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Sample records for hedera helix ivy

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

    Science.gov (United States)

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

    2013-01-01

    Bio-inspiration for novel adhesive development has drawn increasing interest in recent years with the discovery of the nanoscale morphology of the gecko footpad and mussel adhesive proteins. Similar to these animal systems, it was discovered that English ivy (Hedera helix L.) secretes a high strength adhesive containing uniform nanoparticles. Recent studies have demonstrated that the ivy nanoparticles not only contribute to the high strength of this adhesive, but also have ultraviolet (UV) protective abilities, making them ideal for sunscreen and cosmetic fillers, and may be used as nanocarriers for drug delivery. To make these applications a reality, the chemical nature of the ivy nanoparticles must be elucidated. In the current work, a method was developed to harvest bulk ivy nanoparticles from an adventitious root culture system, and the chemical composition of the nanoparticles was analysed. UV/visible spectroscopy, inductively coupled plasma mass spectrometry, Fourier transform infrared spectroscopy and electrophoresis were used in this study to identify the chemical nature of the ivy nanoparticles. Based on this analysis, we conclude that the ivy nanoparticles are proteinaceous. PMID:23883948

  2. Dust particulate absorption by ivy (Hedera helix L) on historic walls in urban environments

    International Nuclear Information System (INIS)

    Sternberg, Troy; Viles, Heather; Cathersides, Alan; Edwards, Mona

    2010-01-01

    The potential bio-protective role of urban greenery and how it interacts with airborne dust and pollutants has been the subject of much recent research. As particulate pollution has been implicated in both the deterioration of building materials and in damaging human health, understanding how it interacts with urban greenery is of great applied interest. Common or English Ivy (Hedera helix L) grows widely on urban walls in many parts of the world, and thus any bio-protective role it might play is of broad relevance. Using Scanning Electron Microscopy ivy leaves collected on roadways were examined to determine if ivy can absorb dust and pollutants that can instigate decay processes on stone walls and impact human health in urban environments. Results showed that ivy acts as a 'particle sink', absorbing particulate matter, particularly in high-traffic areas. It was effective in adhering fine ( 10 per m 2 . Our findings suggest that through absorbing pollutant particles ivy can retard bio-deteriorative processes on historic walls and reduce human exposure to respiratory problems caused by vehicle pollutants.

  3. [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.

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

    Science.gov (United States)

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

    2015-01-01

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

  5. Isolation of a phytotoxic isocoumarin from Diaporthe eres-infected Hedera helix (English ivy) and synthesis of its phytotoxic analogs.

    Science.gov (United States)

    Meepagala, Kumudini M; Briscoe, William E; Techen, Natascha; Johnson, Robert D; Clausen, Brandon M; Duke, Stephen O

    2018-01-01

    The fungus Diaporthe eres was isolated from a fungal pathogen-infected leaf of Hedera helix (English ivy) exhibiting necrosis. It is hypothesized that the causative fungus produces phytotoxins as evidenced by necrotic lesions on the leaves. The fungus was isolated and grown in Czapek Dox broth culture medium and potato dextrose broth culture medium and identified as Diaporthe eres. The ethyl acetate extracts of the culture broths were phytotoxic to lettuce (Lactuca sativa) and bentgrass (Agrostis stolonifera). 3,4-Dihydro-8-hydroxy-3,5-dimethylisocoumarin (1) and tyrosol (2) were isolated and identified as the phytotoxic constituents. Six analogs of 3,4-dihydro-isocoumarin were synthesized and shown to be phytotoxic. The synthesized 3,4-dihydro-8-hydroxy-3,7-dimethylisocoumarin and 3,4-dihydro-8-hydroxy-3,3,7-trimethylisocoumarin were two- to three-fold more phytotoxic than the naturally occurring 1 in a Lemna paucicostata growth bioassay. Synthesis and herbicidal activities of the several new analogs of 1 are reported for the first time. These promising molecules should be used as templates for synthesis and testing of more analogs. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

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

    Science.gov (United States)

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

    2012-12-01

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

    DEFF Research Database (Denmark)

    Jørs, Erik

    2003-01-01

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

  8. Phylogenetic and paleobotanical evidence for late Miocene diversification of the Tertiary subtropical lineage of ivies (Hedera L., Araliaceae).

    Science.gov (United States)

    Valcárcel, V; Guzmán, B; Medina, N G; Vargas, P; Wen, J

    2017-06-22

    Hedera (ivies) is one of the few temperate genera of the primarily tropical Asian Palmate group of the Araliaceae, which extends its range out of Asia to Europe and the Mediterranean basin. Phylogenetic and phylogeographic results suggested Asia as the center of origin and the western Mediterranean region as one of the secondary centers of diversification. The bird-dispersed fleshy fruits of ivies suggest frequent dispersal over long distances (e.g. Macaronesian archipelagos), although reducing the impact of geographic barriers to gene flow in mainland species. Genetic isolation associated with geographic barriers and independent polyploidization events have been postulated as the main driving forces of diversification. In this study we aim to evaluate past and present diversification patterns in Hedera within a geographic and temporal framework to clarify the biogeographic history of the genus. Phylogenetic (biogeographic, time divergence and diversification) and phylogeographic (coalescence) analyses using four DNA regions (nrITS, trnH-psbA, trnT-trnL, rpl32) revealed a complex spatial pattern of lineage divergence. Scarce geographic limitation to gene flow and limited diversification are observed during the early-mid Miocene, followed by a diversification rate increase related to geographic divergence from the Tortonian/Messinian. Genetic and palaeobotanical evidence points the origin of the Hedera clade in Asia, followed by a gradual E-W Asian extinction and the progressive E-W Mediterranean colonization. The temporal framework for the E Asia - W Mediterranean westward colonization herein reported is congruent with the fossil record. Subsequent range expansion in Europe and back colonization to Asia is also inferred. Uneven diversification among geographic areas occurred from the Tortonian/Messinian onwards with limited diversification in the newly colonized European and Asian regions. Eastern and western Mediterranean regions acted as refugia for Miocene and

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

    Science.gov (United States)

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

    2015-01-01

    Several anti-influenza drugs that reduce disease manifestation exist, and although these drugs provide clinical benefits in infected patients, their efficacy is limited by the emergence of drug-resistant influenza viruses. In the current study, we assessed the therapeutic strategy of enhancing the antiviral efficacy of an existing neuraminidase inhibitor, oseltamivir, by coadministering with the leaf extract from Hedera helix L, commonly known as ivy. Ivy extract has anti-inflammatory, antibacterial, antifungal, and antihelminthic properties. In the present study, we investigated its potential antiviral properties against influenza A/PR/8 (PR8) virus in a mouse model with suboptimal oseltamivir that mimics a poor clinical response to antiviral drug treatment. Suboptimal oseltamivir resulted in insufficient protection against PR8 infection. Oral administration of ivy extract with suboptimal oseltamivir increased the antiviral activity of oseltamivir. Ivy extract and its compounds, particularly hedrasaponin F, significantly reduced the cytopathic effect in PR8-infected A549 cells in the presence of oseltamivir. Compared with oseltamivir treatment alone, coadministration of the fraction of ivy extract that contained the highest proportion of hedrasaponin F with oseltamivir decreased pulmonary inflammation in PR8-infected mice. Inflammatory cytokines and chemokines, including tumor necrosis factor-alpha and chemokine (C-C motif) ligand 2, were reduced by treatment with oseltamivir and the fraction of ivy extract. Analysis of inflammatory cell infiltration in the bronchial alveolar of PR8-infected mice revealed that CD11b+Ly6G+ and CD11b+Ly6Cint cells were recruited after virus infection; coadministration of the ivy extract fraction with oseltamivir reduced infiltration of these inflammatory cells. In a model of suboptimal oseltamivir treatment, coadministration of ivy extract fraction that includes hedrasaponin F increased protection against PR8 infection that could be

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

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    Eun-Hye Hong

    Full Text Available Several anti-influenza drugs that reduce disease manifestation exist, and although these drugs provide clinical benefits in infected patients, their efficacy is limited by the emergence of drug-resistant influenza viruses. In the current study, we assessed the therapeutic strategy of enhancing the antiviral efficacy of an existing neuraminidase inhibitor, oseltamivir, by coadministering with the leaf extract from Hedera helix L, commonly known as ivy. Ivy extract has anti-inflammatory, antibacterial, antifungal, and antihelminthic properties. In the present study, we investigated its potential antiviral properties against influenza A/PR/8 (PR8 virus in a mouse model with suboptimal oseltamivir that mimics a poor clinical response to antiviral drug treatment. Suboptimal oseltamivir resulted in insufficient protection against PR8 infection. Oral administration of ivy extract with suboptimal oseltamivir increased the antiviral activity of oseltamivir. Ivy extract and its compounds, particularly hedrasaponin F, significantly reduced the cytopathic effect in PR8-infected A549 cells in the presence of oseltamivir. Compared with oseltamivir treatment alone, coadministration of the fraction of ivy extract that contained the highest proportion of hedrasaponin F with oseltamivir decreased pulmonary inflammation in PR8-infected mice. Inflammatory cytokines and chemokines, including tumor necrosis factor-alpha and chemokine (C-C motif ligand 2, were reduced by treatment with oseltamivir and the fraction of ivy extract. Analysis of inflammatory cell infiltration in the bronchial alveolar of PR8-infected mice revealed that CD11b+Ly6G+ and CD11b+Ly6Cint cells were recruited after virus infection; coadministration of the ivy extract fraction with oseltamivir reduced infiltration of these inflammatory cells. In a model of suboptimal oseltamivir treatment, coadministration of ivy extract fraction that includes hedrasaponin F increased protection against PR8

  11. Antibacterial Activity of Silver Nanoparticles Synthesized by Using Extracts of Hedera helix

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    Ahmadreza Abbasifar

    2017-01-01

    Full Text Available Background Silver nanoparticles (AgNPs are one of the most widely applicable particles whose application is increasing in Nano world daily. Silver nanoparticles have expressed significant advances owing to wide range of applications in the field of bio-medical, sensors, antimicrobials, catalysts, electronics, optical fibers, agricultural, bio-labeling and the other areas. Green synthesis is the safe and easiest method of producing silver nanoparticles. Because of the production of the silver ions, silver nanoparticles are found to have the antibacterial activity. Objectives The aim of this study was to investigate antibacterial activity of silver nanoparticles synthesized by using extracts of Hedera helix against Bacillus subtilis and Klebsiella pneumoniae. Methods In this experimental study AgNPs were prepared by the reaction of 1mM silver nitrate and extracts of Hedera helix. Antibacterial activity of AgNPs was assessed by using disc diffusion method against Bacillus subtilis and Klebsiella pneumoniae. The AgNPs were characterized by UV-visible (vis spectrophotometer, particle size analyzer by dynamic light scattering (DLS method, transmission electron microscopy (TEM. Results AgNPs obtained showed significantly higher antimicrobial activities against B. subtilis and K. pneumonia in comparison to both AgNO3 and raw plant extracts. Conclusions Biological methods are a good competent for the chemical procedures, which are environment friendly and convenient.

  12. Stomatal Responses to Light and Drought Stress in Variegated Leaves of Hedera helix1

    Science.gov (United States)

    Aphalo, Pedro J.; Sánchez, Rodolfo A.

    1986-01-01

    Direct and indirect mechanisms underlying the light response of stomata were studied in variegated leaves of the juvenile phase of Hedera helix L. Dose response curves of leaf conductance were measured with blue and red light in leaves kept in normal or in an inverted position. In the green portions of the leaves, the sensitivity to blue light was nearly 100 times higher than that to red light. No response to red light was observed in the white portions of the leaves up to 90 micromoles per square meter per second. Red light indirectly affected leaf conductance while blue light had a direct effect. Leaf conductance was found to be more sensitive to drought stress and showed a more persistent aftereffect in the white portions of the leaves. A differential effect of drought stress on the responses to blue and red light was also observed. PMID:16664900

  13. Lead pollution due to exhaust gases. [Celtis occidentalis; fraxinus angustifolia; aesculus hippocastanum; hedera helix

    Energy Technology Data Exchange (ETDEWEB)

    Klinscek, P

    1976-01-01

    An investigation was carried out to establish the changes in the lead content of trees and shrubs on the Margaret island in Budapest as a response to the reduction in motor-vehicle traffic introduced in 1974. Compared to samples of the control area (Vacratot) the Margaret island samples were found to have a considerable higher lead content. As a consequence of the traffic modifying measure a 30% decrease in the lead content of the samples was verified. The lead pollution did not involve changes in the chlorophyll content of samples. Accumulation of lead pollution is a specific feature. Lead pollution is accumulated to a great extent (multiple of other plants) by the pilose-leaved CELTIS occidentalis, the pinnate-leaved FRAXINUS angustifolia, ssp. pannonica and the undulate-leaved AESCULUS hippocastanum as well as from among the evergreen by the stellate-hair HEDERA helix. The green belt bordering the roads by its active lead cumulation plays an important role in lessening the plumb pollution of areas more distant from the road. 14 references 3 tables.

  14. Characterization of physicochemical properties of ivy nanoparticles for cosmetic application

    OpenAIRE

    Huang, Yujian; Lenaghan, Scott C; Xia, Lijin; Burris, Jason N; Stewart, C Neal Jr; Zhang, Mingjun

    2013-01-01

    Abstract Background Naturally occurring nanoparticles isolated from English ivy (Hedera helix) have previously been proposed as an alternative to metallic nanoparticles as sunscreen fillers due to their effective UV extinction property, low toxicity and potential biodegradability. Methods This study focused on analyzing the physicochemical properties of the ivy nanoparticles, specifically, those parameters which are crucial for use as sunscreen fillers, such as pH, temperature, and UV irradia...

  15. Flowering plants of Hedera helix L. in the Grunwald district of the city of Poznań

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    Stanisława Korszun

    2012-12-01

    Full Text Available In the period from September 2008 to July 2009 in the Grunwald district in the city of Poznań, Poland, a total of 609 localities of flowering English ivy were recorded, for which 769 plants were described. These plants were found in different localities, most of them euhemerobic. The biggest number of flowering specimens was recorded in home gardens. Support for climbing plants was mainly provided by trees and shrubs, including fruit trees – pear and apple trees. Among the other tree species, the biggest group comprises Scots pine, common birch, European larch and common locust. Other types of supports included fences, buildings and elements of small architecture. A very high number of specimens in the generative stage in the Grunwald district indicates considerable popularity and at the same time very good adaptation of ivy not only to the climatic conditions of the city of Poznań, but also to anthropogenic changes in the habitat.

  16. Characterization of physicochemical properties of ivy nanoparticles for cosmetic application.

    Science.gov (United States)

    Huang, Yujian; Lenaghan, Scott C; Xia, Lijin; Burris, Jason N; Stewart, C Neal; Zhang, Mingjun

    2013-02-01

    Naturally occurring nanoparticles isolated from English ivy (Hedera helix) have previously been proposed as an alternative to metallic nanoparticles as sunscreen fillers due to their effective UV extinction property, low toxicity and potential biodegradability. This study focused on analyzing the physicochemical properties of the ivy nanoparticles, specifically, those parameters which are crucial for use as sunscreen fillers, such as pH, temperature, and UV irradiation. The visual transparency and cytotoxicity of ivy nanoparticles were also investigated comparing them with other metal oxide nanoparticles. Results from this study demonstrated that, after treatment at 100°C, there was a clear increase in the UV extinction spectra of the ivy nanoparticles caused by the partial decomposition. In addition, the UVA extinction spectra of the ivy nanoparticles gradually reduced slightly with the decrease of pH values in solvents. Prolonged UV irradiation indicated that the influence of UV light on the stability of the ivy nanoparticle was limited and time-independent. Compared to TiO2 and ZnO nanoparticles, ivy nanoparticles showed better visual transparency. Methylthiazol tetrazolium assay demonstrated that ivy nanoparticles exhibited lower cytotoxicity than the other two types of nanoparticles. Results also suggested that protein played an important role in modulating the three-dimensional structure of the ivy nanoparticles. Based on the results from this study it can be concluded that the ivy nanoparticles are able to maintain their UV protective capability at wide range of temperature and pH values, further demonstrating their potential as an alternative to replace currently available metal oxide nanoparticles in sunscreen applications.

  17. Characterization of physicochemical properties of ivy nanoparticles for cosmetic application

    Directory of Open Access Journals (Sweden)

    Huang Yujian

    2013-02-01

    Full Text Available Abstract Background Naturally occurring nanoparticles isolated from English ivy (Hedera helix have previously been proposed as an alternative to metallic nanoparticles as sunscreen fillers due to their effective UV extinction property, low toxicity and potential biodegradability. Methods This study focused on analyzing the physicochemical properties of the ivy nanoparticles, specifically, those parameters which are crucial for use as sunscreen fillers, such as pH, temperature, and UV irradiation. The visual transparency and cytotoxicity of ivy nanoparticles were also investigated comparing them with other metal oxide nanoparticles. Results Results from this study demonstrated that, after treatment at 100°C, there was a clear increase in the UV extinction spectra of the ivy nanoparticles caused by the partial decomposition. In addition, the UVA extinction spectra of the ivy nanoparticles gradually reduced slightly with the decrease of pH values in solvents. Prolonged UV irradiation indicated that the influence of UV light on the stability of the ivy nanoparticle was limited and time-independent. Compared to TiO2 and ZnO nanoparticles, ivy nanoparticles showed better visual transparency. Methylthiazol tetrazolium assay demonstrated that ivy nanoparticles exhibited lower cytotoxicity than the other two types of nanoparticles. Results also suggested that protein played an important role in modulating the three-dimensional structure of the ivy nanoparticles. Conclusions Based on the results from this study it can be concluded that the ivy nanoparticles are able to maintain their UV protective capability at wide range of temperature and pH values, further demonstrating their potential as an alternative to replace currently available metal oxide nanoparticles in sunscreen applications.

  18. Efficacy of dry extract of ivy leaves in children with bronchial asthma--a review of randomized controlled trials.

    Science.gov (United States)

    Hofmann, D; Hecker, M; Völp, A

    2003-03-01

    To investigate if extracts from dried ivy leaves (Hedera helix L.) are effective in the treatment of chronic airway obstruction in children suffering from bronchial asthma. Systematic review of trials documented in the literature with re-analysis of original data. 5 randomized controlled trials investigating the efficacy of ivy leaf extract preparations in chronic bronchitis, 3 of which were conducted in children and met our selection criteria. One compared ivy leaf extract cough drops to placebo, one compared suppositories to drops and one tested syrup against drops. Body-plethysmographic and spirometric measures. Drops were significantly superior to placebo in reducing airway resistance (primary outcome measure; p = 0.04 two-sided) and descriptively superior in all other 'objective' measures. For syrup and suppositories, at least 54%, resp. 35% of the effect against placebo were preserved. The trials included in this review indicate that ivy leaf extract preparations have effects with respect to an improvement of respiratory functions of children with chronic bronchial asthma, but more far-reaching conclusions can hardly be drawn because of a meagre database, including the fact that only one primary trial included a placebo control. Further research, particularly into the long-term efficacy of the herbal extract, is needed.

  19. Pulsed excimer laser radiation influences in vitro culture of Algerian ivy

    Energy Technology Data Exchange (ETDEWEB)

    Al Juboory, K. H.; Williams, D. J.; Nayfeh, M. H.

    1991-07-01

    Use of gamma rays and X rays with in vitro cultures has been used to isolate unique plant types (Chevreau et al., 1989). Exposure of in vitro cultures to gamma and X-ray radiation has resulted in the mutagenesis of grape (Kim et al., 1989) and reduced regeneration of maize lants (Moustafa et al., 1989). Our study was initiated to find an alternative method for the elimination of biological contaminants from in vitro cultures of Algerian ivy (Hedera canariensis L.)

  20. Poison Ivy Rash

    Science.gov (United States)

    Poison ivy rash Overview Poison ivy rash is caused by an allergic reaction to an oily resin called urushiol (u-ROO-she-ol). This oil is in the leaves, stems and roots of poison ivy, poison oak and poison sumac. Wash your ...

  1. Poison Ivy Dermatitis

    Science.gov (United States)

    ... than the other two. Poison ivy clings to tree trunks and other vertical surfaces with hair-like ... urushiol". These are called Rhus plants after the old scientific name (it was changed to toxidendron). A ...

  2. Poison Ivy Dermatitis

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    ... Category: Share: Yes No, Keep Private Poison Ivy Dermatitis Share | "Leaves of three - let it be!" aptly ... is caused by an allergic reaction ( allergic contact dermatitis ) to the oily coating that covers of these ...

  3. Poison ivy - oak - sumac rash

    Science.gov (United States)

    ... this page: //medlineplus.gov/ency/article/000027.htm Poison ivy - oak - sumac rash To use the sharing features on this page, please enable JavaScript. Poison ivy, oak, and sumac are plants that commonly ...

  4. Black-spot poison ivy.

    Science.gov (United States)

    Schram, Sarah E; Willey, Andrea; Lee, Peter K; Bohjanen, Kimberly A; Warshaw, Erin M

    2008-01-01

    In black-spot poison ivy dermatitis, a black lacquerlike substance forms on the skin when poison ivy resin is exposed to air. Although the Toxicodendron group of plants is estimated to be the most common cause of allergic contact dermatitis in the United States, black-spot poison ivy dermatitis is relatively rare.

  5. Triple Helix going abroad?

    DEFF Research Database (Denmark)

    Sørensen, Olav Jull; Hu, Yimei

    2014-01-01

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

  6. Double-helix stellarator

    International Nuclear Information System (INIS)

    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 ∼ 1--1.2. Other advantages include a high enclosed volume, appreciable rotational transform, and a possibility of extreme-high-β 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

  7. Antioxidant, antitumor activities and phyto chemical investigation of hedera nepalensis K. koch, an important medicinal plant from Pakistan

    International Nuclear Information System (INIS)

    Kanwal, S.; Ullah, N.; Ihsan-ul-Haq; Mirza, B.; Afzal, I.

    2011-01-01

    Hedera nepalensis is a ground-creeping evergreen woody plant growing mainly in the Himalayas and Kashmir. This plant is frequently used in folk medicines for the treatment of various ailments. The present research focused on the pharmacological evaluation and phyto chemical analysis of crude methanolic extract (CME) and three fractions, n-hexane (n-HF), ethyl acetate (EAF) and aqueous (AQF). The biological assays used for this study included DPPH free radical values scavenging assay, DNA protection assay and potato disc antitumor assay. Maximum antioxidant activities with IC/sub 50/ of 9.834 ppm and 14.22 ppm were shown by EAF and AQF, respectively. Crude methanolic extract (CME) and the fractions OH induced DNA damage assay, at all the concentrations tested. Both also exhibited significant DNA protection activity in EAF and AQF showed well-defined tumor inhibition in the potato disc antitumor assay, with the lowest IC/sub 50/ values shown by EAF and AQF (less than 1 ppm). Phyto chemical analysis showed the presence of flavonoids, steroids, tannins, terpenoids and cardiac glycosides in the crude extract and its fractions. The present study demonstrated that EAF and AQF of Hedera nepalensis have potent antioxidant and antitumor activity with the presence of effective phytochemicals. (author)

  8. Ivi-Els Schneider : "Eestis on oma feng-shui täiesti olemas"

    Index Scriptorium Estoniae

    2005-01-01

    Sisearhitekt Ivi-Els Schneider (sünd. 1945) endast, eelistustest interjööri kujundamisel, kodukujundamisest, loodusega arvestamisest. Ivi-Els Schneiderist, esinemisest näitustel, omistatud preemiad, olulisemaid kujundatud objekte, loomingut muuseumides. Ill.: Ivi-Els Schneideri värv. portree

  9. On the helix equation

    Directory of Open Access Journals (Sweden)

    Taouil Hajer

    2012-08-01

    Full Text Available This paper is devoted to the helices processes, i.e. the solutions H : ℝ × Ω → ℝd, (t, ω ↦ H(t, ω of the helix equation egin{eqnarray} H(0,o=0; quad H(s+t,o= H(s,Phi(t,o +H(t,oonumber end{eqnarray} H ( 0 ,ω = 0 ;   H ( s + t,ω = H ( s, Φ ( t,ω + H ( t,ω where Φ : ℝ × Ω → Ω, (t, ω ↦ Φ(t, ω is a dynamical system on a measurable space (Ω, ℱ. More precisely, we investigate dominated solutions and non differentiable solutions of the helix equation. For the last case, the Wiener helix plays a fundamental role. Moreover, some relations with the cocycle equation defined by Φ, are investigated. Ce papier est consacré aux hélices, c’est-à-dire les solutions H : ℝ × Ω → ℝd, (t, ω ↦ H(t, ω de l’équation fonctionnelle egin{eqnarray} H(0,o=0; quad H(s+t,o= H(s,Phi(t,o +H(t,o onumber end{eqnarray} H ( 0 ,ω = 0 ;   H ( s + t,ω = H ( s, Φ ( t,ω + H ( t,ω où Φ : ℝ × Ω → Ω, (t, ω ↦ Φ(t, ω est un système dynamique défini sur un espace mesurable (Ω, ℱ. Plus présisément, nous déterminons d’abord les hélices dominées puis nous caractérisons les hélices non différentiables. Dans ce dernier cas, l’hélice de Wiener joue un rôle important. Nous précisons aussi quelques relations des hélices avec les cocycles définis par Φ.

  10. Harold and Kumar Go to the Ivy League

    Science.gov (United States)

    Oppenheimer, Mark

    2008-01-01

    For having achieved a mild cult status after doing the movie "Harold & Kumar Go to White Castle," lead actors John Cho and Kal Penn deserve their fame, their million-dollar paychecks, and their groupies. Do they deserve Ivy League teaching jobs? This spring Penn (whose real name is Kalpen Modi) taught a large lecture class, "Images of Asian…

  11. Retrospective: Ivy Lee and the German Dye Trust.

    Science.gov (United States)

    Hainsworth, Brad E.

    1987-01-01

    Examines the relationship between public relations trailblazer Ivy Lee and the German Dye Trust, which became an agent for the policies of Adolf Hitler. Discusses how Lee's efforts to use this relationship to persuade his contacts to influence the Nazi leadership failed because of his formal connection with this group. (JD)

  12. IViPP: A Tool for Visualization in Particle Physics

    Science.gov (United States)

    Tran, Hieu; Skiba, Elizabeth; Baldwin, Doug

    2011-10-01

    Experiments and simulations in physics generate a lot of data; visualization is helpful to prepare that data for analysis. IViPP (Interactive Visualizations in Particle Physics) is an interactive computer program that visualizes results of particle physics simulations or experiments. IViPP can handle data from different simulators, such as SRIM or MCNP. It can display relevant geometry and measured scalar data; it can do simple selection from the visualized data. In order to be an effective visualization tool, IViPP must have a software architecture that can flexibly adapt to new data sources and display styles. It must be able to display complicated geometry and measured data with a high dynamic range. We therefore organize it in a highly modular structure, we develop libraries to describe geometry algorithmically, use rendering algorithms running on the powerful GPU to display 3-D geometry at interactive rates, and we represent scalar values in a visual form of scientific notation that shows both mantissa and exponent. This work was supported in part by the US Department of Energy through the Laboratory for Laser Energetics (LLE), with special thanks to Craig Sangster at LLE.

  13. Dzūkijos nacionalinio parko Liškiavos botanikos sodas: retų ir nykstančių augalų rūšių natūralizacijos galimybės

    OpenAIRE

    Baranauskas, Alius

    2005-01-01

    PAPER The possibilities of naturalization of rare and vanishing plants’ species are surveyed in master’s study The subject of research - The botanical gardens of Liskiava with the rare and vanishing plants’ species cultured and naturalized there. Objective of the research – Naturalized species of the plants: Turk’s-cap (Lilium martagon), medicinal angelica (Angelica archangelica), perennial satinflower (Lunaria rediviva), and ivy bedstraw (Hedera helix). Also the naturalization in site of rar...

  14. Mis on teie maakonna Pisa testi edu võti? / Raivo Peeters, Ivi Remmelg, Monika Adamson

    Index Scriptorium Estoniae

    Peeters, Raivo

    2014-01-01

    Küsimusele vastavad Saare maavalitsuse haridus- ja sotsiaalosakonna juhataja Raivo Peeters, Hiiu maavalitsuse haridusnõunik Ivi Remmelg, Põlva maavalitsuse haridus- ja sotsiaalosakonna peaspetsialist Monika Adamson

  15. Mis saab ESTERMist? / Tiina Soon, Peeter Päll, Ivi Papstel ; interv. Aili Künstler

    Index Scriptorium Estoniae

    Soon, Tiina

    2008-01-01

    Eesti Õiguskeskuse loodud andmebaasist ESTERM. Vastavad EKI terminoloogiaosakonna juhataja Tiina Soon, EKI keelekorraldusosakonna vanemteadur Peeter Päll, Justiitsministeeriumi avalike suhete talituse juhataja Ivi Papstel

  16. The Cultivation of Ivy. A Saga of the College in America.

    Science.gov (United States)

    Thelin, John R

    The popular image of the Ivy League is one of a slightly awesome bastion of the well-born, well-bred, and soon-to-be-powerful or, less charitably, a haven for "the effete, unAmerican, and hopelessly bookish." This pervasive idea of collegiate personality is analyzed, tracing the evolution of the Ivy League from an incongruous array of…

  17. Whole-Genome Sequence and Classification of 11 Endophytic Bacteria from Poison Ivy (Toxicodendron radicans).

    Science.gov (United States)

    Tran, Phuong N; Tan, Nicholas E H; Lee, Yin Peng; Gan, Han Ming; Polter, Steven J; Dailey, Lucas K; Hudson, André O; Savka, Michael A

    2015-11-19

    Here, we report the whole-genome sequences and annotation of 11 endophytic bacteria from poison ivy (Toxicodendron radicans) vine tissue. Five bacteria belong to the genus Pseudomonas, and six single members from other genera were found present in interior vine tissue of poison ivy. Copyright © 2015 Tran et al.

  18. Whole-Genome Sequence and Classification of 11 Endophytic Bacteria from Poison Ivy (Toxicodendron radicans)

    OpenAIRE

    Tran, Phuong N.; Tan, Nicholas E. H.; Lee, Yin Peng; Gan, Han Ming; Polter, Steven J.; Dailey, Lucas K.; Hudson, Andr? O.; Savka, Michael A.

    2015-01-01

    Here, we report the whole-genome sequences and annotation of 11 endophytic bacteria from poison ivy (Toxicodendron radicans) vine tissue. Five bacteria belong to the genus Pseudomonas, and six single members from other genera were found present in interior vine tissue of poison ivy.

  19. Ivy signs on FLAIR images before and after STA-MCA anastomosis in patients with Moyamoya disease

    Energy Technology Data Exchange (ETDEWEB)

    Ideguchi, Reiko; Enokizono, Mikako; Uetani, Masataka (Dept. of Radiological Sciences, Nagasaki Univ. Graduate School of Biomedical Sciences, Nagasaki (Japan)), e-mail: qqtt37gd9@forest.ocn.ne.jp; Morikawa, Minoru (Dept. of Radiology, Nagasaki Univ. School of Medicine, Nagasaki (Japan)); Ogawa, Yoji (Dept. of Radiology, Hanwa Daini Senboku Hospital, Osaka (Japan)); Nagata, Izumi (Dept. of Neurosurgery, Nagasaki Univ. School of Medicine, Nagasaki (Japan))

    2011-04-15

    Background: Leptomeningeal high signal intensity (ivy sign) on fluid-attenuated inversion-recovery (FLAIR) MR imaging is one of the features of Moyamoya disease. However, the correlation between ivy sign and cerebral perfusion status has not been fully evaluated. Purpose: To characterize ivy sign on FLAIR images in Moyamoya disease and compare this finding with hemodynamic alterations on perfusion single-photon emission CT (SPECT) obtained before and after bypass surgery. Material and Methods: Sixteen patients with angiographically confirmed Moyamoya disease who underwent superficial temporal artery-middle cerebral artery (STA-MCA) anastomosis were included in the study. The presence of ivy sign on FLAIR images was classified as 'negative', 'minimal' and 'positive'. We evaluated the relationship between ivy sign and findings of SPECT, including cerebral vascular reserve (CVR) before and after surgery. Results: Minimal or positive ivy sign was seen in 13 (81%) of 16 patients, and 21 (66%) of 32 hemispheres. CVR in the areas with positive or minimal ivy sign was lower than that in the areas with negative ivy sign. After STA-MCA anastomosis, ivy sign disappeared or decreased in all 21 hemispheres demonstrating ivy sign. SPECT demonstrated apparent hemodynamic improvement in areas demonstrating disappearance or decrease of ivy sign. Conclusion: Ivy sign on FLAIR image is seen in areas with decreased cerebral perfusion. The sign is useful for non-invasive assessment of cerebral hemodynamic status before and after surgery

  20. 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...

  1. FMRFamide receptors of Helix aspersa

    International Nuclear Information System (INIS)

    Payza, K.

    1988-01-01

    A receptor binding assay and an isolated heart bioassay were used to identify and characterize the FMRFamide receptors in Helix. In the heart bioassay, FMRFamide increased myocardial contraction force. A potent FMRFamide analog, desaminoTyr-Phe-norLeu-arg-Phe-amide (daYFnLRFamide), was used as a radioiodinated receptor ligand. The high affinity binding of 125 I-daYFnLRFamide at 0 degree C to Helix brain membranes was reversible, saturable, pH-dependent and specific, with a K D of 13-14 nM. A lower affinity (245 nM) site was also observed. Radioligand binding sites were also identified in the heart, male reproductive organs and digestive organs. The structure-activity relations (SAR) of cardiostimulation correlated with the specificity of 125 I-daYFnLRFamide binding to brain and heart receptors. The SAR were similar to those of other molluscan FMRFamide bioassays, except that they showed a marked preference for some analogs with blocked amino-terminals

  2. Põrandakatete + ja - / Ivi-Els Schneider, Kadri - sisearhitekt Tarbe, Priit Põldme

    Index Scriptorium Estoniae

    Schneider, Ivi-Els, 1945-

    2005-01-01

    Sisearhitektid Ivi-Els Schneider, Kadri Tarbe Pärtelpoeg ja Priit Põldme sellest, millist põrandakattematerjali ja millal eelistada. Vaatluse all on naturaalne laudpõrand ja parkett, laminaatparkett, kork, lihvitud betoon, linoleum, vaipkate, keraamiline plaat, looduskivi

  3. Problem area descriptions : motor vehicle crashes - data analysis and IVI program analysis

    Science.gov (United States)

    In general, the IVI program focuses on the more significant safety problem categories as : indicated by statistical analyses of crash data. However, other factors were considered in setting : program priorities and schedules. For some problem areas, ...

  4. Ivy and neurogliaform interneurons are a major target of μ opioid receptor modulation

    OpenAIRE

    Krook-Magnuson, Esther; Luu, Lillian; Lee, Sang-Hun; Varga, Csaba; Soltesz, Ivan

    2011-01-01

    Mu opioid receptors (μORs) are selectively expressed on interneurons in area CA1 of the hippocampus. Fast-spiking, parvalbumin expressing, basket cells express μORs, but circumstantial evidence suggests that another major, unidentified, GABAergic cell class must also be modulated by μORs. Here we report that the abundant, dendritically targeting, neurogliaform family of cells (Ivy and neurogliaform cells) is a previously unrecognized target of direct modulation by μORs. Ivy and neurogliaform ...

  5. A comparison of two IPv4/IPv6 transition mechanisms - OpenVPN and IVI

    Science.gov (United States)

    Vu, Cong Tuan; Tran, Quang Anh; Jiang, Frank

    2012-09-01

    This document presents a comparison of two IPv4/IPv6 transition mechanisms. They are OpenVPN and IVI. Meanwhile OpenVPN is based on tunneling technology, IVI is a stateless IPv4/IPv6 translation technique which is developed by China Education and Research Network (CERNET). This research focus on the quantitative and qualitative comparison of these two main mechanisms; how they are applied in practical situation by the Internet Service Providers, as well as their advantages and drawbacks.

  6. Sequencing and De Novo Assembly of the Toxicodendron radicans (Poison Ivy) Transcriptome.

    Science.gov (United States)

    Weisberg, Alexandra J; Kim, Gunjune; Westwood, James H; Jelesko, John G

    2017-11-10

    Contact with poison ivy plants is widely dreaded because they produce a natural product called urushiol that is responsible for allergenic contact delayed-dermatitis symptoms lasting for weeks. For this reason, the catchphrase most associated with poison ivy is "leaves of three, let it be", which serves the purpose of both identification and an appeal for avoidance. Ironically, despite this notoriety, there is a dearth of specific knowledge about nearly all other aspects of poison ivy physiology and ecology. As a means of gaining a more molecular-oriented understanding of poison ivy physiology and ecology, Next Generation DNA sequencing technology was used to develop poison ivy root and leaf RNA-seq transcriptome resources. De novo assembled transcriptomes were analyzed to generate a core set of high quality expressed transcripts present in poison ivy tissue. The predicted protein sequences were evaluated for similarity to SwissProt homologs and InterProScan domains, as well as assigned both GO terms and KEGG annotations. Over 23,000 simple sequence repeats were identified in the transcriptome, and corresponding oligo nucleotide primer pairs were designed. A pan-transcriptome analysis of existing Anacardiaceae transcriptomes revealed conserved and unique transcripts among these species.

  7. Ivy Sign on Fluid-Attenuated Inversion Recovery Images in Moyamoya Disease: Correlation with Clinical Severity and Old Brain Lesions

    OpenAIRE

    Seo, Kwon-Duk; Suh, Sang Hyun; Kim, Yong Bae; Kim, Ji Hwa; Ahn, Sung Jun; Kim, Dong-Seok; Lee, Kyung-Yul

    2015-01-01

    Purpose Leptomeningeal collateral, in moyamoya disease (MMD), appears as an ivy sign on fluid-attenuated inversion-recovery (FLAIR) images. There has been little investigation into the relationship between presentation of ivy signs and old brain lesions. We aimed to evaluate clinical significance of ivy signs and whether they correlate with old brain lesions and the severity of clinical symptoms in patients with MMD. Materials and Methods FLAIR images of 83 patients were reviewed. Each cerebr...

  8. IVisTMSA: Interactive Visual Tools for Multiple Sequence Alignments.

    Science.gov (United States)

    Pervez, Muhammad Tariq; Babar, Masroor Ellahi; Nadeem, Asif; Aslam, Naeem; Naveed, Nasir; Ahmad, Sarfraz; Muhammad, Shah; Qadri, Salman; Shahid, Muhammad; Hussain, Tanveer; Javed, Maryam

    2015-01-01

    IVisTMSA is a software package of seven graphical tools for multiple sequence alignments. MSApad is an editing and analysis tool. It can load 409% more data than Jalview, STRAP, CINEMA, and Base-by-Base. MSA comparator allows the user to visualize consistent and inconsistent regions of reference and test alignments of more than 21-MB size in less than 12 seconds. MSA comparator is 5,200% efficient and more than 40% efficient as compared to BALiBASE c program and FastSP, respectively. MSA reconstruction tool provides graphical user interfaces for four popular aligners and allows the user to load several sequence files at a time. FASTA generator converts seven formats of alignments of unlimited size into FASTA format in a few seconds. MSA ID calculator calculates identity matrix of more than 11,000 sequences with a sequence length of 2,696 base pairs in less than 100 seconds. Tree and Distance Matrix calculation tools generate phylogenetic tree and distance matrix, respectively, using neighbor joining% identity and BLOSUM 62 matrix.

  9. Ivy and neurogliaform interneurons are a major target of μ opioid receptor modulation

    Science.gov (United States)

    Krook-Magnuson, Esther; Luu, Lillian; Lee, Sang-Hun; Varga, Csaba; Soltesz, Ivan

    2011-01-01

    Mu opioid receptors (μORs) are selectively expressed on interneurons in area CA1 of the hippocampus. Fast-spiking, parvalbumin expressing, basket cells express μORs, but circumstantial evidence suggests that another major, unidentified, GABAergic cell class must also be modulated by μORs. Here we report that the abundant, dendritically targeting, neurogliaform family of cells (Ivy and neurogliaform cells) is a previously unrecognized target of direct modulation by μORs. Ivy and neurogliaform cells are not only numerous, but also have unique properties, including promiscuous gap junctions formed with various interneuronal subtypes, volume transmission, and the ability to produce a postsynaptic GABAB response after a single presynaptic spike. Using a mouse line expressing green fluorescent protein under the neuropeptide Y promoter, we find that across all layers of CA1, activation of μORs hyperpolarizes Ivy and neurogliaform cells. Further, paired recordings between synaptically coupled Ivy and pyramidal cells show that Ivy cell terminals are dramatically inhibited by μOR-activation. Effects in Ivy and neurogliaform cells are seen at similar concentrations of agonist as those producing inhibition in fast-spiking PV basket cells. We also report that Ivy cells display the recently described phenomenon of persistent firing, a state of continued firing in the absence of continued input, and that induction of persistent firing is inhibited by μOR-activation. Together these findings identify a major, previously unrecognized, target of μOR-modulation. Given the prominence of this cell type in and beyond CA1, as well as its unique role in microcircuitry, opioid modulation of neurogliaform cells has wide implications. PMID:22016519

  10. Ivy and neurogliaform interneurons are a major target of μ-opioid receptor modulation.

    Science.gov (United States)

    Krook-Magnuson, Esther; Luu, Lillian; Lee, Sang-Hun; Varga, Csaba; Soltesz, Ivan

    2011-10-19

    μ-Opioid receptors (μORs) are selectively expressed on interneurons in area CA1 of the hippocampus. Fast-spiking, parvalbumin-expressing, basket cells express μORs, but circumstantial evidence suggests that another major, unidentified, GABAergic cell class must also be modulated by μORs. Here we report that the abundant, dendritically targeting, neurogliaform family of cells (Ivy and neurogliaform cells) is a previously unrecognized target of direct modulation by μORs. Ivy and neurogliaform cells are not only numerous but also have unique properties, including promiscuous gap junctions formed with various interneuronal subtypes, volume transmission, and the ability to produce a postsynaptic GABA(B) response after a single presynaptic spike. Using a mouse line expressing green fluorescent protein under the neuropeptide Y promoter, we find that, across all layers of CA1, activation of μORs hyperpolarizes Ivy and neurogliaform cells. Furthermore, paired recordings between synaptically coupled Ivy and pyramidal cells show that Ivy cell terminals are dramatically inhibited by μOR activation. Effects in Ivy and neurogliaform cells are seen at similar concentrations of agonist as those producing inhibition in fast-spiking parvalbumin basket cells. We also report that Ivy cells display the recently described phenomenon of persistent firing, a state of continued firing in the absence of continued input, and that induction of persistent firing is inhibited by μOR activation. Together, these findings identify a major, previously unrecognized, target of μOR modulation. Given the prominence of this cell type in and beyond CA1, as well as its unique role in microcircuitry, opioid modulation of neurogliaform cells has wide implications.

  11. Helix-Hopes on Finite Hyperfields

    Directory of Open Access Journals (Sweden)

    Thomas Vougiouklis

    2016-12-01

    Full Text Available Hyperstructure theory can overcome restrictions which ordinary algebraic structures have. A hyperproduct on non-square ordinary matrices can be defined by using the so called helix-hyperoperations. We study the helix-hyperstructures on the representations using ordinary fields. The related theory can be faced by defining the hyperproduct on the set of non square matrices. The main tools of the Hyperstructure Theory are the fundamental relations which connect the largest class of hyperstructures, the Hv-structures, with the corresponding classical ones. We focus on finite dimensional helix-hyperstructures and on small Hv-fields, as well.

  12. Unfolding four-helix bundles

    Science.gov (United States)

    Gray, Harry B.; Winkler, Jay R.; Kozak, John J.

    2011-03-01

    A geometrical model has been developed to describe the early stages of unfolding of cytochromes c‧ and c-b562 . Calculations are based on a step-wise extension of the polypeptide chain subject to the constraint that the spatial relationship among the residues of each triplet is fixed by the native-state crystallographic data. The response of each protein to these structural perturbations allows the evolution of each of the four helices in these two proteins to be differentiated. It is found that the two external helices in c‧ unfold before its two internal helices, whereas exactly the opposite behaviour is demonstrated by c-b562 . Each of these cytochromes has an extended, internal, non-helical ('turning') region that initially lags behind the most labile helix but then, at a certain stage (identified for each cytochrome), unravels before any of the four helices present in the native structure. It is believed that these predictions will be useful in guiding future experimental studies on the unfolding of these two cytochromes.

  13. Teaching helix and problems connected with helix using GeoGebra

    Science.gov (United States)

    Bímová, Daniela

    2017-12-01

    The contribution presents the dynamic applets created in GeoGebra that show the origin and main properties of a helix and it also presents some constructive problems connected with the helix. There are created the step by step algorithms of some constructions in the chosen applets. Three-dimensional applets include illustrative helix samples and spatial animations that help students better see problems concerning the helix spatially. There is mentioned the website in the contribution on which there is situated GeoGebra book dedicated to the topic "Helix" and containing the mentioned applets. The created applets and materials of the GeoGebra book "Helix" help in teaching and studying the course Constructive Geometry determined for the students of the Faculty of Mechanical Engineering of the Technical University of Liberec.

  14. Determination of saponins and flavonoids in ivy leaf extracts using HPLC-DAD.

    Science.gov (United States)

    Yu, Miao; Shin, Young June; Kim, Nanyoung; Yoo, Guijae; Park, SeonJu; Kim, Seung Hyun

    2015-04-01

    A new method for the determination of six compounds, chlorogenic acid, rutin, nicotiflorin, hederacoside C, hederasaponin B and α-hederin, in ivy leaf extracts using high-performance liquid chromatography with diode array detector was developed. The chromatographic separation was performed on a YMC Hydrosphere C18 analytical column using a gradient elution of 0.1% phosphoric acid and acetonitrile. The method was validated in terms of specificity, linearity (r(2) > 0.9999), precision [relative standard deviation (RSD) method was successfully applied to quantify all six compounds in a 30% ethanol ivy leaf extract and 13 ivy leaf extract products. The results showed that all the tested products satisfied the minimum requirement for the content of hederacoside C. However, there were some differences between the contents of other constituents. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  15. The swimming of a perfect deforming helix

    Science.gov (United States)

    Koens, Lyndon; Zhang, Hang; Mourran, Ahmed; Lauga, Eric

    2017-11-01

    Many bacteria rotate helical flagellar filaments in order to swim. When at rest or rotated counter-clockwise these flagella are left handed helices but they undergo polymorphic transformations to right-handed helices when the motor is reversed. These helical deformations themselves can generate motion, with for example Rhodobacter sphaeroides using the polymorphic transformation of the flagellum to generate rotation, or Spiroplasma propagating a change of helix handedness across its body's length to generate forward motion. Recent experiments reported on an artificial helical microswimmer generating motion without a propagating change in handedness. Made of a temperature sensitive gel, these swimmers moved by changing the dimensions of the helix in a non-reciprocal way. Inspired by these results and helix's ubiquitous presence in the bacterial world, we investigate how a deforming helix moves within a viscous fluid. Maintaining a single handedness along its entire length, we discuss how a perfect deforming helix can create a non-reciprocal swimming stroke, identify its principle directions of motion, and calculate the swimming kinematics asymptotically.

  16. (Re)membering Basic Writing at a Public Ivy: History for Institutional Redesign

    Science.gov (United States)

    Tassoni, John Paul

    2006-01-01

    This essay offers a history of a basic writing course that began at a public ivy campus in the 1970s. Relying on principles of universal design and on insights derived from his school's studio program about ways the institution's selective functions can impact curricular matters, the author describes how the basic writing course was merely…

  17. 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. © 2016 Wiley Periodicals, Inc.

  18. Triple helix interactions for eco-innovation

    DEFF Research Database (Denmark)

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

    the role of science parks in promoting eco-innovation. This study uses qualitative data gathered in two units of analysis: Panama Canal Authority and City of Knowledge Science Park. The study examines how Triple Helix interactions have built the regional system of eco-innovation at the Panama Canal...

  19. Conformational Diffusion and Helix Formation Kinetics

    International Nuclear Information System (INIS)

    Hummer, Gerhard; Garcia, Angel E.; Garde, Shekhar

    2000-01-01

    The time, temperature, and sequence dependences of helix formation kinetics of fully atomistic peptide models in explicit solvent are described quantitatively by a diffusive search within the coil state with barrierless transitions into the helical state. Conformational diffusion leads to nonexponential kinetics and jump-width dependences in temperature jump experiments. (c) 2000 The American Physical Society

  20. The Discovery of the Double Helix

    CERN Multimedia

    CERN. Geneva

    2011-01-01

    Professor James D. Watson has kindly agreed to make a presentation on the 1953 finding of the Double Helix at the Cavendish Laboratory by Francis Crick and himself. Being one of the greatest scientific discoveries in human history, little else needs to be added.

  1. Solitons in an isolated helix chain

    DEFF Research Database (Denmark)

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

    1997-01-01

    as a generalization of the well-known one-dimensional Fermi-Pasta-Ulam model to include transverse degrees of freedom of the chain molecules. In the particular case of the alpha-helix molecular chain, the intermolecular interactions involved into the model are the point-point bonds connecting the first-, second...

  2. Conformational Diffusion and Helix Formation Kinetics

    Energy Technology Data Exchange (ETDEWEB)

    Hummer, Gerhard [Laboratory of Chemical Physics, Building 5, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520 (United States); Garcia, Angel E. [Theoretical Biology and Biophysics Group T-10, MS K710, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States); Garde, Shekhar [Department of Chemical Engineering, Rensselaer Polytechnic Institute, 110 8th Street, Troy, New York 12180 (United States)

    2000-09-18

    The time, temperature, and sequence dependences of helix formation kinetics of fully atomistic peptide models in explicit solvent are described quantitatively by a diffusive search within the coil state with barrierless transitions into the helical state. Conformational diffusion leads to nonexponential kinetics and jump-width dependences in temperature jump experiments. (c) 2000 The American Physical Society.

  3. Ivy Sign on Fluid-Attenuated Inversion Recovery Images in Moyamoya Disease: Correlation with Clinical Severity and Old Brain Lesions.

    Science.gov (United States)

    Seo, Kwon-Duk; Suh, Sang Hyun; Kim, Yong Bae; Kim, Ji Hwa; Ahn, Sung Jun; Kim, Dong-Seok; Lee, Kyung-Yul

    2015-09-01

    Leptomeningeal collateral, in moyamoya disease (MMD), appears as an ivy sign on fluid-attenuated inversion-recovery (FLAIR) images. There has been little investigation into the relationship between presentation of ivy signs and old brain lesions. We aimed to evaluate clinical significance of ivy signs and whether they correlate with old brain lesions and the severity of clinical symptoms in patients with MMD. FLAIR images of 83 patients were reviewed. Each cerebral hemisphere was divided into 4 regions and each region was scored based on the prominence of the ivy sign. Total ivy score (TIS) was defined as the sum of the scores from the eight regions and dominant hemispheric ivy sign (DHI) was determined by comparing the ivy scores from each hemisphere. According to the degree of ischemic symptoms, patients were classified into four subgroups: 1) nonspecific symptoms without motor weakness, 2) single transient ischemic attack (TIA), 3) recurrent TIA, or 4) complete stroke. TIS was significantly different as follows: 4.86±2.55 in patients with nonspecific symptoms, 5.89±3.10 in patients with single TIA, 9.60±3.98 in patients with recurrent TIA and 8.37±3.39 in patients with complete stroke (p=0.003). TIS associated with old lesions was significantly higher than those not associated with old lesions (9.35±4.22 vs. 7.49±3.37, p=0.032). We found a significant correlation between DHI and motor symptoms (p=0.001). Because TIS has a strong tendency with severity of ischemic motor symptom and the presence of old lesions, the ivy sign may be useful in predicting severity of disease progression.

  4. 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.

  5. Kevlar: Transitioning Helix for Research to Practice

    Science.gov (United States)

    2016-03-01

    x86 binaries, although it can be targeted to any platform that is targeted by IDA Pro. Currently, IDA Pro targets more than 40 processors and...effects its own transformations. Helix/Kevlar then automatically generates SPRI rules for any program variants by essentially performing a “ smart diff...execute permission on the pages of memory it uses, leaving only execute (but not write) permission on the code cache. Strata also watches for attempts

  6. Origin and Diversification of Basic-Helix-Loop-Helix Proteins in Plants

    OpenAIRE

    Pires, Nuno; Dolan, Liam

    2009-01-01

    Basic helix-loop-helix (bHLH) proteins are a class of transcription factors found throughout eukaryotic organisms. Classification of the complete sets of bHLH proteins in the sequenced genomes of Arabidopsis thaliana and Oryza sativa (rice) has defined the diversity of these proteins among flowering plants. However, the evolutionary relationships of different plant bHLH groups and the diversity of bHLH proteins in more ancestral groups of plants are currently unknown. In this study, we use wh...

  7. Designing cooperatively folded abiotic uni- and multimolecular helix bundles

    Science.gov (United States)

    de, Soumen; Chi, Bo; Granier, Thierry; Qi, Ting; Maurizot, Victor; Huc, Ivan

    2018-01-01

    Abiotic foldamers, that is foldamers that have backbones chemically remote from peptidic and nucleotidic skeletons, may give access to shapes and functions different to those of peptides and nucleotides. However, design methodologies towards abiotic tertiary and quaternary structures are yet to be developed. Here we report rationally designed interactional patterns to guide the folding and assembly of abiotic helix bundles. Computational design facilitated the introduction of hydrogen-bonding functionalities at defined locations on the aromatic amide backbones that promote cooperative folding into helix-turn-helix motifs in organic solvents. The hydrogen-bond-directed aggregation of helices not linked by a turn unit produced several thermodynamically and kinetically stable homochiral dimeric and trimeric bundles with structures that are distinct from the designed helix-turn-helix. Relative helix orientation within the bundles may be changed from parallel to tilted on subtle solvent variations. Altogether, these results prefigure the richness and uniqueness of abiotic tertiary structure behaviour.

  8. 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.

  9. Dynamics of competitive population abundance of Lactobacillus plantarum ivi gene mutants in faecel samples after passage through the gastrointestinal tract of mice

    NARCIS (Netherlands)

    Bron, P.A.; Meijer, M.; Bongers, R.S.; Vos, de W.M.; Kleerebezem, M.

    2007-01-01

    This study aims to evaluate the impact of mutation of previously identified in vivo-induced (ivi) genes on the persistence and survival of Lactobacillus plantarum WCFS1 in the gastrointestinal (GI) tract of mice. Methods and Results:¿ Nine Lact. plantarum ivi gene replacement mutants were

  10. Surpluses and Deficits: How University Partners Perceive University-Community Partnerships at One Ivy League Institution

    Directory of Open Access Journals (Sweden)

    Alison Klebanoff Cohen

    2012-07-01

    Full Text Available University-community partnerships are a critical method for how universities can serve the public interest.  Yet key questions remain: how do these partnerships work in practice, and how can university and fill reciprocal and mutual needs effectively?  A participatory evaluation of university-community partnerships in education at an Ivy League university found that university partners had a surplus perspective of the university and a deficit perspective of community partners; practitioners must shift our paradigm towards mutually beneficial, asset-driven university-community partnerships to ensure success.

  11. 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…

  12. 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...

  13. 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…

  14. "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…

  15. Fabrication experiments for large helix heat exchangers

    International Nuclear Information System (INIS)

    Burgsmueller, P.

    1978-01-01

    The helical tube has gained increasing attention as a heat transfer element for various kinds of heat exchangers over the last decade. Regardless of reactor type and heat transport medium, nuclear steam generators of the helix type are now in operation, installlation, fabrication or in the project phase. As a rule, projects are based on the extrapolation of existing technologies. In the particlular case of steam generators for HTGR power stations, however, existing experience is with steam generators of up to about 2 m diameter whereas several projects involve units more than twice as large. For this reason it was felt that a fabrication experiment was necessary in order to verify the feasibility of modern steam generator designs. A test rig was erected in the SULZER steam generator shops at Mantes, France, and skilled personnel and conventional production tools were employed in conducting experiments relating to the coiling, handling and threading of large helices. (Auth.)

  16. FPGA helix tracking algorithm for PANDA

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-07-01

    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 VHDL-based algorithm is tested with different types of events, at different event rate. Furthermore, a study of T0 extraction from the tracking algorithm is performed. A concept of simultaneous tracking and T0 determination is presented.

  17. 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.

  18. Adsorption behavior of ammonium by a bioadsorbent - Boston ivy leaf powder

    Institute of Scientific and Technical Information of China (English)

    Haiwei Liu; Yuanhua Dong; Haiyun Wang; Yun Liu

    2010-01-01

    The adsorption behaviors of ammonium ions from aqueous solution by a novel bioadsorbent,the Boston ivy (Parthenocissus tricuspidata) leaf powder (BPTL) were investigated.The SEM images and FT-IR spectra were used to characterize BPTL.The mathematical models were used to analyze the adsorption kinetics and isotherms.The optimum pH range for ammonium adsorption by BPTL was found to be 5-10.The adsorption reached equilibrium at 14 hr,and the kinetic data were well fitted by the Logistic model.The intraparticle diffusion was the main rate-controlling step of the adsorption process.The high temperature was favorableto the ammonium adsorption by BPTL,indicating that the adsorption was endothermic.The adsorption equilibrium fitted well to both the Langrnuir model and Freundlich model,and the maximum monolayer adsorption capacities calculated from Langmuir model were 3.37,5.28 and 6.59 mg N/g at 15,25 and 35℃,respectively,which were comparable to those by reported minerals.Both the separation factor (RL) from the Langmuir model and Freundlich exponent (n) suggested that the ammonium adsorption by BPTL was favorable.Therefore,the Boston ivy leaf powder could be considered a novel bioadsorbent for ammonium removal from aqueous solution.

  19. Recognition and Binding of a Helix-Loop-Helix Peptide to Carbonic Anhydrase Occurs via Partly Folded Intermediate Structures

    Science.gov (United States)

    Lignell, Martin; Becker, Hans-Christian

    2010-01-01

    Abstract We have studied the association of a helix-loop-helix peptide scaffold carrying a benzenesulfonamide ligand to carbonic anhydrase using steady-state and time-resolved fluorescence spectroscopy. The helix-loop-helix peptide, developed for biosensing applications, is labeled with the fluorescent probe dansyl, which serves as a polarity-sensitive reporter of the binding event. Using maximum entropy analysis of the fluorescence lifetime of dansyl at 1:1 stoichiometry reveals three characteristic fluorescence lifetime groups, interpreted as differently interacting peptide/protein structures. We characterize these peptide/protein complexes as mostly bound but unfolded, bound and partly folded, and strongly bound and folded. Furthermore, analysis of the fluorescence anisotropy decay resulted in three different dansyl rotational correlation times, namely 0.18, 1.2, and 23 ns. Using the amplitudes of these times, we can correlate the lifetime groups with the corresponding fluorescence anisotropy component. The 23-ns rotational correlation time, which appears with the same amplitude as a 17-ns fluorescence lifetime, shows that the dansyl fluorophore follows the rotational diffusion of carbonic anhydrase when it is a part of the folded peptide/protein complex. A partly folded and partly hydrated interfacial structure is manifested in an 8-ns dansyl fluorescence lifetime and a 1.2-ns rotational correlation time. This structure, we believe, is similar to a molten-globule-like interfacial structure, which allows segmental movement and has a higher degree of solvent exposure of dansyl. Indirect excitation of dansyl on the helix-loop-helix peptide through Förster energy transfer from one or several tryptophans in the carbonic anhydrase shows that the helix-loop-helix scaffold binds to a tryptophan-rich domain of the carbonic anhydrase. We conclude that binding of the peptide to carbonic anhydrase involves a transition from a disordered to an ordered structure of the

  20. Rain Uusküla korter Tiskre-Hansu elamurajoonis / Ivi Piho, Stina Kasemägi ; fotod: Toomas Tuul

    Index Scriptorium Estoniae

    Piho, Ivi

    2008-01-01

    7 vaadet; korterelamu projekteeris arhitektuuribüroo Nafta; sisearhitekt Ivi Piho, kelle jooniste järgi on tellitud ka suurem osa mööblist firmast Borg ja Rigor; elutoa seinal Stina Kasemäe maal "Merineitsi"

  1. Kergplokkidest Jämera tüüpmaja Merirahu eramurajoonis / Ivi-Els Schneider, Piret Anier

    Index Scriptorium Estoniae

    Schneider, Ivi-Els, 1945-

    2005-01-01

    I ja II korruse plaan, välisvaade, 10 sisevaadet, värv.; ümberprojekteerimine: arhitekt Piret Anier, AB Zokkel, sisearhitekt Ivi-Els Schneideri jooniste järgi on valmistatud ka enamik mööblist; fotod: Kaido Haagen

  2. Molecular analysis of ivy cells of the hippocampal CA1 stratum radiatum using spectral identification of immunofluorophores

    Directory of Open Access Journals (Sweden)

    Jozsef eSomogyi

    2012-05-01

    Full Text Available Nitric oxide synthase-expressing (NOS+ GABAergic interneurons are common in hippocampal stratum radiatum, but these cells are less well characterised than NOS+ ivy cells in stratum pyramidale or neurogliaform cells in stratum lacunosum-moleculare. Here we have studied the laminar distribution of the axons and dendrites, and the immunoreactivity of these neurons recorded in rat hippocampal slices. We have used spectral analysis of antibody- or streptavidin conjugated fluorophores to improve recognition of genuine signals in reactions for molecules such as NOS and neuropeptide-Y, when immunolabelling was low in the recorded cell. We found that most NOS+ cells with soma in the CA1 area stratum radiatum exhibit characteristic properties of ivy cells; all tested cells were positive for NPY and negative for reelin. However, laminar distributions of their neurites differ from original characterization of ivy cells with the soma close to stratum pyramidale. Both their dendrites and axon are mainly in stratum radiatum and to a lesser extent in stratum oriens. In addition, both the dendrites and axons often extend to stratum lacunosum-moleculare. We conclude that ivy cells in stratum radiatum are predominantly feedforward inhibitory interneurons in the CA1 area, and their axonal output delivering GABA, NPY and NO can influence both the entorhinal cortex innervated and the CA3 innervated zones pre- and postsynaptically. Spectral analysis of fluorophores provides an objective algorithm to analyze signals in immunoreactions for neurochemical markers.

  3. Effects and mode of action of chitosan and ivy fruit saponins on the microbiome, fermentation and methanogenesis in the rumen simulation technique.

    Science.gov (United States)

    Belanche, Alejandro; Pinloche, Eric; Preskett, David; Newbold, C Jamie

    2016-01-01

    This study investigates the effects of supplementing a control diet (CON) with chitosan (CHI) or ivy fruit saponins (IVY) as natural feed additives. Both additives had similar abilities to decrease rumen methanogenesis (-42% and -40%, respectively) using different mechanisms: due to its antimicrobial and nutritional properties CHI promoted a shift in the fermentation pattern towards propionate production which explained about two thirds of the decrease in methanogenesis. This shift was achieved by a simplification of the structure in the bacterial community and a substitution of fibrolytic (Firmicutes and Fibrobacteres) by amylolytic bacteria (Bacteroidetes and Proteobacteria) which led to greater amylase activity, lactate and microbial protein yield with no detrimental effect on feed digestibility. Contrarily, IVY had negligible nutritional properties promoting minor changes in the fermentation pattern and on the bacterial community. Instead, IVY modified the structure of the methanogen community and decreased its diversity. This specific antimicrobial effect of IVY against methanogens was considered its main antimethanogenic mechanism. IVY had however a negative impact on microbial protein synthesis. Therefore, CHI and IVY should be further investigated in vivo to determine the optimum doses which maintain low methanogenesis but prevent negative effects on the rumen fermentation and animal metabolism. © FEMS 2015.

  4. Inheritance of the lysozyme inhibitor Ivy was an important evolutionary step by Yersinia pestis to avoid the host innate immune response.

    Science.gov (United States)

    Derbise, Anne; Pierre, François; Merchez, Maud; Pradel, Elizabeth; Laouami, Sabrina; Ricard, Isabelle; Sirard, Jean-Claude; Fritz, Jill; Lemaître, Nadine; Akinbi, Henry; Boneca, Ivo G; Sebbane, Florent

    2013-05-15

    Yersinia pestis (the plague bacillus) and its ancestor, Yersinia pseudotuberculosis (which causes self-limited bowel disease), encode putative homologues of the periplasmic lysozyme inhibitor Ivy and the membrane-bound lysozyme inhibitor MliC. The involvement of both inhibitors in virulence remains subject to debate. Mutants lacking ivy and/or mliC were generated. We evaluated the mutants' ability to counter lysozyme, grow in serum, and/or counter leukocytes; to produce disease in wild-type, neutropenic, or lysozyme-deficient rodents; and to induce host inflammation. MliC was not required for lysozyme resistance and the development of plague. Deletion of ivy decreased Y. pestis' ability to counter lysozyme and polymorphonuclear neutrophils, but it did not affect the bacterium's ability to grow in serum or resist macrophages. Y. pestis lacking Ivy had attenuated virulence, unless animals were neutropenic or lysozyme deficient. The Ivy mutant induced inflammation to a degree similar to that of the parental strain. Last, Y. pseudotuberculosis did not require Ivy to counter lysozyme and for virulence. Ivy is required to counter lysozyme during infection, but its role as a virulence factor is species dependent. Our study also shows that a gene that is not necessary for the virulence of an ancestral bacterium may become essential in the emergence of a new pathogen.

  5. Poison Ivy

    Science.gov (United States)

    ... been out exploring the woods, you might want to give your pet a shower, too! Reviewed by: Steven Dowshen, MD Date reviewed: February ... Visit the Nemours Web site. Note: All information on KidsHealth® is for ...

  6. Fluctuations in the DNA double helix

    Science.gov (United States)

    Peyrard, M.; López, S. C.; Angelov, D.

    2007-08-01

    DNA is not the static entity suggested by the famous double helix structure. It shows large fluctuational openings, in which the bases, which contain the genetic code, are temporarily open. Therefore it is an interesting system to study the effect of nonlinearity on the physical properties of a system. A simple model for DNA, at a mesoscopic scale, can be investigated by computer simulation, in the same spirit as the original work of Fermi, Pasta and Ulam. These calculations raise fundamental questions in statistical physics because they show a temporary breaking of equipartition of energy, regions with large amplitude fluctuations being able to coexist with regions where the fluctuations are very small, even when the model is studied in the canonical ensemble. This phenomenon can be related to nonlinear excitations in the model. The ability of the model to describe the actual properties of DNA is discussed by comparing theoretical and experimental results for the probability that base pairs open an a given temperature in specific DNA sequences. These studies give us indications on the proper description of the effect of the sequence in the mesoscopic model.

  7. Electrostatic bending response of a charged helix

    Science.gov (United States)

    Zampetaki, A. V.; Stockhofe, J.; Schmelcher, P.

    2018-04-01

    We explore the electrostatic bending response of a chain of charged particles confined on a finite helical filament. We analyze how the energy difference Δ E between the bent and the unbent helical chain scales with the length of the helical segment and the radius of curvature and identify features that are not captured by the standard notion of the bending rigidity, normally used as a measure of bending tendency in the linear response regime. Using Δ E to characterize the bending response of the helical chain we identify two regimes with qualitatively different bending behaviors for the ground state configuration: the regime of small and the regime of large radius-to-pitch ratio, respectively. Within the former regime, Δ E changes smoothly with the variation of the system parameters. Of particular interest are its oscillations with the number of charged particles encountered for commensurate fillings which yield length-dependent oscillations in the preferred bending direction of the helical chain. We show that the origin of these oscillations is the nonuniformity of the charge distribution caused by the long-range character of the Coulomb interactions and the finite length of the helix. In the second regime of large values of the radius-to-pitch ratio, sudden changes in the ground state structure of the charges occur as the system parameters vary, leading to complex and discontinuous variations in the ground state bending response Δ E .

  8. Generating structured light with phase helix and intensity helix using reflection-enhanced plasmonic metasurface at 2 μm

    Science.gov (United States)

    Zhao, Yifan; Du, Jing; Zhang, Jinrun; Shen, Li; Wang, Jian

    2018-04-01

    Mid-infrared (2-20 μm) light has been attracting great attention in many areas of science and technology. Beyond the extended wavelength range from visible and near-infrared to mid-infrared, shaping spatial structures may add opportunities to grooming applications of mid-infrared photonics. Here, we design and fabricate a reflection-enhanced plasmonic metasurface and demonstrate efficient generation of structured light with the phase helix and intensity helix at 2 μm. This work includes two distinct aspects. First, structured light (phase helix, intensity helix) generation at 2 μm, which is far beyond the ability of conventional spatial light modulators, is enabled by the metasurface with sub-wavelength engineered structures. Second, the self-referenced intensity helix against environmental noise is generated without using a spatially separated light. The demonstrations may open up advanced perspectives to structured light applications at 2 μm, such as phase helix for communications and non-communications (imaging, sensing) and intensity helix for enhanced microscopy and advanced metrology.

  9. A toolkit for computerized operating procedure of complex industrial systems with IVI-COM technology

    International Nuclear Information System (INIS)

    Zhou Yangping; Dong Yujie; Huang Xiaojing; Ye Jingliang; Yoshikawa, Hidekazu

    2013-01-01

    A human interface toolkit is proposed to help the user develop computerized operating procedure of complex industrial system such as Nuclear Power Plants (NPPs). Coupled with a friendly graphical interface, this integrated tool includes a database, a procedure editor and a procedure executor. A three layer hierarchy is adopted to express the complexity of operating procedure, which includes mission, process and node. There are 10 kinds of node: entrance, exit, hint, manual input, detector, actuator, data treatment, branch, judgment and plug-in. The computerized operating procedure will sense and actuate the actual industrial systems with the interface based on IVI-COM (Interchangeable Virtual Instrumentation-Component Object Model) technology. A prototype system of this human interface toolkit has been applied to develop a simple computerized operating procedure for a simulated NPP. (author)

  10. Assisted reproductive technologies and fertility "tourism": examples from global Dubai and the Ivy League.

    Science.gov (United States)

    Inhorn, Marcia C; Shrivastav, Pankaj; Patrizio, Pasquale

    2012-01-01

    What motivates the global movements of infertile people searching for assisted reproductive technologies (ARTs)? In this article, we attempt to answer this question by exploring infertile patients' practices of so-called "fertility tourism." Based on ethnographic research carried out with nearly 300 infertile travelers in two major ART centers--one in the global hub of the United Arab Emirates and the other at a major East Coast Ivy League university--we examine a diverse set of reasons for reproductive travel. We argue that reproductive "tourism" should be reconceptualized as reproductive "exile" in that infertile couples feel barred from accessing ARTs in their home countries. Listening to reproductive travel stories is key to understanding infertile couples' transnational "quests for conception." Stories of two couples, one from Lebanon and one from Italy, demonstrate the poignancy of these quests and begin to shed light on the complex calculus of factors governing this global movement of reproductive actors.

  11. Fabrication of Microfiber Patterns with Ivy Shoot-Like Geometries Using Improved Electrospinning.

    Science.gov (United States)

    Jeong, Young Hun; Lee, Jongwan

    2016-04-01

    Fibers and fibrous structures are used extensively in various fields due to their many advantages. Microfibers, as well as nanofibers, are considered to be some of the most valuable forms of advanced materials. Accordingly, various methods for fabricating microfibers have been developed. Electrospinning is a useful fabrication method for continuous polymeric nano- and microfibers with attractive merits. However, this technique has limitations in its ability to control the geometry of fibrous structures. Herein, advanced electrospinning with direct-writing functionality was used to fabricate microfiber patterns with ivy shoot-like geometries after experimentally investigating the effects of the process conditions on the fiber formation. The surface properties of the fibers were also modified by introducing nanoscale pores through the use of higher levels of humidity during the fabrication process.

  12. Controlling chirality with helix inversion in cholesteric liquid crystals

    NARCIS (Netherlands)

    Katsonis, Nathalie Hélène; Lacaze, E.; Ferrarini, A.

    2012-01-01

    The helical organization of cholesteric liquid crystals is omnipresent in living matter. Achieving control over the structure of the cholesteric helix consequently holds great potential for developing stimuli-responsive materials matching the level of sophistication of biological systems. In

  13. A genome-wide survey on basic helix-loop-helix transcription factors in giant panda.

    Directory of Open Access Journals (Sweden)

    Chunwang Dang

    Full Text Available The giant panda (Ailuropoda melanoleuca is a critically endangered mammalian species. Studies on functions of regulatory proteins involved in developmental processes would facilitate understanding of specific behavior in giant panda. 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 fruit fly, zebrafish, mouse and human. Our present study identified 107 bHLH family members being encoded in giant panda genome. Phylogenetic analyses revealed that they belong to 44 bHLH families with 46, 25, 15, 4, 11 and 3 members in group A, B, C, D, E and F, respectively, while the remaining 3 members were assigned into "orphan". Compared to mouse, the giant panda does not encode seven bHLH proteins namely Beta3a, Mesp2, Sclerax, S-Myc, Hes5 (or Hes6, EBF4 and Orphan 1. These results provide useful background information for future studies on structure and function of bHLH proteins in the regulation of giant panda development.

  14. Regulation of TCF ETS-domain transcription factors by helix-loop-helix motifs.

    Science.gov (United States)

    Stinson, Julie; Inoue, Toshiaki; Yates, Paula; Clancy, Anne; Norton, John D; Sharrocks, Andrew D

    2003-08-15

    DNA binding by the ternary complex factor (TCF) subfamily of ETS-domain transcription factors is tightly regulated by intramolecular and intermolecular interactions. The helix-loop-helix (HLH)-containing Id proteins are trans-acting negative regulators of DNA binding by the TCFs. In the TCF, SAP-2/Net/ERP, intramolecular inhibition of DNA binding is promoted by the cis-acting NID region that also contains an HLH-like motif. The NID also acts as a transcriptional repression domain. Here, we have studied the role of HLH motifs in regulating DNA binding and transcription by the TCF protein SAP-1 and how Cdk-mediated phosphorylation affects the inhibitory activity of the Id proteins towards the TCFs. We demonstrate that the NID region of SAP-1 is an autoinhibitory motif that acts to inhibit DNA binding and also functions as a transcription repression domain. This region can be functionally replaced by fusion of Id proteins to SAP-1, whereby the Id moiety then acts to repress DNA binding in cis. Phosphorylation of the Ids by cyclin-Cdk complexes results in reduction in protein-protein interactions between the Ids and TCFs and relief of their DNA-binding inhibitory activity. In revealing distinct mechanisms through which HLH motifs modulate the activity of TCFs, our results therefore provide further insight into the role of HLH motifs in regulating TCF function and how the inhibitory properties of the trans-acting Id HLH proteins are themselves regulated by phosphorylation.

  15. Genome-wide identification and analysis of the chicken basic helix-loop-helix factors.

    Science.gov (United States)

    Liu, Wu-Yi; Zhao, Chun-Jiang

    2010-01-01

    Members of the basic helix-loop-helix (bHLH) family of transcription factors play important roles in a wide range of developmental processes. In this study, we conducted a genome-wide survey using the chicken (Gallus gallus) genomic database, and identified 104 bHLH sequences belonging to 42 gene families in an effort to characterize the chicken bHLH transcription factor family. Phylogenetic analyses revealed that chicken has 50, 21, 15, 4, 8, and 3 bHLH members in groups A, B, C, D, E, and F, respectively, while three members belonging to none of these groups were classified as ''orphans". A comparison between chicken and human bHLH repertoires suggested that both organisms have a number of lineage-specific bHLH members in the proteomes. Chromosome distribution patterns and phylogenetic analyses strongly suggest that the bHLH members should have arisen through gene duplication at an early date. Gene Ontology (GO) enrichment statistics showed 51 top GO annotations of biological processes counted in the frequency. The present study deepens our understanding of the chicken bHLH transcription factor family and provides much useful information for further studies using chicken as a model system.

  16. Genome-Wide Identification and Analysis of the Chicken Basic Helix-Loop-Helix Factors

    Directory of Open Access Journals (Sweden)

    Wu-yi Liu

    2010-01-01

    Full Text Available Members of the basic helix-loop-helix (bHLH family of transcription factors play important roles in a wide range of developmental processes. In this study, we conducted a genome-wide survey using the chicken (Gallus gallus genomic database, and identified 104 bHLH sequences belonging to 42 gene families in an effort to characterize the chicken bHLH transcription factor family. Phylogenetic analyses revealed that chicken has 50, 21, 15, 4, 8, and 3 bHLH members in groups A, B, C, D, E, and F, respectively, while three members belonging to none of these groups were classified as ‘‘orphans’’. A comparison between chicken and human bHLH repertoires suggested that both organisms have a number of lineage-specific bHLH members in the proteomes. Chromosome distribution patterns and phylogenetic analyses strongly suggest that the bHLH members should have arisen through gene duplication at an early date. Gene Ontology (GO enrichment statistics showed 51 top GO annotations of biological processes counted in the frequency. The present study deepens our understanding of the chicken bHLH transcription factor family and provides much useful information for further studies using chicken as a model system.

  17. 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.

  18. Gibberellin-regulated gene in the basal region of rice leaf sheath encodes basic helix-loop-helix transcription factor.

    Science.gov (United States)

    Komatsu, Setsuko; Takasaki, Hironori

    2009-07-01

    Genes regulated by gibberellin (GA) during leaf sheath elongation in rice seedlings were identified using the transcriptome approach. mRNA from the basal regions of leaf sheaths treated with GA3 was analyzed by high-coverage gene expression profiling. 33,004 peaks were detected, and 30 transcripts showed significant changes in the presence of GA3. Among these, basic helix-loop-helix transcription factor (AK073385) was significantly upregulated. Quantitative PCR analysis confirmed that expression of AK073385 was controlled by GA3 in a time- and dose-dependent manner. Basic helix-loop-helix transcription factor (AK073385) is therefore involved in the regulation of gene expression by GA3.

  19. Detection of local inflammation induced by repeated exposure to contact allergens by use of IVIS SpectrumCT analyses

    DEFF Research Database (Denmark)

    Nielsen, Morten M.; Schmidt, Jonas D.; Christensen, Jan P.

    2017-01-01

    Background: Contact allergy is characterized by local skin inflammation that, in some cases, can result in systemic immune activation. Objectives: To investigate whether IVIS SpectrumCT analyses can be used to detect the immune response induced by contact allergens. Methods: Mice were repeatedly...... exposed to vehicle or allergens on the ears. The local and systemic responses were analysed at different times with the ProSense 750 FAST probe in IVIS SpectrumCT measurements. In addition, changes in ear thickness, cytokine profile in the skin and immunological phenotype in the draining lymph nodes...... and spleen were determined. Results: Local inflammation was detected by ProSense 750 FAST and correlated with changes in ear thickness, cytokine profile and immunological phenotype following exposure to the strong contact allergen 2,4-dinitrofluorobenzene. Analysis of the systemic response with ProSense 750...

  20. Performance Evaluation of an Intel Haswell- and Ivy Bridge-Based Supercomputer Using Scientific and Engineering Applications

    Science.gov (United States)

    Saini, Subhash; Hood, Robert T.; Chang, Johnny; Baron, John

    2016-01-01

    We present a performance evaluation conducted on a production supercomputer of the Intel Xeon Processor E5- 2680v3, a twelve-core implementation of the fourth-generation Haswell architecture, and compare it with Intel Xeon Processor E5-2680v2, an Ivy Bridge implementation of the third-generation Sandy Bridge architecture. Several new architectural features have been incorporated in Haswell including improvements in all levels of the memory hierarchy as well as improvements to vector instructions and power management. We critically evaluate these new features of Haswell and compare with Ivy Bridge using several low-level benchmarks including subset of HPCC, HPCG and four full-scale scientific and engineering applications. We also present a model to predict the performance of HPCG and Cart3D within 5%, and Overflow within 10% accuracy.

  1. DNA binding specificity of the basic-helix-loop-helix protein MASH-1.

    Science.gov (United States)

    Meierhan, D; el-Ariss, C; Neuenschwander, M; Sieber, M; Stackhouse, J F; Allemann, R K

    1995-09-05

    Despite the high degree of sequence similarity in their basic-helix-loop-helix (BHLH) domains, MASH-1 and MyoD are involved in different biological processes. In order to define possible differences between the DNA binding specificities of these two proteins, we investigated the DNA binding properties of MASH-1 by circular dichroism spectroscopy and by electrophoretic mobility shift assays (EMSA). Upon binding to DNA, the BHLH domain of MASH-1 underwent a conformational change from a mainly unfolded to a largely alpha-helical form, and surprisingly, this change was independent of the specific DNA sequence. The same conformational transition could be induced by the addition of 20% 2,2,2-trifluoroethanol. The apparent dissociation constants (KD) of the complexes of full-length MASH-1 with various oligonucleotides were determined from half-saturation points in EMSAs. MASH-1 bound as a dimer to DNA sequences containing an E-box with high affinity KD = 1.4-4.1 x 10(-14) M2). However, the specificity of DNA binding was low. The dissociation constant for the complex between MASH-1 and the highest affinity E-box sequence (KD = 1.4 x 10(-14) M2) was only a factor of 10 smaller than for completely unrelated DNA sequences (KD = approximately 1 x 10(-13) M2). The DNA binding specificity of MASH-1 was not significantly increased by the formation of an heterodimer with the ubiquitous E12 protein. MASH-1 and MyoD displayed similar binding site preferences, suggesting that their different target gene specificities cannot be explained solely by differential DNA binding. An explanation for these findings is provided on the basis of the known crystal structure of the BHLH domain of MyoD.

  2. IFITM3 requires an amphipathic helix for antiviral activity.

    Science.gov (United States)

    Chesarino, Nicholas M; Compton, Alex A; McMichael, Temet M; Kenney, Adam D; Zhang, Lizhi; Soewarna, Victoria; Davis, Matthew; Schwartz, Olivier; Yount, Jacob S

    2017-10-01

    Interferon-induced transmembrane protein 3 (IFITM3) is a cellular factor that blocks virus fusion with cell membranes. IFITM3 has been suggested to alter membrane curvature and fluidity, though its exact mechanism of action is unclear. Using a bioinformatic approach, we predict IFITM3 secondary structures and identify a highly conserved, short amphipathic helix within a hydrophobic region of IFITM3 previously thought to be a transmembrane domain. Consistent with the known ability of amphipathic helices to alter membrane properties, we show that this helix and its amphipathicity are required for the IFITM3-dependent inhibition of influenza virus, Zika virus, vesicular stomatitis virus, Ebola virus, and human immunodeficiency virus infections. The homologous amphipathic helix within IFITM1 is also required for the inhibition of infection, indicating that IFITM proteins possess a conserved mechanism of antiviral action. We further demonstrate that the amphipathic helix of IFITM3 is required to block influenza virus hemagglutinin-mediated membrane fusion. Overall, our results provide evidence that IFITM proteins utilize an amphipathic helix for inhibiting virus fusion. © 2017 The Authors.

  3. TOWARDS UNDERSTANDING OF HELIX B BASED CONFORMATIONAL DISEASES IN SERPIN

    Directory of Open Access Journals (Sweden)

    Mohamad Aman Jairajpuri

    2012-12-01

    Full Text Available Serine protease inhibitors (serpins are a unique family of protease inhibitors that are prone to polymer formation due to their metastable nature and a complex inhibition mechanism that involves large scale conformational change. Helix B is in the shutter region near the strand 2A and strand 3A of �-sheet A, where reactive centre loop inserts during the serpin inhibition mechanism. Helix B region in serpins is a mutation hotspot for naturally occurring variants that result in pathological conditions due to polymerization. Helix B residues are completely buried in the native state and loop inserted latent state but not in the inhibitory loop inserted cleaved conformation. Native to cleaved transition during inhibition forms a large cavity in the shutter region, which invariably is the largest cavity in most serpins in native state. In a recent paper we had for the first time hypothesized that exposure of helix B at the N-terminal end is important for smooth insertion of the reactive center loop during serpin inhibition mechanism. It is therefore possible that natural variant that induces conformational deformation of helix B probably alter the cavity size which increases the rate of loop-sheet interaction between the monomers resulting in increased polymerization.

  4. An empirical study of the nuclear explosion-induced lightning seen on IVY-MIKE

    Science.gov (United States)

    Colvin, J. D.; Mitchell, C. K.; Greig, J. R.; Murphy, D. P.; Pechacek, R. E.; Raleigh, M.

    1987-05-01

    We report the results of a unique study of the lightninglike phenomena that were seen to accompany the MIKE shot of operation IVY on October 31 1952. MIKE was a thermonuclear surface burst yielding 10.4 MT, which took place on Enewetak Atoll. During the period of approximately 10 ms after detonation, five discrete luminous channels were seen to start from the ground or sea surface at a distance of approximately 1 km from the burst point and to grow up into the clouds. We have reexamined the original photographic records of IVY-MIKE, obtaining effective brightnesses (optical powers per unit length) for the luminous channels at different altitudes as functions of time. The absolute calibration for the MIKE records was deduced by comparison with the photographic records of other events of that era, laboratory measurements of film sensitivity, and use of atmospheric transmission data taken just prior to the MIKE event. Errors in this analysis lead to an uncertainty of a factor of ˜2 in the brightnesses of the luminous channels. In the laboratory we have used laser-guided electric discharges to create long (100 cm), arclike plasma channels to simulate the observed luminous channels and to allow determination of an empirical relation between the brightness of the channel and the electric current flowing in the channel. These laboratory discharges had peak currents up to 100 kA and periods of ˜2 ms. Spectroscopic analysis showed that the luminous channels consisted primarily of normal air plasma with typical ground-level contaminants. Photographic studies showed that these long-duration discharges are unstable to the m = 1 magnetohydrodynamic (MHD) instability and become severely distorted in less than 1 ms. By direct comparison of the luminous channels seen at MIKE and the laboratory discharges, we deduce: (1) the peak current in the prominent (brightest) channel at MIKE was between 200 and 600 kA. Here the most likely value of the peak current was 250±50 kA, but

  5. Effects of nozzle type and spray angle on spray deposition in ivy pot plants.

    Science.gov (United States)

    Foqué, Dieter; Nuyttens, David

    2011-02-01

    Fewer plant protection products are now authorised for use in ornamental growings. Frequent spraying with the same product or a suboptimal technique can lead to resistance in pests and diseases. Better application techniques could improve the sustainable use of the plant protection products still available. Spray boom systems--instead of the still predominantly used spray guns--might improve crop protection management in greenhouses considerably. The effect of nozzle type, spray pressure and spray angle on spray deposition and coverage in ivy pot plants was studied, with a focus on crop penetration and spraying the bottom side of the leaves in this dense crop. The experiments showed a significant and important effect of collector position on deposition and coverage in the plant. Although spray deposition and coverage on the bottom side of the leaves are generally low, they could be improved 3.0-4.9-fold using the appropriate application technique. When using a spray boom in a dense crop, the nozzle choice, spray pressure and spray angle should be well considered. The hollow-cone, the air-inclusion flat-fan and the standard flat-fan nozzle with an inclined spray angle performed best because of the effect of swirling droplets, droplets with a high momentum and droplet direction respectively. Copyright © 2010 Society of Chemical Industry.

  6. IL-33/ST2 signaling excites sensory neurons and mediates itch response in a mouse model of poison ivy contact allergy.

    Science.gov (United States)

    Liu, Boyi; Tai, Yan; Achanta, Satyanarayana; Kaelberer, Melanie M; Caceres, Ana I; Shao, Xiaomei; Fang, Jianqiao; Jordt, Sven-Eric

    2016-11-22

    Poison ivy-induced allergic contact dermatitis (ACD) is the most common environmental allergic condition in the United States. Case numbers of poison ivy ACD are increasing due to growing biomass and geographical expansion of poison ivy and increasing content of the allergen, urushiol, likely attributable to rising atmospheric CO 2 Severe and treatment-resistant itch is the major complaint of affected patients. However, because of limited clinical data and poorly characterized models, the pruritic mechanisms in poison ivy ACD remain unknown. Here, we aim to identify the mechanisms of itch in a mouse model of poison ivy ACD by transcriptomics, neuronal imaging, and behavioral analysis. Using transcriptome microarray analysis, we identified IL-33 as a key cytokine up-regulated in the inflamed skin of urushiol-challenged mice. We further found that the IL-33 receptor, ST2, is expressed in small to medium-sized dorsal root ganglion (DRG) neurons, including neurons that innervate the skin. IL-33 induces Ca 2+ influx into a subset of DRG neurons through neuronal ST2. Neutralizing antibodies against IL-33 or ST2 reduced scratching behavior and skin inflammation in urushiol-challenged mice. Injection of IL-33 into urushiol-challenged skin rapidly exacerbated itch-related scratching via ST2, in a histamine-independent manner. Targeted silencing of neuronal ST2 expression by intrathecal ST2 siRNA delivery significantly attenuated pruritic responses caused by urushiol-induced ACD. These results indicate that IL-33/ST2 signaling is functionally present in primary sensory neurons and contributes to pruritus in poison ivy ACD. Blocking IL-33/ST2 signaling may represent a therapeutic approach to ameliorate itch and skin inflammation related to poison ivy ACD.

  7. Invasive Shrub Mapping in an Urban Environment from Hyperspectral and LiDAR-Derived Attributes.

    Science.gov (United States)

    Chance, Curtis M; Coops, Nicholas C; Plowright, Andrew A; Tooke, Thoreau R; Christen, Andreas; Aven, Neal

    2016-01-01

    Proactive management of invasive species in urban areas is critical to restricting their overall distribution. The objective of this work is to determine whether advanced remote sensing technologies can help to detect invasions effectively and efficiently in complex urban ecosystems such as parks. In Surrey, BC, Canada, Himalayan blackberry ( Rubus armeniacus ) and English ivy ( Hedera helix ) are two invasive shrub species that can negatively affect native ecosystems in cities and managed urban parks. Random forest (RF) models were created to detect these two species using a combination of hyperspectral imagery, and light detection and ranging (LiDAR) data. LiDAR-derived predictor variables included irradiance models, canopy structural characteristics, and orographic variables. RF detection accuracy ranged from 77.8 to 87.8% for Himalayan blackberry and 81.9 to 82.1% for English ivy, with open areas classified more accurately than areas under canopy cover. English ivy was predicted to occur across a greater area than Himalayan blackberry both within parks and across the entire city. Both Himalayan blackberry and English ivy were mostly located in clusters according to a Local Moran's I analysis. The occurrence of both species decreased as the distance from roads increased. This study shows the feasibility of producing highly accurate detection maps of plant invasions in urban environments using a fusion of remotely sensed data, as well as the ability to use these products to guide management decisions.

  8. Living Labs as boundary-spanners between Triple Helix actors

    NARCIS (Netherlands)

    van Geenhuizen, M.S.

    2016-01-01

    Living labs are an increasingly popular methodology to enhance innovation. Living labs aim to span boundaries between different organizations, among others Triple helix actors, by acting as a network organization typically in a real-life environment to foster co-creation by user-groups. This paper

  9. Extreme bendability of DNA double helix due to bending asymmetry

    NARCIS (Netherlands)

    Salari, H.; Eslami-Mossallam, B.; Nederi, S.; Ejtehadi, M.R.

    2015-01-01

    Experimental data of the DNA cyclization (J-factor) at short length scales exceed the theoretical expectation based on the wormlike chain (WLC) model by several orders of magnitude. Here, we propose that asymmetric bending rigidity of the double helix in the groove direction can be responsible for

  10. Nucleic acid helix structure determination from NMR proton chemical shifts

    Energy Technology Data Exchange (ETDEWEB)

    Werf, Ramon M. van der; Tessari, Marco; Wijmenga, Sybren S., E-mail: S.Wijmenga@science.ru.nl [Radboud University Nijmegen, Department of Biophysical Chemistry, Institute of Molecules and Materials (Netherlands)

    2013-06-15

    We present a method for de novo derivation of the three-dimensional helix structure of nucleic acids using non-exchangeable proton chemical shifts as sole source of experimental restraints. The method is called chemical shift de novo structure derivation protocol employing singular value decomposition (CHEOPS) and uses iterative singular value decomposition to optimize the structure in helix parameter space. The correct performance of CHEOPS and its range of application are established via an extensive set of structure derivations using either simulated or experimental chemical shifts as input. The simulated input data are used to assess in a defined manner the effect of errors or limitations in the input data on the derived structures. We find that the RNA helix parameters can be determined with high accuracy. We finally demonstrate via three deposited RNA structures that experimental proton chemical shifts suffice to derive RNA helix structures with high precision and accuracy. CHEOPS provides, subject to further development, new directions for high-resolution NMR structure determination of nucleic acids.

  11. 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 ...

  12. 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

  13. 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.

  14. 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.

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

    International Nuclear Information System (INIS)

    Peng Wei-Feng; Yang Zhong-Hai; Hu Yu-Lu; Li Jian-Qing; Lu Qi-Ru; Li Bin

    2011-01-01

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

  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. Design and synthesis of DNA four-helix bundles

    International Nuclear Information System (INIS)

    Rangnekar, Abhijit; Gothelf, Kurt V; LaBean, Thomas H

    2011-01-01

    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.

  18. Crosslinked Aspartic Acids as Helix-Nucleating Templates.

    Science.gov (United States)

    Zhao, Hui; Liu, Qi-Song; Geng, Hao; Tian, Yuan; Cheng, Min; Jiang, Yan-Hong; Xie, Ming-Sheng; Niu, Xiao-Gang; Jiang, Fan; Zhang, Ya-Ou; Lao, Yuan-Zhi; Wu, Yun-Dong; Xu, Nai-Han; Li, Zi-Gang

    2016-09-19

    Described is a facile helix-nucleating template based on a tethered aspartic acid at the N-terminus [terminal aspartic acid (TD)]. The nucleating effect of the template is subtly influenced by the substituent at the end of the side-chain-end tether as indicated by circular dichroism, nuclear magnetic resonance, and molecular dynamics simulations. Unlike most nucleating strategies, the N-terminal amine is preserved, thus enabling further modification. Peptidomimetic estrogen receptor modulators (PERMs) constructed using this strategy show improved therapeutic properties. The current strategy can be regarded as a good complement to existing helix-stabilizing methods. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Mechanism of death at high temperatures in Helix and Patella

    Energy Technology Data Exchange (ETDEWEB)

    Grainger, J N.R.

    1975-10-01

    In Patella vulgata and Helix aspersa which had been killed by exposure to high temperatures, the rates of oxygen consumption of gill, foot muscle and hepatopancreas are remarkably steady when measured at lower temperatures, although the absolute levels are in some cases different from normal animals. These tissues are thus substantially metabolically intact in heat dead individuals. In Helix there is a fall in blood sodium and a rise in blood potassium during heat death. In Patella there is a marked rise in blood Na/sup +/ and a consequent disturbance of the Na/sup +//K/sup +/ ratio. These ionic disturbances are thought to be a prime cause of heat death. The significance of the results is discussed.

  20. Facilitating Quintuple helix innovation with urban living labs

    OpenAIRE

    Baccarne, Bastiaan; Schuurman, Dimitri; De Marez, Lieven

    2015-01-01

    This paper discusses the Urban Living Lab approach as a way to put the Quintuple Helix model for innovation into practice. In this analysis we focus on the concepts innovation democracy, ‘mode 3’ knowledge production, the innovation ecosystem as a system of societal subsystems and socioecological transition. The empirical analysis is performed by means of a multidimensional case study design, applied on a project-based ad hoc collaborative innovation development process in an ecological doma...

  1. 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.

  2. Helix Nebula Science Cloud pilot phase open session

    CERN Multimedia

    CERN. Geneva

    2018-01-01

    This Helix Nebula Science Cloud (HNSciCloud) public session is open to everyone and will be webcast. The session will provide the audience with an overview of the HNSciCloud pre-commercial procurement project and the innovative cloud platforms that have been developed. A number of practical use-cases from the physics community will be presented as well as the next steps to be undertaken.

  3. Dimerization of the docking/adaptor protein HEF1 via a carboxy-terminal helix-loop-helix domain.

    Science.gov (United States)

    Law, S F; Zhang, Y Z; Fashena, S J; Toby, G; Estojak, J; Golemis, E A

    1999-10-10

    HEF1, p130(Cas), and Efs define a family of multidomain docking proteins which plays a central coordinating role for tyrosine-kinase-based signaling related to cell adhesion. HEF1 function has been specifically implicated in signaling pathways important for cell adhesion and differentiation in lymphoid and epithelial cells. While the SH3 domains and SH2-binding site domains (substrate domains) of HEF1 family proteins are well characterized and binding partners known, to date the highly conserved carboxy-terminal domains of the three proteins have lacked functional definition. In this study, we have determined that the carboxy-terminal domain of HEF1 contains a divergent helix-loop-helix (HLH) motif. This motif mediates HEF1 homodimerization and HEF1 heterodimerization with a recognition specificity similar to that of the transcriptional regulatory HLH proteins Id2, E12, and E47. We had previously demonstrated that the HEF1 carboxy-terminus expressed as a separate domain in yeast reprograms cell division patterns, inducing constitutive pseudohyphal growth. Here we show that pseudohyphal induction by HEF1 requires an intact HLH, further supporting the idea that this motif has an effector activity for HEF1, and implying that HEF1 pseudohyphal activity derives in part from interactions with yeast helix-loop-helix proteins. These combined results provide initial insight into the mode of function of the HEF1 carboxy-terminal domain and suggest that the HEF1 protein may interact with cellular proteins which control differentiation. Copyright 1999 Academic Press.

  4. The basic helix-loop-helix region of the transcriptional repressor hairy and enhancer of split 1 is preorganized to bind DNA

    NARCIS (Netherlands)

    Popovic, Matija; Wienk, Hans; Coglievina, Maristella; Boelens, Rolf; Pongor, Sándor; Pintar, Alessandro

    2014-01-01

    Hairy and enhancer of split 1, one of the main downstream effectors in Notch signaling, is a transcriptional repressor of the basic helix-loop-helix (bHLH) family. Using nuclear magnetic resonance methods, we have determined the structure and dynamics of a recombinant protein, H1H, which includes an

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

    Science.gov (United States)

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

  6. Tööturg võttis majanduslanguse löögi enda peale / Hanno Pevkur, Raul Eamets, Ivi Proos, Sten Anspal ; intervjueerinud Helle Ruusing

    Index Scriptorium Estoniae

    2010-01-01

    Sotsiaaalminister Hanno Pevkur, Tartu Ülikooli makroökonoomika õppetooli juhataja Raul Eamets, Avatud Ühiskonna Instituudi juhataja Ivi Proos ja Eesti Rakendusuuringute Keskuse CENTAR vanemanalüütik Sten Anspal arutlevad Eesti tööturu olukorra ja tulevikuperspektiivide üle

  7. Stretched versus compressed exponential kinetics in α-helix folding

    International Nuclear Information System (INIS)

    Hamm, Peter; Helbing, Jan; Bredenbeck, Jens

    2006-01-01

    In a recent paper (J. Bredenbeck, J. Helbing, J.R. Kumita, G.A. Woolley, P. Hamm, α-helix formation in a photoswitchable peptide tracked from picoseconds to microseconds by time resolved IR spectroscopy, Proc. Natl. Acad. Sci USA 102 (2005) 2379), we have investigated the folding of a photo-switchable α-helix with a kinetics that could be fit by a stretched exponential function exp(-(t/τ) β ). The stretching factor β became smaller as the temperature was lowered, a result which has been interpreted in terms of activated diffusion on a rugged energy surface. In the present paper, we discuss under which conditions diffusion problems occur with stretched exponential kinetics (β 1). We show that diffusion problems do have a strong tendency to yield stretched exponential kinetics, yet, that there are conditions (strong perturbation from equilibrium, performing the experiment in the folding direction) under which compressed exponential kinetics would be expected instead. We discuss the kinetics on free energy surfaces predicted by simple initiation-propagation models (zipper models) of α-helix folding, as well as by folding funnel models. We show that our recent experiment has been performed under condition for which models with strong downhill driving force, such as the zipper model, would predict compressed, rather than stretched exponential kinetics, in disagreement with the experimental observation. We therefore propose that the free energy surface along a reaction coordinate that governs the folding kinetics must be relatively flat and has a shape similar to a 1D golf course. We discuss how this conclusion can be unified with the thermodynamically well established zipper model by introducing an additional kinetic reaction coordinate

  8. Bacterial morphogenesis and the enigmatic MreB helix.

    Science.gov (United States)

    Errington, Jeff

    2015-04-01

    Work over the past decade has highlighted the pivotal role of the actin-like MreB family of proteins in the determination and maintenance of rod cell shape in bacteria. Early images of MreB localization revealed long helical filaments, which were suggestive of a direct role in governing cell wall architecture. However, several more recent, higher-resolution studies have questioned the existence or importance of the helical structures. In this Opinion article, I navigate a path through these conflicting reports, revive the helix model and summarize the key questions that remain to be answered.

  9. Interactions between the mixotrophic dinoflagellate Takayama helix and common heterotrophic protists.

    Science.gov (United States)

    Ok, Jin Hee; Jeong, Hae Jin; Lim, An Suk; Lee, Kyung Ha

    2017-09-01

    The phototrophic dinoflagellate Takayama helix that is known to be harmful to abalone larvae has recently been revealed to be mixotrophic. Although mixotrophy elevates the growth rate of T. helix by 79%-185%, its absolute growth rate is still as low as 0.3d -1 . Thus, if the mortality rate of T. helix due to predation is high, this dinoflagellate may not easily prevail. To investigate potential effective protistan grazers on T. helix, feeding by diverse heterotrophic dinoflagellates such as engulfment-feeding Oxyrrhis marina, Gyrodinium dominans, Gyrodinium moestrupii, Polykrikos kofoidii, and Noctiluca scintillans, peduncle-feeding Aduncodinium glandula, Gyrodiniellum shiwhaense, Luciella masanensis, and Pfiesteria piscicida, pallium-feeding Oblea rotunda and Protoperidinium pellucidum, and the naked ciliates Pelagostrobilidium sp. (ca. 40μm in cell length) and Strombidinopsis sp. (ca. 150μm in cell length) on T. helix was explored. Among the tested heterotrophic protists, O. marina, G. dominans, G. moestrupii, A. glandula, L. masanensis, P. kofoidii, P. piscicida, and Strombidinopsis sp. were able to feed on T. helix. The growth rates of all these predators except Strombidinopsis sp. with T. helix prey were lower than those without the prey. The growth rate of Strombidinopsis sp. on T. helix was almost zero although the growth rate of Strombidinopsis sp. with T. helix prey was higher than those without the prey. Moreover, T. helix fed on O. marina and P. pellucidum and lysed the cells of P. kofoidii and G. shiwhaense. With increasing the concentrations of T. helix, the growth rates of O. marina and P. kofoidii decreased, but those of G. dominans and L. masanensis largely did not change. Therefore, reciprocal predation, lysis, no feeding, and the low ingestion rates of the common protists preying on T. helix may result in a low mortality rate due to predation, thereby compensating for this species' low growth rate. Copyright © 2017 Elsevier B.V. All rights

  10. Thermodynamic Effects of Replacements of Pro Residues in Helix Interiors of Maltose-Binding Protein

    OpenAIRE

    Prajapati, RS; Lingaraju, GM; Bacchawat, Kiran; Surolia, Avadhesha; Varadarajan, Raghavan

    2003-01-01

    Introduction of Pro residues into helix interiors results in protein destabilization. It is currently unclear if the converse substitution (i.e., replacement of Pro residues that naturally occur in helix interiors would be stabilizing). Maltose-binding protein is a large 370-amino acid protein that contains 21 Pro residues. Of these, three nonconserved residues (P48, P133, and P159) occur at helix interiors. Each of the residues was replaced with Ala and Ser. Stabilities were characterized by...

  11. Leptomeningeal high signal intensity (ivy sign) on fluid-attenuated inversion-recovery (FLAIR) MR images in moyamoya disease

    Energy Technology Data Exchange (ETDEWEB)

    Fujiwara, Hirokazu [Department of Diagnostic Radiology, School of Medicine, Keio University, Tokyo 1608582 (Japan)]. E-mail: hirokazu_fujiwara@ybb.ne.jp; Momoshima, Suketaka [Department of Diagnostic Radiology, School of Medicine, Keio University, Tokyo 1608582 (Japan); Kuribayashi, Sachio [Department of Diagnostic Radiology, School of Medicine, Keio University, Tokyo 1608582 (Japan)

    2005-08-01

    Purpose: There are a few reports on leptomeningeal high signal intensity (LMHI: ivy sign) on fluid-attenuated inversion-recovery (FLAIR) images in moyamoya disease, but the feature of this finding has not been completely understood. The purpose of this study was to characterize LMHI on FLAIR images in moyamoya disease and to assess usefulness of this finding in the diagnosis of moyamoya disease in conventional MR imaging. Material and methods: MR imaging of 28 patients with moyamoya disease was retrospectively reviewed. The grade of LMHI on FLAIR images was classified as 'absent,' 'minimal,' 'moderate' and 'marked.' Fifty-four hemispheres of 28 patients (2 patients had unilateral disease) were assessed for the frequency of visualization and distribution of LMHI. The correlations between LMHI on FLAIR images, moyamoya vessels on T1- and T2-weighted images and MR angiography findings were also analyzed. Results: Moderate and marked LMHI was seen in 31 out of 54 hemispheres (57%). LMHI was seen more prominently in the frontal and parietal lobes than in the temporal and occipital lobes. Although there was a tendency for LMHI on FLAIR images to be prominent in groups with moderate and marked moyamoya vessels on T1- and T2-weighted images, there was no significant correlation. More prominent LMHI was observed in the hemispheres in which cortical branches of the middle cerebral arteries were poorly visualized on MR angiography. Conclusion: Leptomeningeal high signal intensity (ivy sign) on FLAIR images is predominantly seen in the frontal and parietal lobes. Because this sign can be seen in patients with unremarkable moyamoya vessels, LMHI is a useful sign in conventional MR imaging for the diagnosis of moyamoya disease.

  12. Pharmacokinetics of hederacoside C, an active ingredient in AG NPP709, in rats.

    Science.gov (United States)

    Kim, Ju Myung; Yoon, Ji Na; Jung, Ji Won; Choi, Hye Duck; Shin, Young June; Han, Chang Kyun; Lee, Hye Suk; Kang, Hee Eun

    2013-11-01

    1. Hederacoside C (HDC) is one of the active ingredients in Hedera helix leaf extract (Ivy Ex.) and AG NPP709, a new botanical drug to treat acute respiratory infection and chronic inflammatory bronchitis. However, information regarding its pharmacokinetic properties remains limited. 2. Here, we report the pharmacokinetics of HDC in rats after intravenous administration of HDC (3, 12.5, and 25 mg/kg) and after oral administration of HDC, Ivy Ex., and AG NPP709 (equivalent to 12.5, 25, and 50 mg/kg HDC). 3. Linear pharmacokinetics of HDC were identified upon its intravenous administration at doses of 3-25 mg/kg. Intravenous administration of HDC results in relatively slow clearance (1.46-2.08 mL/min/kg) and a small volume of distribution at steady state (138-222 mL/kg), while oral administration results in a low absolute oral bioavailability (F) of 0.118-0.250%. The extremely low F of HDC may be due to poor absorption of HDC from the gastrointestinal (GI) tract and/or its decomposition therein. 4. The oral pharmacokinetics of HDC did not differ significantly among pure HDC, Ivy Ex., and AG NPP709.

  13. Nature of the Charged-Group Effect on the Stability of the C-Peptide Helix

    Science.gov (United States)

    Shoemaker, Kevin R.; Kim, Peter S.; Brems, David N.; Marqusee, Susan; York, Eunice J.; Chaiken, Irwin M.; Stewart, John M.; Baldwin, Robert L.

    1985-04-01

    The residues responsible for the pH-dependent stability of the helix formed by the isolated C-peptide (residues 1-13 of ribonuclease A) have been identified by chemical synthesis of analogues and measurement of their helix-forming properties. Each of the residues ionizing between pH 2 and pH 8 has been replaced separately by an uncharged residue. Protonation of Glu-2- is responsible for the sharp decrease in helix stability between pH 5 and pH 2, and deprotonation of His-12+ causes a similar decrease between pH 5 and pH 8. Glu-9- is not needed for helix stability. The results cannot be explained by the Zimm-Bragg model and host-guest data for α -helix formation, which predict that the stability of the C-peptide helix should increase when Glu-2- is protonated or when His-12+ is deprotonated. Moreover, histidine+ is a strong helix-breaker in host-guest studies. In proteins, acidic and basic residues tend to occur at opposite ends of α -helices: acidic residues occur preferentially near the NH2-terminal end and basic residues near the COOH-terminal end. A possible explanation, based on a helix dipole model, has been given [Blagdon, D. E. & Goodman, M. (1975) Biopolymers 14, 241-245]. Our results are consistent with the helix dipole model and they support the suggestion that the distribution of charged residues in protein helices reflects the helix-stabilizing propensity of those residues. Because Glu-9 is not needed for helix stability, a possible Glu-9-\\cdots His-12+ salt bridge does not contribute significantly to helix stability. The role of a possible Glu-2-\\cdots Arg-10+ salt bridge has not yet been evaluated. A charged-group effect on α -helix stability in water has also been observed in a different peptide system [Ihara, S., Ooi, T. & Takahashi, S. (1982) Biopolymers 21, 131-145]: block copolymers containing (Ala)20 and (Glu)20 show partial helix formation at low temperatures, pH 7.5, where the glutamic acid residues are ionized. (Glu)20(Ala)20Phe forms a

  14. Mechanical unfolding reveals stable 3-helix intermediates in talin and α-catenin.

    Directory of Open Access Journals (Sweden)

    Vasyl V Mykuliak

    2018-04-01

    Full Text Available Mechanical stability is a key feature in the regulation of structural scaffolding proteins and their functions. Despite the abundance of α-helical structures among the human proteome and their undisputed importance in health and disease, the fundamental principles of their behavior under mechanical load are poorly understood. Talin and α-catenin are two key molecules in focal adhesions and adherens junctions, respectively. In this study, we used a combination of atomistic steered molecular dynamics (SMD simulations, polyprotein engineering, and single-molecule atomic force microscopy (smAFM to investigate unfolding of these proteins. SMD simulations revealed that talin rod α-helix bundles as well as α-catenin α-helix domains unfold through stable 3-helix intermediates. While the 5-helix bundles were found to be mechanically stable, a second stable conformation corresponding to the 3-helix state was revealed. Mechanically weaker 4-helix bundles easily unfolded into a stable 3-helix conformation. The results of smAFM experiments were in agreement with the findings of the computational simulations. The disulfide clamp mutants, designed to protect the stable state, support the 3-helix intermediate model in both experimental and computational setups. As a result, multiple discrete unfolding intermediate states in the talin and α-catenin unfolding pathway were discovered. Better understanding of the mechanical unfolding mechanism of α-helix proteins is a key step towards comprehensive models describing the mechanoregulation of proteins.

  15. Clear cell hidradenocarcinoma of the ear helix: report of primary ear helix adnexal carcinoma with regional lymph node metastasis.

    Science.gov (United States)

    Bae, Tae Hui; Kang, Shin Hyuk; Kim, Han Koo; Kim, Woo Seob; Kim, Mi Kyung

    2014-07-01

    Clear cell hidradenocarcinoma is a rare tumor of eccrine sweat gland origin that has a predilection for the head and neck. It has an indolent growth pattern and a higher incidence of regional and distant metastases. Metastasizing adnexal carcinomas are rare; thus, currently there is no uniform treatment guideline. We report a case of an 89-year-old female patient with clear cell hidradenocarcinoma manifesting in the right ear helix that metastasized to the right parotid gland who was treated by wide local excision and radiation therapy.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-02-01

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

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

    Science.gov (United States)

    Urano, Ryo; Okamoto, Yuko

    2015-12-01

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

  18. 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.

  19. Classification and evolutionary analysis of the basic helix-loop-helix gene family in the green anole lizard, Anolis carolinensis.

    Science.gov (United States)

    Liu, Ake; Wang, Yong; Zhang, Debao; Wang, Xuhua; Song, Huifang; Dang, Chunwang; Yao, Qin; Chen, Keping

    2013-08-01

    Helix-loop-helix (bHLH) proteins play essential regulatory roles in a variety of biological processes. These highly conserved proteins form a large transcription factor superfamily, and are commonly identified in large numbers within animal, plant, and fungal genomes. The bHLH domain has been well studied in many animal species, but has not yet been characterized in non-avian reptiles. In this study, we identified 102 putative bHLH genes in the genome of the green anole lizard, Anolis carolinensis. Based on phylogenetic analysis, these genes were classified into 43 families, with 43, 24, 16, 3, 10, and 3 members assigned into groups A, B, C, D, E, and F, respectively, and 3 members categorized as "orphans". Within-group evolutionary relationships inferred from the phylogenetic analysis were consistent with highly conserved patterns observed for introns and additional domains. Results from phylogenetic analysis of the H/E(spl) family suggest that genome and tandem gene duplications have contributed to this family's expansion. Our classification and evolutionary analysis has provided insights into the evolutionary diversification of animal bHLH genes, and should aid future studies on bHLH protein regulation of key growth and developmental processes.

  20. Genome-wide identification and analysis of basic helix-loop-helix domains in dog, Canis lupus familiaris.

    Science.gov (United States)

    Wang, Xu-Hua; Wang, Yong; Liu, A-Ke; Liu, Xiao-Ting; Zhou, Yang; Yao, Qin; Chen, Ke-Ping

    2015-04-01

    The basic helix-loop-helix (bHLH) domain is a highly conserved amino acid motif that defines a group of DNA-binding transcription factors. bHLH proteins play essential regulatory roles in a variety of biological processes in animal, plant, and fungus. The domestic dog, Canis lupus familiaris, is a good model organism for genetic, physiological, and behavioral studies. In this study, we identified 115 putative bHLH genes in the dog genome. Based on a phylogenetic analysis, 51, 26, 14, 4, 12, and 4 dog bHLH genes were assigned to six separate groups (A-F); four bHLH genes were categorized as ''orphans''. Within-group evolutionary relationships inferred from the phylogenetic analysis were consistent with positional conservation, other conserved domains flanking the bHLH motif, and highly conserved intron/exon patterns in other vertebrates. Our analytical results confirmed the GenBank annotations of 89 dog bHLH proteins and provided information that could be used to update the annotations of the remaining 26 dog bHLH proteins. These data will provide good references for further studies on the structures and regulatory functions of bHLH proteins in the growth and development of dogs, which may help in understanding the mechanisms that underlie the physical and behavioral differences between dogs and wolves.

  1. 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.

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

    International Nuclear Information System (INIS)

    Beeby, Alan; Richmond, Larry; Herpe, Florian

    2002-01-01

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

  3. Identification of basic/helix-loop-helix transcription factors reveals candidate genes involved in anthocyanin biosynthesis from the strawberry white-flesh mutant

    OpenAIRE

    Zhao, Fengli; Li, Gang; Hu, Panpan; Zhao, Xia; Li, Liangjie; Wei, Wei; Feng, Jiayue; Zhou, Houcheng

    2018-01-01

    As the second largest transcription factor family in plant, the basic helix-loop-helix (bHLH) transcription factor family, characterized by the conserved bHLH domain, plays a central regulatory role in many biological process. However, the bHLH transcription factor family of strawberry has not been systematically identified, especially for the anthocyanin biosynthesis. Here, we identified a total of 113 bHLH transcription factors and described their chromosomal distribution and bioinformatics...

  4. 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.

  5. Mode conversions by a discontinuous junction of two helix loaded waveguides

    International Nuclear Information System (INIS)

    Choe, J.Y.; Ahn, S.; Ganquly, A.K.; Uhm, H.S.

    1983-01-01

    For various reasons, it is desirable to vary the primary propagating mode from one section of the waveguide to another. We choose the base structure to be the sheath helix loaded waveguide. Specifically, we join two physically different helix loaded waveguides axisymmetrically, thereby providing the required discontinuities at the junction (Z = 0). The helix loaded waveguide is more advantageous to the simple waveguide in that the helix mode that exists uniquely in the helix waveguide in addition to the usual fast wave hybrid modes, is without cutoff and thus behaves like a transmission line. In order to obtain the mode conversion rates, we expand the waves in the both sides of the junction with its own eigenmodes including the evanescent modes, and by matching fields at the junction (Z = 0) obtain the matrix equation for the coefficients for the eigenmodes in both sides. By choosing the propagating incident wave (Z = 0) the resulting outgoing waves in the other end (Z > 0) will be computed from the matrix equation. A computer program is devised to solve the suitably truncated matrix equation, and the numerical examples for the mode conversion rates with the parameter variations will be presented. The relevant physical parameters to yield discontinuities at the junction are the radii of the outer conductor and the helix wire and the pitch angle of the helix. Special emphases are on the conversion rates from the helix mode (Z 0) for the application to the tapered gyrotron amplifier

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

    Czech Academy of Sciences Publication Activity Database

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

    2008-01-01

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

  7. Double helix vortex breakdown in a turbulent swirling annular jet flow

    NARCIS (Netherlands)

    Vanierschot, M.; Perçin, M.; van Oudheusden, B.W.

    2018-01-01

    In this paper, we report on the structure and dynamics of double helix vortex breakdown in a turbulent annular swirling jet. Double helix breakdown has been reported previously for the laminar flow regime, but this structure has rarely been observed in turbulent flow. The flow field is

  8. Selective intercalation of six ligands molecules in a self-assembled triple helix

    NARCIS (Netherlands)

    Mateos timoneda, Miguel; Kerckhoffs, J.M.C.A.; Reinhoudt, David; Crego Calama, Mercedes

    2007-01-01

    The addition of a ligand molecule to an artificial self-assembled triple helix leads to the selective intercalation of two hydrogen-bonded trimers in specific binding pockets. Furthermore, the triple helix suffers large conformational rearrangements in order to accommodate the ligand molecules in a

  9. Assembly of Liposomes Controlled by Triple Helix Formation

    DEFF Research Database (Denmark)

    Vogel, Stefan; Jakobsen, Ulla

    2013-01-01

    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-covalent immobilizat...... analysis (NTA) and dynamic light scattering (DLS) show independently from ultraviolet spectroscopy experiments the formation of liposome aggregates.......-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...... 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...

  10. Apex Dips of Experimental Flux Ropes: Helix or Cusp?

    Energy Technology Data Exchange (ETDEWEB)

    Wongwaitayakornkul, Pakorn; Haw, Magnus A.; Bellan, Paul M. [Applied Physics, California Institute of Technology, Pasadena, CA 91125 (United States); Li, Hui [Theoretical Division, Los Alamos National Laboratory, Mail Stop B227, Los Alamos, NM 87545 (United States); Li, Shengtai, E-mail: pwongwai@caltech.edu, E-mail: mhaw@caltech.edu [Mathematical Modeling and Analysis, Los Alamos National Laboratory, Mail Stop B284, Los Alamos, NM 87545 (United States)

    2017-10-20

    We present a new theory for the presence of apex dips in certain experimental flux ropes. Previously such dips were thought to be projections of a helical loop axis generated by the kink instability. However, new evidence from experiments and simulations suggest that the feature is a 2D cusp rather than a 3D helix. The proposed mechanism for cusp formation is a density pileup region generated by nonlinear interaction of neutral gas cones emitted from fast-gas nozzles. The results indicate that density perturbations can result in large distortions of an erupting flux rope, even in the absence of significant pressure or gravitational forces. The density pileup at the apex also suppresses the m = 1 kink mode by acting as a stationary node. Consequently, more accurate density profiles should be considered when attempting to model the stability and shape of solar and astrophysical flux ropes.

  11. 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.

  12. Yeast Ivy1p Is a Putative I-BAR-domain Protein with pH-sensitive Filament Forming Ability in vitro.

    Science.gov (United States)

    Itoh, Yuzuru; Kida, Kazuki; Hanawa-Suetsugu, Kyoko; Suetsugu, Shiro

    2016-01-01

    Bin-Amphiphysin-Rvs161/167 (BAR) domains mold lipid bilayer membranes into tubules, by forming a spiral polymer on the membrane. Most BAR domains are thought to be involved in forming membrane invaginations through their concave membrane binding surfaces, whereas some members have convex membrane binding surfaces, and thereby mold membranes into protrusions. The BAR domains with a convex surface form a subtype called the inverse BAR (I-BAR) domain or IRSp53-MIM-homology domain (IMD). Although the mammalian I-BAR domains have been studied, those from other organisms remain elusive. Here, we found putative I-BAR domains in Fungi and animal-like unicellular organisms. The fungal protein containing the putative I-BAR-domain is known as Ivy1p in yeast, and is reportedly localized in the vacuole. The phylogenetic analysis of the I-BAR domains revealed that the fungal I-BAR-domain containing proteins comprise a distinct group from those containing IRSp53 or MIM. Importantly, Ivy1p formed a polymer with a diameter of approximately 20 nm in vitro, without a lipid membrane. The filaments were formed at neutral pH, but disassembled when pH was reverted to basic. Moreover, Ivy1p and the I-BAR domain expressed in mammalian HeLa cells was localized at a vacuole-like structure as filaments as revealed by super-resolved microscopy. These data indicate the pH-sensitive polymer forming ability and the functional conservation of Ivy1p in eukaryotic cells.

  13. 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

  14. Double helix vortex breakdown in a turbulent swirling annular jet flow

    Science.gov (United States)

    Vanierschot, M.; Percin, M.; van Oudheusden, B. W.

    2018-03-01

    In this paper, we report on the structure and dynamics of double helix vortex breakdown in a turbulent annular swirling jet. Double helix breakdown has been reported previously for the laminar flow regime, but this structure has rarely been observed in turbulent flow. The flow field is investigated experimentally by means of time-resolved tomographic particle image velocimetry. Notwithstanding the axisymmetric nature of the time-averaged flow, analysis of the instantaneous three-dimensional (3D) vortical structures shows the existence of a vortex core along the central axis which breaks up into a double helix downstream. The winding sense of this double helix is opposite to the swirl direction (m =-2 ) and it is wrapped around a central vortex breakdown bubble. This structure is quite different from double helix breakdown found in laminar flows where the helix is formed in the wake of the bubble and not upstream. The double helix precesses around the central axis of the jet with a precessing frequency corresponding to a Strouhal number of 0.27.

  15. 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.

  16. 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.”...

  17. Genotoxicity of Nicotiana tabacum leaves on Helix aspersa.

    Science.gov (United States)

    da Silva, Fernanda R; Erdtmann, Bernardo; Dalpiaz, Tiago; Nunes, Emilene; Ferraz, Alexandre; Martins, Tales L C; Dias, Johny F; da Rosa, Darlan P; Porawskie, Marilene; Bona, Silvia; da Silva, Juliana

    2013-07-01

    Tobacco farmers are routinely exposed to complex mixtures of inorganic and organic chemicals present in tobacco leaves. In this study, we examined the genotoxicity of tobacco leaves in the snail Helix aspersa as a measure of the risk to human health. DNA damage was evaluated using the micronucleus test and the Comet assay and the concentration of cytochrome P450 enzymes was estimated. Two groups of snails were studied: one fed on tobacco leaves and one fed on lettuce (Lactuca sativa L) leaves (control group). All of the snails received leaves (tobacco and lettuce leaves were the only food provided) and water ad libitum. Hemolymph cells were collected after 0, 24, 48 and 72 h. The Comet assay and micronucleus test showed that exposure to tobacco leaves for different periods of time caused significant DNA damage. Inhibition of cytochrome P450 enzymes occurred only in the tobacco group. Chemical analysis indicated the presence of the alkaloid nicotine, coumarins, saponins, flavonoids and various metals. These results show that tobacco leaves are genotoxic in H. aspersa and inhibit cytochrome P450 activity, probably through the action of the complex chemical mixture present in the plant.

  18. Genotoxicity of Nicotiana tabacum leaves on Helix aspersa

    Directory of Open Access Journals (Sweden)

    Fernanda R. da Silva

    2013-01-01

    Full Text Available Tobacco farmers are routinely exposed to complex mixtures of inorganic and organic chemicals present in tobacco leaves. In this study, we examined the genotoxicity of tobacco leaves in the snail Helix aspersa as a measure of the risk to human health. DNA damage was evaluated using the micronucleus test and the Comet assay and the concentration of cytochrome P450 enzymes was estimated. Two groups of snails were studied: one fed on tobacco leaves and one fed on lettuce (Lactuca sativa L leaves (control group. All of the snails received leaves (tobacco and lettuce leaves were the only food provided and water ad libitum. Hemolymph cells were collected after 0, 24, 48 and 72 h. The Comet assay and micronucleus test showed that exposure to tobacco leaves for different periods of time caused significant DNA damage. Inhibition of cytochrome P450 enzymes occurred only in the tobacco group. Chemical analysis indicated the presence of the alkaloid nicotine, coumarins, saponins, flavonoids and various metals. These results show that tobacco leaves are genotoxic in H. aspersa and inhibit cytochrome P450 activity, probably through the action of the complex chemical mixture present in the plant.

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

    Science.gov (United States)

    de Chadarevian, Soraya

    2003-03-01

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

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

    Directory of Open Access Journals (Sweden)

    Qian Yan

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

  1. An α-Helix-Mimicking 12,13-Helix: Designed α/β/γ-Foldamers as Selective Inhibitors of Protein-Protein Interactions.

    Science.gov (United States)

    Grison, Claire M; Miles, Jennifer A; Robin, Sylvie; Wilson, Andrew J; Aitken, David J

    2016-09-05

    A major current challenge in bioorganic chemistry is the identification of effective mimics of protein secondary structures that act as inhibitors of protein-protein interactions (PPIs). In this work, trans-2-aminocyclobutanecarboxylic acid (tACBC) was used as the key β-amino acid component in the design of α/β/γ-peptides to structurally mimic a native α-helix. Suitably functionalized α/β/γ-peptides assume an α-helix-mimicking 12,13-helix conformation in solution, exhibit enhanced proteolytic stability in comparison to the wild-type α-peptide parent sequence from which they are derived, and act as selective inhibitors of the p53/hDM2 interaction. © 2016 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

  2. Genome-wide identification of basic helix-loop-helix and NF-1 motifs underlying GR binding sites in male rat hippocampus

    DEFF Research Database (Denmark)

    Pooley, John R.; Flynn, Ben P.; Grøntved, Lars

    2017-01-01

    linked to structural and organizational roles, an absence of major tethering partners for GRs, and little or no evidence for binding at negative glucocorticoid response elements. A basic helix-loop-helix motif closely resembling a NeuroD1 or Olig2 binding site was found underlying a subset of GR binding......Glucocorticoids regulate hippocampal function in part by modulating gene expression through the glucocorticoid receptor (GR). GR binding is highly cell type specific, directed to accessible chromatin regions established during tissue differentiation. Distinct classes of GR binding sites...

  3. BAROMETRIC PRESSURE and Other Data from ALPHA HELIX from 19971010 to 19980514 (NODC Accession 9800119)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Hydrophysical, hydrochemical, and other data were collected from CTD casts in the Gulf of Alaska from the R/V Alpha Helix from 10 October 1997 to 14 May 1998. Data...

  4. PRESSURE - WATER and Other Data from ALPHA HELIX from 19981002 to 19990513 (NODC Accession 9900149)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Temperature and salinity profiles were collected from CTD casts from the Alpha Helix from 02 October 1998 to 13 May 1999. These 6 CTD data sets are from two...

  5. Fluorophores, environments, and quantification techniques in the analysis of transmembrane helix interaction using FRET.

    Science.gov (United States)

    Khadria, Ambalika S; Senes, Alessandro

    2015-07-01

    Förster resonance energy transfer (FRET) has been widely used as a spectroscopic tool in vitro to study the interactions between transmembrane (TM) helices in detergent and lipid environments. This technique has been instrumental to many studies that have greatly contributed to quantitative understanding of the physical principles that govern helix-helix interactions in the membrane. These studies have also improved our understanding of the biological role of oligomerization in membrane proteins. In this review, we focus on the combinations of fluorophores used, the membrane mimetic environments, and measurement techniques that have been applied to study model systems as well as biological oligomeric complexes in vitro. We highlight the different formalisms used to calculate FRET efficiency and the challenges associated with accurate quantification. The goal is to provide the reader with a comparative summary of the relevant literature for planning and designing FRET experiments aimed at measuring TM helix-helix associations. © 2015 Wiley Periodicals, Inc.

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

    Directory of Open Access Journals (Sweden)

    Chan-Ki Min

    2008-11-01

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

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

    DEFF Research Database (Denmark)

    Olsen, Kasper; Bohr, Jakob

    2012-01-01

    Two important geometrical properties of N-helix structures are influenced by bending. One is maximizing the volume fraction, which is called optimal-packing, and the other is having a vanishing strain-twist coupling, which is called zero-twist. Zero-twist helices rotate neither in one nor...... helix. General N-helices are discussed, as well as zero-twist helices for N > 1. The derived geometrical restrictions are gradually modified by changing the aspect ratio of the torus....

  8. Emergence of the persistent spin helix in semiconductor quantum wells

    International Nuclear Information System (INIS)

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

    2008-01-01

    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) .2 SU(2) is restored, in principle, when the strength of two dominant SO interactions, the Rashba (alpha) and linear Dresselhaus (beta 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 3) and spin-dependent scattering. When these terms are negligible, the distance over which spin information can propagate is predicted to diverge as alpha approaches beta 1. Here we observe experimentally the emergence of the PSH in GaAs quantum wells (QW's) by independently tuning alpha and beta 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 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

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

    International Nuclear Information System (INIS)

    Koralek, Jake

    2011-01-01

    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 (α) and linear Dresselhaus (β 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 (β 3 ) and spin-dependent scattering. When these terms are negligible, the distance over which spin information can propagate is predicted to diverge as α → β 1 . Here we observe experimentally the emergence of the PSH in GaAs quantum wells (QW's) by independently tuning α and β 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 β 3 as the main SU(2) violating term in our samples. The tunable suppression of spin-relaxation demonstrated in this work is well-suited for application to spintronics.

  10. Intersegment interactions and helix-coil transition within the generalized model of polypeptide chains approach

    Science.gov (United States)

    Badasyan, A. V.; Hayrapetyan, G. N.; Tonoyan, Sh. A.; Mamasakhlisov, Y. Sh.; Benight, A. S.; Morozov, V. F.

    2009-09-01

    The generalized model of polypeptide chains is extended to describe the helix-coil transition in a system comprised of two chains interacting side-by-side. The Hamiltonian of the model takes into account four possible types of interactions between repeated units of the two chains, i.e., helix-helix, helix-coil, coil-helix, and coil-coil. Analysis reveals when the energy Ihh+Icc of (h-h, c-c) interactions overwhelms the energy Ihc+Ich of mixed (h-c, c-h) interactions, the correlation length rises substantially, resulting in narrowing of the transition interval. In the opposite case, when Ihh+Icchelix formation and disfavored intersegment interactions from the same theoretical perspective.

  11. 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.

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

    International Nuclear Information System (INIS)

    Yunus, Abdul S.; Jackson, Trent P.; Crisafi, Katherine; Burimski, Irina; Kilgore, Nicole R.; Zoumplis, Dorian; Allaway, Graham P.; Wild, Carl T.; Salzwedel, Karl

    2010-01-01

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

  13. A Developing and Maintenance Toolkit for Operating Support System of Nuclear Power Plant with IVI-COM Technology

    International Nuclear Information System (INIS)

    Zhou, Yang Ping; Dong, Yu Jie; Huang, Xiao Jing; Yoshikawa, Hidekazu

    2011-01-01

    Because of the development and maturation of computer and related technologies, the digitization is inevitably happening in many fields of complex industrial system such as Nuclear Power Plant (NPP). It is believed that the application of these digital operation support systems is able to improve the safety and reliability of complex industrial system and reduce the worker's work load. However, the design, development and maintenance of operation support system such as digital operating procedure under both operational states and accident conditions require not only a profound understand of design, operation and structure of NPP but also expertise on information technology. Because of the reasons mentioned above, a human interface toolkit is proposed for helping the user to develop the operation support system of complex industrial system. With a friendly graphical interface, this integrated tool includes a database, a procedure editor and a procedure executor. In this database, a three layer hierarchy is adopted to express the complexity of operation procedure, which includes mission, process and node. There are 10 kinds of node: entrance, exit, hint, manual input, detector, actuator, data treatment, branch, judgement and plug-in. With the procedure editor, user can easily develop and maintain the procedure and the finished procedure will be stored in the database. Then, the procedure executor can load the procedure from the database for operation support and thus act as a digital operation support system. The operation support system will sense and actuate the actual industrial systems with the interface based on IVI-COM (Interchangeable Virtual Instrumentation-Component Object Model) technology embedded in detector node and actuator node. With the help of various nodes, processes and missions, the developed digital system can access information from plant, make interaction with operator, call additional application, and so on. According to the design mentioned

  14. A Developing and Maintenance Toolkit for Operating Support System of Nuclear Power Plant with IVI-COM Technology

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, Yang Ping; Dong, Yu Jie; Huang, Xiao Jing [Tsinghua University, Beijing (China); Yoshikawa, Hidekazu [Harbin Engineering University, Harbin (China)

    2011-08-15

    Because of the development and maturation of computer and related technologies, the digitization is inevitably happening in many fields of complex industrial system such as Nuclear Power Plant (NPP). It is believed that the application of these digital operation support systems is able to improve the safety and reliability of complex industrial system and reduce the worker's work load. However, the design, development and maintenance of operation support system such as digital operating procedure under both operational states and accident conditions require not only a profound understand of design, operation and structure of NPP but also expertise on information technology. Because of the reasons mentioned above, a human interface toolkit is proposed for helping the user to develop the operation support system of complex industrial system. With a friendly graphical interface, this integrated tool includes a database, a procedure editor and a procedure executor. In this database, a three layer hierarchy is adopted to express the complexity of operation procedure, which includes mission, process and node. There are 10 kinds of node: entrance, exit, hint, manual input, detector, actuator, data treatment, branch, judgement and plug-in. With the procedure editor, user can easily develop and maintain the procedure and the finished procedure will be stored in the database. Then, the procedure executor can load the procedure from the database for operation support and thus act as a digital operation support system. The operation support system will sense and actuate the actual industrial systems with the interface based on IVI-COM (Interchangeable Virtual Instrumentation-Component Object Model) technology embedded in detector node and actuator node. With the help of various nodes, processes and missions, the developed digital system can access information from plant, make interaction with operator, call additional application, and so on. According to the design

  15. 13-Helix folding of a β/γ-peptide manifold designed from a "minimal-constraint" blueprint.

    Science.gov (United States)

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

    2016-06-14

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

  16. Design, synthesis, and evaluation of an alpha-helix mimetic library targeting protein-protein interactions.

    Science.gov (United States)

    Shaginian, Alex; Whitby, Landon R; Hong, Sukwon; Hwang, Inkyu; Farooqi, Bilal; Searcey, Mark; Chen, Jiandong; Vogt, Peter K; Boger, Dale L

    2009-04-22

    The design and solution-phase synthesis of an alpha-helix mimetic library as an integral component of a small-molecule library targeting protein-protein interactions are described. The iterative design, synthesis, and evaluation of the candidate alpha-helix mimetic was initiated from a precedented triaryl template and refined by screening the designs for inhibition of MDM2/p53 binding. Upon identifying a chemically and biologically satisfactory design and consistent with the screening capabilities of academic collaborators, the corresponding complete library was assembled as 400 mixtures of 20 compounds (20 x 20 x 20-mix), where the added subunits are designed to mimic all possible permutations of the naturally occurring i, i + 4, i + 7 amino acid side chains of an alpha-helix. The library (8000 compounds) was prepared using a solution-phase synthetic protocol enlisting acid/base liquid-liquid extractions for purification on a scale that insures its long-term availability for screening campaigns. Screening of the library for inhibition of MDM2/p53 binding not only identified the lead alpha-helix mimetic upon which the library was based, but also suggests that a digestion of the initial screening results that accompany the use of such a comprehensive library can provide insights into the nature of the interaction (e.g., an alpha-helix mediated protein-protein interaction) and define the key residues and their characteristics responsible for recognition.

  17. Optimized molecular dynamics force fields applied to the helix-coil transition of polypeptides.

    Science.gov (United States)

    Best, Robert B; Hummer, Gerhard

    2009-07-02

    Obtaining the correct balance of secondary structure propensities is a central priority in protein force-field development. Given that current force fields differ significantly in their alpha-helical propensities, a correction to match experimental results would be highly desirable. We have determined simple backbone energy corrections for two force fields to reproduce the fraction of helix measured in short peptides at 300 K. As validation, we show that the optimized force fields produce results in excellent agreement with nuclear magnetic resonance experiments for folded proteins and short peptides not used in the optimization. However, despite the agreement at ambient conditions, the dependence of the helix content on temperature is too weak, a problem shared with other force fields. A fit of the Lifson-Roig helix-coil theory shows that both the enthalpy and entropy of helix formation are too small: the helix extension parameter w agrees well with experiment, but its entropic and enthalpic components are both only about half the respective experimental estimates. Our structural and thermodynamic analyses point toward the physical origins of these shortcomings in current force fields, and suggest ways to address them in future force-field development.

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

    Science.gov (United States)

    Rickman, Doug; Shire, J.; Qualters, J.; Mitchell, K.; Pollard, S.; Rao, R.; Kajumba, N.; Quattrochi, D.; Estes, M., Jr.; Meyer, P.; hide

    2009-01-01

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

  19. Lysine as helix C-capping residue in a synthetic peptide.

    Science.gov (United States)

    Esposito, G; Dhanapal, B; Dumy, P; Varma, V; Mutter, M; Bodenhausen, G

    1997-01-01

    The structure of the synthetic peptide CH3CO(Leu-Ser-Leu-Leu-Leu-Ser-Leu)3Lys-NH2 in trifluoroethanol/water 60/40 (volume ratio) was characterized by two-dimensional nmr spectroscopy. The peptide, closely related to the amphiphilic helix models designed by W. F. De-Grado and co-workers to mimic protein ion channels [(1988) Science, Vol. 240, p. 1177-1181], folds into a regular helix spanning residues 1-20. Evidence for a helix C-terminal capping conformation, involving the terminal lysine residue, was observed from Overhauser effects and checked for consistency by restrained molecular dynamics simulations. The side-chain amino group of Lys22 forms a hydrogen bond with the carbonyl of Leu18, and the distorted helical geometry of the terminal dipeptide allows the inclusion of a water bridge between the backbone NH of the Lys22 residue and the carbonyls of Leu19 and Ser20.

  20. Defining the structural requirements for a helix in 23 S ribosomal RNA that confers erythromycin resistance

    DEFF Research Database (Denmark)

    Douthwaite, S; Powers, T; Lee, J Y

    1989-01-01

    The helix spanning nucleotides 1198 to 1247 (helix 1200-1250) in Escherichia coli 23 S ribosomal RNA (rRNA) is functionally important in protein synthesis, and deletions in this region confer erythromycin resistance. In order to define the structural requirements for resistance, we have dissected...... deletion mutants show a sensitive phenotype. Deletions that extend into the base-pairing between GCC1208 and GGU1240 result in non-functional 23 S RNAs, which consequently do not confer resistance. A number of phylogenetically conserved nucleotides have been shown to be non-essential for 23 S RNA function....... However, removal of either these or non-conserved nucleotides from helix 1200-1250 measurably reduces the efficiency of 23 S RNA in forming functional ribosomes. We have used chemical probing and a modified primer extension method to investigate erythromycin binding to wild-type and resistant ribosomes...

  1. Modulating Transmembrane α-Helix Interactions through pH-Sensitive Boundary Residues.

    Science.gov (United States)

    Ng, Derek P; Deber, Charles M

    2016-08-09

    Changes in pH can alter the structure and activity of proteins and may be used by the cell to control molecular function. This coupling can also be used in non-native applications through the design of pH-sensitive biomolecules. For example, the pH (low) insertion peptide (pHLIP) can spontaneously insert into a lipid bilayer when the pH decreases. We have previously shown that the α-helicity and helix-helix interactions of the TM2 α-helix of the proteolipid protein (PLP) are sensitive to the local hydrophobicity at its C-terminus. Given that there is an ionizable residue (Glu-88) at the C-terminus of this transmembrane (TM) segment, we hypothesized that changing the ionization state of this residue through pH may alter the local hydrophobicity of the peptide enough to affect both its secondary structure and helix-helix interactions. To examine this phenomenon, we synthesized peptide analogues of the PLP TM2 α-helix (wild-type sequence (66)AFQYVIYGTASFFFLYGALLLAEGF(90)). Using circular dichroism and Förster resonance energy transfer in the membrane-mimetic detergent sodium dodecyl sulfate, we found that a decrease in pH increases both peptide α-helicity and the extent of self-association. This pH-dependent effect is due specifically to the presence of Glu-88 at the C-terminus. Additional experiments in which Phe-90 was mutated to residues of varying hydrophobicities indicated that the strength of this effect is dependent on the local hydrophobicity near Glu-88. Our results have implications for the design of TM peptide switches and improve our understanding of how membrane protein structure and activity can be regulated through local molecular environmental changes.

  2. Pre-release efficacy assessment of the leaf-mining moth Digitivalva delaireae (Lepidoptera: Glyphipterigidae), a potential biological control agent for Cape-ivy, Delairea odorata (Asteraceae), in western North America

    Science.gov (United States)

    The leaf-mining moth Digitivalva delaireae Gaedike & Kruger (Lepidoptera: Glyphipterigidae) is a potential biological control agent for the invasive vine Cape-ivy, Delairea odorata Lemaire (Asteraceae), in western North America, where two morphological varieties (stipulate and exstipulate) of Cape-i...

  3. Unraveling the Role of the C-terminal Helix Turn Helix of the Coat-binding Domain of Bacteriophage P22 Scaffolding Protein*

    Science.gov (United States)

    Padilla-Meier, G. Pauline; Gilcrease, Eddie B.; Weigele, Peter R.; Cortines, Juliana R.; Siegel, Molly; Leavitt, Justin C.; Teschke, Carolyn M.; Casjens, Sherwood R.

    2012-01-01

    Many viruses encode scaffolding and coat proteins that co-assemble to form procapsids, which are transient precursor structures leading to progeny virions. In bacteriophage P22, the association of scaffolding and coat proteins is mediated mainly by ionic interactions. The coat protein-binding domain of scaffolding protein is a helix turn helix structure near the C terminus with a high number of charged surface residues. Residues Arg-293 and Lys-296 are particularly important for coat protein binding. The two helices contact each other through hydrophobic side chains. In this study, substitution of the residues of the interface between the helices, and the residues in the β-turn, by aspartic acid was used examine the importance of the conformation of the domain in coat binding. These replacements strongly affected the ability of the scaffolding protein to interact with coat protein. The severity of the defect in the association of scaffolding protein to coat protein was dependent on location, with substitutions at residues in the turn and helix 2 causing the most significant effects. Substituting aspartic acid for hydrophobic interface residues dramatically perturbs the stability of the structure, but similar substitutions in the turn had much less effect on the integrity of this domain, as determined by circular dichroism. We propose that the binding of scaffolding protein to coat protein is dependent on angle of the β-turn and the orientation of the charged surface on helix 2. Surprisingly, formation of the highly complex procapsid structure depends on a relatively simple interaction. PMID:22879595

  4. Progesterone modulation of transmembrane helix-helix interactions between the α-subunit of Na/K-ATPase and phospholipid N-methyltransferase in the oocyte plasma membrane

    Directory of Open Access Journals (Sweden)

    Askari Amir

    2010-05-01

    Full Text Available Abstract Background Progesterone binding to the surface of the amphibian oocyte initiates the meiotic divisions. Our previous studies with Rana pipiens oocytes indicate that progesterone binds to a plasma membrane site within the external loop between the M1 and M2 helices of the α-subunit of Na/K-ATPase, triggering a cascade of lipid second messengers and the release of the block at meiotic prophase. We have characterized this site, using a low affinity ouabain binding isoform of the α1-subunit. Results Preparations of isolated plasma membranes from Rana oocytes demonstrate that physiological levels of progesterone (or the non-metabolizable progestin R5020 successively activate phosphatidylethanolamine-N-methyltransferase (PE-NMT and sphingomyelin synthase within seconds. Inhibition of PE-NMT blocks the progesterone induction of meiosis in intact oocytes, whereas its initial product, phosphatidylmonomethylethanolamine (PME, can itself initiate meiosis in the presence of the inhibitor. Published X-ray crystallographic data on Na/K-ATPase, computer-generated 3D projections, heptad repeat analysis and hydrophobic cluster analysis of the transmembrane helices predict that hydrophobic residues L, V, V, I, F and Y of helix M2 of the α1-subunit interact with F, L, G, L, L and F, respectively, of helix M3 of PE-NMT. Conclusion We propose that progesterone binding to the first external loop of the α1-subunit facilitates specific helix-helix interactions between integral membrane proteins to up-regulate PE-NMT, and, that successive interactions between two or more integral plasma membrane proteins induce the signaling cascades which result in completion of the meiotic divisions.

  5. Gate-controlled switching between persistent and inverse persistent spin helix states

    International Nuclear Information System (INIS)

    Yoshizumi, K.; Sasaki, A.; Kohda, M.; Nitta, J.

    2016-01-01

    We demonstrate gate-controlled switching between persistent spin helix (PSH) state and inverse PSH state, which are detected by quantum interference effect on magneto-conductance. These special symmetric spin states showing weak localization effect give rise to a long spin coherence when the strength of Rashba spin-orbit interaction (SOI) is close to that of Dresselhaus SOI. Furthermore, in the middle of two persistent spin helix states, where the Rashba SOI can be negligible, the bulk Dresselhaus SOI parameter in a modulation doped InGaAs/InAlAs quantum well is determined.

  6. Gate-controlled switching between persistent and inverse persistent spin helix states

    Energy Technology Data Exchange (ETDEWEB)

    Yoshizumi, K.; Sasaki, A.; Kohda, M.; Nitta, J. [Department of Materials Science, Tohoku University, Sendai 980-8579 (Japan)

    2016-03-28

    We demonstrate gate-controlled switching between persistent spin helix (PSH) state and inverse PSH state, which are detected by quantum interference effect on magneto-conductance. These special symmetric spin states showing weak localization effect give rise to a long spin coherence when the strength of Rashba spin-orbit interaction (SOI) is close to that of Dresselhaus SOI. Furthermore, in the middle of two persistent spin helix states, where the Rashba SOI can be negligible, the bulk Dresselhaus SOI parameter in a modulation doped InGaAs/InAlAs quantum well is determined.

  7. The Quadruple Helix Model Enhancing Innovative Performance Of Indonesian Creative Industry

    Directory of Open Access Journals (Sweden)

    Sri Wahyu Lelly Hana Setyanti

    2017-11-01

    Full Text Available The creative industry in Indonesia has contributed positively to the national economic growth. Creative industry grows from the creativity and innovation performance of the business actors. The challenge of creative industry is how to completely understand the creative and innovative processes in business management. Therefore it requires an approach that combines the synergy between academicians entrepreneurs government and society in a quadruple helix model. The objective of this research is to develop a creativity model through a quadruple helix model in improving innovation performance of the creative industry.

  8. Klaasist kodu / Ivi Piho

    Index Scriptorium Estoniae

    Piho, Ivi, 1959-

    2003-01-01

    Klaasikunstniku Agnes Tormi ja Mati Tormi perekonna uus kodu. 145 mø eramu projekteeris arhitekt Heiki Teras. Mööbel valiti IKEA kataloogidest, köögimööbel telliti Eesti firmalt Loo Mööbel, klaasist detailid on valmistatud Disainklaasis. Klaasist on kappide uksed, lauaplaadid, dushikabiin, vannitoa uks jm. 13 ill

  9. Poison ivy - oak - sumac

    Science.gov (United States)

    ... done more than 1 hour after touching the plant's sap. Flush the eyes out with water. Take care to clean under the fingernails well to remove ... room. If you are concerned, call your health care provider or poison control. At the ... Take a sample of the plant with you to the doctor or hospital, if ...

  10. PH4 of petunia is an R2R3-MYB protein that activates vacuolar acidification through interactions with Basic-Helix-Loop-Helix transcription factors of the anthocyanin pathway.

    NARCIS (Netherlands)

    Quattrocchio, F.M.; Verweij, C.W.; Spelt, C.E.; Mol, J.N.M.; Koes, R.E.

    2007-01-01

    The Petunia hybrids genes ANTHOCYANIN1 (AN1) and AN2 encode transcription factors with a basic-helix-loop-helix (BHLH) and a MYB domain, respectively, that are required for anthocyanin synthesis and acidification of the vacuole in petal cells. Mutation of PH4 results in a bluer flower color,

  11. The usefulness of the ivy sign on fluid-attenuated intensity recovery images in improved brain hemodynamic changes after superficial temporal artery-middle cerebral artery anastomosis in adult patients with moyamoya disease.

    Science.gov (United States)

    Lee, Jung Keun; Yoon, Byul Hee; Chung, Seung Young; Park, Moon Sun; Kim, Seong Min; Lee, Do Sung

    2013-10-01

    MR perfusion and single photon emission computerized tomography (SPECT) are well known imaging studies to evaluate hemodynamic change between prior to and following superficial temporal artery (STA)-middle cerebral artery (MCA) anastomosis in moyamoya disease. But their side effects and invasiveness make discomfort to patients. We evaluated the ivy sign on MR fluid attenuated inversion recovery (FLAIR) images in adult patients with moyamoya disease and compared it with result of SPECT and MR perfusion images. We enrolled twelve patients (thirteen cases) who were diagnosed with moyamoya disease and underwent STA-MCA anastomosis at our medical institution during a period ranging from September of 2010 to December of 2012. The presence of the ivy sign on MR FLAIR images was classified as Negative (0), Minimal (1), and Positive (2). Regions were classified into four territories: the anterior cerebral artery (ACA), the anterior MCA, the posterior MCA and the posterior cerebral artery. Ivy signs on preoperative and postoperative MR FLAIR were improved (8 and 4 in the ACA regions, 13 and 4 in the anterior MCA regions and 19 and 9 in the posterior MCA regions). Like this result, the cerebrovascular reserve (CVR) on SPECT was significantly increased in the sum of CVR in same regions after STA-MCA anastomosis. After STA-MCA anastomosis, ivy signs were decreased in the cerebral hemisphere. As compared with conventional diagnostic modalities such as SPECT and MR perfusion images, the ivy sign on MR FLAIR is considered as a useful indicator in detecting brain hemodynamic changes between preoperatively and postoperatively in adult moyamoya patients.

  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

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

    Science.gov (United States)

    Miyagawa, Masamichi; Ichinose, Wataru; Yamaguchi, Masahiko

    2014-01-27

    Chiral silica nanoparticles (70 nm) grafted with (P)-helicene recognized the molecular shape of double helix and random coil (P)-ethynylhelicene oligomers in solution. A mixture of the (P)-nanoparticles and double helix precipitated much faster than a mixture of the (P)-nanoparticles and random coil, and the precipitate contained only the double helix. The mixture of the (P)-nanoparticles and (P)-ethynylhelicene pentamer reversibly dispersed in trifluoromethylbenzene upon heating at 70 °C and precipitated upon cooling at 25 °C. When a 10:90 equilibrium mixture of the double helix and random coil in solution was treated with the (P)-nanoparticles, the double helix was precipitated in 53% yield and was accompanied by equilibrium shift. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

    International Nuclear Information System (INIS)

    Donten, Mateusz L.; Hamm, Peter

    2013-01-01

    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

  15. 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…

  16. The triple helix of collagens - an ancient protein structure that enabled animal multicellularity and tissue evolution.

    Science.gov (United States)

    Fidler, Aaron L; Boudko, Sergei P; Rokas, Antonis; Hudson, Billy G

    2018-04-09

    The cellular microenvironment, characterized by an extracellular matrix (ECM), played an essential role in the transition from unicellularity to multicellularity in animals (metazoans), and in the subsequent evolution of diverse animal tissues and organs. A major ECM component are members of the collagen superfamily -comprising 28 types in vertebrates - that exist in diverse supramolecular assemblies ranging from networks to fibrils. Each assembly is characterized by a hallmark feature, a protein structure called a triple helix. A current gap in knowledge is understanding the mechanisms of how the triple helix encodes and utilizes information in building scaffolds on the outside of cells. Type IV collagen, recently revealed as the evolutionarily most ancient member of the collagen superfamily, serves as an archetype for a fresh view of fundamental structural features of a triple helix that underlie the diversity of biological activities of collagens. In this Opinion, we argue that the triple helix is a protein structure of fundamental importance in building the extracellular matrix, which enabled animal multicellularity and tissue evolution. © 2018. Published by The Company of Biologists Ltd.

  17. 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

  18. 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.

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

    DEFF Research Database (Denmark)

    Bohr, Jakob; Olsen, Kasper

    2010-01-01

    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...

  20. Strong contributions from vertical triads to helix-partner preferences in parallel coiled coils.

    Science.gov (United States)

    Steinkruger, Jay D; Bartlett, Gail J; Woolfson, Derek N; Gellman, Samuel H

    2012-09-26

    Pairing preferences in heterodimeric coiled coils are determined by complementarities among side chains that pack against one another at the helix-helix interface. However, relationships between dimer stability and interfacial residue identity are not fully understood. In the context of the "knobs-into-holes" (KIH) packing pattern, one can identify two classes of interactions between side chains from different helices: "lateral", in which a line connecting the adjacent side chains is perpendicular to the helix axes, and "vertical", in which the connecting line is parallel to the helix axes. We have previously analyzed vertical interactions in antiparallel coiled coils and found that one type of triad constellation (a'-a-a') exerts a strong effect on pairing preferences, while the other type of triad (d'-d-d') has relatively little impact on pairing tendencies. Here, we ask whether vertical interactions (d'-a-d') influence pairing in parallel coiled-coil dimers. Our results indicate that vertical interactions can exert a substantial impact on pairing specificity, and that the influence of the d'-a-d' triad depends on the lateral a' contact within the local KIH motif. Structure-informed bioinformatic analyses of protein sequences reveal trends consistent with the thermodynamic data derived from our experimental model system in suggesting that heterotriads involving Leu and Ile are preferred over homotriads involving Leu and Ile.

  1. Triple helix networks matching knowledge demand and supply in seven Dutch horticulture Greenport regions

    NARCIS (Netherlands)

    Geerling-Eiff, Florentien A.; Hoes, Anne-Charlotte; Dijkshoorn-Dekker, Marijke

    2017-01-01

    This paper investigates the triple helix (industry, knowledge workers and governments) cooperation on knowledge co-production and valorisation for innovation, which took place in seven horticultural regions in the Netherlands. It thus provides more empirical insight into the functioning of this form

  2. 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…

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

    NARCIS (Netherlands)

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

    2014-01-01

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

  4. Restrictions on TWT Helix Voltage Ripple for Acceptable Notch Filter Performance

    Energy Technology Data Exchange (ETDEWEB)

    Hyslop, B.

    1984-12-01

    An ac ripple on the helix voltage of the 1-2 GHz TWT's creates FM sidebands that cause amplitude and phase modulation of the microwave TWT output signal. A limit of 16 volts peak-to-peak is required for acceptable superconducting notch filter performance.

  5. Disruption of the LOV-Jalpha helix interaction activates phototropin kinase activity.

    Science.gov (United States)

    Harper, Shannon M; Christie, John M; Gardner, Kevin H

    2004-12-28

    Light plays a crucial role in activating phototropins, a class of plant photoreceptors that are sensitive to blue and UV-A wavelengths. Previous studies indicated that phototropin uses a bound flavin mononucleotide (FMN) within its light-oxygen-voltage (LOV) domain to generate a protein-flavin covalent bond under illumination. In the C-terminal LOV2 domain of Avena sativa phototropin 1, formation of this bond triggers a conformational change that results in unfolding of a helix external to this domain called Jalpha [Harper, S. M., et al. (2003) Science 301, 1541-1545]. Though the structural effects of illumination were characterized, it was unknown how these changes are coupled to kinase activation. To examine this, we made a series of point mutations along the Jalpha helix to disrupt its interaction with the LOV domain in a manner analogous to light activation. Using NMR spectroscopy and limited proteolysis, we demonstrate that several of these mutations displace the Jalpha helix from the LOV domain independently of illumination. When placed into the full-length phototropin protein, these point mutations display constitutive kinase activation, without illumination of the sample. These results indicate that unfolding of the Jalpha helix is the critical event in regulation of kinase signaling for the phototropin proteins.

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

    Science.gov (United States)

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

    2016-01-01

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

  7. Forced evolution of a regulatory RNA helix in the HIV-1 genome

    NARCIS (Netherlands)

    Berkhout, B.; Klaver, B.; Das, A. T.

    1997-01-01

    The 5'and 3'end of the HIV-1 RNA genome forms a repeat (R) element that encodes a double stem-loop structure (the TAR and polyA hairpins). Phylogenetic analysis of the polyA hairpin in different human and simian immunodeficiency viruses suggests that the thermodynamic stability of the helix is

  8. Influence of season, temperature, and photoperiod on growth of the land snail Helix aperta

    NARCIS (Netherlands)

    Benbellil-Tafoughalt, S.; Koene, J.M.

    2015-01-01

    Growth strategies are often plastic and influenced by environmental conditions. Terrestrial gastropods are particularly affected by seasonal and climatic variables, and growth rate and size at maturity are key traits in their life history. Therefore, we investigated juvenile growth of Helix aperta

  9. Increased helix and protein stability through the introduction of a new tertiary hydrogen bond.

    Science.gov (United States)

    Peterson, R W; Nicholson, E M; Thapar, R; Klevit, R E; Scholtz, J M

    1999-03-12

    In an effort to quantify the importance of hydrogen bonding and alpha-helix formation to protein stability, a capping box motif was introduced into the small phosphocarrier protein HPr. Previous studies had confirmed that Ser46, at the N-cap position of the short helix-B in HPr, serves as an N-cap in solution. Thus, only a single-site mutation was required to produce a canonical S-X-X-E capping box: Lys49 at the N3 position was substituted with a glutamic acid residue. Thermal and chemical denaturation studies on the resulting K49E HPr show that the designed variant is approximately 2 kcal mol-1 more stable than the wild-type protein. However, NMR studies indicate that the side-chain of Glu49 does not participate in the expected capping H-bond interaction, but instead forms a new tertiary H-bond that links helix-B to the four-stranded beta-sheet of HPr. Here, we demonstrate that a strategy in which new non-native H-bonds are introduced can generate proteins with increased stability. We discuss why the original capping box design failed, and compare the energetic consequences of the new tertiary side-chain to main-chain H-bond with a local (helix-capping) side-chain to main-chain H-bond on the protein's global stability. Copyright 1999 Academic Press.

  10. Enhancing the innovative capacity of small firms through triple helix interactions : challenges and opportunities

    NARCIS (Netherlands)

    Ranga, Liana Marina; Miedema, Joost; Jorna, Rene

    2008-01-01

    This paper presents the results of a recent exploratory study aiming to enhance the innovative capacity of small firms in the Northern Netherlands, a region lagging behind the rest of the country in terms of economic growth and innovative capacity. The triple helix perspective is adopted to examine

  11. Networks of entrepreneurs driving the Triple Helix: two cases of the Dutch energy system

    NARCIS (Netherlands)

    Werker, C.; Ubacht, J.; Ligtvoet, A.

    2017-01-01

    Entrepreneurs are often envisioned as small private start-up firms operating against all odds. Here, we investigate how in the context of the Triple Helix various entrepreneurs form communities and drive institutional and technological change. To theoretically shape a socialized view of

  12. One Peptide Reveals the Two Faces of α-Helix Unfolding-Folding Dynamics.

    Science.gov (United States)

    Jesus, Catarina S H; Cruz, Pedro F; Arnaut, Luis G; Brito, Rui M M; Serpa, Carlos

    2018-04-12

    The understanding of fast folding dynamics of single α-helices comes mostly from studies on rationally designed peptides displaying sequences with high helical propensity. The folding/unfolding dynamics and energetics of α-helix conformations in naturally occurring peptides remains largely unexplored. Here we report the study of a protein fragment analogue of the C-peptide from bovine pancreatic ribonuclease-A, RN80, a 13-amino acid residue peptide that adopts a highly populated helical conformation in aqueous solution. 1 H NMR and CD structural studies of RN80 showed that α-helix formation displays a pH-dependent bell-shaped curve, with a maximum near pH 5, and a large decrease in helical content in alkaline pH. The main forces stabilizing this short α-helix were identified as a salt bridge formed between Glu-2 and Arg-10 and the cation-π interaction involving Tyr-8 and His-12. Thus, deprotonation of Glu-2 or protonation of His-12 are essential for the RN80 α-helix stability. In the present study, RN80 folding and unfolding were triggered by laser-induced pH jumps and detected by time-resolved photoacoustic calorimetry (PAC). The photoacid proton release, amino acid residue protonation, and unfolding/folding events occur at different time scales and were clearly distinguished using time-resolved PAC. The partial unfolding of the RN80 α-helix, due to protonation of Glu-2 and consequent breaking of the stabilizing salt bridge between Glu-2 and Arg-10, is characterized by a concentration-independent volume expansion in the sub-microsecond time range (0.8 mL mol -1 , 369 ns). This small volume expansion reports the cost of peptide backbone rehydration upon disruption of a solvent-exposed salt bridge, as well as backbone intrinsic expansion. On the other hand, RN80 α-helix folding triggered by His-12 protonation and subsequent formation of a cation-π interaction leads to a microsecond volume contraction (-6.0 mL mol -1 , ∼1.7 μs). The essential role of two

  13. 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

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

    Directory of Open Access Journals (Sweden)

    Bartjan W Pennink

    2013-01-01

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

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

    International Nuclear Information System (INIS)

    Morgan, Rhodri M. L.; Pal, Mohinder; Roe, S. Mark; Pearl, Laurence H.; Prodromou, Chrisostomos

    2015-01-01

    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) 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

  16. 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.

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

    Directory of Open Access Journals (Sweden)

    Jolene Read

    2015-06-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2001-07-01

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

  19. Analysis of eco-innovation with triple helix approach: case-study of biofloc catfish farming in Yogyakarta

    Science.gov (United States)

    Purwadi, D.; Nurlaily, I.

    2018-03-01

    Concerning environmental into focus of innovation process will expand the number of actor involved. Eco-innovation and triple helix are often frameworks applied to analyse how environmental concern are integrated in innovation process and how different stakeholder groups are having inter relation. Case study from biofloc catfish farming in Yogyakarta is presented to demonstrate a possible approach for researching the success of triple helix frameworks. This case is considered on basic of the result of a survey among farmers, academician and government. The paper concludes the creating of full triple helix encounters problem in practice. It also includes suggestion for further research on fisheries development.

  20. Tunable single photonic defect-mode in cholesteric liquid crystals with laser-induced local modifications of helix

    International Nuclear Information System (INIS)

    Yoshida, Hiroyuki; Lee, Chee Heng; Fujii, Akihiko; Ozaki, Masanori

    2006-01-01

    The authors demonstrate a tunable single photonic defect-mode in a single cholesteric liquid crystal material based on a structural defect introduced by local modification of the helix. An unpolymerized region of cholesteric liquid crystal acting as the defect was left between two polymerized regions via a two-photon excitation laser-lithography process. Upon polymerization, the cholesteric liquid crystal helix elongated and became thermally stable, and a single photonic defect mode was exhibited due to the contrast in the helix pitch at the defect. The defect mode showed tunability upon heating, and a 36 nm redshift was seen over a temperature range of 30 deg. C

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

    DEFF Research Database (Denmark)

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

    2012-01-01

    stakeholder groups are interacting in this connection. Taking the triple helix as the theoretical departure point, this paper discusses the opportunities offered by these triple helix frameworks for analyzing eco-innovation dynamics from both theoretical and practical perspectives. It adds to the debate about......Bringing environmental concerns into focus of innovation processes will in several cases also expand the numbers of actors involved. Eco-innovation and triple helix are often frameworks applied to analyse how environmental concerns are integrated in the innovation processes and how different...

  2. Genome-wide analysis of basic/helix-loop-helix gene family in peanut and assessment of its roles in pod development.

    Directory of Open Access Journals (Sweden)

    Chao Gao

    Full Text Available The basic/helix-loop-helix (bHLH proteins constitute a superfamily of transcription factors that are known to play a range of regulatory roles in eukaryotes. Over the past few decades, many bHLH family genes have been well-characterized in model plants, such as Arabidopsis, rice and tomato. However, the bHLH protein family in peanuts has not yet been systematically identified and characterized. Here, 132 and 129 bHLH proteins were identified from two wild ancestral diploid subgenomes of cultivated tetraploid peanuts, Arachis duranensis (AA and Arachis ipaensis (BB, respectively. Phylogenetic analysis indicated that these bHLHs could be classified into 19 subfamilies. Distribution mapping results showed that peanut bHLH genes were randomly and unevenly distributed within the 10 AA chromosomes and 10 BB chromosomes. In addition, 120 bHLH gene pairs between the AA-subgenome and BB-subgenome were found to be orthologous and 101 of these pairs were highly syntenic in AA and BB chromosomes. Furthermore, we confirmed that 184 bHLH genes expressed in different tissues, 22 of which exhibited tissue-specific expression. Meanwhile, we identified 61 bHLH genes that may be potentially involved in peanut-specific subterranean. Our comprehensive genomic analysis provides a foundation for future functional dissection and understanding of the regulatory mechanisms of bHLH transcription factors in peanuts.

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

    International Nuclear Information System (INIS)

    Villano, C.M.; White, L.A.

    2006-01-01

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

  4. An unusual helix-turn-helix protease inhibitory motif in a novel trypsin inhibitor from seeds of Veronica (Veronica hederifolia L.).

    Science.gov (United States)

    Conners, Rebecca; Konarev, Alexander V; Forsyth, Jane; Lovegrove, Alison; Marsh, Justin; Joseph-Horne, Timothy; Shewry, Peter; Brady, R Leo

    2007-09-21

    The storage tissues of many plants contain protease inhibitors that are believed to play an important role in defending the plant from invasion by pests and pathogens. These proteinaceous inhibitor molecules belong to a number of structurally distinct families. We describe here the isolation, purification, initial inhibitory properties, and three-dimensional structure of a novel trypsin inhibitor from seeds of Veronica hederifolia (VhTI). The VhTI peptide inhibits trypsin with a submicromolar apparent K(i) and is expected to be specific for trypsin-like serine proteases. VhTI differs dramatically in structure from all previously described families of trypsin inhibitors, consisting of a helix-turn-helix motif, with the two alpha helices tightly associated by two disulfide bonds. Unusually, the crystallized complex is in the form of a stabilized acyl-enzyme intermediate with the scissile bond of the VhTI inhibitor cleaved and the resulting N-terminal portion of the inhibitor remaining attached to the trypsin catalytic serine 195 by an ester bond. A synthetic, truncated version of the VhTI peptide has also been produced and co-crystallized with trypsin but, surprisingly, is seen to be uncleaved and consequently forms a noncovalent complex with trypsin. The VhTI peptide shows that effective enzyme inhibitors can be constructed from simple helical motifs and provides a new scaffold on which to base the design of novel serine protease inhibitors.

  5. RelB and RelE of Escherichia coli Form a Tight Complex That Represses Transcription via The Ribbon-Helix-Helix Motif in RelB

    DEFF Research Database (Denmark)

    Overgaard, Martin; Borch, Jonas; Gerdes, Kenn

    2009-01-01

    RelB, the Ribbon-Helix-Helix (RHH) repressor encoded by the relBE toxin-antitoxin locus of Escherichia coli, forms a tight complex with RelE and thereby counteracts the mRNA cleavage activity of RelE. In addition, RelB dimers repress the strong relBE promoter and this repression by RelB is enhanced...... by RelE - that is - RelE functions as a transcriptional co-repressor. RelB is a Lon protease substrate and Lon is required both for activation of relBE transcription and for activation of the mRNA cleavage activity of RelE. Here we characterize the molecular interactions important for transcriptional...... motif recognizes four 6 bp repeats within the bipartite binding site. The spacing between each half-site was found to be essential for cooperative interactions between adjacently bound RelB dimers stabilized by the co-repressor RelE. Kinetic and stoichiometric measurements of the interaction between Rel...

  6. 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.

  7. Identification of a basic helix-loop-helix-type transcription regulator gene in Aspergillus oryzae by systematically deleting large chromosomal segments.

    Science.gov (United States)

    Jin, Feng Jie; Takahashi, Tadashi; Machida, Masayuki; Koyama, Yasuji

    2009-09-01

    We previously developed two methods (loop-out and replacement-type recombination) for generating large-scale chromosomal deletions that can be applied to more effective chromosomal engineering in Aspergillus oryzae. In this study, the replacement-type method is used to systematically delete large chromosomal DNA segments to identify essential and nonessential regions in chromosome 7 (2.93 Mb), which is the smallest A. oryzae chromosome and contains a large number of nonsyntenic blocks. We constructed 12 mutants harboring deletions that spanned 16- to 150-kb segments of chromosome 7 and scored phenotypic changes in the resulting mutants. Among the deletion mutants, strains designated Delta5 and Delta7 displayed clear phenotypic changes involving growth and conidiation. In particular, the Delta5 mutant exhibited vigorous growth and conidiation, potentially beneficial characteristics for certain industrial applications. Further deletion analysis allowed identification of the AO090011000215 gene as the gene responsible for the Delta5 mutant phenotype. The AO090011000215 gene was predicted to encode a helix-loop-helix binding protein belonging to the bHLH family of transcription factors. These results illustrate the potential of the approach for identifying novel functional genes.

  8. Novel Plasma Reactor with Rotary Helix Electrode Used in Coupling of CH4 at Atmospheric Pressure

    International Nuclear Information System (INIS)

    Wang Dawang; Ma Tengcai

    2006-01-01

    At the ambient temperature and pressure a glow discharge plasma was used as a new approach for the coupling of methane with the newly-developed rotary multidentate helix electrode. In the presence of hydrogen, the effects of the input peak voltages and gas flow rates on methane conversion, C 2 single pass yield and selectivity were investigated, and then the results were compared with those from the three-disc multidentate electrode. This demonstrated, on an experimental scale, that the rotary multidentate helix electrode was better than the multidentate three-disc electrode as there was little accumulation of coke, and the C 2 yield per pass was 69.85% and C 2 selectivity over 99.14% with 70.46% methane conversion at an input peak voltage of 2300 V and 60 ml/min gas flow rate

  9. 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.

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

    International Nuclear Information System (INIS)

    Shaharun, M A; Yusoff, A R; Reza, M S; Jalal, K A

    2012-01-01

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

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

    Science.gov (United States)

    dos Santos, Rogério Lacerda; Pithon, Matheus Melo

    2013-01-01

    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. 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 nickel stainless steel alloy had force, resilience, and elastic modulus similar to those made of stainless steel alloy.

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

    Energy Technology Data Exchange (ETDEWEB)

    Fu, Chengfang, E-mail: fchffchf@126.com; Zhao, Bo; Yang, Yudong; Ju, Yongfeng [Faculty of Electronic Information Engineering, Huaiyin Institute of Technology, Huai' an 223003 (China); Wei, Yanyu [School of Physical Electronics, University of Electronic and Technology of China, Chengdu 610054 (China)

    2016-08-15

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

  13. Alternative generation of well-aligned uniform lying helix texture in a cholesteric liquid crystal cell

    Directory of Open Access Journals (Sweden)

    Chia-Hua Yu

    2017-10-01

    Full Text Available This work demonstrates a simple approach for obtaining a well-aligned uniform lying helix (ULH texture and a tri-bistable feature at ambient temperature in a typical 90°-twisted cell filled with a short-pitch cholesteric liquid crystal. This ULH texture is obtained at room temperature from initially field-induced helix-free homeotropic state by gradually decreasing the applied voltage. Depending on the way and rate of reducing the voltage, three stable states (i.e., Grandjean planar, focal conic, and ULH are generated and switching between any two of them is realized. Moreover, the electrical operation of the cell in the ULH state enables the tunability in phase retardation via the deformation of the ULH. The observations made in this work may be useful for applications such as tunable phase modulators and energy-efficient photonic devices.

  14. Academic Spin-off as Triple Helix Element: Case-Study of Russian Regions

    Directory of Open Access Journals (Sweden)

    Konstantin Ivanovich Grasmik

    2016-10-01

    Full Text Available The innovation process is becoming more open. According to the concept of the Triple Helix, this requires the creation of institutions capable of mediating the interaction of agents, primarily related to the different elements of the innovation system. The academic spin-off is not only a form of technology transfer, set up at the university but also the institution that provides the interaction of scientists and entrepreneurs. This article gives an analysis of the implementation of the program of creating academic spin-offs in Russia. The main focus of the study is to analyze the affiliation of university spin-off with other companies, including personal links of founders. Research reveals that linkages are substantially personal: University staff member at the same time could be an entrepreneur. This finding allows not only clarifying the concept of the Triple Helix but also increasing the effectiveness of innovation policy, focusing on employees who can combine science and entrepreneurship.

  15. 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 ...

  16. 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...

  17. Helix-length compensation studies reveal the adaptability of the VS ribozyme architecture

    OpenAIRE

    Lacroix-Labonté, Julie; Girard, Nicolas; Lemieux, Sébastien; Legault, Pascale

    2011-01-01

    Compensatory mutations in RNA are generally regarded as those that maintain base pairing, and their identification forms the basis of phylogenetic predictions of RNA secondary structure. However, other types of compensatory mutations can provide higher-order structural and evolutionary information. Here, we present a helix-length compensation study for investigating structure–function relationships in RNA. The approach is demonstrated for stem-loop I and stem-loop V of the Neurospora VS riboz...

  18. A rare polyglycine type II-like helix motif in naturally occurring proteins.

    Science.gov (United States)

    Warkentin, Eberhard; Weidenweber, Sina; Schühle, Karola; Demmer, Ulrike; Heider, Johann; Ermler, Ulrich

    2017-11-01

    Common structural elements in proteins such as α-helices or β-sheets are characterized by uniformly repeating, energetically favorable main chain conformations which additionally exhibit a completely saturated hydrogen-bonding network of the main chain NH and CO groups. Although polyproline or polyglycine type II helices (PP II or PG II ) are frequently found in proteins, they are not considered as equivalent secondary structure elements because they do not form a similar self-contained hydrogen-bonding network of the main chain atoms. In this context our finding of an unusual motif of glycine-rich PG II -like helices in the structure of the acetophenone carboxylase core complex is of relevance. These PG II -like helices form hexagonal bundles which appear to fulfill the criterion of a (largely) saturated hydrogen-bonding network of the main-chain groups and therefore may be regarded in this sense as a new secondary structure element. It consists of a central PG II -like helix surrounded by six nearly parallel PG II -like helices in a hexagonal array, plus an additional PG II -like helix extending the array outwards. Very related structural elements have previously been found in synthetic polyglycine fibers. In both cases, all main chain NH and CO groups of the central PG II -helix are saturated by either intra- or intermolecular hydrogen-bonds, resulting in a self-contained hydrogen-bonding network. Similar, but incomplete PG II -helix patterns were also previously identified in a GTP-binding protein and an antifreeze protein. © 2017 Wiley Periodicals, Inc.

  19. Salt- and pH-Triggered Helix-Coil Transition of Ionic Polypeptides under Physiology Conditions.

    Science.gov (United States)

    Yuan, Jingsong; Zhang, Yi; Sun, Yue; Cai, Zhicheng; Yang, Lijiang; Lu, Hua

    2018-06-11

    Controlling the helix-coil transition of polypeptides under physiological conditions is an attractive way toward smart functional materials. Here, we report the synthesis of a series of tertiary amine-functionalized ethylene glycol (EG x )-linked polypeptide electrolytes with their secondary structures tunable under physiological conditions. The resultant polymers, denoted as P(EG x DMA-Glu) ( x = 1, 2, and 3), show excellent aqueous solubility (>20 mg/mL) regardless of their charge states. Unlike poly-l-lysine that can form a helix only at pH above 10, P(EG x DMA-Glu) undergo a pH-dependent helix-coil switch with their transition points within the physiological range (pH ∼5.3-6.5). Meanwhile, P(EG x DMA-Glu) exhibit an unusual salt-induced helical conformation presumably owing to the unique properties of EG x linkers. Together, the current work highlights the importance of fine-tuning the linker chemistry in achieving conformation-switchable polypeptides and represents a facile approach toward stimuli-responsive biopolymers for advanced biological applications.

  20. Involvement of Na,K-pump in SEPYLRFamide-mediated reduction of cholinosensitivity in Helix neurons.

    Science.gov (United States)

    Pivovarov, Arkady S; Foreman, Richard C; Walker, Robert J

    2007-02-01

    SEPYLRFamide acts as an inhibitory modulator of acetylcholine (ACh) receptors in Helix lucorum neurones. Ouabain, a specific inhibitor of Na,K-pump, (0.1 mM, bath application) decreased the ACh-induced inward current (ACh-current) and increased the leak current. Ouabain decreased the modulatory SEPYLRFamide effect on the ACh-current. There was a correlation between the effects of ouabain on the amplitude of the ACh-current and on the modulatory peptide effect. Ouabain and SEPYLRFamide inhibited the activity of Helix aspersa brain Na,K-ATPase. Activation of Na,K-pump by intracellular injection of 3 M Na acetate or 3 M NaCl reduced the modulatory peptide effect on the ACh-current. An inhibitor of Na/Ca-exchange, benzamil (25 muM, bath application), and an inhibitor of Ca(2+)-pump in the endoplasmic reticulum, thapsigargin (TG, applied intracellularly), both prevented the effect of ouabain on SEPYLRFamide-mediated modulatory effect. Another inhibitor of Ca(2+)-pump in the endoplasmic reticulum, cyclopiazonic acid (applied intracellularly), did not prevent the effect of ouabain on SEPYLRFamide-mediated modulatory effect. These results indicate that Na,K-pump is responsible for the SEPYLRFamide-mediated inhibition of ACh receptors in Helix neurons. Na/Ca-exchange and intracellular Ca(2+) released from internal pools containing TG-sensitive Ca(2+)-pump are involved in the Na,K-pump pathway for the SEPYLRFamide-mediated inhibition of ACh receptors.

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

    Science.gov (United States)

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

    2007-01-01

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

  2. 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.

  3. Thermodynamic effects of replacements of Pro residues in helix interiors of maltose-binding protein.

    Science.gov (United States)

    Prajapati, R S; Lingaraju, G M; Bacchawat, Kiran; Surolia, Avadhesha; Varadarajan, Raghavan

    2003-12-01

    Introduction of Pro residues into helix interiors results in protein destabilization. It is currently unclear if the converse substitution (i.e., replacement of Pro residues that naturally occur in helix interiors would be stabilizing). Maltose-binding protein is a large 370-amino acid protein that contains 21 Pro residues. Of these, three nonconserved residues (P48, P133, and P159) occur at helix interiors. Each of the residues was replaced with Ala and Ser. Stabilities were characterized by differential scanning calorimetry (DSC) as a function of pH and by isothermal urea denaturation studies as a function of temperature. The P48S and P48A mutants were found to be marginally more stable than the wild-type protein. In the pH range of 5-9, there is an average increase in T(m) values of P48A and P48S of 0.4 degrees C and 0.2 degrees C, respectively, relative to the wild-type protein. The other mutants are less stable than the wild type. Analysis of the effects of such Pro substitutions in MBP and in three other proteins studied to date suggests that substitutions are more likely to be stabilizing if the carbonyl group i-3 or i-4 to the mutation site is not hydrogen bonded in the wild-type protein. Copyright 2003 Wiley-Liss, Inc.

  4. Structure of the membrane anchor of pestivirus glycoprotein E(rns, a long tilted amphipathic helix.

    Directory of Open Access Journals (Sweden)

    Daniel Aberle

    2014-02-01

    Full Text Available E(rns 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 E(rns membrane contact, processing and secretion.

  5. 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

  6. Structure of the membrane anchor of pestivirus glycoprotein E(rns), 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

    2014-02-01

    E(rns) 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 E(rns) membrane contact, processing and secretion.

  7. BAROMETRIC PRESSURE and Other Data from ALPHA HELIX From Chukchi Sea and Others from 19930709 to 19930807 (NODC Accession 9400062)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Conductivity, Temperature and Depth (CTD) and other data were collected in Bering Sea, Chukchi Sea. Data was collected from Ship ALPHA HELIX cruise Aleutian...

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

    Energy Technology Data Exchange (ETDEWEB)

    Gao, Kai [Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 (China); Beijing Key Laboratory of Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 (China); University of Chinese Academy of Sciences, Beijing 100049 (China); Zhang, Yong [Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 (China); Beijing Key Laboratory of Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 (China); Lou, Jizhong, E-mail: jlou@ibp.ac.cn [Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 (China); Beijing Key Laboratory of Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 (China)

    2016-05-13

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

  9. De novo design, synthesis and characterisation of MP3, a new catalytic four-helix bundle hemeprotein.

    Science.gov (United States)

    Faiella, Marina; Maglio, Ornella; Nastri, Flavia; Lombardi, Angela; Lista, Liliana; Hagen, Wilfred R; Pavone, Vincenzo

    2012-12-07

    A new artificial metalloenzyme, MP3 (MiniPeroxidase 3), designed by combining the excellent structural properties of four-helix bundle protein scaffolds with the activity of natural peroxidases, was synthesised and characterised. This new hemeprotein model was developed by covalently linking the deuteroporphyrin to two peptide chains of different compositions to obtain an asymmetric helix-loop-helix/heme/helix-loop-helix sandwich arrangement, characterised by 1) a His residue on one chain that acts as an axial ligand to the iron ion; 2) a vacant distal site that is able to accommodate exogenous ligands or substrates; and 3) an Arg residue in the distal site that should assist in hydrogen peroxide activation to give an HRP-like catalytic process. MP3 was synthesised and characterised as its iron complex. CD measurements revealed the high helix-forming propensity of the peptide, confirming the appropriateness of the model procedure; UV/Vis, MCD and EPR experiments gave insights into the coordination geometry and the spin state of the metal. Kinetic experiments showed that Fe(III)-MP3 possesses peroxidase-like activity comparable to R38A-hHRP, highlighting the possibility of mimicking the functional features of natural enzymes. The synergistic application of de novo design methods, synthetic procedures, and spectroscopic characterisation, described herein, demonstrates a method by which to implement and optimise catalytic activity for an enzyme mimetic. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Structural plasticity of the N-terminal capping helix of the TPR domain of kinesin light chain.

    Directory of Open Access Journals (Sweden)

    The Quyen Nguyen

    Full Text Available Kinesin1 plays a major role in neuronal transport by recruiting many different cargos through its kinesin light chain (KLC. Various structurally unrelated cargos interact with the conserved tetratricopeptide repeat (TPR domain of KLC. The N-terminal capping helix of the TPR domain exhibits an atypical sequence and structural features that may contribute to the versatility of the TPR domain to bind different cargos. We determined crystal structures of the TPR domain of both KLC1 and KLC2 encompassing the N-terminal capping helix and show that this helix exhibits two distinct and defined orientations relative to the rest of the TPR domain. Such a difference in orientation gives rise, at the N-terminal part of the groove, to the formation of one hydrophobic pocket, as well as to electrostatic variations at the groove surface. We present a comprehensive structural analysis of available KLC1/2-TPR domain structures that highlights that ligand binding into the groove can be specific of one or the other N-terminal capping helix orientations. Further, structural analysis reveals that the N-terminal capping helix is always involved in crystal packing contacts, especially in a TPR1:TPR1' contact which highlights its propensity to be a protein-protein interaction site. Together, these results underline that the structural plasticity of the N-terminal capping helix might represent a structural determinant for TPR domain structural versatility in cargo binding.

  11. Net (ERP/SAP2) one of the Ras-inducible TCFs, has a novel inhibitory domain with resemblance to the helix-loop-helix motif.

    Science.gov (United States)

    Maira, S M; Wurtz, J M; Wasylyk, B

    1996-11-01

    The three ternary complex factors (TCFs), Net (ERP/ SAP-2), ELK-1 and SAP-1, are highly related ets oncogene family members that participate in the response of the cell to Ras and growth signals. Understanding the different roles of these factors will provide insights into how the signals result in coordinate regulation of the cell. We show that Net inhibits transcription under basal conditions, in which SAP-1a is inactive and ELK-1 stimulates. Repression is mediated by the NID, the Net Inhibitory Domain of about 50 amino acids, which autoregulates the Net protein and also inhibits when it is isolated in a heterologous fusion protein. Net is particularly sensitive to Ras activation. Ras activates Net through the C-domain, which is conserved between the three TCFs, and the NID is an efficient inhibitor of Ras activation. The NID, as well as more C-terminal sequences, inhibit DNA binding. Net is more refractory to DNA binding than the other TCFs, possibly due to the presence of multiple inhibitory elements. The NID may adopt a helix-loop-helix (HLH) structure, as evidenced by homology to other HLH motifs, structure predictions, model building and mutagenesis of critical residues. The sequence resemblance with myogenic factors suggested that Net may form complexes with the same partners. Indeed, we found that Net can interact in vivo with the basic HLH factor, E47. We propose that Net is regulated at the level of its latent DNA-binding activity by protein interactions and/or phosphorylation. Net may form complexes with HLH proteins as well as SRF on specific promotor sequences. The identification of the novel inhibitory domain provides a new inroad into exploring the different roles of the ternary complex factors in growth control and transformation.

  12. The Bacillus subtilis Conjugative Plasmid pLS20 Encodes Two Ribbon-Helix-Helix Type Auxiliary Relaxosome Proteins That Are Essential for Conjugation.

    Science.gov (United States)

    Miguel-Arribas, Andrés; Hao, Jian-An; Luque-Ortega, Juan R; Ramachandran, Gayetri; Val-Calvo, Jorge; Gago-Córdoba, César; González-Álvarez, Daniel; Abia, David; Alfonso, Carlos; Wu, Ling J; Meijer, Wilfried J J

    2017-01-01

    Bacterial conjugation is the process by which a conjugative element (CE) is transferred horizontally from a donor to a recipient cell via a connecting pore. One of the first steps in the conjugation process is the formation of a nucleoprotein complex at the origin of transfer ( oriT ), where one of the components of the nucleoprotein complex, the relaxase, introduces a site- and strand specific nick to initiate the transfer of a single DNA strand into the recipient cell. In most cases, the nucleoprotein complex involves, besides the relaxase, one or more additional proteins, named auxiliary proteins, which are encoded by the CE and/or the host. The conjugative plasmid pLS20 replicates in the Gram-positive Firmicute bacterium Bacillus subtilis . We have recently identified the relaxase gene and the oriT of pLS20, which are separated by a region of almost 1 kb. Here we show that this region contains two auxiliary genes that we name aux1 LS20 and aux2 LS20 , and which we show are essential for conjugation. Both Aux1 LS20 and Aux2 LS20 are predicted to contain a Ribbon-Helix-Helix DNA binding motif near their N-terminus. Analyses of the purified proteins show that Aux1 LS20 and Aux2 LS20 form tetramers and hexamers in solution, respectively, and that they both bind preferentially to oriT LS20 , although with different characteristics and specificities. In silico analyses revealed that genes encoding homologs of Aux1 LS20 and/or Aux2 LS20 are located upstream of almost 400 relaxase genes of the Rel LS20 family (MOB L ) of relaxases. Thus, Aux1 LS20 and Aux2 LS20 of pLS20 constitute the founding member of the first two families of auxiliary proteins described for CEs of Gram-positive origin.

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

    International Nuclear Information System (INIS)

    Noh, Seol Ah; Choi, Young-Im; Cho, Jin-Seong; Lee, Hyoshin

    2015-01-01

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

  14. MicroRNA-212 post-transcriptionally regulates oocyte-specific basic-helix-loop-helix transcription factor, factor in the germline alpha (FIGLA, during bovine early embryogenesis.

    Directory of Open Access Journals (Sweden)

    Swamy K Tripurani

    Full Text Available Factor in the germline alpha (FIGLA is an oocyte-specific basic helix-loop-helix transcription factor essential for primordial follicle formation and expression of many genes required for folliculogenesis, fertilization and early embryonic survival. Here we report the characterization of bovine FIGLA gene and its regulation during early embryogenesis. Bovine FIGLA mRNA expression is restricted to gonads and is detected in fetal ovaries harvested as early as 90 days of gestation. FIGLA mRNA and protein are abundant in germinal vesicle and metaphase II stage oocytes, as well as in embryos from pronuclear to eight-cell stage but barely detectable at morula and blastocyst stages, suggesting that FIGLA might be a maternal effect gene. Recent studies in zebrafish and mice have highlighted the importance of non-coding small RNAs (microRNAs as key regulatory molecules targeting maternal mRNAs for degradation during embryonic development. We hypothesized that FIGLA, as a maternal transcript, is regulated by microRNAs during early embryogenesis. Computational predictions identified a potential microRNA recognition element (MRE for miR-212 in the 3' UTR of the bovine FIGLA mRNA. Bovine miR-212 is expressed in oocytes and tends to increase in four-cell and eight-cell stage embryos followed by a decline at morula and blastocyst stages. Transient transfection and reporter assays revealed that miR-212 represses the expression of FIGLA in a MRE dependent manner. In addition, ectopic expression of miR-212 mimic in bovine early embryos dramatically reduced the expression of FIGLA protein. Collectively, our results demonstrate that FIGLA is temporally regulated during bovine early embryogenesis and miR-212 is an important negative regulator of FIGLA during the maternal to zygotic transition in bovine embryos.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-06-19

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

  16. The Bacillus subtilis Conjugative Plasmid pLS20 Encodes Two Ribbon-Helix-Helix Type Auxiliary Relaxosome Proteins That Are Essential for Conjugation

    Directory of Open Access Journals (Sweden)

    Andrés Miguel-Arribas

    2017-11-01

    Full Text Available Bacterial conjugation is the process by which a conjugative element (CE is transferred horizontally from a donor to a recipient cell via a connecting pore. One of the first steps in the conjugation process is the formation of a nucleoprotein complex at the origin of transfer (oriT, where one of the components of the nucleoprotein complex, the relaxase, introduces a site- and strand specific nick to initiate the transfer of a single DNA strand into the recipient cell. In most cases, the nucleoprotein complex involves, besides the relaxase, one or more additional proteins, named auxiliary proteins, which are encoded by the CE and/or the host. The conjugative plasmid pLS20 replicates in the Gram-positive Firmicute bacterium Bacillus subtilis. We have recently identified the relaxase gene and the oriT of pLS20, which are separated by a region of almost 1 kb. Here we show that this region contains two auxiliary genes that we name aux1LS20 and aux2LS20, and which we show are essential for conjugation. Both Aux1LS20 and Aux2LS20 are predicted to contain a Ribbon-Helix-Helix DNA binding motif near their N-terminus. Analyses of the purified proteins show that Aux1LS20 and Aux2LS20 form tetramers and hexamers in solution, respectively, and that they both bind preferentially to oriTLS20, although with different characteristics and specificities. In silico analyses revealed that genes encoding homologs of Aux1LS20 and/or Aux2LS20 are located upstream of almost 400 relaxase genes of the RelLS20 family (MOBL of relaxases. Thus, Aux1LS20 and Aux2LS20 of pLS20 constitute the founding member of the first two families of auxiliary proteins described for CEs of Gram-positive origin.

  17. Genome-wide identification, classification, and functional analysis of the basic helix-loop-helix transcription factors in the cattle, Bos Taurus.

    Science.gov (United States)

    Li, Fengmei; Liu, Wuyi

    2017-06-01

    The basic helix-loop-helix (bHLH) transcription factors (TFs) form a huge superfamily and play crucial roles in many essential developmental, genetic, and physiological-biochemical processes of eukaryotes. In total, 109 putative bHLH TFs were identified and categorized successfully in the genomic databases of cattle, Bos Taurus, after removing redundant sequences and merging genetic isoforms. Through phylogenetic analyses, 105 proteins among these bHLH TFs were classified into 44 families with 46, 25, 14, 3, 13, and 4 members in the high-order groups A, B, C, D, E, and F, respectively. The remaining 4 bHLH proteins were sorted out as 'orphans.' Next, these 109 putative bHLH proteins identified were further characterized as significantly enriched in 524 significant Gene Ontology (GO) annotations (corrected P value ≤ 0.05) and 21 significantly enriched pathways (corrected P value ≤ 0.05) that had been mapped by the web server KOBAS 2.0. Furthermore, 95 bHLH proteins were further screened and analyzed together with two uncharacterized proteins in the STRING online database to reconstruct the protein-protein interaction network of cattle bHLH TFs. Ultimately, 89 bHLH proteins were fully mapped in a network with 67 biological process, 13 molecular functions, 5 KEGG pathways, 12 PFAM protein domains, and 25 INTERPRO classified protein domains and features. These results provide much useful information and a good reference for further functional investigations and updated researches on cattle bHLH TFs.

  18. Constitutive Overexpression of the Basic Helix-Loop-Helix Nex1/MATH-2 Transcription Factor Promotes Neuronal Differentiation of PC12 Cells and Neurite Regeneration

    Science.gov (United States)

    Uittenbogaard, Martine; Chiaramello, Anne

    2009-01-01

    Elucidation of the intricate transcriptional pathways leading to neural differentiation and the establishment of neuronal identity is critical to the understanding and design of therapeutic approaches. Among the important players, the basic helix-loop-helix (bHLH) transcription factors have been found to be pivotal regulators of neurogenesis. In this study, we investigate the role of the bHLH differentiation factor Nex1/MATH-2 in conjunction with the nerve growth factor (NGF) signaling pathway using the rat phenochromocytoma PC12 cell line. We report that the expression of Nex1 protein is induced after 5 hr of NGF treatment and reaches maximal levels at 24 hr, when very few PC12 cells have begun extending neurites and ceased cell division. Furthermore, our study demonstrates that Nex1 has the ability to trigger neuronal differentiation of PC12 cells in the absence of neurotrophic factor. We show that Nex1 plays an important role in neurite outgrowth and has the capacity to regenerate neurite outgrowth in the absence of NGF. These results are corroborated by the fact that Nex1 targets a repertoire of distinct types of genes associated with neuronal differentiation, such as GAP-43, βIII-tubulin, and NeuroD. In addition, our findings show that Nex1 up-regulates the expression of the mitotic inhibitor p21WAF1, thus linking neuronal differentiation to cell cycle withdrawal. Finally, our studies show that overexpression of a Nex1 mutant has the ability to block the execution of NGF-induced differentiation program, suggesting that Nex1 may be an important effector of the NGF signaling pathway. PMID:11782967

  19. Conservation of Three-Dimensional Helix-Loop-Helix Structure through the Vertebrate Lineage Reopens the Cold Case of Gonadotropin-Releasing Hormone-Associated Peptide.

    Science.gov (United States)

    Pérez Sirkin, Daniela I; Lafont, Anne-Gaëlle; Kamech, Nédia; Somoza, Gustavo M; Vissio, Paula G; Dufour, Sylvie

    2017-01-01

    GnRH-associated peptide (GAP) is the C-terminal portion of the gonadotropin-releasing hormone (GnRH) preprohormone. Although it was reported in mammals that GAP may act as a prolactin-inhibiting factor and can be co-secreted with GnRH into the hypophyseal portal blood, GAP has been practically out of the research circuit for about 20 years. Comparative studies highlighted the low conservation of GAP primary amino acid sequences among vertebrates, contributing to consider that this peptide only participates in the folding or carrying process of GnRH. Considering that the three-dimensional (3D) structure of a protein may define its function, the aim of this study was to evaluate if GAP sequences and 3D structures are conserved in the vertebrate lineage. GAP sequences from various vertebrates were retrieved from databases. Analysis of primary amino acid sequence identity and similarity, molecular phylogeny, and prediction of 3D structures were performed. Amino acid sequence comparison and phylogeny analyses confirmed the large variation of GAP sequences throughout vertebrate radiation. In contrast, prediction of the 3D structure revealed a striking conservation of the 3D structure of GAP1 (GAP associated with the hypophysiotropic type 1 GnRH), despite low amino acid sequence conservation. This GAP1 peptide presented a typical helix-loop-helix (HLH) structure in all the vertebrate species analyzed. This HLH structure could also be predicted for GAP2 in some but not all vertebrate species and in none of the GAP3 analyzed. These results allowed us to infer that selective pressures have maintained GAP1 HLH structure throughout the vertebrate lineage. The conservation of the HLH motif, known to confer biological activity to various proteins, suggests that GAP1 peptides may exert some hypophysiotropic biological functions across vertebrate radiation.

  20. Conservation of Three-Dimensional Helix-Loop-Helix Structure through the Vertebrate Lineage Reopens the Cold Case of Gonadotropin-Releasing Hormone-Associated Peptide

    Directory of Open Access Journals (Sweden)

    Daniela I. Pérez Sirkin

    2017-08-01

    Full Text Available GnRH-associated peptide (GAP is the C-terminal portion of the gonadotropin-releasing hormone (GnRH preprohormone. Although it was reported in mammals that GAP may act as a prolactin-inhibiting factor and can be co-secreted with GnRH into the hypophyseal portal blood, GAP has been practically out of the research circuit for about 20 years. Comparative studies highlighted the low conservation of GAP primary amino acid sequences among vertebrates, contributing to consider that this peptide only participates in the folding or carrying process of GnRH. Considering that the three-dimensional (3D structure of a protein may define its function, the aim of this study was to evaluate if GAP sequences and 3D structures are conserved in the vertebrate lineage. GAP sequences from various vertebrates were retrieved from databases. Analysis of primary amino acid sequence identity and similarity, molecular phylogeny, and prediction of 3D structures were performed. Amino acid sequence comparison and phylogeny analyses confirmed the large variation of GAP sequences throughout vertebrate radiation. In contrast, prediction of the 3D structure revealed a striking conservation of the 3D structure of GAP1 (GAP associated with the hypophysiotropic type 1 GnRH, despite low amino acid sequence conservation. This GAP1 peptide presented a typical helix-loop-helix (HLH structure in all the vertebrate species analyzed. This HLH structure could also be predicted for GAP2 in some but not all vertebrate species and in none of the GAP3 analyzed. These results allowed us to infer that selective pressures have maintained GAP1 HLH structure throughout the vertebrate lineage. The conservation of the HLH motif, known to confer biological activity to various proteins, suggests that GAP1 peptides may exert some hypophysiotropic biological functions across vertebrate radiation.

  1. SclR, a basic helix-loop-helix transcription factor, regulates hyphal morphology and promotes sclerotial formation in Aspergillus oryzae.

    Science.gov (United States)

    Jin, Feng Jie; Takahashi, Tadashi; Matsushima, Ken-ichiro; Hara, Seiichi; Shinohara, Yasutomo; Maruyama, Jun-ichi; Kitamoto, Katsuhiko; Koyama, Yasuji

    2011-07-01

    Most known basic-region helix-loop-helix (bHLH) proteins belong to a superfamily of transcription factors often involved in the control of growth and differentiation. Therefore, inappropriate expression of genes encoding bHLH proteins is frequently associated with developmental dysfunction. In our previously reported study, a novel bHLH protein-encoding gene (AO090011000215) of Aspergillus oryzae was identified. The gene-disrupted strain was found to produce dense conidia, but sparse sclerotia, relative to the parent strain. Here, to further analyze its function, we generated an overexpressing strain using the A. oryzae amyB gene promoter. Genetic overexpression led to a large number of initial hyphal aggregations and then the formation of mature sclerotia; it was therefore designated sclR (sclerotium regulator). At the same time, the sclR-overexpressing strain also displayed both delayed and decreased conidiation. Scanning electron microscopy indicated that the aerial hyphae of the sclR-overexpressing strain were extremely branched and intertwined with each other. In the generation of the SclR-enhanced green fluorescent protein (EGFP) expression strain, the SclR-EGFP protein fusion was conditionally detected in the nuclei. In addition, the loss of sclR function led to rapid protein degradation and cell lysis in dextrin-polypeptone-yeast extract liquid medium. Taken together, these observations indicate that SclR plays an important role in hyphal morphology, asexual conidiospore formation, and the promotion of sclerotial production, even retaining normal cell function, at least in submerged liquid culture.

  2. Fractional sunburn threshold UVR doses generate equivalent vitamin D and DNA damage in skin types I-VI, but with epidermal DNA damage gradient correlated to skin darkness.

    Science.gov (United States)

    Shih, Barbara B; Farrar, Mark D; Cooke, Marcus S; Osman, Joanne; Langton, Abigail K; Kift, Richard; Webb, Ann R; Berry, Jacqueline L; Watson, Rachel E B; Vail, Andy; de Gruijl, Frank R; Rhodes, Lesley E

    2018-05-03

    Public health guidance recommends limiting sun-exposure to sub-sunburn levels, but it's unknown whether these can gain vitamin D (for musculoskeletal health) whilst avoiding epidermal DNA damage (initiates skin cancer). Well-characterised healthy humans of all skin types (I-VI; lightest to darkest skin) were exposed to a low dose-series of solar simulated UVR of 20-80% their individual sunburn threshold dose (minimal erythemal dose, MED). Significant UVR dose-responses were seen for serum 25(OH)D and whole epidermal CPD, with as little as 0.2 MED concurrently producing 25(OH)D and CPD. Notably, fractional MEDs generated equivalent levels of whole epidermal CPD and 25(OH)D across all skin types. Crucially, we demonstrated an epidermal gradient of CPD formation strongly correlated with skin darkness (r=0.74; Pskin types, ranging from darkest skin, where high CPD levels occurred superficially with none in the germinative basal layer, through to lightest skin where CPD were induced evenly across the epidermal depth. Darker skin people can be encouraged to utilise sub-sunburn UVR-exposure to enhance their vitamin D. In lighter skin people, basal cell damage occurs concurrent with vitamin D synthesis at exquisitely low UVR levels, providing an explanation for their high skin cancer incidence; greater caution is required. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

  3. Interactions between an alpha-helix and a beta-sheet. Energetics of alpha/beta packing in proteins.

    Science.gov (United States)

    Chou, K C; Némethy, G; Rumsey, S; Tuttle, R W; Scheraga, H A

    1985-12-05

    Conformational energy computations have been carried out to determine the favorable ways of packing a right-handed alpha-helix on a right-twisted antiparallel or parallel beta-sheet. Co-ordinate transformations have been developed to relate the position and orientation of the alpha-helix to the beta-sheet. The packing was investigated for a CH3CO-(L-Ala)16-NHCH3 alpha-helix interacting with five-stranded beta-sheets composed of CH3CO-(L-Val)6-NHCH3 chains. All internal and external variables for both the alpha-helix and the beta-sheet were allowed to change during energy minimization. Four distinct classes of low-energy packing arrangements were found for the alpha-helix interacting with both the parallel and the anti-parallel beta-sheet. The classes differ in the orientation of the axis of the alpha-helix relative to the direction of the strands of the right-twisted beta-sheet. In the class with the most favorable arrangement, the alpha-helix is oriented along the strands of the beta-sheet, as a result of attractive non-bonded side-chain-side-chain interactions along the entire length of the alpha-helix. A class with nearly perpendicular orientation of the helix axis to the strands is also of low energy, because it allows similarly extensive attractive interactions. In the other two classes, the helix is oriented diagonally relative to the strands of the beta-sheet. In one of them, it interacts with the convex surface near the middle of the saddle-shaped twisted beta-sheet. In the other, it is oriented along the concave diagonal of the beta-sheet and, therefore, it interacts only with the corner regions of the sheet, so that this packing is energetically less favorable. The packing arrangements involving an antiparallel and a parallel beta-sheet are generally similar, although the antiparallel beta-sheet has been found to be more flexible. The major features of 163 observed alpha/beta packing arrangements in 37 proteins are accounted for in terms of the computed

  4. Triple Helix

    National Research Council Canada - National Science Library

    2008-01-01

    .... In 2008, the FIRST Robotics Competition challenged over 37,000 high-school-aged young people on more than 1,500 teams worldwide to work with 18,000 mentors and 2,000 sponsoring companies to design...

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

    International Nuclear Information System (INIS)

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

    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 and D investments in delivering and exploiting cloud computing resources. While a number of technical evaluations of interesting commercial offerings from global IT enterprises have been performed by various physics labs, further technical, security, sociological, and legal issues need to be address before their large-scale adoption by the research community can be envisaged. Helix Nebula – the Science Cloud is an initiative that explores these questions by joining the forces of three European research institutes (CERN, ESA and EMBL) with leading European commercial IT enterprises. The goals of Helix Nebula are to establish a cloud platform federating multiple commercial cloud providers, along with new business models, which can sustain the cloud marketplace for years to come. This contribution will summarize the participation of CERN in Helix Nebula. We will explain CERN's flagship use-case and the model used to integrate several cloud providers with an LHC experiment's workload management system. During the first proof of concept, this project contributed over 40.000 CPU-days of Monte Carlo production throughput to the ATLAS experiment with marginal manpower required. CERN's experience, together with that of ESA and EMBL, is providing a great insight into the cloud computing industry and highlighted several challenges that are being tackled in order to ease the export of the scientific workloads to the cloud environments.

  6. 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.

  7. The human early-life exposome (HELIX): project rationale and design.

    Science.gov (United States)

    Vrijheid, Martine; 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; Gražulevičienė, 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

    2014-06-01

    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. 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. 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. 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.

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

    International Nuclear Information System (INIS)

    Mamasakhlisov, E.S.; Badasyan, A.V.; Tsarukyan, A.V.; Grigoryan, A.V.; Morozov, V.F.

    2005-07-01

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

  9. Mathematical modeling and design parameters of crushing machines with variable-pitch helix of the screw

    Directory of Open Access Journals (Sweden)

    Pelenko V. V.

    2017-11-01

    Full Text Available From the point of view of the effectiveness of the top cutting unit, the helix angle in the end portion of the screw is the most important and characteristic parameter, as it determines the pressure of the meat material in the zone of interaction of a knife and grate. The importance of solving the problem of mathematical modeling of geometry is due to the need to address the problem of minimizing the reverse flow of the food material when injecting into the cutting zone, as the specified effect of "locking" significantly reduces the performance of the transfer process, increases energy consumption of the equipment and entails the deterioration of the quality of the raw materials output. The problem of determining the length of the helix variable pitch for screw chopper food materials has been formulated and solved by methods of differential geometry. The task of correct description of the law of changing the angle of helix inclination along its length has been defined in this case as a key to provide the required dependence of this angle tangent on the angle of the radius-vector of the circle. It has been taken into account that the reduction in the pitch of the screw in the direction of the product delivery should occur at a decreasing rate. The parametric equation of the helix has been written in the form of three functional dependencies of the corresponding cylindrical coordinates. Based on the wide range analysis and significant number of models of tops from different manufacturers the boundaries of possible changes in the angles of inclination of the helical line of the first and last turns of the screw have been identified. The auger screw length is determined mathematically in the form of an analytical relationship and both as a function of the variable angle of its rise, and as a function of the rotation angle of the radius-vector of the circle generatrix, which makes it possible to expand the design possibilities of this node. Along

  10. Circularly Polarized Planar Helix Phased Antenna Array for 5G Mobile Terminals

    DEFF Research Database (Denmark)

    Syrytsin, Igor A.; Zhang, Shuai; Pedersen, Gert F.

    2017-01-01

    In this paper, a planar helix mobile phased antenna array is proposed for 5th generation communication systems with operating frequency of 28GHz. The proposed array displays circular polarization in the endfire direction. Over 65 degrees of axial ratio beamwidth and 7GHz of axial ratio bandwidth...... has been achieved in the proposed design. The coverage performance of the proposed phased antenna array has also been studied by using the coverage efficiency metric. Coverage efficiency of 50 % at 5 dBi gain is achieved by the proposed phased mobile antenna array....

  11. 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.

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

    International Nuclear Information System (INIS)

    Gaso P, M.I.; Segovia, N.; Zarazua, G.; Montes, F.; Morton, O.; Armienta, M.A.; Hernandez, E.

    2001-01-01

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

  13. Modified Quad Helix for Correction of Severely Rotated Incisors in Cleft Cases

    Directory of Open Access Journals (Sweden)

    Aneesha Ashok Shetty

    2014-01-01

    Full Text Available Clefts of the lip, alveolus and/or palate are often associated with several dental anomalies, the most common of which are severely rotated maxillary incisors. Patients with such congenital deformities seek orthodontic treatment as early as possible, for an esthetic as well as psychosocial benefit. Here, a new clinical technique is demonstrated for correction of a severely rotated maxillary central incisor which can be carried out in the mixed dentition phase itself, by modifying a commonly used palatal expansion appliance: the quad helix.

  14. 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.

  15. Cable-type flexible lithium ion battery based on hollow multi-helix electrodes

    Energy Technology Data Exchange (ETDEWEB)

    Kwon, Yo Han; Woo, Sang-Wook; Jung, Hye-Ran; Yu, Hyung Kyun; Kim, Kitae; Oh, Byung Hun; Ahn, Soonho; Kim, Je Young [Battery R and D, LG Chem, Ltd., 104-1 Moonji-dong, Yuseong-gu, Daejeon (Korea, Republic of); Lee, Sang-Young [School of Chemical Engineering, Kangwon National University, Chuncheon, Kangwondo (Korea, Republic of); Song, Seung-Wan [Graduate School of Green Energy Technology, Department of Fine Chemical Engineering and Applied Chemistry, Chungnam National University, Daejeon (Korea, Republic of); Cho, Jaephil [School of Energy Engineering and Converging Research Center for Innovative Battery Technologies, Ulsan National Institute of Science and Technology (UNIST), Ulsan (Korea, Republic of); Shin, Heon-Cheol [School of Materials Science and Engineering, Pusan National University, Busan (Korea, Republic of)

    2012-10-02

    The mechanical flexibility of a cable-type battery reaches levels far beyond what is possible with conventional designs. The hollow-spiral (helical) multi-helix anode architecture is critical to the robustness under mechanical stress and facilitates electrolyte wetting of the battery components. This design enables the battery to reliably power an LED screen or an MP3 player even under severe mechanical twisting and bending. (Copyright copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  16. A de novo designed monomeric, compact three helix bundle protein on a carbohydrate template

    DEFF Research Database (Denmark)

    Malik, Leila; Nygård, Jesper; Christensen, Niels Johan

    2015-01-01

    De novo design and chemical synthesis of proteins and of other artificial structures, which mimic them, is a central strategy for understanding protein folding and for accessing proteins with novel functions. We have previously described carbohydrates as templates for the assembly of artificial...... the template could facilitate protein folding. Here we report the design and synthesis of 3-helix bundle carboproteins on deoxy-hexopyranosides. The carboproteins were analyzed by CD, AUC, SAXS, and NMR, which revealed the formation of the first compact, and folded monomeric carboprotein distinctly different...

  17. Phason thermal transport of three-helix state in insulating chiral magnets

    Science.gov (United States)

    Tatara, Gen

    2018-06-01

    Thermal dynamics of the three-helix state in a chiral magnet is studied based on a phason representation. Although phason representation is convenient for intuitive description, it is not straightforwardly compatible with microscopic linear response calculation of transport phenomena, because it is a (semi)macroscopic picture obtained by a coarse graining. By separating the slow phason mode and fast magnon mode, we show that phason thermal dynamics is driven by thermal magnon flow via the spin-transfer effect. The magnon and phason velocities are calculated by use of thermal vector potential formalism.

  18. Temperature, salinity, conductivity, pressure, transmissivity measurements collected using CTD from the Alpha Helix in the Chukchi Sea during 1996 (NODC Accession 0061042)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Temperature, salinity, conductivity, pressure, and transmissivity data gathered by CTD from the Alpha Helix (cruise HX194), September 1996

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

    Science.gov (United States)

    Morris, Mark; Uchida, Keven; Do, Tuan

    2006-03-16

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

  20. Human telomeric DNA: G-quadruplex, i-motif and Watson–Crick double helix

    Science.gov (United States)

    Phan, Anh Tuân; Mergny, Jean-Louis

    2002-01-01

    Human telomeric DNA composed of (TTAGGG/CCCTAA)n repeats may form a classical Watson–Crick double helix. Each individual strand is also prone to quadruplex formation: the G-rich strand may adopt a G-quadruplex conformation involving G-quartets whereas the C-rich strand may fold into an i-motif based on intercalated C·C+ base pairs. Using an equimolar mixture of the telomeric oligonucleotides d[AGGG(TTAGGG)3] and d[(CCCTAA)3CCCT], we defined which structures existed and which would be the predominant species under a variety of experimental conditions. Under near-physiological conditions of pH, temperature and salt concentration, telomeric DNA was predominantly in a double-helix form. However, at lower pH values or higher temperatures, the G-quadruplex and/or the i-motif efficiently competed with the duplex. We also present kinetic and thermodynamic data for duplex association and for G-quadruplex/i-motif unfolding. PMID:12409451

  1. Locating the fourth helix: Rethinking the role of civil society in developing smart learning cities

    Science.gov (United States)

    Borkowska, Katarzyna; Osborne, Michael

    2018-06-01

    In the Global North and increasingly in the Global South, smart city technologies are enthusiastically seen as a solution to urban problems and as an alternative to austerity. However, to move beyond a narrow technological focus, it is necessary to explore the degree to which smart initiatives are committed to building socially inclusive innovation with learning at its core. Using the particular case of the Future City Demonstrator Initiative in Glasgow, United Kingdom, the most high-profile initiative of its kind funded by government, the authors of this article assess the extent to which this smart city adopts such an inclusive approach. They use the quadruple helix model (government - academia - industry - civil society) as a starting point and develop an analytic framework composed of four strands: (1) supporting participation of citizens in decision-making; (2) implementing technological innovation which positions citizens as active users; (3) implementing technological innovation to benefit the community; and (4) evaluating technological innovation in the light of the experiences and needs of citizens. Unlike most analyses, the principal focus of this article is on the fourth element of the helix, civil society. The authors argue that Glasgow's rhetoric of smart urbanism, while aspiring to problem-solving, devalues certain principles of human agency. They emphasise that urban change, including the city's desire to become technologically innovative, would more fully facilitate active citizenship, social inclusion and learning opportunities for all if it were underpinned by the broader conceptions and frameworks of learning cities.

  2. Antimicrobial Effects of Helix D-derived Peptides of Human Antithrombin III*

    Science.gov (United States)

    Papareddy, Praveen; Kalle, Martina; Bhongir, Ravi K. V.; Mörgelin, Matthias; Malmsten, Martin; Schmidtchen, Artur

    2014-01-01

    Antithrombin III (ATIII) is a key antiproteinase involved in blood coagulation. Previous investigations have shown that ATIII is degraded by Staphylococcus aureus V8 protease, leading to release of heparin binding fragments derived from its D helix. As heparin binding and antimicrobial activity of peptides frequently overlap, we here set out to explore possible antibacterial effects of intact and degraded ATIII. In contrast to intact ATIII, the results showed that extensive degradation of the molecule yielded fragments with antimicrobial activity. Correspondingly, the heparin-binding, helix d-derived, peptide FFFAKLNCRLYRKANKSSKLV (FFF21) of human ATIII, was found to be antimicrobial against particularly the Gram-negative bacteria Escherichia coli and Pseudomonas aeruginosa. Fluorescence microscopy and electron microscopy studies demonstrated that FFF21 binds to and permeabilizes bacterial membranes. Analogously, FFF21 was found to induce membrane leakage of model anionic liposomes. In vivo, FFF21 significantly reduced P. aeruginosa infection in mice. Additionally, FFF21 displayed anti-endotoxic effects in vitro. Taken together, our results suggest novel roles for ATIII-derived peptide fragments in host defense. PMID:25202017

  3. Antimicrobial effects of helix D-derived peptides of human antithrombin III.

    Science.gov (United States)

    Papareddy, Praveen; Kalle, Martina; Bhongir, Ravi K V; Mörgelin, Matthias; Malmsten, Martin; Schmidtchen, Artur

    2014-10-24

    Antithrombin III (ATIII) is a key antiproteinase involved in blood coagulation. Previous investigations have shown that ATIII is degraded by Staphylococcus aureus V8 protease, leading to release of heparin binding fragments derived from its D helix. As heparin binding and antimicrobial activity of peptides frequently overlap, we here set out to explore possible antibacterial effects of intact and degraded ATIII. In contrast to intact ATIII, the results showed that extensive degradation of the molecule yielded fragments with antimicrobial activity. Correspondingly, the heparin-binding, helix D-derived, peptide FFFAKLNCRLYRKANKSSKLV (FFF21) of human ATIII, was found to be antimicrobial against particularly the Gram-negative bacteria Escherichia coli and Pseudomonas aeruginosa. Fluorescence microscopy and electron microscopy studies demonstrated that FFF21 binds to and permeabilizes bacterial membranes. Analogously, FFF21 was found to induce membrane leakage of model anionic liposomes. In vivo, FFF21 significantly reduced P. aeruginosa infection in mice. Additionally, FFF21 displayed anti-endotoxic effects in vitro. Taken together, our results suggest novel roles for ATIII-derived peptide fragments in host defense. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2012-03-15

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

  5. 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.

  6. Stakeholder engagement in quattro helix model for mobile phone reverse logistics in Indonesia: a conceptual framework

    Science.gov (United States)

    Maheswari, H.; Yudoko, G.; Adhiutama, A.

    2017-12-01

    The number of e-waste from mobile phone industry is still dominating until now. This is happened because there is no mutual commitment from all of parties i.e. businesses, government, and societies to reduce the use of mobile phone that has the shortest product life cycle. There are many researches study about firms’ motivation and government’s role, other discuss about actions of communities in supporting reverse logistics implementation. Unfortunately, research about engagement mechanism that involving all parties is still rare. Therefore, it is important to find the engagement model through this conceptual paper and it is expected useful to build the novel model. Through literature review, the results of this research are establishing the Quattro helix model as the appropriate structure to build the robust team by exploring stakeholder theories; mapping the engagement model either in form of collaboration or participation that consider stakeholders’ role and motivation and finding six types of engagement that consider their interest; and determining the novel model of engagement through Quattro helix model for implementing reverse logistics in handling e-waste by describing the linkage and the gaps among existing model.

  7. Effects of dispersion on electromagnetic parameters of tape-helix Blumlein pulse forming line of accelerator

    International Nuclear Information System (INIS)

    Zhang, Y.; Liu, J.L.; Feng, J.H.

    2012-01-01

    In this paper, the tape-helix model is introduced in the field of intense electron beam accelerator to analyze the dispersion effects on the electromagnetic parameters of helical Blumlein pulse forming line (PFL). Work band and dispersion relation of the PFL are analyzed, and the normalized coefficients of spatial harmonics are calculated. Dispersion effects on the important electromagnetic parameters of PFL, such as phase velocity, slow-wave coefficient, electric length and pulse duration, are analyzed as the central topic. In the PFL, electromagnetic waves with different frequencies in the work band of PFL have almost the same phase velocity. When de-ionized water, transformer oil and air are used as the PFL filling dielectric, respectively, the pulse duration of the helical Blumlein PFL is calculated as 479.6 ns, 81.1 ns and 53.1 ns in order. Electromagnetic wave simulation and experiments are carried out to demonstrate the theoretical calculations of the electric length and pulse duration which directly describe the phase velocity and dispersion of the PFL. Simulation results prove the theoretical analysis and calculation on pulse duration. Experiment is carried out based on the tape-helix Blumlein PFL and magnetic switch system. Experimental results show that the pulse durations are tested as 460 ns, 79 ns and 49 ns in order when de-ionized water, transformer oil and air are used respectively. Experimental results basically demonstrate the theoretical calculations and the analyses of dispersion. (authors)

  8. 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.

  9. Nuclear receptor ligand-binding domains: reduction of helix H12 dynamics to favour crystallization

    Energy Technology Data Exchange (ETDEWEB)

    Nahoum, Virginie; Lipski, Alexandra; Quillard, Fabien; Guichou, Jean-François [INSERM, U554, 34090 Montpellier (France); Université de Montpellier, CNRS, UMR5048, Centre de Biochimie Structurale (CBS), 34090 Montpellier (France); Boublik, Yvan [CNRS, UMR5237, Centre de Recherche de Biochimie Macromoléculaire (CRBM), 34293 Montpellier (France); Pérez, Efrèn [Universidade de Vigo, Departamento de Quimica Organica, Facultad de Química, 36310 Vigo (Spain); Germain, Pierre [Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), BP 10142, 67404 Illkirch CEDEX (France); Lera, Angel R. de [Universidade de Vigo, Departamento de Quimica Organica, Facultad de Química, 36310 Vigo (Spain); Bourguet, William, E-mail: bourguet@cbs.cnrs.fr [INSERM, U554, 34090 Montpellier (France); Université de Montpellier, CNRS, UMR5048, Centre de Biochimie Structurale (CBS), 34090 Montpellier (France)

    2008-07-01

    Attempts have been made to crystallize the ligand-binding domain of the human retinoid X receptor in complex with a variety of newly synthesized ligands. An inverse correlation was observed between the ‘crystallizability’ and the structural dynamics of the various receptor–ligand complexes. Crystallization trials of the human retinoid X receptor α ligand-binding domain (RXRα LBD) in complex with various ligands have been carried out. Using fluorescence anisotropy, it has been found that when compared with agonists these small-molecule effectors enhance the dynamics of the RXRα LBD C-terminal helix H12. In some cases, the mobility of this helix could be dramatically reduced by the addition of a 13-residue co-activator fragment (CoA). In keeping with these observations, crystals have been obtained of the corresponding ternary RXRα LBD–ligand–CoA complexes. In contrast, attempts to crystallize complexes with a highly mobile H12 remained unsuccessful. These experimental observations substantiate the previously recognized role of co-regulator fragments in facilitating the crystallization of nuclear receptor LBDs.

  10. Identification of helix capping and β-turn motifs from NMR chemical shifts

    International Nuclear Information System (INIS)

    Shen Yang; Bax, Ad

    2012-01-01

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

  11. The Penta Helix Model of Innovation in Oman: An HEI Perspective

    Directory of Open Access Journals (Sweden)

    Alrence S Halibas

    2017-05-01

    Full Text Available Aim/Purpose: Countries today strategically pursue regional development and economic diversification to compete in the world market. Higher Education Institutions (HEIs are at the crux of this political strategy. The paper reviews how HEIs can propel regional socio-economic growth and development by way of research innovation and entrepreneurship. Background: Offering an academic perspective about the role of HEIs using the Penta Helix innovation network for business and social innovation, the paper discusses opportunities and challenges in gestating an innovation culture. It likewise seeks, identifies and details strategies and workable programs. Methodology: Best-practice innovation campaigns initiated by Omani HEIs in collaboration with capstone programs organized by the government were parsed from selected local and international literature. The study includes a causal analysis of innovation information contained in 40 out of 44 published OAAA Quality Audit reports about HEIs from 2009 to 2016. The best-practice programs serve as success indicators and will be used as a field metric effect a Penta Helix blueprint for innovation. Contribution: The paper discusses how HEIs can engender, nurture, drive, and sustain innovation and entrepreneurial activity by using an innovation strategic blueprint like the Penta Helix model. It gathers together the recent historical attempts at promoting innovation by HEIs. It likewise suggests the creation of a network channel to allow key players in the innovation network to share innovation information and to collaborate with each other. Furthermore, it contributes to the development of innovation culture in HEIs. Findings: Expectations run high in academia. For one, universities believe that all innovations embryonically begin within their halls. Universities–too–believe it is naturally incumbent on them to stimulate and advance innovation despite that most innovation programs are initiated by the

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

    Energy Technology Data Exchange (ETDEWEB)

    Storrs, Richard Wood [Univ. of California, Berkeley, CA (United States)

    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 31P-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 Å 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 α-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.

  13. 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.

  14. 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. Copyright © 2013 Wiley Periodicals, Inc.

  15. Introduction of potential helix-capping residues into an engineered helical protein.

    Science.gov (United States)

    Parker, M H; Hefford, M A

    1998-08-01

    MB-1 is an engineered protein that was designed to incorporate high percentages of four amino acid residues and to fold into a four-alpha-helix bundle motif. Mutations were made in the putative loop I and III regions of this protein with the aim of increasing the stability of the helix ends. Four variants, MB-3, MB-5, MB-11 and MB-13, have replacements intended to promote formation of an 'N-capping box'. The loop I and III sequences of MB-3 (both GDLST) and MB-11 (GGDST) were designed to cause alphaL C-terminal 'capping' motifs to form in helices I and III. MB-5 has a sequence, GPDST, that places proline in a favourable position for forming beta-turns, whereas MB-13 (GLDST) has the potential to form Schellman C-capping motifs. Size-exclusion chromatography suggested that MB-1, MB-3, MB-5, MB-11 and MB-13 all form dimers, or possibly trimers. Free energies for the unfolding of each of these variants were determined by urea denaturation, with the loss of secondary structure followed by CD spectroscopy. Assuming an equilibrium between folded dimer and unfolded monomer, MB-13 had the highest apparent stability (40.5 kJ/mol, with +/-2.5 kJ/mol 95% confidence limits), followed by MB-11 (39.3+/-5.9 kJ/mol), MB-3 (36.4+/-1.7 kJ/mol), MB-5 (34.7+/-2.1 kJ/mol) and MB-1 (29.3+/-1.3 kJ/mol); the same relative stabilities of the variants were found when a folded trimer to unfolded monomer model was used to calculate stabilities. All of the variants were relatively unstable for dimeric proteins, but were significantly more stable than MB-1. These findings suggest that it might be possible to increase the stability of a protein for which the three-dimensional structure is unknown by placing amino acid residues in positions that have the potential to form helix- and turn-stabilizing motifs.

  16. Helix-helix inversion of an optically-inactive π-conjugated foldamer triggered by concentration changes of a single enantiomeric guest leading to a change in the helical stability.

    Science.gov (United States)

    Liu, Lijia; Ousaka, Naoki; Horie, Miki; Mamiya, Fumihiko; Yashima, Eiji

    2016-09-27

    A preferred-handed helicity induced in an optically-inactive poly(phenyleneethynylene)-based foldamer bearing carboxylic acid pendants upon complexation with a single enantiomeric diamine was subsequently inverted into the opposite helix upon further addition of the diamine, accompanied by a remarkable change in the stability of the helices.

  17. Survival probabilities of first and second clutches of blackbird (Turdus merula in an urban environment

    Directory of Open Access Journals (Sweden)

    Kurucz Kornelia

    2010-01-01

    Full Text Available The breeding success of blackbirds was investigated in April and June 2008 and 2009 in the Botanical Garden of the University of Pecs, with a total of 50 artificial nests at each of the four sessions (with 1 quail egg and 1 plasticine egg placed in every nest. In all four study periods of the two years, 2 nests (4% were destroyed by predators. Six nests (12%, of the nests were not discovered in either of the cases. The survival probability of artificial nests was greater in April than in June (both years, but the difference was significant only in 2008. Nests placed into a curtain of ivy (Hedera helix on a wall were located higher up than those in bushes, yet their predation rates were quite similar. The predation values of quail vs. plasticine eggs did not differ in 2008. In the year 2009, however, significantly more quail eggs were discovered (mostly removed, than plasticine eggs. Marks that were left on plasticine eggs originated mostly from small mammals and small-bodied birds, but the disappearance of a large number of quail and plasticine eggs was probably caused by larger birds, primarily jays.

  18. 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)

    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. PMID:24740008

  19. Yang-Lee zeros for a Potts model of helix-coil transition with nontrivial topology

    International Nuclear Information System (INIS)

    Ananikian, N.; Ananikyan, L.; Artuso, R.; Sargsyan, K.

    2007-07-01

    The Yang-Lee partition function zeros of the Q-state Potts model on a zigzag ladder are studied by a transfer-matrix approach. This Q-state model has a non-trivial topology induced by three-site interactions on a zigzag ladder and is proposed as a description of helix-coil transition in homo-polymers. The Yang-Lee zeros are associated to complex values of the solvent-related coupling constant K (magnetic field) and they are exactly derived for arbitrary values of the system parameters: Q, J (coupling constant of hydrogen binding) and temperature. It is shown that there is only a quasi-phase transition for all temperatures. The densities of the Yang-Lee zeros are singular at the edge singularity points and the critical exponent σ = -1/2. (author)

  20. 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.

  1. 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

  2. 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.

  3. Steady-state configurations and dynamics of the MreB helix within bacteria

    Science.gov (United States)

    Rutenberg, Andrew; Allard, Jun

    2007-03-01

    We present a quantitative model of the actin-like MreB cytoskeleton that is present in many prokaryotes. Individual MreB polymers are bundled into a supra-molecular array to make up helical cables. The cell wall imposes constraint forces through a global elasticity model. With variational techniques and stochastic simulations we obtain relationships between observable quantities such as the pitch of the helix, the total abundance of MreB molecules, and the thickness of the MreB cables. We address changes expected with slow cell growth, as well as turnover dynamics that are relevant to FRAP studies. We also address polarized macromolecular trafficking along the MreB cables without motor proteins.

  4. Bridge helix bending promotes RNA polymerase II backtracking through a critical and conserved threonine residue

    KAUST Repository

    Da, Lin-Tai; Pardo-Avila, Fá tima; Xu, Liang; Silva, Daniel-Adriano; Zhang, Lu; Gao, Xin; Wang, Dong; Huang, Xuhui

    2016-01-01

    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.

  5. Communication: Role of explicit water models in the helix folding/unfolding processes

    Science.gov (United States)

    Palazzesi, Ferruccio; Salvalaglio, Matteo; Barducci, Alessandro; Parrinello, Michele

    2016-09-01

    In the last years, it has become evident that computer simulations can assume a relevant role in modelling protein dynamical motions for their ability to provide a full atomistic image of the processes under investigation. The ability of the current protein force-fields in reproducing the correct thermodynamics and kinetics systems behaviour is thus an essential ingredient to improve our understanding of many relevant biological functionalities. In this work, employing the last developments of the metadynamics framework, we compare the ability of state-of-the-art all-atom empirical functions and water models to consistently reproduce the folding and unfolding of a helix turn motif in a model peptide. This theoretical study puts in evidence that the choice of the water models can influence the thermodynamic and the kinetics of the system under investigation, and for this reason cannot be considered trivial.

  6. Broadband and high-efficiency vortex beam generator based on a hybrid helix array.

    Science.gov (United States)

    Fang, Chaoqun; Wu, Chao; Gong, Zhijie; Zhao, Song; Sun, Anqi; Wei, Zeyong; Li, Hongqiang

    2018-04-01

    The vortex beam which carries the orbital angular momentum has versatile applications, such as high-resolution imaging, optical communications, and particle manipulation. Generating vortex beams with the Pancharatnam-Berry (PB) phase has drawn considerable attention for its unique spin-to-orbital conversion features. Despite the PB phase being frequency independent, an optical element with broadband high-efficiency circular polarization conversion feature is still needed for the broadband high-efficiency vortex beam generation. In this work, a broadband and high-efficiency vortex beam generator based on the PB phase is built with a hybrid helix array. Such devices can generate vortex beams with arbitrary topological charge. Moreover, vortex beams with opposite topological charge can be generated with an opposite handedness incident beam that propagates backward. The measured efficiency of our device is above 65% for a wide frequency range, with the relative bandwidth of 46.5%.

  7. A cosmic double helix in the archetypical quasar 3C273.

    Science.gov (United States)

    Lobanov, A P; Zensus, J A

    2001-10-05

    Finding direct evidence for plasma instability in extragalactic jets is crucial for understanding the nature of relativistic outflows from active galactic nuclei. Our radio interferometric observations of the quasar 3C273 made with the orbiting radio telescope, HALCA, and an array of ground telescopes have yielded an image in which the emission across the jet is resolved, revealing two threadlike patterns that form a double helix inside the jet. This double helical structure is consistent with a Kelvin-Helmholtz instability, and at least five different instability modes can be identified and modeled by a light jet with a Lorentz factor of 2 and Mach number of 3.5. The model reproduces in detail the internal structure of the jet on scales of up to 30 milli-arc seconds ( approximately 300 parsecs) and is consistent with the general morphology of the jet on scales of up to 1 kiloparsec.

  8. A "bulged" double helix in a RNA-protein contact site

    DEFF Research Database (Denmark)

    Peattie, D A; Douthwaite, S; Garrett, R A

    1981-01-01

    as a singly bulged nucleotide extending the Fox and Woese central helix by two base pairs in the E. coli sequence (to positions 16-23/60-68) as well as in each of 61 (prokaryotic and eukaryotic) aligned 5S RNA sequences. In each case, the single bulged nucleotide is at the relative position of adenosine-66...... in the RNA sequences. The presence of this putative bulged nucleotide appears to have been conserved in 5S RNA sequences throughout evolution, and its identity varies with major phylogenetic divisions. This residue is likely involved in specific 5S RNA-protein recognition or interaction in prokaryotic...... and eukaryotic ribosomes. The uridine-65 to adenosine-66 internucleotide bond is protected from RNase A digestion in the complex, and carbethoxylation of E. coli adenosine-66 prior to L18 binding affects formation of a stable RNA-protein complex. Thus, we identify a region of E. coli 5S RNA protected...

  9. NMR studies of abasic sites in DNA duplexes: Deoxyadenosine stacks into the helix opposite acyclic lesions

    International Nuclear Information System (INIS)

    Kalnik, M.W.; Chang, Chienneng; Johnson, F.; Grollman, A.P.; Patel, D.J.

    1989-01-01

    Proton and phosphorus NMR studies are reported for two complementary nonanucleotide duplexes containing acyclic abasic sites. The first duplex, d(C-A-T-G-A-G-T-A-C)·d(G-T-A-C-P-C-A-T-G), contains an acyclic propanyl moiety, P, located opposite a deoxyadenosine at the center of the helix (designated AP P 9-mer duplex). The second duplex, d(C-A-T-G-A-G-T-A-C-)·d(G-T-A-C-E-C-A-T-G), contains a similarly located acyclic ethanyl moiety, E (designated AP E 9-mer duplex). The ethanyl moiety is one carbon shorter than the natural carbon-phosphodiester backbone of a single nucleotide unit of DNA. The majority of the exchangeable and nonexchangeable base and sugar protons in both the AP P 9-mer and AP E 9-mer duplexes, including those at the abasic site, have been assigned by recording and analyzing two-dimensional phase-sensitive NOESY data sets in H 2 O and D 2 O solution between -5 and 5 degree C. These spectroscopic observations establish that A5 inserts into the helix opposite the abasic site (P14 and El14) and stacks between the flanking G4·C15 and G6·C13 Watson-Crick base pairs in both the AP P 9-mer and AP E 9-mer duplexes. Proton NMR parameters for the Ap P 9-mer and AP E 9-mer duplexes are similar to those reported previously. These proton NMR experiments demonstrate that the structures at abasic sites are very similar whether the five-membered ring is open or closed or whether the phosphodiester backbone is shortened by one carbon atom. Phosphorus spectra of the AP P 9-mer and AP E 9-mer duplexes (5 degree C) indicate that the backbone conformation is similarly perturbed at three phosphodiester backbone torsion angles

  10. 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.

  11. Oxidation of Helix-3 methionines precedes the formation of PK resistant PrP.

    Directory of Open Access Journals (Sweden)

    Tamar Canello

    2010-07-01

    Full Text Available While elucidating the peculiar epitope of the alpha-PrP mAb IPC2, we found that PrPSc exhibits the sulfoxidation of residue M213 as a covalent signature. Subsequent computational analysis predicted that the presence of sulfoxide groups at both Met residues 206 and 213 destabilize the alpha-fold, suggesting oxidation may facilitate the conversion of PrPC into PrPSc. To further study the effect of oxidation on prion formation, we generated pAbs to linear PrP peptides encompassing the Helix-3 region, as opposed to the non-linear complexed epitope of IPC2. We now show that pAbs, whose epitopes comprise Met residues, readily detected PrPC, but could not recognize most PrPSc bands unless they were vigorously reduced. Next, we showed that the alpha-Met pAbs did not recognize newly formed PrPSc, as is the case for the PK resistant PrP present in lines of prion infected cells. In addition, these reagents did not detect intermediate forms such as PK sensitive and partially aggregated PrPs present in infected brains. Finally, we show that PrP molecules harboring the pathogenic mutation E200K, which is linked to the most common form of familial CJD, may be spontaneously oxidized. We conclude that the oxidation of methionine residues in Helix-3 represents an early and important event in the conversion of PrPC to PrPSc. We believe that further investigation into the mechanism and role of PrP oxidation will be central in finally elucidating the mechanism by which a normal cell protein converts into a pathogenic entity that causes fatal brain degeneration.

  12. DNA binding and unwinding by Hel308 helicase requires dual functions of a winged helix domain.

    Science.gov (United States)

    Northall, Sarah J; Buckley, Ryan; Jones, Nathan; Penedo, J Carlos; Soultanas, Panos; Bolt, Edward L

    2017-09-01

    Hel308 helicases promote genome stability linked to DNA replication in archaea, and have homologues in metazoans. In the crystal structure of archaeal Hel308 bound to a tailed DNA duplex, core helicase domains encircle single-stranded DNA (ssDNA) in a "ratchet" for directional translocation. A winged helix domain (WHD) is also present, but its function is mysterious. We investigated the WHD in full-length Hel308, identifying that mutations in a solvent exposed α-helix resulted in reduced DNA binding and unwinding activities. When isolated from the rest of Hel308, the WHD protein alone bound to duplex DNA but not ssDNA, and DNA binding by WHD protein was abolished by the same mutations as were analyzed in full-length Hel308. Isolated WHD from a human Hel308 homologue (HelQ) also bound to duplex DNA. By disrupting the interface between the Hel308 WHD and a RecA-like domain, a topology typical of Ski2 helicases, we show that this is crucial for ATPase and helicase activities. The data suggest a model in which the WHD promotes activity of Hel308 directly, through binding to duplex DNA that is distinct from ssDNA binding by core helicase, and indirectly through interaction with the RecA-like domain. We propose how the WHD may contribute to ssDNA translocation, resulting in DNA helicase activity or in removal of other DNA bound proteins by "reeling" ssDNA. Copyright © 2017 Elsevier B.V. All rights reserved.

  13. The third helix of the murine Hoxc8 homeodomain facilitates protein transduction in mammalian cells

    International Nuclear Information System (INIS)

    Kong, Kyoung-Ah; Gadi, Jogeswar; Park, Hyoung Woo; Bok, Jinwoong; Kim, Myoung Hee

    2008-01-01

    Previously, we have demonstrated that purified Hoxc8 homeoprotein has the ability to penetrate the cellular membrane and can be transduced efficiently into COS-7 cells. Moreover, the Hoxc8 protein is able to form a complex with DNA molecules in vitro and helps the DNA be delivered intracellularly, serving as a gene delivery vehicle. Here, we further analyzed the membrane transduction activity of Hoxc8 protein and provide the evidence that the 16 amino acid (a.a.191-206, 2.23 kDa) third helix of murine Hoxc8 protein is an efficient protein transduction domain (PTD). When the 16 amino acid peptide was fused at the carboxyl terminal of enhanced green fluorescence protein (EGFP), the fusion proteins were transduced efficiently into the primary pig fetal fibroblast cells. The transduction efficiency increased in a concentration-dependent manner up to 1 μM, and appeared to plateau above a concentration of 1 μM. When tandem multimers of PTD, EGFP-PTD(2), EGFP-PTD(3), EGFP-PTD(4), and EGFP-PTD(5), were analyzed at 500 nM of concentration, the penetrating efficiency increased in a dose-dependent manner. As the number of PTDs increased, the EGFP signal also increased, although the signal maintained plateau after EGFP-PTD(3). These results indicate that the 16 amino acid third helix is the key element responsible for the membrane transduction activity of Hoxc8 proteins, and further suggest that the small peptide could serve as a therapeutic delivery vehicle for large cargo proteins

  14. An Amphipathic Helix Directs Cellular Membrane Curvature Sensing and Function of the BAR Domain Protein PICK1.

    Science.gov (United States)

    Herlo, Rasmus; Lund, Viktor K; Lycas, Matthew D; Jansen, Anna M; Khelashvili, George; Andersen, Rita C; Bhatia, Vikram; Pedersen, Thomas S; Albornoz, Pedro B C; Johner, Niklaus; Ammendrup-Johnsen, Ina; Christensen, Nikolaj R; Erlendsson, Simon; Stoklund, Mikkel; Larsen, Jannik B; Weinstein, Harel; Kjærulff, Ole; Stamou, Dimitrios; Gether, Ulrik; Madsen, Kenneth L

    2018-05-15

    BAR domains are dimeric protein modules that sense, induce, and stabilize lipid membrane curvature. Here, we show that membrane curvature sensing (MCS) directs cellular localization and function of the BAR domain protein PICK1. In PICK1, and the homologous proteins ICA69 and arfaptin2, we identify an amphipathic helix N-terminal to the BAR domain that mediates MCS. Mutational disruption of the helix in PICK1 impaired MCS without affecting membrane binding per se. In insulin-producing INS-1E cells, super-resolution microscopy revealed that disruption of the helix selectively compromised PICK1 density on insulin granules of high curvature during their maturation. This was accompanied by reduced hormone storage in the INS-1E cells. In Drosophila, disruption of the helix compromised growth regulation. By demonstrating size-dependent binding on insulin granules, our finding highlights the function of MCS for BAR domain proteins in a biological context distinct from their function, e.g., at the plasma membrane during endocytosis. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

  15. 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,...

  16. 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.

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

    DEFF Research Database (Denmark)

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

    1993-01-01

    arrangement were performed in two ways: (1) by the use of a Poisson-Boltzmann approach which allows for an estimate of the screening effect, and (2) by the use of a uniform dielectric model (Coulomb's law). It is found that the alpha-helix is stabilized by approximately 5-10 kcal/mol due to electrostatic...

  18. The N-terminal tail of hERG contains an amphipathic α-helix that regulates channel deactivation.

    Directory of Open Access Journals (Sweden)

    Chai Ann Ng

    Full Text Available The cytoplasmic N-terminal domain of the human ether-a-go-go related gene (hERG K+ channel is critical for the slow deactivation kinetics of the channel. However, the mechanism(s by which the N-terminal domain regulates deactivation remains to be determined. Here we show that the solution NMR structure of the N-terminal 135 residues of hERG contains a previously described Per-Arnt-Sim (PAS domain (residues 26-135 as well as an amphipathic α-helix (residues 13-23 and an initial unstructured segment (residues 2-9. Deletion of residues 2-25, only the unstructured segment (residues 2-9 or replacement of the α-helix with a flexible linker all result in enhanced rates of deactivation. Thus, both the initial flexible segment and the α-helix are required but neither is sufficient to confer slow deactivation kinetics. Alanine scanning mutagenesis identified R5 and G6 in the initial flexible segment as critical for slow deactivation. Alanine mutants in the helical region had less dramatic phenotypes. We propose that the PAS domain is bound close to the central core of the channel and that the N-terminal α-helix ensures that the flexible tail is correctly orientated for interaction with the activation gating machinery to stabilize the open state of the channel.

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

    DEFF Research Database (Denmark)

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

    2007-01-01

    Escherichia coli strains with inactivated rluD genes were previously found to lack the conserved pseudouridines in helix 69 of 23S ribosomal RNA and to grow slowly. A suppressor mutant was isolated with a near normal growth rate that had changed the conserved Glu-172 codon to a Lys codon in prf...

  1. Cesium-134 assimilation and retention in the landsnail Helix aspersa Muller 1974. Its potential usefulness as bioindicator for radioactive contamination

    International Nuclear Information System (INIS)

    Alfonso, L.A.; Carvalho, F.P.

    1986-01-01

    Cesium-134 retention was experimentally studied on two groups (n=20 in each) of the land-snail Helix aspersa, labelled either through ingestion of labelled food or the radionuclide injection into the foot muscle. Cesium elimination was found to be not dependent from the labelling technique used. The mean biological half-life for Cs retention in both Helix groups was 53.6+- 0.8 d for the largest retention component, accounting for 0.88 of the initally absorbed Cs. Another experiment runned on a similar size Helix group allowed the gravimetric determination of food ingestion rate (8.8 mg/ g/day) and food assimilation efficiency (0.70+-0.20). Predictive modelling of Cs accumulation by Helix indicates a relatively high bioaccumulation potential in this species. This fact, together with the long biological half-life found for Cs retention, indicate that land snails could be used as suitable bioindicators for radioactive pollution in restrict terrestrial areas. (author)

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

    DEFF Research Database (Denmark)

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

    1981-01-01

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

  3. Basic Tilted Helix Bundle – A new protein fold in human FKBP25/FKBP3 and HectD1

    International Nuclear Information System (INIS)

    Helander, Sara; Montecchio, Meri; Lemak, Alexander; Farès, Christophe; Almlöf, Jonas; Li, Yanjun; Yee, Adelinda; Arrowsmith, Cheryl H.; Dhe-Paganon, Sirano; Sunnerhagen, Maria

    2014-01-01

    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 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

  4. Chain length dependence of the helix orientation in Langmuir-Blodgett monolayers of alpha-helical diblock copolypeptides

    NARCIS (Netherlands)

    Nguyen, Le-Thu T.; Ardana, Aditya; Vorenkamp, Eltjo J.; ten Brinke, Gerrit; Schouten, Arend J.

    2010-01-01

    The effect of chain length on the helix orientation of alpha-helical diblock copolypeptides in Langmuir and Langmuir-Blodgett monolayers is reported for the first time. Amphiphilic diblock copolypeptides (PLGA-b-PMLGSLGs) of poly(alpha-L-glutamic acid) (PLGA) and

  5. Hydrated and Dehydrated Tertiary Interactions–Opening and Closing–of a Four-Helix Bundle Peptide

    Science.gov (United States)

    Lignell, Martin; Tegler, Lotta T.; Becker, Hans-Christian

    2009-01-01

    Abstract The structural heterogeneity and thermal denaturation of a dansyl-labeled four-helix bundle homodimeric peptide was studied with steady-state and time-resolved fluorescence spectroscopy and with circular dichroism (CD). At room temperature the fluorescence decay of the polarity-sensitive dansyl, located in the hydrophobic core region, can be described by a broad distribution of fluorescence lifetimes, reflecting the heterogeneous microenvironment. However, the lifetime distribution is nearly bimodal, which we ascribe to the presence of two major conformational subgroups. Since the fluorescence lifetime reflects the water content of the four-helix bundle conformations, we can use the lifetime analysis to monitor the change in hydration state of the hydrophobic core of the four-helix bundle. Increasing the temperature from 9°C to 23°C leads to an increased population of molten-globule-like conformations with a less ordered helical backbone structure. The fluorescence emission maximum remains constant in this temperature interval, and the hydrophobic core is not strongly affected. Above 30°C the structural dynamics involve transient openings of the four-helix bundle structure, as evidenced by the emergence of a water-quenched component and less negative CD. Above 60°C the homodimer starts to dissociate, as shown by the increasing loss of CD and narrow, short-lived fluorescence lifetime distributions. PMID:19619472

  6. 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…

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

    Science.gov (United States)

    Villarreal de la Garza, Sonia

    2011-01-01

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

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

    NARCIS (Netherlands)

    Koene, J M; Chase, R.

    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

  9. 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

    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

  10. 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…

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

    DEFF Research Database (Denmark)

    Lou, Chenguang; Martos-Maldonado, Manuel C.; Madsen, Charlotte Stahl

    2016-01-01

    Peptide-based structures can be designed to yield artificial proteins with specific folding patterns and functions. Template-based assembly of peptide units is one design option, but the use of two orthogonal self-assembly principles, oligonucleotide triple helix and a coiled coil protein domain ...

  12. Lipid-mediated interactions tune the association of glycophorin A helix and its disruptive mutants in membranes

    NARCIS (Netherlands)

    Sengupta, Durba; Marrink, Siewert J.

    2010-01-01

    The specific and non-specific driving forces of helix association within membranes are still poorly understood. Here, we use coarse-grain molecular dynamics simulations to study the association behavior of glycophorin A and two disruptive mutants, T87F and a triple mutant of the GxxxG motif

  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. Flood-inundation maps for Suwanee Creek from the confluence of Ivy Creek to the Noblin Ridge Drive bridge, Gwinnett County, Georgia

    Science.gov (United States)

    Musser, Jonathan W.

    2012-01-01

    Digital flood-inundation maps for a 6.9-mile reach of Suwanee Creek, from the confluence of Ivy Creek to the Noblin Ridge Drive bridge, were developed by the U.S. Geological Survey (USGS) in cooperation with Gwinnett County, Georgia. The inundation maps, which can be accessed through the USGS Flood Inundation Mapping Science Web site at http://water.usgs.gov/osw/flood_inundation/, depict estimates of the areal extent and depth of flooding corresponding to selected water levels (stages) at the USGS streamgage at Suwanee Creek at Suwanee, Georgia (02334885). Current stage at this USGS streamgage may be obtained at http://waterdata.usgs.gov/ and can be used in conjunction with these maps to estimate near real-time areas of inundation. The National Weather Service (NWS) is incorporating results from this study into the Advanced Hydrologic Prediction Service (AHPS) flood-warning system (http://water.weather.gov/ahps/). The NWS forecasts flood hydrographs at many places that commonly are collocated at USGS streamgages. The forecasted peak-stage information for the USGS streamgage at Suwanee Creek at Suwanee (02334885), available through the AHPS Web site, may be used in conjunction with the maps developed in this study to show predicted areas of flood inundation. A one-dimensional step-backwater model was developed using the U.S. Army Corps of Engineers HEC-RAS software for Suwanee Creek and was used to compute flood profiles for a 6.9-mile reach of the creek. The model was calibrated using the most current stage-discharge relations at the Suwanee Creek at Suwanee streamgage (02334885). The hydraulic model was then used to determine 19 water-surface profiles for flood stages at the Suwanee Creek streamgage at 0.5-foot intervals referenced to the streamgage. The profiles ranged from just above bankfull stage (7.0 feet) to approximately 1.7 feet above the highest recorded water level at the streamgage (16.0 feet). The simulated water-surface profiles were then combined

  15. Pollination biology of fruit-bearing hedgerow plants and the role of flower-visiting insects in fruit-set.

    Science.gov (United States)

    Jacobs, Jennifer H; Clark, Suzanne J; Denholm, Ian; Goulson, Dave; Stoate, Chris; Osborne, Juliet L

    2009-12-01

    In the UK, the flowers of fruit-bearing hedgerow plants provide a succession of pollen and nectar for flower-visiting insects for much of the year. The fruits of hedgerow plants are a source of winter food for frugivorous birds on farmland. It is unclear whether recent declines in pollinator populations are likely to threaten fruit-set and hence food supply for birds. The present study investigates the pollination biology of five common hedgerow plants: blackthorn (Prunus spinosa), hawthorn (Crataegus monogyna), dog rose (Rosa canina), bramble (Rubus fruticosus) and ivy (Hedera helix). The requirement for insect pollination was investigated initially by excluding insects from flowers by using mesh bags and comparing immature and mature fruit-set with those of open-pollinated flowers. Those plants that showed a requirement for insect pollination were then tested to compare fruit-set under two additional pollination service scenarios: (1) reduced pollination, with insects excluded from flowers bagged for part of the flowering period, and (2) supplemental pollination, with flowers hand cross-pollinated to test for pollen limitation. The proportions of flowers setting fruit in blackthorn, hawthorn and ivy were significantly reduced when insects were excluded from flowers by using mesh bags, whereas fruit-set in bramble and dog rose were unaffected. Restricting the exposure of flowers to pollinators had no significant effect on fruit-set. However, blackthorn and hawthorn were found to be pollen-limited, suggesting that the pollination service was inadequate in the study area. Ensuring strong populations of insect pollinators may be essential to guarantee a winter fruit supply for birds in UK hedgerows.

  16. Salt bridge interactions within the β2 integrin α7 helix mediate force-induced binding and shear resistance ability.

    Science.gov (United States)

    Zhang, Xiao; Li, Linda; Li, Ning; Shu, Xinyu; Zhou, Lüwen; Lü, Shouqin; Chen, Shenbao; Mao, Debin; Long, Mian

    2018-01-01

    The functional performance of the αI domain α 7 helix in β 2 integrin activation depends on the allostery of the α 7 helix, which axially slides down; therefore, it is critical to elucidate what factors regulate the allostery. In this study, we determined that there were two conservative salt bridge interaction pairs that constrain both the upper and bottom ends of the α 7 helix. Molecular dynamics (MD) simulations for three β 2 integrin members, lymphocyte function-associated antigen-1 (LFA-1; α L β 2 ), macrophage-1 antigen (Mac-1; α M β 2 ) and α x β 2 , indicated that the magnitude of the salt bridge interaction is related to the stability of the αI domain and the strength of the corresponding force-induced allostery. The disruption of the salt bridge interaction, especially with double mutations in both salt bridges, significantly reduced the force-induced allostery time for all three members. The effects of salt bridge interactions of the αI domain α 7 helix on β 2 integrin conformational stability and allostery were experimentally validated using Mac-1 constructs. The results demonstrated that salt bridge mutations did not alter the conformational state of Mac-1, but they did increase the force-induced ligand binding and shear resistance ability, which was consistent with MD simulations. This study offers new insight into the importance of salt bridge interaction constraints of the αI domain α 7 helix and external force for β 2 integrin function. © 2017 Federation of European Biochemical Societies.

  17. Çivi Yazılı Hukukta Kölelere Verilen Cezalar Punishments Given To Slaves In Cuneiform Law

    Directory of Open Access Journals (Sweden)

    Yusuf KILIÇ

    2013-09-01

    varlığını yararlı görmüşlerdir. Böylece savaş tutsakları, kötü veya hastalıklı ürün yıllarından dolayı istenilen miktarda hasat elde edemeyip fakir düşerek mülkünü başkasına devretmek zorunda kalan insanlar, borcunu ödeyemeyen borçlular, ailesine karşı gelen ve bu sebeple cezalandırılarak evlatlıktan çıkarılan kişilerden bir köle sınıfı oluşturmuşlardır. Köleleri ucuz ve daimi emek olarak görenbu toplumlar bu sınıfın sürekliliğini sağlamak için kölelerin bazı davranışlarını suç kabul ederek, gelir-geçer olan hukuki normlarında buna karşılık bazı cezai müeyyideler öngörmüşlerdir. Bu çalışmanın amacı kölelerin hukuk nazarında suç kabul edilen fiillerine karşılık verilen cezaları ortaya koymaktır. Bu noktada çivi yazılı hukuk sistemine sahip olan Eski Mezopotamya toplumları Sümer, Babil ve Asur ile Anadolu’daki Hititlerin neşredilmiş olan kanun metinleriüzerinde inceleme yapılmıştır. Söz konusu toplumların çivi yazılı kanun metinlerinden çıkarılan neticelere göre, kölelerin cezalandırılmasını gerektiren davranışlar şunlardır: KöleninEfendisinin Evinden Kaçması, Bir Cariyenin (kadın kölenin Efendisinden Habersiz Başını Örtmesi, KöleninHırsızlık Yapması ve KöleninEfendisineKarşı Gelmesi. Bu tür davranışlarda bulunan kölelere bazı organları sakatlanmaktadır. Bununla birlikte evden kaçan bir köleyi saklayan kişiye ise ölüm cezası verilmektedir.

  18. Helix Nebula - the Science Cloud: a public-private partnership to build a multidisciplinary cloud platform for data intensive science

    Science.gov (United States)

    Jones, Bob; Casu, Francesco

    2013-04-01

    The feasibility of using commercial cloud services for scientific research is of great interest to research organisations such as CERN, ESA and EMBL, to the suppliers of cloud-based services and to the national and European funding agencies. Through the Helix Nebula - the Science Cloud [1] initiative and with the support of the European Commission, these stakeholders are driving a two year pilot-phase during which procurement processes and governance issues for a framework of public/private partnership will be appraised. Three initial flagship use cases from high energy physics, molecular biology and earth-observation are being used to validate the approach, enable a cost-benefit analysis to be undertaken and prepare the next stage of the Science Cloud Strategic Plan [2] to be developed and approved. The power of Helix Nebula lies in a shared set of services for initially 3 very different sciences each supporting a global community and thus building a common e-Science platform. Of particular relevance is the ESA sponsored flagship application SuperSites Exploitation Platform (SSEP [3]) that offers the global geo-hazard community a common platform for the correlation and processing of observation data for supersites monitoring. The US-NSF Earth Cube [4] and Ocean Observatory Initiative [5] (OOI) are taking a similar approach for data intensive science. The work of Helix Nebula and its recent architecture model [6] has shown that is it technically feasible to allow publicly funded infrastructures, such as EGI [7] and GEANT [8], to interoperate with commercial cloud services. Such hybrid systems are in the interest of the existing users of publicly funded infrastructures and funding agencies because they will provide "freedom of choice" over the type of computing resources to be consumed and the manner in which they can be obtained. But to offer such freedom-of choice across a spectrum of suppliers, various issues such as intellectual property, legal responsibility

  19. Helix-coil transition of a four-way DNA junction observed by multiple fluorescence parameters.

    Science.gov (United States)

    Vámosi, György; Clegg, Robert M

    2008-10-16

    The thermal denaturation of immobile four-way DNA ("Holliday-") junctions with 17 base pair arms was studied via fluorescence spectroscopic measurements. Two arms of the molecule were labeled at the 5'-end with fluorescein and tetramethylrhodamine, respectively. Melting was monitored by the fluorescence intensity of the dyes, the fluorescence anisotropy of tetramethylrhodamine, and Forster resonance energy transfer (FRET) between fluorescein and rhodamine. To fit the thermal denaturation curves of the four-way junctions, two basic thermodynamic models were tested: (1) all-or-none transitions assuming a molecularity of one, two, or four and (2) a statistical "zipper" model. The all-or-none models correspond to reaction mechanisms assuming that the cooperative melting unit (that is, the structure changing from complete helix to complete coil) consists of (1) one arm, (2) two neighboring arms (which have one continuous strand common to the two arms), or (3) all four arms. In each case, the melting of the cooperative unit takes place in a single step. The tetramolecular reaction model (four-arm melting) yielded unrealistically low van't Hoff enthalpy and entropy values, whereas the monomolecular model (one-arm melting) resulted in a poor fit to the experimental data. The all-or-none bimolecular (two neighboring arm model) fit gave intermediate standard enthalpy change (Delta H) values between those expected for the melting of a duplex with a total length between the helix lengths of one and two arms (17 and 34 base pairs). Simulations according to the zipper model fit the experimental curves best when the length of the simulated duplex was assumed to be 34 base pairs, the length of a single strand. This suggests that the most important parameter determining the melting behavior of the molecule is the end-to-end distance of the strands (34 bases) rather than the length of the individual arms (17 base pairs) and that the equilibrium concentration of partially denatured

  20. Overlapping effector interfaces define the multiple functions of the HIV-1 Nef polyproline helix

    Directory of Open Access Journals (Sweden)

    Kuo Lillian S

    2012-05-01

    proteins. To the N- and C- terminal sides of the polyproline helix are multifunctional protein interaction sites. The polyproline segment is also adapted to downregulate MHCI with a non-canonical binding surface. Our results demonstrate that Nef polyproline helix is highly adapted to directly interact with multiple host cell proteins.

  1. 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

  2. Evidence for an RNA pseudoknot loop-helix interaction essential for efficient -1 ribosomal frameshifting.

    Science.gov (United States)

    Liphardt, J; Napthine, S; Kontos, H; Brierley, I

    1999-05-07

    RNA pseudoknots are structural elements that participate in a variety of biological processes. At -1 ribosomal frameshifting sites, several types of pseudoknot have been identified which differ in their organisation and functionality. The pseudoknot found in infectious bronchitis virus (IBV) is typical of those that possess a long stem 1 of 11-12 bp and a long loop 2 (30-164 nt). A second group of pseudoknots are distinguishable that contain stems of only 5 to 7 bp and shorter loops. The NMR structure of one such pseudoknot, that of mouse mammary tumor virus (MMTV), has revealed that it is kinked at the stem 1-stem 2 junction, and that this kinked conformation is essential for efficient frameshifting. We recently investigated the effect on frameshifting of modulating stem 1 length and stability in IBV-based pseudoknots, and found that a stem 1 with at least 11 bp was needed for efficient frameshifting. Here, we describe the sequence manipulations that are necessary to bypass the requirement for an 11 bp stem 1 and to convert a short non-functional IBV-derived pseudoknot into a highly efficient, kinked frameshifter pseudoknot. Simple insertion of an adenine residue at the stem 1-stem 2 junction (an essential feature of a kinked pseudoknot) was not sufficient to create a functional pseudoknot. An additional change was needed: efficient frameshifting was recovered only when the last nucleotide of loop 2 was changed from a G to an A. The requirement for an A at the end of loop 2 is consistent with a loop-helix contact similar to those described in other RNA tertiary structures. A mutational analysis of both partners of the proposed interaction, the loop 2 terminal adenine residue and two G.C pairs near the top of stem 1, revealed that the interaction was essential for efficient frameshifting. The specific requirement for a 3'-terminal A residue was lost when loop 2 was increased from 8 to 14 nt, suggesting that the loop-helix contact may be required only in those

  3. Poison Ivy, Oak, and Sumac

    Science.gov (United States)

    ... Registration General information Housing & travel Education Exhibit hall Mobile app 2019 Annual Meeting Derm Exam Prep Course ... SkinPAC State societies Scope of practice Truth in advertising NP/PA laws Action center Public and patients ...

  4. 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.

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

    DEFF Research Database (Denmark)

    Stelzer, Walter; Scharnagl, Christina; Leurs, Ulrike

    2016-01-01

    The transmembrane helix of the amyloid precursor protein is subject to proteolytic cleavages by γ-secretase at different sites resulting in Aβ peptides of different length and toxicity. A number of point mutations within this transmembrane helix alter the cleavage pattern thus enhancing production...... destabilizes amide hydrogen bonds in the hinge which connects dimerization and cleavage regions. Weaker intrahelical hydrogen bonds at the hinge may enhance helix bending and thereby affect recognition of the transmembrane substrate by the enzyme and/or presentation of its cleavage sites to the catalytic cleft....

  6. The type II collagen fragments Helix-II and CTX-II reveal different enzymatic pathways of human cartilage collagen degradation

    DEFF Research Database (Denmark)

    Charni-Ben Tabassi, N; Desmarais, S; Jensen, Anne-Christine Bay

    2008-01-01

    human recombinant cathepsins (Cats) and matrix-metalloproteases (MMPs). Next, we analyzed the spontaneous release of Helix-II and CTX-II from cartilage sections of patients with knee OA who were immediately deep frozen after joint replacement to preserve endogenous enzyme activity until assay. Cartilage....... Cat D was unable to digest intact cartilage. MMPs-1, -3, -7, -9, and -13 efficiently released CTX-II, but only small amount of Helix-II. Neither CTX-II nor Helix-II alone was able to reflect accurately the collagenolytic activity of Cats and MMPs as reflected by the release of hydroxyproline. In OA...

  7. 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.

  8. The Role of Triple Helix Actors for Agro-Tourism Development in West Sumatera

    Directory of Open Access Journals (Sweden)

    Widya Fitriana

    2017-12-01

    Full Text Available Agricultural sector as a main contributor to GDP formation in West Sumatera is required to be able to diversify its business in order to highest achieving economic and social development. One diversified agricultural business prospective to be developed is agro-tourism. The development of agro-tourism requires collaboration and synergy between academician, businessman and government as known as triple helix actors. This study is designed with aim to (i map the agro-tourism potential in west Sumatera; (ii analyze the role of each actors, so they may take action in accelerating Agro-tourism development. This research uses observation, depth interview method, literature study and focus group discussion. The result shows that agro-tourism in West Sumatra is more prominent of great natural and cultural value, small scale and lack of local facilities. It also requires relatively high level of investment relative to its return. Therefore government support is likely an essential element of agro-tourism development and the effort may be better directed toward consolidating with intellectual and business also.

  9. Triple-helix molecular switch-based aptasensors and DNA sensors.

    Science.gov (United States)

    Bagheri, Elnaz; Abnous, Khalil; Alibolandi, Mona; Ramezani, Mohammad; Taghdisi, Seyed Mohammad

    2018-07-15

    Utilization of traditional analytical techniques is limited because they are generally time-consuming and require high consumption of reagents, complicated sample preparation and expensive equipment. Therefore, it is of great interest to achieve sensitive, rapid and simple detection methods. It is believed that nucleic acids assays, especially aptamers, are very important in modern life sciences for target detection and biological analysis. Aptamers and DNA-based sensors have been widely used for the design of various sensors owing to their unique features. In recent years, triple-helix molecular switch (THMS)-based aptasensors and DNA sensors have been broadly utilized for the detection and analysis of different targets. The THMS relies on the formation of DNA triplex via Watson-Crick and Hoogsteen base pairings under optimal conditions. This review focuses on recent progresses in the development and applications of electrochemical, colorimetric, fluorescence and SERS aptasensors and DNA sensors, which are based on THMS. Also, the advantages and drawbacks of these methods are discussed. Copyright © 2018 Elsevier B.V. All rights reserved.

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

    Directory of Open Access Journals (Sweden)

    Bruno Bonnemain

    2005-01-01

    Full Text Available The land helix, or snail, has been used in medicine since antiquity and prepared according to several formulations. This historical report traces the understanding of their properties from the time of Hippocrates, who proposed the use of snail mucus against protoccle and Pliny who thought that the snail increased the speed of delivery and was “a sovereign remedy to treat pain related to burns, abscesses and other wounds”, Galien recommended snails against hydrops foetails. In the 18th century, various snail “preparations” were also recommended for external use with dermatological disorders and internally for symptoms associated with tuberculosis and nephritis. Surprisingly, the 19th century saw a renewed interest in the pharmaceutical and medical use of snails with numerous indications for snail preparations. This interest in snails did not stop at the end of the 19th century. The 1945 edition of Dorvault devotes an entire paragraph to snails, indicating that the therapeutic usage of snails was still alive at that time. Recently the FDA has also shown an interest in snails. Ziconotide (SNXIII, a synthetic peptide coming from snail venom, has been under FDA review since 1999. Pre-clinical and clinical studies of this new drug are promising.

  11. 4-twist helix snake to maintain polarization in multi-GeV proton rings

    Directory of Open Access Journals (Sweden)

    F. Antoulinakis

    2017-09-01

    Full Text Available Solenoid Siberian snakes have successfully maintained polarization in particle rings below 1 GeV, but never in multi-GeV rings, because the spin rotation by a solenoid is inversely proportional to the beam momentum. High energy rings, such as Brookhaven’s 255 GeV Relativistic Heavy Ion Collider (RHIC, use only odd multiples of pairs of transverse B-field Siberian snakes directly opposite each other. When it became impractical to use a pair of Siberian Snakes in Fermilab’s 120  GeV/c Main Injector, we searched for a new type of single Siberian snake that could overcome all depolarizing resonances in the 8.9–120  GeV/c range. We found that a snake made of one 4-twist helix and 2 dipoles could maintain the polarization. This snake design could solve the long-standing problem of significant polarization loss during acceleration of polarized protons from a few GeV to tens of GeV, such as in the AGS, before injecting them into multi-hundred GeV rings, such as RHIC.

  12. 4-twist helix snake to maintain polarization in multi-GeV proton rings

    Science.gov (United States)

    Antoulinakis, F.; Chen, Y.; Dutton, A.; Rossi De La Fuente, E.; Haupert, S.; Ljungman, E. A.; Myers, P. D.; Thompson, J. K.; Tai, A.; Aidala, C. A.; Courant, E. D.; Krisch, A. D.; Leonova, M. A.; Lorenzon, W.; Raymond, R. S.; Sivers, D. W.; Wong, V. K.; Yang, T.; Derbenev, Y. S.; Morozov, V. S.; Kondratenko, A. M.

    2017-09-01

    Solenoid Siberian snakes have successfully maintained polarization in particle rings below 1 GeV, but never in multi-GeV rings, because the spin rotation by a solenoid is inversely proportional to the beam momentum. High energy rings, such as Brookhaven's 255 GeV Relativistic Heavy Ion Collider (RHIC), use only odd multiples of pairs of transverse B-field Siberian snakes directly opposite each other. When it became impractical to use a pair of Siberian Snakes in Fermilab's 120 GeV /c Main Injector, we searched for a new type of single Siberian snake that could overcome all depolarizing resonances in the 8.9 - 120 GeV /c range. We found that a snake made of one 4-twist helix and 2 dipoles could maintain the polarization. This snake design could solve the long-standing problem of significant polarization loss during acceleration of polarized protons from a few GeV to tens of GeV, such as in the AGS, before injecting them into multi-hundred GeV rings, such as RHIC.

  13. 4-twist helix snake to maintain polarization in multi-GeV proton rings

    International Nuclear Information System (INIS)

    Antoulinakis, F.; Chen, Y.; Dutton, A.; Rossi De La Fuente, E.; Haupert, S.

    2017-01-01

    Solenoid Siberian snakes have successfully maintained polarization in particle rings below 1 GeV, but never in multi-GeV rings, because the spin rotation by a solenoid is inversely proportional to the beam momentum. High energy rings, such as Brookhaven’s 255 GeV Relativistic Heavy Ion Collider (RHIC), use only odd multiples of pairs of transverse B-field Siberian snakes directly opposite each other. When it became impractical to use a pair of Siberian Snakes in Fermilab’s 120 GeV/c Main Injector, we searched for a new type of single Siberian snake that could overcome all depolarizing resonances in the 8.9–120 GeV/c range. We found that a snake made of one 4-twist helix and 2 dipoles could maintain the polarization. Here, this snake design could solve the long-standing problem of significant polarization loss during acceleration of polarized protons from a few GeV to tens of GeV, such as in the AGS, before injecting them into multi-hundred GeV rings, such as RHIC.

  14. Mirror symmetry breaking of silicon polymers--from weak bosons to artificial helix.

    Science.gov (United States)

    Fujiki, Michiya

    2009-01-01

    From elemental particles to human beings, matter and living worlds in our universe are dissymmetric with respect to mirror symmetry. Since the early 19th century, the origin of biomolecular handedness has been puzzling scientists. Nature's elegant bottom-up preference, however, sheds light on new concepts of generating, amplifying, and switching artificial polymers, supramolecules, liquid crystals, and organic crystals that can exhibit ambidextrous circular dichroism in the UV/Visible region with efficiency in production under milder ambient conditions. In the 1920s, Kipping, who first synthesized polysilanes with phenyl groups, had much interest in the handedness of inorganic and organic substances from 1898 to 1909 in his early research life. Polysilanes--which are soluble Si-Si bonded chain-like near-UV chromophores that carry a rich variety of organic groups--may become a bridge between animate and inanimate polymer systems. The present account focuses on several mirror symmetry breaking phenomena exemplified in polysilanes carrying chiral and/or achiral side groups, which are in isotropic dilute solution, as polymer particles dispersed in solution, and in a double layer film immobilized at the solid surface, and subtle differences in the helix, by dictating ultimately ultraweak chiral forces at subatomic, atomic, and molecular levels. Copyright 2009 The Japan Chemical Journal Forum and Wiley Periodicals, Inc.

  15. Diverse functions of myosin VI elucidated by an isoform-specific α-helix domain.

    Science.gov (United States)

    Wollscheid, Hans-Peter; Biancospino, Matteo; He, Fahu; Magistrati, Elisa; Molteni, Erika; Lupia, Michela; Soffientini, Paolo; Rottner, Klemens; Cavallaro, Ugo; Pozzoli, Uberto; Mapelli, Marina; Walters, Kylie J; Polo, Simona

    2016-04-01

    Myosin VI functions in endocytosis and cell motility. Alternative splicing of myosin VI mRNA generates two distinct isoform types, myosin VI(short) and myosin VI(long), which differ in the C-terminal region. Their physiological and pathological roles remain unknown. Here we identified an isoform-specific regulatory helix, named the α2-linker, that defines specific conformations and hence determines the target selectivity of human myosin VI. The presence of the α2-linker structurally defines a new clathrin-binding domain that is unique to myosin VI(long) and masks the known RRL interaction motif. This finding is relevant to ovarian cancer, in which alternative myosin VI splicing is aberrantly regulated, and exon skipping dictates cell addiction to myosin VI(short) in tumor-cell migration. The RRL interactor optineurin contributes to this process by selectively binding myosin VI(short). Thus, the α2-linker acts like a molecular switch that assigns myosin VI to distinct endocytic (myosin VI(long)) or migratory (myosin VI(short)) functional roles.

  16. 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.

  17. 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.

  18. Physics and application of persistent spin helix state in semiconductor heterostructures

    Science.gov (United States)

    Kohda, Makoto; Salis, Gian

    2017-07-01

    In order to utilize the spin degree of freedom in semiconductors, control of spin states and transfer of the spin information are fundamental requirements for future spintronic devices and quantum computing. Spin orbit (SO) interaction generates an effective magnetic field for moving electrons and enables spin generation, spin manipulation and spin detection without using external magnetic field and magnetic materials. However, spin relaxation also takes place due to a momentum dependent SO-induced effective magnetic field. As a result, SO interaction is considered to be a double-edged sword facilitating spin control but preventing spin transport over long distances. The persistent spin helix (PSH) state solves this problem since uniaxial alignment of the SO field with SU(2) symmetry enables the suppression of spin relaxation while spin precession can still be controlled. Consequently, understanding the PSH becomes an important step towards future spintronic technologies for classical and quantum applications. Here, we review recent progress of PSH in semiconductor heterostructures and its device application. Fundamental physics of SO interaction and the conditions of a PSH state in semiconductor heterostructures are discussed. We introduce experimental techniques to observe a PSH and explain both optical and electrical measurements for detecting a long spin relaxation time and the formation of a helical spin texture. After emphasizing the bulk Dresselhaus SO coefficient γ, the application of PSH states for spin transistors and logic circuits are discussed.

  19. Theoretical study for volume changes associated with the helix-coil transition of peptides.

    Science.gov (United States)

    Imai, T; Harano, Y; Kovalenko, A; Hirata, F

    2001-12-01

    We calculate the partial molar volumes and their changes associated with the coil(extended)-to-helix transition of two types of peptide, glycine-oligomer and glutamic acid-oligomer, in aqueous solutions by using the Kirkwood-Buff solution theory coupled with the three-dimensional reference interaction site model (3D-RISM) theory. The volume changes associated with the transition are small and positive. The volume is analyzed by decomposing it into five contributions following the procedure proposed by Chalikian and Breslauer: the ideal volume, the van der Waals volume, the void volume, the thermal volume, and the interaction volume. The ideal volumes and the van der Waals volumes do not change appreciably upon the transition. In the both cases of glycine-peptide and glutamic acid-peptide, the changes in the void volumes are positive, while those in the thermal volumes are negative, and tend to balance those in the void volumes. The change in the interaction volume of glycine-peptide does not significantly contribute, while that of glutamic acid-peptide makes a negative contribution. Copyright 2001 John Wiley & Sons, Inc. Biopolymers 59: 512-519, 2001

  20. Role of collagen triple helix repeat containing-1 in tumor and inflammatory diseases

    Directory of Open Access Journals (Sweden)

    Qian Wu

    2017-01-01

    Full Text Available Initially, collagen triple helix repeat containing-1 (CTHRC1 is expressed mainly in adventitial fibroblasts and neointimal smooth muscle cells of balloon-injured vessels, and increases cell migration, promotes tissue repair in response to injury. A variety of studies demonstrated that over-expression of CTHRC1 in solid tumors results in enhancement of migration and invasion of tumor cells, and is associated with decreased overall survival and disease-free survival. CTHRC1 expression is elevated in hepatitis B virus-infected patients and highly correlated with hepatocellular carcinoma progression as well. Furthermore, CTHRC1 plays a pivotal role in a great many fields, including increases bone mass, prevents myelination, reverses collagen synthesis in keloid fibroblasts, and increases fibroblast-like synoviocytes migration speed and abundant production of arthritic pannus in rheumatoid arthritis. Therefore, it will provide new insight into the pathogenesis of tumor and autoimmune diseases, and will shed new light on the therapy of related clinical diseases.

  1. Antiproliferation effects of an androgen receptor triple-helix forming oligonucleotide on prostate cancer cells

    International Nuclear Information System (INIS)

    Zhang Yong; Chen Weizhen; Xie Yao; Gao Jinhui

    2005-01-01

    Objective: To provide experimental basis for antigene radiation therapy through exploring the effects of antigene strategy on androgen receptor (AR) expression and proliferation of prostate cancer cells. Methods: The triple-helix forming oligonucleotide (TFO) targeting 2447-2461nt of AR cDNA was designed and transfected LNCaP prostate cancer cells with liposome. 24-72 h after transfection, the cellular proliferation was detected by 3 H-thymidine (TdR) incorporation test, the expression of AR gene was examined by reverse transcription-polymerase chain reaction (RT-PCR) and expression of AR protein was performed by radioligand binding assay. The results of TFO were compared with antisense oligonucleotide (ASON). Results: At all time points, the AR expression levels in TFO group were markedly lower than that of ASON group (P<0.05). The inhibitory rate of TFO for cellular proliferation was significantly higher than that of ASON (P<0.05). Conclusion: The TFO was a potent inhibitor for AR expression and cell proliferation of LNCaP cells , and could be used in antigene radiotherapy. (authors)

  2. Probing α-3(10) transitions in a voltage-sensing S4 helix.

    Science.gov (United States)

    Kubota, Tomoya; Lacroix, Jérôme J; Bezanilla, Francisco; Correa, Ana M

    2014-09-02

    The S4 helix of voltage sensor domains (VSDs) transfers its gating charges across the membrane electrical field in response to changes of the membrane potential. Recent studies suggest that this process may occur via the helical conversion of the entire S4 between α and 310 conformations. Here, using LRET and FRET, we tested this hypothesis by measuring dynamic changes in the transmembrane length of S4 from engineered VSDs expressed in Xenopus oocytes. Our results suggest that the native S4 from the Ciona intestinalis voltage-sensitive phosphatase (Ci-VSP) does not exhibit extended and long-lived 310 conformations and remains mostly α-helical. Although the S4 of NavAb displays a fully extended 310 conformation in x-ray structures, its transplantation in the Ci-VSP VSD scaffold yielded similar results as the native Ci-VSP S4. Taken together, our study does not support the presence of long-lived extended α-to-310 helical conversions of the S4 in Ci-VSP associated with voltage activation. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  3. 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.

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

    Directory of Open Access Journals (Sweden)

    Nikačević N.M.

    2015-01-01

    Full Text Available Flow pattern analysis in a spiral Helix reactor is conducted, for the application in the commercial surfactant production. Step change response curves (SCR were obtained from numerical tracer experiments by three-dimensional computational fluid dynamics (CFD simulations. Non-reactive flow is simulated, though viscosity is treated as variable in the direction of flow, as it increases during the reaction. The design and operating parameters (reactor diameter, number of coils and inlet velocity are varied in CFD simulations, in order to examine the effects on the flow pattern. Given that 3D simulations are not practical for fast computations needed for optimization, scale-up and control, CFD flow model is reduced to one-dimensional axial dispersion (AD model with spatially variable dispersion coefficient. Dimensionless dispersion coefficient (Pe is estimated under different conditions and results are analyzed. Finally, correlation which relates Pe number with Reynolds number and number of coils from the reactor entrance is proposed for the particular reactor application and conditions.

  5. 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.

  6. Lipid Binding of the Amphipathic Helix Serving as Membrane Anchor of Pestivirus Glycoprotein Erns.

    Science.gov (United States)

    Aberle, Daniel; Oetter, Kay-Marcus; Meyers, Gregor

    2015-01-01

    Pestiviruses express a peculiar protein named Erns representing envelope glycoprotein and RNase, which is important for control of the innate immune response and persistent infection. The latter functions are connected with secretion of a certain amount of Erns from the infected cell. Retention/secretion of Erns is most likely controlled by its unusual membrane anchor, a long amphipathic helix attached in plane to the membrane. Here we present results of experiments conducted with a lipid vesicle sedimentation assay able to separate lipid-bound from unbound protein dissolved in the water phase. Using this technique we show that a protein composed of tag sequences and the carboxyterminal 65 residues of Erns binds specifically to membrane vesicles with a clear preference for compositions containing negatively charged lipids. Mutations disturbing the helical folding and/or amphipathic character of the anchor as well as diverse truncations and exchange of amino acids important for intracellular retention of Erns had no or only small effects on the proteins membrane binding. This result contrasts the dramatically increased secretion rates observed for Erns proteins with equivalent mutations within cells. Accordingly, the ratio of secreted versus cell retained Erns is not determined by the lipid affinity of the membrane anchor.

  7. Lipid Binding of the Amphipathic Helix Serving as Membrane Anchor of Pestivirus Glycoprotein Erns.

    Directory of Open Access Journals (Sweden)

    Daniel Aberle

    Full Text Available Pestiviruses express a peculiar protein named Erns representing envelope glycoprotein and RNase, which is important for control of the innate immune response and persistent infection. The latter functions are connected with secretion of a certain amount of Erns from the infected cell. Retention/secretion of Erns is most likely controlled by its unusual membrane anchor, a long amphipathic helix attached in plane to the membrane. Here we present results of experiments conducted with a lipid vesicle sedimentation assay able to separate lipid-bound from unbound protein dissolved in the water phase. Using this technique we show that a protein composed of tag sequences and the carboxyterminal 65 residues of Erns binds specifically to membrane vesicles with a clear preference for compositions containing negatively charged lipids. Mutations disturbing the helical folding and/or amphipathic character of the anchor as well as diverse truncations and exchange of amino acids important for intracellular retention of Erns had no or only small effects on the proteins membrane binding. This result contrasts the dramatically increased secretion rates observed for Erns proteins with equivalent mutations within cells. Accordingly, the ratio of secreted versus cell retained Erns is not determined by the lipid affinity of the membrane anchor.

  8. 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.

  9. Coherent helix vacancy phonon and its ultrafast dynamics waning in topological Dirac semimetal C d3A s2

    Science.gov (United States)

    Sun, Fei; Wu, Q.; Wu, Y. L.; Zhao, H.; Yi, C. J.; Tian, Y. C.; Liu, H. W.; Shi, Y. G.; Ding, H.; Dai, X.; Richard, P.; Zhao, Jimin

    2017-06-01

    We report an ultrafast lattice dynamics investigation of the topological Dirac semimetal C d3A s2 . A coherent phonon beating among three evenly spaced A1 g optical phonon modes (of frequencies 1.80, 1.96, and 2.11 THz, respectively) is unambiguously observed. The two side modes originate from the counter helixes composing Cd vacancies. Significantly, such helix vacancy-induced phonon (HVP) modes experience prominent extra waning in their ultrafast dynamics as temperature increases, which is immune to the central mode. Above 200 K, the HVP becomes inactive, which may potentially affect the topological properties. Our results in the lattice degree of freedom suggest the indispensable role of temperature in considering topological properties of such quantum materials.

  10. Evaluation of a Pilot Surveillance System: Health and Environment Linked for Information Exchange in Atlanta (HELIX-Atlanta)

    Science.gov (United States)

    Meyer, P.; Shire, J.; Qualters, Judy; Daley, Randolph; Fiero, Leslie Todorov; Autry, Andy; Avchen, Rachel; Stock, Allison; Correa, Adolofo; Siffel, Csaba; hide

    2007-01-01

    CDC and its partners established the Health and Environment Linked for Information Exchange, Atlanta (HELIX-Atlanta) demonstration project, to develop linking and analysis methods that could be used by the National Environmental Public Health Tracking (EPHT) Network. Initiated in October 2003, the Metropolitan Atlanta-based collaborative conducted four projects: asthma and particulate air pollution, birth defects and ozone and particulate air pollution, childhood leukemia and traffic emissions, and children's blood lead testing and neighborhood risk factors for lead poisoning. This report provides an overview of the HELIX-Atlanta projects' goals, methods and outcomes. We discuss priority attributes and common issues and challenges and offer recommendations for implementation of the nascent national environmental public health tracking network.

  11. 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.

  12. On the mechanism of irradiation effect on the function of Helix pomatia neuron Na+, K+-pump

    International Nuclear Information System (INIS)

    Ajrapetyan, S.N.; Egorova, E.G.; Sagiyan, A.A.; Dadalyan, S.S.; Dvoretskij, A.I.; Sulejmonyan, M.A.

    1987-01-01

    Mechanism of irradiation effect on passive permeability, Na + /Ca 2+ exchange, Na + , K + -pump function intensity, the number of membrane functionally active pump units (Na + , K + -ATP-ase molecules) was determined using Helix pomatia and nervous ganglions isolated from them and irradiated by 5.16 Kl/kg dose. The data obtained show that ionizing radiation leads to obvious destructions in the mechanisms of neuron Na + , K + -pump functioning

  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. © 2014 Wiley Periodicals, Inc.

  14. Modulating immunogenic properties of HIV-1 gp41 membrane-proximal external region by destabilizing six-helix bundle structure

    Energy Technology Data Exchange (ETDEWEB)

    Banerjee, Saikat; Shi, Heliang; Habte, Habtom H.; Qin, Yali; Cho, Michael W., E-mail: mcho@iastate.edu

    2016-03-15

    The C-terminal alpha-helix of gp41 membrane-proximal external region (MPER; {sup 671}NWFDITNWLWYIK{sup 683}) encompassing 4E10/10E8 epitopes is an attractive target for HIV-1 vaccine development. We previously reported that gp41-HR1-54Q, a trimeric protein comprised of the MPER in the context of a stable six-helix bundle (6HB), induced strong immune responses against the helix, but antibodies were directed primarily against the non-neutralizing face of the helix. To better target 4E10/10E8 epitopes, we generated four putative fusion intermediates by introducing double point mutations or deletions in the heptad repeat region 1 (HR1) that destabilize 6HB in varying degrees. One variant, HR1-∆10-54K, elicited antibodies in rabbits that targeted W672, I675 and L679, which are critical for 4E10/10E8 recognition. Overall, the results demonstrated that altering structural parameters of 6HB can influence immunogenic properties of the MPER and antibody targeting. Further exploration of this strategy could allow development of immunogens that could lead to induction of 4E10/10E8-like antibodies. - Highlights: • Four gp41 MPER-based immunogens that resemble fusion intermediates were generated. • C-terminal region of MPER that contains 4E10/10E8 epitopes was highly immunogenic. • Altering 6HB structure can influence immunogenic properties of the MPER. • Induced antibodies targeted multiple residues critical for 4E10/10E8 binding. • Development of immunogens based on fusion intermediates is a promising strategy.

  15. A Speculation into the Origin of Neutral Globules In Planetary Nebulae: Could the Helix's Comets Really Be Comets?

    OpenAIRE

    Gussie, Grant

    1995-01-01

    A novel explanation for the origin of the cometary globules within NGC 7293 (the "Helix" planetary nebula) is examined; that these globules originate as massive cometary bodies at large astrocentric radii. The mass of such hypothetical cometary bodies would have to be several orders of magnitude larger than any such bodies observed in our solar system in order to supply the observed mass of neutral gas. It is however shown that comets at "outer Oort cloud" like distances are likely to survive...

  16. Crystallization and preliminary electron diffraction study to 3. 7 A of DNA helix-destabilizing protein gp32*I

    Energy Technology Data Exchange (ETDEWEB)

    Chiu, W; Hosoda, J

    1978-01-01

    A two-dimensionally large and thin crystal has been obtained from gp32*I, a proteolytically digested product of a DNA helix-destabilizing protein coded by gene 32 in bacteriophage T4. High-resolution electron diffraction patterns (approx. 3.7 A) are recorded from both unstained and stained protein crystals embedded in glucose. The crystal is of orthorhombic space group with a = 62.9 A and b = 47.3 A.

  17. Effect of ionizing radiation on the functional status of Helix pomatia neurons. Glucose metabolism and atp level

    International Nuclear Information System (INIS)

    Dvoretskij, A.I.; Egorova, E.G.; Shainskaya, A.M.; Stepchenko, L.N.; Ajrapetyan, S.N.; AN Armyanskoj SSR, Erevan. Inst. Ehksperimental'noj Biologii)

    1988-01-01

    The ATP level in nerve ganglia of Helix pomatia was shown to decrease 15 and 30 min, and 1 and 3 h following irradiation (5.16 C/kg). The decrease was maximum in 60 min. The absorption and utilization of glucose via a pentose-phosphate route and in the Kerbs cycle did not substantially change. It is concluded that the energy supply of nerve cells under study is not responsible for the decrease in the ATP level

  18. Glass-like dynamics of the strain-induced coil/helix transition on a permanent polymer network.

    Science.gov (United States)

    Ronsin, O; Caroli, C; Baumberger, T

    2016-02-14

    We study the stress response to a step strain of covalently bonded gelatin gels in the temperature range where triple helix reversible crosslink formation is prohibited. We observe slow stress relaxation towards a T-dependent finite asymptotic level. We show that this is assignable to the strain-induced coil → helix transition, previously evidenced by Courty et al. [Proc. Natl. Acad. Sci. U. S. A. 102, 13457 (2005)], of a fraction of the polymer strands. Relaxation proceeds, in a first stage, according to a stretched exponential dynamics, then crosses over to a terminal simple exponential decay. The respective characteristic times τK and τf exhibit an Arrhenius-like T-dependence with an associated energy E incompatibly larger than the activation barrier height for the isomerisation process which sets the clock for an elementary coil → helix transformation event. We tentatively assign this glass-like slowing down of the dynamics to the long-range couplings due to the mechanical noise generated by the local elementary events in this random elastic medium.

  19. 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.

  20. Evidence for a central role of PrP helix 2 in the nucleation of amyloid fibrils.

    Science.gov (United States)

    Honda, Ryo; Kuwata, Kazuo

    2018-02-01

    Amyloid fibrils are filamentous protein aggregates associated with the pathogenesis of a wide variety of human diseases. The formation of such aggregates typically follows nucleation-dependent kinetics, wherein the assembly and structural conversion of amyloidogenic proteins into oligomeric aggregates (nuclei) is the rate-limiting step of the overall reaction. In this study, we sought to gain structural insights into the oligomeric nuclei of the human prion protein (PrP) by preparing a series of deletion mutants lacking 14-44 of the C-terminal 107 residues of PrP and examined the kinetics and thermodynamics of these mutants in amyloid formation. An analysis of the experimental data using the concepts of the Φ-value analysis indicated that the helix 2 region (residues 168-196) acquires an amyloid-like β-sheet during nucleation, whereas the other regions preserves a relatively disordered structure in the nuclei. This finding suggests that the helix 2 region serves as the nucleation site for the assembly of amyloid fibrils.-Honda, R., Kuwata, K. Evidence for a central role of PrP helix 2 in the nucleation of amyloid fibrils.

  1. The N-terminal amphipathic helix of the topological specificity factor MinE is associated with shaping membrane curvature.

    Directory of Open Access Journals (Sweden)

    Yu-Ling Shih

    Full Text Available Pole-to-pole oscillations of the Min proteins in Escherichia coli are required for the proper placement of the division septum. Direct interaction of MinE with the cell membrane is critical for the dynamic behavior of the Min system. In vitro, this MinE-membrane interaction led to membrane deformation; however, the underlying mechanism remained unclear. Here we report that MinE-induced membrane deformation involves the formation of an amphipathic helix of MinE(2-9, which, together with the adjacent basic residues, function as membrane anchors. Biochemical evidence suggested that the membrane association induces formation of the helix, with the helical face, consisting of A2, L3, and F6, inserted into the membrane. Insertion of this helix into the cell membrane can influence local membrane curvature and lead to drastic changes in membrane topology. Accordingly, MinE showed characteristic features of protein-induced membrane tubulation and lipid clustering in in vitro reconstituted systems. In conclusion, MinE shares common protein signatures with a group of membrane trafficking proteins in eukaryotic cells. These MinE signatures appear to affect membrane curvature.

  2. BAROMETRIC PRESSURE and Other Data from ALPHA HELIX From Prince William Sound (Gulf of Alaska) from 1989-05-05 to 1989-05-11 (NODC Accession 8900192)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The University of Alaska, Institute of Marine Science is responsible for this data collected aboard the R/V Alpha Helix on cruise number HX123 between May 5, 1989 to...

  3. Chemical and depth data from the ALPHA HELIX using bottle casts in the Bering Sea from 1987-09-07 to 1988-06-11 (NODC Accession 0000263)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Chemical and depth data were collected from the ALPHA HELIX from September 7, 1987 to June 11, 1988. Data were submitted by the University of Alaska - Fairbanks;...

  4. Cloud amount/frequency, NITRATE and other data from ALPHA HELIX in the Chukchi Sea from 1992-09-21 to 1992-10-04 (NODC Accession 9300097)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Conductivity, Temperature and Depth (CTD) and other data were collected in Chukchi Sea. Data was collected from Ship ALPHA HELIX. The data was collected over a...

  5. Temperature and salinity profiles from CTD casts from ALPHA HELIX from NE Pacific (limit-180) from 09 February 1991 to 25 February 1991 (NODC Accession 9100097)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CTD data was collected from the R/V ALPHA HELIX from the NE Pacific (limit-180). Data were collected by the University of Alaska - Fairbanks; Institute of Marine...

  6. Nutrients data collected from the ALPHA HELIX from the coastal waters of Alaska from 03 March 1998 to 07 December 1999 (NODC Accession 0000637)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Nutrients data were collected from bottle casts from the ALPHA HELIX in the coastal waters of Alaska from 08 March 1998 to 07 December 1999. Data include...

  7. Cloud amount/frequency, NITRATE and other data from ALPHA HELIX in the Bering Sea from 1993-06-12 to 1993-07-01 (NODC Accession 9400026)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Conductivity, Temperature and Depth (CTD) and other data were collected in Bering Sea. Data was collected from Ship ALPHA HELIX cruise HX 171. The data was...

  8. BAROMETRIC PRESSURE and Other Data from ALPHA HELIX From North Pacific Ocean and Others from 19931016 to 19931103 (NODC Accession 9400051)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Conductivity, Temperature and Depth (CTD) and other data were collected in Bering Sea and North Pacific Ocean. Data was collected from Ship ALPHA HELIX cruise...

  9. Oceanographic profile Biomass, temperature salinity and other measurements collected using bottle from Alpha Helix in the Pacific Ocean from 1976 (NODC Accession 0002070)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Temperature profile, nutrients, and meteorological data were collected using bottle casts from the ALPHA HELIX in the Pacific Ocean. Data were collected from 06...

  10. BuD, a helix–loop–helix DNA-binding domain for genome modification

    Energy Technology Data Exchange (ETDEWEB)

    Stella, Stefano [Spanish National Cancer Research Centre (CNIO), Calle de Melchor Fernández Almagro 3, 28029 Madrid (Spain); University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen (Denmark); Molina, Rafael; López-Méndez, Blanca [Spanish National Cancer Research Centre (CNIO), Calle de Melchor Fernández Almagro 3, 28029 Madrid (Spain); Juillerat, Alexandre; Bertonati, Claudia; Daboussi, Fayza [Cellectis, 8 Rue de la Croix Jarry, 75013 Paris (France); Campos-Olivas, Ramon [Spanish National Cancer Research Centre (CNIO), Calle de Melchor Fernández Almagro 3, 28029 Madrid (Spain); Duchateau, Phillippe [Cellectis, 8 Rue de la Croix Jarry, 75013 Paris (France); Montoya, Guillermo, E-mail: guillermo.montoya@cpr.ku.dk [Spanish National Cancer Research Centre (CNIO), Calle de Melchor Fernández Almagro 3, 28029 Madrid (Spain); University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen (Denmark)

    2014-07-01

    Crystal structures of BurrH and the BurrH–DNA complex are reported. DNA editing offers new possibilities in synthetic biology and biomedicine for modulation or modification of cellular functions to organisms. However, inaccuracy in this process may lead to genome damage. To address this important problem, a strategy allowing specific gene modification has been achieved through the addition, removal or exchange of DNA sequences using customized proteins and the endogenous DNA-repair machinery. Therefore, the engineering of specific protein–DNA interactions in protein scaffolds is key to providing ‘toolkits’ for precise genome modification or regulation of gene expression. In a search for putative DNA-binding domains, BurrH, a protein that recognizes a 19 bp DNA target, was identified. Here, its apo and DNA-bound crystal structures are reported, revealing a central region containing 19 repeats of a helix–loop–helix modular domain (BurrH domain; BuD), which identifies the DNA target by a single residue-to-nucleotide code, thus facilitating its redesign for gene targeting. New DNA-binding specificities have been engineered in this template, showing that BuD-derived nucleases (BuDNs) induce high levels of gene targeting in a locus of the human haemoglobin β (HBB) gene close to mutations responsible for sickle-cell anaemia. Hence, the unique combination of high efficiency and specificity of the BuD arrays can push forward diverse genome-modification approaches for cell or organism redesign, opening new avenues for gene editing.

  11. Computational study of elements of stability of a four-helix bundle protein biosurfactant

    Science.gov (United States)

    Schaller, Andrea; Connors, Natalie K.; Dwyer, Mirjana Dimitrijev; Oelmeier, Stefan A.; Hubbuch, Jürgen; Middelberg, Anton P. J.

    2015-01-01

    Biosurfactants are surface-active molecules produced principally by microorganisms. They are a sustainable alternative to chemically-synthesized surfactants, having the advantages of being non-toxic, highly functional, eco-friendly and biodegradable. However they are currently only used in a few industrial products due to costs associated with production and purification, which exceed those for commodity chemical surfactants. DAMP4, a member of a four-helix bundle biosurfactant protein family, can be produced in soluble form and at high yield in Escherichia coli, and can be recovered using a facile thermal phase-separation approach. As such, it encompasses an interesting synergy of biomolecular and chemical engineering with prospects for low-cost production even for industrial sectors. DAMP4 is highly functional, and due to its extraordinary thermal stability it can be purified in a simple two-step process, in which the combination of high temperature and salt leads to denaturation of all contaminants, whereas DAMP4 stays stable in solution and can be recovered by filtration. This study aimed to characterize and understand the fundamental drivers of DAMP4 stability to guide further process and surfactant design studies. The complementary use of experiments and molecular dynamics simulation revealed a broad pH and temperature tolerance for DAMP4, with a melting point of 122.4 °C, suggesting the hydrophobic core as the major contributor to thermal stability. Simulation of systematically created in silico variants of DAMP4 showed an influence of number and location of hydrophilic mutations in the hydrophobic core on stability, demonstrating a tolerance of up to three mutations before a strong loss in stability occurred. The results suggest a consideration of a balance of stability, functionality and kinetics for new designs according to their application, aiming for maximal functionality but at adequate stability to allow for cost-efficient production using thermal

  12. Structure, stability, and thermodynamics of a short intermolecular purine-purine-pyrimidine triple helix

    International Nuclear Information System (INIS)

    Pilch, D.S.; Shafer, R.H.; Levenson, C.

    1991-01-01

    The authors have investigated the structure and physical chemistry of the d(C 3 T 4 C 3 )·2[d(G 3 A 4 G 3 )] triple helix by polyacrylamide gel electrophoresis (PAGE), 1 H NMR, and ultraviolet (UV) absorption spectroscopy. The triplex was stabilized with MgCl 2 at neutral pH. PAGE studies verify the stoichiometry of the strands comprising the triplex and indicate that the orientation of the third strand in purine-purine-pyrimidine (pur-pur-pyr) triplexes is antiparallel with respect to the purine strand of the underlying duplex. Imino proton NMR spectra provide evidence for the existence of new purine-purine (pur·pur) hydrogen bonds, in addition to those of the Watson-Crick (W-C) base pairs, in the triplex structure. These new hydrogen bonds are likely to correspond to the interaction between third-strand guanine NH1 imino protons and the N7 atoms of guanine residues on the puring strand of the underlying duplex. Thermal denaturation of the triplex proceeds to single strands in one step, under the conditions used in this study. Binding of the third strand appears to enhance the thermal stability of the duplex by 1-3 C, depending on the DNA concentration. This marked enhancement in stability, coupled with the lack of an acidic pH requirement, suggests that pur-pur-pyr triplexes are appealing choices for use in applications involving oligonucleotide targeting of duplex DNA in vitro and in vivo

  13. Mapping the active site helix-to-strand conversion of CxxxxC peroxiredoxin Q enzymes.

    Science.gov (United States)

    Perkins, Arden; Gretes, Michael C; Nelson, Kimberly J; Poole, Leslie B; Karplus, P Andrew

    2012-09-25

    Peroxiredoxins (Prx) make up a family of enzymes that reduce peroxides using a peroxidatic cysteine residue; among these, members of the PrxQ subfamily are proposed to be the most ancestral-like yet are among the least characterized. In many PrxQ enzymes, a second "resolving" cysteine is located five residues downstream from the peroxidatic Cys, and these residues form a disulfide during the catalytic cycle. Here, we describe three hyperthermophilic PrxQ crystal structures originally determined by the RIKEN structural genomics group. We reprocessed the diffraction data and conducted further refinement to yield models with R(free) values lowered by 2.3-7.2% and resolution extended by 0.2-0.3 Å, making one, at 1.4 Å, one of the best resolved peroxiredoxins to date. Comparisons of two matched thiol and disulfide forms reveal that the active site conformational change required for disulfide formation involves a transition of ~20 residues from a pair of α-helices to a β-hairpin and 3(10)-helix. Each conformation has ~10 residues with a high level of disorder providing slack that allows the dramatic shift, and the two conformations are anchored to the protein core by distinct nonpolar side chains that fill three hydrophobic pockets. Sequence conservation patterns confirm the importance of these and a few additional residues for function. From a broader perspective, this study raises the provocative question of how to make use of the valuable information in the Protein Data Bank generated by structural genomics projects but not described in the literature, perhaps remaining unrecognized and certainly underutilized.

  14. Pore helix domain is critical to camphor sensitivity of transient receptor potential vanilloid 1 channel.

    Science.gov (United States)

    Marsakova, Lenka; Touska, Filip; Krusek, Jan; Vlachova, Viktorie

    2012-04-01

    The recent discovery that camphor activates and strongly desensitizes the capsaicin-sensitive and noxious heat-sensitive channel transient receptor potential vanilloid subfamily member 1 (TRPV1) has provided new insights and opened up new research paths toward understanding why this naturally occurring monoterpene is widely used in human medicine for its local counter-irritant, antipruritic, and anesthetic properties. However, the molecular basis for camphor sensitivity remains mostly unknown. The authors attempt to explore the nature of the activation pathways evoked by camphor and narrow down a putative interaction site at TRPV1. The authors transiently expressed wild-type or specifically mutated recombinant TRPV1 channels in human embryonic kidney cells HEK293T and recorded cation currents with the whole cell, patch clamp technique. To monitor changes in the spatial distribution of phosphatidylinositol 4,5-bisphosphate, they used fluorescence resonance energy transfer measurements from cells transfected with the fluorescent protein-tagged pleckstrin homology domains of phospholipase C. The results revealed that camphor modulates TRPV1 channel through the outer pore helix domain by affecting its overall gating equilibrium. In addition, camphor, which generally is known to decrease the fluidity of cell plasma membranes, may also regulate the activity of TRPV1 by inducing changes in the spatial distribution of phosphatidylinositol-4,5-bisphosphate on the inner leaflet of the plasma membrane. The findings of this study provide novel insights into the structural basis for the modulation of TRPV1 channel by camphor and may provide an explanation for the mechanism by which camphor modulates thermal sensation in vivo.

  15. Collagen triple helix repeat containing 1 is a new promigratory marker of arthritic pannus.

    Science.gov (United States)

    Shekhani, Mohammed Talha; Forde, Toni S; Adilbayeva, Altynai; Ramez, Mohamed; Myngbay, Askhat; Bexeitov, Yergali; Lindner, Volkhard; Adarichev, Vyacheslav A

    2016-07-19

    The formation of destructive hypercellular pannus is critical to joint damage in rheumatoid arthritis (RA). The collagen triple helix repeat containing 1 (CTHRC1) protein expressed by activated stromal cells of diverse origin has previously been implicated in tissue remodeling and carcinogenesis. We recently discovered that the synovial Cthrc1 mRNA directly correlates with arthritis severity in mice. This study characterizes the role of CTHRC1 in arthritic pannus formation. Synovial joints of mice with collagen antibody-induced arthritis (CAIA) and human RA-fibroblast-like synoviocytes (FLS) were immunostained for CTHRC1, FLS and macrophage-specific markers. CTHRC1 levels in plasma from patients with RA were measured using sandwich ELISA. The migratory response of fibroblasts was studied with a transwell migration assay and time-lapse microscopy. Velocity and directness of cell migration was analyzed by recording the trajectories of cells treated with rhCTHRC1. Immunohistochemical analysis of normal and inflamed synovium revealed highly inducible expression of CTHRC1 in arthritis (10.9-fold). At the tissue level, CTHRC1-expressing cells occupied the same niche as large fibroblast-like cells positive for α-smooth muscle actin (α-SMA) and cadherin 11 (CDH11). CTHRC1 was produced by activated FLS predominantly located at the synovial intimal lining and at the bone-pannus interface. Cultured RA-FLS expressed CDH11, α-SMA, and CTHRC1. Upon treatment with exogenous rhCTHRC1, embryonic fibroblasts and RA-FLS significantly increased migration velocity, directness, and cell length along the front-tail axis (1.4-fold, p pannus.

  16. Triptolide Upregulates Myocardial Forkhead Helix Transcription Factor p3 Expression and Attenuates Cardiac Hypertrophy

    Science.gov (United States)

    Ding, Yuan-Yuan; Li, Jing-Mei; Guo, Feng-Jie; Liu, Ya; Tong, Yang-Fei; Pan, Xi-Chun; Lu, Xiao-Lan; Ye, Wen; Chen, Xiao-Hong; Zhang, Hai-Gang

    2016-01-01

    The forkhead/winged helix transcription factor (Fox) p3 can regulate the expression of various genes, and it has been reported that the transfer of Foxp3-positive T cells could ameliorate cardiac hypertrophy and fibrosis. Triptolide (TP) can elevate the expression of Foxp3, but its effects on cardiac hypertrophy remain unclear. In the present study, neonatal rat ventricular myocytes (NRVM) were isolated and stimulated with angiotensin II (1 μmol/L) to induce hypertrophic response. The expression of Foxp3 in NRVM was observed by using immunofluorescence assay. Fifty mice were randomly divided into five groups and received vehicle (control), isoproterenol (Iso, 5 mg/kg, s.c.), one of three doses of TP (10, 30, or 90 μg/kg, i.p.) for 14 days, respectively. The pathological morphology changes were observed after Hematoxylin and eosin, lectin and Masson’s trichrome staining. The levels of serum brain natriuretic peptide (BNP) and troponin I were determined by enzyme-linked immunosorbent assay and chemiluminescence, respectively. The mRNA and protein expressions of α- myosin heavy chain (MHC), β-MHC and Foxp3 were determined using real-time PCR and immunohistochemistry, respectively. It was shown that TP (1, 3, 10 μg/L) treatment significantly decreased cell size, mRNA and protein expression of β-MHC, and upregulated Foxp3 expression in NRVM. TP also decreased heart weight index, left ventricular weight index and, improved myocardial injury and fibrosis; and decreased the cross-scetional area of the myocardium, serum cardiac troponin and BNP. Additionally, TP markedly reduced the mRNA and protein expression of myocardial β-MHC and elevated the mRNA and protein expression of α-MHC and Foxp3 in a dose-dependent manner. In conclusion, TP can effectively ameliorate myocardial damage and inhibit cardiac hypertrophy, which is at least partly related to the elevation of Foxp3 expression in cardiomyocytes. PMID:27965581

  17. A 'FIREWORK' OF H2 KNOTS IN THE PLANETARY NEBULA NGC 7293 (THE HELIX NEBULA)

    International Nuclear Information System (INIS)

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

    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 μm H 2 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 from the CS), the knot often show a 'tadpole' shape, an elliptical head with a bright crescent inside and a long tail opposite to the CS. In detail, there are variations in the tadpole shapes, such as narrowing tails, widening tails, meandering tails, or multipeaks within a tail. In the outer ring (4.'5-6.'4 from the CS), the shapes are more fractured, and the tails do not collimate into a single direction. The transition in knot morphology from the inner edge to the outer ring is clearly seen. The number density of knots governs the H 2 surface brightness in the inner ring: H 2 exists only within the knots. Possible mechanisms which contribute to the shaping of the knots are discussed, including photoionization and streaming motions. A plausible interpretation of our images is that inner knots are being overrun by a faster wind, but that this has not (yet) reached the outer knots. Based on H 2 formation and destruction rates, H 2 gas can survive in knots from formation during the late asymptotic giant branch phase throughout the PN phase. These observations provide new constraints on the formation and evolution of knots, and on the physics of molecular gas embedded within ionized gas.

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

    Science.gov (United States)

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

    2009-08-01

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

  19. α-helix to β-hairpin transition of human amylin monomer

    Science.gov (United States)

    Singh, Sadanand; Chiu, Chi-cheng; Reddy, Allam S.; de Pablo, Juan J.

    2013-04-01

    The human islet amylin polypeptide is produced along with insulin by pancreatic islets. Under some circumstances, amylin can aggregate to form amyloid fibrils, whose presence in pancreatic cells is a common pathological feature of Type II diabetes. A growing body of evidence indicates that small, early stage aggregates of amylin are cytotoxic. A better understanding of the early stages of the amylin aggregation process and, in particular, of the nucleation events leading to fibril growth could help identify therapeutic strategies. Recent studies have shown that, in dilute solution, human amylin can adopt an α-helical conformation, a β-hairpin conformation, or an unstructured coil conformation. While such states have comparable free energies, the β-hairpin state exhibits a large propensity towards aggregation. In this work, we present a detailed computational analysis of the folding pathways that arise between the various conformational states of human amylin in water. A free energy surface for amylin in explicit water is first constructed by resorting to advanced sampling techniques. Extensive transition path sampling simulations are then employed to identify the preferred folding mechanisms between distinct minima on that surface. Our results reveal that the α-helical conformer of amylin undergoes a transformation into the β-hairpin monomer through one of two mechanisms. In the first, misfolding begins through formation of specific contacts near the turn region, and proceeds via a zipping mechanism. In the second, misfolding occurs through an unstructured coil intermediate. The transition states for these processes are identified. Taken together, the findings presented in this work suggest that the inter-conversion of amylin between an α-helix and a β-hairpin is an activated process and could constitute the nucleation event for fibril growth.

  20. Loop-to-helix transition in the structure of multidrug regulator AcrR at the entrance of the drug-binding cavity

    Energy Technology Data Exchange (ETDEWEB)

    Manjasetty, Babu A.; Halavaty, Andrei S.; Luan, Chi-Hao; Osipiuk, Jerzy; Mulligan, Rory; Kwon, Keehwan; Anderson, Wayne F.; Joachimiak, Andrzej

    2016-04-01

    Multidrug transcription regulator AcrR from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 belongs to the tetracycline repressor family, one of the largest groups of bacterial transcription factors. The crystal structure of dimeric AcrR was determined and refined to 1.56 Å resolution. The tertiary and quaternary structures of AcrR are similar to those of its homologs. The multidrug binding site was identified based on structural alignment with homologous proteins and has a di(hydroxyethyl)ether molecule bound. Residues from helices a4 and a7 shape the entry into this binding site. The structure of AcrR reveals that the extended helical conformation of helix a4 is stabilized by the hydrogen bond between Glu67 (helix a4) and Gln130 (helix a7). Based on the structural comparison with the closest homolog structure, the Escherichia coli AcrR, we propose that this hydrogen bond is responsible for control of the loop-to-helix transition within helix a4. This local conformational switch of helix a4 may be a key step in accessing the multidrug binding site and securing ligands at the binding site. Solution smallmolecule binding studies suggest that AcrR binds ligands with their core chemical structure resembling the tetracyclic ring of cholesterol.

  1. Loop-to-helix transition in the structure of multidrug regulator AcrR at the entrance of the drug-binding cavity.

    Science.gov (United States)

    Manjasetty, Babu A; Halavaty, Andrei S; Luan, Chi-Hao; Osipiuk, Jerzy; Mulligan, Rory; Kwon, Keehwan; Anderson, Wayne F; Joachimiak, Andrzej

    2016-04-01

    Multidrug transcription regulator AcrR from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 belongs to the tetracycline repressor family, one of the largest groups of bacterial transcription factors. The crystal structure of dimeric AcrR was determined and refined to 1.56Å resolution. The tertiary and quaternary structures of AcrR are similar to those of its homologs. The multidrug binding site was identified based on structural alignment with homologous proteins and has a di(hydroxyethyl)ether molecule bound. Residues from helices α4 and α7 shape the entry into this binding site. The structure of AcrR reveals that the extended helical conformation of helix α4 is stabilized by the hydrogen bond between Glu67 (helix α4) and Gln130 (helix α7). Based on the structural comparison with the closest homolog structure, the Escherichia coli AcrR, we propose that this hydrogen bond is responsible for control of the loop-to-helix transition within helix α4. This local conformational switch of helix α4 may be a key step in accessing the multidrug binding site and securing ligands at the binding site. Solution small-molecule binding studies suggest that AcrR binds ligands with their core chemical structure resembling the tetracyclic ring of cholesterol. Copyright © 2016. Published by Elsevier Inc.

  2. Representing environment-induced helix-coil transitions in a coarse grained peptide model

    Science.gov (United States)

    Dalgicdir, Cahit; Globisch, Christoph; Sayar, Mehmet; Peter, Christine

    2016-10-01

    Coarse grained (CG) models are widely used in studying peptide self-assembly and nanostructure formation. One of the recurrent challenges in CG modeling is the problem of limited transferability, for example to different thermodynamic state points and system compositions. Understanding transferability is generally a prerequisite to knowing for which problems a model can be reliably used and predictive. For peptides, one crucial transferability question is whether a model reproduces the molecule's conformational response to a change in its molecular environment. This is of particular importance since CG peptide models often have to resort to auxiliary interactions that aid secondary structure formation. Such interactions take care of properties of the real system that are per se lost in the coarse graining process such as dihedral-angle correlations along the backbone or backbone hydrogen bonding. These auxiliary interactions may then easily overstabilize certain conformational propensities and therefore destroy the ability of the model to respond to stimuli and environment changes, i.e. they impede transferability. In the present paper we have investigated a short peptide with amphiphilic EALA repeats which undergoes conformational transitions between a disordered and a helical state upon a change in pH value or due to the presence of a soft apolar/polar interface. We designed a base CG peptide model that does not carry a specific (backbone) bias towards a secondary structure. This base model was combined with two typical approaches of ensuring secondary structure formation, namely a C α -C α -C α -C α pseudodihedral angle potential or a virtual site interaction that mimics hydrogen bonding. We have investigated the ability of the two resulting CG models to represent the environment-induced conformational changes in the helix-coil equilibrium of EALA. We show that with both approaches a CG peptide model can be obtained that is environment-transferable and that

  3. Channel Gating Dependence on Pore Lining Helix Glycine Residues in Skeletal Muscle Ryanodine Receptor.

    Science.gov (United States)

    Mei, Yingwu; Xu, Le; Mowrey, David D; Mendez Giraldez, Raul; Wang, Ying; Pasek, Daniel A; Dokholyan, Nikolay V; Meissner, Gerhard

    2015-07-10

    Type 1 ryanodine receptors (RyR1s) release Ca(2+) from the sarcoplasmic reticulum to initiate skeletal muscle contraction. The role of RyR1-G4934 and -G4941 in the pore-lining helix in channel gating and ion permeation was probed by replacing them with amino acid residues of increasing side chain volume. RyR1-G4934A, -G4941A, and -G4941V mutant channels exhibited a caffeine-induced Ca(2+) release response in HEK293 cells and bound the RyR-specific ligand [(3)H]ryanodine. In single channel recordings, significant differences in the number of channel events and mean open and close times were observed between WT and RyR1-G4934A and -G4941A. RyR1-G4934A had reduced K(+) conductance and ion selectivity compared with WT. Mutations further increasing the side chain volume at these positions (G4934V and G4941I) resulted in reduced caffeine-induced Ca(2+) release in HEK293 cells, low [(3)H]ryanodine binding levels, and channels that were not regulated by Ca(2+) and did not conduct Ca(2+) in single channel measurements. Computational predictions of the thermodynamic impact of mutations on protein stability indicated that although the G4934A mutation was tolerated, the G4934V mutation decreased protein stability by introducing clashes with neighboring amino acid residues. In similar fashion, the G4941A mutation did not introduce clashes, whereas the G4941I mutation resulted in intersubunit clashes among the mutated isoleucines. Co-expression of RyR1-WT with RyR1-G4934V or -G4941I partially restored the WT phenotype, which suggested lessening of amino acid clashes in heterotetrameric channel complexes. The results indicate that both glycines are important for RyR1 channel function by providing flexibility and minimizing amino acid clashes. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  4. SU-E-T-564: Multi-Helix Rotating Shield Brachytherapy for Cervical Cancer

    Energy Technology Data Exchange (ETDEWEB)

    Dadkhah, H; Wu, X [University of Iowa, Iowa City, IA (United States); Flynn, R; Kim, Y [University of Iowa Hospitals and Clinics, Iowa City, IA (United States)

    2015-06-15

    Purpose: To present a novel and practical brachytherapy technique, called multi-helix rotating shield brachytherapy (H-RSBT), for the precise positioning of a partial shield in a curved applicator. H-RSBT enables RSBT delivery using only translational motion of the radiation source/shield combination. H-RSBT overcomes the challenges associated with previously proposed RSBT approaches based on a serial (S-RSBT) step-and-shoot delivery technique, which required independent translational and rotational motion. Methods: A Fletcher-type applicator, compatible with the combination of a Xoft Axxent™ electronic brachytherapy source and a 0.5 mm thick tungsten shield, is proposed. The wall of the applicator contains six evenly-spaced helical keyways that rigidly define the emission direction of the shield as a function of depth. The shield contains three protruding keys and is attached to the source such that it rotates freely. S-RSBT and H-RSBT treatment plans with 180° and 45° azimuthal emission angles were generated for five cervical cancer patients representative of a wide range of high-risk clinical target volume (HR-CTV) shapes and applicator positions. The number of beamlets used in the treatment planning process was nearly constant for S-RSBT and H-RSBT by using dwell positions separated by 5 and 1.7 mm, respectively, and emission directions separated by 22.5° and 60°, respectively. For all the treatment plans the EQD2 of the HR-CTV was escalated until the EQD{sub 2cc} tolerance of either the bladder, rectum, or sigmoid colon was reached. Results: Treatment times for H-RSBT tended to be shorter than for S-RSBT, with changes of −38.47% to 1.12% with an average of −8.34%. The HR-CTV D{sub 90} changed by −8.81% to 2.08% with an average of −2.46%. Conclusion: H-RSBT is a mechanically feasible technique in the curved applicators needed for cervical cancer brachytherapy. S-RSBT and H-RSBT dose distributions were clinically equivalent for all patients

  5. Constraining the Lateral Helix of Respiratory Complex I by Cross-linking Does Not Impair Enzyme Activity or Proton Translocation.

    Science.gov (United States)

    Zhu, Shaotong; Vik, Steven B

    2015-08-21

    Complex I (NADH:ubiquinone oxidoreductase) is a multisubunit, membrane-bound enzyme of the respiratory chain. The energy from NADH oxidation in the peripheral region of the enzyme is used to drive proton translocation across the membrane. One of the integral membrane subunits, nuoL in Escherichia coli, has an unusual lateral helix of ∼75 residues that lies parallel to the membrane surface and has been proposed to play a mechanical role as a piston during proton translocation (Efremov, R. G., Baradaran, R., and Sazanov, L. A. (2010) Nature 465, 441-445). To test this hypothesis we have introduced 11 pairs of cysteine residues into Complex I; in each pair one is in the lateral helix, and the other is in a nearby region of subunit N, M, or L. The double mutants were treated with Cu(2+) ions or with bi-functional methanethiosulfonate reagents to catalyze cross-link formation in membrane vesicles. The yields of cross-linked products were typically 50-90%, as judged by immunoblotting, but in no case did the activity of Complex I decrease by >10-20%, as indicated by deamino-NADH oxidase activity or rates of proton translocation. In contrast, several pairs of cysteine residues introduced at other interfaces of N:M and M:L subunits led to significant loss of activity, in particular, in the region of residue Glu-144 of subunit M. The results do not support the hypothesis that the lateral helix of subunit L functions like a piston, but rather, they suggest that conformational changes might be transmitted more directly through the functional residues of the proton translocation apparatus. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  6. NMR studies of abasic sites in DNA duplexes: deoxyadenosine stacks into the helix opposite the cyclic analog of 2-deoxyribose

    International Nuclear Information System (INIS)

    Kalnik, M.W.; Chang, C.N.; Grollman, A.P.; Patel, D.J.

    1988-01-01

    Proton and phosphorus NMR studies are reported for the complementary d(C-A-T-G-A-G-T-A-C) x d(G-T-A-C-F-C-A-T-G) nonanucleotide duplex (designated AP/sub F/ 9-mer duplex) which contains a stable abasic site analog, F, in the center of the helix. This oligodeoxynucleotide contains a modified tetrahydrofuran moiety, isosteric with 2-deoxyribofuranose, which serves as a structural analog of a natural apurinic/apyrimidinic site. Exchangeable and nonexchangeable base and sugar protons, including those located at the abasic site, have been assigned in the complementary AP/sub F/ 9-mer duplex by recording and analyzing two-dimensional phase-sensitive NOESY data sets in H 2 O and D 2 O solution at low temperature (0 0 C). These studies indicate that A5 inserts into the helix opposite the abasic site F14 and stacks with flanking G4 x C15 and G6 x C13 Watson-Crick base pairs. Base-sugar proton NOE connectivities were measured through G4-A5-G6 on the unmodified strand and between the base protons of C15 and the sugar protons of the 5'-flanking residue F14 on the modified strand. These studies establish that all glycosidic torsion angles are anti and that the helix is right-handed at and adjacent to the abasic site in the AP/sub F/ 9-mer duplex. Two of the 16 phosphodiester groups exhibit phosphorus resonances outside the normal spectral dispersion indicative of altered torsion angles at two of the phosphate groups in the backbone of the AP/sub F/ 9-mer duplex

  7. A double-helix and cross-patterned solenoid used as a wirelessly powered receiver for medical implants

    Science.gov (United States)

    Mao, Shitong; Wang, Hao; Mao, Zhi-Hong; Sun, Mingui

    2018-05-01

    Many medical implants need to be designed in the shape of a cylinder (rod), a cuboid or a capsule in order to adapt to a specific site within the human body or facilitate the implantation procedure. In order to wirelessly power these types of implants, a pair of coils, one is located inside the human body and one is outside, is often used. Since most organs such as major muscles, blood vessels, and nerve bundles are anatomically parallel to the body surface, the most desired wireless power transfer (WPT) direction is from the external power transmission pad (a planar coil) to the lateral surface of the implant. However, to obtain optimal coupling, the currently used solenoid coil requires being positioned perpendicular to the body surface, which is often medically or anatomically unacceptable. In this research, a concentric double-helix (DH) coil with an air core is presented for use in implantable devices. Two helical coils are tilted at opposite angles (±45 degrees) to form a cross pattern. The WPT system is designed using the magnetic resonance concept for wireless power transfer (MR-WPT). The power transfer efficiency (PTE) relies on the near-field magnetic coupling which is closely related to the location and orientation of the DH coil. We explain how the novel structure of the DH solenoid magnifies the mutual inductance with the widely adopted circular planner coil and how the PTE is improved in comparison to the case of the conventional solenoid coil. We also study an important case where the double-helix power reception coil is laterally and angularly misaligned with the transmitter. Finally, our computational study using the finite element method and experimental study with actually constructed prototypes are presented which have proven our new double-helix coil design.

  8. A double-helix and cross-patterned solenoid used as a wirelessly powered receiver for medical implants

    Directory of Open Access Journals (Sweden)

    Shitong Mao

    2018-05-01

    Full Text Available Many medical implants need to be designed in the shape of a cylinder (rod, a cuboid or a capsule in order to adapt to a specific site within the human body or facilitate the implantation procedure. In order to wirelessly power these types of implants, a pair of coils, one is located inside the human body and one is outside, is often used. Since most organs such as major muscles, blood vessels, and nerve bundles are anatomically parallel to the body surface, the most desired wireless power transfer (WPT direction is from the external power transmission pad (a planar coil to the lateral surface of the implant. However, to obtain optimal coupling, the currently used solenoid coil requires being positioned perpendicular to the body surface, which is often medically or anatomically unacceptable. In this research, a concentric double-helix (DH coil with an air core is presented for use in implantable devices. Two helical coils are tilted at opposite angles (±45 degrees to form a cross pattern. The WPT system is designed using the magnetic resonance concept for wireless power transfer (MR-WPT. The power transfer efficiency (PTE relies on the near-field magnetic coupling which is closely related to the location and orientation of the DH coil. We explain how the novel structure of the DH solenoid magnifies the mutual inductance with the widely adopted circular planner coil and how the PTE is improved in comparison to the case of the conventional solenoid coil. We also study an important case where the double-helix power reception coil is laterally and angularly misaligned with the transmitter. Finally, our computational study using the finite element method and experimental study with actually constructed prototypes are presented which have proven our new double-helix coil design.

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

    DEFF Research Database (Denmark)

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

    1985-01-01

    Adenosine-66 is unpaired within helix II of Escherichia coli 5S RNA and lies in the binding site of ribosomal protein L18. It has been proposed as a recognition site for protein L18. We have investigated further the structural importance of this nucleotide by deleting it. The 5S RNA gene of the rrn...... plasmid derived from pKK3535. Binding studies with protein L18 revealed that the protein bound much more weakly to the mutated 5S RNA. We consider the most likely explanation of this result is that L18 interacts with adenosine-66, and we present a tentative model for an interaction between the unpaired...

  10. Helix Nebula: Enabling federation of existing data infrastructures and data services to an overarching cross-domain e-infrastructure

    Science.gov (United States)

    Lengert, Wolfgang; Farres, Jordi; Lanari, Riccardo; Casu, Francesco; Manunta, Michele; Lassalle-Balier, Gerard

    2014-05-01

    Helix Nebula has established a growing public private partnership of more than 30 commercial cloud providers, SMEs, and publicly funded research organisations and e-infrastructures. The Helix Nebula strategy is to establish a federated cloud service across Europe. Three high-profile flagships, sponsored by CERN (high energy physics), EMBL (life sciences) and ESA/DLR/CNES/CNR (earth science), have been deployed and extensively tested within this federated environment. The commitments behind these initial flagships have created a critical mass that attracts suppliers and users to the initiative, to work together towards an "Information as a Service" market place. Significant progress in implementing the following 4 programmatic goals (as outlined in the strategic Plan Ref.1) has been achieved: × Goal #1 Establish a Cloud Computing Infrastructure for the European Research Area (ERA) serving as a platform for innovation and evolution of the overall infrastructure. × Goal #2 Identify and adopt suitable policies for trust, security and privacy on a European-level can be provided by the European Cloud Computing framework and infrastructure. × Goal #3 Create a light-weight governance structure for the future European Cloud Computing Infrastructure that involves all the stakeholders and can evolve over time as the infrastructure, services and user-base grows. × Goal #4 Define a funding scheme involving the three stake-holder groups (service suppliers, users, EC and national funding agencies) into a Public-Private-Partnership model to implement a Cloud Computing Infrastructure that delivers a sustainable business environment adhering to European level policies. Now in 2014 a first version of this generic cross-domain e-infrastructure is ready to go into operations building on federation of European industry and contributors (data, tools, knowledge, ...). This presentation describes how Helix Nebula is being used in the domain of earth science focusing on geohazards. The

  11. Structural factors involved in the recognition of helix distortions in uv-damaged DNA by model peptides

    Energy Technology Data Exchange (ETDEWEB)

    Lang, H; Zimmer, C [Akademie der Wissenschaften der DDR, Jena. Forschungszentrum fuer Molekularbiologie und Medizin

    1977-02-28

    On the basis of our previous and present results concerning conformational changes of DNA after uv-irradiation some conclusions on the structure of DNA double helix in uv-damaged regions were drawn. From the results it appears that local distortions like denaturation or premelting should be excluded. Furthermore it was shown that the thymine dimerization strongly depends on the adjacent nucleic acid bases. By means of a strong binding effect of the oligopeptide netropsin to DNA irradiated at low uv-doses it is concluded that such local distortions in DNA together with a specific sequence-dependent variation of the conformation could act as recognition sites for endonucleases.

  12. Modeling of arylamide helix mimetics in the p53 peptide binding site of hDM2 suggests parallel and anti-parallel conformations are both stable.

    Directory of Open Access Journals (Sweden)

    Jonathan C Fuller

    Full Text Available The design of novel α-helix mimetic inhibitors of protein-protein interactions is of interest to pharmaceuticals and chemical genetics researchers as these inhibitors provide a chemical scaffold presenting side chains in the same geometry as an α-helix. This conformational arrangement allows the design of high affinity inhibitors mimicking known peptide sequences binding specific protein substrates. We show that GAFF and AutoDock potentials do not properly capture the conformational preferences of α-helix mimetics based on arylamide oligomers and identify alternate parameters matching solution NMR data and suitable for molecular dynamics simulation of arylamide compounds. Results from both docking and molecular dynamics simulations are consistent with the arylamides binding in the p53 peptide binding pocket. Simulations of arylamides in the p53 binding pocket of hDM2 are consistent with binding, exhibiting similar structural dynamics in the pocket as simulations of known hDM2 binders Nutlin-2 and a benzodiazepinedione compound. Arylamide conformations converge towards the same region of the binding pocket on the 20 ns time scale, and most, though not all dihedrals in the binding pocket are well sampled on this timescale. We show that there are two putative classes of binding modes for arylamide compounds supported equally by the modeling evidence. In the first, the arylamide compound lies parallel to the observed p53 helix. In the second class, not previously identified or proposed, the arylamide compound lies anti-parallel to the p53 helix.

  13. 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. Copyright © 2013 Wiley Periodicals, Inc.

  14. 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.

  15. Bimodal voltage dependence of TRPA1: mutations of a key pore helix residue reveal strong intrinsic voltage-dependent inactivation.

    Science.gov (United States)

    Wan, Xia; Lu, Yungang; Chen, Xueqin; Xiong, Jian; Zhou, Yuanda; Li, Ping; Xia, Bingqing; Li, Min; Zhu, Michael X; Gao, Zhaobing

    2014-07-01

    Transient receptor potential A1 (TRPA1) is implicated in somatosensory processing and pathological pain sensation. Although not strictly voltage-gated, ionic currents of TRPA1 typically rectify outwardly, indicating channel activation at depolarized membrane potentials. However, some reports also showed TRPA1 inactivation at high positive potentials, implicating voltage-dependent inactivation. Here we report a conserved leucine residue, L906, in the putative pore helix, which strongly impacts the voltage dependency of TRPA1. Mutation of the leucine to cysteine (L906C) converted the channel from outward to inward rectification independent of divalent cations and irrespective to stimulation by allyl isothiocyanate. The mutant, but not the wild-type channel, displayed exclusively voltage-dependent inactivation at positive potentials. The L906C mutation also exhibited reduced sensitivity to inhibition by TRPA1 blockers, HC030031 and ruthenium red. Further mutagenesis of the leucine to all natural amino acids individually revealed that most substitutions at L906 (15/19) resulted in inward rectification, with exceptions of three amino acids that dramatically reduced channel activity and one, methionine, which mimicked the wild-type channel. Our data are plausibly explained by a bimodal gating model involving both voltage-dependent activation and inactivation of TRPA1. We propose that the key pore helix residue, L906, plays an essential role in responding to the voltage-dependent gating.

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

    Science.gov (United States)

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

    2016-12-15

    In this work, an ultrasensitive electrochemical sensor was developed for detection of Hg(2+). Gold nanoparticles decorated bovine serum albumin reduction of graphene oxide (AuNP-BSA-rGO) were used as subsurface material for the immobilization of triple-helix DNA. The triple-helix DNA containing a thiol labelled single-stranded DNA (sDNA) and a thymine-rich DNA (T-rich DNA), which could be unwinded in the present of Hg(2+) to form more stable thymine-Hg(2+)-thymine (T-Hg(2+)-T) complex. T-Hg(2+)-T complex was then removed and the sDNA was left on the electrode. At this time, gold nanoparticle carrying thiol labelled cytosine-rich complementary DNA (cDNA-AuNP) could bind with the free sDNA. Meanwhile, the other free cDNA on AuNP could bind with each other in the present of Ag(+) to form the stable cytosine-Ag(+)-cytosine (C-Ag(+)-C) complex and circle amplification. Plenty of C-Ag(+)-C could form silver nanoclusters by electrochemical reduction and the striping signal of Ag could be measured for purpose of the final electrochemical detection of Hg(2+). This sensor could detect Hg(2+) over a wide concentration range from 0.1 to 130nM with a detection limit of 0.03nM. Copyright © 2016 Elsevier B.V. All rights reserved.

  17. Computational analysis of protein-protein interfaces involving an alpha helix: insights for terphenyl-like molecules binding.

    Science.gov (United States)

    Isvoran, Adriana; Craciun, Dana; Martiny, Virginie; Sperandio, Olivier; Miteva, Maria A

    2013-06-14

    Protein-Protein Interactions (PPIs) are key for many cellular processes. The characterization of PPI interfaces and the prediction of putative ligand binding sites and hot spot residues are essential to design efficient small-molecule modulators of PPI. Terphenyl and its derivatives are small organic molecules known to mimic one face of protein-binding alpha-helical peptides. In this work we focus on several PPIs mediated by alpha-helical peptides. We performed computational sequence- and structure-based analyses in order to evaluate several key physicochemical and surface properties of proteins known to interact with alpha-helical peptides and/or terphenyl and its derivatives. Sequence-based analysis revealed low sequence identity between some of the analyzed proteins binding alpha-helical peptides. Structure-based analysis was performed to calculate the volume, the fractal dimension roughness and the hydrophobicity of the binding regions. Besides the overall hydrophobic character of the binding pockets, some specificities were detected. We showed that the hydrophobicity is not uniformly distributed in different alpha-helix binding pockets that can help to identify key hydrophobic hot spots. The presence of hydrophobic cavities at the protein surface with a more complex shape than the entire protein surface seems to be an important property related to the ability of proteins to bind alpha-helical peptides and low molecular weight mimetics. Characterization of similarities and specificities of PPI binding sites can be helpful for further development of small molecules targeting alpha-helix binding proteins.

  18. Clepsis dumicolana (Lepidoptera: Tortricidae), new to the Belgian fauna

    NARCIS (Netherlands)

    de Prins, W.; Baugnée, J.-Y.

    2008-01-01

    On 17 August 2008 a specimen of Clepsis dumicolana (Zeller, 1847) (Lepidoptera: Tortricidae) was caught at Liège, leg. J.-Y. Baugnée. It was resting on Hedera helix, in the vicinity of the Kennedy bridge. During the following days, about 40 specimens were seen in two localities of the slope to the

  19. Bioinformatic analysis of the L polymerase gene leads to discrimination of new rhabdoviruses

    Czech Academy of Sciences Publication Activity Database

    Petrzik, Karel

    2012-01-01

    Roč. 160, 7-8 (2012), s. 377-381 ISSN 0931-1785 R&D Projects: GA ČR GAP501/12/1747 Institutional research plan: CEZ:AV0Z50510513 Institutional support: RVO:60077344 Keywords : Cytorhabdovirus * RNA polymerase * Hedera helix Subject RIV: EE - Microbiology, Virology Impact factor: 1.000, year: 2012

  20. Antithrombin activity of medicinal plants of the Azores.

    Science.gov (United States)

    de Medeiros, J M; Macedo, M; Contancia, J P; Nguyen, C; Cunningham, G; Miles, D H

    2000-09-01

    A chromogenic bioassay was utilized to determine the antithrombin activity of methylene chloride and methanol extracts prepared from 50 plants of Azores. Extracts of the six plants Hedychium gardneranum, Tropaeolum majus, Gunnera tinctoria, Hedera helix, Festuca jubata and Laurus azorica demonstrated activity of 78% or higher in this bioassay system.

  1. Differences between water permeability of astomatous and stomatous cuticular membranes: effects of air humidity in two species of contrasting drought-resistance strategy

    Czech Academy of Sciences Publication Activity Database

    Karbulková, J.; Schreiber, L.; Macek, Petr; Šantrůček, Jiří

    2008-01-01

    Roč. 59, č. 14 (2008), s. 3987-3995 ISSN 0022-0957 R&D Projects: GA AV ČR(CZ) IAA601410505 Institutional research plan: CEZ:AV0Z50510513; CEZ:AV0Z60050516 Keywords : Hedera helix * stomatal conductance * Zamioculcas zamiifolia Subject RIV: EF - Botanics Impact factor: 4.001, year: 2008

  2. Use of 1–4 interaction scaling factors to control the conformational equilibrium between α-helix and β-strand

    Energy Technology Data Exchange (ETDEWEB)

    Pang, Yuan-Ping, E-mail: pang@mayo.edu

    2015-02-06

    Highlights: • 1–4 interaction scaling factors are used to adjust conformational energy. • This article reports the effects of these factors on protein conformations. • Reducing these factors changes a helix to a strand in molecular dynamics simulation. • Increasing these factors causes the reverse conformational change. • These factors control the conformational equilibrium between helix and strand. - Abstract: 1–4 interaction scaling factors are used in AMBER forcefields to reduce the exaggeration of short-range repulsion caused by the 6–12 Lennard-Jones potential and a nonpolarizable charge model and to obtain better agreements of small-molecule conformational energies with experimental data. However, the effects of these scaling factors on protein secondary structure conformations have not been investigated until now. This article reports the finding that the 1–4 interactions among the protein backbone atoms separated by three consecutive covalent bonds are more repulsive in the α-helix conformation than in two β-strand conformations. Therefore, the 1–4 interaction scaling factors of protein backbone torsions ϕ and ψ control the conformational equilibrium between α-helix and β-strand. Molecular dynamics simulations confirm that reducing the ϕ and ψ scaling factors readily converts the α-helix conformation of AcO-(AAQAA){sub 3}-NH{sub 2} to a β-strand conformation, and the reverse occurs when these scaling factors are increased. These results suggest that the ϕ and ψ scaling factors can be used to generate the α-helix or β-strand conformation in situ and to control the propensities of a forcefield for adopting secondary structure elements.

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

    Science.gov (United States)

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

    2014-08-29

    G protein activation by G protein-coupled receptors is one of the critical steps for many cellular signal transduction pathways. Previously, we and other groups reported that the α5 helix in the G protein α subunit plays a major role during this activation process. However, the precise signaling pathway between the α5 helix and the guanosine diphosphate (GDP) binding pocket remains elusive. Here, using structural, biochemical, and computational techniques, we probed different residues around the α5 helix for their role in signaling. Our data showed that perturbing the Phe-336 residue disturbs hydrophobic interactions with the β2-β3 strands and α1 helix, leading to high basal nucleotide exchange. However, mutations in β strands β5 and β6 do not perturb G protein activation. We have highlighted critical residues that leverage Phe-336 as a relay. Conformational changes are transmitted starting from Phe-336 via β2-β3/α1 to Switch I and the phosphate binding loop, decreasing the stability of the GDP binding pocket and triggering nucleotide release. When the α1 and α5 helices were cross-linked, inhibiting the receptor-mediated displacement of the C-terminal α5 helix, mutation of Phe-336 still leads to high basal exchange rates. This suggests that unlike receptor-mediated activation, helix 5 rotation and translocation are not necessary for GDP release from the α subunit. Rather, destabilization of the backdoor region of the Gα subunit is sufficient for triggering the activation process. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

  4. High-resolution orientation and depth of insertion of the voltage-sensing S4 helix of a potassium channel in lipid bilayers.

    Science.gov (United States)

    Doherty, Tim; Su, Yongchao; Hong, Mei

    2010-08-27

    The opening and closing of voltage-gated potassium (Kv) channels are controlled by several conserved Arg residues in the S4 helix of the voltage-sensing domain. The interaction of these positively charged Arg residues with the lipid membrane has been of intense interest for understanding how membrane proteins fold to allow charged residues to insert into lipid bilayers against free-energy barriers. Using solid-state NMR, we have now determined the orientation and insertion depth of the S4 peptide of the KvAP channel in lipid bilayers. Two-dimensional (15)N correlation experiments of macroscopically oriented S4 peptide in phospholipid bilayers revealed a tilt angle of 40 degrees and two possible rotation angles differing by 180 degrees around the helix axis. Remarkably, the tilt angle and one of the two rotation angles are identical to those of the S4 helix in the intact voltage-sensing domain, suggesting that interactions between the S4 segment and other helices of the voltage-sensing domain are not essential for the membrane topology of the S4 helix. (13)C-(31)P distances between the S4 backbone and the lipid (31)P indicate a approximately 9 A local thinning and 2 A average thinning of the DMPC (1,2-dimyristoyl-sn-glycero-3-phosphochloline)/DMPG (1,2-dimyristoyl-sn-glycero-3-phosphatidylglycerol) bilayer, consistent with neutron diffraction data. Moreover, a short distance of 4.6 A from the guanidinium C(zeta) of the second Arg to (31)P indicates the existence of guanidinium phosphate hydrogen bonding and salt bridges. These data suggest that the structure of the Kv gating helix is mainly determined by protein-lipid interactions instead of interhelical protein-protein interactions, and the S4 amino acid sequence encodes sufficient information for the membrane topology of this crucial gating helix. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

  5. Use of 1–4 interaction scaling factors to control the conformational equilibrium between α-helix and β-strand

    International Nuclear Information System (INIS)

    Pang, Yuan-Ping

    2015-01-01

    Highlights: • 1–4 interaction scaling factors are used to adjust conformational energy. • This article reports the effects of these factors on protein conformations. • Reducing these factors changes a helix to a strand in molecular dynamics simulation. • Increasing these factors causes the reverse conformational change. • These factors control the conformational equilibrium between helix and strand. - Abstract: 1–4 interaction scaling factors are used in AMBER forcefields to reduce the exaggeration of short-range repulsion caused by the 6–12 Lennard-Jones potential and a nonpolarizable charge model and to obtain better agreements of small-molecule conformational energies with experimental data. However, the effects of these scaling factors on protein secondary structure conformations have not been investigated until now. This article reports the finding that the 1–4 interactions among the protein backbone atoms separated by three consecutive covalent bonds are more repulsive in the α-helix conformation than in two β-strand conformations. Therefore, the 1–4 interaction scaling factors of protein backbone torsions ϕ and ψ control the conformational equilibrium between α-helix and β-strand. Molecular dynamics simulations confirm that reducing the ϕ and ψ scaling factors readily converts the α-helix conformation of AcO-(AAQAA) 3 -NH 2 to a β-strand conformation, and the reverse occurs when these scaling factors are increased. These results suggest that the ϕ and ψ scaling factors can be used to generate the α-helix or β-strand conformation in situ and to control the propensities of a forcefield for adopting secondary structure elements

  6. The effect of k-cubic Dresselhaus spin—orbit coupling on the decay time of persistent spin helix states in semiconductor two-dimensional electron gases

    International Nuclear Information System (INIS)

    Chai Zheng; Hu Mao-Jin; Wang Rui-Qiang; Hu Liang-Bin

    2014-01-01

    We study the theoretical effect of k-cubic (i.e. cubic-in-momentum) Dresselhaus spin—orbit coupling on the decay time of persistent spin helix states in semiconductor two-dimensional electron gases. We show that the decay time of persistent spin helix states may be suppressed substantially by k-cubic Dresselhaus spin—orbit coupling, and after taking the effect of k-cubic Dresselhaus spin—orbit interaction into account, the theoretical results obtained accord both qualitatively and quantitatively with other recent experimental results. (condensed matter: electronic structure, electrical, magnetic, and optical properties)

  7. Health and Environment Linked for Information Exchange (HELIX)-Atlanta: A CDC-NASA Joint Environmental Public Health Tracking Collaborative Project

    Science.gov (United States)

    Al-Hamdan, Mohammad; Luvall, Jeff; Crosson, Bill; Estes, Maury; Limaye, Ashutosh; Quattrochi, Dale; Rickman, Doug

    2008-01-01

    HELIX-Atlanta was developed to support current and future state and local EPHT programs to implement data linking demonstration projects which could be part of the CDC EPHT Network. HELIX-Atlanta is a pilot linking project in Atlanta for CDC to learn about the challenges the states will encounter. NASA/MSFC and the CDC are partners in linking environmental and health data to enhance public health surveillance. The use of NASA technology creates value added geospatial products from existing environmental data sources to facilitate public health linkages. Proving the feasibility of the approach is the main objective

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

    DEFF Research Database (Denmark)

    Gao, Yuchen; Hu, Yimei; Wang, Jingyi

    2015-01-01

    and transition economies where governments are transforming their roles. Thus the main purpose of this study is to investigate how private venture capitals’ investment willingness on university spin-offs are influenced by universities and governments under the Chinese context based on the triple helix model....... Through an in-depth case study on the interactions of triple helix actors of Tsinghua University’s spin-offs, it is found that government and university developing an environment of marketization exert positive influences on the investment willingness of private venture capitals. Whilst financial direct...

  9. Precise determination of cosmogenic Ne in CREU-1 quartz standard, using the Helix-MC Plus mass spectrometer

    Science.gov (United States)

    Hamilton, D.; Honda, M.; Zhang, X.; Phillips, D.; Matchan, E.

    2017-12-01

    The Helix-MC Plus multi-collector noble gas mass spectrometer at the Australian National University is uniquely equipped with three high mass resolution collectors on H2, Axial and L2 positions. Their mass resolution and mass resolving power are as high as 1,800 and 8,000, respectively. The Helix-MC Plus can totally separate 20Ne+ from 40Ar++ isobaric interference and also partially separate 21Ne+ from 20NeH+ and 22Ne+ from 12C16O2++. By adjusting collector positions, we are able to measure interference-free Ne isotope intensities and have re-determined the 21Ne abundance in air [1]. Analyses by Honda et al. [1] demonstrated that 20Ne1H contributes approximately 2% to previously determined atmospheric 21Ne values [2], and a new atmospheric 21Ne/20Ne ratio of 0.002906 was calculated. Using the Helix-MC Plus mass spectrometer, we measured Ne abundances in the CREU-1 quartz standard [3] and determined cosmogenic concentrations by subtraction of atmospheric Ne with the new atmospheric 21Ne/20Ne value. The average concentration of cosmogenic 21Ne determined from four repeated analyses is 338 ± 12 × 106 atom/g (2σ). This compares with the average concentration of 348 ± 10 × 106 atom/g (2σ) from 45 analyses determined by several laboratories [3], where Ne isotope analyses were undertaken by conventional low resolution mass spectrometers and atmospheric Ne was subtracted using the conventional atmospheric 21Ne/20Ne [2]. On this basis, for a sample with abundant cosmogenic Ne, like CREU-1 quartz, previously measured by low mass resolution mass spectrometers are likely valid and their geological implications are unaffected. However, for low 21Ne concentration samples, combining new generation of mass spectrometers as well as the new atmospheric ratio may have significance for cosmogenic 21Ne surface exposure dating. References: [1] Honda M., et. al., International Journal of Mass Spectrometry, 387, 1 (2015). [2] Eberhardt P., et. al., Zeitschrift fur Naturforschung, 20

  10. PH4 of petunia is an R2R3-MYB protein that activates vacuolar acidification through interactions with Basic-Helix-Loop transcription factors of the anthocyanin pathway.

    NARCIS (Netherlands)

    Quattrocchio, F.M.; Verweij, C.W.; Kroon, A.R.; Spelt, C.E.; Mol, J.N.M.; Koes, R.E.

    2006-01-01

    The Petunia hybrids genes ANTHOCYANIN1 (AN1) and AN2 encode transcription factors with a basic-helix-loop-helix (BHLH) and a MYB domain, respectively, that are required for anthocyanin synthesis and acidification of the vacuole in petal cells. Mutation of PH4 results in a bluer flower color,

  11. Topotactic conversion of β-helix-layered silicate into AST-type zeolite through successive interlayer modifications.

    Science.gov (United States)

    Asakura, Yusuke; Takayama, Ryosuke; Shibue, Toshimichi; Kuroda, Kazuyuki

    2014-02-10

    AST-type zeolite with a plate morphology can be synthesized by topotactic conversion of a layered silicate (β-helix-layered silicate; HLS) by using N,N-dimethylpropionamide (DPA) to control the layer stacking of silicate layers and the subsequent interlayer condensation. Treatment of HLS twice with 1) hydrochloric acid/ethanol and 2) dimethylsulfoxide (DMSO) are needed to remove interlayer hydrated Na ions and tetramethylammonium (TMA) ions in intralayer cup-like cavities (intracavity TMA ions), both of which are introduced during the preparation of HLS. The utilization of an amide molecule is effective for the control of the stacking sequence of silicate layers. This method could be applicable to various layered silicates that cannot be topotactically converted into three-dimensional networks by simple interlayer condensation by judicious choice of amide molecules. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. The Development Model of Small and Medium Enterprises in Textile Sector (Batik, Weaving and Embroidery with Triple Helix in Medan

    Directory of Open Access Journals (Sweden)

    Frida Ramadini

    2016-09-01

    Full Text Available This research is focusing to the identification of the condition and problems of small and medium enterprises (SMEs textile sector consist batik, woven and embroidery SME in Medan to face the ASEAN Economics Community (AEC, and is giving solution to the problems that they have to approach AEC. This research use qualitative methods. The sample is selected by purposive sampling and snowball sampling. The numbers of informant are 10 people. Data Analysis was performed by Triple Helix models. The results show that the main causes for the inability of Batik SMEs to compete in Medan are laborer, entrepreneur, networking and market penetration, government support, production and consumers. Synergy could be done among academicians, businessmen (SME and government. Synergy is conducted as a strategy and concrete steps of comprehensive development of SME.

  13. Dual-purpose linker for alpha helix stabilization and imaging agent conjugation to glucagon-like peptide-1 receptor ligands.

    Science.gov (United States)

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

    2015-02-18

    Peptides display many characteristics of efficient imaging agents such as rapid targeting, fast background clearance, and low non-specific cellular uptake. However, poor stability, low affinity, and loss of binding after labeling often preclude their use in vivo. Using glucagon-like peptide-1 receptor (GLP-1R) ligands exendin and GLP-1 as a model system, we designed a novel α-helix-stabilizing linker to simultaneously address these limitations. The stabilized and labeled peptides showed an increase in helicity, improved protease resistance, negligible loss or an improvement in binding affinity, and excellent in vivo targeting. The ease of incorporating azidohomoalanine in peptides and efficient reaction with the dialkyne linker enable this technique to potentially be used as a general method for labeling α helices. This strategy should be useful for imaging beta cells in diabetes research and in developing and testing other peptide targeting agents.

  14. DISCOVERY OF A HALO AROUND THE HELIX NEBULA NGC 7293 IN THE WISE ALL-SKY SURVEY

    International Nuclear Information System (INIS)

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

    2012-01-01

    We report the discovery of an extended halo (∼40' in diameter) around the planetary nebula NGC 7293 (the Helix Nebula) observed in the 12 μm band from the Wide-field Infrared Survey Explorer all-sky survey. The mid-infrared halo has an axisymmetric structure with a sharp boundary to the northeast and a more diffuse boundary to the southwest, suggesting an interaction between the stellar wind and the interstellar medium (ISM). The symmetry axis of the halo is well aligned with that of a northeast arc, suggesting that the two structures are physically associated. We have attempted to fit the observed geometry with a model of a moving steady-state stellar wind interacting with the ISM. Possible combinations of the ISM density and the stellar velocity are derived from these fittings. The discrepancies between the model and the observations suggest that the stellar mass loss has a more complicated history, including possible time and angle dependences.

  15. Involvement of Mζ-Like Protein Kinase in the Mechanisms of Conditioned Food Aversion Memory Reconsolidation in the Helix lucorum.

    Science.gov (United States)

    Solntseva, S V; Kozyrev, S A; Nikitin, V P

    2015-06-01

    We studied the involvement of Mζ-like protein kinase (PKMζ) into mechanisms of conditioned food aversion memory reconsolidation in Helix lucorum. Injections PKMζ inhibitor ZIP in a dose of 5 mg/kg on day 2 or 10 after learning led to memory impairment and amnesia development. Injections of the inhibitor in doses of 1.5 or 2.5 mg/kg had no effect. Repeated training on day 11 after induction of amnesia resulted in the formation of memory on the same type of food aversion similar to first training. The number of combinations of conditional (food) and reinforcing (electrical shock) stimuli was similar during initial and repeated training. We hypothesize that the inhibition of Mζ-like protein kinase erases the memory trace and a new memory is formed during repeated training.

  16. Effects of hydrophobic helix length and side chain chemistry on biomimicry in peptoid analogues of SP-C.

    Science.gov (United States)

    Brown, Nathan J; Wu, Cindy W; Seurynck-Servoss, Shannon L; Barron, Annelise E

    2008-02-12

    The hydrophobic proteins of lung surfactant (LS), SP-B and SP-C, are critical constituents of an effective surfactant replacement therapy for the treatment of respiratory distress syndrome. Because of concerns and difficulties associated with animal-derived surfactants, recent investigations have focused on the creation of synthetic analogues of the LS proteins. However, creating an accurate mimic of SP-C that retains its biophysical surface activity is extraordinarily challenging given the lipopeptide's extreme hydrophobicity and propensity to misfold and aggregate. One successful approach that overcomes these difficulties is the use of poly-N-substituted glycines, or peptoids, to mimic SP-C. To develop a non-natural, bioactive mimic of SP-C and to investigate the effects of side chain chemistry and length of the helical hydrophobic region, we synthesized, purified, and performed in vitro testing of two classes of peptoid SP-C mimics: those having a rigid alpha-chiral aromatic helix and those having a biomimetic alpha-chiral aliphatic helix. The length of the two classes of mimics was also systematically altered. Circular dichroism spectroscopy gave evidence that all of the peptoid-based mimics studied here emulated SP-C's secondary structure, forming stable helical structures in solution. Langmuir-Wilhelmy surface balance, fluorescence microscopy, and pulsating bubble surfactometry experiments provide evidence that the aromatic-based SP-C peptoid mimics, in conjunction with a synthetic lipid mixture, have superior surface activity and biomimetic film morphology in comparison to the aliphatic-based mimics and that there is an increase in surface activity corresponding to increasing helical length.

  17. Structural Variation and Uniformity among Tetraloop-Receptor Interactions and Other Loop-Helix Interactions in RNA Crystal Structures

    Science.gov (United States)

    Wu, Li; Chai, Dinggeng; Fraser, Marie E.; Zimmerly, Steven

    2012-01-01

    Tetraloop-receptor interactions are prevalent structural units in RNAs, and include the GAAA/11-nt and GNRA-minor groove interactions. In this study, we have compiled a set of 78 nonredundant loop-helix interactions from X-ray crystal structures, and examined them for the extent of their sequence and structural variation. Of the 78 interactions in the set, only four were classical GAAA/11-nt motifs, while over half (48) were GNRA-minor groove interactions. The GNRA-minor groove interactions were not a homogeneous set, but were divided into five subclasses. The most predominant subclass is characterized by two triple base pair interactions in the minor groove, flanked by two ribose zipper contacts. This geometry may be considered the “standard” GNRA-minor groove interaction, while the other four subclasses are alternative ways to form interfaces between a minor groove and tetraloop. The remaining 26 structures in the set of 78 have loops interacting with mostly idiosyncratic receptors. Among the entire set, a number of sequence-structure correlations can be identified, which may be used as initial hypotheses in predicting three-dimensional structures from primary sequences. Conversely, other sequence patterns are not predictive; for example, GAAA loop sequences and GG/CC receptors bind to each other with three distinct geometries. Finally, we observe an example of structural evolution in group II introns, in which loop-receptor motifs are substituted for each other while maintaining the larger three-dimensional geometry. Overall, the study gives a more complete view of RNA loop-helix interactions that exist in nature. PMID:23152878

  18. Characterisation of an ion source on the Helix MC Plus noble gas mass spectrometer - pressure dependent mass discrimination

    Science.gov (United States)

    Zhang, X.

    2017-12-01

    Characterisation of an ion source on the Helix MC Plusnoble gas mass spectrometer - pressure dependent mass discrimination Xiaodong Zhang* dong.zhang@anu.edu.au Masahiko Honda Masahiko.honda@anu.edu.au Research School of Earth Sciences, The Australian National University, Canberra, Australia To obtain reliable measurements of noble gas elemental and isotopic abundances in a geological sample it is essential that the mass discrimination (instrument-induced isotope fractionation) of the mass spectrometer remain constant over the working range of noble gas partial pressures. It is known, however, that there are pressure-dependent variations in sensitivity and mass discrimination in conventional noble gas mass spectrometers [1, 2, 3]. In this study, we discuss a practical approach to ensuring that the pressure effect in the Helix MC Plus high resolution, multi-collector noble gas mass spectrometer is minimised. The isotopic composition of atmospheric Ar was measured under a range of operating conditions to test the effects of different parameters on Ar mass discrimination. It was found that the optimised ion source conditions for pressure independent mass discrimination for Ar were different from those for maximised Ar sensitivity. The optimisation can be achieved by mainly adjusting the repeller voltage. It is likely that different ion source settings will be required to minimise pressure-dependent mass discrimination for different noble gases. A recommended procedure for tuning an ion source to reduce pressure dependent mass discrimination will be presented. References: Honda M., et al., Geochim. Cosmochim. Acta, 57, 859 -874, 1993. Burnard P. G., and Farley K. A., Geochemistry Geophysics Geosystems, Volume 1, 2000GC00038, 2000. Mabry J., et al., Journal of Analytical Atomic Spectrometry, 27, 1012 - 1017, 2012.

  19. Effect of TFE on the Helical Content of AK17 and HAL-1 Peptides: Theoretical Insights into the Mechanism of Helix Stabilization.

    Science.gov (United States)

    Vymětal, Jiří; Bednárová, Lucie; Vondrášek, Jiří

    2016-02-18

    Fluorinated alcohols such as 2,2,2-trifluoroethanol (TFE) are among the most frequently used cosolvents in experiment studies of peptides. They have significant effects on secondary structure and a particularly strong promotion of α-helix is induced by TFE. In this study we validated recently proposed force field parameters for TFE in molecular dynamics simulations with two model peptides-alanine-rich AK-17 and antimicrobial peptide halictine-1 (HAL-1). In the case of HAL-1, we characterized the effect of TFE on this peptide experimentally by ECD spectroscopy. Our TFE model in question reproduced the helix-promoting effect of TFE and provided insight into the mechanisms of TFE action on peptides. Our simulations confirmed the preferential interaction of TFE molecules with α-helices, although the TFE molecules accumulate in the vicinity of the peptides in various conformations. Moreover, we observed a significant effect of TFE on the thermodynamics of the helix-coil transition and a change in local conformational preferences in the unfolded (coil) state induced by TFE. In addition, our simulation-based analysis suggests that different mechanisms participate in helix stabilization in both model peptides in water and TFE solution. Our results thus support the picture of complex TFE action on peptides that is further diversified by the identity and intrinsic properties of the peptide.

  20. A new assay format for NF-kappaB based on a DNA triple helix and a fluorescence resonance energy transfer.

    Science.gov (United States)

    Altevogt, Dominik; Hrenn, Andrea; Kern, Claudia; Clima, Lilia; Bannwarth, Willi; Merfort, Irmgard

    2009-10-07

    Herein we report a feasibility study for a new concept to detect DNA binding protein NF-kappaB based on a DNA triple helix formation in combination with a fluorescence resonance energy transfer (FRET). The new principle avoids expensive antibodies and radioactivity and might have implications for assays of other DNA binding proteins.

  1. Probing the mechanistic role of the long α-helix in subunit L of respiratory Complex I from Escherichia coli by site-directed mutagenesis

    Science.gov (United States)

    Belevich, Galina; Knuuti, Juho; Verkhovsky, Michael I; Wikström, Mårten; Verkhovskaya, Marina

    2011-01-01

    The C-terminus of the NuoL subunit of Complex I includes a long amphipathic α-helix positioned parallel to the membrane, which has been considered to function as a piston in the proton pumping machinery. Here, we have introduced three types of mutations into the nuoL gene to test the piston-like function. First, NuoL was truncated at its C- and N-termini, which resulted in low production of a fragile Complex I with negligible activity. Second, we mutated three partially conserved residues of the amphipathic α-helix: Asp and Lys residues and a Pro were substituted for acidic, basic or neutral residues. All these variants exhibited almost a wild-type phenotype. Third, several substitutions and insertions were made to reduce rigidity of the amphipathic α-helix, and/or to change its geometry. Most insertions/substitutions resulted in a normal growth phenotype, albeit often with reduced stability of Complex I. In contrast, insertion of six to seven amino acids at a site of the long α-helix between NuoL and M resulted in substantial loss of proton pumping efficiency. The implications of these results for the proton pumping mechanism of Complex I are discussed. PMID:22060017

  2. Identification of the roles of individual amino acid residues of the helix E of the major antenna of photosystem II (LHCII) by alanine scanning mutagenesis.

    Science.gov (United States)

    Liu, Cheng; Rao, Yan; Zhang, Lei; Yang, Chunhong

    2014-10-01

    The functions of the helix E (W97-F105), an amphiphilic lumenal 310 helix of the major antenna of photosystem II (LHCII), are still unidentified. To elucidate the roles of individual amino acid residue of the helix E, alanine scanning mutagenesis has been performed to mutate every residue of this domain to alanine. The influence of every alanine substitution on the structure and function of LHCII has been investigated biochemically and spectroscopically. The results show that all mutations have little impact on the pigment binding and configuration. However, many mutants presented decreased thermo- or photo-stability compared with the wild type, highlighting the significance of this helix to the stability of LHCII. The most critical residue for stability is W97. The mutant W97A yielded very fragile trimeric pigment protein complexes. The structural analysis revealed that the hydrogen bonding and aromatic interactions between W97, F195, F194 and a water molecule contributed greatly to the stability of LHCII. Moreover, Q103A and F105A have been identified to be able to reinforce the tendency of aggregation in vitro. The structural analysis suggested that the enhancement in aggregation formation for Q103A and F105A might be attributed to the changing hydrophobicity of the region. © The Authors 2014. Published by Oxford University Press on behalf of the Japanese Biochemical Society. All rights reserved.

  3. Single-photon absorption of isolated collagen mimetic peptides and triple-helix models in the VUV-X energy range

    NARCIS (Netherlands)

    Schwob, Lucas; Lalande, Mathieu; Rangama, Jimmy; Egorov, Dmitrii; Hoekstra, Ronnie; Pandey, Rahul; Eden, Samuel; Schlathölter, Thomas; Vizcaino, Violaine; Poully, Jean-Christophe

    2017-01-01

    Cartilage and tendons owe their special mechanical properties to the fibrous collagen structure. These strong fibrils are aggregates of a sub-unit consisting of three collagen proteins wound around each other in a triple helix. Even though collagen is the most abundant protein in the human body, the

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

    Directory of Open Access Journals (Sweden)

    Paloma Aivar

    Full Text Available Kv7.2 and Kv7.3 are the main components of the neuronal voltage-dependent M-current, which is a subthreshold potassium conductance that exerts an important control on neuronal excitability. Despite their predominantly intracellular distribution, these channels must reach the plasma membrane in order to control neuronal activity. Thus, we analyzed the amino acid sequence of Kv7.2 to identify intrinsic signals that may control its surface expression. Removal of the interlinker connecting helix A and helix B of the intracellular C-terminus produces a large increase in the number of functional channels at the plasma membrane. Moreover, elimination of this linker increased the steady-state amount of protein, which was not associated with a decrease of protein degradation. The magnitude of this increase was inversely correlated with the number of helix A - helix B linkers present in the tetrameric channel assemblies. In contrast to the remarkable effect on the amount of Kv7.2 protein, removal of the Kv7.2 linker had no detectable impact on the steady-state levels of Kv7.3 protein.

  5. Dual catalytic purpose of the tungsten filament during the synthesis of single-helix carbon microcoils by hot-wire CVD

    CSIR Research Space (South Africa)

    Oliphant, CJ

    2009-10-01

    Full Text Available This paper reports on the deposition of crystalline single-helix carbon microcoils, in the as-deposited state, by the hot-wire chemical vapor deposition process without any special preparation of nano-sized transition metal catalysts and subsequent...

  6. RT-173: Helix, 2017 Helix Technical Report

    Science.gov (United States)

    2018-01-16

    and to coordinate across the problem domain and solution domain. Categories include: communication; listening and comprehension ; working in a...proficiency set as a useful and comprehensive model. The forces identified in Figure 1 – experiences, mentoring, education and training – are linked

  7. An Intramolecular Salt Bridge in Bacillus thuringiensis Cry4Ba Toxin Is Involved in the Stability of Helix α-3, Which Is Needed for Oligomerization and Insecticidal Activity.

    Science.gov (United States)

    Pacheco, Sabino; Gómez, Isabel; Sánchez, Jorge; García-Gómez, Blanca-Ines; Soberón, Mario; Bravo, Alejandra

    2017-10-15

    Bacillus thuringiensis three-domain Cry toxins kill insects by forming pores in the apical membrane of larval midgut cells. Oligomerization of the toxin is an important step for pore formation. Domain I helix α-3 participates in toxin oligomerization. Here we identify an intramolecular salt bridge within helix α-3 of Cry4Ba (D111-K115) that is conserved in many members of the family of three-domain Cry toxins. Single point mutations such as D111K or K115D resulted in proteins severely affected in toxicity. These mutants were also altered in oligomerization, and the mutant K115D was more sensitive to protease digestion. The double point mutant with reversed charges, D111K-K115D, recovered both oligomerization and toxicity, suggesting that this salt bridge is highly important for conservation of the structure of helix α-3 and necessary to promote the correct oligomerization of the toxin. IMPORTANCE Domain I has been shown to be involved in oligomerization through helix α-3 in different Cry toxins, and mutations affecting oligomerization also elicit changes in toxicity. The three-dimensional structure of the Cry4Ba toxin reveals an intramolecular salt bridge in helix α-3 of domain I. Mutations that disrupt this salt bridge resulted in changes in Cry4Ba oligomerization and toxicity, while a double point reciprocal mutation that restored the salt bridge resulted in recovery of toxin oligomerization and toxicity. These data highlight the role of oligomer formation as a key step in Cry4Ba toxicity. Copyright © 2017 American Society for Microbiology.

  8. 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.

  9. Phytophthora niederhauserii sp. nov., a polyphagous species associated with ornamentals, fruit trees and native plants in 13 countries.

    Science.gov (United States)

    Abad, Z Gloria; Abad, Jorge A; Cacciola, Santa Olga; Pane, Antonella; Faedda, Roberto; Moralejo, Eduardo; Pérez-Sierra, Ana; Abad-Campos, Paloma; Alvarez-Bernaola, Luis A; Bakonyi, József; Józsa, András; Herrero, Maria Luz; Burgess, Treena I; Cunnington, James H; Smith, Ian W; Balci, Yilmaz; Blomquist, Cheryl; Henricot, Béatrice; Denton, Geoffrey; Spies, Chris; Mcleod, Adele; Belbahri, Lassaad; Cooke, David; Kageyama, Koji; Uematsu, Seiji; Kurbetli, Ilker; Değirmenci, Kemal

    2014-01-01

    A non-papillate, heterothallic Phytophthora species first isolated in 2001 and subsequently from symptomatic roots, crowns and stems of 33 plant species in 25 unrelated botanical families from 13 countries is formally described here as a new species. Symptoms on various hosts included crown and stem rot, chlorosis, wilting, leaf blight, cankers and gumming. This species was isolated from Australia, Hungary, Israel, Italy, Japan, the Netherlands, Norway, South Africa, Spain, Taiwan, Turkey, the United Kingdom and United States in association with shrubs and herbaceous ornamentals grown mainly in greenhouses. The most prevalent hosts are English ivy (Hedera helix) and Cistus (Cistus salvifolius). The association of the species with acorn banksia (Banksia prionotes) plants in natural ecosystems in Australia, in affected vineyards (Vitis vinifera) in South Africa and almond (Prunus dulcis) trees in Spain and Turkey in addition to infection of shrubs and herbaceous ornamentals in a broad range of unrelated families are a sign of a wide ecological adaptation of the species and its potential threat to agricultural and natural ecosystems. The morphology of the persistent non-papillate ellipsoid sporangia, unique toruloid lobate hyphal swellings and amphigynous antheridia does not match any of the described species. Phylogenetic analysis based on sequences of the ITS rDNA, EF-1α, and β-tub supported that this organism is a hitherto unknown species. It is closely related to species in ITS clade 7b with the most closely related species being P. sojae. The name Phytophthora niederhauserii has been used in previous studies without the formal description of the holotype. This name is validated in this manuscript with the formal description of Phytophthora niederhauserii Z.G. Abad et J.A. Abad, sp. nov. The name is coined to honor Dr John S. Niederhauser, a notable plant pathologist and the 1990 World Food Prize laureate. © 2014 by The Mycological Society of America.

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

    Directory of Open Access Journals (Sweden)

    Soares E.D.R.

    2003-01-01

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

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

    Science.gov (United States)

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

    2015-12-15

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

  12. Role of Achiral Nucleobases in Multicomponent Chiral Self-Assembly: Purine-Triggered Helix and Chirality Transfer.

    Science.gov (United States)

    Deng, Ming; Zhang, Li; Jiang, Yuqian; Liu, Minghua

    2016-11-21

    Chiral self-assembly is a basic process in biological systems, where many chiral biomolecules such as amino acids and sugars play important roles. Achiral nucleobases usually covalently bond to saccharides and play a significant role in the formation of the double helix structure. However, it remains unclear how the achiral nucleobases can function in chiral self-assembly without the sugar modification. Herein, we have clarified that purine nucleobases could trigger N-(9-fluorenylmethox-ycarbonyl) (Fmoc)-protected glutamic acid to self-assemble into helical nanostructures. Moreover, the helical nanostructure could serve as a matrix and transfer the chirality to an achiral fluorescence probe, thioflavin T (ThT). Upon chirality transfer, the ThT showed not only supramolecular chirality but also circular polarized fluorescence (CPL). Without the nucleobase, the self-assembly processes cannot happen, thus providing an example where achiral molecules played an essential role in the expression and transfer of the chirality. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. Evidence for a possible role for nitric oxide in the modulation of heart activity in Achatina fulica and Helix aspersa.

    Science.gov (United States)

    White, A R; Curtis, S A; Walker, R J

    2004-02-01

    The effects of nitric oxide (NO) donors, S-nitroso-N-acetylpenicillamine, S-nitroso-l-glutathione, sodium nitroprusside and sodium nitrite were investigated on the activity of the isolated hearts of Achatina fulica and Helix aspersa. NO donors inhibited heart activity in a concentration-dependent manner. The only exception was sodium nitroprusside, which excited H. aspersa heart. The inhibitory effects of these NO donors were reduced by the NO scavenger, methylene blue, the guanylyl cyclase inhibitor, 1H-(1,2,4) Oxadiazolo(4,3-a)quinoxalin-1-one (ODQ), and potentiated by 8-Br-cGMP and the phosphodiesterase inhibitor 3-isobutyl-1-methylxanthine (IBMX). Acetylcholine also inhibited the heart activity, and this inhibition was reduced by methylene blue and ODQ. Positive NADPH-diaphorase staining was located in the outer pericardial layer of the heart of A. fulica. The present results provide evidence that NO may modulate the activity of gastropod hearts, and this modulation may modify the inhibitory action of acetylcholine on heart activity.

  14. 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}).

  15. Haemocyanins from Rapana venosa and Helix vulgaris display an antitumour activity via specific activation of spleen lymphocytes

    International Nuclear Information System (INIS)

    Iliev, I.; Toshkova, R.; Yossifova, L.; Zacharieva, S.; Dolashka-Angelova, P.; Hristova, R.; Yaneva, J.

    2008-01-01

    We have determined and analysed some immuno-adjuvant properties of haemocyanins isolated from the haemolymph of the snails Rapana venosa (RvH) and Helix vulgaris (HvH) acting via activation of cell-mediated immunity. As a result of nonspecific activation of the immune system in tumour-bearing animals treated with RvH and HvH, an increased resistance against Guerin ascites tumour progression was observed in comparison with controls (non-immunized animals). The investigations were focused on elucidation of the different mechanisms of immune response of spleen lymphocytes from experimental animals preliminary immunized with vaccines supplemented with either RvH or HvH. Experimental data showed significant immune activation, much higher than that in the control group immunized with Keyhole limpet haemocyanin (KLH). Supporting these data are the results on the survival rate determination of tumour-bearing animals immunized with each of the haemocyanins or conjugates haemocyanin/tumour antigen showing highest survival in animals treated with HvH, RvH and KLH in comparison with non immunized animals. (authors)

  16. Helix-sense-selective co-precipitation for preparing optically active helical polymer nanoparticles/graphene oxide hybrid nanocomposites.

    Science.gov (United States)

    Huang, Huajun; Li, Weifei; Shi, Yan; Deng, Jianping

    2017-05-25

    Constructing optically active helical polymer based nanomaterials without using expensive and limited chirally helical polymers has become an extremely attractive research topic in both chemical and materials science. In this study, we prepared a series of optically active helical polymer nanoparticles/graphene oxide (OAHPNs/GO) hybrid nanocomposites through an unprecedented strategy-the co-precipitation of optically inactive helical polymers and chirally modified GO. This approach is named helix-sense-selective co-precipitation (HSSCP), in which the chirally modified GO acted as a chiral source for inducing and further stabilizing the predominantly one-handed helicity in the optically inactive helical polymers. SEM and TEM images show quite similar morphologies of all the obtained OAHPNs/GO nanocomposites; specifically, the chirally modified GO sheets were uniformly decorated with spherical polymer nanoparticles. Circular dichroism (CD) and UV-vis absorption spectra confirmed the preferentially induced helicity in the helical polymers and the optical activity of the nanocomposites. The established HSSCP strategy is thus proven to be widely applicable and is expected to produce numerous functional OAHPNs/GO nanocomposites and even the analogues.

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

    International Nuclear Information System (INIS)

    Arakaki, Tracy; Neely, Helen; Boni, Erica; Mueller, Natasha; Buckner, Frederick S.; Van Voorhis, Wesley C.; Lauricella, Angela; DeTitta, George; Luft, Joseph; Hol, Wim G. J.; Merritt, Ethan A.

    2007-01-01

    The crystal structure of a phosphatidylethanolamine-binding protein from P. vivax, a homolog of Raf-kinase inhibitor protein (RKIP), has been solved to a resolution of 1.3 Å. The inferred interaction surface near the anion-binding site is found to include a distinctive left-handed α-helix. The structure of a putative Raf kinase inhibitor protein (RKIP) homolog from the eukaryotic parasite Plasmodium vivax has been studied to a resolution of 1.3 Å using multiple-wavelength anomalous diffraction at the Se K edge. This protozoan protein is topologically similar to previously studied members of the phosphatidylethanolamine-binding protein (PEBP) sequence family, but exhibits a distinctive left-handed α-helical region at one side of the canonical phospholipid-binding site. Re-examination of previously determined PEBP structures suggests that the P. vivax protein and yeast carboxypeptidase Y inhibitor may represent a structurally distinct subfamily of the diverse PEBP-sequence family

  18. In Vitro Antiviral Activity of Circular Triple Helix Forming Oligonucleotide RNA towards Feline Infectious Peritonitis Virus Replication

    Directory of Open Access Journals (Sweden)

    Oi Kuan Choong

    2014-01-01

    Full Text Available Feline Infectious Peritonitis (FIP is a severe fatal immune-augmented disease in cat population. It is caused by FIP virus (FIPV, a virulent mutant strain of Feline Enteric Coronavirus (FECV. Current treatments and prophylactics are not effective. The in vitro antiviral properties of five circular Triple-Helix Forming Oligonucleotide (TFO RNAs (TFO1 to TFO5, which target the different regions of virulent feline coronavirus (FCoV strain FIPV WSU 79-1146 genome, were tested in FIPV-infected Crandell-Rees Feline Kidney (CRFK cells. RT-qPCR results showed that the circular TFO RNAs, except TFO2, inhibit FIPV replication, where the viral genome copy numbers decreased significantly by 5-fold log10 from 1014 in the virus-inoculated cells to 109 in the circular TFO RNAs-transfected cells. Furthermore, the binding of the circular TFO RNA with the targeted viral genome segment was also confirmed using electrophoretic mobility shift assay. The strength of binding kinetics between the TFO RNAs and their target regions was demonstrated by NanoITC assay. In conclusion, the circular TFOs have the potential to be further developed as antiviral agents against FIPV infection.

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

    Science.gov (United States)

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

    2014-01-01

    Feline Infectious Peritonitis (FIP) is a severe fatal immune-augmented disease in cat population. It is caused by FIP virus (FIPV), a virulent mutant strain of Feline Enteric Coronavirus (FECV). Current treatments and prophylactics are not effective. The in vitro antiviral properties of five circular Triple-Helix Forming Oligonucleotide (TFO) RNAs (TFO1 to TFO5), which target the different regions of virulent feline coronavirus (FCoV) strain FIPV WSU 79-1146 genome, were tested in FIPV-infected Crandell-Rees Feline Kidney (CRFK) cells. RT-qPCR results showed that the circular TFO RNAs, except TFO2, inhibit FIPV replication, where the viral genome copy numbers decreased significantly by 5-fold log10 from 10(14) in the virus-inoculated cells to 10(9) in the circular TFO RNAs-transfected cells. Furthermore, the binding of the circular TFO RNA with the targeted viral genome segment was also confirmed using electrophoretic mobility shift assay. The strength of binding kinetics between the TFO RNAs and their target regions was demonstrated by NanoITC assay. In conclusion, the circular TFOs have the potential to be further developed as antiviral agents against FIPV infection.

  20. European business venturing in times of digitisation - An analysis of for-profit business incubators in a triple helix context

    DEFF Research Database (Denmark)

    Brem, Alexander; Kreusel, Nico; Roth, Natalie

    2018-01-01

    Business incubators have been developed as a key component of entrepreneurial activities in countries all over Europe. These incubators have a non-profit or a for-profit profile, with one-third located in Germany. The increased engagement of private business in what was a public-dominated incubat......Business incubators have been developed as a key component of entrepreneurial activities in countries all over Europe. These incubators have a non-profit or a for-profit profile, with one-third located in Germany. The increased engagement of private business in what was a public......-dominated incubation landscape may influence established theoretical frameworks. Within this context, this paper analyses 11 German business incubators to look at the most common types of for-profit business incubators in Germany and their main characteristics. Moreover, it introduces classification criteria...... for these incubators. Another aspect of the analysis is the effect of the triple helix dimensions of the different incubation types. The results show that two additional types of incubators can be identified in addition to the traditional public business incubator model, namely 'company builders' and 'accelerators...

  1. Fluorescence Imaging of Streptococcus pneumoniae with the Helix pomatia agglutinin (HPA As a Potential, Rapid Diagnostic Tool

    Directory of Open Access Journals (Sweden)

    Mirian Domenech

    2017-07-01

    Full Text Available Streptococcus pneumoniae is a common human pathogen and a major causal agent of life-threatening infections that can either be respiratory or non-respiratory. It is well known that the Helix pomatia (edible snail agglutinin (HPA lectin shows specificity for terminal αGalNAc residues present, among other locations, in the Forssman pentasaccharide (αGalNAc1→3βGalNAc1→3αGal1→4βGal1→4βGlc. Based on experiments involving choline-independent mutants and different growth conditions, we propose here that HPA recognizes the αGalNAc terminal residues of the cell wall teichoic and lipoteichoic acids of S. pneumoniae. In addition, experimental evidence showing that pneumococci can be specifically labeled with HPA when growing as planktonic cultures as well as in mixed biofilms of S. pneumoniae and Haemophilus influenzae has been obtained. It should be underlined that pneumococci were HPA-labeled despite of the presence of a capsule. Although some non-pneumococcal species also bind the agglutinin, HPA-binding combined with fluorescence microscopy constitutes a suitable tool for identifying S. pneumoniae and, if used in conjunction with Gram staining and/or other suitable technique like antigen detection, it may potentially facilitate a fast and accurate diagnosis of pneumococcal infections.

  2. The BID Domain of Type IV Secretion Substrates Forms a Conserved Four-Helix Bundle Topped with a Hook.

    Science.gov (United States)

    Stanger, Frédéric V; de Beer, Tjaart A P; Dranow, David M; Schirmer, Tilman; Phan, Isabelle; Dehio, Christoph

    2017-01-03

    The BID (Bep intracellular delivery) domain functions as secretion signal in a subfamily of protein substrates of bacterial type IV secretion (T4S) systems. It mediates transfer of (1) relaxases and the attached DNA during bacterial conjugation, and (2) numerous Bartonella effector proteins (Beps) during protein transfer into host cells infected by pathogenic Bartonella species. Furthermore, BID domains of Beps have often evolved secondary effector functions within host cells. Here, we provide crystal structures for three representative BID domains and describe a novel conserved fold characterized by a compact, antiparallel four-helix bundle topped with a hook. The conserved hydrophobic core provides a rigid scaffold to a surface that, despite a few conserved exposed residues and similarities in charge distribution, displays significant variability. We propose that the genuine function of BID domains as T4S signal may primarily depend on their rigid structure, while the plasticity of their surface may facilitate adaptation to secondary effector functions. Copyright © 2016 Elsevier Ltd. All rights reserved.

  3. Food-chain transfer of cadmium and zinc from contaminated Urtica dioica to Helix aspersa and Lumbricus terrestris.

    Science.gov (United States)

    Sinnett, Danielle E; Hodson, Mark E; Hutchings, Tony R

    2009-08-01

    The present study examines the potential of Urtica dioica as an ecologically relevant species for use in ecotoxicological testing. It is prevalent in degraded ecosystems and is a food source for invertebrates. Urtica dioica grown in hydroponic solutions containing from less than 0.003 to 5.7 mg Cd/L or from 0.02 to 41.9 mg Zn/L accumulated metals resulting in leaf tissue concentrations in the range of 0.10 to 24.9 mg Cd/kg or 22.5 to 2,772.0 mg Zn/kg. No toxicological effects were apparent except at the highest concentrations tested, suggesting that this species may be an important pathway for transfer of metals to primary plant consumers. Helix aspersa and Lumbricus terrestris were fed the Cd- and Zn-rich leaves of U. dioica for six and four weeks, respectively. Cadmium and Zn body load increased with increasing metal concentration in the leaves (p nettle leaves with concentrations of approximately 23 mg Cd/kg and 3,400 mg Zn/kg. Models demonstrate that L. terrestris Cd tissue concentrations (r2 = 0.74, p < 0.001) and H. aspersa Zn tissue concentrations (r(2) = 0.69, p < 0.001) can be estimated from concentrations of Cd and Zn within the leaves of U. dioica and suggest that reasonably reproducible results can be obtained using these species for ecotoxicological testing.

  4. The Triple Helix Model as an Effective Instrument for the Innovation Development of Industrial Enterprises within the National Economy

    Directory of Open Access Journals (Sweden)

    M. N. Dudin

    2014-06-01

    Full Text Available In the context of the transformation of the economies of developed countries towards a new type – knowledge economics – there has emerged the need for the creation and development of effective mechanisms for producing and commercializing knowledge based on the coordination of state, corporate, and academic interests. The subject of the article is topical, since innovation infrastructure is a fundamental factor in innovation development, and its development is a priority focus area in the state’s economic policy. In an era of transformations in the practice of production and knowledge transfer, it is important to analyze the links between theoretical knowledge and industrial information. The article provides a rationale for the fact that the model for the innovation development of industry (the Triple Helix Model, thanks to the multitude of entities engaged in innovation activity and the building of an extensive horizontally structured network, into which the elements of the “triple helix” are integrated, is capable of ensuring a synergistic effect and, consequently, is an effective instrument for boosting the innovation development of industry.

  5. An α‐Helix‐Mimicking 12,13‐Helix: Designed α/β/γ‐Foldamers as Selective Inhibitors of Protein–Protein Interactions

    Science.gov (United States)

    Grison, Claire M.; Miles, Jennifer A.; Robin, Sylvie

    2016-01-01

    Abstract A major current challenge in bioorganic chemistry is the identification of effective mimics of protein secondary structures that act as inhibitors of protein–protein interactions (PPIs). In this work, trans‐2‐aminocyclobutanecarboxylic acid (tACBC) was used as the key β‐amino acid component in the design of α/β/γ‐peptides to structurally mimic a native α‐helix. Suitably functionalized α/β/γ‐peptides assume an α‐helix‐mimicking 12,13‐helix conformation in solution, exhibit enhanced proteolytic stability in comparison to the wild‐type α‐peptide parent sequence from which they are derived, and act as selective inhibitors of the p53/hDM2 interaction. PMID:27467859

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

    DEFF Research Database (Denmark)

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

    2008-01-01

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

  7. Inactivation of Mechanically Activated Piezo1 Ion Channels Is Determined by the C-Terminal Extracellular Domain and the Inner Pore Helix

    Directory of Open Access Journals (Sweden)

    Jason Wu

    2017-11-01

    Full Text Available Piezo proteins form mechanically activated ion channels that are responsible for our sense of light touch, proprioception, and vascular blood flow. Upon activation by mechanical stimuli, Piezo channels rapidly inactivate in a voltage-dependent manner through an unknown mechanism. Inactivation of Piezo channels is physiologically important, as it modulates overall mechanical sensitivity, gives rise to frequency filtering of repetitive mechanical stimuli, and is itself the target of numerous human disease-related channelopathies that are not well understood mechanistically. Here, we identify the globular C-terminal extracellular domain as a structure that is sufficient to confer the time course of inactivation and a single positively charged lysine residue at the adjacent inner pore helix as being required for its voltage dependence. Our results are consistent with a mechanism for inactivation that is mediated through voltage-dependent conformations of the inner pore helix and allosteric coupling with the C-terminal extracellular domain.

  8. Characterization of the biomechanical properties of T4 pili expressed by Streptococcus pneumoniae--a comparison between helix-like and open coil-like pili.

    Science.gov (United States)

    Castelain, Mickaël; Koutris, Efstratios; Andersson, Magnus; Wiklund, Krister; Björnham, Oscar; Schedin, Staffan; Axner, Ove

    2009-07-13

    Bacterial adhesion organelles, known as fimbria or pili, are expressed by gram-positive as well as gram-negative bacteria families. These appendages play a key role in the first steps of the invasion and infection processes, and they therefore provide bacteria with pathogenic abilities. To improve the knowledge of pili-mediated bacterial adhesion to host cells and how these pili behave under the presence of an external force, we first characterize, using force measuring optical tweezers, open coil-like T4 pili expressed by gram-positive Streptococcus pneumoniae with respect to their biomechanical properties. It is shown that their elongation behavior can be well described by the worm-like chain model and that they possess a large degree of flexibility. Their properties are then compared with those of helix-like pili expressed by gram-negative uropathogenic Escherichia coli (UPEC), which have different pili architecture. The differences suggest that these two types of pili have distinctly dissimilar mechanisms to adhere and sustain external forces. Helix-like pili expressed by UPEC bacteria adhere to host cells by single adhesins located at the distal end of the pili while their helix-like structures act as shock absorbers to dampen the irregularly shear forces induced by urine flow and to increase the cooperativity of the pili ensemble, whereas open coil-like pili expressed by S. pneumoniae adhere to cells by a multitude of adhesins distributed along the pili. It is hypothesized that these two types of pili represent different strategies of adhering to host cells in the presence of external forces. When exposed to significant forces, bacteria expressing helix-like pili remain attached by distributing the external force among a multitude of pili, whereas bacteria expressing open coil-like pili sustain large forces primarily by their multitude of binding adhesins which presumably detach sequentially.

  9. A conserved degron containing an amphipathic helix regulates the cholesterol-mediated turnover of human squalene monooxygenase, a rate-limiting enzyme in cholesterol synthesis.

    Science.gov (United States)

    Chua, Ngee Kiat; Howe, Vicky; Jatana, Nidhi; Thukral, Lipi; Brown, Andrew J

    2017-12-08

    Cholesterol biosynthesis in the endoplasmic reticulum (ER) is tightly controlled by multiple mechanisms to regulate cellular cholesterol levels. Squalene monooxygenase (SM) is the second rate-limiting enzyme in cholesterol biosynthesis and is regulated both transcriptionally and post-translationally. SM undergoes cholesterol-dependent proteasomal degradation when cholesterol is in excess. The first 100 amino acids of SM (designated SM N100) are necessary for this degradative process and represent the shortest cholesterol-regulated degron identified to date. However, the fundamental intrinsic characteristics of this degron remain unknown. In this study, we performed a series of deletions, point mutations, and domain swaps to identify a 12-residue region (residues Gln-62-Leu-73), required for SM cholesterol-mediated turnover. Molecular dynamics and circular dichroism revealed an amphipathic helix within this 12-residue region. Moreover, 70% of the variation in cholesterol regulation was dependent on the hydrophobicity of this region. Of note, the earliest known Doa10 yeast degron, Deg1, also contains an amphipathic helix and exhibits 42% amino acid similarity with SM N100. Mutating SM residues Phe-35/Ser-37/Leu-65/Ile-69 into alanine, based on the key residues in Deg1, blunted SM cholesterol-mediated turnover. Taken together, our results support a model whereby the amphipathic helix in SM N100 attaches reversibly to the ER membrane depending on cholesterol levels; with excess, the helix is ejected and unravels, exposing a hydrophobic patch, which then serves as a degradation signal. Our findings shed new light on the regulation of a key cholesterol synthesis enzyme, highlighting the conservation of critical degron features from yeast to humans. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

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

    Science.gov (United States)

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

    2015-12-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2001-10-30

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

  12. Space confinement and rotation stress induced self-organization of double-helix nanostructure: a nanotube twist with a moving catalyst head.

    Science.gov (United States)

    Zhao, Meng-Qiang; Zhang, Qiang; Tian, Gui-Li; Huang, Jia-Qi; Wei, Fei

    2012-05-22

    Inorganic materials with double-helix structure have attracted intensive attention due to not only their elegant morphology but also their amazing morphology-related potential applications. The investigation on the formation mechanism of the inorganic double-helix nanostructure is the first step for the fundamental studies of their materials or physical properties. Herein, we demonstrated the space confinement and rotation stress induced self-organization mechanism of the carbon nanotube (CNT)-array double helices under scanning electron microscopy by directly observing their formation process from individual layered double hydroxide flakes, which is a kind of hydrotalcite-like material composed of positively charged layers and charge-balancing interlayer anions. Space confinement is considered to be the most important extrinsic factor for the formation of CNT-array double helices. Synchronous growth of the CNT arrays oppositely from LDH flakes with space confinement on both sides at the same time is essential for the growth of CNT-array double helices. Coiling of the as-grown CNT arrays into double helices will proceed by self-organization, tending to the most stable morphology in order to release their internal rotation stress. Based on the demonstrated mechanism, effective routes were carried out to improve the selectivity for CNT-array double helices. The work provides a promising method for the fabrication of double-helix nanostructures with their two helices connected at the end by self-assembly.

  13. Analysis of α-helix unfolding in the pine nut peptide Lys-Cys-His-Lys-Pro induced by pulsed electric field.

    Science.gov (United States)

    Xing, Jie; Zhang, Sitian; Zhang, Mingdi; Lin, Songyi

    2017-09-01

    A variety of analytical techniques were applied to explore the effects of pulsed electric field (PEF) on α-helix structural changes in the novel antioxidant peptide Lys-Cys-His-Lys-Pro (KCHKP, 611.76 Da). The relative α-helix content of the KCHKP peptide was significantly altered from 100% to 89.91 ± 0.97% when the electric pulse frequency was 1800 Hz and the field intensity was 10 kV cm -1 . Moreover, the 1,1-diphenyl-2-pycryl-hydrazyl (DPPH) and 2,2-azinobis diammonium salt (ABTS) radical-scavenging activities of PEF-treated KCHKP were increased from 56.31% ± 0.74% to 84.33% ± 1.23% and from 40.56% ± 0.78% to 51.33% ± 0.27%, respectively. PEF treatment increased peptide linkage stretch vibration and altered hydrogen bonding of KCHKP. The stability of the α-helix structure was influenced by hydrogen bonds within the peptide linkage of KCHKP induced by PEF and was related to changes in antioxidant activity. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

  14. Intermediate conformation between native β-sheet and non-native α-helix is a precursor of trifluoroethanol-induced aggregation of Human Carbonic Anhydrase-II

    International Nuclear Information System (INIS)

    Gupta, Preeti; Deep, Shashank

    2014-01-01

    Highlights: • HCAII forms amyloid-like aggregates at moderate concentration of trifluoroethanol. • Protein adopts a state between β-sheet and α-helix at moderate % of TFE. • Hydrophobic surface(s) of partially structured conformation forms amyloid. • High % of TFE induces stable α-helical state preventing aggregation. - Abstract: In the present work, we examined the correlation between 2,2,2-trifluoroethanol (TFE)-induced conformational transitions of human carbonic anhydrase II (HCAII) and its aggregation propensity. Circular dichroism data indicates that protein undergoes a transition from β-sheet to α-helix on addition of TFE. The protein was found to aggregate maximally at moderate concentration of TFE at which it exists somewhere between β-sheet and α-helix, probably in extended non-native β-sheet conformation. Thioflavin-T (ThT) and Congo-Red (CR) assays along with fluorescence microscopy and transmission electron microscopy (TEM) data suggest that the protein aggregates induced by TFE possess amyloid-like features. Anilino-8-naphthalene sulfonate (ANS) binding studies reveal that the exposure of hydrophobic surface(s) was maximum in intermediate conformation. Our study suggests that the exposed hydrophobic surface and/or the disruption of the structural features protecting a β-sheet protein might be the major reason(s) for the high aggregation propensity of non-native intermediate conformation of HCAII

  15. CTD, current meter, meteorological buoy, and bottle data from the Gulf of Mexico from the ALPHA HELIX and other platforms in support of LATEX A from 18 March 1993 to 23 September 1993 (NODC Accession 9400149)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CTD, current meter, meteorological buoy, and bottle data were collected from the Gulf of Mexico from the ALPHA HELIX and other platforms. Data were collected by...

  16. Profile nutrients data from bottle casts from the R/V Alpha Helix in the Bering Sea, Gulf of Alaska and Northeast Pacific from 16 August 1983 to 30 July 1989 (NODC Accession 0000252)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Profile nutrients and other data were collected from the R/V ALPHA HELIX from August 16, 1983 to July 30, 1989. Data were submitted by University of Alaska -...

  17. Cloud amount/frequency, NITRATE and other data from ALPHA HELIX in the Gulf of Alaska from 1990-09-11 to 1990-12-16 (NODC Accession 9100042)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Conductivity, Temperature and Depth (CTD) data were collected from Gulf of Alaska using Ship ALPHA HELIX during three cruises HX14-HX145. The data was collected...

  18. Physical profile data from CTD casts in the Gulf of Alaska from the R/V ALPHA HELIX from 2001-04-18 to 2001-12-11 (NODC Accession 0000739)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Physical profile data were collected from CTD casts in the Gulf of Alaska from the R/V Alpha Helix. Data were collected by Western Washington University (WWU) and...

  19. Physical profile data from the R/V ALPHA HELIX in the Gulf of Alaska as part of the GLOBEC Project from 02 October 1998 to 07 December 1999 (NODC Accession 0000238)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Physical profile data were collected from the R/V ALPHA HELIX in the Gulf of Alaska from October 2, 1998 to December 7, 1999. Data were submitted by the University...

  20. Nutrients data from bottle casts in the Bering Sea from the R/V ALPHA HELIX as part of the Inner Shelf Transport and Recycling Project 04 July 1986 to 25 September 1986 (NODC Accession 0000293)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Nitrate, nitrite, phosphate, silicate, and other data were collected from the R/V ALPHA HELIX from July 4, 1986 to September 25, 1986. Data were submitted by...

  1. Physical and nutrient profile data from bottle casts from the R/V ALPHA HELIX in Gulf of Alaska from 03 December 1990 to 11 December 1998 (NODC Accession 0000221)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Physical and nutrients data were collected using bottle casts from the R/V ALPHA HELIX in Gulf of Alaska from December 3, 1980 to December 11, 1998. These data were...

  2. Turbidity, cloud amount/frequency and other data from ALPHA HELIX in the Gulf of Alaska and Bering Sea from 1989-10-04 to 1990-06-26 (NODC Accession 9100032)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Conductivity, Temperature and Depth (CTD) and Benthic data were collected from Gulf of Alaska and Bering Sea using NOAA Ship Alpha Helix. The data was collected...

  3. Cloud amount/frequency, NITRATE and other data from ALPHA HELIX in the Gulf of Alaska from 1988-09-14 to 1988-09-29 (NODC Accession 8800279)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The University of Alaska, Institute of Marine Science is responsible for this data collected aboard the R/V Alpha Helix on cruise number HX118 between September 14,...

  4. Cloud amount/frequency, NITRATE and other data from ALPHA HELIX in the Bering Sea and Chukchi Sea from 1993-09-09 to 1993-10-10 (NODC Accession 9400036)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Conductivity, Temperature and Depth (CTD) and other data were collected in Bering Sea and Chukchi Sea. Data was collected from Ship ALPHA HELIX. The data was...

  5. Current components, physical, and other data from moored current meters and CTD casts from the ALPHA HELIX and other platforms from Gulf of Alaska from 1988-04-28 to 1988-06-29 (NODC Accession 8800237)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Current components, physical, and other data were collected by moored current meters and CTD casts in the Gulf of Alaska from the ALPHA HELIX and other platforms....

  6. Cloud amount/frequency, TRANSMISSIVITY and other data from ALPHA HELIX and LITTLE DIPPER in the Gulf of Alaska from 1992-01-28 to 1992-04-22 (NODC Accession 9200146)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Conductivity, Temperature and Depth (CTD) and other data were collected in Gulf of Alaska. Data was collected from Ships ALPHA HELIX and LITTLE DIPPER. The data...

  7. Nutrients data from the R/V ALPHA HELIX and T.G. THOMPSON as part of the Inner Shelf Transfer and Recycling Project from 17 April 1987 to 21 July 1988 (NODC Accession 0000296)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Nitrate, nitrite, phosphate, silicate, and other data were collected from the R/V ALPHA HELIX and THOMAS G. THOMPSON from April 17, 1987 to July 21, 1988. Data were...

  8. Depth, salinity, and other data were collected from the R/V ALPHA HELIX in the Bering Sea as part of the Inner Shelf Transport and Recycling Project (ISHTAR) from 17 September 1986 to 25 September 1986 (NODC Accession 0000275)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Depth, fluorescence, oxygen, salinity, and water temperature data were collected from the R/V ALPHA HELIX from September 17, 1986 to September 25, 1986. Data were...

  9. Nutrients profile data from the R/V ALPHA HELIX in the Bering Sea in support of the Inner Shelf Transport and Recycling Project (ISHTAR) from 13 July 1985 to 14 October 1985 (NODC Accession 0000276)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Ammonium, nitrate, nitrite, phosphate, silicate, and urea data were collected from the R/V ALPHA HELIX from July 13, 1985 to October 14, 1985. Data were submitted by...

  10. Cloud amount/frequency, NITRATE and other data from ALPHA HELIX in the Coastal Waters of S. Alaska from 1991-07-24 to 1991-11-14 (NODC Accession 9200039)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Conductivity, Temperature and Depth (CTD) and other data were collected in Coastal Waters of S. Alaska. Data was collected in five cruises from Ship ALPHA HELIX....

  11. Beta2-adrenergic receptor homodimers: Role of transmembrane domain 1 and helix 8 in dimerization and cell surface expression.

    Science.gov (United States)

    Parmar, Vikas K; Grinde, Ellinor; Mazurkiewicz, Joseph E; Herrick-Davis, Katharine

    2017-09-01

    Even though there are hundreds of reports in the published literature supporting the hypothesis that G protein-coupled receptors (GPCR) form and function as dimers this remains a highly controversial area of research and mechanisms governing homodimer formation are poorly understood. Crystal structures revealing homodimers have been reported for many different GPCR. For adrenergic receptors, a potential dimer interface involving transmembrane domain 1 (TMD1) and helix 8 (H8) was identified in crystal structures of the beta 1 -adrenergic (β 1 -AR) and β 2 -AR. The purpose of this study was to investigate a potential role for TMD1 and H8 in dimerization and plasma membrane expression of functional β 2 -AR. Charged residues at the base of TMD1 and in the distal portion of H8 were replaced, singly and in combination, with non-polar residues or residues of opposite charge. Wild type and mutant β 2 -AR, tagged with YFP and expressed in HEK293 cells, were evaluated for plasma membrane expression and function. Homodimer formation was evaluated using bioluminescence resonance energy transfer, bimolecular fluorescence complementation, and fluorescence correlation spectroscopy. Amino acid substitutions at the base of TMD1 and in the distal portion of H8 disrupted homodimer formation and caused receptors to be retained in the endoplasmic reticulum. Mutations in the proximal region of H8 did not disrupt dimerization but did interfere with plasma membrane expression. This study provides biophysical evidence linking a potential TMD1/H8 interface with ER export and the expression of functional β 2 -AR on the plasma membrane. This article is part of a Special Issue entitled: Interactions between membrane receptors in cellular membranes edited by Kalina Hristova. Copyright © 2016 Elsevier B.V. All rights reserved.

  12. Mapping the Active Site Helix-to-Strand Conversion of CxxxxC Peroxiredoxin Q Enzymes †

    Science.gov (United States)

    Perkins, Arden; Gretes, Michael C.; Nelson, Kimberly J.; Poole, Leslie B.; Karplus, P. Andrew

    2012-01-01

    Peroxiredoxins (Prx) are a family of enzymes which reduce peroxides using a peroxidatic cysteine residue; among these, the PrxQ subfamily members are proposed to be the most ancestral-like yet are among the least characterized. In many PrxQ enzymes, a second “resolving” cysteine is located six residues downstream from the peroxidatic Cys, and these residues form a disulfide during the catalytic cycle. Here, we describe three hyperthermophilic PrxQ crystal structures originally solved by the RIKEN structural genomics group. We reprocessed the diffraction data and carried out further refinement to yield models with Rfree lowered by 2.3–7.2% and resolution extended by 0.2–0.3 Å, making one, at 1.4 Å, the best resolved peroxiredoxin to date. Comparisons of two matched thiol and disulfide forms reveal that the active site conformational change required for disulfide formation involves a transition of about 20 residues from a pair of α-helices to a β-hairpin and 310-helix. Each conformation has about 10 residues with high disorder providing slack that enables the dramatic shift, and the two conformations are anchored to the protein core by distinct non-polar side chains that fill three hydrophobic pockets. Sequence conservation patterns confirm the importance of these and a few additional residues for function. From a broader perspective, this study raises the provocative question of how to make use of the valuable information in the protein data bank generated by structural genomics projects but not described in the literature, perhaps remaining unrecognized and certainly underutilized. PMID:22928725

  13. Sensitivity of immune response quality to influenza helix 190 antigen structure displayed on a modular virus-like particle.

    Science.gov (United States)

    Anggraeni, Melisa R; Connors, Natalie K; Wu, Yang; Chuan, Yap P; Lua, Linda H L; Middelberg, Anton P J

    2013-09-13

    Biomolecular engineering enables synthesis of improved proteins through synergistic fusion of modules from unrelated biomolecules. Modularization of peptide antigen from an unrelated pathogen for presentation on a modular virus-like particle (VLP) represents a new and promising approach to synthesize safe and efficacious vaccines. Addressing a key knowledge gap in modular VLP engineering, this study investigates the underlying fundamentals affecting the ability of induced antibodies to recognize the native pathogen. Specifically, this quality of immune response is correlated to the peptide antigen module structure. We modularized a helical peptide antigen element, helix 190 (H190) from the influenza hemagglutinin (HA) receptor binding region, for presentation on murine polyomavirus VLP, using two strategies aimed to promote H190 helicity on the VLP. In the first strategy, H190 was flanked by GCN4 structure-promoting elements within the antigen module; in the second, dual H190 copies were arrayed as tandem repeats in the module. Molecular dynamics simulation predicted that tandem repeat arraying would minimize secondary structural deviation of modularized H190 from its native conformation. In vivo testing supported this finding, showing that although both modularization strategies conferred high H190-specific immunogenicity, tandem repeat arraying of H190 led to a strikingly higher immune response quality, as measured by ability to generate antibodies recognizing a recombinant HA domain and split influenza virion. These findings provide new insights into the rational engineering of VLP vaccines, and could ultimately enable safe and efficacious vaccine design as an alternative to conventional approaches necessitating pathogen cultivation. Copyright © 2013 Elsevier Ltd. All rights reserved.

  14. Triple Helix - in Action?

    DEFF Research Database (Denmark)

    Helms, Niels Henrik; Tellerup, Susanne

    This paper presents a project i-Space about learning and playful applications, which could also document performance. The target group is mentally impaired citizens. The project is used as reference to a discussion on structures within innovation processes. This discussion leads to a discussion o...... of the user as a sense-making category in multi-disciplinary settings....

  15. Suvi õues / Ivi-Els Schneider

    Index Scriptorium Estoniae

    Schneider, Ivi-Els, 1945-

    2004-01-01

    Õuemööblit Eesti kodudest. 9 ill.: Verner Pantoni kavandatud plastiktool, Albero Medea kavandatud lamamistool, dirigent Tõnu Kaljuste pink mererannas, viljapeksumasina hammasrattast laud, puust kiikhobune jm.

  16. "Külaline" Võrumaal / Ivi Kaarna

    Index Scriptorium Estoniae

    Kaarna, Ivi

    2007-01-01

    Võrumaal jätkusid Suurbritannia-Saksamaa-Soome-Eesti ühisfilmi "Külaline" võtted, režissöör Jukka-Pekka Valkeapää, operaator Tuomo Hutri, produtsent Exitfilmist Anneli Ahven, peaosades Vitali Bobrov, Emilia Ikäheimo, Pavel Liski

  17. Measuring the Value of an Ivy Degree.

    Science.gov (United States)

    Gose, Ben

    2000-01-01

    Study examining the earnings of students accepted by elite colleges but who chose to attend less-selective institutions finds that students do not enhance earnings by graduating from colleges with high average Scholastic Assessment Test scores, suggesting that admissions decisions fail to account for intangibles such as students' ambition,…

  18. The Agenda-Setting of Ivy Lee.

    Science.gov (United States)

    Olasky, Marvin N.

    Journalism historians in recent years have made good use of agenda-setting theory in research, but there has been one drawback: in concentrating on the political and economic views of publishers, editors, and reporters, the agendas of those working behind the scenes, the public relations men and women have been overlooked. The public relations…

  19. Outsmarting Poison Ivy and Other Poisonous Plants

    Science.gov (United States)

    ... poison sumac. Protectants such as baking soda or colloidal oatmeal relieve minor irritation and itching. Aluminum acetate ... Food and Drug Administration 10903 New Hampshire Avenue Silver Spring, MD 20993 1-888-INFO-FDA (1- ...

  20. Liivakujud : kaunid ja unustusse vajuvad / Ivi Kaarna

    Index Scriptorium Estoniae

    Kaarna, Ivi

    2008-01-01

    Tamula järve ääres liivalinnas valminud liivaskulptuuridest. Tutvustatakse hollandlase Jaap Ticheneri (festivali võitja), Kimmo Frosti, Ferenc Monostori, Rodrigo Ferreira, Irina Kudrjavtseva, Kalle Pruudeni töid