WorldWideScience

Sample records for caracol helix aspersa

  1. Efecto de la humedad relativa sobre la reproducción del caracol de tierra (Helix aspersa Müller

    Directory of Open Access Journals (Sweden)

    H. Á. Fernández

    2013-01-01

    Full Text Available En El Alto, Ferreñafe, Perú, en vista de resultados pobres en la cantidad de huevos por puesta y en el porcentaje de eclosión del caracol de tierra (Helix aspersa Müller, se asumió que bajos porcentajes de Humedad Relativa podría estar afectando a estas variables. En el presente experimento se implementaron cajas de incubación con diferentes niveles de HR; evaluándose el efecto de cuatro porcentajes de HR (50, T1; 60, T2; 70, T3, y 80, T4 sobre la postura, duración de la incubación y porcentaje de eclosión. Respectivamente, para T1 hasta T4, se obtuvo: 47.9c, 68.6b, 85.8a y 100.7a huevos puestos por caracol; 22.3a, 18.4b, 15.5c y 13.9d días de incubación; 38.4d, 62.6c, 68.9b y 76.2a% de eclosión por postura.

  2. 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

  3. Efecto de las condiciones micro-climáticas en el comportamiento reproductivo del Helix aspersa

    Directory of Open Access Journals (Sweden)

    Hugo Ángel Fernández Cabrera

    2013-01-01

    Full Text Available El objetivo del presente estudio fue evaluar el efecto factores microclimáticos (temperatura y humedad relativa en la reproducción de caracoles de tierra (Helix aspersa. Para esto se acondicionaron cámaras de incubación con cuatro niveles de humedad relativa y de temperatura. Se evaluaron como respuestas la postura, duración de la incubación y porcentaje de eclosión. Se concluye que a 81,0 ± 0,63% de humedad relativa y 23,9 ± 0,39 °C de temperatura se logran los mejores resultados.

  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. [Stages of organogenesis and cytodifferentiation of the albumen gland in the snail Helix aspersa Muller].

    Science.gov (United States)

    Courtot, A M; Gomot, L

    1982-01-01

    The differentiation of the albumen gland of the pulmonate stylommatophora Helix aspersa has been divided into five stages. An ultrastructural study showed, the differentiation of undifferentiated epithelial cells into two cell types: ciliated cells and secretory cells. The glandular differentiation of epithelial cells was characterized by the development of ergastoplasma and the Golgi apparatus which were both involved in protein and galactogen synthesis.

  6. Evidence for genetic control of adult weight plasticity in the snail Helix aspersa

    DEFF Research Database (Denmark)

    Ros, Mathieu; Sorensen, Daniel; Waagepetersen, Rasmus Plenge

    2004-01-01

    of adult weight in the snail Helix aspersa. Several models of heterogeneous variance are fitted using a Bayesin, MCMC approach. Exploratory analyses using posterior predictive model checking and model comparisons based on the deviance information criterion favor a model postulating a genetically structured...... is illustrated numerically using estimates of parameters derived from the snail data set....

  7. Unpredictable responses of garden snail (Helix aspersa) populations to climate change

    NARCIS (Netherlands)

    Bezemer, T.M.; Knight, K.J.

    2001-01-01

    We studied the impact of climate change on the population dynamics of the garden snail (Helix aspersa) in the Ecotron controlled environment facility. The experimental series ran for three plant generations, allowing the snails to reproduce. We investigated the isolated and combined effects of eleva

  8. Development of the feline lungworms Aelurostrongylus abstrusus and Troglostrongylus brevior in Helix aspersa snails.

    Science.gov (United States)

    Giannelli, Alessio; Ramos, Rafael Antonio Nascimento; Annoscia, Giada; Di Cesare, Angela; Colella, Vito; Brianti, Emanuele; Dantas-Torres, Filipe; Mutafchiev, Yasen; Otranto, Domenico

    2014-04-01

    Aelurostrongylus abstrusus (Strongylida, Angiostrongylidae) and Troglostrongylus brevior (Strongylida, Crenosomatidae) are regarded as important lungworm species of domestic felids, with the latter considered an emerging threat in the Mediterranean region. The present study aimed to assess their concurrent development in the mollusc Helix aspersa (Pulmonata, Helicidae). Thirty snails were infested with 100 first-stage larvae (L1) of A. abstrusus and T. brevior, isolated from a naturally infested kitten. Larval development was checked by digesting five specimens at 2, 6 and 11 days post infestation. Larvae retrieved were morphologically described and their identification was confirmed by specific PCR and sequencing. All H. aspersa snails were positive for A. abstrusus and T. brevior, whose larval stages were simultaneously detected at each time point. In addition, snails were exposed to outdoor conditions and examined after overwintering, testing positive up to 120 days post infestation. Data herein presented suggest that A. abstrusus and T. brevior develop in H. aspersa snails and may eventually co-infest cats. Data on the morphology of both parasitic species in H. aspersa provide additional information on their development and identification, to better understand the population dynamics of these lungworms in receptive snails and paratenic hosts.

  9. 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.

  10. Comparative Study on the Adaptation and Growth Dynamics of the Helix pomatia and Helix aspersa Muller Terrestrial Snails Under Different Feeding Regimes

    Directory of Open Access Journals (Sweden)

    Adrian Toader-Williams

    2010-05-01

    Full Text Available We used Helix pomatia and Helix aspersa species and measure their growth as the snails were approaching the hibernation season. Helix pomatia 2yo shown a decrease in weight while being raised in enclosed parcels of 4sqm the younger Helix pomatia 1yo as well as Helix aspersa Muller demonstrated the ability to adapt relatively fast to the same conditions. We established 5 experimental lots in a Helix pomatia farm, GPS coordinates N46.606040 E23.599950. Control lot contained Taraxacum officinales, Sonchus oleraceus, Equisetum arvense and Atriplex hortensis, wild flora found within the farm. The other lots contained the same plants as the control lot plus different combinations of imported plants from other areals. The H. pomatia 2yo weight decreased in the control lot by a mean of -3.86% while H. aspersa 1yo marked an increase of +16.89% in the same lot during the same period. The lot containing lupinus polyphyllus delivered snails with weight gain of +24.66% for H. pomatia 2yo and an increase of only +1.98% for H. aspersa 1yo. As a contrast, H. pomatia 2yo gained only +7.72% while H. aspersa 1yo gained +28.89%, in the lot containing Lavanda officinalis, Foeniculum vulgare and Hyssopus officinalis among the other plants.

  11. Characterization by immunocytochemistry of ionic channels in Helix aspersa suboesophageal brain ganglia neurons.

    Science.gov (United States)

    Azanza, M J; Pérez-Castejón, C; Pes, N; Pérez-Bruzón, R N; Aisa, J; Junquera, C; Maestú, C; Lahoz, M; Martínez-Ciriano, C; Vera-Gil, A; Del Moral, A

    2008-04-01

    The aim of this work was to characterize several ionic channels in nervous cells of the suboesophageal visceral, left and right parietal, and left and right pleural brain ganglia complex of the snail Helix aspersa by immunocytochemistry. We have studied the immunostaining reaction for a wide panel of eleven polyclonal antibodies raised against mammal antigens as follows: voltage-gated-Na+ channel; voltage-gated-delayed-rectifier-K+ channel; SK2-small-conductance-Ca2+-dependent-K+ channel apamin sensitive; SK3 potassium channel; charybdotoxin-sensitive voltage-dependent potassium channel; BKCa-maxi-conductance-Ca2+-dependent-K+ channel; hyperpolarization-activated cyclic nucleotide-gated potassium channel 4; G-protein-activated inwardly rectifying potassium channel GIRK2 and voltage-gated-calcium of L, N and P/Q type channels. Our results show positive reaction in neurons, but neither in glia cells nor in processes in the Helix suboesophageal ganglia. Our results suggest the occurrence of molecules in Helix neurons sharing antigenic determinants with mammal ionic channels. The reaction density and distribution of immunoreactive staining within neurons is specific for each one of the antisera tested. The studies of co-localization of immunoreaction, on alternate serial sections of the anterior right parietal ganglion, have shown for several recognized mapped neurons that they can simultaneously be expressed among two and seven different ionic protein channels. These results are considered a key structural support for the interpretation of Helix aspersa neuron electrophysiological activity.

  12. 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.

  13. Estudio del hepatopáncreas de Helix Aspersa en situación normal y tras ayuno

    OpenAIRE

    Almendros Gallego, Antonio Manuel

    2013-01-01

    Se hace un estudio a microscopia electrónica de los diversos tipos celulares que componen el hepatopancreas de Helix Aspersa atendiendo a los componentes celulares característicos de cada uno de ellos tanto en situación normal como a diversos periodos de ayuno

  14. Direct and correlated responses to individual selection for large adult weight in the edible snail Helix aspersa Muller.

    Science.gov (United States)

    Dupont-Nivet, M; Mallard, J; Bonnet, J C; Blanc, J M

    2000-06-15

    A selection experiment for large adult weight based on individual performance was conducted for three generations in Helix aspersa aspersa. A second line was kept as an unselected control line. Direct response measured as deviation from the control line was 3.55 g after three generations of artificial selection, which averaged 13%. Realized heritability was 0.38 +/- 0.04. Correlated responses to selection showed a significant increase in weight after hibernation, mean egg weight and mean weight of newly-hatched snails with selection. For adult age, egg number, and hatching rate, no significant change correlated to selection was found, but this is to be confirmed.

  15. 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.

  16. Imidacloprid induced alterations in enzyme activities and energy reserves of the land snail, Helix aspersa.

    Science.gov (United States)

    Radwan, M A; Mohamed, M S

    2013-09-01

    The in vivo sublethal toxic effects (0.2 and 0.6 LD50) of topically applied imidacloprid on biochemical biomarkers in the land snail, Helix aspersa was examined. Biochemical perturbations were assessed by measuring the three enzymatic (Acetylcholinesterase, AChE; catalase, CAT and glutathione-S-transferase, GST) activities and three energy reserves (protein, glycogen and lipids) in the snails. Snail samples were taken from each sublethal dose and control groups at 1, 3 and 7 days after treatment. The results revealed that there were overall decrease in AChE activity as well as depletion of lipids and glycogen contents in the imidacloprid-treated snails compared to control groups. The CAT and GST activities of treated snails with the sublethal doses of imidacloprid were significantly higher than those of untreated controls along the three times of exposure. Moreover, an increase in the level of total proteins was observed in animals treated with 0.6 LD50 imidacloprid compared to control groups. The alterations in all tested biochemical perturbations were most pronounced with the 0.6 LD50 than 0.2 LD50. This study suggests that alterations of the enzyme activities and energy reserves in this species that could be useful as biomarkers of imidacloprid exposure in the evaluation of terrestrial impacts of this insecticide.

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

    Science.gov (United States)

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

    2005-12-15

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

  18. 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}).

  19. Localization of connexins in neurons and glia cells of the Helix aspersa suboesophageal brain ganglia by immunocytochemistry.

    Science.gov (United States)

    Azanza, M J; Pes, N; Pérez-Bruzón, R N; Aisa, J; Raso, M; Junquera, C; Lahoz, J M; Maestú, C; Martínez-Ciriano, C; Pérez-Castejón, C; Vera-Gil, A; Del Moral, A

    2007-05-01

    The aim of the present study was to examine the distribution of cells expressing connexin 26 (Cx26) in the suboesophageal visceral, left and right parietal and left and right pleural ganglia of the snail Helix aspersa by immunocytochemistry. Altogether we have found approximately 452 immunoreactive neurons which represent the 4.7% of the total neurons counted. The stained large neurons (measured diameter 55-140 microm) occurred mostly on the peripheral surface of the ganglia while the small immunostained cells (5-25 microm diameter) were observed in groups near the neuropil. The number of large neurons giving positive Cx26-like immunostaining was small in comparison with that for medium (30-50 microm diameter) and small sized cells. The expression of Cx26 was also observed in the processes of glia cells localized among neurons somata and in the neuropil showing that the antiserum recognized epitopes in both protoplasmic and fibrous glia cells of Helix aspersa. The neuropils of all ganglia showed fibers densely immunostained. While we have observed a good specificity for Cx26-antiserum in neurons, a lack of reaction for Cx43 antiserum was observed in neurons and glia cells. The reaction for enolase antiserum in neurons was light and non-specific and a lack of reaction in glia cells and processes for GFAP antiserum was observed. Although the percentage of positive neurons for Cx26 antiserum was low is suggested that in normal physiological conditions or under stimulation the expression of connexin could be increased. The observed results can be considered of interest in the interpretation of Helix aspersa elemental two neuron networks synchronizing activity, observed under applied extremely low frequency magnetic fields.

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

    Directory of Open Access Journals (Sweden)

    Adrian Toader-Williams

    2010-05-01

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

  1. 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.

  2. 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.

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

    Directory of Open Access Journals (Sweden)

    Claudemir Martins Soares

    2002-04-01

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

  4. Effects of a freezing event during hibernation on further survival, reproduction and growth in the partially freezing tolerant land snail Helix aspersa muller (Gastropoda: helicidae).

    Science.gov (United States)

    Ansart, Armelle; Vernon, Philippe; Daguzan, Jacques

    2002-01-01

    Tolerance of ectothermic animals to freezing is often estimated by assessing survival a few days after the treatment. However, in the long term, ice formation in the body tissues can affect survival, as well as reproductive capability and growth. The land snail Helix aspersa survives only short durations with ice in its tissues, to a lethal limit of 40 to 60 % of its body water frozen. Adult and immature snails were treated during their winter dormancy period to a freezing event above this limit; their survival was observed both in the short and long term, as well as their ability to reproduce (adults) and grow (immature snails). Treated snails were compared with a control group, which was not frozen. No difference appeared in the survival, reproduction and growth of control and frozen snails. This study confirms partial freezing tolerance in this population of Helix aspersa.

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

    Directory of Open Access Journals (Sweden)

    B.F. Vasconcellos

    2006-04-01

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

  6. 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.

  7. Short-term changes in Ca, Pb, Zn and Cd concentrations of the garden snail Helix aspersa Muller from a central London car park

    Energy Technology Data Exchange (ETDEWEB)

    Beeby, A.; Eaves, S.L.

    1983-03-01

    Helix aspersa were collected from a car park with a high degree of Pb and Zn pollution over a period of 102 days following the end of aestivation. Analysis of whole soft tissues demonstrates a high variability in both Pb and Ca levels in the short term, possibly associated with shell formation. Pb, Zn and Ca concentrations are also shown to vary with age-class. No simple relationship between total Ca and total heavy metal levels was found, and it is concluded that Ca does not account for the high variability between individuals. The rate of loss of each metal is shown to vary with age-class.

  8. Uptake of lead, zinc, cadmium, and copper by the pulmonate mollusc, Helix aspersa Muller, and its relevance to the monitoring of heavy metal contamination of the environment

    Energy Technology Data Exchange (ETDEWEB)

    Coughtrey, P.J.; Martin, M.H.

    1977-01-13

    The occurrence of lead, zinc, cadmium, and copper in individuals of Helix aspersa from two sites of varying degrees of contamination was studied. Zinc, cadmium, and copper were shown to increase in a linear fashion with animal weight. The rate of uptake for zinc and cadmium in particular was significantly greater at the more contaminated site. Statistical analysis of the data, using correlation and regression techniques, provided information on apparent intermetallic effects. It is concluded that because metal uptake and body weight show a positive linear relationship only the use of animals of similar weight and/or size can be used for monitoring purposes. Even then, different patterns of uptake into different organs and interactions between metal uptakes are such as to seriously question the use of Helix, and other molluscs, for monitoring purposes unless specific organs from comparably sized and/or aged animals are used.

  9. Variação na disponibilidade de oxigênio e respostas antioxidantes no gastrópode Helix aspersa

    OpenAIRE

    2011-01-01

    O gastrópode terrestre Helix aspersa (Müller) é um herbívoro generalista, que habita a região mediterrânea. Os gastrópodes terrestres em geral entram em estados dormentes durante o seu ciclo de vida. A dormência é uma forma de inatividade associada a uma redução na taxa metabólica, sem grandes alterações no estado hídrico do animal (Withers & Cooper, 2010). Os gastrópodes terrestres quando saem de um estado dormente podem apresentar um aumento na produção de espécies reativas de oxigênio (ROS...

  10. Contamination of terrestrial gastropods Helix aspersa maxima with {sup 137}Cs, {sup 85}Sr, {sup 133}Ba and {sup 123m}Te by direct and trophic pathways

    Energy Technology Data Exchange (ETDEWEB)

    Madoz-Escande, C.; Querrec, N.; Bonhomme, T.; Poncet-Bonnard, D. [CEA Cadarache (DEI/SECRE/LRE), Laboratory of Radioecology and Ecotoxicology, Institute for Radioprotection and Nuclear Safety, 13 - Saint-Paul-lez-Durance (France)

    2004-07-01

    Contaminations of terrestrial gastropod Helix aspersa Maxima by direct deposition or labelled food ingestion of {sup 137}Cs, {sup 85}Sr, {sup 133}Ba and {sup 123m}Te were carried out in laboratory conditions. This study was performed to compare the two pathways of contamination: direct and trophic in terms of individual mortality and, radionuclide uptake, depuration and tissular distribution. A first group of 30 snails (2-year old) was exposed to radioactive aerosols during a twenty-hour period. These aerosols were supposed to be representative of those produced during a nuclear accident occurring on a PWR. A second group of 40 snails (same ages) was submitted to twice-a-week ingestion of food during 10 days (flour at a feeding rate of about 0,2 g) contaminated by these same aerosols. During the 21 days observation period, comparison among the two groups and a reference group (not contaminated by radionuclides) was performed. No significant difference between the three groups was observed neither on the growth nor on the mortality. One day after the deposit, the cesium was the most bioavailable element, distributed homogeneously within the whole body (from 15 to 25% of total Cs respectively in shell and muscle). The strontium accumulated in the shell (about 70%). The barium was found in the muscle (20%) and the shell (65%). Tellurium was mainly present in the shell (70%) and in digestive gland (20%), Later, this element was mostly present in faeces. As regards the contamination by ingestion, it was mainly accumulated in digestive gland. (author)

  11. 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

  12. Sanitary diagnosis in different snail breeding places in Colombia: main pathogen agents affecting the snail Helix aspersa (O.F. Muller, 1774 in every phase of its biological process

    Directory of Open Access Journals (Sweden)

    Felipe A. Moncada Reyes

    2007-12-01

    Full Text Available The snail culture is an activity that requires of investigative processes for his optimal development. In Colombia the advances documented on the subject are almost inexistent. Therefore, it is responsibility of the veterinary doctor to create studies that generate a real knowledge on topics as the disease prevention within the snail breeding place. This investigation tries to make a sanitary diagnosis in each phase of the biological cycle of the snail Helix aspersa (O.F. Muller, 1774 bred in captivity. It also determines how different environmental factors (temperature, humidity, altitude above sea level, etc., and different forms of handling can be or no implied in the presentation of any disease. Thus, it identifies and classifies the main pathogenic agents of the land Helix snails in different environmental conditions of regions appropriate for the snail culture in Colombia. This study also makes an analysis of nonparametric observations studies, by observing particular pathological cases, exposed or not, to different risk factors. They measure the prevalence of every disease after applying a survey epidemiologist of risks, determining the pathologies related to the presented symptomatology and carrying out a microbiological isolation of the main contained pathogenic agents in each snail breeding place. The most significant pathologies will be documented inside the snail breeding place, based on the analysis of results through associations, and the rates of incidence for each disease, the presented relative risk, and the main factors of risk will be determined. Finally, with suitable breeding practices established after this study, we can foresee the presence of these alterations in the production of the snail in Colombia.

  13. Contamination of terrestrial gastropods, Helix aspersa maxima, with {sup 137}Cs, {sup 85}Sr, {sup 133}Ba and {sup 123m}Te by direct, trophic and combined pathways

    Energy Technology Data Exchange (ETDEWEB)

    Madoz-Escande, C. [Laboratory of Radioecology and Ecotoxicology, Institute for Radioprotection and Nuclear Safety, IRSN/DEI/SECRE/LRE, Cadarache, Bld 186, BP 3, 13115 St-Paul-lez-Durance Cedex (France)]. E-mail: chantal.madoz-escande@irsn.fr; Simon, O. [Laboratory of Radioecology and Ecotoxicology, Institute for Radioprotection and Nuclear Safety, IRSN/DEI/SECRE/LRE, Cadarache, Bld 186, BP 3, 13115 St-Paul-lez-Durance Cedex (France)

    2006-07-01

    {sup 137}Cs, {sup 85}Sr, {sup 133}Ba and {sup 123m}Te contaminations of terrestrial gastropods, Helix aspersa maxima, by direct deposition, labelled food ingestion or combined (trophic and direct pathways) exposure were carried out under laboratory conditions. The aim of this study was to compare the three contamination pathways: direct, trophic and combined, in terms of individual mortality, radionuclide uptake, depuration and distribution in the tissues. An initial group of 30 snails (2 years old) was exposed to radioactive aerosols during a 20-h period. These aerosols were assumed to be representative of those that would be released during a nuclear accident occurring in a PWR. A second group of 50 snails (same age) was submitted to an ingestion of commercial food contaminated by the same aerosols, twice a week for 21 days (flour at a feeding rate of about 0.2 g). A third group of 40 snails was submitted to a combined exposure: exposure to radioactive aerosols (20 h), followed by ingestion of flour contaminated by the same aerosols, twice a week for 21 days. No significant difference between the three groups and a reference group of 10 snails was observed, neither in growth nor in mortality. Concerning the direct pathway, at the end of direct deposition (about 1 day after the beginning), cesium was the most bioavailable element, distributed rather homogeneously throughout the whole body (13% of the total Cs in all organs excepting the digestive system and 28% in the muscle). Strontium was measured in the shell (about 70%). Barium was found in the muscle (20%) and in the shell (65%). Tellurium was mainly present in the shell (70%) and in the digestive system (20%). After 21 days of depuration, the faeces eliminated 42% of the Te. As for contamination by ingestion, Te mainly accumulated in the digestive system (72% of Te present in the total body), Ba accumulated in the muscle (75%) and Sr in the shell (70%). Concerning contamination by combined pathways, at the

  14. 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.

  15. 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

  16. Histofisiología del epitelio renal de helix aspersa (mollusca, gastropoda, pulmonata, stylommatophora)

    OpenAIRE

    Sánchez Aguayo, Inmaculada

    1983-01-01

    La excreción es, por definición, la separación de los productos de desecho de los fluidos tisulares y corporales, y su eliminación del organismo. Además, se considera como el resultado de la filtración del líquido de la sangre, de la reabsorción de ciertos compuestos y de la secreción de sustancias en el interior de túbulos excretores. Los productos de desecho son el resultado del metabolismo celular. Aunque en general son productos finales de procesos catabólicos, también pueden incluir ...

  17. Caracoles terrestres (Mollusca: Gastropoda) de Iturbide, Nuevo León, México

    OpenAIRE

    Correa Sandoval, Alfonso

    2015-01-01

    Catorce especies de caracoles terrestres son informadas del municipio de Iturbide, Nuevo León, México. El tipo de vegetación más rico en moluscos (11 especies) es el bosque de galería de Populus-Quercus-Juglans, con cobertura vegetal total y escasa pendiente. La distribución panamericana es el principal componente zoogeográfico Fourteen species of land snails are reported from the municipality of Iturbide, Nuevo León, México. The vegetation type with more species ( 1 1) is the Populus-Quer...

  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)

    EDINSON ANDRÉS ACOSTA

    2009-01-01

    Full Text Available El caracol Pala, Strombus gigas (Strombidae, es de gran importancia ecológica y so- cioeconómica 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.

  20. 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

  1. Dynamic and static calcium gradients inside large snail (Helix aspersa) neurones detected with calcium-sensitive microelectrodes

    OpenAIRE

    Thomas, Roger C.; Postma, Marten

    2007-01-01

    We have used quartz Ca2+-sensitive microelectrodes (CASMs) in large voltage-clamped snail neurones to investigate the inward spread of Ca2+ after a brief depolarisation. Both steady state and [Ca2+] i transients changed with depth of penetration. When the CASM tip was within 20 μm of the far side of the cell the [Ca2+] i transient time to peak was 4.4 ± 0.5 s, rising to 14.7 ± 0.7 s at a distance of 80 μm. We estimate that the Ca2+ transients travelled centripetally at an average speed of 6 μ...

  2. Dynamic and static calcium gradients inside large snail (Helix aspersa) neurones detected with calcium-sensitive microelectrodes.

    Science.gov (United States)

    Thomas, Roger C; Postma, Marten

    2007-04-01

    We have used quartz Ca2+-sensitive microelectrodes (CASMs) in large voltage-clamped snail neurones to investigate the inward spread of Ca2+ after a brief depolarisation. Both steady state and [Ca2+]i transients changed with depth of penetration. When the CASM tip was within 20 microm of the far side of the cell the [Ca2+]i transient time to peak was 4.4+/-0.5s, rising to 14.7+/-0.7s at a distance of 80 microm. We estimate that the Ca2+ transients travelled centripetally at an average speed of 6 microm2 s(-1) and decreased in size by half over a distance of about 45 microm. Cyclopiazonic acid had little effect on the size and time to peak of Ca2+ transients but slowed their recovery significantly. This suggests that the endoplasmic reticulum curtails rather than reinforces the transients. Injecting the calcium buffer BAPTA made the Ca2+ transients more uniform in size and increased their times to peak and rates of recovery near the membrane. We have developed a computational model for the transients, which includes diffusion, uptake and Ca2+ extrusion. Good fits were obtained with a rather large apparent diffusion coefficient of about 90+/-20 microm2 s(-1). This may assist fast recovery by extrusion.

  3. 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.

  4. Double-helix stellarator

    Energy Technology Data Exchange (ETDEWEB)

    Moroz, P.E.

    1997-09-01

    A new stellarator configuration, the Double-Helix Stellarator (DHS), is introduced. This novel configuration features a double-helix center post as the only helical element of the stellarator coil system. The DHS configuration has many unique characteristics. One of them is the extreme low plasma aspect ratio, A {approx} 1--1.2. Other advantages include a high enclosed volume, appreciable rotational transform, and a possibility of extreme-high-{beta} MHD equilibria. Moreover, the DHS features improved transport characteristics caused by the absence of the magnetic field ripple on the outboard of the torus. Compactness, simplicity and modularity of the coil system add to the DHS advantages for fusion applications.

  5. Composición de ácidos grasos de los caracoles marinos Phyllonotus pomum y Chicoreus brevifrons (Gastropoda: Muricidae)

    OpenAIRE

    2009-01-01

    Se comparó el contenido de ácidos grasos en los lípidos totales de los caracoles Phyllonotus pomum y Chicoreus brevifrons, recolectados en tres diferentes épocas del año en Punta Arena, estado Sucre, Venezuela. Las concentraciones lipídicas oscilaron entre 0.87 y 1.85%, correspondiendo el valor mínimo y el máximo a C. brevifrons colectado en lluvia y sequía, respectivamente. La esterificación de los ácidos grasos presentes en estos lípidos seguida de la cromatografía de gases permitió la cara...

  6. 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.

  7. 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.

  8. Caracterización de la ovoposición del caracol Pomacea flagellata (Say, 1827 bajo condiciones experimentales

    Directory of Open Access Journals (Sweden)

    Alberto de Jesús-Navarrete

    2016-12-01

    Full Text Available Pomacea flagellata es un caracol conspicuo de zonas tropicales y subtropicales de América, que se ha consumido desde tiempos prehispánicos y actualmente es considerado sobreexplotado. Se realizó un experimento de cultivo de cuatro meses para determinar: la selección del substrato por la hembra, el tamaño de las huevas, el nivel del agua elegido para colocar la masa de huevos, el número de crías, y el tiempo de eclosión. Se utilizaron tres tinas de plástico que se llenaron con 100 L de agua, por duplicado y se colocaron tres sustratos: raíces de mangle, carrizo y tubo de PVC. Se registraron 57 huevas, 26 de ellas eclosionaron produciendo 5037 crías. Hubo más huevas en la “pared” de las tinas, donde se registraron 35 huevas, en raíces de mangle (18, en PVC 3 y en carrizo una hueva. Hubo diferencias significativas en la selección del sustrato, mientras que no se observaron diferencias significativas entre el número de huevas y las proporciones de sexos. La longitud promedio de la masa fue 32.99 ± 10.92, el ancho 16.44 ± 5.1 y grosor 8.08 ± 3.87 mm. La altura promedio de la puesta fue 15.66 ± 3.42 cm, con un tiempo medio de eclosión, de 13.30 ± 2.6 días, obteniéndose entre 94 a 301 crías por desove. Los caracoles utilizaron preferentemente las paredes de las tinas y es difícil determinar si no seleccionan sustrato para la puesta. El nivel del agua empleado es óptimo y permite que los organismos puedan colocar las masas de huevo, la producción de crías es adecuada y suficiente para iniciar programas de cultivo de producción de carne o de repoblación del medio natural.

  9. 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.

  10. Ion-mediated nucleic acid helix-helix interactions.

    Science.gov (United States)

    Tan, Zhi-Jie; Chen, Shi-Jie

    2006-07-15

    Salt ions are essential for the folding of nucleic acids. We use the tightly bound ion (TBI) model, which can account for the correlations and fluctuations for the ions bound to the nucleic acids, to investigate the electrostatic free-energy landscape for two parallel nucleic acid helices in the solution of added salt. The theory is based on realistic atomic structures of the helices. In monovalent salt, the helices are predicted to repel each other. For divalent salt, while the mean-field Poisson-Boltzmann theory predicts only the repulsion, the TBI theory predicts an effective attraction between the helices. The helices are predicted to be stabilized at an interhelix distance approximately 26-36 A, and the strength of the attractive force can reach -0.37 k(B)T/bp for helix length in the range of 9-12 bp. Both the stable helix-helix distance and the strength of the attraction are strongly dependent on the salt concentration and ion size. With the increase of the salt concentration, the helix-helix attraction becomes stronger and the most stable helix-helix separation distance becomes smaller. For divalent ions, at very high ion concentration, further addition of ions leads to the weakening of the attraction. Smaller ion size causes stronger helix-helix attraction and stabilizes the helices at a shorter distance. In addition, the TBI model shows that a decrease in the solvent dielectric constant would enhance the ion-mediated attraction. The theoretical findings from the TBI theory agree with the experimental measurements on the osmotic pressure of DNA array as well as the results from the computer simulations.

  11. La dinámica de la especulación bursátil: la formación de sociedades anónimas y el mineral de Caracoles, 1870-18781

    OpenAIRE

    2016-01-01

    El descubrimiento de Caracoles y la bonanza en Chile El dominio de las esferas mercantil y financiera sobre la actividad productiva (minera, agraria, artesanal o industrial) parece ser una constante en la historia colonial y republicana de Chile tanto como la orientación marcadamente exógena de su economía, sujeta, por ello mismo, a las vicisitudes del mercado mundial. El descubrimiento, en 1870, del mineral de Caracoles, entonces situado en territorio boliviano, sucedió cuando la economía ch...

  12. 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.

  13. Effects of the fruit essential oil of Cuminum cyminum Linn. (Apiaceae) on pentylenetetrazol-induced epileptiform activity in F1 neurones of Helix aspersa.

    Science.gov (United States)

    Janahmadi, Mahyar; Niazi, Farshad; Danyali, Samira; Kamalinejad, Mohammad

    2006-03-08

    The effect of the fruit essential oil of Cuminum cyminum Linn. (Apiaceae) (syn. Cuminum odorum Salisb) on the epileptiform activity induced by pentylenetetrazol (PTZ) was evaluated, using intracellular technique. The results demonstrated that extracellular application of the essential oil of Cuminum cyminum (1% and 3%) dramatically decreased the frequency of spontaneous activity induced by PTZ in a time and concentration dependent manner. In addition it showed protection against pentylenetetrazol-induced epileptic activity by increasing the duration, decreasing the amplitude of after hyperpolarization potential (AHP) following the action potential, the peak of action potential, and inhibition of the firing rate. These membrane effects suggest cellular mechanisms by which the essential oil of Cuminum cyminum can inhibit the PTZ-induced epileptic activity.

  14. 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.

  15. 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.

  16. The Caracol Disk of Chichén Itzá (929-932 CE. Some Throughts on Epigraphy and Iconography

    Directory of Open Access Journals (Sweden)

    Péter Bíró

    2016-06-01

    Full Text Available The sculpture referred to as the ‘Tenoned Disk’, which was recovered from the Caracol building at Chichén Itzá, is a monument decorated with a bass-relief carving displaying historical figures and accompanying hieroglyphic text that is located on the rim of the monument. This text makes reference to several persons named using a Maya Yucatec language. The date of 8 Ajaw is also recorded on the sculpture. For some unknown reason this monument has been overlooked by scholars who have sought to reconstruct the chronology of the site. Crucially, this monument records an important moment in the history of Chichén Itzá and of Yucatán in general: the arrival of the “Mexican-Toltec” people, and the re-foundation of the city under a new social construct that included foreigners and local nobility.

  17. 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.

  18. 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

  19. 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.

  20. Molecular structure of the collagen triple helix.

    Science.gov (United States)

    Brodsky, Barbara; Persikov, Anton V

    2005-01-01

    The molecular conformation of the collagen triple helix confers strict amino acid sequence constraints, requiring a (Gly-X-Y)(n) repeating pattern and a high content of imino acids. The increasing family of collagens and proteins with collagenous domains shows the collagen triple helix to be a basic motif adaptable to a range of proteins and functions. Its rodlike domain has the potential for various modes of self-association and the capacity to bind receptors, other proteins, GAGs, and nucleic acids. High-resolution crystal structures obtained for collagen model peptides confirm the supercoiled triple helix conformation, and provide new information on hydrogen bonding patterns, hydration, sidechain interactions, and ligand binding. For several peptides, the helix twist was found to be sequence dependent, and such variation in helix twist may serve as recognition features or to orient the triple helix for binding. Mutations in the collagen triple-helix domain lead to a variety of human disorders. The most common mutations are single-base substitutions that lead to the replacement of one Gly residue, breaking the Gly-X-Y repeating pattern. A single Gly substitution destabilizes the triple helix through a local disruption in hydrogen bonding and produces a discontinuity in the register of the helix. Molecular information about the collagen triple helix and the effect of mutations will lead to a better understanding of function and pathology.

  1. 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.

  2. 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...

  3. Thioamides in the collagen triple helix.

    Science.gov (United States)

    Newberry, Robert W; VanVeller, Brett; Raines, Ronald T

    2015-06-14

    To probe noncovalent interactions within the collagen triple helix, backbone amides were replaced with a thioamide isostere. This subtle substitution is the first in the collagen backbone that does not compromise thermostability. A triple helix with a thioamide as a hydrogen bond donor was found to be more stable than triple helices assembled from isomeric thiopeptides.

  4. 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...

  5. Kevlar: Transitioning Helix from Research to Practice

    Science.gov (United States)

    2015-04-01

    KEVLAR : TRANSITIONING HELIX FROM RESEARCH TO PRACTICE UNIVERSITY OF VIRGINIA APRIL 2015 FINAL TECHNICAL REPORT...DATES COVERED (From - To) FEB 2013 – NOV 2014 4. TITLE AND SUBTITLE KEVLAR : TRANSITIONING HELIX FROM RESEARCH TO PRACTICE 5a. CONTRACT NUMBER...possible exploitation. Our technology, called Kevlar , includes key security technologies are protective transformations and targeted recovery. The

  6. 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.

  7. Influencia de la cosmovisión del pueblo mixteco de Pinotepa de Don Luis, Oaxaca, México, en el uso y manejo del caracol púrpura, Plicopurpura pansa (Gould, 1853

    Directory of Open Access Journals (Sweden)

    Griselda Ma. Eugenia Hernández Rodríguez

    2009-01-01

    Full Text Available En la cosmovisión mesoamericana, la naturaleza, fuente de recursos para la subsistencia del ser humano, se considera como una entidad viva y sagrada. Esta concepción, aunada a la visión holística de la relación especie humanaambiente y al conocimiento sistemático del movimiento de los cuerpos estelares y del entorno inmediato, son el fundamento de las estrategias tradicionales de aprovechamiento y conservación de los recursos naturales. En este trabajo, el objetivo general fue el de identificar y analizar los fundamentos culturales que regulan el uso del tinte que produce el caracol púrpura Plicopurpura pansa, el cual ha sido utilizado, tradicionalmente, por los tintoreros de Pinotepa de don Luis para teñir el algodón de los textiles mixtecos. La investigación se basó en los procedimientos metodológicos de la Teoría Fundamentada. De esta forma, las concepciones cosmogónicas sobre los fenómenos y elementos que influyen en el uso del tinte que produce el caracol púrpura, resultaron el tema central. El análisis reflexivo de dicha categoría reveló que uno de los aspectos que destaca en el pensamiento mixteco es la persistencia de la concepción femenina del entorno. Específicamente, las concepciones sobre yoo (luna, ndikaandii (sol, Nduta ñuu ("la mar" y Dzavui (lluvia regulan el manejo del caracol púrpura.

  8. Primer registro del caracol manzano exótico Pomacea canaliculata (Gastropoda: Ampullariidae) en México, con comentarios sobre su propagación en el bajo río Colorado

    OpenAIRE

    Ernesto Campos; Gorgonio Ruiz-Campos; José Delgadillo

    2013-01-01

    Se registra por primera vez para México el caracol manzano Pomacea canaliculata (Lamarck, 1822). La especie fue descubierta en varias localidades vecinas a la presa derivadora Matamoros-1950, Algodones, Baja California. La propagación de P. canaliculata en aguas mexicanas fue a través de los afluentes del río Colorado de la población inicialmente introducida en las vecindades de Yuma, Arizona, EUA en el 2005. Hasta el momento no han sido detectados efectos dañinos sobre los cultivos agrícolas...

  9. 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...

  10. Rosalind Franklin and the Double Helix

    Science.gov (United States)

    Elkin, Lynne Osman

    2003-03-01

    Although she made essential contributions toward elucidating the structure of DNA, Rosalind Franklin is known to many only as seen through the distorting lens of James Watson's book, The Double Helix.

  11. The triple helix perspective of innovation systems

    NARCIS (Netherlands)

    Leydesdorff, L.; Zawdie, G.

    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, organisations and technological opportunities. Ho

  12. Radioimmunoassay in Ascidiella aspersa of a gonadoliberin (GnRH)-like factor with an apparent molecular weight higher than that of mammalian decapeptide

    Energy Technology Data Exchange (ETDEWEB)

    Dufour, S.; Monniot, F.; Monniot, C. and others

    1988-02-21

    A radioimmunoassay (RIA) for mammalian gonadoliberin (mGnRH) showed the presence of a GnRH-like factor in the neural complex of a Protochordate, Ascidiella aspersa (about 0.6 pg eq mGnRH/complex). The slope of the displacement curves was slightly lower than with mGnRH indicating antigene differences. No cross reactive material was found in mantle and siphonal area. The KD on Sephadex G25 was 0.45 versus 0.90 with mGnRH. That suggests that the molecular weight of the Ascidian GnRH-like factor is higher than that of known Vertebrate GnRH's, possibly due to a different processing of the precursor.

  13. 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.

  14. Challenges in Targeting a Basic Helix-Loop-Helix Transcription Factor with Hydrocarbon-Stapled Peptides

    NARCIS (Netherlands)

    Edwards, Amanda L; Meijer, Dimphna H; Guerra, Rachel M; Molenaar, Remco J; Alberta, John A; Bernal, Federico; Bird, Gregory H; Stiles, Charles D; Walensky, Loren D

    2016-01-01

    Basic helix-loop-helix (bHLH) transcription factors play critical roles in organism development and disease by regulating cell proliferation and differentiation. Transcriptional activity, whether by bHLH homo- or heterodimerization, is dependent on protein-protein and protein-DNA interactions mediat

  15. Biochemical analysis of the basic helix-loop-helix transcription factor Olig2

    NARCIS (Netherlands)

    Meijer, D.H.M.

    2014-01-01

    The basic helix-loop-helix (bHLH) transcription factors oligodendrocyte transcription factor 1 (Olig1) and Olig2 are structurally similar and, to a first approximation, coordinately expressed in the developing CNS and postnatal brain. Notwithstanding these similarities, it was apparent from early on

  16. The collagen triple-helix structure.

    Science.gov (United States)

    Brodsky, B; Ramshaw, J A

    1997-03-01

    Recent advances, principally through the study of peptide models, have led to an enhanced understanding of the structure and function of the collagen triple helix. In particular, the first crystal structure has clearly shown the highly ordered hydration network critical for stabilizing both the molecular conformation and the interactions between triple helices. The sequence dependent nature of the conformational features is also under active investigation by NMR and other techniques. The triple-helix motif has now been identified in proteins other than collagens, and it has been established as being important in many specific biological interactions as well as being a structural element. The nature of recognition and the degree of specificity for interactions involving triple helices may differ from globular proteins. Triple-helix binding domains consist of linear sequences along the helix, making them amenable to characterization by simple model peptides. The application of structural techniques to such model peptides can serve to clarify the interactions involved in triple-helix recognition and binding and can help explain the varying impact of different structural alterations found in mutant collagens in diseased states.

  17. Triple helix interactions for eco-innovation

    DEFF Research Database (Denmark)

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

    Authority with insights from consultants, universities and donnor agencies. The proximity of the science park to the canal, has hitherto not yielded with the creation of a “green cluster”, which could be a precedent to promote eco-innovations. These findings suggest that, Triple Helix interactions...... 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...... are not institutionalized but take place through adhoc projects. Further, science parks could become mediators in Triple Helix interactions between industry, universities and governments....

  18. Chirality-specific lift forces of helix under shear flows: Helix perpendicular to shear plane.

    Science.gov (United States)

    Zhang, Qi-Yi

    2017-02-01

    Chiral objects in shear flow experience a chirality-specific lift force. Shear flows past helices in a low Reynolds number regime were studied using slender-body theory. The chirality-specific lift forces in the vorticity direction experienced by helices are dominated by a set of helix geometry parameters: helix radius, pitch length, number of turns, and helix phase angle. Its analytical formula is given. The chirality-specific forces are the physical reasons for the chiral separation of helices in shear flow. Our results are well supported by the latest experimental observations.

  19. 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%.

  20. A triple helix-loop-helix/basic helix-loop-helix cascade controls cell elongation downstream of multiple hormonal and environmental signaling pathways in Arabidopsis.

    Science.gov (United States)

    Bai, Ming-Yi; Fan, Min; Oh, Eunkyoo; Wang, Zhi-Yong

    2012-12-01

    Environmental and endogenous signals, including light, temperature, brassinosteroid (BR), and gibberellin (GA), regulate cell elongation largely by influencing the expression of the paclobutrazol-resistant (PRE) family helix-loop-helix (HLH) factors, which promote cell elongation by interacting antagonistically with another HLH factor, IBH1. However, the molecular mechanism by which PREs and IBH1 regulate gene expression has remained unknown. Here, we show that IBH1 interacts with and inhibits a DNA binding basic helix-loop-helix (bHLH) protein, HBI1, in Arabidopsis thaliana. Overexpression of HBI1 increased hypocotyl and petiole elongation, whereas dominant inactivation of HBI1 and its homologs caused a dwarf phenotype, indicating that HBI1 is a positive regulator of cell elongation. In vitro and in vivo experiments showed that HBI1 directly bound to the promoters and activated two EXPANSIN genes encoding cell wall-loosening enzymes; HBI1's DNA binding and transcriptional activities were inhibited by IBH1, but the inhibitory effects of IBH1 were abolished by PRE1. The results indicate that PREs activate the DNA binding bHLH factor HBI1 by sequestering its inhibitor IBH1. Altering each of the three factors affected plant sensitivities to BR, GA, temperature, and light. Our study demonstrates that PREs, IBH1, and HBI1 form a chain of antagonistic switches that regulates cell elongation downstream of multiple external and endogenous signals.

  1. Molecular recognition in helix-loop-helix and helix-loop-helix-leucine zipper domains. Design of repertoires and selection of high affinity ligands for natural proteins.

    Science.gov (United States)

    Ciarapica, Roberta; Rosati, Jessica; Cesareni, Gianni; Nasi, Sergio

    2003-04-04

    Helix-loop-helix (HLH) and helix-loop-helix-leucine zipper (HLHZip) are dimerization domains that mediate selective pairing among members of a large transcription factor family involved in cell fate determination. To investigate the molecular rules underlying recognition specificity and to isolate molecules interfering with cell proliferation and differentiation control, we assembled two molecular repertoires obtained by directed randomization of the binding surface in these two domains. For this strategy we selected the Heb HLH and Max Zip regions as molecular scaffolds for the randomization process and displayed the two resulting molecular repertoires on lambda phage capsids. By affinity selection, many domains were isolated that bound to the proteins Mad, Rox, MyoD, and Id2 with different levels of affinity. Although several residues along an extended surface within each domain appeared to contribute to dimerization, some key residues critically involved in molecular recognition could be identified. Furthermore, a number of charged residues appeared to act as switch points facilitating partner exchange. By successfully selecting ligands for four of four HLH or HLHZip proteins, we have shown that the repertoires assembled are rather general and possibly contain elements that bind with sufficient affinity to any natural HLH or HLHZip molecule. Thus they represent a valuable source of ligands that could be used as reagents for molecular dissection of functional regulatory pathways.

  2. 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

  3. 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.

  4. 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

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

    OpenAIRE

    Carayannis, Elias G.; 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...

  6. FPGA helix tracking algorithm for PANDA

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-07-01

    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 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 algorithm for helix tracking reconstruction in the solenoidal field is shown. The tracking algorithm is composed by two parts, a road finding module followed by an iterative helix parameter calculation module. A performance study using C++ and the status of the VHDL implementation are presented.

  7. 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.

  8. 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.

  9. 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 ...

  10. Thermal stability of collagen triple helix.

    Science.gov (United States)

    Xu, Yujia

    2009-01-01

    Chief among the challenges of characterizing the thermal stability of the collagen triple helix are the lack of the reversibility of the thermal transition and the presence of multiple folding-unfolding steps during the thermal transition which rarely follows the simple two-state, all-or-none mechanism. Despite of the difficulties inherited in the quantitative depiction of the thermal transition of collagen, biophysical studies combined with proteolysis and mutagenesis approaches using full-chain collagens, short synthetic peptides, and recombinant collagen fragments have revealed molecular features of the thermal unfolding of the subdomains of collagen and led to a better understanding of the diverse biological functions of this versatile protein. The subdomain of collagen generally refers to a segment of the long, rope-like triple helical molecule that can unfold cooperatively as an independent unit whose properties (their size, location, and thermal stability) are considered essential for the molecular recognition during the self-assembly of collagen and during the interactions of collagen with other macromolecules. While the unfolding of segments of the triple helix at temperatures below the apparent melting temperature of the molecule has been used to interpret much of the features of the thermal unfolding of full-chain collagens, the thermal studies of short, synthetic peptides have firmly established the molecular basis of the subdomains by clearly demonstrating the close dependence of the thermal stability of a triple helix on the constituent amino acid residues at the X and the Y positions of the characteristic Gly-X-Y repeating sequence patterns of the triple helix. Studies using recombinant collagen fragments further revealed that in the context of the long, linear molecule, the stability of a segment of the triple helix is also modulated by long-range impact of the local interactions such as the interchain salt bridges. Together, the combined approaches

  11. 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

  12. Control of Collagen Triple Helix Stability by Phosphorylation.

    Science.gov (United States)

    Acevedo-Jake, Amanda M; Ngo, Daniel H; Hartgerink, Jeffrey D

    2017-03-10

    The phosphorylation of the collagen triple helix plays an important role in collagen synthesis, assembly, signaling, and immune response, although no reports detailing the effect this modification has on the structure and stability of the triple helix exist. Here we investigate the changes in stability and structure resulting from the phosphorylation of collagen. Additionally, the formation of pairwise interactions between phosphorylated residues and lysine is examined. In all tested cases, phosphorylation increases helix stability. When charged-pair interactions are possible, stabilization via phosphorylation can play a very large role, resulting inasmuch as a 13.0 °C increase in triple helix stability. Two-dimensional NMR and molecular modeling are used to study the local structure of the triple helix. Our results suggest a mechanism of action for phosphorylation in the regulation of collagen and also expand upon our understanding of pairwise amino acid stabilization of the collagen triple helix.

  13. 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.

  14. 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.

  15. 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.

  16. 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

  17. 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

  18. 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.

  19. Government and Governance of Regional Triple Helix Interactions

    Science.gov (United States)

    Danson, Mike; Todeva, Emanuela

    2016-01-01

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

  20. "Special Issue": Regional Dimensions of the Triple Helix Model

    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…

  1. 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…

  2. Time-programmed helix inversion in phototunable liquid crystals.

    Science.gov (United States)

    Asshoff, Sarah J; Iamsaard, Supitchaya; Bosco, Alessandro; Cornelissen, Jeroen J L M; Feringa, Ben L; Katsonis, Nathalie

    2013-05-14

    Doping cholesteric liquid crystals with photo-responsive molecules enables controlling the colour and polarisation of the light they reflect. However, accelerating the rate of relaxation of these photo-controllable liquid crystals remains challenging. Here we show that the relaxation rate of the cholesteric helix is fully determined by helix inversion of the molecular dopants.

  3. The Triple Helix of the Organizational Knowledge

    Directory of Open Access Journals (Sweden)

    Contantin BRĂTIANU

    2013-09-01

    Full Text Available 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 three different "elds: cognitiveknowledge, emotional knowledge and spiritual knowledge. These "elds are nonuniform,nonhomogeneous and they interact in a dynamic way. Cognitive "eld contains knowledgeabout what is, emotional "eld contains knowledge about how we feel, and the spiritual "eldcontains knowledge about people’s aspirations and life values. This new perspective opens anew opportunity in understanding the challenges for the 21st century management.

  4. 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.

  5. 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.

  6. Hexa Helix: Modified Quad Helix Appliance to Correct Anterior and Posterior Crossbites in Mixed Dentition

    Directory of Open Access Journals (Sweden)

    Syed Mohammed Yaseen

    2012-01-01

    Full Text Available Among the commonly encountered dental irregularities which constitute developing malocclusion is the crossbite. During primary and mixed dentition phase, the crossbite is seen very often and if left untreated during these phases then a simple problem may be transformed into a more complex problem. Different techniques have been used to correct anterior and posterior crossbites in mixed dentition. This case report describes the use of hexa helix, a modified version of quad helix for the management of anterior crossbite and bilateral posterior crossbite in early mixed dentition. Correction was achieved within 15 weeks with no damage to the tooth or the marginal periodontal tissue. The procedure is a simple and effective method for treating anterior and bilateral posterior crossbites simultaneously.

  7. 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.

  8. Mutations in TWIST, a basic helix-loop-helix transcription factor, in Saethre-Chotzen syndrome.

    Science.gov (United States)

    Howard, T D; Paznekas, W A; Green, E D; Chiang, L C; Ma, N; Ortiz de Luna, R I; Garcia Delgado, C; Gonzalez-Ramos, M; Kline, A D; Jabs, E W

    1997-01-01

    Saethre-Chotzen syndrome is one of the most common autosomal dominant disorders of craniosynostosis in humans and is characterized by craniofacial and limb anomalies. The locus for Saethre-Chotzen syndrome maps to chromosome 7p21-p22. We have evaluated TWIST, a basic helix-loop-helix transcription factor, as a candidate gene for this condition because its expression pattern and mutant phenotypes in Drosophila and mouse are consistent with the Saethre-Chotzen phenotype. We mapped TWIST to human chromosome 7p21-p22 and mutational analysis reveals nonsense, missense, insertion and deletion mutations in patients. These mutations occur within the basic DNA binding, helix I and loop domains, or result in premature termination of the protein. Studies in Drosophila indicate that twist may affect the transcription of fibroblast growth factor receptors (FGFRs), another gene family implicated in human craniosynostosis. The emerging cascade of molecular components involved in craniofacial and limb development now includes TWIST, which may function as an upstream regulator of FGFRs.

  9. Can synergy in Triple Helix relations be quantified? A review of the development of the Triple Helix indicator

    NARCIS (Netherlands)

    Leydesdorff, L.; Park, H.W.

    2014-01-01

    Triple Helix arrangements of bi- and trilateral relations can be considered as adaptive ecosystems. During the last decade, we have further developed a Triple Helix indicator of synergy as reduction of uncertainty in niches that can be shaped among three or more sets of relations. Reduction of uncer

  10. Electrostatic free energy landscapes for nucleic acid helix assembly

    OpenAIRE

    Tan, Zhi-Jie; Chen, Shi-Jie

    2006-01-01

    Metal ions are crucial for nucleic acid folding. From the free energy landscapes, we investigate the detailed mechanism for ion-induced collapse for a paradigm system: loop-tethered short DNA helices. We find that Na + and Mg2+ play distinctive roles in helix–helix assembly. High [Na+] (>0.3 M) causes a reduced helix–helix electrostatic repulsion and a subsequent disordered packing of helices. In contrast, Mg2+ of concentration >1 mM is predicted to induce helix–helix attraction and results i...

  11. Concentration-temperature superposition of helix folding rates in gelatin.

    Science.gov (United States)

    Gornall, J L; Terentjev, E M

    2007-07-13

    Using optical rotation as the primary technique, we have characterized the kinetics of helix renaturation in water solutions of gelatin. By covering a wide range of solution concentrations we identify a universal exponential dependence of folding rate on concentration and quench temperature. We demonstrate a new concentration-temperature superposition of data at all temperatures and concentrations, and build the corresponding master curve. The normalized rate constant is consistent with helix lengthening. Nucleation of the triple helix occurs rapidly and contributes less to the helical onset than previously thought.

  12. Silver conical helix broadband plasmonic nanoantenna

    Science.gov (United States)

    Sobhkhiz, Nader; Moshaii, Ahmad

    2014-01-01

    The discrete dipole approximation method is used to investigate the optical extinction spectra and the electric field enhancement of Ag conical helix (CH) nanostructures. Based on an expected similarity between the radio frequency response of the antenna with the infrared and the visible response of the nanoantenna, the Ag CH nanostructures were designed as a broadband nanoantenna. It is shown that with engineering the structure parameters of the CH nanostructure the plasmonic response of the nanostructure can be designed for a desirable application. In addition, the change of the substrate material for the nanohelix growth is shown to have infinitesimal effect on the resonance peaks of the conical nanohelix. However, varying the surrounding medium can lead to considerable red-shifting of the plasmonic resonance peaks (up to 230 nm). Calculations of the near field around the helical nanoantenna show that the smaller and the larger sides of the CH are related to the plasmonic resonance peaks at low and high wavelengths, respectively. The calculation result for the extinction spectrum has also been compared with similar experimental data for a 2-pitch Ag conical nanohelix and a relatively good agreement between the numerical calculation and the experiment has been obtained.

  13. 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...

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

    Directory of Open Access Journals (Sweden)

    Domínguez-Ojeda, Delia

    2009-02-01

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

  15. Structural alignment of RNA with triple helix structure.

    Science.gov (United States)

    Wong, Thomas K F; Yiu, S M

    2012-04-01

    Structural alignment is useful in identifying members of ncRNAs. Existing tools are all based on the secondary structures of the molecules. There is evidence showing that tertiary interactions (the interaction between a single-stranded nucleotide and a base-pair) in triple helix structures are critical in some functions of ncRNAs. In this article, we address the problem of structural alignment of RNAs with the triple helix. We provide a formal definition to capture a simplified model of a triple helix structure, then develop an algorithm of O(mn(3)) time to align a query sequence (of length m) with known triple helix structure with a target sequence (of length n) with an unknown structure. The resulting algorithm is shown to be useful in identifying ncRNA members in a simulated genome.

  16. 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.

  17. The Triple Helix of University-Industry-Government Relations

    OpenAIRE

    Leydesdorff, Loet

    2012-01-01

    Etzkowitz & Leydesdorff (2000) further elaborated the Triple Helix of University-Industry-Government Relations (cf. Etzkowitz & Leydesdorff, 1995; Lowe, 1982) into a model for studying knowledge-based economies. A series of workshops, conferences, and special issues of journals have developed under this title since 1996. In various countries, the Triple Helix concept has also been used as an operational strategy for regional development and to further the knowledge-based economy. This short r...

  18. 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.

  19. Saúde infantil em áreas pobres: resultados de um estudo de base populacional nos municípios de Caracol, Piauí, e Garrafão do Norte, Pará, Brasil Child health in poor areas: findings from a population-based study in Caracol, Piauí, and Garrafão do Norte, Pará, Brazil

    Directory of Open Access Journals (Sweden)

    Juraci A. Cesar

    2009-04-01

    Full Text Available Este estudo teve por objetivo conhecer indicadores básicos de saúde infantil nos municípios de Caracol, Piauí, e Garrafão do Norte, Pará, Brasil. Mediante visitas domiciliares por amostragem sistemática, aplicaram-se questionários às mães de menores de cinco anos, investigando nível sócio-econômico, condições de habitação e saneamento da família, características demográficas, padrão de morbidade, de utilização de serviços de saúde e de assistência recebida durante a gestação e o parto. A análise consistiu da comparação de indicadores entre os dois municípios e foi avaliada através dos testes t e qui-quadrado. Das 1.728 crianças estudadas, 60% de suas famílias possuíam renda inferior a um salário mínimo mensal; 41% não contavam com qualquer tipo de sanitário; 10% de suas mães não realizaram uma única consulta de pré-natal; 30% nasceram no domicilio; 30% foram levadas à consulta médica nos últimos três meses; 20% apresentavam déficit > 2 desvios-padrão para o indicador altura/idade. Todos os indicadores estudados foram ruins em ambos os municípios, sobretudo em Garrafão do Norte. Aumentar a oferta de cuidados em saúde e melhorar as condições de habitação e saneamento deveriam ser prioridades nessas localidades.The aim of this study was to evaluate child health indicators in the municipalities (counties of Caracol, Piauí State, and Garrafão do Norte, Pará State, Brazil. Through household visits using systematic sampling, previously trained interviewers applied a standard questionnaire to mothers of under-five children, investigating socioeconomic status, housing and environmental sanitation, demographic characteristics, disease patterns, and prenatal and childbirth care. The analysis used the t-test and chi-square test to compare indicators between the two municipalities. Of the 1,728 children studied, 60% were from families with incomes less than one monthly minimum wage (approximately U

  20. A directional nucleation-zipping mechanism for triple helix formation.

    Science.gov (United States)

    Alberti, Patrizia; Arimondo, Paola B; Mergny, Jean-Louis; Garestier, Thérèse; Hélène, Claude; Sun, Jian-Sheng

    2002-12-15

    A detailed kinetic study of triple helix formation was performed by surface plasmon resonance. Three systems were investigated involving 15mer pyrimidine oligonucleotides as third strands. Rate constants and activation energies were validated by comparison with thermodynamic values calculated from UV-melting analysis. Replacement of a T.A base pair by a C.G pair at either the 5' or the 3' end of the target sequence allowed us to assess mismatch effects and to delineate the mechanism of triple helix formation. Our data show that the association rate constant is governed by the sequence of base triplets on the 5' side of the triplex (referred to as the 5' side of the target oligopurine strand) and provides evidence that the reaction pathway for triple helix formation in the pyrimidine motif proceeds from the 5' end to the 3' end of the triplex according to the nucleation-zipping model. It seems that this is a general feature for all triple helices formation, probably due to the right-handedness of the DNA double helix that provides a stronger base stacking at the 5' than at the 3' duplex-triplex junction. Understanding the mechanism of triple helix formation is not only of fundamental interest, but may also help in designing better triple helix-forming oligonucleotides for gene targeting and control of gene expression.

  1. Hydroxyproline Ring Pucker Causes Frustration of Helix Parameters in the Collagen Triple Helix.

    Science.gov (United States)

    Chow, W Ying; Bihan, Dominique; Forman, Chris J; Slatter, David A; Reid, David G; Wales, David J; Farndale, Richard W; Duer, Melinda J

    2015-07-29

    Collagens, the most abundant proteins in mammals, are defined by their triple-helical structures and distinctive Gly-Xaa-Yaa repeating sequence, where Xaa is often proline and Yaa, hydroxyproline (Hyp/O). It is known that hydroxyproline in the Yaa position stabilises the triple helix, and that lack of proline hydroxylation in vivo leads to dysfunctional collagen extracellular matrix assembly, due to a range of factors such as a change in hydration properties. In addition, we note that in model peptides, when Yaa is unmodified proline, the Xaa proline has a strong propensity to adopt an endo ring conformation, whilst when Yaa is hydroxyproline, the Xaa proline adopts a range of endo and exo conformations. Here we use a combination of solid-state NMR spectroscopy and potential energy landscape modelling of synthetic triple-helical collagen peptides to understand this effect. We show that hydroxylation of the Yaa proline causes the Xaa proline ring conformation to become metastable, which in turn confers flexibility on the triple helix.

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

    Science.gov (United States)

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

    2010-04-01

    Common ivy (Hedera helix subsp. helix) is a well-known native and ornamental plant in Europe. Reports on contact dermatitis from ivy have regularly appeared since 1899. Recently, it has been suggested that allergic contact dermatitis from the plant may be under-diagnosed, partly due to lack of commercial patch test allergens. The objective of the article is to present the results of aimed patch testing with the main common ivy allergen, falcarinol, during a 16-year period and review the newer literature. Consecutive patients tested with falcarinol 0.03% petrolatum from May 1993 to May 2009 were included. Cases published since 1987 were retrieved from the PubMed database. One hundred and twenty-seven Danish patients were tested with falcarinol and 10 (7.9%) tested positive. Seven were occupationally sensitized. Between 1994 and 2009, 28 new cases of contact dermatitis from ivy were reported, 2 of which were occupational. Only 11 of the 28 patients were tested with pure allergens. Falcarinol is not only widely distributed in the ivy family, but also in the closely related Apiaceae. Sensitization may occur in childhood or in adults pruning ivy plants or handling them in an occupational setting. In view of the ubiquity of falcarinol-containing plants and the relatively high prevalence of positive reactions in aimed patch testing, falcarinol should be the next plant allergen to be commercially available and included in the plant series worldwide.

  3. Challenges in Targeting a Basic Helix-Loop-Helix Transcription Factor with Hydrocarbon-Stapled Peptides.

    Science.gov (United States)

    Edwards, Amanda L; Meijer, Dimphna H; Guerra, Rachel M; Molenaar, Remco J; Alberta, John A; Bernal, Federico; Bird, Gregory H; Stiles, Charles D; Walensky, Loren D

    2016-11-18

    Basic helix-loop-helix (bHLH) transcription factors play critical roles in organism development and disease by regulating cell proliferation and differentiation. Transcriptional activity, whether by bHLH homo- or heterodimerization, is dependent on protein-protein and protein-DNA interactions mediated by α-helices. Thus, α-helical decoys have been proposed as potential targeted therapies for pathologic bHLH transcription. Here, we developed a library of stabilized α-helices of OLIG2 (SAH-OLIG2) to test the capacity of hydrocarbon-stapled peptides to disrupt OLIG2 homodimerization, which drives the development and chemoresistance of glioblastoma multiforme, one of the deadliest forms of human brain cancer. Although stapling successfully reinforced the α-helical structure of bHLH constructs of varying length, sequence-specific dissociation of OLIG2 dimers from DNA was not achieved. Re-evaluation of the binding determinants for OLIG2 self-association and stability revealed an unanticipated role of the C-terminal domain. These data highlight potential pitfalls in peptide-based targeting of bHLH transcription factors given the liabilities of their positively charged amino acid sequences and multifactorial binding determinants.

  4. Hydroxyproline Ring Pucker Causes Frustration of Helix Parameters in the Collagen Triple Helix

    Science.gov (United States)

    Ying Chow, W.; Bihan, Dominique; Forman, Chris J.; Slatter, David A.; Reid, David G.; Wales, David J.; Farndale, Richard W.; Duer, Melinda J.

    2015-07-01

    Collagens, the most abundant proteins in mammals, are defined by their triple-helical structures and distinctive Gly-Xaa-Yaa repeating sequence, where Xaa is often proline and Yaa, hydroxyproline (Hyp/O). It is known that hydroxyproline in the Yaa position stabilises the triple helix, and that lack of proline hydroxylation in vivo leads to dysfunctional collagen extracellular matrix assembly, due to a range of factors such as a change in hydration properties. In addition, we note that in model peptides, when Yaa is unmodified proline, the Xaa proline has a strong propensity to adopt an endo ring conformation, whilst when Yaa is hydroxyproline, the Xaa proline adopts a range of endo and exo conformations. Here we use a combination of solid-state NMR spectroscopy and potential energy landscape modelling of synthetic triple-helical collagen peptides to understand this effect. We show that hydroxylation of the Yaa proline causes the Xaa proline ring conformation to become metastable, which in turn confers flexibility on the triple helix.

  5. 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.

  6. 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.

  7. Polyproline and triple helix motifs in host-pathogen recognition.

    Science.gov (United States)

    Berisio, Rita; Vitagliano, Luigi

    2012-12-01

    Secondary structure elements often mediate protein-protein interactions. Despite their low abundance in folded proteins, polyproline II (PPII) and its variant, the triple helix, are frequently involved in protein-protein interactions, likely due to their peculiar propensity to be solvent-exposed. We here review the role of PPII and triple helix in mediating hostpathogen interactions, with a particular emphasis to the structural aspects of these processes. After a brief description of the basic structural features of these elements, examples of host-pathogen interactions involving these motifs are illustrated. Literature data suggest that the role played by PPII motif in these processes is twofold. Indeed, PPII regions may directly mediate interactions between proteins of the host and the pathogen. Alternatively, PPII may act as structural spacers needed for the correct positioning of the elements needed for adhesion and infectivity. Recent investigations have highlighted that collagen triple helix is also a common target for bacterial adhesins. Although structural data on complexes between adhesins and collagen models are rather limited, experimental and theoretical studies have unveiled some interesting clues of the recognition process. Interestingly, very recent data show that not only is the triple helix used by pathogens as a target in the host-pathogen interaction but it may also act as a bait in these processes since bacterial proteins containing triple helix regions have been shown to interact with host proteins. As both PPII and triple helix expose several main chain non-satisfied hydrogen bond acceptors and donors, both elements are highly solvated. The preservation of the solvation state of both PPII and triple helix upon protein-protein interaction is an emerging aspect that will be here thoroughly discussed.

  8. 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.

  9. 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.

  10. 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.

  11. 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

  12. 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.

  13. Stabilization of magnetic helix in exchange-coupled thin films.

    Science.gov (United States)

    Dzemiantsova, L V; Meier, G; Röhlsberger, R

    2015-11-05

    Based on micromagnetic simulations, we report on a novel magnetic helix in a soft magnetic film that is sandwiched between and exchange-coupled to two hard magnetic layers with different anisotropies. We show that such a confined helix stays stable without the presence of an external magnetic field. The magnetic stability is determined by the energy minimization and is a result of an internal magnetic field created by the exchange interaction. We show that this internal field stores a magnetic energy density of a few kJ/m(3). We also find that it dramatically modifies ferromagnetic resonances, such that the helix can be used as a ferromagnetic resonance filter and a fast acting attenuator.

  14. Universal kinetics of helix-coil transition in gelatin.

    Science.gov (United States)

    Gornall, J L; Terentjev, E M

    2008-03-01

    By covering a much wider concentration range than previous studies we find a very unusual exponential dependence of the rate of helix formation on concentration of gelatin in water and ethylene glycol solutions. By applying a procedure of concentration-temperature superposition we build a master curve describing the initial renaturation rates in both solvents. The growth of the normalized helical fraction chi(t) is a first-order process, with a rate constant consistent with cis-trans isomerization, in most situations. We propose that association of three separate chains to form a triple helical nucleus occurs rapidly and contributes less to the helical onset than previously thought. The measured helix content is a result of lengthening of the triple helix after nucleation, by zipping from the associated nuclei.

  15. 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

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

    Science.gov (United States)

    Rainey, Jan K; Goh, M Cynthia

    2002-11-01

    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, no high-resolution structure of any entire protein is yet available. Given the drastic morphological differences in self-assembled collagen structures with subtle changes in assembly conditions, a detailed knowledge of the relative locations of charged and sterically bulky residues in collagen is desirable. Its repetitive primary sequence and highly conserved secondary structure make collagen, and the triple-helix in general, an ideal candidate for a general parameterization for prediction of residue locations and for the use of a helical wheel in the prediction of residue orientation. Herein, a statistical analysis of the currently available high-resolution X-ray crystal structures of model triple-helical peptides is performed to produce an experimentally based parameter set for predicting peptide backbone and C(beta) atom locations for the triple-helix. Unlike existing homology models, this allows easy prediction of an entire triple-helix structure based on all existing high-resolution triple-helix structures, rather than only on a single structure or on idealized parameters. Furthermore, regional differences based on the helical propensity of residues may be readily incorporated. The parameter set is validated in terms of the predicted bond lengths, backbone dihedral angles, and interchain hydrogen bonding.

  17. 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...

  18. Solution structure of the ETS domain from murine Ets-1: a winged helix-turn-helix DNA binding motif.

    OpenAIRE

    Donaldson, L W; Petersen, J.M.; Graves, B J; McIntosh, L. P.

    1996-01-01

    Ets-1 is the prototypic member of the ets family of transcription factors. This family is characterized by the conserved ETS domain that mediates specific DNA binding. Using NMR methods, we have determined the structure of a fragment of murine Ets-1 composed of the 85 residue ETS domain and a 25 amino acid extension that ends at its native C-terminus. The ETS domain folds into a helix-turn-helix motif on a four-stranded anti-parallel beta-sheet scaffold. This structure places Ets-1 in the win...

  19. Type VIa β-turn-fused helix N-termini: A novel helix N-cap motif containing cis proline.

    Science.gov (United States)

    Dasgupta, Rubin; Ganguly, Himal K; Modugula, E K; Basu, Gautam

    2017-01-01

    Helix N-capping motifs often form hydrogen bonds with terminal amide groups which otherwise would be free. Also, without an amide hydrogen, proline (trans) is over-represented at helix N-termini (N1 position) because this naturally removes the need to hydrogen bond one terminal amide. However, the preference of cisPro, vis-à-vis helix N-termini, is not known. We show that cisPro (αR or PPII ) often appears at the N-cap position (N0) of helices. The N-cap cisPro(αR ) is associated with a six-residue sequence motif - X(-2) -X(-1) -cisPro-X(1) -X(2) -X(3) - with preference for Glu/Gln at X(-1) , Phe/Tyr/Trp at X(1) and Ser/Thr at X(3) . The motif, formed by the fusion of a helix and a type VIa β-turn, contains a hydrogen bond between the side chain of X(-1) and the side chain/backbone of X(3) , a α-helical hydrogen bond between X(-2) and X(2) and stacking interaction between cisPro and an aromatic residue at X(1) . NMR experiments on peptides containing the motif and its variants showed that local interactions associated with the motif, as found in folded proteins, were not enough to significantly tilt the cis/trans equilibrium towards cisPro. This suggests that some other evolutionary pressure must select the cisPro motif (over transPro) at helix N-termini. Database analysis showed that >C = O of the pre-cisPro(αR ) residue at the helix N-cap, directed opposite to the N→C helical axis, participates in long-range interactions. We hypothesize that the cisPro(αR ) motif is preferred at helix N-termini because it allows the helix to participate in long-range interactions that may be structurally and functionally important.

  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. Organizing product innovation: hierarchy, market or triple-helix networks?

    Science.gov (United States)

    Fitjar, Rune Dahl; Gjelsvik, Martin; Rodríguez-Pose, Andrés

    This paper assesses the extent to which the organization of the innovation effort in firms, as well as the geographical scale at which this effort is pursued, affects the capacity to benefit from product innovations. Three alternative modes of organization are studied: hierarchy, market and triple-helix-type networks. Furthermore, we consider triple-helix networks at three geographical scales: local, national and international. These relationships are tested on a random sample of 763 firms located in five urban regions of Norway which reported having introduced new products or services during the preceding 3 years. The analysis shows that firms exploiting internal hierarchy or triple-helix networks with a wide range of partners managed to derive a significantly higher share of their income from new products, compared to those that mainly relied on outsourcing within the market. In addition, the analysis shows that the geographical scale of cooperation in networks, as well as the type of partner used, matters for the capacity of firms to benefit from product innovation. In particular, firms that collaborate in international triple-helix-type networks involving suppliers, customers and R&D institutions extract a higher share of their income from product innovations, regardless of whether they organize the processes internally or through the network.

  2. Spontaneous Helix Hand Reversal and Tendril Perversion in Climbing Plants

    Science.gov (United States)

    Goriely, Alain; Tabor, Michael

    1998-02-01

    The helix hand reversal exhibited by the tendrils of climbing plants when attached to a support is investigated. Modeled as a thin elastic rod with intrinsic curvature, a linear and nonlinear stability analysis shows the problem to be a paradigm for curvature induced morphogenesis in which symmetry breaking is constrained by a global invariant.

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

    NARCIS (Netherlands)

    Leydesdorff, L.; Meyer, M.

    2010-01-01

    The Triple Helix model of university-industry-government relations can be generalized from a neo-institutional model of networks of relations to a neo-evolutionary model of how three selection environments operate upon one another. Two selection mechanisms operating upon each other can mutually shap

  4. Collagen model peptides: Sequence dependence of triple-helix stability.

    Science.gov (United States)

    Persikov, A V; Ramshaw, J A; Brodsky, B

    2000-01-01

    The triple helix is a specialized protein motif, found in all collagens as well as in noncollagenous proteins involved in host defense. Peptides will adopt a triple-helical conformation if the sequence contains its characteristic features of Gly as every third residue and a high content of Pro and Hyp residues. Such model peptides have proved amenable to structural studies by x-ray crystallography and NMR spectroscopy, suitable for thermodynamic and kinetic analysis, and a valuable tool in characterizing the binding activities of the collagen triple helix. A systematic approach to understanding the amino acid sequence dependence of the collagen triple helix has been initiated, based on a set of host-guest peptides of the form, (Gly-Pro-Hyp)(3)-Gly-X-Y-(Gly-Pro-Hyp)(4). Comparison of their thermal stabilities has led to a propensity scale for the X and Y positions, and the additivity of contributions of individual residues is now under investigation. The local and global stability of the collagen triple helix is normally modulated by the residues in the X and Y positions, with every third position occupied by Gly in fibril-forming collagens. However, in collagen diseases, such as osteogenesis imperfecta, a single Gly may be substituted by another residue. Host-guest studies where the Gly is replaced by various amino acids suggest that the identity of the residue in the Gly position affects the degree of destabilization and the clinical severity of the disease.

  5. 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.

  6. Surface simulation synthesis: a new strategy to spy alpha-helix structure.

    Science.gov (United States)

    Dong, Xiao-Nan; Chen, Yu; Chen, Ying-Hua

    2007-09-04

    In key proteins, there are always some alpha-helix structures, which play important role in the structure and functions. Many epitopes lie on the surface of alpha-helix. These epitopes are not easy to be recruited into the vaccine development, because they are conformation dependent epitopes. Can such epitopes on alpha-helix be mimicked synthetically? Our findings undoubtedly validate the feasibility of surface simulation synthesis with short linear peptide to mimic the antigenic side of alpha-helix structure.

  7. Iron-binding E3 ligase mediates iron response in plants by targeting basic helix-loop-helix transcription factors.

    Science.gov (United States)

    Selote, Devarshi; Samira, Rozalynne; Matthiadis, Anna; Gillikin, Jeffrey W; Long, Terri A

    2015-01-01

    Iron uptake and metabolism are tightly regulated in both plants and animals. In Arabidopsis (Arabidopsis thaliana), BRUTUS (BTS), which contains three hemerythrin (HHE) domains and a Really Interesting New Gene (RING) domain, interacts with basic helix-loop-helix transcription factors that are capable of forming heterodimers with POPEYE (PYE), a positive regulator of the iron deficiency response. BTS has been shown to have E3 ligase capacity and to play a role in root growth, rhizosphere acidification, and iron reductase activity in response to iron deprivation. To further characterize the function of this protein, we examined the expression pattern of recombinant ProBTS::β-GLUCURONIDASE and found that it is expressed in developing embryos and other reproductive tissues, corresponding with its apparent role in reproductive growth and development. Our findings also indicate that the interactions between BTS and PYE-like (PYEL) basic helix-loop-helix transcription factors occur within the nucleus and are dependent on the presence of the RING domain. We provide evidence that BTS facilitates 26S proteasome-mediated degradation of PYEL proteins in the absence of iron. We also determined that, upon binding iron at the HHE domains, BTS is destabilized and that this destabilization relies on specific residues within the HHE domains. This study reveals an important and unique mechanism for plant iron homeostasis whereby an E3 ubiquitin ligase may posttranslationally control components of the transcriptional regulatory network involved in the iron deficiency response.

  8. 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

  9. 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.

  10. Helix-helix interconversion rates of short 13C-labeled helical peptides as measured by dynamic NMR spectroscopy.

    Science.gov (United States)

    Kubasik, Matthew; Kotz, James; Szabo, Christopher; Furlong, Theresa; Stace, Justin

    2005-06-05

    The rates at which a peptide hexamer and a peptide octamer interconvert between left- and right-handed helical forms in CD2Cl2 solution have been characterized by 13C dynamic NMR (DNMR) spectroscopy. The peptide esters studied are Fmoc-(Aib)n-OtBu (n = 6 and 8), where Fmoc is 9-fluorenylmethyoxycarbonyl and Aib is the strongly helix-forming residue alpha-aminoisobutyric acid. Because the Aib residue is itself achiral, homooligomers of this residue form a 50/50 mixture of enantiomeric 3(10)-helices in solution. It has been demonstrated (R.-P. Hummel, C. Toniolo, and G. Jung, Angewandte Chemie International Edition, 1987, Vol. 26, pp. 1150-1152) that oligomers of Aib interconvert on the millisecond timescale. We have performed lineshape analysis of 13C-NMR spectra collected for our peptides enriched with 13C at a single residue. Rate constants for the octamer range from 6 s(-1) at 196 K to about 56,500 s(-1) at 320 K. At all temperatures, the hexamer interconverts about three times faster than the octamer. Eyring plots of the data reveal experimentally indistinguishable DeltaH++ values for the hexamer and octamer of 37.8 +/- 0.6 and 37.6 +/- 0.4 kJ mol(-1) respectively. The difference in the rates of interconversion is dictated by entropic factors. The hexamer and octamer exhibit negative DeltaS++ values of -29.0(-1) +/- 2.5 and -37.3 +/- 1.7 J K(-1) mol(-1), respectively. A mechanism for the helix-helix interconversion is proposed. and calculated DeltaG++ values are compared to the estimate for a decamer undergoing a helix-helix interconversion.

  11. Playing with peptides: how to build a supramolecular peptide nanostructure by exploiting helix···helix macrodipole interactions.

    Science.gov (United States)

    Gatto, E; Porchetta, A; Scarselli, M; De Crescenzi, M; Formaggio, F; Toniolo, C; Venanzi, M

    2012-02-07

    A novel method to build bicomponent peptide self-assembled monolayers (SAMs) has been developed, by exploiting helix···helix macrodipole interactions. In this work, a peptide-based self-assembled monolayer composed of two helical peptides was immobilized on a gold surface. Specifically, a pyrene-containing octapeptide, devoid of any sulfur atom (A8Pyr), and a hexapeptide, functionalized at the N-terminus with (S,R) lipoic acid, for binding to gold substrates (SSA4WA) via a Au-S linkage, have been employed. Both peptides investigated attain a helical structure, because they are almost exclusively formed by strongly folding inducer C(α)-tetrasubstituted α-amino acids. We demonstrate that the two peptides generate a stable supramolecular nanostructure (a densely packed bicomponent peptide monolayer), where A8Pyr is incorporated into the SSA4WA palisade by exploiting helix···helix macrodipole interactions. The presence of both peptides on the gold surface was investigated by spectroscopic and electrochemical techniques, while the morphology of the monolayer was analyzed by ultra high-vacuum scanning tunnelling microscopy. The composition of the bicomponent SAM on the surface was studied by a combination of electrochemical and spectroscopic techniques. In particular, the amount of Au-S linkages from the sulfur-containing peptides was quantified from reductive desorption of the peptide-based SAM, while the amount of A8Pyr was estimated by fluorescence spectroscopy. The antiparallel orientation of the A8Pyr and SSA4WA peptide chains minimizes the interaction energy between the helix dipoles, suggesting that this kind of electrostatic phenomenon is the driving force that stabilizes the bicomponent SAM.

  12. 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

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

    Science.gov (United States)

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

    2016-04-11

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

  14. Crowding effect on helix-coil transition: Beyond entropic stabilization

    Energy Technology Data Exchange (ETDEWEB)

    Koutsioubas, A.; Lairez, D.; Combet, S.; Longeville, S. [Laboratoire Leon Brillouin, CEA/CNRS UMR 12, CEA-Saclay, 91191 Gif-sur-Yvette Cedex (France); Fadda, G. C. [Laboratoire Leon Brillouin, CEA/CNRS UMR 12, CEA-Saclay, 91191 Gif-sur-Yvette Cedex (France); Universite Paris 13, UFR SMBH, 93017 Bobigny (France); Zalczer, G. [Service de Physique de l' Etat Condense, CEA-Saclay, 91191 Gif-sur-Yvette Cedex (France)

    2012-06-07

    We report circular dichroism measurements on the helix-coil transition of poly(L-glutamic acid) in solution with polyethylene glycol (PEG) as a crowding agent. The PEG solutions have been characterized by small angle neutron scattering and are well described by the picture of a network of mesh size {xi}, usual for semi-dilute chains in good solvent. We show that the increase of PEG concentration stabilizes the helices and increases the transition temperature. But more unexpectedly, we also notice that the increase of concentration of crowding agent reduces the mean helix extent at the transition, or in other words reduces its cooperativity. This result cannot be taken into account for by an entropic stabilization mechanism. Comparing the mean length of helices at the transition and the mesh size of the PEG network, our results strongly suggest two regimes: helices shorter or longer than the mesh size.

  15. Rational design of a triple helix-specific intercalating ligand.

    Science.gov (United States)

    Escudé, C; Nguyen, C H; Kukreti, S; Janin, Y; Sun, J S; Bisagni, E; Garestier, T; Hélène, C

    1998-03-31

    DNA triple helices offer new perspectives toward oligonucleotide-directed gene regulation. 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. Molecular modeling and thermal denaturation experiments suggest that benzo[f]pyrido[3, 4-b]quinoxaline derivatives intercalate into triple helices by stacking preferentially with the Hoogsteen-paired bases. Based on this model, it was predicted that a benzo[f]quino[3,4-b]quinoxaline derivative, which possesses an additional aromatic ring, could engage additional stacking interactions with the pyrimidine strand of the Watson-Crick double helix upon binding of this pentacyclic ligand to a triplex structure. This compound was synthesized. Thermal denaturation experiments and inhibition of restriction enzyme cleavage show that this new compound can indeed stabilize triple helices with great efficiency and specificity and/or induce triple helix formation under physiological conditions.

  16. Design and synthesis of DNA four-helix bundles

    Energy Technology Data Exchange (ETDEWEB)

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

    2011-06-10

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

  17. Soliton solutions for Davydov solitons in α-helix proteins

    Science.gov (United States)

    Taghizadeh, N.; Zhou, Qin; Ekici, M.; Mirzazadeh, M.

    2017-02-01

    The propagation equation for describing Davydov solitons in α-helix proteins has been investigated analytically. There are seven integration tools to extract analytical soliton solutions. They are the Ricatti equation expansion approach, ansatz scheme, improved extended tanh-equation method, the extend exp(-Ψ(τ)) -expansion method, the extended Jacobi elliptic function expansion method, the extended trial equation method and the extended G ' / G - expansion method.

  18. AND BUSINESS INCUBATORS INTO THE TRIPLE HELIX CONCEPT

    Directory of Open Access Journals (Sweden)

    Sizova, Y.S.

    2016-04-01

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

  19. 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.

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

    Science.gov (United States)

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

    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.

  1. Classical scattering of charged particles confined on an inhomogeneous helix

    CERN Document Server

    Zampetaki, A V; Krönke, S; Schmelcher, P

    2013-01-01

    We explore the effects arising due to the coupling of the center of mass and relative motion of two charged particles confined on an inhomogeneous helix with a locally modified radius. It is first proven that a separation of the center of mass and the relative motion is provided if and only if the confining manifold represents a homogeneous helix. In this case bound states of repulsively Coulomb interacting particles occur. For an inhomogeneous helix, the coupling of the center of mass and relative motion induces an energy transfer between the collective and relative motion, leading to dissociation of initially bound states in a scattering process. Due to the time reversal symmetry, a binding of the particles out of the scattering continuum is thus equally possible. We identify the regimes of dissociation for different initial conditions and provide an analysis of the underlying phase space via Poincar\\'e surfaces of section. Bound states inside the inhomogeneity as well as resonant states are identified.

  2. 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.

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

    Science.gov (United States)

    Barre, F X; Ait-Si-Ali, S; Giovannangeli, C; Luis, R; Robin, P; Pritchard, L L; Helene, C; Harel-Bellan, A

    2000-03-28

    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 treated with psoralen-linked TFOs followed by UV irradiation, thus generating highly mutagenic covalent crosslinks at the target site whose repair could restore gene function; the number of revertants and spectrum of mutations generated were quantified. Results showed that a phosphoramidate TFO indeed reaches its target sequence, forms crosslinks, and generates mutations at the expected site via a triplex-mediated mechanism: (i) under identical conditions, no mutations were generated by the same TFO at two other loci in the target strain, nor in an isogenic control strain carrying a modified target sequence incapable of supporting triple-helix formation; (ii) for a given target sequence, whether the triplex was formed in vivo on an endogenous gene or in vitro on an exogenous plasmid, the nature of the mutations generated was identical, and consistent with the repair of a psoralen crosslink at the target site. Although the mutation efficiency was probably too low for therapeutic applications, our results confirm the validity of the triple-helix approach and provide a means of evaluating the effectiveness of new chemically modified TFOs and analogs.

  4. 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.

  5. Lipid solvation effects contribute to the affinity of Gly-xxx-Gly motif-mediated helix-helix interactions.

    Science.gov (United States)

    Johnson, Rachel M; Rath, Arianna; Melnyk, Roman A; Deber, Charles M

    2006-07-18

    Interactions between transmembrane helices are mediated by the concave Gly-xxx-Gly motif surface. Whether Gly residues per se are sufficient for selection of this motif has not been established. Here, we used the in vivo TOXCAT assay to measure the relative affinities of all 18 combinations of Gly, Ala, and Ser "small-xxx-small" mutations in glycophorin A (GpA) and bacteriophage M13 major coat protein (MCP) homodimers. Affinity values were compared with the accessibility to a methylene-sized probe of the total surface area of each helix monomer as a measure of solvation by membrane components. A strong inverse correlation was found between nonpolar-group lipid accessibility and dimer affinity (R = 0.75 for GpA, p = 0.013, and R = 0.81 for MCP, p = 0.004), suggesting that lipid as a poor membrane protein solvent, conceptually analogous to water in soluble protein folding, can contribute to dimer stability and help to define helix-helix interfaces.

  6. 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

  7. 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.

  8. Genetic Analysis in Translational Medicine: The 2010 GOLDEN HELIX Symposium.

    Science.gov (United States)

    Patrinos, George P; Innocenti, Federico; Cox, Nancy; Fortina, Paolo

    2011-06-01

    The 2010 GOLDEN HELIX Symposium "Genetic Analysis in Translational Medicine" was held in Athens, Greece, 1-4 December 2010. The scientific program covered all aspects of this discipline, including genome-wide association studies, genomics of cancer and human disorders, molecular cytogenetics, advances in genomic technology, next-generation sequencing applications, pharmacogenomics, and bioinformatics. In addition, various topics on genetics and society and genetic analysis in clinical practice were discussed. We provide an overview of the plenary lectures and the topics discussed in the symposium.

  9. 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

  10. 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.

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

    DEFF Research Database (Denmark)

    Bohr, Jakob; Olsen, Kasper

    2010-01-01

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

  12. Biophysical studies of matrix metalloproteinase/triple-helix complexes.

    Science.gov (United States)

    Fields, Gregg B

    2014-01-01

    Several members of the zinc-dependent matrix metalloproteinase (MMP) family catalyze collagen degradation. The structures of MMPs, in solution and solid state and in the presence and absence of triple-helical collagen models, have been assessed by NMR spectroscopy, small-angle X-ray scattering, and X-ray crystallography. Structures observed in solution exhibit flexibility between the MMP catalytic (CAT) and hemopexin-like (HPX) domains, while solid-state structures are relatively compact. Evaluation of the maximum occurrence (MO) of MMP-1 conformations in solution found that, for all the high MO conformations, the CAT and HPX domains are not in tight contact, and the residues of the HPX domain reported to be responsible for the binding to the collagen triple-helix are solvent exposed. A mechanism for collagenolysis has been developed based on analysis of MMP solution structures. Information obtained from solid-state structures has proven valuable for analyzing specific contacts between MMPs and the collagen triple-helix.

  13. 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.

  14. 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...

  15. 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.

  16. Conformational preferences of substituted prolines in the collagen triple helix.

    Science.gov (United States)

    Mooney, Sean D; Kollman, Peter A; Klein, Teri E

    2002-07-05

    Researchers have recently questioned the role hydroxylated prolines play in stabilizing the collagen triple helix. To address these issues, we have developed new molecular mechanics parameters for the simulation of peptides containing 4(R)-fluoroproline (Flp), 4(R)-hydroxyproline (Hyp), and 4(R)-aminoproline (Amp). Simulations of peptides based on these parameters can be used to determine the components that stabilize hydroxyproline over proline in the triple helix. The dihedrals F-C-C-N, O-C-C-N, and N-C-C-N were built using a N-beta-ethyl amide model. One nanosecond simulations were performed on the trimers [(Pro-Pro-Gly)(10)](3), [(Pro-Hyp-Gly)(10)](3), [(Pro-Amp-Gly)(10)](3), [(Pro-Amp(1+)-Gly)(10)](3), and [(Pro-Flp-Gly)(10)](3) in explicit solvent. The results of our simulations suggest that pyrrolidine ring conformation is mediated by the strength of the gauche effect and classical electrostatic interactions.

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

  18. 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.

  19. 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.

  20. Structure of bacteriophage phi29 head fibers has a supercoiled triple repeating helix-turn-helix motif.

    Science.gov (United States)

    Xiang, Ye; Rossmann, Michael G

    2011-03-22

    The tailed bacteriophage 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 Å in length. The crystal structure of the C-terminal fibrous portion (residues 112-280) has been determined to a resolution of 1.6 Å. The structure is about 150 Å 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 29 suggest that the fibers might enhance the attachment of the virions onto the host cell wall.

  1. 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.

  2. Caught red-handed: Rc encodes a basic helix-loop-helix protein conditioning red pericarp in rice.

    Science.gov (United States)

    Sweeney, Megan T; Thomson, Michael J; Pfeil, Bernard E; McCouch, Susan

    2006-02-01

    Rc is a domestication-related gene required for red pericarp in rice (Oryza sativa). The red grain color is ubiquitous among the wild ancestors of O. sativa, in which it is closely associated with seed shattering and dormancy. Rc encodes a basic helix-loop-helix (bHLH) protein that was fine-mapped to an 18.5-kb region on rice chromosome 7 using a cross between Oryza rufipogon (red pericarp) and O. sativa cv Jefferson (white pericarp). Sequencing of the alleles from both mapping parents as well as from two independent genetic stocks of Rc revealed that the dominant red allele differed from the recessive white allele by a 14-bp deletion within exon 6 that knocked out the bHLH domain of the protein. A premature stop codon was identified in the second mutant stock that had a light red pericarp. RT-PCR experiments confirmed that the Rc gene was expressed in both red- and white-grained rice but that a shortened transcript was present in white varieties. Phylogenetic analysis, supported by comparative mapping in rice and maize (Zea mays), showed that Rc, a positive regulator of proanthocyanidin, is orthologous with INTENSIFIER1, a negative regulator of anthocyanin production in maize, and is not in the same clade as rice bHLH anthocyanin regulators.

  3. 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.

  4. A genome-wide survey on basic helix-loop-helix transcription factors in rat and mouse.

    Science.gov (United States)

    Zheng, Xiaodong; Zheng, X; Wang, Yong; Wang, Y; Yao, Qin; Yao, Q; Yang, Zhe; Yang, Z; Chen, Keping; Chen, K

    2009-04-01

    The basic helix-loop-helix (bHLH) proteins play essential roles in a wide range of developmental processes in higher organisms. bHLH family members have been identified in over 20 organisms, including nematode, fruit fly, and human. Our study identified 114 rat and 14 additional mouse bHLH members in rat and mouse genomes, respectively. Phylogenetic analyses revealed that both rat and mouse had 49, 26, 15, 4, 12, and 4 bHLH members in groups A, B, C, D, E, and F, respectively. Only the rat Mxi1 gene has two copies in the genome. All other rat bHLH genes and all mouse bHLH genes are single-copy genes. The chromosomal distribution pattern of mouse, rat, and human bHLH genes suggests the emergence of some bHLH genes through gene duplication, which probably happened at least before the divergence of vertebrates from invertebrates. The present study provides useful information for future studies using rat as a model animal for mammalian development.

  5. In vivo analysis of the helix-turn-helix motif of the fushi tarazu homeo domain of Drosophila melanogaster.

    Science.gov (United States)

    Furukubo-Tokunaga, K; Müller, M; Affolter, M; Pick, L; Kloter, U; Gehring, W J

    1992-06-01

    We report a systematic mutational analysis of the helix-turn-helix motif (HTH) of the fushi tarazu (ftz) homeo domain (HD) of Drosophila. We started out by testing the function of chimeric ftz proteins containing either a part of the Sex combs reduced (Scr) or the muscle segment homeobox (msh) HDs. By complementation tests in transgenic flies, cotransfection assays in cultured Drosophila cells and in vitro DNA-binding assays, we have found that the ftz activity is retained in the ftz-Scr chimera but is lost in the ftz-msh chimera, which is defective in binding to an Antennapedia (Antp)-class target site. Further studies with a series of back-mutants of the ftz-msh chimera have revealed that a set of class-specific DNA backbone-contacting residues in the HTH, particularly Arg-28 and Arg-43, are required for efficient target site recognition and, hence, full ftz activity both in vitro and in vivo.

  6. Triple Helix Systems: An Analytical Framework for Innovation Policy and Practice in the Knowledge Society

    Science.gov (United States)

    Ranga, Marina; Etzkowitz, Henry

    2013-01-01

    This paper introduces the concept of Triple Helix systems as an analytical construct that synthesizes the key features of university--industry--government (Triple Helix) interactions into an "innovation system" format, defined according to systems theory as a set of components, relationships and functions. Among the components of Triple…

  7. Triple helix conformation-specific blinking of Cy3 in DNA.

    Science.gov (United States)

    Kawai, Kiyohiko; Maruyama, Atsushi

    2015-03-21

    We report that Cy3 undergoes triple helix conformation-specific blinking in DNA. Blinking patterns were affected by the stabilization of the Hoogsteen base-pair, suggesting that not only the presence but also the fluctuating behaviour of the triple helix can be monitored by the changes in the Cy3 blinking patterns.

  8. 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.

  9. Design of Formed Milling Cutter for Double-Helix Screw Based on Noninstantaneous Envelope Method

    Directory of Open Access Journals (Sweden)

    Yun Li

    2013-01-01

    Full Text Available The design theory and method of formed milling cutter for double-helix screw of progressing cavity pump are presented. Through analyzing the shape and characteristic parameters of double-helix screw, the helicoids equation and axial curve equation of double-helix screw were established. According to the relative position relations between formed milling cutter and double-helix screw in the machining process, the geometric mapping relationship of screw coordinate system and formed milling cutter coordinate system was established by using the coordinate transformation theory. Based on noninstantaneous envelope method and the meshing conditions between formed milling cutter and double-helix screw, the contact line equations were established by minimum value method. By analyzing the machining errors caused by resharpening the formed milling cutter, the tooth back curve equation was established based on spiral of Archimedes, and the profile equation of formed milling cutter with constant back angle was got. On this basis, the formed milling cutter of processing double-helix screw was designed, and the cutter head and tool post were manufactured, respectively. The measuring results have shown that this method can satisfy the requirements of machining accuracy for double-helix screw. So this is an effective method to get formed milling cutter profile for double-helix screw.

  10. 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...

  11. Assembly of Liposomes Controlled by Triple Helix Formation

    DEFF Research Database (Denmark)

    Vogel, Stefan; Jakobsen, Ulla

    2013-01-01

    -covalent immobilization of oligonucleotides on the surface of soft nanoparticles (e.g. liposomes) and the subsequent controlled assembly by DNA triple helix formation. The non-covalent approach avoids tedious surface chemistry and necessary purification procedures and can simplify and extend the available methodology......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 non...... 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 proof the reversible and reproducible formation of liposome aggregates during thermal denaturation cycles. Nanoparticle tracking...

  12. [Allergic contact dermatitis to common ivy (Hedera helix L.)].

    Science.gov (United States)

    Ozdemir, C; Schneider, L A; Hinrichs, R; Staib, G; Weber, L; Weiss, J M; Scharffetter-Kochanek, K

    2003-10-01

    Common ivy (Hedera helix L.) is a ubiquitous plant in Europe whose major allergen falcarinol has moderate allergic potential. It is not related to poison ivy (Toxicodendron spp.). There are no cross reactions between the allergens of common ivy (falcarinol) and poison ivy (urushiol). Contact with common ivy or falcarinol may lead to sensitization and then a delayed hypersensitivity reaction. There are only few cases described in the literature. We report on a male hobby gardener with appropriate clinical history and positive patch test. The pathogenic mechanism is a type IV reaction following a sensitization exposure. Gardeners and landscape architects with frequent exposure to common ivy and thus a high risk of sensitization should wear appropriate protective clothing.

  13. 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.

  14. 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.

  15. 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

  16. 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.

  17. Procollagen triple helix assembly: an unconventional chaperone-assisted folding paradigm.

    Science.gov (United States)

    Makareeva, Elena; Leikin, Sergey

    2007-10-10

    Fibers composed of type I collagen triple helices form the organic scaffold of bone and many other tissues, yet the energetically preferred conformation of type I collagen at body temperature is a random coil. In fibers, the triple helix is stabilized by neighbors, but how does it fold? The observations reported here reveal surprising features that may represent a new paradigm for folding of marginally stable proteins. We find that human procollagen triple helix spontaneously folds into its native conformation at 30-34 degrees C but not at higher temperatures, even in an environment emulating Endoplasmic Reticulum (ER). ER-like molecular crowding by nonspecific proteins does not affect triple helix folding or aggregation of unfolded chains. Common ER chaperones may prevent aggregation and misfolding of procollagen C-propeptide in their traditional role of binding unfolded polypeptide chains. However, such binding only further destabilizes the triple helix. We argue that folding of the triple helix requires stabilization by preferential binding of chaperones to its folded, native conformation. Based on the triple helix folding temperature measured here and published binding constants, we deduce that HSP47 is likely to do just that. It takes over 20 HSP47 molecules to stabilize a single triple helix at body temperature. The required 50-200 microM concentration of free HSP47 is not unusual for heat-shock chaperones in ER, but it is 100 times higher than used in reported in vitro experiments, which did not reveal such stabilization.

  18. Experimental investigation of initial steps of helix propagation in model peptides.

    Science.gov (United States)

    Goch, Grazyna; Maciejczyk, Maciej; Oleszczuk, Marta; Stachowiak, Damian; Malicka, Joanna; Bierzyński, Andrzej

    2003-06-10

    It is not certain whether the helix propagation parameters s(n)() (i.e., the equilibrium constants between (n - 1)- and n-residue long alpha-helices) determined from numerous studies of rather long model peptides are applicable for description of the initial steps of the helix formation during the protein folding process. From fluorescence, NMR, and calorimetric studies of a series of model peptides, containing the La(3+)-binding sequence nucleating the helix (Siedlecka, M., Goch, G., Ejchart, A., Sticht, H., and Bierzynski, A. (1999) Proc. Natl. Acad. Sci. U.S.A. 96, 903-908), we have determined, at 25 degrees C, the average values of the enthalpy DeltaH(n)() and of the helix growth parameters s(n)() describing the first four steps of helix propagation in polyalanine. The absolute values of the C-cap parameters, describing the contribution of the C-terminal residues to the helix free energy, have also been estimated for alanine (1.2 +/- 0.5) and NH(2) group (1.6 +/- 0.7). The initial four steps of the helix growth in polyalanine can be described by a common propagation parameter s = 1.54 +/- 0.04. The enthalpy DeltaH(n)() is also constant and equals -980 +/- 100 cal mol(-)(1).

  19. 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.

  20. Modulation of the oligomerization of myelin proteolipid protein by transmembrane helix interaction motifs.

    Science.gov (United States)

    Ng, Derek P; Deber, Charles M

    2010-08-17

    Proteolipid protein (PLP) is a highly hydrophobic 276-residue integral membrane protein that constitutes more than 50% of the total protein in central nervous system myelin. Previous studies have shown that this protein exists in myelin as an oligomer rather than as a monomer, and mutations in PLP that lead to neurological disorders such as Pelizaeus-Merzbacher disease and spastic paraplegia type 2 have been reported to affect its normal oligomerization. Here we employ peptide-based and in vivo approaches to examine the role of the TM domain in the formation of PLP quaternary structure through homo-oligomeric helix-helix interactions. Focusing on the TM4 alpha-helix (sequence (239)FIAAFVGAAATLVSLLTFMIAATY(262)), the site of several disease-causing point mutations that involve putative small residue helix-helix interaction motifs in the TM4 sequence, we used SDS-PAGE, fluorescence resonance energy transfer, size-exclusion chromatography, and TOXCAT assays in an Escherichia coli membrane to show that the PLP TM4 helix readily assembles into varying oligomeric states. In addition, through targeted studies of the PLP TM4 alpha-helix with point mutations that selectively eliminate these small residue motifs via substitution of Gly, Ala, or Ser residues with Ile residues, we describe a potential mechanism through which disease-causing point mutations can lead to aberrant PLP assembly. The overall results suggest that TM segments in misfolded PLP monomers that expose and/or create surface-exposed helix-helix interaction sites that are normally masked may have consequences for disease.

  1. Solvent-Directed Switch of a Left-Handed 10/12-Helix into a Right-Handed 12/10-Helix in Mixed β-Peptides.

    Science.gov (United States)

    Thodupunuri, Prashanth; Katukuri, Sirisha; Ramakrishna, Kallaganti V S; Sharma, Gangavaram V M; Kunwar, Ajit C; Sarma, Akella V S; Hofmann, Hans-Jörg

    2017-02-17

    Present study describes the synthesis and conformational analysis of β-peptides from C-linked carbo-β-amino acids [β-Caa(l)] with a d-lyxo furanoside side chain and β-hGly in 1:1 alternation. NMR and CD investigations on peptides with an (S)-β-Caa(l) monomer at the N-terminus revealed a right-handed 10/12-mixed helix. An unprecedented solvent-directed "switch" both in helical pattern and handedness was observed when the sequence begins with a β-hGly residue instead of a (S)-β-Caa(l) constituent. NMR studies on these peptides in chloroform indicated a left-handed 10/12-helix, while the CD spectrum in methanol inferred a right-handed secondary structure. The NMR data for these peptides in CD3OH showed the presence of a right-handed 12/10-helix. NMR investigations in acetonitrile indicated the coexistence of both helix types. Quantum chemical studies predicted a small energy difference of 0.3 kcal/mol between the two helix types, which may explain the possibility of solvent influence. Examples for a solvent-directed switch of both the H-bonding pattern and the handedness of foldamer helices are rare so far. A comparable solvent effect was not found in the corresponding peptides with (R)-β-Caa(l) residues, where right-handed 12/10-helices are predominating.

  2. Statistical thermodynamics of the collagen triple-helix/coil transition. Free energies for amino acid substitutions within the triple-helix.

    Science.gov (United States)

    Doig, Andrew J

    2008-11-27

    Collagen sequences frequently deviate from the most thermally stable (Gly-Pro-Hyp)(n) pattern, with many mutations causing osteogenesis imperfecta (or "brittle bone disease"). The effects of collagen mutations have been studied in short peptides. The analysis of this work is problematic, however, as triple-helices fray from their ends, making the coil/triple-helix equilibrium non-two-state. Here, I develop a statistical thermodynamic model to handle this equilibrium that is applicable to peptides that follow the (G-X-Y)(n) pattern, where Gly is present at every third position and where all three chains are identical. Parameters for substitutions at each position are included, as well as a penalty for initiating triple-helix formation. The model is applied to equilibrium experimental data at 37 degrees C to show that the extension of a triple-helix by a three residue unit stabilizes the triple-helix by 0.76 kcal/mol for Gly-Pro-Hyp and 0.33 kcal/mol for Gly-Pro-Pro. The replacement of Hyp by Arg, Asp, or Trp destabilizes the triple-helix by 1.5, 2.4, and 2.9 kcal/mol, respectively, where the substitution is present once in each chain. The model can thus be used to quantitatively interpret data on collagen peptides, giving free energies that can help rationalize mutations that affect collagen stability, and to design new collagen sequences.

  3. 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.

  4. Adsorption of Pb2+, Zn2+ and Ni2+ from Aqueous Solution by Helix aspera Shell

    OpenAIRE

    A. S. Ekop; Eddy, N. O.

    2009-01-01

    The adsorption capacity of Helix aspera shell for Pb2+, Zn2+ and Ni2+ has been studied. This shell has the potential of adsorbing Pb2+, Zn2+ and Ni2+ from aqueous solution. The adsorption potentials of Helix aspera shell is largely influenced by the ionic character of the ions and occurred according to the order Pb2+ > Ni2+ > Zn2+. The adsorption of Pb(II), Zn(II) and Ni(II) ions from aqueous solutions by Helix aspera shell is thermodynamically feasible and is consistent with the models of La...

  5. Allergic and irritant contact dermatitis from falcarinol and didehydrofalcarinol in common ivy (Hedera helix L.).

    Science.gov (United States)

    Hausen, B M; Bröhan, J; König, W A; Faasch, H; Hahn, H; Bruhn, G

    1987-07-01

    Experimental and chemical investigations revealed that common ivy (Hedera helix susp. helix) contains 3 compounds which are powerful irritants and moderate sensitizers. Only 2 of these constituents, falcarinol and didehydrofalcarinol, are present in the plant during the whole year. Besides Panax ginseng and Schefflera arboricola, this is the third species of the Araliaceae in which these polyacetylenic sensitizers have been found. Falcarinol and didehydrofalcarinol also occur in Hedera helix subsp. canariensis. 4 patients have been patch tested. Even in low concentrations (0.03%), the main allergen falcarinol elicited strong reactions in all of them. One of the authors became sensitized during the investigations.

  6. 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.

  7. Thermal helix-coil transition in UV irradiated collagen from rat tail tendon.

    Science.gov (United States)

    Sionkowska, A; Kamińska, A

    1999-05-01

    The thermal helix-coil transition in UV irradiated collagen solution, collagen film and pieces of rat tail tendon (RTT) were compared. Their thermal stability's were determined by differential scanning calorimeter (DSC) and by viscometric measurements. The denaturation temperatures of collagen solution, film and pieces of RTT were different. The helix-coil transition occur near 40 degrees C in collagen solution, near 112 degrees C in collagen film, and near 101 degrees C in pieces of RTT. After UV irradiation the thermal helix-coil transition of collagen samples were changed. These changes depend on the degree of hydratation.

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

    Science.gov (United States)

    Tronci, Giuseppe; Russell, Stephen J; Wood, David J

    2013-08-14

    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, (1)H-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 functionalized collagen precursors. Photo-activated hydrogels demonstrated an increased denaturation temperature (DSC) with respect to native collagen, suggesting that the formation of the covalent network successfully stabilized collagen triple helices. Moreover, biocompatibility and mechanical competence of obtained hydrogels were successfully demonstrated under physiologically-relevant conditions. These results demonstrate that this novel synthetic approach enabled the formation of biocompatible collagen systems with defined network architecture and programmable macroscopic properties, which can only partially be obtained with current synthetic methods.

  9. 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.

  10. Helix kinks are equally prevalent in soluble and membrane proteins.

    Science.gov (United States)

    Wilman, Henry R; Shi, Jiye; Deane, Charlotte M

    2014-09-01

    Helix kinks are a common feature of α-helical membrane proteins, but are thought to be rare in soluble proteins. In this study we find that kinks are a feature of long α-helices in both soluble and membrane proteins, rather than just transmembrane α-helices. The apparent rarity of kinks in soluble proteins is due to the relative infrequency of long helices (≥20 residues) in these proteins. We compare length-matched sets of soluble and membrane helices, and find that the frequency of kinks, the role of Proline, the patterns of other amino acid around kinks (allowing for the expected differences in amino acid distributions between the two types of protein), and the effects of hydrogen bonds are the same for the two types of helices. In both types of protein, helices that contain Proline in the second and subsequent turns are very frequently kinked. However, there are a sizeable proportion of kinked helices that do not contain a Proline in either their sequence or sequence homolog. Moreover, we observe that in soluble proteins, kinked helices have a structural preference in that they typically point into the solvent.

  11. New nucleic acid triple helix, Poly(AAU)

    Energy Technology Data Exchange (ETDEWEB)

    Broitman, S.L.; Im, D.D.; Fresco, J.R.

    1987-05-01

    A polynucleotide helical structure containing two strands of poly(A) and one of poly(U) has been discovered. The stoichiometry of the complex was determined by continuous variation titrations and isosbestic wavelength analysis. Thermal denaturation profiles were used to examine complex stability over a wide range of conditions. The complex forms only when the poly(A) strands are of molecular weight between 9000-50,000 Daltons (dp approx. 28-150), whereas the size of the poly(U) strand has no effect. This limitation may explain why poly(AAU) was not observed in previous investigations. The complex shows inverse dependence of stability on ionic strength, but is not favored by decreasing pH. This behavior, together with the intermediate poly(A) size requirement suggest that the conformational entropy of the poly(A) strands is a critical determinant of the stability of this complex. The potential of the poly(A) tails of mRNA for formation of this triple helix, and of AAU/T triplet formation to contribute to the binding of unique sequence RNA strands to gene-encoding nucleic acid double helices are noted.

  12. Double helix boron-10 powder thermal neutron detector

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Zhehui; Morris, Christopher L.; Bacon, Jeffrey D.

    2015-06-02

    A double-helix Boron-10 powder detector having intrinsic thermal neutron detection efficiency comparable to 36'' long, 2-in diameter, 2-bar Helium-3 detectors, and which can be used to replace such detectors for use in portal monitoring, is described. An embodiment of the detector includes a metallic plate coated with Boron-10 powder for generating alpha and Lithium-7 particles responsive to neutrons impinging thereon supported by insulators affixed to at least two opposing edges; a grounded first wire wound in a helical manner around two opposing insulators; and a second wire having a smaller diameter than that of the first wire, wound in a helical manner around the same insulators and spaced apart from the first wire, the second wire being positively biased. A gas, disposed within a gas-tight container enclosing the plate, insulators and wires, and capable of stopping alpha and Lithium-7 particles and generating electrons produces a signal on the second wire which is detected and subsequently related to the number of neutrons impinging on the plate.

  13. Dynamic headspace time-extended helix liquid-phase microextraction.

    Science.gov (United States)

    Huang, Shih-Pin; Chen, Pai-Shan; Huang, Shang-Da

    2009-05-15

    Liquid-phase microextraction (LPME) has been proved to be a fast, inexpensive and effective sample pre-treatment technique for the analyses of pesticides and many other compounds. In this investigation, a new headspace microextraction technique, dynamic headspace time-extended helix liquid-phase microextraction (DHS-TEH-LPME), is presented. In this work, use of a solvent cooling system, permits the temperature of the extraction solvent to be lowered. Lowering the temperature of the extraction solvent not only reduces solvent loss but also extends the feasible extraction time, thereby improving extraction efficiency. Use of a larger volume of the solvent not only extends the feasible extraction time but also, after extraction, leaves a larger volume to be directly injected into the gas chromatography (GC) to increase extraction efficiency and instrument signal. The DHS-TEH-LPME technique was used to extract six organochlorine pesticides (OCPs) from 110ml water samples that had been spiked with the analytes at ng/l levels, and stirred for 60min. The proposed method attained enrichments up to 2121 fold. The effects of extraction solvent identity, sample agitation, extraction time, extraction temperature, and salt concentration on extraction performance were also investigated. The method detection limits (MDLs) varied from 0.2 to 25ng/l. The calibration curves were linear for at least 2 orders of magnitude with R(2)>==0.996. Relative recoveries in river water were more than 86%.

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

    Energy Technology Data Exchange (ETDEWEB)

    Soenmezoglu, Savas, E-mail: svssonmezoglu@kmu.edu.tr [Department of Physics, Faculty of Kamil Ozdag Science, Karamanoglu Mehmetbey University, 70100, Karaman (Turkey); Ates Soenmezoglu, Ozlem [Department of Biology, Faculty of Kamil Ozdag Science, Karamanoglu Mehmetbey University, 70100, Karaman (Turkey)

    2011-12-01

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

  15. The development of bioactive triple helix-forming oligonucleotides.

    Science.gov (United States)

    Seidman, Michael M; Puri, Nitin; Majumdar, Alokes; Cuenoud, Bernard; Miller, Paul S; Alam, Rowshon

    2005-11-01

    We are developing triple helix-forming oligonucleotides (TFOs) as gene targeting reagents in mammalian cells. We have described psoralen-conjugated TFOs containing 2'-O-methyl (2'OMe) and 2'-O-aminoethoxy (AE) ribose substitutions. TFOs with a cluster of 3-4 AE residues, with all other sugars as 2'OMe, were bioactive in a gene knockout assay in mammalian cells. In contrast, TFOs with one or two clustered, or three dispersed, AE residues were inactive. Thermal stability analysis of the triplexes indicated that there were only incremental differences between the active and inactive TFOs. However the active and inactive TFOs could be distinguished by their association kinetics. The bioactive TFOs showed markedly greater on-rates than the inactive TFOs. It appears that the on-rate is a better predictor of TFO bioactivity than thermal stability. Our data are consistent with a model in which a cluster of 3-4 AE residues stabilizes the nucleation event that precedes formation of a complete triplex. It is likely that triplexes in cells are much less stable than triplexes in vitro probably as a result of elution by chromatin-associated translocases and helicases. Consequently the biologic assay will favor TFOs that can bind and rebind genomic targets quickly.

  16. Hydration dynamics of the collagen triple helix by NMR.

    Science.gov (United States)

    Melacini, G; Bonvin, A M; Goodman, M; Boelens, R; Kaptein, R

    2000-07-28

    The hydration of the collagen-like Ac-(Gly-Pro-Hyp)(6)-NH(2) triple-helical peptide in solution was investigated using an integrated set of high-resolution NMR hydration experiments, including different recently developed exchange-network editing methods. This approach was designed to explore the hydration dynamics in the proximity of labile groups, such as the hydroxyproline hydroxyl group, and revealed that the first shell of hydration in collagen-like triple helices is kinetically labile with upper limits for water molecule residence times in the nanosecond to sub-nanosecond range. This result is consistent with a "hopping" hydration model in which solvent molecules are exchanged in and out of solvation sites at a rate that is not directly correlated to the degree of site localization. The hopping model thus reconciles the dynamic view of hydration revealed by NMR with the previously suggested partially ordered semi-clathrate-like cylinder of hydration. In addition, the nanosecond to sub-nanosecond upper limits for water molecule residence times imply that hydration-dehydration events are not likely to be the rate-limiting step for triple helix self-recognition, complementing previous investigations on water dynamics in collagen fibers. This study has also revealed labile proton features expected to facilitate the characterization of the structure and folding of triple helices in collagen peptides.

  17. 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.”...

  18. 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...

  19. 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...

  20. 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.

  1. Gold triple-helix mid-infrared metamaterial by STED-inspired laser lithography.

    Science.gov (United States)

    Kaschke, Johannes; Wegener, Martin

    2015-09-01

    In analogy to wire-grid polarizers for linear polarization, metal-helix metamaterials can act as broadband circular polarizers. This concept has brought circular-polarization capabilities to mid-infrared and terahertz frequencies, which were previously difficult to access. Due to the lack of rotational symmetry, however, single-helix metamaterials exhibit unwanted circular-polarization conversions. Recent theoretical work showed that conversions can be fully eliminated by intertwining N=3 or 4 helices within each unit cell. While direct laser writing in positive-tone photo-resist yielded good results for single-helix metamaterials operating at mid-infrared frequencies, the axial resolution is insufficient for N-helix metamaterials. Here, we use stimulated emission depletion-inspired three-dimensional laser lithography to fabricate such microstructures. We measure all entries of the Jones transmission and reflection matrices and show experimentally that polarization conversions are minimized, in good agreement with theory.

  2. 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).

  3. Adsorption of Pb2+, Zn2+ and Ni2+ from Aqueous Solution by Helix aspera Shell

    Directory of Open Access Journals (Sweden)

    A. S. Ekop

    2009-01-01

    Full Text Available The adsorption capacity of Helix aspera shell for Pb2+, Zn2+ and Ni2+ has been studied. This shell has the potential of adsorbing Pb2+, Zn2+ and Ni2+ from aqueous solution. The adsorption potentials of Helix aspera shell is largely influenced by the ionic character of the ions and occurred according to the order Pb2+ > Ni2+ > Zn2+. The adsorption of Pb(II, Zn(II and Ni(II ions from aqueous solutions by Helix aspera shell is thermodynamically feasible and is consistent with the models of Langmuir and Freundlich adsorption isotherms. From the results of the study, the shell of Helix aspera is recommended for use in the removal of Pb2+, Zn2+ and Ni2+ from aqueous solution.

  4. Intramolecular triple helix as a model for regular polyribonucleotide (CAA)(n).

    Science.gov (United States)

    Efimov, Alexander V; Spirin, Alexander S

    2009-10-09

    The regular (CAA)(n) polyribonucleotide, as well as the omega leader sequence containing (CAA)-rich core, have recently been shown to form cooperatively melted and compact structures. In this report, we propose a structural model for the (CAA)(n) sequence in which the polyribonucleotide chain is folded upon itself, so that it forms an intramolecular triple helix. The triple helix is stabilized by hydrogen bonding between bases thus forming coplanar triads, and by stacking interactions between the base triads. A distinctive feature of the proposed triple helix is that it does not contain the canonical double-helix elements. The difference from the known triple helices is that Watson-Crick hydrogen bond pairings do not take place in the interactions between the bases within the base triads.

  5. El caracol acuático neozelandés del cieno (Potamopyrgus antipodarum: impactos ecológicos y distribución de esta especie exótica en la península ibérica

    Directory of Open Access Journals (Sweden)

    A. Alonso

    2015-01-01

    Full Text Available Las especies exóticas invasoras constituyen una de las principales causas de pérdida de biodiversidad. Debido a la complejidad del proceso de invasión, algunas especies muestran comportamiento invasor en unos ecosistemas pero no en otros. Una especie con un comportamiento ambiguo respecto a su carácter invasor es el caracol del cieno de Nueva Zelanda (Potamopyrgus antipodarum. La inclusión de esta especie en el reciente catálogo español de especies exóticas invasoras obliga a establecer su seguimiento e incrementar el conocimiento sobre su distribución en España. En el presente estudio se ha revisado la distribución de la especie en la península ibérica y los impactos ecológicos que ocasiona. En España la especie se ha citado en 30 de las 46 provincias, mientras que en Portugal aparece en 6 de 18. Muchas de las provincias afectadas son costeras, especialmente las que cuentan con las citas más antiguas. Respecto a los impactos más destacables que genera destaca su capacidad para cambiar la estructura de las comunidades de invertebrados a las que afecta, aunque en determinados casos no se han descrito tales cambios. La revisión de trabajos muestra una carencia de estudios que indiquen los mecanismos de dispersión de la especie entre distintas cuencas en la Península Ibérica, aspecto muy importante para evitar la expansión de la especie en los ecosistemas acuáticos peninsulares.

  6. Macroscopic control of helix orientation in films dried from cholesteric liquid crystalline cellulose nanocrystal suspensions


    OpenAIRE

    2014-01-01

    The intrinsic ability of cellulose nanocrystals (CNCs) to self-organize into films and bulk materials with helical order in a cholesteric liquid crystal is scientifically intriguing and potentially important for the production of renewable multifunctional materials with attractive optical properties. A major obstacle, however, has been the lack of control of helix direction, which results in a defect-rich, mosaic-like domain structure. Herein, a method for guiding the helix during film format...

  7. The triple helix model and dynamics of innovation: a case study

    OpenAIRE

    Natário, Maria Manuela; Couto, João Pedro Almeida; Almeida, Carlos Fernandes

    2012-01-01

    Copyright © 2012 Emerald Group Publishing Limited. The purpose of this paper is to analyze the dynamics of the triple helix model in less favoured regions, examining the role of three spheres: universities, firms, and government. The paper identifies profiles of behavior in terms of triple helix model performance from the firm's perspective and recognizes key factors for successful innovation dynamics in a less favored region of Portugal.

  8. 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.

  9. [Study of collagen mimetic peptide's triple-helix structure and its thermostability by circular dichroism].

    Science.gov (United States)

    Zhang, Zhi-Bao; Wang, Jing-Jie; Chen, Hui-Juan; Xiong, Qing-Qing; Liu, Ling-Rong; Zhang, Qi-Qing

    2014-04-01

    In the present study, the authors explore the triple-helix conformation and thermal stability of collagen mimetic peptides (CMPs) as a function of peptide sequence and/or chain length by circular dichroism(CD). Five CMPs were designed and synthetized varying the number of POG triplets or incorporating an integrin alpha2beta1 binding motif Gly-Phe-Hyp-Gly-Glu-Arg (GFOGER). CD spectroscopy from 260 to 190 nm was recorded to confirm the existence of triple-helix conformation at room temperature, while thermal melting and thermal annealing of triple-helix (thermal unfolding and refolding of triple-helix, respectively) was characterized by monitoring ellipticity at 225 nm as a function of temperature. The results demonstrated that all the CMPs adopted triple-helix conformation, and the thermal stability of the CMPs was enhanced with increasing the number of POG triplets. In contrast to natural collagen, the thermal denaturation processes of CMPs were reversible, i. e. the triple-helix unfolded upon heating while refolded upon cooling. Meanwhile, the phenomenon of "hysteresis" was observed by comparing melting and thermal curves. These findings add new insights to the mechanisms of collagen and CMPs assembly, as well as provide an alternative approach to the fabrication of artificial collagen-likes biomaterials.

  10. Small-signal analysis of a rectangular helix structure traveling-wave-tube

    Institute of Scientific and Technical Information of China (English)

    Fu Cheng-Fang; Wei Yan-Yu; Duan Zhao-Yun; Wang Wen-Xiang; Gong Yu-Bin

    2009-01-01

    This paper investigates the properties of traveling wave-beam interaction in a rectangular helix traveling-wave-tube (TWT) for a solid sheet electron beam. The 'hot' dispersion equation is obtained by means of the self-consistent field theory. The small signal analysis, which includes the effects of the beam parameters and slow-wave structure (SWS)parameters, is carried out by theoretical computation. The numerical results show that the bandwidth and the smallsignal gain of the rectangular helix TWT increase as the beam current increases; and the beam voltage not obviously influences the small signal gain. Among different rectangular helix structures, the small-signal gain increases as the width of the rectangular helix SWS increases, however, the bandwidth decreases whether structure parameters a and Lor ψ and L are fixed or not. In addition, a comparison of the small-signal gain of this structure with a conventional round helix is made. The presented analysis will be useful for the design of the TWT with a rectangular helix circuit.

  11. 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.

  12. 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

  13. 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.

  14. A routine for measuring synergy in university-industry-government relations: mutual information as a Triple-Helix and Quadruple-Helix indicator

    NARCIS (Netherlands)

    Leydesdorff, L.; Park, H.W.; Lengyel, B.

    2014-01-01

    Mutual information in three (or more) dimensions can be considered as a Triple-Helix indicator of possible synergy in university-industry-government relations. An open-source routine th4.exe makes the computation of this indicator interactively available at the internet, and thus applicable to large

  15. The triple helix, quadruple helix, ..., and an N-tuple of helices: explanatory models for analyzing the knowledge-based economy?

    NARCIS (Netherlands)

    Leydesdorff, L.

    2012-01-01

    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 expe

  16. 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.

  17. 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...

  18. Position and motions of the S4 helix during opening of the Shaker potassium channel.

    Science.gov (United States)

    Phillips, L Revell; Swartz, Kenton J

    2010-12-01

    The four voltage sensors in voltage-gated potassium (Kv) channels activate upon membrane depolarization and open the pore. The location and motion of the voltage-sensing S4 helix during the early activation steps and the final opening transition are unresolved. We studied Zn(2+) bridges between two introduced His residues in Shaker Kv channels: one in the R1 position at the outer end of the S4 helix (R362H), and another in the S5 helix of the pore domain (A419H or F416H). Zn(2+) bridges readily form between R362H and A419H in open channels after the S4 helix has undergone its final motion. In contrast, a distinct bridge forms between R362H and F416H after early S4 activation, but before the final S4 motion. Both bridges form rapidly, providing constraints on the average position of S4 relative to the pore. These results demonstrate that the outer ends of S4 and S5 remain in close proximity during the final opening transition, with the S4 helix translating a significant distance normal to the membrane plane.

  19. Effect of sterically demanding substituents on the conformational stability of the collagen triple helix.

    Science.gov (United States)

    Erdmann, Roman S; Wennemers, Helma

    2012-10-17

    The effect of sterically demanding groups at proline residues on the conformational stability of the collagen triple helix was examined. The thermal stabilities (T(m) and ΔG) of eight different triple helices derived from collagen model peptides with (4R)- or (4S)-configured amidoprolines bearing either methyl or bulkier tert-butyl groups in the Xaa or Yaa position were determined and served as a relative measure for the conformational stability of the corresponding collagen triple helices. The results show that sterically demanding substituents are tolerated in the collagen triple helix when they are attached to (4R)-configured amidoprolines in the Xaa position or to (4S)-configured amidoprolines in the Yaa position. Structural studies in which the preferred conformation of (4R)- or (4S)-configured amidoproline were overlaid with the Pro and Hyp residues within a crystal structure of collagen revealed that the sterically demanding groups point to the outside of these two triple helices and thereby do not interfere with the formation of the triple helix. In all of the other examined collagen derivatives with lower stability of the triple helices, the acetyl or pivaloyl residues point toward the inside of the triple helix and clash with a residue of the neighboring strand. The results also revealed that unfavorable steric dispositions affect the conformational stability of the collagen triple helix more than unfavorable ring puckers of the proline residues. The results are useful for the design of functionalized collagen based materials.

  20. Contribution of dipole-dipole interactions to the stability of the collagen triple helix.

    Science.gov (United States)

    Improta, Roberto; Berisio, Rita; Vitagliano, Luigi

    2008-05-01

    Unveiling sequence-stability and structure-stability relationships is a major goal of protein chemistry and structural biology. Despite the enormous efforts devoted, answers to these issues remain elusive. In principle, collagen represents an ideal system for such investigations due to its simplified sequence and regular structure. However, the definition of the molecular basis of collagen triple helix stability has hitherto proved to be a difficult task. Particularly puzzling is the decoding of the mechanism of triple helix stabilization/destabilization induced by imino acids. Although the propensity-based model, which correlates the propensities of the individual imino acids with the structural requirements of the triple helix, is able to explicate most of the experimental data, it is unable to predict the rather high stability of peptides embedding Gly-Hyp-Hyp triplets. Starting from the available X-ray structures of this polypeptide, we carried out an extensive quantum chemistry analysis of the mutual interactions established by hydroxyproline residues located at the X and Y positions of the Gly-X-Y motif. Our data clearly indicate that the opposing rings of these residues establish significant van der Waals and dipole-dipole interactions that play an important role in triple helix stabilization. These findings suggest that triple helix stabilization can be achieved by distinct structural mechanisms. The interplay of these subtle but recurrent effects dictates the overall stability of this widespread structural motif.

  1. N-terminal helix-cap in α-helix 2 modulates β-state misfolding in rabbit and hamster prion proteins.

    Science.gov (United States)

    Sweeting, Braden; Brown, Eric; Khan, M Qasim; Chakrabartty, Avijit; Pai, Emil F

    2013-01-01

    Susceptibility of a particular species to prion disease is affected by small differences in the sequence of PrP and correlates with the propensity of its PrP to assume the β-state. A helix-cap motif in the β2-α2-loop of native α-helical rabbit PrP, a resistant species, contains sequence differences that influence intra- and interspecies transmission. To determine the effect the helix-cap motif on β-state refolding propensity, we mutated S170N, S174N, and S170N/S174N of the rabbit PrP helix-cap to resemble that of hamster PrP and conversely, N170S, N174S, and N170S/N174S of hamster PrP to resemble the helix-cap of rabbit PrP. High-resolution crystal structures (1.45-1.6 Å) revealed that these mutations ablate hydrogen-bonding interactions within the helix-cap motif in rabbit PrP(C). They also alter the β-state-misfolding propensity of PrP; the serine mutations in hamster PrP decrease the propensity up to 35%, whereas the asparagine mutations in rabbit PrP increase it up to 42%. Rapid dilution of rabbit and hamster into β-state buffer conditions causes quick conversion to β-state monomers. Kinetic monitoring using size-exclusion chromatography showed that the monomer population decreases exponentially mirrored by an increase in an octameric species. The monomer-octamer transition rates are faster for hamster than for rabbit PrP. The N170S/N174S mutant of hamster PrP has a smaller octamer component at the endpoint compared to the wild-type, whereas the kinetics of octamer formation in mutant and wild-type rabbit PrP are comparable. These findings demonstrate that the sequence of the β2-α2 helix-cap affects refolding to the β-state and subsequently, may influence susceptibility to prion disease.

  2. Light and electron microscopy study of late embryonic development in the land snail Limicolaria flammea (Müller (Pulmonata, Achatinidae Microscopias óptica e eletrônica dos estágios embrionários do caracol Limicolaria flammea (Müller (Pulmonata, Achatinidae

    Directory of Open Access Journals (Sweden)

    Rosemary I. Egonmwan

    2007-06-01

    Full Text Available The late stages of embryogenesis in the achatinid land snail Limicolariaflammea (Müller, 1774 were described using light and electron microscopy. Embryos at various stages of development were present in the eggs during the first hour after they were laid, from 4-cell blastulae to morulae and fairly advanced stages. The advanced embryo which was fully developed on the second day bears a long cephalic sac, first to be developed, attached to the embryo and a podocyst which is attached to the foot of the embryo. Both of these structures are reduced in size as embryogenesis progresses until they finally disappear at about the 7th day after the egg was deposited. The embryonic shell was apparent on the second day and spiral coiling was apparent at about day 5. The spiral shell had one whorl when formed and more spirals were added so that at hatching the young snails had three whorls.Os estágios finais da embriogênese do caracol Limicolariaflammea (Müller, 1774 foram descritos por meio de observações a partir de microscopia óptica e eletrônica. Embriões em vários estágios de desenvolvimento estavam presentes em ovos durante a primeira hora ou logo após a desova, de blástulas tetra celulares a mórulas e estágios avançados. Embriões avançados, totalmente desenvolvidos no segundo dia, apresentaram uma longa base cefálica, a primeira a desenvolver-se, aderida ao embrião e um podocisto aderido ao pé do embrião. Ambas estruturas reduziram de tamanho à medida que a embriogênese progrediu, até finalmente desaparecer próximo do sétimo dia após a oviposição. A concha embriogênica foi evidenciada no segundo dia e o enrolamento espiral foi aparente próximo ao quinto. A concha espiralada possuia uma volta quando formada e mais espirais foram adicionadas e assim, quando da eclosão, o jovem tinha três voltas.

  3. 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.

  4. 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.

  5. Discovery of HIV fusion inhibitors targeting gp41 using a comprehensive α-helix mimetic library

    Science.gov (United States)

    Whitby, Landon R.; Boyle, Kristopher E.; Cai, Lifeng; Yu, Xiaoqian; Gochin, Miriam; Boger, Dale L.

    2012-01-01

    The evaluation of a comprehensive α-helix mimetic library for binding the gp41 NHR hydrophobic pocket recognizing an intramolecular CHR α-helix provided a detailed depiction of structural features required for binding and led to the discovery of small molecule inhibitors (Ki 0.6–1.3 µM) that not only match or exceed the potency of those disclosed over the past decade, but that also exhibit effective activity in a cell–cell fusion assay (IC50 5–8 µM). PMID:22424973

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

    Institute of Scientific and Technical Information of China (English)

    FU Cheng-Fang; WEI Yan-Yu; WANG Wen-Xiang; GONG Yu-Bin

    2008-01-01

    A new type of printed rectangular he/ix 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.

  7. 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%.

  8. An octopaminergic system in the CNS of the snails, Lymnaea stagnalis and Helix pomatia

    OpenAIRE

    1998-01-01

    Octopamine (OA) levels in each ganglion of the terrestrial snail, Helix pomatia, and the pond snail, Lymnaea stagnalis, were measured by using the HPLC technique. In both species an inhomogeneous distribution of OA was found in the central nervous system. The buccal ganglia contained a concentration of OA (12.6 pmol mg-1 and 18.8 pmol mg-1) that was two to three times higher than the pedal (4.93 pmol mg-1 and 9.2 pmol mg-1) or cerebral (4.46 pmol mg-1 and 4.9 pmol mg-1) ganglia of Helix and L...

  9. 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

  10. 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

  11. A secondary structural transition in the C-helix promotes gating of cyclic nucleotide-regulated ion channels.

    Science.gov (United States)

    Puljung, Michael C; Zagotta, William N

    2013-05-03

    Cyclic nucleotide-regulated ion channels bind second messengers like cAMP to a C-terminal domain, consisting of a β-roll, followed by two α-helices (B- and C-helices). We monitored the cAMP-dependent changes in the structure of the C-helix of a C-terminal fragment of HCN2 channels using transition metal ion FRET between fluorophores on the C-helix and metal ions bound between histidine pairs on the same helix. cAMP induced a change in the dimensions of the C-helix and an increase in the metal binding affinity of the histidine pair. cAMP also caused an increase in the distance between a fluorophore on the C-helix and metal ions bound to the B-helix. Stabilizing the C-helix of intact CNGA1 channels by metal binding to a pair of histidines promoted channel opening. These data suggest that ordering of the C-helix is part of the gating conformational change in cyclic nucleotide-regulated channels.

  12. Rotational symmetry and the transformation of innovation systems in a Triple Helix of university-industry-government relations

    NARCIS (Netherlands)

    Ivanova, I.A.; Leydesdorff, L.

    2014-01-01

    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 Append

  13. Infrared spectroscopic studies of cells and tissues: triple helix proteins as a potential biomarker for tumors.

    Science.gov (United States)

    Stelling, Allison L; Toher, Deirdre; Uckermann, Ortrud; Tavkin, Jelena; Leipnitz, Elke; Schweizer, Julia; Cramm, Holger; Steiner, Gerald; Geiger, Kathrin D; Kirsch, Matthias

    2013-01-01

    In this work, the infrared (IR) spectra of living neural cells in suspension, native brain tissue, and native brain tumor tissue were investigated. Methods were developed to overcome the strong IR signal of liquid water so that the signal from the cellular biochemicals could be seen. Measurements could be performed during surgeries, within minutes after resection. Comparison between normal tissue, different cell lineages in suspension, and tumors allowed preliminary assignments of IR bands to be made. The most dramatic difference between tissues and cells was found to be in weaker IR absorbances usually assigned to the triple helix of collagens. Triple helix domains are common in larger structural proteins, and are typically found in the extracellular matrix (ECM) of tissues. An algorithm to correct offsets and calculate the band heights and positions of these bands was developed, so the variance between identical measurements could be assessed. The initial results indicate the triple helix signal is surprisingly consistent between different individuals, and is altered in tumor tissues. Taken together, these preliminary investigations indicate this triple helix signal may be a reliable biomarker for a tumor-like microenvironment. Thus, this signal has potential to aid in the intra-operational delineation of brain tumor borders.

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

    Science.gov (United States)

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

    2012-10-01

    Type XXV collagen, or collagen-like amyloidogenic component, 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 was incorporated between (GPO)(n) domains. Circular dichroism and nuclear magnetic resonance (NMR) spectroscopy showed the GNNQQNY peptide formed a random coil structure, whereas the hybrid peptide contained a central disordered GNNQQNY region transitioning to triple-helical ends. Light scattering confirmed the GNNQQNY peptide had a high propensity to form amyloid fibrils, whereas amyloidogenesis was delayed in the hybrid peptide. NMR data suggested the triple-helix constraints on the GNNQQNY sequence within the hybrid peptide may disfavor the conformational change necessary for aggregation. Independent addition of a triple-helical peptide to the GNNQQNY peptide under aggregating conditions delayed nucleation and amyloid fibril growth. The inhibition of amyloid nucleation depended on the Gly-Xaa-Yaa sequence and required the triple-helix conformation. The inhibitory effect of the collagen triple-helix on an amyloidogenic sequence, when in the same molecule or when added separately, suggests Type XXV collagen, and possibly other collagens, may play a role in regulating amyloid fibril formation.

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

    Science.gov (United States)

    Halilem, Norrin

    2010-01-01

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

  17. Structural insights into the stabilization of MALAT1 noncoding RNA by a bipartite triple helix.

    Science.gov (United States)

    Brown, Jessica A; Bulkley, David; Wang, Jimin; Valenstein, Max L; Yario, Therese A; Steitz, Thomas A; Steitz, Joan A

    2014-07-01

    Metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) is a highly abundant nuclear long noncoding RNA that promotes malignancy. A 3'-stem-loop structure is predicted to confer stability by engaging a downstream A-rich tract in a triple helix, similar to the expression and nuclear retention element (ENE) from the KSHV polyadenylated nuclear RNA. The 3.1-Å-resolution crystal structure of the human MALAT1 ENE and A-rich tract reveals a bipartite triple helix containing stacks of five and four U•A-U triples separated by a C+•G-C triplet and C-G doublet, extended by two A-minor interactions. In vivo decay assays indicate that this blunt-ended triple helix, with the 3' nucleotide in a U•A-U triple, inhibits rapid nuclear RNA decay. Interruption of the triple helix by the C-G doublet induces a 'helical reset' that explains why triple-helical stacks longer than six do not occur in nature.

  18. Infrared spectroscopic studies of cells and tissues: triple helix proteins as a potential biomarker for tumors.

    Directory of Open Access Journals (Sweden)

    Allison L Stelling

    Full Text Available In this work, the infrared (IR spectra of living neural cells in suspension, native brain tissue, and native brain tumor tissue were investigated. Methods were developed to overcome the strong IR signal of liquid water so that the signal from the cellular biochemicals could be seen. Measurements could be performed during surgeries, within minutes after resection. Comparison between normal tissue, different cell lineages in suspension, and tumors allowed preliminary assignments of IR bands to be made. The most dramatic difference between tissues and cells was found to be in weaker IR absorbances usually assigned to the triple helix of collagens. Triple helix domains are common in larger structural proteins, and are typically found in the extracellular matrix (ECM of tissues. An algorithm to correct offsets and calculate the band heights and positions of these bands was developed, so the variance between identical measurements could be assessed. The initial results indicate the triple helix signal is surprisingly consistent between different individuals, and is altered in tumor tissues. Taken together, these preliminary investigations indicate this triple helix signal may be a reliable biomarker for a tumor-like microenvironment. Thus, this signal has potential to aid in the intra-operational delineation of brain tumor borders.

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

    Energy Technology Data Exchange (ETDEWEB)

    Donten, Mateusz L. [Institute of Physical Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich (Switzerland); Hamm, Peter, E-mail: phamm@pci.uzh.ch [Institute of Physical Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich (Switzerland)

    2013-08-30

    Highlights: ► pH-jump as truly biomimetic tool to initiate non-equilibrium dynamics of biomolecules. ► Design criteria to widen the applicability of pH-jumps are developed. ► Folding of poly-L-Glu in dependence of starting pH, pH jump size and helix length. ► Length dependence provides strong evidence for a nucleation–propagation scenario. - Abstract: 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.

  1. 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.

  2. Modelling packing interactions in parallel helix bundles: pentameric bundles of nicotinic receptor M2 helices.

    Science.gov (United States)

    Sankararamakrishnan, R; Sansom, M S

    1995-11-01

    The transbilayer pore of the nicotinic acetylcholine receptor (nAChR) is formed by a pentameric bundle of M2 helices. Models of pentameric bundles of M2 helices have been generated using simulated annealing via restrained molecular dynamics. The influence of: (a) the initial C alpha template; and (b) screening of sidechain electrostatic interactions on the geometry of the resultant M2 helix bundles is explored. Parallel M2 helices, in the absence of sidechain electrostatic interactions, pack in accordance with simple ridges-in-grooves considerations. This results in a helix crossing angle of ca. +12 degrees, corresponding to a left-handed coiled coil structure for the bundle as a whole. Tilting of M2 helices away from the central pore axis at their C-termini and/or inclusion of sidechain electrostatic interactions may perturb such ridges-in-grooves packing. In the most extreme cases right-handed coiled coils are formed. An interplay between inter-helix H-bonding and helix bundle geometry is revealed. The effects of changes in electrostatic screening on the dimensions of the pore mouth are described and the significance of these changes in the context of models for the nAChR pore domain is discussed.

  3. 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...

  4. 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

  5. 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...

  6. Efficient Fatigue Analysis of Helix Elements in Umbilicals and Flexible Risers: Theory and Applications

    Directory of Open Access Journals (Sweden)

    Geir Skeie

    2012-01-01

    Full Text Available Fatigue analysis of structural components such as helix tensile armors and steel tubes is a critical design issue for dynamic umbilicals and flexible pipes. The basis for assessment of fatigue damage of such elements is the long-term stress cycle distribution at critical locations on the helix elements caused by long-term environmental loading on the system. The long-term stress cycle distribution will hence require global dynamic time domain analysis followed by a detailed cross-sectional analysis in a large number of irregular sea states. An overall computational consistent and efficient fatigue analysis scheme is outlined with due regard of the cross-sectional analysis technique required for fatigue stress calculation with particular attention to the helix elements. The global cross-section is exposed to pure bending, tensile, torsion, and pressure loading. The state of the different cross-section elements is based on the global response. Special emphasis is placed on assessment of friction stresses caused by the stick-slip behavior of helix elements in bending that are of special importance for fatigue life assessments. The described cross-sectional analysis techniques are based on an extensive literature survey and are hence considered to represent industry consensus. The performance of the described calculation scheme is illustrated by case studies.

  7. 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....

  8. 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…

  9. Nano-mechanical characterization of tension-sensitive helix bundles in talin rod.

    Science.gov (United States)

    Maki, Koichiro; Nakao, Nobuhiko; Adachi, Taiji

    2017-03-04

    Tension-induced exposure of a cryptic signaling binding site is one of the most fundamental mechanisms in molecular mechanotransduction. Helix bundles in rod domains of talin, a tension-sensing protein at focal adhesions, unfurl under tension to expose cryptic vinculin binding sites. Although the difference in their mechanical stabilities would determine which helix bundle is tension-sensitive, their respective mechanical behaviors under tension have not been characterized. In this study, we evaluated the mechanical behaviors of residues 486-654 and 754-889 of talin, which form helix bundles with low and high tension-sensitivity, by employing AFM nano-tensile testing. As a result, residues 754-889 exhibited lower unfolding energy for complete unfolding than residues 486-654. In addition, we found that residues 754-889 transition into intermediate conformations under lower tension than residues 486-654. Furthermore, residues 754-889 showed shorter persistence length in the intermediate conformation than residues 486-654, suggesting that residues 754-889 under tension exhibit separated α-helices, while residues 486-654 assume a compact conformation with inter-helix interactions. Therefore, we suggest that residues 754-889 of talin work as a tension-sensitive domain to recruit vinculin at the early stage of focal adhesion development, while residues 486-654 contribute to rather robust tension-sensitivity by recruiting vinculin under high tension.

  10. 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

  11. 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

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

    DEFF Research Database (Denmark)

    Jofre, Sergio; Andersen, Per Dannemand

    2009-01-01

    , are transforming the profile of the triple helix relationships. This transformation is bringing the American and the Japanese innovation system to an unprecedented level of commonality and the EU to a yet uncertain stage of transition characterized by the conflict between national and supranational priorities...

  13. A Role-Based Approach to Adult Development: The Triple-Helix Model.

    Science.gov (United States)

    Juhasz, Anne McCreary

    1989-01-01

    Presents triple-helix model of adult development which incorporates three major roles: family, work, and self, each powered by drive for self-esteem. Asserts that this approach accommodates wide range of possible patterns and varied timing of life events relative to career options, family and relationship choices, and emphasis on self-development.…

  14. The triple-helix model of smart cities: a neo-evolutionary perspective

    NARCIS (Netherlands)

    Leydesdorff, L.; Deakin, M.

    2011-01-01

    This paper sets out to demonstrate how the triple-helix model enables us to study the knowledge base of an urban economy in terms of its civil society's support for the evolution of the city as a key component of an innovation system. It argues that cities can be considered as densities in networks

  15. The University in the Knowledge Economy: The Triple Helix Model and Its Implications

    Science.gov (United States)

    Zheng, Peijun; Harris, Michael

    2007-01-01

    In the context of the global knowledge economy, the three major players--university, industry, and government--are becoming increasingly interdependent. As more intensified interactions and relationships of increasing complexity among the institutions evolve, the Triple Helix model attempts to describe not only interactions among university,…

  16. 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…

  17. 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...

  18. Structural determinants of salmon calcitonin bioactivity: the role of the Leu-based amphipathic alpha-helix.

    Science.gov (United States)

    Andreotti, Giuseppina; Méndez, Blanca López; Amodeo, Pietro; Morelli, Maria A Castiglione; Nakamuta, Hiromichi; Motta, Andrea

    2006-08-25

    Salmon calcitonin (sCT) forms an amphipathic helix in the region 9-19, with the C-terminal decapeptide interacting with the helix (Amodeo, P., Motta, A., Strazzullo, G., Castiglione Morelli, M. A. (1999) J. Biomol. NMR 13, 161-174). To uncover the structural requirements for the hormone bioactivity, we investigated several sCT analogs. They were designed so as to alter the length of the central helix by removal and/or replacement of flanking residues and by selectively mutating or deleting residues inside the helix. The helix content was assessed by circular dichroism and NMR spectroscopies; the receptor binding affinity in human breast cancer cell line T 47D and the in vivo hypocalcemic activity were also evaluated. In particular, by NMR spectroscopy and molecular dynamics calculations we studied Leu(23),Ala(24)-sCT in which Pro(23) and Arg(24) were replaced by helix inducing residues. Compared with sCT, it assumes a longer amphipathic alpha-helix, with decreased binding affinity and one-fifth of the hypocalcemic activity, therefore supporting the idea of a relationship between a definite helix length and bioactivity. From the analysis of other sCT mutants, we inferred that the correct helix length is located in the 9-19 region and requires long range interactions and the presence of specific regions of residues within the sequence for high binding affinity and hypocalcemic activity. Taken together, the structural and biological data identify well defined structural parameters of the helix for sCT bioactivity.

  19. 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

  20. 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

  1. 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

  2. An important base triple anchors the substrate helix recognition surface within the Tetrahymena ribozyme active site.

    Science.gov (United States)

    Szewczak, A A; Ortoleva-Donnelly, L; Zivarts, M V; Oyelere, A K; Kazantsev, A V; Strobel, S A

    1999-09-28

    Key to understanding the structural biology of catalytic RNA is determining the underlying networks of interactions that stabilize RNA folding, substrate binding, and catalysis. Here we demonstrate the existence and functional importance of a Hoogsteen base triple (U300.A97-U277), which anchors the substrate helix recognition surface within the Tetrahymena group I ribozyme active site. Nucleotide analog interference suppression analysis of the interacting functional groups shows that the U300.A97-U277 triple forms part of a network of hydrogen bonds that connect the P3 helix, the J8/7 strand, and the P1 substrate helix. Product binding and substrate cleavage kinetics experiments performed on mutant ribozymes that lack this base triple (C A-U, U G-C) or replace it with the isomorphous C(+).G-C triple show that the A97 Hoogsteen triple contributes to the stabilization of both substrate helix docking and the conformation of the ribozyme's active site. The U300. A97-U277 base triple is not formed in the recently reported crystallographic model of a portion of the group I intron, despite the presence of J8/7 and P3 in the RNA construct [Golden, B. L., Gooding, A. R., Podell, E. R. & Cech, T. R. (1998) Science 282, 259-264]. This, along with other biochemical evidence, suggests that the active site in the crystallized form of the ribozyme is not fully preorganized and that substantial rearrangement may be required for substrate helix docking and catalysis.

  3. 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.

  4. 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.

  5. Location of glycine mutations within a bacterial collagen protein affects degree of disruption of triple-helix folding and conformation.

    Science.gov (United States)

    Cheng, Haiming; Rashid, Shayan; Yu, Zhuoxin; Yoshizumi, Ayumi; Hwang, Eileen; Brodsky, Barbara

    2011-01-21

    The hereditary bone disorder osteogenesis imperfecta is often caused by missense mutations in type I collagen that change one Gly residue to a larger residue and that break the typical (Gly-Xaa-Yaa)(n) sequence pattern. Site-directed mutagenesis in a recombinant bacterial collagen system was used to explore the effects of the Gly mutation position and of the identity of the residue replacing Gly in a homogeneous collagen molecular population. Homotrimeric bacterial collagen proteins with a Gly-to-Arg or Gly-to-Ser replacement formed stable triple-helix molecules with a reproducible 2 °C decrease in stability. All Gly replacements led to a significant delay in triple-helix folding, but a more dramatic delay was observed when the mutation was located near the N terminus of the triple-helix domain. This highly disruptive mutation, close to the globular N-terminal trimerization domain where folding is initiated, is likely to interfere with triple-helix nucleation. A positional effect of mutations was also suggested by trypsin sensitivity for a Gly-to-Arg replacement close to the triple-helix N terminus but not for the same replacement near the center of the molecule. The significant impact of the location of a mutation on triple-helix folding and conformation could relate to the severe consequences of mutations located near the C terminus of type I and type III collagens, where trimerization occurs and triple-helix folding is initiated.

  6. Triple helix stabilization by covalently linked DNA-bisbenzimidazole conjugate synthesized by maleimide-thiol coupling chemistry.

    Science.gov (United States)

    Jain, Akash K; Awasthi, Satish Kumar; Tandon, Vibha

    2006-09-15

    Tethering of BBZPNH2, an analogue of the Hoechst 33258, with a 14 nucleotide long DNA sequence with the help of succinimidyl-4-(N-maleimidomethyl)cyclohexane-1-carboxylate (SMCC), a heterobifunctional crosslinking reagent, using DMF/ water as solvent yields a conjugate which effectively stabilizes the triple helix. The above conjugate was hybridized with 26 bp long double stranded (ds) DNA having 14 bp long polypurine-polypyrimidine stretch to form a pyrimidine motif triple helix. The above conjugate increases the thermal stability of both the transitions, that is, triple helix to double helix by 12 degrees C and double helix to single strand transition by 16 degrees C for the triple helix formed with conjugated TFO over the triple helix made from non-conjugated TFO. Fluorescence and circular dichroism spectra recorded at different temperatures confirm the presence of minor groove binding bisbenzimidazole in the AT-rich minor groove of dsDNA even after the major groove bound TFO separates out.

  7. Osteogenesis imperfecta model peptides: incorporation of residues replacing Gly within a triple helix achieved by renucleation and local flexibility.

    Science.gov (United States)

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

    2011-07-20

    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 coefficients allowed the identification of partially folded species. When Gly was replaced by Ala, the Ala residue was incorporated into a fully folded triple helix, whereas replacement of Gly by Ser or Arg resulted in the presence of some partially folded species, suggesting a folding barrier. Increasing the triple-helix stability of the sequence N-terminal to a Gly-to-Ser replacement allowed complete triple-helix folding, whereas with the substitution of Arg, with its large side chain, the peptide achieved full folding only after flexible residues were introduced N-terminal to the mutation site. These studies shed light on the factors important for accommodation of Gly mutations within the triple helix and may relate to the varying severity of OI.

  8. Stereoelectronic and steric effects in the collagen triple helix: toward a code for strand association.

    Science.gov (United States)

    Hodges, Jonathan A; Raines, Ronald T

    2005-11-16

    Collagen is the most abundant protein in animals. The protein consists of a helix of three strands, each with sequence X-Y-Gly. Natural collagen is most stable when X is (2S)-proline (Pro) and Y is (2S,4R)-4-hydroxyproline (4R-Hyp). We had shown previously that triple helices in which X is (2S,4S)-4-fluoroproline (4S-Flp) or Y is (2S,4R)-4-fluoroproline (4R-Flp) display hyperstability. This hyperstability arises from stereoelectronic effects that preorganize the main-chain dihedral angles in the conformation found in the triple helix. Here, we report the synthesis of strands containing both 4S-Flp in the X-position and 4R-Flp in the Y-position. We find that these strands do not form a stable triple helix, presumably because of an unfavorable steric interaction between fluoro groups on adjacent strands. Density functional theory calculations indicate that (2S,3S)-3-fluoroproline (3S-Flp), like 4S-Flp, should preorganize the main chain properly for triple-helix formation but without a steric conflict. Synthetic strands containing 3S-Flp in the X-position and 4R-Flp in the Y-position do form a triple helix. This helix is, however, less stable than one with Pro in the X-position, presumably because of an unfavorable inductive effect that diminishes the strength of the interstrand 3S-FlpC=O...H-NGly hydrogen bond. Thus, other forces can counter the benefits derived from the proper preorganization. Although (Pro-Pro-Gly)7 and (4S-Flp-4R-Flp-Gly)7 do not form stable homotrimeric helices, mixtures of these two peptides form stable heterotrimeric helices containing one (Pro-Pro-Gly)7 strand and two (4S-Flp-4R-Flp-Gly)7 strands. This stoichiometry can be understood by considering the cross sections of the two possible heterotrimeric helices. This unexpected finding portends the development of a "code" for the self-assembly of determinate triple helices from two or three strands.

  9. 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

  10. Hierarchical self-assembly of designed 2x2-alpha-helix bundle proteins on Au(111) surfaces

    DEFF Research Database (Denmark)

    Wackerbarth, Hainer; Tofteng, A.P.; Jensen, K.J.

    2006-01-01

    Self-assembled monolayers of biomolecules on atomically planar surfaces offer the prospect of complex combinations of controlled properties, e. g., for bioelectronics. We have prepared a novel hemi-4-alpha-helix bundle protein by attaching two alpha-helical peptides to a cyclo-dithiothreitol (cyclo...... proteins retained. The surface properties of the DTT and 2 x 2- R-helix bundle protein adlayer were characterized by interfacial capacitance and impedance techniques. Reductive desorption was used to determine the coverage of the adlayers, giving values of 65 and 16 mu C cm(-2) for DTT and 2 x 2-helix...

  11. 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.

  12. Molecular characterization of cold-responsive basic helix-loop-helix transcription factors MabHLHs that interact with MaICE1 in banana fruit.

    Science.gov (United States)

    Peng, Huan-Huan; Shan, Wei; Kuang, Jian-Fei; Lu, Wang-Jin; Chen, Jian-Ye

    2013-11-01

    Basic helix-loop-helix (bHLH) transcription factors (TFs) are ubiquitously involved in the response of higher plants to various abiotic stresses. However, little is known about bHLH TFs involved in the cold stress response in economically important fruits. Here, five novel full-length bHLH genes, designated as MabHLH1-MabHLH5, were isolated and characterized from banana fruit. Gene expression profiles revealed that MabHLH1/2/4 were induced by cold stress and methyl jasmonate (MeJA) treatment. Transient assays in tobacco BY2 protoplasts showed that MabHLH1/2/4 promoters were activated by cold stress and MeJA treatments. Moreover, protein-protein interaction analysis demonstrated that MabHLH1/2/4 not only physically interacted with each other to form hetero-dimers in the nucleus, but also interacted with an important upstream component of cold signaling MaICE1, with different interaction domains at their N-terminus. These results indicate that banana fruit cold-responsive MabHLHs may form a big protein complex in the nucleus with MaICE1. Taken together, our findings advance our understanding of the possible involvement of bHLH TFs in the regulatory network of ICE-CBF cold signaling pathway.

  13. Mutations within or upstream of the basic helix-loop-helix domain of the TWIST gene are specific to Saethre-Chotzen syndrome.

    Science.gov (United States)

    El Ghouzzi, V; Lajeunie, E; Le Merrer, M; Cormier-Daire, V; Renier, D; Munnich, A; Bonaventure, J

    1999-01-01

    Saethre-Chotzen syndrome (ACS III) is an autosomal dominant craniosynostosis syndrome recently ascribed to mutations in the TWIST gene, a basic helix-loop-helix (b-HLH) transcription factor regulating head mesenchyme cell development during cranial neural tube formation in mouse. Studying a series of 22 unrelated ACS III patients, we have found TWIST mutations in 16/22 cases. Interestingly, these mutations consistently involved the b-HLH domain of the protein. Indeed, mutant genotypes included frameshift deletions/insertions, nonsense and missense mutations, either truncating or disrupting the b-HLH motif of the protein. This observation gives additional support to the view that most ACS III cases result from loss-of-function mutations at the TWIST locus. The P250R recurrent FGFR 3 mutation was found in 2/22 cases presenting mild clinical manifestations of the disease but 4/22 cases failed to harbour TWIST or FGFR 3 mutations. Clinical re-examination of patients carrying TWIST mutations failed to reveal correlations between the mutant genotype and severity of the phenotype. Finally, since no TWIST mutations were detected in 40 cases of isolated coronal craniosynostosis, the present study suggests that TWIST mutations are specific to Saethre-Chotzen syndrome.

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

    Directory of Open Access Journals (Sweden)

    Gutmann Anja

    2010-01-01

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

  15. 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.

  16. 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.

  17. 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.

  18. Genomics into Healthcare: the 5th Pan Arab Human Genetics Conference and 2013 Golden Helix Symposium.

    Science.gov (United States)

    Fortina, Paolo; Al Khaja, Najib; Al Ali, Mahmoud Taleb; Hamzeh, Abdul Rezzak; Nair, Pratibha; Innocenti, Federico; Patrinos, George P; Kricka, Larry J

    2014-05-01

    The joint 5th Pan Arab Human Genetics conference and 2013 Golden Helix Symposium, "Genomics into Healthcare" was coorganized by the Center for Arab Genomic Studies (http://www.cags.org.ae) in collaboration with the Golden Helix Foundation (http://www.goldenhelix.org) in Dubai, United Arab Emirates from 17 to 19 November, 2013. The meeting was attended by over 900 participants, doctors and biomedical students from over 50 countries and was organized into a series of nine themed sessions that covered cancer genomics and epigenetics, genomic and epigenetic studies, genomics of blood and metabolic disorders, cytogenetic diagnosis and molecular profiling, next-generation sequencing, consanguinity and hereditary diseases, clinical genomics, clinical applications of pharmacogenomics, and genomics in public health.

  19. Water-mediated conformational transitions in nicotinic receptor M2 helix bundles: a molecular dynamics study.

    Science.gov (United States)

    Sankararamakrishnan, R; Sansom, M S

    1995-12-27

    The ion channel of the nicotinic acetylcholine receptor is a water-filled pore formed by five M2 helix segments, one from each subunit. Molecular dynamics simulations on bundles of five M2 alpha 7 helices surrounding a central column of water and with caps of water molecules at either end of the pore have been used to explore the effects of intrapore water on helix packing. Interactions of water molecules with the N-terminal polar sidechains lead to a conformational transition from right- to left-handed supercoils during these stimulations. These studies reveal that the pore formed by the bundle of M2 helices is flexible. A structural role is proposed for water molecules in determining the geometry of bundles of isolated pore-forming helices.

  20. 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...

  1. The Effect of a Helix-Coil Transition on the Extension Elasticity

    Science.gov (United States)

    Buhot, Arnaud; Halperin, Avi

    2000-03-01

    The secondary structure of a polymer affects its deformation behavior in accordance with the Le Chatelier principle. An important example of such secondary structure is the alpha helix encountered in polypeptides. Similar structure was recently proposed for PEO in aqueous media. Our discussion concerns the coupling of the cooperative helix-coil transition and the extension elasticity. In particular, we analyze the extension of a long single chain by use of optical tweezers or AFM. We consider chains that exist in the coil-state when unperturbed. The transition nevertheless occurs because the extension favors the low entropy helical state. As a result, the corresponding force law exhibits a plateau. The analysis of this situation involves two ingredients: (I) the stretching free energy penalty for a rod-coil mutiblock copolymer (II) the entropy associated with the possible placements of the rod and coil blocks.

  2. 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...

  3. Modeling of helix molecules formation on a surface of nanotube and inside it

    Directory of Open Access Journals (Sweden)

    Belolipetskaya Anna

    2017-01-01

    Full Text Available “On-surface” synthesis of large molecules and assemblies is a great challenge in molecular electronics, biomedical devices, sensors, energy harnessing and catalysis. Usually, plane surfaces are used for these purposes. We study a possibility of macro molecules formation on the surface of nanotube and inside it. It can be used for synthesis of helix molecules, particularly, organic and biological. Nanotubes of different structures were considered. Point-like approximation is used for atoms. The Lennard-Jones 6-12 potential is taken as the interaction potential. Possibilities of helix molecules and ring-like molecules formations were shown. A hypothesis of such processes influence on the organic molecules formation during the early Earth history is suggested and discussed.

  4. 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 ...

  5. 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.

  6. 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.

  7. 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.

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

    Directory of Open Access Journals (Sweden)

    Rajamani

    2014-01-01

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

  9. 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.

  10. 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.

  11. 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.

  12. Mechanism of stabilization of a bacterial collagen triple helix in the absence of hydroxyproline.

    Science.gov (United States)

    Mohs, Angela; Silva, Teresita; Yoshida, Takeshi; Amin, Ravish; Lukomski, Slawomir; Inouye, Masayori; Brodsky, Barbara

    2007-10-12

    The Streptococcus pyogenes cell-surface protein Scl2 contains a globular N-terminal domain and a collagen-like domain, (Gly-Xaa-X'aa)(79), which forms a triple helix with a thermal stability close to that seen for mammalian collagens. Hyp is a major contributor to triple-helix stability in animal collagens, but is not present in bacteria, which lack prolyl hydroxylase. To explore the basis of bacterial collagen triple-helix stability in the absence of Hyp, biophysical studies were carried out on recombinant Scl2 protein, the isolated collagen-like domain from Scl2, and a set of peptides modeling the Scl2 highly charged repetitive (Gly-Xaa-X'aa)(n) sequences. At pH 7, CD spectroscopy, dynamic light scattering, and differential scanning calorimetry of the Scl2 protein all showed a very sharp thermal transition near 36 degrees C, indicating a highly cooperative unfolding of both the globular and triple-helix domains. The collagen-like domain isolated by trypsin digestion showed a sharp transition at the same temperature, with an enthalpy of 12.5 kJ/mol of tripeptide. At low pH, Scl2 and its isolated collagen-like domain showed substantial destabilization from the neutral pH value, with two thermal transitions at 24 and 27 degrees C. A similar destabilization at low pH was seen for Scl2 charged model peptides, and the degree of destabilization was consistent with the strong pH dependence arising from the GKD tripeptide unit. The Scl2 protein contained twice as much charge as human fibril-forming collagens, and the degree of electrostatic stabilization observed for Scl2 was similar to the contribution Hyp makes to the stability of mammalian collagens. The high enthalpic contribution to the stability of the Scl2 collagenous domain supports the presence of a hydration network in the absence of Hyp.

  13. Triple Helix model of relations among university, industry and governments: a critical analysis

    OpenAIRE

    González de la Fe, Teresa

    2009-01-01

    In this essay, I attend to the Triple Helix Model of rela tions among university, industry and government, broadly used in innovation studies. The model was proposed by Henry Etzkowitz and Löet Leyersdorf and it has been very succesful as a heuristic for analysis of innovation process and as a normative guide for innovation policies. Moreover, its theoretical foundations are suited with perspectives from evolutive and institutionalist theories of economic science, at the same time that it tak...

  14. Systematische Untersuchungen zum Helix-Knäuel-Übergang in meta-Phenylenethinylen Polymeren

    OpenAIRE

    Kaiser, Christian

    2010-01-01

    The Sonogashira-Polycondensation, based on chiral AB’-monomers, can be used to construct different substituted and chiral, defect-free structures of PmPE`s. The optical properties of the polymers can be investigated by the methods of absorption-, fluorescence- or CD-spectroscopy. For synthesized PmPE`s the helix-coil-transition from a helical ordered state to an extended random conformation is characteristic, originating from solvophobic interactions with the solvent. Thereby, a different beh...

  15. 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...

  16. Contributions of cation-π interactions to the collagen triple helix stability.

    Science.gov (United States)

    Chen, Chia-Ching; Hsu, Wei; Hwang, Kuo-Chu; Hwu, Jih Ru; Lin, Chun-Cheng; Horng, Jia-Cherng

    2011-04-01

    Cation-π interactions are found to be an important noncovalent force in proteins. Collagen is a right-handed triple helix composed of three left-handed PPII helices, in which (X-Y-Gly) repeats dominate in the sequence. Molecular modeling indicates that cation-π interactions could be formed between the X and Y positions in adjacent collagen strands. Here, we used a host-guest peptide system: (Pro-Hyp-Gly)(3)-(Pro-Y-Gly-X-Hyp-Gly)-(Pro-Hyp-Gly)(3), where X is an aromatic residue and Y is a cationic residue, to study the cation-π interaction in the collagen triple helix. Circular dichroism (CD) measurements and Tm data analysis show that the cation-π interactions involving Arg have a larger contribution to the conformational stability than do those involving Lys, and Trp forms a weaker cation-π interaction with cationic residues than expected as a result of steric effects. The results also show that the formation of cation-π interactions between Arg and Phe depends on their relative positions in the strand. Moreover, the fluorinated and methylated Phe substitutions show that an electron-withdrawing or electron-donating substituent on the aromatic ring can modulate its π-electron density and the cation-π interaction in collagen. Our data demonstrate that the cation-π interaction could play an important role in stabilizing the collagen triple helix.

  17. Rational design of a non-canonical "sticky-ended" collagen triple helix.

    Science.gov (United States)

    Jalan, Abhishek A; Jochim, Katherine A; Hartgerink, Jeffrey D

    2014-05-28

    In a canonical collagen triple helix, three peptides self-assemble into a supercoiled motif with a one-amino-acid offset between the peptide chains. Design of triple helices that contain more than one residue offset is lucrative, as it leaves the non-covalent interactions unsatisfied at the termini and renders the termini "sticky" to further self-assemble into collagen-like nanofibers. Here we use lysine-glutamate axial salt-bridges to design a heterotrimeric collagen triple helix, ABC-1, containing a non-canonical offset of four residues between the peptide chains. The four-residue offset is necessary to prevent aggregation, which would prevent characterization of the non-canonical chain arrangement at the molecular level by NMR spectroscopy. A second heterotrimer, ABC-2, also stabilized by axial salt-bridges, is designed containing a canonical one-amino-acid offset to facilitate comparison of structure and stability by CD and NMR. ABC-1 and ABC-2 demonstrate our ability to modulate chain offset in a collagen triple helix. This lays the groundwork to design longer, and therefore stickier, offsets allowing access to a new class of collagen-related nanostructures.

  18. The lncRNA HOTAIR impacts on mesenchymal stem cells via triple helix formation.

    Science.gov (United States)

    Kalwa, Marie; Hänzelmann, Sonja; Otto, Sabrina; Kuo, Chao-Chung; Franzen, Julia; Joussen, Sylvia; Fernandez-Rebollo, Eduardo; Rath, Björn; Koch, Carmen; Hofmann, Andrea; Lee, Shih-Han; Teschendorff, Andrew E; Denecke, Bernd; Lin, Qiong; Widschwendter, Martin; Weinhold, Elmar; Costa, Ivan G; Wagner, Wolfgang

    2016-12-15

    There is a growing perception that long non-coding RNAs (lncRNAs) modulate cellular function. In this study, we analyzed the role of the lncRNA HOTAIR in mesenchymal stem cells (MSCs) with particular focus on senescence-associated changes in gene expression and DNA-methylation (DNAm). HOTAIR binding sites were enriched at genomic regions that become hypermethylated with increasing cell culture passage. Overexpression and knockdown of HOTAIR inhibited or stimulated adipogenic differentiation of MSCs, respectively. Modification of HOTAIR expression evoked only very moderate effects on gene expression, particularly of polycomb group target genes. Furthermore, overexpression and knockdown of HOTAIR resulted in DNAm changes at HOTAIR binding sites. Five potential triple helix forming domains were predicted within the HOTAIR sequence based on reverse Hoogsteen hydrogen bonds. Notably, the predicted triple helix target sites for these HOTAIR domains were also enriched in differentially expressed genes and close to DNAm changes upon modulation of HOTAIR Electrophoretic mobility shift assays provided further evidence that HOTAIR domains form RNA-DNA-DNA triplexes with predicted target sites. Our results demonstrate that HOTAIR impacts on differentiation of MSCs and that it is associated with senescence-associated DNAm. Targeting of epigenetic modifiers to relevant loci in the genome may involve triple helix formation with HOTAIR.

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

    Science.gov (United States)

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

    2015-02-03

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

  20. Statistical mechanical model for a closed loop plectoneme with weak helix specific forces.

    Science.gov (United States)

    Lee, Dominic J O'

    2017-04-12

    We develop a statistical mechanical framework, based on a variational approximation, to describe closed loop plectonemes. This framework incorporates weak helix structure dependent forces into the determination of the free energy and average structure of a plectoneme. Notably, due to their chiral nature, helix structure dependent forces break the symmetry between left and right handed supercoiling. The theoretical approach, presented here, also provides a systematic way of enforcing the topological constraint of closed loop supercoiling in the variational approximation. At large plectoneme lengths, by considering correlation functions in an expansion in terms of the spatial mean twist density about its thermally averaged value, it can be argued that topological constraint may be approximated by replacing twist and writhe by their thermal averages. A Lagrange multiplier, containing the sum of average twist and writhe, can be added to the free energy to conveniently inforce this result. The average writhe can be calculated through the thermal average of the Gauss' integral in the variational approximation. Furthermore, this approach allows for a possible way to calculate finite size corrections due to the topological constraint. Using interaction energy terms from the mean-field Kornyshev-Leikin theory, for parameter values that correspond to weak helix dependent forces, we calculate the free energy, fluctuation magnitudes and mean geometric parameters for the plectoneme. We see a slight asymmetry, where interestingly, left handed supercoils have a looser structure than right handed ones, although with a lower free energy, unlike what the previous ground state calculations would suggest.

  1. Structure of the Membrane Anchor of Pestivirus Glycoprotein Erns, a Long Tilted Amphipathic Helix

    Science.gov (United States)

    Aberle, Daniel; Muhle-Goll, Claudia; Bürck, Jochen; Wolf, Moritz; Reißer, Sabine; Luy, Burkhard; Wenzel, Wolfgang; Ulrich, Anne S.; Meyers, Gregor

    2014-01-01

    Erns is an essential virion glycoprotein with RNase activity that suppresses host cellular innate immune responses upon being partially secreted from the infected cells. Its unusual C-terminus plays multiple roles, as the amphiphilic helix acts as a membrane anchor, as a signal peptidase cleavage site, and as a retention/secretion signal. We analyzed the structure and membrane binding properties of this sequence to gain a better understanding of the underlying mechanisms. CD spectroscopy in different setups, as well as Monte Carlo and molecular dynamics simulations confirmed the helical folding and showed that the helix is accommodated in the amphiphilic region of the lipid bilayer with a slight tilt rather than lying parallel to the surface. This model was confirmed by NMR analyses that also identified a central stretch of 15 residues within the helix that is fully shielded from the aqueous layer, which is C-terminally followed by a putative hairpin structure. These findings explain the strong membrane binding of the protein and provide clues to establishing the Erns membrane contact, processing and secretion. PMID:24586172

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

    Institute of Scientific and Technical Information of China (English)

    SU; Yanhui(苏彦辉); QU; Hong(曲红); Vachon; Vincent; LUO; Jingchu(罗静初); ZHANG; Jie(张杰); Laprade; Raynald; ZHU; Yuxian(朱玉贤)

    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.

  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. 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.

  5. Structural dynamics of a single-stranded RNA–helix junction using NMR

    Science.gov (United States)

    Eichhorn, Catherine D.; Al-Hashimi, Hashim M.

    2014-01-01

    Many regulatory RNAs contain long single strands (ssRNA) that adjoin secondary structural elements. Here, we use NMR spectroscopy to study the dynamic properties of a 12-nucleotide (nt) ssRNA tail derived from the prequeuosine riboswitch linked to the 3′ end of a 48-nt hairpin. Analysis of chemical shifts, NOE connectivity, 13C spin relaxation, and residual dipolar coupling data suggests that the first two residues (A25 and U26) in the ssRNA tail stack onto the adjacent helix and assume an ordered conformation. The following U26-A27 step marks the beginning of an A6-tract and forms an acute pivot point for substantial motions within the tail, which increase toward the terminal end. Despite substantial internal motions, the ssRNA tail adopts, on average, an A-form helical conformation that is coaxial with the helix. Our results reveal a surprising degree of structural and dynamic complexity at the ssRNA–helix junction, which involves a fine balance between order and disorder that may facilitate efficient pseudoknot formation on ligand recognition. PMID:24742933

  6. Left-handed polyproline-II helix revisited: proteins causing proteopathies.

    Science.gov (United States)

    Adzhubei, Alexei A; Anashkina, Anastasia A; Makarov, Alexander A

    2016-09-28

    Left-handed polyproline-II type helix is a regular conformation of polypeptide chain not only of fibrous, but also of folded and natively unfolded proteins and peptides. It is the only class of regular secondary structure substantially represented in non-fibrous proteins and peptides on a par with right-handed alpha-helix and beta-structure. In this study, we have shown that polyproline-II helix is abundant in several peptides and proteins involved in proteopathies, the amyloid-beta peptides, protein tau and prion protein. Polyproline-II helices form two interaction sites in the amyloid-beta peptides, which are pivotal for pathogenesis of Alzheimer's disease (AD). It also with high probability is the structure of the majority of tau phosphorylation sites, important for tau hyperphosphorylation and formation of neurofibrillary tangles, a hallmark of AD. Polyproline-II helices form large parts of the structure of the folded domain of prion protein. They can undergo conversion to beta-structure as a result of relatively small change of one torsional angle of polypeptide chain. We hypothesize that in prions and amyloids, in general polyproline-II helices can serve as structural elements of the normal structure as well as dormant nuclei of structure conversion, and thus play important role in structure changes leading to the formation of fibrils.

  7. Different effects of 4-hydroxyproline and 4-fluoroproline on the stability of collagen triple helix.

    Science.gov (United States)

    Nishi, Yoshinori; Uchiyama, Susumu; Doi, Masamitsu; Nishiuchi, Yuji; Nakazawa, Takashi; Ohkubo, Tadayasu; Kobayashi, Yuji

    2005-04-26

    Differential scanning calorimetry (DSC) analyses of a series of collagen model peptides suggest that 4-hydroxyproline (Hyp) and 4-fluoroproline (fPro) have different effects on the stability of the collagen triple helices according to the sequence of amino acids and stereochemistry at the 4 positions of these imino acids. The thermodynamic parameters indicate that the enhanced stabilities are classified into two different types: the enthalpy term is primarily responsible for the enhanced stability of the triple helix of (Pro-Hyp(R)-Gly)(10), whereas the entropy term dominates the enhanced stability of (Pro-fPro(R)-Gly)(10). The difference between the molecular volumes observed in solution and intrinsic molecular volumes calculated from the crystal structure indicates the different hydration states of these peptides. (Pro-Hyp(R)-Gly)(10) is highly hydrated compared to (Pro-Pro-Gly)(10), which contributes to the larger enthalpy. In contrast, the volume of (Pro-fPro(R)-Gly)(10) shows a smaller degree of hydration than that of (Pro-Pro-Gly)(10). The entropic cost of forming the triple helix of the fPro-containing peptides is compensated by a decrease in an ordered structure of water molecules surrounding the peptide molecule, although the contribution of enthalpy originating from the hydration is reduced. These arguments about the different contribution of entropic and enthalpic terms were successfully applied to interpret the stability of the triple helix of (fPro(S)-Pro-Gly)(10) as well.

  8. Role of side chains in collagen triple helix stabilization and partner recognition.

    Science.gov (United States)

    Berisio, Rita; De Simone, Alfonso; Ruggiero, Alessia; Improta, Roberto; Vitagliano, Luigi

    2009-03-01

    Collagen is a widespread protein family involved in a variety of biological processes. The complexity of collagen and its fibrous nature prevent detailed investigations on the full-length protein. Reductionist approaches conducted by dissecting the protein complexity through the use of model peptides have proved to be quite effective. There are, however, several issues regarding structure-stability relationships, aggregation in higher-order assemblies, and partner recognition that are still extensively investigated. In this review, we discuss the role that side chains play in triple helix stabilization and in partner recognition. On the basis of recent literature data, we show that collagen triple helix stability is the result of the interplay of different factors. As a general trend, interactions established by amino/imino acid side chains within the triple helix scaffold effectively modulate the intrinsic residue propensity for this common structural motif. The use of peptide models has also highlighted the role that side chains play in collagen self-association and in its interactions with receptors. Valuable examples in these fields are illustrated. Finally, future actions required to obtain more detailed information on the structure and the function of this complex protein are also delineated.

  9. A triple helix within a pseudoknot is a conserved and essential element of telomerase RNA.

    Science.gov (United States)

    Shefer, Kinneret; Brown, Yogev; Gorkovoy, Valentin; Nussbaum, Tamar; Ulyanov, Nikolai B; Tzfati, Yehuda

    2007-03-01

    Telomerase copies a short template within its integral telomerase RNA onto eukaryotic chromosome ends, compensating for incomplete replication and degradation. Telomerase action extends the proliferative potential of cells, and thus it is implicated in cancer and aging. Nontemplate regions of telomerase RNA are also crucial for telomerase function. However, they are highly divergent in sequence among species, and their roles are largely unclear. Using in silico three-dimensional modeling, constrained by mutational analysis, we propose a three-dimensional model for a pseudoknot in telomerase RNA of the budding yeast Kluyveromyces lactis. Interestingly, this structure includes a U-A.U major-groove triple helix. We confirmed the triple-helix formation in vitro using oligoribonucleotides and showed that it is essential for telomerase function in vivo. While triplex-disrupting mutations abolished telomerase function, triple compensatory mutations that formed pH-dependent G-C.C(+) triples restored the pseudoknot structure in a pH-dependent manner and partly restored telomerase function in vivo. In addition, we identified a novel type of triple helix that is formed by G-C.U triples, which also partly restored the pseudoknot structure and function. We propose that this unusual structure, so far found only in telomerase RNA, provides an essential and conserved telomerase-specific function.

  10. Crystal structure of the collagen triple helix model [(Pro-Pro-Gly)(10)](3).

    Science.gov (United States)

    Berisio, Rita; Vitagliano, Luigi; Mazzarella, Lelio; Zagari, Adriana

    2002-02-01

    The first report of the full-length structure of the collagen-like polypeptide [(Pro-Pro-Gly)(10)](3) is given. This structure was obtained from crystals grown in a microgravity environment, which diffracted up to 1.3 A, using synchrotron radiation. The final model, which was refined to an R(factor) of 0.18, is the highest-resolution description of a collagen triple helix reported to date. This structure provides clues regarding a series of aspects related to collagen triple helix structure and assembly. The strict dependence of proline puckering on the position inside the Pro-Pro-Gly triplets and the correlation between backbone and side chain dihedral angles support the propensity-based mechanism of triple helix stabilization/destabilization induced by hydroxyproline. Furthermore, the analysis of [(Pro-Pro-Gly)(10)](3) packing, which is governed by electrostatic interactions, suggests that charges may act as locking features in the axial organization of triple helices in the collagen fibrils.

  11. Does alpha-helix folding necessarily provide an energy source for the protein-lipid binding?

    Science.gov (United States)

    Gursky, Olga

    2007-01-01

    Lipid-induced alpha-helix folding, which occurs in many lipid surface-binding proteins and peptides such as apolipoproteins and synucleins, has been proposed to provide an energy source for protein-lipid interactions. We propose that in a system comprised of a phospholipid surface and a small polypeptide that is unfolded in solution and binds reversibly to lipid surface, helical folding involves expenditure of free energy as compared to a similar polypeptide that is alpha-helical in solution. This is a consequence of the entropic cost of helix folding that is illustrated in a simple thermodynamic model and exemplifies the general "key-into-lock" paradigm of protein-ligand binding. Even though this simple model does not explicitly address the protein-induced lipid re-arrangement and may not directly apply to large proteins that undergo significant tertiary structural changes upon lipid binding, it suggests that the notion of helix folding as an energy source for lipid binding should be treated with caution.

  12. 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.

  13. 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

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

  14. 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)....

  15. Personas as a method for applying gender theory in Triple Helix constellations:experiences from two research projects

    OpenAIRE

    Wikberg-Nilsson, Åsa; Källhammer, Eva; Fältholm, Ylva; Abrahamsson, Lena

    2010-01-01

    In focus in this paper is the use of the Persona method for applying gender theory in Triple Helix systems. Whereas such systems often are considered gender neutral, we in contrast emphasize the need for understanding the process of ‘doing gender' within those constellations. The aim of this paper is to describe our experiences of developing Persona as a method for gender equality interventions within two Triple Helix constellations. The personas are fictional characters addressing issues and...

  16. Alterations in tumorigenicity of embryonal carcinoma cells by IGF-I triple-helix induced changes in immunogenicity and apoptosis.

    Science.gov (United States)

    Ly, A; Francois, J C; Upegui-Gonzalez, L C; Swiercz, B; Bedel, C; Duc, H T; Bout, D; Trojan, J

    2000-12-08

    IGF-I antisense gene therapy has been applied successfully to animal models of glioma, hepatoma and teratocarcinoma. The antisense strategy has shown that tumor cells transfected with vectors encoding IGF-I antisense RNA lose tumorigenicity, become immunogenic and are associated with tumor specific immune response involving CD8+ lymphocytes. An IGF-I triple helix approach to gene therapy for glioma was recently described. The approach we have taken is to establish parameters of change using the IGF-I triple helix strategy. PCC-3 embryonal carcinoma cells derived from murine teratocarcinoma which express IGF-I were used as a model. The cells were transfected with vector which encodes an oligoribonucleotide that forms RNA-IGF-I DNA triple-helix structure. The triple-helix stops the production of IGF-I. Cells transfected in this manner underwent changes in phenotype and an increase in MHC-I and B-7 cell surface molecules. They also showed enhancement in the production of apoptotic cells (60-70%). The "triple helix" transfected cells lost the ability to induce tumor when injected subcutaneously in syngeneic 129 Sv mice. When co-transfected in vitro with expression vectors encoding both MHC-I and B-7 cDNA in antisense orientation, the "triple-helix" transfected cells were down-regulated in expression of MHC-I and B-7 and the number of apoptotic cells was significantly decreased. Injection of the doubly co-transfected cells into 129 Sv mice was associated with induction of teratocarcinoma. Comparison between antisense and triple-helix transfected cells strategies showed similar immunogenic and apoptotic changes. The findings suggest that triple-helix technology may offer a new clinical approach to treatement of tumors expressing IGF-I.

  17. Encoding physico-chemical cues in synthetic hydrogels by triple helix assembly of collagen mimetic peptides

    Science.gov (United States)

    Stahl, Patrick

    The ECM is a complex natural system evolved to promote proliferation and differentiation of cells during tissue development. In order to create synthetic biomaterials for studying cell-scaffold interactions and ultimately for engineering tissues, scientists strive to recapitulate many characteristics of ECM by developing hydrogels that contain mechanical cues and biochemical signals such as adhesion moieties and cell growth factors. While synthetic hydrogels bypass limitations of naturally-derived materials (e.g. transfer of pathogens), nature provides inspiration to enhance the functionality of synthetic hydrogels through biomimetic approaches. The collagen triple helix is the basis for the supramolecular structure of collagen in the ECM, and its adaptation in collagen mimetic peptides (CMPs) has provided hybridization mechanisms that can be employed in the formation and functionalization of synthetic hydrogels. The aim of this dissertation is to develop novel poly(ethylene glycol) (PEG)-based hydrogels that employ CMP triple helix assembly as a non-covalent yet target-specific tool to encode physical and chemical cues into the hydrogel with spatial control. We demonstrate that multi-arm PEG functionalized with CMPs form hydrogels supported by physical crosslinks mediated by CMP triple helix. Particle tracking microrheology shows that these physical crosslinks are sensitive to temperature as well as addition of exogenous CMPs that can disrupt crosslinks by competing for triple helix formation. This physical crosslink disruption enables the modulation of bulk hydrogel elasticity and the introduction of local stiffness gradients in PEG-CMP hydrogels. We also present photopolymerized PEG diacrylate (PEGDA) hydrogels displaying CMPs that can be further conjugated to CMPs with bioactive moieties via triple helix hybridization. Encoding these hydrogels with cell-adhesive CMPs induces cell spreading and proliferation. We further demonstrate generation of gradients and

  18. Structure and Biophysical Properties of a Triple-Stranded Beta-Helix Comprising the Central Spike of Bacteriophage T4.

    Science.gov (United States)

    Buth, Sergey A; Menin, Laure; Shneider, Mikhail M; Engel, Jürgen; Boudko, Sergei P; Leiman, Petr G

    2015-08-18

    Gene product 5 (gp5) of bacteriophage T4 is a spike-shaped protein that functions to disrupt the membrane of the target cell during phage infection. Its C-terminal domain is a long and slender β-helix that is formed by three polypeptide chains wrapped around a common symmetry axis akin to three interdigitated corkscrews. The folding and biophysical properties of such triple-stranded β-helices, which are topologically related to amyloid fibers, represent an unsolved biophysical problem. Here, we report structural and biophysical characterization of T4 gp5 β-helix and its truncated mutants of different lengths. A soluble fragment that forms a dimer of trimers and that could comprise a minimal self-folding unit has been identified. Surprisingly, the hydrophobic core of the β-helix is small. It is located near the C-terminal end of the β-helix and contains a centrally positioned and hydrated magnesium ion. A large part of the β-helix interior comprises a large elongated cavity that binds palmitic, stearic, and oleic acids in an extended conformation suggesting that these molecules might participate in the folding of the complete β-helix.

  19. Structure and Biophysical Properties of a Triple-Stranded Beta-Helix Comprising the Central Spike of Bacteriophage T4

    Directory of Open Access Journals (Sweden)

    Sergey A. Buth

    2015-08-01

    Full Text Available Gene product 5 (gp5 of bacteriophage T4 is a spike-shaped protein that functions to disrupt the membrane of the target cell during phage infection. Its C-terminal domain is a long and slender β-helix that is formed by three polypeptide chains wrapped around a common symmetry axis akin to three interdigitated corkscrews. The folding and biophysical properties of such triple-stranded β-helices, which are topologically related to amyloid fibers, represent an unsolved biophysical problem. Here, we report structural and biophysical characterization of T4 gp5 β-helix and its truncated mutants of different lengths. A soluble fragment that forms a dimer of trimers and that could comprise a minimal self-folding unit has been identified. Surprisingly, the hydrophobic core of the β-helix is small. It is located near the C-terminal end of the β-helix and contains a centrally positioned and hydrated magnesium ion. A large part of the β-helix interior comprises a large elongated cavity that binds palmitic, stearic, and oleic acids in an extended conformation suggesting that these molecules might participate in the folding of the complete β-helix.

  20. 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

  1. Basic helix-loop-helix transcription factor Bmsage is involved in regulation of fibroin H-chain gene via interaction with SGF1 in Bombyx mori.

    Science.gov (United States)

    Zhao, Xiao-Ming; Liu, Chun; Li, Qiong-Yan; Hu, Wen-Bo; Zhou, Meng-Ting; Nie, Hong-Yi; Zhang, Yin-Xia; Peng, Zhang-Chuan; Zhao, Ping; Xia, Qing-You

    2014-01-01

    Silk glands are specialized in the synthesis of several secretory proteins. Expression of genes encoding the silk proteins in Bombyx mori silk glands with strict territorial and developmental specificities is regulated by many transcription factors. In this study, we have characterized B. mori sage, which is closely related to sage in the fruitfly Drosophila melanogaster. It is termed Bmsage; it encodes transcription factor Bmsage, which belongs to the Mesp subfamily, containing a basic helix-loop-helix motif. Bmsage transcripts were detected specifically in the silk glands of B. mori larvae through RT-PCR analysis. Immunoblotting analysis confirmed the Bmsage protein existed exclusively in B. mori middle and posterior silk gland cells. Bmsage has a low level of expression in the 4th instar molting stages, which increases gradually in the 5th instar feeding stages and then declines from the wandering to the pupation stages. Quantitative PCR analysis suggested the expression level of Bmsage in a high silk strain was higher compared to a lower silk strain on day 3 of the larval 5th instar. Furthermore, far western blotting and co-immunoprecipitation assays showed the Bmsage protein interacted with the fork head transcription factor silk gland factor 1 (SGF1). An electrophoretic mobility shift assay showed the complex of Bmsage and SGF1 proteins bound to the A and B elements in the promoter of fibroin H-chain gene(fib-H), respectively. Luciferase reporter gene assays confirmed the complex of Bmsage and SGF1 proteins increased the expression of fib-H. Together, these results suggest Bmsage is involved in the regulation of the expression of fib-H by being together with SGF1 in B. mori PSG cells.

  2. A genome-wide identification and analysis of the basic helix-loop-helix transcription factors in the ponerine ant, Harpegnathos saltator

    Directory of Open Access Journals (Sweden)

    Liu Ake

    2012-08-01

    Full Text Available Abstract Background The basic helix-loop-helix (bHLH transcription factors and their homologs form a superfamily that plays essential roles in transcriptional networks of multiple developmental processes. bHLH family members have been identified in over 20 organisms, including fruit fly, zebrafish, human and mouse. Result In this study, we conducted a genome-wide survey for bHLH sequences, and identified 57 bHLH sequences encoded in complete genome sequence of the ponerine ant, Harpegnathos saltator. Phylogenetic analysis of the bHLH domain sequences classified these genes into 38 bHLH families with 23, 14, 10, 1, 8 and 1 members in group A, B, C, D, E and F, respectively. The number of PabHLHs (ponerine ant bHLHs with introns is higher than many other insect species, and they are found to have introns with average lengths only inferior to those of pea aphid. In addition, two H. saltator bHLHs named PaCrp1 and PaSide locate on two separate contigs in the genome. Conclusions A putative full set of PabHLH genes is comparable with other insect species and genes encoding Oligo, MyoRb and Figα were not found in genomes of all insect species of which bHLH family members have been identified. Moreover, in-family phylogenetic analyses indicate that the PabHLH genes are more closely related with Apis mellifera than others. The present study will serve as a solid foundation for further investigations into the structure and function of bHLH proteins in the regulation of H. saltator development.

  3. Temperature-Triggered Switchable Helix-Helix Inversion of Poly(phenylacetylene Bearing l-Valine Ethyl Ester Pendants and Its Chiral Recognition Ability

    Directory of Open Access Journals (Sweden)

    Yanli Zhou

    2016-11-01

    Full Text Available A phenylacetylene containing the l-valine ethyl ester pendant (PAA-Val was synthesized and polymerized by an organorhodium catalyst (Rh(nbdBPh4 to produce the corresponding one-handed helical cis-poly(phenylacetylene (PPAA-Val. PPAA-Val showed a unique temperature-triggered switchable helix-sense in chloroform, while it was not observed in highly polar solvents, such as N,N′-dimethylformamide (DMF. By heating the solution of PPAA-Val in chloroform, the sign of the CD absorption became reversed, but recovered after cooling the solution to room temperature. Even after six cycles of the heating-cooling treatment, the helix sense of the PPAA-Val’s backbone was still switchable without loss of the CD intensity. The PPAA-Val was then coated on silica gel particles to produce novel chiral stationary phases (CSPs for high-performance liquid chromatography (HPLC. These novel PPAA-Val based CSPs showed a high chiral recognition ability for racemic mandelonitrile (α = 2.18 and racemic trans-N,N′-diphenylcyclohexane-1,2-dicarboxamide (α = 2.60. Additionally, the one-handed helical cis-polyene backbone of PPAA-Val was irreversibly destroyed to afford PPAA-Val-H by heating in dimethyl sulfoxide (DMSO accompanied by the complete disappearance of the Cotton effect. Although PPAA-Val-H had the same l-valine ethyl ester pendants as its cis-isomer PPAA-Val, it showed no chiral recognition. It was concluded that the one-handed helical cis-polyene backbone of PPAA-Val plays an important role in the chiral recognition ability.

  4. 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.

  5. The Thermo Scientific HELIX-SFT noble gas mass spectrometer: (preliminary) performance for 40Ar/39Ar geochronology

    Science.gov (United States)

    Barfod, D. N.; Mark, D. F.; Morgan, L. E.; Tomkinson, T.; Stuart, F.; Imlach, J.; Hamilton, D.

    2011-12-01

    The Thermo Scientific HELIX-platform Split Flight Tube (HELIX-SFT) noble gas mass spectrometer is specifically designed for simultaneous collection of helium isotopes. The high mass spur houses a switchable 1011 - 1012 Ω resistor Faraday cup and the low mass spur a digital pulse-counting secondary electron multiplier (SEM). We have acquired the HELIX-SFT with the specific intention to measure argon isotopes for 40Ar/39Ar geochronology. This contribution will discuss preliminary performance (resolution, reproducibility, precision etc.) with respect to measuring argon isotope ratios for 40Ar/39Ar dating of geological materials. We anticipate the greatest impact for 40Ar/39Ar dating will be increased accuracy and precision, especially as we approach the techniques younger limit. Working with Thermo Scientific we have subtly modified the source, alpha and collector slits of the HELIX-SFT mass spectrometer to improve its resolution for resolving isobaric interferences at masses 36 to 40. The enhanced performance will allow for accurate and precise measurement of argon isotopes. Preliminary investigations show that we can obtain a valley resolution of >700 and >1300 (compared to standard HELIX-SFT specifications of >400 and >700) for the high and low mass spurs, respectively. The improvement allows for full resolution of hydrocarbons (C3+) at masses 37 - 40 and almost full resolution at mass 36. The HELIX-SFT will collect data in dual collection mode with 40Ar+ ion beams measured using the switchable 1011 - 1012 Ω resistor Faraday cup and 39Ar through 36Ar measured using the SEM. The HELIX-SFT requires Faraday-SEM inter-calibration but negates the necessity to inter-calibrate multiple electron multipliers. We will further present preliminary data from the dating of mineral standards: Alder Creek sanidine, Fish Canyon sanidine and Mount Dromedary biotite (GA1550).

  6. Fullerene-Assisted Photoinduced Charge Transfer of Single-Walled Carbon Nanotubes through a Flavin Helix.

    Science.gov (United States)

    Mollahosseini, Mehdi; Karunaratne, Erandika; Gibson, George N; Gascón, Jose A; Papadimitrakopoulos, Fotios

    2016-05-11

    One of the greatest challenges with single-walled carbon nanotube (SWNT) photovoltaics and nanostructured devices is maintaining the nanotubes in their pristine state (i.e., devoid of aggregation and inhomogeneous doping) so that their unique spectroscopic and transport characteristics are preserved. To this effect, we report on the synthesis and self-assembly of a C60-functionalized flavin (FC60), composed of PCBM and isoalloxazine moieties attached on either ends of a linear, C-12 aliphatic spacer. Small amounts of FC60 (up to 3 molar %) were shown to coassembly with an organic soluble derivative of flavin (FC12) around SWNTs and impart effective dispersion and individualization. A key annealing step was necessary to perfect the isoalloxazine helix and expel the C60 moiety away from the nanotubes. Steady-state and transient absorption spectroscopy illustrate that 1% or higher incorporation of FC60 allows for an effective photoinduced charge transfer quenching of the encased SWNTs through the seamless helical encase. This is enabled via the direct π-π overlap between the graphene sidewalls, isoalloxazine helix, and the C60 cage that facilitates SWNT exciton dissociation and electron transfer to the PCBM moiety. Atomistic molecular simulations indicate that the stability of the complex originates from enhanced van der Waals interactions of the flexible spacer wrapped around the fullerene that brings the C60 in π-π overlap with the isoalloxazine helix. The remarkable spectral purity (in terms of narrow E(S)ii line widths) for the resulting ground-state complex signals a new class of highly organized supramolecular nanotube architecture with profound importance for advanced nanostructured devices.

  7. The NC2 domain of type IX collagen determines the chain register of the triple helix.

    Science.gov (United States)

    Boudko, Sergei P; Bächinger, Hans Peter

    2012-12-28

    Precise mapping and unraveling the mechanism of interaction or degradation of a certain type of collagen triple helix requires the generation of short and stable collagenous fragments. This is a great challenge especially for hetero-trimeric collagens, where chain composition and register (stagger) are important factors. No system has been reported that can be efficiently used to generate a natural collagenous fragment with exact chain composition and desired chain register. The NC2 domain (only 35-50 residues) of FACIT collagens is a potent trimerization domain. In the case of type IX collagen it provides the efficient selection and hetero-trimerization of three distinct chains. The ability of the NC2 domain to determine the chain register of the triple helix is studied. We generated three possible sequence combinations (α1α1α2, α1α2α1, α2α1α1) of a type I collagen fragment (the binding region for the von Willebrand factor A3 domain) attached to the NC2 domain. In addition, two control combinations were produced that constitute homo-trimers of (α1)(3) or (α2)(3). For the hetero-trimeric constructs, α1α1α2 demonstrated a higher melting temperature than the other two. Binding experiments with the von Willebrand factor A3 domain revealed the homo-trimer of (α1)(3) as the strongest binding construct, whereas the homo-trimer of (α2)(3) showed no binding. For hetero-trimers, α1α1α2 was found to be the strongest binding construct. Differences in thermal stability and binding to the A3 domain unambiguously demonstrate that the NC2 domain of type IX collagen determines not only the chain composition but also the chain register of the adjacent triple helix.

  8. Helix-like biopolymers can act as dampers of force for bacteria in flows.

    Science.gov (United States)

    Zakrisson, Johan; Wiklund, Krister; Axner, Ove; Andersson, Magnus

    2012-06-01

    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 for moderate flows (~25 mm/s) the force experienced by the adhesin-receptor interaction at the tip of the pilus can be reduced by a factor of ~6 and ~4, respectively. The uncoiling ability provides a bacterium with a "go with the flow" possibility that acts as a damping. It is surmised that this can be an important factor for the initial part of the adhesion process, in particular in turbulent flows, and thereby be of use for bacteria in their striving to survive a natural defense such as fluid rinsing actions.

  9. 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.

  10. Sodium ascorbate improves yield of urinary steroids during hydrolysis with Helix pomatia juice.

    Science.gov (United States)

    Christakoudi, Sofia; Cowan, David A; Taylor, Norman F

    2008-03-01

    Urinary steroid profile analysis requires enzymatic hydrolysis of glucuronide and sulfate conjugates and this is achieved simultaneously using Helix pomatia juice (HPJ), but steroids with 3beta-hydroxy-5-ene structure undergo transformation and yield of 5alpha-reduced corticosteroid glucuronides is poor. We describe the use of sodium ascorbate to solve these problems and provide a basis for its mode of action. Steroid conjugates were extracted from urine, hydrolyzed in acetate buffer with HPJ and sodium ascorbate and analyzed as methyloxime-trimethylsilylether derivatives by gas chromatography-mass spectrometry. Ranges of temperature, pH and ascorbate, substrate and HPJ concentrations were compared for urine and pure standards. Activity of other antioxidants and that of bacterial cholesterol oxidase were examined. Helix pomatia enzyme preparations from different commercial sources were compared. Loss of 3beta-hydroxy-5-ene steroids was enzyme-dependant, since it required HPJ, was saturable, subject to substrate competition and heat-inactivated. Products were 3-oxo-4-ene steroids and 4,6-diene and 6-oxy derivatives of these but the latter were not formed from 3-oxo-4-ene precursors. Ascorbate, other antioxidants or oxygen exclusion diminished activity. These characteristics were shared by cholesterol oxidase. Yield of 5alpha-reduced steroids was diminished by pre-incubation of HPJ before ascorbate addition and this was reversed if ascorbate was added to the pre-incubation mixture. We conclude that transformation of 3beta-hydroxy-5-ene steroids by HPJ is due to cholesterol oxidase and is diminished by antioxidants or oxygen denial. Yield of 5alpha-reduced steroids is low due to oxidative damage of beta-glucuronidase during hydrolysis, prevented by ascorbate. These features are shared by most commercial Helix pomatia enzyme preparations tested.

  11. 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.

  12. 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.

  13. Sequence selective recognition of double-stranded RNA using triple helix-forming peptide nucleic acids.

    Science.gov (United States)

    Zengeya, Thomas; Gupta, Pankaj; Rozners, Eriks

    2014-01-01

    Noncoding RNAs are attractive targets for molecular recognition because of the central role they play in gene expression. Since most noncoding RNAs are in a double-helical conformation, recognition of such structures is a formidable problem. Herein, we describe a method for sequence-selective recognition of biologically relevant double-helical RNA (illustrated on ribosomal A-site RNA) using peptide nucleic acids (PNA) that form a triple helix in the major grove of RNA under physiologically relevant conditions. Protocols for PNA preparation and binding studies using isothermal titration calorimetry are described in detail.

  14. 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.

  15. Modified quad helix appliance for thumb sucking and cross bite correction

    Directory of Open Access Journals (Sweden)

    C Vinay

    2013-01-01

    Full Text Available Digit sucking habit is a learned pattern of behavior commonly seen in children of preschool age. Prolonged digit sucking beyond the preschool age, lead to the development of malocclusion such as anterior open bite, maxillary constriction and posterior crossbite. Treatment strategies include interception of habit and correction of the malocclusion. The present case report describes a modified quad helix appliance used successfully in a 9-year-old child to intercept thumb sucking habit and simultaneous correction of posterior crossbite. The appliance has the advantage of easy fabrication, being versatile and more patients compliant.

  16. The Human Early-Life Exposome (HELIX): Project Rationale and Design

    Science.gov (United States)

    Slama, Rémy; Robinson, Oliver; Chatzi, Leda; Coen, Muireann; van den Hazel, Peter; Thomsen, Cathrine; Wright, John; Athersuch, Toby J.; Avellana, Narcis; Basagaña, Xavier; Brochot, Celine; Bucchini, Luca; Bustamante, Mariona; Carracedo, Angel; Casas, Maribel; Estivill, Xavier; Fairley, Lesley; van Gent, Diana; Gonzalez, Juan R.; Granum, Berit; Gražulevicˇiene˙, Regina; Gutzkow, Kristine B.; Julvez, Jordi; Keun, Hector C.; Kogevinas, Manolis; McEachan, Rosemary R.C.; Meltzer, Helle Margrete; Sabidó, Eduard; Schwarze, Per E.; Siroux, Valérie; Sunyer, Jordi; Want, Elizabeth J.; Zeman, Florence; Nieuwenhuijsen, Mark J.

    2014-01-01

    Background: Developmental periods in early life may be particularly vulnerable to impacts of environmental exposures. Human research on this topic has generally focused on single exposure–health effect relationships. The “exposome” concept encompasses the totality of exposures from conception onward, complementing the genome. Objectives: The Human Early-Life Exposome (HELIX) project is a new collaborative research project that aims to implement novel exposure assessment and biomarker methods to characterize early-life exposure to multiple environmental factors and associate these with omics biomarkers and child health outcomes, thus characterizing the “early-life exposome.” Here we describe the general design of the project. Methods: In six existing birth cohort studies in Europe, HELIX will estimate prenatal and postnatal exposure to a broad range of chemical and physical exposures. Exposure models will be developed for the full cohorts totaling 32,000 mother–child pairs, and biomarkers will be measured in a subset of 1,200 mother–child pairs. Nested repeat-sampling panel studies (n = 150) will collect data on biomarker variability, use smartphones to assess mobility and physical activity, and perform personal exposure monitoring. Omics techniques will determine molecular profiles (metabolome, proteome, transcriptome, epigenome) associated with exposures. Statistical methods for multiple exposures will provide exposure–response estimates for fetal and child growth, obesity, neurodevelopment, and respiratory outcomes. A health impact assessment exercise will evaluate risks and benefits of combined exposures. Conclusions: HELIX is one of the first attempts to describe the early-life exposome of European populations and unravel its relation to omics markers and health in childhood. As proof of concept, it will form an important first step toward the life-course exposome. Citation: Vrijheid M, Slama R, Robinson O, Chatzi L, Coen M, van den Hazel P

  17. 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.

  18. Phytophthora tropicalis on Hedera helix and Epipremnum aureum in Polish greenhouses.

    Science.gov (United States)

    Orlikowski, L B; Trzewik, A; Wiejacha, K

    2006-01-01

    Phytophthora tropicalis was isolated from Hedera helix and Epipremnum aureum showing discoloration of leaves, necrosis of shoot base, spread upwards and on roots. The species was detected from 7/8 plants of Hedera and 3/4 of Epipremnum. Additionally Botrytis cinerea, Fusarium avenaceum and Rhizoctonia solani were recovered from some of diseased plants. P. tropicalis caused leaf necrosis of 13 plant species and tomato seedlings. The quickest spread of necrosis was observed on leaves of Peperomia magnoliaefolia, Pelargonium zonale and Phalaenopsis x hybridum. The disease developed at temperature ranged from 10 degrees to 32.5 degrees C with optimum 30 degrees C.

  19. 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.

  20. Effects of some heavy metals on the action potentials of an identified Helix pomatia photosensitive neuron.

    Science.gov (United States)

    Kartelija, Gordana; Radenović, Lidija; Todorović, Natasa; Nedeljković, Miodrag

    2005-06-01

    In the photosensitive MB neuron in the left parietal ganglion of Helix pomatia, the onset of light prolongs significantly (by about 40%) the duration of the action potential. The broadening of the action potential after the onset of light was found to be due to its calcium component and could not be induced after blocking Ca(2+) channels by Cd(2+) and Pb(2+) and in absence of Ca(2+) in medium. The blocking effect of both compounds was reversible. It was found that CdCl(2) exhibited a more intense blocking effect than PbCl(2).

  1. 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.

  2. Modelling H2 Infrared Emission of the Helix Nebula Cometary Knots

    CERN Document Server

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

    2010-01-01

    In the present work, we use a photoionisation code to study the H2 emission of the Helix nebula (NGC 7293) cometary knots, particularly that produced in the interface H+/H0 of the knot, where a significant fraction of the H2 1-0 S(1) emission seems to be produced. Our results show that the production of molecular hydrogen in such region may explain several characteristics of the observed emission, particularly the high excitation temperature of the H2 infrared lines.

  3. 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.

  4. The effect of C-terminal helix on the stability of FF domain studied by molecular dynamics simulation.

    Science.gov (United States)

    Zhao, Liling; Cao, Zanxia; Wang, Jihua

    2012-01-01

    To investigate the effect of C-terminal helix on the stability of the FF domain, we studied the native domain FF3-71 from human HYPA/FBP11 and the truncated version FF3-60 with C-terminal helix being deleted by molecular dynamics simulations with GROMACS package and GROMOS 43A1 force field. The results indicated that the structures of truncated version FF3-60 were evident different from those of native partner FF3-71. Compared with FF3-71, the FF3-60 lost some native contacts and exhibited some similar structural characters to those of intermediate state. The C-terminal helix played a major role in stabilizing the FF3-71 domain. To a certain degree, the FF domain had a tendency to form an intermediate state without the C-terminal helix. In our knowledge, this was the first study to examine the role of C-terminal helix of FF domain in detail by molecular dynamics simulations, which was useful to understand the three-state folding mechanism of the small FF domain.

  5. 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.

  6. A hydrophobic patch surrounding Trp154 in human neuroserpin controls the helix F dynamics with implications in inhibition and aggregation

    Science.gov (United States)

    Ali, Mohammad Farhan; Kaushik, Abhinav; Kapil, Charu; Gupta, Dinesh; Jairajpuri, Mohamad Aman

    2017-01-01

    Neuroserpin (NS) mediated inhibition of tissue-type plasminogen activator (tPA) is important for brain development, synapse formation and memory. Aberrations in helix F and β-sheet A movement during inhibition can directly lead to epilepsy or dementia. Conserved W154 residue in a hydrophobic patch between helix F and β-sheet A is ideally placed to control their movement during inhibition. Molecular Dynamics (MD) simulation on wild type (WT) NS and its two variants (W154A and W154P) demonstrated partial deformation in helix F and conformational differences in strands 1A and 2A only in W154P. A fluorescence and Circular Dichroism (CD) analysis with purified W154 variants revealed a significant red-shift and an increase in α-helical content in W154P as compared to W154A and WT NS. Kinetics of tPA inhibition showed a decline in association rates (ka) for W154A as compared to WT NS with indication of complex formation. Appearance of cleaved without complex formation in W154P indicates that the variant acts as substrate due to conformational misfolding around helix F. Both the variants however showed increased rate of aggregation as compared to WT NS. The hydrophobic patch identified in this study may have importance in helix F dynamics of NS. PMID:28230174

  7. 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

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. Mechanical evaluation of quad-helix appliance made of low-nickel stainless steel wire

    Directory of Open Access Journals (Sweden)

    Rogério Lacerda dos Santos

    2013-06-01

    Full Text Available OBJECTIVE: The objective of this study was to test the hypothesis that there is no difference between stainless steel and low-nickel stainless steel wires as regards mechanical behavior. Force, resilience, and elastic modulus produced by Quad-helix appliances made of 0.032-inch and 0.036-inch wires were evaluated. METHODS: Sixty Quad-helix appliances were made, thirty for each type of alloy, being fifteen for each wire thickness, 0.032-in and 0.036-in. All the archwires were submitted to mechanical compression test using an EMIC DL-10000 machine simulating activations of 4, 6, 9, and 12 mm. Analysis of variance (ANOVA with multiple comparisons and Tukey's test were used (p < 0.05 to assess force, resilience, and elastic modulus. RESULTS: Statistically significant difference in the forces generated, resilience and elastic modulus were found between the 0.032-in 0.036-in thicknesses (p < 0.05. CONCLUSIONS: Appliances made of low-nickel stainless steel alloy had force, resilience, and elastic modulus similar to those made of stainless steel alloy.

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

    Science.gov (United States)

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

    2014-02-01

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

  14. 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.

  15. ELISA for Determination of Human Growth Hormone: Recognition of Helix 4 Epitopes

    Directory of Open Access Journals (Sweden)

    Moura Juliana F.

    2004-01-01

    Full Text Available Human growth hormone (hGH signal transduction initiates with a receptor dimerization in which one molecule binds to the receptor through sites 1 and 2. A sandwich enzyme-linked immunosorbent assay was developed for quantifying hGH molecules that present helix 4 from binding site 1. For this, horse anti-rhGH antibodies were eluted by an immunoaffinity column constituted by sepharose-rhGH. These antibodies were purified through a second column with synthetic peptide correspondent to hGH helix 4, immobilized to sepharose, and used as capture antibodies. Those that did not recognize synthetic peptide were used as a marker antibody. The working range was of 1.95 to 31.25 ng/mL of hGH. The intra-assay coefficient of variation (CV was between 4.53% and 6.33%, while the interassay CV was between 6.00% and 8.27%. The recovery range was between 96.0% to 103.8%. There was no cross-reactivity with human prolactin. These features show that our assay is an efficient method for the determination of hGH.

  16. Helix stabilization of amphipathic peptides by hydrocarbon stapling increases cholesterol efflux by the ABCA1 transporter.

    Science.gov (United States)

    Sviridov, D O; Ikpot, I Z; Stonik, J; Drake, S K; Amar, M; Osei-Hwedieh, D O; Piszczek, G; Turner, S; Remaley, A T

    2011-07-08

    Apolipoprotein mimetic peptides are short amphipathic peptides that efflux cholesterol from cells by the ABCA1 transporter and are being investigated as therapeutic agents for cardiovascular disease. We examined the role of helix stabilization of these peptides in cholesterol efflux. A 23-amino acid long peptide (Ac-VLEDSFKVSFLSALEEYTKKLNTQ-NH2) based on the last helix of apoA-I (A10) was synthesized, as well as two variants, S1A10 and S2A10, in which the third and fourth and third and fifth turn of each peptide, respectively, were covalently joined by hydrocarbon staples. By CD spectroscopy, the stapled variants at 24 °C were more helical in aqueous buffer than A10 (A10 17%, S1A10 62%, S2A10 97%). S1A10 and S2A10 unlike A10 were resistant to proteolysis by pepsin and chymotrypsin. S1A10 and S2A10 showed more than a 10-fold increase in cholesterol efflux by the ABCA1 transporter compared to A10. In summary, hydrocarbon stapling of amphipathic peptides increases their helicity, makes them resistant to proteolysis and enhances their ability to promote cholesterol efflux by the ABCA1 transporter, indicating that this peptide modification may be useful in the development of apolipoprotein mimetic peptides.

  17. Poly(A) Tail Recognition by a Viral RNA Element Through Assembly of a Triple Helix

    Energy Technology Data Exchange (ETDEWEB)

    M Mitton-Fry; S DeGregorio; J Wang; T Steitz; J Steitz

    2011-12-31

    Kaposi's sarcoma-associated herpesvirus produces a highly abundant, nuclear noncoding RNA, polyadenylated nuclear (PAN) RNA, which contains an element that prevents its decay. The 79-nucleotide expression and nuclear retention element (ENE) was proposed to adopt a secondary structure like that of a box H/ACA small nucleolar RNA (snoRNA), with a U-rich internal loop that hybridizes to and protects the PAN RNA poly(A) tail. The crystal structure of a complex between the 40-nucleotide ENE core and oligo(A){sub 9} RNA at 2.5 angstrom resolution reveals that unlike snoRNAs, the U-rich loop of the ENE engages its target through formation of a major-groove triple helix. A-minor interactions extend the binding interface. Deadenylation assays confirm the functional importance of the triple helix. Thus, the ENE acts as an intramolecular RNA clamp, sequestering the PAN poly(A) tail and preventing the initiation of RNA decay.

  18. 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.

  19. Nonlinear optical response of the collagen triple helix and second harmonic microscopy of collagen liquid crystals

    Science.gov (United States)

    Deniset-Besseau, A.; De Sa Peixoto, P.; Duboisset, J.; Loison, C.; Hache, F.; Benichou, E.; Brevet, P.-F.; Mosser, G.; Schanne-Klein, M.-C.

    2010-02-01

    Collagen is characterized by triple helical domains and plays a central role in the formation of fibrillar and microfibrillar networks, basement membranes, as well as other structures of the connective tissue. Remarkably, fibrillar collagen exhibits efficient Second Harmonic Generation (SHG) and SHG microscopy proved to be a sensitive tool to score fibrotic pathologies. However, the nonlinear optical response of fibrillar collagen is not fully characterized yet and quantitative data are required to further process SHG images. We therefore performed Hyper-Rayleigh Scattering (HRS) experiments and measured a second order hyperpolarisability of 1.25 10-27 esu for rat-tail type I collagen. This value is surprisingly large considering that collagen presents no strong harmonophore in its amino-acid sequence. In order to get insight into the physical origin of this nonlinear process, we performed HRS measurements after denaturation of the collagen triple helix and for a collagen-like short model peptide [(Pro-Pro-Gly)10]3. It showed that the collagen large nonlinear response originates in the tight alignment of a large number of weakly efficient harmonophores, presumably the peptide bonds, resulting in a coherent amplification of the nonlinear signal along the triple helix. To illustrate this mechanism, we successfully recorded SHG images in collagen liquid solutions by achieving liquid crystalline ordering of the collagen triple helices.

  20. On the Helix Propensity in Generalized Born Solvent Descriptions of Modeling the Dark Proteome

    Science.gov (United States)

    Olson, Mark A.

    2017-01-01

    Intrinsically disordered proteins that populate the so-called “Dark Proteome” offer challenging benchmarks of atomistic simulation methods to accurately model conformational transitions on a multidimensional energy landscape. This work explores the application of parallel tempering with implicit solvent models as a computational framework to capture the conformational ensemble of an intrinsically disordered peptide derived from the Ebola virus protein VP35. A recent X-ray crystallographic study reported a protein-peptide interface where the VP35 peptide underwent a folding transition from a disordered form to a helix-β-turn-helix topological fold upon molecular association with the Ebola protein NP. An assessment is provided of the accuracy of two generalized Born solvent models (GBMV2 and GBSW2) using the CHARMM force field and applied with temperature-based replica exchange dynamics to calculate the disorder propensity of the peptide and its probability density of states in a continuum solvent. A further comparison is presented of applying an explicit/implicit solvent hybrid replica exchange simulation of the peptide to determine the effect of modeling water interactions at the all-atom resolution. PMID:28197405

  1. 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.

  2. Vibron-polaron in a three-dimensional model of alpha-helix proteins

    CERN Document Server

    Falvo, C; Falvo, Cyril; Pouthier, Vincent J.C.

    2005-01-01

    The vibron dynamics associated to amide-I vibrations in a 3D alpha-helix protein is described according to a generalized Davydov model. The protein is modeled by three spines of hydrogen-bonded peptide units linked via covalent bonds. To remove the vibron-phonon coupling, a Lang-Firsov transformation is performed and a mean field procedure is applied to reach the dressed vibron point of view. It is shown that the vibron dynamics results from the competition between inter-spine and intra-spine vibron hops and that the two kinds of hopping processes do not experience the same dressing mechanism. Therefore, at low temperature (or weak vibron-phonon coupling), the polaron behaves as an undressed vibron delocalized over all the spines whereas at biological temperature (or strong vibron-phonon coupling), the dressing effect strongly reduces the vibrational exchanges between different spines. As a result the polaron propagates along a single spine as in the 1D Davydov model. Although the helix supports both acoustic...

  3. Role of the future creative universities in the triple helix of science and technology corridors

    Directory of Open Access Journals (Sweden)

    Iraj nabipour

    2015-01-01

    Full Text Available The science and technology corridor is a complex cluster containing universities, science parks, research centers, high-tech companies, venture capital, institutional and physical infrastructures, and human capital in a defined geography with its unique management and legal structure in association with the business space and knowledge-based products. In fact, the science and technology corridor reflects the concept of development based on the knowledge region (the especial region for science and technology. The knowledge region is clearly a triple helix phenomenon par excellence: universities, governments and businesses combine their efforts to construct a common advantage which they would not be able to offer on their own. The future creative universities in connection with the knowledge city-regions not only will deal with innovation and entrepreneurial training but also produce a competitive, vibrant environment with high indices for quality of life and full of green technologies. In this article, we will present functional interactions of the creative universities in the triple helix, particularly the missions for the Iranian universities of medical sciences. As a theoretical model, the complex interactions of Bushehr University of Medical Sciences and Health Services with Bushehr Science and Technology Corridor will be discussed.

  4. Molecular mechanism of polyacrylate helix sense switching across its free energy landscape.

    Science.gov (United States)

    Pietropaolo, Adriana; Nakano, Tamaki

    2013-04-17

    Helical polymers with switchable screw sense are versatile frameworks for chiral functional materials. In this work, we reconstructed the free energy landscape of helical poly(2,7-bis(4-tert-butylphenyl)fluoren-9-yl acrylate) [poly(BBPFA)], as its racemization is selectively driven by light without any rearrangement of chemical bonds. The chirality inversion was enforced by atomistic free energy simulations using chirality indices as reaction coordinates. The free energy landscape reproduced the experimental electronic circular dichroism spectra. We propose that the chirality inversion of poly(BBPFA) proceeds from a left-handed 31 helix via multistate free energy pathways to reach the right-handed 31 helix. The inversion is triggered by the rotation of biphenyl units with an activation barrier of 38 kcal/mol. To the best of our knowledge, this is the first report on the chiral inversion mechanism of a helical polymer determined in a quantitative way in the framework of atomistic free energy simulations.

  5. STIM1 activates CRAC channels through rotation of the pore helix to open a hydrophobic gate

    Science.gov (United States)

    Yamashita, Megumi; Yeung, Priscilla S.-W.; Ing, Christopher E.; McNally, Beth A.; Pomès, Régis; Prakriya, Murali

    2017-02-01

    Store-operated Ca2+ release-activated Ca2+ (CRAC) channels constitute a major pathway for Ca2+ influx and mediate many essential signalling functions in animal cells, yet how they open remains elusive. Here, we investigate the gating mechanism of the human CRAC channel Orai1 by its activator, stromal interacting molecule 1 (STIM1). We find that two rings of pore-lining residues, V102 and F99, work together to form a hydrophobic gate. Mutations of these residues to polar amino acids produce channels with leaky gates that conduct ions in the resting state. STIM1-mediated channel activation occurs through rotation of the pore helix, which displaces the F99 residues away from the pore axis to increase pore hydration, allowing ions to flow through the V102-F99 hydrophobic band. Pore helix rotation by STIM1 also explains the dynamic coupling between CRAC channel gating and ion selectivity. This hydrophobic gating mechanism has implications for CRAC channel function, pharmacology and disease-causing mutations.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. A Novel Approach for Modeling and Simulation of Helix Twisting Structure Based on Mass-Spring Model

    Directory of Open Access Journals (Sweden)

    Zhongbin Wang

    2013-01-01

    Full Text Available In order to improve the modeling efficiency and realize the deformation simulation of helix twisting structure, a computer-aided design system based on mass-spring model is developed. The geometry structure of helix twisting structure is presented and mass-spring model is applied in the deformation simulation. Moreover, the key technologies such as coordinate mapping, system render and system architecture are elaborated. Finally, a prototype system is developed with Visual C++ and OpenGL, and the proposed system is proved efficient through a comparison experiment.

  11. Crystal Structure of the Signaling Helix Coiled-coil Domain of the b1 Subunit of the Soluble guanylyl Cyclase

    Energy Technology Data Exchange (ETDEWEB)

    Ma, X.; Beuve, A; van den Akker, F

    2010-01-01

    The soluble guanylyl cyclase (sGC) is a heterodimeric enzyme that, upon activation by nitric oxide, stimulates the production of the second messenger cGMP. Each sGC subunit harbor four domains three of which are used for heterodimerization: H-NOXA/H-NOBA domain, coiled-coil domain (CC), and catalytic guanylyl cyclase domain. The CC domain has previously been postulated to be part of a larger CC family termed the signaling helix (S-helix) family. Homodimers of sGC have also been observed but are not functionally active yet are likely transient awaiting their intended heterodimeric partner. To investigate the structure of the CC S-helix region, we crystallized and determined the structure of the CC domain of the sGC{beta}1 subunit comprising residues 348-409. The crystal structure was refined to 2.15 {angstrom} resolution. The CC structure of sGC{beta}1 revealed a tetrameric arrangement comprised of a dimer of CC dimers. Each monomer is comprised of a long a-helix, a turn near residue P399, and a short second a-helix. The CC structure also offers insights as to how sGC homodimers are not as stable as (functionally) active heterodimers via a possible role for inter-helix salt-bridge formation. The structure also yielded insights into the residues involved in dimerization. In addition, the CC region is also known to harbor a number of congenital and man-made mutations in both membrane and soluble guanylyl cyclases and those function-affecting mutations have been mapped onto the CC structure. This mutant analysis indicated an importance for not only certain dimerization residue positions, but also an important role for other faces of the CC dimer which might perhaps interact with adjacent domains. Our results also extend beyond guanylyl cyclases as the CC structure is, to our knowledge, the first S-helix structure and serves as a model for all S-helix containing family members.

  12. Crystal structure of the signaling helix coiled-coil domain of the β1 subunit of the soluble guanylyl cyclase

    Directory of Open Access Journals (Sweden)

    van den Akker Focco

    2010-01-01

    Full Text Available Abstract Background The soluble guanylyl cyclase (sGC is a heterodimeric enzyme that, upon activation by nitric oxide, stimulates the production of the second messenger cGMP. Each sGC subunit harbor four domains three of which are used for heterodimerization: H-NOXA/H-NOBA domain, coiled-coil domain (CC, and catalytic guanylyl cyclase domain. The CC domain has previously been postulated to be part of a larger CC family termed the signaling helix (S-helix family. Homodimers of sGC have also been observed but are not functionally active yet are likely transient awaiting their intended heterodimeric partner. Results To investigate the structure of the CC S-helix region, we crystallized and determined the structure of the CC domain of the sGCβ1 subunit comprising residues 348-409. The crystal structure was refined to 2.15 Å resolution. Conclusions The CC structure of sGCβ1 revealed a tetrameric arrangement comprised of a dimer of CC dimers. Each monomer is comprised of a long a-helix, a turn near residue P399, and a short second a-helix. The CC structure also offers insights as to how sGC homodimers are not as stable as (functionally active heterodimers via a possible role for inter-helix salt-bridge formation. The structure also yielded insights into the residues involved in dimerization. In addition, the CC region is also known to harbor a number of congenital and man-made mutations in both membrane and soluble guanylyl cyclases and those function-affecting mutations have been mapped onto the CC structure. This mutant analysis indicated an importance for not only certain dimerization residue positions, but also an important role for other faces of the CC dimer which might perhaps interact with adjacent domains. Our results also extend beyond guanylyl cyclases as the CC structure is, to our knowledge, the first S-helix structure and serves as a model for all S-helix containing family members.

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

    DEFF Research Database (Denmark)

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

    1993-01-01

    directed from the beta-turn region toward the receptor-binding region. This overall dipole moment is antiparallel to the dipole moment of the alpha-helix caused by alignment of the peptide dipoles parallel to the helix. Calculations of the stabilization energy for this antiparallel dipole moment...... forces alone when the screening effect is considered. This energy is of the same order of magnitude as the enthalpy change for the unfolding of avian PP (approximately 30 kcal/mol), strongly indicating that the charge-dipole interactions are of significant importance for the stability of the three...

  14. Snail meat: Significance and consumption

    OpenAIRE

    Dragićević Olgica; Baltić Milan Ž.

    2005-01-01

    The consumption of snail meat goes back to prehistoric times. Different ancient nations had snails on their menu, but Helices culture as a productive activity was born as a Roman culture. Some of the most economically important edible species are: Helix aspersa (Mtiller) Helixpomatia (Linne), Helix iucorum (Linne), Helix aperta (Born), Eobania vermiculata (Miiller). Together with its tasie, snail meat has several advantages over others: quite low lipid rate and calorie values versus rich mine...

  15. 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

    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...

  16. 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.

  17. 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.

  18. Formation of the triple-stranded polynucleotide helix, poly(A.A.U).

    Science.gov (United States)

    Broitman, S L; Im, D D; Fresco, J R

    1987-08-01

    A polynucleotide helical structure containing two strands of poly(A) and one of poly(U) is reported. As shown by spectroscopic observations, the complex only forms when the poly(A) strands are of Mr between 9000 and 50,000 (degree of polymerization congruent to 28-150), whereas the size of the poly(U) strand has no effect. This limitation may explain why poly(A.A.U) was not seen in previous investigations. The potential of the poly(A) tails of mRNA for formation of this triple helix and of A.A.U or/and A.A.T triplet formation to contribute to the binding of specific RNA strands to gene-encoding nucleic acid double helices are noted.

  19. Control of Spin Helix Symmetry in Semiconductor Quantum Wells by Crystal Orientation

    Science.gov (United States)

    Kammermeier, Michael; Wenk, Paul; Schliemann, John

    2016-12-01

    We investigate the possibility of spin-preserving symmetries due to the interplay of Rashba and Dresselhaus spin-orbit coupling in n -doped zinc-blende semiconductor quantum wells of general crystal orientation. It is shown that a conserved spin operator can be realized if and only if at least two growth direction Miller indices agree in modulus. The according spin-orbit field has in general both in-plane and out-of-plane components and is always perpendicular to the shift vector of the corresponding persistent spin helix. We also analyze higher-order effects arising from the Dresselhaus term, and the impact of our results on weak (anti)localization corrections.

  20. A Debris Disk around the Central Star of the Helix Nebula?

    CERN Document Server

    Su, K Y L; Rieke, G H; Huggins, P J; Gruendl, R; Napiwotzki, R; Rauch, T; Latter, W B; Volk, K; Su, Kate Y. L.

    2007-01-01

    Excess emission from a point-like source coincident with the central star of the Helix Nebula is detected with Spitzer at 8, 24, and 70 um. At 24 um, the central source is superposed on an extended diffuse emission region. While the [OIV] 25.89 um line contributes to the diffuse emission, a 10-35 um spectrum of the central source shows a strong thermal continuum. The excess emission from the star most likely originates from a dust disk with blackbody temperatures of 90--130 K. Assuming a simple optically thin debris disk model, the dust is distributed in a ring between ~35 and ~150 AU from the central star, possibly arising from collisions of Kuiper-Belt-like Objects or the break-up of comets from an Oort-like cloud that have survived from the post-main-sequence evolution of the central star.

  1. Solvent-Exposed Salt Bridges Influence the Kinetics of α-Helix Folding and Unfolding.

    Science.gov (United States)

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

    2014-03-06

    Salt bridges are known to play an essential role in the thermodynamic stability of the folded conformation of many proteins, but their influence on the kinetics of folding remains largely unknown. Here, we investigate the effect of Glu-Arg salt bridges on the kinetics of α-helix folding using temperature-jump transient-infrared spectroscopy and steady-state UV circular dichroism. We find that geometrically optimized salt bridges (Glu(-) and Arg(+) are spaced four peptide units apart, and the Glu/Arg order is such that the side-chain rotameric preferences favor salt-bridge formation) significantly speed up folding and slow down unfolding, whereas salt bridges with unfavorable geometry slow down folding and slightly speed up unfolding. Our observations suggest a possible explanation for the surprising fact that many biologically active proteins contain salt bridges that do not stabilize the native conformation: these salt bridges might have a kinetic rather than a thermodynamic function.

  2. Postembryonic neurogenesis in the procerebrum of the terrestrial snail, Helix lucorum L

    Science.gov (United States)

    Zakharov, I. S.; Hayes, N. L.; Ierusalimsky, V. N.; Nowakowski, R. S.; Balaban, P. M.

    1998-01-01

    Neuronogenesis during posthatching development of the procerebrum of the terrestrial snail Helix lucorum was analyzed using bromodeoxyuridine immunohistochemistry to label proliferating cells. Comparison of the distribution of labeled cells in a series of animals which differed in age at the time of incubation with bromodeoxyuridine, in survival time after incubation, and in age at sacrifice reveals a clear pattern and developmental sequence in neuron origin. First, the proliferating cells are located only at the apical portion of the procerebrum. Second, cells which are produced at any particular age remain, for the most part, confined to a single layer in the procerebrum. Third, as development proceeds, each layer of previously produced neurons is displaced toward the basal part of the procerebrum by the production of additional neurons. Our results suggest that the vast majority of the neurons (probably about 70-80%) of the snail procerebrum are produced during the first 1-2 months of posthatching development.

  3. 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. Investigation of the effects of electron plasma frequency on the operation of a helix TWT

    Science.gov (United States)

    Oksuz, Lutfi; Haytural, Necati; Uygun, Emre; Bozduman, Ferhat; Yesiltepe, Hakan; Gulec, Ali

    2016-10-01

    The oscillations of electrons are an important subject for the design procedure of linear beam tubes such as klystrons and TWTs. These oscillation frequencies may be affected by the finite region of the tube if the plasma wavelength of the electrons are larger than the bounding region of the device, leading to a reduced plasma frequency which further leads to an increase in wavelength. Following the Pierce's theory on traveling wave tubes, it is seen that the reduced plasma frequency takes place in space charge terms which also include the Pierce's gain parameter C. In this study the effects of plasma frequency on the operation of a helix TWT are investigated using CST Particle Studio. This project is supported by TUBITAK with project number: 1140075.

  5. Biochemical characterization and helix stabilizing properties of HSNP-C' from the thermoacidophilic archaeon Sulfolobus acidocaldarius.

    Science.gov (United States)

    Celestina, F; Suryanarayana, T

    2000-01-19

    Helix stabilizing nucleoid protein HSNP-C' from the thermophilic archaeon Sulfolobus acidocaldarius has been characterized with respect to its interactions with nucleic acids by gel retardation assay, affinities to immobilized matrices, electron microscopy, and fluorescence titration. The amino acids implicated in the DNA binding site of the protein have been shown by selectively modifying specific amino acyl functional groups and looking at their effects on the DNA binding properties of the protein. Lysine, arginine, tryptophan, and tyrosine residues of the protein HSNP-C' were modified with pyridoxal-5-phosphate; 2,3-butanedione; BNPS-skatole; and tetranitromethane, respectively. The modification of residues was assessed according to standard procedures. The effect of the chemical modification on the function of the protein HSNP-C' with respect to DNA protein interactions was studied and the results indicate the definite involvement of tyrosines and also the significant involvement of the flanking tryptophan residues in the DNA binding domain on the protein.

  6. 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

    targeting. Disruptive mutations (L348R or Δ324-339) lowered the secretory amplitude by decreasing vesicle priming, whereas P335A markedly increased priming and secretory amplitude. The mutants displayed unchanged kinetics and Ca(2+) dependence of fusion, indicating that the mutations specifically affect...... the vesicle priming step. Mutation of a nearby tyrosine (Y337A), which interacts with closed syntaxin-1, mildly increased secretory amplitude. This correlated with results from an in vitro fusion assay probing the functions of Munc18-1, indicating an easier transition to the extended state in the mutant. Our...... findings support the notion that a conformational transition within the Munc18-1 domain 3a helix 12 leads to opening of a closed Munc18-1:syntaxin complex, followed by productive SNARE complex assembly and vesicle priming. SIGNIFICANCE STATEMENT: The essential postdocking role of Munc18-1 in vesicular...

  7. The double helix revisited: a paradox of science and a paradigm of human behaviour

    Directory of Open Access Journals (Sweden)

    Argüelles, Juan Carlos

    2007-06-01

    Full Text Available In the modern history of Science, few breakthroughs have caused an impact comparative to the Double Helix, the three-dimensional structure of DNA proposed by Watson & Crick in 1953, an event whose 50th anniversary was widely celebrated in the non-specialist media, three years ago. Although the discovery had little transcendence at the time, it has unquestionably been of great importance ever since. The Double Helix has underlined the true biological value of nucleic acids compared with proteins, demonstrating that genes are not amorphous entities but have a specific chemical composition and adopt an ordered spatial folding pattern. Elucidation of this key configuration made it possible to establish a direct relationship between the structure and the function of macromolecules, a relationship which is not so clear in the case of proteins. During these last fifty years much has been written and argued about the circumstances surrounding the discovery and about the behaviour and attitudes of many of the protagonists. Besides Watson & Crick, other scientists, whose contribution has not been adequately recognised, played an important part in solving the Double Helix mystery. This article contains some ethical and scientific reflections which revise some of these essential contributions and throws light on the role played in history by these comparatively «unknown soldiers» of science. The Double Helix story is undoubtedly a manifestation of the human side of science and many scientists believe that the available evidence taken as a whole permits an alternative story to be written.

    En la desarrollo histórico de la Ciencia moderna, pocos descubrimientos han causado un impacto comparativo a las repercusiones de la Doble Hélice, la estructura tridimensional del ADN, propuesta por Watson y Crick en 1953. El 50º aniversario de aquel evento fue ampliamente celebrado hace tres años, incluso por los medios no especializados en informaci

  8. 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.

  9. 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.

  10. 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.

  11. Hoogsteen-position pyrimidines promote the stability and function of the MALAT1 RNA triple helix.

    Science.gov (United States)

    Brown, Jessica A; Kinzig, Charles G; DeGregorio, Suzanne J; Steitz, Joan A

    2016-05-01

    Triple-stranded RNA was first deduced to form in vitro more than 50 years ago and has since been implicated in RNA catalysis, stability, and small molecule binding. Despite the emerging biological significance of RNA triple helices, it remains unclear how their nucleotide composition contributes to their thermodynamic stability and cellular function. To investigate these properties, we used in vitro RNA electrophoretic mobility shift assays (EMSAs) and in vivo intronless β-globin reporter assays to measure the relative contribution of 20 RNA base triples (N•A-U, N•G-C, N•C-G, N•U-A, and N•G-U) to triple-helical stability. These triples replaced a single internal U•A-U within the known structure of the triple-helical RNA stability element of human metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), which contains 10 major-groove base triples. In addition to the canonical C•G-C triple, the noncanonical base triples U•G-C, U•G-U, C•C-G, and U•C-G exhibited at least 30% stability relative to the wild-type U•A-U base triple in both assays. Of these triples, only U•A-U, C•G-C, and U•G-C, when tested as four successive triples, formed stabilizing structures that allowed accumulation of the intronless β-globin reporter. Overall, we find that Hoogsteen-position pyrimidines support triple helix stability and function and that thermodynamic stability, based on EMSA results, is necessary but not sufficient for stabilization activity of the MALAT1 triple helix in cells. These results suggest that additional RNA triple helices containing noncanonical triples likely exist in nature.

  12. Kinetic analysis of oligodeoxyribonucleotide-directed triple-helix formation on DNA.

    Science.gov (United States)

    Maher, L J; Dervan, P B; Wold, B J

    1990-09-18

    Pyrimidine oligonucleotides recognize extended purine sequences in the major groove of double-helical DNA by triple-helix formation. The resulting local triple helices are relatively stable and can block DNA recognition by sequence-specific DNA binding proteins such as restriction endonucleases. Association and dissociation kinetics for the oligodeoxyribonucleotide 5'-CTCTTTCCTCTCTTTTTCCCC (bold C's indicate 5-methylcytosine residues) are now measured with a restriction endonuclease protection assay. When oligonucleotides are present in greater than 10-fold excess over the DNA target site, the binding reaction kinetics are pseudo first order in oligonucleotide concentration. Under our standard conditions (37 degrees C, 25 mM Tris-acetate, pH 6.8, 70 mM sodium chloride, 20 mM magnesium chloride, 0.4 mM spermine tetrahydrochloride, 10 mM beta-mercaptoethanol, 0.1 mg/mL bovine serum albumin) the value of the observed pseudo-first-order association rate constant, k2obs, is 1.8 x 10(3) +/- 1.9 x 10(2) L.(mol of oligomer-1.s-1. Measurement of the dissociation rate constant yields an equilibrium dissociation constant of approximately 10 nM. Increasing sodium ion concentration slightly decreased the association rate, substantially increased the dissociation rate, and thereby reduced the equilibrium binding constant. This effect was reversible by increasing multivalent cation concentration, confirming the significant role of multivalent cations in oligonucleotide-directed triple-helix formation under these conditions. Finally, a small reduction in association rate, a large increase in dissociation rate, and a resulting reduction in the equilibrium binding constant were observed upon increasing the pH between 6.8 and 7.2.

  13. 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.

  14. [Fifty years ago, the double helix gave birth to molecular biology].

    Science.gov (United States)

    Lunardi, J

    2003-01-01

    Fifty years ago, a paper signed by two young scientists, James Watson and Francis Crick, and reporting a model for DNA based on a double helix structure was published in the scientific review Nature in date of april 25, 1953. Although this model of striking simplicity and rare elegance was actually worked out in a few months by the two men, it was the result of quite 100 years of research aimed at the definition of the structure of the genetic material present in living organisms. The double helix was the outcome of a multidisciplinary approach initiated in the mid 19th century by the genetic laws of Gregor Mendel and the discovery of the chemical nature of the desoxyribonucleic acid by Johann Friedrich Miesher. The discovery of the DNA structure had been at the origin of major scientific progress regarding mechanisms that rule the replication and the expression of the genetic information. Theses researches have given birth to a new scientific field, molecular biology, which everyone will see very soon is actually part in a quasi symbiotic manner of all other biological fields dealing with life. The spectacular development of molecular biology during the last fifty years was in great part possible thanks to a concomitant enormous development of the different methods of investigation of the biological molecules and structure. The present rising of biotechnology applications is the direct consequence of the tremendous amount of fundamental knowledge gained during the last few decennia. They open very important and attractive perspectives both on medical or on socio-economic point of views. There is no doubt that the next fifty years will be as fruitful as the last ones.

  15. Interactions of H562 in the S5 helix with T618 and S621 in the pore helix are important determinants of hERG1 potassium channel structure and function.

    Science.gov (United States)

    Lees-Miller, James P; Subbotina, Julia O; Guo, Jiqing; Yarov-Yarovoy, Vladimir; Noskov, Sergei Y; Duff, Henry J

    2009-05-06

    hERG1 is a member of the cyclic nucleotide binding domain family of K(+) channels. Alignment of cyclic nucleotide binding domain channels revealed an evolutionary conserved sequence HwX(A/G)C in the S5 domain. We reasoned that histidine 562 in hERG1 could play an important structure-function role. To explore this role, we created in silica models of the hERG1 pore domain based on the KvAP crystal structure with Rosetta-membrane modeling and molecular-dynamics simulations. Simulations indicate that the H562 residue in the S5 helix spans the gap between the S5 helix and the pore helix, stabilizing the pore domain, and that mutation at the H562 residue leads to a disruption of the hydrogen bonding to T618 and S621, resulting in distortion of the selectivity filter. Analysis of the simulated point mutations at positions 562/618/621 showed that the reciprocal double mutations H562W/T618I would partially restore the orientation of the 562 residue. Matching hydrophobic interactions between mutated W562 residue and I618 partially compensate for the disrupted hydrogen bonding. Complementary in vitro electrophysiological studies confirmed the results of the molecular-dynamics simulations on single mutations at positions 562, 618, and 621. Experimentally, mutations of the H562 to tryptophan produced a functional channel, but with slowed deactivation and shifted V(1/2) of activation. Furthermore, the double mutation T618I/H562W rescued the defects seen in activation, deactivation, and potassium selectivity seen with the H562W mutation. In conclusion, interactions between H562 in the S5 helix and amino acids in the pore helix are important determinants of hERG1 potassium channel function, as confirmed by theory and experiment.

  16. Use of Molecular Dynamics Data in Biochemistry Courses: An Amphipathy Scale to Determine Protein [alpha]-Helix Transmembrane Segments

    Science.gov (United States)

    Mazze, Fernanda M.; Fuzo, Carlos A.; Degreve, Leo; Ciancaglini, Pietro

    2008-01-01

    The aim of this manuscript is to explain the application of an amphipathy scale obtained from molecular dynamics simulations and to demonstrate how it can be useful in the protein structure field. It is shown that this scale is easy to be used with the advantage of revealing domains of transmembrane [alpha]-helix of proteins without the need of…

  17. 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.

  18. Porphyrinic metal-organic framework as electrochemical probe for DNA sensing via triple-helix molecular switch.

    Science.gov (United States)

    Ling, Pinghua; Lei, Jianping; Ju, Huangxian

    2015-09-15

    An electrochemical DNA sensor was developed based on the electrocatalysis of porphyrinic metal-organic framework (MOF) and triple-helix molecular switch for signal transduction. The streptavidin functionalized zirconium-porphyrin MOF (PCN-222@SA) was prepared as signal nanoprobe via covalent method and demonstrated high electrocatalysis for O2 reduction. Due to the large steric effect, the designed nanoprobe was blocked for the interaction with the biotin labeled triple-helix immobilized on the surface of glassy carbon electrode. In the presence of target DNA, the assistant DNA in triple-helix will hybridize with target DNA, resulting in the disassembly of triple-helix molecular. Consequently, the end biotin away from the electrode was ''activated'' for easy access to the signal nanoprobe, PCN-222@SA, on the basis of biotin-streptavidin biorecognition. The introduction of signal nanoprobe to a sensor surface led to a significantly amplified electrocatalytic current towards oxygen reduction. Integrating with DNA recycling amplification of Exonuclease III, the sensitivity of the biosensor was improved significantly with detection limit of 0.29 fM. Moreover, the present method has been successfully applied to detect DNA in complex serum matrix. This porphyrinic MOF-based strategy has promising application in the determination of various analytes for signal transduction and has great potential in bioassays.

  19. 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.

  20. When Triple Helix Unravels: A Multi-Case Analysis of Failures in Industry-University Cooperative Research Centres

    Science.gov (United States)

    Gray, Denis; Sundstrom, Eric; Tornatzky, Louis G.; McGowen, Lindsey

    2011-01-01

    Cooperative research centres (CRCs) increasingly foster Triple Helix (industry-university-government) collaboration and represent significant vehicles for cooperation across sectors, the promotion of knowledge and technology transfer and ultimately the acceleration of innovation. A growing social science literature on CRCs focuses on their…

  1. 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

  2. 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

  3. 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 r...

  4. Defining the transmembrane helix of M2 protein from influenza A by molecular dynamics simulations in a lipid bilayer

    NARCIS (Netherlands)

    Forrest, LR; Tieleman, DP; Sansom, MSP

    1999-01-01

    Integral membrane proteins containing at least one transmembrane (TM) alpha-helix are believed to account for between 20% and 30% of most genomes. There are several algorithms that accurately predict the number and position of TM helices within,a membrane protein sequence. However, these methods ten

  5. Human maximization test of falcarinol, the principal contact allergen of English ivy and Algerian ivy (Hedera helix, H. canariensis).

    Science.gov (United States)

    Gafner, F; Epstein, W; Reynolds, G; Rodriguez, E

    1988-08-01

    In a human maximization test of 5% falcarinol isolated from Hedera helix, 10 of 20 subjects were sensitized. No subjects gave irritant reactions to 5%, 10 became sensitive to 1%, and 7 to 0.05%, with 3 of these giving 3+ to 4+ bullous reactions.

  6. 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.

  7. Temperature, salinity and transmissivity data from the Alpha Helix in the Arctic Ocean, 2000 - 2004 (NODC Accession 0059005)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This is calibrated CTD downcast data from five Alpha Helix cruises: HX235, 8/1/2000 - 9/30/2000 HX250, 9/1/2001 - 9/30/2001 HX260, 6/1/2002 - 6/30/2002 HX274,...

  8. 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

    In studies of the ensembles of unfolded structures of a four-helix bundle protein, we have detected the presence of potential precursors of native tertiary structures. These observations were based on the perturbation of NMR chemical shifts of the protein backbone atoms by single site mutations. ...

  9. 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 prfB,...

  10. What Reading "The Double Helix" and "The Dark Lady of DNA" Can Teach Students (and Their Teachers) about Science

    Science.gov (United States)

    Othman, Jazilah Bte

    2008-01-01

    Very often science is taught in schools devoid of the people and events behind the research. Yet there is much that can be discovered about the nature of science when we examine the lives of scientists. Recently I read James Watson's "The Double Helix" and Brenda Maddox's biography of Rosalind Franklin, "Rosalind Franklin The Dark Lady of DNA." It…

  11. 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…

  12. 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.

  13. Two states of the triple helix in the thermal transition of the collagen model peptide (Pro-Pro-Gly)10.

    Science.gov (United States)

    Kai, T; Uchiyama, S; Nishi, Y; Kobayashi, Y; Tomiyama, T

    2004-08-01

    The collagen model peptide (Pro-Pro-Gly)10 is known to fold into a triple helix in solution. So far, the triple helix has been considered to exist as a single state. However, our previous study of (Pro-Pro-Gly)10 in solution has indicated the presence of two different states of the triple helix, a lower (HL) and a higher temperature state (HH). In the present study, these triple-helical states were investigated in more detail by NMR. Complete stereospecific assignments of the methylene protons of the proline residues were accomplished by the use of NOESY and TOCSY spectra. The temperature dependence of the 1H chemical shifts showed that the HL-to-HH thermal transition can be attributed to a conformational change of the first proline (Pro1) residues of the (Pro-Pro-Gly) triplets. Since TOCSY spectra with a 10 ms mixing-time confirmed a down puckering of these Pro residues in the HL state, but interconverting down and up puckerings in the HH state, the HL-to-HH thermal transition corresponds to conformational changes of the pyrrolidine rings of the Pro1 residues from an uniform down puckering to a more flexible state. The results confirm that thermal unfolding of the triple helix proceeds through the intermediate HH state.

  14. Multi-Level Evaluation of Cooperative Research Centers: Bridging between the Triple Helix and the Science of Team Science

    Science.gov (United States)

    Gray, Denis O.; Sundstrom, Eric

    2010-01-01

    Two emergent conceptual models for fostering the development of innovative technology through applied science at Cooperative Research Centers (CRCs)--the Triple Helix and the science of team science--have proved highly productive in stimulating research into how the innovation process works. Although the two arenas for fostering innovation have…

  15. Measurement of the second-order hyperpolarizability of the collagen triple helix and determination of its physical origin.

    Science.gov (United States)

    Deniset-Besseau, Ariane; Duboisset, Julien; Benichou, Emmanuel; Hache, François; Brevet, Pierre-François; Schanne-Klein, Marie-Claire

    2009-10-08

    We performed Hyper-Rayleigh Scattering (HRS) experiments to measure the second-order nonlinear optical response of the collagen triple helix and determine the physical origin of second harmonic signals observed in collagenous tissues. HRS experiments yielded a second-order hyperpolarizability of 1.25 x 10(-27) esu for rat-tail type I collagen, a surprisingly large value considering that collagen presents no strong harmonophore in its amino acid sequence. Polarization-resolved experiments showed intramolecular coherent contributions to the HRS signal along with incoherent contributions that are the only contributions for molecules with dimensions much smaller than the excitation wavelength. We therefore modeled the effective second-order hyperpolarizability of the 290 nm long collagen triple helix by summing coherently the nonlinear response of well-aligned moieties along the triple helix axis. This model was confirmed by HRS measurements after denaturation of the collagen triple helix and for a collagen-like short model peptide [(Pro-Pro-Gly)(10)](3). We concluded that the large collagen nonlinear response originates in the tight alignment of a large number of small and weakly efficient harmonophores, presumably the peptide bonds, resulting in a coherent amplification of the nonlinear signal.

  16. From Knowledge Flows to the Triple Helix. The Transformation of Academic-Industry Relations in the USA.

    Science.gov (United States)

    Etzkowitz, Henry

    1996-01-01

    In contrast to the knowledge flows model (one-way from research to innovation), the triple-helix model has interlocking spheres of university, government, and industry with overlapping roles. Massachusetts Institute of Technology is an example of the emerging entrepreneurial university being transformed by the "second academic…

  17. A simulation model of the Triple Helix of university-industry-government relations and the decomposition of the redundancy

    NARCIS (Netherlands)

    Ivanova, I.A.; Leydesdorff, L.

    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

  18. Measuring the knowledge base of an economy in terms of triple-helix relations among 'technology, organization, and territory'

    NARCIS (Netherlands)

    Leydesdorff, L.; Dolfsma, W.; van der Panne, G.; Viale, R.; Etzkowitz, H.

    2010-01-01

    Can the knowledge base of an economy be measured? In this study, we combine the perspective of regional economics on the interrelationships among technology, organization, and territory with the triple-helix model, and offer the mutual information in three dimensions as an indicator of the configura

  19. 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.…

  20. 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.

  1. 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.

  2. 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.

  3. The self-assembly of a mini-fibril with axial periodicity from a designed collagen-mimetic triple helix.

    Science.gov (United States)

    Kaur, Parminder Jeet; Strawn, Rebecca; Bai, Hanying; Xu, Ke; Ordas, Gabriel; Matsui, Hiroshi; Xu, Yujia

    2015-04-03

    In this work we describe the self-assembly of a collagen-like periodic mini-fibril from a recombinant triple helix. The triple helix, designated Col108, is expressed in Escherichia coli using an artificial gene and consists of a 378-residue triple helix domain organized into three pseudo-repeating sequence units. The peptide forms a stable triple helix with a melting temperature of 41 °C. Upon increases of pH and temperature, Col108 self-assembles in solution into smooth mini-fibrils with the cross-striated banding pattern typical of fibrillar collagens. The banding pattern is characterized by an axially repeating feature of ∼35 nm as observed by transmission electron microscopy and atomic force microscopy. Both the negatively stained and the positively stained transmission electron microscopy patterns of the Col108 mini-fibrils are consistent with a staggered arrangement of triple helices having a staggering value of 123 residues, a value closely connected to the size of one repeat sequence unit. A mechanism is proposed for the mini-fibril formation of Col108 in which the axial periodicity is instigated by the built-in sequence periodicity and stabilized by the optimized interactions between the triple helices in a 1-unit staggered arrangement. Lacking hydroxyproline residues and telopeptides, two factors implicated in the fibrillogenesis of native collagen, the Col108 mini-fibrils demonstrate that sequence features of the triple helical domain alone are sufficient to "code" for axially repeating periodicity of fibrils. To our knowledge, Col108 is the first designed triple helix to self-assemble into periodic fibrils and offers a unique opportunity to unravel the specific molecular interactions of collagen fibrillogenesis.

  4. A case report of bilateral Brodie bite in early mixed dentition using bonded constriction quad-helix appliance.

    Science.gov (United States)

    Nojima, Kunihiko; Takaku, Sakiko; Murase, Chiaki; Nishii, Yasushi; Sueishi, Kenji

    2011-01-01

    Brodie bite is a comparatively rare type of malocclusion found in primary and mixed dentition. It not only adversely affects chewing and muscle functions, but also impairs normal growth and development of the mandible. This report describes the therapeutic results of a patient with bilateral Brodie bite in early mixed dentition after using a bonded constriction quad-helix appliance. The patient, a boy aged 9 years and 2 months, first visited our hospital after occlusal abnormality in the molar region was detected at a local dental clinic. Case analysis resulted in a diagnosis of bilateral Brodie bite with slight mandibular retrognathism. Treatment objectives were to reduce the arch width of the maxillary dentition and expand the mandibular arch in order to establish and stabilize molar occlusion and to achieve a Class I molar relation and appropriate overbite and overjet. Treatment comprised covering the occlusal surface of the maxillary molars with resin and attaching a bonded constriction quad-helix appliance joined with a 0.040-inch quad-helix wire. A bi-helix appliance was also fixed to the mandibular dentition. Brodie bite visibly improved after 5 months. Cervical headgear was then fitted and the patient observed until eruption of the permanent dentition was complete. Class I molar relation was achieved after 2 years and 6 months, although spacing remained in the maxillary and mandibular dentitions. Treatment of bilateral Brodie bite in mixed dentition by means of a bonded constriction quad-helix appliance attached to the maxillary dentition enabled effective bite opening and reduction in the width of maxillary arch independent of the patient's cooperation, providing good therapeutic outcome in a short time period.

  5. Molecular weight recognition in the multiple-stranded helix of a synthetic polymer without specific monomer-monomer interaction.

    Science.gov (United States)

    Kumaki, Jiro; Kawauchi, Takehiro; Ute, Koichi; Kitayama, Tatsuki; Yashima, Eiji

    2008-05-21

    Stereoregular isotactic and syndiotactic poly(methyl methacrylate)s (it- and st-PMMAs) are known to form a multiple-stranded complementary helix, so-called stereocomplex (SC) through van der Waals interactions, which is a rare example of helical supramolecular structures formed by a commodity polymer. In this study, we prepared SCs by using uniform it- and st-PMMAs and those with a narrow molecular weight distribution having different molecular weights and investigated their structures in detail using high-resolution atomic force microscopy as a function of the molecular weight and molecular weight distribution of the component PMMAs. We found that complementary it- and st-PMMAs with the longer molecular length determine the total length of the SC, and molecules of the shorter component associate until they fill up or cover the longer component. These observations support a supramolecular triple-stranded helical structure of the SCs composed of a double-stranded helix of two intertwined it-PMMA chains included in a single helix of st-PMMA, and this triple-stranded helix model of the SCs appears to be applicable to the it- and st-PMMAs having a wide range of molecular weights we employed in this study. In homogeneous double-stranded helices of it-PMMA, it has been found that, in mixtures of two it-PMMAs with different molecular weights, chains of the same molecular weight selectively form a double-stranded it-PMMA helix, or recognize the molecular weights of each other ("molecular sorting"). We thus demonstrate that molecular weight recognition is possible, without any specific interaction between monomer units, through the formation of a topological multiple-stranded helical structure based upon van der Waals interaction.

  6. 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

    Directory of Open Access Journals (Sweden)

    Pan Ma

    2014-01-01

    Full Text Available 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.

  7. NMR shows hydrophobic interactions replace glycine packing in the triple helix at a natural break in the (Gly-X-Y)n repeat.

    Science.gov (United States)

    Li, Yingjie; Brodsky, Barbara; Baum, Jean

    2007-08-03

    Little is known about the structural consequences of the more than 20 breaks in the (Gly-X-Y)(n) repeating sequence found in the long triple helix domain of basement membrane type IV collagen. NMR triple resonance studies of doubly labeled residues within a set of collagen model peptides provide distance and dihedral angle restraints that allow determination of model structures of both a standard triple helix and of a triple helix with a break in solution. Although the standard triple helix cannot continue when Gly is not every third residue, the NMR data support rod-like molecules that have standard triple-helical structures on both sides of a well defined and highly localized perturbation. The GAAVM break region may be described as a "pseudo triple helix," because it preserves the standard one-residue stagger of the triple helix but introduces hydrophobic interactions at the position normally occupied by the much smaller and hydrogen-bonded Gly residue of the repeating (Gly-X-Y)(n) sequence. This structure provides a rationale for the consensus presence of hydrophobic residues in breaks of similar length and defines a novel variant of a triple helix that could be involved in recognition.

  8. Binding of helix-threading peptides to E. coli 16S ribosomal RNA and inhibition of the S15-16S complex.

    Science.gov (United States)

    Gooch, Barry D; Krishnamurthy, Malathy; Shadid, Mohammad; Beal, Peter A

    2005-12-01

    Helix-threading peptides (HTPs) constitute a new class of small molecules that bind selectively to duplex RNA structures adjacent to helix defects and project peptide functionality into the dissimilar duplex grooves. To further explore and develop the capabilities of the HTP design for binding RNA selectively, we identified helix 22 of the prokaryotic ribosomal RNA 16S as a target. This helix is a component of the binding site for the ribosomal protein S15. In addition, the S15-16S RNA interaction is important for the ordered assembly of the bacterial ribosome. Here we present the synthesis and characterization of helix-threading peptides that bind selectively to helix 22 of E. coli 16S RNA. These compounds bind helix 22 by threading intercalation placing the N termini in the minor groove and the C termini in the major groove. Binding is dependent on the presence of a highly conserved purine-rich internal loop in the RNA, whereas removal of the loop minimally affects binding of the classical intercalators ethidium bromide and methidiumpropyl-EDTAFe (MPEFe). Moreover, binding selectivity translates into selective inhibition of formation of the S15-16S complex.

  9. 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.

  10. 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

  11. 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.

  12. Non-uniform helix unwinding of cholesteric liquid crystals in cells with interdigitated electrodes.

    Science.gov (United States)

    Rumi, Mariacristina; Tondiglia, Vincent P; Natarajan, Lalgudi V; White, Timothy J; Bunning, Timothy J

    2014-05-19

    A microspectrophotometer was used to elucidate the local optical properties of cholesteric liquid crystals (CLCs) in cells with interdigitated electrodes as a function of applied voltage. The spectra collected from a spatially selective and micron-sized sampling area allow for new insights into the spectral properties of CLCs in the gaps between patterned electrodes. The microscopic electro-optic response is shown to be highly dependent on the cell thickness and the electrode periodicity. Specifically, the helix unwinding of the CLC superstructure does not always occur uniformly in the sample, as a result of field gradients through the cell thickness: for cells with relatively narrow gaps and electrodes, the redshift occurs initially only in the CLC layers closest to the substrate with the electrodes, leading to broad reflection spectra and different reflection colors depending on which side of the cell is illuminated. Theoretical estimates of the expected shift in the reflection band gap based on the critical field for a given CLC material and the spatial variation of electric field in the cell are found to be in good agreement with the complex behavior observed experimentally. In contrast, in thin cells with wider gaps, the pitch increase affects the whole CLC layer uniformly, because the electric field gradient is small.

  13. Myriad Triple-Helix-Forming Structures in the Transposable Element RNAs of Plants and Fungi

    Directory of Open Access Journals (Sweden)

    Kazimierz T. Tycowski

    2016-05-01

    Full Text Available The ENE (element for nuclear expression is a cis-acting RNA structure that protects viral or cellular noncoding RNAs (ncRNAs from nuclear decay through triple-helix formation with the poly(A tail or 3′-terminal A-rich tract. We expanded the roster of nine known ENEs by bioinformatic identification of ∼200 distinct ENEs that reside in transposable elements (TEs of numerous non-metazoan and one fish species and in four Dicistrovirus genomes. Despite variation within the ENE core, none of the predicted triple-helical stacks exceeds five base triples. Increased accumulation of reporter transcripts in human cells demonstrated functionality for representative ENEs. Location close to the poly(A tail argues that ENEs are active in TE transcripts. Their presence in intronless, but not intron-containing, hAT transposase genes supports the idea that TEs acquired ENEs to counteract the RNA-destabilizing effects of intron loss, a potential evolutionary consequence of TE horizontal transfer in organisms that couple RNA silencing to splicing deficits.

  14. 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.

  15. Myriad Triple-Helix-Forming Structures in the Transposable Element RNAs of Plants and Fungi.

    Science.gov (United States)

    Tycowski, Kazimierz T; Shu, Mei-Di; Steitz, Joan A

    2016-05-10

    The ENE (element for nuclear expression) is a cis-acting RNA structure that protects viral or cellular noncoding RNAs (ncRNAs) from nuclear decay through triple-helix formation with the poly(A) tail or 3'-terminal A-rich tract. We expanded the roster of nine known ENEs by bioinformatic identification of ∼200 distinct ENEs that reside in transposable elements (TEs) of numerous non-metazoan and one fish species and in four Dicistrovirus genomes. Despite variation within the ENE core, none of the predicted triple-helical stacks exceeds five base triples. Increased accumulation of reporter transcripts in human cells demonstrated functionality for representative ENEs. Location close to the poly(A) tail argues that ENEs are active in TE transcripts. Their presence in intronless, but not intron-containing, hAT transposase genes supports the idea that TEs acquired ENEs to counteract the RNA-destabilizing effects of intron loss, a potential evolutionary consequence of TE horizontal transfer in organisms that couple RNA silencing to splicing deficits.

  16. 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.

  17. A novel colorimetric triple-helix molecular switch aptasensor for ultrasensitive detection of tetracycline.

    Science.gov (United States)

    Ramezani, Mohammad; Mohammad Danesh, Noor; Lavaee, Parirokh; Abnous, Khalil; Mohammad Taghdisi, Seyed

    2015-08-15

    Detection methods of antibiotic residues in blood serum and animal derived foods are of great interest. In this study a colorimetric aptasensor was designed for sensitive, selective and fast detection of tetracycline based on triple-helix molecular switch (THMS) and gold nanoparticles (AuNPs). As a biosensor, THMS shows distinct advantages including high stability, sensitivity and preserving the selectivity and affinity of the original aptamer. In the absence of tetracycline, THMS is stable, leading to the aggregation of AuNPs by salt and an obvious color change from red to blue. In the presence of tetracycline, aptamer binds to its target, signal transduction probe (STP) leaves the THMS and adsorbs on the surface of AuNPs. So the well-dispersed AuNPs remain stable against salt-induced aggregation with a red color. The presented aptasensor showed high selectivity toward tetracyclines with a limit of detection as low as 266 pM for tetracycline. The designed aptasensor was successfully applied to detect tetracycline in serum and milk.

  18. Comparative NMR analysis of collagen triple helix organization from N- to C-termini.

    Science.gov (United States)

    Acevedo-Jake, Amanda M; Jalan, Abhishek A; Hartgerink, Jeffrey D

    2015-01-12

    The collagen triple helix consists of three supercoiled solvent-exposed polypeptide chains, and by dry weight it is the most abundant fold in mammalian tissues. Many factors affecting the structure and stability of collagen have been determined through the use of short synthetically prepared peptides, generally called collagen-mimetic peptides (CMPs). NMR (nuclear magnetic resonance spectroscopy) investigations into the molecular structure of CMPs have suffered from large amounts of signal overlap and degeneracy because of collagen's repetitive primary sequence, the close and symmetric packing of the three chains and the identical peptide sequences found in homotrimers. In this paper a peptide library is prepared in which a single isotopic (15)N-Gly label is moved sequentially along the peptide backbone. Our approach allows for a more explicit examination of local topology than available in past reports. This reveals larger regions of disorder at the C-terminus than previously detected by crystallographic or NMR studies, and here C-terminal fraying is seen to extend for six amino acids in a (POG)10 sequence. Furthermore, small sequence changes at the N-terminus greatly influence the degree of this localized disorder and may be useful in the future design of CMPs to maximize collagen's interstrand hydrogen bonding pattern. Our approach and data serves as a reference for future CMP characterizations to determine the quality and extent of folding.

  19. 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.

  20. 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.

  1. Measurements of Drag Coefficients and Rotation Rates of Free-Falling Helixes

    KAUST Repository

    Al-Omari, Abdulrhaman A.

    2016-05-01

    The motion of bacteria in the environment is relevant to several fields. At very small scales and with simple helical shapes, we are able to describe experimentally and mathematically the motion of solid spirals falling freely within a liquid pool. Using these shapes we intend to mimic the motion of bacteria called Spirochetes. We seek to experimentally investigate the linear and the rotational motion of such shapes. A better understanding of the dynamics of this process will be practical not only on engineering and physics, but the bioscience and environmental as well. In the following pages, we explore the role of the shape on the motion of passive solid helixes in different liquids. We fabricate three solid helical shapes and drop them under gravity in water, glycerol and a mixture of 30% glycerol in water. That generated rotation due to helical angle in water. However, we observe the rotation disappear in glycerol. The movement of the solid helical shapes is imaged using a high-speed video camera. Then, the images are analyzed using the supplied software and a computer. Using these simultaneous measurements, we examine the terminal velocity of solid helical shapes. Using this information we computed the drag coefficient and the drag force. We obtain the helical angular velocity and the torque applied to the solid. The results of this study will allow us to more accurately predict the motion of solid helical shape. This analysis will also shed light onto biological questions of bacteria movement.

  2. 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.

  3. The control of transmembrane helix transverse position in membranes by hydrophilic residues.

    Science.gov (United States)

    Krishnakumar, Shyam S; London, Erwin

    2007-12-14

    The ability of hydrophilic residues to shift the transverse position of transmembrane (TM) helices within bilayers was studied in model membrane vesicles. Transverse shifts were detected by fluorescence measurements of the membrane depth of a Trp residue at the center of a hydrophobic sequence. They were also estimated from the effective length of the TM-spanning sequence, derived from the stability of the TM configuration under conditions of negative hydrophobic mismatch. Hydrophilic residues (at the fifth position in a 21-residue hydrophobic sequence composed of alternating Leu and Ala residues and flanked on both ends by two Lys) induced transverse shifts that moved the hydrophilic residue closer to the membrane surface. At pH 7, the dependence of the extent of shift upon the identity of the hydrophilic residue increased in the order: L snorkeling). Additional experiments showed that shift was also modulated by the position of the hydrophilic residue in the sequence and the hydrophobicity of the sequence moved out of the bilayer core upon shifting. Combined, these studies show that the insertion boundaries of TM helices are very sensitive to sequence, and can be altered even by weakly hydrophilic residues. Thus, many TM helices may have the capacity to exist in more than one transverse position. Knowledge of the magnitudes of transverse shifts induced by different hydrophilic residues should be useful for design of mutagenesis studies measuring the effect of transverse TM helix position upon function.

  4. Flexoelectro-optic properties of chiral nematic liquid crystals in the uniform standing helix configuration.

    Science.gov (United States)

    Castles, F; Morris, S M; Coles, H J

    2009-09-01

    The flexoelectro-optic effect describes the rotation of the optic axis of a short-pitch chiral nematic liquid crystal under the application of an electric field. We investigate the effect in the uniform standing helix, or "Grandjean" configuration. An in-plane electric field is applied. The director profile is determined numerically using a static one-dimensional continuum model with strong surface anchoring. The Berreman method is used to solve for plane-wave solutions to Maxwell's equations, and predict the optical properties of the resulting structure in general cases. By using a chiral nematic with short pitch between crossed polarizers an optical switch may be generated. With no applied field the configuration is nontransmissive at normal incidence, but becomes transmissive with an applied field. For this case, numerical results using the Berreman method are supplemented with an analytic theory and found to be in good agreement. The transmitted intensity as a function of tilt, the contrast ratio, and the tilt required for full intensity modulation are presented. The angular dependence of the transmission is calculated and the isocontrast curves are plotted. For typical material and cell parameters a switching speed of 0.017 ms and contrast ratio of 1500:1 at normal incidence are predicted, at a switch-on tilt of 41.5 degrees. Experimental verification of the analytic and numerical models is provided.

  5. Interaction of collagen triple-helix with carbon nanotubes: Geometric property of rod-like molecules.

    Science.gov (United States)

    Kuboki, Yoshinori; Terada, Michiko; Kitagawa, Yoshimasa; Abe, Shigeaki; Uo, Motohiro; Watari, Fumio

    2009-01-01

    The interactions between carbon nanotubes and important biomolecules, above all collagen molecules, have not been studied in detail. This situation is partly due to the fact that CNT are solid entities, while most of the biomolecules can be prepared in solution. We used turbidity as a means of evaluating the interaction between CNT and collagen molecules. To a stable suspension of CNT (10 ppm in 0.1% Triton), collagen solution was added to obtain a final concentration of 25 ppm. The degree of aggregation was evaluated by measuring the turbidity of the suspension at 660 nm. It was found that native collagen induced distinct aggregation with CNT, while denaturation of this protein at 60 degrees C for 1 hr deprived the molecules of their ability to aggregate with CNT. Also other globular molecules, albumin and lysozyme, did not induce aggregation of CNT. These results indicate that the rigid rod-like structure of the native collagen triple helix is essential for interaction with CNT to cause aggregation. The mechanisms are considered to be dependent upon geometric properties of rod-like collagen molecules. The findings in this paper will open a new avenue to clarify the detailed mechanism of the interaction between collagen molecules and CNT.

  6. After the double helix: Rosalind Franklin's research on Tobacco mosaic virus.

    Science.gov (United States)

    Creager, Angela N H; Morgan, Gregory J

    2008-06-01

    Rosalind Franklin is best known for her informative X-ray diffraction patterns of DNA that provided vital clues for James Watson and Francis Crick's double-stranded helical model. Her scientific career did not end when she left the DNA work at King's College, however. In 1953 Franklin moved to J. D. Bernal's crystallography laboratory at Birkbeck College, where she shifted her focus to the three-dimensional structure of viruses, obtaining diffraction patterns of Tobacco mosaic virus (TMV) of unprecedented detail and clarity. During the next five years, while making significant headway on the structural determination of TMV, Franklin maintained an active correspondence with both Watson and Crick, who were also studying aspects of virus structure. Developments in TMV research during the 1950s illustrate the connections in the emerging field of molecular biology between structural studies of nucleic acids and of proteins and viruses. They also reveal how the protagonists of the "race for the double helix" continued to interact personally and professionally during the years when Watson and Crick's model for the double-helical structure of DNA was debated and confirmed.

  7. [Selected adjuvants as carriers of a dry extract of common ivy (Hedera helix L.)].

    Science.gov (United States)

    Marczyński, Zbigniew; Zgoda, Marian Mikołaj; Bodek, Kazimiera Henryka

    2011-01-01

    The usefulness was tested of selected adjuvants: Vivapur 112, Carmellose calcium, Calcium carbonate CA 740, Calcium carbonate CA 800, Hypromellose as carriers of a dry extract of common ivy (Hedera helix L.) leaves in the process of direct tableting. The quality of the produced tablets was determined by examining their appearance, diameter, thickness, mass resistance to abrasion, crushing and disintegration time. Furthermore, the rate of release of biologically active components from the produced drug form to acceptor fluid was tested in accordance with the requirements of Polish Pharmacopoeia VII (PPVII). An attempt was made to estimate the effect of the used adjuvants on the course of this process. The applied adjuvants and acceptor fluid osmolarity decide significantly about the pharmaceutical availability of the therapeutic agents contained in the extract. The obtained model tablets are characterized by controlled release of biologically active substances, in majority of batches they fulfil the requirements as regards physicochemical properties. The formulation composition of the first batch (Extr. Hederae helices e fol.spir. sicc., Vivapur 112, Carmellose calcium, Sodium Stearyl Fumarate) appeared to be the most effective. The worked out method is optimal and provides technological reproducibility and high durability of the drug form.

  8. 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.

  9. 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.

  10. Conformational effects of Gly-X-Gly interruptions in the collagen triple helix.

    Science.gov (United States)

    Bella, Jordi; Liu, Jingsong; Kramer, Rachel; Brodsky, Barbara; Berman, Helen M

    2006-09-15

    The collagen model peptide with sequence (Pro-Hyp-Gly)4-Pro-Gly-(Pro-Hyp-Gly)5 contains a central Gly-Pro-Gly interruption in the consensus collagen sequence. Its high-resolution crystal structure defines the molecular consequences of such an interruption for the collagen triple-helical conformation, and provides insight into possible structural and biological roles of similar interruptions in the -Gly-X-Y- repeating pattern found in non-fibrillar collagens. The peptide (denoted as the Hyp minus peptide or Hyp-) forms a rod-like triple helix structure without any bend or kink, and crystallizes in a quasi-hexagonal lattice. The two Pro-Hyp-Gly zones adopt the typical triple-helical collagen conformation with standard Rich and Crick II hydrogen bonding topology. Notably, the central zone containing the Gly-Pro-Gly interruption deviates from the standard structure in terms of hydrogen bonding topology, torsion angles, helical, and superhelical parameters. These deviations are highly localized, such that the standard features are regained within one to two residues on either side. Conformational variations and high temperature factors seen for the six chains of the asymmetric unit in the zone around the interruption point to the presence of a local region of considerable plasticity and flexibility embedded within two highly rigid and ordered standard triple-helical segments. The structure suggests a role for Gly-X-Gly interruptions as defining regions of flexibility and molecular recognition in the otherwise relatively uniform repeating collagen conformation.

  11. Interruptions between the triple helix peptides can promote the formation of amyloid-like fibrils

    Science.gov (United States)

    Parmar, Avanish; Hwang, Eileen; Brodsky, Barbara

    2010-03-01

    It has been reported that collagen can initiate or accelerate the formation of amyloid fibrils. Non-fibrillar collagen types have sites where the repeating (Gly-Xaa-Yaa)n sequences are interrupted by non- Gly-Xaa-Yaa sequences, and we are investigating the hypothesis that some of these interruptions can promote amyloid formation. Our experimental data show that model peptides containing an 8 or 9 residue interruption sequence between (Gly-Pro-Hyp)n domains have a strong propensity for self association to form fibrous structures. A peptide containing only the 9-residue interruption sequence forms amyloid like fibrils with anti-parallel β sheet. Computational analysis predicts that 33 out of 374 naturally occurring human non-fibrillar collagen sequences within or between triple-helical sequences have significant cross-β aggregation potential, including the 8 and 9 residue sequences studied in peptides. Further studies are in progress to investigate whether a triple-helix peptide promotes amyloidogenesis and whether amyloid interferes with collagen fibrillogenesis.

  12. Targeting collagen strands by photo-triggered triple-helix hybridization.

    Science.gov (United States)

    Li, Yang; Foss, Catherine A; Summerfield, Daniel D; Doyle, Jefferson J; Torok, Collin M; Dietz, Harry C; Pomper, Martin G; Yu, S Michael

    2012-09-11

    Collagen remodeling is an integral part of tissue development, maintenance, and regeneration, but excessive remodeling is associated with various pathologic conditions. The ability to target collagens undergoing remodeling could lead to new diagnostics and therapeutics as well as applications in regenerative medicine; however, such collagens are often degraded and denatured, making them difficult to target with conventional approaches. Here, we present caged collagen mimetic peptides (CMPs) that can be photo-triggered to fold into triple helix and bind to collagens denatured by heat or by matrix metalloproteinase (MMP) digestion. Peptide-binding assays indicate that the binding is primarily driven by stereo-selective triple-helical hybridization between monomeric CMPs of high triple-helical propensity and denatured collagen strands. Photo-triggered hybridization allows specific staining of collagen chains in protein gels as well as photo-patterning of collagen and gelatin substrates. In vivo experiments demonstrate that systemically delivered CMPs can bind to collagens in bones, as well as prominently in articular cartilages and tumors characterized by high MMP activity. We further show that CMP-based probes can detect abnormal bone growth activity in a mouse model of Marfan syndrome. This is an entirely new way to target the microenvironment of abnormal tissues and could lead to new opportunities for management of numerous pathologic conditions associated with collagen remodeling and high MMP activity.

  13. (Un)folding of a high-temperature stable polyalanine helix from first principles

    Science.gov (United States)

    Blum, Volker; Rossi, Mariana; Tkatchenko, Alex; Scheffler, Matthias

    2010-03-01

    Peptides in vacuo offer a unique, well-defined testbed to match experiments directly against first-principles approaches that predict the intramolecular interactions that govern peptide and protein folding. In this respect, the polyalanine-based peptide Ac-Ala15-LysH^+ is particularly interesting, as it is experimentally known to form helices in vacuo, with stable secondary structure up to 750 K [1]. Room-temperature folding and unfolding timescales are usually not accessible by direct first-principles simulations, but this high T scale allows a rare direct first-principles view. We here use van der Waals corrected [2] density functional theory in the PBE generalized gradient approximation as implemented in the all-electron code FHI-aims [3] to show by Born-Oppenheimer ab initio molecular dynamics that Ac-Ala15-LysH^+ indeed unfolds rapidly (within a few ps) at T=800 K and 1000 K, but not at 500 K. We show that the structural stability of the α helix at 500 K is critically linked to a correct van der Waals treatment, and that the designed LysH^+ ionic termination is essential for the observed helical secondary structure. [1] M. Kohtani et al., JACS 126, 7420 (2004). [2] A. Tkatchenko, M. Scheffler, PRL 102, 073005 (2009). [3] V. Blum et al, Comp. Phys. Comm. 180, 2175 (2009).

  14. 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.

  15. 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.

  16. 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.

  17. 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 ...

  18. 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.

  19. 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.

  20. Using Triple Helix Forming Peptide Nucleic Acids for Sequence-selective Recognition of Double-stranded RNA

    Science.gov (United States)

    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 grove of RNA helix. The strategy developed uses chemically modified nucleobases, such as 2-aminopyridine (M) that enables strong triple helical binding at physiologically relevant conditions, and 2-pyrimidinone (P) and 3-oxo-2,3-dihydropyridazine (E) that enable recognition of isolated pyrimidines in the purine rich strand of the RNA duplex. Detailed protocols for preparation of modified PNA monomers, solid-phase synthesis and HPLC purification of PNA oligomers, and measuring dsRNA binding affinity using isothermal titration calorimetry are included. PMID:25199637

  1. 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.

  2. 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.

  3. 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.

  4. 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

    2016-12-01

    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.

  5. 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.

  6. Effect of intrachain hydrogen bond on the formation of L amino acids along α helix of peptide

    Institute of Scientific and Technical Information of China (English)

    梅镇岳

    1995-01-01

    The model of right-handed α helix of peptide,in which the intrachain hydrogen bonds be-tween amino acid residues are in the direction of the axis of the helix,is used to compute the energy differ-ences between D-and L-form residues.The dominant intramolecular interactions involved are the Coulombinteraction for the residues with charged and polarized R group and van der Waals interaction for thehydrophobic residues respectively.The results obtained show that the energy states of L-forms are lower thanthose of the corresponding D-forms.Therefore,L-form states are more stable.The racemization of the aminoacid after the residue has been dislocated from the peptide chain is interpreted as the consequence of the pari-ty conservation of the electromagnetic interaction.

  7. 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.

  8. Asymmetry in the triple helix of collagen-like heterotrimers confirms that external bonds stabilize collagen structure.

    Science.gov (United States)

    Slatter, David A; Miles, Christopher A; Bailey, Allen J

    2003-05-23

    Heating and subsequent cooling mixtures of (Pro-Pro-Gly)(10) and (Pro-Hyp-Gly)(10) peptides leads to formation of model heterotrimeric collagen helices that can be isolated by HPLC. These heterotrimeric collagen peptide helices are shown to be fundamentally unstable as denaturing then renaturing experiments result in heterotrimeric/homotrimeric mixtures. As the proportion of hydroxyproline-containing chains in the trimers increases, differential scanning calorimetry shows that the helix melting temperatures and denaturation enthalpies increasing non-linearly. Three types of Rich-Crick hydrogen bonds observed by NMR allow modelling of heterotrimeric structures based on published homotrimeric X-ray data. This revealed a small axial movement of (Pro-Hyp-Gly)(10) chains towards the C-terminal of the helix, demonstrating heterotrimeric asymmetry.

  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. 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.

  11. 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.

  12. Programmable DNA triple-helix molecular switch in biosensing applications: from in homogenous solutions to in living cells.

    Science.gov (United States)

    Tang, Pinting; Zheng, Jing; Tang, Jianru; Ma, Dandan; Xu, Weijian; Li, Jishan; Cao, Zhong; Yang, Ronghua

    2017-02-21

    Herein, we demonstrated a new gold nanoparticles (AuNPs)-integrated programmable triple-helix molecular switch (THMS) to realize the biosensing of multiple targets from in homogenous solution to in living cells. The results demonstrated that this proposed programmable THMS could be successfully used for imaging multiple messenger RNA (mRNA) in living cells and it significantly extends the scope of the THMS sensing platform.

  13. Sequence and conformational preferences at termini of α-helices in membrane proteins: role of the helix environment.

    Science.gov (United States)

    Shelar, Ashish; Bansal, Manju

    2014-12-01

    α-Helices are amongst the most common secondary structural elements seen in membrane proteins and are packed in the form of helix bundles. These α-helices encounter varying external environments (hydrophobic, hydrophilic) that may influence the sequence preferences at their N and C-termini. The role of the external environment in stabilization of the helix termini in membrane proteins is still unknown. Here we analyze α-helices in a high-resolution dataset of integral α-helical membrane proteins and establish that their sequence and conformational preferences differ from those in globular proteins. We specifically examine these preferences at the N and C-termini in helices initiating/terminating inside the membrane core as well as in linkers connecting these transmembrane helices. We find that the sequence preferences and structural motifs at capping (Ncap and Ccap) and near-helical (N' and C') positions are influenced by a combination of features including the membrane environment and the innate helix initiation and termination property of residues forming structural motifs. We also find that a large number of helix termini which do not form any particular capping motif are stabilized by formation of hydrogen bonds and hydrophobic interactions contributed from the neighboring helices in the membrane protein. We further validate the sequence preferences obtained from our analysis with data from an ultradeep sequencing study that identifies evolutionarily conserved amino acids in the rat neurotensin receptor. The results from our analysis provide insights for the secondary structure prediction, modeling and design of membrane proteins.

  14. The Helix Nebula Viewed in HCO+: Large-scale Mapping of the J = 1 → 0 Transition

    Science.gov (United States)

    Zeigler, N. R.; Zack, L. N.; Woolf, N. J.; Ziurys, L. M.

    2013-11-01

    The J = 1 → 0 transition of HCO+ at 89 GHz has been mapped across the Helix Nebula (NGC 7293) with 70'' spatial resolution (1.68 km s-1 velocity resolution) using the Arizona Radio Observatory 12 m telescope. This work is the first large-scale mapping project of a dense gas tracer (n(H2) ~ 105 cm-3) in old planetary nebulae. Observations of over 200 positions encompassing the classical optical image were conducted with a 3σ noise level of ~20 mK. HCO+ was detected at most positions, often exhibiting multiple velocity components indicative of complex kinematic structures in dense gas. The HCO+ spectra suggest that the Helix is composed of a bipolar, barrel-like structure with red- and blue-shifted halves, symmetric with respect to the central star and oriented ~10° east from the line of sight. A second bipolar, higher velocity outflow exists as well, situated along the direction of the Helix "plumes." The column density of HCO+ across the Helix is N tot ~ 1.5 × 1010-5.0 × 1011 cm-2, with an average value N ave ~ 1 × 1011 cm-2, corresponding to an abundance, relative to H2, of f ~ 1.4 × 10-8. This value is similar to that observed in young PN, and contradicts chemical models, which predict that the abundance of HCO+ decreases with nebular age. This study indicates that polyatomic molecules readily survive the ultraviolet field of the central white dwarf, and can be useful in tracing nebular morphology in the very late stages of stellar evolution.

  15. Mean-field interactions between nucleic-acid-base dipoles can drive the formation of the double helix

    Science.gov (United States)

    He, Yi; Maciejczyk, Maciej; Ołdziej, Stanisław; Scheraga, Harold A.; Liwo, Adam

    2013-01-01

    A proposed coarse-grained model of nucleic acids demonstrates that average interactions between base dipoles, together with chain connectivity and excluded-volume interactions, are sufficient to form double-helical structures of DNA and RNA molecules. Additionally, local interactions determine helix handedness and direction of strand packing. This result, and earlier research on reduced protein models, suggest that mean-field multipole-multipole interactions are the principal factors responsible for the formation of regular structure of biomolecules. PMID:23496746

  16. [Double action potentials in the command neurons of Helix pomatia in response to the action of cobalt ions].

    Science.gov (United States)

    Palikhova, T A; Khludova, L K; Sokolov, E N

    1987-01-01

    Cobalt chloride (20 mmol/l) in physiological solution results in generation of doublets of spikes in Helix pomatia command neurons in response to intracellularly injected depolarizing current. The extraspikes arise in arborizations of neuron and are determined by influx sodium ions. It is supposed that facilitation of extraspikes in apparently due to long-lasting blockade of calcium-dependent potassium current by Co2+ ions.

  17. 50 Hz-Sinusoidal magnetic field induced effects on the bioelectric activity of single unit neurone cells

    Science.gov (United States)

    Azanza, María. J.; Calvo, Ana C.; del Moral, A.

    2001-05-01

    Neurones recruiting and synchronized bioelectric activity recorded from Helix aspersa brain ganglia, under exposure to 50 Hz sinusoidal magnetic fields of 1-15 mT intensity, is reported. We show recruiting responses from single neurones and the synchronization of pairs of neurones activity. Experimental evidence and model theoretical explanation for the spreading of synchronization are presented.

  18. Pyrimidine motif triple helix in the Kluyveromyces lactis telomerase RNA pseudoknot is essential for function in vivo.

    Science.gov (United States)

    Cash, Darian D; Cohen-Zontag, Osnat; Kim, Nak-Kyoon; Shefer, Kinneret; Brown, Yogev; Ulyanov, Nikolai B; Tzfati, Yehuda; Feigon, Juli

    2013-07-02

    Telomerase is a ribonucleoprotein complex that extends the 3' ends of linear chromosomes. The specialized telomerase reverse transcriptase requires a multidomain RNA (telomerase RNA, TER), which includes an integral RNA template and functionally important template-adjacent pseudoknot. The structure of the human TER pseudoknot revealed that the loops interact with the stems to form a triple helix shown to be important for activity in vitro. A similar triple helix has been predicted to form in diverse fungi TER pseudoknots. The solution NMR structure of the Kluyveromyces lactis pseudoknot, presented here, reveals that it contains a long pyrimidine motif triple helix with unexpected features that include three individual bulge nucleotides and a C(+)•G-C triple adjacent to a stem 2-loop 2 junction. Despite significant differences in sequence and base triples, the 3D shape of the human and K. lactis TER pseudoknots are remarkably similar. Analysis of the effects of nucleotide substitutions on cell growth and telomere lengths provides evidence that this conserved structure forms in endogenously assembled telomerase and is essential for telomerase function in vivo.

  19. A sensitive and versatile "signal-on" electrochemical aptasensor based on a triple-helix molecular switch.

    Science.gov (United States)

    Wang, Xiuzhong; Jiang, Aiwen; Hou, Ting; Li, Feng

    2014-12-07

    In the present study, a versatile "signal-on" electrochemical aptasensor based on a triple-helix molecular switch has been developed. An aptamer probe is designed to hybridize with the methylene blue (MB)-modified DNA capture probe immobilized on the gold electrode to form rigid triple-helix DNA, impeding the efficient electron transfer of MB to the electrode and resulting in the decreased oxidation peak current of MB. However, upon introduction of the perfectly matched target, for example, human α-thrombin (Tmb), the interaction between Tmb and the aptamer probe leads to the dissociation of the triple-helix DNA structure and thereby liberates the MB-modified end of the capture probe, allowing the MB to collide with the electrode surface and resulting in an increase of the oxidation peak currents of MB. Therefore, the sensitive signal-on detection of Tmb is realized, and the detection limit of Tmb is 0.12 nM. The proposed approach also demonstrates excellent regenerability, reproducibility and stability. Additionally, it also has the advantages of simplicity in design and easy operation. The success in the present biosensor provides a promising alternative to the electrochemical detection of a variety of analytes and may have potential applications in point-of-care testing and clinical diagnosis.

  20. The roles of helix I and strand 5A in the folding, function and misfolding of α1-antitrypsin.

    Directory of Open Access Journals (Sweden)

    Anja S Knaupp

    Full Text Available α(1-Antitrypsin, the archetypal member of the serpin superfamily, is a metastable protein prone to polymerization when exposed to stressors such as elevated temperature, low denaturant concentrations or through the presence of deleterious mutations which, in a physiological context, are often associated with disease. Experimental evidence suggests that α(1-Antitrypsin can polymerize via several alternative mechanisms in vitro. In these polymerization mechanisms different parts of the molecule are proposed to undergo conformational change. Both strand 5 and helix I are proposed to adopt different conformations when forming the various polymers, and possess a number of highly conserved residues however their role in the folding and misfolding of α(1-Antitrypsin has never been examined. We have therefore created a range of α(1Antitypsin variants in order to explore the role of these conserved residues in serpin folding, misfolding, stability and function. Our data suggest that key residues in helix I mediate efficient folding from the folding intermediate and residues in strand 5A ensure native state stability in order to prevent misfolding. Additionally, our data indicate that helix I is involved in the inhibitory process and that both structural elements undergo differing conformational rearrangements during unfolding and misfolding. These findings suggest that the ability of α(1-Antitrypsin to adopt different types of polymers under different denaturing conditions may be due to subtle conformational differences in the transiently populated structures adopted prior to the I and M* states.