WorldWideScience

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. Trace metallic elements in Helix aspersa terrestrial snails of a semiarid ecosystem; Elementos metalicos traza en caracoles terrestres Helix aspersa de un ecosistema semiarido

    Energy Technology Data Exchange (ETDEWEB)

    Gaso P, M.I.; Segovia, N.; Zarazua, G.; Montes, F. [Instituto Nacional de Investigaciones Nucleares, A.P. 18-1027, 11801 Mexico D.F. (Mexico); Morton, O.; Armienta, M.A.; Hernandez, E. [IGF-UNAM, Ciudad Universitaria, 04510 Mexico D.F. (Mexico)

    2001-07-01

    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)

  3. Helix aspersa Müller in Holland

    NARCIS (Netherlands)

    Vernhout, J.H.

    1912-01-01

    In „Nachrichtsblatt der Deutschen Malakozool. Gesellsch. 1910, p. 134” Mr. V. Franz (Helgoland) gives a note on the occurrence of Helix aspersa in Holland at Vlissingen. He suggests that the animals have been transported fortuitously to that locality. Now I will not discuss the possibility this havi

  4. Preparation and evaluation of appertized from snail Helix aspersa M

    Directory of Open Access Journals (Sweden)

    Nelson Loyola López

    2015-01-01

    Full Text Available This study includes the development and evaluation of snails (Helix aspersa M. appertized, collected at a heliciculture breeding center, located in Los Niches sector, Curico, Maule region, South-central of Chile. The test was conducted at the Laboratory of Sciences of the Catholic University of Maule, Nuestra Señora del Carmen Campus, Curico. The main objective of this work was to study the influence of appertized on sensory attributes and commercial durability of snail Helix aspersa M. Additionally, some specific objectives were proposed as follow: to provide this mollusc with a commercial alternative for it consume, to evaluate its organoleptic characteristics and guarantee the product from both the microbiological and nutritional points of view. Three media cover were used (T0: water + NaCl 2%; T1: Water + NaCl 2% + citric acid 0.5% + kilol and T2: extra virgin olive oil + spices + tocopherol. The product was assessed at two different times, after 30 and 90 days of storage. Two sensory evaluations were conducted to measure various organoleptic attributes and acceptability of the appertized by 14 trained panelists. Amino acid, vitamins, cholesterol, acidity, heavy metals, phosphorus and organochlorines analysis were performed. The presence of both total and fecal contaminant microorganisms was determined. Attributes such as color, flavor, aroma, texture and overall acceptability were also measured. Preserves made by T0 and T1 treatments were equally accepted by the panelists. However, preserve from treatment T2 was rejected because of the detection in them of a very dark color, odor and mealy texture. Positive results regarding the content of amino acids, vitamin C and low cholesterol, as well as the absence of pathogenic microorganisms were obtained for the three treatments.

  5. 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

  6. Effects and uptake of polycyclic aromatic compounds in snails (Helix aspersa).

    Science.gov (United States)

    Sverdrup, Line Emilie; De Vaufleury, Annette; Hartnik, Thomas; Hagen, Snorre B; Loibner, Andreas Paul; Jensen, John

    2006-07-01

    The International Standardization Organization recently launched a soil toxicity test with snails (Helix aspersa). We assessed the sensitivity of this test for seven polycyclic aromatic compounds. Control animals had 100% survival and low variability for growth measurements. Maximum exposure concentrations of 2800 mg/kg (4000 mg/kg for acridine) had no effect on survival. Similarly, growth (biomass and shell size) was not affected by pyrene, fluoranthene, fluorene, carbazole, phenanthrene, or acridine, whereas dibenzothiophene gave a 10% effect concentration of 1600 mg/kg. Measured internal concentrations of carbazole, dibenzothiophene, and acridine increased with increasing soil concentrations, but biota-soil accumulation factors were low (0.002-0.1). Compared to previously tested organisms, with all being exposed in the same soil type and under similar test conditions, the H. aspersa test was relatively insensitive to all substances.

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

    Directory of Open Access Journals (Sweden)

    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.

  8. 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

  9. 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

  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. 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

  12. Structural studies of Helix aspersa agglutinin complexed with GalNAc: A lectin that serves as a diagnostic tool.

    Science.gov (United States)

    Pietrzyk, Agnieszka J; Bujacz, Anna; Mak, Paweł; Potempa, Barbara; Niedziela, Tomasz

    2015-11-01

    Lectins belong to a differentiated group of proteins known to possess sugar-binding properties. Due to this fact, they are interesting research targets in medical diagnostics. Helix aspersa agglutinin (HAA) is a lectin that recognizes the epitopes containing α-d-N-acetylgalactosamine (GalNAc), which is present at the surface of metastatic cancer cells. Although several reports have already described the use of HAA as a diagnostic tool, this protein was not characterized on the molecular level. Here, we present for the first time the structural information about lectin isolated from mucus of Helix aspersa (garden snail). The amino acid sequence of this agglutinin was determined by Edman degradation and tertiary as well as quaternary structure by X-ray crystallography. The high resolution crystal structure (1.38Å) and MALDI-TOF mass spectrometry analysis provide the detailed information about a large part of the HAA natural glycan chain. The topology of the GalNAc binding cleft and interaction with lectin are very well defined in the structure and fully confirmed by STD HSQC NMR spectroscopy. Together, this provides structural clues regarding HAA specificity and opens possibilities to rational modifications of this important diagnostic tool.

  13. Changes in the reproductive system of the snail Helix aspersa caused by mucus from the love dart.

    Science.gov (United States)

    Koene, J M; Chase, R

    1998-08-01

    The function of the love dart in certain species of terrestrial snails is unknown. In Helix aspersa, the dart is a sharp calcareous structure that is used to pierce the partner's skin during courtship. When expelled, the dart is covered with a thick mucus. The hypothesis tested here is that the mucus contains a biologically active substance. Extracts of the digitiform glands that produce this mucus were applied to parts of the reproductive system in vitro. The extracts triggered an initial reconfiguration of the copulatory canal that caused the bursa tract diverticulum to become more accessible to the spermatophore. The reconfiguration of the copulatory canal also closed off the tract leading to the bursa copulatrix, a sperm-digesting organ. A few minutes after the initial contraction, the peristaltic contractions in the diverticulum became significantly more frequent. This latter effect continued for at least 1 h, provided that the mucus extract remained in the saline bath. The minimum effective dosage was less than the 2.2 mg of mucus transferred with the dart. Sperm competition is expected in Helix aspersa since multiple matings occur before eggs are laid. By influencing the female organs involved in the processing of foreign sperm, the dart shooter may increase the chance that his sperm will fertilise eggs.

  14. 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.

  15. 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

  16. 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.

  17. 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

  18. Biology of the invasive ascidian Ascidiella aspersa in its native habitat: Reproductive patterns and parasite load

    Science.gov (United States)

    Lynch, Sharon A.; Darmody, Grainne; O'Dwyer, Katie; Gallagher, Mary Catherine; Nolan, Sinead; McAllen, Rob; Culloty, Sarah C.

    2016-11-01

    The European sea squirt Ascidiella aspersa is a solitary tunicate native to the northeastern Atlantic, commonly found in shallow and sheltered marine ecosystems where it is capable of forming large clumps and outcompeting other invertebrate fauna at settlement. To date, there have been relatively few studies looking at the reproductive biology and health status of this invasive species. Between 2006 and 2010 sampling of a native population took place to investigate gametogenesis and reproductive cycle and to determine the impact of settlement depth on reproduction. In addition, parasite diversity and impact was assessed. A staging system to assess reproductive development was determined. The study highlighted that from year to year the tunicate could change its reproductive strategy from single sex to hermaphrodite, with spawning possible throughout the year. Depth did not impact on sex determination, however, gonad maturation and spawning occurred earlier in individuals in deeper waters compared to shallow depth and it also occurred later in A. aspersa at sites further away from the open sea. Four significant parasite groups including eugregarines, ciliates, trematodes and turbellarians were detected and prevalence of parasite infections increased in A. aspersa at sites with a reduced water flow rate. This study demonstrates the high biotic potential of this ascidian bioinvader to have a negative impact on native fauna in an introduced ecosystem, due to its highly efficient reproductive and resource allocation strategies. Artificial structures such as mooring lines can harbour large aggregations of A. aspersa, however, these manmade habitats may facilitate the colonisation and establishment of this invasive species in the benthos. Additionally, the parasite communities that A. aspersa harbour may also exacerbate its negative impact, both ecologically and economically, in an introduced area by possibly leading to the emergence of new disease in native species i

  19. 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

  20. 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...

  1. 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...

  2. Terrestrial gastropods (Helix spp) as sentinels of primary DNA damage for biomonitoring purposes: a validation study.

    Science.gov (United States)

    Angeletti, Dario; Sebbio, Claudia; Carere, Claudio; Cimmaruta, Roberta; Nascetti, Giuseppe; Pepe, Gaetano; Mosesso, Pasquale

    2013-04-01

    We validated the alkaline comet assay in two species of land snail (Helix aspersa and Helix vermiculata) to test their suitability as sentinels for primary DNA damage in polluted environments. The study was conducted under the framework of a biomonitoring program for a power station in Central Italy that had recently been converted from oil to coal-fired plant. After optimizing test conditions, the comet assay was used to measure the % Tail DNA induced by in vitro exposure of hemocytes to different concentrations of a reactive oxygen species (H2 O2 ). The treatment induced significant increases in this parameter with a concentration effect, indicating the effectiveness of the assay in snail hemocytes. After evaluating possible differences between the two species, we sampled them in three field sites at different distances from the power station, and in two reference sites assumed to have low or no levels of pollution. No species differences emerged. Percent Tail DNA values in snails from the sites near the power station were higher than those from control sites. An inverse correlation emerged between % Tail DNA and distance from the power station, suggesting that the primary DNA damage decreased as distance increased away from the pollution source. Detection of a gradient of heavy metal concentration in snail tissues suggests that these pollutants are a potential cause of the observed pattern. The comet assay appears to be a suitable assay and Helix spp. populations suitable sentinels to detect the genotoxic impact of pollutants. PMID:23444166

  3. Miradas fotográficas y construcción de huellas documentales El nacimiento de los Caracoles zapatistas

    Directory of Open Access Journals (Sweden)

    Diana Guillén

    2014-01-01

    Full Text Available El presente artículo tiene como objetivo analizar un tipo de mirada que, en tanto representación y a la vez huella documental de la realidad que capta, contribuye a construir y/o reproducir imaginarios sobre los procesos societales que nos circundan, y abre ventanas para que a través de ojos ajenos los observemos. La idea es recuperar algunos de los registros fotográficos que se realizaron durante la inauguración de los Caracoles en agosto de 2003 y, en función de la iconicidad y textualidad asociada a ellos, identificar fragmentos de las narrativas que se han desarrollado alrededor del zapatismo.

  4. 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.

  5. On the establishment of two more alien mollusca (Chama aspersa Reeve, 1846 and Chama asperella Lamarck, 1819 in the eastern Mediterranean

    Directory of Open Access Journals (Sweden)

    P. OVALIS

    2012-12-01

    Full Text Available The Indo-Pacific bivalvia Chama aspersa Reeve, 1846 and Chama asperella Lamarck, 1819 are recorded for the first time in Greek waters. These findings represent a considerable expansion in the eastern Mediterranean. Ship fouling is assumed as the most probable transportation means. However, natural dispersal via the Suez Canal is feasible as well.

  6. 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 ...

  7. 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.

  8. 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.

  9. Application of Failure Mode and Effect Analysis (FMEA) and cause and effect analysis in conjunction with ISO 22000 to a snails (Helix aspersa) processing plant; A case study.

    Science.gov (United States)

    Arvanitoyannis, Ioannis S; Varzakas, Theodoros H

    2009-08-01

    Failure Mode and Effect Analysis (FMEA) has been applied for the risk assessment of snails manufacturing. A tentative approach of FMEA application to the snails industry was attempted in conjunction with ISO 22000. Preliminary Hazard Analysis was used to analyze and predict the occurring failure modes in a food chain system (snails processing plant), based on the functions, characteristics, and/or interactions of the ingredients or the processes, upon which the system depends. Critical Control points have been identified and implemented in the cause and effect diagram (also known as Ishikawa, tree diagram, and fishbone diagram). In this work a comparison of ISO22000 analysis with HACCP is carried out over snails processing and packaging. However, the main emphasis was put on the quantification of risk assessment by determining the RPN per identified processing hazard. Sterilization of tins, bioaccumulation of heavy metals, packaging of shells and poisonous mushrooms, were the processes identified as the ones with the highest RPN (280, 240, 147, 144, respectively) and corrective actions were undertaken. Following the application of corrective actions, a second calculation of RPN values was carried out leading to considerably lower values (below the upper acceptable limit of 130). It is noteworthy that the application of Ishikawa (Cause and Effect or Tree diagram) led to converging results thus corroborating the validity of conclusions derived from risk assessment and FMEA. Therefore, the incorporation of FMEA analysis within the ISO22000 system of a snails processing industry is considered imperative.

  10. Application of Failure Mode and Effect Analysis (FMEA) and cause and effect analysis in conjunction with ISO 22000 to a snails (Helix aspersa) processing plant; A case study.

    Science.gov (United States)

    Arvanitoyannis, Ioannis S; Varzakas, Theodoros H

    2009-08-01

    Failure Mode and Effect Analysis (FMEA) has been applied for the risk assessment of snails manufacturing. A tentative approach of FMEA application to the snails industry was attempted in conjunction with ISO 22000. Preliminary Hazard Analysis was used to analyze and predict the occurring failure modes in a food chain system (snails processing plant), based on the functions, characteristics, and/or interactions of the ingredients or the processes, upon which the system depends. Critical Control points have been identified and implemented in the cause and effect diagram (also known as Ishikawa, tree diagram, and fishbone diagram). In this work a comparison of ISO22000 analysis with HACCP is carried out over snails processing and packaging. However, the main emphasis was put on the quantification of risk assessment by determining the RPN per identified processing hazard. Sterilization of tins, bioaccumulation of heavy metals, packaging of shells and poisonous mushrooms, were the processes identified as the ones with the highest RPN (280, 240, 147, 144, respectively) and corrective actions were undertaken. Following the application of corrective actions, a second calculation of RPN values was carried out leading to considerably lower values (below the upper acceptable limit of 130). It is noteworthy that the application of Ishikawa (Cause and Effect or Tree diagram) led to converging results thus corroborating the validity of conclusions derived from risk assessment and FMEA. Therefore, the incorporation of FMEA analysis within the ISO22000 system of a snails processing industry is considered imperative. PMID:19582641

  11. 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.

  12. 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.

  13. 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

  14. 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

  15. 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.

  16. Microfluidic 3D Helix Mixers

    Directory of Open Access Journals (Sweden)

    Georgette B. Salieb-Beugelaar

    2016-10-01

    Full Text Available Polymeric microfluidic systems are well suited for miniaturized devices with complex functionality, and rapid prototyping methods for 3D microfluidic structures are increasingly used. Mixing at the microscale and performing chemical reactions at the microscale are important applications of such systems and we therefore explored feasibility, mixing characteristics and the ability to control a chemical reaction in helical 3D channels produced by the emerging thread template method. Mixing at the microscale is challenging because channel size reduction for improving solute diffusion comes at the price of a reduced Reynolds number that induces a strictly laminar flow regime and abolishes turbulence that would be desired for improved mixing. Microfluidic 3D helix mixers were rapidly prototyped in polydimethylsiloxane (PDMS using low-surface energy polymeric threads, twisted to form 2-channel and 3-channel helices. Structure and flow characteristics were assessed experimentally by microscopy, hydraulic measurements and chromogenic reaction, and were modeled by computational fluid dynamics. We found that helical 3D microfluidic systems produced by thread templating allow rapid prototyping, can be used for mixing and for controlled chemical reaction with two or three reaction partners at the microscale. Compared to the conventional T-shaped microfluidic system used as a control device, enhanced mixing and faster chemical reaction was found to occur due to the combination of diffusive mixing in small channels and flow folding due to the 3D helix shape. Thus, microfluidic 3D helix mixers can be rapidly prototyped using the thread template method and are an attractive and competitive method for fluid mixing and chemical reactions at the microscale.

  17. 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...

  18. Square Helix TWT for THz Frequencies

    DEFF Research Database (Denmark)

    Kotiranta, Mikko; Krozer, Viktor; Zhurbenko, Vitaliy

    2010-01-01

    A helix slow-wave structure with a square shape has been designed for use in traveling-wave tubes operating at terahertz frequencies. The square shape makes it compatible with microfabrication methods. A 3-D particle-in-cell simulation of a traveling-wave tube with such a helix indicates a gain...

  19. Helix-packing motifs in membrane proteins.

    Science.gov (United States)

    Walters, R F S; DeGrado, W F

    2006-09-12

    The fold of a helical membrane protein is largely determined by interactions between membrane-imbedded helices. To elucidate recurring helix-helix interaction motifs, we dissected the crystallographic structures of membrane proteins into a library of interacting helical pairs. The pairs were clustered according to their three-dimensional similarity (rmsd universe of common transmembrane helix-pairing motifs is relatively simple. The largest cluster, which comprises 29% of the library members, consists of an antiparallel motif with left-handed packing angles, and it is frequently stabilized by packing of small side chains occurring every seven residues in the sequence. Right-handed parallel and antiparallel structures show a similar tendency to segregate small residues to the helix-helix interface but spaced at four-residue intervals. Position-specific sequence propensities were derived for the most populated motifs. These structural and sequential motifs should be quite useful for the design and structural prediction of membrane proteins.

  20. 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...

  1. 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...

  2. 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.

  3. 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%.

  4. 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-...

  5. 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.

  6. Triple helix interactions for eco-innovation

    DEFF Research Database (Denmark)

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

    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...

  7. Helix reactor: great potential for flow chemistry

    NARCIS (Netherlands)

    Geerdink, P.; Runstraat, A. van den; Roelands, C.P.M.; Goetheer, E.L.V.

    2009-01-01

    The Helix reactor is highly suited for precise reaction control based on good hydrodynamics. The hydrodynamics are controlled by the Dean vortices, which create excellent heat transfer properties, approach plug flow and avoid turbulence. The flexibility of this reactor has been demonstrated using a

  8. 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.

  9. 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

  10. 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...

  11. Helix Scan: A Scan Design for Diagnosis

    Institute of Scientific and Technical Information of China (English)

    WANG Fei; HU Yu; LI Xiaowei

    2007-01-01

    Scan design is a widely used design-for-testability technique to improve test quality and efficiency. For the scan-designed circuit, test and diagnosis of the scan chain and the circuit is an important process for silicon debug and yield learning. However, conventional scan designs and diagnosis methods abort the subsequent diagnosis process after diagnosing the scan chain if the scan chain is faulty. In this work, we propose a design-for-diagnosis scan strategy called helix scan and a diagnosis algorithm to address this issue. Unlike previous proposed methods, helix scan has the capability to carry on the diagnosis process without losing information when the scan chain is faulty. What is more, it simplifies scan chain diagnosis and achieves high diagnostic resolution as well as accuracy. Experimental results demonstrate the effectiveness of our design.

  12. The double helix and the 'wronged heroine'.

    Science.gov (United States)

    Maddox, Brenda

    2003-01-23

    In 1962, James Watson, Francis Crick and Maurice Wilkins received the Nobel prize for the discovery of the structure of DNA. Notably absent from the podium was Rosalind Franklin, whose X-ray photographs of DNA contributed directly to the discovery of the double helix. Franklin's premature death, combined with misogynist treatment by the male scientific establishment, cast her as a feminist icon. This myth overshadowed her intellectual strength and independence both as a scientist and as an individual.

  13. 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.

  14. 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 ...

  15. 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 ...

  16. 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 ...

  17. Chatter Prediction for Variable Pitch and Variable Helix Milling

    Directory of Open Access Journals (Sweden)

    Yong Wang

    2015-01-01

    Full Text Available 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 predicted and observed performance of variable pitch and variable helix against uniform pitch and uniform helix milling is presented. It is shown that variable pitch and variable helix milling can obtain larger stable cutting area than uniform pitch and uniform helix milling. Thus, it is concluded that variable pitch and variable helix milling are an effective way for suppressing chatter.

  18. Site-specific unfolding thermodynamics of a helix-turn-helix protein.

    Science.gov (United States)

    Amunson, Krista E; Ackels, Loren; Kubelka, Jan

    2008-07-01

    The thermal unfolding of a 40-residue helix-turn-helix subdomain of the P22 viral coat protein was investigated using circular dichroism (CD) and Fourier transform infrared spectroscopy (FTIR) with site-specific 13C isotopic labeling. Helix-turn-helix is the simplest alpha-helical structural motif that combines both secondary and tertiary structural elements. The CD of individual helical fragments reveals that the P22 subdomain is stabilized by tertiary interhelical interactions. Overall the temperature-dependent CD and FTIR data can be described by a three-state process with a partially folded intermediate. However, the analysis of the site-specific 13C IR signals reveals distinct unfolding thermodynamics for each of the labeled sites. The thermodynamic parameters of the thermal unfolding of each of the labeled segments were obtained using singular value decomposition in combination with target transformation and global fitting. The P22 subdomain unfolds from the N-terminus toward the helical segments near the turn. Our results show that as few as two 13C labeled residues can be detected in a 40 residue protein and provide local, site-specific structural information about protein unfolding, which is not resolved by standard, nonsite-specific spectroscopic probes.

  19. A Classification of Basic Helix-Loop-Helix Transcription Factors of Soybean

    Directory of Open Access Journals (Sweden)

    Karen A. Hudson

    2015-01-01

    Full Text Available The complete genome sequence of soybean allows an unprecedented opportunity for the discovery of the genes controlling important traits. In particular, the potential functions of regulatory genes are a priority for analysis. The basic helix-loop-helix (bHLH family of transcription factors is known to be involved in controlling a wide range of systems critical for crop adaptation and quality, including photosynthesis, light signalling, pigment biosynthesis, and seed pod development. Using a hidden Markov model search algorithm, 319 genes with basic helix-loop-helix transcription factor domains were identified within the soybean genome sequence. These were classified with respect to their predicted DNA binding potential, intron/exon structure, and the phylogeny of the bHLH domain. Evidence is presented that the vast majority (281 of these 319 soybean bHLH genes are expressed at the mRNA level. Of these soybean bHLH genes, 67% were found to exist in two or more homeologous copies. This dataset provides a framework for future studies on bHLH gene function in soybean. The challenge for future research remains to define functions for the bHLH factors encoded in the soybean genome, which may allow greater flexibility for genetic selection of growth and environmental adaptation in this widely grown crop.

  20. 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

  1. HELIX: The High Energy Light Isotope Experiment

    Science.gov (United States)

    Wakely, Scott

    This is the lead proposal for a new suborbital program, HELIX (High-Energy Light Isotope eXperiment), designed to make measurements of the isotopic composition of light cosmic-ray nuclei from ~200 MeV/nuc to ~10 GeV/nuc. Past measurements of this kind have provided profound insights into the nature and origin of cosmic rays, revealing, for instance, information on acceleration and confinement time scales, and exposing some conspicuous discrepancies between solar and cosmic-ray abundances. The most detailed information currently available comes from the ACE/CRIS mission, but is restricted to energies below a few 100 MeV/nuc. HELIX aims at extending this energy range by over an order of magnitude, where, in most cases, no measurements of any kind exist, and where relativistic time dilation affects the apparent lifetime of radioactive clock nuclei. The HELIX measurements will provide essential information for understanding the propagation history of cosmic rays in the galaxy. This is crucial for properly interpreting several intriguing anomalies reported in recent cosmic-ray measurements, pertaining to the energy spectra of protons, helium, and heavier nuclei, and to the anomalous rise in the positron fraction at higher energy. HELIX employs a high-precision magnet spectrometer to provide measurements which are not achievable by any current or planned instrument. The superconducting magnet originally used for the HEAT payload in five successful high-altitude flights will be combined with state-of-the-art detectors to measure the charge, time-of-flight, magnetic rigidity, and velocity of cosmic-ray particles with high precision. The instrumentation includes plastic scintillators, silicon-strip detectors repurposed from Fermilab's CDF detector, a high-performance gas drift chamber, and a ring-imaging Cherenkov counter employing aerogel radiators and silicon photomultipliers. To reduce cost and technical risk, the HELIX program will be structured in two stages. The first

  2. The bridge helix coordinates movements of modules in RNA polymerase

    Directory of Open Access Journals (Sweden)

    Landick Robert

    2010-11-01

    Full Text Available Abstract The RNA polymerase 'bridge helix' is a metastable α-helix that spans the leading edge of the enzyme active-site cleft. A new study published in BMC Biology reveals surprising tolerance to helix-disrupting changes in a region previously thought crucial for translocation, and suggests roles for two hinge-like segments of the bridge helix in coordinating modules that move during the nucleotide-addition cycle. See Research article: http://www.biomedcentral.com/1741-7007/8/134

  3. [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

  4. Importance of Hydrophilic Hydration and Intramolecular Interactions in the Thermodynamics of Helix-Coil Transition and Helix-Helix Assembly in a Deca-Alanine Peptide.

    Science.gov (United States)

    Tomar, Dheeraj S; Weber, Valéry; Pettitt, B Montgomery; Asthagiri, D

    2016-01-14

    For a model deca-alanine peptide the cavity (ideal hydrophobic) contribution to hydration favors the helix state over extended states and the paired helix bundle in the assembly of two helices. The energetic contributions of attractive protein-solvent interactions are separated into quasi-chemical components consisting of a short-range part arising from interactions with solvent in the first hydration shell and the remaining long-range part that is well described by a Gaussian. In the helix-coil transition, short-range attractive protein-solvent interactions outweigh hydrophobic hydration and favor the extended 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 favoring folding. In the pairing of two helices, the cavity contribution outweighs the short-range attractive protein-water interactions. However, long-range, protein-solvent attractive interactions can either enhance or reverse this trend depending on the mutual orientation of the helices. In helix-helix assembly, change in enthalpy arising from change in attractive protein-solvent interactions favors disassembly. In helix pairing as well, favorable protein intramolecular interactions are found to be as important as hydration effects. Overall, hydrophilic protein-solvent interactions and protein intramolecular interactions are found to play a significant role in the thermodynamics of folding and assembly in the system studied.

  5. Solitons in an isolated helix chain

    DEFF Research Database (Denmark)

    Christiansen, Peter Leth; Zolotaryuk, Alexander; Savin, A.V.

    1997-01-01

    propagating together with localized transverse thickening (bulge) and torsional stretching (untwisting) have been found. The stability properties of these (three-component) soliton solutions have been studied by using numerical techniques developed for seeking solitary-wave solutions in complex molecular...... as a generalization of the well-known one-dimensional Fermi-Pasta-Ulam model to include transverse degrees of freedom of the chain molecules. In the particular case of the alpha-helix molecular chain, the intermolecular interactions involved into the model are the point-point bonds connecting the first-, second......-, and third-nearest neighbors. The set of nonlinear field equations with respect to the longitudinal and transverse (torsional and radial) displacements of the chain molecules has been derived and treated. Stable nontopological soliton solutions which describe supersonic pulses of longitudinal compression...

  6. 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.

  7. 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.

  8. Regional Dimensions of the Triple Helix Model: Setting the Context

    Science.gov (United States)

    Todeva, Emanuela; Danson, Mike

    2016-01-01

    This paper introduces the rationale for the special issue and its contributions, which bridge the literature on regional development and the Triple Helix model. The concept of the Triple Helix at the sub-national, and specifically regional, level is established and examined, with special regard to regional economic development founded on…

  9. 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 ...

  10. The Membrane- and Soluble-Protein Helix-Helix Interactome: Similar Geometry via Different Interactions

    OpenAIRE

    Zhang, Shao-Qing; Kulp, Daniel W.; Schramm, Chaim A.; Mravic, Marco; Samish, Ilan; DeGrado, William F

    2015-01-01

    Alpha-helices are a basic unit of protein secondary structure and therefore the interaction between helices is crucial to understanding tertiary and higher-order folds. Comparing subtle variations in the structural and sequence motifs between membrane and soluble proteins sheds light on the different constraints faced by each environment and elucidates the complex puzzle of membrane protein folding. Here, we demonstrate that membrane and water-soluble helix pairs share a small number of simil...

  11. 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

  12. The membrane- and soluble-protein helix-helix interactome: similar geometry via different interactions.

    Science.gov (United States)

    Zhang, Shao-Qing; Kulp, Daniel W; Schramm, Chaim A; Mravic, Marco; Samish, Ilan; DeGrado, William F

    2015-03-01

    α Helices are a basic unit of protein secondary structure and therefore the interaction between helices is crucial to understanding tertiary and higher-order folds. Comparing subtle variations in the structural and sequence motifs between membrane and soluble proteins sheds light on the different constraints faced by each environment and elucidates the complex puzzle of membrane protein folding. Here, we demonstrate that membrane and water-soluble helix pairs share a small number of similar folds with various interhelical distances. The composition of the residues that pack at the interface between corresponding motifs shows that hydrophobic residues tend to be more enriched in the water-soluble class of structures and small residues in the transmembrane class. The latter group facilitates packing via sidechain- and backbone-mediated hydrogen bonds within the low-dielectric membrane milieu. The helix-helix interactome space, with its associated sequence preferences and accompanying hydrogen-bonding patterns, should be useful for engineering, prediction, and design of protein structure. PMID:25703378

  13. 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 ...

  14. 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)

  15. 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...

  16. 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...

  17. 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.

  18. 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...

  19. 6th Golden Helix Pharmacogenomics Day: pharmacogenomics and individualized therapy

    Directory of Open Access Journals (Sweden)

    Stojiljkovic Maja

    2012-09-01

    Full Text Available Abstract The Golden Helix Pharmacogenomics Days are international scientific meetings aiming to educate healthcare professionals and biomedical scientists about pharmacogenomics and personalized medicine. In this meeting report, we provide an overview of the scientific lectures and the topics discussed during the 6th Golden Helix Pharmacogenomics Day that was held in Belgrade, Serbia last June 5, 2012. The scientific program included lectures by the local and international speakers from Europe and the United States.

  20. Slow Wave Characteristics of Helix Structure with Elliptical Cross Section

    Institute of Scientific and Technical Information of China (English)

    XIE Jian-Xiang; WEI Yan-Yu; GONG Yu-Bin; Fu Cheng-Fang; YUE Ling-Na; WANG Wen-Xiang

    2007-01-01

    We present a novel helix slow wave structure with an elliptical cross section shielded by an elliptical waveguide.The rf characteristics including dispersion properties,interaction impedance of zero mode in this structure have been studied in detail.The theoretical results reveal that weaker dispersion even abnormal dispersion characteristics is obtained with the increasing eccentricity of the elliptical waveguide,while the interaction impedance is enhanced by enlarging the eccentricity of elliptical helix.

  1. 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.

  2. 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.

  3. 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

  4. 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

  5. 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.

  6. Structure, stability and folding of the alpha-helix.

    Science.gov (United States)

    Doig, A J; Andrew, C D; Cochran, D A; Hughes, E; Penel, S; Sun, J K; Stapley, B J; Clarke, D T; Jones, G R

    2001-01-01

    Pauling first described the alpha-helix nearly 50 years ago, yet new features of its structure continue to be discovered, using peptide model systems, site-directed mutagenesis, advances in theory, the expansion of the Protein Data Bank and new experimental techniques. Helical peptides in solution form a vast number of structures, including fully helical, fully coiled and partly helical. To interpret peptide results quantitatively it is essential to use a helix/coil model that includes the stabilities of all these conformations. Our models now include terms for helix interiors, capping, side-chain interactions, N-termini and 3(10)-helices. The first three amino acids in a helix (N1, N2 and N3) and the preceding N-cap are unique, as their amide NH groups do not participate in backbone hydrogen bonding. We surveyed their structures in proteins and measured their amino acid preferences. The results are predominantly rationalized by hydrogen bonding to the free NH groups. Stabilizing side-chain-side-chain energies, including hydrophobic interactions, hydrogen bonding and polar/non-polar interactions, were measured accurately in helical peptides. Helices in proteins show a preference for having approximately an integral number of turns so that their N- and C-caps lie on the same side. There are also strong periodic trends in the likelihood of terminating a helix with a Schellman or alpha L C-cap motif. The kinetics of alpha-helix folding have been studied with stopped-flow deep ultraviolet circular dichroism using synchrotron radiation as the light source; this gives a far superior signal-to-noise ratio than a conventional instrument. We find that poly(Glu), poly(Lys) and alanine-based peptides fold in milliseconds, with longer peptides showing a transient overshoot in helix content.

  7. An unusual helix turn helix motif in the catalytic core of HIV-1 integrase binds viral DNA and LEDGF.

    Directory of Open Access Journals (Sweden)

    Hayate Merad

    Full Text Available BACKGROUND: Integrase (IN of the type 1 human immunodeficiency virus (HIV-1 catalyzes the integration of viral DNA into host cellular DNA. We identified a bi-helix motif (residues 149-186 in the crystal structure of the catalytic core (CC of the IN-Phe185Lys variant that consists of the alpha(4 and alpha(5 helices connected by a 3 to 5-residue turn. The motif is embedded in a large array of interactions that stabilize the monomer and the dimer. PRINCIPAL FINDINGS: We describe the conformational and binding properties of the corresponding synthetic peptide. This displays features of the protein motif structure thanks to the mutual intramolecular interactions of the alpha(4 and alpha(5 helices that maintain the fold. The main properties are the binding to: 1- the processing-attachment site at the LTR (long terminal repeat ends of virus DNA with a K(d (dissociation constant in the sub-micromolar range; 2- the whole IN enzyme; and 3- the IN binding domain (IBD but not the IBD-Asp366Asn variant of LEDGF (lens epidermal derived growth factor lacking the essential Asp366 residue. In our motif, in contrast to the conventional HTH (helix-turn-helix, it is the N terminal helix (alpha(4 which has the role of DNA recognition helix, while the C terminal helix (alpha(5 would rather contribute to the motif stabilization by interactions with the alpha(4 helix. CONCLUSION: The motif, termed HTHi (i, for inverted emerges as a central piece of the IN structure and function. It could therefore represent an attractive target in the search for inhibitors working at the DNA-IN, IN-IN and IN-LEDGF interfaces.

  8. 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

  9. 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

  10. 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

  11. 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.

  12. 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...

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

    DEFF Research Database (Denmark)

    Wittung, P; Nielsen, Peter E.; Buchardt, O;

    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...... acid (PNA) is a DNA analogue with a backbone consisting of N-(2-aminoethyl)glycine units (Fig. 1) which has been shown to mimic DNA in forming Watson-Crick complementary duplexes with normal DNA. Using circular dichroism spectroscopy we show here that two complementary PNA strands can hybridize to one...

  14. 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.

  15. 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. ...

  16. 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.

  17. 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…

  18. 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 ...

  19. 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

  20. Alpha- and beta-hemocyanin of Helix pomatia

    NARCIS (Netherlands)

    Dijk, Jan

    1971-01-01

    This thesis deals with several aspects of the protein structure of Alpha- and Beta -hemocyanin of Helix pomatia. a- and 0-hemocyanin possess a virtually identical amino acid composition; it closely resembles the amino acid com- positions of hemocyanins of other MOLLUSCA and ARTHROPODA. All hemocyani

  1. 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 ...

  2. A catastrophe theory model of the conflict helix, with tests.

    Science.gov (United States)

    Rummel, R J

    1987-10-01

    Macro social field theory has undergone extensive development and testing since the 1960s. One of these has been the articulation of an appropriate conceptual micro model--called the conflict helix--for understanding the process from conflict to cooperation and vice versa. Conflict and cooperation are viewed as distinct equilibria of forces in a social field; the movement between these equilibria is a jump, energized by a gap between social expectations and power, and triggered by some minor event. Quite independently, there also has been much recent application of catastrophe theory to social behavior, but usually without a clear substantive theory and lacking empirical testing. This paper uses catastrophe theory--namely, the butterfly model--mathematically to structure the conflict helix. The social field framework and helix provide the substantive interpretation for the catastrophe theory; and catastrophe theory provides a suitable mathematical model for the conflict helix. The model is tested on the annual conflict and cooperation between India and Pakistan, 1948 to 1973. The results are generally positive and encouraging.

  3. Archaeal MBF1 binds to 30S and 70S ribosomes via its helix-turn-helix domain

    NARCIS (Netherlands)

    Blombach, F.; Launay, H.; Snijders, A.P.; Zorraquino, V.; Wu, H.; Koning, de B.; Brouns, S.J.J.; Ettema, T.J.; Camilloni, C.; Cavalli, A.; Vendruscolo, M.; Dickman, M.J.; Cabrita, L.D.; Teana, La A.; Benelli, D.; Londei, P.; Christodoulou, J.; Oost, van der J.

    2014-01-01

    MBF1 (multi-protein bridging factor 1) is a protein containing a conserved HTH (helix–turn–helix) domain in both eukaryotes and archaea. Eukaryotic MBF1 has been reported to function as a transcriptional co-activator that physically bridges transcription regulators with the core transcription initia

  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 th...

  5. Structural and functional aspects of winged-helix domains at the core of transcription initiation complexes.

    Science.gov (United States)

    Teichmann, Martin; Dumay-Odelot, Hélène; Fribourg, Sébastien

    2012-01-01

    The winged helix (WH) domain is found in core components of transcription systems in eukaryotes and prokaryotes. It represents a sub-class of the helix-turn-helix motif. The WH domain participates in establishing protein-DNA and protein-protein-interactions. Here, we discuss possible explanations for the enrichment of this motif in transcription systems.

  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. 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

  8. Bent helix formation between RNA hairpins with complementary loops.

    Science.gov (United States)

    Marino, J P; Gregorian, R S; Csankovszki, G; Crothers, D M

    1995-06-01

    The initial interaction between the ColE1 plasmid specific transcripts RNA I and RNA II, which function as antisense regulators of plasmid replication, comprises a transient complex between complementary loops found within the RNA secondary structures. Multidimensional heteronuclear magnetic resonance spectroscopy was used to characterize complexes formed between model RNA hairpins having seven nucleotide complementary loops. Seven base pairs are formed in the loop-loop helix, with continuous helical stacking of the loop residues on the 3' side of their helical stems. A sharp bend in the loop-loop helix, documented by gel electrophoresis, narrows the major groove and allows bridging of the phosphodiester backbones across the major groove in order to close the hairpin loops at their 5'-ends. The bend is further enhanced by the binding of Rom, a ColE1 encoded protein that regulates replication. PMID:7539549

  9. 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)

  10. 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.

  11. 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.

  12. 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...

  13. 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...

  14. 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...

  15. 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.

  16. Partial Agonists Activate PPARgamma Using a Helix 12 Independent Mechanism

    Energy Technology Data Exchange (ETDEWEB)

    Bruning, J.B.; Chalmers, M.J.; Prasad, S.; Bushby, S.A.; Kamenecka, T.A.; He, Y.; Nettles, K.W.; Griffin, P.R.

    2009-05-28

    Binding to helix 12 of the ligand-binding domain of PPAR{gamma} is required for full agonist activity. Previously, the degree of stabilization of the activation function 2 (AF-2) surface was thought to correlate with the degree of agonism and transactivation. To examine this mechanism, we probed structural dynamics of PPAR{gamma} with agonists that induced graded transcriptional responses. Here we present crystal structures and amide H/D exchange (HDX) kinetics for six of these complexes. Amide HDX revealed each ligand induced unique changes to the dynamics of the ligand-binding domain (LBD). Full agonists stabilized helix 12, whereas intermediate and partial agonists did not at all, and rather differentially stabilized other regions of the binding pocket. The gradient of PPAR{gamma} transactivation cannot be accounted for solely through changes to the dynamics of AF-2. Thus, our understanding of allosteric signaling must be extended beyond the idea of a dynamic helix 12 acting as a molecular switch.

  17. 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.

  18. 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.

  19. 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

  20. 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.

  1. 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 ...

  2. 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

  3. 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

  4. 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.

  5. 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

  6. 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.

  7. 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

  8. pH jump induced α-helix folding.

    Directory of Open Access Journals (Sweden)

    Donten M. L.

    2013-03-01

    Full Text Available pH can be used to impact the folding equilibrium of peptides and proteins. This fact is utilized, similarly to temperature jumps, in pH jump experiments employing laser time-resolved spectroscopy to study the function and structural dynamics of these molecules. Here the application of pH jumps in folding experiments was investigated. Experiments with poly-L-glutamic acid alpha-helix formation shown the critical aspects of pH jump experiments and yielded direct information about the folding kinetics monitored with the amide I IR band.

  9. 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 ...

  10. 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.

  11. 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.

  12. HelixFlex: bioinspired maneuverable instrument for skull base surgery.

    Science.gov (United States)

    Gerboni, Giada; Henselmans, Paul W J; Arkenbout, Ewout A; van Furth, Wouter R; Breedveld, Paul

    2015-12-01

    Endoscopic endonasal surgery is currently regarded as the 'gold standard' for operating on pituitary gland tumors, and is becoming more and more accepted for treatment of other skull base lesions. However, endoscopic surgical treatment of most skull base pathologies, including certain pituitary tumors, is severely impaired by current instruments lack of maneuverability. Especially, gaining access to, and visibility of, difficult-to-reach anatomical corners without interference with surrounding neurovascular structures or other instruments, is a challenge. In this context there is the need for instruments that are able to provide a stable shaft position, while both the orientation and the position of the end-effector can be independently controlled. Current instruments that allow for this level of maneuverability are usually mechanically complex, and hence less suitable for mass production. This study therefore focuses on the development of a new actuation technique that allows for the required maneuverability while reducing the construction complexity. This actuation technique, referred to as multi-actuation, integrates multiple cable routings into a single steerable structure. Multi-actuation has been successfully integrated and tested in a handheld prototype instrument called HelixFlex. HelixFlex contains a 4 degrees of freedom maneuverable 5.8 mm (diameter) tip and shows promising results concerning its maneuverability and potential rigidity.

  13. 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

  14. Genes and the physics of the DNA double-helix.

    Science.gov (United States)

    Yeramian, E

    2000-09-19

    The processing of the genetic information stored in the double-helical DNA implies the separation of the two strands, the physics of which is described by the helix-coil transition model. Is there a relationship between genetic maps and DNA physical stability maps that plot the sequence-specific propensity for the thermal disruption of the double-helix? Here, with appropriate methodological formulations, such maps are derived for a large set of sequences, including complete genomes. The superposition of the two maps leads to a contrasted picture with correlations ranging between two extremes: from almost perfect (with the genes precisely delineated as stable regions) to more or less complete unrelatedness. The simplest explanation for the results is that the observed striking correlations correspond to the relics of a primeval organisation of the genetic message, with the physics of DNA playing a role in the delimitation of coding regions. In order to trace the evolutionary fate of this signal further, a detailed study of the yeast complete genome is performed. In this study, the superposition of the genetic and physical stability maps is examined in the light of information concerning gene duplication. On the basis of this analysis it is concluded that the 'signature' associated with the supposed archaic signal is in the process of being erased, most probably because the underlying feature is no longer under selective pressure. There are many evolutionary implications for the results presented and for their proposed interpretations, notably concerning models of mutational dynamics in relation to erasure processes.

  15. 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...

  16. 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.

  17. 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.

  18. A basic helix-loop-helix transcription factor DvIVS determines flower color intensity in cyanic dahlia cultivars.

    Science.gov (United States)

    Ohno, Sho; Deguchi, Ayumi; Hosokawa, Munetaka; Tatsuzawa, Fumi; Doi, Motoaki

    2013-08-01

    The study was aimed to identify the factors that regulate the intensity of flower color in cyanic dahlia (Dahlia variabilis), using fifteen cultivars with different color intensities in their petals. The cultivars were classified into three groups based on their flavonoid composition: ivory white cultivars with flavones; purple and pink cultivars with flavones and anthocyanins; and red cultivars with flavones, anthocyanins, and chalcones. Among the purple, pink, and ivory white cultivars, an inverse relationship was detected between lightness, which was used as an indicator for color intensity and anthocyanin content. A positive correlation was detected between anthocyanin contents and the expression of some structural genes in the anthocyanin synthesis pathway that are regulated by DvIVS, a basic helix-loop-helix transcription factor. A positive correlation between anthocyanin content and expression of DvIVS was also found. The promoter region of DvIVS was classified into three types, with cultivars carrying Type 1 promoter exhibited deep coloring, those carrying Type 2 and/or Type 3 exhibited pale coloring, and those carrying Type 1 and Type 2 and/or Type 3 exhibited medium coloring. The transcripts of the genes from these promoters encoded full-length predicted proteins. These results suggested that the genotype of the promoter region in DvIVS is one of the key factors determining the flower color intensity. PMID:23689377

  19. 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.

  20. Structure of bacteriophage [phi]29 head fibers has a supercoiled triple repeating helix-turn-helix motif

    Energy Technology Data Exchange (ETDEWEB)

    Xiang, Ye; Rossmann, Michael G. (Purdue)

    2011-12-22

    The tailed bacteriophage {phi}29 capsid is decorated with 55 fibers attached to quasi-3-fold symmetry positions. Each fiber is a homotrimer of gene product 8.5 (gp8.5) and consists of two major structural parts, a pseudohexagonal base and a protruding fibrous portion that is about 110 {angstrom} in length. The crystal structure of the C-terminal fibrous portion (residues 112-280) has been determined to a resolution of 1.6 {angstrom}. The structure is about 150 {angstrom} long and shows three distinct structural domains designated as head, neck, and stem. The stem region is a unique three-stranded helix-turn-helix supercoil that has not previously been described. When fitted into a cryoelectron microscope reconstruction of the virus, the head structure corresponded to a disconnected density at the distal end of the fiber and the neck structure was located in weak density connecting it to the fiber. Thin section studies of Bacillus subtilis cells infected with fibered or fiberless {phi}29 suggest that the fibers might enhance the attachment of the virions onto the host cell wall.

  1. Helix versus sheet formation in a small peptide

    Science.gov (United States)

    Peng, Yong; Hansmann, Ulrich H.

    2003-10-01

    Segments with the amino acid sequence EKAYLRT (glutamine-lysine-alanine-tyrosine-leucine-arginine-threonine) appear in naturally occurring proteins both in α-helices and β-sheets. For this reason, we have used this peptide to study how secondary structure formation in proteins depends on the local environment. Our data rely on multicanonical Monte Carlo simulations where the interactions among all atoms are taken into account. Results in gas phase are compared with that in an implicit solvent. We find that both the solvated molecule and EKAYLRT in gas phase form an α-helix when not interacting with other molecules. However, in the vicinity of a β-strand, the peptide forms a β-strand. Because of this change in secondary structure our peptide may provide a simple model for the α→β transition that is supposedly related to the outbreak of prion diseases and similar illnesses.

  2. 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...

  3. 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

  4. 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

  5. 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.

  6. 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

  7. 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.)

  8. 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.

  9. ZmZHOUPI, an endosperm-specific basic helix-loop-helix transcription factor involved in maize seed development.

    Science.gov (United States)

    Grimault, Aurélie; Gendrot, Ghislaine; Chamot, Sophy; Widiez, Thomas; Rabillé, Hervé; Gérentes, Marie-France; Creff, Audrey; Thévenin, Johanne; Dubreucq, Bertrand; Ingram, Gwyneth C; Rogowsky, Peter M; Depège-Fargeix, Nathalie

    2015-11-01

    In angiosperm seeds the embryo is embedded within the endosperm, which is in turn enveloped by the seed coat, making inter-compartmental communication essential for coordinated seed growth. In this context the basic helix-loop-helix domain transcription factor AtZHOUPI (AtZOU) fulfils a key role in both the lysis of the transient endosperm and in embryo cuticle formation in Arabidopsis thaliana. In maize (Zea mays), a cereal with a persistent endosperm, a single gene, ZmZOU, falls into the same phylogenetic clade as AtZOU. Its expression is limited to the endosperm where it peaks during the filling stage. In ZmZOU-RNA interference knock-down lines embryo size is slightly reduced and the embryonic suspensor and the adjacent embryo surrounding region show retarded breakdown. Ectopic expression of ZmZOU reduces stomatal number, possibly due to inappropriate protein interactions. ZmZOU forms functional heterodimers with AtICE/AtSCREAM and the closely related maize proteins ZmICEb and ZmICEc, but its interaction is more efficient with the ZmICEa protein, which shows sequence divergence and only has close homologues in other monocotyledonous species. Consistent with the observation that these complexes can trans-activate target gene promoters from Arabidopsis, ZmZOU partially complements the Atzou-4 mutant. However, structural, trans-activation and gene expression data support the hypothesis that ZmZOU and ZmICEa may have coevolved to form a functional complex unique to monocot seeds. This divergence may explain the reduced functionality of ZmZOU in Arabidopsis, and reflect functional specificities which are unique to the monocotyledon lineage. PMID:26361885

  10. Discrete step model of helix-coil kinetics: Distribution of fluctuation times

    Science.gov (United States)

    Poland, Douglas

    1996-07-01

    A method is outlined for the computer simulation of the cooperative kinetics required to construct the distribution function for time intervals between fluctuations in conformational states in macromolecules. Using the helix-coil transition in polyamino acids as an example, we develop a Monte Carlo cellular automata approximation of the kinetics of this system in discrete time. This approximation is tested against a number of exact solutions for homopolymers and is then used to calculate moments of the distribution function for the time intervals between switches in conformational state at a given site (e.g., given a switch from coil to helix at zero time, how long will it take before the state switches back). The maximum-entropy method is used to construct the very broad distribution function from the moments. In heteropolymers the diffusion of helix-coil boundaries is reduced, helix being more localized on strong helix-forming residues. We investigate the effect of a specific sequence of amino acid residues on conformational fluctuations by using the known σ and s values for the naturally occurring amino acids to simulate the kinetics of helix formation (limiting the range of cooperativity to the α-helix) in sperm whale myoglobin, giving the time evolution to the equilibrium probability profile in this system.

  11. 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.

  12. 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.

  13. 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.

  14. 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 ...

  15. 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...

  16. Helix Induction to Polysilane Chain Upon Wrapping by Sugar Derivatives and Related Chemistry

    Institute of Scientific and Technical Information of China (English)

    M.Tanaka; T.Sanji; Nobu; Kato; Y.Sato

    2007-01-01

    1 Results Helix induction to polymer chains is an active area of research these days. In most cases,optically-active units are attached to the polymers to induce helical conformation. Scheme 1Since the properties of σ-conjugated polymers like polysilanes are dependent on the conformation of the chain,it is particularly interesting to induce helix to oligo-and polysilanes. We have been working on the helix induction by host-guest complexation with sugar derivatives such as cyclodextrine and amylose.The l...

  17. 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...

  18. Extension of Helix 12 in Munc18-1 Induces Vesicle Priming

    DEFF Research Database (Denmark)

    Munch, Anders S; Kedar, Girish H; van Weering, Jan R T;

    2016-01-01

    interaction with synaptobrevin-2/VAMP2 (vesicle-associated membrane protein 2), leading to SNARE complex formation. To test this hypothesis in living cells, we examined secretion from Munc18-1-null mouse adrenal chromaffin cells expressing Munc18-1 mutants designed to either perturb the extension of helix 12...... exocytosis has remained elusive, but recent data led to the hypothesis that the extension of helix 12 in Munc18 within domain 3a leads to synaptobrevin-2/VAMP2 interaction and SNARE complex formation. Using both lack-of-function and gain-of-function mutants, we here report that the conformation of helix 12...

  19. 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

  20. 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.

  1. 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

  2. Portrait of a discovery. Watson, Crick, and the double helix.

    Science.gov (United States)

    de Chadarevian, Soraya

    2003-03-01

    This essay examines an iconic image of twentieth-century science: Antony Barrington Brown's photograph of James Watson, Francis Crick, and the double-helical model of DNA. The detailed reconstruction of the production, reception, and uses of the photograph reveals the central role of the image in making the discovery it portrays. Taken in May 1953, two full months after the scientists built the model, to accompany a report on the structure in Time magazine, the photograph (like the report) was never published. It came into circulation only fifteen years later, as an illustration in Watson's best-selling book The Double Helix. While the image served as a historical document and advertisement for the book, only the book provided the description that made the image as well as the people and the model it represented famous. The history of the image provides insights into the retrospective construction of the discovery, which has since been celebrated as the origin of a new science of life. PMID:12725105

  3. 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

  4. 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.”...

  5. Knots in the Helix Nebula found in H2

    CERN Document Server

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

    2009-01-01

    We present a deep and wide field-of-view (4'x 7') image of the planetary nebula (PN) NGC 7293 (the Helix Nebula) in the 2.12 micron H2 v=1-0 S(1) line. The excellent seeing (0.4'') at the Subaru Telescope, allows the details of cometary knots to be examined. The knots are found at distances of 2.2'-6.4' from the central star (CS). At the inner edge and in the inner ring (up to 4.5' fromthe CS), the knot often show a `tadpole' shape, an elliptical head with a bright crescent inside and a long tail opposite to the CS. In detail, there are variations in the tadpole shapes, such as narrowing tails, widening tails, meandering tails, or multi-peaks within a tail. In the outer ring (4.5'-6.4' from the CS), the shapes are more fractured, and the tails do not collimate into a single direction. The transition in knot morphology from the inner edge to the outer ring is clearly seen. The number density of knots governs the H2 surface brightness in the inner ring: H2 exists only within the knots. Possible mechanisms which...

  6. 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...

  7. Fluorescence Resonance Energy Transfer (FRET as a method to calculate the dimerization strength of basic Helix-Loop-Helix (bHLH proteins

    Directory of Open Access Journals (Sweden)

    Centonze Victoria E.

    2004-01-01

    Full Text Available Post-translational modifications such as phosphorylation play a vital role in the regulation of protein function. In our study of the basic Helix-loop-Helix (bHLH transcription factor HAND1, we show that HAND1 is phosphorylated during the trophoblast giant cell differentiation on residues residing in Helix I of the bHLH domain. Our hypothesis is that these modifications result in changes in HAND1 dimerization affinities with other bHLH factors. To test this idea, we employed FRET to measure the protein-protein interactions of HAND1 and HAND1 point mutants in HEK293 cells using YFP and CFP fusion proteins and laser scanning confocal microscopy.

  8. 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...

  9. 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.

  10. 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).

  11. 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...

  12. Helix-Sense-Selective Polymerization of N,N-Diphenyl(Meth)acrylamide by Anionic Catalysts

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    In this paper, the helix-sense-selective polymerization of N,N-diphenyl acrylamide (DPAA) and N,N-diphenyl methacrylamide(DPMAA) were studied with living helix prepolymer as anionic initiator, and the chiral optical properties of the obtained polymers were investigated too.It was shown that optically active polymers of DPAA and DPMAA could be obtained under the experimental condition, and exhibited the same screw sense as that of the prepolymer.

  13. 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 ...

  14. 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.

  15. 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.

  16. 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

  17. 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.

  18. Heterogeneity of myotubes generated by the MyoD and E12 basic helix-loop-helix transcription factors in otherwise non-differentiation growth conditions.

    Science.gov (United States)

    Grubišić, Vladimir; Gottipati, Manoj K; Stout, Randy F; Grammer, J Robert; Parpura, Vladimir

    2014-02-01

    We used a synthetic biology approach to produce myotubes from mammalian C2C12 myoblasts in non-differentiation growth conditions using the expression of basic helix-loop-helix transcription factors, MyoD and E12, in various combinations and configurations. Our approach not only recapitulated the basics of muscle development and physiology, as the obtained myotubes showed qualities similar to those seen in striated muscle fibers in vivo, but also allowed for the synthesis of populations of myotubes which assumed distinct morphology, myofibrillar development and Ca(2+) dynamics. This fashioned class of biomaterials is suitable for the building blocks of soft actuators in micro-scale biomimetic robotics. This production line strategy can be embraced in reparative medicine as synthetic human myotubes with predetermined morphological/functional properties could be obtained using this very approach. This methodology can be adopted beyond striated muscle for the engineering of other tissue components/cells whose differentiation is governed by the principles of basic helix-loop-helix transcription factors, as in the case, for example, of neural or immune cell types.

  19. 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

  20. 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...

  1. 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.

  2. 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.

  3. Helix-like structure formation of a semi-flexible chain confined in a cylinder channel

    Science.gov (United States)

    Wen, Xiaohui; Sun, Tieyu; Zhang, Wei-Bing; Lam, Chi-Hang; Zhang, Linxi; Zang, Huaping

    2016-09-01

    Molecular dynamics method is used to study the conformation behavior of a semi-flexible polymer chain confined in a cylinder channel. A novel helix-like structure is found to form during the simulation. Moreover, the detailed characteristic parameters and formation probability of these helix-like structures under moderate conditions are investigated. We find that the structure is not a perfect helix, but a bundle of elliptical turns. In addition, we conduct a statistical analysis for the chain monomer distribution along the radial direction. This research contributes to our understanding of the microscopic conformation of polymer chains in confined environments filled with a solvent. Project supported by the National Natural Science Foundation of China (Grant Nos. 11504033 and 11404290) and the General Research Fund of Hong Kong Research Council of China (Grant No. 15301014).

  4. 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)

  5. The auto-inhibitory role of the EPAC hinge helix as mapped by NMR.

    Directory of Open Access Journals (Sweden)

    Rajeevan Selvaratnam

    Full Text Available The cyclic-AMP binding domain (CBD is the central regulatory unit of exchange proteins activated by cAMP (EPAC. The CBD maintains EPAC in a state of auto-inhibition in the absence of the allosteric effector, cAMP. When cAMP binds to the CBD such auto-inhibition is released, leading to EPAC activation. It has been shown that a key feature of such cAMP-dependent activation process is the partial destabilization of a structurally conserved hinge helix at the C-terminus of the CBD. However, the role of this helix in auto-inhibition is currently not fully understood. Here we utilize a series of progressive deletion mutants that mimic the hinge helix destabilization caused by cAMP to show that such helix is also a pivotal auto-inhibitory element of apo-EPAC. The effect of the deletion mutations on the auto-inhibitory apo/inactive vs. apo/active equilibrium was evaluated using recently developed NMR chemical shift projection and covariance analysis methods. Our results show that, even in the absence of cAMP, the C-terminal region of the hinge helix is tightly coupled to other conserved allosteric structural elements of the CBD and perturbations that destabilize the hinge helix shift the auto-inhibitory equilibrium toward the apo/active conformations. These findings explain the apparently counterintuitive observation that cAMP binds more tightly to shorter than longer EPAC constructs. These results are relevant for CBDs in general and rationalize why substrates sensitize CBD-containing systems to cAMP. Furthermore, the NMR analyses presented here are expected to be generally useful to quantitatively evaluate how mutations affect conformational equilibria.

  6. The auto-inhibitory role of the EPAC hinge helix as mapped by NMR.

    Science.gov (United States)

    Selvaratnam, Rajeevan; Mazhab-Jafari, Mohammad T; Das, Rahul; Melacini, Giuseppe

    2012-01-01

    The cyclic-AMP binding domain (CBD) is the central regulatory unit of exchange proteins activated by cAMP (EPAC). The CBD maintains EPAC in a state of auto-inhibition in the absence of the allosteric effector, cAMP. When cAMP binds to the CBD such auto-inhibition is released, leading to EPAC activation. It has been shown that a key feature of such cAMP-dependent activation process is the partial destabilization of a structurally conserved hinge helix at the C-terminus of the CBD. However, the role of this helix in auto-inhibition is currently not fully understood. Here we utilize a series of progressive deletion mutants that mimic the hinge helix destabilization caused by cAMP to show that such helix is also a pivotal auto-inhibitory element of apo-EPAC. The effect of the deletion mutations on the auto-inhibitory apo/inactive vs. apo/active equilibrium was evaluated using recently developed NMR chemical shift projection and covariance analysis methods. Our results show that, even in the absence of cAMP, the C-terminal region of the hinge helix is tightly coupled to other conserved allosteric structural elements of the CBD and perturbations that destabilize the hinge helix shift the auto-inhibitory equilibrium toward the apo/active conformations. These findings explain the apparently counterintuitive observation that cAMP binds more tightly to shorter than longer EPAC constructs. These results are relevant for CBDs in general and rationalize why substrates sensitize CBD-containing systems to cAMP. Furthermore, the NMR analyses presented here are expected to be generally useful to quantitatively evaluate how mutations affect conformational equilibria.

  7. Helix A Stabilization Precedes Amino-terminal Lobe Activation upon Calcium Binding to Calmodulin

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Baowei [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Lowry, David [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Mayer, M. Uljana [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Squier, Thomas C. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2008-08-09

    The structural coupling between opposing domains of CaM was investigated using the conformationally sensitive biarsenical probe 4,5-bis(1,3,2-dithioarsolan-2-yl)-resorufin (ReAsH), which upon binding to an engineered tetracysteine binding motif near the end of helix A (Thr-5 to Phe-19) becomes highly fluorescent. Changes in conformation and dynamics are reflective of the native CaM structure, as there is no change in the 1H-15N HSQC NMR spectrum in comparison to wild-type CaM. We find evidence of a conformational intermediate associated with CaM activation, where calcium occupancy of sites in the amino-terminal and carboxyl-terminal lobes of CaM differentially affect the fluorescence intensity of bound ReAsH. Insight into the structure of the conformational intermediate is possible from a consideration of calcium-dependent changes in rates of ReAsH binding and helix A mobility, which respectively distinguish secondary structural changes associated with helix A stabilization from the tertiary structural reorganization of the amino-terminal lobe of CaM necessary for high-affinity binding to target proteins. Helix A stabilization is associated with calcium occupancy of sites in the carboxyl-terminal lobe (Kd = 0.36 ± 0.04 μM), which results in a reduction in the rate of ReAsH binding from 4900 M-1 sec-1 to 370 M-1 sec-1. In comparison, tertiary structural changes involving helix A and other structural elements in the amino-terminal lobe requires calcium-occupancy of amino-terminal sites (Kd = 18 ± 3 μM). Observed secondary and tertiary structural changes involving helix A in response to the sequential calcium occupancy of carboxyl- and amino-terminal lobe calcium binding sites suggest an important involvement of helix A in mediating the structural coupling between the opposing domains of CaM. These results are discussed in terms of a model in which carboxyl-terminal lobe calcium activation induces

  8. 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

  9. 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.

  10. THE COUPLING IMPEDANCE OF VANE-LOADED TAPE HELIX SLOW-WAVE STRUCTURE

    Institute of Scientific and Technical Information of China (English)

    Chen Qingyou; Wang Zicheng; Wu Hongshi

    2001-01-01

    Based on the actual vane-loaded tape helix slow wave structure, a new theoretical analytic model for calculating coupling impedance is proposed by Chen Qingyou, et al.(1999)with calculated values of dispersion in good agreement with measured ones. In this paper, it is continued to use this model to calculate the coupling impedance of such a structure, and analyze the effects of the propagation power within vane gaps and the helix gap on the coupling impedance.As a result, the theoretical values are found to be in good agreement with the measured ones,with the maximum difference less than ±18%.

  11. 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

    , 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...

  12. Effect of four-alpha-helix bundle cavity size on volatile anesthetic binding energetics.

    Science.gov (United States)

    Manderson, Gavin A; Michalsky, Stuart J; Johansson, Jonas S

    2003-09-30

    Currently, it is thought that inhalational anesthetics cause anesthesia by binding to ligand-gated ion channels. This is being investigated using four-alpha-helix bundles, small water-soluble analogues of the transmembrane domains of the "natural" receptor proteins. The study presented here specifically investigates how multiple alanine-to-valine substitutions (which each decrease the volume of the internal binding cavity by 38 A(3)) affect structure, stability, and anesthetic binding affinity of the four-alpha-helix bundles. Structure remains essentially unchanged when up to four alanine residues are changed to valine. However, stability increases as the number of these substitutions is increased. Anesthetic binding affinities are also affected. Halothane binds to the four-alpha-helix bundle variants with 0, 1, and 2 substitutions with equivalent affinities but binds to the variants with 3 and 4 more tightly. The same order of binding affinities was observed for chloroform, although for a particular variant, chloroform was bound less tightly. The observed differences in binding affinities may be explained in terms of a modulation of van der Waals and hydrophobic interactions between ligand and receptor. These, in turn, could result from increased four-alpha-helix bundle binding cavity hydrophobicity, a decrease in cavity size, or improved ligand/receptor shape complementarity.

  13. 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;

    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 hydropho......)) and melting points in chemical and thermal denaturation experiments....

  14. 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...

  15. 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...

  16. A Helix-Stabilizing Linker Improves Subcutaneous Bioavailability of a Helical Peptide Independent of Linker Lipophilicity.

    Science.gov (United States)

    Zhang, Liang; Navaratna, Tejas; Thurber, Greg M

    2016-07-20

    Stabilized peptides address several limitations to peptide-based imaging agents and therapeutics such as poor stability and low affinity due to conformational flexibility. There is also active research in developing these compounds for intracellular drug targeting, and significant efforts have been invested to determine the effects of helix stabilization on intracellular delivery. However, much less is known about the impact on other pharmacokinetic parameters such as plasma clearance and bioavailability. We investigated the effect of different fluorescent helix-stabilizing linkers with varying lipophilicity on subcutaneous (sc) bioavailability using the glucagon-like peptide-1 (GLP-1) receptor ligand exendin as a model system. The stabilized peptides showed significantly higher protease resistance and increased bioavailability independent of linker hydrophilicity, and all subcutaneously delivered conjugates were able to successfully target the islets of Langerhans with high specificity. The lipophilic peptide variants had slower absorption and plasma clearance than their respective hydrophilic conjugates, and the absolute bioavailability was also lower likely due to the longer residence times in the skin. Their ease and efficiency make double-click helix stabilization chemistries a useful tool for increasing the bioavailability of peptide therapeutics, many of which suffer from rapid in vivo protease degradation. Helix stabilization using linkers of varying lipophilicity can further control sc absorption and clearance rates to customize plasma pharmacokinetics. PMID:27327034

  17. 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

    of dimers and revealed a cooperative stabilization of helix A4 in this process. This emphasizes its special role in the structure formation in the denatured state of ACBP. No dimers are formed in the presence of guanidine hydrochloride, which underlines the fundamental difference between the nature...

  18. 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...

  19. 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

  20. 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

  1. 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 ...

  2. 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…

  3. 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

  4. 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

  5. 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…

  6. Reversible helix sense inversion in surface-grafted poly(beta-phenethyl-L-aspartate) films

    NARCIS (Netherlands)

    Luijten, Jeroen; Vorenkamp, Eltjo J.; Schouten, Arend J.

    2007-01-01

    The reversible manipulation of the helix screw sense in surface-grafted poly(beta-phenethyl-L-aspartate) (PPELA) films by means of external stimuli was investigated. Ringopening polymerization of beta-phenethyl-L-aspartate N-carboxyanhydride initiated from primary amino-functionalized silicon and qu

  7. Reversible Helix Sense Inversion in Surface-Grafted Poly(β-phenethyl-L-aspartate) Films

    NARCIS (Netherlands)

    Luijten, Jeroen; Vorenkamp, Eltjo J.; Schouten, Arend J.

    2007-01-01

    The reversible manipulation of the helix screw sense in surface-grafted poly(β-phenethyl-L-aspartate) (PPELA) films by means of external stimuli was investigated. Ringopening polymerization of β-phenethyl-L-aspartate N-carboxyanhydride initiated from primary amino-functionalized silicon and quartz s

  8. 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

  9. Identification of a site critical for kinase regulation on the central processing unit (CPU) helix of the aspartate receptor.

    Science.gov (United States)

    Trammell, M A; Falke, J J

    1999-01-01

    Ligand binding to the homodimeric aspartate receptor of Escherichia coli and Salmonella typhimurium generates a transmembrane signal that regulates the activity of a cytoplasmic histidine kinase, thereby controlling cellular chemotaxis. This receptor also senses intracellular pH and ambient temperature and is covalently modified by an adaptation system. A specific helix in the cytoplasmic domain of the receptor, helix alpha6, has been previously implicated in the processing of these multiple input signals. While the solvent-exposed face of helix alpha6 possesses adaptive methylation sites known to play a role in kinase regulation, the functional significance of its buried face is less clear. This buried region lies at the subunit interface where helix alpha6 packs against its symmetric partner, helix alpha6'. To test the role of the helix alpha6-helix alpha6' interface in kinase regulation, the present study introduces a series of 13 side-chain substitutions at the Gly 278 position on the buried face of helix alpha6. The substitutions are observed to dramatically alter receptor function in vivo and in vitro, yielding effects ranging from kinase superactivation (11 examples) to complete kinase inhibition (one example). Moreover, four hydrophobic, branched side chains (Val, Ile, Phe, and Trp) lock the kinase in the superactivated state regardless of whether the receptor is occupied by ligand. The observation that most side-chain substitutions at position 278 yield kinase superactivation, combined with evidence that such facile superactivation is rare at other receptor positions, identifies the buried Gly 278 residue as a regulatory hotspot where helix packing is tightly coupled to kinase regulation. Together, helix alpha6 and its packing interactions function as a simple central processing unit (CPU) that senses multiple input signals, integrates these signals, and transmits the output to the signaling subdomain where the histidine kinase is bound. Analogous CPU

  10. 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.

  11. Transmembrane helix dynamics of bacterial chemoreceptors supports a piston model of signalling.

    Directory of Open Access Journals (Sweden)

    Benjamin A Hall

    2011-10-01

    Full Text Available Transmembrane α-helices play a key role in many receptors, transmitting a signal from one side to the other of the lipid bilayer membrane. Bacterial chemoreceptors are one of the best studied such systems, with a wealth of biophysical and mutational data indicating a key role for the TM2 helix in signalling. In particular, aromatic (Trp and Tyr and basic (Arg residues help to lock α-helices into a membrane. Mutants in TM2 of E. coli Tar and related chemoreceptors involving these residues implicate changes in helix location and/or orientation in signalling. We have investigated the detailed structural basis of this via high throughput coarse-grained molecular dynamics (CG-MD of Tar TM2 and its mutants in lipid bilayers. We focus on the position (shift and orientation (tilt, rotation of TM2 relative to the bilayer and how these are perturbed in mutants relative to the wildtype. The simulations reveal a clear correlation between small (ca. 1.5 Å shift in position of TM2 along the bilayer normal and downstream changes in signalling activity. Weaker correlations are seen with helix tilt, and little/none between signalling and helix twist. This analysis of relatively subtle changes was only possible because the high throughput simulation method allowed us to run large (n = 100 ensembles for substantial numbers of different helix sequences, amounting to ca. 2000 simulations in total. Overall, this analysis supports a swinging-piston model of transmembrane signalling by Tar and related chemoreceptors.

  12. 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

  13. 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.

  14. 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

  15. 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

  16. 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.

  17. Structural characterizations of fusion peptide analogs of influenza virus hemagglutinin. Implication of the necessity of a helix-hinge-helix motif in fusion activity.

    Science.gov (United States)

    Hsu, Chun-Hua; Wu, Shih-Hsiung; Chang, Ding-Kwo; Chen, Chinpan

    2002-06-21

    Infection by enveloped viruses initially involves membrane fusion between viral and host cell membranes. The fusion peptide plays a crucial role in triggering this reaction. To clarify how the fusion peptide exerts this specific function, we carried out biophysical studies of three fusion peptide analogs of influenza virus hemagglutinin HA2, namely E5, G13L, and L17A. E5 exhibits an activity similar to the native fusion peptide, whereas G13L and L17A, which are two point mutants of the E5 analog, possess much less fusion activity. Our CD data showed that the conformations of these three analogs in SDS micelles are pH-dependent, with higher alpha-helical contents at acidic pH. Tryptophan fluorescence emission experiments indicated that these three analogs insert deeper into lipid bilayers at acidic pH. The three-dimensional structure of the E5 analog in SDS micelles at pH 4.0 revealed that two segments, Leu(2)-Glu(11) and Trp(14)-Ile(18), form amphipathic helical conformations, with Gly(12)-Gly(13) forming a hinge. The hydrophobic residues in the N- and C-terminal helices form a hydrophobic cluster. At neutral pH, however, the C-terminal helix of Trp(14)-Ile(18) reduces dramatically, and the hydrophobic core observed at acidic pH is severely disrupted. We suggest that the disruption of the C-terminal helix renders the E5 analog fusion-inactive at neutral pH. Furthermore, the decrease of the hinge and the reduction of fusion activity in G13L reveal the importance of the hinge in fusion activity. Also, the decrease in the C-terminal helix and the reduction of fusion activity in L17A demonstrates the importance of the C-terminal helix in fusion activity. Based on these biophysical studies, we propose a model that illustrates the structural change of the HA2 fusion peptide analog and explains how the analog interacts with the lipid bilayer at different pH values.

  18. 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;

    2010-01-01

    . Some mutations change the chemical shifts of residues remote from the site of mutation indicating the presence of an interaction between the mutated and the remote residues, suggesting that the formation of helix segments and helix-helix interactions is cooperative. We can begin to track down...... the 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...

  19. 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......Bringing environmental concerns into focus of innovation processes will in several cases also expand the numbers of actors involved. Eco-innovation and triple helix are often frameworks applied to analyse how environmental concerns are integrated in the innovation processes and how different...

  20. 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

  1. Characterization of Mycobacterium tuberculosis EsxA membrane insertion: roles of N- and C-terminal flexible arms and central helix-turn-helix motif.

    Science.gov (United States)

    Ma, Yue; Keil, Verena; Sun, Jianjun

    2015-03-13

    EsxA (ESAT-6), an important virulence factor of Mycobacterium tuberculosis, plays an essential role in phagosome rupture and bacterial cytosolic translocation within host macrophages. Our previous study showed that EsxA exhibits a unique membrane-interacting activity that is not found in its ortholog from nonpathogenic Mycobacterium smegmatis. However, the molecular mechanism of EsxA membrane insertion remains unknown. In this study, we generated truncated EsxA proteins with deletions of the N- and/or C-terminal flexible arm. Using a fluorescence-based liposome leakage assay, we found that both the N- and C-terminal arms were required for membrane disruption. Moreover, we found that, upon acidification, EsxA converted into a more organized structure with increased α-helical content, which was evidenced by CD analysis and intrinsic tryptophan fluorescence. Finally, using an environmentally sensitive fluorescent dye, we obtained direct evidence that the central helix-turn-helix motif of EsxA inserted into the membranes and formed a membrane-spanning pore. A model of EsxA membrane insertion is proposed and discussed.

  2. 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

  3. 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

  4. 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.

  5. 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...

  6. 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...

  7. Effects of Boundary Condition and Helix Angle On Meshing Performance of TI Worm Gearing

    Institute of Scientific and Technical Information of China (English)

    SUN Yue-hai; DUAN Lu-qian; WANG Shu-ren; ZHANG Ce

    2006-01-01

    To exactly describe the contact state and contact area oftooth surface oftoroidalinvolute(TI) worm gearing.the authors introduced boundary condition into contact line analysis.With helix angle chosen as parameter,the criterion for the existence of meshing boundary line on the surface of TI worm gearing is derived.Results show that there can be four situations for meshing boundary line on the tooth surface of gear.namely,inexistence of meshing boundary line.a unique line,two lines,and two coincident lines.If the helix angle is equal to or slightly smaller than the bigger angle,which makes two meshing boundary lines superpose,a preferable meshing performance is obtained.Computer simulation proves the validity Of the above conclusion.

  8. 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.

  9. 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 ...

  10. Nanofiber-Based Double-Helix Dipole Trap for Cold Neutral Atoms

    CERN Document Server

    Reitz, D

    2012-01-01

    A double-helix optical trapping potential for cold atoms can be straightforwardly created inside the evanescent field of an optical nanofiber. It suffices to send three circularly polarized light fields through the nanofiber; two counterpropagating and far red-detuned with respect to the atomic transition and the third far blue-detuned. Assuming realistic experimental parameters, the transverse confinement of the resulting potential allows one to reach the one-dimensional regime with cesium atoms for temperatures of several \\muK. Moreover, by locally varying the nanofiber diameter, the radius and pitch of the double-helix can be modulated, thereby opening a realm of applications in cold-atom physics.

  11. 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.

  12. One-dimensional nonlinear theory for rectangular helix traveling-wave tube

    Science.gov (United States)

    Fu, Chengfang; Wei, Yanyu; Zhao, Bo; Yang, Yudong; Ju, Yongfeng

    2016-08-01

    A 1-D nonlinear theory of a rectangular helix traveling-wave tube (TWT) interacting with a ribbon beam is presented in this paper. The RF field is modeled by a transmission line equivalent circuit, the ribbon beam is divided into a sequence of thin rectangular electron discs with the same cross section as the beam, and the charges are assumed to be uniformly distributed over these discs. Then a method of computing the space-charge field by solving Green's Function in the Cartesian Coordinate-system is fully described. Nonlinear partial differential equations for field amplitudes and Lorentz force equations for particles are solved numerically using the fourth-order Runge-Kutta technique. The tube's gain, output power, and efficiency of the above TWT are computed. The results show that increasing the cross section of the ribbon beam will improve a rectangular helix TWT's efficiency and reduce the saturated length.

  13. Globular structures of a helix-coil copolymer: Self-consistent treatment

    Science.gov (United States)

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

    2007-01-01

    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.

  14. 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

  15. Conservation of Hydrophobic and Hydrophilic Residues in Four-Helix Bundle

    Institute of Scientific and Technical Information of China (English)

    秦猛; 王骏; 王炜

    2003-01-01

    The conservation of the hydrophobic and the hydrophilic residue sites obtained from 1000 designed sequences with the Z-score method for a four-helix bundle has been studied. The folding dynamic and thermodynamic features of the designed sequences and their different mutations are also studied. It is found that this conservation is related to the stability and the fast folding of the model proteins. Our results are consistent with the experimental results.

  16. 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...

  17. 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...

  18. Beyond the nearest-neighbor Zimm-Bragg model for helix-coil transition in peptides.

    Science.gov (United States)

    Murza, Adrian; Kubelka, Jan

    2009-02-01

    The nearest-neighbor (micro = 1) variant of the Zimm and Bragg (ZB) model has been extensively used to describe the helix-coil transition in biopolymers. In this work, we investigate the helix-coil transition for a 21-residue alanine peptide (AP) with the ZB model up to fourth nearest neighbor (micro = 1, 2, 3, and 4). We use a matrix approach that takes into account combinations of any number of helical stretches of any length and therefore gives the exact statistical weight of the chain within the assumptions of the ZB model. The parameters of the model are determined by fitting the temperature-dependent circular dichroism and Fourier transform infrared experimental spectra of the AP. All variants of the model fit the experimental data, thus giving similar results in terms of the macroscopic observables, such as temperature-dependent fractional helicity. However, the resulting microscopic parameters, such as distributions of the individual residue helical probabilities and free energy surfaces, vary significantly depending on the variant of the model. Overall, the mean residue enthalpy and entropy (in the absolute value) both increase with micro, but combined yield essentially the same "effective" value of the ZB propagation parameters for all micro. Greater helical probabilities for individual residues are predicted for larger micro, in particular, near the center of the sequence. The ZB nucleation parameters increase with increasing micro, which results in a lower free energy barrier to helix nucleation and lower apparent "cooperativity" of the transition. The significance of the long-range interactions for the predictions of ZB model for helix-coil transition, the calculated model parameters and the limitations of the model are discussed.

  19. 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...

  20. Coupled-mode analysis for single-helix chiral fiber gratings with small core-offset

    Institute of Scientific and Technical Information of China (English)

    Li Yang; Linlin Xue; Jue Su; Jingren Qian

    2011-01-01

    Using conventional coupled-mode theory,a set of coupled-mode equations are formulated for single-helix chiral fiber long-period gratings.A helical-core fiber is analyzed as an example.The analysis is simple in mathematical form and intuitive in physical concept.Based on the analysis,the polarization independence of mode coupling in special fiber gratings is revealed.The transmission characteristics of helical-core fibers are also simulated and discussed.

  1. Convention of Optical Vortices in Two-Helix Long-Period Fiber Gratings

    Institute of Scientific and Technical Information of China (English)

    Xiao-Qiang Zhang; Rui-Shan Chen; Yong Zhou; Hai Ming; An-Ting Wang

    2016-01-01

    An effective method to fabricate two-helix long-period fiber gratings (TH-LFGs) is presented.Based on the coupling mode theory,the conversion of optical vortices (OVs) in TH-LFGs are analyzed in detail.The conversions of OVs with different topological charges:0 → ±2 and 1 → 3 are simulated as three examples and the conversion efficiency higher than 98% can be realized.

  2. 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 ...

  3. 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...

  4. 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...

  5. 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 ...

  6. 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...

  7. 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...

  8. 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...

  9. 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...

  10. 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 ...

  11. 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...

  12. 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...

  13. 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...

  14. 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...

  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. 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.

  18. 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...

  19. 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.

  20. 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...

  1. 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.

  2. 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

  3. Antiferromagnetic nuclear spin helix and topological superconductivity in 13C nanotubes

    Science.gov (United States)

    Hsu, Chen-Hsuan; Stano, Peter; Klinovaja, Jelena; Loss, Daniel

    2015-12-01

    We investigate the Ruderman-Kittel-Kasuya-Yosida (RKKY) interaction arising from the hyperfine coupling between localized nuclear spins and conduction electrons in interacting 13C carbon nanotubes. Using the Luttinger liquid formalism, we show that the RKKY interaction is sublattice dependent, consistent with the spin susceptibility calculation in noninteracting carbon nanotubes, and it leads to an antiferromagnetic nuclear spin helix in finite-size systems. The transition temperature reaches up to tens of mK, due to a strong boost by a positive feedback through the Overhauser field from ordered nuclear spins. Similar to GaAs nanowires, the formation of the helical nuclear spin order gaps out half of the conduction electrons, and is therefore observable as a reduction of conductance by a factor of 2 in a transport experiment. The nuclear spin helix leads to a density wave combining spin and charge degrees of freedom in the electron subsystem, resulting in synthetic spin-orbit interaction, which induces nontrivial topological phases. As a result, topological superconductivity with Majorana fermion bound states can be realized in the system in the presence of proximity-induced superconductivity without the need of fine tuning the chemical potential. We present the phase diagram as a function of system parameters, including the pairing gaps, the gap due to the nuclear spin helix, and the Zeeman field perpendicular to the helical plane.

  4. 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...

  5. The toxicity test and hypothetical model of Bacillus thuringiensis Cry1Aa helix4

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Development of targeted biological agents against agricultural insect pests is of prime importance for the elaboration and implementation of integrated pest management strategies that are environment-friendly, respectful of bio-diversity and safer to human health through reduced use of chemical pesticides. A major goal to understand how Bt toxins work is to elucidate the functions of their three domains. Domains II and III are involved in binding specificity and structural integrity, but the function of Domain I remains poorly understood. Using a Manduca sexta BBMV (brush border membrane vesicles) system, we analyzed its responses to Cry1Aa 15 single-point mutations with altered Domain I helix 4 residues. Light scattering assay showed that toxicity was almost lost in 3 mutants, and we observed significantly reduced toxicity in other 7 mutants. However, 5 mutants retained wild-type toxicity. Using computer software, we simulated the three-dimensional structures of helix 4. Both experimental and bioinformatic analysis showed that residues in Cry1Aa Domain I helix 4 were involved in the formation of ion channels that is critical for its insect toxicity.

  6. 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.

  7. 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...

  8. pH-jump induced α-helix folding of poly-L-glutamic acid

    Science.gov (United States)

    Donten, Mateusz L.; Hamm, Peter

    2013-08-01

    pH jumps are a truly biomimetic technique to initiate non-equilibrium dynamics of biomolecules. In this work, the pH jump induced α-helix folding of poly-L-glutamic acid is investigated upon proton release from o-nitrobenzaldehyde. The aim of this work is twofold: On the one hand, design criteria of pH jump experiments are discussed, on the other hand, the folding mechanism of poly-L-glutamic acid is clarified by probing the IR response of the amide I band. Its folding kinetics is studied in dependence of the starting pD, the size of the pD jump and the length of the helix. While no dependence on the first two parameters could be detected, the folding time varies from 0.6 μs to 1.8 μs for helix lengths of 20 residue to 440 residue, respectively. It converges to a long-length limit at about 50 residue, a result which is attributed to a nucleation-propagation mechanism.

  9. 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)....

  10. 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...

  11. 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...

  12. 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...

  13. 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

  14. 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.

  15. 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.

  16. 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

  17. Engineering D-helix of antithrombin in alpha-1-proteinase inhibitor confers antiinflammatory properties on the chimeric serpin.

    Science.gov (United States)

    Yang, L; Dinarvand, P; Qureshi, S H; Rezaie, A R

    2014-07-01

    Antithrombin (AT) is a heparin-binding serpin in plasma which regulates the proteolytic activity of procoagulant proteases of the clotting cascade. In addition to being an anticoagulant, AT also exhibits antiinflammatory activities when it binds to cell surface heparan sulfate proteoglycans (HSPGs) on the endothelium via its basic residues of D-helix to elicit intracellular signalling responses. By contrast to AT, α1-proteinase inhibitor (α1-PI) is a non-heparin-binding serpin that exhibits very slow reactivity with coagulation proteases and possesses no HSPG-dependent antiinflammatory properties. To determine whether the antiinflammatory signaling specificity of AT can be transferred to α1-PI, we replaced the D-helix of human α1-PI with the corresponding sequence of human AT and expressed the chimeric serpin α1-PI/D-helix) in a bacterial expression system. High molecular weight heparin bound to α1-PI/D-helix and accelerated the inhibition of thrombin by the serpin mutant by a template mechanism reminiscent of the cofactor effect of heparin on inhibition of thrombin by AT. Like AT, α1-PI/D-helix exhibited antiinflammatory properties in both cellular and animal models. Thus, α1-PI/D-helix inhibited the barrier-disruptive effect of proinflammatory cytokines and inhibited the activation of nuclear factor-κB transcription factor in lipopolysaccharide-stimulated endothelial cells by a concentration-dependent manner. Furthermore, the chimeric serpin reduced lipopolysaccharide-mediated lethality, elicited a vascular protective effect and inhibited infiltration of activated leukocytes to the peritoneal cavity of mice in an HMGB1-mediated inflammatory model. These results suggest that grafting the D-helix of AT to α1-PI confers antiinflammatory properties on the serpin and that the chimeric serpin may have therapeutic utility for treating inflammatory disorders. PMID:24522239

  18. 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)

  19. 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.

  20. 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.

  1. Protein folding of the SAP domain, a naturally occurring two-helix bundle.

    Science.gov (United States)

    Dodson, Charlotte A; Arbely, Eyal

    2015-07-01

    The SAP domain from the Saccharomyces cerevisiae Tho1 protein is comprised of just two helices and a hydrophobic core and is one of the smallest proteins whose folding has been characterised. Φ-value analysis revealed that Tho1 SAP folds through a transition state where helix 1 is the most extensively formed element of secondary structure and flickering native-like core contacts from Leu35 are also present. The contacts that contribute most to native state stability of Tho1 SAP are not formed in the transition state.

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

    DEFF Research Database (Denmark)

    Jofre, Sergio; Andersen, Per Dannemand

    2009-01-01

    in the European Union and its closer competitors, Japan and the United States. Main results suggest that the innovation systems in this study are in a transition stage at different degrees of change. Such transitions, broadly motivated by the challenge of globalization and sustainable development......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...

  3. 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.

  4. 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.

  5. 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.

  6. 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...

  7. 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...

  8. 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.

  9. Modulation of unpolarized light in planar aligned subwavelength-pitch deformed-helix ferroelectric liquid crystals

    CERN Document Server

    Kesaev, Vladimir V; Kiselev, Alexei D

    2016-01-01

    We study the electro-optic properties of subwavelength-pitch deformed-helix ferroelectric liquid crystals (DHFLC) illuminated with unpolarized light. In the experimental setup based on the Mach-Zehnder interferometer, it was observed that the reference and the sample beams being both unpolarized produce the interference pattern which is insensitive to rotation of in-plane optical axes of the DHFLC cell. We find that the field-induced shift of the interference fringes can be described in terms of the electrically dependent Pancharatnam relative phase determined by the averaged phase shift, whereas the visibility of the fringes is solely dictated by the phase retardation.

  10. 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...

  11. 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/...

  12. Point Defects in Double Helix Induced by Interaction of Silver Nanoparticles with DNA

    CERN Document Server

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

    2012-01-01

    Interaction of DNA-silver nanoparticles (AgNPs) complexes with H3O+, Cu2+ and Cl- has been studied by spectro-photometric, spectro-fluorimetric and differential scanning micro calorimetric methods. It is shown that DNA is a catalyst in redox reactions taking place in AgNPs adsorbed on its surface. We also demonstrate that Ag+ ions that are freed after corrosion of nanoparticles show absorption into the inner part of DNA double helix, i.e. they make the so-called cross-links between complementary base pairs of DNA. The cross-links present point defects of DNA which leads in-vivo to cell death.

  13. OsbHLH148, a basic helix-loop-helix protein, interacts with OsJAZ proteins in a jasmonate signaling pathway leading to drought tolerance in rice.

    Science.gov (United States)

    Seo, Ju-Seok; Joo, Joungsu; Kim, Min-Jeong; Kim, Yeon-Ki; Nahm, Baek Hie; Song, Sang Ik; Cheong, Jong-Joo; Lee, Jong Seob; Kim, Ju-Kon; Choi, Yang Do

    2011-03-01

    Jasmonates play important roles in development, stress responses and defense in plants. Here, we report the results of a study using a functional genomics approach that identified a rice basic helix-loop-helix domain gene, OsbHLH148, that conferred drought tolerance as a component of the jasmonate signaling module in rice. OsbHLH148 transcript levels were rapidly increased by treatment with methyl jasmonate (MeJA) or abscisic acid, and abiotic stresses including dehydration, high salinity, low temperature and wounding. Transgenic over-expression of OsbHLH148 in rice confers plant tolerance to drought stress. Expression profiling followed by DNA microarray and RNA gel-blot analyses of transgenic versus wild-type rice identified genes that are up-regulated by OsbHLH148 over-expression. These include OsDREB and OsJAZ genes that are involved in stress responses and the jasmonate signaling pathway, respectively. OsJAZ1, a rice ZIM domain protein, interacted with OsbHLH148 in yeast two-hybrid and pull-down assays, but it interacted with the putative OsCOI1 only in the presence of coronatine. Furthermore, the OsJAZ1 protein was degraded by rice and Arabidopsis extracts in the presence of coronatine, and its degradation was inhibited by MG132, a 26S proteasome inhibitor, suggesting 26S proteasome-mediated degradation of OsJAZ1 via the SCF(OsCOI1) complex. The transcription level of OsJAZ1 increased upon exposure of rice to MeJA. These results show that OsJAZ1 could act as a transcriptional regulator of the OsbHLH148-related jasmonate signaling pathway leading to drought tolerance. Thus, our study suggests that OsbHLH148 acts on an initial response of jasmonate-regulated gene expression toward drought tolerance, constituting the OsbHLH148-OsJAZ-OsCOI1 signaling module in rice.

  14. 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

  15. Design and analysis of post-fusion 6-helix bundle of heptad repeat regions from Newcastle disease virus F protein.

    Science.gov (United States)

    Zhu, Jieqing; Li, Pengyun; Wu, Tinghe; Gao, Feng; Ding, Yi; Zhang, Catherine W-H; Rao, Zihe; Gao, George F; Tien, Po

    2003-05-01

    Fusion of paramyxovirus to the cell involves receptor binding of the HN glycoprotein and a number of conformational changes of F glycoprotein. The F protein is expressed as a homotrimer on the virus surface. In the present model, there are at least three conformations of F protein, i.e. native form, pre-hairpin intermediate and the post-fusion state. In the post-fusion state, the two highly conserved heptad repeat (HR) regions of F protein form a stable 6-helix coiled-coil bundle. However, no crystal structure is known for this state for the Newcastle disease virus, although the crystal structure of the F protein native form has been solved recently. Here we deployed an Escherichia coli in vitro expression system to engineer this 6-helix bundle by fusion of either the two HR regions (HR1, linker and HR2) or linking the 6-helix [3 x (HR1, linker and HR2)] together as a single chain. Subsequently, both of them form a stable 6-helix bundle in vitro judging by gel filtration and chemical cross-linking and the proteins show salient features of an alpha-helix structure. Crystals diffracting X-rays have been obtained from both protein preparations and the structure determination is under way. This method could be used for crystallization of the post-fusion state HR structures of other viruses.

  16. 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.

  17. 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.

  18. 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.

  19. MATE1 has an external COOH terminus, consistent with a 13-helix topology.

    Science.gov (United States)

    Zhang, Xiaohong; Wright, Stephen H

    2009-08-01

    The mammalian members of the Multidrug And Toxin Extruder family, i.e., MATE1 and MATE2-K, are suspected of mediating the luminal step in renal secretion of organic cations. The 1,000+ prokaryotic/fungal/plant MATE family members are predicted to have 12 transmembrane helices (TMHs), whereas MATE1/2-K appear to have an additional (13th) COOH-terminal helix. Here, we determined whether rabbit MATE1 has an external COOH terminus, consistent with the presence of 13 TMHs. A V5 epitope tag at the COOH terminus of MATE1 was freely accessible to external V5 antibody, whereas tags at the NH(2) terminus, or at sites of truncation within the long cytoplasmic loop between predicted TMHs 12 and 13, were only accessible to the V5 antibody following permeabilization of the membrane. The truncated mutants that lacked TMH13 still retained transport activity, indicating that the terminal helix was not necessary for transport function. Cells that expressed a mutant lacking only TMH13 displayed similar K(t) and J(max) values to those of the full-length protein, although when normalized to protein expressed at the plasma membrane, the transport rate of the mutant was COOH terminus was freely accessible to maleimide biotin. These data are consistent with a mammalian MATE topology that includes 13 TMHs and indicate that the terminal TMH, although not necessary for transport function, may influence the turnover characteristics of the transporter.

  20. 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

  1. 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

  2. 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.

  3. Scaling and alpha-helix regulation of protein relaxation in a lipid bilayer

    Science.gov (United States)

    Qiu, Liming; Buie, Creighton; Cheng, Kwan Hon; Vaughn, Mark W.

    2014-12-01

    Protein conformation and orientation in the lipid membrane plays a key role in many cellular processes. Here we use molecular dynamics simulation to investigate the relaxation and C-terminus diffusion of a model helical peptide: beta-amyloid (Aβ) in a lipid membrane. We observed that after the helical peptide was initially half-embedded in the extracelluar leaflet of phosphatidylcholine (PC) or PC/cholesterol (PC/CHOL) membrane, the C-terminus diffused across the membrane and anchored to PC headgroups of the cytofacial lipid leaflet. In some cases, the membrane insertion domain of the Aβ was observed to partially unfold. Applying a sigmoidal fit to the process, we found that the characteristic velocity of the C-terminus, as it moved to its anchor site, scaled with θu-4/3, where θu is the fraction of the original helix that was lost during a helix to coil transition. Comparing this scaling with that of bead-spring models of polymer relaxation suggests that the C-terminus velocity is highly regulated by the peptide helical content, but that it is independent of the amino acid type. The Aβ was stabilized by the attachment of the positive Lys28 side chain to the negative phosphate of PC or 3β oxygen of CHOL in the extracellular lipid leaflet and of the C-terminus to its anchor site in the cytofacial lipid leaflet.

  4. 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)

  5. 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

  6. 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.

  7. 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

  8. 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

  9. 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

  10. 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.

  11. 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.

  12. 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.

  13. The MCL-1 BH3 helix is an exclusive MCL-1 inhibitor and apoptosis sensitizer

    Energy Technology Data Exchange (ETDEWEB)

    Stewart, Michelle L.; Fire, Emiko; Keating, Amy E.; Walensky, Loren D. (MIT); (DFCI)

    2010-08-30

    The development of selective inhibitors for discrete anti-apoptotic BCL-2 family proteins implicated in pathologic cell survival remains a formidable but pressing challenge. Such precisely tailored compounds would serve as molecular probes and targeted therapies to study and treat human diseases driven by specific anti-apoptotic blockades. In particular, MCL-1 has emerged as a major resistance factor in human cancer. By screening a library of stabilized alpha-helix of BCL-2 domains (SAHBs), we determined that the MCL-1 BH3 helix is itself a potent and exclusive MCL-1 inhibitor. X-ray crystallography and mutagenesis studies defined key binding and specificity determinants, including the capacity to harness the hydrocarbon staple to optimize affinity while preserving selectivity. MCL-1 SAHB directly targets MCL-1, neutralizes its inhibitory interaction with pro-apoptotic BAK and sensitizes cancer cells to caspase-dependent apoptosis. By leveraging nature's solution to ligand selectivity, we generated an MCL-1-specific agent that defines the structural and functional features of targeted MCL-1 inhibition.

  14. 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 different PAMPs. HBI1 overexpression leads to reduced PAMP-triggered responses. This inhibition correlates with reduced steady-state expression of immune marker genes, leading to increased susceptibility to the bacterium Pseudomonas syringae. Overexpression of the HBI1-related bHLHs brassinosteroid enhanced...

  15. 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.

  16. 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

  17. 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.

  18. 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.

  19. Right- and left-handed three-helix proteins. I. Experimental and simulation analysis of differences in folding and structure.

    Science.gov (United States)

    Glyakina, Anna V; Pereyaslavets, Leonid B; Galzitskaya, Oxana V

    2013-09-01

    Despite the large number of publications on three-helix protein folding, there is no study devoted to the influence of handedness on the rate of three-helix protein folding. From the experimental studies, we make a conclusion that the left-handed three-helix proteins fold faster than the right-handed ones. What may explain this difference? An important question arising in this paper is whether the modeling of protein folding can catch the difference between the protein folding rates of proteins with similar structures but with different folding mechanisms. To answer this question, the folding of eight three-helix proteins (four right-handed and four left-handed), which are similar in size, was modeled using the Monte Carlo and dynamic programming methods. The studies allowed us to determine the orders of folding of the secondary-structure elements in these domains and amino acid residues which are important for the folding. The obtained data are in good correlation with each other and with the experimental data. Structural analysis of these proteins demonstrated that the left-handed domains have a lesser number of contacts per residue and a smaller radius of cross section than the right-handed domains. This may be one of the explanations of the observed fact. The same tendency is observed for the large dataset consisting of 332 three-helix proteins (238 right- and 94 left-handed). From our analysis, we found that the left-handed three-helix proteins have some less-dense packing that should result in faster folding for some proteins as compared to the case of right-handed proteins.

  20. 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 ...

  1. 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.

  2. The effect of α-helix comformation on interaction between model oligopeptides and polymers

    Institute of Scientific and Technical Information of China (English)

    LI JiHong; DANG QinQin; SUN HongWei; CHA RuiTao; YUAN Zhi

    2008-01-01

    The study of interactions between peptides and synthetic polymers has aroused considerable interest recently. In the present paper, the interaction mechanism between adsorbent DMAPAM and two pep-tides, VVRGCTWW(V8) and CTWW(C4), was investigated at molecular level by NMR and molecular stimulation. The results demonstrated that the conformation of oligopeptides played a vital role in their adsorption capacity on the adsorbent. Weak interactions could incorporate with each other between V8 and DMAPAM because there was a hydrophobic cleavage in α-helix conformation of V8. So the ad-sorption capacity of DMAPAM to V8 was higher. This was significant to explore the interaction mecha-nism between peptides and biomaterials.

  3. Analysis of Dielectric Loss in a Helix Slow-wave Structure

    Directory of Open Access Journals (Sweden)

    S. K. Datta

    2009-09-01

    Full Text Available Equivalent circuit analysis of a helix slow-wave structure was carried out and closed form expressions were derived for the shunt capacitance and shunt conductance per unit length of the transmission-line equivalent circuit of the structure. These equivalent circuit parameters were interpreted for the dielectric attenuation constant of the slow-wave structure. The analysis was computationally simple and showsed excellent agreement with published results. The analysis was furthered for predicting the dielectric loss in typical C-Ku band and Ka band helical slow-wave structures, and variation of dielectric loss with temperature.Defence Science Journal, 2009, 59(5, pp.549-552, DOI:http://dx.doi.org/10.14429/dsj.59.1558

  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. 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.

  6. 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

  7. 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.

  8. 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.

  9. 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

  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. 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.

  12. 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.

  13. Solitary waves of α-helix propagation in media with arbitrary inhomogeneities

    Science.gov (United States)

    Mvogo, Alain; Ben-Bolie, Germain Hubert; Kofané, Timoléon Crépin

    2013-05-01

    We study the dynamics of solitary waves in α-helical proteins going beyond the standard nearest-neighbour interaction by taking into account influence long-range dipole-dipole interactions of the Kac-Baker type. By means of the coherent state representation of operators, the model Hamiltonian is transformed into a pair of classical lattice equations, which is further reduced to a sole nonlinear Schrödinger (NLS) equation using the continuum approximation of which the dispersive coefficient depends on the long-range interactions (LRI) parameter. It comes out from our results that the bright-like solitons, solitary waves which govern the energy transfer in α-helix, are deeply influenced by the LRI. At the end, we transform the NLS equation for more currently-important inhomogeneous NLS models in media with inhomogeneities. Application of this transformation to two example models is illustrated and soliton-like solutions are also graphically discussed.

  14. Flows along cometary tails in the Helix planetary nebula NGC 7293

    CERN Document Server

    Meaburn, John

    2009-01-01

    Previous velocity images which reveal flows of ionized gas along the most prominent cometary tail (from Knot 38) in the Helix planetary nebula are compared with that taken at optical wavelengths with the Hubble Space Telescope and with an image in the emission from molecular hydrogen. The flows from the second most prominent tail from Knot 14 are also considered. The kinematics of the tail from the more complex Knot 32, shown here for the first time, also reveals an acceleration away from the central star. All of the tails are explained as accelerating ionized flows of ablated material driven by the previous, mildly supersonic, AGB wind from the central star. The longest tail of ionized gas, even though formed by this mechanism in a very clumpy medium, as revealed by the emission from molecular hydrogen, appears to be a coherent outflowing feature.

  15. 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

  16. 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.

  17. 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

  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. 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)

  20. 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.

  1. The nucleotide addition cycle of RNA polymerase is controlled by two molecular hinges in the Bridge Helix domain

    Directory of Open Access Journals (Sweden)

    Weinzierl Robert OJ

    2010-10-01

    Full Text Available Abstract Background Cellular RNA polymerases (RNAPs are complex molecular machines that combine catalysis with concerted conformational changes in the active center. Previous work showed that kinking of a hinge region near the C-terminus of the Bridge Helix (BH-HC plays a critical role in controlling the catalytic rate. Results Here, new evidence for the existence of an additional hinge region in the amino-terminal portion of the Bridge Helix domain (BH-HN is presented. The nanomechanical properties of BH-HN emerge as a direct consequence of the highly conserved primary amino acid sequence. Mutations that are predicted to influence its flexibility cause corresponding changes in the rate of the nucleotide addition cycle (NAC. BH-HN displays functional properties that are distinct from BH-HC, suggesting that conformational changes in the Bridge Helix control the NAC via two independent mechanisms. Conclusions The properties of two distinct molecular hinges in the Bridge Helix of RNAP determine the functional contribution of this domain to key stages of the NAC by coordinating conformational changes in surrounding domains.

  2. 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…

  3. Relative Stability of the Scleroglucan Triple-Helix and Single Strand: an Insight from Computational and Experimental Techniques

    Science.gov (United States)

    Bocchinfuso, Gianfranco; Mazzuca, Claudia; Conflitti, Paolo; Cori, Davide; Coviello, Tommasina; Palleschi, Antonio

    2016-09-01

    Scleroglucan (Sclg) is a polysaccharide that exhibits a triple helix conformation (triplex), both in aqueous solution and in the solid state, which is lost in DMSO solution, at high temperature and at high pH values. The triplex conformation is characterized by a high rigidity, responsible of Sclg peculiar properties. Although the relative stability of triplex and single strand has already been investigated, different structural details are still missing. In the present study, we analyse the structural properties and the factors stabilizing the single chain and the triple helix of Sclg in different conditions. To this end, we simulated both systems in water and in DMSO. The triple helix has been also simulated in the presence of chemical damages on one of the three strands (to reproduce in silico the effect of sonication) or by inducing a partial unfolding of the triplex structure. The computational results have been compared with experimental evidences in which the triplex denaturation, at alkaline pH values, has been followed by monitoring the UV and CD spectra of Congo red, used as a probe molecule. Our results indicate that sonication breaks the Sclg chains without appreciably changing the stability of the other tracts of triple helix. The simulated perturbed or partially unfolded triplexes show a clear tendency to form less ordered aggregates. Finally, our simulations put in evidence an important role of the hydrophobic interactions both in the triplex stability and in the aggregation processes observed after induced denaturation.

  4. 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.

  5. 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.

  6. 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

  7. A Grounded Theory for Regional Development through the IT Offshoring Industry with the Triple-Helix Involvment

    Science.gov (United States)

    Villarreal de la Garza, Sonia

    2011-01-01

    The purpose of this qualitative grounded study was to explore the thoughts, experiences, and needs of potential clients and of the triple-helix members with the intention to establish a framework to support the development of the regional economy through the information technology (IT) and business processing outsourcing (BPO) offshoring industry.…

  8. 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

  9. 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

  10. 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

  11. 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.

  12. National and international dimensions of the Triple Helix in Japan: University-industry-government versus international coauthorship relations

    NARCIS (Netherlands)

    L. Leydesdorff; Y. Sun

    2009-01-01

    International co-authorship relations and university-industry-government (Triple Helix) relations have hitherto been studied separately. Using Japanese publication data for the 1981-2004 period, we were able to study both kinds of relations in a single design. In the Japanese file, 1,277,030 article

  13. Behavioural modification of the optic tentacle of Helix pom atia; effect of puromycin, activity of S-100

    DEFF Research Database (Denmark)

    Christoffersen, Gert Rene Juul; Frederiksen, K; Johansen, Jørgen;

    1981-01-01

    1. 1. A long-term learning phenomenon in the tentacle of Helix pomatia has been observed.   2. 2. Repeated mechanical stimulation of the optic tentacle led to habituation of the associated withdrawal-extension action pattern whereas repeated combined mechanical and electrical stimulation potentia...

  14. 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

  15. 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.

  16. 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.

  17. Conformation and sequence evidence for two-fold symmetry in left-handed beta-helix fold.

    Science.gov (United States)

    Shen, Xiaojuan

    2011-09-21

    The left-handed beta-helix (LβH) has received interest recently as it folds as a possible solution for the structure of misfolded proteins associated with prion and Huntington's diseases. Through a combination of sequence and structure analysis, we uncover a novel feature that is common to this unique fold: a two-fold symmetry in both sequence and structure, and this feature always coupled with extended loops in the middle of the helix. Since the results reveal a two-fold symmetric pattern both in the sequence and structure, it may indicate that the symmetry in tertiary structure is coded by the symmetry in primary sequence, which agrees with Anfisen's proposal that a protein's amino-acid sequence specify its three-dimensional structure. It may also indicate that LβH adopts a two-fold repeat pattern during the evolution process and symmetry helps maintaining the stability of the helix structure. The two-fold symmetric pattern and extended loops might be important in maintaining stability of helix proteins. This discovery can be useful in understanding the folding mechanisms of this protein fold and provide insights in the relation between sequences and structures.

  18. 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

  19. 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.

  20. 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

  1. Influence of thread pitch, helix angle, and compactness on micromotion of immediately loaded implants in three types of bone quality: a three-dimensional finite element analysis.

    Science.gov (United States)

    Ma, Pan; Xiong, Wei; Tan, Baosheng; Geng, Wei; Liu, Jiaqiang; Li, Weihong; Li, Dehua

    2014-01-01

    This study investigated the influence of thread pitch, helix angle, and compactness on micromotion in immediately loaded implants in bone of varying density (D2, D3, and D4). Five models of the three-dimensional finite element (0.8 mm pitch, 1.6 mm pitch, 2.4 mm pitch, double-threaded, and triple-threaded implants) in three types of bone were created using Pro/E, Hypermesh, and ABAQUS software. The study had three groups: Group 1, different pitches (Pitch Group); Group 2, same compactness but different helix angles (Angle Group); and Group 3, same helix angle but different compactness (Compact Group). Implant micromotion was assessed as the comprehensive relative displacement. We found that vertical relative displacement was affected by thread pitch, helix angle, and compactness. Under vertical loading, displacement was positively correlated with thread pitch and helix angle but negatively with compactness. Under horizontal loading in D2, the influence of pitch, helix angle, and compactness on implant stability was limited; however, in D3 and D4, the influence of pitch, helix angle, and compactness on implant stability is increased. The additional evidence was provided that trabecular bone density has less effect on implant micromotion than cortical bone thickness. Bone type amplifies the influence of thread pattern on displacement. PMID:25110716

  2. An amphipathic alpha-helix controls multiple roles of brome mosaic virus protein 1a in RNA replication complex assembly and function.

    Directory of Open Access Journals (Sweden)

    Ling Liu

    2009-03-01

    Full Text Available Brome mosaic virus (BMV protein 1a has multiple key roles in viral RNA replication. 1a localizes to perinuclear endoplasmic reticulum (ER membranes as a peripheral membrane protein, induces ER membrane invaginations in which RNA replication complexes form, and recruits and stabilizes BMV 2a polymerase (2a(Pol and RNA replication templates at these sites to establish active replication complexes. During replication, 1a provides RNA capping, NTPase and possibly RNA helicase functions. Here we identify in BMV 1a an amphipathic alpha-helix, helix A, and use NMR analysis to define its structure and propensity to insert in hydrophobic membrane-mimicking micelles. We show that helix A is essential for efficient 1a-ER membrane association and normal perinuclear ER localization, and that deletion or mutation of helix A abolishes RNA replication. Strikingly, mutations in helix A give rise to two dramatically opposite 1a function phenotypes, implying that helix A acts as a molecular switch regulating the intricate balance between separable 1a functions. One class of helix A deletions and amino acid substitutions markedly inhibits 1a-membrane association and abolishes ER membrane invagination, viral RNA template recruitment, and replication, but doubles the 1a-mediated increase in 2a(Pol accumulation. The second class of helix A mutations not only maintains efficient 1a-membrane association but also amplifies the number of 1a-induced membrane invaginations 5- to 8-fold and enhances viral RNA template recruitment, while failing to stimulate 2a(Pol accumulation. The results provide new insights into the pathways of RNA replication complex assembly and show that helix A is critical for assembly and function of the viral RNA replication complex, including its central role in targeting replication components and controlling modes of 1a action.

  3. 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.

  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. 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.

  6. Lectin Histochemical Study of Cell Surface Glycoconjugate in Gastric Carcinoma Using Helix Pomatia Agglutinin

    Directory of Open Access Journals (Sweden)

    Mohammad Reza Arab

    2010-07-01

    Full Text Available "nAltered glycosylation of proteins in cancer cells is one of the main processes responsible for anaplasia, invasion and metastatic potential of neoplastic cells. Lectins are nonimmunogenetic compounds which specifically detect certain terminal sugars of glycoconjugates. The aim of the present study was to identify the N-acetylgalactosamine (GalNac containing glycoconjugates in cancer cells in all grades of gastric carcinoma. Paraffin blocks belong to 30 patients of gastric carcinoma (10 cases from each grade was collected from pathology file of Ali-Ebn-Abitaleb Hospital in Zahedan during 2005-2007. Prepared sections (5-7μm in thickness were stained by Alcian Blue, hematoxylin and eosin (H&E and helix pomatia agglutinin (HPA conjugated lectin. Lectin diluted up to 10μg/ml in PBS (0.1M, pH=6.8. Lectin reactivity was visualized by 0.03% diaminobenzidine (DAB solution. Sections were graded according to staining intensity to lectin (0-4+. Although there was some difference for lectin staining intensity between cancer cells in different grades of gastric carcinoma, statistical analysis showed that there was only a significant difference for cancer cells reactivity between histopathological grades of II and III. The pattern of reactivity to HPA lectin were also different from all histopathological grades. It seems that in cancer cells, the amount and distribution of GalNac containing glycoconjugate differ from neoplastic cells of different histopathological grades in gastric carcinoma.

  7. Lectin Histochemical Study of Cell Surface Glycoconjugate in Gastric Carcinoma Using Helix Pomatia Agglutinin

    Directory of Open Access Journals (Sweden)

    Mohammad Reza Arab

    2010-08-01

    Full Text Available Altered glycosylation of proteins in cancer cells is one of the main processes responsible for anaplasia, invasion and metastatic potential of neoplastic cells. Lectins are nonimmunogenetic compounds which specifically detect certain terminal sugars of glycoconjugates. The aim of the present study was to identify the N-acetylgalactosamine (GalNac containing glycoconjugates in cancer cells in all grades of gastric carcinoma. Paraffin blocks belong to 30 patients of gastric carcinoma (10 cases from each grade was collected from pathology file of Ali-Ebn-Abitaleb Hospital in Zahedan during 2005-2007. Prepared sections (5-7μm in thickness were stained by Alcian Blue, hematoxylin and eosin (H&E and helix pomatia agglutinin (HPA conjugated lectin. Lectin diluted up to 10μg/ml in PBS (0.1M, pH=6.8. Lectin reactivity was visualized by 0.03% diaminobenzidine (DAB solution. Sections were graded according to staining intensity to lectin (0-4+. Although there was some difference for lectin staining intensity between cancer cells in different grades of gastric carcinoma, statistical analysis showed that there was only a significant difference for cancer cells reactivity between histopathological grades of II and III. The pattern of reactivity to HPA lectin were also different from all histopathological grades. It seems that in cancer cells, the amount and distribution of GalNac containing glycoconjugate differ from neoplastic cells of different histopathological grades in gastric carcinoma.

  8. 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.

  9. 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.

  10. 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

  11. 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

  12. 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.

  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. 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.

  16. De Novo Design of Metalloproteins and Metalloenzymes in a Three-Helix Bundle.

    Science.gov (United States)

    Plegaria, Jefferson S; Pecoraro, Vincent L

    2016-01-01

    For more than two decades, de novo protein design has proven to be an effective methodology for modeling native proteins. De novo design involves the construction of metal-binding sites within simple and/or unrelated α-helical peptide structures. The preparation of α3D, a single polypeptide that folds into a native-like three-helix bundle structure, has significantly expanded available de novo designed scaffolds. Devoid of a metal-binding site (MBS), we incorporated a 3Cys and 3His motif in α3D to construct a heavy metal and a transition metal center, respectively. These efforts produced excellent functional models for native metalloproteins/metalloregulatory proteins and metalloenzymes. Morever, these α3D derivatives serve as a foundation for constructing redox active sites with either the same (e.g., 4Cys) or mixed (e.g., 2HisCys) ligands, a feat that could be achieved in this preassembled framework. Here, we describe the process of constructing MBSs in α3D and our expression techniques.

  17. 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.

  18. 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

  19. The involvement of collagen triple helix repeat containing 1 in muscular dystrophies.

    Science.gov (United States)

    Spector, Itai; Zilberstein, Yael; Lavy, Adi; Genin, Olga; Barzilai-Tutsch, Hila; Bodanovsky, Ana; Halevy, Orna; Pines, Mark

    2013-03-01

    Fibrosis is the main complication of muscular dystrophies. We identified collagen triple helix repeat containing 1 (Cthrc1) in skeletal and cardiac muscles of mice, representing Duchenne and congenital muscle dystrophies (DMD and CMD, respectively), and dysferlinopathy. In all of the mice, Cthrc1 was associated with high collagen type I levels; no Cthrc1 or collagen was observed in muscles of control mice. High levels of Cthrc1 were also observed in biopsy specimens from patients with DMD, in whom they were reversibly correlated with that of β-dystroglycan, whereas collagen type I levels were elevated in all patients with DMD. At the muscle sites where collagen and Cthrc1 were adjacent, collagen fibers appeared smaller, suggesting involvement of Cthrc1 in collagen turnover. Halofuginone, an inhibitor of Smad3 phosphorylation downstream of the transforming growth factor-β signaling, reduced Cthrc1 levels in skeletal and cardiac muscles of mice, representing DMD, CMD, and dysferlinopathy. The myofibroblasts infiltrating the dystrophic muscles of the murine models of DMD, CMD, and dysferlinopathy were the source of Cthrc1. Transforming growth factor-β did not affect Cthrc1 levels in the mdx fibroblasts but decreased them in the control fibroblasts, in association with increased migration of mdx fibroblasts and dystrophic muscle invasion by myofibroblasts. To our knowledge, this is the first demonstration of Cthrc1 as a marker of the severity of the disease progression in the dystrophic muscles, and as a possible target for therapy.

  20. 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

  1. Modelling the Warm H2 Infrared Emission of the Helix Nebula Cometary Knots

    CERN Document Server

    Aleman, Isabel; Matsuura, Mikako; Gruenwald, Ruth; Kimura, Rafael K

    2011-01-01

    Molecular hydrogen emission is commonly observed in planetary nebulae. Images taken in infrared H2 emission lines show that at least part of the molecular emission is produced inside the ionised region. In the best-studied case, the Helix nebula, the H2 emission is produced inside cometary knots (CKs), comet-shaped structures believed to be clumps of dense neutral gas embedded within the ionised gas. Most of the H2 emission of the CKs seems to be produced in a thin layer between the ionised diffuse gas and the neutral material of the knot, in a mini photodissociation region (PDR). However, PDR models published so far cannot fully explain all the characteristics of the H2 emission of the CKs. In this work, we use the photoionisation code \\textsc{Aangaba} to study the H2 emission of the CKs, particularly that produced in the interface H^+/H^0 of the knot, where a significant fraction of the H2 1-0S(1) emission seems to be produced. Our results show that the production of molecular hydrogen in such a region may ...

  2. The molecular structure of the left-handed supra-molecular helix of eukaryotic polyribosomes.

    Science.gov (United States)

    Myasnikov, Alexander G; Afonina, Zhanna A; Ménétret, Jean-François; Shirokov, Vladimir A; Spirin, Alexander S; Klaholz, Bruno P

    2014-11-07

    During protein synthesis, several ribosomes bind to a single messenger RNA (mRNA) forming large macromolecular assemblies called polyribosomes. Here we report the detailed molecular structure of a 100 MDa eukaryotic poly-ribosome complex derived from cryo electron tomography, sub-tomogram averaging and pseudo-atomic modelling by crystal structure fitting. The structure allowed the visualization of the three functional parts of the polysome assembly, the central core region that forms a rather compact left-handed supra-molecular helix, and the more open regions that harbour the initiation and termination sites at either ends. The helical region forms a continuous mRNA channel where the mRNA strand bridges neighbouring exit and entry sites of the ribosomes and prevents mRNA looping between ribosomes. This structure provides unprecedented insights into protein- and RNA-mediated inter-ribosome contacts that involve conserved sites through 40S subunits and long protruding RNA expansion segments, suggesting a role in stabilizing the overall polyribosomal assembly.

  3. Sequence-dependent stability test of a left-handed β-helix motif.

    Science.gov (United States)

    Hayre, Natha R; Singh, Rajiv R P; Cox, Daniel L

    2012-03-21

    The left-handed β-helix (LHBH) is an intriguing, rare structural pattern in polypeptides that has been implicated in the formation of amyloid aggregates. We used accurate all-atom replica-exchange molecular dynamics (REMD) simulations to study the relative stability of diverse sequences in the LHBH conformation. Ensemble-average coordinates from REMD served as a scoring criterion to identify sequences and threadings optimally suited to the LHBH, as in a fold recognition paradigm. We examined the repeatability of our REMD simulations, finding that single simulations can be reliable to a quantifiable extent. We find expected behavior for the positive and negative control cases of a native LHBH and intrinsically disordered sequences, respectively. Polyglutamine and a designed hexapeptide repeat show remarkable affinity for the LHBH motif. A structural model for misfolded murine prion protein was also considered, and showed intermediate stability under the given conditions. Our technique is found to be an effective probe of LHBH stability, and promises to be scalable to broader studies of this and potentially other novel or rare motifs. The superstable character of the designed hexapeptide repeat suggests theoretical and experimental follow-ups.

  4. 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.

  5. The Bridge Helix of RNA Polymerase Acts as a Central Nanomechanical Switchboard for Coordinating Catalysis and Substrate Movement

    Directory of Open Access Journals (Sweden)

    Robert O. J. Weinzierl

    2011-01-01

    Full Text Available The availability of in vitro assembly systems to produce recombinant archaeal RNA polymerases (RNAPs offers one of the most powerful experimental tools for investigating the still relatively poorly understood molecular mechanisms underlying RNAP function. Over the last few years, we pioneered new robot-based high-throughput mutagenesis approaches to study structure/function relationships within various domains surrounding the catalytic center. The Bridge Helix domain, which appears in numerous X-ray structures as a 35-amino-acid-long alpha helix, coordinates the concerted movement of several other domains during catalysis through kinking of two discrete molecular hinges. Mutations affecting these kinking mechanisms have a direct effect on the specific catalytic activity of RNAP and can in some instances more than double it. Molecular dynamics simulations have established themselves as exceptionally useful for providing additional insights and detailed models to explain the underlying structural motions.

  6. Features of Motion of Soliton Transported Bio-energy in Aperiodic α-Helix Protein Molecules with Three Channels

    Institute of Scientific and Technical Information of China (English)

    PANG Xiao-Feng; LIU Mei-Jie

    2009-01-01

    The structure aperiodicities can influence seriously the features of motion of soliton excited in the α-helix protein molecules with three channels. We study the influence of structure aperiodicities on the features of the soliton in the improved model by numerical simulation and Runge-Kulta method. The results obtained show that the new soliton is very robust against the structure aperiodieities including large disorder in the sequence of mass of the amino acids and fluctuations of spring constant, coupling constant, dipole-dipole interactional constant, ground state energy and chain-chain interaction. However, very strong structure aperiodicities can also destroy the stability of the soliton in the α-helix protein molecules.

  7. Performance of the High Resolution, Multi-collector Helix MC Plus Noble Gas Mass Spectrometer at the Australian National University

    Science.gov (United States)

    Zhang, Xiaodong; Honda, Masahiko; Hamilton, Doug

    2016-09-01

    Performance of the Helix MC Plus noble gas mass spectrometer installed at the Australian National University (ANU) is reported. Results for sensitivity, mass discrimination and their linearity against partial pressure of noble gases, and mass resolution of the mass spectrometer are presented, and the results are compared with those of conventional noble gas mass spectrometers. The application of the five detectors on the Helix MC Plus in measuring various noble gas isotopes in multi-collector modes and the integration of the software drivers of peripheral hardware devices into the controlling program Qtegra of the mass spectrometer are discussed. High mass resolution (>1800) and mass resolving power (>8000) make this mass spectrometer unique in noble gas cosmo-geochemistry. It provides the capability to measure isobaric interference-free noble gas isotopes in multi-collector mode, significantly improves the accuracy to determine isotopic ratios, and greatly increases the efficiency of data acquisition.

  8. 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.

  9. 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.

  10. Comparison of Oct-2-enyl and Oct-4-enyl Staples for Their Formation and α-Helix Stabilizing Effects

    Energy Technology Data Exchange (ETDEWEB)

    Pham, Thanh K.; Yoo, Jiyeon; Kim, Youngwoo [Dongguk Univ., Seoul (Korea, Republic of)

    2013-09-15

    The all-hydrocarbon i,i+4 stapling system using an oct-4-enyl crosslink is one of the most widely employed chemical tools to stabilize an α-helical conformation of a short peptide. This crosslinking system has greatly extended our ability to modulate intracellular protein-macromolecule interactions. The helix-inducing property of the i,i+4 staple has shown to be highly dependent on the length and the stereochemistry of the oct-4-enyl crosslink. Here we show that changing the double bond position within the i,i+4 staple has a considerable impact not only on the formation of the crosslink but also on α-helix induction. The data further increases the understanding of the structure-activity relationships of this valuable chemical tool.

  11. 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...

  12. 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)

  13. 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...

  14. 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.

  15. Triple Helix and European Union (EU Funding: The case of Latin America, especially Mexico and the Seventh European Framework Program

    Directory of Open Access Journals (Sweden)

    Jürgen Haberleithner

    2010-05-01

    Full Text Available The following analysis not only seeks to develop new potential intervention models; it also aims to create a detailed analysis of the existing problems with regards to communication among the active participants of Triple Helix (especially in Mexico. The special situation in Latin America with regards to existing corruption, the unequal distribution of power between the government and the private sector, dependence on other economies and other social issues will be analysed in accordance with the main focus of the investigation. The subsequent linking of potential partners to the development of an initiative for submitting a future Triple Helix/FP7 project represent an important contribution to a longer-term perspective on the preceding investigation. The potential partnerships between Europe and Latin America (in addition to other possible world regions, such as, for example, Pacific Asia will create an initial project draft within the scope of the conference.

  16. Right- and left-handed three-helix proteins. II. Similarity and differences in mechanical unfolding of proteins.

    Science.gov (United States)

    Glyakina, Anna V; Likhachev, Ilya V; Balabaev, Nikolay K; Galzitskaya, Oxana V

    2014-01-01

    Here, we study mechanical properties of eight 3-helix proteins (four right-handed and four left-handed ones), which are similar in size under stretching at a constant speed and at a constant force on the atomic level using molecular dynamics simulations. The analysis of 256 trajectories from molecular dynamics simulations with explicit water showed that the right-handed three-helix domains are more mechanically resistant than the left-handed domains. Such results are observed at different extension velocities studied (192 trajectories obtained at the following conditions: v = 0.1, 0.05, and 0.01 Å ps(-1) , T = 300 K) and under constant stretching force (64 trajectories, F = 800 pN, T = 300 K). We can explain this by the fact, at least in part, that the right-handed domains have a larger number of contacts per residue and the radius of cross section than the left-handed domains.

  17. 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 ...

  18. 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...

  19. 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...

  20. 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...

  1. 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...

  2. 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...

  3. 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...

  4. 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...

  5. 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...

  6. 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...

  7. 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

  8. 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

    human recombinant cathepsins (Cats) and matrix-metalloproteases (MMPs). Next, we analyzed the spontaneous release of Helix-II and CTX-II from cartilage sections of patients with knee OA who were immediately deep frozen after joint replacement to preserve endogenous enzyme activity until assay. Cartilage...... 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 activated...... sections were then incubated for up to 84h in the presence or absence of E-64 and GM6001, inhibitors of cysteine proteases and MMPs, respectively. RESULTS: In vitro, Cats K, L and S generated large amount of Helix-II, but not CTX-II. Cat B generated CTX-II fragment, but destroyed Helix-II immunoreactivity...

  9. 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...

  10. 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 ...

  11. 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.

  12. 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.

  13. 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

  14. 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

  15. 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.

  16. A conserved phenylalanine as a relay between the α5 helix and the GDP binding region of heterotrimeric Gi protein α subunit.

    Science.gov (United States)

    Kaya, Ali I; Lokits, Alyssa D; Gilbert, James A; Iverson, Tina M; Meiler, Jens; Hamm, Heidi E

    2014-08-29

    G protein activation by G protein-coupled receptors is one of the critical steps for many cellular signal transduction pathways. Previously, we and other groups reported that the α5 helix in the G protein α subunit plays a major role during this activation process. However, the precise signaling pathway between the α5 helix and the guanosine diphosphate (GDP) binding pocket remains elusive. Here, using structural, biochemical, and computational techniques, we probed different residues around the α5 helix for their role in signaling. Our data showed that perturbing the Phe-336 residue disturbs hydrophobic interactions with the β2-β3 strands and α1 helix, leading to high basal nucleotide exchange. However, mutations in β strands β5 and β6 do not perturb G protein activation. We have highlighted critical residues that leverage Phe-336 as a relay. Conformational changes are transmitted starting from Phe-336 via β2-β3/α1 to Switch I and the phosphate binding loop, decreasing the stability of the GDP binding pocket and triggering nucleotide release. When the α1 and α5 helices were cross-linked, inhibiting the receptor-mediated displacement of the C-terminal α5 helix, mutation of Phe-336 still leads to high basal exchange rates. This suggests that unlike receptor-mediated activation, helix 5 rotation and translocation are not necessary for GDP release from the α subunit. Rather, destabilization of the backdoor region of the Gα subunit is sufficient for triggering the activation process.

  17. 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

  18. 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

  19. 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

  20. Communication routes in ARID domains between distal residues in helix 5 and the DNA-binding loops.

    Directory of Open Access Journals (Sweden)

    Gaetano Invernizzi

    2014-09-01

    Full Text Available ARID is a DNA-binding domain involved in several transcriptional regulatory processes, including cell-cycle regulation and embryonic development. ARID domains are also targets of the Human Cancer Protein Interaction Network. Little is known about the molecular mechanisms related to conformational changes in the family of ARID domains. Thus, we have examined their structural dynamics to enrich the knowledge on this important family of regulatory proteins. In particular, we used an approach that integrates atomistic simulations and methods inspired by graph theory. To relate these properties to protein function we studied both the free and DNA-bound forms. The interaction with DNA not only stabilizes the conformations of the DNA-binding loops, but also strengthens pre-existing paths in the native ARID ensemble for long-range communication to those loops. Residues in helix 5 are identified as critical mediators for intramolecular communication to the DNA-binding regions. In particular, we identified a distal tyrosine that plays a key role in long-range communication to the DNA-binding loops and that is experimentally known to impair DNA-binding. Mutations at this tyrosine and in other residues of helix 5 are also demonstrated, by our approach, to affect the paths of communication to the DNA-binding loops and alter their native dynamics. Overall, our results are in agreement with a scenario in which ARID domains exist as an ensemble of substates, which are shifted by external perturbation, such as the interaction with DNA. Conformational changes at the DNA-binding loops are transmitted long-range by intramolecular paths, which have their heart in helix 5.

  1. Communication routes in ARID domains between distal residues in helix 5 and the DNA-binding loops.

    Science.gov (United States)

    Invernizzi, Gaetano; Tiberti, Matteo; Lambrughi, Matteo; Lindorff-Larsen, Kresten; Papaleo, Elena

    2014-09-01

    ARID is a DNA-binding domain involved in several transcriptional regulatory processes, including cell-cycle regulation and embryonic development. ARID domains are also targets of the Human Cancer Protein Interaction Network. Little is known about the molecular mechanisms related to conformational changes in the family of ARID domains. Thus, we have examined their structural dynamics to enrich the knowledge on this important family of regulatory proteins. In particular, we used an approach that integrates atomistic simulations and methods inspired by graph theory. To relate these properties to protein function we studied both the free and DNA-bound forms. The interaction with DNA not only stabilizes the conformations of the DNA-binding loops, but also strengthens pre-existing paths in the native ARID ensemble for long-range communication to those loops. Residues in helix 5 are identified as critical mediators for intramolecular communication to the DNA-binding regions. In particular, we identified a distal tyrosine that plays a key role in long-range communication to the DNA-binding loops and that is experimentally known to impair DNA-binding. Mutations at this tyrosine and in other residues of helix 5 are also demonstrated, by our approach, to affect the paths of communication to the DNA-binding loops and alter their native dynamics. Overall, our results are in agreement with a scenario in which ARID domains exist as an ensemble of substates, which are shifted by external perturbation, such as the interaction with DNA. Conformational changes at the DNA-binding loops are transmitted long-range by intramolecular paths, which have their heart in helix 5.

  2. 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.

  3. 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.

  4. 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...

  5. 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...

  6. 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...

  7. 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

  8. 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

  9. Electrochemical DNA probe for Hg(2+) detection based on a triple-helix DNA and Multistage Signal Amplification Strategy.

    Science.gov (United States)

    Wang, Huan; Zhang, Yihe; Ma, Hongmin; Ren, Xiang; Wang, Yaoguang; Zhang, Yong; Wei, Qin

    2016-12-15

    In this work, an ultrasensitive electrochemical sensor was developed for detection of Hg(2+). Gold nanoparticles decorated bovine serum albumin reduction of graphene oxide (AuNP-BSA-rGO) were used as subsurface material for the immobilization of triple-helix DNA. The triple-helix DNA containing a thiol labelled single-stranded DNA (sDNA) and a thymine-rich DNA (T-rich DNA), which could be unwinded in the present of Hg(2+) to form more stable thymine-Hg(2+)-thymine (T-Hg(2+)-T) complex. T-Hg(2+)-T complex was then removed and the sDNA was left on the electrode. At this time, gold nanoparticle carrying thiol labelled cytosine-rich complementary DNA (cDNA-AuNP) could bind with the free sDNA. Meanwhile, the other free cDNA on AuNP could bind with each other in the present of Ag(+) to form the stable cytosine-Ag(+)-cytosine (C-Ag(+)-C) complex and circle amplification. Plenty of C-Ag(+)-C could form silver nanoclusters by electrochemical reduction and the striping signal of Ag could be measured for purpose of the final electrochemical detection of Hg(2+). This sensor could detect Hg(2+) over a wide concentration range from 0.1 to 130nM with a detection limit of 0.03nM.

  10. Peptide-oligonucleotide conjugates as nanoscale building blocks for assembly of an artificial three-helix protein mimic

    Science.gov (United States)

    Lou, Chenguang; Martos-Maldonado, Manuel C.; Madsen, Charlotte S.; Thomsen, Rasmus P.; Midtgaard, Søren Roi; Christensen, Niels Johan; Kjems, Jørgen; Thulstrup, Peter W.; Wengel, Jesper; Jensen, Knud J.

    2016-07-01

    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 high degree of α-helicity for the peptide moieties in the assemblies. The results validate the use of orthogonal self-assembly principles as a paradigm for de novo protein design.

  11. Peptide–oligonucleotide conjugates as nanoscale building blocks for assembly of an artificial three-helix protein mimic

    Science.gov (United States)

    Lou, Chenguang; Martos-Maldonado, Manuel C.; Madsen, Charlotte S.; Thomsen, Rasmus P.; Midtgaard, Søren Roi; Christensen, Niels Johan; Kjems, Jørgen; Thulstrup, Peter W.; Wengel, Jesper; Jensen, Knud J.

    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 high degree of α-helicity for the peptide moieties in the assemblies. The results validate the use of orthogonal self-assembly principles as a paradigm for de novo protein design. PMID:27464951

  12. 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

  13. Structural polymorphism of the major capsid protein of a double-stranded RNA virus: an amphipathic alpha helix as a molecular switch.

    Science.gov (United States)

    Saugar, Irene; Luque, Daniel; Oña, Ana; Rodríguez, José F; Carrascosa, José L; Trus, Benes L; Castón, José R

    2005-07-01

    The infectious bursal disease virus T=13 viral particle is composed of two major proteins, VP2 and VP3. Here, we show that the molecular basis of the conformational flexibility of the major capsid protein precursor, pVP2, is an amphipatic alpha helix formed by the sequence GFKDIIRAIR. VP2 containing this alpha helix is able to assemble into the T=13 capsid only when expressed as a chimeric protein with an N-terminal His tag. An amphiphilic alpha helix, which acts as a conformational switch, is thus responsible for the inherent structural polymorphism of VP2. The His tag mimics the VP3 C-terminal region closely and acts as a molecular triggering factor. Using cryo-electron microscopy difference imaging, both polypeptide elements were detected on the capsid inner surface. We propose that electrostatic interactions between these two morphogenic elements are transmitted to VP2 to acquire the competent conformations for capsid assembly.

  14. 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.

  15. 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...

  16. 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

  17. 一种GPCR跨膜螺旋形变的建模方法%Method for Modeling the Distortions of Transmembrane Helix in G-protein Couple Receptor

    Institute of Scientific and Technical Information of China (English)

    陈荣; 吕强; 吴宏杰; 陈沙沙

    2012-01-01

    跨膜螺旋是GPCR的最主要特征,单个螺旋的预测精度直接影响GPCR整体三维结构的预测.GPCR螺旋形变预测是一个挑战性的难题.该形变用发生形变的残基位置和该位置前后两端螺旋的夹角表示.基于目前已知的所有GPCR的跨膜螺旋结构,根据螺旋序列相似度进行聚类,然后在每类中对形变角度用连续型yon Mises概率分布来建模.对建模后GPCR跨膜螺旋的形变角度进行了回归和预测测试.基于本文方法的模型,只需进行15次采样,就会有一次的采样结果近似符合天然螺旋的形变角度,这在很大程度上能够帮助跨膜螺旋空间结构的预测.%Transmembrane helix is main feature of the GPCR,and the accuracy of single helix prediction directly affects the prediction is of entire GPCR structure. It is a challenge problem to predict the distortion of the GPCR helix. The distortion is represented by using the kink residue place and the angle of two fragment helix around the distortion position. Based on the all known GPCR's helixes structure currently, the helixes are clustered according to the helix sequence similarity, and the bend angles in each cluster are modeled by using continuous von mises probability distribution. The modeled GPCR TM kink angles are tested by using the regression and forecast testing method. Based on this article's model,only fifteen times sampling would have a sample result close to the native TM distortion angle, which will help to improve the TM-helix structure prediction.

  18. 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...

  19. 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.)

  20. 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

  1. A single amino acid substitution in IIIf subfamily of basic helix-loop-helix transcription factor AtMYC1 leads to trichome and root hair patterning defects by abolishing its interaction with partner proteins in Arabidopsis.

    Science.gov (United States)

    Zhao, Hongtao; Wang, Xiaoxue; Zhu, Dandan; Cui, Sujuan; Li, Xia; Cao, Ying; Ma, Ligeng

    2012-04-20

    Plant trichomes and root hairs are powerful models for the study of cell fate determination. In Arabidopsis thaliana, trichome and root hair initiation requires a combination of three groups of proteins, including the WD40 repeat protein transparent TESTA GLABRA1 (TTG1), R2R3 repeat MYB protein GLABRA1 (GL1), or werewolf (WER) and the IIIf subfamily of basic helix-loop-helix (bHLH) protein GLABRA3 (GL3) or enhancer of GLABRA3 (EGL3). The bHLH component acts as a docking site for TTG1 and MYB proteins. Here, we isolated a mutant showing defects in trichome and root hair patterning that carried a point mutation (R173H) in AtMYC1 that encodes the fourth member of IIIf bHLH family protein. Genetic analysis revealed partial redundant yet distinct function between AtMYC1 and GL3/EGL3. GLABRA2 (GL2), an important transcription factor involved in trichome and root hair control, was down-regulated in Atmyc1 plants, suggesting the requirement of AtMYC1 for appropriate GL2 transcription. Like its homologs, AtMYC1 formed a complex with TTG1 and MYB proteins but did not dimerized. In addition, the interaction of AtMYC1 with MYB proteins and TTG1 was abrogated by the R173H substitution in Atmyc1-1. We found that this amino acid (Arg) is conserved in the AtMYC1 homologs GL3/EGL3 and that it is essential for their interaction with MYB proteins and for their proper functions. Our findings indicate that AtMYC1 is an important regulator of trichome and root hair initiation, and they reveal a novel amino acid necessary for protein-protein interactions and gene function in IIIf subfamily bHLH transcription factors.

  2. Detection of initiation sites in protein folding of the four helix bundle ACBP by chemical shift analysis

    DEFF Research Database (Denmark)

    Modig, K.; Jürgensen, Vibeke Würtz; Lindorff-Larsen, K.;

    2007-01-01

    A simple alternative method for obtaining "random coil" chemical shifts by intrinsic referencing using the protein's own peptide sequence is presented. These intrinsic random coil backbone shifts were then used to calculate secondary chemical shifts, that provide important information on the resi......A simple alternative method for obtaining "random coil" chemical shifts by intrinsic referencing using the protein's own peptide sequence is presented. These intrinsic random coil backbone shifts were then used to calculate secondary chemical shifts, that provide important information...... on the residual secondary structure elements in the acid-denatured state of an acylcoenzyme A binding protein. This method reveals a clear correlation between the carbon secondary chemical shifts and the amide secondary chemical shifts 3-5 residues away in the primary sequence. These findings strongly suggest...... transient formation of short helix-like segments, and identify unique sequence segments important for protein folding....

  3. Structural regularities of helicoidally-like biopolymers in the framework of algebraic topology: II. {alpha}-Helix and DNA structures

    Energy Technology Data Exchange (ETDEWEB)

    Samoylovich, M. I., E-mail: samoylovich@technomash.ru [Central Research Technological Institute ' Technomash' (Russian Federation); Talis, A. L. [Russian Academy of Sciences, Nesmeyanov Institute of Organoelement Compounds (Russian Federation)

    2013-09-15

    The developed apparatus of the 'structural application' of algebraic geometry and topology makes it possible to determine topologically stable helicoidally-like packings of polyhedra (clusters). A packing found is limited by a minimal surface with zero instability index; this surface is set by the Weierstrass representation and corresponds to the bifurcation point. The symmetries of the packings under consideration are determined by four-dimensional polyhedra (polytopes) from a closed sequence, which begins with diamondlike polytope (240). One example of these packings is a packing of tetrahedra, which arises as a result of the multiplication of a peculiar starting aggregation of tetrahedra by a fractional 40/11 axis with an angle of helical rotation of 99 Degree-Sign . The arrangement of atoms in particular positions of this starting aggregation allows one to obtain a model of the {alpha}-helix. This apparatus makes it possible to determine a priori the symmetry parameters of DNA double helices.

  4. 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.

  5. 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. .

  6. Knowledge-Based Innovation Systems and the Model of a Triple Helix of University-Industry-Government Relations

    CERN Document Server

    Leydesdorff, Loet

    2010-01-01

    The (neo-)evolutionary model of a Triple Helix of University-Industry-Government Relations focuses on the overlay of expectations, communications, and interactions that potentially feed back on the institutional arrangements among the carrying agencies. From this perspective, the evolutionary perspective in economics can be complemented with the reflexive turn from sociology. The combination provides a richer understanding of how knowledge-based systems of innovation are shaped and reconstructed. The communicative capacities of the carrying agents become crucial to the system's further development, whereas the institutional arrangements (e.g., national systems) can be expected to remain under reconstruction. The tension of the differentiation no longer needs to be resolved, since the network configurations are reproduced by means of translations among historically changing codes. Some methodological and epistemological implications for studying innovation systems are explicated.

  7. High stability of the hinge region in the membrane-active peptide helix of zervamicin: paramagnetic relaxation enhancement studies.

    Science.gov (United States)

    Shenkarev, Zakhar O; Paramonov, Alexander S; Balashova, Tamara A; Yakimenko, Zoya A; Baru, Michael B; Mustaeva, Leila G; Raap, Jan; Ovchinnikova, Tatyana V; Arseniev, Alexander S

    2004-12-17

    Zervamicin IIB is a 16 amino acid peptaibol that forms voltage dependent ion channels with multilevel conductance states in planar lipid bilayers and vesicular systems. Stability of the hinge region and intermolecular interactions were investigated in the N- and C-terminally spin-labelled peptide analogues. Intermolecular and intramolecular paramagnetic enhancement indicates that zervamicin behaves as a rigid helical rod in methanol solution. There are no high amplitude hinge-bending motions, and the peptaibol is monomeric up to concentration 1.5 mM. Stability of the hinge region illustrates the helix stabilising propensity of the Pro residue in membrane mimic environments and implies absence of significant conformational rearrangement due to voltage peptaibol activation.

  8. 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

    2016-02-14

    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.

  9. 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

  10. 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.

  11. 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

  12. The Impact of the ‘Austrian’ Mutation of the Amyloid Precursor Protein Transmembrane Helix is Communicated to the Hinge Region

    DEFF Research Database (Denmark)

    Stelzer, Walter; Scharnagl, Christina; Leurs, Ulrike;

    2016-01-01

    destabilizes amide hydrogen bonds in the hinge which connects dimerization and cleavage regions. Weaker intrahelical hydrogen bonds at the hinge may enhance helix bending and thereby affect recognition of the transmembrane substrate by the enzyme and/or presentation of its cleavage sites to the catalytic cleft....

  13. 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...

  14. 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

  15. Pressure-dependent helix inversion of poly(quinoxaline-2,3-diyl)s containing chiral side chains in non-aqueous solvents.

    Science.gov (United States)

    Nagata, Yuuya; Takeda, Ryohei; Suginome, Michinori

    2015-06-30

    Poly(quinoxaline-2,3-diyl)s with chiral (S)-2-butoxymethyl side chains dissolved in 1,2-dichloroethane experience a reversible pressure-dependent helix inversion from P- to M-helical structures between 0.1 MPa and 200 MPa.

  16. 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...

  17. The Triple Helix of university-industry-government relations at the country level and Its dynamic evolution under the pressures of globalization

    NARCIS (Netherlands)

    F.Y. Ye; S.S. Yu; L. Leydesdorff

    2013-01-01

    Using data from the Web of Science (WoS), we analyze the mutual information among university, industry, and government addresses (U-I-G) at the country level for a number of countries. The dynamic evolution of the Triple Helix can thus be compared among developed and developing nations in terms of c

  18. 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.

  19. Surface expression and subunit specific control of steady protein levels by the Kv7.2 helix A-B linker.

    Science.gov (United States)

    Aivar, Paloma; Fernández-Orth, Juncal; Gomis-Perez, Carolina; Alberdi, Araitz; Alaimo, Alessandro; Rodríguez, Manuel S; Giraldez, Teresa; Miranda, Pablo; Areso, Pilar; Villarroel, Alvaro

    2012-01-01

    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.

  20. 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

  1. Helix stability in succinylated and acetylated ovalbumins: effect of high pH, urea and guanidine hydrochloride.

    Science.gov (United States)

    Batra, P P; Uetrecht, D

    1990-08-01

    Previous studies (Batra, P.P., Roebuck, M.A. and Uetrecht, D. (1990) J. Protein Chem. 9, 37-44) showed that succinylation or acetylation of 75% of the lysine residues has little effect on the secondary structure of ovalbumin. The acylation of the remaining 25% lysine residues, which apparently are partially buried, results in a substantial loss of the helical structure. These conformational changes may be due not only to electrostatic repulsions introduced by succinylation or acetylation of the positively charged epsilon-amino groups but also to steric hindrance, since an increase in the ionic strength failed to reverse the loss of the helical structure. An increase in pH to 12.2 results in a complete helix-to-coil transition in the maximally succinylated ovalbumin (but not in the partially succinylated or in any of the acetylated ovalbumins including the maximally acetylated derivative), perhaps because it is most expanded and its molecular interior most accessible to solvent as succinylation replaces +1 charge of epsilon-amino group with a -1 charge so that a net of -2 charge per succinyl group is placed on the protein molecule. This helix-to-coil transition in the maximally succinylated ovalbumin induced by high pH is fully reversed by increasing the ionic strength, indicating that only electrostatic effects are responsible for this disruption. Studies have also shown that although there is no loss of the helical structure until after the 75% surface lysine residues have been acylated, the helical structure does become progressively destabilized with increasing degree of modification, a conclusion drawn from urea unfolding curves. This destabilization of the helical structure is due primarily to electrostatic effects, as an increase in the ionic strength led to an increase in the urea transition mid-point. Unlike urea, the guanidine hydrochloride unfolding curves indicate that the transition mid-point for the native protein, as well as for the maximally

  2. The structure of the XPF-ssDNA complex underscores the distinct roles of the XPF and ERCC1 helix- hairpin-helix domains in ss/ds DNA recognition.

    Science.gov (United States)

    Das, Devashish; Folkers, Gert E; van Dijk, Marc; Jaspers, Nicolaas G J; Hoeijmakers, Jan H J; Kaptein, Robert; Boelens, Rolf

    2012-04-01

    Human XPF/ERCC1 is a structure-specific DNA endonuclease that nicks the damaged DNA strand at the 5' end during nucleotide excision repair. We determined the structure of the complex of the C-terminal domain of XPF with 10 nt ssDNA. A positively charged region within the second helix of the first HhH motif contacts the ssDNA phosphate backbone. One guanine base is flipped out of register and positioned in a pocket contacting residues from both HhH motifs of XPF. Comparison to other HhH-containing proteins indicates a one-residue deletion in the second HhH motif of XPF that has altered the hairpin conformation, thereby permitting ssDNA interactions. Previous nuclear magnetic resonance studies showed that ERCC1 in the XPF-ERCC1 heterodimer can bind dsDNA. Combining the two observations gives a model that underscores the asymmetry of the human XPF/ERCC1 heterodimer in binding at an ss/ds DNA junction.

  3. 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.

  4. 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...

  5. '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

  6. Pseudouridylation of helix 69 of 23S rRNA is necessary for an effective translation termination

    DEFF Research Database (Denmark)

    Ejby, Morten; Sørensen, Michael A; Pedersen, Steen

    2007-01-01

    Escherichia coli strains with inactivated rluD genes were previously found to lack the conserved pseudouridines in helix 69 of 23S ribosomal RNA and to grow slowly. A suppressor mutant was isolated with a near normal growth rate that had changed the conserved Glu-172 codon to a Lys codon in prf......B, encoding translation termination factor RF2. When nonsense suppression in strains with all combinations of prfB(+)/prfB(E172K) and rluD(+)/rluD::cat was analyzed, misreading of all three stop codons as sense codons was found to be increased by rluD inactivation: Nonsense suppression was increased 2-fold...... at UAG codons, 9-fold at UAA, and 14-fold at UGA. The increased read-through at UGA corresponds to reading UGA as a sense codon in 30% of the cases. In contrast, the accuracy of reading sense codons appeared unaffected by loss of rluD. When the inactivated rluD gene was combined with the altered prf...

  7. 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.

  8. Does unpaired adenosine-66 from helix II of Escherichia coli 5S RNA bind to protein L18?

    DEFF Research Database (Denmark)

    Christiansen, J; Douthwaite, S R; Christensen, A;

    1985-01-01

    Adenosine-66 is unpaired within helix II of Escherichia coli 5S RNA and lies in the binding site of ribosomal protein L18. It has been proposed as a recognition site for protein L18. We have investigated further the structural importance of this nucleotide by deleting it. The 5S RNA gene of the rrn......B operon of E. coli was subjected to primer-directed mutagenesis. To produce the deletion it was necessary to use simultaneously the mutagenic dodecamer dCGGCGCACGGCG and the universal M13 primer dCCCAGTCACGACGTT, and to employ forced annealing conditions. The mutated gene was expressed in an overproducing...... plasmid derived from pKK3535. Binding studies with protein L18 revealed that the protein bound much more weakly to the mutated 5S RNA. We consider the most likely explanation of this result is that L18 interacts with adenosine-66, and we present a tentative model for an interaction between the unpaired...

  9. In vitro antiviral activity of circular triple helix forming oligonucleotide RNA towards Feline Infectious Peritonitis virus replication.

    Science.gov (United States)

    Choong, Oi Kuan; Mehrbod, Parvaneh; Tejo, Bimo Ario; Omar, Abdul Rahman

    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-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 10(14) in the virus-inoculated cells to 10(9) 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.

  10. Functional role of an endophytic Bacillus amyloliquefaciens in enhancing growth and disease protection of invasive English ivy (Hedera helix L.)

    Science.gov (United States)

    Soares, Marcos Antonio; Li, Jai-Yan; Bergen, Marshall; da Silva, Joaquim Manoel; Kowalski, Kurt P.; White, James Francis

    2015-01-01

    BackgroundWe hypothesize that invasive English ivy (Hedera helix) harbors endophytic microbes that promote plant growth and survival. To evaluate this hypothesis, we examined endophytic bacteria in English ivy and evaluated effects on the host plant.MethodsEndophytic bacteria were isolated from multiple populations of English ivy in New Brunswick, NJ. Bacteria were identified as a single species Bacillus amyloliquefaciens. One strain of B. amyloliquefaciens, strain C6c, was characterized for indoleacetic acid (IAA) production, secretion of hydrolytic enzymes, phosphate solubilization, and antibiosis against pathogens. PCR was used to amplify lipopeptide genes and their secretion into culture media was detected by MALDI-TOF mass spectrometry. Capability to promote growth of English ivy was evaluated in greenhouse experiments. The capacity of C6c to protect plants from disease was evaluated by exposing B+ (bacterium inoculated) and B− (non-inoculated) plants to the necrotrophic pathogen Alternaria tenuissima.ResultsB. amyloliquefaciens C6c systemically colonized leaves, petioles, and seeds of English ivy. C6c synthesized IAA and inhibited plant pathogens. MALDI-TOF mass spectrometry analysis revealed secretion of antifungal lipopeptides surfactin, iturin, bacillomycin, and fengycin. C6c promoted the growth of English ivy in low and high soil nitrogen conditions. This endophytic bacterium efficiently controlled disease caused by Alternaria tenuissima.ConclusionsThis study suggests that B. amyloliquefaciens plays an important role in enhancing growth and disease protection of English ivy.

  11. Soj/ParA stalls DNA replication by inhibiting helix formation of the initiator protein DnaA.

    Science.gov (United States)

    Scholefield, Graham; Errington, Jeff; Murray, Heath

    2012-03-21

    Control of DNA replication initiation is essential for normal cell growth. A unifying characteristic of DNA replication initiator proteins across the kingdoms of life is their distinctive AAA+ nucleotide-binding domains. The bacterial initiator DnaA assembles into a right-handed helical oligomer built upon interactions between neighbouring AAA+ domains, that in vitro stretches DNA to promote replication origin opening. The Bacillus subtilis protein Soj/ParA has previously been shown to regulate DnaA-dependent DNA replication initiation; however, the mechanism underlying this control was unknown. Here, we report that Soj directly interacts with the AAA+ domain of DnaA and specifically regulates DnaA helix assembly. We also provide critical biochemical evidence indicating that DnaA assembles into a helical oligomer in vivo and that the frequency of replication initiation correlates with the extent of DnaA oligomer formation. This work defines a significant new regulatory mechanism for the control of DNA replication initiation in bacteria. PMID:22286949

  12. One 4-Twist Helix Snake to Maintain Polarization in 8-120 GeV Proton Rings

    CERN Document Server

    Antoulinakis, F; Tai, A; Aidala, C A; Courant, E D; Krisch, A D; Lorenzon, W; Myers, P D; Raymond, R S; Sivers, D W; Leonova, M A; Derbenev, Y S; Morozov, V S; Kondratenko, A M

    2013-01-01

    Solenoid Siberian snakes have successfully maintained polarization in particle rings below 1 GeV, but never in multi-GeV rings because the Lorentz contraction of a solenoid's integral B dl would require impractically long high-field solenoids. High energy rings, such as Brookhaven's 255 GeV Relativistic Heavy Ion Collider (RHIC), use only odd multiples of pairs of transverse B-field Siberian snakes directly opposite each other. When it became impractical to use a pair of Siberian Snakes in Fermilab's 120 GeV Main Injector, we searched for a new type of single Siberian snake, which should overcome all depolarizing resonances in the 8.9 - 120 GeV range. We found that one snake made of one 4-twist helix and 2 short dipoles could maintain the polarization. This snake design might also be used at other rings, such as Japan's 30 GeV J-PARC, the 12 - 24 GeV NICA proton-deuteron collider at JINR-Dubna, and perhaps RHIC's injector, the 25 GeV AGS.

  13. 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.

  14. Polarizability of Six-Helix Bundle and Triangle DNA Origami and Their Escape Characteristics from a Dielectrophoretic Trap.

    Science.gov (United States)

    Gan, Lin; Camacho-Alanis, Fernanda; Ros, Alexandra

    2015-12-15

    DNA nanoassemblies, such as DNA origamis, hold promise in biosensing, drug delivery, nanoelectronic circuits, and biological computing, which require suitable methods for migration and precision positioning. Insulator-based dielectrophoresis (iDEP) has been demonstrated as a powerful migration and trapping tool for μm- and nm-sized colloids as well as DNA origamis. However, little is known about the polarizability of origami species, which is responsible for their dielectrophoretic migration. Here, we report the experimentally determined polarizabilities of the six-helix bundle origami (6HxB) and triangle origami by measuring the migration times through a potential landscape exhibiting dielectrophoretic barriers. The resulting migration times correlate to the depth of the dielectrophoretic potential barrier and the escape characteristics of the origami according to an adapted Kramer's rate model, allowing their polarizabilities to be determined. We found that the 6HxB polarizability is larger than that of the triangle origami, which correlates with the variations in charge density of both origamis. Further, we discuss the orientation of both origami species in the dielectrophoretic trap and discuss the influence of diffusion during the escape process. Our study provides detailed insight into the factors contributing to the migration through dielectrophoretic potential landscapes, which can be exploited for applications with DNA and other nanoassemblies based on dielectrophoresis. PMID:26570981

  15. Path to Collagenolysis: COLLAGEN V TRIPLE-HELIX MODEL BOUND PRODUCTIVELY AND IN ENCOUNTERS BY MATRIX METALLOPROTEINASE-12.

    Science.gov (United States)

    Prior, Stephen H; Byrne, Todd S; Tokmina-Roszyk, Dorota; Fields, Gregg B; Van Doren, Steven R

    2016-04-01

    Collagenolysis is essential in extracellular matrix homeostasis, but its structural basis has long been shrouded in mystery. We have developed a novel docking strategy guided by paramagnetic NMR that positions a triple-helical collagen V mimic (synthesized with nitroxide spin labels) in the active site of the catalytic domain of matrix metalloproteinase-12 (MMP-12 or macrophage metalloelastase) primed for catalysis. The collagenolytically productive complex forms by utilizing seven distinct subsites that traverse the entire length of the active site. These subsites bury ∼1,080 Å(2)of surface area, over half of which is contributed by the trailing strand of the synthetic collagen V mimic, which also appears to ligate the catalytic zinc through the glycine carbonyl oxygen of its scissile G∼VV triplet. Notably, the middle strand also occupies the full length of the active site where it contributes extensive interfacial contacts with five subsites. This work identifies, for the first time, the productive and specific interactions of a collagen triple helix with an MMP catalytic site. The results uniquely demonstrate that the active site of the MMPs is wide enough to accommodate two strands from collagen triple helices. Paramagnetic relaxation enhancements also reveal an extensive array of encounter complexes that form over a large part of the catalytic domain. These transient complexes could possibly facilitate the formation of collagenolytically active complexes via directional Brownian tumbling. PMID:26887942

  16. Reproducible In-Silico Folding of a Four Helix 60 Amino Acid Protein in a Transferable All-Atom Forcefield

    Science.gov (United States)

    Schug, Alexander

    2005-03-01

    For predicting the protein tertiary structure one approach describes the native state of a protein as the global minimum of an appropiate free-energy forcefield. We have recently developed such a all-atom protein forcefield (PFF01). As major challenge remains the search for the global minimum for which we developed efficient methods. Using these we were able to predict the structure of helical proteins from different families ranging in size from 20 to 60 amino acids starting with random configurations. For the four helix 60 amino acid protein Bacterial Ribosomal Protein L20 (pdb code: 1GYZ) we used a simple client-master model for distributed computing. Starting from a set of random structures three phases of different folding simulations refined this set to a final one with 50 configurations. During this process the amount of native-like structures increased strongly. Six out of the ten structures best in energy approached the native structure within 5 åbackbone rmsd. The conformation with the lowest energy had a backbone rmsd value of 4.6 åtherefore correctly predicting the tertiary structure of 1GYZ.ReferencesA. Schug et al, Phys. Rev. Letters, 91:158102, 2003A. Schug et al, J. Am. Chem. Soc. (in press), 2004

  17. 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

  18. Mechanism of intramolecular charge transfer in DNA helix as probed by the use of the fluorescent 2-aminopurine

    Institute of Scientific and Technical Information of China (English)

    ZHANG Huijuan; WANG Peng; WANG Xuefei; FENG Juan; XU Sichuan; AI Xicheng; ZHANG Xingkang; ZHANG Jianping

    2004-01-01

    As a structural analogue of adenine, 2-aminopurine (2Ap) is often used as a fluorescent probe to study the intramolecular charge transfer reaction in DNA. We have designed and synthesized a series of model DNA helix with the variation in the distance between the 2Ap probe and the GGG sequence, and have investigated, by means of picosecond time-resolved fluorescence spectroscopy, the effect of the length of the bridge (consisting of a number of transfer dynamics. The fluorescence dynamics of 2Ap exhibited three exponential decay components, the one with a time constant of a few hundred picoseconds is assigned to the intramolecular charge transfer from GGG to 2Ap. Within 2.4 nm of the donor-acceptor separation,the rate of charge transfer decreased exponentially upon increasing the separation, from which the decay factor ,β is determined to be 1.3 nm-1. Beyond 2.4 nm, however, the rate started to increase, this abnormal behavior of charge transfer is interpreted in terms of the match of electronic energies between the I-bridge and the donor/acceptor couple.

  19. 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

  20. In vitro antiviral activity of circular triple helix forming oligonucleotide RNA towards Feline Infectious Peritonitis virus replication.

    Science.gov (United States)

    Choong, Oi Kuan; Mehrbod, Parvaneh; Tejo, Bimo Ario; Omar, Abdul Rahman

    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-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 10(14) in the virus-inoculated cells to 10(9) 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. PMID:24707494

  1. Combination and cleavage of HBV DNA fragments by triple helix-forming oligonucleotides modified with manganese porphyrin in vitro

    Institute of Scientific and Technical Information of China (English)

    光丽霞; 袁发焕; 奚敏; 赵聪敏; 刘立; 温恩懿; 艾友萍

    2003-01-01

    Objective To observe the ability of triple helix-forming oligonucleotides (TFOs) modified with manganese porphyrin to combine with and cleave HBV DNA fractions. Methods TFO were modified with manganese porphyrin and acridines, and then reacted with the 32P labeled HBV DNA fragments at 37℃ in vitro (pH 7.4). Electrophoretic mobility shift assays and Dnase Ⅰ footprinting tests were used to show the affinity and specificity of TFO to bind to target sequences. The ability of TFO to cleave HBV DNA fragments was tested by cleavage experiments. Results TFO modified with manganese porphyrin and acridine could bind to the target sequence in a sequence-dependent manner, with a Kd value of 3.5×10-7 mol/L and a relative affinity of 0.008. In the presence of potassium monopersulfate (KHSO5), TFO modified with manganese porphyrin and acridine could cleave the target sequence where the triplex DNA was formed. Conclusion In the presence of KHSO5, TFO modified with manganese porphyrin and acridine could bind and cleave the target HBV-DNA in a sequence-dependent manner.

  2. The structure of Plasmodium vivax phosphatidylethanolamine-binding protein suggests a functional motif containing a left-handed helix

    Energy Technology Data Exchange (ETDEWEB)

    Arakaki, Tracy; Neely, Helen; Boni, Erica; Mueller, Natasha [Structural Genomics of Pathogenic Protozoa (SGPP) Consortium (United States); Department of Biochemistry, University of Washington, Seattle, WA 98195-7742 (United States); Buckner, Frederick S.; Van Voorhis, Wesley C. [Structural Genomics of Pathogenic Protozoa (SGPP) Consortium (United States); Department of Medicine, University of Washington, Seattle, WA 98195-7185 (United States); Lauricella, Angela; DeTitta, George; Luft, Joseph [Structural Genomics of Pathogenic Protozoa (SGPP) Consortium (United States); Hauptman-Woodward Institute, Buffalo, NY 14203 (United States); Hol, Wim G. J. [Structural Genomics of Pathogenic Protozoa (SGPP) Consortium (United States); Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195 (United States); Merritt, Ethan A., E-mail: merritt@u.washington.edu [Structural Genomics of Pathogenic Protozoa (SGPP) Consortium (United States); Department of Biochemistry, University of Washington, Seattle, WA 98195-7742 (United States)

    2007-03-01

    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.

  3. Flexible Wire-Shaped Supercapacitors in Parallel Double Helix Configuration with Stable Electrochemical Properties under Static/Dynamic Bending.

    Science.gov (United States)

    Guo, Kai; Ma, Ying; Li, Huiqiao; Zhai, Tianyou

    2016-02-24

    Wire-shaped flexible supercapacitors (SCs) have aroused much attention due to their small size, light weight, high flexibility, and deformability. However, the previously reported wire-shaped SCs usually involve complex assembly processes, encounter potential structural instabilities, and the influence of dynamic bending on the electrochemical stability of wire-shaped SCs is also not clear. Here, a parallel double helix wire-shaped supercapacitor (PDWS) protocol has been developed with two symmetric titanium@MnO2 fiber electrodes winded on a flexible nylon fiber by a simple and reliable process. The PDWSs show an operate voltage of 0.8 V, a high capacitance of 15.6 mF cm(-2) and an energy density of 1.4 µWh cm(-2) . Due to rational structure design, the PDWSs demonstrate excellent mechanical and electrochemical stability under both static and dynamic deformations. Over 3500 bending cycles, 88.0% of the initial capacitance can still be retained. In terms of dynamic bending, it is found that the cyclic voltammetry curves show periodically fluctuations simultaneously with the bending frequency and the intensity of fluctuation increases with higher bending frequency, while the dynamic capacitance is almost not affected. With extraordinary mechanical flexibility and excellent electrochemical stability, the high performance PDWS is considered to be a promising power source for wearable electronics. PMID:26725220

  4. The structure of DinB from Geobacillus stearothermophilus: a representative of a unique four-helix-bundle superfamily

    International Nuclear Information System (INIS)

    The structure of DinB from G. stearothermophilus is described and compared with a number of recently reported structures of this unusual fold. Structural similarities are revealed that unite several distant protein families. The crystal structure of the dinB gene product from Geobacillus stearothermophilus (GsDinB) is reported at 2.5 Å resolution. The dinB gene is one of the DNA-damage-induced genes and the corresponding protein, DinB, is the founding member of a Pfam family with no known function. The protein contains a four-helix up–down–down–up bundle that has previously been described in the literature in three disparate proteins: the enzyme MDMPI (mycothiol-dependent maleylpyruvate isomerase), YfiT and TTHA0303, a member of a small DUF (domain of unknown function). However, a search of the DALI structural database revealed similarities to a further 11 new unpublished structures contributed by structural genomics centers. The sequences of these proteins are quite divergent and represent several Pfam families, yet their structures are quite similar and most (but not all) seem to have the ability to coordinate a metal ion using a conserved histidine-triad motif. The structural similarities of these diverse proteins suggest that a new Pfam clan encompassing the families that share this fold should be created. The proteins that share this fold exhibit four different quaternary structures: monomeric and three different dimeric forms

  5. 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.

  6. Mutations in conserved helix 69 of 23S rRNA of Thermus thermophilus that affect capreomycin resistance but not posttranscriptional modifications

    DEFF Research Database (Denmark)

    Monshupanee, Tanakarn; Gregory, Steven T; Douthwaite, Stephen;

    2008-01-01

    for resistance to the tuberactinomycin antibiotic capreomycin. Two base substitutions, A1913U and mU1915G, and a single base deletion, DeltamU1915, were identified in helix 69 of 23S rRNA, a structural element that forms part of an interribosomal subunit bridge with the decoding center of 16S rRNA, the site...... to capreomycin. Finally, none of the mutations in helix 69 interferes with methylation at C1920 or with pseudouridylation at positions 1911 and 1917. We conclude that the resistance phenotype is a consequence of structural changes introduced by the mutations....... of previously reported capreomycin resistance base substitutions. Capreomycin resistance in other bacteria has been shown to result from inactivation of the TlyA methyltransferase which 2'-O methylates C1920 of 23S rRNA. Inactivation of the tlyA gene in T. thermophilus does not affect its sensitivity...

  7. A model for the [C+-GxC]n triple helix derived from observation of the C+-GxC base triplet in a crystal structure.

    Science.gov (United States)

    Nunn, C M; Trent, J O; Neidle, S

    1997-10-13

    A molecular modelling study on the [C+-GxC]n triple helix is reported. We have observed the C+-GxC base triplet in the crystal structure of an oligonucleotide-drug complex, between the minor-groove drug netropsin and the decanucleotide d(CGCAATTGCG)2. The complex was crystallised at pH 7.0, but the crystal structure, at a resolution of 2.4 A, shows that a terminal cytosine has become protonated and participates in a parallel C+-GxC base triplet. The structure of this triplet and its associated sugar-phosphate backbones have been energy-refined and then used to generate a triple helix. This has characteristics of the B-type family of DNA structures for two strands, with the third, the C+ strand, having backbone conformations closer to the A family. PMID:9369239

  8. Private Venture Capital’s Investment on University Spin-Offs: A Case Study of Tsinghua University Based on Triple Helix Model

    DEFF Research Database (Denmark)

    Gao, Yuchen; Hu, Yimei; Wang, Jingyi

    2015-01-01

    University spin-offs is a key form of university-industry collaboration, while venture capitals play a critical role for the creation and growth of these spin-offs. However, research on investment from venture capitals towards university spin-offs is still scant, especially in emerging...... and transition economies where governments are transforming their roles. Thus the main purpose of this study is to investigate how private venture capitals’ investment willingness on university spin-offs are influenced by universities and governments under the Chinese context based on the triple helix model....... Through an in-depth case study on the interactions of triple helix actors of Tsinghua University’s spin-offs, it is found that government and university developing an environment of marketization exert positive influences on the investment willingness of private venture capitals. Whilst financial direct...

  9. In-silico folding of a three helix protein and characterization of its free-energy landscape in an all-atom forcefield

    CERN Document Server

    Herges, T

    2003-01-01

    We report the reproducible first-principles folding of the 40 amino acid, three-helix headpiece of the HIV accessory protein in a recently developed all-atom free-energy forcefield. Six of twenty simulations using an adapted basin-hopping method converged to better than 3 \\AA backbone RMS deviation to the experimental structure. Using over 60,000 low-energy conformations of this protein, we constructed a decoy tree that completely characterizes its folding funnel.

  10. Plant Pathogenic Bacteria Utilize Biofilm Growth-associated Repressor (BigR), a Novel Winged-helix Redox Switch, to Control Hydrogen Sulfide Detoxification under Hypoxia*

    Science.gov (United States)

    Guimarães, Beatriz G.; Barbosa, Rosicler L.; Soprano, Adriana S.; Campos, Bruna M.; de Souza, Tiago A.; Tonoli, Celisa C. C.; Leme, Adriana F. P.; Murakami, Mario T.; Benedetti, Celso E.

    2011-01-01

    Winged-helix transcriptional factors play important roles in the control of gene expression in many organisms. In the plant pathogens Xylella fastidiosa and Agrobacterium tumefaciens, the winged-helix protein BigR, a member of the ArsR/SmtB family of metal sensors, regulates transcription of the bigR operon involved in bacterial biofilm growth. Previous studies showed that BigR represses transcription of its own operon through the occupation of the RNA polymerase-binding site; however, the signals that modulate its activity and the biological function of its operon are still poorly understood. Here we show that although BigR is a homodimer similar to metal sensors, it functions as a novel redox switch that derepresses transcription upon oxidation. Crystal structures of reduced and oxidized BigR reveal that formation of a disulfide bridge involving two critical cysteines induces conformational changes in the dimer that remarkably alter the topography of the winged-helix DNA-binding interface, precluding DNA binding. This structural mechanism of DNA association-dissociation is novel among winged-helix factors. Moreover, we demonstrate that the bigR operon is required for hydrogen sulfide detoxification through the action of a sulfur dioxygenase (Blh) and sulfite exporter. As hydrogen sulfide strongly inhibits cytochrome c oxidase, it must be eliminated to allow aerobic growth under low oxygen tension, an environmental condition found in bacterial biofilms, xylem vessels, and root tissues. Accordingly, we show that the bigR operon is critical to sustain bacterial growth under hypoxia. These results suggest that BigR integrates the transcriptional regulation of a sulfur oxidation pathway to an oxidative signal through a thiol-based redox switch. PMID:21632538

  11. Nonlocal effect of a varying in-space Zeeman field on supercurrent and helix state in a spin-orbit-coupled s -wave superconductor

    Science.gov (United States)

    Mal'shukov, A. G.

    2016-02-01

    A weak parallel Zeeman field combined with spin-orbit coupling can induce the supercurrent in an s -wave two-dimensional superconductor. At the same time, the thermodynamic equilibrium state of such a system is characterized by the helix phase in which the order parameter varies in space as exp(i Q .r ) . In this state, the electric current that is induced by the Zeeman interaction is exactly counterbalanced by the current produced by the gradient of the order parameter. We studied the interplay of the helix state and magnetoelectric current in the case of a varying in-space Zeeman field, as it might be realized in hybrid heterostructures with magnetic and superconducting layers. The theoretical analysis was based on Usadel equations for Green functions in a dirty superconductor. It is shown that even weak inhomogeneity produces a strong long-range effect on the magnetoelectric current and the order-parameter phase. Consequently, depending on the macroscopic shape of such an inhomogeneity, either the helix state with the zero supercurrent, or a locally uniform state with the finite supercurrent, is realized. A mixture of these two extreme situations is also possible. It is also shown that the current can be induced at a large distance from a ferromagnetic island embedded into a superconductor. Quantum effects associated with the magnetoelectric effect are briefly discussed for multiply connected systems. The theory proposes an alternative point of view on the interplay of the magnetoelectric effect and helix phase in spin-orbit coupled superconductors. It also suggests an interesting method that enables us to couple superconducting and magnetic circuits.

  12. In Silico Folding of a Three Helix Protein and Characterization of Its Free-Energy Landscape in an All-Atom Force Field

    Science.gov (United States)

    Herges, T.; Wenzel, W.

    2005-01-01

    We report the reproducible first-principles folding of the 40 amino-acid, three-helix headpiece of the HIV accessory protein in a recently developed all-atom free-energy force field. Six of 20 simulations using an adapted basin-hopping method converged to better than 3Å backbone rms deviation to the experimental structure. Using over 60 000 low-energy conformations of this protein, we constructed a decoy tree that completely characterizes its folding funnel.

  13. Hederagenin from the leaves of ivy (Hedera helix L.) induces apoptosis in human LoVo colon cells through the mitochondrial pathway

    OpenAIRE

    Liu, Bao-Xin-Zi; Zhou, Jin-Yong; Li, Yu; Zou, Xi; Wu, Jian; Gu, Jun-Fei; YUAN, JIA-RUI; Zhao, Bing-Jie; Feng, Liang; JIA, XIAO-BIN; Wang, Rui-ping

    2014-01-01

    Background Colorectal cancer has become one of the leading cause of cancer morbidity and mortality throughout world. Hederagenin, a derivative of oleanolic acid isolated from the leaves of ivy (Hedera helix L.), has been shown to have potential anti-tumor activity. The study was conducted to evaluate whether hederagenin could induce apoptosis of human colon cancer LoVo cells and explore the possible mechanism. Methods MTT assay was used for evaluating cell viability while Annexin V-FITC/PI as...

  14. Coadministration of Hedera helix L. Extract Enabled Mice to Overcome Insufficient Protection against Influenza A/PR/8 Virus Infection under Suboptimal Treatment with Oseltamivir

    OpenAIRE

    Eun-Hye Hong; Jae-Hyoung Song; Aeri Shim; Bo-Ra Lee; Bo-Eun Kwon; Hyuk-Hwan Song; Yeon-Jeong Kim; Sun-Young Chang; Hyeon Gun Jeong; Jong Geal Kim; Sang-Uk Seo; HyunPyo Kim; YongSoo Kwon; Hyun-Jeong Ko

    2015-01-01

    Several anti-influenza drugs that reduce disease manifestation exist, and although these drugs provide clinical benefits in infected patients, their efficacy is limited by the emergence of drug-resistant influenza viruses. In the current study, we assessed the therapeutic strategy of enhancing the antiviral efficacy of an existing neuraminidase inhibitor, oseltamivir, by coadministering with the leaf extract from Hedera helix L, commonly known as ivy. Ivy extract has anti-inflammatory, antiba...

  15. "helix Nebula - the Science Cloud", a European Science Driven Cross-Domain Initiative Implemented in via AN Active Ppp Set-Up

    Science.gov (United States)

    Lengert, W.; Mondon, E.; Bégin, M. E.; Ferrer, M.; Vallois, F.; DelaMar, J.

    2015-12-01

    Helix Nebula, a European science cross-domain initiative building on an active PPP, is aiming to implement the concept of an open science commons[1] while using a cloud hybrid model[2] as the proposed implementation solution. This approach allows leveraging and merging of complementary data intensive Earth Science disciplines (e.g. instrumentation[3] and modeling), without introducing significant changes in the contributors' operational set-up. Considering the seamless integration with life-science (e.g. EMBL), scientific exploitation of meteorological, climate, and Earth Observation data and models open an enormous potential for new big data science. The work of Helix Nebula has shown that is it feasible to interoperate publicly funded infrastructures, such as EGI [5] and GEANT [6], 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 and choice" over the type of computing resources to be consumed and the manner in which they can be obtained. But to offer such freedom and choice across a spectrum of suppliers, various issues such as intellectual property, legal responsibility, service quality agreements and related issues need to be addressed. Finding solutions to these issues is one of the goals of the Helix Nebula initiative. [1] http://www.egi.eu/news-and-media/publications/OpenScienceCommons_v3.pdf [2] http://www.helix-nebula.eu/events/towards-the-european-open-science-cloud [3] e.g. https://sentinel.esa.int/web/sentinel/sentinel-data-access [5] http://www.egi.eu/ [6] http://www.geant.net/

  16. Collagen triple-helix formation in all-trans chains proceeds by a nucleation/growth mechanism with a purely entropic barrier

    OpenAIRE

    Bachmann, Annett; Kiefhaber, Thomas; Boudko, Sergei; Engel, Jürgen; Bächinger, Hans Peter

    2005-01-01

    Collagen consists of repetitive Gly–Xaa–Yaa tripeptide units with proline and hydroxyproline frequently found in the Xaa and Yaa position, respectively. This sequence motif allows the formation of a highly regular triple helix that is stabilized by steric (entropic) restrictions in the constituent polyproline-II-helices and backbone hydrogen bonds between the three strands. Concentration-dependent association reactions and slow prolyl isomerization steps have been identified as major rate-lim...

  17. Parametrization, molecular dynamics simulation and calculation of electron spin resonance spectra of a nitroxide spin label on a poly-alanine alpha helix

    OpenAIRE

    Sezer, Deniz; Freed, Jack H.; Roux, Benoît

    2008-01-01

    The nitroxide spin label 1-oxyl-2,2,5,5-tetramethylpyrroline-3-methyl-methanethiosulfonate (MTSSL), commonly used in site-directed spin labeling of proteins, is studied with molecular dynamics (MD) simulations. After developing force field parameters for the nitroxide moiety and the spin label linker, we simulate MTSSL attached to a poly-alanine alpha helix in explicit solvent to elucidate the factors affecting its conformational dynamics. Electron spin resonance spectra at 9 and 250 GHz are ...

  18. A distinct three-helix centipede toxin SSD609 inhibits I(ks) channels by interacting with the KCNE1 auxiliary subunit.

    Science.gov (United States)

    Sun, Peibei; Wu, Fangming; Wen, Ming; Yang, Xingwang; Wang, Chenyang; Li, Yiming; He, Shufang; Zhang, Longhua; Zhang, Yun; Tian, Changlin

    2015-01-01

    KCNE1 is a single-span transmembrane auxiliary protein that modulates the voltage-gated potassium channel KCNQ1. The KCNQ1/KCNE1 complex in cardiomyocytes exhibited slow activated potassium (I(ks)) currents. Recently, a novel 47-residue polypeptide toxin SSD609 was purified from Scolopendra subspinipes dehaani venom and showed I(ks) current inhibition. Here, chemically synthesized SSD609 was shown to exert I(ks) inhibition in extracted guinea pig cardiomyocytes and KCNQ1/KCNE1 current attenuation in CHO cells. The K(+) current attenuation of SSD609 showed decent selectivity among different auxiliary subunits. Solution nuclear magnetic resonance analysis of SSD609 revealed a distinctive three-helix conformation that was stabilized by a new disulfide bonding pattern as well as segregated surface charge distribution. Structure-activity studies demonstrated that negatively charged Glu19 in the amphipathic extracellular helix of KCNE1 was the key residue that interacted with SSD609. The distinctive three-helix centipede toxin SSD609 is known to be the first polypeptide toxin acting on channel auxiliary subunit KCNE1, which suggests a new type of pharmacological regulation for ion channels in cardiomyocytes. PMID:26307551

  19. Effect of secondary structure on the potential of mean force for poly-L-lysine in the alpha-Helix and beta-sheet conformations

    Energy Technology Data Exchange (ETDEWEB)

    Grigsby, J.J.; Blanch, H.W.; Prausnitz, J.M.

    2001-10-30

    Because poly-L-lysine (PLL) can exist in the {alpha}-helix or {beta}-sheet conformation depending on solution preparation and solution conditions, PLL is a suitable candidate to probe the dependence of protein interactions on secondary structure. The osmotic second virial coefficient and weight-average molecular weight are reported from low-angle laser-light scattering measurements for PLL as a function of NaCl concentration, pH, and {alpha}-helix or {beta}-sheet content. Interactions between PLL molecules become more attractive as salt concentration increases due to screening of PLL charge by salt ions and at low salt concentration become more attractive as pH increases due to decreased net charge on PLL. The experimental results show that interactions are stronger for the {beta}-sheet conformation than for the {alpha}-helix conformation. A spherically-symmetric model for the potential of mean force is used to account for specific interactions not described by DLVO theory and to show how differences in secondary structure affect PLL interactions.

  20. On the Use of Cross-Correlation between Volume Scattering and Helix Scattering from Polarimetric SAR Data for the Improvement of Ship Detection

    Directory of Open Access Journals (Sweden)

    Jujie Wei

    2016-01-01

    Full Text Available Synthetic Aperture Radar (SAR ship detection is an important maritime application. However, azimuth ambiguities caused by the finite sampling of the Doppler spectrum are often visible in SAR images and are always mistaken as ships by classic detection techniques, like the Constant False Alarm Rate (CFAR. It is known that radar targets and azimuth ambiguities have different characteristics in polarimetric SAR (PolSAR data, i.e., first ambiguities usually have strong odd- or double-bounce scattering and the maximum amplitude of the first ambiguity in SHV is always considerably smaller than that of the corresponding target for zero or high velocity. On the basis of this characteristics, this paper finds that first ambiguities usually have low volume scattering power relative to ships and almost have no helix scattering by Yamaguchi decomposition. But some residual ambiguities still exit in the volume scattering power and have similar scattering intensity to small ships, and some parts of a ship also have zero helix scattering owing to some physical factors (e.g., ship structure, radar incidence angle, etc.. Thus, for high-precision ship detection, a new ship detection method based on cross-correlation between the volume and helix scattering mechanisms derived from Yamaguchi decomposition is proposed to avoid false alarms caused by azimuth ambiguities and enhance Target-to-Clutter Ratio (TCR for improving the miss detection rate of small ships. By experiments, it is proved that our method can work effectively and has high detection accuracy.