binds specifically double-stranded DNA (dsDNA) containing the ColEl oriT. Amino acid sequence comparison and secondary structure prediction imply that MbeC is related to the ribbon-helix-helix (RHH) protein family. Alignment with RHH members pointed to a conserved arginine (R13...

  3. Role of amphipathic helix of a herpesviral protein in membrane deformation and T cell receptor downregulation.

    Directory of Open Access Journals (Sweden)

    Chan-Ki Min

    2008-11-01

    Full Text Available Lipid rafts are membrane microdomains that function as platforms for signal transduction and membrane trafficking. Tyrosine kinase interacting protein (Tip of T lymphotropic Herpesvirus saimiri (HVS is targeted to lipid rafts in T cells and downregulates TCR and CD4 surface expression. Here, we report that the membrane-proximal amphipathic helix preceding Tip's transmembrane (TM domain mediates lipid raft localization and membrane deformation. In turn, this motif directs Tip's lysosomal trafficking and selective TCR downregulation. The amphipathic helix binds to the negatively charged lipids and induces liposome tubulation, the TM domain mediates oligomerization, and cooperation of the membrane-proximal helix with the TM domain is sufficient for localization to lipid rafts and lysosomal compartments, especially the mutivesicular bodies. These findings suggest that the membrane-proximal amphipathic helix and TM domain provide HVS Tip with the unique ability to deform the cellular membranes in lipid rafts and to downregulate TCRs potentially through MVB formation.

  4. Electric Field-induced Conformational Transition of Bovine Serum Albumin from α -helix to β -sheet

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    The irreversible conformational transition of bovine serum albumin (BSA) from α -helix to β -sheet, induced by electric field near the electrode surface, was monitored by circular dichroism (CD) with a long optical path thin layer cell (LOPTLC).

  5. Herschel spectral mapping of the Helix nebula (NGC 7293): Extended CO photodissociation and OH+ emission

    OpenAIRE

    Etxaluze, M.; Cernicharo, J.; Goicoechea, J. R.; van Hoof, P. A. M.; Van de Steene, G. C.; Groenewegen, M. A. T.; Swinyard, B. M.; Barlow, M.J.; Matsuura, M.; Lim, T. L.; Pearson, C.; Polehampton, E. T.; Kerschbaum, F.; Lique, F.; Royer, P.

    2014-01-01

    Context. The Helix nebula (NGC 7293) is our closest planetary nebulae. Therefore, it is an ideal template for photochemical studies at small spatial scales in planetary nebulae. Aims. We aim to study the spatial distribution of the atomic and the molecular gas, and the structure of the photodissociation region along the western rims of the Helix nebula as seen in the submillimeter range with Herschel. Methods. We used five SPIRE FTS pointing observations to make atomic and molecular spectral ...

  6. The Antiinflammatory and Antiarthritic Properties of Ethanol Extract of Hedera helix

    OpenAIRE

    Anuradha Rai

    2013-01-01

    The ethanol Hedera helix plant extract was tested for its antiinflammatory properties. Intraperitoneal injections of 7.5 ml/kg wt ethanol extract showed antiinflammatory activity with 88.89% inhibition as compared to reference drug diclofenac, which showed 94.44% inhibition in formalin-induced paw oedema. As formalin-induced paw oedema closely resembles human arthritis, the antiarthritic property of ethanol extract of Hedera helix was also investigated. The visible reduction in arthritic symp...

  7. Herschel imaging of the dust in the Helix nebula (NGC 7293)

    OpenAIRE

    Van de Steene, G. C.; van Hoof, P. A. M.; Exter, K. M.; Barlow, M.J.; Cernicharo, J.; Etxaluze, M.; Gear, W. K.; Goicoechea, J. R.; Gomez, H. L.; Groenewegen, M. A. T.; Hargrave, P.C.; Ivison, R. J.; Leeks, S. J.; Lim, T. L.; Matsuura, M.

    2015-01-01

    Aims: In our series of papers presenting the Herschel imaging of evolved planetary nebulae, we present images of the dust distribution in the Helix nebula (NGC 7293). Methods: Images at 70, 160, 250, 350, and 500 μm were obtained with the PACS and SPIRE instruments on board the Herschel satellite. Results: The broadband maps show the dust distribution over the main Helix nebula to be clumpy and predominantly present in the barrel wall. We determined the spectral energy distribution of t...

  8. A novel quadrifilar helix antenna for use in LEO satellite communications

    OpenAIRE

    Mirkamali, Ali; Akhoondzadeh, Lida; Keyghobad, Kiyan; Soleimani, Mohammad

    2003-01-01

    A spherical quadrifilar helix antenna (SQHA) is introduced for producing a saddle point shaped radiation pattern. Radiation characteristics of the antenna have been simulated and the results have been compared with the characteristics of the cylindrical quadrifilar helix antenna (CQHA) which was previously used for this purpose. The results show an improvement in radiation pattern of the proposed antenna in comparison with the previous antenna.

  9. Emergence of the Persistent Spin Helix in Semiconductor Quantum Wells

    Energy Technology Data Exchange (ETDEWEB)

    Koralek, Jake; Weber, Chris; Orenstein, Joe; Bernevig, Andrei; Zhang, Shoucheng; Mack, Shawn; Awschalom, David

    2011-08-24

    According to Noether's theorem, for every symmetry in nature there is a corresponding conservation law. For example, invariance with respect to spatial translation corresponds to conservation of momentum. In another well-known example, invariance with respect to rotation of the electron's spin, or SU(2) symmetry, leads to conservation of spin polarization. For electrons in a solid, this symmetry is ordinarily broken by spin-orbit (SO) coupling, allowing spin angular momentum to flow to orbital angular momentum. However, it has recently been predicted that SU(2) can be recovered in a two-dimensional electron gas (2DEG), despite the presence of SO coupling. The corresponding conserved quantities include the amplitude and phase of a helical spin density wave termed the 'persistent spin helix' (PSH). SU(2) is restored, in principle, when the strength of two dominant SO interactions, the Rashba ({alpha}) and linear Dresselhaus ({beta}{sub 1}), are equal. This symmetry is predicted to be robust against all forms of spin-independent scattering, including electron-electron interactions, but is broken by the cubic Dresselhaus term ({beta}{sub 3}) and spin-dependent scattering. When these terms are negligible, the distance over which spin information can propagate is predicted to diverge as {alpha} {yields} {beta}{sub 1}. Here we observe experimentally the emergence of the PSH in GaAs quantum wells (QW's) by independently tuning {alpha} and {beta}{sub 1}. Using transient spin-grating spectroscopy (TSG), we find a spin-lifetime enhancement of two orders of magnitude near the symmetry point. Excellent quantitative agreement with theory across a wide range of sample parameters allows us to obtain an absolute measure of all relevant SO terms, identifying {beta}{sub 3} as the main SU(2) violating term in our samples. The tunable suppression of spin-relaxation demonstrated in this work is well-suited for application to spintronics.

  10. TAL2, a helix-loop-helix gene activated by the (7; 9)(q34; q32) translocation in human T-cell leukemia

    Energy Technology Data Exchange (ETDEWEB)

    Ying Xia; Brown, L.; Yang, C.Y.; Tsan, J.T.; Baer, R.J. (Univ. of Texas, Dallas (United States)); Siciliano, M.J. (Univ. of Texas, Houston (United States)); Espinosa, R. III; Le Beau, M.M. (Univ. of Chicago, IL (United States))

    1991-12-15

    Tumor-specific alteration of the TAL1 gene occurs in almost 25% of patients with T-cell acute lymphoblastic leukemia (T-ALL). The authors now report the identification of TAL2, a distinct gene that was isolated on the basis of its sequence homology with TAL1. The TAL2 gene is located 33 kilobase pairs from the chromosome 9 breakpoint of t(7;9)(q34;q32), a recurring translocation specifically associated with T-ALL. As a consequence of t(7;9)(q34;q32), TAL2 is juxtaposed with sequences from the T-cell receptor {beta}-chain gene on chromosome 7. TAL2 sequences are actively transcribed in SUP-T3, a T-ALL cell line that harbors the t(7;9)(q34;q32). The TAL2 gene product includes a helix-loop-helix protein dimerization and DNA binding domain that is especially homologous to those encoded by the TAL1 and LYL1 protooncogenes. Hence, TAL2, TAL1, and LYL1 constitute a discrete subgroup of helix-loop-helix proteins, each of which can potentially contribute to the development of T-ALL.

  11. CFD analysis and flow model reduction for surfactant production in helix reactor = CFD analiza i redukcija modela strujanja za proizvodnju surfaktanta u helix reaktoru

    NARCIS (Netherlands)

    Nikačević, N.M.; Thielen, L.; Twerda, A.; Hof, P.M.J. van den

    2015-01-01

    Flow pattern analysis in a spiral Helix reactor is conducted, for the application in commercial surfactant production. Step change response curves (SCR) were obtained from numerical tracer experiments by three-dimensional computational fluid dynamics (CFD) simulations. Non-reactive flow is simulated

  12. The C-Terminal RpoN Domain of sigma54 Forms an unpredictedHelix-Turn-Helix Motif Similar to domains of sigma70

    Energy Technology Data Exchange (ETDEWEB)

    Doucleff, Michaeleen; Malak, Lawrence T.; Pelton, Jeffrey G.; Wemmer, David E.

    2005-11-01

    The ''{delta}'' subunit of prokaryotic RNA-polymerase allows gene-specific transcription initiation. Two {sigma} families have been identified, {sigma}{sup 70} and {sigma}{sup 54}, which use distinct mechanisms to initiate transcription and share no detectable sequence homology. Although the {sigma}{sup 70}-type factors have been well characterized structurally by x-ray crystallography, no high-resolution structural information is available for the {sigma}{sup 54}-type factors. Here we present the NMR derived structure of the C-terminal domain of {sigma}{sup 54} from Aquifex aeolicus. This domain (Thr323 to Gly389), which contains the highly conserved RpoN box sequence, consists of a poorly structured N-terminal tail followed by a three-helix bundle, which is surprisingly similar to domains of the {sigma}{sup 70}-type proteins. Residues of the RpoN box, which have previously been shown to be critical for DNA binding, form the second helix of an unpredicted helix-turn-helix motif. This structure's homology with other DNA binding proteins, combined with previous biochemical data, suggest how the C-terminal domain of {sigma}{sup 54} binds to DNA.

  13. Elevated temperature triggers human respiratory syncytial virus F protein six-helix bundle formation

    International Nuclear Information System (INIS)

    Human respiratory syncytial virus (RSV) is a major cause of severe lower respiratory tract infection in infants, immunocompromised patients, and the elderly. The RSV fusion (F) protein mediates fusion of the viral envelope with the target cell membrane during virus entry and is a primary target for antiviral drug and vaccine development. The F protein contains two heptad repeat regions, HR1 and HR2. Peptides corresponding to these regions form a six-helix bundle structure that is thought to play a critical role in membrane fusion. However, characterization of six-helix bundle formation in native RSV F protein has been hindered by the fact that a trigger for F protein conformational change has yet to be identified. Here we demonstrate that RSV F protein on the surface of infected cells undergoes a conformational change following exposure to elevated temperature, resulting in the formation of the six-helix bundle structure. We first generated and characterized six-helix bundle-specific antibodies raised against recombinant peptides modeling the RSV F protein six-helix bundle structure. We then used these antibodies as probes to monitor RSV F protein six-helix bundle formation in response to a diverse array of potential triggers of conformational changes. We found that exposure of 'membrane-anchored' RSV F protein to elevated temperature (45-55 deg. C) was sufficient to trigger six-helix bundle formation. Antibody binding to the six-helix bundle conformation was detected by both flow cytometry and cell-surface immunoprecipitation of the RSV F protein. None of the other treatments, including interaction with a number of potential receptors, resulted in significant binding by six-helix bundle-specific antibodies. We conclude that native, untriggered RSV F protein exists in a metastable state that can be converted in vitro to the more stable, fusogenic six-helix bundle conformation by an increase in thermal energy. These findings help to better define the mechanism of

  14. The triple helix frame for Small and Medium-sized Enterprises for innovation and development of offshore wind energy

    DEFF Research Database (Denmark)

    Brink, Tove; Madsen, Svend Ole

    2016-01-01

    -term support of industry knowledge spaces for offshore wind energy. Governmental bodies would actively enhance political growth strategies regulating competition and collaboration. Universities can contribute actively towards knowledge creation and dissemination. All three helices could benefit from this...... from integrating SMEs in a triple helix context. The triple helix approach with government, university and industry participants typically include larger organisations. The research indicates that SMEs could join the triple helix and both contribute and receive benefit from their presence. The findings...

  15. Osteogenesis Imperfecta Model Peptides: Incorporation of Residues Replacing Gly within a Triple Helix Achieved by Renucleation and Local Flexibility

    OpenAIRE

    Xiao, Jianxi; Madhan, Balaraman; Li, Yingjie; Brodsky, Barbara; Baum, Jean

    2011-01-01

    Missense mutations, which replace one Gly with a larger residue in the repeating sequence of the type I collagen triple helix, lead to the hereditary bone disorder osteogenesis imperfecta (OI). Previous studies suggest that these mutations may interfere with triple-helix folding. NMR was used to investigate triple-helix formation in a series of model peptides where the residue replacing Gly, as well as the local sequence environment, was varied. NMR measurement of translational diffusion coef...

  16. 13-Helix folding of a β/γ-peptide manifold designed from a "minimal-constraint" blueprint.

    Science.gov (United States)

    Grison, Claire M; Robin, Sylvie; Aitken, David J

    2016-06-14

    A bottom-up design rationale was adopted to devise β/γ-peptide foldamer manifolds which would adopt preferred 13-helix conformations, relying on minimal steric imposition brought by the constituent amino acid residues. In this way, a well-defined 13-helix conformer was revealed for short oligomers of trans-2-aminocyclobutanecarboxylic acid and γ(4)-amino acids in alternation, which gave good topological superposition upon an α-helix motif. PMID:27230541

  17. What can triple helix frameworks offer to the analysis of eco-innovation dynamics? Theoretical and methodological considerations

    DEFF Research Database (Denmark)

    Yang, Yan; Holgaard, Jette Egelund; Remmen, Arne

    2012-01-01

    stakeholder groups are interacting in this connection. Taking the triple helix as the theoretical departure point, this paper discusses the opportunities offered by these triple helix frameworks for analyzing eco-innovation dynamics from both theoretical and practical perspectives. It adds to the debate about...... stakeholder dynamics in eco-innovation processes by using the discourse of a proactive company to argue for the need for, and a conceptual framing of, a fourth actor in the helix of eco-innovation....

  18. Cytotoxic helix-rich oligomer formation by melittin and pancreatic polypeptide.

    Directory of Open Access Journals (Sweden)

    Pradeep K Singh

    Full Text Available Conversion of amyloid fibrils by many peptides/proteins involves cytotoxic helix-rich oligomers. However, their toxicity and biophysical studies remain largely unknown due to their highly dynamic nature. To address this, we chose two helical peptides (melittin, Mel and pancreatic polypeptide, PP and studied their aggregation and toxicity. Mel converted its random coil structure to oligomeric helical structure upon binding to heparin; however, PP remained as helix after oligomerization. Interestingly, similar to Parkinson's associated α-synuclein (AS oligomers, Mel and PP also showed tinctorial properties, higher hydrophobic surface exposure, cellular toxicity and membrane pore formation after oligomerization in the presence of heparin. We suggest that helix-rich oligomers with exposed hydrophobic surface are highly cytotoxic to cells irrespective of their disease association. Moreover as Mel and PP (in the presence of heparin instantly self-assemble into stable helix-rich amyloidogenic oligomers; they could be represented as models for understanding the biophysical and cytotoxic properties of helix-rich intermediates in detail.

  19. Vibrations of ordered counterions around left- and right-handed DNA double helixes

    Science.gov (United States)

    Perepelytsya, S. M.; Volkov, S. N.

    2013-06-01

    The vibrations of ordered counterions around right- and left-handed DNA double helix are studied. To determine the modes of DNA conformational vibrations the structure of the double helix with counterions is considered as ionic lattice (ion-phosphate lattice). Using the developed approach the frequencies and Raman intensities for right-handed B-form and left-handed Z-form of the double helix with Na+, K+, Rb+, Cs+, and Mg2+ counterions are calculated. The obtained frequencies of vibrations of internal structure elements of the double helix (mass and charge. The frequencies of ion-phosphate vibrations of alkali metal counterions decrease from 180 to 100 cm-1, while their Raman intensities increase as the counterion mass increases for the both B- and Z-DNA. In the case of Z-DNA new mode of ion-phosphate vibrations near 150 cm-1 is found. This mode is characterized by vibrations of Mg2+ counterions with respect to the phosphates of different strands of the double helix. Our results explain the experimental Raman spectra of Z-DNA.

  20. Vibrations of ordered counterions around left- and right-handed DNA double helixes

    International Nuclear Information System (INIS)

    The vibrations of ordered counterions around right- and left-handed DNA double helix are studied. To determine the modes of DNA conformational vibrations the structure of the double helix with counterions is considered as ionic lattice (ion-phosphate lattice). Using the developed approach the frequencies and Raman intensities for right-handed B-form and left-handed Z-form of the double helix with Na+, K+, Rb+, Cs+, and Mg2+ counterions are calculated. The obtained frequencies of vibrations of internal structure elements of the double helix (−1) weakly depend on counterion type. In contrast, the vibrations of the ion-phosphate lattice are determined by counterion mass and charge. The frequencies of ion-phosphate vibrations of alkali metal counterions decrease from 180 to 100 cm−1, while their Raman intensities increase as the counterion mass increases for the both B- and Z-DNA. In the case of Z-DNA new mode of ion-phosphate vibrations near 150 cm−1 is found. This mode is characterized by vibrations of Mg2+ counterions with respect to the phosphates of different strands of the double helix. Our results explain the experimental Raman spectra of Z-DNA.

  1. Radio-Frequency Characteristics of a Printed Rectangular Helix Slow-Wave Structure

    International Nuclear Information System (INIS)

    A new type of printed rectangular helix slow-wave structure (SWS) is investigated using the field-matching method and the electromagnetic integral equations at the boundaries. The radio-frequency characteristics including the dispersion equation and the coupling impedance for transverse antisymmetric (odd) modes of this structure are analysed. The numerical results agree well with the results obtained by the EM simulation software HFSS. It is shown that the dispersion of the rectangular helix circuit is weakened, the phase velocity is reduced after filling the dielectric materials in the rectangular helix SWS. As a planar slow-wave structure, this structure has potential applications in compact TWTs. (cross-disciplinary physics and related areas of science and technology)

  2. Health and Environment Linked for Information Exchange in Atlanta (HELIX-Atlanta): A Pilot Tracking System

    Science.gov (United States)

    Rickman, Doug; Shire, J.; Qualters, J.; Mitchell, K.; Pollard, S.; Rao, R.; Kajumba, N.; Quattrochi, D.; Estes, M., Jr.; Meyer, P.; Crosson, W.; Limaye, A.; Al-Hamdan, M.; Khan, M.; Bayakly, R.; Staley, F.; Hallisey, E.; Young, J.; Ward, K.; Tolbert, P.; Tolsma, D.; Sinclair, A.; Strickland, M.; Adeniyi, K.; Rainisch, G.

    2009-01-01

    Objectives. To provide an overview of four environmental public health surveillance projects developed by CDC and its partners for the Health and Environment Linked for Information Exchange, Atlanta (HELIX-Atlanta) and to illustrate common issues and challenges encountered in developing an environmental public health tracking system. Methods. HELIX-Atlanta, initiated in October 2003 to develop data linkage and analysis methods that can be used by the National Environmental Public Health Tracking Network (Tracking Network), conducted four projects. We highlight the projects' work, assess attainment of the HELIX-Atlanta goals and discuss three surveillance attributes. Results. Among the major challenges was the complexity of analytic issues which required multidiscipline teams with technical expertise. This expertise and the data resided across multiple organizations. Conclusions:Establishing formal procedures for sharing data, defining data analysis standards and automating analyses, and committing staff with appropriate expertise is needed to support wide implementation of environmental public health tracking.

  3. The Drosophila dysfusion basic helix-loop-helix (bHLH)-PAS gene controls tracheal fusion and levels of the trachealess bHLH-PAS protein.

    Science.gov (United States)

    Jiang, Lan; Crews, Stephen T

    2003-08-01

    The development of the mature insect trachea requires a complex series of cellular events, including tracheal cell specification, cell migration, tubule branching, and tubule fusion. Here we describe the identification of the Drosophila melanogaster dysfusion gene, which encodes a novel basic helix-loop-helix (bHLH)-PAS protein conserved between Caenorhabditis elegans, insects, and humans, and controls tracheal fusion events. The Dysfusion protein functions as a heterodimer with the Tango bHLH-PAS protein in vivo to form a putative DNA-binding complex. The dysfusion gene is expressed in a variety of embryonic cell types, including tracheal-fusion, leading-edge, foregut atrium cells, nervous system, hindgut, and anal pad cells. RNAi experiments indicate that dysfusion is required for dorsal branch, lateral trunk, and ganglionic branch fusion but not for fusion of the dorsal trunk. The escargot gene, which is also expressed in fusion cells and is required for tracheal fusion, precedes dysfusion expression. Analysis of escargot mutants indicates a complex pattern of dysfusion regulation, such that dysfusion expression is dependent on escargot in the dorsal and ganglionic branches but not the dorsal trunk. Early in tracheal development, the Trachealess bHLH-PAS protein is present at uniformly high levels in all tracheal cells, but since the levels of Dysfusion rise in wild-type fusion cells, the levels of Trachealess in fusion cells decline. The downregulation of Trachealess is dependent on dysfusion function. These results suggest the possibility that competitive interactions between basic helix-loop-helix-PAS proteins (Dysfusion, Trachealess, and possibly Similar) may be important for the proper development of the trachea. PMID:12897136

  4. The signaling helix: a common functional theme in diverse signaling proteins

    Directory of Open Access Journals (Sweden)

    Aravind L

    2006-09-01

    Full Text Available Abstract Background The mechanism by which the signals are transmitted between receptor and effector domains in multi-domain signaling proteins is poorly understood. Results Using sensitive sequence analysis methods we identify a conserved helical segment of around 40 residues in a wide range of signaling proteins, including numerous sensor histidine kinases such as Sln1p, and receptor guanylyl cyclases such as the atrial natriuretic peptide receptor and nitric oxide receptors. We term this helical segment the signaling (S-helix and present evidence that it forms a novel parallel coiled-coil element, distinct from previously known helical segments in signaling proteins, such as the Dimerization-Histidine phosphotransfer module of histidine kinases, the intra-cellular domains of the chemotaxis receptors, inter-GAF domain helical linkers and the α-helical HAMP module. Analysis of domain architectures allowed us to reconstruct the domain-neighborhood graph for the S-helix, which showed that the S-helix almost always occurs between two signaling domains. Several striking patterns in the domain neighborhood of the S-helix also became evident from the graph. It most often separates diverse N-terminal sensory domains from various C-terminal catalytic signaling domains such as histidine kinases, cNMP cyclase, PP2C phosphatases, NtrC-like AAA+ ATPases and diguanylate cyclases. It might also occur between two sensory domains such as PAS domains and occasionally between a DNA-binding HTH domain and a sensory domain. The sequence conservation pattern of the S-helix revealed the presence of a unique constellation of polar residues in the dimer-interface positions within the central heptad of the coiled-coil formed by the S-helix. Conclusion Combining these observations with previously reported mutagenesis studies on different S-helix-containing proteins we suggest that it functions as a switch that prevents constitutive activation of linked downstream

  5. Dispersion Features of Conducting Sheath Helix Embedded Elliptical and Circular Fibers with Chiral Nihility Core

    Directory of Open Access Journals (Sweden)

    N. Iqbal

    2015-01-01

    Full Text Available Discussions have been made of the electromagnetic wave propagation through optical fibers of elliptical and circular cross-sections with the loadings of conducting sheath helix at the core-clad interface with particular orientations. In both geometrical situations, the core section of fiber is assumed to be composed of chiral nihility medium, and the clad remains linear, homogeneous, isotropic, and nonmagnetic dielectric. Dispersion relations are deduced for both fiber structures, followed by the analysis of dispersion features considering a few low-order EH modes. Furthermore, the effects of conducting helix pitch angle on the features of wave propagation are also discussed.

  6. Sodium Dodecyl Sulfate Monomers Induce XAO Peptide Polyproline II to α-Helix Transition

    OpenAIRE

    Hong, Zhenmin; Damodaran, Krishnan; Asher, Sanford A.

    2014-01-01

    XAO peptide (Ac–X2A7O2–NH2; X: diaminobutyric acid side chain, −CH2CH2NH3 +; O: ornithine side chain, −CH2CH2CH2NH3 +) in aqueous solution shows a predominantly polyproline II (PPII) conformation without any detectable α-helix-like conformations. Here we demonstrate by using circular dichroism (CD), ultraviolet resonance Raman (UVRR) and nuclear magnetic resonance (NMR) spectroscopy that sodium dodecyl sulfate (SDS) monomers bind to XAO and induce formation of α-helix-like conformations. The ...

  7. End-to-end and end-to-middle interhelical interactions: new classes of interacting helix pairs in protein structures

    International Nuclear Information System (INIS)

    New classes of helix–helix interactions in protein structures are reported in which interactions only occur at the terminal regions or between the terminal region of one helix and the middle region of another helix. Helix–helix interactions are important for the structure, stability and function of α-helical proteins. Helices that either cross in the middle or show extensive contacts between each other, such as coiled coils, have been investigated in previous studies. Interactions between two helices can also occur only at the terminal regions or between the terminal region of one helix and the middle region of another helix. Examples of such helix pairs are found in aquaporin, H+/Cl− transporter and Bcl-2 proteins. The frequency of the occurrence of such ‘end-to-end’ (EE) and ‘end-to-middle’ (EM) helix pairs in protein structures is not known. Questions regarding the residue preferences in the interface and the mode of interhelical interactions in such helix pairs also remain unanswered. In this study, high-resolution structures of all-α proteins from the PDB have been systematically analyzed and the helix pairs that interact only in EE or EM fashion have been extracted. EE and EM helix pairs have been categorized into five classes (N–N, N–C, C–C, N–MID and C–MID) depending on the region of interaction. Nearly 13% of 5725 helix pairs belonged to one of the five classes. Analysis of single-residue propensities indicated that hydrophobic and polar residues prefer to occur in the C-terminal and N-terminal regions, respectively. Hydrophobic C-terminal interacting residues and polar N-terminal interacting residues are also highly conserved. A strong correlation exists between some of the residue properties (surface area/volume and length of side chains) and their preferences for occurring in the interface of EE and EM helix pairs. In contrast to interacting non-EE/EM helix pairs, helices in EE and EM pairs are farther apart. In these helix

  8. Dynamic Antagonism between Phytochromes and PIF Family Basic Helix-Loop-Helix Factors Induces Selective Reciprocal Responses to Light and Shade in a Rapidly Responsive Transcriptional Network in Arabidopsis

    Science.gov (United States)

    Plants respond to shade-modulated light signals via phytochrome (phy)-induced adaptive changes, termed shade avoidance. To examine the roles of Phytochrome-Interacting basic helix-loop-helix Factors, PIF1, 3, 4, and 5, in relaying such signals to the transcriptional network, we compared the shade-re...

  9. Equilibrium shift in solution: molecular shape recognition and precipitation of a synthetic double helix using helicene-grafted silica nanoparticles.

    Science.gov (United States)

    Miyagawa, Masamichi; Ichinose, Wataru; Yamaguchi, Masahiko

    2014-01-27

    Chiral silica nanoparticles (70 nm) grafted with (P)-helicene recognized the molecular shape of double helix and random coil (P)-ethynylhelicene oligomers in solution. A mixture of the (P)-nanoparticles and double helix precipitated much faster than a mixture of the (P)-nanoparticles and random coil, and the precipitate contained only the double helix. The mixture of the (P)-nanoparticles and (P)-ethynylhelicene pentamer reversibly dispersed in trifluoromethylbenzene upon heating at 70 °C and precipitated upon cooling at 25 °C. When a 10:90 equilibrium mixture of the double helix and random coil in solution was treated with the (P)-nanoparticles, the double helix was precipitated in 53% yield and was accompanied by equilibrium shift. PMID:24382663

  10. Symmetrical-geometry constructions defining helicoidal biostructures. The case of alpha-helix

    CERN Document Server

    Samoylovich, Mikhail

    2016-01-01

    The chain of algebraic geometry constructions permits to transfer from the minimal surface with zero instability index, and from the lattice over the ring of cyclotomic integers to the tetra-block helix. The tetra-block is the 7-vertex joining of four tetrahedra sharing common faces; it is considered as a building unit for structures approximated by the chains of regular tetrahedra. The minimality condition of the 7 - vertex tetrablock as a building unit is the consequence of its unique mapping by the Klein's quartic (which is characterized by the minimal hyperbolic Schwartz triangle) into the minimal finite projective geometry. The topological stability of this helix provided by the pitch to radius ratio H/R of 2{\\pi}/({\\tau}+1) ({\\tau} is the golden section) and by the local rotation axis order of 40/11=40exp(-H/R). These parameters determine the helix of C{\\alpha} atoms inside the alpha - helix with the accuracy of up to 2%. They explain also the bonding relationship i -- i+4 between the i-th amide group a...

  11. A note on the pollen representation of ivy (Hedera helix L.)

    NARCIS (Netherlands)

    Bottema, S

    2001-01-01

    Pollen productivity and dispersal of ivy (Hedera helix) is discussed on the basis of a simple surface sample study in a situation that has been followed for about 30 yr. The pollen production of a special ivy plant was estimated for the flowering season of 1998. Hedera pollen dispersal was followed

  12. Geometry of the toroidal N-helix: optimal-packing and zero-twist

    DEFF Research Database (Denmark)

    Olsen, Kasper; Bohr, Jakob

    2012-01-01

    Two important geometrical properties of N-helix structures are influenced by bending. One is maximizing the volume fraction, which is called optimal-packing, and the other is having a vanishing strain-twist coupling, which is called zero-twist. Zero-twist helices rotate neither in one nor in the ...

  13. CFD analysis and flow model reduction for surfactant production in helix reactor

    NARCIS (Netherlands)

    Nikačević, N.M.; Thielen, L.; Twerda, A.; Hof, P.M.J. van den

    2014-01-01

    Flow pattern analysis in a spiral Helix reactor is conducted, for the application in the commercial surfactant production. Step change response curves (SCR) were obtained from numerical tracer experiments by three-dimensional computational fluid dynamics (CFD) simulations. Non-reactive flow is simul

  14. Rendezvous of the "Third Kind": Triple Helix Origins and Future Possibilities

    Science.gov (United States)

    Etzkowitz, Henry

    2015-01-01

    The Triple Helix, representing university-industry-government interactions, was rooted in a 1993 International Workshop on University-Industry Relations at UNAM's Centro Para la Innovacion Technologica in Mexico City. Impelled by Mexican reality, where university-industry interactions and the institutions themselves operated within a governmental…

  15. Structures and Energetics of Four Adjacent G·U Pairs That Stabilize an RNA Helix.

    Science.gov (United States)

    Gu, Xiaobo; Mooers, Blaine H M; Thomas, Leonard M; Malone, Joshua; Harris, Steven; Schroeder, Susan J

    2015-10-22

    Consecutive G·U base pairs inside RNA helices can be destabilizing, while those at the ends of helices are thermodynamically stabilizing. To determine if this paradox could be explained by differences in base stacking, we determined the high-resolution (1.32 Å) crystal structure of (5'-GGUGGCUGUU-3')2 and studied three sequences with four consecutive terminal G·U pairs by NMR spectroscopy. In the crystal structure of (5'-GGUGGCUGUU-3')2, the helix is overwound but retains the overall features of A-form RNA. The penultimate base steps at each end of the helix have high base overlap and contribute to the unexpectedly favorable energetic contribution for the 5'-GU-3'/3'-UG-5' motif in this helix position. The balance of base stacking and helical twist contributes to the positional dependence of G·U pair stabilities. The energetic stabilities and similarity to A-form RNA helices suggest that consecutive G·U pairs would be recognized by RNA helix binding proteins, such as Dicer and Ago. Thus, these results will aid future searches for target sites of small RNAs in gene regulation. PMID:26425937

  16. Tuning of Collagen Triple-Helix Stability in Recombinant Telechelic Polymers

    NARCIS (Netherlands)

    Silva, da C.I.; Skrzeszewska, P.J.; Golinska, M.D.; Werten, M.W.T.; Eggink, G.; Wolf, de F.A.

    2012-01-01

    The melting properties of various triblock copolymers with random coil middle blocks (100–800 amino acids) and triple helix-forming (Pro-Gly-Pro)n end blocks (n = 6–16) were compared. These gelatin-like molecules were produced as secreted proteins by recombinant yeast. The investigated series shows

  17. The close-packed triple helix as a possible new structural motif for collagen

    CERN Document Server

    Bohr, Jakob

    2010-01-01

    The one-dimensional problem of selecting the triple helix with the highest volume fraction is solved and hence the condition for a helix to be close-packed is obtained. The close-packed triple helix is shown to have a pitch angle of $v_{CP} =43.3 ^\\circ$. Contrary to the conventional notion, we suggest that close packing form the underlying principle behind the structure of collagen, and the implications of this suggestion are considered. Further, it is shown that the unique zero-twist structure with no strain-twist coupling is practically identical to the close-packed triple helix. Some of the difficulties for the current understanding of the structure of collagen are reviewed: The ambiguity in assigning crystal structures for collagen-like peptides, and the failure to satisfactorily calculate circular dichroism spectra. Further, the proposed new geometrical structure for collagen is better packed than both the 10/3 and the 7/2 structure. A feature of the suggested collagen structure is the existence of a ce...

  18. Inside the Triple Helix: An Integrative Conceptual Framework of the Academic Researcher's Activities, a Systematic Review

    Science.gov (United States)

    Halilem, Norrin

    2010-01-01

    In the Triple Helix of University-Industry-Government relations, the academic researcher plays a predominant role as he participates in research, which provides opportunities for innovation; in teaching, which develops highly qualified personnel; and in entrepreneurialism, which represents the transformation of knowledge in a more usable form, and…

  19. Open Innovation, Triple Helix and Regional Innovation Systems: Exploring CATAPULT Centres in the UK

    Science.gov (United States)

    Kerry, Christopher; Danson, Michael

    2016-01-01

    Through the lens of UK CATAPULT Centres this conceptual paper presents an examination of the links between open innovation, the Triple Helix model and regional innovation systems. Highlighting the importance of boundary-spanning intermediaries, the combined role of these concepts is explored in detail. A conceptual model is then proposed which…

  20. Reversible Dimerization of Acid-Denatured ACBP Controlled by Helix A4

    DEFF Research Database (Denmark)

    Fieber, Wolfgang; Kragelund, Birthe Brandt; Meldal, Morten Peter;

    2005-01-01

    denaturing conditions at pH 2.3, helix conformations are still populated in 24% of the ensemble of molecules. The structure of HA4 at atomic resolution was assessed using nuclear magnetic resonance (NMR) spectroscopy. Long-range NOEs between remote residues at opposite peptide ends suggested the formation of...

  1. Democracy and environment as references for quadruple and quintuple helix innovation systems

    Science.gov (United States)

    Carayannis, Elias G.; Campbell, David F. J.; Orr, Barron J.

    2015-04-01

    The perspective of democracy and the ecological context define key references for knowledge production and innovation in innovation systems. Particularly under conditions of environmental change where enhancing the potential for adaptation is critical, this requires a closer look at ecological responsibility and sensitivity in the different innovation models and governance regimes. The "Quintuple Helix" innovation model is an approach that stresses the necessary socio-ecological transition of society and economy by adding an environment helix to an innovation system already made up of three (university-industry-government) or four (civil society relations) helices in a way that supports adaptation by incorporating global warming as both a challenge to and a driver of innovation. There is the proposition that knowledge production and innovation co-evolve with democracy (Carayannis and Campbell, 2014). In the Triple Helix model (Etzkowitz and Leydesdorff, 2000) the existence of a democracy does not appear to be necessary for knowledge production and innovation. However, the Quadruple Helix (Carayannis and Campbell, 2009, 2010 and 2014) is defined and represented by additional key attributes and components: "media-based and culture-based public", "civil society" and "arts, artistic research and arts-based innovation" (Bast, Carayannis and Campbell, 2015). Implications of this are that the fourth helix in the Quadruple Helix innovation systems brings in and represents the perspective of "dimension of democracy" or the "context of democracy" for knowledge in general and knowledge production and innovation in more particular. Within theories of democracy there is a competition between narrow and broader concepts of democracy (Campbell, 2013). This is particularly true when democracy is to be understood to transcend more substantially the narrow understanding of being primarily based on or being primarily rooted in government institutions (within a Triple Helix

  2. From Family Based to Industrial Based Production: Local Economic Development Initiatives and the HELIX Model

    Directory of Open Access Journals (Sweden)

    Bartjan W Pennink

    2013-01-01

    Full Text Available To build a strong local economy, good practice tells us that each community should undertake a collaborative, strategically planned process to understand and then act upon its own strengths, weaknesses, opportunities and threats. From this perspective we start with the local communities but how is this related to the perspective from the Helix model in which three actors are explicitly introduced: the Government, the Industry and the Universities? The purpose of local economic development (LED is to build up the economic capacity of a local area to improve its economic future and the quality of life for all. To support  the Local Economic Development in remote areas,   a program  has been developed based on the LED frame work of the world bank. This approach and  the experiences over  the past years with this program are  described in the first part.  In the second part of the paper, We analyse work done with that program with the help of the social capital concept and the triple helix model.  In all cases it is important to pay attention to who is taken the initiative after the first move (and it is not always the governance as actor and for the triple helix we suggest  that the concepts of (national Government, Industry and University need a translation to Local Governance Agency, Cooperation or other ways of cooperation of local communities and Local Universities. Although a push from outside might help  a local region in development the endogenous factors are  also needed. Keywords: Triple Helix model, Local Economic Development, Local Actors, Double Triangle within the Helix Model

  3. Sodium dodecyl sulfate monomers induce XAO peptide polyproline II to α-helix transition.

    Science.gov (United States)

    Hong, Zhenmin; Damodaran, Krishnan; Asher, Sanford A

    2014-09-11

    XAO peptide (Ac-X2A7O2-NH2; X: diaminobutyric acid side chain, -CH2CH2NH3(+); O: ornithine side chain, -CH2CH2CH2NH3(+)) in aqueous solution shows a predominantly polyproline II (PPII) conformation without any detectable α-helix-like conformations. Here we demonstrate by using circular dichroism (CD), ultraviolet resonance Raman (UVRR) and nuclear magnetic resonance (NMR) spectroscopy that sodium dodecyl sulfate (SDS) monomers bind to XAO and induce formation of α-helix-like conformations. The stoichiometry and the association constants of SDS and XAO were determined from the XAO-SDS diffusion coefficients measured by pulsed field gradient NMR. We developed a model for the formation of XAO-SDS aggregate α-helix-like conformations. Using UVRR spectroscopy, we calculated the Ramachandran ψ angle distributions of aggregated XAO peptides. We resolved α-, π- and 3(10)-helical conformations and a turn conformation. XAO nucleates SDS aggregation at SDS concentrations below the SDS critical micelle concentration. The XAO4-SDS16 aggregates have four SDS molecules bound to each XAO to neutralize the four side chain cationic charges. We propose that the SDS alkyl chains partition into a hydrophobic core to minimize the hydrophobic area exposed to water. Neutralization of the flanking XAO charges enables α-helix formation. Four XAO-SDS4 aggregates form a complex with an SDS alkyl chain-dominated hydrophobic core and a more hydrophilic shell where one face of the α-helix peptide contacts the water environment. PMID:25121643

  4. Tah1 helix-swap dimerization prevents mixed Hsp90 co-chaperone complexes

    Energy Technology Data Exchange (ETDEWEB)

    Morgan, Rhodri M. L.; Pal, Mohinder; Roe, S. Mark; Pearl, Laurence H., E-mail: laurence.pearl@sussex.ac.uk; Prodromou, Chrisostomos, E-mail: laurence.pearl@sussex.ac.uk [University of Sussex, Falmer, Brighton BN1 9RQ (United Kingdom)

    2015-05-01

    A helix swap involving the fifth helix between two adjacently bound Tah1 molecules restores the normal binding environment of the conserved MEEVD peptide of Hsp90. Dimerization also explains how other monomeric TPR-domain proteins are excluded from forming inappropriate mixed co-chaperone complexes with Hsp90 and Tah1. Specific co-chaperone adaptors facilitate the recruitment of client proteins to the Hsp90 system. Tah1 binds the C-terminal conserved MEEVD motif of Hsp90, thus linking an eclectic set of client proteins to the R2TP complex for their assembly and regulation by Hsp90. Rather than the normal complement of seven α-helices seen in other tetratricopeptide repeat (TPR) domains, Tah1 unusually consists of the first five only. Consequently, the methionine of the MEEVD peptide remains exposed to solvent when bound by Tah1. In solution Tah1 appears to be predominantly monomeric, and recent structures have failed to explain how Tah1 appears to prevent the formation of mixed TPR domain-containing complexes such as Cpr6–(Hsp90){sub 2}–Tah1. To understand this further, the crystal structure of Tah1 in complex with the MEEVD peptide of Hsp90 was determined, which shows a helix swap involving the fifth α-helix between two adjacently bound Tah1 molecules. Dimerization of Tah1 restores the normal binding environment of the bound Hsp90 methionine residue by reconstituting a TPR binding site similar to that in seven-helix-containing TPR domain proteins. Dimerization also explains how other monomeric TPR-domain proteins are excluded from forming inappropriate mixed co-chaperone complexes.

  5. Site-specific cleavage of genomic DNA mediated by triple helix formation

    Energy Technology Data Exchange (ETDEWEB)

    Strobel, S.A.

    1992-01-01

    Physical isolation of large segments of chromosomal DNA is a major goal of human genetics. This would be greatly assisted by a generalizable technique for the cleavage of chromosomal DNA at a single site. Pyrimidine oligonucleotide directed triple helix formation is a generalizable motif for the site specific recognition of duplex DNA. This thesis describes the application of oligonucleotide directed triple helix formation to bind unique target sites in bacteriophage [lambda], yeast, and human genomic DNA. Cleavage at the binding sites are achieved by affinity cleaving with EDTA[center dot]Fe(II) derivatized oligonucleotides, alkylation with bromoacetyl derivatized oligonucleotides, and by site specific triple helix mediated methylase inhibition followed by digestion with the cognate endonuclease. Cleavage of genomic substrates with progressively greater complexity is described. Bacteriophage [lambda] genomic DNA (48.5 kilobase pairs) was targeted at a single endogenous homopurine site within the origin of replication. This substrate was also used to demonstrate cooperative binding of heterologous oligonucleotides to duplex DNA at contiguous binding sites. An engineered target site on yeast chromosome III (340 kilobase pairs) was cut quantitatively at a single site within total yeast genomic DNA (14 megabase pairs) by both chemical and enzymatic techniques. Techniques for the identification of endogenous triple helix target sites within unsequenced genetic markers were developed and successfully used to characterize a target site on human chromosome 4, proximal to the Huntington disease gene. As a test for the site specific cleavage of gigabase DNA, this site near the end of human chromosome 4 was cleaved by triple helix mediated enzymatic cleavage. This generated a specific 3.6 Mb fragment in greater than 80% yield that contained the entire candidate region for the Huntington mutation.

  6. Stereochemical punctuation marks in protein structures: glycine and proline containing helix stop signals.

    Science.gov (United States)

    Gunasekaran, K; Nagarajaram, H A; Ramakrishnan, C; Balaram, P

    1998-02-01

    An analysis on the nature of alpha-helix stop signals has been carried out, using a dataset of 1057 helices identified from 250 high resolution (helix stop signals, alphaL and E-terminated helices, were further examined for sequence preferences. Gly residues were found to have an overwhelming preference to occur as the "alphaL-terminator (T)" resulting in the classical Schellman motif, with a strong preference for hydrophobic residues at position T-4 and T+1. In the case of E-terminated helices His, Asn, Leu and Phe were found to occur with high propensity at position T. Quite remarkably Pro residues, with single exception, were absent at position T, but had the highest propensity at position T+1. Examination of the frequencies of hydrophobic (h) and polar (p) residues at positions flanking Gly/Pro permitted delineation of exclusive patterns and predictive rules for Gly-terminated helices and Pro-terminated helices. The analysis reveals that Pro residues flanked by polar amino acids have a very strong tendency to terminate helices. Examination of a segment ranging from T-4 to T+3 appeared to be necessary to determine whether helix termination or continuation occur at Gly residues. The two types of helix termination (alphaL, E) signals also differed dramatically in their solvent accessibility. Gly and Pro residues at helix termini appeared to be strongly conserved in homologous sequences. PMID:9480777

  7. Utilization of shells of the snail Achatina fulica Bowdich, 1822 (Mollusca, Gastropoda by the hermit crab Clibanarius vittatus (Bosc, 1802 (Decapoda, Anomura in the São Vicente Estuary, São Paulo, Brazil Utilización de conchas de caracoles terrestres Achatina fulica Bowdich, 1822 (Mollusca, Gastropoda por el cangrejo ermitaño Clibanarius vittatus (Bosc, 1802 (Decapoda, Anomura en el estuario de São Vicente, São Paulo, Brasil

    Directory of Open Access Journals (Sweden)

    Bruno S. Sant'Anna

    2005-11-01

    Full Text Available Hermit crabs depend on mollusc shells for housing. In this study, an unusual resource is reported for a hermit crab that usually inhabits marine gastropod shells. During a field study conducted from May 2001 to April 2003 in an estuarine area in São Vicente, state of São Paulo, Brazil, 21 individuals of Clibanarius vittatus (Bosc, 1802 were found inhabiting the shells of the terrestrial gastropod Achatina fulica Bowdich, 1822. A. fulica occurs in nearshore grass patches, where occasional contact with sea water kills them, and their shells then become available to the hermit crabsEl cangrejo ermitaño depende de conchas de moluscos para hacer de ella su casa. Este estudio ha descubierto una manera inusual de como vive este cangrejo, que generalmente habita la concha de gastrópodos marinos. El estudio fue realizado en la estación marítima de São Vicente, provincia de São Paulo, de mayo de 2001 hasta abril de 2003. Durante ese periodo, un total de 21 cangrejos Clibanarius vittatus (Bosc, 1802 fueron encontrados viviendo en las conchas del caracol terrestre Achatina fulica Bowdich, 1822. A. fulica ocurre en áreas de césped cercanos a la costa, donde el contacto ocasional con el agua de mar provoca su muerte y sus conchas quedan disponibles para el cangrejo ermitaño

  8. Reovirus FAST Proteins Drive Pore Formation and Syncytiogenesis Using a Novel Helix-Loop-Helix Fusion-Inducing Lipid Packing Sensor.

    Directory of Open Access Journals (Sweden)

    Jolene Read

    2015-06-01

    Full Text Available Pore formation is the most energy-demanding step during virus-induced membrane fusion, where high curvature of the fusion pore rim increases the spacing between lipid headgroups, exposing the hydrophobic interior of the membrane to water. How protein fusogens breach this thermodynamic barrier to pore formation is unclear. We identified a novel fusion-inducing lipid packing sensor (FLiPS in the cytosolic endodomain of the baboon reovirus p15 fusion-associated small transmembrane (FAST protein that is essential for pore formation during cell-cell fusion and syncytiogenesis. NMR spectroscopy and mutational studies indicate the dependence of this FLiPS on a hydrophobic helix-loop-helix structure. Biochemical and biophysical assays reveal the p15 FLiPS preferentially partitions into membranes with high positive curvature, and this partitioning is impeded by bis-ANS, a small molecule that inserts into hydrophobic defects in membranes. Most notably, the p15 FLiPS can be functionally replaced by heterologous amphipathic lipid packing sensors (ALPS but not by other membrane-interactive amphipathic helices. Furthermore, a previously unrecognized amphipathic helix in the cytosolic domain of the reptilian reovirus p14 FAST protein can functionally replace the p15 FLiPS, and is itself replaceable by a heterologous ALPS motif. Anchored near the cytoplasmic leaflet by the FAST protein transmembrane domain, the FLiPS is perfectly positioned to insert into hydrophobic defects that begin to appear in the highly curved rim of nascent fusion pores, thereby lowering the energy barrier to stable pore formation.

  9. Expression of the helix-loop-helix protein inhibitor of DNA binding-1 (ID-1) is activated by all-trans retinoic acid in normal human keratinocytes

    International Nuclear Information System (INIS)

    The ID (inhibitor of differentiation or DNA binding) helix-loop-helix proteins are important mediators of cellular differentiation and proliferation in a variety of cell types through regulation of gene expression. Overexpression of the ID proteins in normal human keratinocytes results in extension of culture lifespan, indicating that these proteins are important for epidermal differentiation. Our hypothesis is that the ID proteins are targets of the retinoic acid signaling pathway in keratinocytes. Retinoids, vitamin A analogues, are powerful regulators of cell growth and differentiation and are widely used in the prevention and treatment of a variety of cancers in humans. Furthermore, retinoic acid is necessary for the maintenance of epithelial differentiation and demonstrates an inhibitory action on skin carcinogenesis. We examined the effect of all-trans retinoic acid on expression of ID-1, -2, -3, and -4 in normal human keratinocytes and found that exposure of these cells to all-trans retinoic acid causes an increase in both ID-1 and ID-3 gene expression. Furthermore, our data show that this increase is mediated by increased transcription involving several cis-acting elements in the distal portion of the promoter, including a CREB-binding site, an Egr1 element, and an YY1 site. These data demonstrate that the ID proteins are direct targets of the retinoic acid signaling pathway. Given the importance of the ID proteins to epidermal differentiation, these results suggest that IDs may be mediating some of the effects of all-trans retinoic acid in normal human keratinocytes

  10. Agrobacterium tumefaciens VirC2 enhances T-DNA transfer and virulence through its C-terminal ribbon-helix-helix DNA-binding fold.

    Science.gov (United States)

    Lu, Jun; den Dulk-Ras, Amke; Hooykaas, Paul J J; Glover, J N Mark

    2009-06-16

    Agrobacterium tumefaciens VirC2 stimulates processing of single-stranded T-DNA that is translocated into plants to induce tumor formation, but how VirC2 functions is unclear. Here, we report the 1.7-A X-ray crystal structure of its trypsin-resistant C-terminal domain, VirC2(82-202), which reveals a form of the ribbon-helix-helix (RHH) DNA-binding fold contained within a single polypeptide chain. DNA-binding assays and mutagenesis indicate that VirC2 uses this RHH fold to bind double-stranded DNA but not single-stranded DNA. Mutations that severely affect VirC2 DNA binding are highly deleterious for both T-DNA transfer into yeast and the virulence of A. tumefaciens in different plants including Nicotiana glauca and Kalanchoe daigremontiana. These data suggest that VirC2 enhances T-DNA transfer and virulence through DNA binding with its RHH fold. The RHH fold of VirC2 is the first crystal structure representing a group of predicted RHH proteins that facilitate endonucleolytic processing of DNA for horizontal gene transfer. PMID:19482939

  11. Elevated endogenous expression of the dominant negative basic helix-loop-helix protein ID1 correlates with significant centrosome abnormalities in human tumor cells

    Directory of Open Access Journals (Sweden)

    Gutmann Anja

    2010-01-01

    Full Text Available Abstract Background ID proteins are dominant negative inhibitors of basic helix-loop-helix transcription factors that have multiple functions during development and cellular differentiation. Ectopic (over-expression of ID1 extends the lifespan of primary human epithelial cells. High expression levels of ID1 have been detected in multiple human malignancies, and in some have been correlated with unfavorable clinical prognosis. ID1 protein is localized at the centrosomes and forced (over-expression of ID1 results in errors during centrosome duplication. Results Here we analyzed the steady state expression levels of the four ID-proteins in 18 tumor cell lines and assessed the number of centrosome abnormalities. While expression of ID1, ID2, and ID3 was detected, we failed to detect protein expression of ID4. Expression of ID1 correlated with increased supernumerary centrosomes in most cell lines analyzed. Conclusions This is the first report that shows that not only ectopic expression in tissue culture but endogenous levels of ID1 modulate centrosome numbers. Thus, our findings support the hypothesis that ID1 interferes with centrosome homeostasis, most likely contributing to genomic instability and associated tumor aggressiveness.

  12. Identification and functional analysis of porcine basic helix-loop-helix transcriptional factor 3 (TCF3) and its alternative splicing isoforms.

    Science.gov (United States)

    Yang, Fan; Wang, Ning; Liu, Yajun; Wang, Huayan

    2016-04-01

    The transcription factor 3 (TCF3) is a basic helix-loop-helix transcription factor and is essential for lymphocyte development and epithelial-mesenchymal transition. The splicing isoform, genomic organization and physiological roles of TCF3 have not been elucidated well in pig. Based on RNA-seq database, four alternative splicing isoforms were identified. Splicing isoforms TCF3(E12), TCF3(E47), and TCF3A expressed globally in porcine tissues, but TCF3B mainly expressed in spleen and endoderm derived tissues, such as pancreas and lung. The functional analysis showed that TCF3(E12), TCF3(E47), and TCF3B were translocated exclusively into nuclei, yet TCF3A was distributed in cytoplasm. The investigation of clinical specimens showed that TCF3 expression was significantly reduced in spleen tissues that were infected by classical swine fever virus (CSFV). This study is for the first time to report two novel splicing isoforms TCF3A and TCF3B, which may play an important role in lymphocyte maturation and have the correlation with CSFV evasion. PMID:27033898

  13. DEC1, a Basic Helix-Loop-Helix Transcription Factor and a Novel Target Gene of the p53 Family, Mediates p53-dependent Premature Senescence*

    Science.gov (United States)

    Qian, Yingjuan; Zhang, Jin; Yan, Bingfang; Chen, Xinbin

    2014-01-01

    Cellular senescence plays an important role in tumor suppression. p53 tumor suppressor has been reported to be crucial in cellular senescence. However, the underlying mechanism is poorly understood. In this regard, a cDNA microarray assay was performed to identify p53 targets involved in senescence. Among the many candidates is DEC1, a basic helix-loop-helix transcription factor that has been recently shown to be up-regulated in K-ras-induced premature senescence. However, it is not clear whether DEC1 is capable of inducing senescence. Here, we found that DEC1 is a novel target gene of the p53 family and mediates p53-dependent premature senescence. Specifically, we showed that DEC1 is induced by the p53 family and DNA damage in a p53-dependent manner. We also found that the p53 family proteins bind to, and activate, the promoter of the DEC1 gene. In addition, we showed that overexpression of DEC1 induces G1 arrest and promotes senescence. Moreover, we found that targeting endogenous DEC1 attenuates p53-mediated premature senescence in response to DNA damage. Furthermore, overexpression of DEC1 induces cellular senescence in p53-knockdown cells, albeit to a lesser extent. Finally, we showed that DEC1-induced senescence is p21-independent. Taken together, our data provided strong evidence that DEC1 is one of the effectors downstream of p53 to promote premature senescence. PMID:18025081

  14. Ligatoxin B, a new cytotoxic protein with a novel helix-turn-helix DNA-binding domain from the mistletoe Phoradendron liga.

    Science.gov (United States)

    Li, Shi-Sheng; Gullbo, Joachim; Lindholm, Petra; Larsson, Rolf; Thunberg, Eva; Samuelsson, Gunnar; Bohlin, Lars; Claeson, Per

    2002-09-01

    A new basic protein, designated ligatoxin B, containing 46 amino acid residues has been isolated from the mistletoe Phoradendron liga (Gill.) Eichl. (Viscaceae). The protein's primary structure, determined unambiguously using a combination of automated Edman degradation, trypsin enzymic digestion, and tandem MS analysis, was 1-KSCCPSTTAR-NIYNTCRLTG-ASRSVCASLS-GCKIISGSTC-DSGWNH-46. Ligatoxin B exhibited in vitro cytotoxic activities on the human lymphoma cell line U-937-GTB and the primary multidrug-resistant renal adenocarcinoma cell line ACHN, with IC50 values of 1.8 microM and 3.2 microM respectively. Sequence alignment with other thionins identified a new member of the class 3 thionins, ligatoxin B, which is similar to the earlier described ligatoxin A. As predicted by the method of homology modelling, ligatoxin B shares a three-dimensional structure with the viscotoxins and purothionins and so may have the same mode of cytotoxic action. The novel similarities observed by structural comparison of the helix-turn-helix (HTH) motifs of the thionins, including ligatoxin B, and the HTH DNA-binding proteins, led us to propose the working hypothesis that thionins represent a new group of DNA-binding proteins. This working hypothesis could be useful in further dissecting the molecular mechanisms of thionin cytotoxicity and of thionin opposition to multidrug resistance, and useful in clarifying the physiological function of thionins in plants. PMID:12049612

  15. Structural Basis for Elastic Mechanical Properties of the DNA Double Helix

    Science.gov (United States)

    Kim, Young-Joo; Kim, Do-Nyun

    2016-01-01

    In this article, we investigate the principal structural features of the DNA double helix and their effects on its elastic mechanical properties. We develop, in the pursuit of this purpose, a helical continuum model consisting of a soft helical core and two stiff ribbons wrapping around it. The proposed model can reproduce the negative twist-stretch coupling of the helix successfully as well as its global stretching, bending, and torsional rigidities measured experimentally. Our parametric study of the model using the finite element method further reveals that the stiffness of phosphate backbones is a crucial factor for the counterintuitive overwinding behavior of the duplex and its extraordinarily high torsional rigidity, the major-minor grooves augment the twist-stretch coupling, and the change of the helicity might be responsible for the transition from a negative to a positive twist-stretching coupling when a tensile force is applied to the duplex. PMID:27055239

  16. Local equilibria and state transfer of charged classical particles on a helix in an electric field

    CERN Document Server

    Plettenberg, J; Zampetaki, A V; Schmelcher, P

    2016-01-01

    We explore the effects of a homogeneous external electric field on the static properties and dynamical behavior of two charged particles confined to a helix. In contrast to the field-free setup which provides a separation of the center-of-mass and relative motion, the existence of an external force perpendicular to the helix axis couples the center-of-mass to the relative degree of freedom leading to equilibria with a localized center of mass. By tuning the external field various fixed points are created and/or annihilated through different bifurcation scenarios. We provide a detailed analysis of these bifurcations based on which we demonstrate a robust state transfer between essentially arbitrary equilibrium configurations of the two charges that can be induced by making the external force time-dependent.

  17. Three-dimensional simulation of helix traveling-wave tube cold-test characteristics using MAFIA

    Energy Technology Data Exchange (ETDEWEB)

    Kory, C.L. [Analex Corp., Cleveland, OH (United States)

    1996-12-31

    A critically important step in the traveling-wave tube (TWT) design process is the cold-testing of the slow-wave circuit for dispersion, beam interaction impedance and RF losses. Experimental cold-tests can be very time-consuming and expensive, thus limiting the freedom to examine numerous variations to the test circuit. This makes the need for computational methods crucial as they can lower cost, reduce tube development time and allow the freedom to introduce novel and improved designs. The cold-test parameters have been calculated for a C-Band Northrop-Grumman helix TWT slow-wave circuit using MAFIA, the three-dimensional electromagnetic finite-integration computer code. Measured and simulated cold-test data for the Northrop-Grumman helix TWT including dispersion, impedance and attenuation will be presented. Close agreement between simulated and measured values of the dispersion, impedance and attenuation has been obtained.

  18. Globular structures of a helix-coil copolymer: self-consistent treatment.

    Science.gov (United States)

    Nowak, C; Rostiashvili, V G; Vilgis, T A

    2007-01-21

    A self-consistent-field theory was developed in the grand canonical ensemble formulation to study transitions in a helix-coil multiblock globule. Helical and coil parts are treated as stiff rods and self-avoiding walks of variable lengths correspondingly. The resulting field theory takes, in addition to the conventional Zimm-Bragg, [J. Chem. Phys. 31, 526 (1959)] parameters, also three-dimensional interaction terms into account. The appropriate differential equations which determine the self-consistent fields were solved numerically with finite element method. Three different phase states are found: open chain, amorphous globule, and nematic liquid-crystalline (LC) globule. The LC-globule formation is driven by the interplay between the hydrophobic helical segment attraction and the anisotropic globule surface energy of an entropic nature. The full phase diagram of the helix-coil copolymer was calculated and thoroughly discussed. The suggested theory shows a clear interplay between secondary and tertiary structures in globular homopolypeptides. PMID:17249898

  19. A triple Helix Approach to the Future Innovation Flagship of Europe:

    DEFF Research Database (Denmark)

    Jofre, Sergio; Andersen, Per Dannemand

    2009-01-01

    This paper explores the strategic context of the implementation of the European Institute of Innovation and Technology (EIT). The analytical framework is based on a comparative study of National Innovation Systems (NIS) and the particular Triple Helix of University-Government-Industry relationship......, are transforming the profile of the triple helix relationships. This transformation is bringing the American and the Japanese innovation system to an unprecedented level of commonality and the EU to a yet uncertain stage of transition characterized by the conflict between national and supranational...... priorities, and the different innovation capabilities of its Member States. The paper argues that in such conditions, the current strategy to deploy the EIT is not appropriated and an alternative strategy is proposed....

  20. The Triple Helix Model and the Meta-Stabilization of Urban Technologies in Smart Cities

    CERN Document Server

    Leydesdorff, Loet

    2010-01-01

    The Triple Helix model of university-industry-government relations can be generalized from a neo-institutional model of networks to a neo-evolutionary model of how three selection environments operate upon one another. The neo-evolutionary model enables us to appreciate both organizational integration in university-industry-government relations and differentiation among functions like the generation of intellectual capital, creation of wealth, and their attending legislation. The specification of innovation systems in terms of nations, sectors, cities, and regions can then be formulated as empirical questions: is synergy generated among functions in networks of relations? This Triple Helix model enables us to study the knowledge base of an urban economy in terms of a trade-off between locally stabilized and (potentially locked-in) trajectories versus the techno-economic and cultural development regimes which work with one more degree of freedom at the global level. The meta-stabilizing potentials of urban tec...

  1. Performance of Process Damping in Machining Titanium Alloys at Low Cutting Speed with Different Helix Tools

    International Nuclear Information System (INIS)

    Titanium is a strong, lustrous, corrosion-resistant and transition metal with a silver color to produce strong lightweight alloys for industrial process, automotive, medical instruments and other applications. However, it is very difficult to machine the titanium due to its poor machinability. When machining titanium alloys with the conventional tools, the wear rate of the tool is rapidly accelerate and it is generally difficult to achieve at high cutting speed. In order to get better understanding of machining titanium alloy, the interaction between machining structural system and the cutting process which result in machining instability will be studied. Process damping is a useful phenomenon that can be exploited to improve the limited productivity of low speed machining. In this study, experiments are performed to evaluate the performance of process damping of milling under different tool helix geometries. The results showed that the helix of 42° angle is significantly increase process damping performance in machining titanium alloy.

  2. Helix Nebula and CERN: A Symbiotic approach to exploiting commercial clouds

    CERN Document Server

    Barreiro Megino, Fernando Harald; Kucharczyk, Katarzyna; Medrano Llamas, Ramón; van der Ster, Daniel

    2014-01-01

    The recent paradigm shift toward cloud computing in IT, and general interest in "Big Data" in particular, have demonstrated that the computing requirements of HEP are no longer globally unique. Indeed, the CERN IT department and LHC experiments have already made significant R&D investments in delivering and exploiting cloud computing resources. While a number of technical evaluations of interesting commercial offerings from global IT enterprises have been performed by various physics labs, further technical, security, sociological, and legal issues need to be address before their large-scale adoption by the research community can be envisaged. Helix Nebula - the Science Cloud is an initiative that explores these questions by joining the forces of three European research institutes (CERN, ESA and EMBL) with leading European commercial IT enterprises. The goals of Helix Nebula are to establish a cloud platform federating multiple commercial cloud providers, along with new business models, which can sustain ...

  3. Conformational Heterogeneity of Bax Helix 9 Dimer for Apoptotic Pore Formation

    Science.gov (United States)

    Liao, Chenyi; Zhang, Zhi; Kale, Justin; Andrews, David W.; Lin, Jialing; Li, Jianing

    2016-07-01

    Helix α9 of Bax protein can dimerize in the mitochondrial outer membrane (MOM) and lead to apoptotic pores. However, it remains unclear how different conformations of the dimer contribute to the pore formation on the molecular level. Thus we have investigated various conformational states of the α9 dimer in a MOM model — using computer simulations supplemented with site-specific mutagenesis and crosslinking of the α9 helices. Our data not only confirmed the critical membrane environment for the α9 stability and dimerization, but also revealed the distinct lipid-binding preference of the dimer in different conformational states. In our proposed pathway, a crucial iso-parallel dimer that mediates the conformational transition was discovered computationally and validated experimentally. The corroborating evidence from simulations and experiments suggests that, helix α9 assists Bax activation via the dimer heterogeneity and interactions with specific MOM lipids, which eventually facilitate proteolipidic pore formation in apoptosis regulation.

  4. Helix Nebula and CERN: A Symbiotic approach to exploiting commercial clouds

    CERN Multimedia

    Barreiro Megino, Fernando Harald; Kucharczyk, Katarzyna; Medrano Llamas, Ramón; van der Ster, Daniel

    2013-01-01

    The recent paradigm shift toward cloud computing in IT, and general interest in "Big Data" in particular, have demonstrated that the computing requirements of HEP are no longer globally unique. Indeed, the CERN IT department and LHC experiments have already made significant R&D; investments in delivering and exploiting cloud computing resources. While a number of technical evaluations of interesting commercial offerings from global IT enterprises have been performed by various physics labs, further technical, security, sociological, and legal issues need to be address before their large-scale adoption by the research community can be envisaged. Helix Nebula - the Science Cloud is an initiative that explores these questions by joining the forces of three European research institutes (CERN, ESA and EMBL) with leading European commercial IT enterprises. The goals of Helix Nebula are to establish a cloud platform federating multiple commercial cloud providers, along with new business models, which can sustain...

  5. Conformational Heterogeneity of Bax Helix 9 Dimer for Apoptotic Pore Formation.

    Science.gov (United States)

    Liao, Chenyi; Zhang, Zhi; Kale, Justin; Andrews, David W; Lin, Jialing; Li, Jianing

    2016-01-01

    Helix α9 of Bax protein can dimerize in the mitochondrial outer membrane (MOM) and lead to apoptotic pores. However, it remains unclear how different conformations of the dimer contribute to the pore formation on the molecular level. Thus we have investigated various conformational states of the α9 dimer in a MOM model - using computer simulations supplemented with site-specific mutagenesis and crosslinking of the α9 helices. Our data not only confirmed the critical membrane environment for the α9 stability and dimerization, but also revealed the distinct lipid-binding preference of the dimer in different conformational states. In our proposed pathway, a crucial iso-parallel dimer that mediates the conformational transition was discovered computationally and validated experimentally. The corroborating evidence from simulations and experiments suggests that, helix α9 assists Bax activation via the dimer heterogeneity and interactions with specific MOM lipids, which eventually facilitate proteolipidic pore formation in apoptosis regulation. PMID:27381287

  6. Effects of environmental exposure: Interplay between helix-distorting and oxidative DNA lesions and their repair

    OpenAIRE

    Lakså, Solveig Margrethe B.

    2012-01-01

    DNA lesions are introduced in all living organisms every day, both via endogenous processes and by exposure to an array of DNA damaging agents. DNA lesions require repair for the sustenance of life. Base excision repair (BER) and nucleotide excision repair (NER) are DNA repair pathways involved in removal of oxidative DNA lesions and helix-distorting DNA lesions, respectively. Several studies suggest interactions or crosstalk between these pathways, involving overlapping activities for remova...

  7. Helix and Drugs: Snails for Western Health Care From Antiquity to the Present

    OpenAIRE

    Bruno Bonnemain

    2005-01-01

    The land helix, or snail, has been used in medicine since antiquity and prepared according to several formulations. This historical report traces the understanding of their properties from the time of Hippocrates, who proposed the use of snail mucus against protoccle and Pliny who thought that the snail increased the speed of delivery and was “a sovereign remedy to treat pain related to burns, abscesses and other wounds”, Galien recommended snails against hydrops foetails. In the 18th centu...

  8. Energy patterns in coupled α-helix protein chains with diagonal and off-diagonal couplings

    Science.gov (United States)

    Tabi, C. B.; Ondoua, R. Y.; Ekobena Fouda, H. P.; Kofané, T. C.

    2016-07-01

    We introduce off-diagonal effects in the three-stranded model of α-helix chains, which bring about additional nonlinear terms to enhance the way energy spreads among the coupled spines. This is analyzed through the modulational instability theory. The linear stability analysis of plane wave solutions is performed and the competitive effects of diagonal and off-diagonal interactions are studied, followed by direct numerical simulations. Some features of the obtained solitonic structures are discussed.

  9. Evaluation of Common Interfaces in a Multi-supplier Cloud Environment for Helix Nebula

    OpenAIRE

    Tsikiridis, Artem; Cinquilli, Mattia

    2013-01-01

    Abstract The Helix Nebula initiative is a partnership between leading European IT-intense scientific research organisations (CERN, EMBL and ESA) and leading IT cloud providers. Its goal is to form a federated Cloud Computing infrastructure that will satisfy the growing demand of scientists for computing power. The concept of the federated cloud requires a standard framework named BlueBox so that current and future cloud providers are able to smoothly interface their system to the existing...

  10. Nanoparticle biofabrication using English ivy (Hedera helix)

    OpenAIRE

    Burris Jason N; Lenaghan Scott C; Zhang Mingjun; Stewart C

    2012-01-01

    Abstract Background English ivy (Hedera helix) is well known for its adhesive properties and climbing ability. Essential to its ability to adhere to vertical surfaces is the secretion of a nanocomposite adhesive containing spherical nanoparticles, 60–85 nm in diameter, produced exclusively by root hairs present on adventitious roots. These organic nanoparticles have shown promise in biomedical and cosmetic applications, and represent a safer alternative to metal oxide nanoparticles currently ...

  11. Expectorant and Antitussive Effect of Hedera helix and Rhizoma coptidis Extracts Mixture

    OpenAIRE

    Song, Kee Jae; Shin, Young-June; Lee, Kang Ro; Lee, Eun Jung; Suh, Yun Suk; Kim, Kyung-Su

    2015-01-01

    Purpose This study aims to investigate the additive effect of the Hedera helix (HH) and Rhizoma coptidis (RC) extracts mixture on antitussive and expectorant activities in animals. Materials and Methods The expectorant assay was performed with phenol red secretion in mice trachea. Mice or guinea pigs were randomly divided into groups of 8 each, including negative and positive control groups. After gastric administration of the test extracts in mice, 2.5% phenol red solution (0.2 mL) was intra...

  12. Isolation and chemical analysis of nanoparticles from English ivy (Hedera helix L.)

    OpenAIRE

    Lenaghan, Scott C; Jason N Burris; Chourey, Karuna; Huang, Yujian; Xia, Lijin; Lady, Belinda; Sharma, Ritin; Pan, Chongle; LeJeune, Zorabel; Foister, Shane; Hettich, Robert L.; Stewart, C. Neal; Zhang, Mingjun

    2013-01-01

    Bio-inspiration for novel adhesive development has drawn increasing interest in recent years with the discovery of the nanoscale morphology of the gecko footpad and mussel adhesive proteins. Similar to these animal systems, it was discovered that English ivy (Hedera helix L.) secretes a high strength adhesive containing uniform nanoparticles. Recent studies have demonstrated that the ivy nanoparticles not only contribute to the high strength of this adhesive, but also have ultraviolet (UV) pr...

  13. Antinociceptive Effect of Hydroalcoholic Leaf Extract of Hedera helix in Male Rat

    OpenAIRE

    shahidi, S.; S. Mohammadi; Mahmoudi, M.

    2013-01-01

    Introduction & Objective: The consumption of chemical compounds and medicinal herbs are different ways to control pain. On the other hand, the complications of chemical drugs and their expensiveness cause people to use herbal medicines The aim of this study was to inves-tigate the antinociceptive effect of hydroalcoholic leaf extract of Hedera helix in male rats. Materials & Methods: In this experimental study, 36 adult male rats were divided into 6 groups: control, morphine (1mg/kg), Hedera ...

  14. Structure, attachment properties, and ecological importance of the attachment system of English ivy (Hedera helix)

    OpenAIRE

    Melzer, Björn; Seidel, Robin; Steinbrecher, Tina; Speck, Thomas

    2011-01-01

    Root climbers such as English ivy (Hedera helix) rely on specialized adventitious roots for attachment, enabling the plants to climb on a wide range of natural and artificial substrates. Despite their importance for the climbing habit, the biomechanical properties of these specialized adventitious roots compared with standard roots and their performance in the attachment to different host species or inert substrates have not been studied. Here organs and tissues involved in the attachment are...

  15. A peptide study of the relationship between the collagen triple-helix and amyloid

    OpenAIRE

    Parmar, Avanish S.; Nunes, Ana Monica; Baum, Jean; Brodsky, Barbara

    2012-01-01

    Type XXV collagen, or Collagen-Like Amyloidogenic Component (CLAC), is a component of amyloid plaques, and recent studies suggest this collagen affects amyloid fibril elongation and has a genetic association with Alzheimer’s disease. The relationship between the collagen triple helix and amyloid fibrils was investigated by studying peptide models, including a very stable triple helical peptide (Pro-Hyp-Gly)10; an amyloidogenic peptide GNNQQNY; and a hybrid peptide where the GNNQQNY sequence w...

  16. Transient Collagen Triple-Helix Binding to a Key Metalloproteinase in Invasion and Development

    OpenAIRE

    Zhao, Yingchu; Marcink, Thomas C.; Gari, Raghavendar Reddy Sanganna; Marsh, Brendan P.; King, Gavin M.; Stawikowska, Roma; Fields, Gregg B.; Van Doren, Steven R.

    2015-01-01

    Skeletal development and invasion by tumor cells depends on proteolysis of collagen by the pericellular metalloproteinase MT1-MMP. Its hemopexin-like (HPX) domain binds to collagen substrates to facilitate their digestion. Spin labeling and paramagnetic NMR detection have revealed how the HPX domain docks to collagen I-derived triple-helix. Mutations impairing triple-helical peptidase activity corroborate the interface. Saturation transfer difference NMR suggests rotational averaging around t...

  17. Technology Entreprenurship in the Changing Business Environment – A Triple Helix Performance Model

    OpenAIRE

    Maja Levi Jaksić; Milica Jovanović; Jasna Petković

    2015-01-01

    In this paper the contribution of technology management and entrepreneurship to sustainable development is emphasized and the Triple Helix (TH) model is used to analyse the performance of different actors in accomplishing the activities of Technology Innovation Management and Entrepreneurship (TIME). By analysing TH model (Government – University – Industry) in relation to accomplishing TIME main functions: Planning, Organizing and Control (POC), we created a general model which measures TIME...

  18. Triple helix-forming oligonucleotides target psoralen adducts to specific chromosomal sequences in human cells.

    OpenAIRE

    Oh, D H; Hanawalt, P C

    1999-01-01

    The ability to target photochemical adducts to specific genomic DNA sequences in cells is useful for studying DNA repair and mutagenesis in intact cells, and also as a potential mode of gene-specific therapy. Triple helix-forming DNA oligonucleotides linked to psoralen (psoTFOs) were designed to deliver UVA-induced psoralen photoadducts to two distinct sequences within the human interstitial collagenase gene. A primer extension assay demonstrated that the appropriate psoTFO selectively damage...

  19. Specificity of DNA triple helix formation analyzed by a FRET assay

    OpenAIRE

    Reither Sabine; Jeltsch Albert

    2002-01-01

    Abstract Background A third DNA strand can bind into the major groove of a homopurine duplex DNA to form a DNA triple helix. Sequence specific triplex formation can be applied for gene targeting, gene silencing and mutagenesis. Results We have analyzed triplex formation of two polypurine triplex forming oligodeoxynucleotides (TFOs) using fluorescence resonance energy transfer (FRET). Under our conditions, the TFOs bind to their cognate double strand DNAs with binding constants of 2.6 × 105 an...

  20. Covalent crosslinks introduced via a triple helix-forming oligonucleotide coupled to psoralen are inefficiently repaired.

    OpenAIRE

    Barre, F X; Giovannangeli, C.; Hélène, C; Harel-Bellan, A

    1999-01-01

    Triple helix-forming oligonucleotides (TFOs) represent potentially powerful tools to artificially modulate gene activity. In particular, they can be used to specifically introduce a lesion into a selected target sequence: interstrand crosslinks and monoadducts can be introduced via TFOs coupled to psoralen. The efficiency of these strategies depends on the cell ability to repair these lesions, an issue which is still controversial. Here we show, using psoralen-coupled TFOs and the yeast as a ...

  1. Exploring the Cellular Activity of Camptothecin-Triple-Helix-Forming Oligonucleotide Conjugates†

    OpenAIRE

    Arimondo, Paola B.; Thomas, Craig J.; Oussedik, Kahina; Baldeyrou, Brigitte; Mahieu, Christine; Halby, Ludovic; Guianvarc'h, Dominique; Lansiaux, Amélie; Hecht, Sidney M.; Bailly, Christian; Giovannangeli, Carine

    2006-01-01

    Topoisomerase I is a ubiquitous DNA-cleaving enzyme and an important therapeutic target in cancer chemotherapy for camptothecins (CPTs). These drugs stimulate DNA cleavage by topoisomerase I but exhibit little sequence preference, inducing toxicity and side effects. A convenient strategy to confer sequence specificity consists of the linkage of topoisomerase poisons to DNA sequence recognition elements. In this context, triple-helix-forming oligonucleotides (TFOs) covalently linked to CPTs we...

  2. Human Replication Protein A Melts a DNA Triple Helix Structure in a Potent and Specific Manner†

    OpenAIRE

    Wu, Yuliang; Rawtani, Nina; Thazhathveetil, Arun Kalliat; Kenny, Mark K.; Seidman, Michael M.; Brosh, Robert M.

    2008-01-01

    Alternate DNA structures other than double-stranded B-form DNA can potentially impede cellular processes such as transcription and replication. The DNA triplex helix and G4 tetraplex structures that form by Hoogsteen hydrogen bonding are two examples of alternate DNA structures that can be a source of genomic instability. In this study, we have examined the ability of human replication protein A (RPA), a single-stranded DNA binding protein that is implicated in all facets of DNA metabolism, t...

  3. Drug binding to higher ordered DNA structures: netropsin complexation with a nucleic acid triple helix.

    OpenAIRE

    Park, Y. W.; Breslauer, K J

    1992-01-01

    We have used a combination of spectroscopic and calorimetric techniques to characterize how netropsin, a ligand that binds in the minor groove of DNA, influences the properties of a DNA triple helix. Specifically, our data allow us to reach the following conclusions: (i) netropsin binds to the triplex without displacing the major-groove-bound third strand; (ii) netropsin binding to the triplex exhibits a lower saturation binding density (7.0 base triplets per netropsin bound) than netropsin b...

  4. Triple helix DNA alters nucleosomal histone-DNA interactions and acts as a nucleosome barrier.

    OpenAIRE

    Westin, L; Blomquist, P.; Milligan, J F; Wrange, O

    1995-01-01

    Oligonucleotides which form triple helical complexes on double-stranded DNA have been previously reported to selectively inhibit transcription both in vitro and in vivo by physically blocking RNA polymerase or transcription factor access to the DNA template. Here we show that a 16mer oligonucleotide, which forms triple helix DNA by binding to a 16 bp homopurine segment, alters the formation of histone-DNA contacts during in vitro nucleosome reconstitution. This effect was DNA sequence-specifi...

  5. Predicting RNA 3D structure using a coarse-grain helix-centered model

    OpenAIRE

    Kerpedjiev, Peter; Höner zu Siederdissen, Christian; Hofacker, Ivo L

    2015-01-01

    A 3D model of RNA structure can provide information about its function and regulation that is not possible with just the sequence or secondary structure. Current models suffer from low accuracy and long running times and either neglect or presume knowledge of the long-range interactions which stabilize the tertiary structure. Our coarse-grained, helix-based, tertiary structure model operates with only a few degrees of freedom compared with all-atom models while preserving the ability to sampl...

  6. Water permeation through gramicidin A: Desformylation and the double helix: A molecular dynamics study

    OpenAIRE

    de Groot, B.; Tieleman, D.; Pohl, P.; Grubmueller, H.

    2002-01-01

    Multinanosecond molecular dynamics simulations of gramicidin A embedded in a dimyristoylphosphatidylcholine bilayer show a remarkable structural stability for both experimentally determined conformations: the head-to-head helical dimer and the double helix. Water permeability was found to be much higher in the double helical conformation, which is explained by lower hydrogen bond-mediated enthalpic barriers at the channel entrance and its larger pore size. Free-energy perturbation calculation...

  7. 拷问双螺旋%To interrogate the double helix

    Institute of Scientific and Technical Information of China (English)

    徐有成

    2009-01-01

    Is DNA really right-handed (plectonemic) double helix? The author asked several questions and proved that the linking number of a plasmid could be zero,which is a phenomenon unexplainable by the traditional double helix model.Based on this observation and several other evidences,a hypothesis about the double helix was proposed.It is called ambidextrous double helix,in which the two strands are supposed to wind in both directions.This essay is provided for discussion.It is hoped that the readers can block their first impression,keep their minds open,to think carefully,independently,critically on the novel ideas that were not written in textbooks and to make their own judgments.%DNA真的完全是右旋的双螺旋吗(plectonemic)?作者提出了一些疑问,并用实验证明质粒分子的拓扑环挠数可以为零,这是经典双螺旋结构不能解释的现象.据此实验观察以及若干其他证据,作者提出了关于DNA双螺旋结构的假说--左右旋共存的双螺旋(ambidextrous),供研究和讨论.希望读者能革除先入之见,用开放的态度来独立思考、分辨是非、认真审视本文中不见于教材的新观点,从而作出自己明智的判断.

  8. Symmetrical-geometry constructions defining helicoidal biostructures. The case of alpha-helix

    OpenAIRE

    Samoylovich, Mikhail; Talis, Alexander

    2016-01-01

    The chain of algebraic geometry constructions permits to transfer from the minimal surface with zero instability index, and from the lattice over the ring of cyclotomic integers to the tetra-block helix. The tetra-block is the 7-vertex joining of four tetrahedra sharing common faces; it is considered as a building unit for structures approximated by the chains of regular tetrahedra. The minimality condition of the 7 - vertex tetrablock as a building unit is the consequence of its unique mappi...

  9. Long-Circulating 15 nm Micelles Based on Amphiphilic 3-Helix Peptide-PEG Conjugates

    OpenAIRE

    Dong, He; Dube, Nikhil; Shu, Jessica Y.; Seo, Jai W.; Mahakian, Lisa M; Ferrara, Katherine W.; Xu, Ting

    2012-01-01

    Generating stable, multi-functional organic nanocarriers will have a significant impact on drug formulation. However, it remains a significant challenge to generate organic nanocarriers with a long circulation half-life, effective tumor penetration and efficient clearance of metabolites. We have advanced this goal by designing a new family of amphiphiles based on coiled-coil 3-helix bundle forming peptide-poly(ethylene glycol) conjugates. The amphiphiles self-assemble into monodisperse micell...

  10. BILATERAL PERICHONDRITIS OF PINNA FOLLOWING PIERCING OF HELIX – A CASE REPORT

    OpenAIRE

    Rajamani; Santhosh Kumar

    2014-01-01

    Piercing of Helix of pinna is a social custom of certain communities in Northern Tamil Nadu. Such a “high helical” piercing is well known to cause Perichondritis of Pinna. Most of the times such a Perichondritis is unilateral. Here we present a case of Bilateral Perichondritis of pinna, following ear piercing, first time from India subcontinent. We also highlight some practical points on management of such cases.

  11. BILATERAL PERICHONDRITIS OF PINNA FOLLOWING PIERCING OF HELIX – A CASE REPORT

    Directory of Open Access Journals (Sweden)

    Rajamani

    2014-01-01

    Full Text Available Piercing of Helix of pinna is a social custom of certain communities in Northern Tamil Nadu. Such a “high helical” piercing is well known to cause Perichondritis of Pinna. Most of the times such a Perichondritis is unilateral. Here we present a case of Bilateral Perichondritis of pinna, following ear piercing, first time from India subcontinent. We also highlight some practical points on management of such cases.

  12. Strong Binding of Myosin Heads Stretches and Twists the Actin Helix

    OpenAIRE

    Tsaturyan, Andrey K.; Koubassova, Natalia; Ferenczi, Michael A.; Narayanan, Theyencheri; Roessle, Manfred; Bershitsky, Sergey Y.

    2004-01-01

    Calculation of the size of the power stroke of the myosin motor in contracting muscle requires knowledge of the compliance of the myofilaments. Current estimates of actin compliance vary significantly introducing uncertainty in the mechanical parameters of the motor. Using x-ray diffraction on small bundles of permeabilized fibers from rabbit muscle we show that strong binding of myosin heads changes directly the actin helix. The spacing of the 2.73-nm meridional x-ray reflection increased by...

  13. Accurate axial localization by conical diffraction beam shaping generating a dark-helix PSF

    Science.gov (United States)

    Fallet, Clement; Lassalle, Astrid; Dubois-Delumeau, Maxime; Sirat, Gabriel Y.

    2016-02-01

    We present here a new PSF-shaping technique using biaxial crystals to generate a highly z-dependent distribution in single molecule localization microscopy (SMLM). This distribution features two zeros of intensity that rotate together with defocus. This PSF features similarities to the double-helix introduced by Moerner and Piestun and thus has been dubbed dark-helix since we track zeros of intensity. Preliminary numerical studies based on Cramer-Rao Lower Bound (CRLB) show that this PSF has the potential to obtain up to 20nm localization precision. This PSF can be easily generated by a very simple, monolithic add-on added in front of the detection camera. Additionally, the PSF remains of the approximate size of the Airy PSF, the x-y localization precision is not substantially affected and no trade-off is required. The xy compacity of the PSF also enables theoretically a higher density of emitters than the double-helix which spreads on a larger scale. Limiting factors for SMLM such as loss of photons, complexity and robustness will be discussed and considerations about the practical implementation of such techniques will be given.

  14. Herschel spectral-mapping of the Helix Nebula (NGC 7293): Extended CO photodissociation and OH+ emission

    CERN Document Server

    Etxaluze, M; Goicoechea, J R; van Hoof, P A M; Swinyard, B M; Barlow, M J; van de Steene, G C; Groenewegen, M A T; Kerschbaum, F; Lim, T L; Lique, F; Matsuura, M; Pearson, C; Polehampton, E T; Royer, P; Ueta, T

    2014-01-01

    The Helix Nebula (NGC 7293) is the closest planetary nebulae. Therefore, it is an ideal template for photochemical studies at small spatial scales in planetary nebulae. We aim to study the spatial distribution of the atomic and the molecular gas, and the structure of the photodissociation region along the western rims of the Helix Nebula as seen in the submillimeter range with Herschel. We use 5 SPIRE FTS pointing observations to make atomic and molecular spectral maps. We analyze the molecular gas by modeling the CO rotational lines using a non-local thermodynamic equilibrium (non-LTE) radiative transfer model. For the first time, we have detected extended OH+ emission in a planetary nebula. The spectra towards the Helix Nebula also show CO emission lines (from J= 4 to 8), [NII] at 1461 GHz from ionized gas, and [CI] (2-1), which together with the OH+ lines, trace extended CO photodissociation regions along the rims. The estimated OH+ column density is (1-10)x1e12 cm-2. The CH+ (1-0) line was not detected at...

  15. Transient collagen triple helix binding to a key metalloproteinase in invasion and development.

    Science.gov (United States)

    Zhao, Yingchu; Marcink, Thomas C; Sanganna Gari, Raghavendar Reddy; Marsh, Brendan P; King, Gavin M; Stawikowska, Roma; Fields, Gregg B; Van Doren, Steven R

    2015-02-01

    Skeletal development and invasion by tumor cells depends on proteolysis of collagen by the pericellular metalloproteinase MT1-MMP. Its hemopexin-like (HPX) domain binds to collagen substrates to facilitate their digestion. Spin labeling and paramagnetic nuclear magnetic resonance (NMR) detection have revealed how the HPX domain docks to collagen I-derived triple helix. Mutations impairing triple-helical peptidase activity corroborate the interface. Saturation transfer difference NMR suggests rotational averaging around the longitudinal axis of the triple-helical peptide. Part of the interface emerges as unique and potentially targetable for selective inhibition. The triple helix crosses the junction of blades I and II at a 45° angle to the symmetry axis of the HPX domain, placing the scissile Gly∼Ile bond near the HPX domain and shifted ∼25 Å from MMP-1 complexes. This raises the question of the MT1-MMP catalytic domain folding over the triple helix during catalysis, a possibility accommodated by the flexibility between domains suggested by atomic force microscopy images. PMID:25651059

  16. A molecular mechanical model to predict the helix twist angles of B-DNA.

    Science.gov (United States)

    Tung, C S; Harvey, S C

    1984-04-11

    We present here a model for the prediction of helix twist angles in B-DNA, a model composed of a collection of torsional springs. Statistically averaged conformational energy calculations show that, for a specified basepair step, the basepair-basepair conformational energy is quadratically dependent on the helix twist angle, so the calculations provide the spring parameters for the basepair-basepair interactions. Torsional springs can also be used to model the effects of the backbone on the helix twist, and the parameters for those springs are derived by fitting the model to experimental data. The model predicts a macroscopic torsional stiffness and a longitudinal compressibility (Young's modulus) which are both in good agreement with experiment. One biological consequence of the model is examined, the sequence specificity of the Eco RI restriction endonuclease, and it is shown that the discriminatory power of the enzyme receives a substantial contribution from the energetic cost of torsional deformations of the DNA when wrong sequences are forced into the enzyme binding site. PMID:6326059

  17. Herschel imaging of the dust in the Helix Nebula (NGC 7293)

    CERN Document Server

    Van de Steene, G C; Exter, K M; Barlow, M J; Cernicharo, J; Etxaluze, M; Gear, W K; Goicoechea, J R; Gomez, H L; Groenewegen, M A T; Hargrave, P C; Ivison, R J; Leeks, S J; Lim, T L; Matsuura, M; Olofsson, G; Polehampton, E T; Swinyard, B M; Ueta, T; Van Winckel, H; Waelkens, C; Wesson, R

    2014-01-01

    In our series of papers presenting the Herschel imaging of evolved planetary nebulae, we present images of the dust distribution in the Helix nebula (NGC 7293). Images at 70, 160, 250, 350, and 500 micron were obtained with the PACS and SPIRE instruments on board the Herschel satellite. The broadband maps show the dust distribution over the main Helix nebula to be clumpy and predominantly present in the barrel wall. We determined the spectral energy distribution of the main nebula in a consistent way using Herschel, IRAS, and Planck flux values. The emissivity index of 0.99 +/- 0.09, in combination with the carbon rich molecular chemistry of the nebula, indicates that the dust consists mainly of amorphous carbon. The dust excess emission from the central star disk is detected at 70 micron and the flux measurement agree with previous measurement. We present the temperature and dust column density maps. The total dust mass across the Helix nebula (without its halo) is determined to be 0.0035 solar mass at a dis...

  18. Forster Resonance Energy Transfer and Laser Fluorescent Analysis of Defects in DNA Double Helix

    CERN Document Server

    Bregadze, Vasil G; Giorgadze, Tamar G; Jaliashvili, Zaza V; Chkhaberidze, Jemal G; Monaselidze, Jamlet R; Khuskivadze, Temur B

    2013-01-01

    Real time laser induced fluorescence spectroscopy usage for microanalysis of DNA double helix defects is shown. The method is based on Forster resonance energy transfer (FRET) in intercalator-donor pair (acridine orange as a donor and ethidium bromide as an acceptor). Transition metal ions such as Cu(II), Cu(I), Ag(I), silver nanoparticles (AgNPs), photo- and thermo effects were used to cause double helix defects in DNA. FRET radii were experimentally estimated in background electrolyte solution (0.01 M NaNO3) and proved to be 3.9 +- 0.3 nm and the data are in satisfactory agreement with the theoretically calculated value Ro = 3.5 +- 0.3 nm. Concentration of DNA sites, exposed to Cu(II), Cu(I), Ag(I) ions, AgNPs impact as well as laser irradiation ({\\lambda} = 457 nm) and temperature, which are applicable for intercalation, were estimated in relative units. FRET method allows to estimate the concentration of double helix areas with high quality stability applicable for intercalation in DNA after it was subjec...

  19. Contact Stress Analysis for Gears of Different Helix Angle Using Finite Element Method

    Directory of Open Access Journals (Sweden)

    Patil Santosh

    2014-07-01

    Full Text Available The gear contact stress problem has been a great point of interest for many years, but still an extensive research is required to understand the various parameters affecting this stress. Among such parameters, helix angle is one which has played a crucial role in variation of contact stress. Numerous studies have been carried out on spur gear for contact stress variation. Hence, the present work is an attempt to study the contact stresses among the helical gear pairs, under static conditions, by using a 3D finite element method. The helical gear pairs on which the analysis is carried are 0, 5, 15, 25 degree helical gear sets. The Lagrange multiplier algorithm has been used between the contacting pairs to determine the stresses. The helical gear contact stress is evaluated using FE model and results have also been found at different coefficient of friction, varying from 0.0 to 0.3. The FE results have been further compared with the analytical calculations. The analytical calculations are based upon Hertz and AGMA equations, which are modified to include helix angle. The commercial finite element software was used in the study and it was shown that this approach can be applied to gear design efficiently. The contact stress results have shown a decreasing trend, with increase in helix angle.

  20. Ruby-Helix: an implementation of helical image processing based on object-oriented scripting language.

    Science.gov (United States)

    Metlagel, Zoltan; Kikkawa, Yayoi S; Kikkawa, Masahide

    2007-01-01

    Helical image analysis in combination with electron microscopy has been used to study three-dimensional structures of various biological filaments or tubes, such as microtubules, actin filaments, and bacterial flagella. A number of packages have been developed to carry out helical image analysis. Some biological specimens, however, have a symmetry break (seam) in their three-dimensional structure, even though their subunits are mostly arranged in a helical manner. We refer to these objects as "asymmetric helices". All the existing packages are designed for helically symmetric specimens, and do not allow analysis of asymmetric helical objects, such as microtubules with seams. Here, we describe Ruby-Helix, a new set of programs for the analysis of "helical" objects with or without a seam. Ruby-Helix is built on top of the Ruby programming language and is the first implementation of asymmetric helical reconstruction for practical image analysis. It also allows easier and semi-automated analysis, performing iterative unbending and accurate determination of the repeat length. As a result, Ruby-Helix enables us to analyze motor-microtubule complexes with higher throughput to higher resolution. PMID:16996276

  1. Cysteine scanning reveals minor local rearrangements of the horizontal helix of respiratory complex I.

    Science.gov (United States)

    Steimle, Stefan; Schnick, Christian; Burger, Eva-Maria; Nuber, Franziska; Krämer, Dorothée; Dawitz, Hannah; Brander, Sofia; Matlosz, Bartlomiej; Schäfer, Jacob; Maurer, Katharina; Glessner, Udo; Friedrich, Thorsten

    2015-10-01

    The NADH:ubiquinone oxidoreductase, respiratory complex I, couples electron transfer from NADH to ubiquinone with the translocation of protons across the membrane. The complex consists of a peripheral arm catalyzing the redox reaction and a membrane arm catalyzing proton translocation. The membrane arm is almost completely aligned by a 110 Å unique horizontal helix that is discussed to transmit conformational changes induced by the redox reaction in a piston-like movement to the membrane arm driving proton translocation. Here, we analyzed such a proposed movement by cysteine-scanning of the helix of the Escherichia coli complex I. The accessibility of engineered cysteine residues and the flexibility of individual positions were determined by labeling the preparations with a fluorescent marker and a spin-probe, respectively, in the oxidized and reduced states. The differences in fluorescence labeling and the rotational flexibility of the spin probe between both redox states indicate only slight conformational changes at distinct positions of the helix but not a large movement. PMID:26115017

  2. A role of helix 12 of the vitamin D receptor in SMRT corepressor interaction

    International Nuclear Information System (INIS)

    To repress gene transcription, the unliganded nuclear receptor (NR) recruits the N-CoR and SMRT corepressors via its direct association with the conserved motif within bipartite NR-interaction domains (IDs) of corepressors. We recently reported that SMRT is directly involved in the VDR-mediated repression via an ID1-specific interaction with the VDR. Here we show that removal of helix 12 from VDR (VDRΔAF2) converts it to a more potent repressor through additional interaction between the VDR and SMRT-ID2 in yeast and mammalian systems. These data suggest that the VDR helix 12 actively regulates the ID1 preference of the VDR by inhibiting ID2-VDR association. Using the one- plus two-hybrid system, we identified specific residues within the extended helix motif of SMRT-ID2 that are required for VDRΔAF2 binding. Analyses of these mutants also revealed the specific residues of SMRT-ID2 generally required for optimal NR binding as well as those involved in preferential interaction with specific NRs.

  3. Exploring the membrane fusion mechanism through force-induced disassembly of HIV-1 six-helix bundle.

    Science.gov (United States)

    Gao, Kai; Zhang, Yong; Lou, Jizhong

    2016-05-13

    Enveloped virus, such as HIV-1, employs membrane fusion mechanism to invade into host cell. HIV-1 gp41 ectodomain uses six-helix bundle configuration to accomplish this process. Using molecular dynamic simulations, we confirmed the stability of this six-helix bundle by showing high occupancy of hydrogen bonds and hydrophobic interactions. Key residues and interactions important for the bundle integration were characterized by force-induced unfolding simulations of six-helix bundle, exhibiting the collapse order of these groups of interactions. Moreover, our results in some way concerted with a previous theory that the formation of coiled-coil choose a route which involved cooperative interactions between the N-terminal and C-terminal helix. PMID:27079239

  4. Threatened Neotropical mollusks: analysis of shape differences in three endemic snails from High Paraná River by geometric morphometrics Moluscos neotropicales amenazados: análisis de diferencias de forma en tres caracoles endémicos del río Alto Paraná mediante morfometría geométrica

    Directory of Open Access Journals (Sweden)

    Roberto E. Vogler

    2012-12-01

    Full Text Available Variation in shape among a living and 2 extinct aquatic snails of the genus Aylacostoma, using a geometric morphometric method of thin plate splines and multivariate analysis was investigated. The analysis was performed to evaluate the diagnostic capability of this method and to explore shell shape differences, due to the lack of other data, in an attempt to answer why only 1 of the species persisted in the wild. Sixteen landmarks in a bi-dimensional space for 32 shells of type, paratype and reference specimens deposited in museums of Argentina were defined. Analysis was successful in assigning individual specimens to particular species. Statistically significant differences in last whorl, aperture, and spire were found for the first 4 non-uniform components explaining an 85% of local variation observed. Differences could be related to a differential use of habitat and/or to the degree of exposure to water current. More globose shell found in the extinct species could be associated to habitats and substrata with the highest water currents, whereas the more stylized shell in the third species could be related to a preference for more protected habitats, like those where it presently occurs.La variación de forma entre una especie viviente y dos extintas de caracoles acuáticos del género Aylacostoma, fue investigada mediante el método de morfometría geométrica de "thin plate splines" y análisis multivariado. El análisis se realizó para evaluar la capacidad diagnóstica del método y explorar las diferencias de forma de conchilla, debido a la falta de otros datos, en un intento por responder por qué sólo una de las especies persistió en la naturaleza. Dieciséis "landmarks" fueron definidos en un espacio bi-dimensional para 32 conchillas de ejemplares tipo, paratipo y de referencia depositados en museos de Argentina. El análisis fue exitoso en la asignación de los individuos a especies particulares. Se encontraron diferencias

  5. Praevalensen afhud- og slimhindesymptomer blandt gartnere der omgås Ficus benjamina (stuebirk) og Hedera helix (vedbend). Et tvaersnitsstudie

    DEFF Research Database (Denmark)

    Jørs, Erik

    2003-01-01

    Allergic and toxic initiative symptoms from skin, eyes and respiratory tract are well known among gardeners This study reports the prevalence of these symptoms among gardeners working with Ficus Benjamina (Fb) and Hedera helix (Hh).......Allergic and toxic initiative symptoms from skin, eyes and respiratory tract are well known among gardeners This study reports the prevalence of these symptoms among gardeners working with Ficus Benjamina (Fb) and Hedera helix (Hh)....

  6. Evaluation of backbone-cyclized HER2-binding 2-helix Affibody molecule for In Vivo molecular imaging

    OpenAIRE

    HONARVAR, HADIS; Jokilaakso, Nima; Andersson, Karl; Malmberg, Jennie; Rosik, Daniel; Orlova, Anna; Karlstrom, Amelie Eriksson; Tolmachev, Vladimir; Jarver, Peter

    2013-01-01

    Introduction Affibody molecules, small scaffold proteins, have demonstrated an appreciable potential as imaging probes. Affibody molecules are composed of three alpha-helices. Helices 1 and 2 are involved in molecular recognition, while helix 3 provides stability. The size of Affibody molecules can be reduced by omitting the third alpha-helix and cross-linking the two remaining, providing a smaller molecule with better extravasation and quicker clearance of unbound tracer. The goal of this st...

  7. Activation of the pseudokinase MLKL unleashes the four-helix bundle domain to induce membrane localization and necroptotic cell death

    OpenAIRE

    Hildebrand, Joanne M.; Tanzer, Maria C; Lucet, Isabelle S; Young, Samuel N.; Spall, Sukhdeep K; Sharma, Pooja; Pierotti, Catia; Garnier, Jean-Marc; Dobson, Renwick C. J.; Andrew I Webb; Tripaydonis, Anne; Babon, Jeffrey J.; Mulcair, Mark D.; Scanlon, Martin J.; Alexander, Warren S

    2014-01-01

    The four-helix bundle (4HB) domain of Mixed Lineage Kinase Domain-Like (MLKL) bears two clusters of residues that are required for cell death by necroptosis. Mutations within a cluster centered on the α4 helix of the 4HB domain of MLKL prevented its membrane translocation, oligomerization, and ability to induce necroptosis. This cluster is composed principally of acidic residues and therefore challenges the idea that the 4HB domain engages negatively charged phospholipid membranes via a conve...

  8. Rotational Symmetry and the Transformation of Innovation Systems in a Triple Helix of University-Industry-Government Relations

    OpenAIRE

    Ivanova, Inga A.; Leydesdorff, Loet

    2012-01-01

    Using a mathematical model, we show that a Triple Helix (TH) system contains self-interaction, and therefore self-organization of innovations can be expected in waves, whereas a Double Helix (DH) remains determined by its linear constituents. (The mathematical model is fully elaborated in the Appendices.) The ensuing innovation systems can be expected to have a fractal structure: innovation systems at different scales can be considered as spanned in a Cartesian space with the dimensions of (S...

  9. O aparelho quadrihélice (Quad-helix e suas variações The Quad-helix appliance and their variations

    Directory of Open Access Journals (Sweden)

    Mario Sergio Duarte

    2006-04-01

    Full Text Available O presente artigo objetivou mostrar a eficiência dos vários desenhos do aparelho quadrihélice, de Ricketts, na correção das desarmonias dentoalveolares. Devido às suas várias formas de confecção, assim como de sua ativação, o quadrihélice tornou-se um acessório útil não somente na sobrecorreção da discrepância transversal e sagital, mas também no tratamento das más oclusões da Classe II, divisão 1, de Angle, principalmente nos casos em que a rotação do molar é desejada como parte do tratamento. Também é relevante o seu efeito no tratamento das mordidas abertas anteriores, atuando como coadjuvante no tratamento dos fatores ambientais que contribuem, muitas vezes, para exacerbar o desenvolvimento das más oclusões. Em relação ao alinhamento do arco dentário, o quadrihélice abrevia essa fase do tratamento em 4 a 5 meses (o tratamento convencional levaria muito mais tempo e pelo menos uma grande série de troca de arcos em mecânicas de nivelamento. Portanto, este trabalho tem a intenção de mostrar algumas das ativações possíveis do aparelho quadrihélice, bem como algumas de suas variações, que contribuem para conseguir resultados estáveis em longo prazo.The aim of this present article was to show the efficiency of several drawings of Ricketts Quad-helix appliance in the correction of dentoalveolar disharmonies. Due its varied forms, as well as its activation, the Quad-helix became a useful accessory not only in overcorrecting the transversal discrepancy and sagittal, but also in treating Angle Class II Division 1 malocclusions, mainly when molar rotation is a necessary part of the treatment. It is also relevant its effect in the treatment of anterior open-bites. It gives support in the treatment of environmental factors that contribute to exacerbate the development of malocclusions. In relation to dental arch alignment, the Quad-helix appliance abbreviate this treatment phase in 4 to 5 months, what would

  10. atonal- and achaete-scute-related genes in the annelid Platynereis dumerilii: insights into the evolution of neural basic-Helix-Loop-Helix genes

    Directory of Open Access Journals (Sweden)

    Arendt Detlev

    2008-06-01

    Full Text Available Abstract Background Functional studies in model organisms, such as vertebrates and Drosophila, have shown that basic Helix-loop-Helix (bHLH proteins have important roles in different steps of neurogenesis, from the acquisition of neural fate to the differentiation into specific neural cell types. However, these studies highlighted many differences in the expression and function of orthologous bHLH proteins during neural development between vertebrates and Drosophila. To understand how the functions of neural bHLH genes have evolved among bilaterians, we have performed a detailed study of bHLH genes during nervous system development in the polychaete annelid, Platynereis dumerilii, an organism which is evolutionary distant from both Drosophila and vertebrates. Results We have studied Platynereis orthologs of the most important vertebrate neural bHLH genes, i.e. achaete-scute, neurogenin, atonal, olig, and NeuroD genes, the latter two being genes absent of the Drosophila genome. We observed that all these genes have specific expression patterns during nervous system formation in Platynereis. Our data suggest that in Platynereis, like in vertebrates but unlike Drosophila, (i neurogenin is the main proneural gene for the formation of the trunk central nervous system, (ii achaete-scute and olig genes are involved in neural subtype specification in the central nervous system, in particular in the specification of the serotonergic phenotype. In addition, we found that the Platynereis NeuroD gene has a broad and early neuroectodermal expression, which is completely different from the neuronal expression of vertebrate NeuroD genes. Conclusion Our analysis suggests that the Platynereis bHLH genes have both proneural and neuronal specification functions, in a way more akin to the vertebrate situation than to that of Drosophila. We conclude that these features are ancestral to bilaterians and have been conserved in the vertebrates and annelids lineages, but

  11. The poplar basic helix-loop-helix transcription factor BEE3 – Like gene affects biomass production by enhancing proliferation of xylem cells in poplar

    Energy Technology Data Exchange (ETDEWEB)

    Noh, Seol Ah, E-mail: s6022029@korea.ac.kr; Choi, Young-Im, E-mail: yichoi99@forest.go.kr; Cho, Jin-Seong, E-mail: jinsung3932@gmail.com; Lee, Hyoshin, E-mail: hslee@forest.go.kr

    2015-06-19

    Brassinosteroids (BRs) play important roles in many aspects of plant growth and development, including regulation of vascular cambium activities and cell elongation. BR-induced BEE3 (brassinosteroid enhanced expression 3) is required for a proper BR response. Here, we identified a poplar (Populus alba × Populus glandulosa) BEE3-like gene, PagBEE3L, encoding a putative basic helix-loop-helix (bHLH)-type transcription factor. Expression of PagBEE3L was induced by brassinolide (BL). Transcripts of PagBEE3L were mainly detected in stems, with the internode having a low level of transcription and the node having a relatively higher level. The function of the PagBEE3L gene was investigated through phenotypic analyses with PagBEE3L-overexpressing (ox) transgenic lines. This work particularly focused on a potential role of PagBEE3L in stem growth and development of polar. The PagBEE3L-ox poplar showed thicker and longer stems than wild-type plants. The xylem cells from the stems of PagBEE3L-ox plants revealed remarkably enhanced proliferation, resulting in an earlier thickening growth than wild-type plants. Therefore, this work suggests that xylem development of poplar is accelerated in PagBEE3L-ox plants and PagBEE3L plays a role in stem growth by increasing the proliferation of xylem cells to promote the initial thickening growth of poplar stems. - Highlights: • We identify the BEE3-like gene form hybrid poplar (Populus alba × Populus glandulosa). • We examine effects of overexpression of PagBEE3L on growth in poplar. • We found that 35S:BEE3L transgenic plants showed more rapid growth than wild-type plants. • BEE3L protein plays an important role in the development of plant stem.

  12. Intermolecular recognition revealed by the complex structure of human CLOCK-BMAL1 basic helix-loop-helix domains with E-box DNA

    Institute of Scientific and Technical Information of China (English)

    Zixi Wang; Yaling Wu; Lanfen Li; Xiao-Dong Su

    2013-01-01

    CLOCK (circadian locomotor output cycles kaput) and BMAL1 (brain and muscle ARNT-like 1) are both transcription factors of the circadian core loop in mammals.Recently published mouse CLOCK-BMAL1 bHLH (basic helix-loop-helix)-PAS (period-ARNT-single-minded) complex structure sheds light on the mechanism for heterodimer formation,but the structural details of the protein-DNA recognition mechanisms remain elusive.Here we have elucidated the crystal structure of human CLOCK-BMAL1 bHLH domains bound to a canonical E-box DNA.We demonstrate that CLOCK and BMAL1 bHLH domains can be mutually selected,and that hydrogen-bonding networks mediate their E-box recognition.We identified a hydrophobic contact between BMAL1 Ile80 and a fianking thymine nucleotide,suggesting that CLOCK-BMAL1 actually reads 7-bp DNA and not the previously believed 6-bp DNA.To find potential non-canonical E-boxes that could be recognized by CLOCK-BMAL1,we constructed systematic single-nucleotide mutations on the E-box and measured their relevant affinities.We defined two non-canonical E-box patterns with high affinities,AACGTGA and CATGTGA,in which the flanking A7-T7' base pair is indispensable for recognition.These results will help us to identify functional CLOCK-BMAL1-binding sites in vivo and to search for clock-controlled genes.Furthermore,we assessed the inhibitory role of potential phosphorylation sites in bHLH regions.We found that the phospho-mimicking mutation on BMAL1 Ser78 could efficiently block DNA binding as well as abolish normal circadian oscillation in cells.We propose that BMAL1 Ser78 should be a key residue mediating input signal-regulated transcriptional inhibition for external cues to entrain the circadian clock by kinase cascade.

  13. The poplar basic helix-loop-helix transcription factor BEE3 – Like gene affects biomass production by enhancing proliferation of xylem cells in poplar

    International Nuclear Information System (INIS)

    Brassinosteroids (BRs) play important roles in many aspects of plant growth and development, including regulation of vascular cambium activities and cell elongation. BR-induced BEE3 (brassinosteroid enhanced expression 3) is required for a proper BR response. Here, we identified a poplar (Populus alba × Populus glandulosa) BEE3-like gene, PagBEE3L, encoding a putative basic helix-loop-helix (bHLH)-type transcription factor. Expression of PagBEE3L was induced by brassinolide (BL). Transcripts of PagBEE3L were mainly detected in stems, with the internode having a low level of transcription and the node having a relatively higher level. The function of the PagBEE3L gene was investigated through phenotypic analyses with PagBEE3L-overexpressing (ox) transgenic lines. This work particularly focused on a potential role of PagBEE3L in stem growth and development of polar. The PagBEE3L-ox poplar showed thicker and longer stems than wild-type plants. The xylem cells from the stems of PagBEE3L-ox plants revealed remarkably enhanced proliferation, resulting in an earlier thickening growth than wild-type plants. Therefore, this work suggests that xylem development of poplar is accelerated in PagBEE3L-ox plants and PagBEE3L plays a role in stem growth by increasing the proliferation of xylem cells to promote the initial thickening growth of poplar stems. - Highlights: • We identify the BEE3-like gene form hybrid poplar (Populus alba × Populus glandulosa). • We examine effects of overexpression of PagBEE3L on growth in poplar. • We found that 35S:BEE3L transgenic plants showed more rapid growth than wild-type plants. • BEE3L protein plays an important role in the development of plant stem

  14. The generalized model of polypeptide chain describing the helix-coil transition in biopolymers

    International Nuclear Information System (INIS)

    In this paper we summarize some results of our theoretical investigations of helix-coil transition both in single-strand (polypeptides) and two-strand (polynucleotides) macromolecules. The Hamiltonian of the Generalized Model of Polypeptide Chain (GMPC) is introduced to describe the system in which the conformations are correlated over some dimensional range Δ (it equals 3 for polypeptide, because one H-bond fixes three pairs of rotation, for double strand DNA it equals to one chain rigidity because of impossibility of loop formation on the scale less than Δ). The Hamiltonian does not contain any parameter designed especially for helix-coil transition and uses pure molecular microscopic parameters (the energy of hydrogen bond formation, reduced partition function of repeated unit, the number of repeated units fixed by one hydrogen bond, the energies of interaction between the repeated units and the solvent molecules). To calculate averages we evaluate the partition function using the transfer-matrix approach. The GMPC allowed to describe the influence of a number of factors, affecting the transition, basing on a unified microscopic approach. Thus we obtained, that solvents change transition temperature and interval in different ways, depending on type of solvent and on energy of solvent- macromolecule interaction; stacking on the background of H-bonding increases stability and decreases cooperativity of melting. For heterogeneous DNA we could analytically derive well known formulae for transition temperature and interval. In the framework of GMPC we calculate and show the difference of two order parameters of helix-coil transition - the helicity degree, and the average fraction of repeated units in helical conformation. Given article has the aim to review the results obtained during twenty years in the context of GMPC. (author)

  15. Helix Nebula and CERN: A Symbiotic approach to exploiting commercial clouds

    Science.gov (United States)

    Barreiro Megino, Fernando H.; Jones, Robert; Kucharczyk, Katarzyna; Medrano Llamas, Ramón; van der Ster, Daniel

    2014-06-01

    The recent paradigm shift toward cloud computing in IT, and general interest in "Big Data" in particular, have demonstrated that the computing requirements of HEP are no longer globally unique. Indeed, the CERN IT department and LHC experiments have already made significant R&D investments in delivering and exploiting cloud computing resources. While a number of technical evaluations of interesting commercial offerings from global IT enterprises have been performed by various physics labs, further technical, security, sociological, and legal issues need to be address before their large-scale adoption by the research community can be envisaged. Helix Nebula - the Science Cloud is an initiative that explores these questions by joining the forces of three European research institutes (CERN, ESA and EMBL) with leading European commercial IT enterprises. The goals of Helix Nebula are to establish a cloud platform federating multiple commercial cloud providers, along with new business models, which can sustain the cloud marketplace for years to come. This contribution will summarize the participation of CERN in Helix Nebula. We will explain CERN's flagship use-case and the model used to integrate several cloud providers with an LHC experiment's workload management system. During the first proof of concept, this project contributed over 40.000 CPU-days of Monte Carlo production throughput to the ATLAS experiment with marginal manpower required. CERN's experience, together with that of ESA and EMBL, is providing a great insight into the cloud computing industry and highlighted several challenges that are being tackled in order to ease the export of the scientific workloads to the cloud environments.

  16. Helix Nebula and CERN: A Symbiotic approach to exploiting commercial clouds

    International Nuclear Information System (INIS)

    The recent paradigm shift toward cloud computing in IT, and general interest in 'Big Data' in particular, have demonstrated that the computing requirements of HEP are no longer globally unique. Indeed, the CERN IT department and LHC experiments have already made significant R and D investments in delivering and exploiting cloud computing resources. While a number of technical evaluations of interesting commercial offerings from global IT enterprises have been performed by various physics labs, further technical, security, sociological, and legal issues need to be address before their large-scale adoption by the research community can be envisaged. Helix Nebula – the Science Cloud is an initiative that explores these questions by joining the forces of three European research institutes (CERN, ESA and EMBL) with leading European commercial IT enterprises. The goals of Helix Nebula are to establish a cloud platform federating multiple commercial cloud providers, along with new business models, which can sustain the cloud marketplace for years to come. This contribution will summarize the participation of CERN in Helix Nebula. We will explain CERN's flagship use-case and the model used to integrate several cloud providers with an LHC experiment's workload management system. During the first proof of concept, this project contributed over 40.000 CPU-days of Monte Carlo production throughput to the ATLAS experiment with marginal manpower required. CERN's experience, together with that of ESA and EMBL, is providing a great insight into the cloud computing industry and highlighted several challenges that are being tackled in order to ease the export of the scientific workloads to the cloud environments.

  17. In vivo targeting of HER2-positive tumor using 2-helix affibody molecules

    OpenAIRE

    Ren, Gang; Webster, Jack M.; LIU, ZHE; Zhang, Rong; Miao, Zheng; Liu, Hongguang; Gambhir, Sanjiv S.; Syud, Faisal A.; Cheng, Zhen

    2011-01-01

    Molecular imaging of human epidermal growth factor receptor type 2 (HER2) expression has drawn significant attention because of the unique role of the HER2 gene in diagnosis, therapy and prognosis of human breast cancer. In our previous research, a novel cyclic 2-helix small protein, MUT-DS, was discovered as an anti-HER2 Affibody analog with high affinity through rational protein design and engineering. MUT-DS was then evaluated for positron emission tomography (PET) of HER2-positive tumor b...

  18. An evolutionary triple helix to strengthen energy regulation: Implications for management

    Energy Technology Data Exchange (ETDEWEB)

    Rizzi, Francesco; Borzoni, Matteo

    2010-09-15

    Regulation is the basic tool to implement energy policy. The evolution of the regulation is influenced by its impacts on the industrial activities. Consequently, entrepreneurs acts in a continuously adapting-by-interacting environment. Both from a systemic and an atomistic perspective, this paper provides a theoretical framework for energy regulation development in order to support management implications. This work builds on the triple helix model and extends it to energy regulation development processes. It concludes that the analysis of intangible resources and their related services at inter-organizational level is fundamental to guide companies in designing win-win corporate strategies and in their operazionalization.

  19. Regulation of the RNA-dependent protein kinase by triple helix formation

    OpenAIRE

    Vuyisich, Momchilo; Beal, Peter A.

    2000-01-01

    The RNA-dependent protein kinase (PKR) is an interferon-induced, RNA-activated enzyme that phosphorylates the α-subunit of the translation initiation factor eIF-2, inhibiting its function. PKR is activated in vitro by binding to double-stranded RNA (dsRNA) molecules of ~30 bp or longer. Here we show that triple helix forming oligonucleotides (TFOs) inhibit dsRNA binding to the isolated RNA binding domain of PKR. The inhibition is specific to the targeted RNA and dependent on TFO length. Bindi...

  20. Recombination induced by triple-helix-targeted DNA damage in mammalian cells.

    OpenAIRE

    Faruqi, A F; Seidman, M M; Segal, D J; Carroll, D; Glazer, P M

    1996-01-01

    Gene therapy has been hindered by the low frequency of homologous recombination in mammalian cells. To stimulate recombination, we investigated the use of triple-helix-forming oligonucleotides (TFOs) to target DNA damage to a selected site within cells. By treating cells with TFOs linked to psoralen, recombination was induced within a simian virus 40 vector carrying two mutant copies of the supF tRNA reporter gene. Gene conversion events, as well as mutations at the target site, were also obs...

  1. Alpha-helix <-> random coil phase transition: analysis of ab initio theory predictions

    DEFF Research Database (Denmark)

    Solov'yov, Ilia; Yakubovich, Alexander V.; Solov'yov, Andrey V.;

    2008-01-01

    In the present paper we present results of calculations obtained with the use of the theoretical method described in our preceding paper [Eur. Phys. J. D, DOI 10.1140/epjd/e2007-00328-9] and perform detail analysis of -helix random coil transition in alanine polypeptides of different length. We...... have calculated the potential energy surfaces of polypeptides with respect to their twisting degrees of freedom and construct a parameter-free partition function of the polypeptide using the suggested method [Eur. Phys. J. D, DOI 10.1140/epjd/e2007-00328-9]. From the build up partition function we...

  2. Mapping the Structural Requirements in the CB1 Cannabinoid Receptor Transmembrane Helix II for Signal Transduction

    OpenAIRE

    Kapur, Ankur; Samaniego, Patrick; Thakur, Ganesh A.; Makriyannis, Alexandros; Abood, Mary E.

    2008-01-01

    Amino acid residues in the transmembrane domains of the CB1 receptor are important for ligand recognition and signal transduction. We used site-directed mutagenesis to identify the role of two novel and adjacent residues in the transmembrane helix II domain, Ile2.62 and Asp2.63. We investigated the role of the conserved, negatively charged aspartate at position 2.63 in cannabinoid receptor (CB1) function by substituting it with asparagine (D2.63N) and glutamate (D2.63E). In addition, the effe...

  3. An Exact SU(2) Symmetry and Persistent Spin Helix in a Spin-Orbit Coupled System

    Energy Technology Data Exchange (ETDEWEB)

    Bernevig, Andrei

    2010-02-10

    Spin-orbit coupled systems generally break the spin rotation symmetry. However, for a model with equal Rashba and Dresselhauss coupling constant (the ReD model), and for the [110] Dresselhauss model, a new type of SU(2) spin rotation symmetry is discovered. This symmetry is robust against spin-independent disorder and interactions, and is generated by operators whose wavevector depends on the coupling strength. It renders the spin lifetime infinite at this wavevector, giving rise to a Persistent Spin Helix (PSH). We obtain the spin fluctuation dynamics at, and away, from the symmetry point, and suggest experiments to observe the PSH.

  4. Monosaccharide templates for de novo designed 4-alpha-helix bundle proteins: template effects in carboproteins

    DEFF Research Database (Denmark)

    Brask, Jesper; Dideriksen, J.M.; Nielsen, John; Jensen, Knud Jørgen

    2003-01-01

    De novo design and total chemical synthesis of proteins provide powerful approaches to critically test our understanding of protein folding, structure, and stability. The 4-alpha-helix bundle is a frequently studied structure in which four amphiphilic alpha-helical peptide strands form a...... hydrophobic core. Assembly of protein models on a template has been suggested as a way to reduce the entropy of folding. We have previously developed the concept of carbohydrates as templates in the de novo design of protein models termed 'carboproteins'. Here we present the chemical synthesis of three 8.1 k...... melting points in chemical and thermal denaturation experiments....

  5. Solvent-Exposed Salt Bridges Influence the Kinetics of alpha-Helix Folding and Unfolding

    OpenAIRE

    Meuzelaar, Heleen; Tros, Martijn; Huerta-Viga, Adriana; Chris N. van Dijk; Vreede, Jocelyne; Woutersen, Sander

    2014-01-01

    Salt bridges are known to play an essential role in the thermodynamic stability of the folded conformation of many proteins, but their influence on the kinetics of folding remains largely unknown. Here, we investigate the effect of Glu-Arg salt bridges on the kinetics of α-helix folding using temperature-jump transient-infrared spectroscopy and steady-state UV circular dichroism. We find that geometrically optimized salt bridges (Glu– and Arg+ are spaced four peptide units apart, and the Glu/...

  6. Analysis of the axial electric field in a plasma-loaded-helix travelling wave tube

    Institute of Scientific and Technical Information of China (English)

    Xie Hong-Quan; Liu Pu-Kun

    2006-01-01

    A helix type slow wave structure filled with plasma is immersed in a strong longitudinal magnetic field. Taking into account the effect of the plasma and the dielectric, the system is separated radially into three regions. By means of the sheath model and Maxwell equation, the distribution of the electromagnetic field is established. Using the boundary conditions of each region, the dispersion relation of the slow wave structure is derived. The trend of change for the radial profile of the axial electric field is analysed respectively in different plasma densities, plasma column radius and dielectric constant by numerical computation. Some useful results are obtained on the basis of the discussion.

  7. CAXIAS DO SUL TECHNOLOGY INCUBATOR: TECHNOLOGICAL INNOVATION THROUGH THE TRIPLE HELIX

    Directory of Open Access Journals (Sweden)

    Priscila Bresolin Tisott

    2014-09-01

    on investment in the form of registered patents, attracting new students and recognition as a technological, entrepreneurial and innovative university. The perceived benefits for the industrial sector are training and development for businesses and entrepreneurs, while the municipal government perceives the reduced number of businesses failing and the financial returns, in the form of taxes, as benefits. The findings show that the Triple Helix concept developed by Etzkowitz (2009 plays a cooperative and participatory role in the Technology Incubator, even though it could be applied to more segments of society.

  8. A Phosphoserine–Lysine Salt Bridge within an α-Helical Peptide, the Strongest α-Helix Side-Chain Interaction Measured to Date†

    OpenAIRE

    Errington, Neil; Doig, Andrew J.

    2005-01-01

    Phosphorylation is ubiquitous in control of protein activity, yet its effects on protein structure are poorly understood. Here we investigate the effect of serine phosphorylation in the interior of an α-helix when a salt bridge is present between the phosphate group and a positively charged side chain (in this case lysine) at i,i + 4 spacing. The stabilization of the helix is considerable and can overcome the intrinsically low preference of phosphoserine for the interior of the helix. The eff...

  9. Reversible folding/unfolding of small α-helix in explicit solvent investigated by ABEEMσπ/MM

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    We have performed molecular dynamics simulations on the reversible folding/unfolding of small α-helix(short Ala based peptide Ala5) in explicit water solvent in terms of ABEEMσπ/MM.A dynamics analysis shows that the α-helical turn can be preserved up to a period of about 2 ns at 300 K,which supports the conclusions of Margulis et al.The time trajectory of the root mean square deviation between the heavy atoms of the backbone and the helical reference structure indicate that "helix melting and formation occurs rapidly on a time scale of 0.1 ns at 300 K" is not a felicitous conclusion.We first quantificationally concluded that the helix nucleation can maintain 2 ns,1―1.5 ns and 0.8 ns for Ala5 at 300 K,400 K and 500 K,respectively.Furthermore,increasing temperature dose not alter the pathway of folding/unfolding,but change the rate.An analysis of structures in a "transition-state ensemble" shows that helix-to-coil transitions occurs predominantly through breaking of hydrogen bonds at the helix ends(92%),particularly at the C-terminus(50%).Hydrogen bonds’ breaking and formation occurs on a time scale of 0.1 ns.

  10. Reversible folding/unfolding of small α-helix in explicit solvent investigated by ABEEMσπ/MM

    Institute of Scientific and Technical Information of China (English)

    LIU Cui; YANG ZhongZhi

    2009-01-01

    We have performed molecular dynamics simulations on the reversible folding/unfolding of small α-helix (shod Ala based peptide Ala_5) in explicit water solvent in terms of ABEEMσπ/MM.A dynamics analysis shows that the α-helical turn can be preserved up to a period of about 2 ns at 300 K,which supports the conclusions of Margulis et al.The time trajectory of the root mean square deviation between the heavy atoms of the backbone and the helical reference structure indicate that "helix melting and formation occurs rapidly on a time scale of 0.1 ns at 300 K" is not a felicitous conclusion.We first quantificationally concluded that the helix nucleation can maintain 2 ns,1-1.5 ns and 0.8 ns for Ala_5 at 300 K,400 K and 500 K,respectively.Furthermore,increasing temperature dose not alter the pathway of folding/unfolding,but change the rate.An analysis of structures in a "transition-state ensemble" shows that helix-to-coil transitions occurs predominantly through breaking of hydrogen bonds at the helix ends (92%),particularly at the C-terminus(50%).Hydrogen bonds' breaking and formation occurs on a time scale of 0.1 ns.

  11. A self-consistent nonlinear theory of a premodulated electron beam propagating through a helix-loaded waveguide

    International Nuclear Information System (INIS)

    A self-consistent nonlinear theory of a relativistic electron beam propagating through a waveguide loaded with a sheath helix is developed by making use of Maxwell equations. A closed integrodifferential equation is obtained for the normalized beam current described in terms of the normalized time θ and propagation distance ζ. An analytical investigation of the partial integrodifferential equation of the current modulation is carried out by Fourier decomposing the current modulation with harmonic number scr(l). The mode strength cscr(l)(ζ) is obtained in terms of the spatial oscillation frequency ηscr(l) and growth rate ξscr(l) of the mode amplitude, which are, in turn, determined in terms of the electrostatic and helix effects. The spatial oscillation frequency increases as the electrostatic effect (gscr(l)) increases. On the other hand, the growth rate increases with the strength of the helix effect. It is found that the mode strength cscr(l) is oscillatory and that it grows during propagation when the spatial frequency ηscr(l) (the electrostatic effect) is considerably larger than the growth rate ξscr(l) (the helix effect). Otherwise, the exponential growth dominates. Investigation of the helix mode must include the electrostatic effect for an intense beam

  12. Functional diversity of human basic helix-loop-helix transcription factor TCF4 isoforms generated by alternative 5' exon usage and splicing.

    Directory of Open Access Journals (Sweden)

    Mari Sepp

    Full Text Available BACKGROUND: Transcription factor 4 (TCF4 alias ITF2, E2-2, ME2 or SEF2 is a ubiquitous class A basic helix-loop-helix protein that binds to E-box DNA sequences (CANNTG. While involved in the development and functioning of many different cell types, recent studies point to important roles for TCF4 in the nervous system. Specifically, human TCF4 gene is implicated in susceptibility to schizophrenia and TCF4 haploinsufficiency is the cause of the Pitt-Hopkins mental retardation syndrome. However, the structure, expression and coding potential of the human TCF4 gene have not been described in detail. PRINCIPAL FINDINGS: In the present study we used human tissue samples to characterize human TCF4 gene structure and TCF4 expression at mRNA and protein level. We report that although widely expressed, human TCF4 mRNA expression is particularly high in the brain. We demonstrate that usage of numerous 5' exons of the human TCF4 gene potentially yields in TCF4 protein isoforms with 18 different N-termini. In addition, the diversity of isoforms is increased by alternative splicing of several internal exons. For functional characterization of TCF4 isoforms, we overexpressed individual isoforms in cultured human cells. Our analysis revealed that subcellular distribution of TCF4 isoforms is differentially regulated: Some isoforms contain a bipartite nuclear localization signal and are exclusively nuclear, whereas distribution of other isoforms relies on heterodimerization partners. Furthermore, the ability of different TCF4 isoforms to regulate E-box controlled reporter gene transcription is varied depending on whether one or both of the two TCF4 transcription activation domains are present in the protein. Both TCF4 activation domains are able to activate transcription independently, but act synergistically in combination. CONCLUSIONS: Altogether, in this study we have described the inter-tissue variability of TCF4 expression in human and provided evidence

  13. Accurate prediction of helix interactions and residue contacts in membrane proteins.

    Science.gov (United States)

    Hönigschmid, Peter; Frishman, Dmitrij

    2016-04-01

    Accurate prediction of intra-molecular interactions from amino acid sequence is an important pre-requisite for obtaining high-quality protein models. Over the recent years, remarkable progress in this area has been achieved through the application of novel co-variation algorithms, which eliminate transitive evolutionary connections between residues. In this work we present a new contact prediction method for α-helical transmembrane proteins, MemConP, in which evolutionary couplings are combined with a machine learning approach. MemConP achieves a substantially improved accuracy (precision: 56.0%, recall: 17.5%, MCC: 0.288) compared to the use of either machine learning or co-evolution methods alone. The method also achieves 91.4% precision, 42.1% recall and a MCC of 0.490 in predicting helix-helix interactions based on predicted contacts. The approach was trained and rigorously benchmarked by cross-validation and independent testing on up-to-date non-redundant datasets of 90 and 30 experimental three dimensional structures, respectively. MemConP is a standalone tool that can be downloaded together with the associated training data from http://webclu.bio.wzw.tum.de/MemConP. PMID:26851352

  14. Pressure-dependent changes in the structure of the melittin {alpha}-helix determined by NMR

    Energy Technology Data Exchange (ETDEWEB)

    Iwadate, Mitsuo; Asakura, Tetsuo [Tokyo University of Agriculture and Technology, Department of Biotechnology (Japan); Dubovskii, Peter V.; Yamada, Hiroaki; Akasaka, Kazuyuki [Kobe University, Graduate School of Science and Technology and Department of Chemistry of Faculty of Science (Japan); Williamson, Michael P. [University of Sheffield, Department of Molecular Biology and Biotechnology (United Kingdom)

    2001-02-15

    A novel method is described, which uses changes in NMR chemical shifts to characterise the structural change in a protein with pressure. Melittin in methanol is a small {alpha}-helical protein, and its chemical shifts change linearly and reversibly with pressure between 1 and 2000 bar. An improved relationship between structure and HN shift has been calculated, and used to drive a molecular dynamics-based calculation of the change in structure. With pressure, the helix is compressed, with the H-O distance of the NH-O=C hydrogen bonds decreased by 0.021 {+-} 0.039 A, leading to an overall compression along the entire helix of about 0.4 A, corresponding to a static compressibility of 6 x10{sup -6} bar{sup -1}. The backbone dihedral angles {phi} and {psi} are altered by no more than {+-} 3 deg. for most residues with a negative correlation coefficient of -0.85 between {phi}{sub i} and {psi}{sub i-1}, indicating that the local conformation alters to maintain hydrogen bonds in good geometries. The method is shown to be capable of calculating structural change with high precision, and the results agree with structural changes determined using other methodologies.

  15. Investigation and direct mapping of the persistent spin helix in confined structures

    Science.gov (United States)

    Schwemmer, Markus; Weingartner, Matthias; Völkl, Roland; Oltscher, Martin; Schuh, Dieter; Bougeard, Dominique; Korn, Tobias; Schüller, Christian

    The spin-orbit field in GaAs-based quantum well (QW) structures typically consists of two different contributions: Dresselhaus and Rashba field. The geometry of the Dresselhaus field, which arises due to the bulk inversion asymmetry, is mostly determined by the growth direction of the quantum well. The Rashba field instead is caused by a structure inversion asymmetry, which can be controlled, e.g. by the modulation doping. For the specific case of a (001)-grown GaAs quantum well with equal strength of Dresselhaus and Rashba fields, the effective spin-orbit field is oriented along the in-plane [110] direction for all k values and the spin splitting for this direction vanishes. For optically injected spins, which are initially oriented perpendicular to the QW plane, a persistent spin helix (PSH) state forms. We use a femtosecond pulsed TiSa-Laser system combined with a magneto-optical Kerr effect microscope for time- and space-resolved mapping of the PSH. With this technique, we investigate the PSH behavior in confined structures, e.g., thin channels along the helix direction. Hence we find that lateral confinement increases the effective PSH lifetime drastically. In more complex structures, we observe that PSH formation is even stable under a forced direction change. Financial support by the DFG via SFB 689 and SPP 1285 is gratefully acknowledged.

  16. Design and construction of superconducting helix cavities for heavy-ion acceleration

    International Nuclear Information System (INIS)

    In a first step we shall investigate the grounds which led us to define the characteristic values of beam energy and spread for the tandem Van de Graaf Booster. We have very accurately measured by the perturbation method the electromagnetic field distribution for the fundamental mode inside the cavity. We have been obliged to use an experimental method because the lack of axial symmetry does not allow us to compute the field distribution with a good accuracy. Characteristic parameters as: shunt impedance, geometrical factor. Q value have been measured. From these measurements we have optimized the helix geometry and estimated the energy gain per charge. The liquid helium temperature properties of the cavity have been measured. The main parameter is then the Q value. We measured it at different field levels, and we used second sound wave propagation in superfluid helium to determine the spot position where the increase of temperature leads to quench. The variations of the eigen-frequency of the resonators have been investigated. We have also estimated the RF losses due to the trapped magnetic flux (Meissner Effect). To realize construction prototype cavities we have investigated the resonance frequency dependence upon the geometrical parameters. We have also tested the slow tuning system which tunes the cavity by mechanical deformation of the helix. The prototype cavity with an ion beam has been tested, we have checked the behaviour of the transit time factor and studied the optic along the beam trasport line

  17. The Molecular Mechanism of Opening the Helix Bundle Crossing (HBC) Gate of a Kir Channel

    Science.gov (United States)

    Meng, Xuan-Yu; Liu, Shengtang; Cui, Meng; Zhou, Ruhong; Logothetis, Diomedes E.

    2016-01-01

    Inwardly rectifying K+ (Kir) channels, serving as natural molecular nanomachines, transport potassium ions across the plasma membrane of the cell. Along the ion permeation pathway, three relatively narrow regions (the selectivity filter (SF), the inner helix bundle crossing (HBC), and the cytosolic G loop) may serve as gates to control ion permeation. Our previous molecular dynamics simulations based on the crystal structure of a Kir3.1 chimera revealed the possible gating mechanism of the G loop gate. Here, we introduced a proline mutation in the inner helix and obtained a channel model of the open HBC gate. The open HBC gate reaches 0.6 nm in diameter, which allows partial hydrated K+ ions to pass through. During the gating process, both the transmembrane helices TM1 and TM2 cooperatively rotate in a counterclockwise direction (viewed from the extracellular side) with the aid of the phospholipid PIP2. Only when all the transmembrane helices adopt a counterclockwise rotation, the HBC gate can be stabilized in the open state. We estimate that introduction of the proline mutation decreases the energy required to open the HBC gate by about 1.4 kcal/mol (ΔΔG). PMID:27439597

  18. A triple-helix forming oligonucleotide targeting genomic DNA fails to induce mutation.

    Science.gov (United States)

    Reshat, Reshat; Priestley, Catherine C; Gooderham, Nigel J

    2012-11-01

    Purine tracts in duplex DNA can bind oligonucleotide strands in a sequence specific manner to form triple-helix structures. Triple-helix forming oligonucleotides (TFOs) targeting supFG1 constructs have previously been shown to be mutagenic raising safety concerns for oligonucleotide-based pharmaceuticals. We have engineered a TFO, TFO27, to target the genomic Hypoxanthine-guanine phosphoribosyltransferase (HPRT) locus to define the mutagenic potential of such structures at genomic DNA. We report that TFO27 was resistant to nuclease degradation and readily binds to its target motif in a cell free system. Contrary to previous studies using the supFG1 reporter construct, TFO27 failed to induce mutation within the genomic HPRT locus. We suggest that it is possible that previous reports of triplex-mediated mutation using the supFG1 reporter construct could be confounded by DNA quadruplex formation. Although the present study indicates that a TFO targeting a genomic locus lacks mutagenic activity, it is unclear if this finding can be generalised to all TFOs and their targets. For the present, we suggest that it is prudent to avoid large purine stretches in oligonucleotide pharmaceutical design to minimise concern regarding off-target genotoxicity. PMID:22914677

  19. Priming DNA Replication from Triple Helix Oligonucleotides: Possible Threestranded DNA in DNA Polymerases

    Directory of Open Access Journals (Sweden)

    Patrick P. Lestienne

    2011-01-01

    Full Text Available Triplex associate with a duplex DNA presenting the same polypurine or polypyrimidine-rich sequence in an antiparallel orientation. So far, triplex forming oligonucleotides (TFOs are known to inhibit transcription, replication, and to induce mutations. A new property of TFO is reviewed here upon analysis of DNA breakpoint yielding DNA rearrangements; the synthesized sequence of the first direct repeat displays a skewed polypurine- rich sequence. This synthesized sequence can bind the second homologous duplex sequence through the formation of a triple helix, which is able to prime further DNA replication. In these case, the d(G-rich Triple Helix Primers (THP bind the homologous strand in a parallel manner, possibly via a RecA-like mechanism. This novel property is shared by all tested DNA polymerases: phage, retrovirus, bacteria, and human. These features may account for illegitimate initiation of replication upon single-strand breakage and annealing to a homologous sequence where priming may occur. Our experiments suggest that DNA polymerases can bind three instead of two polynucleotide strands in their catalytic centre.

  20. Specificity of DNA triple helix formation analyzed by a FRET assay

    Directory of Open Access Journals (Sweden)

    Reither Sabine

    2002-09-01

    Full Text Available Abstract Background A third DNA strand can bind into the major groove of a homopurine duplex DNA to form a DNA triple helix. Sequence specific triplex formation can be applied for gene targeting, gene silencing and mutagenesis. Results We have analyzed triplex formation of two polypurine triplex forming oligodeoxynucleotides (TFOs using fluorescence resonance energy transfer (FRET. Under our conditions, the TFOs bind to their cognate double strand DNAs with binding constants of 2.6 × 105 and 2.3 × 106 M-1. Our data confirm that the polypurine TFO binds in an antiparallel orientation with respect to the polypurine DNA strand and that triplex formation requires Mg2+ions whereas it is inhibited by K+ions. The rate of formation of triple helices is slow with bimolecular rate constants of 5.6 × 104 and 8.1 × 104 min-1 M-1. Triplex dissociation was not detectable over at least 30 hours. Triplex formation is sequence specific; alteration of a single base pair within the 13 base pairs long TFOs prevents detectable triplex formation. Conclusion We have applied a FRET assay to investigate the specificity of DNA triple helix formation. This assay is homogeneous, continuous and specific, because the appearance of the FRET signal is directly correlated to triplex formation. We show that polypurine TFOs bind highly specifically to polypurine stretches in double stranded DNA. This is a prerequisite for biotechnical applications of triple helices to mediate sequence specific recognition of DNA.

  1. Priming DNA replication from triple helix oligonucleotides: possible threestranded DNA in DNA polymerases.

    Science.gov (United States)

    Lestienne, Patrick P

    2011-01-01

    Triplex associate with a duplex DNA presenting the same polypurine or polypyrimidine-rich sequence in an antiparallel orientation. So far, triplex forming oligonucleotides (TFOs) are known to inhibit transcription, replication, and to induce mutations. A new property of TFO is reviewed here upon analysis of DNA breakpoint yielding DNA rearrangements; the synthesized sequence of the first direct repeat displays a skewed polypurine- rich sequence. This synthesized sequence can bind the second homologous duplex sequence through the formation of a triple helix, which is able to prime further DNA replication. In these case, the d(G)-rich Triple Helix Primers (THP) bind the homologous strand in a parallel manner, possibly via a RecA-like mechanism. This novel property is shared by all tested DNA polymerases: phage, retrovirus, bacteria, and human. These features may account for illegitimate initiation of replication upon single-strand breakage and annealing to a homologous sequence where priming may occur. Our experiments suggest that DNA polymerases can bind three instead of two polynucleotide strands in their catalytic centre. PMID:22229092

  2. Aptamer/target binding-induced triple helix forming for signal-on electrochemical biosensing.

    Science.gov (United States)

    Mao, Yinfei; Liu, Jinquan; He, Dinggen; He, Xiaoxiao; Wang, Kemin; Shi, Hui; Wen, Li

    2015-10-01

    Owing to its diversified structures, high affinity, and specificity for binding a wide range of non-nucleic acid targets, aptamer is a useful molecular recognition tool for the design of various biosensors. Herein, we report a new signal-on electrochemical biosensing platform which is based on an aptamer/target binding-induced strand displacement and triple-helix forming. The biosensing platform is composed of a signal transduction probe (STP) modified with a methylene blue (MB) and a sulfhydryl group, a triplex-forming oligonucleotides probe (TFO) and a target specific aptamer probe (Apt). Through hybridization with the TFO probe and the Apt probe, the self-assembled STP on Au electrode via Au-S bonding keeps its rigid structure. The MB on the STP is distal to the Au electrode surface. It is eT off state. Target binding releases the Apt probe and liberates the end of the MB tagged STP to fold back and form a triplex-helix structure with TFO (STP/TFO/STP), allowing MB to approach the Au electrode surface and generating measurable electrochemical signals (eT ON). As test for the feasibility and universality of this signal-on electrochemical biosensing platform, two aptamers which bind to adenosine triphosphate (ATP) and human α-thrombin (Tmb), respectively, are selected as models. The detection limit of ATP was 7.2 nM, whereas the detection limit of Tmb was 0.86 nM. PMID:26078174

  3. Comparison of heat transfer performances of helix baffled heat exchangers with different baffle configurations

    Institute of Scientific and Technical Information of China (English)

    Cong Dong; Yaping Chen; Jiafeng Wu

    2015-01-01

    Numerical simulations were performed on flow and heat transfer performances of heat exchangers having six helical baffles of different baffle shapes and assembly configurations, i.e., two trisection baffle schemes, two quadrant baffle schemes, and two continuous helical baffle schemes. The temperature contour or the pressure contour and velocity contour plots with superimposed velocity vectors on meridian, transverse and unfolded concentric hexagonal slices are presented to obtain a full angular view. For the six helix baffled heat exchangers, the different patterns of the single vortex secondary flow and the shortcut leakage flow were depicted as wel as the heat transfer properties were compared. The results show that the optimum scheme among the six configurations is a circumferential overlap trisection helix baffled heat exchanger with a baffle incline angle of 20° (20°TCO) scheme with an anti-shortcut baffle structure, which exhibits the second highest pressure dropΔpo, the highest overal heat transfer coefficient K, shel-side heat transfer coefficient ho and shel-side average comprehensive index ho/Δpo.

  4. Unified description of solvent effects in the helix-coil transition

    Science.gov (United States)

    Badasyan, Artem; Tonoyan, Shushanik A.; Giacometti, Achille; Podgornik, Rudolf; Parsegian, V. Adrian; Mamasakhlisov, Yevgeni Sh.; Morozov, Vladimir F.

    2014-02-01

    We analyze the problem of the helix-coil transition in explicit solvents analytically by using spin-based models incorporating two different mechanisms of solvent action: explicit solvent action through the formation of solvent-polymer hydrogen bonds that can compete with the intrinsic intra-polymer hydrogen bonded configurations (competing interactions) and implicit solvent action, where the solvent-polymer interactions tune biopolymer configurations by changing the activity of the solvent (non-competing interactions). The overall spin Hamiltonian is comprised of three terms: the background in vacuo Hamiltonian of the "Generalized Model of Polypeptide Chain" type and two additive terms that account for the two above mechanisms of solvent action. We show that on this level the solvent degrees of freedom can be explicitly and exactly traced over, the ensuing effective partition function combining all the solvent effects in a unified framework. In this way we are able to address helix-coil transitions for polypeptides, proteins, and DNA, with different buffers and different external constraints. Our spin-based effective Hamiltonian is applicable for treatment of such diverse phenomena as cold denaturation, effects of osmotic pressure on the cold and warm denaturation, complicated temperature dependence of the hydrophobic effect as well as providing a conceptual base for understanding the behavior of intrinsically disordered proteins and their analogues.

  5. A magnetic torsional wave near the Galactic Centre traced by a 'double helix' nebula.

    Science.gov (United States)

    Morris, Mark; Uchida, Keven; Do, Tuan

    2006-03-16

    The magnetic field in the central few hundred parsecs of the Milky Way has a dipolar geometry and is substantially stronger than elsewhere in the Galaxy, with estimates ranging up to a milligauss (refs 1-6). Characterization of the magnetic field at the Galactic Centre is important because it can affect the orbits of molecular clouds by exerting a drag on them, inhibit star formation, and could guide a wind of hot gas or cosmic rays away from the central region. Here we report observations of an infrared nebula having the morphology of an intertwined double helix about 100 parsecs from the Galaxy's dynamical centre, with its axis oriented perpendicular to the Galactic plane. The observed segment is about 25 parsecs in length, and contains about 1.25 full turns of each of the two continuous, helically wound strands. We interpret this feature as a torsional Alfvén wave propagating vertically away from the Galactic disk, driven by rotation of the magnetized circumnuclear gas disk. The direct connection between the circumnuclear disk and the double helix is ambiguous, but the images show a possible meandering channel that warrants further investigation. PMID:16541066

  6. Experiments on Broadband EMP Radiation with an Axial Mode Helix Antenna

    International Nuclear Information System (INIS)

    To produce broadband electromagnetic pulse (EMP) radiation, we design and test a sub-ns pulse system which is utilized to drive an axial mode helix antenna. This sub-ns pulse system consists of a 10-stage Marx generator, an intermediate storage capacitor, an impedance transforming line, and can generate a high voltage of 570 kV with a rise time of 1–1.5 ns on a 300-Ω-resistance load. The diameter, pitch and turns of the helix antenna are 29 cm, 19.5 cm and 5, respectively, with a design frequency of 300 MHz. When the charging voltage of the Marx generator is 30 kV, the electric field of radiated EMP measured 3m from the source is 35 kV/m with a central frequency of 250 MHz. The relatively spectral bandwidth is 25%. The radiated EMP results are reproducible and the system will work in repetition mode if the available dc power is utilized. (general)

  7. Long Circulating Micelles based on Helix Bundle-Forming Peptide-Polymer Conjugates

    Science.gov (United States)

    Shu, Jessica; Dong, He; Dube, Nikhil; Seo, Jai Woong; Ma, Yu Fei; Ferrara, Katherine; Xu, Ting

    2012-02-01

    Stable, multi-functional organic nanoparticles that combine long in vivo circulation, the ability to cross vessel walls to reach tumor tissues and controlled disassembly for eventual clearance will have a significant impact in nanomedicine. Although current self-assemblies of amphiphiles provide a versatile platform to generate modular organic nanoparticles, it remains a significant challenge to simultaneously control nanoparticle size in the range of 10-30 nm, enhance particle stability and tailor disassembly within suitable timescales. We have advanced this goal by designing a new family of amphiphiles based on coiled-coil 3-helix bundle forming peptide-polymer conjugates. By attaching a polymer chain to the middle of a helical peptide, the protein tertiary structures are used to position entropic forces of compressed polymer chains comprising the headgroups so as to effectively slow down the subunit desorption rate and enhance the in vivo stability. The resultant monodispersed nanoparticles are composed of subunits, polymer chain with a common protein structure, i.e. coiled-coil helix bundle, and a lipid core, self-assembled nanoparticles have been engineered with tunable stability and disassembly.

  8. Chiral selection of single helix formed by diblock copolymers confined in nanopores.

    Science.gov (United States)

    Deng, Hanlin; Qiang, Yicheng; Zhang, Tingting; Li, Weihua; Yang, Tao

    2016-09-21

    Chiral selection has attracted tremendous attention from the scientific communities, especially from biologists, due to the mysterious origin of homochirality in life. The self-assembly of achiral block copolymers confined in nanopores offers a simple but useful model of forming helical structures, where the helical structures possess random chirality selection, i.e. equal probability of left-handedness and right-handedness. Based on this model, we study the stimulus-response of chiral selection to external conditions by introducing a designed chiral pattern onto the inner surface of a nanopore, aiming to obtain a defect-free helix with controllable homochirality. A cell dynamics simulation based on the time-dependent Ginzburg-Landau theory is carried out to demonstrate the tuning effect of the patterned surface on the chiral selection. Our results illustrate that the chirality of the helix can be successfully controlled to be consistent with that of the tailored surface patterns. This work provides a successful example for the stimulus response of the chiral selection of self-assembled morphologies from achiral macromolecules to external conditions, and hence sheds light on the understanding of the mechanism of the stimulus response. PMID:27536966

  9. Identification of helix capping and {beta}-turn motifs from NMR chemical shifts

    Energy Technology Data Exchange (ETDEWEB)

    Shen Yang; Bax, Ad, E-mail: bax@nih.gov [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)

    2012-03-15

    We present an empirical method for identification of distinct structural motifs in proteins on the basis of experimentally determined backbone and {sup 13}C{sup {beta}} chemical shifts. Elements identified include the N-terminal and C-terminal helix capping motifs and five types of {beta}-turns: I, II, I Prime , II Prime and VIII. Using a database of proteins of known structure, the NMR chemical shifts, together with the PDB-extracted amino acid preference of the helix capping and {beta}-turn motifs are used as input data for training an artificial neural network algorithm, which outputs the statistical probability of finding each motif at any given position in the protein. The trained neural networks, contained in the MICS (motif identification from chemical shifts) program, also provide a confidence level for each of their predictions, and values ranging from ca 0.7-0.9 for the Matthews correlation coefficient of its predictions far exceed those attainable by sequence analysis. MICS is anticipated to be useful both in the conventional NMR structure determination process and for enhancing on-going efforts to determine protein structures solely on the basis of chemical shift information, where it can aid in identifying protein database fragments suitable for use in building such structures.

  10. [Secondary liver lesions studied with double-helix spiral computed tomography: first experience].

    Science.gov (United States)

    Vannucchi, L; Zanfranceschi, G; Simonelli, P; Niccolai, F; Piperno, G

    1996-06-01

    The authors report their early personal experience with double-helix spiral CT (CT Twin Elscint) in the study of liver metastases. This work was aimed at optimizing the study technique and at assessing the diagnostic accuracy of this method. The high temperature developed by CT Twin and the presence of a double row of detectors permit to acquire proper length sequences (with 6.5 mm slice thickness) within a short scanning time which is easy for the patient to tolerate without breathing and moving. Two hundred and thirty patients were examined with US for focal hepatic lesions and then submitted to spiral CT: spatial and density resolution were higher with spiral CT than with US, and the former technique permitted the whole liver to be studied without any partial volume artifacts, which allowed us to confirm all the lesions depicted with US and to detect other lesions, missed at US, in 20% of patients. The choice of the proper time between contrast administration and sequence acquisition is sufficient to permit the detection of focal lesions, if the liver is studied in the portal phase. The authors stress the yield of spiral CT, especially with the double-helix technique, in studying liver metastases. PMID:8830364

  11. Antagonistic regulation of growth and immunity by the Arabidopsis basic helix-loop-helix transcription factor homolog of brassinosteroid enhanced expression2 interacting with increased leaf inclination1 binding bHLH1

    DEFF Research Database (Denmark)

    Malinovsky, Frederikke Gro; Batoux, Martine; Schwessinger, Benjamin;

    2014-01-01

    mechanisms is needed. Here, we identify the basic helix-loop-helix (bHLH) transcription factor homolog of brassinosteroid enhanced expression2 interacting with IBH1 (HBI1) as a negative regulator of PTI signaling in Arabidopsis (Arabidopsis thaliana). HBI1 expression is down-regulated in response to......Plants need to finely balance resources allocated to growth and immunity to achieve optimal fitness. A tradeoff between pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) and brassinosteroid (BR)-mediated growth was recently reported, but more information about the underlying...

  12. Antiviral Activity of Hederasaponin B from Hedera helix against Enterovirus 71 Subgenotypes C3 and C4a.

    Science.gov (United States)

    Song, Jaehyoung; Yeo, Sang-Gu; Hong, Eun-Hye; Lee, Bo-Ra; Kim, Jin-Won; Kim, Jeonghoon; Jeong, Hyeongun; Kwon, Yongsoo; Kim, Hyunpyo; Lee, Sangwon; Park, Jae-Hak; Ko, Hyun-Jeong

    2014-01-01

    Enterovirus 71 (EV71) is the predominant cause of hand, foot and mouth disease (HFMD). The antiviral activity of hederasaponin B from Hedera helix against EV71 subgenotypes C3 and C4a was evaluated in vero cells. In the current study, the antiviral activity of hederasaponin B against EV71 C3 and C4a was determined by cytopathic effect (CPE) reduction method and western blot assay. Our results demonstrated that hederasaponin B and 30% ethanol extract of Hedera helix containing hederasaponin B showed significant antiviral activity against EV71 subgenotypes C3 and C4a by reducing the formation of a visible CPE. Hederasaponin B also inhibited the viral VP2 protein expression, suggesting the inhibition of viral capsid protein synthesis.These results suggest that hederasaponin B and Hedera helix extract containing hederasaponin B can be novel drug candidates with broad-spectrum antiviral activity against various subgenotypes of EV71. PMID:24596620

  13. Spontaneous helix formation in non-chiral bent-core liquid crystals with fast linear electro-optic effect

    Science.gov (United States)

    Sreenilayam, Sithara P.; Panarin, Yuri P.; Vij, Jagdish K.; Panov, Vitaly P.; Lehmann, Anne; Poppe, Marco; Prehm, Marko; Tschierske, Carsten

    2016-05-01

    Liquid crystals (LCs) represent one of the foundations of modern communication and photonic technologies. Present display technologies are based mainly on nematic LCs, which suffer from limited response time for use in active colour sequential displays and limited image grey scale. Herein we report the first observation of a spontaneously formed helix in a polar tilted smectic LC phase (SmC phase) of achiral bent-core (BC) molecules with the axis of helix lying parallel to the layer normal and a pitch much shorter than the optical wavelength. This new phase shows fast (~30 μs) grey-scale switching due to the deformation of the helix by the electric field. Even more importantly, defect-free alignment is easily achieved for the first time for a BC mesogen, thus providing potential use in large-scale devices with fast linear and thresholdless electro-optical response.

  14. Conservation of a helix-stabilizing dipole moment in the PP-fold family of regulatory peptides

    DEFF Research Database (Denmark)

    Bjørnholm, B; Jørgensen, Flemming Steen; Schwartz, T W

    1993-01-01

    arrangement were performed in two ways: (1) by the use of a Poisson-Boltzmann approach which allows for an estimate of the screening effect, and (2) by the use of a uniform dielectric model (Coulomb's law). It is found that the alpha-helix is stabilized by approximately 5-10 kcal/mol due to electrostatic...... directed from the beta-turn region toward the receptor-binding region. This overall dipole moment is antiparallel to the dipole moment of the alpha-helix caused by alignment of the peptide dipoles parallel to the helix. Calculations of the stabilization energy for this antiparallel dipole moment...... forces alone when the screening effect is considered. This energy is of the same order of magnitude as the enthalpy change for the unfolding of avian PP (approximately 30 kcal/mol), strongly indicating that the charge-dipole interactions are of significant importance for the stability of the three...

  15. Structural studies of polypeptides: Mechanism of immunoglobin catalysis and helix propagation in hybrid sequence, disulfide containing peptides

    Energy Technology Data Exchange (ETDEWEB)

    Storrs, R.W.

    1992-08-01

    Catalytic immunoglobin fragments were studied Nuclear Magnetic Resonance spectroscopy to identify amino acid residues responsible for the catalytic activity. Small, hybrid sequence peptides were analyzed for helix propagation following covalent initiation and for activity related to the protein from which the helical sequence was derived. Hydrolysis of p-nitrophenyl carbonates and esters by specific immunoglobins is thought to involve charge complementarity. The pK of the transition state analog P-nitrophenyl phosphate bound to the immunoglobin fragment was determined by {sup 31}P-NMR to verify the juxtaposition of a positively charged amino acid to the binding/catalytic site. Optical studies of immunoglobin mediated photoreversal of cis, syn cyclobutane thymine dimers implicated tryptophan as the photosensitizing chromophore. Research shows the chemical environment of a single tryptophan residue is altered upon binding of the thymine dimer. This tryptophan residue was localized to within 20 {Angstrom} of the binding site through the use of a nitroxide paramagnetic species covalently attached to the thymine dimer. A hybrid sequence peptide was synthesized based on the bee venom peptide apamin in which the helical residues of apamin were replaced with those from the recognition helix of the bacteriophage 434 repressor protein. Oxidation of the disufide bonds occured uniformly in the proper 1-11, 3-15 orientation, stabilizing the 434 sequence in an {alpha}-helix. The glycine residue stopped helix propagation. Helix propagation in 2,2,2-trifluoroethanol mixtures was investigated in a second hybrid sequence peptide using the apamin-derived disulfide scaffold and the S-peptide sequence. The helix-stop signal previously observed was not observed in the NMR NOESY spectrum. Helical connectivities were seen throughout the S-peptide sequence. The apamin/S-peptide hybrid binded to the S-protein (residues 21-166 of ribonuclease A) and reconstituted enzymatic activity.

  16. Structural studies of polypeptides: Mechanism of immunoglobin catalysis and helix propagation in hybrid sequence, disulfide containing peptides

    Energy Technology Data Exchange (ETDEWEB)

    Storrs, R.W.

    1992-08-01

    Catalytic immunoglobin fragments were studied Nuclear Magnetic Resonance spectroscopy to identify amino acid residues responsible for the catalytic activity. Small, hybrid sequence peptides were analyzed for helix propagation following covalent initiation and for activity related to the protein from which the helical sequence was derived. Hydrolysis of p-nitrophenyl carbonates and esters by specific immunoglobins is thought to involve charge complementarity. The pK of the transition state analog P-nitrophenyl phosphate bound to the immunoglobin fragment was determined by [sup 31]P-NMR to verify the juxtaposition of a positively charged amino acid to the binding/catalytic site. Optical studies of immunoglobin mediated photoreversal of cis, syn cyclobutane thymine dimers implicated tryptophan as the photosensitizing chromophore. Research shows the chemical environment of a single tryptophan residue is altered upon binding of the thymine dimer. This tryptophan residue was localized to within 20 [Angstrom] of the binding site through the use of a nitroxide paramagnetic species covalently attached to the thymine dimer. A hybrid sequence peptide was synthesized based on the bee venom peptide apamin in which the helical residues of apamin were replaced with those from the recognition helix of the bacteriophage 434 repressor protein. Oxidation of the disufide bonds occured uniformly in the proper 1-11, 3-15 orientation, stabilizing the 434 sequence in an [alpha]-helix. The glycine residue stopped helix propagation. Helix propagation in 2,2,2-trifluoroethanol mixtures was investigated in a second hybrid sequence peptide using the apamin-derived disulfide scaffold and the S-peptide sequence. The helix-stop signal previously observed was not observed in the NMR NOESY spectrum. Helical connectivities were seen throughout the S-peptide sequence. The apamin/S-peptide hybrid binded to the S-protein (residues 21-166 of ribonuclease A) and reconstituted enzymatic activity.

  17. Antiviral Activity of Hederasaponin B from Hedera helix against Enterovirus 71 Subgenotypes C3 and C4a

    OpenAIRE

    Song, Jaehyoung; Yeo, Sang-Gu; Hong, Eun-Hye; Lee, Bo-Ra; Kim, Jin-Won; Kim, Jeonghoon; Jeong, HyeonGun; Kwon, YongSoo; Kim, HyunPyo; Lee, Sangwon; Park, Jae-Hak; Ko, Hyun-Jeong

    2014-01-01

    Enterovirus 71 (EV71) is the predominant cause of hand, foot and mouth disease (HFMD). The antiviral activity of hederasaponin B from Hedera helix against EV71 subgenotypes C3 and C4a was evaluated in vero cells. In the current study, the antiviral activity of hederasaponin B against EV71 C3 and C4a was determined by cytopathic effect (CPE) reduction method and western blot assay. Our results demonstrated that hederasaponin B and 30% ethanol extract of Hedera helix containing hederasaponin B ...

  18. Experiments on Broadband EMP Radiation with an Axial Mode Helix Antenna

    Institute of Scientific and Technical Information of China (English)

    SUN Qi-Zhi; FANG Dong-Fan; LIU Wei; LIU Zheng-Fen; CHI Yuan; DAI Wen-Feng; HAN Wen-Hui

    2011-01-01

    @@ To produce broadband electromagnetic pulse(EMP)radiation,we design and test a sub-ns pulse system which is utilized to drive an axial mode helix antenna.This sub-ns pulse system consists of a 10-stage Marx generator,an intermediate storage capacitor,an impedance transforming line,and can generate a high voltage of 570kV with a rise time of 1-1.5ns on a 300-Ω-resistance load.The diameter,pitch and turns of the helix antenna are 29 cm,19.5cm and 5,respectively,with a design frequency of 300 MHz.When the charging voltage of the Marx generator is 30kV,the electric field of radiated EMP measured 3m from the source is 35kV/m with a central frequency of 250MHz.The relatively spectral bandwidth is 25%.The radiated EMP results are reproducible and the system will work in repetition mode if the available do power is utilized.%To produce broadband electromagnetic pulse (EMP) radiation, we design and test a sub-ns pulse system which is utilized to drive an axial mode helix antenna. This sub-ns pulse system consists of a 10-stage Marx generator, an intermediate storage capacitor, an impedance transforming line, and can generate a high voltage of 570kV with a rise time of 1-1.5 ns on a 300-Q-resistance load. The diameter, pitch and turns of the hetix antenna are 29 cm, 19.5 cm and 5, respectively, with a design frequency of 300 MHz. When the charging voltage of the Marx generator is 30 kV, the electric field of radiated EMP measured 3m from the source is 35kV/m with a central frequency of 250 MHz. The relatively spectra] bandwidth is 25%. The radiated EMP results are reproducible and the system will work in repetition mode if the available dc power is utilized.

  19. Structure and dynamics of the pore-lining helix of the nicotinic receptor : MD simulations in water, lipid bilayers, and transbilayer bundles

    NARCIS (Netherlands)

    Law, RJ; Forrest, LR; Ranatunga, KM; La Rocca, P; Tieleman, DP; Sansom, MSP

    2000-01-01

    Multiple nanosecond duration molecular dynamics simulations on the pore-lining M2 helix of the nicotinic acetylcholine receptor reveal how its structure and dynamics change as a function of environment. In water, the M2 helix partially unfolds to form a molecular hinge in the vicinity of a central L

  20. Conformational flexibility of PPII-helix: A density functional theory study

    Science.gov (United States)

    Guo, Ping; Lei, Xiaoling; Gao, Yi

    2016-05-01

    Poly-proline fragments form the distinctive PPII-helix in a high percentage in proteins and peptides, which plays an important role in signal transduction and protein complex assembly. But why and how this helical structure works is still unknown. In this work, we applied the density functional calculations to investigate the different preferences of prolines on Cγ-endo and Cγ-exo conformers, in which non-covalent interactions play important roles. As a result, Cγ-exo conformers are favored for short-oligomers with stronger n → π* interaction formed by the backbone, while Cγ-endo conformers are favored for longer oligomers with stronger dipole interactions between side groups.

  1. Current-voltage characteristics of seven-helix proteins from a cubic array of amino acids

    Science.gov (United States)

    Alfinito, Eleonora; Reggiani, Lino

    2016-06-01

    The electrical properties of a set of seven-helix transmembrane proteins, whose space arrangement [three-dimensional (3D) structure] is known, are investigated by using regular arrays of the amino acids. These structures, specifically cubes, have topological features similar to those shown by the chosen proteins. The theoretical results show a good agreement between the predicted current-voltage characteristics obtained from a cubic array and those obtained from a detailed 3D structure. The agreement is confirmed by available experiments on bacteriorhodopsin. Furthermore, all the analyzed proteins are found to share the same critical behavior of the voltage-dependent conductance and of its variance. In particular, the cubic arrangement evidences a short plateau of the excess conductance and its variance at high voltages. The results of the present investigation show the possibility to predict the I -V characteristics of a multiple-protein sample even in the absence of detailed knowledge of the proteins' 3D structure.

  2. Postembryonic neurogenesis in the procerebrum of the terrestrial snail, Helix lucorum L

    Science.gov (United States)

    Zakharov, I. S.; Hayes, N. L.; Ierusalimsky, V. N.; Nowakowski, R. S.; Balaban, P. M.

    1998-01-01

    Neuronogenesis during posthatching development of the procerebrum of the terrestrial snail Helix lucorum was analyzed using bromodeoxyuridine immunohistochemistry to label proliferating cells. Comparison of the distribution of labeled cells in a series of animals which differed in age at the time of incubation with bromodeoxyuridine, in survival time after incubation, and in age at sacrifice reveals a clear pattern and developmental sequence in neuron origin. First, the proliferating cells are located only at the apical portion of the procerebrum. Second, cells which are produced at any particular age remain, for the most part, confined to a single layer in the procerebrum. Third, as development proceeds, each layer of previously produced neurons is displaced toward the basal part of the procerebrum by the production of additional neurons. Our results suggest that the vast majority of the neurons (probably about 70-80%) of the snail procerebrum are produced during the first 1-2 months of posthatching development.

  3. Phenolic Compounds and Antifungal Activity of Hedera helix L. (Ivy Flowers and Fruits

    Directory of Open Access Journals (Sweden)

    Marcel PARVU

    2015-04-01

    Full Text Available Identification and quantitative analysis of the phenolic compounds from Hedera helix L. (ivy flower and fruit ethanol extracts by LC/MS, in vitro germination and growth inhibition effects on Aspergillus niger, Botrytis cinerea, Fusarium oxysporum f.sp. tulipae, Penicillium gladioli and Sclerotinia sclerotiorum were performed. In the non-hydrolyzed samples of flower and fruit extracts were determined, in different amounts, five polyphenols (p-coumaric acid, ferulic acid, rutoside, quercetol and kaempferol while quercitrin was identified only in the ivy flower extract. The hydrolyzed samples of the same ivy extracts indicated four phenolic compounds (p-coumaric acid, ferulic acid, quercetol and kaempferol, in different concentrations, whereas sinapic acid was only detected in the ivy fruit extract. The antifungal activity of the fresh flower extract was stronger than that of the fresh fruit extract and was compared to that of an antimycotic drug.

  4. Stomatal Responses to Light and Drought Stress in Variegated Leaves of Hedera helix1

    Science.gov (United States)

    Aphalo, Pedro J.; Sánchez, Rodolfo A.

    1986-01-01

    Direct and indirect mechanisms underlying the light response of stomata were studied in variegated leaves of the juvenile phase of Hedera helix L. Dose response curves of leaf conductance were measured with blue and red light in leaves kept in normal or in an inverted position. In the green portions of the leaves, the sensitivity to blue light was nearly 100 times higher than that to red light. No response to red light was observed in the white portions of the leaves up to 90 micromoles per square meter per second. Red light indirectly affected leaf conductance while blue light had a direct effect. Leaf conductance was found to be more sensitive to drought stress and showed a more persistent aftereffect in the white portions of the leaves. A differential effect of drought stress on the responses to blue and red light was also observed. PMID:16664900

  5. Yang-Lee zeros for a Potts model of helix-coil transition with nontrivial topology

    International Nuclear Information System (INIS)

    The Yang-Lee partition function zeros of the Q-state Potts model on a zigzag ladder are studied by a transfer-matrix approach. This Q-state model has a non-trivial topology induced by three-site interactions on a zigzag ladder and is proposed as a description of helix-coil transition in homo-polymers. The Yang-Lee zeros are associated to complex values of the solvent-related coupling constant K (magnetic field) and they are exactly derived for arbitrary values of the system parameters: Q, J (coupling constant of hydrogen binding) and temperature. It is shown that there is only a quasi-phase transition for all temperatures. The densities of the Yang-Lee zeros are singular at the edge singularity points and the critical exponent σ = -1/2. (author)

  6. Non-dipole interaction of helix inclusions in metamaterials with artificial permeability

    Science.gov (United States)

    Starostenko, Sergey N.; Rozanov, Konstantin N.

    2015-06-01

    An analytic approach to calculate induced permeability of metamaterial filled with helix inclusions is developed. For an electrically small coil, the dynamic magnetization is determined by lumped inductance, capacitance, and resistance that are calculated from the coil design. The susceptibility of a coil is shown to be close to that of diamagnetic ellipsoid of the same elongation. Contrary to permeable particles in a composite, the coils screen each other thus decreasing the magnetic response of metamaterial compared to total response of comprised coils. The filling effect on magnetic spectrum of metamaterial is analyzed and verified by measurements for the case of identical coaxially placed coreless coils. The critical filling where magnetic response of metamaterial is maximal depends on coil shape and resistance. The coil-filled metamaterials may find applications as permeable EMI suppressors or microwave absorbers free of Snoek or Acher limitations on the high-frequency permeability, as well as of Curie limitation on the high-temperature magnetic performance.

  7. The double helix revisited: a paradox of science and a paradigm of human behaviour

    Directory of Open Access Journals (Sweden)

    Argüelles, Juan Carlos

    2007-06-01

    Full Text Available In the modern history of Science, few breakthroughs have caused an impact comparative to the Double Helix, the three-dimensional structure of DNA proposed by Watson & Crick in 1953, an event whose 50th anniversary was widely celebrated in the non-specialist media, three years ago. Although the discovery had little transcendence at the time, it has unquestionably been of great importance ever since. The Double Helix has underlined the true biological value of nucleic acids compared with proteins, demonstrating that genes are not amorphous entities but have a specific chemical composition and adopt an ordered spatial folding pattern. Elucidation of this key configuration made it possible to establish a direct relationship between the structure and the function of macromolecules, a relationship which is not so clear in the case of proteins. During these last fifty years much has been written and argued about the circumstances surrounding the discovery and about the behaviour and attitudes of many of the protagonists. Besides Watson & Crick, other scientists, whose contribution has not been adequately recognised, played an important part in solving the Double Helix mystery. This article contains some ethical and scientific reflections which revise some of these essential contributions and throws light on the role played in history by these comparatively «unknown soldiers» of science. The Double Helix story is undoubtedly a manifestation of the human side of science and many scientists believe that the available evidence taken as a whole permits an alternative story to be written.

    En la desarrollo histórico de la Ciencia moderna, pocos descubrimientos han causado un impacto comparativo a las repercusiones de la Doble Hélice, la estructura tridimensional del ADN, propuesta por Watson y Crick en 1953. El 50º aniversario de aquel evento fue ampliamente celebrado hace tres años, incluso por los medios no especializados en informaci

  8. The effect of cooling on the acetylcholine-induced current of identified Helix pomatia Br neuron.

    Science.gov (United States)

    Nedeljkovic, Miodrag; Kartelija, Gordana; Radenovic, Lidija; Todorovic, Natasa

    2005-05-01

    The Br neuron of the snail Helix pomatia, involved in neuronal regulation of various homeostatic and adaptive mechanisms, represents an interesting model for studying effects of temperature changes on neuronal activity of poikilotherms. The acetylcholine (ACh) induces a transient, inward dose-dependent current in the identified Br neuron. In the work presented, we analyses the effects of cooling on the ACh-induced inward current. The amplitude of ACh-induced inward current was markedly decreased after cooling and the speed of the decay of ACh response was decreased. Sensitivity to cooling of Ach-activated current on the Br neuron is mediated by a mechanism that does not involve change in the apparent receptor affinity or the cooperativity of binding. PMID:15759140

  9. The Mutual Information of University-Industry-Government Relations: An Indicator of the Triple Helix Dynamics

    CERN Document Server

    Leydesdorff, Loet

    2009-01-01

    University-industry-government relations provide a networked infrastructure for knowledge-based innovation systems. This infrastructure organizes the dynamic fluxes locally and the knowledge base remains emergent given these conditions. Whereas the relations between the institutions can be measured as variables, the interacting fluxes generate a probabilistic entropy. The mutual information among the three institutional dimensions provides us with an indicator of this entropy. When this indicator is negative, self-organization can be expected. The self-organizing dynamic may temporarily be stabilized in the overlay of communications among the carrying agencies. The various dynamics of Triple Helix relations at the global and national levels, in different databases, and in different regions of the world, are distinguished by applying this indicator to scientometric and webometric data.

  10. The high radial velocity of an outer filament of the Helix nebula (NGC 7293)

    International Nuclear Information System (INIS)

    An echelle spectrography was used to obtain a series of long-slit high-resolution line profiles of Hα and [NII] from the centre of the Helix nebula (NGC 7293) to the filament 11 arcmin east. This filament shows a blue-shifted velocity of about 50 km s-1 with respect to the nebula velocity, i.e. larger than the approximately 25 km s-1 expansion of the bright helical ring. It is suggested that this feature may be part of a radially expanding ellipsoidal shell whose long axis is inclined towards the line-of-sight. Possible mechanisms for the formation of such a high-velocity feature are discussed. (author)

  11. [The "condensation" and "ligand" theory in describing DNA helix-coil transition: comparative analysis].

    Science.gov (United States)

    Sorokin, V A; Gladchenko, G O; Galkin, V L; Volchok, I V; Blagoĭ, Iu P

    1996-01-01

    Experimental data on DNA melting in the presence of magnesium and calcium ions are compared with the calculated results by the "ligand" theory and "condensation" theory developed by de Marky and Manning (TMM). The maximum is observed in TMM dependences of DNA melting temperature change (delta Tm) on the ion concentration (D), absent in the experimental dependences and the "ligand" theory. The main cause of the discrepancy of calculated and experimental dependences delta Tm (D) is the fact that TMM neglects Na+ ion effects on Me2+ ion binding ("condensation") to DNA. The results obtained show that in comparison with TMM the "ligand" theory describes more adequately DNA helix-coil transition in the presence of divalent metal ions in the region of both low and high ionic strengths of solution. PMID:9044618

  12. Solvent-Exposed Salt Bridges Influence the Kinetics of α-Helix Folding and Unfolding.

    Science.gov (United States)

    Meuzelaar, Heleen; Tros, Martijn; Huerta-Viga, Adriana; van Dijk, Chris N; Vreede, Jocelyne; Woutersen, Sander

    2014-03-01

    Salt bridges are known to play an essential role in the thermodynamic stability of the folded conformation of many proteins, but their influence on the kinetics of folding remains largely unknown. Here, we investigate the effect of Glu-Arg salt bridges on the kinetics of α-helix folding using temperature-jump transient-infrared spectroscopy and steady-state UV circular dichroism. We find that geometrically optimized salt bridges (Glu(-) and Arg(+) are spaced four peptide units apart, and the Glu/Arg order is such that the side-chain rotameric preferences favor salt-bridge formation) significantly speed up folding and slow down unfolding, whereas salt bridges with unfavorable geometry slow down folding and slightly speed up unfolding. Our observations suggest a possible explanation for the surprising fact that many biologically active proteins contain salt bridges that do not stabilize the native conformation: these salt bridges might have a kinetic rather than a thermodynamic function. PMID:24634715

  13. Time-resolved two-dimensional vibrational spectroscopy of a short α-helix in water

    Science.gov (United States)

    Woutersen, Sander; Hamm, Peter

    2001-10-01

    Nonlinear two-dimensional (2D) vibrational spectroscopy has been used to investigate the amide I band of an alanine-based 21-residue α-helical peptide in aqueous solution. Whereas the linear absorption spectrum consists of a single, broad amide I band, the 2D vibrational spectrum clearly reveals that this band is composed of two amide I transitions, which are assigned to the A and E1 modes. The A-E1 frequency splitting is found to be approximately 10 cm-1. We find that the amide I band is inhomogeneously broadened due to conformational disorder of the helix. The 2D line shapes can be well described using distributions of the dihedral angles (φ,ψ) around their average values with a width of 20°, confirming previous molecular-dynamics studies. Time-resolved 2D measurements show that the conformation fluctuates on a time scale of picoseconds.

  14. A cosmic double helix in the archetypical quasar 3C273.

    Science.gov (United States)

    Lobanov, A P; Zensus, J A

    2001-10-01

    Finding direct evidence for plasma instability in extragalactic jets is crucial for understanding the nature of relativistic outflows from active galactic nuclei. Our radio interferometric observations of the quasar 3C273 made with the orbiting radio telescope, HALCA, and an array of ground telescopes have yielded an image in which the emission across the jet is resolved, revealing two threadlike patterns that form a double helix inside the jet. This double helical structure is consistent with a Kelvin-Helmholtz instability, and at least five different instability modes can be identified and modeled by a light jet with a Lorentz factor of 2 and Mach number of 3.5. The model reproduces in detail the internal structure of the jet on scales of up to 30 milli-arc seconds ( approximately 300 parsecs) and is consistent with the general morphology of the jet on scales of up to 1 kiloparsec. PMID:11588254

  15. Synthetic Aperture Focusing for a Single Element Transducer undergoing Helix Motion

    DEFF Research Database (Denmark)

    Andresen, Henrik; Nikolov, Svetoslav Ivanov; Jensen, Jørgen Arendt

    2011-01-01

    This paper describes the application of 3D synthetic aperture focusing (SAF) to a single element trans-rectal ultrasound transducer. The transducer samples a 3D volume by simultaneous rotation and translation giving a helix motion. Two different 3D SAF methods are investigated, a direct and a two......-step approach. Both methods perform almost identical for simulated scatterers and give a significant improvement in azimuth resolution and a constant resolution in elevation. Sidelobes below -60 dB is achievable for both methods. Validation of the method is achieved by scanning a simple wire phantom and a...... complex phantom containing wires in azimuth and elevation. The simple wire phantom shows the same results as that found through simulation. The complex phantom shows simultaneous focusing in azimuth and elevation for the wire scatterers. Considerations on processing requirements for both 3D SAF methods...

  16. Bridge helix bending promotes RNA polymerase II backtracking through a critical and conserved threonine residue

    KAUST Repository

    Da, Lin-Tai

    2016-04-19

    The dynamics of the RNA polymerase II (Pol II) backtracking process is poorly understood. We built a Markov State Model from extensive molecular dynamics simulations to identify metastable intermediate states and the dynamics of backtracking at atomistic detail. Our results reveal that Pol II backtracking occurs in a stepwise mode where two intermediate states are involved. We find that the continuous bending motion of the Bridge helix (BH) serves as a critical checkpoint, using the highly conserved BH residue T831 as a sensing probe for the 3′-terminal base paring of RNA:DNA hybrid. If the base pair is mismatched, BH bending can promote the RNA 3′-end nucleotide into a frayed state that further leads to the backtracked state. These computational observations are validated by site-directed mutagenesis and transcript cleavage assays, and provide insights into the key factors that regulate the preferences of the backward translocation.

  17. From keys to bulldozers: expanding roles for winged helix domains in nucleic-acid-binding proteins.

    Science.gov (United States)

    Harami, Gábor M; Gyimesi, Máté; Kovács, Mihály

    2013-07-01

    The winged helix domain (WHD) is a widespread nucleic-acid-binding protein structural element found in all kingdoms of life. Although the overall structure of the WHD is conserved, its functional properties and interaction profiles are extremely versatile. WHD-containing proteins can exploit nearly the full spectrum of nucleic acid structural features for recognition and even covalent modification or noncovalent rearrangement of target molecules. WHD functions range from sequence-recognizing keys in transcription factors and bulldozer-like strand-separating wedges in helicases to mediators of protein-protein interactions (PPIs). Further investigations are needed to understand the contribution of WHD structural dynamics to nucleic-acid-modifying enzymatic functions. PMID:23768997

  18. Immobilization of the N-terminal helix stabilizes prefusion paramyxovirus fusion proteins.

    Science.gov (United States)

    Song, Albert S; Poor, Taylor A; Abriata, Luciano A; Jardetzky, Theodore S; Dal Peraro, Matteo; Lamb, Robert A

    2016-07-01

    Parainfluenza virus 5 (PIV5) is an enveloped, single-stranded, negative-sense RNA virus of the Paramyxoviridae family. PIV5 fusion and entry are mediated by the coordinated action of the receptor-binding protein, hemagglutinin-neuraminidase (HN), and the fusion protein (F). Upon triggering by HN, F undergoes an irreversible ATP- and pH-independent conformational change, going down an energy gradient from a metastable prefusion state to a highly stable postfusion state. Previous studies have highlighted key conformational changes in the F-protein refolding pathway, but a detailed understanding of prefusion F-protein metastability remains elusive. Here, using two previously described F-protein mutations (S443D or P22L), we examine the capacity to modulate PIV5 F stability and the mechanisms by which these point mutants act. The S443D mutation destabilizes prefusion F proteins by disrupting a hydrogen bond network at the base of the F-protein globular head. The introduction of a P22L mutation robustly rescues destabilized F proteins through a local hydrophobic interaction between the N-terminal helix and a hydrophobic pocket. Prefusion stabilization conferred by a P22L-homologous mutation is demonstrated in the F protein of Newcastle disease virus, a paramyxovirus of a different genus, suggesting a conserved stabilizing structural element within the paramyxovirus family. Taken together, the available data suggest that movement of the N-terminal helix is a necessary early step for paramyxovirus F-protein refolding and presents a novel target for structure-based drug design. PMID:27335462

  19. Aptamer contained triple-helix molecular switch for rapid fluorescent sensing of acetamiprid.

    Science.gov (United States)

    Liu, Xin; Li, Ying; Liang, Jing; Zhu, Wenyue; Xu, Jingyue; Su, Ruifang; Yuan, Lei; Sun, Chunyan

    2016-11-01

    In this study, an aptamer-based fluorescent sensing platform using triple-helix molecular switch (THMS) was developed for the pesticide screening represented by acetamiprid. The THMS was composed of two tailored DNA probes: a label-free central target specific aptamer sequence flanked by two arm segments acting as a recognition probe; a hairpin-shaped structure oligonucleotide serving as a signal transduction probe (STP), labeled with a fluorophore and a quencher at the 3' and 5'-end, respectively. In the absence of acetamiprid, complementary bindings of two arm segments of the aptamers with the loop sequence of STP enforce the formation of THMS with the "open" configuration of STP, and the fluorescence of THMS is on. In the presence of target acetamiprid, the aptamer-target binding results in the formation of a structured aptamer/target complex, which disassembles the THMS and releases the STP. The free STP is folded to a stem loop structure, and the fluorescence is quenched. The quenched fluorescence intensity was proportional to the concentration of acetamiprid in the range from 100 to 1200nM, with the limit of detection (LOD) as low as 9.12nM. In addition, this THMS-based method has been successfully used to test and quantify acetamiprid in Chinese cabbage with satisfactory recoveries, and the results were in full agreement with those from LC-MS. The aptamer-based THMS presents distinct advantages, including high stability, remarkable sensitivity, and preservation of the affinity and specificity of the original aptamer. Most importantly, this strategy is convenient and generalizable by virtue of altering the aptamer sequence without changing the triple-helix structure. So, it is expected that this aptamer-based fluorescent assay could be extensively applied in the field of food safety inspection. PMID:27591592

  20. Innovative Development of Kazakhstan on The Basis of Triple Helix and Cluster Approach

    Directory of Open Access Journals (Sweden)

    Farkhat Musayevich Dnishev

    2015-06-01

    Full Text Available The aim of the research is to study the Triple Helix model feasibility in developing innovations and using cluster approach in Kazakhstan. There are possible points of the emergence of clusters in Kazakhstan. However, there are a lot of constraining factors. First of all, institutional and social factors: the culture of business, unfair competition, low trust of economic agents to each other and to power institutes, low psychological readiness for cooperation of the enterprises of various branches and regions, poor development of chambers of commerce, and industrial associations. For the time being, the majority of regions of Kazakhstan are characterized by a limited set of high technology industrial branches, and a sharp shortage of universities generating innovation and research institutes. The research results show that the open innovation model is realized in a limited scale that does not allow to export innovations into external markets, to participate in global technology chains and international research networks. At the same time, some interaction schemes and preconditions for the development of the Triple Helix model are emerging. However, in general, the innovation policy is not systemic; it does not unite actions in the sphere of science and technology, education, industry, and regional initiatives. As the result of the research, some policy implications are given. For the development of clusters in Kazakhstan, it is desirable to use such a way, as integration into global cluster networks. It is necessary to make use of foreign experience at which various specialized state agencies become participants of clusters. It is necessary to focus not only on science but also industry, which should play the central role in the innovation process.

  1. A novel slotted helix slow-wave structure for high power Ka-band traveling-wave tubes

    International Nuclear Information System (INIS)

    A novel slotted helix slow-wave structure (SWS) is proposed to develop a high power, wide-bandwidth, and high reliability millimeter-wave traveling-wave tube (TWT). This novel structure, which has higher heat capacity than a conventional helix SWS, evolves from conventional helix SWS with three parallel rows of rectangular slots made in the outside of the helix tape. In this paper, the electromagnetic characteristics and the beam-wave interaction of this novel structure operating in the Ka-band are investigated. From our calculations, when the designed beam voltage and beam current are set to be 18.45 kV and 0.2 A, respectively, this novel circuit can produce over 700-W average output power in a frequency range from 27.5 GHz to 32.5 GHz, and the corresponding conversion efficiency values vary from 19% to 21.3%, and the maximum output power is 787 W at 30 GHz. (interdisciplinary physics and related areas of science and technology)

  2. Temperature, salinity and transmissivity data from the Alpha Helix in the Arctic Ocean, 2000 - 2004 (NODC Accession 0059005)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This is calibrated CTD downcast data from five Alpha Helix cruises: HX235, 8/1/2000 - 9/30/2000 HX250, 9/1/2001 - 9/30/2001 HX260, 6/1/2002 - 6/30/2002 HX274,...

  3. A simulation model of the Triple Helix of university-industry-government relations and the decomposition of the redundancy

    NARCIS (Netherlands)

    I.A. Ivanova; L. Leydesdorff

    2014-01-01

    A Triple Helix (TH) network of bi- and trilateral relations among universities, industries, and governments can be considered as an ecosystem in which uncertainty can be reduced when functions become synergetic. The functions are based on correlations among distributions of relations, and therefore

  4. Self-assembled RNA-triple-helix hydrogel scaffold for microRNA modulation in the tumour microenvironment

    Science.gov (United States)

    Conde, João; Oliva, Nuria; Atilano, Mariana; Song, Hyun Seok; Artzi, Natalie

    2016-03-01

    The therapeutic potential of miRNA (miR) in cancer is limited by the lack of efficient delivery vehicles. Here, we show that a self-assembled dual-colour RNA-triple-helix structure comprising two miRNAs--a miR mimic (tumour suppressor miRNA) and an antagomiR (oncomiR inhibitor)--provides outstanding capability to synergistically abrogate tumours. Conjugation of RNA triple helices to dendrimers allows the formation of stable triplex nanoparticles, which form an RNA-triple-helix adhesive scaffold upon interaction with dextran aldehyde, the latter able to chemically interact and adhere to natural tissue amines in the tumour. We also show that the self-assembled RNA-triple-helix conjugates remain functional in vitro and in vivo, and that they lead to nearly 90% levels of tumour shrinkage two weeks post-gel implantation in a triple-negative breast cancer mouse model. Our findings suggest that the RNA-triple-helix hydrogels can be used as an efficient anticancer platform to locally modulate the expression of endogenous miRs in cancer.

  5. CBR antimicrobials inhibit RNA polymerase via at least two bridge-helix cap-mediated effects on nucleotide addition

    Energy Technology Data Exchange (ETDEWEB)

    Bae, Brian [Rockefeller Univ., New York, NY (United States); Nayak, Dhananjaya [Univ. of Wisconsin, Madison, WI (United States); Ray, Ananya [Univ. of Wisconsin, Madison, WI (United States); Mustaev, Arkady [New Jersey Medical School, Newark, NJ (United States); Landick, Robert [Univ. of Wisconsin, Madison, WI (United States); Darst, Seth A. [Rockefeller Univ., New York, NY (United States)

    2015-07-20

    RNA polymerase inhibitors like the CBR class that target the enzyme’s complex catalytic center are attractive leads for new antimicrobials. The catalysis by RNA polymerase involves multiple rearrangements of bridge helix, trigger loop, and active-center side chains that isomerize the triphosphate of bound NTP and two Mg2+ ions from a preinsertion state to a reactive configuration. CBR inhibitors target a crevice between the N-terminal portion of the bridge helix and a surrounding cap region within which the bridge helix is thought to rearrange during the nucleotide addition cycle. Here, we report crystal structures of CBR inhibitor/Escherichia coli RNA polymerase complexes as well as biochemical tests that establish two distinct effects of the inhibitors on the RNA polymerase catalytic site. One effect involves inhibition of trigger-loop folding via the F loop in the cap, which affects both nucleotide addition and hydrolysis of 3'-terminal dinucleotides in certain backtracked complexes. The second effect is trigger-loop independent, affects only nucleotide addition and pyrophosphorolysis, and may involve inhibition of bridge-helix movements that facilitate reactive triphosphate alignment.

  6. MOLECULAR-DYNAMICS SIMULATION OF THE STABILITY OF A 22-RESIDUE ALPHA-HELIX IN WATER AND 30-PERCENT TRIFLUOROETHANOL

    NARCIS (Netherlands)

    VANBUUREN, AR; BERENDSEN, HJC

    1993-01-01

    A molecular dynamics (MD) simulation was performed on the alpha-helix H8-HC5, the C-terminal part of myoglobin (residue 132-153), under periodic boundary conditions in two different solutions, water and water with 30% (v/v) 2,2,2-trifluoroethanol (TFE), at 300 K to investigate the stability of the h

  7. Basic Tilted Helix Bundle – A new protein fold in human FKBP25/FKBP3 and HectD1

    International Nuclear Information System (INIS)

    Highlights: • We describe the structure of a novel fold in FKBP25 and HectD. • The new fold is named the Basic Tilted Helix Bundle (BTHB) domain. • A conserved basic surface patch is presented, suggesting a functional role. - Abstract: In this paper, we describe the structure of a N-terminal domain motif in nuclear-localized FKBP251–73, a member of the FKBP family, together with the structure of a sequence-related subdomain of the E3 ubiquitin ligase HectD1 that we show belongs to the same fold. This motif adopts a compact 5-helix bundle which we name the Basic Tilted Helix Bundle (BTHB) domain. A positively charged surface patch, structurally centered around the tilted helix H4, is present in both FKBP25 and HectD1 and is conserved in both proteins, suggesting a conserved functional role. We provide detailed comparative analysis of the structures of the two proteins and their sequence similarities, and analysis of the interaction of the proposed FKBP25 binding protein YY1. We suggest that the basic motif in BTHB is involved in the observed DNA binding of FKBP25, and that the function of this domain can be affected by regulatory YY1 binding and/or interactions with adjacent domains

  8. Basic Tilted Helix Bundle – A new protein fold in human FKBP25/FKBP3 and HectD1

    Energy Technology Data Exchange (ETDEWEB)

    Helander, Sara; Montecchio, Meri [Department of Physics, Chemistry and Biology, Division of Chemistry, Linköping University, SE-58183 Linköping (Sweden); Lemak, Alexander [Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7 (Canada); Northeast Structural Genomics Consortium, Toronto, Ontario (Canada); Farès, Christophe [Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7 (Canada); Almlöf, Jonas [Department of Physics, Chemistry and Biology, Division of Chemistry, Linköping University, SE-58183 Linköping (Sweden); Li, Yanjun [Structural Genomics Consortium, University of Toronto, 101 College St, Toronto, Ontario M5G 1L7 (Canada); Yee, Adelinda [Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7 (Canada); Northeast Structural Genomics Consortium, Toronto, Ontario (Canada); Arrowsmith, Cheryl H. [Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7 (Canada); Northeast Structural Genomics Consortium, Toronto, Ontario (Canada); Structural Genomics Consortium, University of Toronto, 101 College St, Toronto, Ontario M5G 1L7 (Canada); Dhe-Paganon, Sirano [Structural Genomics Consortium, University of Toronto, 101 College St, Toronto, Ontario M5G 1L7 (Canada); Sunnerhagen, Maria, E-mail: maria.sunnerhagen@liu.se [Department of Physics, Chemistry and Biology, Division of Chemistry, Linköping University, SE-58183 Linköping (Sweden)

    2014-04-25

    Highlights: • We describe the structure of a novel fold in FKBP25 and HectD. • The new fold is named the Basic Tilted Helix Bundle (BTHB) domain. • A conserved basic surface patch is presented, suggesting a functional role. - Abstract: In this paper, we describe the structure of a N-terminal domain motif in nuclear-localized FKBP25{sub 1–73}, a member of the FKBP family, together with the structure of a sequence-related subdomain of the E3 ubiquitin ligase HectD1 that we show belongs to the same fold. This motif adopts a compact 5-helix bundle which we name the Basic Tilted Helix Bundle (BTHB) domain. A positively charged surface patch, structurally centered around the tilted helix H4, is present in both FKBP25 and HectD1 and is conserved in both proteins, suggesting a conserved functional role. We provide detailed comparative analysis of the structures of the two proteins and their sequence similarities, and analysis of the interaction of the proposed FKBP25 binding protein YY1. We suggest that the basic motif in BTHB is involved in the observed DNA binding of FKBP25, and that the function of this domain can be affected by regulatory YY1 binding and/or interactions with adjacent domains.

  9. Modulating immunogenic properties of HIV-1 gp41 membrane-proximal external region by destabilizing six-helix bundle structure.

    Science.gov (United States)

    Banerjee, Saikat; Shi, Heliang; Habte, Habtom H; Qin, Yali; Cho, Michael W

    2016-03-01

    The C-terminal alpha-helix of gp41 membrane-proximal external region (MPER; (671)NWFDITNWLWYIK(683)) encompassing 4E10/10E8 epitopes is an attractive target for HIV-1 vaccine development. We previously reported that gp41-HR1-54Q, a trimeric protein comprised of the MPER in the context of a stable six-helix bundle (6HB), induced strong immune responses against the helix, but antibodies were directed primarily against the non-neutralizing face of the helix. To better target 4E10/10E8 epitopes, we generated four putative fusion intermediates by introducing double point mutations or deletions in the heptad repeat region 1 (HR1) that destabilize 6HB in varying degrees. One variant, HR1-∆10-54K, elicited antibodies in rabbits that targeted W672, I675 and L679, which are critical for 4E10/10E8 recognition. Overall, the results demonstrated that altering structural parameters of 6HB can influence immunogenic properties of the MPER and antibody targeting. Further exploration of this strategy could allow development of immunogens that could lead to induction of 4E10/10E8-like antibodies. PMID:26803471

  10. A Triple Helix Strategy for Promoting SME Development: The Case of a Dried Banana Community Enterprise in Thailand

    Science.gov (United States)

    Yuwawutto, Sauwapa; Smitinont, Thitapha; Charoenanong, Numtip; Yokakul, Nattaka; Chatratana, Sonchai; Zawdie, Girma

    2010-01-01

    This paper examines the university-industry-government relationship as a mechanism for enhancing the efficiency and competitiveness of small and medium-sized enterprises (SMEs). The case of a community enterprise producing dried banana products in the north of Thailand is used to demonstrate the significance of the Triple Helix model for business…

  11. Measurement of the second-order hyperpolarizability of the collagen triple helix and determination of its physical origin.

    Science.gov (United States)

    Deniset-Besseau, Ariane; Duboisset, Julien; Benichou, Emmanuel; Hache, François; Brevet, Pierre-François; Schanne-Klein, Marie-Claire

    2009-10-01

    We performed Hyper-Rayleigh Scattering (HRS) experiments to measure the second-order nonlinear optical response of the collagen triple helix and determine the physical origin of second harmonic signals observed in collagenous tissues. HRS experiments yielded a second-order hyperpolarizability of 1.25 x 10(-27) esu for rat-tail type I collagen, a surprisingly large value considering that collagen presents no strong harmonophore in its amino acid sequence. Polarization-resolved experiments showed intramolecular coherent contributions to the HRS signal along with incoherent contributions that are the only contributions for molecules with dimensions much smaller than the excitation wavelength. We therefore modeled the effective second-order hyperpolarizability of the 290 nm long collagen triple helix by summing coherently the nonlinear response of well-aligned moieties along the triple helix axis. This model was confirmed by HRS measurements after denaturation of the collagen triple helix and for a collagen-like short model peptide [(Pro-Pro-Gly)(10)](3). We concluded that the large collagen nonlinear response originates in the tight alignment of a large number of small and weakly efficient harmonophores, presumably the peptide bonds, resulting in a coherent amplification of the nonlinear signal. PMID:19754079

  12. Hierarchical self-assembly of designed 2x2-alpha-helix bundle proteins on Au(111) surfaces

    DEFF Research Database (Denmark)

    Wackerbarth, Hainer; Tofteng, A.P.; Jensen, K.J.;

    2006-01-01

    Self-assembled monolayers of biomolecules on atomically planar surfaces offer the prospect of complex combinations of controlled properties, e. g., for bioelectronics. We have prepared a novel hemi-4-alpha-helix bundle protein by attaching two alpha-helical peptides to a cyclo-dithiothreitol (cyclo......-DTT) template. The protein was de novo designed to self-assemble in solution to form a 4-alpha-helix bundle, whereas the disulfide moiety enables the formation of a self-assembled monolayer on a Au(111) surface by opening of the disulfide, thus giving rise to a two-step self-assembly process. The 2 x 2-alpha......, respectively. The 2 x 2-alpha-helix bundle protein adlayers were imaged by in situ STM. The images indicated a dense monolayer according with the voltammetric data. No long-range order could be detected, but two clearly distinct STM contrasts were assigned to 2 x 2-alpha-helix bundle protein molecules oriented...

  13. Solvent effects in the helix-coil transition model can explain the unusual biophysics of intrinsically disordered proteins

    Science.gov (United States)

    Badasyan, Artem; Mamasakhlisov, Yevgeni Sh.; Podgornik, Rudolf; Parsegian, V. Adrian

    2015-07-01

    We analyze a model statistical description of the polypeptide chain helix-coil transition, where we take into account the specificity of its primary sequence, as quantified by the phase space volume ratio of the number of all accessible states to the number corresponding to a helical conformation. The resulting transition phase diagram is then juxtaposed with the unusual behavior of the secondary structures in Intrinsically Disordered Proteins (IDPs) and a number of similarities are observed, even if the protein folding is a more complex transition than the helix-coil transition. In fact, the deficit in bulky and hydrophobic amino acids observed in IDPs, translated into larger values of phase space volume, allows us to locate the region in parameter space of the helix-coil transition that would correspond to the secondary structure transformations that are intrinsic to conformational transitions in IDPs and that is characterized by a modified phase diagram when compared to globular proteins. Here, we argue how the nature of this modified phase diagram, obtained from a model of the helix-coil transition in a solvent, would illuminate the turned-out response of IDPs to the changes in the environment conditions that follow straightforwardly from the re-entrant (cold denaturation) branch in their folding phase diagram.

  14. The Use of GIS and Remotely Sensed Data in Environmental Public Health Tracking (EPHT): The HELIX-Atlanta Experience

    Science.gov (United States)

    Al-Hamdan, Mohammad Z.; Crosson, William L.; Limaye, Ashutosh S.; Estes, Maurice G., Jr.; Watts, Carol; Rickman, Douglas L.; Quattrochi, Dale A.; Qualters, Judith R.; Sinclair, Amber H.; Tolsma, Dennis D.; Adeniyi, Kafayat A.

    2007-01-01

    As part of the National Environmental Public Health Tracking Network (EPHTN), the National Center for Environmental Health (NCEH) at the Centers for Disease Control and Prevention (CDC) is leading a project in collaboration with the NASA Marshall Space Flight Center (NASA/MSFC) called Health and Environment Linked for Information Exchange (HELIX-Atlanta). HELIX-Atlanta's goal is to examine the feasibility of building an integrated electronic health and environmental data network in five counties of metropolitan Atlanta, GA. Under HELIX-Atlanta, pilot projects are being conducted to develop methods to characterize exposure; link health and environmental data; analyze the relationship between health and environmental factors; and communicate findings. There is evidence in the research literature that asthmatic persons are at increased risk of developing asthma exacerbations with exposure to environmental factors, including PM(sub 2.5). Thus, HELIX-Atlanta is focusing on methods for characterizing population exposure to PM(sub 2.5) for the Atlanta metropolitan area that could be used in ongoing surveillance. NASA/MSFC is working with CDC to combine NASA earth science satellite observations related to air quality and environmental monitoring data to model surface estimates of fine particulate matter (PM(sub 2.5)) concentrations in a Geographic Information System (GIS) that can be linked with clinic visits for asthma on the aggregated grid level as well as the individual level at the geographic locations of the patients' residences.

  15. Design and modular parallel synthesis of a MCR derived α-helix mimetic protein-protein interaction inhibitor scaffold

    NARCIS (Netherlands)

    Antuch, Walfrido; Menon, Sanjay; Chen, Quin-Zene; Lu, Yingchun; Sakamuri, Sukumar; Beck, Barbara; Schauer-Vukašinović, Vesna; Agarwal, Seema; Hess, Sibylle; Dömling, Alexander

    2006-01-01

    A terphenyl α-helix mimetic scaffold recognized to be capable of disrupting protein-protein interactions was structurally morphed into an easily amenable and versatile multicomponent reaction (MCR) backbone. The design, modular in-parallel library synthesis, initial cell based biological data, and p

  16. Use of Molecular Dynamics Data in Biochemistry Courses: An Amphipathy Scale to Determine Protein [alpha]-Helix Transmembrane Segments

    Science.gov (United States)

    Mazze, Fernanda M.; Fuzo, Carlos A.; Degreve, Leo; Ciancaglini, Pietro

    2008-01-01

    The aim of this manuscript is to explain the application of an amphipathy scale obtained from molecular dynamics simulations and to demonstrate how it can be useful in the protein structure field. It is shown that this scale is easy to be used with the advantage of revealing domains of transmembrane [alpha]-helix of proteins without the need of…

  17. Virginia Biotechnology Summit Oct. 13-15 to Celebrate 50th Anniversary Of DNA Double Helix Discovery

    OpenAIRE

    Schroder, Beth

    2003-01-01

    The 2003 Virginia Biotechnology Summit will be held Oct. 13 to 15 to celebrate the 50th anniversary of the discovery of the DNA double helix. The seventh annual event, with Virginia Tech as its platinum sponsor, was organized by the Virginia Biotechnology Association and Tech's Continuing and Professional Education and will be held at the Hilton Hotel in Tyson's Corner.

  18. L-band compact printed quadrifilar helix antenna with ‘Iso-Flux' radiating pattern for stratospheric balloons telemetry

    OpenAIRE

    Fonseca, Nelson; Hebib, Sami; Aubert, Hervé

    2008-01-01

    International audience Two sinusoidal profile compact printed quadrifilar helix antennas have been presented. Particular care has been given to the co and cross-polarization patterns during the parametric design process to produce antennas with performances very similar to the conventional one in those aspects. A size reduction ranging from 30 to 40% is confirmed. Experimental validation will be presented at the conference.

  19. 50 Hz-Sinusoidal magnetic field induced effects on the bioelectric activity of single unit neurone cells

    International Nuclear Information System (INIS)

    Neurones recruiting and synchronized bioelectric activity recorded from Helix aspersa brain ganglia, under exposure to 50 Hz sinusoidal magnetic fields of 1-15 mT intensity, is reported. We show recruiting responses from single neurones and the synchronization of pairs of neurones activity. Experimental evidence and model theoretical explanation for the spreading of synchronization are presented

  20. Helix Nebula - the Science Cloud: a public-private partnership to build a multidisciplinary cloud platform for data intensive science

    Science.gov (United States)

    Jones, Bob; Casu, Francesco

    2013-04-01

    The feasibility of using commercial cloud services for scientific research is of great interest to research organisations such as CERN, ESA and EMBL, to the suppliers of cloud-based services and to the national and European funding agencies. Through the Helix Nebula - the Science Cloud [1] initiative and with the support of the European Commission, these stakeholders are driving a two year pilot-phase during which procurement processes and governance issues for a framework of public/private partnership will be appraised. Three initial flagship use cases from high energy physics, molecular biology and earth-observation are being used to validate the approach, enable a cost-benefit analysis to be undertaken and prepare the next stage of the Science Cloud Strategic Plan [2] to be developed and approved. The power of Helix Nebula lies in a shared set of services for initially 3 very different sciences each supporting a global community and thus building a common e-Science platform. Of particular relevance is the ESA sponsored flagship application SuperSites Exploitation Platform (SSEP [3]) that offers the global geo-hazard community a common platform for the correlation and processing of observation data for supersites monitoring. The US-NSF Earth Cube [4] and Ocean Observatory Initiative [5] (OOI) are taking a similar approach for data intensive science. The work of Helix Nebula and its recent architecture model [6] has shown that is it technically feasible to allow publicly funded infrastructures, such as EGI [7] and GEANT [8], to interoperate with commercial cloud services. Such hybrid systems are in the interest of the existing users of publicly funded infrastructures and funding agencies because they will provide "freedom of choice" over the type of computing resources to be consumed and the manner in which they can be obtained. But to offer such freedom-of choice across a spectrum of suppliers, various issues such as intellectual property, legal responsibility

  1. Symmetry-adapted digital modeling II. The double-helix B-DNA.

    Science.gov (United States)

    Janner, A

    2016-05-01

    The positions of phosphorus in B-DNA have the remarkable property of occurring (in axial projection) at well defined points in the three-dimensional space of a projected five-dimensional decagonal lattice, subdividing according to the golden mean ratio τ:1:τ [with τ = (1+\\sqrt {5})/2] the edges of an enclosing decagon. The corresponding planar integral indices n1, n2, n3, n4 (which are lattice point coordinates) are extended to include the axial index n5 as well, defined for each P position of the double helix with respect to the single decagonal lattice ΛP(aP, cP) with aP = 2.222 Å and cP = 0.676 Å. A finer decagonal lattice Λ(a, c), with a = aP/6 and c = cP, together with a selection of lattice points for each nucleotide with a given indexed P position (so as to define a discrete set in three dimensions) permits the indexing of the atomic positions of the B-DNA d(AGTCAGTCAG) derived by M. J. P. van Dongen. This is done for both DNA strands and the single lattice Λ. Considered first is the sugar-phosphate subsystem, and then each nucleobase guanine, adenine, cytosine and thymine. One gets in this way a digital modeling of d(AGTCAGTCAG) in a one-to-one correspondence between atomic and indexed positions and a maximal deviation of about 0.6 Å (for the value of the lattice parameters given above). It is shown how to get a digital modeling of the B-DNA double helix for any given code. Finally, a short discussion indicates how this procedure can be extended to derive coarse-grained B-DNA models. An example is given with a reduction factor of about 2 in the number of atomic positions. A few remarks about the wider interest of this investigation and possible future developments conclude the paper. PMID:27126108

  2. Technology Entreprenurship in the Changing Business Environment – A Triple Helix Performance Model

    Directory of Open Access Journals (Sweden)

    Maja Levi Jaksić

    2015-02-01

    Full Text Available In this paper the contribution of technology management and entrepreneurship to sustainable development is emphasized and the Triple Helix (TH model is used to analyse the performance of different actors in accomplishing the activities of Technology Innovation Management and Entrepreneurship (TIME. By analysing TH model (Government – University – Industry in relation to accomplishing TIME main functions: Planning, Organizing and Control (POC, we created a general model which measures TIME effectiveness related to the key elements of the TH model. The general model – TMD-TH (Technology Management and Development – Triple Helix represents the framework for further more specific research into the relations of the observed dimensions. From the general model, three sub-models are excluded: TMD-G (Government, TMD-U (University and TMD-I (Industry, and each of TH dimensions is observed by a set of indicators classified from the perspective of the specific function (POC of TIME. This provides better categorization of TIME indicators and linkage with the actors in the TH model. The applicability of the suggested general model was tested by a set of indicators at the example of Serbia, Austria and Finland and comparison of these countries was made from a perspective of innovativeness and sustainable development. Since technology, innovation and entrepreneurship are considered as the main forces leading to sustainable development at different levels of the economy and society, it is of paramount importance to develop our capacities to better monitor, analyse and develop these forces. A model is developed with a set of indicators that enables the systematic analysis in concrete situations in practice. In this paper, the model is applied at the level of the national economy, the results obtained point to the most critical activities of the actors in the TH model in accomplishing TIME. The performance model represents a base for developing policies

  3. Overlapping effector interfaces define the multiple functions of the HIV-1 Nef polyproline helix

    Directory of Open Access Journals (Sweden)

    Kuo Lillian S

    2012-05-01

    proteins. To the N- and C- terminal sides of the polyproline helix are multifunctional protein interaction sites. The polyproline segment is also adapted to downregulate MHCI with a non-canonical binding surface. Our results demonstrate that Nef polyproline helix is highly adapted to directly interact with multiple host cell proteins.

  4. Helix and Drugs: Snails for Western Health Care From Antiquity to the Present

    Directory of Open Access Journals (Sweden)

    Bruno Bonnemain

    2005-01-01

    Full Text Available The land helix, or snail, has been used in medicine since antiquity and prepared according to several formulations. This historical report traces the understanding of their properties from the time of Hippocrates, who proposed the use of snail mucus against protoccle and Pliny who thought that the snail increased the speed of delivery and was “a sovereign remedy to treat pain related to burns, abscesses and other wounds”, Galien recommended snails against hydrops foetails. In the 18th century, various snail “preparations” were also recommended for external use with dermatological disorders and internally for symptoms associated with tuberculosis and nephritis. Surprisingly, the 19th century saw a renewed interest in the pharmaceutical and medical use of snails with numerous indications for snail preparations. This interest in snails did not stop at the end of the 19th century. The 1945 edition of Dorvault devotes an entire paragraph to snails, indicating that the therapeutic usage of snails was still alive at that time. Recently the FDA has also shown an interest in snails. Ziconotide (SNXIII, a synthetic peptide coming from snail venom, has been under FDA review since 1999. Pre-clinical and clinical studies of this new drug are promising.

  5. A novel colorimetric triple-helix molecular switch aptasensor for ultrasensitive detection of tetracycline.

    Science.gov (United States)

    Ramezani, Mohammad; Mohammad Danesh, Noor; Lavaee, Parirokh; Abnous, Khalil; Mohammad Taghdisi, Seyed

    2015-08-15

    Detection methods of antibiotic residues in blood serum and animal derived foods are of great interest. In this study a colorimetric aptasensor was designed for sensitive, selective and fast detection of tetracycline based on triple-helix molecular switch (THMS) and gold nanoparticles (AuNPs). As a biosensor, THMS shows distinct advantages including high stability, sensitivity and preserving the selectivity and affinity of the original aptamer. In the absence of tetracycline, THMS is stable, leading to the aggregation of AuNPs by salt and an obvious color change from red to blue. In the presence of tetracycline, aptamer binds to its target, signal transduction probe (STP) leaves the THMS and adsorbs on the surface of AuNPs. So the well-dispersed AuNPs remain stable against salt-induced aggregation with a red color. The presented aptasensor showed high selectivity toward tetracyclines with a limit of detection as low as 266 pM for tetracycline. The designed aptasensor was successfully applied to detect tetracycline in serum and milk. PMID:25814407

  6. The double helix of cultural assimilationism and neo-liberalism: citizenship in contemporary governmentality.

    Science.gov (United States)

    Schinkel, Willem; Van Houdt, Friso

    2010-12-01

    In this article the recent transformations of citizenship in the Netherlands are analysed in relation to a developing form of governmentality. We regard citizenship as a state regulated technique of in- and exclusion and a crucial instrument in the management of populations. Taking the Dutch contexts of immigration and integration as our case, we argue that cultural assimilationism and neo-liberalism appear in a double helix: they combine to form a new governmental strategy we call neo-liberal communitarianism. Neo-liberal communitarianism is the underlying rationale of a population management that operates both in an individualizing (citizenship as individual participation and responsibility) and a de-individualizing way ('community' at various aggregate and localized levels as frame of 'integration'). It thus combines a communitarian care of a Dutch culturally grounded national community - conceived as traditionally'enlightened' and 'liberal'- with a neo-liberal emphasis on the individual's responsibility to achieve membership of that community. 'Community' is thereby selectively seen as mobilized and present (when immigrant integration is concerned) or as latently present and still in need of mobilization (when indigenous Dutch are concerned). Concomitantly, a repressive responsibilization and a facilitative responsibilization are aimed at these two governmentally differentiated populations. PMID:21138428

  7. Dust particulate absorption by ivy (Hedera helix L) on historic walls in urban environments

    Energy Technology Data Exchange (ETDEWEB)

    Sternberg, Troy, E-mail: troy.sternberg@geog.ox.ac.uk [School of Geography and the Environment, University of Oxford, South Parks Road, Oxford OX1 3QY UK (United Kingdom); Viles, Heather, E-mail: heather.viles@ouce.ox.ac.uk [School of Geography and the Environment, University of Oxford, South Parks Road, Oxford OX1 3QY UK (United Kingdom); Cathersides, Alan, E-mail: alan.cathersides@english-heritage.org.uk [Conservation Department, English Heritage, Kemble Drive, Swindon, SN2 2GZ UK (United Kingdom); Edwards, Mona, E-mail: mona.edwards@ouce.ox.ac.uk [School of Geography and the Environment, University of Oxford, South Parks Road, Oxford OX1 3QY UK (United Kingdom)

    2010-12-01

    The potential bio-protective role of urban greenery and how it interacts with airborne dust and pollutants has been the subject of much recent research. As particulate pollution has been implicated in both the deterioration of building materials and in damaging human health, understanding how it interacts with urban greenery is of great applied interest. Common or English Ivy (Hedera helix L) grows widely on urban walls in many parts of the world, and thus any bio-protective role it might play is of broad relevance. Using Scanning Electron Microscopy ivy leaves collected on roadways were examined to determine if ivy can absorb dust and pollutants that can instigate decay processes on stone walls and impact human health in urban environments. Results showed that ivy acts as a 'particle sink', absorbing particulate matter, particularly in high-traffic areas. It was effective in adhering fine (< 2.5 {mu}m) and ultra-fine (< 1 {mu}m) particles at densities of up to 2.9 x 10{sup 10} per m{sup 2}. Our findings suggest that through absorbing pollutant particles ivy can retard bio-deteriorative processes on historic walls and reduce human exposure to respiratory problems caused by vehicle pollutants.

  8. Dust particulate absorption by ivy (Hedera helix L) on historic walls in urban environments

    International Nuclear Information System (INIS)

    The potential bio-protective role of urban greenery and how it interacts with airborne dust and pollutants has been the subject of much recent research. As particulate pollution has been implicated in both the deterioration of building materials and in damaging human health, understanding how it interacts with urban greenery is of great applied interest. Common or English Ivy (Hedera helix L) grows widely on urban walls in many parts of the world, and thus any bio-protective role it might play is of broad relevance. Using Scanning Electron Microscopy ivy leaves collected on roadways were examined to determine if ivy can absorb dust and pollutants that can instigate decay processes on stone walls and impact human health in urban environments. Results showed that ivy acts as a 'particle sink', absorbing particulate matter, particularly in high-traffic areas. It was effective in adhering fine (10 per m2. Our findings suggest that through absorbing pollutant particles ivy can retard bio-deteriorative processes on historic walls and reduce human exposure to respiratory problems caused by vehicle pollutants.

  9. Triple Helix of university-industry-government relationships in West Africa

    Directory of Open Access Journals (Sweden)

    Eustache Mêgnigbêto

    2013-01-01

    Full Text Available The West African countries′ scientific publications data are downloaded from Web of Science. Analyses focus on university-industry-government collaboration. We compute data on each sector′s production and collaboration among them. Particularly, the industrial production is extracted; the network, it induces is built and its structure analyzed with social network analysis methods and techniques, using Pajek. Results show that the university is the biggest information producer, followed by government; the number of industrial publications is meaningless; even some countries have no industrial output. Consequently, collaboration between the university and government is more visible. Collaboration between the three Triple Helix spheres occurred only in Nigeria. The mutual information between university, industry, and government is weak, illustrating the low level of knowledge flow between innovation actors in the region. These results could explain the negligible share of the developing countries in general and African and West African countries particularly to the World economy, and also the low level of development the region.

  10. Non-dipole interaction of helix inclusions in metamaterials with artificial permeability

    Energy Technology Data Exchange (ETDEWEB)

    Starostenko, Sergey N.; Rozanov, Konstantin N.

    2015-06-01

    An analytic approach to calculate induced permeability of metamaterial filled with helix inclusions is developed. For an electrically small coil, the dynamic magnetization is determined by lumped inductance, capacitance, and resistance that are calculated from the coil design. The susceptibility of a coil is shown to be close to that of diamagnetic ellipsoid of the same elongation. Contrary to permeable particles in a composite, the coils screen each other thus decreasing the magnetic response of metamaterial compared to total response of comprised coils. The filling effect on magnetic spectrum of metamaterial is analyzed and verified by measurements for the case of identical coaxially placed coreless coils. The critical filling where magnetic response of metamaterial is maximal depends on coil shape and resistance. The coil-filled metamaterials may find applications as permeable EMI suppressors or microwave absorbers free of Snoek or Acher limitations on the high-frequency permeability, as well as of Curie limitation on the high-temperature magnetic performance. - Highlights: • The field of a coreless coil is close to that of a conductive ellipsoid. • The self-resonance parameters of a coil are calculated basing on its size and winding. • The coil size and winding define the dynamic susceptibility of coil-inscribed ellipsoid. • Susceptibility of metamaterial of regularly placed coils depends on intercoil distance. • There is a critical filling, where the metamaterial susceptibility reaches maximum.

  11. Lead pollution due to exhaust gases. [Celtis occidentalis; fraxinus angustifolia; aesculus hippocastanum; hedera helix

    Energy Technology Data Exchange (ETDEWEB)

    Klinscek, P.

    1976-01-01

    An investigation was carried out to establish the changes in the lead content of trees and shrubs on the Margaret island in Budapest as a response to the reduction in motor-vehicle traffic introduced in 1974. Compared to samples of the control area (Vacratot) the Margaret island samples were found to have a considerable higher lead content. As a consequence of the traffic modifying measure a 30% decrease in the lead content of the samples was verified. The lead pollution did not involve changes in the chlorophyll content of samples. Accumulation of lead pollution is a specific feature. Lead pollution is accumulated to a great extent (multiple of other plants) by the pilose-leaved CELTIS occidentalis, the pinnate-leaved FRAXINUS angustifolia, ssp. pannonica and the undulate-leaved AESCULUS hippocastanum as well as from among the evergreen by the stellate-hair HEDERA helix. The green belt bordering the roads by its active lead cumulation plays an important role in lessening the plumb pollution of areas more distant from the road. 14 references 3 tables.

  12. CFD analysis and flow model reduction for surfactant production in helix reactor

    Directory of Open Access Journals (Sweden)

    Nikačević N.M.

    2015-01-01

    Full Text Available Flow pattern analysis in a spiral Helix reactor is conducted, for the application in the commercial surfactant production. Step change response curves (SCR were obtained from numerical tracer experiments by three-dimensional computational fluid dynamics (CFD simulations. Non-reactive flow is simulated, though viscosity is treated as variable in the direction of flow, as it increases during the reaction. The design and operating parameters (reactor diameter, number of coils and inlet velocity are varied in CFD simulations, in order to examine the effects on the flow pattern. Given that 3D simulations are not practical for fast computations needed for optimization, scale-up and control, CFD flow model is reduced to one-dimensional axial dispersion (AD model with spatially variable dispersion coefficient. Dimensionless dispersion coefficient (Pe is estimated under different conditions and results are analyzed. Finally, correlation which relates Pe number with Reynolds number and number of coils from the reactor entrance is proposed for the particular reactor application and conditions.

  13. Preparation and application of triple helix forming oligonucleotides and single strand oligonucleotide donors for gene correction.

    Science.gov (United States)

    Alam, Rowshon; Thazhathveetil, Arun Kalliat; Li, Hong; Seidman, Michael M

    2014-01-01

    Strategies for site-specific modulation of genomic sequences in mammalian cells require two components. One must be capable of recognizing and activating a specific target sequence in vivo, driving that site into an exploitable repair pathway. Information is transferred to the site via participation in the pathway by the second component, a donor nucleic acid, resulting in a permanent change in the target sequence. We have developed biologically active triple helix forming oligonucleotides (TFOs) as site-specific gene targeting reagents. These TFOs, linked to DNA reactive compounds (such as a cross-linking agent), activate pathways that can engage informational donors. We have used the combination of a psoralen-TFO and single strand oligonucleotide donors to generate novel cell lines with directed sequence changes at the target site. Here we describe the synthesis and purification of bioactive psoralen-linked TFOs, their co-introduction into mammalian cells with donor nucleic acids, and the identification of cells with sequence conversion of the target site. We have emphasized details in the synthesis and purification of the oligonucleotides that are essential for preparation of reagents with optimal activity. PMID:24557899

  14. Antiproliferation effects of an androgen receptor triple-helix forming oligonucleotide on prostate cancer cells

    International Nuclear Information System (INIS)

    Objective: To provide experimental basis for antigene radiation therapy through exploring the effects of antigene strategy on androgen receptor (AR) expression and proliferation of prostate cancer cells. Methods: The triple-helix forming oligonucleotide (TFO) targeting 2447-2461nt of AR cDNA was designed and transfected LNCaP prostate cancer cells with liposome. 24-72 h after transfection, the cellular proliferation was detected by 3H-thymidine (TdR) incorporation test, the expression of AR gene was examined by reverse transcription-polymerase chain reaction (RT-PCR) and expression of AR protein was performed by radioligand binding assay. The results of TFO were compared with antisense oligonucleotide (ASON). Results: At all time points, the AR expression levels in TFO group were markedly lower than that of ASON group (P<0.05). The inhibitory rate of TFO for cellular proliferation was significantly higher than that of ASON (P<0.05). Conclusion: The TFO was a potent inhibitor for AR expression and cell proliferation of LNCaP cells , and could be used in antigene radiotherapy. (authors)

  15. Field-induced Gap and Quantized Charge Pumping in Nano-helix

    Energy Technology Data Exchange (ETDEWEB)

    Qi, Xiao-Liang; /Stanford U., Phys. Dept. /Tsinghua U., Beijing; Zhang, Shou-Cheng; /Stanford U., Phys. Dept.

    2010-02-15

    We propose several novel physical phenomena based on nano-scale helical wires. Applying a static electric field transverse to the helical wire induces a metal to insulator transition, with the band gap determined by the applied voltage. Similar idea can be applied to 'geometrically' constructing one-dimensional systems with arbitrary external potential. With a quadrupolar electrode configuration, the electric field could rotate in the transverse plane, leading to a quantized dc charge current proportional to the frequency of the rotation. Such a device could be used as a new standard for the high precession measurement of the electric current. The inverse effect implies that passing an electric current through a helical wire in the presence of a transverse static electric field can lead to a mechanical rotation of the helix. This effect can be used to construct nano-scale electro-mechanical motors. Finally, our methodology also enables new ways of controlling and measuring the electronic properties of helical biological molecules such as the DNA.

  16. Non-dipole interaction of helix inclusions in metamaterials with artificial permeability

    International Nuclear Information System (INIS)

    An analytic approach to calculate induced permeability of metamaterial filled with helix inclusions is developed. For an electrically small coil, the dynamic magnetization is determined by lumped inductance, capacitance, and resistance that are calculated from the coil design. The susceptibility of a coil is shown to be close to that of diamagnetic ellipsoid of the same elongation. Contrary to permeable particles in a composite, the coils screen each other thus decreasing the magnetic response of metamaterial compared to total response of comprised coils. The filling effect on magnetic spectrum of metamaterial is analyzed and verified by measurements for the case of identical coaxially placed coreless coils. The critical filling where magnetic response of metamaterial is maximal depends on coil shape and resistance. The coil-filled metamaterials may find applications as permeable EMI suppressors or microwave absorbers free of Snoek or Acher limitations on the high-frequency permeability, as well as of Curie limitation on the high-temperature magnetic performance. - Highlights: • The field of a coreless coil is close to that of a conductive ellipsoid. • The self-resonance parameters of a coil are calculated basing on its size and winding. • The coil size and winding define the dynamic susceptibility of coil-inscribed ellipsoid. • Susceptibility of metamaterial of regularly placed coils depends on intercoil distance. • There is a critical filling, where the metamaterial susceptibility reaches maximum

  17. Interstrand dipole-dipole interactions can stabilize the collagen triple helix.

    Science.gov (United States)

    Shoulders, Matthew D; Raines, Ronald T

    2011-07-01

    The amino acid sequence of collagen is composed of GlyXaaYaa repeats. A prevailing paradigm maintains that stable collagen triple helices form when (2S)-proline (Pro) or Pro derivatives that prefer the C(γ)-endo ring pucker are in the Xaa position and Pro derivatives that prefer the C(γ)-exo ring pucker are in the Yaa position. Anomalously, an amino acid sequence in an invertebrate collagen has (2S,4R)-4-hydroxyproline (Hyp), a C(γ)-exo-puckered Pro derivative, in the Xaa position. In certain contexts, triple helices with Hyp in the Xaa position are now known to be hyperstable. Most intriguingly, the sequence (GlyHypHyp)(n) forms a more stable triple helix than does the sequence (GlyProHyp)(n). Competing theories exist for the physicochemical basis of the hyperstability of (GlyHypHyp)(n) triple helices. By synthesizing and analyzing triple helices with different C(γ)-exo-puckered proline derivatives in the Xaa and Yaa positions, we conclude that interstrand dipole-dipole interactions are the primary determinant of their additional stability. These findings provide a new framework for understanding collagen stability. PMID:21482820

  18. Myriad Triple-Helix-Forming Structures in the Transposable Element RNAs of Plants and Fungi.

    Science.gov (United States)

    Tycowski, Kazimierz T; Shu, Mei-Di; Steitz, Joan A

    2016-05-10

    The ENE (element for nuclear expression) is a cis-acting RNA structure that protects viral or cellular noncoding RNAs (ncRNAs) from nuclear decay through triple-helix formation with the poly(A) tail or 3'-terminal A-rich tract. We expanded the roster of nine known ENEs by bioinformatic identification of ∼200 distinct ENEs that reside in transposable elements (TEs) of numerous non-metazoan and one fish species and in four Dicistrovirus genomes. Despite variation within the ENE core, none of the predicted triple-helical stacks exceeds five base triples. Increased accumulation of reporter transcripts in human cells demonstrated functionality for representative ENEs. Location close to the poly(A) tail argues that ENEs are active in TE transcripts. Their presence in intronless, but not intron-containing, hAT transposase genes supports the idea that TEs acquired ENEs to counteract the RNA-destabilizing effects of intron loss, a potential evolutionary consequence of TE horizontal transfer in organisms that couple RNA silencing to splicing deficits. PMID:27134163

  19. Dissociation of Bak α1 helix from the core and latch domains is required for apoptosis.

    Science.gov (United States)

    Alsop, Amber E; Fennell, Stephanie C; Bartolo, Ray C; Tan, Iris K L; Dewson, Grant; Kluck, Ruth M

    2015-01-01

    During apoptosis, Bak permeabilizes mitochondria after undergoing major conformational changes, including poorly defined N-terminal changes. Here, we characterize those changes using 11 antibodies that were epitope mapped using peptide arrays and mutagenesis. After Bak activation by Bid, epitopes throughout the α1 helix are exposed indicating complete dissociation of α1 from α2 in the core and from α6-α8 in the latch. Moreover, disulfide tethering of α1 to α2 or α6 blocks cytochrome c release, suggesting that α1 dissociation is required for further conformational changes during apoptosis. Assaying epitope exposure when α1 is tethered shows that Bid triggers α2 movement, followed by α1 dissociation. However, α2 reaches its final position only after α1 dissociates from the latch. Thus, α1 dissociation is a key step in unfolding Bak into three major components, the N terminus, the core (α2-α5) and the latch (α6-α8). PMID:25880232

  20. Rigid multibody simulation of a helix-like structure: the dynamics of bacterial adhesion pili.

    Science.gov (United States)

    Zakrisson, Johan; Wiklund, Krister; Servin, Martin; Axner, Ove; Lacoursière, Claude; Andersson, Magnus

    2015-07-01

    We present a coarse-grained rigid multibody model of a subunit assembled helix-like polymer, e.g., adhesion pili expressed by bacteria, that is capable of describing the polymer's force-extension response. With building blocks representing individual subunits, the model appropriately describes the complex behavior of pili expressed by the gram-negative uropathogenic Escherichia coli bacteria under the action of an external force. Numerical simulations show that the dynamics of the model, which include the effects of both unwinding and rewinding, are in good quantitative agreement with the characteristic force-extension response as observed experimentally for type 1 and P pili. By tuning the model, it is also possible to reproduce the force-extension response in the presence of anti-shaft antibodies, which dramatically changes the mechanical properties. Thus, the model and results in this work give enhanced understanding of how a pilus unwinds under the action of external forces and provide a new perspective of the complex bacterial adhesion processes. PMID:25851543

  1. Measurements of Drag Coefficients and Rotation Rates of Free-Falling Helixes

    KAUST Repository

    Al-Omari, Abdulrhaman A.

    2016-05-01

    The motion of bacteria in the environment is relevant to several fields. At very small scales and with simple helical shapes, we are able to describe experimentally and mathematically the motion of solid spirals falling freely within a liquid pool. Using these shapes we intend to mimic the motion of bacteria called Spirochetes. We seek to experimentally investigate the linear and the rotational motion of such shapes. A better understanding of the dynamics of this process will be practical not only on engineering and physics, but the bioscience and environmental as well. In the following pages, we explore the role of the shape on the motion of passive solid helixes in different liquids. We fabricate three solid helical shapes and drop them under gravity in water, glycerol and a mixture of 30% glycerol in water. That generated rotation due to helical angle in water. However, we observe the rotation disappear in glycerol. The movement of the solid helical shapes is imaged using a high-speed video camera. Then, the images are analyzed using the supplied software and a computer. Using these simultaneous measurements, we examine the terminal velocity of solid helical shapes. Using this information we computed the drag coefficient and the drag force. We obtain the helical angular velocity and the torque applied to the solid. The results of this study will allow us to more accurately predict the motion of solid helical shape. This analysis will also shed light onto biological questions of bacteria movement.

  2. Knowledge-enhancing Helix: An Approach for Developing Key Academic Skills at Universities. A Case Study

    Directory of Open Access Journals (Sweden)

    Nadja Boeller

    2008-08-01

    Full Text Available In an increasingly e-literate society, new and media technologies are proliferating and traditional teaching approaches are challenged to meet new requirements. Other aspects such as teamwork and knowledge exchange are also becoming more important. Collaborative working methods are more dominant in the networked business environment. The vocational training at universities is therefore continuously facing with new challenges. The objective of this paper is to show how the implementation of a holistic teaching approach including the idea of blended learning can be an effective way to train students in collaborative and academic working skills, methodological expertise, information literacy, as well as making students aware of new developments in media literacy. This approach follows our proposed concept DIAMOND (Didactical Approach for Media Competence Development with a main focus on the implementation of the "knowledgeenhancing helix." This pedagogical concept was developed corresponding the requirements for "good online learning." The paper accordingly discusses the theoretical framework and presents a case study where the concept was implemented in practice.

  3. Characterization of English ivy (Hedera helix) adhesion force and imaging using atomic force microscopy

    International Nuclear Information System (INIS)

    English ivy (Hedera helix) is well known for its ability to climb onto and strongly adhere to a variety of solid substrates. It has been discovered that the ivy aerial rootlet secretes an adhesive composed of polysaccharide and spherical nanoparticles. This study aims to characterize the mechanical properties of the nanocomposite adhesive using atomic force microscopy (AFM). The adhesive was first imaged by AFM to visualize the nanocomposite. Mechanical properties were then determined at various time points, from secretion to hardening. The experimental results indicate that the ivy adhesive exhibited strong adhesion strength and high elasticity. There was a decrease in adhesive force over time, from 298 to 202 nN during the 24-h study. Accompanying with it were the limited changes in extension length and Young’s modulus. The limited curing process of the ivy adhesive helps fill gaps in the attaching surface, leading to more intimate contact and increased van der Waals interactions with the surface. However, study based on a mechanical model indicated that van der Waals force alone is not significant enough to account for all of the measured force. Other chemical interactions and cross linking likely contribute to the strong adhesion strength of ivy.

  4. A three-dimensional time-dependent theory for helix traveling wave tubes in beam-wave interaction

    Institute of Scientific and Technical Information of China (English)

    Peng Wei-Feng; Hu Yu-Lu; Yang Zhong-Hai; Li Jian-Qing; Lu Qi-Ru; Li Bin

    2011-01-01

    This paper presents a three-dimensional time-dependent nonlinear theory of helix traveling wave tubes for beam-wave interaction. The radio frequency electromagnetic fields are represented as the superposition of azimuthally symmetric Waves in a vacuum sheath helix. Coupling impedance is introduced to the electromagnetic field equations' stimulating sources, which makes the theory easier and more flexible to realize. The space charge fields are calculated by electron beam space-charge waves expressed as the superposition solutions of Helmholtz equations. The focusing forces due to either a solenoidal field or a periodic permanent magnetic field is also included. The dynamical equations of electrons are Lorentz equations associating with electromagnetic fields, focusing fields and space-charge fields. The numerically simulated results of a tube are presented.

  5. Peptide-oligonucleotide conjugates as nanoscale building blocks for assembly of an artificial three-helix protein mimic

    DEFF Research Database (Denmark)

    Lou, Chenguang; Martos-Maldonado, Manuel C; Madsen, Charlotte S;

    2016-01-01

    Peptide-based structures can be designed to yield artificial proteins with specific folding patterns and functions. Template-based assembly of peptide units is one design option, but the use of two orthogonal self-assembly principles, oligonucleotide triple helix and a coiled coil protein domain...... formation have never been realized for de novo protein design. Here, we show the applicability of peptide-oligonucleotide conjugates for self-assembly of higher-ordered protein-like structures. The resulting nano-assemblies were characterized by ultraviolet-melting, gel electrophoresis, circular dichroism...... (CD) spectroscopy, small-angle X-ray scattering and transmission electron microscopy. These studies revealed the formation of the desired triple helix and coiled coil domains at low concentrations, while a dimer of trimers was dominating at high concentration. CD spectroscopy showed an extraordinarily...

  6. Liquid holdup measurement with double helix capacitance sensor in horizontal oil-water two-phase flow pipes

    Institute of Scientific and Technical Information of China (English)

    Lusheng Zhai; Ningde Jin; Zhongke Gao; Zhenya Wang

    2015-01-01

    This paper presents the characteristics of a double helix capacitance sensor for measurement of the liquid holdup in horizontal oil–water two-phase flow. The finite element method is used to calculate the sensitivity field of the sensor in a pipe with 20 mm inner diameter and the effect of sensor geometry on the distribution of sensitivity field is presented. Then, a horizontal oil–water two-phase flow experiment is carried out to measure the response of the double helix capacitance sensor, in which a novel method is proposed to calibrate the liquid holdup based on three pairs of paral el-wire capacitance probes. The performance of the sensor is analyzed in terms of the flow structures detected by mini-conductance array probes.

  7. EFFECT OF GEAR WIDTH AND HELIX ANGLE ON FACTOR OF DYNAMIC LOAD OF DOUBLE CIRCULAR ARC HELICAL GEARING

    Institute of Scientific and Technical Information of China (English)

    Wu Baolin

    2004-01-01

    Based on theory of mechanical dynamics, meshing characteristic as well as the dynamic model of double circular arc helical gearing, an analysis approach and a computer program have been developed for studying the state of dynamic load and factor of dynamic load of the gearing, the changing situation of dynamic load and dynamic load factor vs some affecting factors such as gear width, helix angle and accuracy grade etc are investigated. A series of conclusions are obtained: ①With the increasing in the values of gear width, the dynamic load factor appears slow decreasing tendency in most region of gear width. ② When the accuracy grades of the gearing are improved, the values of dynamic load factor decrease. ③ The value of dynamic load factor appears a decreasing tendency with the increasing of value of helix angle at the same ratio of critical rotational speed.

  8. A three-dimensional time-dependent theory for helix traveling wave tubes in beam-wave interaction

    International Nuclear Information System (INIS)

    This paper presents a three-dimensional time-dependent nonlinear theory of helix traveling wave tubes for beam-wave interaction. The radio frequency electromagnetic fields are represented as the superposition of azimuthally symmetric waves in a vacuum sheath helix. Coupling impedance is introduced to the electromagnetic field equations' stimulating sources, which makes the theory easier and more flexible to realize. The space charge fields are calculated by electron beam space-charge waves expressed as the superposition solutions of Helmholtz equations. The focusing forces due to either a solenoidal field or a periodic permanent magnetic field is also included. The dynamical equations of electrons are Lorentz equations associating with electromagnetic fields, focusing fields and space-charge fields. The numerically simulated results of a tube are presented. (cross-disciplinary physics and related areas of science and technology)

  9. Remarkable optics of short-pitch deformed helix ferroelectric liquid crystals: symmetries, exceptional points and polarization-resolved angular patterns

    CERN Document Server

    Kiselev, Alexei D

    2014-01-01

    In order to explore electric-field-induced transformations of polarization singularities in the polarization-resolved angular (conoscopic) patterns emerging after deformed helix ferroelectric liquid crystal (DHFLC) cells with subwavelength helix pitch, we combine the transfer matrix formalism with the results for the effective dielectric tensor of biaxial FLCs evaluated using an improved technique of averaging over distorted helical structures. Within the framework of the transfer matrix method, we deduce a number of symmetry relations and show that the symmetry axis of L lines (curves of linear polarization) is directed along the major in-plane optical axis which rotates under the action of the electric field. When the angle between this axis and the polarization plane of incident linearly polarized light is above its critical value, the C points (points of circular polarization) appear in the form of symmetrically arranged chains of densely packed star-monstar pairs. We also emphasize the role of phase sing...

  10. Evaluation of a Pilot Surveillance System: Health and Environment Linked for Information Exchange in Atlanta (HELIX-Atlanta)

    Science.gov (United States)

    Meyer, P.; Shire, J.; Qualters, Judy; Daley, Randolph; Fiero, Leslie Todorov; Autry, Andy; Avchen, Rachel; Stock, Allison; Correa, Adolofo; Siffel, Csaba; Devine, Owen; Gotway, Carol; Crawford; Mitchell, Ken; Pollard, Solomon; Rao, Ravi; Kajumba, Ntale; Rickman, Doug; Quattrochi, Dale; Estes, Maury; Meyer, Paul; Crosson, Bill; Limaye, Ashutosh; Al-Hamdan, Mohammad; Khan, Maudood

    2007-01-01

    CDC and its partners established the Health and Environment Linked for Information Exchange, Atlanta (HELIX-Atlanta) demonstration project, to develop linking and analysis methods that could be used by the National Environmental Public Health Tracking (EPHT) Network. Initiated in October 2003, the Metropolitan Atlanta-based collaborative conducted four projects: asthma and particulate air pollution, birth defects and ozone and particulate air pollution, childhood leukemia and traffic emissions, and children's blood lead testing and neighborhood risk factors for lead poisoning. This report provides an overview of the HELIX-Atlanta projects' goals, methods and outcomes. We discuss priority attributes and common issues and challenges and offer recommendations for implementation of the nascent national environmental public health tracking network.

  11. Thermodynamic origin of α-helix stabilization by side-chain cross-links in a small protein.

    Science.gov (United States)

    Haney, Conor M; Werner, Halina M; McKay, James J; Horne, W Seth

    2016-06-15

    Peptide cross-linking has been widely explored as a means of constraining short sequences into stable folded conformations, most commonly α-helices. The prevailing hypothesis for the origin of helix stabilization is an entropic effect resulting from backbone pre-organization; however, obtaining direct evidence bearing on this hypothesis is challenging. Here, we compare the folding thermodynamics of a small helix-rich protein domain and analogues containing one of three common cross-linking motifs. Analysis of the folding free energy landscapes of linear vs. cyclized species reveal consistent trends in the effect of cyclization on folding energetics, as well as subtle differences based on the chemistry of the cross link. Stabilization in all three systems arises entirely from a reduction in the entropic penalty of folding that more than compensates for an enthalpic destabilization of the folded state. PMID:27006192

  12. Electric Field-Driven Disruption of a Native β-Sheet Protein Conformation and Generation of a Helix-Structure

    OpenAIRE

    Ojeda-May, Pedro; Garcia, Martin E.

    2010-01-01

    We demonstrate that an external constant electric field is able to modify the secondary structure of a protein and induce a transition from a β-sheet into a helix-like conformation. This dramatic change is driven by a global rearrangement of the dipole moments at the amide planes. We also predict electric-field-induced modifications of the intermediate states of the protein.

  13. HIV-1 Envelope Proteins Complete Their Folding into Six-helix Bundles Immediately after Fusion Pore Formation

    OpenAIRE

    Markosyan, Ruben M; Cohen, Fredric S.; Melikyan, Grigory B.

    2003-01-01

    Fusion proteins of many viruses, including HIV-1 envelope protein (Env), fold into six-helix bundle structures. Fusion between individual Env-expressing cells and target cells was studied by fluorescence microscopy, and a temperature jump technique, to determine whether folding of Env into a bundle is complete by the time fusion pores have formed. Lowering temperature to 4°C immediately after a pore opened halted pore growth, which quickly resumed when temperature was raised again. HIV gp41-d...

  14. Systematic Review of Clinical Trials Assessing the Effectiveness of Ivy Leaf (Hedera Helix) for Acute Upper Respiratory Tract Infections

    OpenAIRE

    Holzinger, Felix; Chenot, Jean-François

    2011-01-01

    Introduction. Among nonantibiotic cough remedies, herbal preparations containing extracts from leaves of ivy (Hedera helix) enjoy great popularity. Objective. A systematic review to assess the effectiveness and tolerability of ivy for acute upper respiratory tract infections (URTIs). Methods. We searched for randomized controlled trials (RCTs), nonrandomized controlled clinical trials and observational studies evaluating the efficacy of ivy preparations for acute URTIs. Study quality was asse...

  15. Phenolic Compounds and Antifungal Activity of Hedera helix L. (Ivy) Flowers and Fruits

    OpenAIRE

    Marcel PARVU; Laurian VLASE; Alina E. PARVU; Oana ROSCA-CASIAN; GHELDIU, ANA-MARIA; Ovidiu PARVU

    2015-01-01

    Identification and quantitative analysis of the phenolic compounds from Hedera helix L. (ivy) flower and fruit ethanol extracts by LC/MS, in vitro germination and growth inhibition effects on Aspergillus niger, Botrytis cinerea, Fusarium oxysporum f.sp. tulipae, Penicillium gladioli and Sclerotinia sclerotiorum were performed. In the non-hydrolyzed samples of flower and fruit extracts were determined, in different amounts, five polyphenols (p-coumaric acid, ferulic acid, rutoside, quercetol a...

  16. Biological characteristics of the species Hedera helix L. and its use in controlling erosion in shady places

    OpenAIRE

    Stavretović N.

    2007-01-01

    Controlling erosion in shady places is among the most serious problems of environment protection, one that requires persistent and strenuous efforts. Ivy (Hedera helix L.) is exceptionally shade-tolerant, covers the ground surface nicely, and is easy to cultivate. For these reasons, it can be used more successfully than any other ground cover to control erosion in shady places. Hardening of ivy cuttings is accomplished with semi-lignified and lignified cuttings. In hardening of cuttings in pl...

  17. Systematic Review of Clinical Trials Assessing the Effectiveness of Ivy Leaf (Hedera Helix) for Acute Upper Respiratory Tract Infections

    OpenAIRE

    Holzinger, Felix; Chenot, Jean-François

    2010-01-01

    Introduction. Among nonantibiotic cough remedies, herbal preparations containing extracts from leaves of ivy (Hedera helix) enjoy great popularity. Objective. A systematic review to assess the effectiveness and tolerability of ivy for acute upper respiratory tract infections (URTIs). Methods. We searched for randomized controlled trials (RCTs), nonrandomized controlled clinical trials and observational studies evaluating the efficacy of ivy preparations for acute URTIs. Study quality was asse...

  18. The winged helix transcription factor HFH-4 is expressed during choroid plexus epithelial development in the mouse embryo

    OpenAIRE

    Lim, Lorena; Zhou, Heping; Costa, Robert H.

    1997-01-01

    Mammalian hepatocyte nuclear factor-3 (HNF-3) and the Drosophila homeotic gene fork head proteins are prototypes of an extensive family of cell-specific transcription factors that share homology in the winged helix DNA-binding domain. One of these mammalian family members, HNF-3/fork head homolog-4 (HFH-4), was isolated by PCR amplification of rodent brain cDNA and exhibits abundant expression in the adult bronchiolar epithelium. In this study, we performed in ...

  19. Using Triple Helix Forming Peptide Nucleic Acids for Sequence-selective Recognition of Double-stranded RNA

    OpenAIRE

    Hnedzko, Dziyana; Cheruiyot, Samwel K.; Rozners, Eriks

    2014-01-01

    Non-coding RNAs play important roles in regulation of gene expression. Specific recognition and inhibition of these biologically important RNAs that form complex double-helical structures will be highly useful for fundamental studies in biology and practical applications in medicine. This protocol describes a strategy developed in our laboratory for sequence-selective recognition of double-stranded RNA (dsRNA) using triple helix forming peptide nucleic acids (PNAs) that bind in the major grov...

  20. P/CAF-mediated acetylation regulates the function of the basic helix–loop–helix transcription factor TAL1/SCL

    OpenAIRE

    Huang, Suming; Qiu, Yi; Shi, Yubin; Xu, Zhixiong; Brandt, Stephen J.

    2000-01-01

    The basic helix–loop–helix transcription factor TAL1 (or SCL) is a critical regulator of hematopoietic and vascular development and is misexpressed in the majority of patients with T-cell acute lymphoblastic leukemia. We found previously that TAL1 could interact with transcriptional co-activator and co-repressor complexes possessing histone acetyltransferase and deacetylase activities, respectively. Here, we report that TAL1 is subject to acetylation in vivo and can be acetylated by p300 and ...

  1. Chain length dependence of the helix orientation in Langmuir-Blodgett monolayers of alpha-helical diblock copolypeptides

    OpenAIRE

    Nguyen, Le-Thu T; Ardana, Aditya; Vorenkamp, Eltjo J.; ten Brinke, Gerrit; Schouten, Arend J.

    2010-01-01

    The effect of chain length on the helix orientation of alpha-helical diblock copolypeptides in Langmuir and Langmuir-Blodgett monolayers is reported for the first time. Amphiphilic diblock copolypeptides (PLGA-b-PMLGSLGs) of poly(alpha-L-glutamic acid) (PLGA) and poly(gamma-methyl-L-glutamate-ran-gamma-stearyl-L-glutamate) with 30 mol% of stearyl substituents (PMLGSLG) of various block lengths were studied. The tilt angle between the helices and the substrate-normal decreases upon increasing ...

  2. Helix Stability of Oligoglycine, Oligoalanine and Oligo-β-alanine Dodecamers Reflected by Hydrogen-Bond Persistence

    OpenAIRE

    Liu, Chengyu; Ponder, Jay W.; Marshall, Garland R.

    2014-01-01

    Helices are important structural/recognition elements in proteins and peptides. Stability and conformational differences between helices composed of α- and β-amino acids as scaffolds for mimicry of helix recognition has become a theme in medicinal chemistry. Furthermore, helices formed by β-amino acids are experimentally more stable than those formed by α-amino acids. This is paradoxical because the larger sizes of the hydrogen-bonding rings required by the extra methylene groups should lead ...

  3. In Vitro Antiviral Activity of Circular Triple Helix Forming Oligonucleotide RNA towards Feline Infectious Peritonitis Virus Replication

    OpenAIRE

    Oi Kuan Choong; Parvaneh Mehrbod; Bimo Ario Tejo; Abdul Rahman Omar

    2014-01-01

    Feline Infectious Peritonitis (FIP) is a severe fatal immune-augmented disease in cat population. It is caused by FIP virus (FIPV), a virulent mutant strain of Feline Enteric Coronavirus (FECV). Current treatments and prophylactics are not effective. The in vitro antiviral properties of five circular Triple-Helix Forming Oligonucleotide (TFO) RNAs (TFO1 to TFO5), which target the different regions of virulent feline coronavirus (FCoV) strain FIPV WSU 79-1146 genome, were tested in FIPV-infect...

  4. Triple-Helix Formation Induces Recombination in Mammalian Cells via a Nucleotide Excision Repair-Dependent Pathway

    OpenAIRE

    Faruqi, A. Fawad; Datta, Hirock J.; Carroll, Dana; Seidman, Michael M.; Glazer, Peter M.

    2000-01-01

    The ability to stimulate recombination in a site-specific manner in mammalian cells may provide a useful tool for gene knockout and a valuable strategy for gene therapy. We previously demonstrated that psoralen adducts targeted by triple-helix-forming oligonucleotides (TFOs) could induce recombination between tandem repeats of a supF reporter gene in a simian virus 40 vector in monkey COS cells. Based on work showing that triple helices, even in the absence of associated psoralen adducts, are...

  5. CD and UV Resonance Raman Indicate Little arg-glu Side Chain α-helix Peptide Stabilization

    OpenAIRE

    Hong, Zhenmin; Ahmed, Zeeshan; Asher, Sanford A.

    2011-01-01

    Electrostatic interactions between side chains can control the conformation and folding of peptides and proteins. We used CD and UV resonance Raman spectroscopy (UVRR) to examine the impact of side chain charge on the conformations of two 21 residue mainly polyala peptides with a few arg and glu residues. We expected that attractions between arg-10 and glu-14 side chains would stabilize the α-helix conformation compared to a peptide with an arg-14. Surprisingly, CD suggests that the peptide w...

  6. The helix nebula viewed in HCO+: Large-scale mapping of the J = 1 → 0 transition

    International Nuclear Information System (INIS)

    The J = 1 → 0 transition of HCO+ at 89 GHz has been mapped across the Helix Nebula (NGC 7293) with 70'' spatial resolution (1.68 km s–1 velocity resolution) using the Arizona Radio Observatory 12 m telescope. This work is the first large-scale mapping project of a dense gas tracer (n(H2) ∼ 105 cm–3) in old planetary nebulae. Observations of over 200 positions encompassing the classical optical image were conducted with a 3σ noise level of ∼20 mK. HCO+ was detected at most positions, often exhibiting multiple velocity components indicative of complex kinematic structures in dense gas. The HCO+ spectra suggest that the Helix is composed of a bipolar, barrel-like structure with red- and blue-shifted halves, symmetric with respect to the central star and oriented ∼10° east from the line of sight. A second bipolar, higher velocity outflow exists as well, situated along the direction of the Helix 'plumes'. The column density of HCO+ across the Helix is N tot ∼ 1.5 × 1010-5.0 × 1011 cm–2, with an average value N ave ∼ 1 × 1011 cm–2, corresponding to an abundance, relative to H2, of f ∼ 1.4 × 10–8. This value is similar to that observed in young PN, and contradicts chemical models, which predict that the abundance of HCO+ decreases with nebular age. This study indicates that polyatomic molecules readily survive the ultraviolet field of the central white dwarf, and can be useful in tracing nebular morphology in the very late stages of stellar evolution.

  7. PSOFuzzySVM-TMH: identification of transmembrane helix segments using ensemble feature space by incorporated fuzzy support vector machine.

    Science.gov (United States)

    Hayat, Maqsood; Tahir, Muhammad

    2015-08-01

    Membrane protein is a central component of the cell that manages intra and extracellular processes. Membrane proteins execute a diversity of functions that are vital for the survival of organisms. The topology of transmembrane proteins describes the number of transmembrane (TM) helix segments and its orientation. However, owing to the lack of its recognized structures, the identification of TM helix and its topology through experimental methods is laborious with low throughput. In order to identify TM helix segments reliably, accurately, and effectively from topogenic sequences, we propose the PSOFuzzySVM-TMH model. In this model, evolutionary based information position specific scoring matrix and discrete based information 6-letter exchange group are used to formulate transmembrane protein sequences. The noisy and extraneous attributes are eradicated using an optimization selection technique, particle swarm optimization, from both feature spaces. Finally, the selected feature spaces are combined in order to form ensemble feature space. Fuzzy-support vector Machine is utilized as a classification algorithm. Two benchmark datasets, including low and high resolution datasets, are used. At various levels, the performance of the PSOFuzzySVM-TMH model is assessed through 10-fold cross validation test. The empirical results reveal that the proposed framework PSOFuzzySVM-TMH outperforms in terms of classification performance in the examined datasets. It is ascertained that the proposed model might be a useful and high throughput tool for academia and research community for further structure and functional studies on transmembrane proteins. PMID:26054033

  8. Inhibition of spontaneous receptor phosphorylation by residues in a putative alpha-helix in the KIT intracellular juxtamembrane region.

    Science.gov (United States)

    Ma, Y; Cunningham, M E; Wang, X; Ghosh, I; Regan, L; Longley, B J

    1999-05-01

    KIT receptor kinase activity is repressed, prior to stem cell factor binding, by unknown structural constraints. Using site-directed mutagenesis, we examined the role of KIT intracellular juxtamembrane residues Met-552 through Ile-563 in controlling receptor autophosphorylation. Alanine substitution for Tyr-553, Trp-557, Val-559, or Val-560, all sitting along the hydrophobic side of an amphipathic alpha-helix (Tyr-553-Ile-563) predicted by the Chou-Fasman algorithm, resulted in substantially increased spontaneous receptor phosphorylation, revealing inhibitory roles for these residues. Alanine substitution for other residues, most of which are on the hydrophilic side of the helix, caused no or slightly increased basal receptor phosphorylation. Converting Tyr-553 or Trp-557 to phenylalanine generated slight or no elevation, respectively, in basal KIT phosphorylation, indicating that the phenyl ring of Tyr-553 and the hydrophobicity of Trp-557 are critical for the inhibition. Although alanine substitution for Lys-558 had no effect on receptor phosphorylation, its substitution with proline produced high spontaneous receptor phosphorylation, suggesting that the predicted alpha-helical conformation is involved in the inhibition. A synthetic peptide comprising Tyr-553 through Ile-563 showed circular dichroism spectra characteristic of alpha-helix, supporting the structural prediction. Thus, the KIT intracellular juxtamembrane region contains important residues which, in a putative alpha-helical conformation, exert inhibitory control on the kinase activity of ligand-unoccupied receptor. PMID:10224103

  9. Recent expansion and relic survival: Phylogeography of the land snail genus Helix (Mollusca, Gastropoda) from south to north Europe.

    Science.gov (United States)

    Fiorentino, V; Manganelli, G; Giusti, F; Ketmaier, V

    2016-05-01

    Little is known about the evolutionary history of Helix, despite the fact that it includes the largest land snails in the western Palaearctic, some of which (e.g. H. pomatia Linnaeus, 1758) are valuable human food. We compared two groups of Helix with apparently contrasting evolutionary histories: the widespread species H. pomatia and the group distributed along the Italian Apennine chain, a relatively unknown set of species with a restricted distribution over a range of altitudes. To reconstruct the evolutionary trajectories of these two groups, we analysed morphological (shell and genitalia) and molecular characters (mitochondrial and nuclear markers) in a total of 59 populations from northern and central Europe (H. pomatia) and along the Apennine chain (various species). We also reconstructed the phylogeny and the evolutionary history of the genus by combining our data with that currently available in the literature. We found that spatial changes did not merely imply fragmentation of populations, but also implied environmental changes (woodlands vs. grasslands) that may have triggered the observed phenotypic diversification. We also found that Anatolia is the ancestral range of Helix and is therefore an important area for the Palaearctic diversity. The results provide insights into the evolutionary history of species richness and more generally into the processes that may have shaped the distribution and diversification of these organisms across Europe and the peri-Mediterranean area. PMID:26926944

  10. Glass-like dynamics of the strain-induced coil/helix transition on a permanent polymer network.

    Science.gov (United States)

    Ronsin, O; Caroli, C; Baumberger, T

    2016-02-14

    We study the stress response to a step strain of covalently bonded gelatin gels in the temperature range where triple helix reversible crosslink formation is prohibited. We observe slow stress relaxation towards a T-dependent finite asymptotic level. We show that this is assignable to the strain-induced coil → helix transition, previously evidenced by Courty et al. [Proc. Natl. Acad. Sci. U. S. A. 102, 13457 (2005)], of a fraction of the polymer strands. Relaxation proceeds, in a first stage, according to a stretched exponential dynamics, then crosses over to a terminal simple exponential decay. The respective characteristic times τK and τf exhibit an Arrhenius-like T-dependence with an associated energy E incompatibly larger than the activation barrier height for the isomerisation process which sets the clock for an elementary coil → helix transformation event. We tentatively assign this glass-like slowing down of the dynamics to the long-range couplings due to the mechanical noise generated by the local elementary events in this random elastic medium. PMID:26874501

  11. Zooplankton, salinity, and other data from the ALPHA HELIX using nets in the Bering Sea from 22 July 1999 to 14 August 1999 (NODC Accession 0000262)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Zooplankton, salinity, fluorescence, and temperature data were collected from the ALPHA HELIX from July 22, 1999 to August 14, 1999. Data were submitted by...

  12. Chemical and depth data from the ALPHA HELIX using bottle casts in the Bering Sea from 1987-09-07 to 1988-06-11 (NODC Accession 0000263)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Chemical and depth data were collected from the ALPHA HELIX from September 7, 1987 to June 11, 1988. Data were submitted by the University of Alaska - Fairbanks;...

  13. Nutrients data collected from the ALPHA HELIX from the coastal waters of Alaska from 03 March 1998 to 07 December 1999 (NODC Accession 0000637)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Nutrients data were collected from bottle casts from the ALPHA HELIX in the coastal waters of Alaska from 08 March 1998 to 07 December 1999. Data include...

  14. The type II collagen fragments Helix-II and CTX-II reveal different enzymatic pathways of human cartilage collagen degradation

    DEFF Research Database (Denmark)

    Charni-Ben Tabassi, N; Desmarais, S; Jensen, Anne-Christine Bay;

    2008-01-01

    OBJECTIVE: Cartilage degradation in osteoarthritis (OA) generates the type II collagen fragments, Helix-II and CTX-II that can be used as clinical biological markers. Helix-II and C-telopeptide of type II collagen (CTX-II) levels are associated independently with progression of OA suggesting that...... they may be generated through different collagenolytic pathways. In this study we analyzed the release of Helix-II and CTX-II from human cartilage collagen by the proteinases reported to play a role in cartilage degradation. METHODS: In vitro, human articular cartilage extract was incubated with...... enzymatic pathways. Helix-II and CTX-II alone reflect only partially overall cartilage collagen degradation. These findings may explain why these two biological markers could provide complementary information on disease progression in OA....

  15. Triple helix formation: binding avidity of acridine-conjugated AG motif third strands containing natural, modified and surrogate bases opposed to pyrimidine interruptions in a polypurine target.

    OpenAIRE

    Orson, F M; Klysik, J; Bergstrom, D E; Ward, B; Glass, G A; P. Hua; Kinsey, B M

    1999-01-01

    A critical issue for the general application of triple-helix-forming oligonucleotides (TFOs) as modulators of gene expression is the dramatically reduced binding of short TFOs to targets that contain one or two pyrimidines within an otherwise homopurine sequence. Such targets are often found in gene regulatory regions, which represent desirable sites for triple helix formation. Using intercalator-conjugated AG motif TFOs, we compared the efficacy and base selectivity of 13 different bases or ...

  16. Loop-to-helix transition in the structure of multidrug regulator AcrR at the entrance of the drug-binding cavity

    Energy Technology Data Exchange (ETDEWEB)

    Manjasetty, Babu A.; Halavaty, Andrei S.; Luan, Chi-Hao; Osipiuk, Jerzy; Mulligan, Rory; Kwon, Keehwan; Anderson, Wayne F.; Joachimiak, Andrzej

    2016-04-01

    Multidrug transcription regulator AcrR from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 belongs to the tetracycline repressor family, one of the largest groups of bacterial transcription factors. The crystal structure of dimeric AcrR was determined and refined to 1.56 Å resolution. The tertiary and quaternary structures of AcrR are similar to those of its homologs. The multidrug binding site was identified based on structural alignment with homologous proteins and has a di(hydroxyethyl)ether molecule bound. Residues from helices a4 and a7 shape the entry into this binding site. The structure of AcrR reveals that the extended helical conformation of helix a4 is stabilized by the hydrogen bond between Glu67 (helix a4) and Gln130 (helix a7). Based on the structural comparison with the closest homolog structure, the Escherichia coli AcrR, we propose that this hydrogen bond is responsible for control of the loop-to-helix transition within helix a4. This local conformational switch of helix a4 may be a key step in accessing the multidrug binding site and securing ligands at the binding site. Solution smallmolecule binding studies suggest that AcrR binds ligands with their core chemical structure resembling the tetracyclic ring of cholesterol.

  17. Structure, stability, and thermodynamics of a short intermolecular purine-purine-pyrimidine triple helix

    Energy Technology Data Exchange (ETDEWEB)

    Pilch, D.S.; Shafer, R.H. (Univ. of California, San Francisco (United States)); Levenson, C. (Cetus Corp., Emeryville, CA (United States))

    1991-06-25

    The authors have investigated the structure and physical chemistry of the d(C{sub 3}T{sub 4}C{sub 3}){center dot}2(d(G{sub 3}A{sub 4}G{sub 3})) triple helix by polyacrylamide gel electrophoresis (PAGE), {sup 1}H NMR, and ultraviolet (UV) absorption spectroscopy. The triplex was stabilized with MgCl{sub 2} at neutral pH. PAGE studies verify the stoichiometry of the strands comprising the triplex and indicate that the orientation of the third strand in purine-purine-pyrimidine (pur-pur-pyr) triplexes is antiparallel with respect to the purine strand of the underlying duplex. Imino proton NMR spectra provide evidence for the existence of new purine-purine (pur{center dot}pur) hydrogen bonds, in addition to those of the Watson-Crick (W-C) base pairs, in the triplex structure. These new hydrogen bonds are likely to correspond to the interaction between third-strand guanine NH1 imino protons and the N7 atoms of guanine residues on the puring strand of the underlying duplex. Thermal denaturation of the triplex proceeds to single strands in one step, under the conditions used in this study. Binding of the third strand appears to enhance the thermal stability of the duplex by 1-3 C, depending on the DNA concentration. This marked enhancement in stability, coupled with the lack of an acidic pH requirement, suggests that pur-pur-pyr triplexes are appealing choices for use in applications involving oligonucleotide targeting of duplex DNA in vitro and in vivo.

  18. Structure, stability, and thermodynamics of a short intermolecular purine-purine-pyrimidine triple helix

    International Nuclear Information System (INIS)

    The authors have investigated the structure and physical chemistry of the d(C3T4C3)·2[d(G3A4G3)] triple helix by polyacrylamide gel electrophoresis (PAGE), 1H NMR, and ultraviolet (UV) absorption spectroscopy. The triplex was stabilized with MgCl2 at neutral pH. PAGE studies verify the stoichiometry of the strands comprising the triplex and indicate that the orientation of the third strand in purine-purine-pyrimidine (pur-pur-pyr) triplexes is antiparallel with respect to the purine strand of the underlying duplex. Imino proton NMR spectra provide evidence for the existence of new purine-purine (pur·pur) hydrogen bonds, in addition to those of the Watson-Crick (W-C) base pairs, in the triplex structure. These new hydrogen bonds are likely to correspond to the interaction between third-strand guanine NH1 imino protons and the N7 atoms of guanine residues on the puring strand of the underlying duplex. Thermal denaturation of the triplex proceeds to single strands in one step, under the conditions used in this study. Binding of the third strand appears to enhance the thermal stability of the duplex by 1-3 C, depending on the DNA concentration. This marked enhancement in stability, coupled with the lack of an acidic pH requirement, suggests that pur-pur-pyr triplexes are appealing choices for use in applications involving oligonucleotide targeting of duplex DNA in vitro and in vivo

  19. BuD, a helix–loop–helix DNA-binding domain for genome modification

    International Nuclear Information System (INIS)

    Crystal structures of BurrH and the BurrH–DNA complex are reported. DNA editing offers new possibilities in synthetic biology and biomedicine for modulation or modification of cellular functions to organisms. However, inaccuracy in this process may lead to genome damage. To address this important problem, a strategy allowing specific gene modification has been achieved through the addition, removal or exchange of DNA sequences using customized proteins and the endogenous DNA-repair machinery. Therefore, the engineering of specific protein–DNA interactions in protein scaffolds is key to providing ‘toolkits’ for precise genome modification or regulation of gene expression. In a search for putative DNA-binding domains, BurrH, a protein that recognizes a 19 bp DNA target, was identified. Here, its apo and DNA-bound crystal structures are reported, revealing a central region containing 19 repeats of a helix–loop–helix modular domain (BurrH domain; BuD), which identifies the DNA target by a single residue-to-nucleotide code, thus facilitating its redesign for gene targeting. New DNA-binding specificities have been engineered in this template, showing that BuD-derived nucleases (BuDNs) induce high levels of gene targeting in a locus of the human haemoglobin β (HBB) gene close to mutations responsible for sickle-cell anaemia. Hence, the unique combination of high efficiency and specificity of the BuD arrays can push forward diverse genome-modification approaches for cell or organism redesign, opening new avenues for gene editing

  20. BuD, a helix–loop–helix DNA-binding domain for genome modification

    Energy Technology Data Exchange (ETDEWEB)

    Stella, Stefano [Spanish National Cancer Research Centre (CNIO), Calle de Melchor Fernández Almagro 3, 28029 Madrid (Spain); University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen (Denmark); Molina, Rafael; López-Méndez, Blanca [Spanish National Cancer Research Centre (CNIO), Calle de Melchor Fernández Almagro 3, 28029 Madrid (Spain); Juillerat, Alexandre; Bertonati, Claudia; Daboussi, Fayza [Cellectis, 8 Rue de la Croix Jarry, 75013 Paris (France); Campos-Olivas, Ramon [Spanish National Cancer Research Centre (CNIO), Calle de Melchor Fernández Almagro 3, 28029 Madrid (Spain); Duchateau, Phillippe [Cellectis, 8 Rue de la Croix Jarry, 75013 Paris (France); Montoya, Guillermo, E-mail: guillermo.montoya@cpr.ku.dk [Spanish National Cancer Research Centre (CNIO), Calle de Melchor Fernández Almagro 3, 28029 Madrid (Spain); University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen (Denmark)

    2014-07-01

    Crystal structures of BurrH and the BurrH–DNA complex are reported. DNA editing offers new possibilities in synthetic biology and biomedicine for modulation or modification of cellular functions to organisms. However, inaccuracy in this process may lead to genome damage. To address this important problem, a strategy allowing specific gene modification has been achieved through the addition, removal or exchange of DNA sequences using customized proteins and the endogenous DNA-repair machinery. Therefore, the engineering of specific protein–DNA interactions in protein scaffolds is key to providing ‘toolkits’ for precise genome modification or regulation of gene expression. In a search for putative DNA-binding domains, BurrH, a protein that recognizes a 19 bp DNA target, was identified. Here, its apo and DNA-bound crystal structures are reported, revealing a central region containing 19 repeats of a helix–loop–helix modular domain (BurrH domain; BuD), which identifies the DNA target by a single residue-to-nucleotide code, thus facilitating its redesign for gene targeting. New DNA-binding specificities have been engineered in this template, showing that BuD-derived nucleases (BuDNs) induce high levels of gene targeting in a locus of the human haemoglobin β (HBB) gene close to mutations responsible for sickle-cell anaemia. Hence, the unique combination of high efficiency and specificity of the BuD arrays can push forward diverse genome-modification approaches for cell or organism redesign, opening new avenues for gene editing.

  1. Homology modeling of major intrinsic proteins in rice, maize and Arabidopsis: comparative analysis of transmembrane helix association and aromatic/arginine selectivity filters

    Directory of Open Access Journals (Sweden)

    Sankararamakrishnan Ramasubbu

    2007-04-01

    Full Text Available Abstract Background The major intrinsic proteins (MIPs facilitate the transport of water and neutral solutes across the lipid bilayers. Plant MIPs are believed to be important in cell division and expansion and in water transport properties in response to environmental conditions. More than 30 MIP sequences have been identified in Arabidopsis thaliana, maize and rice. Plasma membrane intrinsic proteins (PIPs, tonoplast intrinsic proteins (TIPs, Nod26-like intrinsic protein (NIPs and small and basic intrinsic proteins (SIPs are subfamilies of plant MIPs. Despite sequence diversity, all the experimentally determined structures belonging to the MIP superfamily have the same "hour-glass" fold. Results We have structurally characterized 39 rice and 31 maize MIPs and compared them with that of Arabidopsis. Homology models of 105 MIPs from all three plant species were built. Structure-based sequence alignments were generated and the residues in the helix-helix interfaces were analyzed. Small residues (Gly/Ala/Ser/Thr are found to be highly conserved as a group in the helix-helix interface of MIP structures. Individual families sometimes prefer one or another of the residues from this group. The narrow aromatic/arginine (ar/R selectivity filter in MIPs has been shown to provide an important constriction for solute permeability. Ar/R regions were analyzed and compared between the three plant species. Seventeen TIP, NIP and SIP members from rice and maize have ar/R signatures that are not found in Arabidopsis. A subgroup of rice and maize NIPs has small residues in three of the four positions in the ar/R tetrad, resulting in a wider constriction. These MIP members could transport larger solute molecules. Conclusion Small residues are group-conserved in the helix-helix interface of MIP structures and they seem to be important for close helix-helix interactions. Such conservation might help to preserve the hour-glass fold in MIP structures. Analysis and

  2. SU-E-T-564: Multi-Helix Rotating Shield Brachytherapy for Cervical Cancer

    International Nuclear Information System (INIS)

    Purpose: To present a novel and practical brachytherapy technique, called multi-helix rotating shield brachytherapy (H-RSBT), for the precise positioning of a partial shield in a curved applicator. H-RSBT enables RSBT delivery using only translational motion of the radiation source/shield combination. H-RSBT overcomes the challenges associated with previously proposed RSBT approaches based on a serial (S-RSBT) step-and-shoot delivery technique, which required independent translational and rotational motion. Methods: A Fletcher-type applicator, compatible with the combination of a Xoft Axxent™ electronic brachytherapy source and a 0.5 mm thick tungsten shield, is proposed. The wall of the applicator contains six evenly-spaced helical keyways that rigidly define the emission direction of the shield as a function of depth. The shield contains three protruding keys and is attached to the source such that it rotates freely. S-RSBT and H-RSBT treatment plans with 180° and 45° azimuthal emission angles were generated for five cervical cancer patients representative of a wide range of high-risk clinical target volume (HR-CTV) shapes and applicator positions. The number of beamlets used in the treatment planning process was nearly constant for S-RSBT and H-RSBT by using dwell positions separated by 5 and 1.7 mm, respectively, and emission directions separated by 22.5° and 60°, respectively. For all the treatment plans the EQD2 of the HR-CTV was escalated until the EQD2cc tolerance of either the bladder, rectum, or sigmoid colon was reached. Results: Treatment times for H-RSBT tended to be shorter than for S-RSBT, with changes of −38.47% to 1.12% with an average of −8.34%. The HR-CTV D90 changed by −8.81% to 2.08% with an average of −2.46%. Conclusion: H-RSBT is a mechanically feasible technique in the curved applicators needed for cervical cancer brachytherapy. S-RSBT and H-RSBT dose distributions were clinically equivalent for all patients considered, with

  3. SU-E-T-564: Multi-Helix Rotating Shield Brachytherapy for Cervical Cancer

    Energy Technology Data Exchange (ETDEWEB)

    Dadkhah, H; Wu, X [University of Iowa, Iowa City, IA (United States); Flynn, R; Kim, Y [University of Iowa Hospitals and Clinics, Iowa City, IA (United States)

    2015-06-15

    Purpose: To present a novel and practical brachytherapy technique, called multi-helix rotating shield brachytherapy (H-RSBT), for the precise positioning of a partial shield in a curved applicator. H-RSBT enables RSBT delivery using only translational motion of the radiation source/shield combination. H-RSBT overcomes the challenges associated with previously proposed RSBT approaches based on a serial (S-RSBT) step-and-shoot delivery technique, which required independent translational and rotational motion. Methods: A Fletcher-type applicator, compatible with the combination of a Xoft Axxent™ electronic brachytherapy source and a 0.5 mm thick tungsten shield, is proposed. The wall of the applicator contains six evenly-spaced helical keyways that rigidly define the emission direction of the shield as a function of depth. The shield contains three protruding keys and is attached to the source such that it rotates freely. S-RSBT and H-RSBT treatment plans with 180° and 45° azimuthal emission angles were generated for five cervical cancer patients representative of a wide range of high-risk clinical target volume (HR-CTV) shapes and applicator positions. The number of beamlets used in the treatment planning process was nearly constant for S-RSBT and H-RSBT by using dwell positions separated by 5 and 1.7 mm, respectively, and emission directions separated by 22.5° and 60°, respectively. For all the treatment plans the EQD2 of the HR-CTV was escalated until the EQD{sub 2cc} tolerance of either the bladder, rectum, or sigmoid colon was reached. Results: Treatment times for H-RSBT tended to be shorter than for S-RSBT, with changes of −38.47% to 1.12% with an average of −8.34%. The HR-CTV D{sub 90} changed by −8.81% to 2.08% with an average of −2.46%. Conclusion: H-RSBT is a mechanically feasible technique in the curved applicators needed for cervical cancer brachytherapy. S-RSBT and H-RSBT dose distributions were clinically equivalent for all patients

  4. Triple Helix Model in Developing Technological Innovation: The Case of Computer Based Interlocking

    Directory of Open Access Journals (Sweden)

    Erry Ricardo Nurzal

    2013-01-01

    Full Text Available Computer Based Interlocking (CBI is the most important part of the electric railway signalingsystem which serves as the “brain” that controls the operation of electrical signaling system thatreplaces the role of the electromagnetic relay which has gradually been abandoned. Developmentof CBI is based on the fact that until recently the signaling system in Indonesia is still reliedheavily on the CBI products from foreign vendors. Therefore, the development of domestic CBIproducts is really necessary in order to decrease the dependence on technology from foreignvendors that at the same time is also be able to support the accelerated development of railwayinfrastructure in Indonesia.The CBI development is conducted in the form of a collaboration involving the government,universities, and industry. This paper explores and analyzes the roles and interactions betweendifferent actors in the triple helix perspective, and identifies how the innovation ecosystemfunctioning with support from the government.Based on the data collected through in-depth interview with the actors involved in the CBI casestudy, this paper gives some key findings. First, government role is very important in establishingan innovation ecosystem for CBI development. Second, the leader in the development of CBItechnological innovation should be the industry supported by governmental R & D institutionsand universities. Third, R & D consortium is an effective vehicle for creating an interactionamong industry, academia, and government.Such findings may provide conceptual direction which is important for the development oftechnological innovation in Indonesia. In addition, in providing support for R&D activities, thegovernment needs to direct its R & D incentives to the industry as a business practitioner with itsown technology roadmap. The possible further research may include some research issues. First,is the pattern occurred in the CBI case also applied in the other cases of

  5. Helix geometry, hydration, and G.A mismatch in a B-DNA decamer.

    Science.gov (United States)

    Privé, G G; Heinemann, U; Chandrasegaran, S; Kan, L S; Kopka, M L; Dickerson, R E

    1987-10-23

    The DNA double helix is not a regular, featureless barberpole molecule. Different base sequences have their own special signature, in the way that they influence groove width, helical twist, bending, and mechanical rigidity or resistance to bending. These special features probably help other molecules such as repressors to read and recognize one base sequence in preference to another. Single crystal x-ray structure analysis is beginning to show us the various structures possible in the B-DNA family. The DNA decamer C-C-A-A-G-A-T-T-G-G appears to be a better model for mixed-sequence B-DNA than was the earlier C-G-C-G-A-A-T-T-C-G-C-G, which is more akin to regions of poly(dA).poly(dT). The G.A mismatch base pairs at the center of the decamer are in the anti-anti conformation about their bonds from base to sugar, in agreement with nuclear magnetic resonance evidence on this and other sequences, and in contrast to the anti-syn geometry reported for G.A pairs in C-G-C-G-A-A-T-T-A-G-C-G. The ordered spine of hydration seen earlier in the narrow-grooved dodecamer has its counterpart, in this wide-grooved decamer, in two strings of water molecules lining the walls of the minor groove, bridging from purine N3 or pyrimidine O2, to the following sugar O4'. The same strings of hydration are present in the phosphorothioate analog of G-C-G-C-G-C. Unlike the spine, which is broken up by the intrusion of amine groups at guanines, these water strings are found in general, mixed-sequence DNA because they can pass by unimpeded to either side of a guanine N2 amine. The spine and strings are perceived as two extremes of a general pattern of hydration of the minor groove, which probably is the dominant factor in making B-DNA the preferred form at high hydration. PMID:3310237

  6. Analysis of the function of E. coli 23S rRNA helix-loop 69 by mutagenesis

    Directory of Open Access Journals (Sweden)

    Maiväli Ülo

    2005-07-01

    Full Text Available Abstract Background The ribosome is a two-subunit enzyme known to exhibit structural dynamism during protein synthesis. The intersubunit bridges have been proposed to play important roles in decoding, translocation, and the peptidyl transferase reaction; yet the physical nature of their contributions is ill understood. An intriguing intersubunit bridge, B2a, which contains 23S rRNA helix 69 as a major component, has been implicated by proximity in a number of catalytically important regions. In addition to contacting the small ribosomal subunit, helix 69 contacts both the A and P site tRNAs and several translation factors. Results We scanned the loop of helix 69 by mutagenesis and analyzed the mutant ribosomes using a plasmid-borne IPTG-inducible expression system. We assayed the effects of 23S rRNA mutations on cell growth, contribution of mutant ribosomes to cellular polysome pools and the ability of mutant ribosomes to function in cell-free translation. Mutations A1912G, and A1919G have very strong growth phenotypes, are inactive during in vitro protein synthesis, and under-represented in the polysomes. Mutation Ψ1917C has a very strong growth phenotype and leads to a general depletion of the cellular polysome pool. Mutation A1916G, having a modest growth phenotype, is apparently defective in the assembly of the 70S ribosome. Conclusion Mutations A1912G, A1919G, and Ψ1917C of 23S rRNA strongly inhibit translation. Mutation A1916G causes a defect in the 50S subunit or 70S formation. Mutations Ψ1911C, A1913G, C1914A, Ψ1915C, and A1918G lack clear phenotypes.

  7. Properties of Soliton-Transported Bio-energy in α-Helix Protein Molecules with Three Channels

    International Nuclear Information System (INIS)

    We study numerically the propagating properties of soliton-transported bio-energy excited in the α-helix protein molecules with three channels in the cases of the short-time and long-time motions and its features of collision at temperature T = 0 and biological temperature T = 300 K by the dynamic equations in the improved Davydov theory and fourth-order Runge-Kutta method, respectively. From these simulation experiments we see that the new solitons in the improved model can move without dispersion at a constant speed retaining its shape and energy in the cases of motion of both short-time or T = 0 and long time or T = 300 K and can go through each other without scattering in their collisions. In these cases its lifetime is, at least, 120 ps at 300 K, in which the soliton can travel over about 700 amino acid residues. This result is consistent with analytic result obtained by quantum perturbed theory in this model. In the meanwhile, the influences of structure disorder of α-helix protein molecules, including the inhomogeneous distribution of amino acids with different masses and fluctuations of spring constant, dipole-dipole interaction, exciton-phonon coupling constant and diagonal disorder, on the solitons are also studied by the fourth-order Runge-Kutta method. The results show that the soliton still is very robust against the structure disorders and thermal perturbation of proteins at biological temperature 300 K. Therefore we can conclude that the new soliton in the α-helix protein molecules with three channels is a possible carrier of bio-energy transport and the improved model is possibly a candidate for the mechanism of this transport.

  8. The hot hELicon eXperiment (HELIX) and the large experiment on instabilities and anisotropy (LEIA)

    Science.gov (United States)

    Scime, E. E.; Keiter, P. A.; Balkey, M. M.; Kline, J. L.; Sun, X.; Keesee, A. M.; Hardin, R. A.; Biloiu, I. A.; Houshmandyar, S.; Chakraborty Thakur, S.; Carr, J.; Galante, M.; McCarren, D.; Sears, S.

    2015-01-01

    The West Virginia University Hot hELIcon eXperiment (HELIX) provides variable density and ion temperature plasmas, with controllable levels of thermal anisotropy, for space relevant laboratory experiments in the Large Experiment on Instabilities and Anisotropy (LEIA) as well as fundamental studies of helicon source physics in HELIX. Through auxiliary ion heating, the ion temperature anisotropy (T ⊥/T ∥) is variable from 1 to 20 for parallel plasma beta (β = 8πnkT i∥/B 2) values that span the range of 0.0001 to 0.01 in LEIA. The ion velocity distribution function is measured throughout the discharge volume in steady-state and pulsed plasmas with laser induced fluorescence (LIF). The wavelengths of very short wavelength electrostatic fluctuations are measured with a coherent microwave scattering system. Operating at low neutral pressures triggers spontaneous formation of a current-free electric double layer. Ion acceleration through the double layer is detected through LIF. LIF-based velocity space tomography of the accelerated beam provides a two-dimensional mapping of the bulk and beam ion distribution functions. The driving frequency for the m = 1 helical antenna is continuously variable from 8.5 to 16 MHz and frequency dependent variations of the RF coupling to the plasma allow the spontaneously appearing double layers to be turned on and off without modifying the plasma collisionality or magnetic field geometry. Single and multi-species plasmas are created with argon, helium, nitrogen, krypton, and xenon. The noble gas plasmas have steep neutral density gradients, with ionization levels reaching 100% in the core of the plasma source. The large plasma density in the source enables the study of Aflvén waves in the HELIX device.

  9. NMR studies of abasic sites in DNA duplexes: deoxyadenosine stacks into the helix opposite the cyclic analog of 2-deoxyribose

    International Nuclear Information System (INIS)

    Proton and phosphorus NMR studies are reported for the complementary d(C-A-T-G-A-G-T-A-C) x d(G-T-A-C-F-C-A-T-G) nonanucleotide duplex (designated AP/sub F/ 9-mer duplex) which contains a stable abasic site analog, F, in the center of the helix. This oligodeoxynucleotide contains a modified tetrahydrofuran moiety, isosteric with 2-deoxyribofuranose, which serves as a structural analog of a natural apurinic/apyrimidinic site. Exchangeable and nonexchangeable base and sugar protons, including those located at the abasic site, have been assigned in the complementary AP/sub F/ 9-mer duplex by recording and analyzing two-dimensional phase-sensitive NOESY data sets in H2O and D2O solution at low temperature (00C). These studies indicate that A5 inserts into the helix opposite the abasic site F14 and stacks with flanking G4 x C15 and G6 x C13 Watson-Crick base pairs. Base-sugar proton NOE connectivities were measured through G4-A5-G6 on the unmodified strand and between the base protons of C15 and the sugar protons of the 5'-flanking residue F14 on the modified strand. These studies establish that all glycosidic torsion angles are anti and that the helix is right-handed at and adjacent to the abasic site in the AP/sub F/ 9-mer duplex. Two of the 16 phosphodiester groups exhibit phosphorus resonances outside the normal spectral dispersion indicative of altered torsion angles at two of the phosphate groups in the backbone of the AP/sub F/ 9-mer duplex

  10. A novel {sup 18}F-labeled two-helix scaffold protein for PET imaging of HER2-positive tumor

    Energy Technology Data Exchange (ETDEWEB)

    Miao, Zheng; Ren, Gang; Jiang, Lei; Liu, Hongguang; Cheng, Zhen [Stanford University, Molecular Imaging Program at Stanford (MIPS), Department of Radiology, Stanford Cancer Center, Bio-X Program, Stanford, CA (United States); Webster, Jack M.; Zhang, Rong; Syud, Faisal [General Electric Company, Global Research, Niskayuna, NY (United States); Namavari, Mohammad; Gambhir, Sanjiv S. [Stanford University, MIPS, Departments of Radiology and Bioengineering, Stanford Cancer Center, Bio-X Program, Stanford, CA (United States)

    2011-11-15

    Two-helix scaffold proteins ({proportional_to} 5 kDa) against human epidermal growth factor receptor type 2 (HER2) have been discovered in our previous work. In this research we aimed to develop an {sup 18}F-labeled two-helix scaffold protein for positron emission tomography (PET) imaging of HER2-positive tumors. An aminooxy-functionalized two-helix peptide (AO-MUT-DS) with high HER2 binding affinity was synthesized through conventional solid phase peptide synthesis. The purified linear peptide was cyclized by I{sub 2} oxidation to form a disulfide bridge. The cyclic peptide was then conjugated with a radiofluorination synthon, 4-{sup 18}F-fluorobenzyl aldehyde ({sup 18}F-FBA), through the aminooxy functional group at the peptide N terminus (30% yield, non-decay corrected). The binding affinities of the peptides were analyzed by Biacore analysis. Cell uptake assay of the resulting PET probe, {sup 18}F-FBO-MUT-DS, was performed at 37 C. {sup 18}F-FBO-MUT-DS with high specific activity (20-32 MBq/nmol, 88-140 {mu}Ci/{mu}g, end of synthesis) was injected into mice xenograft model bearing SKOV3 tumor. MicroPET and biodistribution and metabolic stability studies were then conducted. Cell uptake assays showed high and specific cell uptake ({proportional_to}12% applied activity at 1 h) by incubation of {sup 18}F-FBO-MUT-DS with HER2 high-expressing SKOV3 ovarian cancer cells. The affinities (K{sub D}) of AO-MUT-DS and FBO-MUT-DS as tested by Biacore analysis were 2 and 1 nM, respectively. In vivo small animal PET demonstrated fast tumor targeting, high tumor accumulation, and good tumor to normal tissue contrast of {sup 18}F-FBO-MUT-DS. Biodistribution studies further revealed that the probe had excellent tumor uptake (6.9%ID/g at 1 h post-injection) and was cleared through both liver and kidneys. Co-injection of the probe with 500 {mu}g of HER2 Affibody protein reduced the tumor uptake (6.9 vs 1.8%ID/g, p < 0.05). F-FBO-MUT-DS displays excellent HER2 targeting ability

  11. Persistent spin helix on a wurtzite ZnO(101-bar0) surface. First-principles density-functional study

    International Nuclear Information System (INIS)

    The persistent spin helix (PSH) that has been widely and exclusively studied in zinc-blende structures is revealed for the first time on the surface of a wurtzite structure. Through first principles calculations of the surface of ZnO(101-bar0), a quasi-one-dimensional orientation of the spin textures is identified. Furthermore, the wavelength of this particular PSH is smaller than that observed in various zinc-blende quantum well structures, thus indicating that wurtzite-structured surfaces are suitable for spintronics applications. (author)

  12. Cooperative formation of native-like tertiary contacts in the ensemble of unfolded states of a four-helix protein

    DEFF Research Database (Denmark)

    Bruun, Susanne W; Iesmantavicius, Vytautas; Danielsson, Jens; Poulsen, Flemming Martin

    2010-01-01

    In studies of the ensembles of unfolded structures of a four-helix bundle protein, we have detected the presence of potential precursors of native tertiary structures. These observations were based on the perturbation of NMR chemical shifts of the protein backbone atoms by single site mutations...... folding mechanism of this protein using only experimental data by combining the information available for the rate limiting structure formation during the folding process with measurements of the site specific hydrogen bond formation in the burst phase, and with the existence prior to the folding reaction...... of tertiary structures in the ensemble of otherwise unfolded structures observed in the present study....

  13. Design of a novel triple helix-forming oligodeoxyribonucleotide directed to the major promoter of the c-myc gene

    OpenAIRE

    McGuffie, E M; Catapano, C. V.

    2002-01-01

    Altered expression of c-myc is implicated in pathogenesis and progression of many human cancers. Triple helix-forming oligonucleotides (TFOs) directed to a polypurine/polypyrimidine sequence in a critical regulatory region near the c-myc P2 promoter have been shown to inhibit c-myc transcription in vitro and in cells. However, these guanine-rich TFOs had moderate binding affinity and required high concentrations for activity. The 23 bp myc P2 sequence is split equally into AT- and GC-rich tra...

  14. Super-specific DNA methylation by a DNA methyltransferase coupled with a triple helix-forming oligonucleotide

    OpenAIRE

    Maluszynska-Hoffman, Maria

    2008-01-01

    In this work, an engineered variant of the DNA cytosine-C5 methyltransferase (MTase) M.SssI has been conjugated with a triple helix-forming oligonucleotide (TFO) and the properties of the enzyme-TFO conjugate were evaluated using a variety of biochemical and biophysical methods. M.SssI is the only known prokaryotic DNA MTase which shares the 5’-CG-3’ recognition sequence (CpG) with mammalian DNA MTases. It has been rendered a super-specific MTase by conjugation with a TFO designed to bind a t...

  15. Self-replication of chemical systems based on recognition within a double or a triple helix - A realistic hypothesis

    Science.gov (United States)

    Kanavarioti, Anastassia

    1992-01-01

    A scenario is proposed for the non-enzymatic self-replication of short RNA molecules. The self-replication of an oligopyrimidine strand is considered and the process of template-directed synthesis based on recognition within a double helix is discussed. Replication mechanisms are suggested for selected oligonucleotides. The mechanisms are based on Watson-Crick base pairing between complementary nucleotides as well as Hoogsteen base pairing between a duplex and the complementary third strand. It is suggested that self-replication based on these mechanisms may be accomplished but may result in a substantial amount of misinformation transfer when mixed oligonucleotides are used.

  16. Expression cloning of cDNA encoding a seven-helix receptor from human placenta with affinity for opioid ligands

    OpenAIRE

    1992-01-01

    Here we report the expression cloning of cDNA encoding a putative opioid receptor from a human placenta cDNA library. Placental opioid receptors are of the kappa type. As the dynorphin opioid peptides are kappa-selective, a dynorphin ligand was used in an affinity-enrichment (panning) procedure to select transiently transfected COS-7 cells expressing kappa receptor binding sites. The cloned cDNA encodes a 440-residue protein of the seven-helix guanine nucleotide-binding protein (G-protein)-co...

  17. Helix Nebula: Enabling federation of existing data infrastructures and data services to an overarching cross-domain e-infrastructure

    Science.gov (United States)

    Lengert, Wolfgang; Farres, Jordi; Lanari, Riccardo; Casu, Francesco; Manunta, Michele; Lassalle-Balier, Gerard

    2014-05-01

    Helix Nebula has established a growing public private partnership of more than 30 commercial cloud providers, SMEs, and publicly funded research organisations and e-infrastructures. The Helix Nebula strategy is to establish a federated cloud service across Europe. Three high-profile flagships, sponsored by CERN (high energy physics), EMBL (life sciences) and ESA/DLR/CNES/CNR (earth science), have been deployed and extensively tested within this federated environment. The commitments behind these initial flagships have created a critical mass that attracts suppliers and users to the initiative, to work together towards an "Information as a Service" market place. Significant progress in implementing the following 4 programmatic goals (as outlined in the strategic Plan Ref.1) has been achieved: × Goal #1 Establish a Cloud Computing Infrastructure for the European Research Area (ERA) serving as a platform for innovation and evolution of the overall infrastructure. × Goal #2 Identify and adopt suitable policies for trust, security and privacy on a European-level can be provided by the European Cloud Computing framework and infrastructure. × Goal #3 Create a light-weight governance structure for the future European Cloud Computing Infrastructure that involves all the stakeholders and can evolve over time as the infrastructure, services and user-base grows. × Goal #4 Define a funding scheme involving the three stake-holder groups (service suppliers, users, EC and national funding agencies) into a Public-Private-Partnership model to implement a Cloud Computing Infrastructure that delivers a sustainable business environment adhering to European level policies. Now in 2014 a first version of this generic cross-domain e-infrastructure is ready to go into operations building on federation of European industry and contributors (data, tools, knowledge, ...). This presentation describes how Helix Nebula is being used in the domain of earth science focusing on geohazards. The

  18. A Composite Element that Binds Basic Helix Loop Helix and Basic Leucine Zipper Transcription Factors Is Important for Gonadotropin-Releasing Hormone Regulation of the Follicle-Stimulating Hormone β Gene

    Science.gov (United States)

    Ciccone, Nick A.; Lacza, Charlemagne T.; Hou, Melody Y.; Gregory, Susan J.; Kam, Kyung-Yoon; Xu, Shuyun; Kaiser, Ursula B.

    2008-01-01

    Although FSH plays an essential role in controlling gametogenesis, the biology of FSHβ transcription remains poorly understood, but is known to involve the complex interplay of multiple endocrine factors including GnRH. We have identified a GnRH-responsive element within the rat FSHβ promoter containing an E-box and partial cAMP response element site that are bound by the basic helix loop helix transcription factor family members, upstream stimulating factor (USF)-1/USF-2, and the basic leucine zipper member, cAMP response element-binding protein (CREB), respectively. Expression studies with CREB, USF-1/USF-2, and activating protein-1 demonstrated that the USF transcription factors increased basal transcription, an effect not observed if the cognate binding site was mutated. Conversely, expression of a dominant negative CREB mutant or CREB knockdown attenuated induction by GnRH, whereas dominant negative Fos or USF had no effect on the GnRH response. GnRH stimulation specifically induced an increase in phosphorylated CREB occupation of the FSHβ promoter, leading to the recruitment of CREB-binding protein to enhance gene transcription. In conclusion, a composite element bound by both USF and CREB serves to integrate signals for basal and GnRH-stimulated transcription of the rat FSHβ gene. PMID:18550775

  19. Exposed hydrophobic residues in human immunodeficiency virus type 1 Vpr helix-1 are important for cell cycle arrest and cell death.

    Directory of Open Access Journals (Sweden)

    R Anthony Barnitz

    Full Text Available The human immunodeficiency virus type 1 (HIV-1 accessory protein viral protein R (Vpr is a major determinant for virus-induced G2/M cell cycle arrest and cytopathicity. Vpr is thought to perform these functions through the interaction with partner proteins. The NMR structure of Vpr revealed solvent exposed hydrophobic amino acids along helices 1 and 3 of Vpr, which could be putative protein binding domains. We previously showed that the hydrophobic patch along helix-3 was important for G2/M blockade and cytopathicity. Mutations of the exposed hydrophobic residues along helix-1 were found to reduce Vpr-induced cell cycle arrest and cell death as well. The levels of toxicity during virion delivery of Vpr correlated with G2/M arrest. Thus, the exposed hydrophobic amino acids in the amino-terminal helix-1 are important for the cell cycle arrest and cytopathicity functions of Vpr.

  20. Rapid Determination of α-Hederin and Hederacoside C in Extracts of Hedera helix Leaves Available in the Czech Republic and Poland.

    Science.gov (United States)

    Havliková, Lucie; Macáková, Kateřina; Opleta, Lubomir; Solich, Petr

    2015-09-01

    Leaf extracts of Hedera helix L. are widely used in the treatment of upper respiratory diseases. The saponins a-hederin and hederacoside C are considered to be the main compounds responsible for the biological activity. a-Hederin and hederacoside C were determined in H. helix leaf extracts using a fast, simple and validated HPLC method. An XTerra MS C18 column and mobile phase composed of 10 mM ammonium acetate at pH 8.5 (adjusted with triethylamine) and acetonitrile were used for the chromatography at 1.2 mL min(-1). The column was kept at 30°C. Detection was performed at 220 nm. An approach utilizing a basic pH of the aqueous part of the mobile phase enabled analysis in 5 minutes in isocratic mode. The method was validated and used for the quality control of H. helix leaf ethanolic extracts. PMID:26594750

  1. Effects of chain length of an amphipathic polypeptide carrying the repeated amino acid sequence (LETLAKA)(n) on α-helix and fibrous assembly formation.

    Science.gov (United States)

    Takei, Toshiaki; Hasegawa, Kazuya; Imada, Katsumi; Namba, Keiichi; Tsumoto, Kouhei; Kuriki, Yukino; Yoshino, Masakuni; Yazaki, Kazumori; Kojima, Shuichi; Takei, Tsunetomo; Ueda, Takuya; Miura, Kin-ichiro

    2013-04-23

    Polypeptide α3 (21 residues), with three repeats of a seven-amino-acid sequence (LETLAKA)(3), forms an amphipathic α-helix and a long fibrous assembly. Here, we investigated the ability of α3-series polypeptides (with 14-42 residues) of various chain lengths to form α-helices and fibrous assemblies. Polypeptide α2 (14 residues), with two same-sequence repeats, did not form an α-helix, but polypeptide α2L (15 residues; α2 with one additional leucine residue on its carboxyl terminal) did form an α-helix and fibrous assembly. Fibrous assembly formation was associated with polypeptides at least as long as polypeptide α2L and with five leucine residues, indicating that the C-terminal leucine has a critical element for stabilization of α-helix and fibril formation. In contrast, polypeptides α5 (35 residues) and α6 (42 residues) aggregated easily, although they formed α-helices. A 15-35-residue chain was required for fibrous assembly formation. Electron microscopy and X-ray fiber diffraction showed that the thinnest fibrous assemblies of polypeptides were about 20 Å and had periodicities coincident with the length of the α-helix in a longitudinal direction. These results indicated that the α-helix structures were orientated along the fibrous axis and assembled into a bundle. Furthermore, the width and length of fibrous assemblies changed with changes in the pH value, resulting in variations in the charged states of the residues. Our results suggest that the formation of fibrous assemblies of amphipathic α-helices is due to the assembly of bundles via the hydrophobic faces of the helices and extension with hydrophobic noncovalent bonds containing a leucine. PMID:23530905

  2. Use of 1–4 interaction scaling factors to control the conformational equilibrium between α-helix and β-strand

    International Nuclear Information System (INIS)

    Highlights: • 1–4 interaction scaling factors are used to adjust conformational energy. • This article reports the effects of these factors on protein conformations. • Reducing these factors changes a helix to a strand in molecular dynamics simulation. • Increasing these factors causes the reverse conformational change. • These factors control the conformational equilibrium between helix and strand. - Abstract: 1–4 interaction scaling factors are used in AMBER forcefields to reduce the exaggeration of short-range repulsion caused by the 6–12 Lennard-Jones potential and a nonpolarizable charge model and to obtain better agreements of small-molecule conformational energies with experimental data. However, the effects of these scaling factors on protein secondary structure conformations have not been investigated until now. This article reports the finding that the 1–4 interactions among the protein backbone atoms separated by three consecutive covalent bonds are more repulsive in the α-helix conformation than in two β-strand conformations. Therefore, the 1–4 interaction scaling factors of protein backbone torsions ϕ and ψ control the conformational equilibrium between α-helix and β-strand. Molecular dynamics simulations confirm that reducing the ϕ and ψ scaling factors readily converts the α-helix conformation of AcO-(AAQAA)3-NH2 to a β-strand conformation, and the reverse occurs when these scaling factors are increased. These results suggest that the ϕ and ψ scaling factors can be used to generate the α-helix or β-strand conformation in situ and to control the propensities of a forcefield for adopting secondary structure elements

  3. Common interruptions in the repeating tripeptide sequence of non-fibrillar collagens: Sequence analysis and structural studies on triple-helix peptide models

    OpenAIRE

    Thiagarajan, Geetha; Li, Yingjie; Mohs, Angela; Strafaci, Christopher; Popiel, Magdalena; Baum, Jean; Brodsky, Barbara

    2007-01-01

    Interruptions in the repeating (Gly-X1-X2)n amino acid sequence pattern are found in the triple-helix domains of all non-fibrillar collagens, and perturbations to the triple-helix at such sites are likely to play a role in collagen higher order structure and function. This report defines the sequence features and structural consequences of the most common interruption, where one residue is missing in the tripeptide pattern, Gly-X1-X2-Gly-AA1-Gly-X1-X2, designated as G1G interruptions. Residue...

  4. Agrobacterium tumefaciens VirC2 enhances T-DNA transfer and virulence through its C-terminal ribbon–helix–helix DNA-binding fold

    OpenAIRE

    Lu, Jun; den Dulk-Ras, Amke; Hooykaas, Paul J. J.; Glover, J. N. Mark

    2009-01-01

    Agrobacterium tumefaciens VirC2 stimulates processing of single-stranded T-DNA that is translocated into plants to induce tumor formation, but how VirC2 functions is unclear. Here, we report the 1.7-Å X-ray crystal structure of its trypsin-resistant C-terminal domain, VirC282–202, which reveals a form of the ribbon-helix-helix (RHH) DNA-binding fold contained within a single polypeptide chain. DNA-binding assays and mutagenesis indicate that VirC2 uses this RHH fold to bind double-stranded DN...

  5. Health and Environment Linked for Information Exchange (HELIX)-Atlanta: A CDC-NASA Joint Environmental Public Health Tracking Collaborative Project

    Science.gov (United States)

    Al-Hamdan, Mohammad; Luvall, Jeff; Crosson, Bill; Estes, Maury; Limaye, Ashutosh; Quattrochi, Dale; Rickman, Doug

    2008-01-01

    HELIX-Atlanta was developed to support current and future state and local EPHT programs to implement data linking demonstration projects which could be part of the CDC EPHT Network. HELIX-Atlanta is a pilot linking project in Atlanta for CDC to learn about the challenges the states will encounter. NASA/MSFC and the CDC are partners in linking environmental and health data to enhance public health surveillance. The use of NASA technology creates value added geospatial products from existing environmental data sources to facilitate public health linkages. Proving the feasibility of the approach is the main objective

  6. Active-Site α-Helix in Papain and the Stability of the Ion Pair RS- · · · ImH+. Ab initio Molecular Orbital Study

    OpenAIRE

    Duijnen, P.Th. van; Thole, B.Th.; Broer, Ria; Nieuwpoort, W. C.

    1980-01-01

    Ab initio MO calculations, using both minimal (STO-3G) and extended (Roos-Siegbahn) basis sets are reported for the systems methanethiol-imidazole, methanethiol-imidazole-formaldehyde, and methanethiol-imidazole-formamide, which, together with a point-change representation of a long α-helix, form models for the active site of papain. It is shown that the large electric field exerted by the helix in the active-site region is responsible for the presence of the essential residues Cys 25 and His...

  7. A Study of Low pH-Induced Refolding of Env of Avian Sarcoma and Leukosis Virus into a Six-Helix Bundle

    OpenAIRE

    Markosyan, R. M.; P. Bates; Cohen, F S; Melikyan, G B

    2004-01-01

    The fusion protein of avian sarcoma and leukosis virus is likely to fold into a six-helix bundle as part of its final configuration. A peptide, R99, inhibits fusion, probably by binding into the grooves of the triple-stranded coiled coil that becomes the central core of the six-helix bundle. The stages at which the envelope protein (Env) of avian sarcoma and leukosis virus subgroup A folds into a bundle during low pH-induced fusion were determined. Effector cells expressing Env were bound to ...

  8. A novel 18F-labeled two-helix scaffold protein for PET imaging of HER2-positive tumor

    International Nuclear Information System (INIS)

    Two-helix scaffold proteins (∝ 5 kDa) against human epidermal growth factor receptor type 2 (HER2) have been discovered in our previous work. In this research we aimed to develop an 18F-labeled two-helix scaffold protein for positron emission tomography (PET) imaging of HER2-positive tumors. An aminooxy-functionalized two-helix peptide (AO-MUT-DS) with high HER2 binding affinity was synthesized through conventional solid phase peptide synthesis. The purified linear peptide was cyclized by I2 oxidation to form a disulfide bridge. The cyclic peptide was then conjugated with a radiofluorination synthon, 4-18F-fluorobenzyl aldehyde (18F-FBA), through the aminooxy functional group at the peptide N terminus (30% yield, non-decay corrected). The binding affinities of the peptides were analyzed by Biacore analysis. Cell uptake assay of the resulting PET probe, 18F-FBO-MUT-DS, was performed at 37 C. 18F-FBO-MUT-DS with high specific activity (20-32 MBq/nmol, 88-140 μCi/μg, end of synthesis) was injected into mice xenograft model bearing SKOV3 tumor. MicroPET and biodistribution and metabolic stability studies were then conducted. Cell uptake assays showed high and specific cell uptake (∝12% applied activity at 1 h) by incubation of 18F-FBO-MUT-DS with HER2 high-expressing SKOV3 ovarian cancer cells. The affinities (KD) of AO-MUT-DS and FBO-MUT-DS as tested by Biacore analysis were 2 and 1 nM, respectively. In vivo small animal PET demonstrated fast tumor targeting, high tumor accumulation, and good tumor to normal tissue contrast of 18F-FBO-MUT-DS. Biodistribution studies further revealed that the probe had excellent tumor uptake (6.9%ID/g at 1 h post-injection) and was cleared through both liver and kidneys. Co-injection of the probe with 500 μg of HER2 Affibody protein reduced the tumor uptake (6.9 vs 1.8%ID/g, p 18F-based PET probes. (orig.)

  9. The neurogenic basic helix-loop-helix transcription factor NeuroD6 enhances mitochondrial biogenesis and bioenergetics to confer tolerance of neuronal PC12-NeuroD6 cells to the mitochondrial stressor rotenone

    International Nuclear Information System (INIS)

    The fundamental question of how and which neuronal specific transcription factors tailor mitochondrial biogenesis and bioenergetics to the need of developing neuronal cells has remained largely unexplored. In this study, we report that the neurogenic basic helix-loop-helix transcription factor NeuroD6 possesses mitochondrial biogenic properties by amplifying the mitochondrial DNA content and TFAM expression levels, a key regulator for mitochondrial biogenesis. NeuroD6-mediated increase in mitochondrial biogenesis in the neuronal progenitor-like PC12-NEUROD6 cells is concomitant with enhanced mitochondrial bioenergetic functions, including increased expression levels of specific subunits of respiratory complexes of the electron transport chain, elevated mitochondrial membrane potential and ATP levels produced by oxidative phosphorylation. Thus, NeuroD6 augments the bioenergetic capacity of PC12-NEUROD6 cells to generate an energetic reserve, which confers tolerance to the mitochondrial stressor, rotenone. We found that NeuroD6 induces an adaptive bioenergetic response throughout rotenone treatment involving maintenance of the mitochondrial membrane potential and ATP levels in conjunction with preservation of the actin network. In conclusion, our results support the concept that NeuroD6 plays an integrative role in regulating and coordinating the onset of neuronal differentiation with acquisition of adequate mitochondrial mass and energetic capacity to ensure energy demanding events, such as cytoskeletal remodeling, plasmalemmal expansion, and growth cone formation. -- Highlights: ► NeuroD6 induces mitochondrial biogenesis in neuroprogenitor-like cells. ► NeuroD6 augments the bioenergetic reserve of the neuronal PC12-NeuroD6 cells. ► NeuroD6 increases the mitochondrial membrane potential and ATP levels. ► NeuroD6 confers tolerance to rotenone via an adaptive mitochondrial response.

  10. The neurogenic basic helix-loop-helix transcription factor NeuroD6 enhances mitochondrial biogenesis and bioenergetics to confer tolerance of neuronal PC12-NeuroD6 cells to the mitochondrial stressor rotenone

    Energy Technology Data Exchange (ETDEWEB)

    Baxter, Kristin Kathleen; Uittenbogaard, Martine [Department of Anatomy and Regenerative Biology, George Washington University Medical Center, Washington, DC (United States); Chiaramello, Anne, E-mail: achiaram@gwu.edu [Department of Anatomy and Regenerative Biology, George Washington University Medical Center, Washington, DC (United States)

    2012-10-15

    The fundamental question of how and which neuronal specific transcription factors tailor mitochondrial biogenesis and bioenergetics to the need of developing neuronal cells has remained largely unexplored. In this study, we report that the neurogenic basic helix-loop-helix transcription factor NeuroD6 possesses mitochondrial biogenic properties by amplifying the mitochondrial DNA content and TFAM expression levels, a key regulator for mitochondrial biogenesis. NeuroD6-mediated increase in mitochondrial biogenesis in the neuronal progenitor-like PC12-NEUROD6 cells is concomitant with enhanced mitochondrial bioenergetic functions, including increased expression levels of specific subunits of respiratory complexes of the electron transport chain, elevated mitochondrial membrane potential and ATP levels produced by oxidative phosphorylation. Thus, NeuroD6 augments the bioenergetic capacity of PC12-NEUROD6 cells to generate an energetic reserve, which confers tolerance to the mitochondrial stressor, rotenone. We found that NeuroD6 induces an adaptive bioenergetic response throughout rotenone treatment involving maintenance of the mitochondrial membrane potential and ATP levels in conjunction with preservation of the actin network. In conclusion, our results support the concept that NeuroD6 plays an integrative role in regulating and coordinating the onset of neuronal differentiation with acquisition of adequate mitochondrial mass and energetic capacity to ensure energy demanding events, such as cytoskeletal remodeling, plasmalemmal expansion, and growth cone formation. -- Highlights: Black-Right-Pointing-Pointer NeuroD6 induces mitochondrial biogenesis in neuroprogenitor-like cells. Black-Right-Pointing-Pointer NeuroD6 augments the bioenergetic reserve of the neuronal PC12-NeuroD6 cells. Black-Right-Pointing-Pointer NeuroD6 increases the mitochondrial membrane potential and ATP levels. Black-Right-Pointing-Pointer NeuroD6 confers tolerance to rotenone via an adaptive

  11. Comparison of an Atomic Model and Its Cryo-EM Image at the Central Axis of a Helix

    Science.gov (United States)

    He, Jing; Zeil, Stephanie; Hallak, Hussam; McKaig, Kele; Kovacs, Julio; Wriggers, Willy

    2016-01-01

    Cryo-electron microscopy (cryo-EM) is an important biophysical technique that produces three-dimensional (3D) density maps at different resolutions. Because more and more models are being produced from cryo-EM density maps, validation of the models is becoming important. We propose a method for measuring local agreement between a model and the density map using the central axis of the helix. This method was tested using 19 helices from cryo-EM density maps between 5.5 Å and 7.2 Å resolution and 94 helices from simulated density maps. This method distinguished most of the well-fitting helices, although challenges exist for shorter helices.

  12. On features of the radiation from an electron moving along a helix inside a cylindrical hole in a homogeneous dielectric

    CERN Document Server

    Arzumanyan, S R; Khachatryan, H F; Kotanjyan, A S; Saharian, A A

    2007-01-01

    The radiation from a charge moving along a helical trajectory inside a cylindrical hole in homogeneous dielectric medium is investigated. Prompted by availability of materials with large dielectric permittivity $\\epsilon $ and small absorption, we discuss the features of this type of radiation for media with $\\epsilon \\gg 1$. It is shown that there are high peaks in the angular distribution of radiation intensity at well-defined harmonics. The conditions are specified for the cavity-to-helix radii ratio, $\\rho_{1}/\\rho_{0}$, under which the angle-integrated radiation intensity on some harmonics exceeds that in the empty space. Though the amplification of radiation intensity increases with increasing $\\epsilon $, the corresponding "resonant" values of $\\rho _{1}/\\rho_{0}$ ratio are practically independent of the dielectric permittivity of surrounding medium. It is shown that an analogous amplification of radiation takes place essentially for the same values of $\\rho_{1}/\\rho_{0}$ also for the radiation in a cy...

  13. Modification of the acetylcholine-induced current of the snail Helix pomatia L. by fast temperature changes

    Directory of Open Access Journals (Sweden)

    Nedeljković M.

    2005-01-01

    Full Text Available Using the single electrode voltage clamp method, we found that acetylcholine (aCh induces transient inward dose-dependent current on the membrane of the identified Helix pomatia Br neuron. We analyzed the effects of fast cooling and heating as well as thermal acclimation on the aCh inward current. the experiments were conducted on active and dormant snails acclimated to either 20 or 7°C for at least four weeks. the Hill coefficient remained approximately 1 in all cases, which means that there is a single aCh binding site on the membrane. Fast temperature alternations induce binding affinity changes. in the work presented, we analyzed the effects of cooling on the aCh-induced inward current. the amplitude of aCh-induced inward current was markedly reduced after cooling, and the speed of decay of the aCh response was lower.

  14. The use of mould-templated surface structures for high-quality uniform-lying-helix liquid-crystal alignment

    Science.gov (United States)

    Outram, B. I.; Elston, S. J.; Tuffin, R.; Siemianowski, S.; Snow, B.

    2013-06-01

    The chiral-flexoelectrooptic effect in a Uniform Lying Helix (ULH) configuration provides a sub-millisecond in-plane rotation of the optic axis with the application of a transverse field. This enables displays with a wide viewing angle without costly in-plane-type electrodes. The salient challenge is one of alignment of the ULH, which is not topologically compatible with uniform alignment surface treatments. Here, we create a micro-grooved surface structure with features on the micron scale by using a replica-moulding technique. When the cell is assembled, the micro-grooves create channels, and using surface-energy considerations, we explain how and show experimentally that the channels align a cholesteric material in the ULH geometry with the helicoidal axis oriented parallel to the channels. The resultant alignment provides a high level of contrast between crossed polarizers and exhibits an electrooptic response with a switching time of the order of tens of microseconds.

  15. Biological characteristics of the species Hedera helix L. and its use in controlling erosion in shady places

    Directory of Open Access Journals (Sweden)

    Stavretović N.

    2007-01-01

    Full Text Available Controlling erosion in shady places is among the most serious problems of environment protection, one that requires persistent and strenuous efforts. Ivy (Hedera helix L. is exceptionally shade-tolerant, covers the ground surface nicely, and is easy to cultivate. For these reasons, it can be used more successfully than any other ground cover to control erosion in shady places. Hardening of ivy cuttings is accomplished with semi-lignified and lignified cuttings. In hardening of cuttings in plastic containers, a substrate composed of garden soil and peat proved to be the most effective. Even when the percentage of ivy cuttings that take is low in shady places subject to erosion, the significance of their presence is great in subsequent years, when the ivy spreads over the ground, covering it and retarding erosion of the soil. .

  16. Efficient trapping of HIV-1 envelope protein by hetero-oligomerization with an N-helix chimera

    Directory of Open Access Journals (Sweden)

    Silver Jonathan

    2005-08-01

    Full Text Available Abstract Background The N-heptad repeat region of the HIV-1 Transmembrane Envelope protein is a trimerization domain that forms part of a "six helix bundle" crucial to Envelope-mediated membrane fusion. N-heptad repeat peptides have been used as extracellular reagents to inhibit virus fusion. Results When expressed intracellularly with wild-type HIV-1 Envelope protein, the N-heptad repeat domain efficiently hetero-oligomerized with Envelope and trapped it in the endoplasmic reticulum or early Golgi, as indicated by lack of transport to the cell surface, absent proteolytic processing, and aberrant glycosylation. Conclusion Post-translational processing of HIV Envelope is very sensitive to an agent that binds to the N-heptad repeat during synthesis, suggesting that it might be possible to modify drugs that bind to this region to have transport-blocking properties.

  17. Mapping the time evolution of a persistent spin helix in GaAs/AlGaAs quantum wells

    International Nuclear Information System (INIS)

    Full text: The spin-orbit interaction in asymmetrically doped GaAs/AlGaAs quantum wells is tuned to a situation with comparable Dresselhaus and Rashba terms. Polarized electron spins are initially pumped with a circularly polarized laser pulse. Using a high numeric aperture lens placed closely to the sample in the cryostat, high-resolution spatial maps of the evolving spin pattern are recorded with a delayed probe pulse. When focusing the pump and probe beam to a diffraction limited spot and scanning the relative spot separation, we can observe the evolution from an initially Gaussian spin polarization to a spin pattern with a wave-like nature related to the persistent spin helix. (author)

  18. Nanoscale stabilization of zintl compounds: 1D ionic Li-P double helix confined inside a carbon nanotube

    Science.gov (United States)

    Ivanov, Alexander S.; Kar, Tapas; Boldyrev, Alexander I.

    2016-02-01

    One-dimensional (1D) ionic nanowires are extremely rare materials due to the difficulty in stabilizing 1D chains of ions under ambient conditions. We demonstrate here a theoretical prediction of a novel hybrid material, a nanotube encapsulated 1D ionic lithium monophosphide (LiP) chain, featuring a unique double-helix structure, which is very unusual in inorganic chemistry. This nanocomposite has been investigated with density functional theory, including molecular dynamics simulations and electronic structure calculations. We find that the formation of the LiP double-helical nanowire is facilitated by strong interactions between LiP and CNTs resulting in a charge transfer. This work suggests that nanostructured confinement may be used to stabilize other polyphosphide 1D chains, thus opening new ways to study the chemistry of zintl compounds at the nanoscale.One-dimensional (1D) ionic nanowires are extremely rare materials due to the difficulty in stabilizing 1D chains of ions under ambient conditions. We demonstrate here a theoretical prediction of a novel hybrid material, a nanotube encapsulated 1D ionic lithium monophosphide (LiP) chain, featuring a unique double-helix structure, which is very unusual in inorganic chemistry. This nanocomposite has been investigated with density functional theory, including molecular dynamics simulations and electronic structure calculations. We find that the formation of the LiP double-helical nanowire is facilitated by strong interactions between LiP and CNTs resulting in a charge transfer. This work suggests that nanostructured confinement may be used to stabilize other polyphosphide 1D chains, thus opening new ways to study the chemistry of zintl compounds at the nanoscale. Electronic supplementary information (ESI) available: Additional DOS, band structures, and Bader charges for LiP@SWCNTs. See DOI: 10.1039/c5nr07713c

  19. Homologue of Protein Kinase Mζ Maintains Context Aversive Memory and Underlying Long-Term Facilitation in Terrestrial Snail Helix.

    Directory of Open Access Journals (Sweden)

    Pavel M. Balaban

    2015-06-01

    Full Text Available It has been shown that a variety of long-term memories in different regions of the brain and in different species are quickly erased by local inhibition of PKMζ. Using antibodies to mammalian PKMζ, we describe in the present study the localization of immunoreactive molecules in the nervous system of the terrestrial snail Helix lucorum. Presence of a homologue of PKMζ was confirmed with transcriptomics. We have demonstrated in behavioral experiments that contextual fear memory disappeared under a blockade of PKMζ with a selective peptide blocker of PKMζ (ZIP, but not with scrambled ZIP. If ZIP was combined with a reminder (20 min in noxious context, no impairment of the long-term contextual memory was observed. In electrophysiological experiments we investigated whether PKMζ takes part in the maintenance of long-term facilitation (LTF in the neural circuit mediating tentacle withdrawal. LTF of excitatory synaptic inputs to premotor interneurons was induced by high-frequency nerve stimulation combined with serotonin bath applications and lasted at least four hours. We found that bath application of 2x10-6 M ZIP at the 90th min after the tetanization reduced the EPSP amplitude to the non-tetanized EPSP values. Applications of the scrambled ZIP peptide at a similar time and concentration didn't affect the EPSP amplitudes. In order to test whether effects of ZIP are specific to the synapses, we performed experiments with LTF of somatic membrane responses to local glutamate applications. It was shown earlier that serotonin application in such an artificial synapse condition elicits LTF of responses to glutamate. It was found that ZIP had no effect on LTF in these conditions, which may be explained by the very low concentration of PKMζ molecules in somata of these identified neurons, as evidenced by immunochemistry. Obtained results suggest that the Helix homologue of PKMζ might be involved in post-induction maintenance of long-term changes in

  20. Structural variation and uniformity among tetraloop-receptor interactions and other loop-helix interactions in RNA crystal structures.

    Directory of Open Access Journals (Sweden)

    Li Wu

    Full Text Available Tetraloop-receptor interactions are prevalent structural units in RNAs, and include the GAAA/11-nt and GNRA-minor groove interactions. In this study, we have compiled a set of 78 nonredundant loop-helix interactions from X-ray crystal structures, and examined them for the extent of their sequence and structural variation. Of the 78 interactions in the set, only four were classical GAAA/11-nt motifs, while over half (48 were GNRA-minor groove interactions. The GNRA-minor groove interactions were not a homogeneous set, but were divided into five subclasses. The most predominant subclass is characterized by two triple base pair interactions in the minor groove, flanked by two ribose zipper contacts. This geometry may be considered the "standard" GNRA-minor groove interaction, while the other four subclasses are alternative ways to form interfaces between a minor groove and tetraloop. The remaining 26 structures in the set of 78 have loops interacting with mostly idiosyncratic receptors. Among the entire set, a number of sequence-structure correlations can be identified, which may be used as initial hypotheses in predicting three-dimensional structures from primary sequences. Conversely, other sequence patterns are not predictive; for example, GAAA loop sequences and GG/CC receptors bind to each other with three distinct geometries. Finally, we observe an example of structural evolution in group II introns, in which loop-receptor motifs are substituted for each other while maintaining the larger three-dimensional geometry. Overall, the study gives a more complete view of RNA loop-helix interactions that exist in nature.

  1. Effect of TFE on the Helical Content of AK17 and HAL-1 Peptides: Theoretical Insights into the Mechanism of Helix Stabilization.

    Science.gov (United States)

    Vymětal, Jiří; Bednárová, Lucie; Vondrášek, Jiří

    2016-02-18

    Fluorinated alcohols such as 2,2,2-trifluoroethanol (TFE) are among the most frequently used cosolvents in experiment studies of peptides. They have significant effects on secondary structure and a particularly strong promotion of α-helix is induced by TFE. In this study we validated recently proposed force field parameters for TFE in molecular dynamics simulations with two model peptides-alanine-rich AK-17 and antimicrobial peptide halictine-1 (HAL-1). In the case of HAL-1, we characterized the effect of TFE on this peptide experimentally by ECD spectroscopy. Our TFE model in question reproduced the helix-promoting effect of TFE and provided insight into the mechanisms of TFE action on peptides. Our simulations confirmed the preferential interaction of TFE molecules with α-helices, although the TFE molecules accumulate in the vicinity of the peptides in various conformations. Moreover, we observed a significant effect of TFE on the thermodynamics of the helix-coil transition and a change in local conformational preferences in the unfolded (coil) state induced by TFE. In addition, our simulation-based analysis suggests that different mechanisms participate in helix stabilization in both model peptides in water and TFE solution. Our results thus support the picture of complex TFE action on peptides that is further diversified by the identity and intrinsic properties of the peptide. PMID:26786280

  2. High constitutive activity of a virus-encoded seven transmembrane receptor in the absence of the conserved DRY motif (Asp-Arg-Tyr) in transmembrane helix 3

    DEFF Research Database (Denmark)

    Rosenkilde, Mette M; Kledal, Thomas N; Schwartz, Thue W

    2005-01-01

    The highly conserved Arg in the so-called DRY motif (Asp-Arg-Tyr) at the intracellular end of transmembrane helix 3 is in general considered as an essential residue for G protein coupling in rhodopsin-like seven transmembrane (7TM) receptors. In the open reading frame 74 (ORF74) receptor encoded by...

  3. INFLUENCE OF AGING ON ANTIBODY-FORMATION INVIVO AFTER IMMUNIZATION WITH THE PRIMARY T-CELL DEPENDENT ANTIGEN HELIX-POMATIA HEMOCYANIN

    NARCIS (Netherlands)

    DEGREEF, GE; KALLENBERG, CGM; VANSTAALDUINEN, GJ; REMARQUE, EJ; TJANDRA, YI; HIJMANS, W

    1992-01-01

    The in vivo antibody response to the primary T-cell dependent antigen Helix pomatia Haemocyanin (HPH) was studied, in order to detect the possible presence of a humoral immune deficiency in ageing. The IgG subclass distribution of the specific antibodies was also determined. In order to define a dos

  4. Surface expression and subunit specific control of steady protein levels by the Kv7.2 helix A-B linker.

    Directory of Open Access Journals (Sweden)

    Paloma Aivar

    Full Text Available Kv7.2 and Kv7.3 are the main components of the neuronal voltage-dependent M-current, which is a subthreshold potassium conductance that exerts an important control on neuronal excitability. Despite their predominantly intracellular distribution, these channels must reach the plasma membrane in order to control neuronal activity. Thus, we analyzed the amino acid sequence of Kv7.2 to identify intrinsic signals that may control its surface expression. Removal of the interlinker connecting helix A and helix B of the intracellular C-terminus produces a large increase in the number of functional channels at the plasma membrane. Moreover, elimination of this linker increased the steady-state amount of protein, which was not associated with a decrease of protein degradation. The magnitude of this increase was inversely correlated with the number of helix A - helix B linkers present in the tetrameric channel assemblies. In contrast to the remarkable effect on the amount of Kv7.2 protein, removal of the Kv7.2 linker had no detectable impact on the steady-state levels of Kv7.3 protein.

  5. Tipping the Scale from Disorder to Alpha-helix: Folding of Amphiphilic Peptides in the Presence of Macroscopic and Molecular Interfaces

    OpenAIRE

    Cahit Dalgicdir; Christoph Globisch; Christine Peter; Mehmet Sayar

    2015-01-01

    RESEARCH ARTICLE Tipping the Scale from Disorder to Alpha-helix: Folding of Amphiphilic Peptides in the Presence of Macroscopic and Molecular Interfaces Cahit Dalgicdir1, Christoph Globisch2, Christine Peter2*, Mehmet Sayar1* 1 College of Engineering, Koç University, Istanbul, Turkey, 2 Theoretical Chemistry, University of Konstanz, Konstanz, Germany * (CP); (MS) Abstract Secondary amphiphilicity is inherent to the...

  6. The PNT domain from Drosophila pointed-P2 contains a dynamic N-terminal helix preceded by a disordered phosphoacceptor sequence.

    Science.gov (United States)

    Lau, Desmond K W; Okon, Mark; McIntosh, Lawrence P

    2012-11-01

    Pointed-P2, the Drosophila ortholog of human ETS1 and ETS2, is a transcription factor involved in Ras/MAP kinase-regulated gene expression. In addition to a DNA-binding ETS domain, Pointed-P2 contains a PNT (or SAM) domain that serves as a docking module to enhance phosphorylation of an adjacent phosphoacceptor threonine by the ERK2 MAP kinase Rolled. Using NMR chemical shift, ¹⁵N relaxation, and amide hydrogen exchange measurements, we demonstrate that the Pointed-P2 PNT domain contains a dynamic N-terminal helix H0 appended to a core conserved five-helix bundle diagnostic of the SAM domain fold. Neither the secondary structure nor dynamics of the PNT domain is perturbed significantly upon in vitro ERK2 phosphorylation of three threonine residues in a disordered sequence immediately preceding this domain. These data thus confirm that the Drosophila Pointed-P2 PNT domain and phosphoacceptors are highly similar to those of the well-characterized human ETS1 transcription factor. NMR-monitored titrations also revealed that the phosphoacceptors and helix H0, as well as region of the core helical bundle identified previously by mutational analyses as a kinase docking site, are selectively perturbed upon ERK2 binding by Pointed-P2. Based on a homology model derived from the ETS1 PNT domain, helix H0 is predicted to partially occlude the docking interface. Therefore, this dynamic helix must be displaced to allow both docking of the kinase, as well as binding of Mae, a Drosophila protein that negatively regulates Pointed-P2 by competing with the kinase for its docking site. PMID:22936607

  7. Evolution of the α-Subunit of Na/K-ATPase from Paramecium to Homo sapiens: Invariance of Transmembrane Helix Topology.

    Science.gov (United States)

    Morrill, Gene A; Kostellow, Adele B; Liu, Lijun; Gupta, Raj K; Askari, Amir

    2016-05-01

    Na/K-ATPase is a key plasma membrane enzyme involved in cell signaling, volume regulation, and maintenance of electrochemical gradients. The α-subunit, central to these functions, belongs to a large family of P-type ATPases. Differences in transmembrane (TM) helix topology, sequence homology, helix-helix contacts, cell signaling, and protein domains of Na/K-ATPase α-subunit were compared in fungi (Beauveria), unicellular organisms (Paramecia), primitive multicellular organisms (Hydra), and vertebrates (Xenopus, Homo sapiens), and correlated with evolution of physiological functions in the α-subunit. All α-subunits are of similar length, with groupings of four and six helices in the N- and C-terminal regions, respectively. Minimal homology was seen for protein domain patterns in Paramecium and Hydra, with high correlation between Hydra and vertebrates. Paramecium α-subunits display extensive disorder, with minimal helix contacts. Increases in helix contacts in Hydra approached vertebrates. Protein motifs known to be associated with membrane lipid rafts and cell signaling reveal significant positional shifts between Paramecium and Hydra vulgaris, indicating that regional membrane fluidity changes occur during evolution. Putative steroid binding sites overlapping TM-3 occurred in all species. Sites associated with G-protein-receptor stimulation occur both in vertebrates and amphibia but not in Hydra or Paramecia. The C-terminus moiety "KETYY," necessary for the Na(+) activation of pump phosphorylation, is not present in unicellular species indicating the absence of classical Na(+)/K(+)-pumps. The basic protein topology evolved earliest, followed by increases in protein domains and ordered helical arrays, correlated with appearance of α-subunit regions known to involve cell signaling, membrane recycling, and ion channel formation. PMID:26961431

  8. Probing the Orientation and Conformation of alpha-Helix and beta-Strand Model Peptides on Self-Assembled Monolayers Using Sum Frequency Generation and NEXAFS Spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Weidner, T.; Apte, J; Gamble, L; Castner, D

    2010-01-01

    The structure and orientation of amphiphilic {alpha}-helix and {beta}-strand model peptide films on self-assembled monolayers (SAMs) have been studied with sum frequency generation (SFG) vibrational spectroscopy and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy. The {alpha}-helix peptide is a 14-mer, and the {beta}-strand is a 15-mer of hydrophilic lysine and hydrophobic leucine residues with hydrophobic periodicities of 3.5 and 2, respectively. These periodicities result in the leucine side chains located on one side of the peptides and the lysine side chains on the other side. The SAMs were prepared from the assembly of either carboxylic acid- or methyl-terminated alkyl thiols onto gold surfaces. For SFG studies, the deuterated analog of the methyl SAM was used. SFG vibrational spectra in the C-H region of air-dried peptides films on both SAMs exhibit strong peaks near 2965, 2940, and 2875 cm{sup -1} related to ordered leucine side chains. The orientation of the leucine side chains was determined from the phase of these features relative to the nonresonant gold background. The relative phase for both the {alpha}-helix and {beta}-strand peptides showed that the leucine side chains were oriented away from the carboxylic acid SAM surface and oriented toward the methyl SAM surface. Amide I peaks observed near 1656 cm{sup -1} for the {alpha}-helix peptide confirm that the secondary structure is preserved on both SAMs. Strong linear dichroism related to the amide {pi}* orbital at 400.8 eV was observed in the nitrogen K-edge NEXAFS spectra for the adsorbed {beta}-strand peptides, suggesting that the peptide backbones are oriented parallel to the SAM surface with the side chains pointing toward or away from the interface. For the {alpha}-helix the dichroism of the amide {pi}* is significantly weaker, probably because of the broad distribution of amide bond orientations in the {alpha}-helix secondary structure.

  9. NMR Structure and CD Titration with Metal Cations of Human Prion α2-Helix-Related Peptides

    Directory of Open Access Journals (Sweden)

    Luisa Ronga

    2007-01-01

    Full Text Available The 173–195 segment corresponding to the helix 2 of the C-globular prion protein domain could be one of several “spots” of intrinsic conformational flexibility. In fact, it possesses chameleon conformational behaviour and gathers several disease-associated point mutations. We have performed spectroscopic studies on the wild-type fragment 173–195 and on its D178N mutant dissolved in trifluoroethanol to mimic the in vivo system, both in the presence and in the absence of metal cations. NMR data showed that the structure of the D178N mutant is characterized by two short helices separated by a kink, whereas the wild-type peptide is fully helical. Both peptides retained these structural organizations, as monitored by CD, in the presence of metal cations. NMR spectra were however not in favour of the formation of definite ion-peptide complexes. This agrees with previous evidence that other regions of the prion protein are likely the natural target of metal cation binding.

  10. Pathogenic C9ORF72 Antisense Repeat RNA Forms a Double Helix with Tandem C:C Mismatches.

    Science.gov (United States)

    Dodd, David W; Tomchick, Diana R; Corey, David R; Gagnon, Keith T

    2016-03-01

    Expansion of a GGGGCC/CCCCGG repeat sequence in the first intron of the C9ORF72 gene is a leading cause of frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS). In this combined disorder, called c9FTD/ALS, the expansion is bidirectionally transcribed into sense and antisense repeat RNA associated with disease. To better understand the role of C9ORF72 repeat RNA in molecular disease pathology, we determined crystal structures of a [(CCCCGG)3(CCCC)] model antisense repeat RNA to 1.47 Å resolution. The RNA structure was an A-form-like double helix composed of repeating and regularly spaced tandem C:C mismatch pairs that perturbed helical geometry and surface charge. Solution studies revealed a preference for A-form-like helical conformations as the repeat number increased. Results provide a structural starting point for rationalizing the contribution of repeat RNA to c9FTD/ALS molecular disease mechanisms and for developing molecules to target C9ORF72 repeat RNA as potential therapeutics. PMID:26878348

  11. Habituation-Like Decrease of Acetylcholine-Induced Inward Current in Helix Command Neurons: Role of Microtubule Motor Proteins.

    Science.gov (United States)

    Vasil'yeva, Natal'ya A; Murzina, Galina B; Pivovarov, Arkady S

    2015-07-01

    The role of kinesin and dynein microtubule-associated molecular motors in the cellular mechanism of depression of acetylcholine-induced inward chloride current (ACh-current) was examined in command neurons of land snails (Helix lucorum) in response to repeated applications of ACh to neuronal soma. This pharmacological stimulation imitated the protocol of tactile stimulation evoking behavioural habituation of the defensive reaction. In this system, a dynein inhibitor (erythro-9-(2-hydroxy-3-nonyl)adenine, 50 µM) decreased the ACh-current depression rate. Kinesin Eg5 inhibitors (Eg5 inhibitor III, 10 µM and Eg5 inhibitor V, trans-24, 15 µM) reduced the degree of current depression, and Eg5 inhibitor V also reduced the initial rate of depression. The results of electrophysiological experiments in combination with mathematical modelling provided evidence of the participation of dyneins and kinesin Eg5 proteins in the radial transport of acetylcholine receptors in command neurons of H. lucorum in the cellular analogue of habituation. Furthermore, these results suggest that the reciprocal interaction between dynein and kinesin proteins located on the same vesicle can lead to reverse their usual direction of transport (dyneins-in exocytosis and kinesin Eg5-in endocytosis). PMID:25687906

  12. In Vitro Antiviral Activity of Circular Triple Helix Forming Oligonucleotide RNA towards Feline Infectious Peritonitis Virus Replication

    Directory of Open Access Journals (Sweden)

    Oi Kuan Choong

    2014-01-01

    Full Text Available Feline Infectious Peritonitis (FIP is a severe fatal immune-augmented disease in cat population. It is caused by FIP virus (FIPV, a virulent mutant strain of Feline Enteric Coronavirus (FECV. Current treatments and prophylactics are not effective. The in vitro antiviral properties of five circular Triple-Helix Forming Oligonucleotide (TFO RNAs (TFO1 to TFO5, which target the different regions of virulent feline coronavirus (FCoV strain FIPV WSU 79-1146 genome, were tested in FIPV-infected Crandell-Rees Feline Kidney (CRFK cells. RT-qPCR results showed that the circular TFO RNAs, except TFO2, inhibit FIPV replication, where the viral genome copy numbers decreased significantly by 5-fold log10 from 1014 in the virus-inoculated cells to 109 in the circular TFO RNAs-transfected cells. Furthermore, the binding of the circular TFO RNA with the targeted viral genome segment was also confirmed using electrophoretic mobility shift assay. The strength of binding kinetics between the TFO RNAs and their target regions was demonstrated by NanoITC assay. In conclusion, the circular TFOs have the potential to be further developed as antiviral agents against FIPV infection.

  13. Where may Synergy be Indicated in the Norwegian Innovation System? Triple-Helix Relations among Technology, Organization, and Geography

    CERN Document Server

    Strand, Øivind

    2011-01-01

    Using entropy statistics and data for all (0.5 million) Norwegian firms, the national and regional innovation systems are decomposed into three subdynamics: (i) economic wealth generation, (ii) technological novelty production, and (iii) government interventions and administrative control. The mutual information in three dimensions can then be used as an indicator of potential synergy, that is, reduction of uncertainty. We aggregate the data at the NUTS3 level for 19 counties, the NUTS2 level for seven regions, and the single NUTS1 level for the nation. 19.6% of the synergy (measured as in-between group reduction of uncertainty) was found at the regional level, whereas only another 2.7% was added by aggregation at the national level of integration. Using this triple-helix indicator, the counties along the west coast are indicated as more knowledge-based than the metropolitan area of Oslo or the geographical environment of the Technical University in Trondheim. Foreign direct investment seems to have larger kn...

  14. The brown adipocyte protein CIDEA promotes lipid droplet fusion via a phosphatidic acid-binding amphipathic helix

    Science.gov (United States)

    Barneda, David; Planas-Iglesias, Joan; Gaspar, Maria L; Mohammadyani, Dariush; Prasannan, Sunil; Dormann, Dirk; Han, Gil-Soo; Jesch, Stephen A; Carman, George M; Kagan, Valerian; Parker, Malcolm G; Ktistakis, Nicholas T; Klein-Seetharaman, Judith; Dixon, Ann M; Henry, Susan A; Christian, Mark

    2015-01-01

    Maintenance of energy homeostasis depends on the highly regulated storage and release of triacylglycerol primarily in adipose tissue, and excessive storage is a feature of common metabolic disorders. CIDEA is a lipid droplet (LD)-protein enriched in brown adipocytes promoting the enlargement of LDs, which are dynamic, ubiquitous organelles specialized for storing neutral lipids. We demonstrate an essential role in this process for an amphipathic helix in CIDEA, which facilitates embedding in the LD phospholipid monolayer and binds phosphatidic acid (PA). LD pairs are docked by CIDEA trans-complexes through contributions of the N-terminal domain and a C-terminal dimerization region. These complexes, enriched at the LD–LD contact site, interact with the cone-shaped phospholipid PA and likely increase phospholipid barrier permeability, promoting LD fusion by transference of lipids. This physiological process is essential in adipocyte differentiation as well as serving to facilitate the tight coupling of lipolysis and lipogenesis in activated brown fat. DOI: http://dx.doi.org/10.7554/eLife.07485.001 PMID:26609809

  15. Systematic review of clinical trials assessing the effectiveness of ivy leaf (hedera helix) for acute upper respiratory tract infections.

    Science.gov (United States)

    Holzinger, Felix; Chenot, Jean-François

    2011-01-01

    Introduction. Among nonantibiotic cough remedies, herbal preparations containing extracts from leaves of ivy (Hedera helix) enjoy great popularity. Objective. A systematic review to assess the effectiveness and tolerability of ivy for acute upper respiratory tract infections (URTIs). Methods. We searched for randomized controlled trials (RCTs), nonrandomized controlled clinical trials and observational studies evaluating the efficacy of ivy preparations for acute URTIs. Study quality was assessed by the Jadad score or the EPHPP tool. Results. 10 eligible studies were identified reporting on 17463 subjects. Studies were heterogeneous in design and conduct; 2 were RCTs. Three studies evaluated a combination of ivy and thyme, 7 studies investigated monopreparations of ivy. Only one RCT (n = 360) investigating an ivy/thyme combination used a placebo control and showed statistically significant superiority in reducing the frequency and duration of cough. All other studies lack a placebo control and show serious methodological flaws. They all conclude that ivy extracts are effective for reducing symptoms of URTI. Conclusion. Although all studies report that ivy extracts are effective to reduce symptoms of URTI, there is no convincing evidence due to serious methodological flaws and lack of placebo controls. The combination of ivy and thyme might be more effective but needs confirmation. PMID:20976077

  16. Systematic Review of Clinical Trials Assessing the Effectiveness of Ivy Leaf (Hedera Helix for Acute Upper Respiratory Tract Infections

    Directory of Open Access Journals (Sweden)

    Felix Holzinger

    2011-01-01

    Full Text Available Introduction. Among nonantibiotic cough remedies, herbal preparations containing extracts from leaves of ivy (Hedera helix enjoy great popularity. Objective. A systematic review to assess the effectiveness and tolerability of ivy for acute upper respiratory tract infections (URTIs. Methods. We searched for randomized controlled trials (RCTs, nonrandomized controlled clinical trials and observational studies evaluating the efficacy of ivy preparations for acute URTIs. Study quality was assessed by the Jadad score or the EPHPP tool. Results. 10 eligible studies were identified reporting on 17463 subjects. Studies were heterogeneous in design and conduct; 2 were RCTs. Three studies evaluated a combination of ivy and thyme, 7 studies investigated monopreparations of ivy. Only one RCT (=360 investigating an ivy/thyme combination used a placebo control and showed statistically significant superiority in reducing the frequency and duration of cough. All other studies lack a placebo control and show serious methodological flaws. They all conclude that ivy extracts are effective for reducing symptoms of URTI. Conclusion. Although all studies report that ivy extracts are effective to reduce symptoms of URTI, there is no convincing evidence due to serious methodological flaws and lack of placebo controls. The combination of ivy and thyme might be more effective but needs confirmation.

  17. A DNA binding winged helix domain in CAF-1 functions with PCNA to stabilize CAF-1 at replication forks

    Science.gov (United States)

    Zhang, Kuo; Gao, Yuan; Li, Jingjing; Burgess, Rebecca; Han, Junhong; Liang, Huanhuan; Zhang, Zhiguo; Liu, Yingfang

    2016-01-01

    Chromatin assembly factor 1 (CAF-1) is a histone H3–H4 chaperone that deposits newly synthesized histone (H3–H4)2 tetramers during replication-coupled nucleosome assembly. However, how CAF-1 functions in this process is not yet well understood. Here, we report the crystal structure of C terminus of Cac1 (Cac1C), a subunit of yeast CAF-1, and the function of this domain in stabilizing CAF-1 at replication forks. We show that Cac1C forms a winged helix domain (WHD) and binds DNA in a sequence-independent manner. Mutations in Cac1C that abolish DNA binding result in defects in transcriptional silencing and increased sensitivity to DNA damaging agents, and these defects are exacerbated when combined with Cac1 mutations deficient in PCNA binding. Similar phenotypes are observed for corresponding mutations in mouse CAF-1. These results reveal a mechanism conserved in eukaryotic cells whereby the ability of CAF-1 to bind DNA is important for its association with the DNA replication forks and subsequent nucleosome assembly. PMID:26908650

  18. The meso Helix: Symmetry and Symmetry-Breaking in Dynamic Oligourea Foldamers with Reversible Hydrogen-Bond Polarity.

    Science.gov (United States)

    Wechsel, Romina; Raftery, James; Cavagnat, Dominique; Guichard, Gilles; Clayden, Jonathan

    2016-08-01

    Oligoureas (up to n=6) of meso cyclohexane-1,2-diamine were synthesized by chain extension with an enzymatically desymmetrized monomer 2. Despite being achiral, the meso oligomers adopt chiral canonical 2.5-helical conformations, the equally populated enantiomeric screw-sense conformers of which are in slow exchange on the NMR timescale, with a barrier to screw-sense inversion of about 70 kJ mol(-1) . Screw-sense inversion in these helical foldamers is coupled with cyclohexane ring-flipping, and results in a reversal of the directionality of the hydrogen bonding in the helix. The termini of the meso oligomers are enantiotopic, and desymmetrized analogues of the oligoureas with differentially and enantioselectively protected termini display moderate screw-sense preferences. A screw-sense preference may furthermore be induced in the achiral, meso oligoureas by formation of a 1:1 hydrogen-bonded complex with the carboxylate anion of Boc-d-proline. The meso oligoureas are the first examples of hydrogen-bonded foldamers with reversible hydrogen-bond directionality. PMID:27298097

  19. 'Supramolecular wrapping chemistry' by helix-forming polysaccharides: a powerful strategy for generating diverse polymeric nano-architectures.

    Science.gov (United States)

    Numata, Munenori; Shinkai, Seiji

    2011-02-21

    We have exploited novel supramolecular wrapping techniques by helix-forming polysaccharides, β-1,3-glucans, which have strong tendency to form regular helical structures on versatile nanomaterials in an induced-fit manner. This approach is totally different from that using the conventional interpolymer interactions seen in both natural and synthetic polymeric architectures, and therefore has potential to create novel polymeric architectures with diverse and unexpected functionalities. The wrapping by β-1,3-glucans enforces the entrapped guest polymer to adopt helical or twisted conformations through the convergent interpolymer interactions. On the contrary, the wrapping by chemically modified semi-artificial β-1,3-glucans can bestow the divergent self-assembling abilities on the entrapped guest polymer to create hierarchical polymeric architectures, where the polymer/β-1,3-glucan composite acts as a huge one-dimensional building block. Based on the established wrapping strategy, we have further extended the wrapping techniques toward the creation of three-dimensional polymeric architectures, in which the polymer/β-1,3-glucan composite behaves as a sort of amphiphilic block copolymers. The present wrapping system would open several paths to accelerate the development of the polymeric supramolecular assembly systems, giving the strong stimuli to the frontier of polysaccharide-based functional chemistry. PMID:21246150

  20. The structure of Plasmodium vivax phosphatidylethanolamine-binding protein suggests a functional motif containing a left-handed helix

    International Nuclear Information System (INIS)

    The crystal structure of a phosphatidylethanolamine-binding protein from P. vivax, a homolog of Raf-kinase inhibitor protein (RKIP), has been solved to a resolution of 1.3 Å. The inferred interaction surface near the anion-binding site is found to include a distinctive left-handed α-helix. The structure of a putative Raf kinase inhibitor protein (RKIP) homolog from the eukaryotic parasite Plasmodium vivax has been studied to a resolution of 1.3 Å using multiple-wavelength anomalous diffraction at the Se K edge. This protozoan protein is topologically similar to previously studied members of the phosphatidylethanolamine-binding protein (PEBP) sequence family, but exhibits a distinctive left-handed α-helical region at one side of the canonical phospholipid-binding site. Re-examination of previously determined PEBP structures suggests that the P. vivax protein and yeast carboxypeptidase Y inhibitor may represent a structurally distinct subfamily of the diverse PEBP-sequence family