WorldWideScience

Sample records for electra mass stranded

  1. Electra Laser Facility

    Data.gov (United States)

    Federal Laboratory Consortium — FUNCTION: The Electra Laser Facility is used to develop the science and technology needed to develop a reliable, efficient, high-energy, repetitively pulsed krypton...

  2. Electra-Clad

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2006-05-04

    The study relates to the use of building-integrated photovoltaics. The Electra-Clad project sought to use steel-based cladding as a substrate for direct fabrication of a fully integrated solar panel of a design similar to the ICP standard glass-based panel. The five interrelated phases of the project are described. The study successfully demonstrated that the principles of the panel design are achievable and sound. But, despite intensive trials, a commercially realistic solar performance has not been achieved: the main failing was the poor solar conversion efficiency as the active area of the panel was increased in size. The problem lies with the coating used on the steel cladding substrates and it was concluded that a new type of coating will be required. ICP Solar Technologies UK carried out the work under contract to the DTI.

  3. Las tres electras

    Directory of Open Access Journals (Sweden)

    Abelardo Forero Benavides

    1965-10-01

    Full Text Available Electra hizo su aparición en el Teatro Colón de Bogotá, después de dos mil cuatrocientos años. Habló en griego moderno. La mayor parte de los espectadores, naturalmente, no entendíamos el texto. Teníamos que llevar en la mente, escritos, los títulos en español. Pero el interés que nos movía a concurrir al espectáculo no tenía nada que ver con el "snobismo". Teníamos el anhelo de admirar, en actuación viva, el coro griego.

  4. Electra-slate. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Lane, M

    2004-09-15

    The aim of this project was to develop a photovoltaic (PV) roofing tile that could safely be installed by any roofer without additional training and supervision on a roof constructed using a traditional truss/rafter/felt/batten approach. It is hoped that such a tile, which would closely resemble conventional roofing tiles, would overcome the conservatism of the UK building industry to new ideas. The project involves improving on the design of 'Electra-Slate', a solar roof slate using thin film silicon that was originally produced in 2003 by ICP Solar Technologies and PV Systems. The overall aim is to design a slate that would be simple to install, robust for site handling, visually similar to standard slates and suitable for distribution through builders merchants. The design specification of the Electra-Slate has now been finalised and prototypes produced to prove the concept in terms of both installation and manufacturing. A laser system that replaces the need for four separate laser systems taking over 20 minutes processing time, a two-part connector (the female on the slate and the male on the wiring loom) and an effective system of mounting the Electra-Slate without the need to drill holes have been developed. ICP will now be able to undertake post qualification production of Electra-Slate and to seek collaborators for large-scale manufacture and launch of the product.

  5. False killer whale Pseudorca crassidens mass stranding at Long ...

    African Journals Online (AJOL)

    A mass stranding of false killer whales Pseudorca crassidens at Long Beach near the village of Kommetjie (34°8.18′ S, 18°9.77′ E) on the Cape Peninsula, South Africa, in May 2009 is described. The estimated size of stranded group was 55 animals, which is close to the median size of P. crassidens groups that have ...

  6. Marine mammal strandings in the New Caledonia region, Southwest Pacific.

    Science.gov (United States)

    Borsa, Philippe

    2006-04-01

    Four hundred twenty three marine mammals, in 72 stranding events, were recorded between 1877 and 2005 in New Caledonia, the Loyalty Islands, and Vanuatu in the southwest Pacific. Sixteen species were represented in this count, including: minke whale, Balaenoptera acutorostrata (1 single stranding), sei whale, B. borealis (1 single stranding), blue whale, B. musculus (1 single stranding), humpback whale, Megaptera novaeangliae (2 single strandings), giant sperm whale, Physeter macrocephalus (18 single strandings, 2 pair strandings), pygmy sperm whale, Kogia breviceps (5 single strandings), dwarf sperm whale, K. sima (2 single strandings, 1 triple stranding), Blainville's beaked whale, Mesoplodon densirostris (2 single strandings), short-finned pilot whale, Globicephala macrorhynchus (4 strandings, 56 individuals), melon-headed whale, Peponocephala electra (1 single stranding and 2 mass strandings totalling 231 individuals), common dolphin, Delphinus delphis (1 single stranding), spinner dolphin, Stenella longirostris (1 pair stranding and 2 mass strandings of groups of approximately 30 individuals each), Indian Ocean bottlenose dolphin, Tursiops aduncus (2 single strandings), dugong, Dugong dugon (14 single strandings), and New Zealand fur seal, Arctocephalus forsteri (3 single strandings). A stranded rorqual identified as an Antarctic minke whale (B. bonaerensis), with coloration patterns that did not match known descriptions, was also reported. Sei whale was recorded for the first time in the tropical Southwest Pacific region and Antarctic minke whale, melon-headed whale, and Indian Ocean bottlenose dolphin were recorded for the first time in New Caledonia. Strandings of sperm whales were most frequent in the spring, but also occurred in autumn months, suggesting a seasonal pattern of occurrence possibly related to seasonal migration. One stranded humpback whale bore the scars of a killer whale's attack and one dugong was injured by a shark. Scars left by

  7. Short Communication A near mass stranding of cetaceans in St ...

    African Journals Online (AJOL)

    A group of 70 false killer whales Pseudorca crassidens and 124 bottlenose dolphins Tursiops sp., and a separate group of 13 Risso's dolphins Grampus griseus, assembled close inshore off a known mass-stranding site in St Helena Bay, South Africa, in October 2003. However, only a single Risso's dolphin attempted to ...

  8. A mass stranding of the squid martialia hyadesi Rochebrune and ...

    African Journals Online (AJOL)

    1997-02-11

    Feb 11, 1997 ... All animals were immature, with females in lower stages of maturity than males. No predatory marine mammals were seen in the area during or after the stranding event. An interpretation of the stranding is presented with reference to historical reports of squid strandings worldwide. Evidence suggests some ...

  9. Implementation of a method to visualize noise-induced hearing loss in mass stranded cetaceans

    Science.gov (United States)

    Morell, Maria; Brownlow, Andrew; McGovern, Barry; Raverty, Stephen A.; Shadwick, Robert E.; André, Michel

    2017-02-01

    Assessment of the impact of noise over-exposure in stranded cetaceans is challenging, as the lesions that lead to hearing loss occur at the cellular level and inner ear cells are very sensitive to autolysis. Distinguishing ante-mortem pathology from post-mortem change has been a major constraint in diagnosing potential impact. Here, we outline a methodology applicable to the detection of noise-induced hearing loss in stranded cetaceans. Inner ears from two mass strandings of long-finned pilot whales in Scotland were processed for scanning electron microscopy observation. In one case, a juvenile animal, whose ears were fixed within 4 hours of death, revealed that many sensory cells at the apex of the cochlear spiral were missing. In this case, the absence of outer hair cells would be compatible with overexposure to underwater noise, affecting the region which transduces the lowest frequencies of the pilot whales hearing spectrum. Perfusion of cochlea with fixative greatly improved preservation and enabled diagnostic imaging of the organ of Corti, even 30 hours after death. This finding supports adopting a routine protocol to detect the pathological legacy of noise overexposure in mass stranded cetaceans as a key to understanding the complex processes and implications that lie behind such stranding events.

  10. Adaptation of the Electra Radio to Support Multiple Receive Channels

    Science.gov (United States)

    Satorius, Edgar H.; Shah, Biren N.; Bruvold, Kristoffer N.; Bell, David J.

    2011-01-01

    Proposed future Mars missions plan communication between multiple assets (rovers). This paper presents the results of a study carried out to assess the potential adaptation of the Electra radio to a multi-channel transceiver. The basic concept is a Frequency Division multiplexing (FDM) communications scheme wherein different receiver architectures are examined. Options considered include: (1) multiple IF slices, A/D and FPGAs each programmed with an Electra baseband modem; (2) common IF but multiple A/Ds and FPGAs and (3) common IF, single A/D and single or multiple FPGAs programmed to accommodate the FDM signals. These options represent the usual tradeoff between analog and digital complexity. Given the space application, a common IF is preferable; however, multiple users present dynamic range challenges (e.g., near-far constraints) that would favor multiple IF slices (Option 1). Vice versa, with a common IF and multiple A/Ds (Option 2), individual AGC control of the A/Ds would be an important consideration. Option 3 would require a common AGC control strategy and would entail multiple digital down conversion paths within the FPGA. In this paper, both FDM parameters as well as the different Electra design options will be examined. In particular, signal channel spacing as a function of user data rates and transmit powers will be evaluated. In addition, tradeoffs between the different Electra design options will be presented with the ultimate goal of defining an augmented Electra radio architecture for potential future missions.

  11. Tailoring Thermal Conductivity of Single-stranded Carbon-chain Polymers through Atomic Mass Modification.

    Science.gov (United States)

    Liao, Quanwen; Zeng, Lingping; Liu, Zhichun; Liu, Wei

    2016-10-07

    Tailoring the thermal conductivity of polymers is central to enlarge their applications in the thermal management of flexible integrated circuits. Progress has been made over the past decade by fabricating materials with various nanostructures, but a clear relationship between various functional groups and thermal properties of polymers remains to be established. Here, we numerically study the thermal conductivity of single-stranded carbon-chain polymers with multiple substituents of hydrogen atoms through atomic mass modification. We find that their thermal conductivity can be tuned by atomic mass modifications as revealed through molecular dynamics simulations. The simulation results suggest that heavy homogeneous substituents do not assist heat transport and trace amounts of heavy substituents can in fact hinder heat transport substantially. Our analysis indicates that carbon chain has the biggest contribution (over 80%) to the thermal conduction in single-stranded carbon-chain polymers. We further demonstrate that atomic mass modifications influence the phonon bands of bonding carbon atoms, and the discrepancies of phonon bands between carbon atoms are responsible for the remarkable drops in thermal conductivity and large thermal resistances in carbon chains. Our study provides fundamental insight into how to tailor the thermal conductivity of polymers through variable substituents.

  12. Markers of Decompression Stress of Mass Stranded/Live Caught and Released vs. Single Stranded Marine Mammals

    Science.gov (United States)

    2014-09-30

    Caught and Released vs. Single Stranded Marine Mammals Michael Moore Biology Department Woods Hole Oceanographic Institution Woods Hole, MA 02543...Society for Marine Mammalogy 2013 Biennial Conference on the Biology of Marine Mammals in New Zealand. Dr. Fahlman’s graduate student Lauren Gonzalez...Harabin, Metabolism and thermoregulation in guinea pigs in hyperbaric hydrogen: Effects of pressure. Journal of Thermal Biology , 1997. 22(1): p. 31-41

  13. Orestes Kinetics Model for the Electra KrF Laser

    Science.gov (United States)

    Giuliani, J. L.; Kepple, P.; Lehmberg, R. H.; Myers, M. C.; Sethian, J. D.; Petrov, G.; Wolford, M.; Hegeler, F.

    2003-10-01

    Orestes is a first principles simulation code for the electron deposition, plasma chemistry, laser transport, and amplified spontaneous emission (ASE) in an e-beam pumped KrF laser. Orestes has been benchmarked against results from Nike at NRL and the Keio laser facility. The modeling tasks are to support ongoing oscillator experiments on the Electra laser ( 500 J), to predict performance of Electra as an amplifier, and to develop scaling relations for larger systems such as envisioned for an inertial fusion energy power plant. In Orestes the energy deposition of the primary beam electrons is assumed to be spatially uniform, but the excitation and ionization of the Ar/Kr/F2 target gas by the secondary electrons is determined from the energy distribution function as calculated by a Boltzmann code. The subsequent plasma kinetics of 23 species subject to over 100 reactions is followed with 1-D spatial resolution along the lasing axis. In addition, the vibrational relaxation among excited electronic states of the KrF molecule are included in the kinetics since lasing at 248 nm can occur from several vibrational lines of the B state. Transport of the lasing photons is solved by the method of characteristics. The time dependent ASE is calculated in 3-D using a ``local look-back'' scheme with discrete ordinates and includes specular reflection off the side walls and rear mirror. Gain narrowing is treated by multi-frequency transport of the ASE. Calculations for the gain, saturation intensity, extraction efficiency, and laser output from the Orestes model will be presented and compared with available data from Electra operated as an oscillator. Potential implications for the difference in optimal F2 concentration will be discussed along with the effects of window transmissivity at 248 nm.

  14. What caused the UK's largest common dolphin (Delphinus delphis mass stranding event?

    Directory of Open Access Journals (Sweden)

    Paul D Jepson

    Full Text Available On 9 June 2008, the UK's largest mass stranding event (MSE of short-beaked common dolphins (Delphinus delphis occurred in Falmouth Bay, Cornwall. At least 26 dolphins died, and a similar number was refloated/herded back to sea. On necropsy, all dolphins were in good nutritive status with empty stomachs and no evidence of known infectious disease or acute physical injury. Auditory tissues were grossly normal (26/26 but had microscopic haemorrhages (5/5 and mild otitis media (1/5 in the freshest cases. Five lactating adult dolphins, one immature male, and one immature female tested were free of harmful algal toxins and had low chemical pollutant levels. Pathological evidence of mud/seawater inhalation (11/26, local tide cycle, and the relative lack of renal myoglobinuria (26/26 suggested MSE onset on a rising tide between 06:30 and 08∶21 hrs (9 June. Potential causes excluded or considered highly unlikely included infectious disease, gas/fat embolism, boat strike, by-catch, predator attack, foraging unusually close to shore, chemical or algal toxin exposure, abnormal weather/climatic conditions, and high-intensity acoustic inputs from seismic airgun arrays or natural sources (e.g., earthquakes. International naval exercises did occur in close proximity to the MSE with the most intense part of the exercises (including mid-frequency sonars occurring four days before the MSE and resuming with helicopter exercises on the morning of the MSE. The MSE may therefore have been a "two-stage process" where a group of normally pelagic dolphins entered Falmouth Bay and, after 3-4 days in/around the Bay, a second acoustic/disturbance event occurred causing them to strand en masse. This spatial and temporal association with the MSE, previous associations between naval activities and cetacean MSEs, and an absence of other identifiable factors known to cause cetacean MSEs, indicates naval activity to be the most probable cause of the Falmouth Bay MSE.

  15. What Caused the UK's Largest Common Dolphin (Delphinus delphis) Mass Stranding Event?

    Science.gov (United States)

    Jepson, Paul D.; Deaville, Robert; Acevedo-Whitehouse, Karina; Barnett, James; Brownlow, Andrew; Brownell Jr., Robert L.; Clare, Frances C.; Davison, Nick; Law, Robin J.; Loveridge, Jan; Macgregor, Shaheed K.; Morris, Steven; Murphy, Sinéad; Penrose, Rod; Perkins, Matthew W.; Pinn, Eunice; Seibel, Henrike; Siebert, Ursula; Sierra, Eva; Simpson, Victor; Tasker, Mark L.; Tregenza, Nick; Cunningham, Andrew A.; Fernández, Antonio

    2013-01-01

    On 9 June 2008, the UK's largest mass stranding event (MSE) of short-beaked common dolphins (Delphinus delphis) occurred in Falmouth Bay, Cornwall. At least 26 dolphins died, and a similar number was refloated/herded back to sea. On necropsy, all dolphins were in good nutritive status with empty stomachs and no evidence of known infectious disease or acute physical injury. Auditory tissues were grossly normal (26/26) but had microscopic haemorrhages (5/5) and mild otitis media (1/5) in the freshest cases. Five lactating adult dolphins, one immature male, and one immature female tested were free of harmful algal toxins and had low chemical pollutant levels. Pathological evidence of mud/seawater inhalation (11/26), local tide cycle, and the relative lack of renal myoglobinuria (26/26) suggested MSE onset on a rising tide between 06∶30 and 08∶21 hrs (9 June). Potential causes excluded or considered highly unlikely included infectious disease, gas/fat embolism, boat strike, by-catch, predator attack, foraging unusually close to shore, chemical or algal toxin exposure, abnormal weather/climatic conditions, and high-intensity acoustic inputs from seismic airgun arrays or natural sources (e.g., earthquakes). International naval exercises did occur in close proximity to the MSE with the most intense part of the exercises (including mid-frequency sonars) occurring four days before the MSE and resuming with helicopter exercises on the morning of the MSE. The MSE may therefore have been a “two-stage process” where a group of normally pelagic dolphins entered Falmouth Bay and, after 3–4 days in/around the Bay, a second acoustic/disturbance event occurred causing them to strand en masse. This spatial and temporal association with the MSE, previous associations between naval activities and cetacean MSEs, and an absence of other identifiable factors known to cause cetacean MSEs, indicates naval activity to be the most probable cause of the Falmouth Bay MSE. PMID

  16. Repeated mass strandings of Miocene marine mammals from Atacama Region of Chile point to sudden death at sea.

    Science.gov (United States)

    Pyenson, Nicholas D; Gutstein, Carolina S; Parham, James F; Le Roux, Jacobus P; Chavarría, Catalina Carreño; Little, Holly; Metallo, Adam; Rossi, Vincent; Valenzuela-Toro, Ana M; Velez-Juarbe, Jorge; Santelli, Cara M; Rogers, David Rubilar; Cozzuol, Mario A; Suárez, Mario E

    2014-04-22

    Marine mammal mass strandings have occurred for millions of years, but their origins defy singular explanations. Beyond human causes, mass strandings have been attributed to herding behaviour, large-scale oceanographic fronts and harmful algal blooms (HABs). Because algal toxins cause organ failure in marine mammals, HABs are the most common mass stranding agent with broad geographical and widespread taxonomic impact. Toxin-mediated mortalities in marine food webs have the potential to occur over geological timescales, but direct evidence for their antiquity has been lacking. Here, we describe an unusually dense accumulation of fossil marine vertebrates from Cerro Ballena, a Late Miocene locality in Atacama Region of Chile, preserving over 40 skeletons of rorqual whales, sperm whales, seals, aquatic sloths, walrus-whales and predatory bony fish. Marine mammal skeletons are distributed in four discrete horizons at the site, representing a recurring accumulation mechanism. Taphonomic analysis points to strong spatial focusing with a rapid death mechanism at sea, before being buried on a barrier-protected supratidal flat. In modern settings, HABs are the only known natural cause for such repeated, multispecies accumulations. This proposed agent suggests that upwelling zones elsewhere in the world should preserve fossil marine vertebrate accumulations in similar modes and densities.

  17. Repeated mass strandings of Miocene marine mammals from Atacama Region of Chile point to sudden death at sea

    Science.gov (United States)

    Pyenson, Nicholas D.; Gutstein, Carolina S.; Parham, James F.; Le Roux, Jacobus P.; Chavarría, Catalina Carreño; Little, Holly; Metallo, Adam; Rossi, Vincent; Valenzuela-Toro, Ana M.; Velez-Juarbe, Jorge; Santelli, Cara M.; Rogers, David Rubilar; Cozzuol, Mario A.; Suárez, Mario E.

    2014-01-01

    Marine mammal mass strandings have occurred for millions of years, but their origins defy singular explanations. Beyond human causes, mass strandings have been attributed to herding behaviour, large-scale oceanographic fronts and harmful algal blooms (HABs). Because algal toxins cause organ failure in marine mammals, HABs are the most common mass stranding agent with broad geographical and widespread taxonomic impact. Toxin-mediated mortalities in marine food webs have the potential to occur over geological timescales, but direct evidence for their antiquity has been lacking. Here, we describe an unusually dense accumulation of fossil marine vertebrates from Cerro Ballena, a Late Miocene locality in Atacama Region of Chile, preserving over 40 skeletons of rorqual whales, sperm whales, seals, aquatic sloths, walrus-whales and predatory bony fish. Marine mammal skeletons are distributed in four discrete horizons at the site, representing a recurring accumulation mechanism. Taphonomic analysis points to strong spatial focusing with a rapid death mechanism at sea, before being buried on a barrier-protected supratidal flat. In modern settings, HABs are the only known natural cause for such repeated, multispecies accumulations. This proposed agent suggests that upwelling zones elsewhere in the world should preserve fossil marine vertebrate accumulations in similar modes and densities. PMID:24573855

  18. Stranding survey as a framework to investigate rare cetacean records of the north and north-eastern Brazilian coasts

    Directory of Open Access Journals (Sweden)

    Alexandra Fernandes Costa

    2017-08-01

    Full Text Available Marine mammal stranding events are used as an important tool for understanding cetacean biology worldwide. Nonetheless, there are vast gaps of knowledge to be filled in for a wide range of species. Reputable information is required regarding species from large baleen whales to sperm and beaked whales, as well as pelagic dolphins. This paper describes new cetacean records from north and north-eastern Brazil, which are both the least surveyed areas regarding aquatic mammals. Regular beach surveys were conducted to recover cetacean carcasses along the coast of Pará beginning November 2005. At the coasts of the Maranhão and Piauí states, the surveys were conducted between 2003 and 2013. From 2003 to 2014, 34 strandings of cetaceans were registered. The study provides four additional species records’ in the area based on strandings (Balaenoptera borealis, Balaenoptera physalus, Peponocephala electra, and Pseudorca crassidens. A mass stranding of Guiana dolphins (Sotalia guianensis, N = 12, the most common species for the region, was reported for the first time. The records presented herein are of special concern, since they expand the knowledge on cetaceans from the Brazilian coast. In addition, this study conducted an analysis to verify the similarity between cetacean compositions described for north and north-eastern Brazil and the southern Caribbean region. The results showed a high similarity between these regions, proving the connection with the Caribbean cetacean fauna.

  19. Stranding survey as a framework to investigate rare cetacean records of the north and north-eastern Brazilian coasts.

    Science.gov (United States)

    Costa, Alexandra Fernandes; Siciliano, Salvatore; Emin-Lima, Renata; Martins, Bruna Maria Lima; Sousa, Maura Elisabeth Moraes; Giarrizzo, Tommaso; Júnior, José de Sousa E Silva

    2017-01-01

    Marine mammal stranding events are used as an important tool for understanding cetacean biology worldwide. Nonetheless, there are vast gaps of knowledge to be filled in for a wide range of species. Reputable information is required regarding species from large baleen whales to sperm and beaked whales, as well as pelagic dolphins. This paper describes new cetacean records from north and north-eastern Brazil, which are both the least surveyed areas regarding aquatic mammals. Regular beach surveys were conducted to recover cetacean carcasses along the coast of Pará beginning November 2005. At the coasts of the Maranhão and Piauí states, the surveys were conducted between 2003 and 2013. From 2003 to 2014, 34 strandings of cetaceans were registered. The study provides four additional species records' in the area based on strandings ( Balaenoptera borealis , Balaenoptera physalus , Peponocephala electra , and Pseudorca crassidens ). A mass stranding of Guiana dolphins ( Sotalia guianensis , N = 12), the most common species for the region, was reported for the first time. The records presented herein are of special concern, since they expand the knowledge on cetaceans from the Brazilian coast. In addition, this study conducted an analysis to verify the similarity between cetacean compositions described for north and north-eastern Brazil and the southern Caribbean region. The results showed a high similarity between these regions, proving the connection with the Caribbean cetacean fauna.

  20. Possible causes of a harbour porpoise mass stranding in Danish waters in 2005

    DEFF Research Database (Denmark)

    Wright, Andrew J.; Maar, Marie; Mohn, Christian

    2013-01-01

    with the actual presence of strandings. Military vessels from various countries were confirmed in the area from the 7th April, en route to the largest naval exercise in Danish waters to date (Loyal Mariner 2005, 11-28 April). Although sonar usage cannot be confirmed, it is likely that ships were testing various...

  1. Tailoring Thermal Conductivity of Single-stranded Carbon-chain Polymers through Atomic Mass Modification

    OpenAIRE

    Liao, Quanwen; Zeng, Lingping; Liu, Zhichun; Liu, Wei

    2016-01-01

    Tailoring the thermal conductivity of polymers is central to enlarge their applications in the thermal management of flexible integrated circuits. Progress has been made over the past decade by fabricating materials with various nanostructures, but a clear relationship between various functional groups and thermal properties of polymers remains to be established. Here, we numerically study the thermal conductivity of single-stranded carbon-chain polymers with multiple substituents of hydrogen...

  2. A data management program for the Electra 800 automatic analyser.

    Science.gov (United States)

    Cambus, J P; Nguyen, F; de Graeve, J; Aragon, B; Valdiguie, P

    1994-10-01

    The Electra 800 automatic coagulation analyser rapidly performs most chronometric coagulation tests with high precision. To facilitate data handling, software, adaptable to any PC running under MS-DOS, was written to manage the analyser. Data are automatically collected via the RS232 interface or can be manually input. The software can handle 64 different analyses, all entirely 'user defined'. An 'electronic worksheet' presents the results in pages of ten patients. This enables the operator to assess the data and to perform verifications or complementary tests if necessary. All results outside a predetermined range can be flagged and results can be deleted, modified or added. A patient's previous files can be recalled as the data are archived at the end of the day. A 120 Mb disk can store approximately 130,000 patient files. A daily archive function can print the day's work in alphabetical order. A communication protocol allows connection to a mainframe computer. This program and the user's manual are available on request, free of charge, from the authors.

  3. Electra: durable repetitively pulsed angularly multiplexed KrF laser system

    Science.gov (United States)

    Wolford, Matthew F.; Myers, Matthew C.; Giuliani, John L.; Sethian, John D.; Burns, Patrick M.; Hegeler, Frank; Jaynes, Reginald

    2008-02-01

    Electra is a repetitively pulsed, electron beam pumped Krypton Fluoride (KrF) laser at the Naval Research Laboratory that is developing the technologies that can meet the Inertial Fusion Energy (IFE) requirements for durability, efficiency, and cost. The technologies developed on Electra should be directly scalable to a full size fusion power plant beam line. As in a full size fusion power plant beam line, Electra is a multistage laser amplifier system which, consists of a commercial discharge laser (LPX 305i, Lambda Physik), 175 keV electron beam pumped (40 ns flat-top) preamplifier, and 530 keV (100 ns flat-top) main amplifier. Angular multiplexing is used in the optical layout to provide pulse length control and to maximize laser extraction from the amplifiers. Single shot yield of 452 J has been extracted from the initial shots of the Electra laser system using a relatively low energy preamplifier laser beam. In rep-rate burst of 5 Hz for durations of one second a total energy of 1.585 kJ (average 317 J/pulse) has been attained. Total energy of 2.5 kJ has been attained over a two second period. For comparison, the main amplifier of Electra in oscillator mode has demonstrated at 2.5 Hz rep-rate average laser yield of 270 J over a 2 hour period.

  4. Cobwebs of Ophiuchus. I. Strands of (C-13)O - the mass distribution

    International Nuclear Information System (INIS)

    Loren, R.B.

    1989-01-01

    A 4.5 deg x 6.5 deg area of the Rho Ophiuchus molecular complex has been mapped in J = 1-0 (C-13)O with a 2.4 arcmin beam. The spatial distribution of (C-13)O, the distribution of clumps according to size, mass, density, and kinetic temperature are described. The distribution of material in the cloud is compared with the magnetic field distribution and with a shocked cloud model. Evidence supporting the role of shock in the cloud is found in the cloud morphology. 48 references

  5. Electra e Orestes: os efebos euripidianos na khóra de Argos

    Directory of Open Access Journals (Sweden)

    Márcia Cristina Lacerda Ribeiro

    2016-03-01

    Full Text Available Este artigo pretende analisar a Electra de Eurípides, sob um ângulo específico – o exame da efebia (ephebeia. O drama de exclusão-inclusão de Electra e Orestes, somado ao espaço de ação, a fronteira, levou-nos a conjecturar que os jovens vivenciam conjuntamente a instituição militar conhecida como efebia, um ritual de iniciação masculino. Em que pese a efebia ser exclusiva do universo masculino, desenvolvemos a ideia de os heróis formarem uma unidade, uma única persona – o vingador/justiceiro; portanto, ambos participam do mesmo ritual. Comparamos alguns aspectos da instituição com as ações desenvolvidas pelos protagonistas e cogitamos da possibilidade de, no nível do texto poético, assistir a efebia trágica.

  6. Stenurus globicephalae Baylis et Daubney, 1925 (Nematoda: Pseudaliidae from a False Killer Whale, Pseudorca crassidens (Cetacea: Delphinidae, Stranded on the Coast of Uruguay

    Directory of Open Access Journals (Sweden)

    María Inés Zylber

    2002-03-01

    Full Text Available Stenurus globicephalae Baylis et Daubney, 1925 (Nematoda: Pseudaliidae was found in the cranial air sinuses of a false killer whale, Pseudorca crassidens (Owen, stranded on the coast of Uruguay in 1999. Although this species has been reported once in P. crassidens from the North Atlantic, this is the first record for South America. A total of 920 specimens were obtained, of which 663 were females (body length: 4.34 ± 0.45 cm and 257 were males (2.99 ± 0.18 cm. Morphometric details are presented for S. globicephalae in this host, which do not show significant differences from those parasitizing Globicephala melas (Traill, but are distinct from those parasitizing Peponocephala electra (Gray. The host's skull revealed loss of osseous mass with the disappearance of the left zygomatic arch, and the left jaw had three osseous fenestrations in the region related to the organ of acoustic reception. These lesions support the hypothesis that this infection, known as stenurosis, was related to the stranding.

  7. Stenurus globicephalae Baylis et Daubney, 1925 (Nematoda: Pseudaliidae) from a false killer whale, Pseudorca crassidens (Cetacea: Delphinidae), stranded on the coast of Uruguay.

    Science.gov (United States)

    Zylber, María Inés; Failla, Gabriela; Le Bas, Alfredo

    2002-03-01

    Stenurus globicephalae Baylis et Daubney, 1925 (Nematoda: Pseudaliidae) was found in the cranial air sinuses of a false killer whale, Pseudorca crassidens (Owen), stranded on the coast of Uruguay in 1999. Although this species has been reported once in P. crassidens from the North Atlantic, this is the first record for South America. A total of 920 specimens were obtained, of which 663 were females (body length: 4.34 +/- 0.45 cm) and 257 were males (2.99 +/- 0.18 cm). Morphometric details are presented for S. globicephalae in this host, which do not show significant differences from those parasitizing Globicephala melas (Traill), but are distinct from those parasitizing Peponocephala electra (Gray). The host's skull revealed loss of osseous mass with the disappearance of the left zygomatic arch, and the left jaw had three osseous fenestrations in the region related to the organ of acoustic reception. These lesions support the hypothesis that this infection, known as stenurosis, was related to the stranding.

  8. Scenario-based approach adopted in the ELECTRA project for deriving innovative control room functionality

    DEFF Research Database (Denmark)

    Marinelli, Mattia; Heussen, Kai; Prostejovsky, Alexander Maria

    2017-01-01

    Here, the authors analyse the operator point of view of the Web-of-Cells concept defined in the EU project ELECTRA, by identifying operator tasks into the supervision of a highly automated power system, and the information requirements to facilitate appropriate operator situation awareness....... The study outlines the methodology adopted, which is based on the cognitive work analysis framework, to provide an overview of the most interesting scenarios and to summarise the requirements analysis results. In order to derive required control room functionality, a set of relevant control room scenarios...

  9. Electra: Repetitively Pulsed Angularly Multiplexed KrF Laser System Performance

    Science.gov (United States)

    Wolford, Matthew; Myers, Matthew; Giuliani, John; Sethian, John; Burns, Patrick; Hegeler, Frank; Jaynes, Reginald

    2008-11-01

    As in a full size fusion power plant beam line, Electra is a multistage laser amplifier system. The multistage amplifier system consists of a commercial discharge laser and two doubled sided electron beam pumped amplifiers. Angular multiplexing is used in the optical layout to provide pulse length control and to maximize laser extraction from the amplifiers. Two angularly multiplexed beams have extracted 30 J of KrF laser light with an aperture 8 x 10 cm^2, which is sufficient to extract over 500 J from the main amplifier and models agree. The main amplifier of Electra in oscillator mode has demonstrated single shot and rep-rate laser energies exceeding 700 J with 100 ns pulsewidth at 248 nm with an aperture 29 x 29 cm^2. Continuous operation of the KrF electron beam pumped oscillator has lasted for more than 2.5 hours without failure at 1 Hz and 2.5 Hz. The measured intensity and pulse energy for durations greater than thousand shots are consistent at measurable rep-rates of 1 Hz, 2.5 Hz and 5 Hz.

  10. Shaping the pain: Lamenting of Euripides’, Kakojannis’ and Liš’ Electra

    Directory of Open Access Journals (Sweden)

    Šijaković Đurđina

    2012-01-01

    Full Text Available This paper is the continuation of a wider research, presented with its first part: Shaping the pain: Ancient Greek Lament and Its Therapeutic Aspect. In the mentioned papers’ focus is creative- therapeutic aspect of a lament. The pain verbalized, revealed and shared with others -becomes itself a more bearable burden both for the woman that laments and for the bereaved family. Related to this therapeutic is the creative aspect of lament: the woman that mourns has to lament in order to make it easier for herself and others; but while lamenting, she is creating something. Deeply rooted in funeral ritual, a lament respects certain ritual rules, and yet it is a spontaneous expression of pain. A role of a lament in ancient Greek ritual is, as always when it comes to the Greek culture, an inexhaustible topic. The theme of a lament within ancient Greek tragedy is particularly interesting. Although tragedy belongs to literary tradition, it is a trustworthy source for ancient Greek ritual practice; a lament within tragedy is thus a ritual lament, and not only a literary one. Therapeutic aspect of a lament is also in the focus of this paper which examines "shaping of the pain" in few case studies. Inspired by laments of Montenegrin women, those that I have heard or read, I am re-reading Euripides’ Electra and Electra by Danilo Kiš (in which both Euripides’ drama and Montenegrin folklore is reflected, I am watching the Michalis Kakojannis’ movie Electra. Electra’s pain for loss, her sorrowful dirge, the one that through despair leads to anger and revengefulness, is found written or filmed: it is captured in a work of art, but it emits folklore and ritual characteristics. From that perspective I am re-reading one of the most beautiful Serbian epic poems, The Death of Jugović's Mother, which tells us about a mother that didn’t lament. [Projekat Ministarstva nauke Republike Srbije, br. 47016: Interdisciplinary Research of Serbian Cultural and

  11. Integrative modelling coupled with ion mobility mass spectrometry reveals structural features of the clamp loader in complex with single-stranded DNA binding protein.

    Science.gov (United States)

    Politis, Argyris; Park, Ah Young; Hall, Zoe; Ruotolo, Brandon T; Robinson, Carol V

    2013-11-29

    DNA polymerase III, a decameric 420-kDa assembly, simultaneously replicates both strands of the chromosome in Escherichia coli. A subassembly of this holoenzyme, the seven-subunit clamp loader complex, is responsible for loading the sliding clamp (β2) onto DNA. Here, we use structural information derived from ion mobility mass spectrometry (IM-MS) to build three-dimensional models of one form of the full clamp loader complex, γ3δδ'ψχ (254 kDa). By probing the interaction between the clamp loader and a single-stranded DNA (ssDNA) binding protein (SSB4) and by identifying two distinct conformational states, with and without ssDNA, we assemble models of ψχ-SSB4 (108 kDa) and the clamp loader-SSB4 (340 kDa) consistent with IM data. A significant increase in measured collision cross-section (~10%) of the clamp loader-SSB4 complex upon DNA binding suggests large conformational rearrangements. This DNA bound conformation represents the active state and, along with the presence of ψχ, stabilises the clamp loader-SSB4 complex. Overall, this study of a large heteromeric complex analysed by IM-MS, coupled with integrative modelling, highlights the potential of such an approach to reveal structural features of previously unknown complexes of high biological importance. Copyright © 2013 Elsevier Ltd. All rights reserved.

  12. A cinema for the unborn: moving pictures, mental pictures and Electra Sparks's New Thought film theory.

    Science.gov (United States)

    Ellis, Patrick

    2017-09-01

    In the 1910s, New York suffragette Electra Sparks wrote a series of essays in the Moving Picture News that advocated for cine-therapy treatments for pregnant women. Film was, in her view, the great democratizer of beautiful images, providing high-cultural access to the city's poor. These positive 'mental pictures' were important for her because, she claimed, in order to produce an attractive, healthy child, the mother must be exposed to quality cultural material. Sparks's championing of cinema during its 'second birth' was founded upon the premise of New Thought. This metaphysical Christian doctrine existed alongside the self-help and esoteric publishing domains and testified, above all, to the possibility of the 'mind-cure' of the body through the positive application of 'mental pictures'. Physiologically, their method began best in the womb, where the thoughts of the mother were of utmost importance: the eventual difference between birthing an Elephant Man or an Adonis. This positive maternal impression was commonplace in New Thought literature; it was Sparks's innovation to apply it to cinema. Investigating Sparks's film theory, practice and programming reveals her to be a harbinger of the abiding analogy between mind and motion picture that occupies film theorists to this day.

  13. [Euripides and Heraclitus on the attitude towards the corpse--an unrecognized fragment of Heraclitus in Electra, v. 289].

    Science.gov (United States)

    Moog, Ferdinand Peter

    2007-01-01

    Among the fragments of Heraclitus preserved to our times there is one saying that corpses ought to be disposed of more urgently than excrements Diels/Kranz 22 B 96. This sentence of an aphoristic nature, as frequently in the case of Heraclitus' scripts, allows many different interpretations. Even in antiquity these words led to vitriolic reactions and perplexed other writers. It is why they have been frequently quoted. Nevertheless, it has been overlooked until now that Euripides, the youngest of the three great Attic tragedians, had inserted them into one of his dramas. In his Electra it is the title figure who uses them while reporting the slaughter of Agamemnon. The quotation bears witness to Euripides' erudition as of one of the earliest men known to have possessed a private library. He must, therefore, have had access to many treatises on various subjects, among them to the work by Heraclitus. The Electra is a kind of homage to the obscure thinker from Ephesus. From this fact, and from the plot of this particular play, we may gain some insight into an ambivalent attitude of the ancient Greeks towards the corpse that certainly influenced ideas about human anatomy in particular and medical knowledge in general. A characteristic feature of the malefactors, namely Aigisthos and Clytaimestra, is the deliberate dishonouring of their victims corpse. By contrast, the noble characters Orestes and Electra never violate the corpse of their arch-enemy Aigisthos, but see to it that he is properly buried. Burial was, particularly in Athens, so essential that in the well-known Arginusai trial the failure to bury the fallen soldiers resulted in capital punishment for the accused. Nevertheless, it is likely that Euripides, following Heraclitus, did not reject the anatomical examination of corpses for scientific purposes, as he was not only in this regard a supporter of science and progress. Perhaps Plato's notion of the human body as the tomb of the soul is foreshadowed here

  14. IntErnationaL eLeCTRicAl storm registry (ELECTRA: Background, rationale, study design, and expected results

    Directory of Open Access Journals (Sweden)

    Federico Guerra

    2017-09-01

    Full Text Available Electrical storm (ES is defined as three or more episodes of ventricular fibrillation (VF or ventricular tachycardia (VT within 24 h and is associated with an increased cardiac and all-cause mortality. ES is a full arrhythmic emergency, its prevalence steadily increasing along with the number of implantable cardioverter-defibrillator implanted every year in developed countries. Nowadays, little evidence exists regarding clinical predictors of ES and their potential association on mortality and heart failure (HF, nor optimal pharmacological and non-pharmacological treatment has ever been codified. The intErnationaL eLeCTRicAl storm registry (ELECTRA is a multicentre, observational, prospective clinical study with two major aims. First, to create an international database on ES encompassing clinical features, pharmacological management, and interventional treatment strategies. Second, to describe mortality and rehospitalization rates in patients with ES over a long follow-up. The primary endpoint is all-cause mortality 3 years after the ES index event. The main secondary endpoint is hospitalization for all causes 3 years after the ES index event. Other secondary endpoints includes ES recurrences, unclustered VTs/VFs recurrences, and hospitalizations for HF worsening. A minimum of 500 patients will be included in the registry, and all patients will be followed-up for a minimum of three years. The present paper describes the background and current rationale of the ELECTRA study and details the study design, from enrolment strategy to data collection methods to planned data analysis. A brief overview of the expected results and their potential clinical and research implications will also be presented (NCT02882139. Keywords: Arrhythmia, Catheter ablation, Electrical storm, Implantable cardioverter-defibrillator, Ventricular fibrillation, Ventricular tachycardia

  15. The Pan-European Reference Grid Developed in the ELECTRA Project for Deriving Innovative Observability Concepts in the Web-of-Cells Framework

    DEFF Research Database (Denmark)

    Marinelli, Mattia; Pertl, Michael; Rezkalla, Michel M.N.

    2016-01-01

    In the ELECTRA EU project, an innovative approach for frequency and voltage control is investigated, with reference to future power system scenarios characterized by massive amounts of distributed energy resources. A control architecture based on dividing the power system into a web of subsystems......, the so-called cells, is proposed. Cells are individual control entities but also need to be coordinated together at system-wide level, in order to ensure secure and reliable overall operation (at Pan-European level). Task 5.4 in the ELECTRA project focuses on deriving novel observability concepts...... at system-wide scale. The methodology proposed in the task analyzes the system performance by investigating typical phenomena peculiar to each stability type and by developing observables necessary for the novel Web-of-Cells based control methods to operate properly at cell- and inter-cell level. Crucial...

  16. Centenario de Electra, de Galdós, símbolo anticlerical de la comunicación creativa

    Directory of Open Access Journals (Sweden)

    Javier Figuero

    2001-01-01

    Full Text Available El 30 de enero de 1901 se estrenaba en el teatro Español de Madrid la Electra de Benito Pérez Galdós, obra de teatro elevada a categoría de símbolo por los anticlericales que los obispos conseguirían prohibir en varias diócesis. Durante la gira que siguió, en algunas capitales se interrumpió la representación para que sonara el Himno de Riego. Futuro apóstol del integrismo, Ramiro de Maeztu, anarquista literario por entonces, acudió a la premiere madrileña con pistola, y sus amigos Pío Baroja y Azorín, que tampoco eran lo que serían, se movieron entre una clá de ácratas que imprecó a los jesuitas cuyas residencias resultarían apedreadas en Valladolid, Valencia, Barcelona, Cádiz, Santander y Zaragoza. La ciudadanía concienciada de Madrid agredió el coche del nuncio, intentó asaltar la sede de los luises y el palacio arzobispal, amenazó la casa central de los ignacianos y cantó La Marsellesa en la Puerta del Sol entre gritos por la libertad y la República, mientras paseó a hombros a Galdós como si de un antipapa se tratara. La prensa liberal le convirtió en lo mismo y la Correspondencia de España le calificó de "héroe legendario... que ha iniciado la libertad".

  17. Detection of double-stranded PCR amplicons at the attomole level electrosprayed from low nanomolar solutions using FT-ICR mass spectrometry.

    Science.gov (United States)

    Hannis, J C; Muddiman, D C

    2001-02-01

    An 82-base-pair polymerase chain reaction (PCR) product was amplified from the tetranucleotide short tandem repeat locus within the human tyrosine hydroxylase gene. PCR amplification was carried out using 100 ng of human nuclear DNA obtained from an individual who is homozygotic for the 9.3 allele resulting in a 50.5 kDa amplicon. To generate sufficient material for these investigations, several reactions were pooled and subsequently purified and quantified using UV-vis spectrophotometry. A serial dilution was carried out from a 2 microM stock solution providing solution concentrations down to 5 nM. Measurements were made using hexapole accumulation and gated trapping strategies in a 4.7 Telsa Fourier transform ion cyclotron resonance mass spectrometer (FTICR-MS) which facilitated detection of the amplicon at the attomole level when electrosprayed from a 5 nM solution with a single acquisition! The signal-to-noise ratio was determined to be 8.3 for the spectrum derived from the 5 nM solution using the magnitude-mode mass spectral peak height for the most abundant charge-state. This remarkable sensitivity for large PCR amplicons will dramatically improve the ability of electrospray ionization mass spectrometry to address important genetic questions for low copy number genes or when the amount of initial template is limited; the latter issue is commonly encountered in DNA forensics. Furthermore, these data represents over 2 orders of magnitude decrease in detection limits over other existing ESI-MS reports concerning PCR products, including those conducted using FTICR-MS.

  18. LHC superconducting strand

    CERN Multimedia

    Patrice Loiez

    1999-01-01

    This cross-section through a strand of superconducting matieral as used in the LHC shows the 8000 Niobium-Titanium filaments embedded like a honeycomb in copper. When cooled to 1.9 degrees above absolute zero in the LHC accelerator, these filaments will have zero resistance and so will carry a high electric current with no energy loss.

  19. Strand SPA & Konverentsikeskus

    Index Scriptorium Estoniae

    2008-01-01

    Strand SPA & Konverentsikeskus on Pärnu suurim äri- ja konverentsiklientidele suunatud hotell, mis klientide seas on hinnatud just selle kompleksuse tõttu, kuna kõik, mida külaline vajab ja soovib, on olemas ühe katuse all

  20. Sea Turtle Stranding Network Reports

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Sea Turtle Stranding and Salvage Network (STSSN) was formally established in 1980 to collect information on and document the stranding of marine turtles along...

  1. Fragmentation in DNA double-strand breaks

    International Nuclear Information System (INIS)

    Wei Zhiyong; Suzhou Univ., Suzhou; Zhang Lihui; Li Ming; Fan Wo; Xu Yujie

    2005-01-01

    DNA double strand breaks are important lesions induced by irradiations. Random breakage model or quantification supported by this concept is suitable to analyze DNA double strand break data induced by low LET radiation, but deviation from random breakage model is more evident in high LET radiation data analysis. In this work we develop a new method, statistical fragmentation model, to analyze the fragmentation process of DNA double strand breaks. After charged particles enter the biological cell, they produce ionizations along their tracks, and transfer their energies to the cells and break the cellular DNA strands into fragments. The probable distribution of the fragments is obtained under the condition in which the entropy is maximum. Under the approximation E≅E 0 + E 1 l + E 2 l 2 , the distribution functions are obtained as exp(αl + βl 2 ). There are two components, the one proportional to exp(βl 2 ), mainly contributes to the low mass fragment yields, the other component, proportional to exp(αl), decreases slowly as the mass of the fragments increases. Numerical solution of the constraint equations provides parameters α and β. Experimental data, especially when the energy deposition is higher, support the statistical fragmentation model. (authors)

  2. Cable degration of SSC strand

    International Nuclear Information System (INIS)

    Warnes, W.H.; Dai, W.; Seuntjens, J.; Capone, D.W. II

    1992-01-01

    Cable degradation of a SSC 40mm cable was studied by comparing the virgin strand and extracted strand measurements of critical current for all thirty strands. Typical degradation values of a few percent are observed in these materials. Image analysis performed on the strand cross sections found the filament deformation to be commensurate with the measured degradation in critical current. A simple model for current sharing in cables with edge damage reduction of Ic was developed and described below. Suggestions for measurements of cable critical current using extracted strands are also presented

  3. Getting to know you: Identification of pygmy killer whales (Feresa attenuata and melon-headed whales (Peponocephala electra under challenging conditions

    Directory of Open Access Journals (Sweden)

    Salvatore Siciliano

    2015-12-01

    Full Text Available Abstract Melon-headed whale (Peponocephala electra and Pygmy killer whale (Feresa attenuata are very poorly known species and are often confused with each other. We examined in detail Figure 3 in MARIGO and GIFFONI (2010 who reported that two melon-headed whales were taken in a surface driftnet about 90 nm off Santos, Brazil. We concluded they were in fact pygmy killer whales and explain our reasoning. To aid in future identifications, we illustrate and describe some of the main differences between these two species of small cetaceans. The incident reported by MARIGO and GIFFONI (2010 might represent the 'tip of the iceberg' regarding the incidental catches of cetaceans by pelagic drift nets off Brazil. Offshore driftnetting operating along the south-southeastern coast of Brazil may threaten pygmy killer whales.

  4. Stranded costs and exit fees

    International Nuclear Information System (INIS)

    2002-01-01

    The New Brunswick Market Design Committee has been directed to examine the issue of stranded costs since it is a major component of restructuring within the electricity sector. When regulated monopolies are faced with competition, they could find that some of their embedded costs cannot be recovered. These costs are referred to as stranded costs. Common sources include large capital investments in uneconomic plants or expensive power purchase contracts or fuel supply contracts. In general, stranded costs do not include gains or losses associated with normal business risks experienced by regulated utilities. This report presents recommendations for mitigation of stranded costs, valuation methodologies and cost-recovery mechanisms. It also presents a summary of experience with stranded costs in other jurisdictions such as California, Rhode Island, Pennsylvania and Ontario. Stranded costs are often recovered through an obligatory charge on all customers, particularly in jurisdictions where retail competition exists. In the New Brunswick market, however, the only customers who can create stranded costs are those eligible to choose their own suppliers. It is argued that since most customers will not have a choice of electricity suppliers, they cannot generate stranded costs and therefore, should not have to pay costs stranded by others. A method to quantify stranded costs is presented, along with a review of transmission-related stranded costs in New Brunswick. Expansion of self-generation in New Brunswick could strand transmission assets. Currently, self-generators only contribute a small amount to fixed charges of the transmission system. However, under new recommended tariffs, the amount could increase. It is likely that the net amount of stranded transmission costs will not be large. 2 refs., 1 fig

  5. Mass

    International Nuclear Information System (INIS)

    Quigg, Chris

    2007-01-01

    In the classical physics we inherited from Isaac Newton, mass does not arise, it simply is. The mass of a classical object is the sum of the masses of its parts. Albert Einstein showed that the mass of a body is a measure of its energy content, inviting us to consider the origins of mass. The protons we accelerate at Fermilab are prime examples of Einsteinian matter: nearly all of their mass arises from stored energy. Missing mass led to the discovery of the noble gases, and a new form of missing mass leads us to the notion of dark matter. Starting with a brief guided tour of the meanings of mass, the colloquium will explore the multiple origins of mass. We will see how far we have come toward understanding mass, and survey the issues that guide our research today.

  6. Single--stranded DNA mycoplasmaviruses

    Energy Technology Data Exchange (ETDEWEB)

    Maniloff, J.; Das, J.; Nowak, J.A.

    1978-01-01

    Two general types of single--stranded DNA bacteriophases have been described, icosahedral virions (e.g., 0X174) and filamentous virions (e.g., M13). Mycoplasmavirus MVL51 appears to represent another type of single--stranded DNA phage, with a genome size close to that of 0X174 and a nonlytic mode of infection like that of filamentous phages. The bullet shaped MVL51 morphology is unlike that of other known phages.

  7. Radiobiology of DNA strand breakage

    International Nuclear Information System (INIS)

    Johansen, I.

    1975-01-01

    The yield of single-strand breaks in lambda DNA within lysogenic host bacteria was measured after exposure to 4-MeV electrons (50 msec) and rapid transfer (45 msec) to alkaline detergent. In nitrogen anoxia the yield was 1.2 x 10 -12 DNA single-strand breaks per rad per dalton, and under full oxygenation the yield increased to 5 x 10 -12 breaks per rad per dalton. A search for the presence of fast repair mechanisms failed to demonstrate the presence of any mechanism for repair of strand breaks operating within a fraction of a second. Strand breaks produced in the presence of oxygen were repaired in 30--40 sec, while breaks produced under anoxia were rejoined even slower. A functional product from the polAl gene was needed for the rejoining of the broken molecules. Intermediate levels of DNA strand breakage seen at low concentrations of oxygen are dependent on the concentration of cellular sulfhydryl compounds, suggesting that in strand breakage oxygen and hydrogen donors compete for reactions with radiation-induced transients in the DNA. Intercomparisons of data on radiation-induced lethality of cells and single-strand breaks in episomal DNA allow the distinction between two classes of radiation-induced radicals, R 1 and R 2 , with different chemical properties; R 1 reacts readily with oxygen and N-oxyls under formation of potentially lethal products. The reactivity of oxygen in this reaction is 30--40 times higher than that of TMPN. R 2 reacts 16 times more readily than R 1 with oxygen under formation of single-strand breaks in the DNA. R 2 does not react with N-oxyls

  8. Si Electra fuese colombiana, se llamaría Rosalba, Ismena, María Eugenia, Vera, Alix María, Patricia, Gloria, Margarita...

    Directory of Open Access Journals (Sweden)

    Marie Estripeaut-Bourjac

    2017-07-01

    Full Text Available Electra se niega a permanecer en silencio mientras no se le haga justicia y los culpables de la muerte de su padre no reciban su merecido castigo: “Si el desafortunado muerto debiera quedarse tendido, condenado a la nada y al polvo, sin que los demás carguen a su vez con la sangrienta culpa, se acabaría para siempre jamás toda conciencia y toda piedad para los hombres” (Sófocles, 1972, p. 146. Su figura hará las veces de brújula para desentrañar las características de la palabra testimonial femenina, ya que, como Rosalba, quien busca sin descanso el cadáver de su hermano, cifra su dignidad en no callarse y, con ella, clama: “Mi dignidad, mi dignidad vale más que todo lo que se perdió” (Rosalba, citada por Franco, Nieto y Rincón, 2010, p. 105.

  9. Discriminating features of echolocation clicks of melon-headed whales (Peponocephala electra), bottlenose dolphins (Tursiops truncatus), and Gray's spinner dolphins (Stenella longirostris longirostris).

    Science.gov (United States)

    Baumann-Pickering, Simone; Wiggins, Sean M; Hildebrand, John A; Roch, Marie A; Schnitzler, Hans-Ulrich

    2010-10-01

    Spectral parameters were used to discriminate between echolocation clicks produced by three dolphin species at Palmyra Atoll: melon-headed whales (Peponocephala electra), bottlenose dolphins (Tursiops truncatus) and Gray's spinner dolphins (Stenella longirostris longirostris). Single species acoustic behavior during daytime observations was recorded with a towed hydrophone array sampling at 192 and 480 kHz. Additionally, an autonomous, bottom moored High-frequency Acoustic Recording Package (HARP) collected acoustic data with a sampling rate of 200 kHz. Melon-headed whale echolocation clicks had the lowest peak and center frequencies, spinner dolphins had the highest frequencies and bottlenose dolphins were nested in between these two species. Frequency differences were significant. Temporal parameters were not well suited for classification. Feature differences were enhanced by reducing variability within a set of single clicks by calculating mean spectra for groups of clicks. Median peak frequencies of averaged clicks (group size 50) of melon-headed whales ranged between 24.4 and 29.7 kHz, of bottlenose dolphins between 26.7 and 36.7 kHz, and of spinner dolphins between 33.8 and 36.0 kHz. Discriminant function analysis showed the ability to correctly discriminate between 93% of melon-headed whales, 75% of spinner dolphins and 54% of bottlenose dolphins.

  10. Arquitectura e industria hidroeléctrica. Las obras de Ignacio Álvarez Castelao y Juan José Elorza para Electra de Viesgo en Asturias

    Directory of Open Access Journals (Sweden)

    Javier Molina Sánchez

    2015-07-01

    Full Text Available La construcción de infraestructuras hidráulicas constituye uno de los ejes mejor conocidos de la política económica del desarrollismo industrial en España desde comienzos de los años cincuenta. Sin embargo, pese a su elevado número e interés, éstas apenas se han estudiado desde el punto de vista arquitectónico. Este artículo estudia las características de las obras hidráulicas que proyectaron juntos el arquitecto Ignacio Álvarez Castelao y el ingeniero Juan José Elorza para la compañía Electra de Viesgo SA en Asturias y en Palencia durante los años cincuenta y sesenta del siglo XX. Todos los casos mencionados tienen en común la fructífera colaboración de distintos profesionales en un equipo multidisciplinar en el que se incluyeron la bellas artes.

  11. Fair Exchange in Strand Spaces

    Directory of Open Access Journals (Sweden)

    Joshua D. Guttman

    2009-10-01

    Full Text Available Many cryptographic protocols are intended to coordinate state changes among principals. Exchange protocols coordinate delivery of new values to the participants, e.g. additions to the set of values they possess. An exchange protocol is fair if it ensures that delivery of new values is balanced: If one participant obtains a new possession via the protocol, then all other participants will, too. Fair exchange requires progress assumptions, unlike some other protocol properties. The strand space model is a framework for design and verification of cryptographic protocols. A strand is a local behavior of a single principal in a single session of a protocol. A bundle is a partially ordered global execution built from protocol strands and adversary activities. The strand space model needs two additions for fair exchange protocols. First, we regard the state as a multiset of facts, and we allow strands to cause changes in this state via multiset rewriting. Second, progress assumptions stipulate that some channels are resilient-and guaranteed to deliver messages-and some principals are assumed not to stop at certain critical steps. This method leads to proofs of correctness that cleanly separate protocol properties, such as authentication and confidentiality, from invariants governing state evolution. G. Wang's recent fair exchange protocol illustrates the approach.

  12. Acute Ischemic Stroke in a Patient with a Native Valvular Strand

    Directory of Open Access Journals (Sweden)

    Hak Young Rhee

    2010-06-01

    Full Text Available Valvular strands are known to be a potential source of cardioembolism but the natural history of native valvular strands has not yet been fully outlined. We report a case of ischemic stroke in a patient with a native valvular strand of the aortic valve and the patient’s clinical course. A previously healthy 21-year-old man suffered acute cerebral infarction in the right posterior cerebral artery territory. On echocardiography, there was a strand-like, oscillating mass on the left coronary cusp of the aortic valve. The patient received 100 mg aspirin daily and the valvular strand was not found on subsequent transthoracic echocardiography performed 10 days after the first examination. Serial echocardiographic examinations have been performed since the stroke and failed to find any abnormality. The patient did not suffer a recurrent stroke over a 3-year follow-up period.

  13. Mortality trends of stranded marine mammals on Cape Cod and southeastern Massachusetts, USA, 2000 to 2006.

    Science.gov (United States)

    Bogomolni, Andrea L; Pugliares, Katie R; Sharp, Sarah M; Patchett, Kristen; Harry, Charles T; LaRocque, Jane M; Touhey, Kathleen M; Moore, Michael

    2010-01-25

    To understand the cause of death of 405 marine mammals stranded on Cape Cod and southeastern Massachusetts between 2000 and 2006, a system for coding final diagnosis was developed and categorized as (1) disease, (2) human interaction, (3) mass-stranded with no significant findings, (4) single-stranded with no significant findings, (5) rock and/or sand ingestion, (6) predatory attack, (7) failure to thrive or dependent calf or pup, or (8) other. The cause of death for 91 animals could not be determined. For the 314 animals that could be assigned a cause of death, gross and histological pathology results and ancillary testing indicated that disease was the leading cause of mortality in the region, affecting 116/314 (37%) of cases. Human interaction, including harassment, entanglement, and vessel collision, fatally affected 31/314 (10%) of all animals. Human interaction accounted for 13/29 (45%) of all determined gray seal Halichoerus grypus mortalities. Mass strandings were most likely to occur in northeastern Cape Cod Bay; 97/106 (92%) of mass stranded animals necropsied presented with no significant pathological findings. Mass strandings were the leading cause of death in 3 of the 4 small cetacean species: 46/67 (69%) of Atlantic white-sided dolphin Lagenorhynchus acutus, 15/21 (71%) of long-finned pilot whale Globicephala melas, and 33/54 (61%) of short-beaked common dolphin Delphinus delphis. These baseline data are critical for understanding marine mammal population health and mortality trends, which in turn have significant conservation and management implications. They not only afford a better retrospective analysis of strandings, but ultimately have application for improving current and future response to live animal stranding.

  14. THE THREE-STRANDED CORD

    Directory of Open Access Journals (Sweden)

    Walter Redmond

    2013-11-01

    Full Text Available The Schoolmen did much of their most interesting and original philosophizing in theology. An example is the dilemma in Renaissance Scholasticism on free will: how can we act freely if God causes and knows our actions? Basic issues are involved here: the antinomy between freedom and determination, modal semantics, tense logic, the logical status of counterfacts. Mexican Jesuits Matías Blanco (d. 1734 and Antonio Peralta (d. 1736 wrote books on the subject. We describe here the “disjunctive” solution that Blanco advanced in his Funiculus triplex (The Three-Stranded Cord, published posthumously in Mexico in 1746. When someone is faced with choosing between B and C, conjectures Blanco, God does not actualize either, but rather their disjunction B-or-C. Blanco calls for a truce in the “war” among the contending schools so that they may consider his solution–for he thinks it may indeed be acceptable to all.

  15. Control of contact resistance by strand surface coating in 36-strands NbTi CICC's

    NARCIS (Netherlands)

    Nijhuis, Arend; ten Kate, Herman H.J.; Duchateau, Jean-Luc; Decool, Patrick

    2001-01-01

    The stability and AC loss of NbTi cable-in-conduit conductors (CICCs) is largely determined by the interstrand contact resistance (Rc). Rc is predominantly established by the strand surface properties. Five 36-strand CICCs, fully identical except for the plating of the strand surface or the presence

  16. Unraveling the strands of Saturn's F ring

    Science.gov (United States)

    Murray, C.D.; Gordon, M.K.; Giuliatti, Winter S.M.

    1997-01-01

    Several high-resolution Voyager 2 images of Saturn's F ring show that it is composed of at least four separate, non-intersecting strands extending ~45?? in longitude. Voyager 1 images show that the two brightest strands appear to intersect, giving rise to a "braided" morphology. From a study of all available Voyager images the detectable radial structure is cataloged and reviewed. Previous indications that there is fine material interior to the orbit of the F ring are confirmed. Evidence is presented that a model of four strands with comparable eccentricities and nearly aligned perichrones is consistent with all the Voyager observations. The observed perichrone offset of the two brightest strands suggests a minimum radial separation of ~20 km, which implies intersection of these strands when their finite radial widths are taken into account. The longitude range of such an intersection includes that observed in the Voyager 1 "braid" images. The proximity of these two strands at some longitudes may account for the apparent differences in the ring between the Voyager encounters, as well as provide a source for the short-lived features detected in the Hubble Space Telescope images of the F ring. There is no evidence that the locations of the individual strands are determined by resonant perturbations with known satellites. It is proposed that the radial structure is formed by the localized action of small satellites orbiting within the strand region. ?? 1997 Academic Press.

  17. Statistical Assessment of Cetacean Stranding Events in Cape Cod (Massachusetts, USA) area.

    Science.gov (United States)

    Zellar, R.; Pulkkinen, A. A.; Moore, K.; Reeb, D.; Karakoylu, E.; Uritskaya, O.

    2017-12-01

    Cetacean (whales, dolphins and porpoises) mass strandings are a longstanding mystery in the field of marine biology that continue to be recorded in coastal environments around the world. For each of these events, anywhere from a few to several hundred otherwise healthy animals strand in onshore environments, often for no apparent reason. While the causes of these events remain unclear, anthropogenic and naturogenic mechanisms have been suggested. We present results of an inter-disciplinary study that draws expertise from space weather, marine mammal biology and ecology, and marine mammal stranding response. This study assessed 16 years of cetacean stranding events in the Cape Cod (Massachusetts, USA) area concurrently with a large dataset of meteorological, geophysical, biological, oceanographic and space weather data to produce inferences about possible causes for these unexplained events.

  18. The stranding anomaly as population indicator

    DEFF Research Database (Denmark)

    Peltier, Helene; Baagøe, Hans J.; Camphuysen, Kees C. J.

    2013-01-01

    Ecological indicators for monitoring strategies are expected to combine three major characteristics: ecological significance, statistical credibility, and cost-effectiveness. Strategies based on stranding networks rank highly in cost-effectiveness, but their ecological significance and statistica...

  19. Bubbles in live-stranded dolphins.

    Science.gov (United States)

    Dennison, S; Moore, M J; Fahlman, A; Moore, K; Sharp, S; Harry, C T; Hoppe, J; Niemeyer, M; Lentell, B; Wells, R S

    2012-04-07

    Bubbles in supersaturated tissues and blood occur in beaked whales stranded near sonar exercises, and post-mortem in dolphins bycaught at depth and then hauled to the surface. To evaluate live dolphins for bubbles, liver, kidneys, eyes and blubber-muscle interface of live-stranded and capture-release dolphins were scanned with B-mode ultrasound. Gas was identified in kidneys of 21 of 22 live-stranded dolphins and in the hepatic portal vasculature of 2 of 22. Nine then died or were euthanized and bubble presence corroborated by computer tomography and necropsy, 13 were released of which all but two did not re-strand. Bubbles were not detected in 20 live wild dolphins examined during health assessments in shallow water. Off-gassing of supersaturated blood and tissues was the most probable origin for the gas bubbles. In contrast to marine mammals repeatedly diving in the wild, stranded animals are unable to recompress by diving, and thus may retain bubbles. Since the majority of beached dolphins released did not re-strand it also suggests that minor bubble formation is tolerated and will not lead to clinically significant decompression sickness.

  20. Mass strandings of various ommastrephid squid species have been ...

    African Journals Online (AJOL)

    spamer

    escape reaction, to jet backwards at speed, is commonly observed. Appearing to work their jets at top pressure with ... north-east of the continental shelf break, in an area influenced by the confluence of Antarctic circumpolar ..... the Indian Ocean sector of the Southern Ocean. Polar Biol. 11(4): 273–275. PRESCOTT, R. 1977 ...

  1. Performance optimization of internal tin process multifilamentary Nb{sub 3}Sn strands

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Ke, E-mail: zhangke@c-wst.com [State Key Laboratory of Solidification Processing, Northwestern Polytechnical University, Xi’an, Shaanxi 710072 (China); Western Superconducting Technologies Co. Ltd, Xi’an, Shaanxi 710018 (China); State Engineering Lab. of Superconducting Material Preparation, Xi’an, Shaanxi 710018 (China); Zhang, Pingxiang [State Key Laboratory of Solidification Processing, Northwestern Polytechnical University, Xi’an, Shaanxi 710072 (China); Western Superconducting Technologies Co. Ltd, Xi’an, Shaanxi 710018 (China); State Engineering Lab. of Superconducting Material Preparation, Xi’an, Shaanxi 710018 (China); Northwest Institute for Non-ferrous Metal Research, Xi’an, Shaanxi 710016 (China); Shi, Yigong; Liu, Jianwei; Gao, Huixian; Li, Jianfeng; Liu, Xianghong; Feng, Yong [Western Superconducting Technologies Co. Ltd, Xi’an, Shaanxi 710018 (China); State Engineering Lab. of Superconducting Material Preparation, Xi’an, Shaanxi 710018 (China)

    2016-11-01

    Highlights: • J{sub c} increases by adding Sn cores in the interspaces, hysteresis loss increases at the same time. • Enlarger the number of filaments with the same Sn proportion will increase J{sub c} and hysteresis loss. • Cu split adopted in each sub-element leads to a low hysteresis loss. - Abstract: In this study, internal tin process Nb{sub 3}Sn strands for the International Thermo-nuclear Experimental Reactor are developed in Western Superconducting Technologies. Short cable-in-conduit conductors manufactured with these strands have been qualified. Mass production is accomplished, and all the performances of the strands meet the requirement of ITER project. Besides, more researches on the effect of strand design on critical current density and hysteresis loss for Nb{sub 3}Sn strands are carried out. It is found that critical current density can be enhanced by reducing filament diameter and increasing Sn content, and hysteresis loss of the strands can be significantly reduced through Cu split adopted in sub-element.

  2. Mechanical properties of rubberwood oriented strand lumber (OSL: The effect of strand length

    Directory of Open Access Journals (Sweden)

    Buhnnum Kyokong

    2005-09-01

    Full Text Available Effect of strand length on mechanical properties (tension, compression and bending of oriented strand lumber (OSL made of rubberwood (Hevea brasiliensis Muell. Arg. was reported. Three strand lengths of 50 mm, 100 mm, and 150 mm with 1 mm thickness and 15 mm width were used. The strands were mixed with 5% pMDI glue (weight basis in a tumble mixer. The OSL specimens were formed by hot pressing process of unidirectionally aligned strands. Average specific gravity and moisture content were 0.76 and 8.34%, respectively. Tension and compression tests were carried out for directions both parallel and perpendicular to grain while bending test was performed only in parallel direction. Ultimate stresses and moduli of elasticity were examined from the stress-strain curves. It was found that for the parallel-to-grain direction, the longer strand OSL gave higher strength. The role of the strand length did not appear for the direction normal to the grain. The relationship between the mechanical properties of OSL and strand length was well described by the modified Hankinson formula.

  3. Initiation signals for complementary strand DNA synthesis on single-stranded plasmid DNA

    NARCIS (Netherlands)

    van der Ende, A.; Teertstra, R.; van der Avoort, H. G.; Weisbeek, P. J.

    1983-01-01

    The bacteriophage 0X174 origin for (+) strand DNA synthesis, when inserted in a plasmid, is in vivo a substrate for the initiator A protein, that is produced by infecting phages. The result of this interaction is the packaging of single-stranded plasmid DNA into preformed phage coats. These plasmid

  4. Coating Thickness of the LHC Superconducting Strands

    CERN Document Server

    Charras, N

    2003-01-01

    In order to determine the time of heat treatment to give to the superconducting Rutherford-type cable, it is essential to know the stabrite (SnAg5%) coating thickness on the superconducting strands. Depending on the heat treatment time applied, the cable will have a contact resistance between strands conform to the LHC specifications. A study on the tin layers thickness was carried out. It concerns the internal and the external strands for all the firms producing these strands for the LHC. The level of control of the tinning process was established for each firm, and correlations between different measuring techniques of the tin layers were achieved, based on the keys process parameters. Finally, a correlation's relationship was found to get an equivalent value of Atomic Adsorption Spectrometry (AAS) from a coulometric result. The AAS measurement gives the total amount of tin in the strand and is the reference nowadays. Thanks to this equivalence, the number of real AAS measurements carried out can be lowered...

  5. Connecting localized DNA strand displacement reactions

    Science.gov (United States)

    Mullor Ruiz, Ismael; Arbona, Jean-Michel; Lad, Amitkumar; Mendoza, Oscar; Aimé, Jean-Pierre; Elezgaray, Juan

    2015-07-01

    Logic circuits based on DNA strand displacement reactions have been shown to be versatile enough to compute the square root of four-bit numbers. The implementation of these circuits as a set of bulk reactions faces difficulties which include leaky reactions and intrinsically slow, diffusion-limited reaction rates. In this paper, we consider simple examples of these circuits when they are attached to platforms (DNA origamis). As expected, constraining distances between DNA strands leads to faster reaction rates. However, it also induces side-effects that are not detectable in the solution-phase version of this circuitry. Appropriate design of the system, including protection and asymmetry between input and fuel strands, leads to a reproducible behaviour, at least one order of magnitude faster than the one observed under bulk conditions.Logic circuits based on DNA strand displacement reactions have been shown to be versatile enough to compute the square root of four-bit numbers. The implementation of these circuits as a set of bulk reactions faces difficulties which include leaky reactions and intrinsically slow, diffusion-limited reaction rates. In this paper, we consider simple examples of these circuits when they are attached to platforms (DNA origamis). As expected, constraining distances between DNA strands leads to faster reaction rates. However, it also induces side-effects that are not detectable in the solution-phase version of this circuitry. Appropriate design of the system, including protection and asymmetry between input and fuel strands, leads to a reproducible behaviour, at least one order of magnitude faster than the one observed under bulk conditions. Electronic supplementary information (ESI) available. See DOI: 10.1039/C5NR02434J

  6. Asymmetric strand segregation: epigenetic costs of genetic fidelity?

    Directory of Open Access Journals (Sweden)

    Diane P Genereux

    2009-06-01

    Full Text Available Asymmetric strand segregation has been proposed as a mechanism to minimize effective mutation rates in epithelial tissues. Under asymmetric strand segregation, the double-stranded molecule that contains the oldest DNA strand is preferentially targeted to the somatic stem cell after each round of DNA replication. This oldest DNA strand is expected to have fewer errors than younger strands because some of the errors that arise on daughter strands during their synthesis fail to be repaired. Empirical findings suggest the possibility of asymmetric strand segregation in a subset of mammalian cell lineages, indicating that it may indeed function to increase genetic fidelity. However, the implications of asymmetric strand segregation for the fidelity of epigenetic information remain unexplored. Here, I explore the impact of strand-segregation dynamics on epigenetic fidelity using a mathematical-modelling approach that draws on the known molecular mechanisms of DNA methylation and existing rate estimates from empirical methylation data. I find that, for a wide range of starting methylation densities, asymmetric -- but not symmetric -- strand segregation leads to systematic increases in methylation levels if parent strands are subject to de novo methylation events. I found that epigenetic fidelity can be compromised when enhanced genetic fidelity is achieved through asymmetric strand segregation. Strand segregation dynamics could thus explain the increased DNA methylation densities that are observed in structured cellular populations during aging and in disease.

  7. The (not so immortal strand hypothesis

    Directory of Open Access Journals (Sweden)

    Cristian Tomasetti

    2015-03-01

    Significance: Utilizing an approach that is fundamentally different from previous efforts to confirm or refute the immortal strand hypothesis, we provide evidence against non-random segregation of DNA during stem cell replication. Our results strongly suggest that parental DNA is passed randomly to stem cell daughters and provides new insight into the mechanism of DNA replication in stem cells.

  8. SAKAMATA : A tool to avoid whale strandings

    NARCIS (Netherlands)

    Benders, F.P.A.; Beerens, S.P.; Verboom, W.C.

    2002-01-01

    World-wide a concern exists about the influence of man-made noise on marine life, and particularly of high power sonar. Most concern lies with marine mammals that use acoustics for hunting, communication and/or navigation. This concern is fed by recent strandings of whales that could be related to

  9. SAKAMATA : A tool to avoid whale strandings

    NARCIS (Netherlands)

    Benders, F.P.A.; Beerens, S.P.; Verboom, W.C.

    2004-01-01

    World-wide a concern exists about the influence of man-made noise on marine life, and particularly of high power sonar. Most concern lies with marine mammals that use acoustics for hunting, communication and/or navigation. This concern is fed by recent strandings of whales that could be related to

  10. Double-Stranded Peptide Nucleic Acids

    DEFF Research Database (Denmark)

    2001-01-01

    A novel class of compounds, known as peptide nucleic acids, form double-stranded structures with one another and with ssDNA. The peptide nucleic acids generally comprise ligands such as naturally occurring DNA bases attached to a peptide backbone through a suitable linker....

  11. Methodology for in situ gas sampling, transport and laboratory analysis of gases from stranded cetaceans.

    Science.gov (United States)

    Bernaldo de Quirós, Yara; González-Díaz, Oscar; Saavedra, Pedro; Arbelo, Manuel; Sierra, Eva; Sacchini, Simona; Jepson, Paul D; Mazzariol, Sandro; Di Guardo, Giovanni; Fernández, Antonio

    2011-01-01

    Gas-bubble lesions were described in cetaceans stranded in spatio-temporal concordance with naval exercises using high-powered sonars. A behaviourally induced decompression sickness-like disease was proposed as a plausible causal mechanism, although these findings remain scientifically controversial. Investigations into the constituents of the gas bubbles in suspected gas embolism cases are highly desirable. We have found that vacuum tubes, insulin syringes and an aspirometer are reliable tools for in situ gas sampling, storage and transportation without appreciable loss of gas and without compromising the accuracy of the analysis. Gas analysis is conducted by gas chromatography in the laboratory. This methodology was successfully applied to a mass stranding of sperm whales, to a beaked whale stranded in spatial and temporal association with military exercises and to a cetacean chronic gas embolism case. Results from the freshest animals confirmed that bubbles were relatively free of gases associated with putrefaction and consisted predominantly of nitrogen.

  12. KARAKTERISTIK ORIENTED STRAND BOARD DARI KAYU AKASIA DAN AFRIKA BERDASARKAN PENYUSUNAN ARAH STRAND

    Directory of Open Access Journals (Sweden)

    Nurhaida

    2008-04-01

    Full Text Available The research objectives arc to evaluate physical and mechanical properties of OSB based on strands orientation; and to evaluate physical and mechanical properties of OSB made from akasia wood (Acacia mangium Wild and afrika wood (Maesopsis eminii Engl. Akasia and afrika wood are used for OSB strand material with phenol formaldehyde (PF as adhesives and addition of paraffin. OSB made in this research is consist of three plies whereas are differed into eight (8 strand orientations. In the making process, hot press was carried out at 160OC and pressure 25kg.cm-2 for 15 minutes. Determination of OSB physical and mechanical properties is referred to JIS A 5908-2003. Result showed that strand orientations has no affect to OSB physical properties except for linicr swelling 24h, but it significantly influence all mechanical properties of OSB. Wood species have an effect on mechanical properties of OSB in the dry test, wet MOE lengthwise test and OSB physical properties, particularly to OSB density and water absorbing capability at 2h and 24h. All of OSB physical properties arc meet JIS A 5908-2003 standard, but not all of the mechanical properties such as dry MOE lengthwise, dry MOE and MOR widthwise. The best physical and mechanical properties is presented by OSB made from akasia wood in strand orientation F, G, Band C whereas all parameters meet JIS A 5908-2003 standard. In comparation with strand orientation B that is frequent used in industry, strand orientation F and G arc proficient to raise the modulus elasticity value (MOE and strength (MOR as much as 167.81-231.65% and 89.73-109.87%, respectively; especially in widthwise board application. Furthermore, strand orientation F and G arc more flexible as structural components

  13. Costs of high-field superconducting strands for particle accelerator magnets

    CERN Document Server

    Cooley, L D; Scanlan, R M; 10.1088/0953-2048/18/4/R01

    2005-01-01

    The costs of superconducting magnet strands are compared by calculating a 'production scaling factor' P that relates purchase data to the cost of raw materials. Using a consistent method, we normalize for different conductor geometries and strand diameters to arrive at cost indices in $ kg/sup -1/, $ m/sup -1/, and $ kA/sup -1/ m/sup -1/. Analyses of Nb47Ti conductors taken from the past 25 years of high-field magnet projects reveal that the price of raw materials and, to a lesser extent, finished strands, have tracked the price of niobium pentoxide. Performance gains during the 1980s produced $ kA /sup -1/ m/sup -1/ indices that fell with time ahead of strand cost in $ m/sup -1/, a situation that may reflect the present status of Nb /sub 3/Sn magnet conductors. Analyses of present materials show that P decreases systematically with billet mass. While production strands in 200-500 kg billets have costs ~3 times the cost of raw materials, the 20-50 kg billet size for internal-tin Nb/sub 3/Sn composites drives ...

  14. Corrosion characteristics of unprotected post-tensioning strands under stress.

    Science.gov (United States)

    2014-05-01

    An investigation was conducted to determine the effect of stress condition : and environmental exposure on corrosion of post-tensioned strands during ungrouted periods. : Exposures for periods of up to 4 weeks of stressed, as-received strand placed i...

  15. Facile synthesis of Graphene Oxide/Double-stranded DNA ...

    Indian Academy of Sciences (India)

    assembled liquid crystals and three-dimensional hydrogels of graphene oxidewith double-stranded DNA by simple mixing in an aqueous buffer media without unwinding double-strandedDNA to single-stranded DNA. The GO/dsDNA hydrogels have ...

  16. G-Strands on symmetric spaces

    Science.gov (United States)

    2017-01-01

    We study the G-strand equations that are extensions of the classical chiral model of particle physics in the particular setting of broken symmetries described by symmetric spaces. These equations are simple field theory models whose configuration space is a Lie group, or in this case a symmetric space. In this class of systems, we derive several models that are completely integrable on finite dimensional Lie group G, and we treat in more detail examples with symmetric space SU(2)/S1 and SO(4)/SO(3). The latter model simplifies to an apparently new integrable nine-dimensional system. We also study the G-strands on the infinite dimensional group of diffeomorphisms, which gives, together with the Sobolev norm, systems of 1+2 Camassa–Holm equations. The solutions of these equations on the complementary space related to the Witt algebra decomposition are the odd function solutions. PMID:28413343

  17. Population Size and Structure of Melon-Headed Whales (Peponocephala Electra) Around the Main Hawaiian Islands: Evidence of Multiple Populations Based on Photographic Data

    Science.gov (United States)

    2010-05-14

    echolocation clicks at night, that foraging is predominantly occurring at night (Baumann- Pickering 2009). Although relatively few stomach contents have...Hawaiian Islands; one on O‘ahu (two animals in 2003) and one on Kaua‘i (150—200 animals in 2004). There are a number of theories as to why mass...headed whales around Hawai‘i. Photo-Identification and Mark-Recapture In simple terms, the theory of mark-recapture (or capture-recapture) is merely a

  18. Double-stranded DNA dissociates into single strands when dragged into a poor solvent.

    Science.gov (United States)

    Cui, Shuxun; Yu, Jin; Kühner, Ferdinand; Schulten, Klaus; Gaub, Hermann E

    2007-11-28

    DNA displays a richness of biologically relevant supramolecular structures, which depend on both sequence and ambient conditions. The effect of dragging double-stranded DNA (dsDNA) from water into poor solvent on the double-stranded structure is still unclear because of condensation. Here, we employed single molecule techniques based on atomic force microscopy and molecular dynamics (MD) simulations to investigate the change in structure and mechanics of DNA during the ambient change. We found that the two strands are split apart when the dsDNA is pulled at one strand from water into a poor solvent. The findings were corroborated by MD simulations where dsDNA was dragged from water into poor solvent, revealing details of the strand separation at the water/poor solvent interface. Because the structure of DNA is of high polarity, all poor solvents show a relatively low polarity. We speculate that the principle of spontaneous unwinding/splitting of dsDNA by providing a low-polarity (in other word, hydrophobic) micro-environment is exploited as one of the catalysis mechanisms of helicases.

  19. The multiple personalities of Watson and Crick strands

    Directory of Open Access Journals (Sweden)

    Graur Dan

    2011-02-01

    Full Text Available Abstract Background In genetics it is customary to refer to double-stranded DNA as containing a "Watson strand" and a "Crick strand." However, there seems to be no consensus in the literature on the exact meaning of these two terms, and the many usages contradict one another as well as the original definition. Here, we review the history of the terminology and suggest retaining a single sense that is currently the most useful and consistent. Proposal The Saccharomyces Genome Database defines the Watson strand as the strand which has its 5'-end at the short-arm telomere and the Crick strand as its complement. The Watson strand is always used as the reference strand in their database. Using this as the basis of our standard, we recommend that Watson and Crick strand terminology only be used in the context of genomics. When possible, the centromere or other genomic feature should be used as a reference point, dividing the chromosome into two arms of unequal lengths. Under our proposal, the Watson strand is standardized as the strand whose 5'-end is on the short arm of the chromosome, and the Crick strand as the one whose 5'-end is on the long arm. Furthermore, the Watson strand should be retained as the reference (plus strand in a genomic database. This usage not only makes the determination of Watson and Crick unambiguous, but also allows unambiguous selection of reference stands for genomics. Reviewers This article was reviewed by John M. Logsdon, Igor B. Rogozin (nominated by Andrey Rzhetsky, and William Martin.

  20. Method of preparing and applying single stranded DNA probes to double stranded target DNAs in situ

    Science.gov (United States)

    Gray, J.W.; Pinkel, D.

    1991-07-02

    A method is provided for producing single stranded non-self-complementary nucleic acid probes, and for treating target DNA for use therewith. The probe is constructed by treating DNA with a restriction enzyme and an exonuclease to form template/primers for a DNA polymerase. The digested strand is resynthesized in the presence of labeled nucleoside triphosphate precursor. Labeled single stranded fragments are separated from the resynthesized fragments to form the probe. Target DNA is treated with the same restriction enzyme used to construct the probe, and is treated with an exonuclease before application of the probe. The method significantly increases the efficiency and specificity of hybridization mixtures by increasing effective probe concentration by eliminating self-hybridization between both probe and target DNAs, and by reducing the amount of target DNA available for mismatched hybridizations. No Drawings

  1. New insights on single-stranded versus double-stranded DNA library preparation for ancient DNA

    DEFF Research Database (Denmark)

    Wales, Nathan; Carøe, Christian; Sandoval-Velasco, Marcela

    2015-01-01

    An innovative single-stranded DNA (ssDNA) library preparation method has sparked great interest among ancient DNA (aDNA) researchers, especially after reports of endogenous DNA content increases >20-fold in some samples. To investigate the behavior of this method, we generated ssDNA...... and conventional double-stranded DNA (dsDNA) libraries from 23 ancient and historic plant and animal specimens. We found ssDNA library preparation substantially increased endogenous content when dsDNA libraries contained...

  2. Refinement of Propellant Strand Burning Method to Suit Aluminised Composite Rocket Propellant

    Science.gov (United States)

    2014-12-01

    from strands. In a DSTO (then WSRL) report published in 1985 by Kempson, et al. [1], a polyvinyl chloride /acetate copolymer solution in...within the firing chamber and produces a large mass of hot aluminium oxide. Those hot particles carry significant thermal energy and are free to...polybutadiene (HTPB) cross-linked with isophorone diisocyanate (IPDI). The formulation is a highly aluminised one containing 18 wt% aluminium (Al) and

  3. The Effect of the Heat Flux on the Self-Ignition of Oriented Strand Board

    Directory of Open Access Journals (Sweden)

    Hirle Siegfried

    2017-06-01

    Full Text Available This article deals with the initiation phase of flaming and smouldering burning of oriented strand board. The influence of heat flux on thermal degradation of OSB boards, time to ignition, heat release rate and mass loss rate using thermal analysis and vertical electrical radiation panel methods were studied. Significant information on the influence of the heat flux density and the thickness of the material on time to ignition was obtained.

  4. Effects of Strand Lay Direction and Crossing Angle on Tribological Behavior of Winding Hoist Rope

    Directory of Open Access Journals (Sweden)

    Xiang-dong Chang

    2017-06-01

    Full Text Available Friction and wear behavior exists between hoisting ropes that are wound around the drums of a multi-layer winding hoist. It decreases the service life of ropes and threatens mine safety. In this research, a series of experiments were conducted using a self-made test rig to study the effects of the strand lay direction and crossing angle on the winding rope’s tribological behavior. Results show that the friction coefficient in the steady-state period shows a decreasing tendency with an increase of the crossing angle in both cross directions, but the variation range is different under different cross directions. Using thermal imaging, the high temperature regions always distribute along the strand lay direction in the gap between adjacent strands, as the cross direction is the same with the strand lay direction (right cross contact. Additionally, the temperature rise in the steady-state increases with the increase of the crossing angle in both cross directions. The differences of the wear scar morphology are obvious under different cross directions, especially for the large crossing angle tests. In the case of right cross, the variation range of wear mass loss is larger than that in left cross. The damage that forms on the wear surface is mainly ploughing, pits, plastic deformation, and fatigue fracture. The major wear mechanisms are adhesive wear, and abrasive and fatigue wear.

  5. Effects of Strand Lay Direction and Crossing Angle on Tribological Behavior of Winding Hoist Rope.

    Science.gov (United States)

    Chang, Xiang-Dong; Peng, Yu-Xing; Zhu, Zhen-Cai; Gong, Xian-Sheng; Yu, Zhang-Fa; Mi, Zhen-Tao; Xu, Chun-Ming

    2017-06-09

    Friction and wear behavior exists between hoisting ropes that are wound around the drums of a multi-layer winding hoist. It decreases the service life of ropes and threatens mine safety. In this research, a series of experiments were conducted using a self-made test rig to study the effects of the strand lay direction and crossing angle on the winding rope's tribological behavior. Results show that the friction coefficient in the steady-state period shows a decreasing tendency with an increase of the crossing angle in both cross directions, but the variation range is different under different cross directions. Using thermal imaging, the high temperature regions always distribute along the strand lay direction in the gap between adjacent strands, as the cross direction is the same with the strand lay direction (right cross contact). Additionally, the temperature rise in the steady-state increases with the increase of the crossing angle in both cross directions. The differences of the wear scar morphology are obvious under different cross directions, especially for the large crossing angle tests. In the case of right cross, the variation range of wear mass loss is larger than that in left cross. The damage that forms on the wear surface is mainly ploughing, pits, plastic deformation, and fatigue fracture. The major wear mechanisms are adhesive wear, and abrasive and fatigue wear.

  6. Biophysical characterization of the association of histones with single-stranded DNA.

    Science.gov (United States)

    Wang, Ying; van Merwyk, Luis; Tönsing, Katja; Walhorn, Volker; Anselmetti, Dario; Fernàndez-Busquets, Xavier

    2017-11-01

    Despite the profound current knowledge of the architecture and dynamics of nucleosomes, little is known about the structures generated by the interaction of histones with single-stranded DNA (ssDNA), which is widely present during replication and transcription. Non-denaturing gel electrophoresis, transmission electron microscopy, atomic force microscopy, magnetic tweezers. Histones have a high affinity for ssDNA in 0.15M NaCl ionic strength, with an apparent binding constant similar to that calculated for their association with double-stranded DNA (dsDNA). The length of DNA (number of nucleotides in ssDNA or base pairs in dsDNA) associated with a fixed core histone mass is the same for both ssDNA and dsDNA. Although histone-ssDNA complexes show a high tendency to aggregate, nucleosome-like structures are formed at physiological salt concentrations. Core histones are able to protect ssDNA from digestion by micrococcal nuclease, and a shortening of ssDNA occurs upon its interaction with histones. The purified (+) strand of a cloned DNA fragment of nucleosomal origin has a higher affinity for histones than the purified complementary (-) strand. At physiological ionic strength histones have high affinity for ssDNA, possibly associating with it into nucleosome-like structures. In the cell nucleus histones may spontaneously interact with ssDNA to facilitate their participation in the replication and transcription of chromatin. Copyright © 2017 Elsevier B.V. All rights reserved.

  7. Hole hopping rates in single strand oligonucleotides

    Energy Technology Data Exchange (ETDEWEB)

    Borrelli, Raffaele [Dipartimento di Scienze Agrarie, Forestali e Alimentari, Università di Torino, Largo Paolo Braccini 2, I-10095 Grugliasco, TO (Italy); Capobianco, Amedeo [Dipartimento di Chimica e Biologia, Università di Salerno, Via Giovanni Paolo II, I-84084 Fisciano, SA (Italy); Peluso, Andrea, E-mail: apeluso@unisa.it [Dipartimento di Chimica e Biologia, Università di Salerno, Via Giovanni Paolo II, I-84084 Fisciano, SA (Italy)

    2014-08-31

    Highlights: • DNA hole transfer rates have been computed. • Delocalized adenine domains significantly affect hole transfer rates in DNA. • Franck–Condon weighted density of state from DFT normal modes. • DNA application in molecular electronics. - Abstract: The rates of hole transfer between guanine and adenine in single strand DNA have been evaluated by using Fermi’s golden rule and Kubo’s generating function approach for the Franck–Condon weighted density of states. The whole sets of the normal modes and vibrational frequencies of the two nucleobases, obtained at DFT/B3LYP level of calculation, have been considered in computations. The results show that in single strand the pyramidalization/planarization mode of the amino groups of both nucleobases plays the major role. At room temperature, the Franck–Condon density of states extends over a wide range of hole site energy difference, 0–1 eV, giving some hints about the design of oligonucleotides of potential technological interest.

  8. Stranded cost recovery in electricity market reforms in the US

    International Nuclear Information System (INIS)

    Woo, C.K.; Lloyd, D.; Karimov, R.; Tishler, A.

    2003-01-01

    An important element of an electricity market reform is stranded cost recovery. This paper explains the cause of stranded costs, describes four recovery mechanisms, evaluates these mechanisms using the criteria of recovery certainty, economic efficiency and equity, reviews the financial performance of 12 utilities in the US in connection to stranded cost recovery, and shows why the mechanism used in California has contributed to the reform failure in that state. (Author)

  9. Patterns of stranding and mortality in common seals (Phoca vitulina) and grey seals (Halichoerus grypus) in The Netherlands between 1979 and 2008.

    Science.gov (United States)

    Osinga, N; Shahi Ferdous, M M; Morick, D; García Hartmann, M; Ulloa, J A; Vedder, L; Udo de Haes, H A; Brakefield, P M; Osterhaus, A D M E; Kuiken, T

    2012-11-01

    Pathological examination of stranded marine mammals provides information on the causes of mortality in their populations. Patterns of stranding and causes of death of dead-stranded seals on the Dutch coast were analyzed over a 30-year period (1979-2008). Stranding data (n=1,286) and post-mortem data (n=379) from common seals (Phoca vitulina) and grey seals (Halichoerus grypus) found dead, or that died before admission to rehabilitation, were obtained from the Seal Rehabilitation and Research Centre database. Data for the years 1988 and 2002, when mass mortality occurred due to phocine distemper virus epidemics, were excluded. Common seal stranding increased from one to nearly 100 per year over this period. This coincides with the increase in the number of common seals in Dutch waters over recent decades. Grey seal stranding increased gradually from one to about 40 per year over the period, reflecting recolonization of Dutch waters by this species. For both species, the trend in stranding of dead seals was found to be in line with that of seals observed in Dutch waters during aerial surveys and did not provide any indications of a relative change in the stranding rate of dead seals. The total monthly stranding rates peaked at more than 120 in June and July for common seals and at nearly 60 in January for grey seals. This coincides with the pupping periods of the two species. Besides phocine distemper, the most common causes of death in investigated common seals (n=286) were by-catch (confirmed and inferred) (19%), pup starvation (7%), intestinal volvulus (7%) and parasitic bronchopneumonia (6%). The most common causes of death in investigated grey seals (n=93) were by-catch (confirmed and inferred) (15%), pup starvation (11%) and trauma (5%). The relative occurrence of by-catch significantly decreased over time for grey seals, but not for common seals. Common seals were affected by infectious disease significantly more often than grey seals, mainly because of a

  10. Radiation-induced DNA double strand breaks in Ehrlich ascites tumour cells and their possible effects on cell survival

    International Nuclear Information System (INIS)

    Bloecher, D.

    1981-01-01

    A method to prepare high-molecular, pure DNA with the aid of enzymes, detergents, and heat treatment is presented. A sedimentation technique with neutral density gradients has been introduced which permits mass separation and molecular mass analysis of high-molecular DNA (msub(r) 10 ). Using this method, the induction of DNA double strand breaks (DSB) in the dose range between 10 Gy [de

  11. Marine mammal strandings and environmental changes: a 15-year study in the St. Lawrence ecosystem.

    Directory of Open Access Journals (Sweden)

    Marie-Hélène Truchon

    Full Text Available Understanding the effects of climatic variability on marine mammals is challenging due to the complexity of ecological interactions. We used general linear models to analyze a 15-year database documenting marine mammal strandings (1994-2008; n = 1,193 and nine environmental parameters known to affect marine mammal survival, from regional (sea ice to continental scales (North Atlantic Oscillation, NAO. Stranding events were more frequent during summer and fall than other seasons, and have increased since 1994. Poor ice conditions observed during the same period may have affected marine mammals either directly, by modulating the availability of habitat for feeding and breeding activities, or indirectly, through changes in water conditions and marine productivity (krill abundance. For most species (75%, n = 6 species, a low volume of ice was correlated with increasing frequency of stranding events (e.g. R(2adj = 0.59, hooded seal, Cystophora cristata. This likely led to an increase in seal mortality during the breeding period, but also to increase habitat availability for seasonal migratory cetaceans using ice-free areas during winter. We also detected a high frequency of stranding events for mysticete species (minke whale, Balaenoptera acutorostrata and resident species (beluga, Delphinapterus leucas, correlated with low krill abundance since 1994. Positive NAO indices were positively correlated with high frequencies of stranding events for resident and seasonal migratory cetaceans, as well as rare species (R(2adj = 0.53, 0.81 and 0.34, respectively. This contrasts with seal mass stranding numbers, which were negatively correlated with a positive NAO index. In addition, an unusual multiple species mortality event (n = 114, 62% of total annual mortality in 2008 was caused by a harmful algal bloom. Our findings provide an empirical baseline in understanding marine mammal survival when faced with climatic variability. This is a

  12. Getting Frustrated: Modelling Emotion Contagion in Stranded Passengers

    NARCIS (Netherlands)

    van der Wal, C. Natalie; Couwenberg, Maik; Bosse, T.

    2017-01-01

    Train passengers can get stranded due to a variety of events, such as a delay, technical malfunctioning or a natural disaster. Stranded passengers can get frustrated, which could escalate in misbehaviours. Examples are verbal and physical violence or dangerous behaviours such as opening emergency

  13. Cetacean strandings along the coast of Izmir Bay, Turkey

    NARCIS (Netherlands)

    Guclusoy, H.; Veryeri, N.; Cirik, S.

    2004-01-01

    The present paper provides information on the stranding of cetaceans in Izmir Bay, Aegean Sea, between 1992 and 2004. The data were collected opportunistically during sightings and stranding data collection for Monk Seals. A total of 12 cetaceans, namely Bottle-nosed Dolphin, Tursiops truncatus

  14. Second-strand cDNA synthesis: classical method

    International Nuclear Information System (INIS)

    Gubler, U.

    1987-01-01

    The classical scheme for the synthesis of double-stranded cDNA as it was reported in 1976 is described. Reverse transcription of mRNA with oligo(dT) as the primer generates first strands with a small loop at the 3' end of the cDNA (the end that corresponds to the 5' end of the mRNA). Subsequent removal of the mRNA by alkaline hydrolysis leaves single-stranded cDNA molecules again with a small 3' loop. This loop can be used by either reverse transcriptase or Klenow fragment of DNA polymerase I as a primer for second-strand synthesis. The resulting products are double-stranded cDNA molecules that are covalently closed at the end corresponding to the 5' end of the original mRNA. Subsequent cleavage of the short piece of single-stranded cDNA within the loop with the single-strand-specific S 1 nuclease generate open double-stranded molecules that can be used for molecular cloning in plasmids or in phage. Useful variations of this scheme have been described

  15. Gamma-ray induced double-strand breaks in DNA resulting from randomly-inflicted single-strand breaks: temporal local denaturation, a new radiation phenomenon?

    NARCIS (Netherlands)

    Schans, G.P. van der

    1978-01-01

    The induction of single- and double-strand breaks in DNA by γ-rays has been measured. The maximum number of nucleotide paris (a) between two independently induced single-strand breaks in opposite strands of the DNA which cannot prevent the occurrence of a double-strand break was found to amount to

  16. Acute Pyelonephritis with Perinephric Stranding on CT

    Directory of Open Access Journals (Sweden)

    Ronald Goubert

    2018-01-01

    Full Text Available History of present illness: A 54-year old female presented to the emergency department with complaints of fevers, dysuria, urinary frequency, and diffuse abdominal pain. Her temperature was 103°F, but the remainder of her vital signs were normal. Upon physical examination, the patient had tenderness to palpation in the left upper and left lower abdomen and left costovertebral angle tenderness. Due to the location of pain (diverticulitis is in the differential for left-sided abdominal pain in this age group and patient’s reported history of nephrolithiasis, a computed tomography (CT scan of the abdomen and pelvis with intravenous (IV contrast was ordered because the physician felt this could best work up both of these possible conditions. Significant findings: A CT abdomen and pelvis with IV contrast showed neither nephrolithiasis nor diverticulitis, and instead showed heterogeneous enhancement of the left kidney with mild edematous enlargement and striated left nephrogram. Significant perinephric stranding (red arrows was also noted and was consistent with severe acute pyelonephritis. Discussion: Acute pyelonephritis (APN is a bacterial infection of the renal parenchyma which can present with a spectrum of symptoms including flank pain, high-grade fever, vomiting, and urinary tract symptoms.1,2 The diagnosis of APN can be made based on these clinical features with associated laboratory findings of bacteriuria, pyuria, positive urine cultures, and leukocytosis.1,2,7 Early diagnosis and treatment of APN is essential to prevent complications such as renal abscess or infarct, which could lead to renal failure, sepsis, and shock.3 CT has a sensitivity and specificity of 86.8% and 87.5%, respectively, for diagnosing APN. Common findings include striated nephrograms or perinephric fat stranding.2 However, imaging is not required for diagnosis and is typically reserved for patients who are immunocompromised, have severe symptoms, or show no clinical

  17. Current redistribution in cables made of insulated, soldered, or oxidized strands

    International Nuclear Information System (INIS)

    Turck, B.

    1979-07-01

    Current redistributions are compared in cables made of insulated strands, soldered, or oxidized strands and insulated strands with periodic joints. After discussing the different current redistributions in the cases of a rapidly changing current and a dc current, several particular situations are investigated: what happens if a strand is broken, or if a local normal zone appears that does not affect all the strands equally, the detection of this normal zone, and the influence of short circuits between strands

  18. Towards quantitative viromics for both double-stranded and single-stranded DNA viruses

    Directory of Open Access Journals (Sweden)

    Simon Roux

    2016-12-01

    Full Text Available Background Viruses strongly influence microbial population dynamics and ecosystem functions. However, our ability to quantitatively evaluate those viral impacts is limited to the few cultivated viruses and double-stranded DNA (dsDNA viral genomes captured in quantitative viral metagenomes (viromes. This leaves the ecology of non-dsDNA viruses nearly unknown, including single-stranded DNA (ssDNA viruses that have been frequently observed in viromes, but not quantified due to amplification biases in sequencing library preparations (Multiple Displacement Amplification, Linker Amplification or Tagmentation. Methods Here we designed mock viral communities including both ssDNA and dsDNA viruses to evaluate the capability of a sequencing library preparation approach including an Adaptase step prior to Linker Amplification for quantitative amplification of both dsDNA and ssDNA templates. We then surveyed aquatic samples to provide first estimates of the abundance of ssDNA viruses. Results Mock community experiments confirmed the biased nature of existing library preparation methods for ssDNA templates (either largely enriched or selected against and showed that the protocol using Adaptase plus Linker Amplification yielded viromes that were ±1.8-fold quantitative for ssDNA and dsDNA viruses. Application of this protocol to community virus DNA from three freshwater and three marine samples revealed that ssDNA viruses as a whole represent only a minor fraction (<5% of DNA virus communities, though individual ssDNA genomes, both eukaryote-infecting Circular Rep-Encoding Single-Stranded DNA (CRESS-DNA viruses and bacteriophages from the Microviridae family, can be among the most abundant viral genomes in a sample. Discussion Together these findings provide empirical data for a new virome library preparation protocol, and a first estimate of ssDNA virus abundance in aquatic systems.

  19. Template role of double-stranded RNA in tombusvirus replication.

    Science.gov (United States)

    Kovalev, Nikolay; Pogany, Judit; Nagy, Peter D

    2014-05-01

    Replication of plus-strand RNA [(+)RNA] viruses of plants is a relatively simple process that involves complementary minus-strand RNA [(-)RNA] synthesis and subsequent (+)RNA synthesis. However, the actual replicative form of the (-)RNA template in the case of plant (+)RNA viruses is not yet established unambiguously. In this paper, using a cell-free replication assay supporting a full cycle of viral replication, we show that replication of Tomato bushy stunt virus (TBSV) leads to the formation of double-stranded RNA (dsRNA). Using RNase digestion, DNAzyme, and RNA mobility shift assays, we demonstrate the absence of naked (-)RNA templates during replication. Time course experiments showed the rapid appearance of dsRNA earlier than the bulk production of new (+)RNAs, suggesting an active role for dsRNA in replication. Radioactive nucleotide chase experiments showed that the mechanism of TBSV replication involves the use of dsRNA templates in strand displacement reactions, where the newly synthesized plus strand replaces the original (+)RNA in the dsRNA. We propose that the use of dsRNA as a template for (+)RNA synthesis by the viral replicase is facilitated by recruited host DEAD box helicases and the viral p33 RNA chaperone protein. Altogether, this replication strategy allows TBSV to separate minus- and plus-strand syntheses in time and regulate asymmetrical RNA replication that leads to abundant (+)RNA progeny. Positive-stranded RNA viruses of plants use their RNAs as the templates for replication. First, the minus strand is synthesized by the viral replicase complex (VRC), which then serves as a template for new plus-strand synthesis. To characterize the nature of the (-)RNA in the membrane-bound viral replicase, we performed complete RNA replication of Tomato bushy stunt virus (TBSV) in yeast cell-free extracts and in plant extracts. The experiments demonstrated that the TBSV (-)RNA is present as a double-stranded RNA that serves as the template for TBSV

  20. Two-dimensional strandness-dependent electrophoresis: a method to characterize single-stranded DNA, double-stranded DNA, and RNA-DNA hybrids in complex samples.

    Science.gov (United States)

    Gunnarsson, Gudmundur H; Gudmundsson, Bjarki; Thormar, Hans G; Alfredsson, Arni; Jonsson, Jon J

    2006-03-01

    We describe two-dimensional strandness-dependent electrophoresis (2D-SDE) for quantification and length distribution analysis of single-stranded (ss) DNA fragments, double-stranded (ds) DNA fragments, RNA-DNA hybrids, and nicked DNA fragments in complex samples. In the first dimension nucleic acid molecules are separated based on strandness and length in the presence of 7 M urea. After the first-dimension electrophoresis all nucleic acid fragments are heat denatured in the gel. During the second-dimension electrophoresis all nucleic acid fragments are single-stranded and migrate according to length. 2D-SDE takes about 90 min and requires only basic skills and equipment. We show that 2D-SDE has many applications in analyzing complex nucleic acid samples including (1) estimation of renaturation efficiency and kinetics, (2) monitoring cDNA synthesis, (3) detection of nicked DNA fragments, and (4) estimation of quality and in vitro damage of nucleic acid samples. Results from 2D-SDE should be useful to validate techniques such as complex polymerase chain reaction, subtractive hybridization, cDNA synthesis, cDNA normalization, and microarray analysis. 2D-SDE could also be used, e.g., to characterize biological nucleic acid samples. Information obtained with 2D-SDE cannot be readily obtained with other methods. 2D-SDE can be used for preparative isolation of ssDNA fragments, dsDNA fragments, and RNA-DNA hybrids.

  1. Two highly thermostable paralogous single-stranded DNA-binding proteins from Thermoanaerobacter tengcongensis.

    Science.gov (United States)

    Olszewski, Marcin; Mickiewicz, Małgorzata; Kur, Józef

    2008-07-01

    The thermophilic bacterium Thermoanaerobacter tengcongensis has two single-stranded DNA-binding (SSB) proteins, designated TteSSB2 and TteSSB3. In a SSB complementation assay in Escherichia coli, only TteSSB3 took over the in vivo function of EcoSSB. We have cloned the ssb genes obtained by PCR and have developed E. coli overexpression systems. The TteSSB2 and TteSSB3 consist of 153 and 150 amino acids with a calculated molecular mass of 17.29 and 16.96 kDa, respectively. They are the smallest known bacterial SSB proteins. The homology between amino acid sequences of these proteins is 40% identity and 53% similarity. They are functional as homotetramers, with each monomer encoding one single-stranded DNA binding domain (OB-fold). In fluorescence titrations with poly(dT), both proteins bind single-stranded DNA with a binding site size of about 40 nt per homotetramer. Thermostability with half-life of about 30 s at 95 degrees C makes TteSSB3 similar to the known SSB of Thermus aquaticus (TaqSSB). The TteSSB2 was fully active even after 6 h incubation at 100 degrees C. Here, we show for the first time paralogous thermostable homotetrameric SSBs, which could be an attractive alternative for known homodimeric thermostable SSB proteins in their applications for molecular biology methods and analytical purposes.

  2. Genetic and environmental influence on DNA strand break repair

    DEFF Research Database (Denmark)

    Garm, Christian; Moreno-Villanueva, Maria; Bürkle, Alexander

    2013-01-01

    factors are likely to influence DNA repair capacity. In order to gain more insight into the genetic and environmental contribution to the molecular basis of DNA repair, we have performed a human twin study, where we focused on the consequences of some of the most abundant types of DNA damage (single-strand...... breaks), and some of the most hazardous lesions (DNA double-strand breaks). DNA damage signaling response (Gamma-H2AX signaling), relative amount of endogenous damage, and DNA-strand break repair capacities were studied in peripheral blood mononuclear cells from 198 twins (94 monozygotic and 104...... dizygotic). We did not detect genetic effects on the DNA-strand break variables in our study. Environ. Mol. Mutagen., 2013. © 2013 Wiley Periodicals, Inc....

  3. Electrical Interconnection Of Superconducting Strands By Electrolytic CU Deposition.

    CERN Document Server

    Scheuerlein, C; Heck, S; Ams, A

    2011-01-01

    The electrical interconnection of Nb3Sn/Cu strands is a key issue for the construction of superconducting devices such as Nb3Sn based insertion devices for third generation light sources. As an alternative connection method for brittle superconducting strands like Nb3Sn/Cu, test joints have been produced by electrolytic deposition of Cu. The resistance of first test joints produced by electrolytic Cu deposition with a strand overlap length of 3 cm at 4.2 K is about 10 n$\\omega$, similar to the resistance measured for joints produced by soft soldering with the same strand overlap length. Interconnection by electrolytic Cu deposition can be done before or after the reaction heat treatment, and it produces a mechanically strong connection. Simulations have been performed with Comsol multiphysics in order to estimate the influence of deposit imperfections on the joint resistance, and to compare the resistance of joints made with different techniques

  4. Corrosion performance of prestressing strands in contact with dissimilar grouts.

    Science.gov (United States)

    2013-01-01

    To improve the corrosion protection provided to prestressing strands, anti-bleed grouts are used to fill voids in post-tensioning : ducts that result from bleeding and shrinkage of older Portland Cement grouts. Environmental differences caused by exp...

  5. The N-terminal strand modulates immunoglobulin light chain fibrillogenesis

    Energy Technology Data Exchange (ETDEWEB)

    Pozo-Yauner, Luis del, E-mail: ldelpozo@inmegen.gob.mx [Instituto Nacional de Medicina Genómica, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, México, D.F. C.P. 14610 (Mexico); Wall, Jonathan S. [Departments of Radiology and Medicine, The University of Tennessee Medical Center, 1924 Alcoa Highway, Knoxville, TN (United States); González Andrade, Martín [Instituto Nacional de Medicina Genómica, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, México, D.F. C.P. 14610 (Mexico); Sánchez-López, Rosana [Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa Cuernavaca, Morelos C.P. 62210 (Mexico); Rodríguez-Ambriz, Sandra L. [Centro de Desarrollo de Productos Bióticos, Instituto Politécnico Nacional, Calle CEPROBI No. 8, Col. San Isidro, Yautepec, Morelos C.P. 62731 (Mexico); Pérez Carreón, Julio I. [Instituto Nacional de Medicina Genómica, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, México, D.F. C.P. 14610 (Mexico); and others

    2014-01-10

    Highlights: •We evaluated the impact of mutations in the N-terminal strand of 6aJL2 protein. •Mutations destabilized the protein in a position-dependent manner. •Destabilizing mutations accelerated the fibrillogenesis by shortening the lag time. •The effect on the kinetic of fibril elongation by seeding was of different nature. •The N-terminal strand is buried in the fibrillar state of 6aJL2 protein. -- Abstract: It has been suggested that the N-terminal strand of the light chain variable domain (V{sub L}) protects the molecule from aggregation by hindering spurious intermolecular contacts. We evaluated the impact of mutations in the N-terminal strand on the thermodynamic stability and kinetic of fibrillogenesis of the V{sub L} protein 6aJL2. Mutations in this strand destabilized the protein in a position-dependent manner, accelerating the fibrillogenesis by shortening the lag time; an effect that correlated with the extent of destabilization. In contrast, the effect on the kinetics of fibril elongation, as assessed in seeding experiments was of different nature, as it was not directly dependant on the degree of destabilization. This finding suggests different factors drive the nucleation-dependent and elongation phases of light chain fibrillogenesis. Finally, taking advantage of the dependence of the Trp fluorescence upon environment, four single Trp substitutions were made in the N-terminal strand, and changes in solvent exposure during aggregation were evaluated by acrylamide-quenching. The results suggest that the N-terminal strand is buried in the fibrillar state of 6aJL2 protein. This finding suggest a possible explanation for the modulating effect exerted by the mutations in this strand on the aggregation behavior of 6aJL2 protein.

  6. The risk of stranded assets for utilities in Canada

    International Nuclear Information System (INIS)

    Schroeder, W.

    1998-01-01

    The problems of dealing with stranded assets in Canada and the United States were discussed. Compared to the United States, the risk associated with stranded assets for utilities in Canada was considered to be relatively low because of the following factors: (1) low variable cost, (2) isolation, (3) lack of transmission interconnection capacity, (4) lack of tight synchronization in North America, (5) the likelihood of an increase in natural gas prices, (6) the absence of jurisdictional disputes such as FERC versus the states, (7) social considerations, (8) the learning curve, (9) politics, (10) weak balance sheets, (11) relatively low electricity prices, (12) the weak Canadian dollar, and (13) the possibility of refinancing at lower interest rates. Ontario Hydro, New Brunswick and Nova Scotia Power are the three Canadian utilities that may have stranded costs. For Ontario Hydro and New Brunswick Power the stranded costs would be related to nuclear generator problems, whereas for Nova Scotia Power, the stranded costs would be related to the thermal generating base, the threat from Sable Island Gas and the changing tax structure of the utility. Some other reasons why stranded assets could be created in Canada would include low variable costs and high fixed costs, over capacity of at least 30 per cent in generation, limited domestic energy growth, competitive threat from gas, reliability and safety of nuclear plants, and technology change. Five factors in terms of which stranded assets can be expressed are: (1) variable cost definition, (2) total cost definition, (3) operating profit definition, (4) wide geographic definition, and (5) free market definition. In calculating stranded assets, the number of years over which the assets are recovered and the discount rate are considered to be key factors. 26 tabs

  7. Mismatch repair balances leading and lagging strand DNA replication fidelity.

    Directory of Open Access Journals (Sweden)

    Scott A Lujan

    Full Text Available The two DNA strands of the nuclear genome are replicated asymmetrically using three DNA polymerases, α, δ, and ε. Current evidence suggests that DNA polymerase ε (Pol ε is the primary leading strand replicase, whereas Pols α and δ primarily perform lagging strand replication. The fact that these polymerases differ in fidelity and error specificity is interesting in light of the fact that the stability of the nuclear genome depends in part on the ability of mismatch repair (MMR to correct different mismatches generated in different contexts during replication. Here we provide the first comparison, to our knowledge, of the efficiency of MMR of leading and lagging strand replication errors. We first use the strand-biased ribonucleotide incorporation propensity of a Pol ε mutator variant to confirm that Pol ε is the primary leading strand replicase in Saccharomyces cerevisiae. We then use polymerase-specific error signatures to show that MMR efficiency in vivo strongly depends on the polymerase, the mismatch composition, and the location of the mismatch. An extreme case of variation by location is a T-T mismatch that is refractory to MMR. This mismatch is flanked by an AT-rich triplet repeat sequence that, when interrupted, restores MMR to > 95% efficiency. Thus this natural DNA sequence suppresses MMR, placing a nearby base pair at high risk of mutation due to leading strand replication infidelity. We find that, overall, MMR most efficiently corrects the most potentially deleterious errors (indels and then the most common substitution mismatches. In combination with earlier studies, the results suggest that significant differences exist in the generation and repair of Pol α, δ, and ε replication errors, but in a generally complementary manner that results in high-fidelity replication of both DNA strands of the yeast nuclear genome.

  8. Withdrawal Strength of Dowels in Plywood and Oriented Strand Board

    OpenAIRE

    ERDİL, Yusuf Z.; ECKELMAN, Carl A.

    2001-01-01

    Plywood and oriented strand board (OSB) are being used increasingly in the construction of upholstered furniture frames. Yet there is little information available concerning the holding strength of various fasteners, and, in particular, dowels in these materials. A study was conducted accordingly, to obtain basic information about the holding strength of dowels in both plywood and oriented strand board. Results of the tests were incorporated into predictive expressions that allow designers to...

  9. Hearing Loss in Stranded Odontocete Dolphins and Whales

    Science.gov (United States)

    Mann, David; Hill-Cook, Mandy; Manire, Charles; Greenhow, Danielle; Montie, Eric; Powell, Jessica; Wells, Randall; Bauer, Gordon; Cunningham-Smith, Petra; Lingenfelser, Robert; DiGiovanni, Robert; Stone, Abigale; Brodsky, Micah; Stevens, Robert; Kieffer, George; Hoetjes, Paul

    2010-01-01

    The causes of dolphin and whale stranding can often be difficult to determine. Because toothed whales rely on echolocation for orientation and feeding, hearing deficits could lead to stranding. We report on the results of auditory evoked potential measurements from eight species of odontocete cetaceans that were found stranded or severely entangled in fishing gear during the period 2004 through 2009. Approximately 57% of the bottlenose dolphins and 36% of the rough-toothed dolphins had significant hearing deficits with a reduction in sensitivity equivalent to severe (70–90 dB) or profound (>90 dB) hearing loss in humans. The only stranded short-finned pilot whale examined had profound hearing loss. No impairments were detected in seven Risso's dolphins from three different stranding events, two pygmy killer whales, one Atlantic spotted dolphin, one spinner dolphin, or a juvenile Gervais' beaked whale. Hearing impairment could play a significant role in some cetacean stranding events, and the hearing of all cetaceans in rehabilitation should be tested. PMID:21072206

  10. Hearing loss in stranded odontocete dolphins and whales.

    Directory of Open Access Journals (Sweden)

    David Mann

    Full Text Available The causes of dolphin and whale stranding can often be difficult to determine. Because toothed whales rely on echolocation for orientation and feeding, hearing deficits could lead to stranding. We report on the results of auditory evoked potential measurements from eight species of odontocete cetaceans that were found stranded or severely entangled in fishing gear during the period 2004 through 2009. Approximately 57% of the bottlenose dolphins and 36% of the rough-toothed dolphins had significant hearing deficits with a reduction in sensitivity equivalent to severe (70-90 dB or profound (>90 dB hearing loss in humans. The only stranded short-finned pilot whale examined had profound hearing loss. No impairments were detected in seven Risso's dolphins from three different stranding events, two pygmy killer whales, one Atlantic spotted dolphin, one spinner dolphin, or a juvenile Gervais' beaked whale. Hearing impairment could play a significant role in some cetacean stranding events, and the hearing of all cetaceans in rehabilitation should be tested.

  11. Red Tide Strands South African Rock Lobsters

    Science.gov (United States)

    2002-01-01

    Although some red tides form a healthy part of phytoplankton production, recurrent harmful or toxic blooms also occur, with results depending upon the type of plankton and on atmospheric and oceanic conditions. At Elands Bay in South Africa's Western Cape province, about 1000 tons of rock lobsters beached themselves during February 2002, when the decay of dense blooms of phytoplankton caused a rapid reduction in the oxygen concentration of nearshore waters. The lobsters (or crayfish, as they are known locally) moved toward the breaking surf in search of oxygen, but were stranded by the retreating tide. The Multi-angle Imaging SpectroRadiometer's nadir camera acquired these red, green, blue composites on February 2 and 18, 2002, during Terra orbits 11315 and 11548. The colors have been accentuated to highlight the bloom, and land and water have been enhanced separately. The two views show the shoreward migration of the algal bloom. Each image represents an area of about 205 kilometers x 330 kilometers. Elands Bay is situated near the mouth of the Doring River, about 75 kilometers northeast of the jutting Cape Columbine. The term 'red tide' is used to refer to a number of different types of phytoplankton blooms of various hues. The wine color of certain parts of this bloom are consistent with the ciliate species Mesodinium rubrum, which has been associated with recurring harmful algal blooms along the Western Cape coast. Under these conditions, the lobsters are not poisoned. During the recent event, government and military staff transported as many of the living lobsters as possible to areas that were less affected by the red tide. At the same time, people came from across South Africa to gather the undersized creatures for food. The effects of the losses on the maritime economy are expected to be felt over the next few years. MISR was built and is managed by NASA's Jet Propulsion Laboratory, Pasadena, CA, for NASA's Office of Earth Science, Washington, DC. The Terra

  12. The importance of becoming double-stranded: Innate immunity and the kinetic model of HIV-1 central plus strand synthesis

    Energy Technology Data Exchange (ETDEWEB)

    Poeschla, Eric, E-mail: poeschla.eric@mayo.edu

    2013-06-20

    Central initiation of plus strand synthesis is a conserved feature of lentiviruses and certain other retroelements. This complication of the standard reverse transcription mechanism produces a transient “central DNA flap” in the viral cDNA, which has been proposed to mediate its subsequent nuclear import. This model has assumed that the important feature is the flapped DNA structure itself rather than the process that produces it. Recently, an alternative kinetic model was proposed. It posits that central plus strand synthesis functions to accelerate conversion to the double-stranded state, thereby helping HIV-1 to evade single-strand DNA-targeting antiviral restrictions such as APOBEC3 proteins, and perhaps to avoid innate immune sensor mechanisms. The model is consistent with evidence that lentiviruses must often synthesize their cDNAs when dNTP concentrations are limiting and with data linking reverse transcription and uncoating. There may be additional kinetic advantages for the artificial genomes of lentiviral gene therapy vectors. - Highlights: • Two main functional models for HIV central plus strand synthesis have been proposed. • In one, a transient central DNA flap in the viral cDNA mediates HIV-1 nuclear import. • In the other, multiple kinetic consequences are emphasized. • One is defense against APOBEC3G, which deaminates single-stranded DNA. • Future questions pertain to antiviral restriction, uncoating and nuclear import.

  13. The importance of becoming double-stranded: Innate immunity and the kinetic model of HIV-1 central plus strand synthesis

    International Nuclear Information System (INIS)

    Poeschla, Eric

    2013-01-01

    Central initiation of plus strand synthesis is a conserved feature of lentiviruses and certain other retroelements. This complication of the standard reverse transcription mechanism produces a transient “central DNA flap” in the viral cDNA, which has been proposed to mediate its subsequent nuclear import. This model has assumed that the important feature is the flapped DNA structure itself rather than the process that produces it. Recently, an alternative kinetic model was proposed. It posits that central plus strand synthesis functions to accelerate conversion to the double-stranded state, thereby helping HIV-1 to evade single-strand DNA-targeting antiviral restrictions such as APOBEC3 proteins, and perhaps to avoid innate immune sensor mechanisms. The model is consistent with evidence that lentiviruses must often synthesize their cDNAs when dNTP concentrations are limiting and with data linking reverse transcription and uncoating. There may be additional kinetic advantages for the artificial genomes of lentiviral gene therapy vectors. - Highlights: • Two main functional models for HIV central plus strand synthesis have been proposed. • In one, a transient central DNA flap in the viral cDNA mediates HIV-1 nuclear import. • In the other, multiple kinetic consequences are emphasized. • One is defense against APOBEC3G, which deaminates single-stranded DNA. • Future questions pertain to antiviral restriction, uncoating and nuclear import

  14. Role of stranded gas in increasing global gas supplies

    Science.gov (United States)

    Attanasi, E.D.; Freeman, P.A.

    2013-01-01

    This report synthesizes the findings of three regional studies in order to evaluate, at the global scale, the contribution that stranded gas resources can make to global natural gas supplies. Stranded gas, as defined for this study, is natural gas in discovered conventional gas and oil fields that is currently not commercially producible for either physical or economic reasons. The regional studies evaluated the cost of bringing the large volumes of undeveloped gas in stranded gas fields to selected markets. In particular, stranded gas fields of selected Atlantic Basin countries, north Africa, Russia, and central Asia are screened to determine whether the volumes are sufficient to meet Europe’s increasing demand for gas imports. Stranded gas fields in Russia, central Asia, Southeast Asia, and Australia are also screened to estimate development, production, and transport costs and corresponding gas volumes that could be supplied to Asian markets in China, India, Japan, and South Korea. The data and cost analysis presented here suggest that for the European market and the markets examined in Asia, the development of stranded gas provides a way to meet projected gas import demands for the 2020-to-2040 period. Although this is a reconnaissance-type appraisal, it is based on volumes of gas that are associated with individual identified fields. Individual field data were carefully examined. Some fields were not evaluated because current technology was insufficient or it appeared the gas was likely to be held off the export market. Most of the evaluated stranded gas can be produced and delivered to markets at costs comparable to historical prices. Moreover, the associated volumes of gas are sufficient to provide an interim supply while additional technologies are developed to unlock gas diffused in shale and hydrates or while countries transition to making a greater use of renewable energy sources.

  15. New Views on Strand Asymmetry in Insect Mitochondrial Genomes

    Science.gov (United States)

    Wei, Shu-Jun; Shi, Min; Chen, Xue-Xin; Sharkey, Michael J.; van Achterberg, Cornelis; Ye, Gong-Yin; He, Jun-Hua

    2010-01-01

    Strand asymmetry in nucleotide composition is a remarkable feature of animal mitochondrial genomes. Understanding the mutation processes that shape strand asymmetry is essential for comprehensive knowledge of genome evolution, demographical population history and accurate phylogenetic inference. Previous studies found that the relative contributions of different substitution types to strand asymmetry are associated with replication alone or both replication and transcription. However, the relative contributions of replication and transcription to strand asymmetry remain unclear. Here we conducted a broad survey of strand asymmetry across 120 insect mitochondrial genomes, with special reference to the correlation between the signs of skew values and replication orientation/gene direction. The results show that the sign of GC skew on entire mitochondrial genomes is reversed in all species of three distantly related families of insects, Philopteridae (Phthiraptera), Aleyrodidae (Hemiptera) and Braconidae (Hymenoptera); the replication-related elements in the A+T-rich regions of these species are inverted, confirming that reversal of strand asymmetry (GC skew) was caused by inversion of replication origin; and finally, the sign of GC skew value is associated with replication orientation but not with gene direction, while that of AT skew value varies with gene direction, replication and codon positions used in analyses. These findings show that deaminations during replication and other mutations contribute more than selection on amino acid sequences to strand compositions of G and C, and that the replication process has a stronger affect on A and T content than does transcription. Our results may contribute to genome-wide studies of replication and transcription mechanisms. PMID:20856815

  16. New views on strand asymmetry in insect mitochondrial genomes.

    Directory of Open Access Journals (Sweden)

    Shu-Jun Wei

    Full Text Available Strand asymmetry in nucleotide composition is a remarkable feature of animal mitochondrial genomes. Understanding the mutation processes that shape strand asymmetry is essential for comprehensive knowledge of genome evolution, demographical population history and accurate phylogenetic inference. Previous studies found that the relative contributions of different substitution types to strand asymmetry are associated with replication alone or both replication and transcription. However, the relative contributions of replication and transcription to strand asymmetry remain unclear. Here we conducted a broad survey of strand asymmetry across 120 insect mitochondrial genomes, with special reference to the correlation between the signs of skew values and replication orientation/gene direction. The results show that the sign of GC skew on entire mitochondrial genomes is reversed in all species of three distantly related families of insects, Philopteridae (Phthiraptera, Aleyrodidae (Hemiptera and Braconidae (Hymenoptera; the replication-related elements in the A+T-rich regions of these species are inverted, confirming that reversal of strand asymmetry (GC skew was caused by inversion of replication origin; and finally, the sign of GC skew value is associated with replication orientation but not with gene direction, while that of AT skew value varies with gene direction, replication and codon positions used in analyses. These findings show that deaminations during replication and other mutations contribute more than selection on amino acid sequences to strand compositions of G and C, and that the replication process has a stronger affect on A and T content than does transcription. Our results may contribute to genome-wide studies of replication and transcription mechanisms.

  17. Accurate strand-specific quantification of viral RNA.

    Directory of Open Access Journals (Sweden)

    Nicole E Plaskon

    Full Text Available The presence of full-length complements of viral genomic RNA is a hallmark of RNA virus replication within an infected cell. As such, methods for detecting and measuring specific strands of viral RNA in infected cells and tissues are important in the study of RNA viruses. Strand-specific quantitative real-time PCR (ssqPCR assays are increasingly being used for this purpose, but the accuracy of these assays depends on the assumption that the amount of cDNA measured during the quantitative PCR (qPCR step accurately reflects amounts of a specific viral RNA strand present in the RT reaction. To specifically test this assumption, we developed multiple ssqPCR assays for the positive-strand RNA virus o'nyong-nyong (ONNV that were based upon the most prevalent ssqPCR assay design types in the literature. We then compared various parameters of the ONNV-specific assays. We found that an assay employing standard unmodified virus-specific primers failed to discern the difference between cDNAs generated from virus specific primers and those generated through false priming. Further, we were unable to accurately measure levels of ONNV (- strand RNA with this assay when higher levels of cDNA generated from the (+ strand were present. Taken together, these results suggest that assays of this type do not accurately quantify levels of the anti-genomic strand present during RNA virus infectious cycles. However, an assay permitting the use of a tag-specific primer was able to distinguish cDNAs transcribed from ONNV (- strand RNA from other cDNAs present, thus allowing accurate quantification of the anti-genomic strand. We also report the sensitivities of two different detection strategies and chemistries, SYBR(R Green and DNA hydrolysis probes, used with our tagged ONNV-specific ssqPCR assays. Finally, we describe development, design and validation of ssqPCR assays for chikungunya virus (CHIKV, the recent cause of large outbreaks of disease in the Indian Ocean

  18. Manufacture of Strand Board Bonded with Disposal Expanded Polystyrene as Binder

    OpenAIRE

    Hermawan, Andi; Ohuchi, Takeshi; Fujimoto, Noboru; 大内, 毅; 藤本, 登留

    2010-01-01

    The objective of this study was to evaluate the physical and mechanical properties of strand board bonded with disposal expanded polystyrene (EPS) as binder. The strand board was manufactured using strand made from Douglas-fir beams selected from construction scrap wood. The strands were oriented, and two types of three-layer (face-core-face) strand board were manufactured: one in which the board bounded with only disposal EPS (P board), and the other in which the board bonded with disposal...

  19. Ketahanan Papan Unting (Oriented Strand Board) terhadap Serangan Rayap Tanah dan Rayap Kayu Kering

    OpenAIRE

    Gea, Bud diman

    2011-01-01

    Oriented strand board is panel of wood raw material from which strand composed of cross and upright structure. In order to oriented strand board can be used for interior and exterior needs, than necessary to be applied various thenology of quality improvement like durabelities and endurance of oriented strand board. For it does found endurance oriented strand board from attack of ground termite and wood dry termite, necessary doing grave yard trial and wood dry termite trial. This research ta...

  20. The Effect of Basepair Mismatch on DNA Strand Displacement.

    Science.gov (United States)

    Broadwater, D W Bo; Kim, Harold D

    2016-04-12

    DNA strand displacement is a key reaction in DNA homologous recombination and DNA mismatch repair and is also heavily utilized in DNA-based computation and locomotion. Despite its ubiquity in science and engineering, sequence-dependent effects of displacement kinetics have not been extensively characterized. Here, we measured toehold-mediated strand displacement kinetics using single-molecule fluorescence in the presence of a single basepair mismatch. The apparent displacement rate varied significantly when the mismatch was introduced in the invading DNA strand. The rate generally decreased as the mismatch in the invader was encountered earlier in displacement. Our data indicate that a single base pair mismatch in the invader stalls branch migration and displacement occurs via direct dissociation of the destabilized incumbent strand from the substrate strand. We combined both branch migration and direct dissociation into a model, which we term the concurrent displacement model, and used the first passage time approach to quantitatively explain the salient features of the observed relationship. We also introduce the concept of splitting probabilities to justify that the concurrent model can be simplified into a three-step sequential model in the presence of an invader mismatch. We expect our model to become a powerful tool to design DNA-based reaction schemes with broad functionality. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  1. DNA-directed mutations. Leading and lagging strand specificity

    Science.gov (United States)

    Sinden, R. R.; Hashem, V. I.; Rosche, W. A.

    1999-01-01

    The fidelity of replication has evolved to reproduce B-form DNA accurately, while allowing a low frequency of mutation. The fidelity of replication can be compromised, however, by defined order sequence DNA (dosDNA) that can adopt unusual or non B-DNA conformations. These alternative DNA conformations, including hairpins, cruciforms, triplex DNAs, and slipped-strand structures, may affect enzyme-template interactions that potentially lead to mutations. To analyze the effect of dosDNA elements on spontaneous mutagenesis, various mutational inserts containing inverted repeats or direct repeats were cloned in a plasmid containing a unidirectional origin of replication and a selectable marker for the mutation. This system allows for analysis of mutational events that are specific for the leading or lagging strands during DNA replication in Escherichia coli. Deletions between direct repeats, involving misalignment stabilized by DNA secondary structure, occurred preferentially on the lagging strand. Intermolecular strand switch events, correcting quasipalindromes to perfect inverted repeats, occurred preferentially during replication of the leading strand.

  2. The superconducting strand for the CMS solenoid conductor

    CERN Document Server

    Curé, B; Campi, D; Goodrich, L F; Horváth, I L; Kircher, F; Liikamaa, R; Seppälä, J; Smith, R P; Teuho, J; Vieillard, L

    2002-01-01

    The Compact Muon Solenoid (CMS) is one of the general-purpose detectors to be provided for the LHC project at CERN. The design field of the CMS superconducting magnet is 4 T, the magnetic length is 12.5 m and the free bore is 6 m. Approximately 2000 km of superconducting strand is under procurement for the conductor of the CMS superconducting solenoid. Each strand length is required to be an integral multiple of 2.75 km. The strand is composed of copper- stabilized multifilamentary Nb-Ti with Nb barrier. Individual strands are identified by distinctive patterns of Nb-Ti filaments selected during stacking of the monofilaments. The statistics of piece length, measurements of I/sub c/, n-value, copper RRR, (Cu+Nb)/Nb-Ti ratio, as well as the results of independent cross checks of these quantities, are presented. A study was performed on the CMS strands to investigate the critical current degradation due to various heat treatments. The degradation versus annealing temperature and duration are reported. (4 refs).

  3. Size distribution of stranded small plastic debris on the coast of Guangdong, South China.

    Science.gov (United States)

    Fok, Lincoln; Cheung, Pui Kwan; Tang, Guangda; Li, Wai Chin

    2017-01-01

    Beach environments are known to be conducive to fragmentation of plastic debris, and highly fragmented plastic particles can interact with smaller organisms. Even through stranded plastic debris may not interact directly with marine organisms, backwash processes may transport this debris back to coastal waters, where it may affect a wide range of marine life at different trophic levels. This study analysed the size distribution of stranded plastic debris (plastic debris by abundance and 71% by weight, indicating that the plastic debris on these coastal beaches was highly fragmented and the majority of the plastic masses belonged to the microplastic size range. The observed size distributions of PS foams and fragments are believed to result from continued fragmentation. Previous studies found that the residence time of beached debris was less than one year on average, and no sign of plastic accumulation with depth in beach sediment was observed. Therefore, coastal beaches may represent a reservoir of highly fragmented and degraded microplastics that may be mobilised and returned to the sea during storm events. Further research on the dynamics and longevity of microplastics on beaches will help reveal the mass balance of microplastics on the shoreline and determine whether shorelines are sinks or sources of microplastics. Copyright © 2016 Elsevier Ltd. All rights reserved.

  4. DNA turnover and strand breaks in Escherichia coli

    International Nuclear Information System (INIS)

    Hanawalt, P.; Grivell, A.; Nakayama, H.

    1975-01-01

    The extent of DNA turnover has been measured in a dnaB mutant of Escherichia coli, temperature sensitive for semiconservative DNA replication. At the nonpermissive temperature about 0.02 percent of the deoxynucleotides in DNA are exchanged per generation period. This turnover rate is markedly depressed in the presence of rifampicin. During thymine starvation strand breaks accumulate in the DNA of E. coli strains that are susceptible to thymineless death. Rifampicin suppresses the appearance of these breaks, consistent with our hypothesis that transcription may be accompanied by repairable single-strand breaks in DNA. DNA turnover is enhanced severalfold in strands containing 5-bromodeoxyuridine in place of thymidine, possibly because the analog (or the deoxyuridine, following debromination) is sometimes recognized and excised

  5. Availability: A Metric for Nucleic Acid Strand Displacement Systems

    Science.gov (United States)

    2016-01-01

    DNA strand displacement systems have transformative potential in synthetic biology. While powerful examples have been reported in DNA nanotechnology, such systems are plagued by leakage, which limits network stability, sensitivity, and scalability. An approach to mitigate leakage in DNA nanotechnology, which is applicable to synthetic biology, is to introduce mismatches to complementary fuel sequences at key locations. However, this method overlooks nuances in the secondary structure of the fuel and substrate that impact the leakage reaction kinetics in strand displacement systems. In an effort to quantify the impact of secondary structure on leakage, we introduce the concepts of availability and mutual availability and demonstrate their utility for network analysis. Our approach exposes vulnerable locations on the substrate and quantifies the secondary structure of fuel strands. Using these concepts, a 4-fold reduction in leakage has been achieved. The result is a rational design process that efficiently suppresses leakage and provides new insight into dynamic nucleic acid networks. PMID:26875531

  6. Crystal structure of four-stranded Oxytricha telomeric DNA

    Science.gov (United States)

    Kang, C.; Zhang, X.; Ratliff, R.; Moyzis, R.; Rich, A.

    1992-01-01

    The sequence d(GGGGTTTTGGGG) from the 3' overhang of the Oxytricha telomere has been crystallized and its three-dimensional structure solved to 2.5 A resolution. The oligonucleotide forms hairpins, two of which join to make a four-stranded helical structure with the loops containing four thymine residues at either end. The guanine residues are held together by cyclic hydrogen bonding and an ion is located in the centre. The four guanine residues in each segment have a glycosyl conformation that alternates between anti and syn. There are two four-stranded molecules in the asymmetric unit showing that the structure has some intrinsic flexibility.

  7. Viable deletions of the M13 complementary strand origin

    OpenAIRE

    Kim, Myoung Hee; Hines, Jane C.; Ray, Dan S.

    1981-01-01

    The single-stranded DNA of bacteriophage M13 is converted to a duplex replicative form by a mechanism involving RNA-primed initiation at a single unique site on the viral DNA. The DNA sequence that specifies the RNA primer is contained largely within one of two adjacent hairpin structures protected from DNase degradation by RNA polymerase. We have used in vitro techniques to construct a series of M13 mutants having deletions in the region of the complementary strand origin. Deletions of the d...

  8. Genetic transformation of Neisseria gonorrhoeae shows a strand preference

    OpenAIRE

    Duffin, Paul M.; Seifert, H. Steven

    2012-01-01

    Natural transformation is the main means of horizontal genetic exchange in the obligate human pathogen Neisseria gonorrhoeae. Neisseria spp. have been shown to preferentially take up and transform their own DNA by recognizing a non-palindromic 10 or 12 nucleotide DNA uptake sequence (DUS10 or DUS12). We investigated the ability of the DUS12 to enhance single-stranded DNA (ssDNA) transformation. Given the non-palindromic nature of the DUS12, we tested whether both strands of the DUS equally en...

  9. Industry participation workshop: Chromium electroplating of superconductor strand. Proceedings

    International Nuclear Information System (INIS)

    1994-01-01

    The primary objective of the workshop was to inform US plating vendors about the opportunity to participate in the effort on Cr plating of large quantities of superconducting wires required for the ITER and the TPX projects and DOE's interest in developing several reliable and high quality suppliers of Chromium plating services for the superconducting strand industry. The objective was also to inform plating vendors about the Cr plating technology developed in LLNL and invite interested plating vendors to get the technology. Finally the workshop was intended to inform the plating vendors about the plan to get verification of capability of two to four vendors for Cr plating of superconducting strands

  10. A single-stranded RNA copy of the Giardia lamblia virus double-stranded RNA genome is present in the infected Giardia lamblia.

    OpenAIRE

    Furfine, E S; White, T C; Wang, A L; Wang, C C

    1989-01-01

    An isolate of Giardia lamblia infected with the double-stranded RNA virus (GLV) has two major species of RNA that are not present in an uninfected isolate. One of these species is the previously characterized double-stranded RNA genome of GLV (1). The second species of RNA appears to be a full length copy of one strand of the double-stranded RNA genome. This full length single-stranded RNA is not present in viral particles isolated from the growth medium. The cellular concentration of the sin...

  11. Elimination of double strand nuclease activity from S1 nuclease prepared from crude alpha amylase.

    Science.gov (United States)

    Hahn, W E; Van Ness, J

    1976-01-01

    Single strand-specific s1 nuclease prepared as previously described from crude alpha amylase by DEAE-cellulose chromatography also contains nuclease which degrades double strand nucleic acid. The double strand activity can be removed by repeating the DEAE-cellulose chromatography procedure at least two additional times. S1 nuclease prepared by this procedure does not degrade double strand sheared DNA as measured by Sephadex chromatography. Under the same conditions single strand DNA is completely degraded. Thus, S1 nuclease prepared by this procedure is suitable for use in removing single strand regions in DNA/DNA duplexes and DNA/RNA hybrids. PMID:940774

  12. DNA replication of single-stranded Escherichia coli DNA phages

    NARCIS (Netherlands)

    Baas, P.D.

    1985-01-01

    Research on single-stranded DNA phages has contributed tremendously to our knowledge of several fundamental life-processes. The small size of their genomes and the fast rate at which they multiply in their host, Escherichia coil, made them attractive candidates for various studies. There

  13. DNA strand exchange catalyzed by molecular crowding in PEG solutions

    KAUST Repository

    Feng, Bobo

    2010-01-01

    DNA strand exchange is catalyzed by molecular crowding and hydrophobic interactions in concentrated aqueous solutions of polyethylene glycol, a discovery of relevance for understanding the function of recombination enzymes and with potential applications to DNA nanotechnology. © 2010 The Royal Society of Chemistry.

  14. Double-Strand DNA Break Repair in Mycobacteria.

    Science.gov (United States)

    Glickman, Michael S

    2014-10-01

    Discontinuity of both strands of the chromosome is a lethal event in all living organisms because it compromises chromosome replication. As such, a diversity of DNA repair systems has evolved to repair double-strand DNA breaks (DSBs). In part, this diversity of DSB repair systems has evolved to repair breaks that arise in diverse physiologic circumstances or sequence contexts, including cellular states of nonreplication or breaks that arise between repeats. Mycobacteria elaborate a set of three genetically distinct DNA repair pathways: homologous recombination, nonhomologous end joining, and single-strand annealing. As such, mycobacterial DSB repair diverges substantially from the standard model of prokaryotic DSB repair and represents an attractive new model system. In addition, the presence in mycobacteria of a DSB repair system that can repair DSBs in nonreplicating cells (nonhomologous end joining) or when DSBs arise between repeats (single-strand annealing) has clear potential relevance to Mycobacterium tuberculosis pathogenesis, although the exact role of these systems in M. tuberculosis pathogenesis is still being elucidated. In this article we will review the genetics of mycobacterial DSB repair systems, focusing on recent insights.

  15. Detection of polymorphisms in leptin gene using single strand ...

    African Journals Online (AJOL)

    student

    Sachs B1 variant. Nucleic Acids Res. 19, 405-406. Barroso, A., Dunner, S. & Cañon, J., 1998. Technical note: detection of bovine kappa-casein variants A, B,. C and E by means of Polymerase Chain Reaction-Single Strand Conformation ...

  16. Guide Strand 3'-End Modifications Regulate siRNA Specificity.

    Science.gov (United States)

    Valenzuela, Rachel A P; Onizuka, Kazumitsu; Ball-Jones, Alexi A; Hu, Tiannan; Suter, Scott R; Beal, Peter A

    2016-12-14

    Short interfering RNA (siRNA)-triggered gene knockdown through the RNA interference (RNAi) pathway is widely used to study gene function, and siRNA-based therapeutics are in development. However, as the guide strand of an siRNA can function like a natural microRNA (miRNA), siRNAs often repress hundreds of off-target transcripts with complementarity only to the seed region (nucleotides 2-8) of the guide strand. Here, we describe novel guide strand 3'-end modifications derived from 1-ethynylribose (1-ER) and copper-catalyzed azide-alkyne cycloaddition reactions and evaluate their impact on target versus miRNA-like off-target knockdown. Surprisingly, when positioned at the guide strand 3'-end, the parent 1-ER modification substantially reduced off-target knockdown while having no measurable effect on on-target knockdown potency. In addition, these modifications were shown to modulate siRNA affinity for the hAgo2 PAZ domain. However, the change in PAZ domain binding affinity was not sufficient to predict the modification's effect on miRNA-like off targeting. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. Characterization of Nb3Sn Strand for ITER

    Energy Technology Data Exchange (ETDEWEB)

    Cheggour, Najib; Goodrich, Loren F

    2012-05-03

    We have an ongoing research program for characterization of superconductor composite strands, the principal output of which is sensitive measurements of critical current Ic over a broad range of the essential parameters: longitudinal strain µ, temperature T, and magnetic field B. This features a new apparatus for integrated measurement of Ic(µ,T,B) on the same, long-conductor sample without remounting.

  18. Chromatin remodelers in the DNA double strand break response

    NARCIS (Netherlands)

    Smeenk, Godelieve

    2012-01-01

    During my PhD project, I studied the role of several chromatin remodelers in the DNA double strand break (DSB) response. We discovered that both CHD4 and SMARCA5 are required for ubiquitin signaling through the E3 ubiquitin ligases RNF8 and RNF168, which is a central signaling event in the response

  19. Applications of Strand-Specific in situ Hybridization

    Energy Technology Data Exchange (ETDEWEB)

    Goodwin, E.H.; Meyne, J.; Bailey, S.M.; Quigley, D.; Smith, L.; Tennyson, R.

    1997-01-01

    This is the final report of a three-year, Laboratory-Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). Fluorescence in situ hybridization (FISH) is used to determine the location of specific DNA sequences on chromosomes. It is an effective tool in genomic mapping and is finding increasing use in medical diagnosis. A ''strand-specific'' version of FISH has been developed in the Life Sciences Division of LANL. The new procedure, named CO-FISH, reveals not only location but also the 5'-to-3'direction of a target sequence, such as the sense strand of a gene. This project was designed to investigate applications of the new technique. Strand-specific FISH was found to be useful and informative for genomic mapping of repetitive DNA sequences. The method provide a valuable new tool for investigating the mechanisms of aneuploidy inducing agents and the cytogenetic phenomena called lateral asymmetry. Finally, using strand-specific FISH, the authors were able to detect certain types of chromosome aberrations (isochromosomes, inversions and Robertsonian translocations) that can be difficult to observe with standard techniques.

  20. Facile synthesis of Graphene Oxide/Double-stranded DNA ...

    Indian Academy of Sciences (India)

    DNA to single-stranded DNA. The GO/dsDNA hydrogels have shown controlled porosity by changing the concentration of the components. The strong binding between dsDNA and graphene is proved by Raman spectroscopy. Keywords. Graphene oxide; DNA; hydrogels; liquid crystals; self-assembly. 1. Introduction.

  1. 75 FR 8113 - Prestressed Concrete Steel Wire Strand From China

    Science.gov (United States)

    2010-02-23

    ... INTERNATIONAL TRADE COMMISSION [Investigation Nos. 701-TA-464 and 731-TA-1160 (Final)] Prestressed Concrete Steel Wire Strand From China AGENCY: United States International Trade Commission. ACTION: Revised schedule for the subject investigations. DATES: Effective Date: February 16, 2010. FOR FURTHER INFORMATION...

  2. 75 FR 4104 - Prestressed Concrete Steel Wire Strand From China

    Science.gov (United States)

    2010-01-26

    ... retarded, by reason of subsidized and less-than-fair-value imports from China of prestressed concrete steel... in prestressed concrete (both pre-tensioned and post- tensioned) applications. The product definition..., producers, or exporters in China of prestressed concrete steel wire strand, and that such products are being...

  3. Short Communication A stranding of Balaenoptera borealis (Lesson ...

    African Journals Online (AJOL)

    Short Communication A stranding of Balaenoptera borealis (Lesson 1828) from Patagonia, Argentina, with notes on parasite infestation and diet. MS Leonardi, MF Grandi, NA García, G Svendsen, MA Romero, R González, EA Crespo ...

  4. Strand asymmetry and codon usage bias in the chloroplast genome of Euglena gracilis

    Science.gov (United States)

    Morton, Brian R.

    1999-01-01

    It is shown that the two strands of the chloroplast genome from Euglena gracilis are asymmetric with regards to nucleotide composition. This asymmetry switches at both the origin of replication and a location that is halfway around the circular genome from the origin. In both halves of the genome the leading strand is G+T-rich, having a bias toward G over C and T over A, and the lagging strand is A+C-rich. This asymmetry is probably the result of a difference in mutation dynamics between the leading and lagging strands. In addition to composition asymmetry, the two strands differ with regards to coding content. In both halves of the genome the vast majority of genes are coded by the leading strand. These two aspects of strand asymmetry are then applied to a statistical test for selection on codon usage. The results indicate that selection on codon usage is limited to genes on the leading strand; no gene on the A+C-rich lagging strand shows evidence for selection, suggesting that highly expressed genes are coded predominantly on the strand of DNA that is the leading strand during replication. On the basis of these observations it is proposed that the coding strand bias is generated by selection to code highly expressed genes on the leading strand to coordinate the direction of replication and transcription, thereby increasing the potential rate of both reactions. PMID:10220429

  5. TrmBL2 from Pyrococcus furiosus Interacts Both with Double-Stranded and Single-Stranded DNA.

    Directory of Open Access Journals (Sweden)

    Sebastian Wierer

    Full Text Available In many hyperthermophilic archaea the DNA binding protein TrmBL2 or one of its homologues is abundantly expressed. TrmBL2 is thought to play a significant role in modulating the chromatin architecture in combination with the archaeal histone proteins and Alba. However, its precise physiological role is poorly understood. It has been previously shown that upon binding TrmBL2 covers double-stranded DNA, which leads to the formation of a thick and fibrous filament. Here we investigated the filament formation process as well as the stabilization of DNA by TrmBL2 from Pyroccocus furiosus in detail. We used magnetic tweezers that allow to monitor changes of the DNA mechanical properties upon TrmBL2 binding on the single-molecule level. Extended filaments formed in a cooperative manner and were considerably stiffer than bare double-stranded DNA. Unlike Alba, TrmBL2 did not form DNA cross-bridges. The protein was found to bind double- and single-stranded DNA with similar affinities. In mechanical disruption experiments of DNA hairpins this led to stabilization of both, the double- (before disruption and the single-stranded (after disruption DNA forms. Combined, these findings suggest that the biological function of TrmBL2 is not limited to modulating genome architecture and acting as a global repressor but that the protein acts additionally as a stabilizer of DNA secondary structure.

  6. Inter-strand resistance measurements in the termination of the ITER SULTAN samples

    International Nuclear Information System (INIS)

    Cau, F; Bruzzone, P

    2009-01-01

    In cabled conductors a perfect uniformity of the current among the strands is hardly reached, due to the non-homogeneity of the contact resistance distribution between the strands and the copper of the electrical terminations. In the case of large current unbalance, the overloaded strands hit the critical surface at high field early, developing a current sharing voltage, which drives the redistribution of the current, mainly in the electrical terminations where the inter-strand resistance is lower than in the high field conductor. If the inter-strand resistance in the termination is low, the voltage levels are sufficiently low to allow an effective redistribution of the current to the less loaded strands. The inter-strand resistance of three different termination layouts of ITER short length samples is measured to make a database available which can be used to qualify the layout of the joints and their capability of redistributing the current among the strands.

  7. Strain measurements by neutron diffraction on Nb3Sn cable with stainless steel reinforcement strands

    International Nuclear Information System (INIS)

    Takahashi, K; Oguro, H; Awaji, S; Watanabe, K; Harjo, S; Aizawa, K

    2012-01-01

    Internal lattice strains under a tensile load for a seven-strand cable consisting of three pre-bent CuNb/Nb 3 Sn and four stainless steel strands were measured by neutron diffraction at room temperature in order to investigate the improvement of mechanical properties of Nb 3 Sn strands. Stress–lattice strain curves of Nb 3 Sn and stainless steel strands were obtained, and the effective stress for a Nb 3 Sn strand was estimated by considering the load sharing of a stainless strand. It was found that the reinforcement with stainless steel strands is an effective way to reduce an applied electromagnetic tensile load for Nb 3 Sn strands for superconducting magnet application. (paper)

  8. Corrosion characteristics of post-tensioning strands in ungrouted ducts : summary.

    Science.gov (United States)

    2011-01-01

    To prevent corrosion of post-tensioning strands, FDOT construction specifications currently require post-tensioning ducts to be grouted within seven calendar days of strand installation. This period challenges construction schedules on large projects...

  9. Functions of Human Rad51 and Other Recombination Factors in DNA Double-Strand Break Repair

    National Research Council Canada - National Science Library

    Sigurdsson, Stefan

    2004-01-01

    ... of. DNA double strand breaks. Genetic and biochemical studies have suggested that the function of genes of the RAD52 group is highly conserved from yeast to humans and interestingly the efficiency of DNA double strand break...

  10. 75 FR 32747 - Prestressed Concrete Steel Wire Strand from Mexico: Rescission of Antidumping Duty Administrative...

    Science.gov (United States)

    2010-06-09

    ... DEPARTMENT OF COMMERCE INTERNATIONAL TRADE ADMINISTRATION [A-201-831] Prestressed Concrete Steel Wire Strand from Mexico: Rescission of Antidumping Duty Administrative Review AGENCY: Import... request an administrative review of the antidumping duty order on prestressed concrete steel wire strand...

  11. Measurement of longitudinal sulfur isotopic variations by laser ablation MC-ICP-MS in single human hair strands.

    Science.gov (United States)

    Santamaria-Fernandez, Rebeca; Giner Martínez-Sierra, Justo; Marchante-Gayón, J M; García-Alonso, J Ignacio; Hearn, Ruth

    2009-05-01

    A new method for the measurement of longitudinal variations of sulfur isotope amount ratios in single hair strands using a laser ablation system coupled to a multicollector inductively coupled plasma mass spectrometer (LA-MC-ICP-MS) is reported here for the first time. Ablation parameters have been optimized for the measurement of sulfur isotope ratios in scalp human hair strands of 80-120-microm thickness and different washing procedures have been evaluated. The repeatability of the method has been tested and the ability to measure sulfur isotopic variations in 1,000-microm-long hair segments has been evaluated. A horse hair sample previously characterized for carbon and nitrogen isotope ratios in an interlaboratory study has been characterized by LA-MC-ICP-MS to be used as an in-house standard for the bracketing of human hair strands. (34)S/(32)S isotope amount ratios have been measured and corrected for instrumental mass bias adopting the external standardization approach using National Institute of Standards and Technology (NIST) RM8553 and full uncertainty budgets have been calculated using the Kragten approach. Results are reported as both (34)S/(32)S isotope amount ratios and deltaS(V-CDT) values (sulfur isotopic differences relative to a reference sample expressed in the Vienna Canyon Diablo Troilite (V-CDT) scale) calculated using NIST RM8553, NIST RM8554, and NIST RM8556 to anchor results to the V-CDT scale. The main advantage of the new method versus conventional gas source isotope ratio mass spectrometry measurements is that longitudinal variations in sulfur isotope amount ratios can be resolved. Proof of concept is shown with human scalp hair strands from three individuals, two UK residents and one traveler (long periods of time abroad). The method enables monitoring of longitudinal isotope ratio variations in single hair strands. Absolute ratios are reported and delta(34)S(V-CDT) values are plotted for comparison. Slight variations of 5 per thousand

  12. Biotechnological mass production of DNA origami

    Science.gov (United States)

    Praetorius, Florian; Kick, Benjamin; Behler, Karl L.; Honemann, Maximilian N.; Weuster-Botz, Dirk; Dietz, Hendrik

    2017-12-01

    DNA nanotechnology, in particular DNA origami, enables the bottom-up self-assembly of micrometre-scale, three-dimensional structures with nanometre-precise features. These structures are customizable in that they can be site-specifically functionalized or constructed to exhibit machine-like or logic-gating behaviour. Their use has been limited to applications that require only small amounts of material (of the order of micrograms), owing to the limitations of current production methods. But many proposed applications, for example as therapeutic agents or in complex materials, could be realized if more material could be used. In DNA origami, a nanostructure is assembled from a very long single-stranded scaffold molecule held in place by many short single-stranded staple oligonucleotides. Only the bacteriophage-derived scaffold molecules are amenable to scalable and efficient mass production; the shorter staple strands are obtained through costly solid-phase synthesis or enzymatic processes. Here we show that single strands of DNA of virtually arbitrary length and with virtually arbitrary sequences can be produced in a scalable and cost-efficient manner by using bacteriophages to generate single-stranded precursor DNA that contains target strand sequences interleaved with self-excising ‘cassettes’, with each cassette comprising two Zn2+-dependent DNA-cleaving DNA enzymes. We produce all of the necessary single strands of DNA for several DNA origami using shaker-flask cultures, and demonstrate end-to-end production of macroscopic amounts of a DNA origami nanorod in a litre-scale stirred-tank bioreactor. Our method is compatible with existing DNA origami design frameworks and retains the modularity and addressability of DNA origami objects that are necessary for implementing custom modifications using functional groups. With all of the production and purification steps amenable to scaling, we expect that our method will expand the scope of DNA nanotechnology in

  13. Adenovirus DNA replication in vitro: Duplication of single-stranded DNA containing a panhandle structure

    NARCIS (Netherlands)

    Leegwater, P.A.J.; Rombouts, R.F.A.; Vliet, P.C. van der

    1988-01-01

    Adenovirus DNA replicates by displacement of one of the parental strands followed by duplication of the displaced parental single strand (complementary strand synthesis). Displacement synthesis has been performed in a reconstituted system composed of viral and cellular proteins, employing either the

  14. Torsional regulation of hRPA-induced unwinding of double-stranded DNA

    NARCIS (Netherlands)

    De Vlaminck, I.; Vidic, I.; Van Loenhout, M.T.J.; Kanaar, R.; Lebbink, J.H.G.; Dekker, C.

    2010-01-01

    All cellular single-stranded (ss) DNA is rapidly bound and stabilized by single stranded DNA-binding proteins (SSBs). Replication protein A, the main eukaryotic SSB, is able to unwind double-stranded (ds) DNA by binding and stabilizing transiently forming bubbles of ssDNA. Here, we study the

  15. DNA strand breaks, repair, and survival in x-irradiated mammalian cells

    International Nuclear Information System (INIS)

    Dugle, D.L.; Gillespie, C.J.; Chapman, J.D.

    1976-01-01

    The yields of unrepairable single- and double-strand breaks in the DNA of x-irradiated Chinese hamster cells were measured by low-speed neutral and alkaline sucrose density gradient sedimentation in order to investigate the relation between these lesions and reproductive death. After maximal single-strand rejoining, at all doses, the number of residual single-strand breaks was twice the number of residual double-strand breaks. Both double-strand and unrepairable single-strand breaks were proportional to the square of absorbed dose, in the range 10-50 krad. No rejoining of double-strand breaks was observed. These observations suggest that, in mammalian cells, most double-strand breaks are not repairable, while all single-strand breaks are repaired except those that are sufficiently close on complementary strands to constitute double-strand breaks. Comparison with cell survival measurements at much lower doses suggests that loss of reproductive capacity corresponds to induction of approximately one double-strand break

  16. Probing electronic coupling between adenine bases in RNA strands from synchrotron radiation circular dichroism experiments

    DEFF Research Database (Denmark)

    Nielsen, Lisbeth Munksgård; Hoffmann, Søren Vrønning; Nielsen, Steen Brøndsted

    2012-01-01

    Circular dichroism spectra (176–330 nm) of RNA adenine oligomers, (rA)n (n = 1–10, 12, 15, and 20), reveal electronic coupling between two bases in short strands. The number of interacting bases in long strands is more and larger than that reported previously for the corresponding DNA strands....

  17. 75 FR 36678 - Prestressed Concrete Steel Wire Strand From China; Determinations

    Science.gov (United States)

    2010-06-28

    ... prestressed concrete steel wire strand (PC strand), provided for in subheading 7312.10.30 of the Harmonized... Publication 4162 (June 2010), entitled Prestressed Concrete Steel Wire Strand from China: Investigation Nos... INTERNATIONAL TRADE COMMISSION [Investigation Nos. 701-TA-464 and 731-TA-1160 (Final)] Prestressed...

  18. 77 FR 2958 - Prestressed Concrete Steel Wire Strand From Thailand: Correction to Notice of Opportunity To...

    Science.gov (United States)

    2012-01-20

    ... DEPARTMENT OF COMMERCE International Trade Administration [A-549-820] Prestressed Concrete Steel Wire Strand From Thailand: Correction to Notice of Opportunity To Request Administrative Review AGENCY... prestressed concrete steel wire strand (``PC Strand'') from Thailand. See Antidumping or Countervailing Duty...

  19. Dynamic protein assembly by programmable DNA strand displacement

    Science.gov (United States)

    Chen, Rebecca P.; Blackstock, Daniel; Sun, Qing; Chen, Wilfred

    2018-03-01

    Inspired by the remarkable ability of natural protein switches to sense and respond to a wide range of environmental queues, here we report a strategy to engineer synthetic protein switches by using DNA strand displacement to dynamically organize proteins with highly diverse and complex logic gate architectures. We show that DNA strand displacement can be used to dynamically control the spatial proximity and the corresponding fluorescence resonance energy transfer between two fluorescent proteins. Performing Boolean logic operations enabled the explicit control of protein proximity using multi-input, reversible and amplification architectures. We further demonstrate the power of this technology beyond sensing by achieving dynamic control of an enzyme cascade. Finally, we establish the utility of the approach as a synthetic computing platform that drives the dynamic reconstitution of a split enzyme for targeted prodrug activation based on the sensing of cancer-specific miRNAs.

  20. Hybrid fur rendering: combining volumetric fur with explicit hair strands

    DEFF Research Database (Denmark)

    Andersen, Tobias Grønbeck; Falster, Viggo; Frisvad, Jeppe Revall

    2016-01-01

    Hair is typically modeled and rendered using either explicitly defined hair strand geometry or a volume texture of hair densities. Taken each on their own, these two hair representations have difficulties in the case of animal fur as it consists of very dense and thin undercoat hairs in combination...... with coarse guard hairs. Explicit hair strand geometry is not well-suited for the undercoat hairs, while volume textures are not well-suited for the guard hairs. To efficiently model and render both guard hairs and undercoat hairs, we present a hybrid technique that combines rasterization of explicitly...... defined guard hairs with ray marching of a prismatic shell volume with dynamic resolution. The latter is the key to practical combination of the two techniques, and it also enables a high degree of detail in the undercoat. We demonstrate that our hybrid technique creates a more detailed and soft fur...

  1. Identification of Cis-Acting Elements on Positive-Strand Subgenomic mRNA Required for the Synthesis of Negative-Strand Counterpart in Bovine Coronavirus

    Directory of Open Access Journals (Sweden)

    Po-Yuan Yeh

    2014-07-01

    Full Text Available It has been demonstrated that, in addition to genomic RNA, sgmRNA is able to serve as a template for the synthesis of the negative-strand [(−-strand] complement. However, the cis-acting elements on the positive-strand [(+-strand] sgmRNA required for (−-strand sgmRNA synthesis have not yet been systematically identified. In this study, we employed real-time quantitative reverse transcription polymerase chain reaction to analyze the cis-acting elements on bovine coronavirus (BCoV sgmRNA 7 required for the synthesis of its (−-strand counterpart by deletion mutagenesis. The major findings are as follows. (1 Deletion of the 5'-terminal leader sequence on sgmRNA 7 decreased the synthesis of the (−-strand sgmRNA complement. (2 Deletions of the 3' untranslated region (UTR bulged stem-loop showed no effect on (−-strand sgmRNA synthesis; however, deletion of the 3' UTR pseudoknot decreased the yield of (−-strand sgmRNA. (3 Nucleotides positioned from −15 to −34 of the sgmRNA 7 3'-terminal region are required for efficient (−-strand sgmRNA synthesis. (4 Nucleotide species at the 3'-most position (−1 of sgmRNA 7 is correlated to the efficiency of (−-strand sgmRNA synthesis. These results together suggest, in principle, that the 5'- and 3'-terminal sequences on sgmRNA 7 harbor cis-acting elements are critical for efficient (−-strand sgmRNA synthesis in BCoV.

  2. Marine Mammals Ashore: A Field Guide for Strandings. Second Edition

    Science.gov (United States)

    2005-01-01

    particularly gillnets, has driven the vaquita to critically low numbers and is a serious threat to other porpoise species throughout their range~ ...... For the... vaquita , as well as all baleen whales except minke, Bryde’s, and gray whales, are also listed under the Endangered Species Act. Stranding response to...Habits: Coastal in bays, estuaries and rivers; frequent offshore banks; weaning at 8-12 months; occur singly, in pairs, or in small groups. Vaquita

  3. Improved single-strand DNA sizing accuracy in capillary electrophoresis.

    OpenAIRE

    Rosenblum, B B; Oaks, F; Menchen, S; Johnson, B

    1997-01-01

    Interpolation algorithms can be developed to size unknown single-stranded (ss) DNA fragments based on their electrophoretic mobilities, when they are compared with the mobilities of standard fragments of known sizes; however, sequence-specific anomalous electrophoretic migration can affect the accuracy and precision of the called sizes of the fragments. We used the anomalous migration of ssDNA fragments to optimize denaturation conditions for capillary electrophoresis. The capillary electroph...

  4. Five strands of math tasks big book : grades pk-2

    CERN Document Server

    Reed, Nat; Forest, Chris

    2009-01-01

    For grades PK-2, our Common Core State Standards-based resource meets the five strands of math concepts addressed by the NCTM standards and encourages the students to learn and review the concepts in unique ways. Included are challenging problem-solving tasks which will push the boundaries of critical thought and demonstrate to students the importance of mathematical problems in Number & Operations, Geometry, Measurement, Data Analysis & Probability and Algebra using real world situations.

  5. Oriented strand board: new material for building construction

    International Nuclear Information System (INIS)

    Paridah Md Tahir; Ong, L.L.

    2001-01-01

    The paper will attempt to show the suitability and competitiveness of oriented strand board (OSB) in building construction. One important factor underlining the success of this product is the availability of the wood raw material. Plantation timbers such as rubberwood, paraserianthes falcataria, acacia crassicarpa, A. auriculiformis and A. mangium have been identified as the major source of this industry. We will focus on the domestic market as well as export market especially on the Asia Pacific region

  6. Formation of double-strand breaks in DNA of γ-irradiated bacteria depending on the function of fast repair processes of DNA single-strand breaks

    International Nuclear Information System (INIS)

    Petrov, S.I.; Gaziev, A.I.

    1980-01-01

    The formation of double-strand breaks in DNA of γ-irradiated ( 60 Co)Ex coli bacteria depending on the function of fast repair processes of DNA single-strand breaks, is investigated. The profiles of sedimentation of DNA Ex coli cells, irradiated at 0-2 deg C in the salt medium and in EDTA-borate buffer, are presented. It is shown that when irradiating cells in EDTA-borate buffer, the output of single- and double strand breaks in DNA is much higher than in the case of their irradiation in the minimum salt medium. The dependence of output of single-strand and double-strand breaks depending on the radiatier doze of E coli cells in the salt medium and EDTA-borate buffer, is studied. The supposition is made on the presence of a regulative interaction between the accumulation of DNA single-breaks and their repair with the formation of double-strand breaks. The functionating of fast and superfast repair processes considerably affects the formation of double-strand breaks in DNA of a bacterium cell. A considerable amount of double-breaks registered immediately after irradiation forms due to a close position of single-strand breaks on the opposite DNA strands

  7. A novel protein that recognizes DNA strand break

    Energy Technology Data Exchange (ETDEWEB)

    Narumi, Issay; Satoh, Katsuya; Kikuchi, Masahiro [Japan Atomic Energy Research Inst., Takasaki, Gunma (Japan). Takasaki Radiation Chemistry Research Establishment

    2002-03-01

    By analyzing a DNA damage-sensitive mutant of the radioresistant bacterium Deinococcus radiodurans, we discovered that a novel protein participates in the extreme radiation resistance of this bacterium. The protein (designated PprA for promoting prominent repair) can recognize DNA strand breaks. PprA could bind to double-stranded DNA (dsDNA) in the open circular form and to linear dsDNA, but could not bind to either dsDNA in the closed circular form or single-stranded DNA (ssDNA). Further, under conditions where a substantial amount of degradation of naked DNA fragments would normally result from the activity of E. coli exonuclease III, no DNA degradation was observed when the DNA fragments were preincubated with PprA. These suggest that PprA would protect irradiation-damaged DNA from exonuclease-mediated degradation and consequent DNA repair processes could function. Beside DNA-binding ability, PprA could promote the activities of DNA repair enzymes such as DNA ligase and RecA, suggesting that PprA functions as a DNA repair-promoting protein to potentiate the effectiveness of DNA repair. These properties enable PprA to use the widespread application in vivo and in vitro. (author)

  8. Paul Strand y las paradojas de la modernidad americana

    Directory of Open Access Journals (Sweden)

    Vicente Sánchez Biosca

    2010-06-01

    Full Text Available As contribuições de Strand para o cinema estão estreitamente relacionadas com seus trabalhos fotográficos da época e mesmo com um olhar que, apesar de suas múltiplas diferenças, possui muitos pontos em comum. Se em Manhatta (1920, Strand (em colaboração com Sheeler oferece uma síntese da natureza e da modernidade, em Redes (1934 o que predomina, em contrapartida, é a experiência da arte muralista mexicana e a influência de Eisenstein (em suas andanças por México são os fatores que determinam seus esforços na construção de uma épica dos operários. Mas sem dúvida, o projeto mais ambicioso de Strand (ao mando da produtora Frontier Films foi Native Land, o filme que atendeu às demandas do American Popular Front e as moldou nas palavras dos fundadores da pátria americana.

  9. Commercial possibilities for stranded conventional gas from Alaska's North Slope

    Science.gov (United States)

    Attanasi, E.D.; Freeman, P.A.

    2014-01-01

    Stranded gas resources are defined for this study as gas resources in discrete accumulations that are not currently commercially producible, or producible at full potential, for either physical or economic reasons. Approximately 35 trillion cubic feet (TCF) of stranded gas was identified on Alaska’s North Slope. The commercialization of this resource requires facilities to transport gas to markets where sales revenue will be sufficient to offset the cost of constructing and operating a gas delivery system. With the advent of the shale gas revolution, plans for a gas pipeline to the conterminous US have been shelved (at least temporarily) and the State and resource owners are considering a liquefied natural gas (LNG) export project that targets Asian markets. This paper focuses on competitive conditions for Asian gas import markets by estimating delivered costs of competing supplies from central Asia, Russia, Indonesia, Malaysia, and Australia in the context of a range of import gas demand projections for the period from 2020 to 2040. These suppliers’ costs are based on the cost of developing, producing, and delivering to markets tranches of the nearly 600 TCF of recoverable gas from their own conventional stranded gas fields. The results of these analyses imply that Alaska’s gas exports to Asia will likely encounter substantial competitive challenges. The sustainability of Asia’s oil-indexed LNG pricing is also discussed in light of a potentially intense level of competition.

  10. Human DNA polymerase η accommodates RNA for strand extension.

    Science.gov (United States)

    Su, Yan; Egli, Martin; Guengerich, F Peter

    2017-11-03

    Ribonucleotides are the natural analogs of deoxyribonucleotides, which can be misinserted by DNA polymerases, leading to the most abundant DNA lesions in genomes. During replication, DNA polymerases tolerate patches of ribonucleotides on the parental strands to different extents. The majority of human DNA polymerases have been reported to misinsert ribonucleotides into genomes. However, only PrimPol, DNA polymerase α, telomerase, and the mitochondrial human DNA polymerase (hpol) γ have been shown to tolerate an entire RNA strand. Y-family hpol η is known for translesion synthesis opposite the UV-induced DNA lesion cyclobutane pyrimidine dimer and was recently found to incorporate ribonucleotides into DNA. Here, we report that hpol η is able to bind DNA/DNA, RNA/DNA, and DNA/RNA duplexes with similar affinities. In addition, hpol η, as well as another Y-family DNA polymerase, hpol κ, accommodates RNA as one of the two strands during primer extension, mainly by inserting dNMPs opposite unmodified templates or DNA lesions, such as 8-oxo-2'-deoxyguanosine or cyclobutane pyrimidine dimer, even in the presence of an equal amount of the DNA/DNA substrate. The discovery of this RNA-accommodating ability of hpol η redefines the traditional concept of human DNA polymerases and indicates potential new functions of hpol η in vivo . © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  11. Programmable autonomous synthesis of single-stranded DNA

    Science.gov (United States)

    Kishi, Jocelyn Y.; Schaus, Thomas E.; Gopalkrishnan, Nikhil; Xuan, Feng; Yin, Peng

    2018-02-01

    DNA performs diverse functional roles in biology, nanotechnology and biotechnology, but current methods for autonomously synthesizing arbitrary single-stranded DNA are limited. Here, we introduce the concept of primer exchange reaction (PER) cascades, which grow nascent single-stranded DNA with user-specified sequences following prescribed reaction pathways. PER synthesis happens in a programmable, autonomous, in situ and environmentally responsive fashion, providing a platform for engineering molecular circuits and devices with a wide range of sensing, monitoring, recording, signal-processing and actuation capabilities. We experimentally demonstrate a nanodevice that transduces the detection of a trigger RNA into the production of a DNAzyme that degrades an independent RNA substrate, a signal amplifier that conditionally synthesizes long fluorescent strands only in the presence of a particular RNA signal, molecular computing circuits that evaluate logic (AND, OR, NOT) combinations of RNA inputs, and a temporal molecular event recorder that records in the PER transcript the order in which distinct RNA inputs are sequentially detected.

  12. The effect of strand bias in Illumina short-read sequencing data

    Directory of Open Access Journals (Sweden)

    Guo Yan

    2012-11-01

    Full Text Available Abstract Background When using Illumina high throughput short read data, sometimes the genotype inferred from the positive strand and negative strand are significantly different, with one homozygous and the other heterozygous. This phenomenon is known as strand bias. In this study, we used Illumina short-read sequencing data to evaluate the effect of strand bias on genotyping quality, and to explore the possible causes of strand bias. Result We collected 22 breast cancer samples from 22 patients and sequenced their exome using the Illumina GAIIx machine. By comparing the consistency between the genotypes inferred from this sequencing data with the genotypes inferred from SNP chip data, we found that, when using sequencing data, SNPs with extreme strand bias did not have significantly lower consistency rates compared to SNPs with low or no strand bias. However, this result may be limited by the small subset of SNPs present in both the exome sequencing and the SNP chip data. We further compared the transition and transversion ratio and the number of novel non-synonymous SNPs between the SNPs with low or no strand bias and those with extreme strand bias, and found that SNPs with low or no strand bias have better overall quality. We also discovered that the strand bias occurs randomly at genomic positions across these samples, and observed no consistent pattern of strand bias location across samples. By comparing results from two different aligners, BWA and Bowtie, we found very consistent strand bias patterns. Thus strand bias is unlikely to be caused by alignment artifacts. We successfully replicated our results using two additional independent datasets with different capturing methods and Illumina sequencers. Conclusion Extreme strand bias indicates a potential high false-positive rate for SNPs.

  13. Autonomous parvovirus LuIII encapsidates equal amounts of plus and minus DNA strands

    Energy Technology Data Exchange (ETDEWEB)

    Bates, R.C.; Snyder, C.E.; Banerjee, P.T.; Mitra, S.

    1984-02-01

    Autonomous parvoviruses are thought to uniquely encapsidate single-stranded DNA of minus polarity. In contrast, the defective adeno-associated viruses separately encapsidate equal amounts of plus and minus DNA strands. The uniqueness of minus strand encapsidation is reexamined for the autonomous parvoviruses. Although it was found that Kilham rat virus and H-1 virus encapsidate varying but small amounts of complementary-strand DNA, it was unexpected to find that LuIII virus encapsidated equal amounts of plus and minus DNA. The extracted LuIII DNA possessed properties of double-stranded replicative-form DNA, including insensitivity to S1 endonuclease, cleavage by restriction enzymes, and conversion to unit-length, single-stranded DNA when electrophoresed under denaturing conditions. However, the inability of this DNA to form single-stranded DNA circles when denatured and then renatured in the presence of formamide and the lack of double-stranded DNA circle formation after treatment with exonuclease III and reannealing shows a lack of sequence homology of the 3' and 5' termini of LuIII DNA, in contrast to adeno-associated virus DNA. Digestion of LuIII double-stranded DNA with EcoRI and HincII and separation of plus and minus DNA strands on composite agarose-acrylamide gels identified a heterogeneity present only in the plus DNA strand. These results suggest that strand specificity of viral DNA encapsidation is not a useful property for differentiation between the autonomous and defective parvoviruses. Furthermore, encapsidation by LuIII of equal amounts of complementary DNA strands in contrast to encapsidation of minus strands by H-1 virus, when propagated in the same host cell type, suggests that selection of strands for encapsidation is a virus-coded rather than host-controlled event.

  14. Bottlenose dolphin (Tursiops truncatus) strandings in South Carolina, 1992-1996

    OpenAIRE

    McFee, Wayne E.; Hopkins-Murphy, Sally R.

    2002-01-01

    From 1992 to 1996, 153 bottlenose dolphin stranded in South Carolina, accounting for 73% of all marine mammal strandings during this period. The objectives of our study were to evaluate data from these strandings to deter-mine 1) annual trends in strandings, 2) seasonal and spatial distribution trends, 3) life history parameters such as sex ratio and age classes, 3) seasonal trends in reproduction, and 4) the extent to which humans have played a role in causing these strandings (human inter-a...

  15. Activation of 2'-5' oligoadenylate synthetase by single-stranded and double-stranded RNA aptamers

    DEFF Research Database (Denmark)

    Hartmann, R; Norby, P L; Martensen, P M

    1998-01-01

    A number of small RNA molecules that are high affinity ligands for the 46-kDa form of human 2'-5' oligoadenylate synthetase have been identified by the SELEX method. Surface plasmon resonance analysis indicates that these RNAs bind to the enzyme with dissociation constants in the nanomolar range....... Competition experiments indicate that the binding site for the small RNAs on the 2'-5' oligoadenylate synthetase molecule at least partially overlaps that for the synthetic double-stranded RNA, poly(I).poly(C). Several of the RNAs function as potent activators of 2'-5' oligoadenylate synthetase in vitro......-stranded RNA, can also be activated by RNA ligands with little secondary structure. Since 2'-5' oligoadenylate synthetase possesses no homology to other known RNA-binding proteins, the development of small specific ligands by SELEX should facilitate studies of RNA-protein interactions and may reveal novel...

  16. Metallographic investigation of fracture behavior in ITER-style Nb$_{3}$Sn superconducting strands

    CERN Document Server

    Jewell, M C; Larbalestier, D C; Nijhuis, A

    2009-01-01

    In this work we specify the extent to which fracture in two ITER-style Nb$_{3}$Sn composite strands occurs in a collective or individual manner, under mechanical tension and bending from the TARSIS apparatus at the University of Twente. A bronze-route strand from European Advanced Superconductors (EAS), which has very uniform, well-spaced filaments, has a widely distributed (200 μm) fracture field and exhibits a composite of individual and collective cracks. An internal tin strand from Oxford Instruments – Superconducting Technology (OST) demonstrates much more localized, collective fracture behavior. The filaments in this strand are about four times larger (in area) than the filaments in the EAS strand, and also agglomerate significantly during heat treatment upon conversion of the Nb to Nb$_{3}$Sn. These results demonstrate that the architecture of the strand can play a significant role in determining the mechanical toughness of the composite, and that strand design should incorporate mechanical consider...

  17. Social factors mediating human-carnivore coexistence: Understanding thematic strands influencing coexistence in Central Romania.

    Science.gov (United States)

    Dorresteijn, Ine; Milcu, Andra Ioana; Leventon, Julia; Hanspach, Jan; Fischer, Joern

    2016-05-01

    Facilitating human-carnivore coexistence depends on the biophysical environment but also on social factors. Focusing on Central Romania, we conducted 71 semi-structured interviews to explore human-bear (Ursus arctos) coexistence. Qualitative content and discourse analysis identified three socially mediated thematic strands, which showed different ways in which perceived interactions between people, bears and the environment shape coexistence. The "landscape-bear strand" described perceptions of the way in which the landscape offers resources for the bear, while the "landscape-human strand" related to ways in which humans experience the landscape. The "management strand" related to the way bears was managed. All three strands highlight both threats and opportunities for the peaceful coexistence of people and bears. Management and policy interventions could be improved by systematically considering the possible effects of interventions on each of the three strands shaping coexistence. Future research should explore the relevance of the identified thematic strands in other settings worldwide.

  18. Programming chemical kinetics: engineering dynamic reaction networks with DNA strand displacement

    Science.gov (United States)

    Srinivas, Niranjan

    Over the last century, the silicon revolution has enabled us to build faster, smaller and more sophisticated computers. Today, these computers control phones, cars, satellites, assembly lines, and other electromechanical devices. Just as electrical wiring controls electromechanical devices, living organisms employ "chemical wiring" to make decisions about their environment and control physical processes. Currently, the big difference between these two substrates is that while we have the abstractions, design principles, verification and fabrication techniques in place for programming with silicon, we have no comparable understanding or expertise for programming chemistry. In this thesis we take a small step towards the goal of learning how to systematically engineer prescribed non-equilibrium dynamical behaviors in chemical systems. We use the formalism of chemical reaction networks (CRNs), combined with mass-action kinetics, as our programming language for specifying dynamical behaviors. Leveraging the tools of nucleic acid nanotechnology (introduced in Chapter 1), we employ synthetic DNA molecules as our molecular architecture and toehold-mediated DNA strand displacement as our reaction primitive. Abstraction, modular design and systematic fabrication can work only with well-understood and quantitatively characterized tools. Therefore, we embark on a detailed study of the "device physics" of DNA strand displacement (Chapter 2). We present a unified view of strand displacement biophysics and kinetics by studying the process at multiple levels of detail, using an intuitive model of a random walk on a 1-dimensional energy landscape, a secondary structure kinetics model with single base-pair steps, and a coarse-grained molecular model that incorporates three-dimensional geometric and steric effects. Further, we experimentally investigate the thermodynamics of three-way branch migration. Our findings are consistent with previously measured or inferred rates for

  19. Mass Stranding of Marine Birds Caused by a Surfactant-Producing Red Tide

    Science.gov (United States)

    Jessup, David A.; Miller, Melissa A.; Ryan, John P.; Nevins, Hannah M.; Kerkering, Heather A.; Mekebri, Abdou; Crane, David B.; Johnson, Tyler A.; Kudela, Raphael M.

    2009-01-01

    In November-December 2007 a widespread seabird mortality event occurred in Monterey Bay, California, USA, coincident with a massive red tide caused by the dinoflagellate Akashiwo sanguinea. Affected birds had a slimy yellow-green material on their feathers, which were saturated with water, and they were severely hypothermic. We determined that foam containing surfactant-like proteins, derived from organic matter of the red tide, coated their feathers and neutralized natural water repellency and insulation. No evidence of exposure to petroleum or other oils or biotoxins were found. This is the first documented case of its kind, but previous similar events may have gone undetected. The frequency and amplitude of red tides have increased in Monterey Bay since 2004, suggesting that impacts on wintering marine birds may continue or increase. PMID:19234604

  20. Heavy Metal Exposure Influences Double Strand Break DNA Repair Outcomes.

    Directory of Open Access Journals (Sweden)

    Maria E Morales

    Full Text Available Heavy metals such as cadmium, arsenic and nickel are classified as carcinogens. Although the precise mechanism of carcinogenesis is undefined, heavy metal exposure can contribute to genetic damage by inducing double strand breaks (DSBs as well as inhibiting critical proteins from different DNA repair pathways. Here we take advantage of two previously published culture assay systems developed to address mechanistic aspects of DNA repair to evaluate the effects of heavy metal exposures on competing DNA repair outcomes. Our results demonstrate that exposure to heavy metals significantly alters how cells repair double strand breaks. The effects observed are both specific to the particular metal and dose dependent. Low doses of NiCl2 favored resolution of DSBs through homologous recombination (HR and single strand annealing (SSA, which were inhibited by higher NiCl2 doses. In contrast, cells exposed to arsenic trioxide preferentially repaired using the "error prone" non-homologous end joining (alt-NHEJ while inhibiting repair by HR. In addition, we determined that low doses of nickel and cadmium contributed to an increase in mutagenic recombination-mediated by Alu elements, the most numerous family of repetitive elements in humans. Sequence verification confirmed that the majority of the genetic deletions were the result of Alu-mediated non-allelic recombination events that predominantly arose from repair by SSA. All heavy metals showed a shift in the outcomes of alt-NHEJ repair with a significant increase of non-templated sequence insertions at the DSB repair site. Our data suggest that exposure to heavy metals will alter the choice of DNA repair pathway changing the genetic outcome of DSBs repair.

  1. Heavy Metal Exposure Influences Double Strand Break DNA Repair Outcomes.

    Science.gov (United States)

    Morales, Maria E; Derbes, Rebecca S; Ade, Catherine M; Ortego, Jonathan C; Stark, Jeremy; Deininger, Prescott L; Roy-Engel, Astrid M

    2016-01-01

    Heavy metals such as cadmium, arsenic and nickel are classified as carcinogens. Although the precise mechanism of carcinogenesis is undefined, heavy metal exposure can contribute to genetic damage by inducing double strand breaks (DSBs) as well as inhibiting critical proteins from different DNA repair pathways. Here we take advantage of two previously published culture assay systems developed to address mechanistic aspects of DNA repair to evaluate the effects of heavy metal exposures on competing DNA repair outcomes. Our results demonstrate that exposure to heavy metals significantly alters how cells repair double strand breaks. The effects observed are both specific to the particular metal and dose dependent. Low doses of NiCl2 favored resolution of DSBs through homologous recombination (HR) and single strand annealing (SSA), which were inhibited by higher NiCl2 doses. In contrast, cells exposed to arsenic trioxide preferentially repaired using the "error prone" non-homologous end joining (alt-NHEJ) while inhibiting repair by HR. In addition, we determined that low doses of nickel and cadmium contributed to an increase in mutagenic recombination-mediated by Alu elements, the most numerous family of repetitive elements in humans. Sequence verification confirmed that the majority of the genetic deletions were the result of Alu-mediated non-allelic recombination events that predominantly arose from repair by SSA. All heavy metals showed a shift in the outcomes of alt-NHEJ repair with a significant increase of non-templated sequence insertions at the DSB repair site. Our data suggest that exposure to heavy metals will alter the choice of DNA repair pathway changing the genetic outcome of DSBs repair.

  2. PROTOCOL FOR GAS SAMPLING AND ANALYSIS IN STRANDED MARINE MAMMALS

    OpenAIRE

    sprotocols

    2015-01-01

    Authors: Yara Bernaldo de Quirós, Óscar González-Díaz, Manuel Arbelo, Marisa Andrada & Antonio Fernández ### Abstract Gas sampling in stranded marine mammals can now be performed in situ using the appropriate vacuum tubes, insulin syringes and an aspirometer. Glass vacuum tubes are used for extraction of gas from cavities such as the intestine, pterigoyd air sacs, pneumothorax or subcapsular emphysema as well as for storage of the gas sample at room temperature and pressure. Insulin s...

  3. Turbulent Flow Validation in the Helios Strand Solver

    Science.gov (United States)

    2014-01-07

    of streamwise velocity and turbulent viscosity profiles for flow over a flat plate atM = 0.2 and Re = 5×106. Figure 20. 137×97 NACA 0012 strand grid 22...6. AUTHORS 7. PERFORMING ORGANIZATION NAMES AND ADDRESSES 15. SUBJECT TERMS b. ABSTRACT 2. REPORT TYPE 17. LIMITATION OF ABSTRACT 15. NUMBER OF...facilitates data exchange between the two mesh types as well as enables relative motion between the mesh systems - i.e. the near-body unstructured rotor

  4. Herpetic keratoconjunctivitis: Therapy with synthetic double-stranded RNA

    Science.gov (United States)

    Friedman, I.; Evans, C.; Meighan, C.W.; Foote, L.J.; Aiello, P.V.; Park, J.H.; Baron, S.

    1968-01-01

    A study was undertaken in rabbits to determine how late in the course of keratoconjunctivitis caused by herpes simplex recovery could be effected by an inducer of interferon. Interferon was induced by means of synthetic double-stranded RNA copolymer formed with polynosinic acid : polycytidilic acid RNA. Therapy promotes recovery from severe and fully established keratoconjunctivitis for which treatment was begun as late as 3 days after virus inoculation. No drug toxicity was observed in the therapeutic dose range. These findings further support the proposed role of the interferon mechanism in the natural recovery of already established viral infection. They also suggest the usefulness of interferon inducers in viral infections of man.

  5. Language Variation and Change in the Australian Curriculum English: Integrating Sub-Strands through a Pedagogy of Metalogue

    Science.gov (United States)

    Willis, Linda-Dianne; Exley, Beryl

    2016-01-01

    The Language Strand of the Australian Curriculum: English (Australian Curriculum, Assessment & Reporting Authority (ACARA), 2016b) includes the sub-strand of "Language Variation and Change". This sub-strand is a marked space for discovery and discussion of the history and politics of language use. As such, this sub-strand points to…

  6. 75 FR 38977 - Pre-Stressed Concrete Steel Wire Strand from the People's Republic of China: Notice of Amended...

    Science.gov (United States)

    2010-07-07

    ... International Trade Administration Pre-Stressed Concrete Steel Wire Strand from the People's Republic of China... concrete steel wire strand (PC strand) from the People's Republic of China (PRC). On June 22, 2010, the ITC...-Stressed Concrete Steel Wire Strand from the People's Republic of China, USITC Pub. 4162, Inv. Nos. 701-TA...

  7. Normal formation and repair of γ-radiation-induced single and double strand DNA breaks in Down syndrome fibroblasts

    International Nuclear Information System (INIS)

    Steiner, M.E.; Woods, W.G.

    1982-01-01

    Fibroblasts from patients with Down syndrome (Trisomy 21) were examined for repair capability of γ-radiation-induced single strand and double strand DNA breaks. Formation and repair of DNA breaks were determined by DNA alkaline and non-denaturing elution techniques. Down syndrome fibroblasts were found to repair single strand and double strand breaks as well as fibroblasts from normal controls. (orig.)

  8. Offshore Earthquakes Do Not Influence Marine Mammal Stranding Risk on the Washington and Oregon Coasts

    Science.gov (United States)

    Grant, Rachel A.; Savirina, Anna

    2018-01-01

    Simple Summary Marine mammals stranding on coastal beaches is not unusual. However, there appears to be no single cause for this, with several causes being probable, such as starvation, contact with humans (for example boat strike or entanglement with fishing gear), disease, and parasitism. We evaluated marine mammal stranding off the Washington and Oregon coasts and looked at offshore earthquakes as a possible contributing factor. Our analysis showed that offshore earthquakes did not make marine mammals more likely to strand. We also analysed a subset of data from the north of Washington State and found that non-adult animals made up a large proportion of stranded animals, and for dead animals the commonest cause of death was disease, traumatic injury, or starvation. Abstract The causes of marine mammals stranding on coastal beaches are not well understood, but may relate to topography, currents, wind, water temperature, disease, toxic algal blooms, and anthropogenic activity. Offshore earthquakes are a source of intense sound and disturbance and could be a contributing factor to stranding probability. We tested the hypothesis that the probability of marine mammal stranding events on the coasts of Washington and Oregon, USA is increased by the occurrence of offshore earthquakes in the nearby Cascadia subduction zone. The analysis carried out here indicated that earthquakes are at most, a very minor predictor of either single, or large (six or more animals) stranding events, at least for the study period and location. We also tested whether earthquakes inhibit stranding and again, there was no link. Although we did not find a substantial association of earthquakes with strandings in this study, it is likely that there are many factors influencing stranding of marine mammals and a single cause is unlikely to be responsible. Analysis of a subset of data for which detailed descriptions were available showed that most live stranded animals were pups, calves, or

  9. Molecular investigation of evaporation of biodroplets containing single-strand DNA on graphene surface.

    Science.gov (United States)

    Akbari, Fahimeh; Foroutan, Masumeh

    2018-02-14

    In this study, the water droplet behaviour of four different types of single-strand DNA with homogeneous base sequence on a graphene substrate during evaporation of the droplet was investigated using molecular dynamics (MD) simulation. The simulation results indicated that the evaporation depended on the DNA sequence. The observed changes can be divided into four parts: (i) vaporization mode, (ii) evaporation flux, (iii) mechanism of single-strand placement on the surface, and (iv) consideration of remaining single strands after evaporation. Our simulation observations indicated different evaporation modes for thymine biodroplets as compared to those for other biodroplets. The evaporation of the thymine biodroplets occurred with an increase in the contact angle, while that of the other biodroplets occur in a constant contact angle mode. Moreover, thymine biodroplets generate the lowest contact line compared to other single strands, and it is always placed far away from the centre of the droplets during evaporation. Investigating variations in the evaporation flux shows that thymine has the highest evaporation flux and guanine has the lowest. Moreover, during initial evaporation, the flux of evaporation increases at the triple point of the biodroplets containing thymine single strands, while it decreases in the other biodroplets. The following observation was obtained from the study of the placement of single strands on the substrate: guanine and thymine interacted slower than other single strands during evaporation with graphene, adenine single strand had a higher folding during evaporation, and guanine single strand showed the lowest end-to-end distance. The investigation of single-strand DNA after evaporation shows that adenine produces the most stable structure at the end of evaporation. In addition, cytosine is the most stretched single-strand DNA due to its lack of internal π-π stacking and hydrogen bonding. Therefore, cytosine single strand is more

  10. Mapping meiotic single-strand DNA reveals a new landscape of DNA double-strand breaks in Saccharomyces cerevisiae.

    Directory of Open Access Journals (Sweden)

    Cyril Buhler

    2007-12-01

    Full Text Available DNA double-strand breaks (DSBs, which are formed by the Spo11 protein, initiate meiotic recombination. Previous DSB-mapping studies have used rad50S or sae2Delta mutants, which are defective in break processing, to accumulate Spo11-linked DSBs, and report large (> or = 50 kb "DSB-hot" regions that are separated by "DSB-cold" domains of similar size. Substantial recombination occurs in some DSB-cold regions, suggesting that DSB patterns are not normal in rad50S or sae2Delta mutants. We therefore developed a novel method to map genome-wide, single-strand DNA (ssDNA-associated DSBs that accumulate in processing-capable, repair-defective dmc1Delta and dmc1Delta rad51Delta mutants. DSBs were observed at known hot spots, but also in most previously identified "DSB-cold" regions, including near centromeres and telomeres. Although approximately 40% of the genome is DSB-cold in rad50S mutants, analysis of meiotic ssDNA from dmc1Delta shows that most of these regions have substantial DSB activity. Southern blot assays of DSBs in selected regions in dmc1Delta, rad50S, and wild-type cells confirm these findings. Thus, DSBs are distributed much more uniformly than was previously believed. Comparisons of DSB signals in dmc1, dmc1 rad51, and dmc1 spo11 mutant strains identify Dmc1 as a critical strand-exchange activity genome-wide, and confirm previous conclusions that Spo11-induced lesions initiate all meiotic recombination.

  11. Human RECQ5 helicase promotes repair of DNA double-strand breaks by synthesis-dependent strand annealing

    Czech Academy of Sciences Publication Activity Database

    Paliwal, S.; Kanagaraj, R.; Sturzenegger, A.; Burdová, Kamila; Janščák, Pavel

    2014-01-01

    Roč. 42, č. 4 (2014), s. 2380-2390 ISSN 0305-1048 R&D Projects: GA ČR GA204/09/0565; GA ČR GAP305/10/0281 Grant - others:Swiss National Science Foundation(CH) 31003A-129747; Swiss National Science Foundation(CH) 31003A_146206 Institutional support: RVO:68378050 Keywords : Human RECQ5 helicase * DNA double-strand breaks * mitotic homologous recombination Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 9.112, year: 2014

  12. Analysis of Double-Stranded RNA from Microbial Communities Identifies Double-Stranded RNA Virus-like Elements

    OpenAIRE

    Decker, Carolyn J.; Parker, Roy

    2014-01-01

    Double-stranded RNA (dsRNA) can function as genetic information and may have served as genomic material before the existence of DNA-based life. By developing a method to purify dsRNA, we have investigated the diversity of dsRNA in microbial populations. We detect large dsRNAs in multiple microbial populations. Analysis of an aquatic microbial population reveals that some dsRNA sequences match metagenomic DNA, suggesting that microbes contain pools of sense-antisense transcripts. In addition, ...

  13. Euler buckling and nonlinear kinking of double-stranded DNA

    Science.gov (United States)

    Fields, Alexander; Axelrod, Kevin; Cohen, Adam

    2012-02-01

    Bare double-stranded DNA is a stiff biopolymer with a persistence length of roughly 53 nm under physiological conditions. Cells and viruses employ extensive protein machinery to overcome this stiffness and bend, twist, and loop DNA to accomplish tasks such as packaging, recombination, gene regulation, and repair. The mechanical properties of DNA are of fundamental importance to the mechanism and thermodynamics of these processes, but physiologically relevant curvature has been difficult to access experimentally. We designed and synthesized a DNA hairpin construct in which base-pairing interactions generated a compressive force on a short segment of duplex DNA, inducing Euler buckling followed by bending to thermally inaccessible radii of curvature. The efficiency of F"orster resonance energy transfer (FRET) between two fluorophores covalently linked to the hairpin indicated the degree of buckling. Bulk and single-molecule measurements yielded distinctly different force-compression curves for intact DNA and for strands with single nicks, base pair mismatches, and damage sites. These results suggest that changes in local mechanical properties may play a significant role in the recognition of these features by DNA-binding proteins.

  14. Amphipathic beta-strand mimics as potential membrane disruptive antibiotics.

    Science.gov (United States)

    Watson, Jessica L; Gillies, Elizabeth R

    2009-08-21

    In recent years, there have been increasing numbers of bacterial strains emerging that are resistant to the currently available antibiotics. In the search for new antibiotics, attention has been focused on natural antimicrobial peptides that act by selectively disrupting the membranes of bacterial cells, a mechanism that is thought to be nonconducive to the development of resistance. It is desirable to mimic the structures and activities of these peptides while introducing properties such as resistance to proteolytic degradation, which make molecules more ideal for development as drugs. Described here is the design and synthesis of beta-strand mimetic oligomers based on alternating alpha-amino acids and azacyclohexenone units that segregate cationic lysine and hydrophobic valine side chains on opposite faces of the beta-strand. (1)H NMR dilution studies demonstrated that despite the incorporation of alternating d- and l-amino acids in order to obtain facial amphiphilicity, these oligomers are capable of dimerizing to beta-sheet mimics in a manner similar to the oligomers containing all l-amino acids. The ability of the molecules to disrupt phospholipid vesicles mimicking the membranes of both bacterial and mammalian cells was investigated using a fluorescent dye leakage assay. Several of the oligomers were found to exhibit activity and selectivity for the bacterial over mammalian membranes. Overall, these studies demonstrate the promise of this class of molecules for the development of new potential antibiotics and provide information on the structural features that are important for activity.

  15. Protection of DNA strand breakage by radiation exposure

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Jeong Ho; Kim, In Gyu; Lee, Kang Suk; Kim, Kug Chan; Shim, Hae Won

    1997-12-01

    Human ceruloplasmin, the plasma copper containing protein, is thought to play an essential role in iron metabolism, but it also has antioxidant properties. Ceruloplasmin directly scavenged hydroxyl radicals (.OH) generated in dithiothreitol/FeCl{sub 3} system besides inhibitory function of hydroxyl radical formation and lipid peroxidation. Polyamines, spermidine and spermine, significantly protected the supercoiled DNA strand breakage by hydroxyl radicals and DNA strand breakage by UV was highly protected by all four polyamines used in this study. In polyamine deficient mutant KL527. It was shown that cell survivability following UV irradiation was slightly increased by exogenous polyamines putrescine and spermidine supplement. However the cell survivability of wild type (MG 1655) was not influenced by polyamine supplement. In {gamma}-irradiated cells, cell survivability of polyamine-deficient mutant strain KL527 was significantly increased by exogenous putrescine supplement and that of wild type strain MG1655 was similar irrespective of polyamine supplement. These results implicate the possibility that polyamines play a potent role in radioprotection of cell and DNA level. (author). 32 refs., 8 figs

  16. Triplex-forming oligonucleotides: a third strand for DNA nanotechnology.

    Science.gov (United States)

    Chandrasekaran, Arun Richard; Rusling, David A

    2018-02-16

    DNA self-assembly has proved to be a useful bottom-up strategy for the construction of user-defined nanoscale objects, lattices and devices. The design of these structures has largely relied on exploiting simple base pairing rules and the formation of double-helical domains as secondary structural elements. However, other helical forms involving specific non-canonical base-base interactions have introduced a novel paradigm into the process of engineering with DNA. The most notable of these is a three-stranded complex generated by the binding of a third strand within the duplex major groove, generating a triple-helical ('triplex') structure. The sequence, structural and assembly requirements that differentiate triplexes from their duplex counterparts has allowed the design of nanostructures for both dynamic and/or structural purposes, as well as a means to target non-nucleic acid components to precise locations within a nanostructure scaffold. Here, we review the properties of triplexes that have proved useful in the engineering of DNA nanostructures, with an emphasis on applications that hitherto have not been possible by duplex formation alone.

  17. Monomer dynamics in single- and double-stranded DNA coils

    Science.gov (United States)

    Tothova, J.; Brutovsky, B.; Lisy, V.

    2007-09-01

    In our paper (Tothova et al., Czech. J. Phys. 55, 221 (2005)), the first observation of the kinetics of individual polymer monomers using the fluorescence correlation technique (R. Shusterman et al., Phys. Rev. Lett. 92, 048303 (2004)) has been interpreted within the bead-spring theory. Optimizing the joint Rouse-Zimm model to the experimental data, the phenomenological parameters for the statistical-mechanical description of the universal behavior of double- and single-stranded DNA and the dominant types of their dynamics have been determined. Recently, these data have been corrected (R. Shusterman et al., Phys. Rev. Lett. 98, 029901 (2007)). In the present work, the fits of the theory to the new data are given. The main conclusions of our preceding paper remain unchanged but some of the polymer parameters have changed. The new data allow a significantly better agreement with the theory than the previous ones. Our calculations confirm that dsDNA follows mainly the classical Zimm-type kinetics rather than the Rouse one as it was proposed by Shusterman et al. Single-stranded DNA also behaves predominantly as the Zimm polymer. To support these conclusions, we analyze the draining effects on the monomer dynamics and the applicability of simple “universal” laws, according to which the monomer mean square displacement scales with the time as t1/2 and t2/3 for the Rouse and Zimm polymers, respectively.

  18. Genome-wide mapping of DNA strand breaks.

    Directory of Open Access Journals (Sweden)

    Frédéric Leduc

    Full Text Available Determination of cellular DNA damage has so far been limited to global assessment of genome integrity whereas nucleotide-level mapping has been restricted to specific loci by the use of specific primers. Therefore, only limited DNA sequences can be studied and novel regions of genomic instability can hardly be discovered. Using a well-characterized yeast model, we describe a straightforward strategy to map genome-wide DNA strand breaks without compromising nucleotide-level resolution. This technique, termed "damaged DNA immunoprecipitation" (dDIP, uses immunoprecipitation and the terminal deoxynucleotidyl transferase-mediated dUTP-biotin end-labeling (TUNEL to capture DNA at break sites. When used in combination with microarray or next-generation sequencing technologies, dDIP will allow researchers to map genome-wide DNA strand breaks as well as other types of DNA damage and to establish a clear profiling of altered genes and/or intergenic sequences in various experimental conditions. This mapping technique could find several applications for instance in the study of aging, genotoxic drug screening, cancer, meiosis, radiation and oxidative DNA damage.

  19. Protection of DNA strand breakage by radiation exposure

    International Nuclear Information System (INIS)

    Lee, Jeong Ho; Kim, In Gyu; Lee, Kang Suk; Kim, Kug Chan; Shim, Hae Won

    1997-12-01

    Human ceruloplasmin, the plasma copper containing protein, is thought to play an essential role in iron metabolism, but it also has antioxidant properties. Ceruloplasmin directly scavenged hydroxyl radicals (.OH) generated in dithiothreitol/FeCl 3 system besides inhibitory function of hydroxyl radical formation and lipid peroxidation. Polyamines, spermidine and spermine, significantly protected the supercoiled DNA strand breakage by hydroxyl radicals and DNA strand breakage by UV was highly protected by all four polyamines used in this study. In polyamine deficient mutant KL527. It was shown that cell survivability following UV irradiation was slightly increased by exogenous polyamines putrescine and spermidine supplement. However the cell survivability of wild type (MG 1655) was not influenced by polyamine supplement. In γ-irradiated cells, cell survivability of polyamine-deficient mutant strain KL527 was significantly increased by exogenous putrescine supplement and that of wild type strain MG1655 was similar irrespective of polyamine supplement. These results implicate the possibility that polyamines play a potent role in radioprotection of cell and DNA level. (author). 32 refs., 8 figs

  20. Single-strand DNA molecule translocation through nanoelectrode gaps

    International Nuclear Information System (INIS)

    Zhao Xiongce; Payne, Christina M; Cummings, Peter T; Lee, James W

    2007-01-01

    Molecular dynamics simulations were performed to investigate the translocation of single-strand DNA through nanoscale electrode gaps under the action of a constant driving force. The application behind this theoretical study is a proposal to use nanoelectrodes as a screening gap as part of a rapid genomic sequencing device. Preliminary results from a series of simulations using various gap widths and driving forces suggest that the narrowest electrode gap that a single-strand DNA can pass is ∼1.5 nm. The minimum force required to initiate the translocation within nanoseconds is ∼0.3 nN. Simulations using DNA segments of various lengths indicate that the minimum initiation force is insensitive to the length of DNA. However, the average threading velocity of DNA varies appreciably from short to long DNA segments. We attribute such variation to the different nature of drag force experienced by the short and long DNA segments in the environment. It is found that DNA molecules deform significantly to fit in the shape of the nanogap during the translocation

  1. The RNA synthesis machinery of negative-stranded RNA viruses

    Energy Technology Data Exchange (ETDEWEB)

    Ortín, Juan, E-mail: jortin@cnb.csic.es [Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología (CSIC) and CIBER de Enfermedades Respiratorias (ISCIII), Madrid (Spain); Martín-Benito, Jaime, E-mail: jmartinb@cnb.csic.es [Department of Macromolecular Structures, Centro Nacional de Biotecnología (CSIC), Madrid (Spain)

    2015-05-15

    The group of Negative-Stranded RNA Viruses (NSVs) includes many human pathogens, like the influenza, measles, mumps, respiratory syncytial or Ebola viruses, which produce frequent epidemics of disease and occasional, high mortality outbreaks by transmission from animal reservoirs. The genome of NSVs consists of one to several single-stranded, negative-polarity RNA molecules that are always assembled into mega Dalton-sized complexes by association to many nucleoprotein monomers. These RNA-protein complexes or ribonucleoproteins function as templates for transcription and replication by action of the viral RNA polymerase and accessory proteins. Here we review our knowledge on these large RNA-synthesis machines, including the structure of their components, the interactions among them and their enzymatic activities, and we discuss models showing how they perform the virus transcription and replication programmes. - Highlights: • Overall organisation of NSV RNA synthesis machines. • Structure and function of the ribonucleoprotein components: Atomic structure of the RNA polymerase complex. • Commonalities and differences between segmented- and non-segmented NSVs. • Transcription versus replication programmes.

  2. The RNA synthesis machinery of negative-stranded RNA viruses

    International Nuclear Information System (INIS)

    Ortín, Juan; Martín-Benito, Jaime

    2015-01-01

    The group of Negative-Stranded RNA Viruses (NSVs) includes many human pathogens, like the influenza, measles, mumps, respiratory syncytial or Ebola viruses, which produce frequent epidemics of disease and occasional, high mortality outbreaks by transmission from animal reservoirs. The genome of NSVs consists of one to several single-stranded, negative-polarity RNA molecules that are always assembled into mega Dalton-sized complexes by association to many nucleoprotein monomers. These RNA-protein complexes or ribonucleoproteins function as templates for transcription and replication by action of the viral RNA polymerase and accessory proteins. Here we review our knowledge on these large RNA-synthesis machines, including the structure of their components, the interactions among them and their enzymatic activities, and we discuss models showing how they perform the virus transcription and replication programmes. - Highlights: • Overall organisation of NSV RNA synthesis machines. • Structure and function of the ribonucleoprotein components: Atomic structure of the RNA polymerase complex. • Commonalities and differences between segmented- and non-segmented NSVs. • Transcription versus replication programmes

  3. Cadmium/zinc-metallothionein induces DNA strand breaks in vitro.

    Science.gov (United States)

    Müller, T; Schuckelt, R; Jaenicke, L

    1991-01-01

    The in vitro DNA strand breaking activity of metallothionein (MT) containing Cd2+ and Zn2+ in a molar ratio of 5:2 is described. Studies with radical scavengers and electron paramagnetic resonance spectroscopy indicate that the DNA damage might be caused by a radical species formed by the native protein (i.e., MT) charged with the heavy metal ions. No DNA strand breaks are detectable with the heat-denatured MT or with Cd2+ or Zn2+ alone. Inhibition studies using EDTA as a metal ion chelator or N-ethylmaleimide to alkylate sulfhydryl groups suggest that both the bound heavy metal ions as well as the SH groups of the various cysteine residues of MT may be involved in the MT-dependent DNA cleavage. Further characterization showed that the DNA cleavage is more likely random than sequence- or base-specific. These observations may provide a clue in the search for initial events in Cd-related carcinogenicity.

  4. Photochemical Acceleration of DNA Strand Displacement by Using Ultrafast DNA Photo-crosslinking.

    Science.gov (United States)

    Nakamura, Shigetaka; Hashimoto, Hirokazu; Kobayashi, Satoshi; Fujimoto, Kenzo

    2017-10-18

    DNA strand displacement is an essential reaction in genetic recombination, biological processes, and DNA nanotechnology. In particular, various DNA nanodevices enable complicated calculations. However, it takes time before the output is obtained, so acceleration of DNA strand displacement is required for a rapid-response DNA nanodevice. Herein, DNA strand displacement by using DNA photo-crosslinking to accelerate this displacement is evaluated. The DNA photo-crosslinking of 3-cyanovinylcarbazole ( CNV K) was accelerated at least 20 times, showing a faster DNA strand displacement. The rate of photo-crosslinking is a key factor and the rate of DNA strand displacement is accelerated through ultrafast photo-crosslinking. The rate of DNA strand displacement was regulated by photoirradiation energy. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. Residual Resistivity Ratio (RRR) Measurements of LHC Superconducting NbTi Cable Strands

    CERN Document Server

    Charifoulline, Z

    2006-01-01

    The Rutherford-type superconducting NbTi cables of the LHC accelerator are currently manufactured by six industrial companies. As a part of the acceptance tests, the Residual Resistivity Ratio (RRR) of superconducting strands is systematically measured on virgin strands to qualify the strands before cabling and on extracted strands to qualify the cables and to check the final heat treatment (controlled oxidation to control interstrand resistance). More than 12000 samples of virgin and extracted strands have been measured during last five years. Results show good correlation with the measurements done by the companies and reflect well the technological process of cable production (strand annealing, cabling, cable heat treatment). This paper presents a description of the RRR-test station and the measurement procedure, the summary of the results over all suppliers and finally the correlation between RRR-values of the cables and the magnets.

  6. Estimation of Prestress Force Distribution in the Multi-Strand System of Prestressed Concrete Structures.

    Science.gov (United States)

    Cho, Keunhee; Park, Sung Yong; Cho, Jeong-Rae; Kim, Sung Tae; Park, Young-Hwan

    2015-06-15

    Prestressed concrete (PSC) is one of the most reliable, durable and widely used construction materials, which overcomes the weakness of concrete in tension by the introduction of a prestress force. Smart strands enabling measurement of the prestress force have recently been developed to maintain PSC structures throughout their lifetime. However, the smart strand cannot give a representative indication of the whole prestress force when used in multi-strand systems since each strand sustains a different prestress force. In this paper, the actual distribution of the prestress force in a multi-strand system is examined using elastomagnetic (EM) sensors to develop a method for tracking representative indicators of the prestress force using smart strands.

  7. Estimation of Prestress Force Distribution in the Multi-Strand System of Prestressed Concrete Structures

    Directory of Open Access Journals (Sweden)

    Keunhee Cho

    2015-06-01

    Full Text Available Prestressed concrete (PSC is one of the most reliable, durable and widely used construction materials, which overcomes the weakness of concrete in tension by the introduction of a prestress force. Smart strands enabling measurement of the prestress force have recently been developed to maintain PSC structures throughout their lifetime. However, the smart strand cannot give a representative indication of the whole prestress force when used in multi-strand systems since each strand sustains a different prestress force. In this paper, the actual distribution of the prestress force in a multi-strand system is examined using elastomagnetic (EM sensors to develop a method for tracking representative indicators of the prestress force using smart strands.

  8. Investigations of radiation-induced strand breaks of poly(U) in aqueous solutions

    International Nuclear Information System (INIS)

    Lemaire, D.G.E.

    1984-01-01

    DNA strand breaks induced by γ irradiation were studied in polyuridylic acid (Poly(U)), a single-strand model substance with a single base. Poly(U) in diluted, aqueous solution was irradiated in a Co-γ source, and the 100 eV yields of strand breaks (Cr values) were determined on the basis of the loss of molecular weight. The molecular weight was determined by small-angle laser light scattering. (orig./PW) [de

  9. DNA double strand breaks as the critical type of damage with regard to inactivation of cells through ionizing radiation

    International Nuclear Information System (INIS)

    Frankenberg, D.

    1985-01-01

    This report presents the results of an investigation into the effects of ionizing radiation on eukaryotic cells, aimed at revealing the molecular mechanisms leading to cell inactivation as a result of ionizing radiation. The quantitative determination of radiation-induced double strand breaks (DSB) is done via sedimentation of the DNA released from the cells in a neutral saccharose gradient in a preparative ultracentrifuge. The 'experimental mass spectrum' of DNA molecules thus obtained, the mean number of DSB per cell is calculated using a special computer program which simulates the stochastic induction of DSB in the DNA of non-irradiated cells and links the 'simulated' mass spectrum with the 'experimental' one on the basis of the least square fit. The experimental and theoretical studies with the eukaryote yeast on the whole allow insight into the relation between energy absorption and the inactivation of irradiated cells. (orig./MG) [de

  10. Radioresistance of GGG sequences to prompt strand break formation from direct-type radiation damage.

    Science.gov (United States)

    Black, Paul J; Miller, Adam S; Hayes, Jeffrey J

    2016-11-01

    As humans, we are constantly exposed to ionizing radiation from natural, man-made and cosmic sources which can damage DNA, leading to deleterious effects including cancer incidence. In this work, we introduce a method to monitor strand breaks resulting from damage due to the direct effect of ionizing radiation and provide evidence for sequence-dependent effects leading to strand breaks. To analyze only DNA strand breaks caused by radiation damage due to the direct effect of ionizing radiation, we combined an established technique to generate dehydrated DNA samples with a technique to analyze single-strand breaks on short oligonucleotide sequences via denaturing gel electrophoresis. We find that direct damage primarily results in a reduced number of strand breaks in guanine triplet regions (GGG) when compared to isolated guanine (G) bases with identical flanking base context. In addition, we observe strand break behavior possibly indicative of protection of guanine bases when flanked by pyrimidines and sensitization of guanine to strand break when flanked by adenine (A) bases in both isolated G and GGG cases. These observations provide insight into the strand break behavior in GGG regions damaged via the direct effect of ionizing radiation. In addition, this could be indicative of DNA sequences that are naturally more susceptible to strand break due to the direct effect of ionizing radiation.

  11. Offshore Earthquakes Do Not Influence Marine Mammal Stranding Risk on the Washington and Oregon Coasts.

    Science.gov (United States)

    Grant, Rachel A; Savirina, Anna; Hoppitt, Will

    2018-01-26

    The causes of marine mammals stranding on coastal beaches are not well understood, but may relate to topography, currents, wind, water temperature, disease, toxic algal blooms, and anthropogenic activity. Offshore earthquakes are a source of intense sound and disturbance and could be a contributing factor to stranding probability. We tested the hypothesis that the probability of marine mammal stranding events on the coasts of Washington and Oregon, USA is increased by the occurrence of offshore earthquakes in the nearby Cascadia subduction zone. The analysis carried out here indicated that earthquakes are at most, a very minor predictor of either single, or large (six or more animals) stranding events, at least for the study period and location. We also tested whether earthquakes inhibit stranding and again, there was no link. Although we did not find a substantial association of earthquakes with strandings in this study, it is likely that there are many factors influencing stranding of marine mammals and a single cause is unlikely to be responsible. Analysis of a subset of data for which detailed descriptions were available showed that most live stranded animals were pups, calves, or juveniles, and in the case of dead stranded mammals, the commonest cause of death was trauma, disease, and emaciation.

  12. Single-stranded regions in transforming deoxyribonucleic acid after uptake by competent Haemophilus influenzae

    Energy Technology Data Exchange (ETDEWEB)

    Sedgwick, B.; Setlow, J.K.

    1976-02-01

    About 15% of donor deoxyribonucleic acid (DNA) is single stranded immediately after uptake into competent Haemophilus influenzae wild-type cells, as judged by its sensitivity to S1 endonuclease. This amount decreases to 4 to 5% by 30 min after uptake. Mutants which are defective in the covalent association of recipient and donor DNA form little or no S1 endonuclease-sensitive donor. At 17 C donor DNA taken up by the wild type contains single-stranded regions although there is no observable association, either covalent or noncovalent. The single-stranded regions are at the ends of donor DNA molecules, as judged by the unchanged sedimentation velocity after S1 endonuclease digestion. The amount of single-stranded donor remains constant at 17 C for more than 60 min after uptake, suggesting that the decrease observed at 37 C is the result of association of single-stranded ends with single-stranded regions of recipient cell DNA. Three sequential steps necessary for the integration of donor DNA into recipient DNA are proposed: the synthesis of single-stranded regions in recipient DNA, the interaction of donor DNA with recipient DNA resulting in the production of single-stranded ends on donor DNA, and the stable pairing of homologous single-stranded regions. (auth)

  13. Workshop on effects of chromium coating on Nb3Sn superconductor strand: Proceedings

    International Nuclear Information System (INIS)

    1994-01-01

    This report discusses the following topics: Chromium coating on superconductor strand -- an overview; technology of chromium plating; comparison of wires plated by different platers; search for chromium in copper; strand manufactures' presentations; chromium plating at the Lawrence Livermore National Laboratory; a first look at a chromium plating process development project tailored for T.P.X. and I.T.E.R. strand; and influence of chromium diffusion and related phenomena on the reference ratios of bare and chromium plated Nb 3 Sn strand

  14. Development of a 10 m quasi-isotropic strand assembled from 2G wires

    Science.gov (United States)

    Kan, Changtao; Wang, Yinshun; Hou, Yanbing; Li, Yan; Zhang, Han; Fu, Yu; Jiang, Zhe

    2018-03-01

    Quasi-isotropic strands made of second generation (2G) high temperature superconducting (HTS) wires are attractive to applications of high-field magnets at low temperatures and power transmission cables at liquid nitrogen temperature in virtue of their high current carrying capability and well mechanical property. In this contribution, a 10 m length quasi-isotropic strand is manufactured and successfully tested in liquid nitrogen to verify the feasibility of an industrial scale production of the strand by the existing cabling technologies. The strand with copper sheath consists of 72 symmetrically assembled 2G wires. The uniformity of critical properties of long quasi-isotropic strands, including critical current and n-value, is very important for their using. Critical currents as well as n-values of the strand are measured every 1 m respectively and compared with the simulation results. Critical current and n-value of the strand are calculated basing on the self-consistent model solved by the finite element method (FEM). Effects of self-field on the critical current and n-value distributions in wires of the strand are analyzed in detail. The simulation results show good agreement with the experimental data and the 10 m quasi-isotropic strand has good critical properties uniformity.

  15. Interactions between Cytochrome c and DNA Strands Self-Assembled at Gold Electrode

    Science.gov (United States)

    Lao, Ruojun; Wang, Lihua; Wan, Ying; Zhang, Jiong; Song, Shiping; Zhang, Zhizhou; Fan, Chunhai; He, Lin

    2007-01-01

    In this work, we reported the investigation on the interaction between DNA strands self-assembled at gold electrodes and an electron transfer protein, cytochrome c. We observed that cytochrome c exhibited well-defined electrochemistry in both double-stranded and single-stranded DNA films. This suggested that the electron transfer reaction of cytochrome c arose possibly due to the electron hopping along DNA strands rather than wiring along the double helix. We also compared the heterogeneous electron transfer rate of cytochrome c with that of a ruthenium complex, which further confirmed this mechanism.

  16. A euryarchaeal histone modulates strand displacement synthesis by replicative DNA polymerases.

    Science.gov (United States)

    Sun, Fei; Huang, Li

    2016-07-01

    Euryarchaeota and Crenarchaeota, the two main lineages of the domain Archaea, encode different chromatin proteins and differ in the use of replicative DNA polymerases. Crenarchaea possess a single family B DNA polymerase (PolB), which is capable of strand displacement modulated by the chromatin proteins Cren7 and Sul7d. Euryarchaea have two distinct replicative DNA polymerases, PolB and PolD, a family D DNA polymerase. Here we characterized the strand displacement activities of PolB and PolD from the hyperthermophilic euryarchaeon Pyrococcus furiosus and investigated the influence of HPfA1, a homolog of eukaryotic histones from P. furiosus, on these activities. We showed that both PolB and PolD were efficient in strand displacement. HPfA1 inhibited DNA strand displacement by both DNA polymerases but exhibited little effect on the displacement of a RNA strand annealed to single-stranded template DNA. This is consistent with the finding that HPfA1 bound more tightly to double-stranded DNA than to a RNA:DNA hybrid. Our results suggest that, although crenarchaea and euryarchaea differ in chromosomal packaging, they share similar mechanisms in modulating strand displacement by DNA polymerases during lagging strand DNA synthesis.

  17. Offshore Earthquakes Do Not Influence Marine Mammal Stranding Risk on the Washington and Oregon Coasts

    Directory of Open Access Journals (Sweden)

    Rachel A. Grant

    2018-01-01

    Full Text Available The causes of marine mammals stranding on coastal beaches are not well understood, but may relate to topography, currents, wind, water temperature, disease, toxic algal blooms, and anthropogenic activity. Offshore earthquakes are a source of intense sound and disturbance and could be a contributing factor to stranding probability. We tested the hypothesis that the probability of marine mammal stranding events on the coasts of Washington and Oregon, USA is increased by the occurrence of offshore earthquakes in the nearby Cascadia subduction zone. The analysis carried out here indicated that earthquakes are at most, a very minor predictor of either single, or large (six or more animals stranding events, at least for the study period and location. We also tested whether earthquakes inhibit stranding and again, there was no link. Although we did not find a substantial association of earthquakes with strandings in this study, it is likely that there are many factors influencing stranding of marine mammals and a single cause is unlikely to be responsible. Analysis of a subset of data for which detailed descriptions were available showed that most live stranded animals were pups, calves, or juveniles, and in the case of dead stranded mammals, the commonest cause of death was trauma, disease, and emaciation.

  18. Flexural behavior of bonded post-tensioned concrete beams under strand corrosion

    International Nuclear Information System (INIS)

    Zhang, Xuhui; Wang, Lei; Zhang, Jianren; Ma, Yafei; Liu, Yongming

    2017-01-01

    Highlights: • Flexural behavior of bonded PT beams with strand corrosion is experimental tested. • Cracking, stiffness, ultimate strength, failure & ductility of beams are clarified. • A coefficient is proposed to measure incompatible strain between strand & concrete. - Abstract: An experimental test is performed to investigate the flexural behavior of bonded post-tensioned concrete beams under strand corrosion. Eight beams are designed and subjected to accelerated method to different corrosion levels. The initial stiffness of beams is observed by cyclic loading-unloading test during the corrosion procedure. Corrosion effects on concrete cracking, post-cracking stiffness, ultimate strength, failure mode and ductility are then clarified by the flexural test. And, a coefficient is introduced to quantify the incompatible strain between corroded strand and concrete. Results show that the prestress force loss of strand has almost the linear relation with corrosion loss. Strand corrosion affects slightly the initial stiffness of beam before flexural cracking, but degrades significantly the post-cracking stiffness of beam as the corrosion loss exceeds 27.0%. Slight corrosion of strand has little effects on beams flexural behavior. The severe corrosion, however, decreases the number of crack, changes the failure mode form the concrete crushing to strand rupture, degrades the ductility and the ultimate strength of beams, and leads to the incompatible strain between strand and concrete. In the present test, the incompatible strain decreases about 20% of the flexural strength as the corrosion loss exceeds 27.0%.

  19. Structure-spectrophotometric selectivity relationship in interactions of quercetin related flavonoids with double stranded and single stranded RNA

    Science.gov (United States)

    Piantanida, Ivo; Mašić, Lozika; Rusak, Gordana

    2009-04-01

    Interactions of five flavonoids with dsRNA and single stranded ssRNA were studied by UV/vis titrations. The results obtained supported the intercalative binding mode as a dominant interaction of studied flavonoids with dsRNA as well as major interaction with ssRNA. Furthermore, changes of the UV/vis spectra of flavonoids induced by addition of poly G or poly C, respectively, are significantly stronger than changes induced by double stranded poly G-poly C, pointing to essential role of the free poly G or poly C sequence (not hydrogen bonded in double helix). Exclusively poly G caused significant batochromic shift of the UV/vis maxima of all studied flavonoids, whereby the intensity of batochromic shift is nicely correlated to the number of OH groups of flavonoid. Unlikely to poly G, addition of poly A and poly U induced measurable changes only in the UV/vis spectra of flavonoids characterised by no OH (galangin) or three OH groups (myricetin) on the phenyl part of the molecule. Consequently, flavonoids with one- or two-OH groups on the phenyl part of the molecule (luteolin, fisetin, kaempferol) specifically differentiate between poly A, poly U (negligible changes in the UV/Vis spectra) and poly G (strong changes in the UV/Vis spectra) as well as poly C (moderate changes in the UV/Vis spectra).

  20. Primary resistance to integrase strand-transfer inhibitors in Europe

    DEFF Research Database (Denmark)

    Casadellà, M; van Ham, P M; Noguera-Julian, M

    2015-01-01

    OBJECTIVES: The objective of this study was to define the natural genotypic variation of the HIV-1 integrase gene across Europe for epidemiological surveillance of integrase strand-transfer inhibitor (InSTI) resistance. METHODS: This was a multicentre, cross-sectional study within the European...... SPREAD HIV resistance surveillance programme. A representative set of 300 samples was selected from 1950 naive HIV-positive subjects newly diagnosed in 2006-07. The prevalence of InSTI resistance was evaluated using quality-controlled baseline population sequencing of integrase. Signature raltegravir......, elvitegravir and dolutegravir resistance mutations were defined according to the IAS-USA 2014 list. In addition, all integrase substitutions relative to HXB2 were identified, including those with a Stanford HIVdb score ≥10 to at least one InSTI. To rule out circulation of minority InSTI-resistant HIV, 65...

  1. Phosphorylation: The Molecular Switch of Double-Strand Break Repair

    Directory of Open Access Journals (Sweden)

    K. C. Summers

    2011-01-01

    Full Text Available Repair of double-stranded breaks (DSBs is vital to maintaining genomic stability. In mammalian cells, DSBs are resolved in one of the following complex repair pathways: nonhomologous end-joining (NHEJ, homologous recombination (HR, or the inclusive DNA damage response (DDR. These repair pathways rely on factors that utilize reversible phosphorylation of proteins as molecular switches to regulate DNA repair. Many of these molecular switches overlap and play key roles in multiple pathways. For example, the NHEJ pathway and the DDR both utilize DNA-PK phosphorylation, whereas the HR pathway mediates repair with phosphorylation of RPA2, BRCA1, and BRCA2. Also, the DDR pathway utilizes the kinases ATM and ATR, as well as the phosphorylation of H2AX and MDC1. Together, these molecular switches regulate repair of DSBs by aiding in DSB recognition, pathway initiation, recruitment of repair factors, and the maintenance of repair mechanisms.

  2. DNA double-strand break repair in Caenorhabditis elegans.

    Science.gov (United States)

    Lemmens, Bennie B L G; Tijsterman, Marcel

    2011-02-01

    Faithful repair of DNA double-strand breaks (DSBs) is vital for animal development, as inappropriate repair can cause gross chromosomal alterations that result in cellular dysfunction, ultimately leading to cancer, or cell death. Correct processing of DSBs is not only essential for maintaining genomic integrity, but is also required in developmental programs, such as gametogenesis, in which DSBs are deliberately generated. Accordingly, DSB repair deficiencies are associated with various developmental disorders including cancer predisposition and infertility. To avoid this threat, cells are equipped with an elaborate and evolutionarily well-conserved network of DSB repair pathways. In recent years, Caenorhabditis elegans has become a successful model system in which to study DSB repair, leading to important insights in this process during animal development. This review will discuss the major contributions and recent progress in the C. elegans field to elucidate the complex networks involved in DSB repair, the impact of which extends well beyond the nematode phylum.

  3. RNA-directed repair of DNA double-strand breaks.

    Science.gov (United States)

    Yang, Yun-Gui; Qi, Yijun

    2015-08-01

    DNA double-strand breaks (DSBs) are among the most deleterious DNA lesions, which if unrepaired or repaired incorrectly can cause cell death or genome instability that may lead to cancer. To counteract these adverse consequences, eukaryotes have evolved a highly orchestrated mechanism to repair DSBs, namely DNA-damage-response (DDR). DDR, as defined specifically in relation to DSBs, consists of multi-layered regulatory modes including DNA damage sensors, transducers and effectors, through which DSBs are sensed and then repaired via DNAprotein interactions. Unexpectedly, recent studies have revealed a direct role of RNA in the repair of DSBs, including DSB-induced small RNA (diRNA)-directed and RNA-templated DNA repair. Here, we summarize the recent discoveries of RNA-mediated regulation of DSB repair and discuss the potential impact of these novel RNA components of the DSB repair pathway on genomic stability and plasticity. Copyright © 2015 Elsevier B.V. All rights reserved.

  4. Assembly of large icosahedral double-stranded RNA viruses.

    Science.gov (United States)

    Poranen, Minna M; Bamford, Dennis H

    2012-01-01

    Double-stranded RNA (dsRNA) viruses are a diverse group of viruses infecting hosts from bacteria to higher eukaryotes. Among the hosts are humans, domestic animals, and economically important plant species. Fine details of high-resolution virion structures have revealed common structural characteristics unique to these viruses including an internal icosahedral capsid built from 60 asymmetric dimers (120 monomers!) of the major coat protein. Here we focus mainly on the structures and assembly principles of large icosahedral dsRNA viruses belonging to the families of Cystoviridae and Reoviridae. It is obvious that there are a variety of assembly pathways utilized by different viruses starting from similar building blocks and reaching in all cases a similar capsid architecture. This is true even with closely related viruses indicating that the assembly pathway per se is not an indicator of relatedness and is achieved with minor changes in the interacting components.

  5. Sulforaphane induces DNA single strand breaks in cultured human cells

    Energy Technology Data Exchange (ETDEWEB)

    Sestili, Piero, E-mail: piero.sestili@uniurb.it [Dipartimento di Scienze Biomolecolari, Via Maggetti, 21, Universita degli Studi di Urbino ' Carlo Bo' , 61029 Urbino, PU (Italy); Paolillo, Marco [Dipartimento di Scienze Biomolecolari, Via Maggetti, 21, Universita degli Studi di Urbino ' Carlo Bo' , 61029 Urbino, PU (Italy); Lenzi, Monia [Dipartimento di Farmacologia, Universita degli Studi di Bologna, Via Irnerio 48, 40126 Bologna (Italy); Colombo, Evelin; Vallorani, Luciana; Casadei, Lucia; Martinelli, Chiara [Dipartimento di Scienze Biomolecolari, Via Maggetti, 21, Universita degli Studi di Urbino ' Carlo Bo' , 61029 Urbino, PU (Italy); Fimognari, Carmela [Dipartimento di Farmacologia, Universita degli Studi di Bologna, Via Irnerio 48, 40126 Bologna (Italy)

    2010-07-07

    Sulforaphane (SFR), an isothiocyanate from cruciferous vegetables, possesses growth-inhibiting and apoptosis-inducing activities in cancer cell lines. Recently, SFR has been shown to promote the mitochondrial formation of reactive oxygen species (ROS) in human cancer cell lines. The present study was undertaken to see whether SFR-derived ROS might cause DNA damage in cultured human cells, namely T limphoblastoid Jurkat and human umbilical vein endothelial cells (HUVEC). 1-3 h treatments with 10-30 {mu}M SFR elicited intracellular ROS formation (as assayed with dihydrorhodamine, DHR, oxidation) as well as DNA breakage (as assessed with fast halo assay, FHA). These effects lacked cell-type specificity, since could be observed in both Jurkat and HUVEC. Differential-pH FHA analysis of damaged DNA showed that SFR causes frank DNA single strand breaks (SSBs); no DNA double strand breaks (DSBs) were found within the considered treatment times (up to 3 h). SFR-derived ROS were formed at the mitochondrial respiratory chain (MRC) level: indeed rotenone or myxothiazol (MRC Complex I and III inhibitors, respectively) abrogated ROS formation. Furthermore ROS were not formed in Jurkat cells pharmacologically depleted of respiring mitochondria (MRC-/Jurkat). Formation of ROS was causally linked to the induction of SSBs: indeed all the experimental conditions capable of preventing ROS formation also prevented the damage of nuclear DNA from SFR-intoxicated cells. As to the toxicological relevance of SSBs, we found that their prevention slightly but significantly attenuated SFR cytotoxicity, suggesting that high-dose SFR toxicity is the result of a complex series of events among which GSH depletion seems to play a pivotal role. In conclusion, the present study identifies a novel mechanism contributing to SFR toxicity which - since DNA damage is a prominent mechanism underlying the cytotoxic activity of established antineoplastic agents - might help to exploit the therapeutic value

  6. Elastic properties of alternative versus single-stranded leveling archwires.

    Science.gov (United States)

    Rucker, Brian K; Kusy, Robert P

    2002-11-01

    The strength, stiffness, and range of single-stranded stainless steel (SS) and superelastic nickel-titanium (NiTi) archwires were compared with those of alternative leveling products, including nylon-coated and multistranded wires. Wire cross-sections were photographed after being potted in polymer, ground, and polished. Because the rectangular wires had rounded or beveled corners, gravimetric measurements and specific gravity calculations quantified the actual polygonal cross-sectional areas versus the ideal rectangular cross-sectional areas. Beveling reduced the cross-sectional areas by 7% to 8%; this decreased the wire stiffnesses by 15% to 19%. Using a testing machine, we measured the yield strengths, the elastic limits, and the ultimate tensile strengths in tension, and wire stiffnesses in 3-point bending. From cyclic loading tests, the elastic limits of the superelastic NiTi wires were approximately 90% and 45% of their ultimate tensile strengths for the round and rectangular wires, respectively. Using the measurements of the mechanical properties and geometric parameters of each wire, we computed the elastic property ratios (EPRs) versus a 16-mil (0.41 mm) NiTi wire. The single-stranded NiTi wires outperformed the alternative wires, whose EPRs varied from 0.05 to 0.32 for strength, from 0.11 to 1.55 for stiffness, and from 0.10 to 0.80 for range. Based on the current study and a review of the orthodontic literature, few superelastic wires are activated sufficiently in vivo to exhibit superelastic behavior. Therefore, the EPR data reported here for superelastic wires truly represent their performance in most clinical situations.

  7. Sulforaphane induces DNA single strand breaks in cultured human cells

    International Nuclear Information System (INIS)

    Sestili, Piero; Paolillo, Marco; Lenzi, Monia; Colombo, Evelin; Vallorani, Luciana; Casadei, Lucia; Martinelli, Chiara; Fimognari, Carmela

    2010-01-01

    Sulforaphane (SFR), an isothiocyanate from cruciferous vegetables, possesses growth-inhibiting and apoptosis-inducing activities in cancer cell lines. Recently, SFR has been shown to promote the mitochondrial formation of reactive oxygen species (ROS) in human cancer cell lines. The present study was undertaken to see whether SFR-derived ROS might cause DNA damage in cultured human cells, namely T limphoblastoid Jurkat and human umbilical vein endothelial cells (HUVEC). 1-3 h treatments with 10-30 μM SFR elicited intracellular ROS formation (as assayed with dihydrorhodamine, DHR, oxidation) as well as DNA breakage (as assessed with fast halo assay, FHA). These effects lacked cell-type specificity, since could be observed in both Jurkat and HUVEC. Differential-pH FHA analysis of damaged DNA showed that SFR causes frank DNA single strand breaks (SSBs); no DNA double strand breaks (DSBs) were found within the considered treatment times (up to 3 h). SFR-derived ROS were formed at the mitochondrial respiratory chain (MRC) level: indeed rotenone or myxothiazol (MRC Complex I and III inhibitors, respectively) abrogated ROS formation. Furthermore ROS were not formed in Jurkat cells pharmacologically depleted of respiring mitochondria (MRC-/Jurkat). Formation of ROS was causally linked to the induction of SSBs: indeed all the experimental conditions capable of preventing ROS formation also prevented the damage of nuclear DNA from SFR-intoxicated cells. As to the toxicological relevance of SSBs, we found that their prevention slightly but significantly attenuated SFR cytotoxicity, suggesting that high-dose SFR toxicity is the result of a complex series of events among which GSH depletion seems to play a pivotal role. In conclusion, the present study identifies a novel mechanism contributing to SFR toxicity which - since DNA damage is a prominent mechanism underlying the cytotoxic activity of established antineoplastic agents - might help to exploit the therapeutic value of

  8. In vivo quantification of DNA double strand breaks

    International Nuclear Information System (INIS)

    Simonsson, M.; Qvarnstroem, F.; Turesson, I.; Johansson, K.-A.; Nyman, J.; Hermansson, I.; Oden, A.; Book, M.

    2003-01-01

    DNA double strand breaks (DSBs) can be introduced in the genome by exposure to exogenous agents such as ionising radiation and radio-mimetic chemicals. The biological importance of these breaks is significant even at low numbers. Inaccurate repair or lack of repair of a single DSB has the potential to kill a cell or lead to tumourigenesis. Thus the induction and repair of DSBs are crucial events in the onset of malignancies. Following the induction of DSBs, the core histone H2AX is rapidly phosphorylated at residue serine 139. This phosphorylated form of H2AX is referred to as gH2AX. Histones wrapped in megabase regions flanking these breaks are involved in this process, which results in the formation of discrete nuclear foci. It has previously been shown that a single DSB is sufficient to produce a detectable focus. So far there has been a lack of methods capable of measuring the amount of DSBs at clinically relevant quantities. Such a method would embrace a wide field of applications. It could be applied as a biological dosimeter when studying carcinogenic effects and provide the basis for an assay predicting individual radiosensitivity. We describe a measurement procedure that detects and quantifies small amounts of DSBs in vivo. This is accomplished using immunofluorescence detection of the molecular marker gH2AX. The gH2AX foci are quantified in histological sections using basic digital image analysis methods as the main component. In a primary assessment of the procedure we analysed the in vivo dose response of prostate cancer patients in clinical practice undergoing radiotherapy. Epidermal nucleated cells in skin biopsies taken 30 minutes following the first single dose delivered show linear dose response for low doses ranging from 0 - 1.2 Gy. The described procedure for double strand break quantification can detect dose changes as low as 0.18 Gy

  9. Complex shapes self-assembled from single-stranded DNA tiles.

    Science.gov (United States)

    Wei, Bryan; Dai, Mingjie; Yin, Peng

    2012-05-30

    Programmed self-assembly of strands of nucleic acid has proved highly effective for creating a wide range of structures with desired shapes. A particularly successful implementation is DNA origami, in which a long scaffold strand is folded by hundreds of short auxiliary strands into a complex shape. Modular strategies are in principle simpler and more versatile and have been used to assemble DNA or RNA tiles into periodic and algorithmic two-dimensional lattices, extended ribbons and tubes, three-dimensional crystals, polyhedra and simple finite two-dimensional shapes. But creating finite yet complex shapes from a large number of uniquely addressable tiles remains challenging. Here we solve this problem with the simplest tile form, a 'single-stranded tile' (SST) that consists of a 42-base strand of DNA composed entirely of concatenated sticky ends and that binds to four local neighbours during self-assembly. Although ribbons and tubes with controlled circumferences have been created using the SST approach, we extend it to assemble complex two-dimensional shapes and tubes from hundreds (in some cases more than one thousand) distinct tiles. Our main design feature is a self-assembled rectangle that serves as a molecular canvas, with each of its constituent SST strands--folded into a 3 nm-by-7 nm tile and attached to four neighbouring tiles--acting as a pixel. A desired shape, drawn on the canvas, is then produced by one-pot annealing of all those strands that correspond to pixels covered by the target shape; the remaining strands are excluded. We implement the strategy with a master strand collection that corresponds to a 310-pixel canvas, and then use appropriate strand subsets to construct 107 distinct and complex two-dimensional shapes, thereby establishing SST assembly as a simple, modular and robust framework for constructing nanostructures with prescribed shapes from short synthetic DNA strands.

  10. Mass production system and technology of NbTi superconductors

    International Nuclear Information System (INIS)

    Fukutsuka, Toshiro; Monju, Yoshiyuki; Tatara, Isamu; Noguchi, Masataka; Yokochi, Katsuhiro; Matsubara, Mitsuharu.

    1984-01-01

    A mass production system for NbTi superconductors is described, involving vacuum arc melting of the alloys, hot hydrostatic extrusion of the composite billets and special drawing and stranding techniques for the rods and wires. The qualities required for superconducting wires are assured by a variety of instrument measurement and inspection techniques drawn from accumulated cryogenic experiences. (author)

  11. Radiation induced strand breaks and time scale for repair of broken strands in superinfecting phage lambda DNA in Escherichia coli lysogenic for lambda

    International Nuclear Information System (INIS)

    Johansen, I.; Boye, E.; Brustad, T.

    1975-01-01

    The production of the first radiation induced break in covalent lambda DNA molecules in pol + and pol A 1 lysogenic host cells was measured after exposure to electrons from a linear accelerator and transfer to alkaline detergent within 100 ms from the onset of irradiation. The results revealed the presence of an oxygen effect in DNA strand breakage. In both pol + and pol A 1 host cells the rate of production in nitrogen was 1.2x10 -12 DNA single strand breaks per rad per dalton as compared to 5x10 -12 in oxygen. The yields of strand breaks in lambda DNA in pol + host cells under oxygenated or anoxic conditions are independent of whether the cells are irradiated in buffer at room temperature, in buffer at ice temperature, or in growth medium at 37 0 C. These results indicate that enzymic repair of DNA strand breaks before analysis is insignificant in these experiments. The presence of an oxygen effect in DNA strand breakage under these conditions suggest that an actual difference exists between initial number of breaks produced in nitrogen and in oxygen. The kinetics of rejoining of broken molecules under optimal growth conditions was measured by incubating the irradiated host cells prior to lysis. In pol + host cells 50% of the lambda DNA molecules broken in presence of oxygen are rejoined within 10 to 20 seconds of incubation. A significantly lower recovery is seen in pol + host cells after irradiation in nitrogen. The rejoining of broken lambda DNA strands in pol A 1 host cells is impaired after irradiation in presence of oxygen as well as under anoxia. These results show that DNA polymerase I is needed for the rapid rejoining of radiation induced strand breaks in the DNA, and that oxygen promoted strand breaks are more easily rejoined than are those produced in nitrogen. (author)

  12. BIOMECHANICS AND HISTOLOGICAL ANALYSIS IN RABBIT FLEXOR TENDONS REPAIRED USING THREE SUTURE TECHNIQUES (FOUR AND SIX STRANDS) WITH EARLY ACTIVE MOBILIZATION.

    Science.gov (United States)

    Severo, Antônio Lourenço; Arenhart, Rodrigo; Silveira, Daniela; Ávila, Aluísio Otávio Vargas; Berral, Francisco José; Lemos, Marcelo Barreto; Piluski, Paulo César Faiad; Lech, Osvandré Luís Canfield; Fukushima, Walter Yoshinori

    2012-01-01

    Analyzing suture time, biomechanics (deformity between the stumps) and the histology of three groups of tendinous surgical repair: Brazil-2 (4-strands) which the end knot (core) is located outside the tendon, Indiana (4-strands) and Tsai (6-strands) with sutures technique which the end knot (core) is inner of the tendon, associated with early active mobilization. The right calcaneal tendons (plantar flexor of the hind paw) of 36 rabbits of the New Zealand breed (Oryctolagus cuniculus) were used in the analysis. This sample presents similar size to human flexor tendon that has approximately 4.5 mm (varying from 2mm). The selected sample showed the same mass (2.5 to 3kg) and were male or female adults (from 8 ½ months). For the flexor tendons of the hind paws, sterile and driven techniques were used in accordance to the Committee on Animal Research and Ethics (CETEA) of the University of the State of Santa Catarina (UDESC), municipality of Lages, in Brazil (protocol # 1.33.09). In the biomechanical analysis (deformity) carried out between tendinous stumps, there was no statistically significant difference (p>0.01). There was no statistical difference in relation to surgical time in all three suture techniques with a mean of 6.0 minutes for Tsai (6- strands), 5.7 minutes for Indiana (4-strands) and 5.6 minutes for Brazil (4-strands) (p>0.01). With the early active mobility, there was qualitative and quantitative evidence of thickening of collagen in 38.9% on the 15(th) day and in 66.7% on the 30(th) day, making the biological tissue stronger and more resistant (p=0.095). This study demonstrated that there was no histological difference between the results achieved with an inside or outside end knot with respect to the repaired tendon and the number of strands did not affect healing, vascularization or sliding of the tendon in the osteofibrous tunnel, which are associated with early active mobility, with the repair techniques applied.

  13. Escherichia coli Single-Stranded DNA-Binding Protein: NanoESI-MS Studies of Salt-Modulated Subunit Exchange and DNA Binding Transactions

    Science.gov (United States)

    Mason, Claire E.; Jergic, Slobodan; Lo, Allen T. Y.; Wang, Yao; Dixon, Nicholas E.; Beck, Jennifer L.

    2013-02-01

    Single-stranded DNA-binding proteins (SSBs) are ubiquitous oligomeric proteins that bind with very high affinity to single-stranded DNA and have a variety of essential roles in DNA metabolism. Nanoelectrospray ionization mass spectrometry (nanoESI-MS) was used to monitor subunit exchange in full-length and truncated forms of the homotetrameric SSB from Escherichia coli. Subunit exchange in the native protein was found to occur slowly over a period of hours, but was significantly more rapid in a truncated variant of SSB from which the eight C-terminal residues were deleted. This effect is proposed to result from C-terminus mediated stabilization of the SSB tetramer, in which the C-termini interact with the DNA-binding cores of adjacent subunits. NanoESI-MS was also used to examine DNA binding to the SSB tetramer. Binding of single-stranded oligonucleotides [one molecule of (dT)70, one molecule of (dT)35, or two molecules of (dT)35] was found to prevent SSB subunit exchange. Transfer of SSB tetramers between discrete oligonucleotides was also observed and is consistent with predictions from solution-phase studies, suggesting that SSB-DNA complexes can be reliably analyzed by ESI mass spectrometry.

  14. Unusual Mortality Events of Harbor Porpoise Strandings in North Carolina, 1997–2009

    Directory of Open Access Journals (Sweden)

    Aleta A. Hohn

    2013-01-01

    Full Text Available A marked increase in the frequency of harbor porpoises (Phocoena phocoena stranded in North Carolina in 2005 was declared as an Unusual Mortality Event (UME. Strandings occurred in January through May when harbor porpoises are seasonally present. Increased stranding rates were measured relative to a threshold to determine that the UME was occurring. The threshold analysis also revealed elevated strandings during 1999, an undeclared UME year. Recovered carcasses during 1999 and 2005 accounted for 39% of 261 strandings during 1997–2009. During 2005, of 43 strandings, primary or secondary causes of mortality included fishery interactions, emaciation, and interspecific aggression. Apart from small but significant differences in timing and condition of strandings, composition of strandings during UME and non-UME years was similar, with most being young-of-the-year and occurring during March and April, north of Cape Hatteras. Porpoises had high levels of parasitic infestation typical for this species. However, no indication of infectious disease and no cause of the 2005 event were found from gross and histologic findings. Response to UMEs is challenging, particularly along the expanses of North Carolina beaches, requiring additional effort to obtain carcasses in sufficiently fresh condition to determine the cause of these events.

  15. Targeting the MicroRNA Passenger Strand for Regulating Therapeutic Transgenes.

    Science.gov (United States)

    Kim, Sung Jin; Lee, Chang Ho; Lee, Seong-Wook

    2015-08-01

    Gene therapy strategies have been developed, which can tissue or disease specifically regulate expression of exogenous transgenes by means of endogenous microRNA (miRNA) activity. However, the use of an endogenous guide strand to regulate an exogenous transgene could affect expression of endogenous miRNA target genes. In this study, we developed a new regulatory system of exogenous transgene expression by targeting the passenger strand. We constructed reporter constructs harboring miRNA-122 guide or passenger target sites with perfect or imperfect complementarity. We observed downregulation of an exogenous transgene harboring the miRNA-122 target sites against either the guide or passenger strand in cells expressing the cognate miRNA or cells stably expressing the miRNA target site. Moreover, the transgene activity as well as the gene expression level increased specifically by intracellular introduction of the antisense RNA against the corresponding strand. Endogenous target gene expression was induced by the transgene construct harboring the miRNA guide strand target sites, but not the passenger strand target sites. Importantly, the therapeutic transgene activity was efficiently regulated by targeting the passenger strand. These results suggested that an approach to passenger strand-regulated expression of therapeutic transgenes could be applied more safely as a therapeutic tool.

  16. Distinct voltage-current characteristics of Nb3Sn strands with dispersed and collective crack distributions

    NARCIS (Netherlands)

    Miyoshi, Y.; van Lanen, E.P.A.; Dhalle, Marc M.J.; Nijhuis, Arend

    2009-01-01

    Two ITER-type Nb3Sn superconductor strands, one prepared with the bronze route and the other with the internal-tin route, were used to investigate the impact of filament cracking on the strand's transport properties. Careful mechanical polishing allowed unambiguous identification of the microscopic

  17. Persistent-current magnetizations of Nb3Sn Rutherford cables and extracted strands

    NARCIS (Netherlands)

    Collings, E.W.; Sumption, M.D.; Myers, C.S.; Wang, Xiao; Dietderich, D.R.; Yagotyntsev, K.; Nijhuis, Arend

    2017-01-01

    The magnetizations of eight high-gradient quadrupole cables designated HQ and QXF and a pair of strands, identical in architecture but with different effective strand diameters extracted from an HQ and a related QXF cable, were measured. In the service of field quality assessment, the cable

  18. Colocalization of multiple DNA double-strand breaks at a single Rad52 repair centre

    DEFF Research Database (Denmark)

    Lisby, M.; Mortensen, Uffe Hasbro; Rothstein, R.

    2003-01-01

    DNA double-strand break repair (DSBR) is an essential process for preserving genomic integrity in all organisms. To investigate this process at the cellular level, we engineered a system of fluorescently marked DNA double-strand breaks (DSBs) in the yeast Saccharomyces cerevisiae to visualize in ...

  19. DNA template strand sequencing of single-cells maps genomic rearrangements at high resolution

    NARCIS (Netherlands)

    Falconer, Ester; Hills, Mark; Naumann, Ulrike; Poon, Steven S. S.; Chavez, Elizabeth A.; Sanders, Ashley D.; Zhao, Yongjun; Hirst, Martin; Lansdorp, Peter M.

    2012-01-01

    DNA rearrangements such as sister chromatid exchanges (SCEs) are sensitive indicators of genomic stress and instability, but they are typically masked by single-cell sequencing techniques. We developed Strand-seq to independently sequence parental DNA template strands from single cells, making it

  20. Nick-initiated homologous recombination: Protecting the genome, one strand at a time

    NARCIS (Netherlands)

    Vriend, Lianne E. M.; Krawczyk, Przemek M.

    2017-01-01

    Homologous recombination (HR) is an essential, widely conserved mechanism that utilizes a template for accurate repair of DNA breaks. Some early HR models, developed over five decades ago, anticipated single-strand breaks (nicks) as initiating lesions. Subsequent studies favored a more double-strand

  1. A Stress Measurement Method for Steel Strands Based on LC Oscillation

    Directory of Open Access Journals (Sweden)

    Dongjun Chen

    2018-01-01

    Full Text Available The prestress loss is one of the main factors affecting the safety of prestressed concrete structure. While the detecting signals like sound and light are difficult to spread in steel strands, there is no effective method for prestress detection of the bonded prestressed steel strands in existing structures yet. In this paper, taking into consideration that the electromagnetic oscillation characteristic can make the signal propagate effectively on the bonded prestressed steel strands, a nondestructive prestress detection method based on the electromagnetic effect to detect oscillation frequency is proposed. In a detection circuit, the steel strands are simulated as an inductance component, in which an induced electromagnetic signal passes through the steel strands to form resonance. And then, a frequency meter is used to detect the oscillation frequency of the resonant circuit. The oscillation frequency is supposed to have relationship with the prestress loading on the steel strands. A section of steel strands with a length of 1.2 m is adopted to test the correlation of stress and oscillation frequency. Both the theoretical and experimental results show that the resonant frequency of the circuit decreases with the increase of the stress of the strand and is linear in a certain range.

  2. When proteome meets genome: the alpha helix and the beta strand ...

    Indian Academy of Sciences (India)

    The avoidance of the -helix and the -strand by splice junctions suggests the existence of a selection pressure against their disruption, perhaps underscoring the investment made by nature in building these intricate secondary structures. A corollary is that the helix and the strand are the smallest integral architectural units ...

  3. Repairing/strengthening of bridges with post-tensioned FRP strands and performance evaluation.

    Science.gov (United States)

    2008-06-01

    The proposed project is to take advantage of some new developments in bridge engineering to apply fiber reinforced polymers (FRP) post-tensioning strands on a selected structure. The use of externally post-tensioned FRP strands to repair/strengthen b...

  4. Regions of incompatibility in single-stranded DNA bacteriophages phi X174 and G4

    NARCIS (Netherlands)

    van der Avoort, H. G.; van der Ende, A.; van Arkel, G. A.; Weisbeek, P. J.

    1984-01-01

    The intracellular presence of a recombinant plasmid containing the intercistronic region between the genes H and A of bacteriophage phi X174 strongly inhibits the conversion of infecting single-stranded phi X DNA to parental replicative-form DNA. Also, transfection with single-stranded or

  5. Sequence dependence of electron-induced DNA strand breakage revealed by DNA nanoarrays

    DEFF Research Database (Denmark)

    Keller, Adrian; Rackwitz, Jenny; Cauët, Emilie

    2014-01-01

    sections for electron induced single strand breaks in specific 13 mer oligonucleotides we used atomic force microscopy analysis of DNA origami based DNA nanoarrays. We investigated the DNA sequences 5'-TT(XYX)3TT with X = A, G, C and Y = T, BrU 5-bromouracil and found absolute strand break cross sections...

  6. Statistical analysis of the Nb3Sn strand production for the ITER toroidal field coils

    Science.gov (United States)

    Vostner, A.; Jewell, M.; Pong, I.; Sullivan, N.; Devred, A.; Bessette, D.; Bevillard, G.; Mitchell, N.; Romano, G.; Zhou, C.

    2017-04-01

    The ITER toroidal field (TF) strand procurement initiated the largest Nb3Sn superconducting strand production hitherto. The industrial-scale production started in Japan in 2008 and finished in summer 2015. Six ITER partners (so-called Domestic Agencies, or DAs) are in charge of the procurement and involved eight different strand suppliers all over the world, of which four are using the bronze route (BR) process and four the internal-tin (IT) process. In total more than 500 tons have been produced including excess material covering losses during the conductor manufacturing process, in particular the cabling. The procurement is based on a functional specification where the main strand requirements like critical current, hysteresis losses, Cu ratio and residual resistance ratio are specified but not the strand production process or layout. This paper presents the analysis on the data acquired during the quality control (QC) process that was carried out to ensure the same conductor performance requirements are met by the different strand suppliers regardless of strand design. The strand QC is based on 100% billet testing and on applying statistical process control (SPC) limits. Throughout the production, samples adjacent to the strand pieces tested by the suppliers are cross-checked (‘verified’) by their respective DAs reference labs. The level of verification was lowered from 100% at the beginning of the procurement progressively to approximately 25% during the final phase of production. Based on the complete dataset of the TF strand production, an analysis of the SPC limits of the critical strand parameters is made and the related process capability indices are calculated. In view of the large-scale production and costs, key manufacturing parameters such as billet yield, number of breakages and piece-length distribution are also discussed. The results are compared among all the strand suppliers, focusing on the difference between BR and IT processes. Following

  7. Structure of the replicative form of bacteriophage φX174 : VI. Studies on alkali-denatured double-stranded φX DNA

    NARCIS (Netherlands)

    Pouwels, P.H.; Knijnenburg, C.M.; Rotterdam, J. van; Cohen, J.A.; Jansz, H.S.

    1968-01-01

    Double-stranded φX DNA which accumulates after infection with bacteriophage φX174 in the presence of chloramphenicol consists mainly of twisted circular double-stranded DNA with no single-strand breaks (component I) and of circular double-stranded DNA, in which single-strand breaks are present

  8. World-Wide Benchmarking of ITER Nb3Sn Strand Test Facilities

    CERN Document Server

    Jewell, MC; Takahashi, Yoshikazu; Shikov, Alexander; Devred, Arnaud; Vostner, Alexander; Liu, Fang; Wu, Yu; Jewell, Matthew C; Boutboul, Thierry; Bessette, Denis; Park, Soo-Hyeon; Isono, Takaaki; Vorobieva, Alexandra; Martovetsky, Nicolai; Seo, Kazutaka

    2010-01-01

    The world-wide procurement of Nb3Sn and NbTi for the ITER superconducting magnet systems will involve eight to ten strand suppliers from six Domestic Agencies (DAs) on three continents. To ensure accurate and consistent measurement of the physical and superconducting properties of the composite strand, a strand test facility benchmarking effort was initiated in August 2008. The objectives of this effort are to assess and improve the superconducting strand test and sample preparation technologies at each DA and supplier, in preparation for the more than ten thousand samples that will be tested during ITER procurement. The present benchmarking includes tests for critical current (I-c), n-index, hysteresis loss (Q(hys)), residual resistivity ratio (RRR), strand diameter, Cu fraction, twist pitch, twist direction, and metal plating thickness (Cr or Ni). Nineteen participants from six parties (China, EU, Japan, South Korea, Russia, and the United States) have participated in the benchmarking. This round, conducted...

  9. Study in regularities in the formation of double stranded DNA breaks in irradiated rat thymocytes

    International Nuclear Information System (INIS)

    Ivannik, B.P.; ProskuryakoV, S.Ya.; Ryabchenko, N.I.

    1979-01-01

    Using low-gradient viscosimetry of neutral detergent nuclear lysates a study was made of postradiation changes in the molecular weight of double-stranded DNA of thymocytes. It was established that 375 eV are needed for one double-stranded break to appear, and a dose of 1 rad is required for 0.275 double-stranded break to occur at the site of DNA with m.w. 10 12 dalton. The repair of double-stranded breaks is only observed when rats are exposed to a dose of 500 R. It is assumed that the absence of repair of double-stranded DNA breaks and the presence of secondary postradiation degradation of DNA are responsible for thymocyte death

  10. Comparison of the electrophoretic method with the sedimentation method for the analysis of DNA strand breaks

    International Nuclear Information System (INIS)

    Yamamoto, Osamu; Ogawa, Masaaki; Hoshi, Masaharu

    1982-01-01

    Application of electrophoresis to the analysis of DNA strand breaks was studied comparing with the sedimentation analysis. A BRL gel electrophoresis system (Type V16) was used for this study. Calf thymus DNA (1 mg/ml) irradiated with 60 Co gamma-rays in SSC solution was applied to both the electrophoretic analysis and the sedimentation analysis. Lamda phage DNA and its fragments were employed as the standard size molecules. In a range from 1 k base pairs to 6 k base pairs in length for double stranded DNA or from 2 k bases to 12 k bases for single stranded DNA, the calculated average molecular weight from the electrophoresis coincided with that from the sedimentation. Number of single strand breaks and double strand breaks were 1.34 x 10 11 breaks/mg/rad (G = 0.215) and 0.48 x 10 5 breaks/mg/rad 2 , respectively. (author)

  11. Magnetization Losses of Roebel Cable Samples with 2G YBCO Coated Conductor Strands

    CERN Document Server

    Yang, Y.; Falorio, I.; Young, E.A.; Kario, A.; Goldacker, W.; Dhallé, M. M. J.; van Nugteren, J.; Kirby, G.; Bottura, L.; Ballarino, A.

    2016-01-01

    Roebel cable with 2G YBCO strands is one of the promising HTS solutions of fully transposed high current conductors for high field accelerator magnets. Following the considerable research effort on the manufacturing of Roebel cables in recent years, sample conductors are now available in useful lengths with reproducible performances to allow detailed characterizations beyond the standard critical current measurements. The ac loss and strands coupling are of significant interest for the field quality of the accelerator magnets. We report a set of systematic ac loss measurements on two different Roebel cable samples prepared for the EuCARD2 collaboration. The measurements were performed over a wide range of temperature between 5 K and 90 K and the results were analyzed in the context of strands architecture and coupling. The results show that the transposed bundles are partially decoupled and the strands in transposition sections behave as an isolated single tape if the strands are insulated.

  12. Enhanced Strain Measurement Range of an FBG Sensor Embedded in Seven-Wire Steel Strands.

    Science.gov (United States)

    Kim, Jae-Min; Kim, Chul-Min; Choi, Song-Yi; Lee, Bang Yeon

    2017-07-18

    FBG sensors offer many advantages, such as a lack of sensitivity to electromagnetic waves, small size, high durability, and high sensitivity. However, their maximum strain measurement range is lower than the yield strain range (about 1.0%) of steel strands when embedded in steel strands. This study proposes a new FBG sensing technique in which an FBG sensor is recoated with polyimide and protected by a polyimide tube in an effort to enhance the maximum strain measurement range of FBG sensors embedded in strands. The validation test results showed that the proposed FBG sensing technique has a maximum strain measurement range of 1.73% on average, which is 1.73 times higher than the yield strain of the strands. It was confirmed that recoating the FBG sensor with polyimide and protecting the FBG sensor using a polyimide tube could effectively enhance the maximum strain measurement range of FBG sensors embedded in strands.

  13. Modelling of current distribution in Nb3Sn multifilamentary strands subjected to bending

    International Nuclear Information System (INIS)

    Miyoshi, Y; Zhou, C; Lanen, E P A van; Dhallé, M M J; Nijhuis, A

    2012-01-01

    In Nb 3 Sn cable-in-conduit conductors (CICCs), strands follow complex trajectories that result in a periodic bending strain acting on the strands upon electromagnetic loading and thermal contraction. Such a periodic bending strain leads to degradation of the overall transport performance of a CICC. Aiming for a better understanding and quantitative correlation between strand degradation and CICC test results, a detailed strand model is essential in combination with accurate intra-strand resistance data, the spatial filament strain distribution, and the associated filament crack distribution. Our novel numerical strand model is a 3D network of resistors including superconducting filaments, normal matrix elements, and an outer stabilizing shell or inner core. Along the strand length, matrix elements have Ohmic resistance, there is a filament-to-matrix contact resistance (R fm ) between filaments and matrix elements, while superconducting filaments have a power-law voltage–current (VI) characteristic with critical current (I c ) and an n-value described by the ITER Nb 3 Sn strain scaling law based on measured strand data. The model simulates the VI characteristic in a periodic bending experiment and provides the associated spatial potential distribution. The VI characteristics representing the low- and high-resistivity limits (LRL and HRL) are identified for periodic and uniform axial bending. The voltage level for the current transfer regime depends on the strand internal resistivities, i.e. the filament-to-matrix contact and the matrix resistivity, the twist pitch and the bending wavelength. The simulation results show good agreement against I c degradation, as experimentally measured by the TARSIS facility, versus the assessed peak bending strain. In addition we discuss different methods for determining the applied peak bending strain. The model provides a basis to find a practical relationship between a strand’s VI characteristic and the periodic bending

  14. Popular theatre and nonformal education in the Third World: Five strands of experience

    Science.gov (United States)

    Kidd, Ross

    1985-09-01

    Popular theatre is gaining increasing attention in the Third World as a tool for popular education and community organizing. It finds expression in a number of forms including drama, music dance, puppetry and poetry and is performed for — and often by — ordinary peasants and workers. Popular theatre is used as a means of bringing people together, building confidence and solidarity, stimulating discussion, exploring alternative options for action, and building a collective commitment to change: starting with people's urgent concerns and issues, it encourages reflection on these issues and possible strategies for change. Popular theatre, however, is not a unified discipline. It is used by different groups for different interests, ranging from a technocratic, message-oriented `domestication theatre' at one end of the spectrum to a process of consciousness-raising, organization-building and struggle at the other end. Five main strands of popular theatre can be distinguished: (a) the struggle for national liberation; (b) mass education and rural extension; (c) community or participatory development; (d) `conscientization' or popular education; and (e) popular education and organizing. At its best, popular theatre is not an isolated performance or a cathartic experience, but part of an ongoing process of education and organizing, aimed at overcoming oppression and dependence, and at securing basic rights.

  15. Interaction of anticancer Ru(III) complexes with single stranded and duplex DNA model systems.

    Science.gov (United States)

    Musumeci, Domenica; Rozza, Lucia; Merlino, Antonello; Paduano, Luigi; Marzo, Tiziano; Massai, Lara; Messori, Luigi; Montesarchio, Daniela

    2015-08-21

    The interaction of the anticancer Ru(iii) complex AziRu - in comparison with its analogue NAMI-A, currently in advanced clinical trials as an antimetastatic agent - with DNA model systems, both single stranded and duplex oligonucleotides, was investigated using a combined approach, including absorption UV-vis spectroscopy, circular dichroism (CD) and electrospray mass spectrometry (ESI-MS) techniques. UV-vis absorption spectra of the Ru complexes were recorded at different times in a pseudo-physiological solution, to monitor the ligand exchange processes in the absence and in the presence of the examined oligonucleotides. CD experiments provided information on the overall conformational changes of the DNA model systems induced by these metal complexes. UV- and CD-monitored thermal denaturation studies were performed to analyse the effects of AziRu and NAMI-A on the stability of the duplex structures. ESI-MS experiments, carried out on the oligonucleotide/metal complex mixtures under investigation, allowed us to detect the formation of stable adducts between the guanine-containing oligomers and the ruthenium complexes. These data unambiguously demonstrate that both AziRu and NAMI-A can interact with the DNA model systems. Although very similar in their structures, the two metal compounds manifest a markedly different reactivity with the examined sequences, respectively, with either a naked Ru(3+) ion or a Ru(Im)(3+) (Im = imidazole) fragment being incorporated into the oligonucleotide structure via stable linkages.

  16. Nominal Mass?

    Science.gov (United States)

    Attygalle, Athula B; Pavlov, Julius

    2017-08-01

    The current IUPAC-recommended definition of the term "nominal mass," based on the most abundant naturally occurring stable isotope of an element, is flawed. We propose that Nominal mass should be defined as the sum of integer masses of protons and neutrons in any chemical species. In this way, all isotopes and isotopologues can be assigned a definitive identifier. Graphical Abstract ᅟ.

  17. Materials, Strands, and Cables for Superconducting Accelerator Magnets. Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Sumption, Mike D. [Ohio State University, Columbia, OH (United States); Collings, Edward W. [Ohio State University, Columbia, OH (United States)

    2014-09-19

    This report focuses on Materials, Strands and Cables for High Energy Physics Particle accelerators. In the materials area, work has included studies of basic reactions, diffusion, transformations, and phase assemblage of Nb3Sn. These materials science aspects have been married to results, in the form of flux pinning, Bc2, Birr, and transport Jc, with an emphasis on obtaining the needed Jc for HEP needs. Attention has also been paid to the “intermediate-temperature superconductor”, magnesium diboride emphasis being placed on (i) irreversibility field enhancement, (ii) critical current density and flux pinning, and (iii) connectivity. We also report on studies of Bi-2212. The second area of the program has been in the area of “Strands” in which, aside from the materials aspect of the conductor, its physical properties and their influence on performance have been studied. Much of this work has been in the area of magnetization estimation and flux jump calculation and control. One of the areas of this work was strand instabilities in high-performance Nb3Sn conductors due to combined fields and currents. Additionally, we investigated quench and thermal propagation in YBCO coated conductors at low temperatures and high fields. The last section, “Cables”, focussed on interstrand contact resistance, ICR, it origins, control, and implications. Following on from earlier work in NbTi, the present work in Nb3Sn has aimed to make ICR intermediate between the two extremes of too little contact (no current sharing) and too much (large and unacceptable magnetization and associated beam de-focussing). Interstrand contact and current sharing measurements are being made on YBCO based Roebel cables using transport current methods. Finally, quench was investigated for YBCO cables and the magnets wound from them, presently with a focus on 50 T solenoids for muon collider applications.

  18. Finite element analysis of contributing factors to the horizontal splitting cracks in concrete crossties pretensioned with seven-wire strands.

    Science.gov (United States)

    2017-04-04

    This paper employs the finite element (FE) modeling : method to investigate the contributing factors to the horizontal : splitting cracks observed in the upper strand plane in some : concrete crossties made with seven-wire strands. The concrete...

  19. Mass spectrometers

    International Nuclear Information System (INIS)

    Manojlov, V.E.; Nedelin, P.N.; Lukichev, A.N.; Sapozhkov, L.K.; Turubarov, V.I.

    1980-01-01

    Mass spectrometers of different types are suggested to use for qualitative and quantitative analyses of gas. The operation principles of static and dynamic mass spectrometer are studied. In static mass spectrometers mass separation of ions is performed by changing the value of accelerating voltage in the ion source when retaining the magnetic field intensity. Such devices are stationary. The device mass is conditioned by the magnet mass. Mass separation in dynamic mass spectrometers is dependent on the degree of energy increment of ions in HF-electric fields. Radio frequency mass spectrometers are used with advantage for studying upper layers of an atmosphere and are installed on radiosondes and satellites. The main technical characteristics of the MX-1330 mass spectrometer, the basis of which is the analyzer with 180 deg deviation of an ion beam in the field of permanent magnet, are presented. The device is intended for controlling the environment and permits to analyze gases with a molecular mass up to 450 using various systems of gas filling. The error of determination of molecular substance is not greater than +-3 %; the magnetic field intensity constitutes 4.8x10 5 A/m; the supply voltage is 380/220 V; the total power is 5.0 kVA [ru

  20. Patterns of evolution of research strands in the hydrologic sciences

    Science.gov (United States)

    Schwartz, F. W.; Fang, Y. C.; Parthasarathy, S.

    2005-03-01

    This paper examines issues of impact and innovation in groundwater research by using bibliometric data and citation analysis.The analysis is based on 3120 papers from the journal Water Resources Research with full contents and their citation data from the ISI Web of Science. The research is designed to develop a better understanding of the way citation numbers can be interpreted by scientists. Not surprisingly, the most highly cited papers appear to be pioneers in the field with papers departing significantly from what has come before and to be effective in creating similar, follow-on papers. Papers that are early contributions to a new research strand that is highly influential will be on average highly cited. However, the importance of a research strand as measured by citations seems to fall with time. The citation patterns of some classic papers show that the activity in the topical area and impact of follow-on papers gradually decline with time, which has similarities with Kuhn's ideas of revolutionary and normal science. The results of this study reinforce the importance of being a pioneer in a research strand, strategically shifting research strands, adopting strategies that can facilitate really major research breakthroughs. L'article examine les problèmes d'impact et d'innovation dans la recherche des eaux souterraines en utilisant les données bibliométriques et l'analyse des citations. L'analyse a été faite sur 3120 articles parus dans Water Resources Research en tenant compte de leur texte complet et de toutes citations parues dans l' ISI Web de la Science. Le but de la recherche a été de mieux comprendre comment le nombre des citations peut être interprété par les scientifiques. Ce n'est pas une surprise que les plus cités articles soient les articles-pionniers dans leurs domaines, qui s'écartent d'une manière significative de ce qui a été écrit auparavant et qui ont été suivi par des nouveaux articles. Les articles qui présentent une

  1. Do DNA Double-Strand Breaks Drive Aging?

    Science.gov (United States)

    White, Ryan R; Vijg, Jan

    2016-09-01

    DNA double-strand breaks (DSBs) are rare, but highly toxic, lesions requiring orchestrated and conserved machinery to prevent adverse consequences, such as cell death and cancer-causing genome structural mutations. DSBs trigger the DNA damage response (DDR) that directs a cell to repair the break, undergo apoptosis, or become senescent. There is increasing evidence that the various endpoints of DSB processing by different cells and tissues are part of the aging phenotype, with each stage of the DDR associated with specific aging pathologies. In this Perspective, we discuss the possibility that DSBs are major drivers of intrinsic aging, highlighting the dynamics of spontaneous DSBs in relation to aging, the distinct age-related pathologies induced by DSBs, and the segmental progeroid phenotypes in humans and mice with genetic defects in DSB repair. A model is presented as to how DSBs could drive some of the basic mechanisms underlying age-related functional decline and death. Copyright © 2016 Elsevier Inc. All rights reserved.

  2. Nuclear proteins hijacked by mammalian cytoplasmic plus strand RNA viruses

    Energy Technology Data Exchange (ETDEWEB)

    Lloyd, Richard E., E-mail: rlloyd@bcm.edu

    2015-05-15

    Plus strand RNA viruses that replicate in the cytoplasm face challenges in supporting the numerous biosynthetic functions required for replication and propagation. Most of these viruses are genetically simple and rely heavily on co-opting cellular proteins, particularly cellular RNA-binding proteins, into new roles for support of virus infection at the level of virus-specific translation, and building RNA replication complexes. In the course of infectious cycles many nuclear-cytoplasmic shuttling proteins of mostly nuclear distribution are detained in the cytoplasm by viruses and re-purposed for their own gain. Many mammalian viruses hijack a common group of the same factors. This review summarizes recent gains in our knowledge of how cytoplasmic RNA viruses use these co-opted host nuclear factors in new functional roles supporting virus translation and virus RNA replication and common themes employed between different virus groups. - Highlights: • Nuclear shuttling host proteins are commonly hijacked by RNA viruses to support replication. • A limited group of ubiquitous RNA binding proteins are commonly hijacked by a broad range of viruses. • Key virus proteins alter roles of RNA binding proteins in different stages of virus replication.

  3. Prion search and cellular prion protein expression in stranded dolphins.

    Science.gov (United States)

    Di Guardo, G; Cocumelli, C; Meoli, R; Barbaro, K; Terracciano, G; Di Francesco, C E; Mazzariol, S; Eleni, C

    2012-01-01

    The recent description of a prion disease (PD) case in a free-ranging bottlenose dolphin (Tursiops truncatus) prompted us to carry out an extensive search for the disease-associated isoform (PrPSc) of the cellular prion protein (PrPC) in the brain and in a range of lymphoid tissues from 23 striped dolphins (Stenella coeruleoalba), 5 bottlenose dolphins and 2 Risso s dolphins (Grampus griseus) found stranded between 2007 and 2012 along the Italian coastline. Three striped dolphins and one bottlenose dolphin showed microscopic lesions of encephalitis, with no evidence of spongiform brain lesions being detected in any of the 30 free-ranging cetaceans investigated herein. Nevertheless, we could still observe a prominent PrPC immunoreactivity in the brain as well as in lymphoid tissues from these dolphins. Although immunohistochemical and Western blot investigations yielded negative results for PrPSc deposition in all tissues from the dolphins under study, the reported occurrence of a spontaneous PD case in a wild dolphin is an intriguing issue and a matter of concern for both prion biology and intra/inter-species transmissibility, as well as for cetacean conservation medicine.

  4. Regulation of Gene Expression with Double-Stranded Phosphorothioate Oligonucleotides

    Science.gov (United States)

    Bielinska, Anna; Shivdasani, Ramesh A.; Zhang, Liquan; Nabel, Gary J.

    1990-11-01

    Alteration of gene transcription by inhibition of specific transcriptional regulatory proteins is necessary for determining how these factors participate in cellular differentiation. The functions of these proteins can be antagonized by several methods, each with specific limitations. Inhibition of sequence-specific DNA-binding proteins was achieved with double-stranded (ds) phosphorothioate oligonucleotides that contained octamer or kappaB consensus sequences. The phosphorothioate oligonucleotides specifically bound either octamer transcription factor or nuclear factor (NF)-kappaB. The modified oligonucleotides accumulated in cells more effectively than standard ds oligonucleotides and modulated gene expression in a specific manner. Octamer-dependent activation of a reporter plasmid or NF-kappaB-dependent activation of the human immunodeficiency virus (HIV) enhancer was inhibited when the appropriate phosphorothioate oligonucleotide was added to a transiently transfected B cell line. Addition of phosphorothioate oligonucleotides that contained the octamer consensus to Jurkat T leukemia cells inhibited interleukin-2 (IL-2) secretion to a degree similar to that observed with a mutated octamer site in the IL-2 enhancer. The ds phosphorothioate oligonucleotides probably compete for binding of specific transcription factors and may provide anti-viral, immunosuppressive, or other therapeutic effects.

  5. Conformational Thermodynamics of DNA Strands in Hydrophilic Nanopores.

    Science.gov (United States)

    Cruz, Fernando J A L; Mota, Jose P B

    2016-08-18

    Enhanced sampling techniques spanning a sub-microsecond timescale reveal that a double-stranded DNA dodecamer can be spontaneously encapsulated into (51,0) and (40,0) single-walled carbon nanotubes under the influence of an electric field, leading to hybrids with a 40 kJ/mol enhanced free-energy. The confinement mechanism allows the nucleic acid to retain its mobility, diffusing anisotropically along the endohedral volume, visiting regions of space determined by entropic factors (diameter, free-volume) and linked by a thermodynamical highway. In spite of the energetic similarities between both topologies (4.1× 103 kJ/mol), the biomolecule favours positioning either parallel to the nanopore central axis, (40,0), or in close contact with the solid walls, (51,0), in the latter encasing a hollow cylindrical domain of diameter 1 - 1.5 nm. Precise physiological conditions allow the extrapolation of results to in vivo systems and constitute a novel and thorough contribution to nanotube technology in the areas of nucleic acid encapsulation/delivery and personalized therapeutics.

  6. Structure-Guided Optimization of HIV Integrase Strand Transfer Inhibitors.

    Science.gov (United States)

    Zhao, Xue Zhi; Smith, Steven J; Maskell, Daniel P; Métifiot, Mathieu; Pye, Valerie E; Fesen, Katherine; Marchand, Christophe; Pommier, Yves; Cherepanov, Peter; Hughes, Stephen H; Burke, Terrence R

    2017-09-14

    Integrase mutations can reduce the effectiveness of the first-generation FDA-approved integrase strand transfer inhibitors (INSTIs), raltegravir (RAL) and elvitegravir (EVG). The second-generation agent, dolutegravir (DTG), has enjoyed considerable clinical success; however, resistance-causing mutations that diminish the efficacy of DTG have appeared. Our current findings support and extend the substrate envelope concept that broadly effective INSTIs can be designed by filling the envelope defined by the DNA substrates. Previously, we explored 1-hydroxy-2-oxo-1,2-dihydro-1,8-naphthyridine-3-carboxamides as an INSTI scaffold, making a limited set of derivatives, and concluded that broadly effective INSTIs can be developed using this scaffold. Herein, we report an extended investigation of 6-substituents as well the first examples of 7-substituted analogues of this scaffold. While 7-substituents are not well-tolerated, we have identified novel substituents at the 6-position that are highly effective, with the best compound (6p) retaining better efficacy against a broad panel of known INSTI resistant mutants than any analogues we have previously described.

  7. Signalling of double strand breaks and deprotected telomeres in Arabidopsis.

    Directory of Open Access Journals (Sweden)

    Simon eAmiard

    2013-10-01

    Full Text Available Failure to repair DNA double strand breaks (DSB can lead to chromosomal rearrangements and eventually to cancer or cell death. Radiation and environmental pollutants induce DSB and this is of particular relevance to plants due to their sessile life style. DSB also occur naturally in cells during DNA replication and programmed induction of DSB initiates the meiotic recombination essential for gametogenesis in most eukaryotes. The linear nature of most eukaryotic chromosomes means that each chromosome has two "broken" ends. Chromosome ends, or telomeres, are protected by nucleoprotein caps which avoid their recognition as DSB by the cellular DNA repair machinery. Deprotected telomeres are recognized as DSB and become substrates for recombination leading to chromosome fusions, the "bridge-breakage-fusion" cycle, genome rearrangements and cell death. The importance of repair of DSB and the severity of the consequences of their misrepair have led to the presence of multiple, robust mechanisms for their detection and repair. After a brief overview of DSB repair pathways to set the context, we present here an update of current understanding of the detection and signalling of DSB in the plant, Arabidopsis thaliana.

  8. Habitat structure and zonation patterns of northwestern Mediterranean shoreline strands

    Directory of Open Access Journals (Sweden)

    Simone Mariani

    2017-06-01

    Full Text Available We studied the habitat structure (macrofaunal assemblages and bottom types and zonation patterns of 29 unvegetated shoreline strands along the 900-km coast of Catalonia (NW Mediterranean Sea. Organisms were sampled with grabs, pitfall traps, sticky traps, clam nets and spades to ensure capture of the different proportions of macrofaunal assemblages from the supra-, medio- and infralittoral levels. We collected 211 taxa: 194 animals and 17 algae. The most abundant and dominant organisms collected with van Veen grabs were Nematoda, Oligochaeta and Collembola at the supralittoral level; the polychaetes Saccocirrus spp. and Pisione remota, the amphipod Corophium orientale, Nematoda, and Turbellaria at the mediolittoral level; and Nematoda at the upper infralittoral level. SIMPER analysis revealed great dissimilarity between the organisms inhabiting the supralittoral and the other littoral levels. Regarding the epifauna, the sticky traps used at the supralittoral level mainly collected Collembola, which were nearly absent in pitfall traps. The qualitative study performed with a clam net and a small spade revealed that Nematoda, Saccocirrus spp., Turbellaria, Nemertea and the polychaete P. remota were the most abundant animals at both the medio- and the infralittoral levels and no differences were found between these levels. Different qualitative sampling methodologies showed that in fine sediments the bivalves Donax trunculus and D. semistriatus determined more than 97% of dissimilarity from coarse-sand sites. Richness increased in protected sandy and cobble shores. Littoral level and bottom-type features were only to a certain extent valid indicators of specific biotic components for a specific habitat.

  9. Ku recruits XLF to DNA double-strand breaks.

    Science.gov (United States)

    Yano, Ken-ichi; Morotomi-Yano, Keiko; Wang, Shih-Ya; Uematsu, Naoya; Lee, Kyung-Jong; Asaithamby, Aroumougame; Weterings, Eric; Chen, David J

    2008-01-01

    XRCC4-like factor (XLF)--also known as Cernunnos--has recently been shown to be involved in non-homologous end-joining (NHEJ), which is the main pathway for the repair of DNA double-strand breaks (DSBs) in mammalian cells. XLF is likely to enhance NHEJ by stimulating XRCC4-ligase IV-mediated joining of DSBs. Here, we report mechanistic details of XLF recruitment to DSBs. Live cell imaging combined with laser micro-irradiation showed that XLF is an early responder to DSBs and that Ku is essential for XLF recruitment to DSBs. Biochemical analysis showed that Ku-XLF interaction occurs on DNA and that Ku stimulates XLF binding to DNA. Unexpectedly, XRCC4 is dispensable for XLF recruitment to DSBs, although photobleaching analysis showed that XRCC4 stabilizes the binding of XLF to DSBs. Our observations showed the direct involvement of XLF in the dynamic assembly of the NHEJ machinery and provide mechanistic insights into DSB recognition.

  10. [Diverse double-stranded RNA viruses infecting fungi].

    Science.gov (United States)

    Chiba, Sotaro; Suzuki, Nobuhiro

    2014-01-01

    Most of reported fungal viruses (mycoviruses) have double-stranded RNA (dsRNA) genomes. This may reflect the simple, easy method for mycovirus hunting that entails detection of dsRNAs as a sign of viral infections. There are an increasing number of screens of various fungi, particularly phytopathogenic fungi for viruses pathogenic to host fungi or able to confer hypovirulence to them. This bases on an attractive research field of biological control of fungal plant diseases using viruses (virocontrol), mainly targeting important phytopathogenic fungi. While isolated viruses usually induce asymptomatic symptoms, they show a considerably high level of diversity. As of 2014, fungal dsRNA viruses are classified into six families: Reoviridae, Totiviridae, Chrysoviridae, Partitiviridae, Megabirnaviridae and Quadriviridae. These exclude unassigned mycoviruses which will definitely be placed into distinct families and/or genera. In this review article, dsRNA viruses isolated from the kingdom Fungi including as-yet-unclassified taxa are overviewed. Some recent achievements in the related field are briefly introduced as well.

  11. Fatigue Characteristic of Chopped Strand Mat/Polyester Composite

    Directory of Open Access Journals (Sweden)

    I Made Astika

    2012-11-01

    Full Text Available The application of composite as an alternatif material to substitute of metal has better properties than metal such as light, high elasticity, corrosion and fatigue resistance. Some components in its application are subjected to millions of varying stress cycles that initiated to fatigue failure such as crack, delamination and fracture. The strength of composite is influenced by construction, fiber type, orientation and fiber fraction. The objective of this experiment is to investigate the fatigue characteristic on SCM composite. Material composite to be used is glass fiber with chopped strand mat (CSM as fiber and Yukalac 157 BQTN-EX with 1% hardener (Mexpox as matrix. The mold process was built with hand lay-up. Fiber volume fractions in composite are 40, 32 and 24 %. The tests to be done on composite are fatigue and tensile test. The research show that the increasing of fiber fraction in composite affects increasing of fatigue life, endurance limit and tensile strength. Fatigue failure modes of composite are debonding, matrix cracking, delamination and fiber fracture.

  12. Enzyme-free colorimetric detection systems based on the DNA strand displacement competition reaction

    DEFF Research Database (Denmark)

    Zhang, Zhao; Birkedal, Victoria; Gothelf, Kurt Vesterager

    2016-01-01

    The strand displacement competition assay is based on the dynamic equilibrium of the competitive hybridization of two oligonucleotides (A and B) to a third oligonucleotide (S). In the presence of an analyte that binds to a specific affinity-moiety conjugated to strand B, the equilibrium shifts, w...... G-quadruplex DNAzyme for colorimetric readout of the detection of streptavidin by the naked eye. Finally, we integrate the whole G-quadruplex DNAzyme system in a single DNA strand and show that it is applicable to colorimetric detection......., which can be detected by a shift in the fluorescence resonance energy transfer signal between dyes attached to the DNA strands. In the present study we have integrated an ATP aptamer in the strand B and demonstrated the optical detection of ATP. Furthermore we explore a new readout method using a split......The strand displacement competition assay is based on the dynamic equilibrium of the competitive hybridization of two oligonucleotides (A and B) to a third oligonucleotide (S). In the presence of an analyte that binds to a specific affinity-moiety conjugated to strand B, the equilibrium shifts...

  13. Dynamic properties of unbonded, multi-strand beams subjected to flexural loading

    Science.gov (United States)

    Asker, Haval K.; Rongong, Jem A.; Lord, Charles E.

    2018-02-01

    Beam-like structures, constructed from many long strands that are constrained rather than bonded together, can provide appreciable levels of structural damping through friction between individual strands. This paper describes experimental and numerical studies, carried out on square-section metal beams, which are aimed at improving understanding of the relationship between construction and performance. A beam is formed from a pack of square-section strands that is held together at various compression loads with pre-calibrated clamps. Flexural deformation of the assembled beam is simulated using standard finite element analysis employing simple Coulomb friction at the interfaces. The validity of the assumptions used in the models is confirmed by comparison with three point bend tests on a regular nine strand construction at several different clamp loads. Dynamic loss factors for this beam are obtained by conducting forced vibration tests, which show that the damping is insensitive to frequency. Subsequent numerical studies are used to investigate the effects of increasing the number of strands whilst maintaining the overall cross-section geometry of the beam. It is found that the system stiffness drops and loss factor increases when more strands are used for a maintained beam cross-section. Interestingly, the energy dissipated by each beam construction is almost the same. These results provide a vital and necessary insight into the physics for stranded structures and materials that are largely prevalent in mechanical (e.g. cables) and electrical (e.g. wires) elements.

  14. Strand Tension Control in Anchor Span for Suspension Bridge Using Dynamic Balance Theory

    Directory of Open Access Journals (Sweden)

    Da Wang

    Full Text Available Abstract Strand tension control is essential in suspension bridge safety. However, few quantitative studies have examined the bending rigidity and boundary condition behavior of strands in the anchor span of suspension bridges because of their special structure and complex configuration. In this paper, a new calculation method for strand tension is explored by using dynamic balance theory to determine the effect of bending rigidity and boundary conditions. The accuracy and effectiveness of the proposed method are tested and confirmed with verification examples and application on Nanxi Yangtze Suspension Bridge in China. The results indicated that only low-order frequency calculation could be used to calculate the strand tension without considering the effect of bending rigidity to ensure control accuracy. The influence of bending rigidity on the control precision is related to the tension and the length of the strands, which is significantly determined by the specific value between the stress rigidity and the bending rigidity. The uncertain boundary conditions of the anchor span cable, which are fixed between consolidated and hinged, also have a major effect on the control accuracy. To improve the accuracy of strand tension control, the least squares method is proposed during the tension construction control of the anchor span. This approach can significantly improve the accuracy of the tension control of the main cable strand. Some recommendations for future bridge analysis are provided based on the results of this study.

  15. Single-stranded DNA library preparation from highly degraded DNA using T4 DNA ligase.

    Science.gov (United States)

    Gansauge, Marie-Theres; Gerber, Tobias; Glocke, Isabelle; Korlevic, Petra; Lippik, Laurin; Nagel, Sarah; Riehl, Lara Maria; Schmidt, Anna; Meyer, Matthias

    2017-06-02

    DNA library preparation for high-throughput sequencing of genomic DNA usually involves ligation of adapters to double-stranded DNA fragments. However, for highly degraded DNA, especially ancient DNA, library preparation has been found to be more efficient if each of the two DNA strands are converted into library molecules separately. We present a new method for single-stranded library preparation, ssDNA2.0, which is based on single-stranded DNA ligation with T4 DNA ligase utilizing a splinter oligonucleotide with a stretch of random bases hybridized to a 3΄ biotinylated donor oligonucleotide. A thorough evaluation of this ligation scheme shows that single-stranded DNA can be ligated to adapter oligonucleotides in higher concentration than with CircLigase (an RNA ligase that was previously chosen for end-to-end ligation in single-stranded library preparation) and that biases in ligation can be minimized when choosing splinters with 7 or 8 random nucleotides. We show that ssDNA2.0 tolerates higher quantities of input DNA than CircLigase-based library preparation, is less costly and better compatible with automation. We also provide an in-depth comparison of library preparation methods on degraded DNA from various sources. Most strikingly, we find that single-stranded library preparation increases library yields from tissues stored in formalin for many years by several orders of magnitude. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  16. Enzymatic induction of DNA double-strand breaks in γ-irradiated Escherichia coli K-12

    International Nuclear Information System (INIS)

    Bonura, T.; Smith, K.C.; Kaplan, H.S.

    1975-01-01

    The polA1 mutation increases the sensitivity of E. coli K-12 to killing by γ-irradiation in air by a factor of 2.9 and increases the yield of DNA double-strand breaks by a factor of 2.5. These additional DNA double-strand breaks appear to be due to the action of nucleases in the polA1 strain rather than to the rejoining of radiation-induced double-strand breaks in the pol + strain. This conclusion is based upon the observation that γ-irradiation at 3 0 did not affect the yield of DNA double-strand breaks in the pol + strain, but decreased the yield in the polA1 strain by a factor of 2.2. Irradiation of the polA1 strain at 3 0 followed by incubation at 3 0 for 20 min before plating resulted in approximately a 1.5-fold increase in the D 0 . The yield of DNA double-strand breaks was reduced by a factor of 1.5. The pol + strain, however, did not show the protective effect of the low temperature incubation upon either survival or DNA double-strand breakage. We suggest that the increased yield of DNA double-strand breaks in the polA 1 strain may be the result of the unsuccessful excision repair of ionizing radiation-induced dna base damage

  17. Induction of DNA strand breaks in 14C-labelled cells

    International Nuclear Information System (INIS)

    Sundell-Bergman, S.; Johanson, K.J.

    1979-01-01

    Chinese hamster cells grown in vitro were labelled with 14 C-thymidine for 18 hours and after 3 hours in non-radioactive medium they were stored at 0 0 C for various periods ( 1 to 12 hours). During this treatment a number of DNA strand breaks were induced by 14 C decay which were not repaired at 0 0 C. The number of DNA strand breaks was determined using the DNA unwinding technique. At 0.5-1 dpm per cell a detectable number of DNA strand breaks were found. Treatment for six hours (1 dpm per cell) reduced the percentage of double-stranded DNA from 80 to 70%, corresponding to about 750 DNA strand breaks per cell. The rejoining of DNA strand breaks was studied after treatment for 12 hours at 0 0 C followed by incubation of the cells for various periods at 37 0 C. Most of the DNA strand breaks induced by 14 C decay at 0 0 C were repaired after incubation at 37 0 C for 15 minutes. Assuming an absorbed dose of 1.8 mGy per 14 C decay to the cell nucleus an RBE value close to 1 was found for internal irradiation from 14 C decay as compared with 60 Co-gamma irradiation. (author)

  18. Diphosphates at the 5' end of the positive strand of yeast L-A double-stranded RNA virus as a molecular self-identity tag.

    Science.gov (United States)

    Fujimura, Tsutomu; Esteban, Rosa

    2016-10-01

    The 5'end of RNA conveys important information on self-identity. In mammalian cells, double-stranded RNA (dsRNA) with 5'di- or triphosphates generated during virus infection is recognized as foreign and elicits the host innate immune response. Here, we analyze the 5' ends of the dsRNA genome of the yeast L-A virus. The positive strand has largely diphosphates with a minor amount of triphosphates, while the negative strand has only diphosphates. Although the virus can produce capped transcripts by cap snatching, neither strand carried a cap structure, suggesting that only non-capped transcripts serve as genomic RNA for encapsidation. We also found that the 5' diphosphates of the positive but not the negative strand within the dsRNA genome are crucial for transcription in vitro. Furthermore, the presence of a cap structure in the dsRNA abrogated its template activity. Given that the 5' diphosphates of the transcripts are also essential for cap acquisition and that host cytosolic RNAs (mRNA, rRNA, and tRNA) are uniformly devoid of 5' pp-structures, the L-A virus takes advantage of its 5' terminal diphosphates, using them as a self-identity tag to propagate in the host cytoplasm. © 2016 John Wiley & Sons Ltd.

  19. The stranding anomaly as population indicator: the case of harbour porpoise Phocoena phocoena in North-Western Europe.

    Directory of Open Access Journals (Sweden)

    Helene Peltier

    Full Text Available Ecological indicators for monitoring strategies are expected to combine three major characteristics: ecological significance, statistical credibility, and cost-effectiveness. Strategies based on stranding networks rank highly in cost-effectiveness, but their ecological significance and statistical credibility are disputed. Our present goal is to improve the value of stranding data as population indicator as part of monitoring strategies by constructing the spatial and temporal null hypothesis for strandings. The null hypothesis is defined as: small cetacean distribution and mortality are uniform in space and constant in time. We used a drift model to map stranding probabilities and predict stranding patterns of cetacean carcasses under H0 across the North Sea, the Channel and the Bay of Biscay, for the period 1990-2009. As the most common cetacean occurring in this area, we chose the harbour porpoise Phocoena phocoena for our modelling. The difference between these strandings expected under H0 and observed strandings is defined as the stranding anomaly. It constituted the stranding data series corrected for drift conditions. Seasonal decomposition of stranding anomaly suggested that drift conditions did not explain observed seasonal variations of porpoise strandings. Long-term stranding anomalies increased first in the southern North Sea, the Channel and Bay of Biscay coasts, and finally the eastern North Sea. The hypothesis of changes in porpoise distribution was consistent with local visual surveys, mostly SCANS surveys (1994 and 2005. This new indicator could be applied to cetacean populations across the world and more widely to marine megafauna.

  20. 75 FR 28557 - Pre-Stressed Concrete Steel Wire Strand from the People's Republic of China: Final Affirmative...

    Science.gov (United States)

    2010-05-21

    ... International Trade Administration Pre-Stressed Concrete Steel Wire Strand from the People's Republic of China... countervailable subsidies are being provided to producers and exporters of pre-stressed concrete steel wire strand... Determination on October 27, 2009. See Pre-Stressed Concrete Steel Wire Strand from the People's Republic of...

  1. Electro-mechanical behaviors of composite superconducting strand with filament breakage

    International Nuclear Information System (INIS)

    Wang, Xu; Gao, Yuanwen; Zhou, Youhe

    2016-01-01

    Highlights: • The electromechanical behaviors of the superconducting (SC) strand are investigated. • A 3D FEM model for bending behaviors and electric properties of strand is developed. • The influence of breakage of filaments on the critical current of SC strand is calculated. • The impact of current transfer length on the electric properties of SC strand is discussed. - Abstract: The bending behaviors of superconducting strand with typical multi-filament twist configuration are investigated based on a three-dimensional finite element method (FEM) model, named as the Multi-filament twist model, of the strand. In this 3D FEM model, the impacts of initial thermal residual stress, filament-breakage and its evaluation are taken into accounts. The mechanical responses of the strand under bending load are studied with the factors taken into consideration one by one. The distribution of the damage of the filaments and its evolution and the movement of the neutral axis caused by it are studied and displayed in detail. Besides, taking the advantages of the Multi-filament twist model, the normalized critical current of the strand under bending load is also calculated based on the invariant temperature and field strain functions. In addition, the non-negligible influences of the pitch length of the filaments on both the mechanical behaviors and the normalized critical current are discussed. The stress-strain characteristics of the strand under tensile load and the normalized critical current of it under axial and bending loads resulting from the Multi-filament twist model show good agreement with the experimental data.

  2. Electro-mechanical behaviors of composite superconducting strand with filament breakage

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Xu [Key Laboratory of Mechanics on Environment and Disaster in Western China, The Ministry of Education of China, Lanzhou, Gansu 730000 (China); Department of Mechanics and Engineering Science, College of Civil Engineering and Mechanics, Lanzhou University, Lanzhou, Gansu 730000 (China); Gao, Yuanwen, E-mail: ywgao@lzu.edu.cn [Key Laboratory of Mechanics on Environment and Disaster in Western China, The Ministry of Education of China, Lanzhou, Gansu 730000 (China); Department of Mechanics and Engineering Science, College of Civil Engineering and Mechanics, Lanzhou University, Lanzhou, Gansu 730000 (China); Zhou, Youhe [Key Laboratory of Mechanics on Environment and Disaster in Western China, The Ministry of Education of China, Lanzhou, Gansu 730000 (China); Department of Mechanics and Engineering Science, College of Civil Engineering and Mechanics, Lanzhou University, Lanzhou, Gansu 730000 (China)

    2016-10-15

    Highlights: • The electromechanical behaviors of the superconducting (SC) strand are investigated. • A 3D FEM model for bending behaviors and electric properties of strand is developed. • The influence of breakage of filaments on the critical current of SC strand is calculated. • The impact of current transfer length on the electric properties of SC strand is discussed. - Abstract: The bending behaviors of superconducting strand with typical multi-filament twist configuration are investigated based on a three-dimensional finite element method (FEM) model, named as the Multi-filament twist model, of the strand. In this 3D FEM model, the impacts of initial thermal residual stress, filament-breakage and its evaluation are taken into accounts. The mechanical responses of the strand under bending load are studied with the factors taken into consideration one by one. The distribution of the damage of the filaments and its evolution and the movement of the neutral axis caused by it are studied and displayed in detail. Besides, taking the advantages of the Multi-filament twist model, the normalized critical current of the strand under bending load is also calculated based on the invariant temperature and field strain functions. In addition, the non-negligible influences of the pitch length of the filaments on both the mechanical behaviors and the normalized critical current are discussed. The stress-strain characteristics of the strand under tensile load and the normalized critical current of it under axial and bending loads resulting from the Multi-filament twist model show good agreement with the experimental data.

  3. Application of pulsed field gel electrophoresis to determine γ-ray-induced double-strand breaks in yeast chromosomal molecules

    International Nuclear Information System (INIS)

    Friedl, A.A.; Hahn, K.; Eckardt-Schupp, F.; Kellerer, A.M.; Beisker, W.

    1993-01-01

    The frequency of DNA double-strand breaks (dsb) was determined in yeast cells exposed to γ-rays under anoxic conditions. Genomic DNA of treated cells was separated by pulsed field gel electrophoresis, and two different approaches for the evaluation of the gels were employed: (1) The DNA mass distribution profile obtained by electrophoresis was compared to computed profiles, and the number of DSB per unit length was then derived in terms of a fitting procedure; (2) hybridization of selected chromosomes was performed, and a comparison of the hybridization signals in treated and untreated samples was then used to derive the frequency of dsb. The two assays gave similar results for the frequency of dsb ((1.07 ± 0.06) x 10 -9 Gy -1 bp -1 and (0.93 ± 0.09) x 10 -9 Gy -1 bp -1 , respectively). The dsb frequency was found to be linearly dependent on dose. (author)

  4. Filament and critical current degradations in extracted strands of SSC cable

    International Nuclear Information System (INIS)

    Seuntjens, J.M.; Capone, D.W. II; Warnes, W.H.

    1991-01-01

    Previous work by Goodrich et al. has shown that virtually all of the voltage in a strand of cable at I c is concentrated locally at the edges where the damage is severest. The authors have worked to characterize this local degradation both microstructurally and electromagnetically. Scanning electron microscopy and image analysis have been used to characterize filament defects and uniformity throughout the edge and flat regions of the strand. A summary of this work is given and is correlated to recent electromagnetic results on the distribution of critical currents along the strand

  5. Filament and critical current degradations in extracted strands of SSC cable

    International Nuclear Information System (INIS)

    Seuntjens, J.M.; Capone, D.W. II; Warnes, W.H.

    1991-03-01

    Previous work by Goodrich et al. has shown that virtually all of the voltage in a strand of cable at I c is concentrated locally at the edges where the damage is severest. We have worked to characterize this local degradation both microstructurally and electromagnetically. Scanning electron microscopy and image analysis have been used to characterize filament defects and uniformity throughout the edge and flat regions of the strand. A summary of this work is given and is correlated to recent electromagnetic results on the distribution of critical currents along the strand. 3 refs., 4 figs., 1 tab

  6. Examination of contacts between strands by electrical measurements and topographical analysis

    CERN Document Server

    Depond, J M; Oberli, L R; Richter, D

    1996-01-01

    The contact resistance (crossing and adjacent) between the strands of Rutherford type superconducting cables has been proven to be an essential parameter for the behaviour of the main magnets in accelerators like the LHC. A strong development program has been launched at CERN. Contact resistances were measured by means of a DC method at 4.2 K. The strand deformation and the chemical conditions at the contacts were analyzed in order to interpret the electrical resistances measured by a 3 contacts method on individual strands as well as the resistances measured independently on cables.

  7. Long-Term Seasonal and Interannual Patterns of Marine Mammal Strandings in Subtropical Western South Atlantic.

    Directory of Open Access Journals (Sweden)

    Jonatas H F Prado

    Full Text Available Understanding temporal patterns of marine mammal occurrence is useful for establishing conservation strategies. We used a 38 yr-long dataset spanning 1976 to 2013 to describe temporal patterns and trends in marine mammal strandings along a subtropical stretch of the east coast of South America. This region is influenced by a transitional zone between tropical and temperate waters and is considered an important fishing ground off Brazil. Generalized Additive Models were used to evaluate the temporal stranding patterns of the most frequently stranded species. Forty species were documented in 12,540 stranding events. Franciscana (n = 4,574, South American fur seal, (n = 3,419, South American sea lion (n = 2,049, bottlenose dolphins (n = 293 and subantarctic fur seal (n = 219 were the most frequently stranded marine mammals. The seasonality of strandings of franciscana and bottlenose dolphin coincided with periods of higher fishing effort and strandings of South American and subantarctic fur seals with post-reproductive dispersal. For South American sea lion the seasonality of strandings is associated with both fishing effort and post-reproductive dispersal. Some clear seasonal patterns were associated with occurrence of cold- (e.g. subantarctic fur seal and warm-water (e.g. rough-toothed dolphin species in winter and summer, respectively. Inter-annual increases in stranding rate were observed for franciscana and South American fur seal and these are likely related to increased fishing effort and population growth, respectively. For subantarctic fur seal the stranding rate showed a slight decline while for bottlenose dolphin it remained steady. No significant year to year variation in stranding rate was observed for South American sea lion. The slight decrease in frequency of temperate/polar marine mammals and the increased occurrence of subtropical/tropical species since the late 1990s might be associated with environmental changes linked to

  8. Recent Progress in Application of Internal Oxidation Technique in Nb3Sn Strands

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Xingchen [Fermilab; Peng, Xuan [Hyper Tech Research Inc.; Sumption, Michael [Ohio State U.; Collings, E. W. [Ohio State U.

    2016-10-13

    The internal oxidation technique can generate ZrO2 nano particles in Nb3Sn strands, which markedly refine the Nb3Sn grain size and boost the high-field critical current density (Jc). This article summarizes recent efforts on implementing this technique in practical Nb3Sn wires and adding Ti as a dopant. It is demonstrated that this technique can be readily incorporated into the present Nb3Sn conductor manufacturing technology. Powder-in-tube (PIT) strands with fine subelements (~25 µm) based on this technique were successfully fabricated, and proper heat treatments for oxygen transfer were explored. Future work for producing strands ready for applications is proposed.

  9. Enzymatic quantification of strand breaks of DNA induced by vacuum-UV radiation

    International Nuclear Information System (INIS)

    Ito, Takashi

    1986-01-01

    Hind3 digested plasmid DNA dried on an aluminum plate was irradiated by vacuum-UV at 160 and 195 nm using a synchrotron irradiation system. A change induced in the DNA, presumably a single strand break, was quantified by the aid of the strand break-derived stimulation of poly(ADP-ribose) synthetase activity. The end group of strand breaks so induced was recognized by the enzyme as effectively as that by DNase 1 treatment, suggesting a nicking as the major lesion inflicted on the DNA. The fluence (UV) dependent stimulation of poly(ADP-ribose) synthetase activity was much higher upon 160 nm irradiation than upon 195 nm irradiation. (Auth.)

  10. Long-Term Seasonal and Interannual Patterns of Marine Mammal Strandings in Subtropical Western South Atlantic

    Science.gov (United States)

    Prado, Jonatas H. F.; Mattos, Paulo H.; Silva, Kleber G.; Secchi, Eduardo R.

    2016-01-01

    Understanding temporal patterns of marine mammal occurrence is useful for establishing conservation strategies. We used a 38 yr-long dataset spanning 1976 to 2013 to describe temporal patterns and trends in marine mammal strandings along a subtropical stretch of the east coast of South America. This region is influenced by a transitional zone between tropical and temperate waters and is considered an important fishing ground off Brazil. Generalized Additive Models were used to evaluate the temporal stranding patterns of the most frequently stranded species. Forty species were documented in 12,540 stranding events. Franciscana (n = 4,574), South American fur seal, (n = 3,419), South American sea lion (n = 2,049), bottlenose dolphins (n = 293) and subantarctic fur seal (n = 219) were the most frequently stranded marine mammals. The seasonality of strandings of franciscana and bottlenose dolphin coincided with periods of higher fishing effort and strandings of South American and subantarctic fur seals with post-reproductive dispersal. For South American sea lion the seasonality of strandings is associated with both fishing effort and post-reproductive dispersal. Some clear seasonal patterns were associated with occurrence of cold- (e.g. subantarctic fur seal) and warm-water (e.g. rough-toothed dolphin) species in winter and summer, respectively. Inter-annual increases in stranding rate were observed for franciscana and South American fur seal and these are likely related to increased fishing effort and population growth, respectively. For subantarctic fur seal the stranding rate showed a slight decline while for bottlenose dolphin it remained steady. No significant year to year variation in stranding rate was observed for South American sea lion. The slight decrease in frequency of temperate/polar marine mammals and the increased occurrence of subtropical/tropical species since the late 1990s might be associated with environmental changes linked to climate change

  11. Double strand breaks in DNA in vivo and in vitro after 60Co-γ-irradiation

    International Nuclear Information System (INIS)

    Huelsewede, J.W.

    1985-01-01

    The questions of what the correlation is between double strand breaks in DNA in the cell and lethal radiation damage and by means of which possible mechanisms DNA double strand breaks could occur were studied. E. coli served as test system. In addition to this the molecular weight of the DNA from irradiated E. coli as a function of the radiation dose under various conditions was measured. This data was compared on the one hand to the survival of the cell and on the other hand to the formation of DNA double strand breaks in an aqueous buffer system, which in its ionic characteristics was similar to cell fluids. (orig./MG) [de

  12. DNA strand breakage by 125I-decay in oligoDNA

    International Nuclear Information System (INIS)

    Lobachevsky, P.; Martin, R.F.

    1996-01-01

    Full text: A double-stranded oligodeoxynucleotide containing 125 I-dC in a defined location, with 5'- or 3'- 32 P-end-labelling of either strand, was used to investigate DNA strand breakage resulting from 125 I decay. Samples of the 32 P-end-labelled and 125 I-dC containing oligoDNA were incubated in 20 mM phosphate buffer (PB), or PB + 2 M dimethylsulphoxide (DMSO) at 4 deg during 18-20 days. The 32 P-end-labelled DNA fragments produced by 125 I decays were separated on denaturing polyacrylamide gels, and the 3P activity in each fragment was determined by scintillation counting after elution from the gel. The fragment size distribution was then converted to a distribution of single stranded break probabilities at each nucleotide position. The results indicate that each 125 I decay event produces at least one break in the 125 I-dC containing strand, and causes breakage of the opposite strand in 75-80% of events. Thus, the double stranded break is produced by 125 I decay with probability ∼0.8. Most of single stranded breaks (around 90%) occurred within 5-6 nucleotides of the 125 I-dC, however DNA breaks were detected up to 18-20 nucleotides from the decay site. The average numbers of single stranded breaks per decay are 3.7 (PB) and 3.3 (PB+DMSO) in 125 I-dC containing strand, and 1.5 (PB) and 1.3 (PB+DMSO) in the opposite strand. Deconvolution of strand break probabilities as a function of separation from the 125 I, in terms of both distance (to target deoxyribosyl carbon atoms, in B-DNA) and nucleotide number, show that the latter is an important parameter for the shorter-range damage. This could indicate a role for attenuation/dissipation of damage through the stacked bases. In summary, the results represent a much more extensive set of data than available from earlier experiments on DNA breakage from l25 I-decay, and may provide new mechanistic insights

  13. BOREAS AFM-03 NCAR Electra 1994 Aircraft Sounding Data

    Data.gov (United States)

    National Aeronautics and Space Administration — Measurements of wind speed and direction, air pressure and temperature, potential temperature, dewpoint, mixing ratio of H2O, CO2 concentration, and ozone...

  14. BOREAS AFM-03 NCAR Electra 1994 Aircraft Sounding Data

    Data.gov (United States)

    National Aeronautics and Space Administration — ABSTRACT: Measurements of wind speed and direction, air pressure and temperature, potential temperature, dewpoint, mixing ratio of H2O, CO2 concentration, and ozone...

  15. Towards modeling future energy infrastructures - the ELECTRA system engineering approach

    DEFF Research Database (Denmark)

    Uslar, Mathias; Heussen, Kai

    2016-01-01

    of the IEC 62559 use case template as well as needed changes to cope particularly with the aspects of controller conflicts and Greenfield technology modeling. From the original envisioned use of the standards, we show a possible transfer on how to properly deal with a Greenfield approach when modeling....

  16. Double-strand break repair-adox: Restoration of suppressed double-strand break repair during mitosis induces genomic instability.

    Science.gov (United States)

    Terasawa, Masahiro; Shinohara, Akira; Shinohara, Miki

    2014-12-01

    Double-strand breaks (DSBs) are one of the severest types of DNA damage. Unrepaired DSBs easily induce cell death and chromosome aberrations. To maintain genomic stability, cells have checkpoint and DSB repair systems to respond to DNA damage throughout most of the cell cycle. The failure of this process often results in apoptosis or genomic instability, such as aneuploidy, deletion, or translocation. Therefore, DSB repair is essential for maintenance of genomic stability. During mitosis, however, cells seem to suppress the DNA damage response and proceed to the next G1 phase, even if there are unrepaired DSBs. The biological significance of this suppression is not known. In this review, we summarize recent studies of mitotic DSB repair and discuss the mechanisms of suppression of DSB repair during mitosis. DSB repair, which maintains genomic integrity in other phases of the cell cycle, is rather toxic to cells during mitosis, often resulting in chromosome missegregation and aberration. Cells have multiple safeguards to prevent genomic instability during mitosis: inhibition of 53BP1 or BRCA1 localization to DSB sites, which is important to promote non-homologous end joining or homologous recombination, respectively, and also modulation of the non-homologous end joining core complex to inhibit DSB repair. We discuss how DSBs during mitosis are toxic and the multiple safeguard systems that suppress genomic instability. © 2014 The Authors. Cancer Science published by Wiley Publishing Asia Pty Ltd on behalf of Japanese Cancer Association.

  17. Analysis of double-stranded RNA from microbial communities identifies double-stranded RNA virus-like elements.

    Science.gov (United States)

    Decker, Carolyn J; Parker, Roy

    2014-05-08

    Double-stranded RNA (dsRNA) can function as genetic information and may have served as genomic material before the existence of DNA-based life. By developing a method to purify dsRNA, we have investigated the diversity of dsRNA in microbial populations. We detect large dsRNAs in multiple microbial populations. Analysis of an aquatic microbial population reveals that some dsRNA sequences match metagenomic DNA, suggesting that microbes contain pools of sense-antisense transcripts. In addition, ∼30% of the dsRNA sequences are not present in the corresponding DNA pool and are strongly biased toward encoding novel proteins. Of these "dsRNA unique" sequences, only a small percentage share similarity to known viruses, a large fraction assemble into RNA virus-like contigs, and the remaining fraction has an unexplained origin. These results have uncovered dsRNA virus-like elements and underscore that dsRNA potentially represents an additional reservoir of genetic information in microbial populations. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

  18. Pleolipoviridae, a newly proposed family comprising archaeal pleomorphic viruses with single-stranded or double-stranded DNA genomes.

    Science.gov (United States)

    Pietilä, Maija K; Roine, Elina; Sencilo, Ana; Bamford, Dennis H; Oksanen, Hanna M

    2016-01-01

    Viruses infecting archaea show a variety of virion morphotypes, and they are currently classified into more than ten viral families or corresponding groups. A pleomorphic virus morphotype is very common among haloarchaeal viruses, and to date, several such viruses have been isolated. Here, we propose the classification of eight such viruses and formation of a new family, Pleolipoviridae (from the Greek pleo for more or many and lipos for lipid), containing three genera, Alpha-, Beta-, and Gammapleolipovirus. The proposal is currently under review by the International Committee on Taxonomy of Viruses (ICTV). The members of the proposed family Pleolipoviridae infect halophilic archaea and are nonlytic. They share structural and genomic features and differ from any other classified virus. The virion of pleolipoviruses is composed of a pleomorphic membrane vesicle enclosing the genome. All pleolipoviruses have two major structural protein species, internal membrane and spike proteins. Although the genomes of the pleolipoviruses are single- or double-stranded, linear or circular DNA molecules, they share the same genome organization and gene synteny and show significant similarity at the amino acid level. The canonical features common to all members of the proposed family Pleolipoviridae show that they are closely related and thus form a new viral family.

  19. Effect of Twist Pitch in the Strands on the Saturation and Losses in the Nb3Sn Strands for the ITER TF CICC

    Energy Technology Data Exchange (ETDEWEB)

    Martovetsky, N N

    2007-12-06

    ITER TF coils will see a significant longitudinal magnetic field in the event of the plasma disruption. This abrupt change of magnetic fields results in the appearance of an additional electrical field in the strands. The mechanism of this electrical field is the induced currents that expel the flux from the strands. This effect was known since the late 1970's [1-3] and most of the details necessary for the analyses given in this report are presented in [4]. Let's assume for simplicity a zero transport current in the strand. When a longitudinal pulsed field is applied, the outer filaments will carry an induced current repelling the change of flux. The current density of this current is 'critical' in the simplification of Bean's critical state model, where superconducting transition is represented as j=j{sub c} at any non-zero electrical field and zero where the electrical field has not penetrated. In reality, since the current density is roughly logarithmic with the electrical field, E=E{sub c}*exp[(j-j{sub c})/jo], Bean's model is just a simplification, and current density is slightly nonuniform in the outer filament and more so for the interior strands. The inner portion of the filaments will carry a current of the opposite sign. Even in the Bean's model it is not uniform, but the assumption that it is uniform and less than critical simplifies mathematics significantly and does not deviate far from the real current density distribution. In certain circumstances, the average electrical field in the strands will be high enough to exceed the take-off electrical field averaged across the cross section. In this case, the multifilamentary strand will become unstable and will experience transition to the normal state. With zero transport current, it will eventually recover, of course. This phenomenon is analogous to the flux jump. If the strand carries a transport current, the situation becomes more complicated. If it goes unstable and

  20. Neutrino mass

    International Nuclear Information System (INIS)

    Robertson, R.G.H.

    1992-01-01

    Despite intensive experimental work since the neutrino's existence was proposed by Pauli 60 years ago, and its first observation by Reines and Cowan almost 40 years ago, the neutrino's fundamental properties remain elusive. Among those properties are the masses of the three known flavors, properties under charge conjugation, parity and time-reversal, and static and dynamic electromagnetic moments. Mass is perhaps the most fundamental, as it constrains the other properties. The present status of the search for neutrino mass is briefly reviewed

  1. MASS SPECTROMETER

    Science.gov (United States)

    White, F.A.

    1960-08-23

    A mass spectrometer is designed with a first adjustable magnetic field for resolving an ion beam into beams of selected masses, a second adjustable magnetic field for further resolving the ion beam from the first field into beams of selected masses, a thin foil disposed in the path of the beam between the first and second magnets to dissociate molecular ions incident thereon, an electrostatic field for further resolving the ion beam from the second field into beams of selected masses, and a detector disposed adjacent to the electrostatic field to receive the ion beam.

  2. Possible lin between elevated accumulation of trace elements and canine distemper virus infection in the Caspian seals (Phoca caspica) stranded in 2000 and 2001

    Science.gov (United States)

    Shinsuke, T.; Takashi, K.; Yasumi, A.; Tokutaka, I.; Reiji, K.

    2003-05-01

    In the Caspian Sea, a die-off of thousands of Caspian seals (Phoca caspica) occurred in 1997 and 2000. While a direct cause for these deaths seems to be canine distemper virus (CDV) infection, immunosuppression due to environmental pollutants is considered as one of the possible explanations for the development of the disease. The purpose of this work is to examine whether exposure to trace metals could be one of the factors involved in the mass mortality of Caspian seals. Concentrations of 13 trace elements weredetermined in liver, kidney and muscle of Caspian seals found stranded along the coasts of the Caspian Sea in 2000 and 2001. Concentrations of toxic elemen ts (Ag, Cd, Hg, Tl and Pb) in the Caspian seals collected in 2000 and 2001 were comparable to or lower than those in healthy Caspian seals collected in 1993 and 1998 and in seals from other regions, suggesting that these elements would not be the causative agent for the death of Caspian seals. In contrast, Zn and Fe concentrations in the stranded Caspian seals were apparently higher than those in seals from other locations. These results suggest the disturbance in homeostatic control and nutritional statu s of essential elements in the stranded Caspian seals.

  3. Location and timing of the deposition of egg strands by perch (Perca fluviatilis L.: the roles of lake hydrology, spawning substrate and female size

    Directory of Open Access Journals (Sweden)

    Čech M.

    2011-10-01

    Full Text Available The reproduction biology of perch Perca fluviatilis was studied in relation to lake hydrology, spawning substrate and female size using SCUBA divers during late April and mid-May 2009 in Chabařovice Lake, Czech Republic. An extreme displacement of water mass, induced by a long-lasting strong wind, caused the abundance of egg strands to differ significantly between individual parts of the lake. On average, 91% of perch spawning activity occurred at depths greater than 3 m. The mean concentration of dissolved organic carbon (DOC indicated that the lake belongs to the category where DOC influencing the penetration of ultraviolet radiation, is not responsible for the deep deposition of egg strands by perch. Most probably, the avoidance of shallow depths (<3 m results from strong wind/waves coming from any direction. Larger perch females started to spawn earlier than their smaller conspecifics and they used shallower depths for depositing their egg strands. As a spawning substrate, perch strongly selected dead submerged vegetation, such as common reed Phragmites communis and worm weed Artemisia sp. These substrates, however, reveal signs of progressive degradation and seem likely to disappear from the lake within several years.

  4. Evidence that single-stranded DNA breaks are a normal feature of koala sperm chromatin, while double-stranded DNA breaks are indicative of DNA damage.

    Science.gov (United States)

    Zee, Yeng Peng; López-Fernández, Carmen; Arroyo, F; Johnston, Stephen D; Holt, William V; Gosalvez, Jaime

    2009-08-01

    In this study, we have used single and double comet assays to differentiate between single- and double-stranded DNA damage in an effort to refine the interpretation of DNA damage in mature koala spermatozoa. We have also investigated the likelihood that single-stranded DNA breakage is part of the natural spermiogenic process in koalas, where its function would be the generation of structural bends in the DNA molecule so that appropriate packaging and compaction can occur. Koala spermatozoa were examined using the sperm chromatin dispersion test (SCDt) and comet assays to investigate non-orthodox double-stranded DNA. Comet assays were conducted under 1) neutral conditions; and 2) neutral followed by alkaline conditions (double comet assay); the latter technique enabled simultaneous visualisation of both single-stranded and double-stranded DNA breaks. Following the SCDt, there was a continuum of nuclear morphotypes, ranging from no apparent DNA fragmentation to those with highly dispersed and degraded chromatin. Dispersion morphotypes were mirrored by a similar diversity of comet morphologies that could be further differentiated using the double comet assay. The majority of koala spermatozoa had nuclei with DNA abasic-like residues that produced single-tailed comets following the double comet assay. The ubiquity of these residues suggests that constitutive alkali-labile sites are part of the structural configuration of the koala sperm nucleus. Spermatozoa with 'true' DNA fragmentation exhibited a continuum of comet morphologies, ranging from a more severe form of alkaline-susceptible DNA with a diffuse single tail to nuclei that exhibited both single- and double-stranded breaks with two comet tails.

  5. Global organization of a positive-strand RNA virus genome.

    Directory of Open Access Journals (Sweden)

    Baodong Wu

    Full Text Available The genomes of plus-strand RNA viruses contain many regulatory sequences and structures that direct different viral processes. The traditional view of these RNA elements are as local structures present in non-coding regions. However, this view is changing due to the discovery of regulatory elements in coding regions and functional long-range intra-genomic base pairing interactions. The ∼4.8 kb long RNA genome of the tombusvirus tomato bushy stunt virus (TBSV contains these types of structural features, including six different functional long-distance interactions. We hypothesized that to achieve these multiple interactions this viral genome must utilize a large-scale organizational strategy and, accordingly, we sought to assess the global conformation of the entire TBSV genome. Atomic force micrographs of the genome indicated a mostly condensed structure composed of interconnected protrusions extending from a central hub. This configuration was consistent with the genomic secondary structure model generated using high-throughput selective 2'-hydroxyl acylation analysed by primer extension (i.e. SHAPE, which predicted different sized RNA domains originating from a central region. Known RNA elements were identified in both domain and inter-domain regions, and novel structural features were predicted and functionally confirmed. Interestingly, only two of the six long-range interactions known to form were present in the structural model. However, for those interactions that did not form, complementary partner sequences were positioned relatively close to each other in the structure, suggesting that the secondary structure level of viral genome structure could provide a basic scaffold for the formation of different long-range interactions. The higher-order structural model for the TBSV RNA genome provides a snapshot of the complex framework that allows multiple functional components to operate in concert within a confined context.

  6. Manipulation of double-stranded DNA melting by force

    Science.gov (United States)

    Singh, Amit Raj; Granek, Rony

    2017-09-01

    By integrating elasticity—as described by the Gaussian network model—with bond binding energies that distinguish between different base-pair identities and stacking configurations, we study the force induced melting of a double-stranded DNA (dsDNA). Our approach is a generalization of our previous study of thermal dsDNA denaturation [J. Chem. Phys. 145, 144101 (2016), 10.1063/1.4964285] to that induced by force at finite temperatures. It allows us to obtain semimicroscopic information about the opening of the chain, such as whether the dsDNA opens from one of the ends or from the interior, forming an internal bubble. We study different types of force manipulation: (i) "end unzipping," with force acting at a single end base pair perpendicular to the helix, (ii) "midunzipping," with force acting at a middle base pair perpendicular to the helix, and (iii) "end shearing," where the force acts at opposite ends along the helix. By monitoring the free-energy landscape and probability distribution of intermediate denaturation states, we show that different dominant intermediate states are stabilized depending on the type of force manipulation used. In particular, the bubble state of the sequence L60B36, which we have previously found to be a stable state during thermal denaturation, is absent for end unzipping and end shearing, whereas very similar bubbles are stabilized by midunzipping, or when the force location is near the middle of the chain. Ours results offer a simple tool for stabilizing bubbles and loops using force manipulations at different temperatures, and may implicate on the mechanism in which DNA enzymes or motors open regions of the chain.

  7. Repair and gamma radiation-induced single- and double-strand breaks in DNA of Escherichia coli

    International Nuclear Information System (INIS)

    Petrov, S.I.

    1981-01-01

    Studies in the kinetics of repair of γ-radiation-induced single- and double-strand breaks in DNA of E. coli cells showed that double-strand DNA breaks are rejoined by the following two ways. The first way is conditioned by repair of single-strand breaks and represents the repair of ''oblique'' double-strand breaks in DNA, whereas the second way is conditioned by functioning of the recombination mechanisms and, to all appearance, represents the repair of ''direct'' double-strand breaks in DNA

  8. Correlation of Free Radical Yields with Strand Break Yields Produced in Plasmid DNA by the Direct Effect of Ionizing Radiation

    OpenAIRE

    Purkayastha, Shubhadeep; Milligan, Jamie R.; Bernhard, William A.

    2005-01-01

    The purpose of this study was to determine how free radical formation (fr) correlates with single strand break (ssb) and double strand break (dsb) formation in DNA exposed to the direct effects of ionizing radiation. Chemical yields have been determined of (i) total radicals trapped on DNA at 4 K, G(∑fr), (ii) radicals trapped on the DNA sugar, Gsugar(fr), (iii) prompt single strand breaks, Gprompt(ssb), (iv) total single strand breaks, Gtotal(ssb), and (v) double strand breaks, G(dsb). These...

  9. Finite element bond models for seven-wire prestressing strands in concrete crossties.

    Science.gov (United States)

    2015-03-23

    Seven-wire strands are commonly used in pretensioned : concrete ties, but its bonding mechanism with concrete needs : further examination to provide a better understanding of some : concrete tie failure modes. As a key component in the finite : eleme...

  10. Screening for Breast Cancer Using Near-Field Infrared Spectroscopy of a Single Strand of Hair

    National Research Council Canada - National Science Library

    Erramilli, Shyamsunder

    2003-01-01

    .... In this study, we have successfully developed a new infrared method for the detection in a single strand of hair the presence of lipid deposits that were the putative cause of the observed x-ray patterns...

  11. Corrosion performance of prestressing strands in contact with dissimilar grouts : technical summary.

    Science.gov (United States)

    2013-01-01

    Inspections of post-tensioned bridges : by the Kansas Department of Transportation : have revealed voids in strand ducts due to : bleeding and shrinkage of older Portland : Cement grouts. The Kansas Department : of Transportation is faced with a deci...

  12. Single slit interference made easy with a strand of hair and a laser

    Science.gov (United States)

    Messer, Rebecca

    2018-01-01

    Students can easily measure the width of a strand of their own hair with a monochromatic light source such as a laser. This inexpensive activity engages students in an application of single slit diffraction using Babinet's principle.

  13. Acute hypoxia and hypoxic exercise induce DNA strand breaks and oxidative DNA damage in humans

    DEFF Research Database (Denmark)

    Møller, P; Loft, S; Lundby, C

    2001-01-01

    The present study investigated the effect of a single bout of exhaustive exercise on the generation of DNA strand breaks and oxidative DNA damage under normal conditions and at high-altitude hypoxia (4559 meters for 3 days). Twelve healthy subjects performed a maximal bicycle exercise test...... exercise in altitude hypoxia. Exercise-induced generation of DNA strand breaks was not seen at sea level. In both environments, the level of FPG and endonuclease III-sensitive sites remained unchanged immediately after exercise. DNA strand breaks and oxidative DNA damage are probably produced by reactive...... oxygen species, generated by leakage of the mitochondrial respiration or during a hypoxia-induced inflammation. Furthermore, the presence of DNA strand breaks may play an important role in maintaining hypoxia-induced inflammation processes. Hypoxia seems to deplete the antioxidant system of its capacity...

  14. Effect of catechins and tannins on depleted uranium-induced DNA strand breaks

    International Nuclear Information System (INIS)

    Emiko Matsuda; Akira Nakajima

    2012-01-01

    The effects of polyphenols on plasmid DNA strand breaks by depleted uranium were studied using four catechins: (+)-catechin, (-)-epicatechin, (-)-epigallocatechin (EGC), and (-)-epigallocatechin gallate (EGCG); seven tannins: Chinese gallotannin, persimmon tannin (PST), mimosa tannin (MMT), myrobalan tannin, quebracho tannin, gambir tannin, and chestnut tannin; and gallic acid. The plasmid DNA strand breaks by uranyl ion (UO 2 2+ ) with hydrogen peroxide (H 2 O 2 ) were strongly enhanced by EGC, EGCG, MMT, and PST (condenced tannins). The obtained results showed that the DNA strand breaks are caused by UO 2 2+ through the direct interaction between the uranyl complex and the negatively charged DNA phosphate backbone. The additional DNA strand breaks by the addition of polyphenols occurred through an indirect process by the reduction of UO 2 2+ to UO 2 + and hydroxyl radical formation through a Fenton-type reaction with H 2 O 2 . (author)

  15. Detection of DNA strand breaks in mammalian cells using the radioresistant bacterium PprA protein

    International Nuclear Information System (INIS)

    Satoh, Katsuya; Wada, Seiichi; Narumi, Issay; Kikuchi, Masahiro; Funayama, Tomoo; Kobayashi, Yasuhiko

    2003-01-01

    We have previously found that the PprA protein from Deinococcus radiodurans possesses ability to recognize DNA carrying strand breaks. In the present study, we attempted to visualize radiation-induced DNA strand breaks with PprA protein using immunofluorescence technique to elucidate the DNA damage response mechanism in mammalian cultured cells. As a result, colocalization of Cy2 and DAPI fluorescent signals was observed. This observation suggests that DNA strand breaks in the nucleus of CHO-K1 cells were effectively detected using the PprA protein. The amount of DNA strand breaks (integrated density of Cy2 fluorescent signals) was increased with the increase in the radiation dose. (author)

  16. Mass Society

    DEFF Research Database (Denmark)

    Borch, Christian

    2017-01-01

    Mass society is a societal diagnosis that emphasizes – usually in a pejorative, modernity critical manner – a series of traits allegedly associated with modern society, such as the leveling of individuality, moral decay, alienation, and isolation. As such, the notion of mass society generalizes...

  17. Genetic transformation of Streptococcus pneumoniae by DNA cloned into the single-stranded bacteriophage f1.

    OpenAIRE

    Barany, F; Boeke, J D

    1983-01-01

    A Staphylococcus aureus plasmid derivative, pFB9, coding for erythromycin and chloramphenicol resistance was cloned into the filamentous Escherichia coli phage f1. Recombinant phage-plasmid hybrids, designated plasmids, were isolated from E. coli and purified by transformation into Streptococcus pneumoniae. Single-stranded DNA was prepared from E. coli cells infected with two different plasmids, fBB101 and fBB103. Introduction of fully or partially single-stranded DNA into Streptococcus pneum...

  18. Low concentration of arsenite exacerbates UVR-induced DNA strand breaks by inhibiting PARP-1 activity

    International Nuclear Information System (INIS)

    Qin Xujun; Hudson, Laurie G.; Liu Wenlan; Timmins, Graham S.; Liu Kejian

    2008-01-01

    Epidemiological studies have associated arsenic exposure with many types of human cancers. Arsenic has also been shown to act as a co-carcinogen even at low concentrations. However, the precise mechanism of its co-carcinogenic action is unknown. Recent studies indicate that arsenic can interfere with DNA-repair processes. Poly(ADP-ribose) polymerase (PARP)-1 is a zinc-finger DNA-repair protein, which can promptly sense DNA strand breaks and initiate DNA-repair pathways. In the present study, we tested the hypothesis that low concentrations of arsenic could inhibit PAPR-1 activity and so exacerbate levels of ultraviolet radiation (UVR)-induced DNA strand breaks. HaCat cells were treated with arsenite and/or UVR, and then DNA strand breaks were assessed by comet assay. Low concentrations of arsenite (≤ 2 μM) alone did not induce significant DNA strand breaks, but greatly enhanced the DNA strand breaks induced by UVR. Further studies showed that 2 μM arsenite effectively inhibited PARP-1 activity. Zinc supplementation of arsenite-treated cells restored PARP-1 activity and significantly diminished the exacerbating effect of arsenite on UVR-induced DNA strand breaks. Importantly, neither arsenite treatment, nor zinc supplementation changed UVR-triggered reactive oxygen species (ROS) formation, suggesting that their effects upon UVR-induced DNA strand breaks are not through a direct free radical mechanism. Combination treatments of arsenite with PARP-1 inhibitor 3-aminobenzamide or PARP-1 siRNA demonstrate that PARP-1 is the target of arsenite. Together, these findings show that arsenite at low concentration exacerbates UVR-induced DNA strand breaks by inhibiting PARP-1 activity, which may represent an important mechanism underlying the co-carcinogenicity of arsenic

  19. Signals for the initiation and termination of synthesis of the viral strand of bacteriophage f1

    International Nuclear Information System (INIS)

    Dotto, G.P.; Horiuchi, K.; Jakes, K.S.; Zinder, N.D.

    1983-01-01

    In this paper the sequence around the plus origin that is required for efficient plus-strand synthesis as well as that necessary for gene-II-protein recognition is described. Results which demonstrate that the nucleotide sequence of the f1 plus origin contains two overlapping but distinct signals, one for initiation and the other for termination of plus-strand synthesis is presented. 29 references, 6 figures, 1 table

  20. Multiple reversals of strand asymmetry in molluscs mitochondrial genomes, and consequences for phylogenetic inferences.

    Science.gov (United States)

    Sun, Shao'e; Li, Qi; Kong, Lingfeng; Yu, Hong

    2018-01-01

    Strand asymmetry in nucleotide composition is a remarkable feature of animal mitochondrial genomes. The strand-specific bias in the nucleotide composition of the mtDNA has been known to be highly problematic for phylogenetic analyses. Here, the strand asymmetry was compared across 140 mollusc species and analyzed for a mtDNA fragment including twelve protein-coding genes. The analyses show that almost all species in Gastropoda (except Heterobranchia) and all species in Bivalvia present reversals of strand bias. The skew values on individual genes for all codon positions (P 123 ), third codon positions (P 3 ), and fourfold redundant third codon positions (P 4FD ) indicated that CG skews are the best indicators of strand asymmetry. The differences in the patterns of strand asymmetry significantly influenced the amino acid composition of the encoded proteins. These biases are most striking for the amino acids Valine, Cysteine, Asparagine and Threonines, which appear to have evolved asymmetrical exchanges in response to shifts in nucleotide composition. Molluscs with strong variability of genome architectures (ARs) are usually characterized by a reversal of the usual strand bias. Phylogenetic analyses show that reversals of asymmetric mutational constraints have consequences on the phylogenetic inferences, as taxa characterized by reverse strand bias (Heterobranchia and Bivalvia) tend to group together due to long-branch attraction (LBA) artifacts. Neutral Transitions Excluded (NTE) model did not overcome the problem of heterogeneous biases present in molluscs mt genomes, suggested it may not be appropriate for molluscs mt genome data. Further refinement phylogenetic models may help us better understand internal relationships among these diverse organisms. Copyright © 2017 Elsevier Inc. All rights reserved.

  1. Analytical model of the critical current of a bent Nb3Sn strand

    International Nuclear Information System (INIS)

    Koizumi, Norikiyo; Murakami, Haruyuki; Hemmi, Tsutomu; Nakajima, Hideo

    2011-01-01

    The critical current performance of a large Nb 3 Sn cable-in-conduit conductor (CICC) was degraded by periodic bending of strands due to a large transverse electromagnetic force. The degradation of each strand due to this bending should be evaluated in calculations of the critical current of a CICC, but a suitable model has not been developed yet. Therefore, the authors have developed a new analytical model which takes into account plastic deformation of copper and bronze and filament breakage. The calculated results were compared with test results for uniformly bent Nb 3 Sn bronze-route strands. The calculated results assuming a high transverse resistance model (HTRM) show good agreement with the test results, a finding which confirms the validity of the model. Because of a much shorter calculation time than for numerical simulation, the developed model seems much more practical for use in calculating the critical current performance of a Nb 3 Sn CICC. In addition, simulation results show that since the neutral axis of a bent strand shifts to the compressive side due to plastic deformation of the copper and bronze, and/or filament breakage, the strand is elongated by bending. This elongation may enhance the strand's critical current performance. Moreover, the calculated results indicate that the dependence of the critical current on the bending strain is affected by the bending history if the strand is excessively bent, especially when filaments are broken. In a real magnet, since a strand in a CICC is normally subject to the maximum electromagnetic force prior to an evaluation of its performance at a lower electromagnetic force, the effect of over-bending should be taken into account in calculations of its critical current performance, especially when filament breakage occurs.

  2. Analysis of marine turtle strandings (Reptilia: Testudine occurring on coast of Bahia State, Brazil

    Directory of Open Access Journals (Sweden)

    Aline Lopes-Souza

    2015-09-01

    Full Text Available This study provides an analysis of the occurrence and the spatial and temporal distribution of marine turtle strandings found in the south of the State of Bahia. Data was collected between January 2006 and June 2008. This study covers an area of 220 km of the southern coast of Bahia State (northeastern Brazil, and spatial analyses were made considering data collected in three bases suported by Petrobras-Petróleo Brasileiro S/A distributed in the area. The records were sorted according to month and year, species, age group and sex. A total of 260 stranding were reported: 183 of Chelonia mydas (74.1%, the most frequent species. The highest number of strandings was recorded in Gamboa do Morro Base. Juveniles presented the highest densities, but no differences between adults and small juveniles were detected. Males were more frequently stranded in Gamboa do Morro Base, while females were more frequent in Ilhéus Base. An increase in the number of stranding between 2006 and 2008 was noted; moreover, the months with more records were January, February, March, October and December. The number of stranding events was discontinuously distributed in the study area. This study also demonstrated the usefulness of implement different strategies of recording marine turtle strandings: direct monitoring efforts (patrol in remote beaches and educational campaigns applied on beaches frequented by tourists. This study demonstrated that, despite spatial nearby, the three bases attend independent biological systems and show different stranding dynamics, thus different conservancy actions should be implemented in order to improve the knowledge on natural history of sea-turtles in the southern coast of Bahia State.

  3. Breaking DNA strands by extreme-ultraviolet laser pulses in vacuum

    Czech Academy of Sciences Publication Activity Database

    Nováková, Eva; Vyšín, Luděk; Burian, Tomáš; Juha, Libor; Davídková, Marie; Múčka, V.; Čuba, V.; Grisham, M. E.; Heinbuch, S.; Rocca, J.J.

    2015-01-01

    Roč. 91, č. 4 (2015), "042718-1"-"042718-8" ISSN 1539-3755 R&D Projects: GA ČR(CZ) GBP108/12/G108; GA ČR GA13-28721S Institutional support: RVO:68378271 ; RVO:61389005 Keywords : XUV * DNA damages * single- strand breaks (SSBs) * double- strand breaks (DSBs) Subject RIV: BO - Biophysics Impact factor: 2.288, year: 2014

  4. Optimizing anti-gene oligonucleotide 'Zorro-LNA' for improved strand invasion into duplex DNA

    DEFF Research Database (Denmark)

    Zaghloul, Eman M; Madsen, Andreas S; Moreno, Pedro M D

    2011-01-01

    established a method, which conclusively demonstrates that an LNA ON can strand invade into duplex DNA. To make Zorros smaller in size and easier to design, we synthesized 3'-5'-5'-3' single-stranded Zorro-LNA (ssZorro) by using both 3'- and 5'-phosphoramidites. With ssZorro, a significantly greater extent......Zorro-LNA (Zorro) is a newly developed, oligonucleotide (ON)-based, Z-shaped construct with the potential of specific binding to each strand of duplex DNA. The first-generation Zorros are formed by two hybridized LNA/DNA mixmers (2-ON Zorros) and was hypothesized to strand invade. We have now...... and rate of double-strand invasion (DSI) was obtained than with conventional 2-ON Zorros. Introducing hydrophilic PEG-linkers connecting the two strands did not significantly change the rate or extent of DSI as compared to ssZorro with a nucleotide-based linker, while the longest alkyl-chain linker tested...

  5. DNA Strand Breaks in Mitotic Germ Cells of Caenorhabditis elegans Evaluated by Comet Assay.

    Science.gov (United States)

    Park, Sojin; Choi, Seoyun; Ahn, Byungchan

    2016-03-01

    DNA damage responses are important for the maintenance of genome stability and the survival of organisms. Such responses are activated in the presence of DNA damage and lead to cell cycle arrest, apoptosis, and DNA repair. In Caenorhabditis elegans, double-strand breaks induced by DNA damaging agents have been detected indirectly by antibodies against DSB recognizing proteins. In this study we used a comet assay to detect DNA strand breaks and to measure the elimination of DNA strand breaks in mitotic germline nuclei of C. elegans. We found that C. elegans brc-1 mutants were more sensitive to ionizing radiation and camptothecin than the N2 wild-type strain and repaired DNA strand breaks less efficiently than N2. This study is the first demonstration of direct measurement of DNA strand breaks in mitotic germline nuclei of C. elegans. This newly developed assay can be applied to detect DNA strand breaks in different C. elegans mutants that are sensitive to DNA damaging agents.

  6. Increase Jc by Improving the Array of Nb3Sn strands for Fusion Application

    Energy Technology Data Exchange (ETDEWEB)

    Peng, Xuan

    2012-12-17

    During Phase I, our efforts were focusing on improving the array of subelement in the tube type strands by hardening the Sn core and the subelement matrix to effectively increase the Jc of the strands. Below is a summary of the results. 1) We were unsuccessful in improving the array using a Cu-Sn matrix approach. 2) We slightly improved the array using Sn with 1.5at%Ti doped core, and a 217-subelement restacked strand was made and drawn down without any breakage. 3) We greatly improved the array using the Glidcop Al-15 to replace the pure Cu sheath in the subelement, and a 217-subelement restacked strand was made and drawn down. Both strands have very good drawability and the array showed good improvement. 4) We also improved the array using improved wire drawing techniques using Hyper Tech's new caterpillar wire drawing machines to enable straight wire drawing for the entire wire drawing process. 5) The 919-subelement restack strand shows its non-Cu Jc over 2100 A/mm2 at 12 T/4.2 K and AC loss of 508 mJ/cm3.

  7. A new cable-in-conduit conductor magnet with insulated strands

    Energy Technology Data Exchange (ETDEWEB)

    Yamaguchi, Satarou; Yamamoto, Junya; Motojima, Osamu

    1995-09-01

    Many studies have used cable-in-conduit conductor (CICC) coils in trying to develop an AC superconducting magnet because of its enormous potential if AC losses were low and insulation voltage was high. The strands in the most recent CICC magnets are coated with chromium or another metal with high electrical resistance to order to induce current re-distribution among the strands and to avoid a quench caused by a current imbalance. Current re-distribution is highly complex and very difficult to analyze because the conditions of the strand surfaces and the contact areas vary greatly with the operation of the conductor. If, however, the cable currents were well-balanced, insulating the strands would be the best way to reduce AC losses. We propose a new CICC magnet structure featuring a current lead that balances the strand currents via its resistance. Having calculated current balances, we find that strand currents are well within the present parameters for nuclear fusion experiments and superconducting magnet energy storages. (author).

  8. Guided ultrasonic waves for non-destructive monitoring of the stress levels in prestressed steel strands.

    Science.gov (United States)

    Chaki, S; Bourse, G

    2009-02-01

    The safety of prestressed civil structures such as bridges, dams, nuclear power plants, etc. directly involves the security of both environment and users. Health monitoring of the tensioning components, such as strands, tendons, bars, anchorage bolts, etc. is an important research topic and a challenging task bringing together the non-destructive evaluation (NDE) and civil engineering communities. This paper deals with a guided ultrasonic wave procedure for monitoring the stress levels in seven-wire steel strands (15.7 mm in diameter). The mechanical and geometrical characteristics of the prestressed strands were taken into account for optimizing the measurement configuration and then the choice of the guided ultrasonic mode at a suitable frequency. Simplified acoustoelastic formulations were derived from the acoustoelasticity theory according to either calibration test or in situ measurement. The results from acoustoelastic measurements on the seven-wire steel strands are presented and discussed in the case of calibration tests and industrially prestressed strands. They show the potential and the suitability of the proposed guided wave method for evaluating the stress levels in the tested seven-wire steel strands.

  9. Status of European manufacture of Toroidal Field conductor and strand for JT-60SA project

    International Nuclear Information System (INIS)

    Zani, Louis; Barabaschi, Pietro; Di Pietro, Enrico

    2013-01-01

    In the framework of the JT-60SA project, part of the Broader Approach (BA) agreement, EURATOM provides to Japan, the Toroidal Field (TF) magnet system, consisting of 18 superconducting coils. The procurement of the conductor for the TF coils is managed by Fusion for Energy, acting as EU representative in the BA agreement. The TF conductor procurement is split into two contracts, one dedicated to the production of Niobium Titanium (NbTi) and Cu strand and the other to TF conductor production through strand cabling and cable jacketing operations. The TF conductor is a rectangular-shaped cable-in-conduit conductor formed by 486 (0.81 mm diameter) strands (2/3 NbTi–1/3 Cu) wrapped in a stainless steel foil and embedded into a stainless steel jacket. The 18 TF coils require (including spares) 115 ‘Unit Lengths’ (UL) of such conductor, each 240 m long for a total of about 28 km. Correspondingly about 10,000 km for NbTi and 5000 km for Cu strand are produced. The Japanese company Furukawa Electric Co. (FEC) is in charge of TF strand manufacture while the Italian company Italian Consortium for Applied Superconductivity (ICAS) is in charge of cabling and jacketing of TF conductor ULs. In the paper, we provide information on the production stages presently achieved in TF strand and conductor contracts

  10. Detection of short single-strand DNA homopolymers with ultrathin Si3N4 nanopores.

    Science.gov (United States)

    Ma, Jian; Qiu, Yinghua; Yuan, Zhishan; Zhang, Yin; Sha, Jingjie; Liu, Lei; Sun, Litao; Ni, Zhonghua; Yi, Hong; Li, Deyu; Chen, Yunfei

    2015-08-01

    A series of nanopores with diameters ranging from 2.5 to 63 nm are fabricated on a reduced Si3N4 membrane by focused ion beam and high energy electron beam. Through measuring the blocked ionic currents for DNA strands threading linearly through those solid-state nanopores, it is found that the blockade ionic current is proportional to the square of the hydrodynamic diameter of the DNA strand. With the nanopore diameter reduced to be comparable with that of DNA strands, the hydrodynamic diameter of the DNA becomes smaller, which is attributed to the size confinement effects. The duration time for the linear DNA translocation events increases monotonically with the nanopore length. By comparing the spatial configurations of DNA strands through nanopores with different diameters, it is found that the nanopore with large diameter has enough space to allow the DNA strand to translocate through with complex conformation. With the decrease of the nanopore diameter, the folded part of the DNA is prone to be straightened by the nanopore, which leads to the increase in the occurrence frequency of the linear DNA translocation events. Reducing the diameter of the nanopore to 2.5 nm allows the detection and discrimination of three nucleotide "G" and three nucleotide "T" homopolymer DNA strands based on differences in their physical dimensions.

  11. A new cable-in-conduit conductor magnet with insulated strands

    International Nuclear Information System (INIS)

    Yamaguchi, Satarou; Yamamoto, Junya; Motojima, Osamu.

    1995-09-01

    Many studies have used cable-in-conduit conductor (CICC) coils in trying to develop an AC superconducting magnet because of its enormous potential if AC losses were low and insulation voltage was high. The strands in the most recent CICC magnets are coated with chromium or another metal with high electrical resistance to order to induce current re-distribution among the strands and to avoid a quench caused by a current imbalance. Current re-distribution is highly complex and very difficult to analyze because the conditions of the strand surfaces and the contact areas vary greatly with the operation of the conductor. If, however, the cable currents were well-balanced, insulating the strands would be the best way to reduce AC losses. We propose a new CICC magnet structure featuring a current lead that balances the strand currents via its resistance. Having calculated current balances, we find that strand currents are well within the present parameters for nuclear fusion experiments and superconducting magnet energy storages. (author)

  12. Breaking DNA strands by extreme-ultraviolet laser pulses in vacuum

    Science.gov (United States)

    Nováková, Eva; Vyšín, Luděk; Burian, Tomáš; Juha, Libor; Davídková, Marie; Múčka, Viliam; Čuba, Václav; Grisham, Michael E.; Heinbuch, Scott; Rocca, Jorge J.

    2015-04-01

    Ionizing radiation induces a variety of DNA damages including single-strand breaks (SSBs), double-strand breaks (DSBs), abasic sites, modified sugars, and bases. Most theoretical and experimental studies have been focused on DNA strand scissions, in particular production of DNA double-strand breaks. DSBs have been proven to be a key damage at a molecular level responsible for the formation of chromosomal aberrations, leading often to cell death. We have studied the nature of DNA damage induced directly by the pulsed 46.9-nm (26.5 eV) radiation provided by an extreme ultraviolet (XUV) capillary-discharge Ne-like Ar laser (CDL). Doses up to 45 kGy were delivered with a repetition rate of 3 Hz. We studied the dependence of the yield of SSBs and DSBs of a simple model of DNA molecule (pBR322) on the CDL pulse fluence. Agarose gel electrophoresis method was used for determination of both SSB and DSB yields. The action cross sections of the single- and double-strand breaks of pBR322 plasmid DNA in solid state were determined. We observed an increase in the efficiency of strand-break induction in the supercoiled DNA as a function of laser pulse fluence. Results are compared to those acquired at synchrotron radiation facilities and other sources of extreme-ultraviolet and soft x-ray radiation.

  13. Breaking DNA strands by extreme-ultraviolet laser pulses in vacuum.

    Science.gov (United States)

    Nováková, Eva; Vyšín, Luděk; Burian, Tomáš; Juha, Libor; Davídková, Marie; Múčka, Viliam; Čuba, Václav; Grisham, Michael E; Heinbuch, Scott; Rocca, Jorge J

    2015-04-01

    Ionizing radiation induces a variety of DNA damages including single-strand breaks (SSBs), double-strand breaks (DSBs), abasic sites, modified sugars, and bases. Most theoretical and experimental studies have been focused on DNA strand scissions, in particular production of DNA double-strand breaks. DSBs have been proven to be a key damage at a molecular level responsible for the formation of chromosomal aberrations, leading often to cell death. We have studied the nature of DNA damage induced directly by the pulsed 46.9-nm (26.5 eV) radiation provided by an extreme ultraviolet (XUV) capillary-discharge Ne-like Ar laser (CDL). Doses up to 45 kGy were delivered with a repetition rate of 3 Hz. We studied the dependence of the yield of SSBs and DSBs of a simple model of DNA molecule (pBR322) on the CDL pulse fluence. Agarose gel electrophoresis method was used for determination of both SSB and DSB yields. The action cross sections of the single- and double-strand breaks of pBR322 plasmid DNA in solid state were determined. We observed an increase in the efficiency of strand-break induction in the supercoiled DNA as a function of laser pulse fluence. Results are compared to those acquired at synchrotron radiation facilities and other sources of extreme-ultraviolet and soft x-ray radiation.

  14. MTE1 Functions with MPH1 in Double-Strand Break Repair.

    Science.gov (United States)

    Yimit, Askar; Kim, TaeHyung; Anand, Ranjith P; Meister, Sarah; Ou, Jiongwen; Haber, James E; Zhang, Zhaolei; Brown, Grant W

    2016-05-01

    Double-strand DNA breaks occur upon exposure of cells to ionizing radiation and certain chemical agents or indirectly through replication fork collapse at DNA damage sites. If left unrepaired, double-strand breaks can cause genome instability and cell death, and their repair can result in loss of heterozygosity. In response to DNA damage, proteins involved in double-strand break repair by homologous recombination relocalize into discrete nuclear foci. We identified 29 proteins that colocalize with recombination repair protein Rad52 in response to DNA damage. Of particular interest, Ygr042w/Mte1, a protein of unknown function, showed robust colocalization with Rad52. Mte1 foci fail to form when the DNA helicase gene MPH1 is absent. Mte1 and Mph1 form a complex and are recruited to double-strand breaks in vivo in a mutually dependent manner. MTE1 is important for resolution of Rad52 foci during double-strand break repair and for suppressing break-induced replication. Together our data indicate that Mte1 functions with Mph1 in double-strand break repair. Copyright © 2016 by the Genetics Society of America.

  15. Structure and development of Nostoc strands in Leiosporoceros dussii (Anthocerotophyta): a novel symbiosis in land plants.

    Science.gov (United States)

    Villarreal A, Juan Carlos; Renzaglia, Karen Sue

    2006-05-01

    The presence of Nostoc in longitudinally oriented schizogenous canals is a feature that separates Leiosporoceros from all other hornworts and represents a novel symbiotic arrangement in land plants. In surface view, Nostoc canals are visible as elongated, dichotomously branched blue-green strands. All other hornworts develop numerous discrete globose colonies through continuous production of mucilage clefts as avenues for multiple invasions within a single thallus. To elucidate the anatomy and development of the unusual Nostoc strands in Leiosporoceros, we examined sporeling development in culture and the structure of strands in field-collected plants using light and electron microscopy. Rosette-like sporelings have mucilage clefts scattered along swollen apices. All field specimens were strap-shaped, contained Nostoc, and lacked mucilage clefts. Nostoc strands are located in the center of the thallus and develop behind the apical cell by separation of the middle lamella between apical derivatives. Strands elongate and branch in synchrony with apical growth, and thus only a single invasion is required for strand production. Two distinct ultrastructural morphotypes in the collections suggest nonspecificity of Nostoc. We speculate that Nostoc enters the thallus in the sporeling stage through mucilage clefts, and once colonies are established, cleft production ceases.

  16. Induction and repair of double- and single-strand DNA breaks in bacteriophage lambda superinfecting Escherichia coli

    International Nuclear Information System (INIS)

    Boye, E.; Krisch, R.E.

    1980-01-01

    Induction and repair of double-and single-strand DNA breaks have been measured after decays of 125 I and 3 H incorporated into the DNA and after external irradiation with 4 MeV electrons. For the decay experiments, cells of wild type Escherichia coli K-12 were superinfected with bacteriophage lambda DNA labelled with 5'-( 125 I)iodo-2'-deoxyuridine or with (methyl- 3 H)thymidine and frozen in liquid nitrogen. Aliquots were thawed at intervals and lysed at neutral pH, and the phage DNA was assayed for double- and single-strand breakage by neutral sucrose gradient centrifugation. The gradients used allowed measurements of both kinds of breaks in the same gradient. Decays of 125 I induced 0.39 single-strand breaks per double-strand break. No repair of either break type could be detected. Each 3 H disintegration caused 0.20 single-strand breaks and very few double-strand breaks. The single-strand breaks were rapidly rejoined after the cells were thawed. For irradiation with 4 MeV electrons, cells of wild type E. coli K-12 were superinfected with phage lambda and suspended in growth medium. Irradiation induced 42 single-strand breaks per double-strand break. The rates of break induction were 6.75 x 10 -14 (double-strand breaks) and 2.82 x 10 -12 (single-strand breaks) per rad and per dalton. The single-strand breaks were rapidly repaired upon incubation whereas the double-strand breaks seemed to remain unrepaired. It is concluded that double-strand breaks in superinfecting bacteriophage lambda DNA are repaired to a very small extent, if at all. (Author)

  17. The helicase DinG responds to stress due to DNA double strand breaks.

    Directory of Open Access Journals (Sweden)

    Stephan A Frye

    Full Text Available Neisseria meningitidis (Nm is a Gram-negative nasopharyngeal commensal that can cause septicaemia and meningitis. The neisserial DNA damage-inducible protein DinG is a helicase related to the mammalian helicases XPD and FANCJ. These helicases belong to superfamily 2, are ATP dependent and exert 5' → 3' directionality. To better understand the role of DinG in neisserial genome maintenance, the Nm DinG (DinGNm enzymatic activities were assessed in vitro and phenotypical characterization of a dinG null mutant (NmΔdinG was performed. Like its homologues, DinGNm possesses 5' → 3' directionality and prefers DNA substrates containing a 5'-overhang. ATPase activity of DinGNm is strictly DNA-dependent and DNA unwinding activity requires nucleoside triphosphate and divalent metal cations. DinGNm directly binds SSBNm with a Kd of 313 nM. Genotoxic stress analysis demonstrated that NmΔdinG was more sensitive to double-strand DNA breaks (DSB induced by mitomycin C (MMC than the Nm wildtype, defining the role of neisserial DinG in DSB repair. Notably, when NmΔdinG cells grown under MMC stress assessed by quantitative mass spectrometry, 134 proteins were shown to be differentially abundant (DA compared to unstressed NmΔdinG cells. Among the DNA replication, repair and recombination proteins affected, polymerase III subunits and recombinational repair proteins RuvA, RuvB, RecB and RecD were significantly down regulated while TopA and SSB were upregulated under stress condition. Most of the other DA proteins detected are involved in metabolic functions. The present study shows that the helicase DinG is probably involved in regulating metabolic pathways as well as in genome maintenance.

  18. Alternaria inhibits double-stranded RNA-induced cytokine production through Toll-like receptor 3.

    Science.gov (United States)

    Wada, Kota; Kobayashi, Takao; Matsuwaki, Yoshinori; Moriyama, Hiroshi; Kita, Hirohito

    2013-01-01

    Fungi may be involved in asthma and chronic rhinosinusitis (CRS). Peripheral blood mononuclear cells from CRS patients produce interleukin (IL)-5, IL-13 and interferon (IFN)-γ in the presence of Alternaria. In addition, Alternaria produces potent Th2-like adjuvant effects in the airway. Therefore, we hypothesized that Alternaria may inhibit Th1-type defense mechanisms against virus infection. Dendritic cells (DCs) were generated from mouse bone marrow. The functional responses were assessed by expression of cell surface molecules by FACS (MHC class II, CD40, CD80, CD86 and OX40L). Production of IL-6, chemokine CXCL10 (IP-10), chemokine CXCL11 (I-TAC) and IFN-β was measured by ELISA. Toll-like receptor 3 (TLR3) mRNA and protein expression was detected by quantitative real-time PCR and Western blot. Alternaria and polyinosinic-polycytidylic acid (poly I:C) enhanced cell surface expression of MHC class II, CD40, CD80, CD86 and OX40L, and IL-6 production in a concentration-dependent manner. However, Alternaria significantly inhibited production of IP-10, I-TAC and IFN-β, induced by viral double-stranded RNA (dsRNA) mimic poly I:C. TLR3 mRNA expression and protein production by poly I:C were significantly inhibited by Alternaria. These reactions are likely caused by heat-stable factor(s) in Alternaria extract with >100 kDa molecular mass. These findings suggest that the fungus Alternaria may inhibit production of IFN-β and other cytokines by DCs by suppressing TLR3 expression. These results indicate that Alternaria may inhibit host innate immunity against virus infection. Copyright © 2013 S. Karger AG, Basel.

  19. Alternaria Inhibits Double-stranded RNA-Induced Cytokines Productions through TLR3

    Science.gov (United States)

    Wada, Kota; Kobayashi, Takao; Matsuwaki, Yoshinori; Moriyama, Hiroshi; Kita, Hirohito

    2014-01-01

    Background Fungi may be involved in asthma and chronic rhinosinusitis (CRS). PBMCs from CRS patients produce IL-5, IL-13 and INF-γ by Alternaria. In addition, Alternaria produces potent Th2-like adjuvant effects in the airway. Therefore, we hypothesized that Alternaria may inhibit Th1-type defense mechanisms against virus infection. Methods Dendritic cells (DCs) were generated from mouse bone marrow. The functional responses were assessed by expression of cell surface molecules by FACS (MHC Class II, CD40, CD80, CD86 and OX40L. Production of IL-6, IP-10, I-TAC and IFN -β were measured by ELISA. TLR3 mRNA and protein expression were detected by quantitative Real time-PCR and Western blot. Results Alternaria and poly I:C enhanced cell surface expression of MHC Class II, CD40, CD80, CD86 and OX40L, and IL-6 production in a concentration-dependent manner. However, Alternaria significantly inhibited IP-10, I-TAC and IFN-β production induced by viral double-stranded RNA (dsRNA)-mimic poly I:C. TLR3 mRNA expression and protein production by poly I:C were significantly inhibited by Alternaria. These reactions are likely caused by heat-stable factor(s) in Alternaria extract with >100 kDa molecular mass. Conclusion These findings suggest that fungus, Alternaria may inhibit production of IFN-β and other cytokines by DCs by suppressing TLR3 expression. These results indicate that Alternaria may inhibit host innate immunity against virus infection. PMID:23711857

  20. Mass hysteria

    CERN Document Server

    Hellemans, Alexander

    2004-01-01

    Considerable research is being undertaken to identify the Higgs particle that is believed to give things their mass. According to the standard model, what we call mass is really an indication of how strongly particles interact with an invisible syrupy substance called the Higgs field. Quantum mechanics say that the mass-giving field can also be thought of as a sea of electrically neutral Higgs particles that should be dislodged in collisions between subatomic particles with high enough energies. Particle physicists expect the Higgs to exist only for a fleeting moment before decaying into other particles, which are caught in a detector. (Edited abstract).

  1. Self-consistent modeling of entangled network strands and linear dangling structures in a single-strand mean-field slip-link model

    DEFF Research Database (Denmark)

    Jensen, Mette Krog; Khaliullin, Renat; Schieber, Jay D.

    2012-01-01

    knowledge about the effect of dangling ends and soluble structures. To interpret our recent experimental results, we exploit a molecular model that can predict LVE data and non-linear stress–strain data. The slip-link model has proven to be a robust tool for both LVE and non-linear stress–strain predictions...... strands in the ensemble are attached to the network in both ends. Next we add dangling strands to the network representing the stoichiometric imbalance, or imperfections during curing. By considering monodisperse network strands without dangling ends, we find that the relative low-frequency plateau, G0/GN......0G0G0N, decreases linearly with the average number of entanglements. The decrease from GN0G0N to G 0 is a result of monomer fluctuations between entanglements, which is similar to “longitudinal modes” in tube theory. It is found that the slope of G′ is dependent on the fraction of network strands...

  2. Complex shapes self–assembled from single–stranded DNA tiles

    Science.gov (United States)

    Wei, Bryan; Dai, Mingjie; Yin, Peng

    2014-01-01

    Programmed self-assembly of strands of nucleic acid has proved highly effective for creating a wide range of structures with desired shapes1–25. A particularly successful implementation is DNA origami, in which a long scaffold strand is folded by hundreds of short auxiliary strands into a complex shape9, 14–16,18–21,25. Modular strategies are in principle simpler and more versatile and have been used to assemble DNA2–5,8,10–13,17,23 or RNA7,22 tiles into periodic3,4,7,22 and algorithmic5 two-dimensional lattices, extended ribbons10,12 and tubes4,12,13, three-dimensional crystals17, polyhedra11 and simple finite two-dimensional shapes7,8. But creating finite yet complex shapes from a large number of uniquely addressable tiles remains challenging. Here we solve this problem with the simplest tile form, a ‘single-stranded tile’ (SST) that consists of a 42-base strand of DNA composed entirely of concatenated sticky ends and that binds to four local neighbours during self-assembly12. Although ribbons and tubes with controlled circumferences12 have been created using the SST approach, we extend it to assemble complex two-dimensional shapes and tubes from hundreds (in some cases more than one thousand) distinct tiles. Our main design feature is a self-assembled rectangle that serves as a molecular canvas, with each of its constituent SST strands—folded into a 3nm-by-7 nm tile and attached to four neighbouring tiles—acting as a pixel. A desired shape, drawn on the canvas, is then produced by one-pot annealing of all those strands that correspond to pixels covered by the target shape; the remaining strands are excluded. We implement the strategy with a master strand collection that corresponds to a 310-pixel canvas, and then use appropriate strand subsets to construct 107 distinct and complex two-dimensional shapes, thereby establishing SST assembly as a simple, modular and robust framework for constructing nanostructures with prescribed shapes from short

  3. Abdominal mass

    Science.gov (United States)

    ... such as CBC and blood chemistry Colonoscopy EGD Isotope study Sigmoidoscopy Alternative Names Mass in the abdomen ... WA. Also reviewed by David Zieve, MD, MHA, Medical Director, Brenda Conaway, Editorial Director, and the A. ...

  4. Scrotal masses

    Science.gov (United States)

    ... in your scrotum. Any new growth in the testicle or scrotum needs to be checked by your provider to determine if it may be testicular cancer. Prevention You can prevent scrotal masses caused by sexually ...

  5. Strand-specific PCR of UV radiation-damaged genomic DNA revealed an essential role of DNA-PKcs in the transcription-coupled repair

    Directory of Open Access Journals (Sweden)

    Wang Yu

    2011-01-01

    , indicating that DNA-PKcs may also be involved in the TCR pathway of DNA damage repair. By means of immunoprecipitation and MALDI-TOF-Mass spectrometric analysis, we have revealed the interaction of DNA-PKcs and cyclin T2, which is a subunit of the human transcription elongation factor (P-TEFb. While the P-TEFb complex can phosphorylate the serine 2 of the carboxyl-terminal domain (CTD of RNA polymerase II and promote transcription elongation. Conclusion A new method of TCR assay was developed based the strand-specific-PCR (SS-PCR. Our data suggest that DNA-PKcs plays a role in the TCR pathway of UV-damaged DNA. One possible mechanistic hypothesis is that DNA-PKcs may function through associating with CyclinT2/CDK9 (P-TEFb to modulate the activity of RNA Pol II, which has already been identified as a key molecule recognizing and initializing TCR.

  6. Tensile and thickness swelling properties of strands from Southern hardwoods and Southern pine : effect of hot-pressing and resin application

    Science.gov (United States)

    Zhiyong Cai; Qinglin Wu; Guangping Han; Jong N. Lee

    2007-01-01

    Tensile and the moisture-induced thickness swelling properties of wood strands are among the most fundamental parameters in modeling and predicting engineering constants of strand-based composites such as oriented strandboard (OSB). The effects of hot-pressing and resin-curing on individual strand properties were investigated in this study. Strands from four Louisiana-...

  7. Continuous Measurement Of Mass Density Of Yarn

    Science.gov (United States)

    Hinkley, Jeffrey A.; Marchello, Joseph M.; Johnston, John D.

    1993-01-01

    Prototype instrument provides measurement data from which one computes mass density of strand of yarn. Includes fixtures placing known length of yarn under known tension across fixed and movable support. Transverse vibrations induced in yarn by moving movable support up and down. Source of light illuminates photodetector at midlength of yarn, and photodetector senses repeated shadowing caused by vibration of yarn through light, thereby measuring vibrations. Also used for continuous real-time monitoring of such yarn-manufacturing processes as coating or impregnation.

  8. Stranded cost recovery: Reregulating the electricity markets in the United States

    Science.gov (United States)

    Wagle, Pushkar Ghanashyam

    2000-10-01

    For the past few years, Stranded Cost recovery has been one of the most contentious issues regarding the restructuring of electricity markets among the regulators, researchers, and the other interested parties. Among the states that have moved towards retail competition, some have already made decisions regarding the levels of the stranded cost recovery. So the question is: how have these states handled the "stranded cost problem"? Following the introduction and the historical perspective of the industry in the first chapter, the second chapter takes a broad view for understanding the overall process of deregulation. It attempts to analyze why some states have made a rapid transition to competition in the electric utility industry, while other states are just beginning to consider the issue. White (1996) and Ando & Palmer (1998) have conducted a similar exercise. We present a more comprehensive and theoretically informed econometric analysis that sheds light over some of the crucial issues involved in restructuring, such as, stranded cost recovery, regulation of transmission and distribution sectors, and establishment of Independent System Operator, etc. This chapter offers the rationale for alternative econometric techniques, and extends the political economy analysis to incorporate actual timings of retail competition. Once we have identified the role of stranded cost in restructuring and the theoretical foundations, we study empirically the political economy of states' decisions to grant stranded cost recovery. This constitutes the third chapter. Here, we concentrate on California and Pennsylvania, two states that are at the frontiers of deregulation, and compare their respective treatments of the stranded cost. We probe the reasons behind Pennsylvania's lead over California on the path towards deregulation.

  9. Slow conduction in mixed cultured strands of primary ventricular cells and stem cell-derived cardiomyocytes

    Directory of Open Access Journals (Sweden)

    Jan Pavel Kucera

    2015-09-01

    Full Text Available Modern concepts for the treatment of myocardial diseases focus on novel cell therapeutic strategies involving stem cell-derived cardiomyocytes (SCMs. However, functional integration of SCMs requires similar electrophysiological properties as primary cardiomyocytes (PCMs and the ability to establish intercellular connections with host myocytes in order to contribute to the electrical and mechanical activity of the heart. The aim of this project was to investigate the properties of cardiac conduction in a co-culture approach using SCMs and PCMs in cultured cell strands. Murine embryonic SCMs were pooled with fetal ventricular cells and seeded in predefined proportions on microelectrode arrays to form patterned strands of mixed cells. Conduction velocity (CV was measured during steady state pacing. SCM excitability was estimated from action potentials measured in single cells using the patch clamp technique. Experiments were complemented with computer simulations of conduction using a detailed model of cellular architecture in mixed cell strands.CV was significantly lower in strands composed purely of SCMs (5.5±1.5 cm/s, n=11 as compared to PCMs (34.9±2.9 cm/s, n=21 at similar refractoriness (100% SCMs: 122±25 ms, n=9; 100% PCMs: 139±67 ms, n=14. In mixed strands combining both cell types, CV was higher than in pure SCMs strands, but always lower than in 100% PCM strands. Computer simulations demonstrated that both intercellular coupling and electrical excitability limit CV.These data provide evidence that in cultures of murine ventricular cardiomyocytes, SCMs cannot restore CV to control levels resulting in slow conduction, which may lead to reentry circuits and arrhythmias.

  10. Genetic Kinship Analyses Reveal That Gray's Beaked Whales Strand in Unrelated Groups.

    Science.gov (United States)

    Patel, Selina; Thompson, Kirsten F; Santure, Anna W; Constantine, Rochelle; Millar, Craig D

    2017-06-01

    Some marine mammals are so rarely seen that their life history and social structure remain a mystery. Around New Zealand, Gray's beaked whales (Mesoplodon grayi) are almost never seen alive, yet they are a commonly stranded species. Gray's are unique among the beaked whales in that they frequently strand in groups, providing an opportunity to investigate their social organization. We examined group composition and genetic kinship in 113 Gray's beaked whales with samples collected over a 20-year period. Fifty-six individuals stranded in 19 groups (2 or more individuals), and 57 whales stranded individually. Mitochondrial control region haplotypes and microsatellite genotypes (16 loci) were obtained for 103 whales. We estimated pairwise relatedness between all pairs of individuals and average relatedness within, and between, groups. We identified 6 mother-calf pairs and 2 half-siblings, including 2 whales in different strandings 17 years and 1500 km apart. Surprisingly, none of the adults stranding together were related suggesting that groups are not formed through the retention of kin. These data suggest that both sexes may disperse from their mothers, and groups consisting of unrelated subadults are common. We also found no instances of paternity within the groups. Our results provide the first insights into dispersal, social organization, and the mating system in this rarely sighted species. Why whales strand is still unknown but, in Gray's beaked whales, the dead can tell us much about the living. © The American Genetic Association 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  11. Characterization of exceptionally thermostable single-stranded DNA-binding proteins from Thermotoga maritima and Thermotoga neapolitana.

    Science.gov (United States)

    Olszewski, Marcin; Grot, Anna; Wojciechowski, Marek; Nowak, Marta; Mickiewicz, Małgorzata; Kur, Józef

    2010-10-15

    In recent years, there has been an increasing interest in SSBs because they find numerous applications in diverse molecular biology and analytical methods. We report the characterization of single-stranded DNA binding proteins (SSBs) from the thermophilic bacteria Thermotoga maritima (TmaSSB) and Thermotoga neapolitana (TneSSB). They are the smallest known bacterial SSB proteins, consisting of 141 and 142 amino acid residues with a calculated molecular mass of 16.30 and 16.58 kDa, respectively. The similarity between amino acid sequences of these proteins is very high: 90% identity and 95% similarity. Surprisingly, both TmaSSB and TneSSB possess a quite low sequence similarity to Escherichia coli SSB (36 and 35% identity, 55 and 56% similarity, respectively). They are functional as homotetramers containing one single-stranded DNA binding domain (OB-fold) in each monomer. Agarose mobility assays indicated that the ssDNA-binding site for both proteins is salt independent, and fluorescence spectroscopy resulted in a size of 68 ± 2 nucleotides. The half-lives of TmaSSB and TneSSB were 10 h and 12 h at 100°C, respectively. When analysed by differential scanning microcalorimetry (DSC) the melting temperature (Tm) was 109.3°C and 112.5°C for TmaSSB and TneSSB, respectively. The results showed that TmaSSB and TneSSB are the most thermostable SSB proteins identified to date, offering an attractive alternative to TaqSSB and TthSSB in molecular biology applications, especially with using high temperature e. g. polymerase chain reaction (PCR).

  12. Characterization of exceptionally thermostable single-stranded DNA-binding proteins from Thermotoga maritima and Thermotoga neapolitana

    Directory of Open Access Journals (Sweden)

    Mickiewicz Małgorzata

    2010-10-01

    Full Text Available Abstract Background In recent years, there has been an increasing interest in SSBs because they find numerous applications in diverse molecular biology and analytical methods. Results We report the characterization of single-stranded DNA binding proteins (SSBs from the thermophilic bacteria Thermotoga maritima (TmaSSB and Thermotoga neapolitana (TneSSB. They are the smallest known bacterial SSB proteins, consisting of 141 and 142 amino acid residues with a calculated molecular mass of 16.30 and 16.58 kDa, respectively. The similarity between amino acid sequences of these proteins is very high: 90% identity and 95% similarity. Surprisingly, both TmaSSB and TneSSB possess a quite low sequence similarity to Escherichia coli SSB (36 and 35% identity, 55 and 56% similarity, respectively. They are functional as homotetramers containing one single-stranded DNA binding domain (OB-fold in each monomer. Agarose mobility assays indicated that the ssDNA-binding site for both proteins is salt independent, and fluorescence spectroscopy resulted in a size of 68 ± 2 nucleotides. The half-lives of TmaSSB and TneSSB were 10 h and 12 h at 100°C, respectively. When analysed by differential scanning microcalorimetry (DSC the melting temperature (Tm was 109.3°C and 112.5°C for TmaSSB and TneSSB, respectively. Conclusion The results showed that TmaSSB and TneSSB are the most thermostable SSB proteins identified to date, offering an attractive alternative to TaqSSB and TthSSB in molecular biology applications, especially with using high temperature e. g. polymerase chain reaction (PCR.

  13. Survey on the presence of non-dioxine-like PCBs (NDL-PCBs) in loggerhead turtles (Caretta caretta) stranded in south Mediterranean coasts (Sicily, Southern Italy).

    Science.gov (United States)

    Cammilleri, Gaetano; Calvaruso, Enza; Pantano, Licia; Cascio, Giovanni Lo; Randisi, Barbara; Macaluso, Andrea; Vazzana, Mirella; Caracappa, Giulia; Giangrosso, Giuseppe; Vella, Antonio; Ferrantelli, Vincenzo

    2017-11-01

    A total of 71 loggerhead turtles (Caretta caretta) stranded along the coasts of Sicily (Southern Italy) were examined for non-dioxine like polychlorinated biphenyl (NDL-PCB) levels in muscle and adipose tissue by a gas chromatography-mass spectrometry/mass spectrometry (GC-MS/MS) method. The results revealed 6 high-indicator congener (∑ 6 PCB IND ) levels in 45% of the loggerhead turtles examined, with mean values of 980.39 ± 2508.39 ng/g wet weight in adipose tissue and 102.53 ± 238.58 ng/g wet weight in muscle tissue. The hexachloro and heptachloro PCB congeners were the most abundant in both the sample types. The highest NDL-PCB levels were reached in an adipose tissue sample of a loggerhead turtle of 80 kg stranded along the coasts of Termini Imerese (14 183.85 ng/g wet wt). No significant correlation was found between modified Fulton's K values of the loggerhead turtles and PCB contents (S = 47 151, p > 0.05). Furthermore, no significant differences were found between sexes (W = 365, p >  0.05). The PCB levels found in the present study were much higher than those found in the literature. The present study is the first report on the existence of NDL-PCBs in loggerhead turtles stranded in Sicilian coasts confirming C. caretta as a valuable indicator of contaminant exposure in the marine environment because of their specific biological and ecological characteristics. Environ Toxicol Chem 2017;36:2997-3002. © 2017 SETAC. © 2017 SETAC.

  14. Site-specific binding of viral plus single-stranded RNA to replicase-containing open virus-like particles of yeast.

    OpenAIRE

    Esteban, R; Fujimura, T; Wickner, R B

    1988-01-01

    X double-stranded RNA is a deletion mutant of L-A double-stranded RNA and is encapsidated in viral particles by the L-A-encoded major coat protein. X double-stranded RNA has all the cis sites necessary to be transcribed, encapsidated, and replicated. We have cloned X double-stranded RNA and sequenced it. The complete X double-stranded RNA sequence deduced indicates that the first 25 bases of the X plus-strand 5' end originated from the 5' end of the L-A plus strand and that most, if not all, ...

  15. Double-Stranded RNA Is Detected by Immunofluorescence Analysis in RNA and DNA Virus Infections, Including Those by Negative-Stranded RNA Viruses.

    Science.gov (United States)

    Son, Kyung-No; Liang, Zhiguo; Lipton, Howard L

    2015-09-01

    Early biochemical studies of viral replication suggested that most viruses produce double-stranded RNA (dsRNA), which is essential for the induction of the host immune response. However, it was reported in 2006 that dsRNA could be detected by immunofluorescence antibody staining in double-stranded DNA and positive-strand RNA virus infections but not in negative-strand RNA virus infections. Other reports in the literature seemed to support these observations. This suggested that negative-strand RNA viruses produce little, if any, dsRNA or that more efficient viral countermeasures to mask dsRNA are mounted. Because of our interest in the use of dsRNA antibodies for virus discovery, particularly in pathological specimens, we wanted to determine how universal immunostaining for dsRNA might be in animal virus infections. We have detected the in situ formation of dsRNA in cells infected with vesicular stomatitis virus, measles virus, influenza A virus, and Nyamanini virus, which represent viruses from different negative-strand RNA virus families. dsRNA was also detected in cells infected with lymphocytic choriomeningitis virus, an ambisense RNA virus, and minute virus of mice (MVM), a single-stranded DNA (ssDNA) parvovirus, but not hepatitis B virus. Although dsRNA staining was primarily observed in the cytoplasm, it was also seen in the nucleus of cells infected with influenza A virus, Nyamanini virus, and MVM. Thus, it is likely that most animal virus infections produce dsRNA species that can be detected by immunofluorescence staining. The apoptosis induced in several uninfected cell lines failed to upregulate dsRNA formation. An effective antiviral host immune response depends on recognition of viral invasion and an intact innate immune system as a first line of defense. Double-stranded RNA (dsRNA) is a viral product essential for the induction of innate immunity, leading to the production of type I interferons (IFNs) and the activation of hundreds of IFN

  16. Characterization of a mitochondrially targeted single-stranded DNA-binding protein in Arabidopsis thaliana.

    Science.gov (United States)

    Edmondson, Andrew C; Song, Daqing; Alvarez, Luis A; Wall, Melisa K; Almond, David; McClellan, David A; Maxwell, Anthony; Nielsen, Brent L

    2005-04-01

    A gene encoding a predicted mitochondrially targeted single-stranded DNA binding protein (mtSSB) was identified in the Arabidopsis thaliana genome sequence. This gene (At4g11060) codes for a protein of 201 amino acids, including a 28-residue putative mitochondrial targeting transit peptide. Protein sequence alignment shows high similarity between the mtSSB protein and single-stranded DNA binding proteins (SSB) from bacteria, including residues conserved for SSB function. Phylogenetic analysis indicates a close relationship between this protein and other mitochondrially targeted SSB proteins. The predicted targeting sequence was fused with the GFP coding region, and the organellar localization of the expressed fusion protein was determined. Specific targeting to mitochondria was observed in in-vitro import experiments and by transient expression of a GFP fusion construct in Arabidopsis leaves after microprojectile bombardment. The mature mtSSB coding region was overexpressed in Escherichia coli and the protein was purified for biochemical characterization. The purified protein binds single-stranded, but not double-stranded, DNA. MtSSB stimulates the homologous strand-exchange activity of E. coli RecA. These results indicate that mtSSB is a functional homologue of the E. coli SSB, and that it may play a role in mitochondrial DNA recombination.

  17. POT1-independent single-strand telomeric DNA binding activities in Brassicaceae.

    Science.gov (United States)

    Shakirov, Eugene V; McKnight, Thomas D; Shippen, Dorothy E

    2009-06-01

    Telomeres define the ends of linear eukaryotic chromosomes and are required for genome maintenance and continued cell proliferation. The extreme ends of telomeres terminate in a single-strand protrusion, termed the G-overhang, which, in vertebrates and fission yeast, is bound by evolutionarily conserved members of the POT1 (protection of telomeres) protein family. Unlike most other model organisms, the flowering plant Arabidopsis thaliana encodes two divergent POT1-like proteins. Here we show that the single-strand telomeric DNA binding activity present in A. thaliana nuclear extracts is not dependent on POT1a or POT1b proteins. Furthermore, in contrast to POT1 proteins from yeast and vertebrates, recombinant POT1a and POT1b proteins from A. thaliana, and from two additional Brassicaceae species, Arabidopsis lyrata and Brassica oleracea (cauliflower), fail to bind single-strand telomeric DNA in vitro under the conditions tested. Finally, although we detected four single-strand telomeric DNA binding activities in nuclear extracts from B. oleracea, partial purification and DNA cross-linking analysis of these complexes identified proteins that are smaller than the predicted sizes of BoPOT1a or BoPOT1b. Taken together, these data suggest that POT1 proteins are not the major single-strand telomeric DNA binding activities in A. thaliana and its close relatives, underscoring the remarkable functional divergence of POT1 proteins from plants and other eukaryotes.

  18. Design and Analysis of Compact DNA Strand Displacement Circuits for Analog Computation Using Autocatalytic Amplifiers.

    Science.gov (United States)

    Song, Tianqi; Garg, Sudhanshu; Mokhtar, Reem; Bui, Hieu; Reif, John

    2018-01-19

    A main goal in DNA computing is to build DNA circuits to compute designated functions using a minimal number of DNA strands. Here, we propose a novel architecture to build compact DNA strand displacement circuits to compute a broad scope of functions in an analog fashion. A circuit by this architecture is composed of three autocatalytic amplifiers, and the amplifiers interact to perform computation. We show DNA circuits to compute functions sqrt(x), ln(x) and exp(x) for x in tunable ranges with simulation results. A key innovation in our architecture, inspired by Napier's use of logarithm transforms to compute square roots on a slide rule, is to make use of autocatalytic amplifiers to do logarithmic and exponential transforms in concentration and time. In particular, we convert from the input that is encoded by the initial concentration of the input DNA strand, to time, and then back again to the output encoded by the concentration of the output DNA strand at equilibrium. This combined use of strand-concentration and time encoding of computational values may have impact on other forms of molecular computation.

  19. Self-Field Effects in Magneto-Thermal Instabilities for Nb-Sn Strands

    CERN Document Server

    Bordini, B; Fehér, S; Rossi, L; Zlobin, A V

    2008-01-01

    Recent advancements in the critical current density (Jc) of Nb3Sn conductors, coupled with a large effective filament size, have drawn attention to the problem of magnetothermal instabilities. At low magnetic fields, the quench current of such high Jc Nb3Sn strands is significantly lower than their critical current because of the above-mentioned instabilities. An adiabatic model to calculate the minimum current at which a strand can quench due to magneto-thermal instabilities is developed. The model is based on an 'integral' approach already used elsewhere [1]. The main difference with respect to the previous model is the addition of the self-field effect that allows to describe premature quenches of non-magnetized Nb3Sn strands and to better calculate the quench current of strongly magnetized strands. The model is in good agreement with experimental results at 4.2 K obtained at Fermilab using virgin Modified Jelly Roll (MJR) strands with a low Residual Resistivity Ratio (RRR) of the stabilizing copper. The p...

  20. Self-assembly of complex two-dimensional shapes from single-stranded DNA tiles.

    Science.gov (United States)

    Wei, Bryan; Vhudzijena, Michelle K; Robaszewski, Joanna; Yin, Peng

    2015-05-08

    Current methods in DNA nano-architecture have successfully engineered a variety of 2D and 3D structures using principles of self-assembly. In this article, we describe detailed protocols on how to fabricate sophisticated 2D shapes through the self-assembly of uniquely addressable single-stranded DNA tiles which act as molecular pixels on a molecular canvas. Each single-stranded tile (SST) is a 42-nucleotide DNA strand composed of four concatenated modular domains which bind to four neighbors during self-assembly. The molecular canvas is a rectangle structure self-assembled from SSTs. A prescribed complex 2D shape is formed by selecting the constituent molecular pixels (SSTs) from a 310-pixel molecular canvas and then subjecting the corresponding strands to one-pot annealing. Due to the modular nature of the SST approach we demonstrate the scalability, versatility and robustness of this method. Compared with alternative methods, the SST method enables a wider selection of information polymers and sequences through the use of de novo designed and synthesized short DNA strands.

  1. Understanding the similarity in thermophoresis between single- and double-stranded DNA or RNA

    Science.gov (United States)

    Reichl, Maren; Herzog, Mario; Greiss, Ferdinand; Wolff, Manuel; Braun, Dieter

    2015-06-01

    Thermophoresis is the movement of molecules in a temperature gradient. For aqueous solutions its microscopic basis is debated. Understanding thermophoresis for this case is, however, important since it proved very useful to detect the binding affinity of biomolecules and since thermophoresis could have played an important role in early molecular evolution. Here we discuss why the thermophoresis of single- and double-stranded oligonucleotides - DNA and RNA - is surprisingly similar. This finding is understood by comparing the spherical capacitor model for single-stranded species with the case of a rod-shaped model for double-stranded oligonucleotides. The approach describes thermophoresis of DNA and RNA with fitted effective charges consistent with electrophoresis measurements and explains the similarity between single- and double-stranded species. We could not confirm the sign change for the thermophoresis of single- versus double-stranded DNA in crowded solutions containing polyethylene glycol [Y. T. Maeda, T. Tlusty, and A. Libchaber, Proc. Natl. Acad. Sci. USA 109, 17972 (2012), 10.1073/pnas.1215764109], but find a salt-independent offset while the Debye length dependence still satisfies the capacitor model. Overall, the analysis documents the continuous progress in the microscopic understanding of thermophoresis.

  2. Increased and imbalanced dNTP pools symmetrically promote both leading and lagging strand replication infidelity.

    Science.gov (United States)

    Buckland, Robert J; Watt, Danielle L; Chittoor, Balasubramanyam; Nilsson, Anna Karin; Kunkel, Thomas A; Chabes, Andrei

    2014-12-01

    The fidelity of DNA replication requires an appropriate balance of dNTPs, yet the nascent leading and lagging strands of the nuclear genome are primarily synthesized by replicases that differ in subunit composition, protein partnerships and biochemical properties, including fidelity. These facts pose the question of whether imbalanced dNTP pools differentially influence leading and lagging strand replication fidelity. Here we test this possibility by examining strand-specific replication infidelity driven by a mutation in yeast ribonucleotide reductase, rnr1-Y285A, that leads to elevated dTTP and dCTP concentrations. The results for the CAN1 mutational reporter gene present in opposite orientations in the genome reveal that the rates, and surprisingly even the sequence contexts, of replication errors are remarkably similar for leading and lagging strand synthesis. Moreover, while many mismatches driven by the dNTP pool imbalance are efficiently corrected by mismatch repair, others are repaired less efficiently, especially those in sequence contexts suggesting reduced proofreading due to increased mismatch extension driven by the high dTTP and dCTP concentrations. Thus the two DNA strands of the nuclear genome are at similar risk of mutations resulting from this dNTP pool imbalance, and this risk is not completely suppressed even when both major replication error correction mechanisms are genetically intact.

  3. Increased and imbalanced dNTP pools symmetrically promote both leading and lagging strand replication infidelity.

    Directory of Open Access Journals (Sweden)

    Robert J Buckland

    2014-12-01

    Full Text Available The fidelity of DNA replication requires an appropriate balance of dNTPs, yet the nascent leading and lagging strands of the nuclear genome are primarily synthesized by replicases that differ in subunit composition, protein partnerships and biochemical properties, including fidelity. These facts pose the question of whether imbalanced dNTP pools differentially influence leading and lagging strand replication fidelity. Here we test this possibility by examining strand-specific replication infidelity driven by a mutation in yeast ribonucleotide reductase, rnr1-Y285A, that leads to elevated dTTP and dCTP concentrations. The results for the CAN1 mutational reporter gene present in opposite orientations in the genome reveal that the rates, and surprisingly even the sequence contexts, of replication errors are remarkably similar for leading and lagging strand synthesis. Moreover, while many mismatches driven by the dNTP pool imbalance are efficiently corrected by mismatch repair, others are repaired less efficiently, especially those in sequence contexts suggesting reduced proofreading due to increased mismatch extension driven by the high dTTP and dCTP concentrations. Thus the two DNA strands of the nuclear genome are at similar risk of mutations resulting from this dNTP pool imbalance, and this risk is not completely suppressed even when both major replication error correction mechanisms are genetically intact.

  4. Methods for the preparation of large quantities of complex single-stranded oligonucleotide libraries.

    Science.gov (United States)

    Murgha, Yusuf E; Rouillard, Jean-Marie; Gulari, Erdogan

    2014-01-01

    Custom-defined oligonucleotide collections have a broad range of applications in fields of synthetic biology, targeted sequencing, and cytogenetics. Also, they are used to encode information for technologies like RNA interference, protein engineering and DNA-encoded libraries. High-throughput parallel DNA synthesis technologies developed for the manufacture of DNA microarrays can produce libraries of large numbers of different oligonucleotides, but in very limited amounts. Here, we compare three approaches to prepare large quantities of single-stranded oligonucleotide libraries derived from microarray synthesized collections. The first approach, alkaline melting of double-stranded PCR amplified libraries with a biotinylated strand captured on streptavidin coated magnetic beads results in little or no non-biotinylated ssDNA. The second method wherein the phosphorylated strand of PCR amplified libraries is nucleolyticaly hydrolyzed is recommended when small amounts of libraries are needed. The third method combining in vitro transcription of PCR amplified libraries to reverse transcription of the RNA product into single-stranded cDNA is our recommended method to produce large amounts of oligonucleotide libraries. Finally, we propose a method to remove any primer binding sequences introduced during library amplification.

  5. Stretching and controlled motion of single-stranded DNA in locally heated solid-state nanopores.

    Science.gov (United States)

    Belkin, Maxim; Maffeo, Christopher; Wells, David B; Aksimentiev, Aleksei

    2013-08-27

    Practical applications of solid-state nanopores for DNA detection and sequencing require the electrophoretic motion of DNA through the nanopores to be precisely controlled. Controlling the motion of single-stranded DNA presents a particular challenge, in part because of the multitude of conformations that a DNA strand can adopt in a nanopore. Through continuum, coarse-grained and atomistic modeling, we demonstrate that local heating of the nanopore volume can be used to alter the electrophoretic mobility and conformation of single-stranded DNA. In the nanopore systems considered, the temperature near the nanopore is modulated via a nanometer-size heater element that can be radiatively switched on and off. The local enhancement of temperature produces considerable stretching of the DNA fragment confined within the nanopore. Such stretching is reversible, so that the conformation of DNA can be toggled between compact (local heating is off) and extended (local heating is on) states. The effective thermophoretic force acting on single-stranded DNA in the vicinity of the nanopore is found to be sufficiently large (4-8 pN) to affect such changes in the DNA conformation. The local heating of the nanopore volume is observed to promote single-file translocation of DNA strands at transmembrane biases as low as 10 mV, which opens new avenues for using solid-state nanopores for detection and sequencing of DNA.

  6. Chirality induction and protonation-induced molecular motions in helical molecular strands.

    Science.gov (United States)

    Kolomiets, Elena; Berl, Volker; Lehn, Jean-Marie

    2007-01-01

    The long oligopyridinedicarboxamide strand 9, containing 15 heterocyclic rings has been synthesized and its helical structure determined by X-ray crystallography. It was shown that the shorter analogue 6 displays induced circular dichroism and amplification of induced chirality upon dissolution in an optically active solvent, diethyl-L-tartrate. A novel class of helical foldamers was prepared, strands 14-16, based on two oligopyridine carboxamide segments linked through a L-tartaric acid derived spacer. These tartro strands display internal chirality induction as well as chirality amplification. NMR spectroscopy (on 8 and 9) and circular dichroism (on 16) studies show that the oligopyridine carboxamide strands undergo reversible unfolding/folding upon protonation. The protonation-induced unfolding has been confirmed by X-ray crystallographic determination of the molecular structure of the extended protonated heptameric form 8(+). The molecular-scale mechano-chemical motions of the protonation-induced structural switching consist of a change of the length of the molecule, from 6 angstroms (6, coiled form) to 29 angstroms (8(+), uncoiled form) for the heptamer and from 12.5 angstroms (9, coiled form, X-ray structure) to 57 angstroms (9(+), uncoiled form, from modeling) for the pentadecamer. Similar unfolding/folding motional processes take place in the L-tartro strands 15 and 16 upon protonation/deprotonation, with loss of helicity-induced circular dichroism on unfolding as shown for the protonated form 16(+).

  7. A METHOD TO PREDICT EDGE STRANDS IN BETA-SHEETS FROM PROTEIN SEQUENCES

    Directory of Open Access Journals (Sweden)

    Antonin Guilloux

    2013-05-01

    Full Text Available There is a need for rules allowing three-dimensional structure information to be derived from protein sequences. In this work, consideration of an elementary protein folding step allows protein sub-sequences which optimize folding to be derived for any given protein sequence. Classical mechanics applied to this system and the energy conservation law during the elementary folding step yields an equation whose solutions are taken over the field of rational numbers. This formalism is applied to beta-sheets containing two edge strands and at least two central strands. The number of protein sub-sequences optimized for folding per amino acid in beta-strands is shown in particular to predict edge strands from protein sequences. Topological information on beta-strands and loops connecting them is derived for protein sequences with a prediction accuracy of 75%. The statistical significance of the finding is given. Applications in protein structure prediction are envisioned such as for the quality assessment of protein structure models.

  8. A method to predict edge strands in beta-sheets from protein sequences

    Directory of Open Access Journals (Sweden)

    Antonin Guilloux

    2013-05-01

    Full Text Available There is a need for rules allowing three-dimensional structure information to be derived from protein sequences. In this work, consideration of an elementary protein folding step allows protein sub-sequences which optimize folding to be derived for any given protein sequence. Classical mechanics applied to this system and the energy conservation law during the elementary folding step yields an equation whose solutions are taken over the field of rational numbers. This formalism is applied to beta-sheets containing two edge strands and at least two central strands. The number of protein sub-sequences optimized for folding per amino acid in beta-strands is shown in particular to predict edge strands from protein sequences. Topological information on beta-strands and loops connecting them is derived for protein sequences with a prediction accuracy of 75%. The statistical significance of the finding is given. Applications in protein structure prediction are envisioned such as for the quality assessment of protein structure models.

  9. Offset configurations for single- and double-strand DNA inside single-walled carbon nanotubes.

    Science.gov (United States)

    Alshehri, Mansoor H; Cox, Barry J; Hill, James M

    2014-01-01

    Nanotechnology is a rapidly expanding research area, and it is believed that the unique properties of molecules at the nano-scale will prove to be of substantial benefit to mankind, especially so in medicine and electronics. Here we use applied mathematical modelling exploiting the basic principles of mechanics and the 6-12 Lennard-Jones potential function together with the continuum approximation, which assumes that intermolecular interactions can be approximated by average atomic surface densities. We consider the equilibrium offset positions for both single-strand and double-strand DNA molecules inside a single-walled carbon nanotube, and we predict offset positions with reference to the cross-section of the carbon nanotube. For the double-strand DNA, the potential energy is determined for the general case for any helical phase angle ϕ, but we also consider a special case when ϕ = π, which leads to a substantial simplification in the analytical expression for the energy. As might be expected, our results confirm that the global minimum energy positions for a single-strand DNA molecule and a double-strand DNA molecule will lie off axis and they become closer to the tube wall as the radius of the tube increases.

  10. TALEN-Induced Double-Strand Break Repair of CTG Trinucleotide Repeats.

    Science.gov (United States)

    Mosbach, Valentine; Poggi, Lucie; Viterbo, David; Charpentier, Marine; Richard, Guy-Franck

    2018-02-20

    Trinucleotide repeat expansions involving CTG/CAG triplets are responsible for several neurodegenerative disorders, including myotonic dystrophy and Huntington's disease. Because expansions trigger the disease, contracting repeat length could be a possible approach to gene therapy for these disorders. Here, we show that a TALEN-induced double-strand break was very efficient at contracting expanded CTG repeats in yeast. We show that RAD51, POL32, and DNL4 are dispensable for double-strand break repair within CTG repeats, the only required genes being RAD50, SAE2, and RAD52. Resection was totally abolished in the absence of RAD50 on both sides of the break, whereas it was reduced in a sae2Δ mutant on the side of the break containing the longest repeat tract, suggesting that secondary structures at double-strand break ends must be removed by the Mre11-Rad50 complex and Sae2. Following the TALEN double-strand break, single-strand annealing occurred between both sides of the repeat tract, leading to repeat contraction. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

  11. First-strand cDNA synthesis primed with oligo(dT)

    International Nuclear Information System (INIS)

    Krug, M.S.; Berger, S.L.

    1987-01-01

    The quality of a cDNA library depends on the integrity of the messenger RNA and the fidelity with which it can be reverse transcribed. RNA cannot be cloned directly; in a reaction catalyzed by reverse transcriptase, the RNA, together with a suitable primer and a supply of deoxyribonucleoside triphosphates (dNTPs), must be converted to a double-stranded molecule. The product contains a complementary strand (first, antisense, or minus-strand cDNA) that is hybridized to what remains of the original RNA template. Such DNA-RNA hybrids can be cloned albeit often with lower efficiency than their double-stranded DNA counterparts. Usually the hybrid molecules are treated as intermediates in a scheme aimed at replacing the fragmented RNA with continuous DNA to form a double-stranded cDNA molecule. From this brief summary of cDNA cloning, it should be obvious that, regardless of the strategy, reverse transcriptase does and how it does it in vitro is discussed

  12. Time-dependent evolution of strand transfer length in pretensioned prestressed concrete members

    Science.gov (United States)

    Caro, L. A.; Martí-Vargas, J. R.; Serna, P.

    2013-11-01

    For design purposes, it is generally considered that prestressing strand transfer length does not change with time. However, some experimental studies on the effect of time on transfer lengths show contradictory results. In this paper, an experimental research to study transfer length changes over time is presented. A test procedure based on the ECADA testing technique to measure prestressing strand force variation over time in pretensioned prestressed concrete specimens has been set up. With this test method, an experimental program that varies concrete strength, specimen cross section, age of release, prestress transfer method, and embedment length has been carried out. Both the initial and long-term transfer lengths of 13-mm prestressing steel strands have been measured. The test results show that transfer length variation exists for some prestressing load conditions, resulting in increased transfer length over time. The applied test method based on prestressing strand force measurements has shown more reliable results than procedures based on measuring free end slips and longitudinal strains of concrete. An additional factor for transfer length models is proposed in order to include the time-dependent evolution of strand transfer length in pretensioned prestressed concrete members.

  13. TALEN-Induced Double-Strand Break Repair of CTG Trinucleotide Repeats

    Directory of Open Access Journals (Sweden)

    Valentine Mosbach

    2018-02-01

    Full Text Available Trinucleotide repeat expansions involving CTG/CAG triplets are responsible for several neurodegenerative disorders, including myotonic dystrophy and Huntington’s disease. Because expansions trigger the disease, contracting repeat length could be a possible approach to gene therapy for these disorders. Here, we show that a TALEN-induced double-strand break was very efficient at contracting expanded CTG repeats in yeast. We show that RAD51, POL32, and DNL4 are dispensable for double-strand break repair within CTG repeats, the only required genes being RAD50, SAE2, and RAD52. Resection was totally abolished in the absence of RAD50 on both sides of the break, whereas it was reduced in a sae2Δ mutant on the side of the break containing the longest repeat tract, suggesting that secondary structures at double-strand break ends must be removed by the Mre11-Rad50 complex and Sae2. Following the TALEN double-strand break, single-strand annealing occurred between both sides of the repeat tract, leading to repeat contraction.

  14. Stable loop in the crystal structure of the intercalated four-stranded cytosine-rich metazoan telomere

    Science.gov (United States)

    Kang, C.; Berger, I.; Lockshin, C.; Ratliff, R.; Moyzis, R.; Rich, A.

    1995-01-01

    In most metazoans, the telomeric cytosine-rich strand repeating sequence is d(TAACCC). The crystal structure of this sequence was solved to 1.9-A resolution. Four strands associate via the cytosine-containing parts to form a four-stranded intercalated structure held together by C.C+ hydrogen bonds. The base-paired strands are parallel to each other, and the two duplexes are intercalated into each other in opposite orientations. One TAA end forms a highly stabilized loop with the 5' thymine Hoogsteen-base-paired to the third adenine. The 5' end of this loop is in close proximity to the 3' end of one of the other intercalated cytosine strands. Instead of being entirely in a DNA duplex, this structure suggests the possibility of an alternative conformation for the cytosine-rich telomere strands.

  15. Influence of strand surface condition on interstrand contact resistance and coupling loss in NbTi-wound Rutherford cables

    CERN Document Server

    Sumption, M D; Scanlan, R M; Nijhuis, A; ten Kate, H H J; Kim, S W; Wake, M; Shintomi, T

    1999-01-01

    Presented in this work are the results of directly measured and AC- loss-derived interstrand contact resistance (ICR) measurements performed magnetically or resistively on bare-Cu and coated-strand pairs, calorimetrically on $9 11-strand Rutherford cables wound with strands that had been coated with various metallic and insulating layers, and calorimetrically and magnetically on 28-strand Rutherford cables (LHC-type) wound with bare-Cu-, Ni-, and $9 stabrite-plated strands. Comparisons are made of the effects of various conditions of heat treatment, HT (time and temperature), and pressure (applied during HT and then either maintained or re-applied during measurement). The $9 resulting ICRs are compared and interpreted in terms of the oxide layer on the strand coating and its response to curing conditions. (66 refs).

  16. Postreplicational formation and repair of DNA double-strand breaks in UV-irradiated Escherichia coli uvrB cells

    International Nuclear Information System (INIS)

    Wang, Tzuchien V.; Smith, K.C.

    1986-01-01

    The number of DNA double-strand breaks formed in UV-irradiated uvrB recF recB cells correlates with the number of unrepaired DNA daughter-strand gaps, and is dependent on DNA synthesis after UV-irradiation. These results are consistent with the model that the DNA double-strand breaks that are produced in UV-irradiated excision-deficient cells occur as the result of breaks in the parental DNA opposite unrepaired DNA daughter-strand gaps. By employing a temperature-sensitive recA200 mutation, we have devised an improved assay for studying the formation and repair of these DNA double-strand breaks. Possible mechanisms for the postreplication repair of DNA double-strand breaks are discussed. (Auth.)

  17. Mass metrology

    CERN Document Server

    Gupta, S V

    2012-01-01

    This book presents the practical aspects of mass measurements. Concepts of gravitational, inertial and conventional mass and details of the variation of acceleration of gravity are described. The Metric Convention and International Prototype Kilogram and BIPM standards are described. The effect of change of gravity on the indication of electronic balances is derived with respect of latitude, altitude and earth topography. The classification of weights by OIML is discussed. Maximum permissible errors in different categories of weights prescribed by national and international organizations are p

  18. Estimation of Prestress Force Distribution in Multi-Strand System of Prestressed Concrete Structures Using Field Data Measured by Electromagnetic Sensor.

    Science.gov (United States)

    Cho, Keunhee; Cho, Jeong-Rae; Kim, Sung Tae; Park, Sung Yong; Kim, Young-Jin; Park, Young-Hwan

    2016-08-18

    The recently developed smart strand can be used to measure the prestress force in the prestressed concrete (PSC) structure from the construction stage to the in-service stage. The higher cost of the smart strand compared to the conventional strand renders it unaffordable to replace all the strands by smart strands, and results in the application of only a limited number of smart strands in the PSC structure. However, the prestress forces developed in the strands of the multi-strand system frequently adopted in PSC structures differ from each other, which means that the prestress force in the multi-strand system cannot be obtained by simple proportional scaling using the measurement of the smart strand. Therefore, this study examines the prestress force distribution in the multi-strand system to find the correlation between the prestress force measured by the smart strand and the prestress force distribution in the multi-strand system. To that goal, the prestress force distribution was measured using electromagnetic sensors for various factors of the multi-strand system adopted on site in the fabrication of actual PSC girders. The results verified the possibility to assume normal distribution for the prestress force distribution per anchor head, and a method computing the mean and standard deviation defining the normal distribution is proposed. This paper presents a meaningful finding by proposing an estimation method of the prestress force based upon field-measured data of the prestress force distribution in the multi-strand system of actual PSC structures.

  19. Stellar Masses

    Indian Academy of Sciences (India)

    later stages of evolution into a red giant differs considerably. It may lead to the formation of a white dwarf via a planetary nebula phase (for stars like the Sun) or the formation of a neutron star via a supernova explosion (for massive stars). The exact course is decided by the mass again. The energy produced is proportional to ...

  20. Mass spectrometry

    DEFF Research Database (Denmark)

    Nyvang Hartmeyer, Gitte; Jensen, Anne Kvistholm; Böcher, Sidsel

    2010-01-01

    Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is currently being introduced for the rapid and accurate identification of bacteria. We describe 2 MALDI-TOF MS identification cases - 1 directly on spinal fluid and 1 on grown bacteria. Rapidly obtained...

  1. Plant viruses of the Amalgaviridae family evolved via recombination between viruses with double-stranded and negative-strand RNA genomes.

    Science.gov (United States)

    Krupovic, Mart; Dolja, Valerian V; Koonin, Eugene V

    2015-03-29

    Plant viruses of the recently recognized family Amalgaviridae have monopartite double-stranded (ds) RNA genomes and encode two proteins: an RNA-dependent RNA polymerase (RdRp) and a putative capsid protein (CP). Whereas the RdRp of amalgaviruses has been found to be most closely related to the RdRps of dsRNA viruses of the family Partitiviridae, the provenance of their CP remained obscure. Here we show that the CP of amalgaviruses is homologous to the nucleocapsid proteins of negative-strand RNA viruses of the genera Phlebovirus (Bunyaviridae) and Tenuivirus. The chimeric genomes of amalgaviruses are a testament to the effectively limitless gene exchange between viruses that shaped the evolution of the virosphere.

  2. Xeroderma pigmentosum complementation group C cells remove pyrimidine dimers selectively from the transcribed strand of active genes

    International Nuclear Information System (INIS)

    Venema, J.; van Hoffen, A.; Karcagi, V.; Natarajan, A.T.; van Zeeland, A.A.; Mullenders, L.H.

    1991-01-01

    The authors have measured the removal of UV-induced pyrimidine dimers from DNA fragments of the adenosine deaminase (ADA) and dihydrofolate reductase (DHFR) genes in primary normal human and xeroderma pigmentosum complementation group C (XP-C) cells. Using strand-specific probes, we show that in normal cells, preferential repair of the 5' part of the ADA gene is due to the rapid and efficient repair of the transcribed strand. Within 8 h after irradiation with UV at 10 J m-2, 70% of the pyrimidine dimers in this strand are removed. The nontranscribed strand is repaired at a much slower rate, with 30% dimers removed after 8 h. Repair of the transcribed strand in XP-C cells occurs at a rate indistinguishable from that in normal cells, but the nontranscribed strand is not repaired significantly in these cells. Similar results were obtained for the DHFR gene. In the 3' part of the ADA gene, however, both normal and XP-C cells perform fast and efficient repair of either strand, which is likely to be caused by the presence of transcription units on both strands. The factor defective in XP-C cells is apparently involved in the processing of DNA damage in inactive parts of the genome, including nontranscribed strands of active genes. These findings have important implications for the understanding of the mechanism of UV-induced excision repair and mutagenesis in mammalian cells

  3. Developing single-molecule TPM experiments for direct observation of successful RecA-mediated strand exchange reaction.

    Science.gov (United States)

    Fan, Hsiu-Fang; Cox, Michael M; Li, Hung-Wen

    2011-01-01

    RecA recombinases play a central role in homologous recombination. Once assembled on single-stranded (ss) DNA, RecA nucleoprotein filaments mediate the pairing of homologous DNA sequences and strand exchange processes. We have designed two experiments based on tethered particle motion (TPM) to investigate the fates of the invading and the outgoing strands during E. coli RecA-mediated pairing and strand exchange at the single-molecule level in the absence of force. TPM experiments measure the tethered bead Brownian motion indicative of the DNA tether length change resulting from RecA binding and dissociation. Experiments with beads labeled on either the invading strand or the outgoing strand showed that DNA pairing and strand exchange occurs successfully in the presence of either ATP or its non-hydrolyzable analog, ATPγS. The strand exchange rates and efficiencies are similar under both ATP and ATPγS conditions. In addition, the Brownian motion time-courses suggest that the strand exchange process progresses uni-directionally in the 5'-to-3' fashion, using a synapse segment with a wide and continuous size distribution.

  4. Repair of ultraviolet light damage in Saccharomyces cerevisiae as studied with double- and single-stranded incoming DNAs

    International Nuclear Information System (INIS)

    Keszenman-Pereyra, D.; Hieda, K.

    1992-01-01

    Purified double- and single-stranded DNAs of the autonomously replicating vector M13RK9-T were irradiated with ultraviolet light (UV) in vitro and introduced into competent whole cells of Saccharomyces cerevisiae. Incoming double-stranded DNA was more sensitive to UV in excision repair-deficient rad2-1 cells than in proficient repair RAD + cells, while single-stranded DNA exhibited high sensitivity in both host cells. The results indicate that in yeast there is no effective rescue of UV-incoming single-stranded DNA by excision repair or other constitutive dark repair processes

  5. A specific subdomain in φ29 DNA polymerase confers both processivity and strand-displacement capacity

    Science.gov (United States)

    Rodríguez, Irene; Lázaro, José M.; Blanco, Luis; Kamtekar, Satwik; Berman, Andrea J.; Wang, Jimin; Steitz, Thomas A.; Salas, Margarita; de Vega, Miguel

    2005-01-01

    Recent crystallographic studies of φ29 DNA polymerase have provided structural insights into its strand displacement and processivity. A specific insertion named terminal protein region 2 (TPR2), present only in protein-primed DNA polymerases, together with the exonuclease, thumb, and palm subdomains, forms two tori capable of interacting with DNA. To analyze the functional role of this insertion, we constructed a φ29 DNA polymerase deletion mutant lacking TPR2 amino acid residues Asp-398 to Glu-420. Biochemical analysis of the mutant DNA polymerase indicates that its DNA-binding capacity is diminished, drastically decreasing its processivity. In addition, removal of the TPR2 insertion abolishes the intrinsic capacity of φ29 DNA polymerase to perform strand displacement coupled to DNA synthesis. Therefore, the biochemical results described here directly demonstrate that TPR2 plays a critical role in strand displacement and processivity. PMID:15845765

  6. Formal Analysis of Fairness in E-Payment Protocol Based on Strand Space

    Science.gov (United States)

    Wang, Hong; Ma, Jianping; Chen, Bo

    Fairness as one of most important properties in E-payment protocol, it is important to verify it through informal and formal analysis approach. In this paper, we present the procedure to analyze iKP protocol in terms of strand space model, which consists of three key steps: First, we use strand space terminology to create the bundle of iKP protocol. Second, we enumerate all possible traces of each participant's strand in the run process of iKP. Third, according to the definition of fairness, determine whether iKP satisfy fairness. Then, we present the algorithm to verify fairness of E-payment protocol in pseudo code and use this algorithm to analyze ISI protocol successfully. This algorithm allows us to automatically verify fairness of E-payment protocol.

  7. Repair of X-ray-induced single-strand breaks by a cell-free system

    International Nuclear Information System (INIS)

    Seki, Shuji; Ikeda, Shogo; Tsutui, Ken; Teraoka, Hirobumi

    1990-01-01

    Repair of X-ray-induced single-strand breaks of DNA was studied in vitro using an exonuclease purified from mouse ascites sarcoma (SR-C3H/He) cells. X-ray-dose-dependent unscheduled DNA synthesis was primed by the exonuclease. Repair of X-ray-induced single-strand breaks in pUC19 plasmid DNA was demonstrated by agarose gel electrophoresis after incubating the damaged DNA with the exonuclease, DNA polymerase (Klenow fragment of DNA polymerase I or DNA polymerase β purified from SR-C3H/He cells), four deoxynucleoside triphosphates, ATP and DNA ligase (T4 DNA ligase or DNA ligase I purified from calf thymus). The present results suggested that the exonuclease is involved in the initiation of repair of X-ray-induced single-strand breaks in removing 3' ends of X-ray-damaged DNA. (author)

  8. DNA-imprinted polymer nanoparticles with monodispersity and prescribed DNA-strand patterns

    Science.gov (United States)

    Trinh, Tuan; Liao, Chenyi; Toader, Violeta; Barłóg, Maciej; Bazzi, Hassan S.; Li, Jianing; Sleiman, Hanadi F.

    2018-02-01

    As colloidal self-assembly increasingly approaches the complexity of natural systems, an ongoing challenge is to generate non-centrosymmetric structures. For example, patchy, Janus or living crystallization particles have significantly advanced the area of polymer assembly. It has remained difficult, however, to devise polymer particles that associate in a directional manner, with controlled valency and recognition motifs. Here, we present a method to transfer DNA patterns from a DNA cage to a polymeric nanoparticle encapsulated inside the cage in three dimensions. The resulting DNA-imprinted particles (DIPs), which are 'moulded' on the inside of the DNA cage, consist of a monodisperse crosslinked polymer core with a predetermined pattern of different DNA strands covalently 'printed' on their exterior, and further assemble with programmability and directionality. The number, orientation and sequence of DNA strands grafted onto the polymeric core can be controlled during the process, and the strands are addressable independently of each other.

  9. Alkaline gel electrophoresis assay to detect DNA strand breaks and repair mechanisms in Escherichia coli

    International Nuclear Information System (INIS)

    Mattos, Jose Carlos Pelielo de; Motta, Ellen Serri da; Oliveira, Marcia Betania Nunes de; Dantas, Flavio Jose da Silva; Araujo, Adriano Caldeira de

    2008-01-01

    Reactive oxygen species (ROS) can induce lesions in different cellular targets, including DNA. Stannous chloride (SnCl 2 ) is a ROS generator, leading to lethality in Escherichia coli (E. coli), with the base excision repair (BER) mechanism playing a role in this process. Many techniques have been developed to detect genotoxicity, as comet assay, in eukaryotic cells, and plasmid DNA agarose gel electrophoresis. In this study, an adaptation of the alkaline gel electrophoresis method was carried out to ascertain the induction of strand breaks by SnCl 2 in bacterial DNA, from E. coli BER mutants, and its repair pathway. Results obtained show that SnCl 2 was able to induce DNA strand breaks in all strains tested. Moreover, endonuclease IV and exonuclease III play a role in DNA repair. On the whole, data has shown that the alkaline gel electrophoresis assay could be used both for studying DNA strand breaks induction and for associated repair mechanisms. (author)

  10. Three methods to determine the yields of DNA double-strand breaks

    International Nuclear Information System (INIS)

    Erzgraeber, G.; Lapidus, I.L.

    1985-01-01

    A possibility of determining the yield of DNA double-strand breaks in cells of the Chinese hamster (V79-4) by finding the amount of DNA released as a result of breaks and by determining the relative sedimentation velocity of DNA-membrane complexes affected by ionizing radiations with different physical characteristics is discussed. Results of the analysis are compared with the data obtained by a traditional method of sedimentation in the neutral sucrose density gradient. Comparative characterization of the methods is discussed. The yields of DNA double-strand breaks determined by the suggested independent methods are in good agreement, which opens possibilities of studying induction and repair of double-strand breaks by means of simpler and more reliable methods

  11. Cell cycle-regulated centers of DNA double-strand break repair

    DEFF Research Database (Denmark)

    Lisby, Michael; Antúnez de Mayolo, Adriana; Mortensen, Uffe H

    2003-01-01

    In eukaryotes, homologous recombination is an important pathway for the repair of DNA double-strand breaks. We have studied this process in living cells in the yeast Saccharomyces cerevisiae using Rad52 as a cell biological marker. In response to DNA damage, Rad52 redistributes itself and forms...... foci specifically during S phase. We have shown previously that Rad52 foci are centers of DNA repair where multiple DNA double-strand breaks colocalize. Here we report a correlation between the timing of Rad52 focus formation and modification of the Rad52 protein. In addition, we show that the two ends...... of a double-strand break are held tightly together in the majority of cells. Interestingly, in a small but significant fraction of the S phase cells, the two ends of a break separate suggesting that mechanisms exist to reassociate and align these ends for proper DNA repair....

  12. Translocation of double-stranded DNA through membrane-adapted phi29 motor protein nanopores

    Science.gov (United States)

    Wendell, David; Jing, Peng; Geng, Jia; Subramaniam, Varuni; Lee, Tae Jin; Montemagno, Carlo; Guo, Peixuan

    2009-11-01

    Biological pores have been used to study the transport of DNA and other molecules, but most pores have channels that allow only the movement of small molecules and single-stranded DNA and RNA. The bacteriophage phi29 DNA-packaging motor, which allows double-stranded DNA to enter the virus during maturation and exit during an infection, contains a connector protein with a channel that is between 3.6 and 6 nm wide. Here we show that a modified version of this connector protein, when reconstituted into liposomes and inserted into planar lipid bilayers, allows the translocation of double-stranded DNA. The measured conductance of a single connector channel was 4.8 nS in 1 M KCl. This engineered and membrane-adapted phage connector is expected to have applications in microelectromechanical sensing, microreactors, gene delivery, drug loading and DNA sequencing.

  13. Theoretical investigation of the production of strand breaks in DNA by water radicals

    International Nuclear Information System (INIS)

    Chatterjee, A.; Magee, J.L.

    1985-01-01

    A calculation has been made of the indirect action of radiation on SV40 DNA in dilute aqueous solution, including the extent of OH reaction with both the sugar moiety and the bases. A realistic DNA model is used along with a track model that gives the correct decay rates of hydrated electrons and OH radicals in pure water with the same calculational techniques. It was found, in agreement with experiment, that 80% of the OH attack on DNA is on the bases and 20% is on the sugar. It is estimated that the probability is almost non-existent ( -6 ) for two OH radicals from the same track or from two tracks to reach sugars on opposite strands within 12 base pairs from each other. Thus double strand breaks that depend linearly on the dose (as we find in a companion experimental programme) must arise from some other mechanism. The calculated single strand break probabilities are in good agreement with experiment. (author)

  14. Correlation of superconductor strand, cable, and dipole critical currents in CBA magnets

    International Nuclear Information System (INIS)

    Tannenbaum, M.J.; Garber, M.; Sampson, W.B.

    1982-01-01

    A calibration between vendor critical current data for 0.0268'' diameter superconductor strand supplied to Fermilab, and the BNL 10 -12 Ωcm critical current specification is presented. Vendor critical current data for over 400 Fermilab type billets are shown, both as supplied by the vendor and converted to BNL units. Predictions of cable critical current are made using the sum of the critical currents of the 23 strands, where all strands from the same half billet are assigned the same critical current. The measured critical current shows excellent correlation to the predicted value and is approximately 14 +- 2 percent below it. Colliding Beam Accelerator (CBA) full length dipoles reach the conductor critical current limit, essentially without training. Magnet performance is predictable from the measured critical current of a short sample of cable to within 2%

  15. Simulating mechanisms for dispersal, production and stranding of small forage fish in temporary wetland habitats

    Science.gov (United States)

    Yurek, Simeon; DeAngelis, Donald L.; Trexler, Joel C.; Jopp, Fred; Donalson, Douglas D.

    2013-01-01

    Movement strategies of small forage fish (wetland habitats affect their overall population growth and biomass concentrations, i.e., availability to predators. These fish are often the key energy link between primary producers and top predators, such as wading birds, which require high concentrations of stranded fish in accessible depths. Expansion and contraction of seasonal wetlands induce a sequential alternation between rapid biomass growth and concentration, creating the conditions for local stranding of small fish as they move in response to varying water levels. To better understand how landscape topography, hydrology, and fish behavior interact to create high densities of stranded fish, we first simulated population dynamics of small fish, within a dynamic food web, with different traits for movement strategy and growth rate, across an artificial, spatially explicit, heterogeneous, two-dimensional marsh slough landscape, using hydrologic variability as the driver for movement. Model output showed that fish with the highest tendency to invade newly flooded marsh areas built up the largest populations over long time periods with stable hydrologic patterns. A higher probability to become stranded had negative effects on long-term population size, and offset the contribution of that species to stranded biomass. The model was next applied to the topography of a 10 km × 10 km area of Everglades landscape. The details of the topography were highly important in channeling fish movements and creating spatiotemporal patterns of fish movement and stranding. This output provides data that can be compared in the future with observed locations of fish biomass concentrations, or such surrogates as phosphorus ‘hotspots’ in the marsh.

  16. Holocene geologic slip rate for the Banning strand of the southern San Andreas Fault, southern California

    Science.gov (United States)

    Gold, Peter O.; Behr, Whitney M.; Rood, Dylan; Sharp, Warren D.; Rockwell, Thomas K.; Kendrick, Katherine; Salin, Aaron

    2015-08-01

    Northwest directed slip from the southern San Andreas Fault is transferred to the Mission Creek, Banning, and Garnet Hill fault strands in the northwestern Coachella Valley. How slip is partitioned between these three faults is critical to southern California seismic hazard estimates but is poorly understood. In this paper, we report the first slip rate measured for the Banning fault strand. We constrain the depositional age of an alluvial fan offset 25 ± 5 m from its source by the Banning strand to between 5.1 ± 0.4 ka (95% confidence interval (CI)) and 6.4 + 3.7/-2.1 ka (95% CI) using U-series dating of pedogenic carbonate clast coatings and 10Be cosmogenic nuclide exposure dating of surface clasts. We calculate a Holocene geologic slip rate for the Banning strand of 3.9 + 2.3/-1.6 mm/yr (median, 95% CI) to 4.9 + 1.0/-0.9 mm/yr (median, 95% CI). This rate represents only 25-35% of the total slip accommodated by this section of the southern San Andreas Fault, suggesting a model in which slip is less concentrated on the Banning strand than previously thought. In rejecting the possibility that the Banning strand is the dominant structure, our results highlight an even greater need for slip rate and paleoseismic measurements along faults in the northwestern Coachella Valley in order to test the validity of current earthquake hazard models. In addition, our comparison of ages measured with U-series and 10Be exposure dating demonstrates the importance of using multiple geochronometers when estimating the depositional age of alluvial landforms.

  17. Reconstitution of DNA strand exchange mediated by Rhp51 recombinase and two mediators.

    Directory of Open Access Journals (Sweden)

    Yumiko Kurokawa

    2008-04-01

    Full Text Available In the fission yeast Schizosaccharomyces pombe, genetic evidence suggests that two mediators, Rad22 (the S. pombe Rad52 homolog and the Swi5-Sfr1 complex, participate in a common pathway of Rhp51 (the S. pombe Rad51 homolog-mediated homologous recombination (HR and HR repair. Here, we have demonstrated an in vitro reconstitution of the central step of DNA strand exchange during HR. Our system consists entirely of homogeneously purified proteins, including Rhp51, the two mediators, and replication protein A (RPA, which reflects genetic requirements in vivo. Using this system, we present the first robust biochemical evidence that concerted action of the two mediators directs the loading of Rhp51 onto single-stranded DNA (ssDNA precoated with RPA. Dissection of the reaction reveals that Rad22 overcomes the inhibitory effect of RPA on Rhp51-Swi5-Sfr1-mediated strand exchange. In addition, Rad22 negates the requirement for a strict order of protein addition to the in vitro system. However, despite the presence of Rad22, Swi5-Sfr1 is still essential for strand exchange. Importantly, Rhp51, but neither Rad22 nor the Swi5-Sfr1 mediator, is the factor that displaces RPA from ssDNA. Swi5-Sfr1 stabilizes Rhp51-ssDNA filaments in an ATP-dependent manner, and this stabilization is correlated with activation of Rhp51 for the strand exchange reaction. Rad22 alone cannot activate the Rhp51 presynaptic filament. AMP-PNP, a nonhydrolyzable ATP analog, induces a similar stabilization of Rhp51, but this stabilization is independent of Swi5-Sfr1. However, hydrolysis of ATP is required for processive strand transfer, which results in the formation of a long heteroduplex. Our in vitro reconstitution system has revealed that the two mediators have indispensable, but distinct, roles for mediating Rhp51 loading onto RPA-precoated ssDNA.

  18. Holocene geologic slip rate for the Banning strand of the southern San Andreas Fault, southern California

    Science.gov (United States)

    Gold, Peter O.; Behr, Whitney M.; Rood, Dylan; Sharp, Warren D.; Rockwell, Thomas; Kendrick, Katherine J.; Salin, Aaron

    2015-01-01

    Northwest directed slip from the southern San Andreas Fault is transferred to the Mission Creek, Banning, and Garnet Hill fault strands in the northwestern Coachella Valley. How slip is partitioned between these three faults is critical to southern California seismic hazard estimates but is poorly understood. In this paper, we report the first slip rate measured for the Banning fault strand. We constrain the depositional age of an alluvial fan offset 25 ± 5 m from its source by the Banning strand to between 5.1 ± 0.4 ka (95% confidence interval (CI)) and 6.4 + 3.7/−2.1 ka (95% CI) using U-series dating of pedogenic carbonate clast coatings and 10Be cosmogenic nuclide exposure dating of surface clasts. We calculate a Holocene geologic slip rate for the Banning strand of 3.9 + 2.3/−1.6 mm/yr (median, 95% CI) to 4.9 + 1.0/−0.9 mm/yr (median, 95% CI). This rate represents only 25–35% of the total slip accommodated by this section of the southern San Andreas Fault, suggesting a model in which slip is less concentrated on the Banning strand than previously thought. In rejecting the possibility that the Banning strand is the dominant structure, our results highlight an even greater need for slip rate and paleoseismic measurements along faults in the northwestern Coachella Valley in order to test the validity of current earthquake hazard models. In addition, our comparison of ages measured with U-series and 10Be exposure dating demonstrates the importance of using multiple geochronometers when estimating the depositional age of alluvial landforms.

  19. A potential new, stable state of the E-cadherin strand-swapped dimer in solution.

    Science.gov (United States)

    Schumann-Gillett, Alexandra; Mark, Alan E; Deplazes, Evelyne; O'Mara, Megan L

    2018-01-01

    E-cadherin is a transmembrane glycoprotein that facilitates inter-cellular adhesion in the epithelium. The ectodomain of the native structure is comprised of five repeated immunoglobulin-like domains. All E-cadherin crystal structures show the protein in one of three alternative conformations: a monomer, a strand-swapped trans homodimer and the so-called X-dimer, which is proposed to be a kinetic intermediate to forming the strand-swapped trans homodimer. However, previous studies have indicated that even once the trans strand-swapped dimer is formed, the complex is highly dynamic and the E-cadherin monomers may reorient relative to each other. Here, molecular dynamics simulations have been used to investigate the stability and conformational flexibility of the human E-cadherin trans strand-swapped dimer. In four independent, 100 ns simulations, the dimer moved away from the starting structure and converged to a previously unreported structure, which we call the Y-dimer. The Y-dimer was present for over 90% of the combined simulation time, suggesting that it represents a stable conformation of the E-cadherin dimer in solution. The Y-dimer conformation is stabilised by interactions present in both the trans strand-swapped dimer and X-dimer crystal structures, as well as additional interactions not found in any E-cadherin dimer crystal structures. The Y-dimer represents a previously unreported, stable conformation of the human E-cadherin trans strand-swapped dimer and suggests that the available crystal structures do not fully capture the conformations that the human E-cadherin trans homodimer adopts in solution.

  20. A single-strand specific lesion drives MMS-induced hyper-mutability at a double-strand break in yeast.

    Science.gov (United States)

    Yang, Yong; Gordenin, Dmitry A; Resnick, Michael A

    2010-08-05

    Localized hyper-mutability (LHM) can be important in evolution, immunity, and genetic diseases. We previously reported that single-strand DNA (ssDNA) can be an important source of damage-induced LHM in yeast. Here, we establish that the generation of LHM by methyl methanesulfonate (MMS) during repair of a chromosomal double-strand break (DSB) can result in over 0.2 mutations/kb, which is approximately 20,000-fold higher than the MMS-induced mutation density without a DSB. The MMS-induced mutations associated with DSB repair were primarily due to substitutions via translesion DNA synthesis at damaged cytosines, even though there are nearly 10 times more MMS-induced lesions at other bases. Based on this mutation bias, the promutagenic lesion dominating LHM is likely 3-methylcytosine, which is single-strand specific. Thus, the dramatic increase in mutagenesis at a DSB is concluded to result primarily from the generation of non-repairable lesions in ssDNA associated with DSB repair along with efficient induction of highly mutagenic ssDNA-specific lesions. These findings with MMS-induced LHM have broad biological implications for unrepaired damage generated in ssDNA and possibly ssRNA. Published by Elsevier B.V.

  1. Rapid Synthesis of a Long Double-Stranded Oligonucleotide from a Single-Stranded Nucleotide Using Magnetic Beads and an Oligo Library.

    Directory of Open Access Journals (Sweden)

    Sumate Pengpumkiat

    Full Text Available Chemical synthesis of oligonucleotides is a widely used tool in the field of biochemistry. Several methods for gene synthesis have been introduced in the growing area of genomics. In this paper, a novel method of constructing dsDNA is proposed. Short (28-mer oligo fragments from a library were assembled through successive annealing and ligation processes, followed by PCR. First, two oligo fragments annealed to form a dsDNA molecule. The double-stranded oligo was immobilized onto magnetic beads (solid support via streptavidin-biotin binding. Next, single-stranded oligo fragments were added successively through ligation to form the complete DNA molecule. The synthesized DNA was amplified through PCR and gel electrophoresis was used to characterize the product. Sanger sequencing showed that more than 97% of the nucleotides matched the expected sequence. Extending the length of the DNA molecule by adding single-stranded oligonucleotides from a basis set (library via ligation enables a more convenient and rapid mechanism for the design and synthesis of oligonucleotides on the go. Coupled with an automated dispensing system and libraries of short oligo fragments, this novel DNA synthesis method would offer an efficient and cost-effective method for producing dsDNA.

  2. Crystal structure of a four-stranded intercalated DNA: d(C4)

    Science.gov (United States)

    Chen, L.; Cai, L.; Zhang, X.; Rich, A.

    1994-01-01

    The crystal structure of d(C4) solved at 2.3-A resolution reveals a four-stranded molecule composed of two interdigitated or intercalated duplexes. The duplexes are held together by hemiprotonated cytosine-cytosine base pairs and are parallel stranded, but the two duplexes point in opposite directions. The molecule has a slow right-handed twist of 12.4 degrees between covalently linked cytosine base pairs, and the base stacking distance is 3.1 A. This is in general agreement with the NMR studies. A biological role for DNA in this conformation is suggested.

  3. Laboratory experiments on stranding of Anopheles larvae under different shoreline environmental conditions.

    Science.gov (United States)

    Endo, Noriko; Kiszewski, Anthony E; Eltahir, Elfatih A B

    2015-01-21

    One of the concerns for future malaria epidemiology is the elevated risks of malaria around an ever-increasing number of dam sites. Controlling larval populations around reservoirs behind dams by manipulating the water levels of reservoirs could be an effective and sustainable measure for suppressing malaria epidemics; however, the effectiveness of the water-level manipulation and the contributing mechanisms have been poorly studied. In this paper, we focus on how water recession may lead to larval stranding. Larvae of An. albimanus were studied to assess their susceptibility to stranding under different conditions representing reservoir shoreline environments in an experimental tank (50 cm × 100 cm). The tank was initially seeded with 80 larvae uniformly, and the numbers of larvae stranded on land and remaining in water were counted (summed up to recovered larvae), following the recession of water. The vertical water drawdown rate and the proportion of stranded larvae to recovered larvae (p) were measured. Shoreline conditions tested were inclinations of shore slopes (2% and 4%) and surface types (smooth, vegetated, rough, ridged). For the 2% slopes, the proportions of stranded larvae (p) increased by about 0.002, 0.004, and 0.010 as the water drawdown rate increased by a centimeter per day on the smooth, rough, and vegetated surfaces, respectively. p for the 4% slopes were smaller than for the 2% slopes. Unlike other surface conditions, no significant correlation between p and the drawdown rate was observed on the ridged surface. Larger proportions of Anopheles larvae were stranded at higher water drawdown rates, on smaller reservoir slopes, and under rough or vegetated surface conditions. Three mechanisms of larval stranding were identified: falling behind shoreline recession; entrapment in small closed water bodies; and inhabitation in shallow areas. Depending on the local vectors of Anopheles mosquitoes, the conditions for their favorable breeding sites

  4. Use of Cellular Decapping Activators by Positive-Strand RNA Viruses

    Directory of Open Access Journals (Sweden)

    Jennifer Jungfleisch

    2016-12-01

    Full Text Available Positive-strand RNA viruses have evolved multiple strategies to not only circumvent the hostile decay machinery but to trick it into being a priceless collaborator supporting viral RNA translation and replication. In this review, we describe the versatile interaction of positive-strand RNA viruses and the 5′-3′ mRNA decay machinery with a focus on the viral subversion of decapping activators. This highly conserved viral trickery is exemplified with the plant Brome mosaic virus, the animal Flock house virus and the human hepatitis C virus.

  5. Laser ablation MC-ICPMS to study longitudinal stable isotopic variations in single human hair strands

    International Nuclear Information System (INIS)

    Santamaria-Fernandez, R.; Hearn, R.; Giner Martinez-Sierra, J.

    2009-01-01

    Full text: There is a need for novel approaches to measure stable isotopic variations in human tissues to provide information regarding the geographical origin and lifestyle of individuals. In this work, a method for the measurement of longitudinal sulfur isotopic variations in single hair strands has been developed. The method validation, uncertainty evaluation, in-house characterization of a horse hair sample and the potential of the method as a forensic tool to obtain information from single hair strands will be discussed. In addition, a new method for carbon isotope ratio measurements by MC-ICPMS has been developed and results will be presented. (author)

  6. Acute hypoxia and hypoxic exercise induce DNA strand breaks and oxidative DNA damage in humans

    DEFF Research Database (Denmark)

    Møller, P; Loft, S; Lundby, C

    2001-01-01

    The present study investigated the effect of a single bout of exhaustive exercise on the generation of DNA strand breaks and oxidative DNA damage under normal conditions and at high-altitude hypoxia (4559 meters for 3 days). Twelve healthy subjects performed a maximal bicycle exercise test...... oxygen species, generated by leakage of the mitochondrial respiration or during a hypoxia-induced inflammation. Furthermore, the presence of DNA strand breaks may play an important role in maintaining hypoxia-induced inflammation processes. Hypoxia seems to deplete the antioxidant system of its capacity...

  7. Cell cycle-regulated centers of DNA double-strand break repair

    DEFF Research Database (Denmark)

    Lisby, Michael; Antúnez de Mayolo, Adriana; Mortensen, Uffe H

    2003-01-01

    In eukaryotes, homologous recombination is an important pathway for the repair of DNA double-strand breaks. We have studied this process in living cells in the yeast Saccharomyces cerevisiae using Rad52 as a cell biological marker. In response to DNA damage, Rad52 redistributes itself and forms...... of a double-strand break are held tightly together in the majority of cells. Interestingly, in a small but significant fraction of the S phase cells, the two ends of a break separate suggesting that mechanisms exist to reassociate and align these ends for proper DNA repair....

  8. Analysis of DNA strand break induction and repair in plants from the vicinity of Chernobyl

    International Nuclear Information System (INIS)

    Syomov, A.B.; Ptitsyna, S.N.; Sergeeva, S.A.

    1992-01-01

    For 3 years following the Chernobyl accident DNA repair efficiency was studied in irradiated and control populations of various plan species. Compared with the control populations, some irradiated populations exhibited increases in the yield of DNA single-strand breaks per unit dose of challenge radiation. The effect was registered in low-dose-rate alpha-irradiated populations, but was absent in plant populations growing in conditions of low-dose-rate beta-irradiation. The efficiency of single-strand DNA repair was identical in control and irradiated populations and approximated 100%. (author). 12 refs.; 1 fig.; 2 tabs

  9. Phylogenetic and functional analysis of the bacteriophage P1 single-stranded DNA-binding protein

    DEFF Research Database (Denmark)

    Bendtsen, Jannick Dyrløv; Nilsson, A.S.; Lehnherr, H.

    2002-01-01

    Bacteriophage P1 encodes a single-stranded DNA-binding protein (SSB-P1), which shows 66% amino acid sequence identity to the SSB protein of the host bacterium Escherichia coli. A phylogenetic analysis indicated that the P1 ssb gene coexists with its E. coli counterpart as an independent unit...

  10. Ion assisted structural collapse of a single stranded DNA: A molecular dynamics approach

    Energy Technology Data Exchange (ETDEWEB)

    Ghosh, Soumadwip; Dixit, Himanshu; Chakrabarti, Rajarshi, E-mail: rajarshi@chem.iitb.ac.in

    2015-09-28

    Highlights: • The dynamics of a single-stranded DNA in presence of different concentrations of Mg{sup 2+} is investigated. • The initial DNA chain collapse is characterized by the formation of non-sequentially stacked base pairs. • The DNA chain re-swells at high concentrations of Mg{sup 2+} as a consequence of overcharging. - Abstract: The structure and dynamics of negatively charged nucleic acids strongly correlate with the concentration and charge of the oppositely charged counterions. It is well known that the structural collapse of DNA is favoured in the presence of additional salt, a source of excess oppositely charged ions. Under such conditions single stranded DNA adopts a collapsed coil like conformation, typically characterized by stacking base pairs. Using atomistic molecular dynamics simulation, we demonstrate that in the presence of additional divalent salt (MgCl{sub 2}) single stranded DNA with base sequence 5′-CGCGAATTCGCG-3′ (Dickerson Drew dodecamer) initially collapses and then expands with increasing salt concentration. This is due to the overcharging induced DNA chain swelling, a dominant factor at a higher divalent salt concentration. In a nutshell, our simulations show how in the presence of divalent salt, non-sequential base stacking and overcharging competes and affect single stranded DNA dynamics unlike a monovalent salt.

  11. Dynamics of RecA filaments on single-stranded DNA

    NARCIS (Netherlands)

    Van Loenhout, M.T.J.; Van der Heijden, T.; Kanaar, R.; Wyman, C.; Dekker, C.

    2009-01-01

    RecA, the key protein in homologous recombination, performs its actions as a helical filament on single-stranded DNA (ssDNA). ATP hydrolysis makes the RecA–ssDNA filament dynamic and is essential for successful recombination. RecA has been studied extensively by single-molecule techniques on

  12. MDA5 Detects the Double-Stranded RNA Replicative Form in Picornavirus-Infected Cells

    Directory of Open Access Journals (Sweden)

    Qian Feng

    2012-11-01

    Full Text Available RIG-I and MDA5 are cytosolic RNA sensors that play a critical role in innate antiviral responses. Major advances have been made in identifying RIG-I ligands, but our knowledge of the ligands for MDA5 remains restricted to data from transfection experiments mostly using poly(I:C, a synthetic dsRNA mimic. Here, we dissected the IFN-α/β-stimulatory activity of different viral RNA species produced during picornavirus infection, both by RNA transfection and in infected cells in which specific steps of viral RNA replication were inhibited. Our results show that the incoming genomic plus-strand RNA does not activate MDA5, but minus-strand RNA synthesis and production of the 7.5 kbp replicative form trigger a strong IFN-α/β response. IFN-α/β production does not rely on plus-strand RNA synthesis and thus generation of the partially double-stranded replicative intermediate. This study reports MDA5 activation by a natural RNA ligand under physiological conditions.

  13. Dual daughter strand incision is processive and increases the efficiency of DNA mismatch repair.

    Science.gov (United States)

    Hermans, Nicolaas; Laffeber, Charlie; Cristovão, Michele; Artola-Borán, Mariela; Mardenborough, Yannicka; Ikpa, Pauline; Jaddoe, Aruna; Winterwerp, Herrie H K; Wyman, Claire; Jiricny, Josef; Kanaar, Roland; Friedhoff, Peter; Lebbink, Joyce H G

    2016-08-19

    DNA mismatch repair (MMR) is an evolutionarily-conserved process responsible for the repair of replication errors. In Escherichia coli, MMR is initiated by MutS and MutL, which activate MutH to incise transiently-hemimethylated GATC sites. MMR efficiency depends on the distribution of these GATC sites. To understand which molecular events determine repair efficiency, we quantitatively studied the effect of strand incision on unwinding and excision activity. The distance between mismatch and GATC site did not influence the strand incision rate, and an increase in the number of sites enhanced incision only to a minor extent. Two GATC sites were incised by the same activated MMR complex in a processive manner, with MutS, the closed form of MutL and MutH displaying different roles. Unwinding and strand excision were more efficient on a substrate with two nicks flanking the mismatch, as compared to substrates containing a single nick or two nicks on the same side of the mismatch. Introduction of multiple nicks by the human MutLα endonuclease also contributed to increased repair efficiency. Our data support a general model of prokaryotic and eukaryotic MMR in which, despite mechanistic differences, mismatch-activated complexes facilitate efficient repair by creating multiple daughter strand nicks. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  14. Beyond Parasitism: Hepatic Lesions in Stranded Harbor Porpoises (Phocoena phocoena) Without Trematode (Campula oblonga) Infections

    NARCIS (Netherlands)

    S. Hiemstra; L. Harkema (Liesbeth); L.C.M. Wiersma (Lidewij); R.I. Keesler

    2015-01-01

    textabstractThe liver can be an indicator of the health of an individual or of a group, which can be especially important to identify agents that can cause disease in multiple species. To better characterize hepatic lesions in stranded harbor porpoises (Phocoena phocoena), we analyzed the livers

  15. PCNA function in the activation and strand direction of MutLα endonuclease in mismatch repair

    Science.gov (United States)

    Pluciennik, Anna; Dzantiev, Leonid; Iyer, Ravi R.; Constantin, Nicoleta; Kadyrov, Farid A.; Modrich, Paul

    2010-01-01

    MutLα (MLH1–PMS2) is a latent endonuclease that is activated in a mismatch-, MutSα-, proliferating cell nuclear antigen (PCNA)-, replication factor C (RFC)-, and ATP-dependent manner, with nuclease action directed to the heteroduplex strand that contains a preexisting break. RFC depletion experiments and use of linear DNAs indicate that RFC function in endonuclease activation is limited to PCNA loading. Whereas nicked circular heteroduplex DNA is a good substrate for PCNA loading and for endonuclease activation on the incised strand, covalently closed, relaxed circular DNA is a poor substrate for both reactions. However, covalently closed supercoiled or bubble-containing relaxed heteroduplexes, which do support PCNA loading, also support MutLα activation, but in this case cleavage strand bias is largely abolished. Based on these findings we suggest that PCNA has two roles in MutLα function: The clamp is required for endonuclease activation, an effect that apparently involves interaction of the two proteins, and by virtue of its loading orientation, PCNA determines the strand direction of MutLα incision. These results also provide a potential mechanism for activation of mismatch repair on nonreplicating DNA, an effect that may have implications for the somatic phase of triplet repeat expansion. PMID:20713735

  16. DNA-mediated strand displacement facilitates sensitive electronic detection of antibodies in human serums.

    Science.gov (United States)

    Dou, Baoting; Yang, Jianmei; Shi, Kai; Yuan, Ruo; Xiang, Yun

    2016-09-15

    We describe here the development of a sensitive and convenient electronic sensor for the detection of antibodies in human serums. The sensor is constructed by self-assembly formation of a mixed monolayer containing the small molecule epitope conjugated double stranded DNA probes on gold electrode. The target antibody binds the epitope on the dsDNA probe and lowers the melting temperature of the duplex, which facilitates the displacement of the antibody-linked strand of the duplex probe by an invading methylene blue-tagged single stranded DNA (MB-ssDNA) through the strand displacement reaction and leads to the capture of many MB-ssDNA on the sensor surface. Subsequent electrochemical oxidation of the methylene blue labels results in amplified current response for sensitive monitoring of the antibodies. The antibody assay conditions are optimized and the sensor exhibits a linear range between 1.0 and 25.0nM with a detection limit of 0.67nM for the target antibody. The sensor is also selective and can be employed to detect the target antibodies in human serum samples. With the advantages of using small molecule epitope as the antibody recognition element over traditional antigen, the versatile manipulability of the DNA probes and the unique properties of the electrochemical transduction technique, the developed sensor thus hold great potential for simple and sensitive detection of different antibodies and other proteins in real samples. Copyright © 2016 Elsevier B.V. All rights reserved.

  17. Toxoplasma gondii in stranded marine mammals from the North Sea and Eastern Atlantic Ocean

    NARCIS (Netherlands)

    Velde, van de Norbert; Devleesschauwer, Brecht; Leopold, Mardik; Begeman, Lineke; IJsseldijk, Lonneke; Hiemstra, Sjoukje; IJzer, Jooske; Brownlow, Andrew; Davison, Nicholas; Haelters, Jan

    2016-01-01

    The occurrence of the zoonotic protozoan parasite Toxoplasma gondii in marine mammals remains a poorly understood phenomenon. In this study, samples from 589 marine mammal species and 34 European otters (Lutra lutra), stranded on the coasts of Scotland, Belgium, France, The Netherlands and

  18. Comparison of DNA strand-break simulated with different DNA models

    International Nuclear Information System (INIS)

    Xie, Wenzhang; Li, Junli; Qiu, Rui; Yan, Congchong; Zeng, Zhi; Li, Chunyan

    2013-01-01

    Full text of the publication follows. In Monte Carlo simulation of DNA damage, the geometric model of DNA is of great importance. To study the influence of DNA model on the simulation of DNA damage, three DNA models were created in this paper. They were a volume model and two atomic models with different parameters. Direct DNA strand-break induced by low-energy electrons were simulated respectively with the three models. The results show that most of the energy depositions in the DNA segments do not lead to strand-breaks. The simple single strand-break (SSB) tends to be the predominant damage type, and the contribution of complex double strand-break (DSB) to the total DSB cannot be neglected. Among the yields of all the three DNA target models applied here, the yields of the volume model are the highest, the yields of the atomic model with double van der Waals radii (r) take the second place, whereas the yields of the atomic model with single r come last. On average, the ratios of SSB yields are approximately equivalent to the corresponding ratios of the models' volume. However, there seems to be no clear relationship between the DSB yields and the models' volume. (authors)

  19. Fundamental simulations of transverse load effects on Nb3Sn strands using finite element analysis

    Science.gov (United States)

    Wang, T.; Chiesa, L.; Takayasu, M.

    2012-06-01

    A 2D finite element elasto-plastic analysis with various property values of the materials in composite Nb3Sn wires has been conducted to simulate the transverse compression effect on a single strand and a 3-strand cable as basic elements of a Cable-in-Conduit Conductor (CICC). The simulation results have been compared with previously reported experimental results. A parametric study of the stress-strain characteristics of copper at 4 K was considered. The simulation results showed that wire and cable deformations due to the transverse load are very sensitive to the elasto-plastic material properties of copper and bronze. In a triplet it is found that the strain distributions inside the superconducting strand are very different along its axis, that is, for a configuration in which two strands lined in parallel to the transverse load direction shows much higher internal strain than other configurations under the same transverse load. The simulation results agree with the reported experimental results indicating a low Young's modulus for Nb3Sn wires under transverse compression. The simulation also supports the reported contact mechanics model for critical current degradation.

  20. Screening for Breast Cancer Using Near Field Infrared Spectroscopy of a Single Strand of Hair

    National Research Council Canada - National Science Library

    Erramilli, Shyamsunder

    2001-01-01

    ... predisposition to breast cancer because of the breast of a mutation of the BRCA1 gene. We would like to develop a new method for the screening of breast cancer based on infrared spectroscopy of a single strand of human hair...

  1. Identification and typing of Brucella spp. in stranded harbour porpoises (Phocoena phocoena) on the Dutch coast.

    NARCIS (Netherlands)

    Maio, E.; Begeman, L.; Bisselink, Y.J.W.M.; Tulden, van P.W.; Wiersma, L.; Hiemstra, S.; Ruuls, R.; Gröne, A.; Roest, H.I.J.; Willemsen, P.T.J.; Giessen, van der J.

    2014-01-01

    The presence of Brucella (B.) spp. in harbour porpoises stranded between 2008 and 2011 along the Dutch coast was studied. A selection of 265 tissue samples from 112 animals was analysed using conventional and molecular methods. In total, 4.5% (5/112) of the animals corresponding with 2.3% (6/265)

  2. Identification and typing of Brucella spp. in stranded harbour porpoises (Phocoena phocoena) on the Dutch coast

    NARCIS (Netherlands)

    Maio, Elisa; Begeman, Lineke; Bisselink, Yvette; van Tulden, Peter; Wiersma, Lidewij; Hiemstra, Sjoukje; Ruuls, Robin; Gröne, Andrea; Roest, Hendrik-Ido-Jan; Willemsen, Peter; van der Giessen, Joke

    2014-01-01

    The presence of Brucella (B.) spp. in harbour porpoises stranded between 2008 and 2011 along the Dutch coast was studied. A selection of 265 tissue samples from 112 animals was analysed using conventional and molecular methods. In total, 4.5% (5/112) of the animals corresponding with 2.3% (6/265)

  3. REV7 counteracts DNA double-strand break resection and affects PARP inhibition

    NARCIS (Netherlands)

    Xu, Guotai; Chapman, J. Ross; Brandsma, Inger; Yuan, Jingsong; Mistrik, Martin; Bouwman, Peter; Bartkova, Jirina; Gogola, Ewa; Warmerdam, Daniël; Barazas, Marco; Jaspers, Janneke E.; Watanabe, Kenji; Pieterse, Mark; Kersbergen, Ariena; Sol, Wendy; Celie, Patrick H. N.; Schouten, Philip C.; van den Broek, Bram; Salman, Ahmed; Nieuwland, Marja; de Rink, Iris; de Ronde, Jorma; Jalink, Kees; Boulton, Simon J.; Chen, Junjie; van Gent, Dik C.; Bartek, Jiri; Jonkers, Jos; Borst, Piet; Rottenberg, Sven

    2015-01-01

    Error-free repair of DNA double-strand breaks (DSBs) is achieved by homologous recombination (HR), and BRCA1 is an important factor for this repair pathway(1). In the absence of BRCA1-mediated HR, the administration of PARP inhibitors induces synthetic lethality of tumour cells of patients with

  4. Chromatin mobility is increased at sites of DNA double-strand breaks

    NARCIS (Netherlands)

    Krawczyk, P. M.; Borovski, T.; Stap, J.; Cijsouw, T.; ten Cate, R.; Medema, J. P.; Kanaar, R.; Franken, N. A. P.; Aten, J. A.

    2012-01-01

    DNA double-strand breaks (DSBs) can efficiently kill cancer cells, but they can also produce unwanted chromosome rearrangements when DNA ends from different DSBs are erroneously joined. Movement of DSB-containing chromatin domains might facilitate these DSB interactions and promote the formation of

  5. Corrosion characteristics of unprotected post-tensioning strands under stress : [summary].

    Science.gov (United States)

    2014-05-01

    Post tensioned concrete is used in many Florida : transportation structures, many of which are : exposed to fresh or salt water. The steel strands : that supply the tension are encased in a plastic : duct which is later filled with grout, so the stra...

  6. When proteome meets genome: the alpha helix and the beta strand ...

    Indian Academy of Sciences (India)

    Unknown

    gions using a custom Java tool. The junctions were ini- tially classified as avoiding or dissecting the structures. (helices and strands). Those dissecting the structures were further divided on the basis of whether they were one, two or three amino acid residues into the structure. To check the Ensembl database for accuracy, ...

  7. Rapid construction of Pacific Street Bridge with o.7 inch strands.

    Science.gov (United States)

    2010-10-01

    The Pacific Street Bridge over I-680 in Omaha, NE is the first bridge in the United States to use 0.7-in.-diameter prestressing : strands in pretensioned concrete girders. This project was funded by FHWA through NDOR under the Innovative Bridge Resea...

  8. On the linearity of the dose-effect relationship of DNA double strand breaks

    International Nuclear Information System (INIS)

    Chadwick, K.H.; Leenhouts, H.P.

    1994-01-01

    Most radiation biologists believe that DNA double-strand breaks are induced linearly with radiation dose for all types of radiation. Since 1985, with the advent of elution and gel electrophoresis techniques which permit the measurement of DNA double-strand breaks induced in mammalian cells at doses having radiobiological relevance, the true nature of the dose-effect relationship has been brought into some doubt. Many investigators measured curvilinear dose-effect relationships and a few found good correlations between the induction of the DNA double-strand breaks and cell survival. We approach the problem pragmatically by assuming that the induction of DNA double-strand breaks by 125 I Auger electron emitters incorporated into the DNA of the cells is a linear function of the number of 125 I decays, and by comparing the dose-effect relationship for sparsely ionizing radiation against this standard. The conclusion drawn that the curvilinear dose-effect relationships and the correlations with survival are real. (Author)

  9. Local Strain Measurement of Kevlar Strand with Fiber Optic Bragg Grating

    Science.gov (United States)

    Banks, Curtis E.; Grant, Joseph; Russell, Sam; Arnett, Shawn

    2008-01-01

    1987 DuPont manufactured 4560 denier Kevlar/Epoxy Strands were instrumented with nine and three sensors each. Stress tests were performed at 30,45,60,70 and 80% of ultimate strength with dwell times of 10,000 seconds. FBG showed uneven stress levels which is contrary to conventional observation.

  10. Phenylketonuria in The Netherlands : 93% of the mutations are detected by single-strand conformation analysis

    NARCIS (Netherlands)

    vanderSijsBos, CJM; Diepstraten, CM; Juyn, JA; Plaisier, M; Giltay, JC; vanSpronsen, FJ; Smit, GPA; Berger, R; Smeitink, JAM; PollThe, BT; vanAmstel, JKP

    1996-01-01

    Single-strand conformational analysis was used to screen for genetic defects in all thirteen exons of the phenylalanine hydroxylase gene (PAH) in phenylketonuria and hyperphenylalaninemia patients in the Netherlands. Exons that showed a bandshift were sequenced directly, In this way, we were able to

  11. Regulation of DNA double-strand break repair by ubiquitin and ubiquitin-like modifiers

    DEFF Research Database (Denmark)

    Schwertman, Petra; Bekker-Jensen, Simon; Mailand, Niels

    2016-01-01

    DNA double-strand breaks (DSBs) are highly cytotoxic DNA lesions. The swift recognition and faithful repair of such damage is crucial for the maintenance of genomic stability, as well as for cell and organismal fitness. Signalling by ubiquitin, SUMO and other ubiquitin-like modifiers (UBLs...

  12. Sequencing of first-strand cDNA library reveals full-length transcriptomes.

    Science.gov (United States)

    Agarwal, Saurabh; Macfarlan, Todd S; Sartor, Maureen A; Iwase, Shigeki

    2015-01-21

    Massively parallel strand-specific sequencing of RNA (ssRNA-seq) has emerged as a powerful tool for profiling complex transcriptomes. However, many current methods for ssRNA-seq suffer from the underrepresentation of both the 5' and 3' ends of RNAs, which can be attributed to second-strand cDNA synthesis. The 5' and 3' ends of RNA harbour crucial information for gene regulation; namely, transcription start sites (TSSs) and polyadenylation sites. Here we report a novel ssRNA-seq method that does not involve second-strand cDNA synthesis, as we Directly Ligate sequencing Adaptors to the First-strand cDNA (DLAF). This novel method with fewer enzymatic reactions results in a higher quality of the libraries than the conventional method. Sequencing of DLAF libraries followed by a novel analysis pipeline enables the profiling of both 5' ends and polyadenylation sites at near-base resolution. Therefore, DLAF offers the first genomics tool to obtain the 'full-length' transcriptome with a single library.

  13. 18 CFR 35.26 - Recovery of stranded costs by public utilities and transmitting utilities.

    Science.gov (United States)

    2010-04-01

    ...) Definitions—1) Wholesale stranded cost means any legitimate, prudent and verifiable cost incurred by a public utility or a transmitting utility to provide service to: (i) A wholesale requirements customer that subsequently becomes, in whole or in part, an unbundled wholesale transmission services customer of such public...

  14. The Ku Heterodimer and the Metabolism of Single-Ended DNA Double-Strand Breaks

    NARCIS (Netherlands)

    A. Balestrini (Alessia); D. Ristic (Dejan); I. Dionne (Isabelle); X.Z. Liu (Xiao); C. Wyman (Claire); R.J. Wellinger (Raymund); J.H.J. Petrini (John)

    2013-01-01

    textabstractSingle-ended double-strand breaks (DSBs) are a common form of spontaneous DNA break, generated when the replisome encounters a discontinuity in the DNA template. Given their prevalence, understanding the mechanisms governing the fate(s) of single-ended DSBs is important. We describe the

  15. North American oriented strand board markets, arbitrage activity, and market price dynamics: A smooth transition approach

    Science.gov (United States)

    Barry Goodwin; Matthew Holt; Jeffrey P. Prestemon

    2011-01-01

    Price dynamics for North American oriented strand board markets are examined. The role of transactions costs are explored vis-à-vis the law of one price. Nonlinearities induced by unobservable transactions costs are modeled by estimating time-varying smooth transition autoregressions (TV-STARs). Results indicate that nonlinearity and structural change are important...

  16. Detection of grey seal Halichoerus grypus DNA in attack wounds on stranded harbour porpoises Phocoena phocoena

    NARCIS (Netherlands)

    van Blijswijk, Judith; Begeman, Lineke; Witte, H.; IJsseldijk, Lonneke; Brasseur, Sophie; Gröne, Andrea; Leopold, Mardik F

    2014-01-01

    DNA was analysed from external wounds on 3 dead harbour porpoises Phocoena phocoena that were stranded in the Netherlands. Puncture wounds as well as the edges of large open wounds were sampled with sterile cotton swabs. With specific primers that target the mtDNA control region of grey seal

  17. Zinc chromate induces chromosome instability and DNA double strand breaks in human lung cells

    International Nuclear Information System (INIS)

    Xie Hong; Holmes, Amie L.; Young, Jamie L.; Qin Qin; Joyce, Kellie; Pelsue, Stephen C.; Peng Cheng; Wise, Sandra S.; Jeevarajan, Antony S.; Wallace, William T.; Hammond, Dianne; Wise, John Pierce

    2009-01-01

    Hexavalent chromium Cr(VI) is a respiratory toxicant and carcinogen, with solubility playing an important role in its carcinogenic potential. Zinc chromate, a water insoluble or 'particulate' Cr(VI) compound, has been shown to be carcinogenic in epidemiology studies and to induce tumors in experimental animals, but its genotoxicity is poorly understood. Our study shows that zinc chromate induced concentration-dependent increases in cytotoxicity, chromosome damage and DNA double strand breaks in human lung cells. In response to zinc chromate-induced breaks, MRE11 expression was increased and ATM and ATR were phosphorylated, indicating that the DNA double strand break repair system was initiated in the cells. In addition, our data show that zinc chromate-induced double strand breaks were only observed in the G2/M phase population, with no significant amount of double strand breaks observed in G1 and S phase cells. These data will aid in understanding the mechanisms of zinc chromate toxicity and carcinogenesis

  18. Design and structural analysis of a thermostable nine-beta-stranded immunoglobulin scaffold.

    NARCIS (Netherlands)

    Roo, de G.; Francoijs, C.J.J.; Ippel, J.H.; Houtzager, E.; Vijn, I.M.C.; Burgers, K.; Willebrands, W.; Verwoerd, T.C.; Linden, van der R.; Vervoort, J.J.M.; Sijmons, P.C.

    2010-01-01

    A small and stable protein scaffold, consisting of nine beta-strands and able to functionally present affinity peptide loops, was designed. Computational methods were used to predict sequences with low free energy derived from a naturally occurring single-chain camel antibody. Genes for two

  19. NbTi Strands Verification for ITER PF CICC Process Qualification of CNDA

    Science.gov (United States)

    Liu, F.; Liu, H.; Liu, S.; Liu, B.; Lei, L.; Wu, Y.

    2014-05-01

    China is in charge of most of Poloidal Field (PF) conductors production for the International Thermonuclear Experimental Reactor (ITER). The execution for PF conductors shall be in three main phases. According to ITER Procurement Arrangement (PA), the Domestic Agency (DA) shall be required to verify the room and low temperature acceptance tests carried out by the strand suppliers. As the reference laboratory of Chinese DA (CNDA), the superconducting strands test laboratory of Institute of Plasma Physics, Chinese Academy of Sciences (ASIPP) was undertaking the task of strands verification for ITER conductors. The verification test includes: diameter, Nickel plating thickness, copper-to-non-copper volume ratio, twist pitch direction and length, standard critical current (IC) and resistive transition index (n), residual resistance ration (RRR), and hysteresis loss. 48 NbTi strands with 7 billets were supplied for the PF Cable-In-Conduit Conductor (CICC) process qualification. In total, 54 samples were measured. The verification level for PF CICC process qualification was 100%. The test method, facility and results of each item are described in detail in this publication.

  20. Structural basis for DNA strand separation by a hexameric replicative helicase

    Science.gov (United States)

    Chaban, Yuriy; Stead, Jonathan A.; Ryzhenkova, Ksenia; Whelan, Fiona; Lamber, Ekaterina P.; Antson, Alfred; Sanders, Cyril M.; Orlova, Elena V.

    2015-01-01

    Hexameric helicases are processive DNA unwinding machines but how they engage with a replication fork during unwinding is unknown. Using electron microscopy and single particle analysis we determined structures of the intact hexameric helicase E1 from papillomavirus and two complexes of E1 bound to a DNA replication fork end-labelled with protein tags. By labelling a DNA replication fork with streptavidin (dsDNA end) and Fab (5′ ssDNA) we located the positions of these labels on the helicase surface, showing that at least 10 bp of dsDNA enter the E1 helicase via a side tunnel. In the currently accepted ‘steric exclusion’ model for dsDNA unwinding, the active 3′ ssDNA strand is pulled through a central tunnel of the helicase motor domain as the dsDNA strands are wedged apart outside the protein assembly. Our structural observations together with nuclease footprinting assays indicate otherwise: strand separation is taking place inside E1 in a chamber above the helicase domain and the 5′ passive ssDNA strands exits the assembly through a separate tunnel opposite to the dsDNA entry point. Our data therefore suggest an alternative to the current general model for DNA unwinding by hexameric helicases. PMID:26240379

  1. Effects of single-stranded DNA binding proteins on primer extension by telomerase.

    Science.gov (United States)

    Cohen, Shlomit; Jacob, Eyal; Manor, Haim

    2004-08-12

    We present a biochemical analysis of the effects of three single-stranded DNA binding proteins on extension of oligonucleotide primers by the Tetrahymena telomerase. One of them, a human protein designated translin, which was shown to specifically bind the G-rich Tetrahymena and human telomeric repeats, slightly stimulated the primer extension reactions at molar ratios of translin/primer of primers, rather than by a direct interaction of this protein with telomerase. A second protein, the general human single-stranded DNA binding protein Replication Protein A (RPA), similarly affected the primer extension by telomerase, even though its mode of binding to DNA differs from that of translin. A third protein, the E. coli single-stranded DNA binding protein (SSB), whose binding to DNA is highly cooperative, caused more substantial stimulation and inhibition at the lower and the higher molar ratios of SSB/primer, respectively. Both telomere-specific and general single-stranded DNA binding proteins are found in living cells in telomeric complexes. Based on our data, we propose that these proteins may exert either stimulatory or inhibitory effects on intracellular telomerases, depending on their local concentrations. Copyright 2004 Elsevier B.V.

  2. Acheta domesticus Volvovirus, a Novel Single-Stranded Circular DNA Virus of the House Cricket.

    Science.gov (United States)

    Pham, Hanh T; Bergoin, Max; Tijssen, Peter

    2013-03-14

    The genome of a novel virus of the house cricket consists of a 2,517-nucleotide (nt) circular single-stranded DNA (ssDNA) molecule with 4 open reading frames (ORFs). One ORF had a low identity to circovirus nucleotide sequences (NS). The unique properties of this volvovirus suggested that it belongs to a new virus family or genus.

  3. Acheta domesticus Volvovirus, a Novel Single-Stranded Circular DNA Virus of the House Cricket

    OpenAIRE

    Pham, Hanh T.; Bergoin, Max; Tijssen, Peter

    2013-01-01

    International audience; The genome of a novel virus of the house cricket consists of a 2,517-nucleotide (nt) circular single-stranded DNA (ssDNA) molecule with 4 open reading frames (ORFs). One ORF had a low identity to circovirus nucleotide sequences (NS). The unique properties of this volvovirus suggested that it belongs to a new virus family or genus.

  4. Branch migration prevents DNA loss during double-strand break repair.

    Directory of Open Access Journals (Sweden)

    Julia S P Mawer

    2014-08-01

    Full Text Available The repair of DNA double-strand breaks must be accurate to avoid genomic rearrangements that can lead to cell death and disease. This can be accomplished by promoting homologous recombination between correctly aligned sister chromosomes. Here, using a unique system for generating a site-specific DNA double-strand break in one copy of two replicating Escherichia coli sister chromosomes, we analyse the intermediates of sister-sister double-strand break repair. Using two-dimensional agarose gel electrophoresis, we show that when double-strand breaks are formed in the absence of RuvAB, 4-way DNA (Holliday junctions are accumulated in a RecG-dependent manner, arguing against the long-standing view that the redundancy of RuvAB and RecG is in the resolution of Holliday junctions. Using pulsed-field gel electrophoresis, we explain the redundancy by showing that branch migration catalysed by RuvAB and RecG is required for stabilising the intermediates of repair as, when branch migration cannot take place, repair is aborted and DNA is lost at the break locus. We demonstrate that in the repair of correctly aligned sister chromosomes, an unstable early intermediate is stabilised by branch migration. This reliance on branch migration may have evolved to help promote recombination between correctly aligned sister chromosomes to prevent genomic rearrangements.

  5. 75 FR 28560 - Prestressed Concrete Steel Wire Strand From the People's Republic of China: Final Determination...

    Science.gov (United States)

    2010-05-21

    ... Wire Strand From the People's Republic of China: Final Determination of Sales at Less Than Fair Value...'') published its notice of preliminary determination of sales at less than fair value (``LTFV'') in the... Fair Value, 74 FR 68232 (December 23, 2009) (``Preliminary Determination''). FOR FURTHER INFORMATION...

  6. A role for small RNAs in DNA double-strand break repair

    DEFF Research Database (Denmark)

    Wei, W.; Ba, Z.; Wu, Y.

    2012-01-01

    Eukaryotes have evolved complex mechanisms to repair DNA double-strand breaks (DSBs) through coordinated actions of protein sensors, transducers, and effectors. Here we show that ∼21-nucleotide small RNAs are produced from the sequences in the vicinity of DSB sites in Arabidopsis and in human cells...

  7. Ago2 facilitates Rad51 recruitment and DNA double-strand break repair by homologous recombination

    DEFF Research Database (Denmark)

    Gao, Min; Wei, Wei; Li, Ming Hua

    2014-01-01

    DNA double-strand breaks (DSBs) are highly cytotoxic lesions and pose a major threat to genome stability if not properly repaired. We and others have previously shown that a class of DSB-induced small RNAs (diRNAs) is produced from sequences around DSB sites. DiRNAs are associated with Argonaute...

  8. SCAI promotes DNA double-strand break repair in distinct chromosomal contexts

    DEFF Research Database (Denmark)

    Hansen, Rebecca Kring; Mund, Andreas; Poulsen, Sara Lund

    2016-01-01

    DNA double-strand breaks (DSBs) are highly cytotoxic DNA lesions, whose accurate repair by non-homologous end-joining (NHEJ) or homologous recombination (HR) is crucial for genome integrity and is strongly influenced by the local chromatin environment. Here, we identify SCAI (suppressor of cancer...

  9. The lichens of Fakahatchee Strand Preserve State Park, Florida: Proceedings from the 18th Tuckerman Workshop

    Science.gov (United States)

    Robert Lucking; Frederick Seavey; Ralph S. Common; Sean Q. Beeching; Othmar Breuss; William R. Buck; Lee Crane; Malcolm Hodges; Brendan P. Hodkinson; Elisabeth Lay; James C. Lendemer; R. Troy McMullin; Joel Mercado

    2011-01-01

    Fakahatchee Strand Preserve State Park is located in Collier County at the extreme southwestern corner of Florida, close to Everglades National Park and Big Cypress National Preserve. The 18th Tuckerman Workshop, an annual gathering of professional and amateur lichenologists and mycologists from the United States and Canada, this time with additional participants from...

  10. Viral Proteins That Bind Double-Stranded RNA: Countermeasures Against Host Antiviral Responses

    OpenAIRE

    Krug, Robert M.

    2014-01-01

    Several animal viruses encode proteins that bind double-stranded RNA (dsRNA) to counteract host dsRNA-dependent antiviral responses. This article discusses the structure and function of the dsRNA-binding proteins of influenza A virus and Ebola viruses (EBOVs).

  11. Baculovirus-mediated gene silencing in insect cells using intracellularly produced long double-stranded RNA

    NARCIS (Netherlands)

    Huang, Yi; Deng, F.; Hu, Z.H.; Vlak, J.M.; Wang, H.

    2007-01-01

    Double-stranded RNA-mediated interference (RNAi) has recently emerged as a powerful reverse genetics tool to silence gene expression in multiple organisms, including plants, nematodes and insects. In this study, DNA vectors capable of promoting the synthesis of long hairpin dsRNAs in vivo from a DNA

  12. DOUBLE-STRANDED-RNA MYCOVIRUSES IN MYCELIUM OF PLEUROTUS-OSTREATUS

    NARCIS (Netherlands)

    VANDERLENDE, TR; HARMSEN, MC; GO, SJ

    1995-01-01

    Mycelium of Pleurotus ostreatus var. florida with a decreased growth rate contained seven double-stranded RNA segments and isometrical virus particles with diameters of 24 and 30 nm. Mycelium with a normal growth rate lacked dsRNA. Protoclones from virus-containing mycelium contained one to seven of

  13. Effects of the environment on the electric conductivity of double-stranded DNA molecules

    NARCIS (Netherlands)

    Malyshev, A. V.; Diaz, E.; Dominguez-Adame, F.; Malyshev, V. A.

    2009-01-01

    We present a theoretical analysis of the effects of the environment on charge transport in double-stranded synthetic poly(G)-poly(C) DNA molecules attached to two ideal leads. Coupling of the DNA to the environment results in two effects: (i) localization of carrier functions due to static disorder

  14. Effects of hyperthermia on repair of radiation-induced DNA strand breaks

    International Nuclear Information System (INIS)

    Mills, M.D.; Meyn, R.E.

    1981-01-01

    Previous reports have suggested a relationship between the heat-induced changes in nucleoprotein and the hyperthermic enhancement of radiation sensitivity. In an effort to further understand these relationships, we measured the level of initial DNA strand break damage and the DNA strand break rejoining kinetics in Chinese hamster ovary cells following combined hyperthermia and ionizing radiation treatments. The amount of protein associated with DNA measured as the ratio of [ 3 H)leucine to [ 14 C]thymidine was also compared in chromatin isolated from both heated and unheated cells. The results of these experiments show that the initial level of radiation-induced DNA strand breaks is significantly enhanced by a prior hyperthermia treatment of 43 0 C for 30 min. Treatments at higher temperatures and longer treatments at the same temperature magnified this effect. Hyperthermia was also shown to cause a substantial inhibition of the DNA strand break rejoining after irradiation. Both the initial level of DNA damage and the rejoining kinetics recovered to normal levels with incubation at 37 0 C between the hyperthermia and radiation treatments. Recovery of these parameters coincided with the return of the amount of protein associated with DNA to normal values, further suggesting a relationship between the changes in nucleoprotein and the hyperthermic enhancement of radiation sensivivity

  15. Increased rate of repair of ultraviolet-induced DNA strand breaks in mitogen stimulated lymphocytes

    International Nuclear Information System (INIS)

    Hamlet, S.M.; Lavin, M.F.; Jennings, P.A.; Queensland Univ., St. Lucia; Queensland Univ. St. Lucia

    1982-01-01

    Previous results have shown that phytohaemagglutinin-stimulated bovine lymphocytes exhibit a peak of ultraviolet-induced DNA repair synthesis 3 to 4 days after addition of mitogen. The level of repair synthesis was approximately tenfold higher than that in unstimulated lymphocytes. These studies have been extended to examine the rate of repair of strand breaks in U.V.-irradiated bovine lymphocytes. The extent of breakage of DNA was shown to be the same in mitogen-stimulated and unstimulated lymphocytes from two breeds of cattle, when determined by sedimentation of nucleoids on sucrose gradients. However, in mitogen-stimulated cells the time taken to repair DNA strand breaks was 6 hours compared with 12 hours in stationary phase lymphocytes after a U.V. dose of 5 J/m 2 . These results suggest that the increased rate of repair of strand breaks is due to the induction of enzymes involved at the post-incision stage of DNA repair. Thus the increased level of repair synthesis observed in earlier work correlates with an increased rate of repair of DNA strand breaks in phytohaemagglutinin-stimulated bovine lymphocytes. (author)

  16. Monophosphate end groups produced in radiation induced strand breakage in DNA

    International Nuclear Information System (INIS)

    Kay, E.; Ward, J.F.

    1976-01-01

    A solution of DNA was gamma-irradiated and treated with monophosphatase for studies on the amount of inorganic phosphate released as a function of time. Studies were also conducted on: effect of alkali on yield of monophosphate end groups; induction of DNA strand breaks by treatment with DNAase; initial G values for monophosphate termini; and effect of alkali on radioinduced DNA damage

  17. Comparative Measurements of ITER Nb3Sn Strands between Two Laboratories

    NARCIS (Netherlands)

    Lu, Jun; Hill, Scott; McGuire, David; Dellinger, Keagan; Nijhuis, Arend; Wessel, W. A.; Krooshoop, H. J.G.; Chan, Kevin; Martovetsky, Nicolai

    2017-01-01

    ITER Nb3Sn strand quality verification tests require large quantities of precise measurements. Therefore, regular cross-checking between testing laboratories is critically important. In this paper, we present results from a cross-checking test of 140 samples between the National High Magnetic Field

  18. Requirements for DNA strand transfer during reverse transcription in mutant HIV-1 virions

    NARCIS (Netherlands)

    Berkhout, B.; van Wamel, J.; Klaver, B.

    1995-01-01

    Retroviruses convert their RNA genome into a DNA form by means of reverse transcription. According to the current model of reverse transcription, two strand transfer reactions are needed to synthesize a full-length DNA genome. Because reverse transcription is initiated close to the 5' end of the RNA

  19. Long DNA passenger strand highly improves the activity of RNA/DNA hybrid siRNAs.

    Science.gov (United States)

    Ida, Hiroyuki; Fukuda, Kosuke; Tachibana, Akira; Tanabe, Toshizumi

    2014-04-01

    Small interfering RNAs (siRNAs) are potent tools in biomedical research, which can reduce the expression level of target proteins through RNAi pathway. They are composed of 19-25 bp double strand RNA (dsRNAs), therefore, stimulate dsRNAs dependent interferon responses in a non-specific manner. This problem has prevented siRNAs from being applied as new therapeautic agents. In the present paper, we tried to circumvent interferon responses using RNA/DNA hetero siRNAs (HsiRNAs) composed of RNA guide and DNA passenger strands. It was previously reported that siRNAs which were partially substituted with DNA had RNAi activity and that DNA substitution often caused the activity loss. In our results, HsiRNAs, in which the passenger strand of siRNAs were exchanged with DNA also showed much lower activity than that of parental siRNAs. Here, we found that attachment of 5' flanking sequence to DNA passenger strand improved the activity of HsiRNAs. Furthermore, the effective HsiRNAs induced much lower interferon responses than parental siRNAs. Thus, HsiRNAs with 5' flanking sequence are expected to be novel siRNA drug candidates. Copyright © 2013 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

  20. When proteome meets genome: the alpha helix and the beta strand ...

    Indian Academy of Sciences (India)

    Unknown

    Comparison of pre-mRNA splice junctions with the three-dimensional architecture of its protein product from different eukaryotes revealed that the junctions were far less likely to occur inside the α-helices and β-strands of proteins than within the more flexible linker regions ('turns' and 'loops') con- necting them. The splice ...

  1. Bacterial single-stranded DNA-binding proteins are phosphorylated on tyrosine

    DEFF Research Database (Denmark)

    Mijakovic, Ivan; Petranovic, Dina; Macek, B

    2006-01-01

    by kinase YwqD and phosphatase YwqE. Phosphorylation of B.subtilis SSB increased binding almost 200-fold to single-stranded DNA in vitro. Tyrosine phosphorylation of B.subtilis, S.coelicolor and Escherichia coli SSBs occured while they were expressed in E.coli, indicating that tyrosine phosphorylation...

  2. DNA double-strand break rejoining in human follicular lymphoma and glioblastoma tumor cells

    NARCIS (Netherlands)

    Macann, AMJ; Britten, RA; Poppema, S; Pearcey, R; Rosenberg, E; Allalunis-Turner, MJ; Murray, D

    2000-01-01

    Follicle center cell lymphoma is among the most radioresponsive of human cancers. To assess whether this radioresponsiveness might be a result of a compromised ability of the tumor cells to accomplish the biologically-effective repair of DNA double-strand breaks (DSBs), we have measured i) the

  3. Distinct genetic control of homologous recombination repair of Cas9-induced double-strand breaks, nicks and paired nicks

    NARCIS (Netherlands)

    Vriend, Lianne E. M.; Prakash, Rohit; Chen, Chun-Chin; Vanoli, Fabio; Cavallo, Francesca; Zhang, Yu; Jasin, Maria; Krawczyk, Przemek M.

    2016-01-01

    DNA double-strand breaks (DSBs) are known to be powerful inducers of homologous recombination (HR), but single-strand breaks (nicks) have also been shown to trigger HR. Both DSB- and nick-induced HR ((nick)HR) are exploited in advanced genome-engineering approaches based on the bacterial RNA-guided

  4. Viral counterdefense on RNA silencing : analysis of RNA silencing suppressors from arthropod-borne negative strand RNA plant viruses

    NARCIS (Netherlands)

    Schnettler, E.

    2010-01-01

    This thesis describes that RNA silencing suppressor (RSS) proteins encoded by negative-stranded RNA plant viruses are able to interfere with different RNA silencing pathways in a variety of organisms by interacting with double stranded (ds)RNA molecules. These RSS proteins are able to counteract the

  5. DMPD: Transcriptional signaling by double-stranded RNA: role of TLR3. [Dynamic Macrophage Pathway CSML Database

    Lifescience Database Archive (English)

    Full Text Available 15733829 Transcriptional signaling by double-stranded RNA: role of TLR3. Sen GC, Sa...rkar SN. Cytokine Growth Factor Rev. 2005 Feb;16(1):1-14. (.png) (.svg) (.html) (.csml) Show Transcriptional sign...aling by double-stranded RNA: role of TLR3. PubmedID 15733829 Title Transcriptional signaling by double

  6. Critical Mass

    CERN Multimedia

    AUTHOR|(CDS)2070299

    2017-01-01

    Critical Mass is a cycling event typically held on the last Friday of every month; its purpose is not usually formalized beyond the direct action of meeting at a set location and time and traveling as a group through city or town streets on bikes. The event originated in 1992 in San Francisco; by the end of 2003, the event was being held in over 300 cities around the world. At CERN it is held once a year in conjunction with the national Swiss campaing "Bike to work".

  7. MO-AB-BRA-04: Radiation Measurements with a DNA Double-Strand-Break Dosimeter

    International Nuclear Information System (INIS)

    Obeidat, M; Cline, K; Stathakis, S; Papanikolaou, N; Rasmussen, K; Gutierrez, A; Ha, CS; Lee, SE; Shim, EY; Kirby, N

    2016-01-01

    Purpose: Many types of dosimeters are used to measure radiation, but none of them directly measures the biological effect of this dose. The purpose here is to create a dosimeter that can measure the probability of double-strand breaks (DSB) for DNA, which is directly related to the biological effect of radiation. Methods: The dosimeter has DNA strands, which are labeled on one end with biotin and on the other with fluorescein. The biotin attaches these strands to magnetic beads. We suspended the DNA dosimeter in phosphate-buffered saline (PBS) as it matches the internal environment of the body. We placed small volumes (50µL) of the DNA dosimeter into tubes and irradiated these samples in a water-equivalent plastic phantom with several doses (three samples per dose). After irradiating the samples, a magnet was placed against the tubes. The fluorescein attached to broken DNA strands was extracted (called the supernatant) and placed into a different tube. The fluorescein on the unbroken strands remained attached to the beads in the tube and was re-suspended with 50µL of PBS. A fluorescence reader was used to measure the fluorescence for both the re-suspended beads and supernatant. To prove that we are measuring DSB, we tested dosimeter response with two different lengths of attached DNA strands (1 and 4 kilo-base pair). Results: The probability of DSB at the dose levels of 5, 10, 25, and 50 Gy were 0.05, 0.08, 0.12, and 0.19, respectively, while the coefficients of variation were 0.14, 0.07, 0.02, and 0.01, respectively. The 4 kilo-base-pair dosimeter produced 5.3 times the response of the 1 kilo-base-pair dosimeter. Conclusion: The DNA dosimeter yields a measurable response to dose that scales with the DNA strand length. The goal now is to refine the dosimeter fabrication to reproducibly create a low coefficient of variation for the lower doses. This work was supported in part by Yarmouk University (Irbid, Jordan) and CPRIT (RP140105)

  8. MO-AB-BRA-04: Radiation Measurements with a DNA Double-Strand-Break Dosimeter

    Energy Technology Data Exchange (ETDEWEB)

    Obeidat, M; Cline, K; Stathakis, S; Papanikolaou, N; Rasmussen, K; Gutierrez, A; Ha, CS; Lee, SE; Shim, EY; Kirby, N [University of Texas HSC SA, San Antonio, TX (United States)

    2016-06-15

    Purpose: Many types of dosimeters are used to measure radiation, but none of them directly measures the biological effect of this dose. The purpose here is to create a dosimeter that can measure the probability of double-strand breaks (DSB) for DNA, which is directly related to the biological effect of radiation. Methods: The dosimeter has DNA strands, which are labeled on one end with biotin and on the other with fluorescein. The biotin attaches these strands to magnetic beads. We suspended the DNA dosimeter in phosphate-buffered saline (PBS) as it matches the internal environment of the body. We placed small volumes (50µL) of the DNA dosimeter into tubes and irradiated these samples in a water-equivalent plastic phantom with several doses (three samples per dose). After irradiating the samples, a magnet was placed against the tubes. The fluorescein attached to broken DNA strands was extracted (called the supernatant) and placed into a different tube. The fluorescein on the unbroken strands remained attached to the beads in the tube and was re-suspended with 50µL of PBS. A fluorescence reader was used to measure the fluorescence for both the re-suspended beads and supernatant. To prove that we are measuring DSB, we tested dosimeter response with two different lengths of attached DNA strands (1 and 4 kilo-base pair). Results: The probability of DSB at the dose levels of 5, 10, 25, and 50 Gy were 0.05, 0.08, 0.12, and 0.19, respectively, while the coefficients of variation were 0.14, 0.07, 0.02, and 0.01, respectively. The 4 kilo-base-pair dosimeter produced 5.3 times the response of the 1 kilo-base-pair dosimeter. Conclusion: The DNA dosimeter yields a measurable response to dose that scales with the DNA strand length. The goal now is to refine the dosimeter fabrication to reproducibly create a low coefficient of variation for the lower doses. This work was supported in part by Yarmouk University (Irbid, Jordan) and CPRIT (RP140105)

  9. Genetic and biochemical identification of a novel single-stranded DNA binding complex in Haloferax volcanii

    Directory of Open Access Journals (Sweden)

    Amy eStroud

    2012-06-01

    Full Text Available Single-stranded DNA binding proteins play an essential role in DNA replication and repair. They use oligosaccharide-binding folds, a five-stranded ß-sheet coiled into a closed barrel, to bind to single-stranded DNA thereby protecting and stabilizing the DNA. In eukaryotes the single-stranded DNA binding protein is known as replication protein A (RPA and consists of three distinct subunits that function as a heterotrimer. The bacterial homolog is termed single-stranded DNA-binding protein (SSB and functions as a homotetramer. In the archaeon Haloferax volcanii there are three genes encoding homologs of RPA. Two of the rpa genes (rpa1 and rpa3 exist in operons with a novel gene specific to Euryarchaeota, this gene encodes a protein that we have termed rpa-associated protein (RPAP. The rpap genes encode proteins belonging to COG3390 group and feature oligosaccharide-binding folds, suggesting that they might cooperate with RPA in binding to single-stranded DNA. Our genetic analysis showed that rpa1 and rpa3 deletion mutants have differing phenotypes; only ∆rpa3 strains are hypersensitive to DNA damaging agents. Deletion of the rpa3-associated gene rpap3 led to similar levels of DNA damage sensitivity, as did deletion of the rpa3 operon, suggesting that RPA3 and RPAP3 function in the same pathway. Protein pull-downs involving recombinant hexahistidine-tagged RPAs showed that RPA3 co-purifies with RPAP3, and RPA1 co-purifies with RPAP1. This indicates that the RPAs interact only with their respective associated proteins; this was corroborated by the inability to construct rpa1 rpap3 and rpa3 rpap1 double mutants. This is the first report investigating the individual function of the archaeal COG3390 RPA-associated proteins. We have shown genetically and biochemically that the RPAPs interact with their respective RPAs, and have uncovered a novel single-stranded DNA binding complex that is unique to Euryarchaeota.

  10. Quantitating subcellular metabolism with multi-isotope imaging mass spectrometry

    OpenAIRE

    Steinhauser, Matthew L.; Bailey, Andrew; Senyo, Samuel E.; Guillermier, Christelle; Perlstein, Todd S.; Gould, Alex P.; Lee, Richard T.; Lechene, Claude P.

    2012-01-01

    Mass spectrometry with stable isotope labels has been seminal in discovering the dynamic state of living matter 1,2 but is limited to bulk tissues or cells. We developed multi-isotope imaging mass spectrometry (MIMS) that allowed us to view and measure stable isotope incorporation with sub-micron resolution 3,4 . Here we apply MIMS to diverse organisms, including Drosophila, mice, and humans. We test the “immortal strand hypothesis,” which predicts that during asymmetric stem cell division ch...

  11. Mass/Count Variation: A Mereological, Two-Dimensional Semantics

    Directory of Open Access Journals (Sweden)

    Peter R Sutton

    2016-12-01

    Full Text Available We argue that two types of context are central to grounding the semantics for the mass/count distinction. We combine and develop the accounts of Rothstein (2010 and Landman (2011, which emphasize (non-overlap at a context. We also adopt some parts of Chierchia’s (2010 account which uses precisifying contexts. We unite these strands in a two-dimensional semantics that covers a wide range of the puzzling variation data in mass/count lexicalization. Most importantly, it predicts where we should expect to find such variation for some classes of nouns but not for others, and also explains why.

  12. Cause-specific temporal and spatial trends in green sea turtle strandings in the Hawaiian Archipelago (1982-2003)

    Science.gov (United States)

    Chaloupka, Milani; Work, Thierry M.; Balazs, George H.; Murakawa, Shawn K. K.; Morris, Robert

    2008-01-01

    We investigated cause-specific temporal and spatial trends in sea turtle strandings in the Hawaiian Archipelago. Five species of sea turtle were recorded in 3,861 strandings over a 22-year period (1982–2003). Green turtles comprised 97% of these strandings with size and gender composition reflecting the demographic structure of the resident green turtle population and relative green turtle abundance in Hawaiian waters. The cause of strandings was determined by necropsy based on a complete gross external and internal examination. Totally 75% of the 3,732 green turtle strandings were from Oahu where strandings occur year-round. The most common known cause of the green turtle strandings was the tumour-forming disease, fibropapillomatosis (28%) followed by hook-and-line fishing gear-induced trauma (7%), gillnet fishing gear-induced trauma (5%), boat strike (2.5%), and shark attack (2.7%). Miscellaneous causes comprised 5.4% of strandings whereas 49% of green turtle strandings could not be attributed to any known cause. Green turtle strandings attributable to boat strike were more likely from Kauai and Oahu while fibropapilloma strandings were more likely from Oahu and Maui. Hook-and-line gear strandings were more likely from Oahu due to higher per capita inshore fishing effort. The specific mortality rate (conditional probability) for fibropapillomatosis was 88%, 69% for gillnet gear and 52% for hook-and-line gear. The probability of a dead green turtle stranding increased from 1982 but levelled off by the mid-1990s. The declining mortality risk was because the prevalence and severity of fibropapillomatosis has decreased recently and so has the mortality risk attributable to gillnet gear. Despite exposure to disease and inshore fishing gears, the Hawaiian green turtle stock continues to recover following protection since the late 1970s. Nevertheless, measures to reduce incidental capture of sea turtles in coastal Hawaiian fisheries would be prudent, especially since

  13. Role of teh Rad52 Amino-terminal DNA Binding Activity in DNA Strand Capture in Homologous Recombination

    DEFF Research Database (Denmark)

    Shi, Idina; Hallwyl, Swee Chuang Lim; Seong, Changhyun

    2009-01-01

    Saccharomyces cerevisiae Rad52 protein promotes homologous recombination by nucleating the Rad51 recombinase onto replication protein A-coated single-stranded DNA strands and also by directly annealing such strands. We show that the purified rad52-R70A mutant protein, with a compromised amino......-terminal DNA binding domain, is capable of Rad51 delivery to DNA but is deficient in DNA annealing. Results from chromatin immunoprecipitation experiments find that rad52-R70A associates with DNA double-strand breaks and promotes recruitment of Rad51 as efficiently as wild-type Rad52. Analysis of gene...... conversion intermediates reveals that rad52-R70A cells can mediate DNA strand invasion but are unable to complete the recombination event. These results provide evidence that DNA binding by the evolutionarily conserved amino terminus of Rad52 is needed for the capture of the second DNA end during homologous...

  14. Method for detecting DNA strand breaks in mammalian cells using the Deinococcus radiodurans PprA protein

    International Nuclear Information System (INIS)

    Satoh, Katsuya; Wada, Seiichi; Kikuchi, Masahiro; Funayama, Tomoo; Narumi, Issay; Kobayashi, Yasuhiko

    2006-01-01

    In a previous study, we identified the novel protein PprA that plays a critical role in the radiation resistance of Deinococcus radiodurans. In this study, we focussed on the ability of PprA protein to recognize and bind to double-stranded DNA carrying strand breaks, and attempted to visualize radiation-induced DNA strand breaks in mammalian cultured cells by employing PprA protein using an immunofluorescence technique. Increased PprA protein binding to CHO-K1 nuclei immediately following irradiation suggests the protein is binding to DNA strand breaks. By altering the cell permeabilization conditions, PprA protein binding to CHO-K1 mitochondria, which is probably resulted from DNA strand break immediately following irradiation, was also detected. The method developed and detailed in this study will be useful in evaluating DNA damage responses in cultured cells, and could also be applicable to genotoxic tests in the environmental and pharmaceutical fields

  15. What is DNA damage? Risk of double-strand break and its individual variation

    International Nuclear Information System (INIS)

    Hanaoka, Fumio

    2011-01-01

    The author discusses about the title subject in an aspect of possible spreading of Fukushima radioactive substances mainly in eastern north area of Japan where carcinogenic incidence may be increased as the ionizing radiation injures the gene (DNA). At first, explained is that cancer is a disease of genes with infinitive proliferation of cells, there are systems to prevent it by repairing the damaged DNA and by other mechanisms like exclusion of cells damaged too much or killing cancer cells with immunity, and individual difference of the repairing capability exists. DNA is always damaged even under ordinary living conditions by sunlight UV ray, cosmic radiation and chemicals externally and by active oxygen species and thermal water movement internally. Concomitantly, DNA damaged by many mechanisms like deletion, dimmer formation, chemical modification of bases, single and double strand breaks is always repaired by concerned enzymes. Double-strand damage by high-energy radiation like gamma ray is quite risky because its repair sometimes accompanies error as concerned enzymes are from more multiple genes. There are many syndromes derived from gene deficit of those repairing enzymes. The diseases concerned with repair of the double-strand damage teach that fetus and infant are more sensitive to radiation than adult as their young body cells are more actively synthesizing DNA, during which, if DNA is injured by radiation, risk of repairing error is higher as the double strand break more frequently occurs. It cannot be simply said that a certain radiation dose limit is generally permissible. There is an individual difference of radiation sensitivity and a possible method to find out an individual weak to radiation is the lymphocyte screening in vitro using anticancer bleomycin which breaks the double strand. (T.T.)

  16. Genetics of x-ray induced double strand break repair in saccharomyces cerevisiae

    International Nuclear Information System (INIS)

    Budd, M.E.

    1982-07-01

    The possible fates of x-ray-induced double-strand breaks in Saccharomyces cerevisiae were examined. One possible pathway which breaks can follow, the repair pathway, was studied by assaying strains with mutations in the RAD51, RAD54, and RAD57 loci for double-strand break repair. In order of increasing radiation sensitivity one finds: rad57-1(23 0 )> rad51-1(30 0 )> rad54-3(36 0 ). At 36 0 , rad54-3 cells cannot repair double-strand breaks, while 23 0 , they can. Strains with the rad57-1 mutation can rejoin broken chromosomes at both temperatures. However, the low survival at 36 0 shows that the assay is not distinguishing large DNA fragments which allow cell survival from those which cause cell death. A rad51-1 strain could also rejoin broken chromosomes, and was thus capable of incomplete repair. The data can be explained with the hypothesis that rad54-3 cells are blocked in an early step of repair, while rad51-1 and rad57-1 strains are blocked in a later step of repair. The fate of double-strand breaks when they are left unrepaired was investigated with the rad54-3 mutation. If breaks are prevented from entering the RAD54 repair pathway they become uncommitted lesions. These lesions are repaired slower than the original breaks. One possible fate for an uncommitted lesion is conversion into a fixed lesion, which is likely to be an unrepairable or misrepaired double-strand break. The presence of protein synthesis after irradiation increases the probability that a break will enter the repair pathway. Evidence shows that increased probability of repair results from enhanced synthesis of repair proteins shortly after radiation

  17. Protection of free-radical induced DNA strand breaks in vitro by flavonoids

    International Nuclear Information System (INIS)

    Fisher, L.; Anderson, R.F.

    1998-01-01

    Full text: We have used both plasmid and cosmid test systems to assay the effect of antioxidant flavonoids (AO) on DNA strand breakage in supercoiled closed circular DNA (DNA SC ) following the formation oxidative radical damage on DNA (DNA OXID + . ) in aqueous solution. Single strand breaks in DNA SC result in the formation of the relaxed circular form (DNA RC ) and double strand breaks give linear DNA (DNA L ). Dose response curves were constructed for the log of the loss of [DNA S C] against dose (0-600 Gy). The D 37 (dose for 37% unchanged DNA SC ) values determined in the presence of increasing amounts of flavonoids were compared as ratios to the D 37 control value to give dose modification factor (DMF). Irradiations were carried out under 'constant scavenging' conditions to separate out the effect of direct radical scavenging from the possible electron transfer reaction. Control irradiation experiments, were performed in aerated TRIS buffer, concentration 10 mM, which has a scavenging capacity, k s (defined as the summation of the rate constants for the reaction of OH radicals with all species in solution, multiplied by their concentrations) of 1.5 x 10 7 s -1 . The concentration of TRIS was reduced upon addition of AO to maintain k s at this level. Data will be presented for examples from all four major types of flavonoids (flavonols, isoflavones, flavones and flavon-3-ols) showing DMF values plateau at near 2.0 even at low concentrations (ca. 20 μM) of the flavonoids. Increased DNA strand breaks following post irradiation incubation with endo III protein was unaffected by having the flavonoids present at the time of irradiation. This result suggests that the protection afforded by the flavonoids is unlikely to be in repairing radical damage on pyrimidine bases that are precursors of DNA strand breaks. Overall these studies provide evidence for an additional mechanism of antioxidant activity

  18. Genetics of x-ray induced double strand break repair in saccharomyces cerevisiae

    Energy Technology Data Exchange (ETDEWEB)

    Budd, M.E.

    1982-07-01

    The possible fates of x-ray-induced double-strand breaks in Saccharomyces cerevisiae were examined. One possible pathway which breaks can follow, the repair pathway, was studied by assaying strains with mutations in the RAD51, RAD54, and RAD57 loci for double-strand break repair. In order of increasing radiation sensitivity one finds: rad57-1(23/sup 0/)> rad51-1(30/sup 0/)> rad54-3(36/sup 0/). At 36/sup 0/, rad54-3 cells cannot repair double-strand breaks, while 23/sup 0/, they can. Strains with the rad57-1 mutation can rejoin broken chromosomes at both temperatures. However, the low survival at 36/sup 0/ shows that the assay is not distinguishing large DNA fragments which allow cell survival from those which cause cell death. A rad51-1 strain could also rejoin broken chromosomes, and was thus capable of incomplete repair. The data can be explained with the hypothesis that rad54-3 cells are blocked in an early step of repair, while rad51-1 and rad57-1 strains are blocked in a later step of repair. The fate of double-strand breaks when they are left unrepaired was investigated with the rad54-3 mutation. If breaks are prevented from entering the RAD54 repair pathway they become uncommitted lesions. These lesions are repaired slower than the original breaks. One possible fate for an uncommitted lesion is conversion into a fixed lesion, which is likely to be an unrepairable or misrepaired double-strand break. The presence of protein synthesis after irradiation increases the probability that a break will enter the repair pathway. Evidence shows that increased probability of repair results from enhanced synthesis of repair proteins shortly after radiation. (ERB)

  19. First-In-Class Small Molecule Inhibitors of the Single-Strand DNA Cytosine Deaminase APOBEC3G

    Energy Technology Data Exchange (ETDEWEB)

    Li, Ming; Shandilya, Shivender M.D.; Carpenter, Michael A.; Rathore, Anurag; Brown, William L.; Perkins, Angela L.; Harki, Daniel A.; Solberg, Jonathan; Hook, Derek J.; Pandey, Krishan K.; Parniak, Michael A.; Johnson, Jeffrey R.; Krogan, Nevan J.; Somasundaran, Mohan; Ali, Akbar; Schiffer, Celia A.; Harris, Reuben S. (Pitt); (UMASS, MED); (SLUHSC); (UCSF); (UMM)

    2012-04-04

    APOBEC3G is a single-stranded DNA cytosine deaminase that comprises part of the innate immune response to viruses and transposons. Although APOBEC3G is the prototype for understanding the larger mammalian polynucleotide deaminase family, no specific chemical inhibitors exist to modulate its activity. High-throughput screening identified 34 compounds that inhibit APOBEC3G catalytic activity. Twenty of 34 small molecules contained catechol moieties, which are known to be sulfhydryl reactive following oxidation to the orthoquinone. Located proximal to the active site, C321 was identified as the binding site for the inhibitors by a combination of mutational screening, structural analysis, and mass spectrometry. Bulkier substitutions C321-to-L, F, Y, or W mimicked chemical inhibition. A strong specificity for APOBEC3G was evident, as most compounds failed to inhibit the related APOBEC3A enzyme or the unrelated enzymes E. coli uracil DNA glycosylase, HIV-1 RNase H, or HIV-1 integrase. Partial, but not complete, sensitivity could be conferred to APOBEC3A by introducing the entire C321 loop from APOBEC3G. Thus, a structural model is presented in which the mechanism of inhibition is both specific and competitive, by binding a pocket adjacent to the APOBEC3G active site, reacting with C321, and blocking access to substrate DNA cytosines.

  20. IER5 is involved in DNA Double-Strand Breaks Repair in Association with PAPR1 in Hela Cells.

    Science.gov (United States)

    Yu, Xin-Ping; Wu, Yu-Mei; Liu, Yang; Tian, Ming; Wang, Jian-Dong; Ding, Ku-Ke; Ma, Teng; Zhou, Ping-Kun

    2017-01-01

    The immediate early response gene 5 ( IER 5) is a radiation response gene induced in a dose-independent manner, and has been suggested to be a molecular biomarker for biodosimetry purposes upon radiation exposure. Here, we investigated the function of IER5 in DNA damage response and repair. We found that interference on IER5 expression significantly decreased the efficiency of repair of DNA double-strand breaks induced by ionizing radiations in Hela cells. We found that IER5 participates in the non-homologous end-joining pathway of DNA breaks repair. Additionally, we identified a number of potential IER5-interacting proteins through mass spectrometry-based protein assays. The interaction of IER5 protein with poly(ADP-Ribose) polymerase 1 (PARP1) and Ku70 was further confirmed by immunoprecipitation assays. We also found that Olaparib, a PARP1 inhibitor, affected the stability of IER5. These results indicate that targeting of IER5 may be a novel DNA damage response-related strategy to use during cervical cancer radiotherapy or chemotherapy.

  1. The complete genome sequence of a double-stranded RNA mycovirus from Fusarium graminearum strain HN1.

    Science.gov (United States)

    Wang, Luan; Wang, Shuangchao; Yang, Xiufen; Zeng, Hongmei; Qiu, Dewen; Guo, Lihua

    2017-07-01

    The complete nucleotide sequence of a double-stranded RNA (dsRNA) mycovirus, Fusarium graminearum dsRNA virus 5 (FgV5), was identified and characterized. The FgV5 genome comprises two dsRNA genome segments of 2030 bp and 1740 bp. FgV5 dsRNA1 contains a single open reading frame (ORF1), which is predicted to encode a protein of 613 amino acids (aa) with a molecular mass of 70.4 kDa and has a conserved RNA-dependent RNA polymerase (RdRp) motif. FgV5 dsRNA2 is predicted to contain two discontinuous ORFs (ORF2 and ORF3) that code for products of unknown function. Sequence comparisons showed that FgV5 has the highest aa sequence identities to Fusarium graminearum virus 4 (FgV4) (83.01% for ORF1, 78.70% for ORF2, and 76.27% for ORF3), suggesting that FgV5 and FgV4 should be regarded as members of different species. Phylogenetic analysis indicated that FgV5 belongs to a taxonomically unassigned dsRNA mycovirus group that is related to the families Amalgaviridae and Partitiviridae. Here, we propose that FgV5 and related viruses are members of a yet to be named and formally recognized new family.

  2. Thioflavin T binds dimeric parallel-stranded GA-containing non-G-quadruplex DNAs: a general approach to lighting up double-stranded scaffolds.

    Science.gov (United States)

    Liu, Shuangna; Peng, Pai; Wang, Huihui; Shi, Lili; Li, Tao

    2017-12-01

    A molecular rotor thioflavin T (ThT) is usually used as a fluorescent ligand specific for G-quadruplexes. Here, we demonstrate that ThT can tightly bind non-G-quadruplex DNAs with several GA motifs and dimerize them in a parallel double-stranded mode, accompanied by over 100-fold enhancement in the fluorescence emission of ThT. The introduction of reverse Watson-Crick T-A base pairs into these dimeric parallel-stranded DNA systems remarkably favors the binding of ThT into the pocket between G•G and A•A base pairs, where ThT is encapsulated thereby restricting its two rotary aromatic rings in the excited state. A similar mechanism is also demonstrated in antiparallel DNA duplexes where several motifs of two consecutive G•G wobble base pairs are incorporated and serve as the active pockets for ThT binding. The insight into the interactions of ThT with non-G-quadruplex DNAs allows us to introduce a new concept for constructing DNA-based sensors and devices. As proof-of-concept experiments, we design a DNA triplex containing GA motifs in its Hoogsteen hydrogen-bonded two parallel strands as a pH-driven nanoswitch and two GA-containing parallel duplexes as novel metal sensing platforms where C-C and T-T mismatches are included. This work may find further applications in biological systems (e.g. disease gene detection) where parallel duplex or triplex stretches are involved. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  3. Arabidopsis DNA ligase IV is induced by gamma-irradiation and interacts with an Arabidopsis homologue of the double strand break repair protein XRCC4.

    Science.gov (United States)

    West, C E; Waterworth, W M; Jiang, Q; Bray, C M

    2000-10-01

    Rejoining of single- and double-strand breaks (DSBs) introduced in DNA during replication, recombination, and DNA damage is catalysed by DNA ligase enzymes. Eukaryotes possess multiple DNA ligase enzymes, each having distinct roles in cellular metabolism. Double-strand breaks in DNA, which can occur spontaneously in the cell or be induced experimentally by gamma-irradiation, represent one of the most serious threats to genomic integrity. Non-homologous end joining (NHEJ) rather than homologous recombination is the major pathway for repair of DSBs in organisms with complex genomes, including humans and plants. DNA ligase IV in Saccharomyces cerevisiae and humans catalyses the final step in the NHEJ pathway of DSB repair. In this study we identify an Arabidopsis thaliana homologue (AtLIG4) of human and S. cerevisiae DNA ligase IV which is shown to encode an ATP-dependent DNA ligase with a theoretical molecular mass of 138 kDa and 48% similarity in amino-acid sequence to the human DNA ligase IV. Yeast two-hybrid analysis demonstrated a strong interaction between A. thaliana DNA ligase IV and the A. thaliana homologue of the human DNA ligase IV-binding protein XRCC4. This interaction is shown to be mediated via the tandem BRCA C-terminal domains of A. thaliana DNA ligase IV protein. Expression of AtLIG4 is induced by gamma-irradiation but not by UVB irradiation, consistent with an in vivo role for the A. thaliana DNA ligase IV in DSB repair.

  4. Influence of age, sex and body condition on zinc, copper, cadmium and metallothioneins in common guillemots (Uria aalge) stranded at the Belgian coast.

    Science.gov (United States)

    Debacker, V; Schiettecatte, L S; Jauniaux, T; Bouquegneau, J M

    2001-12-01

    The common guillemots, Uria aalge, found stranded at the Belgian coast, display high levels of Cu in both liver and kidneys. The condition index of the animals, defined as the ratio of liver to kidneys mass (Wenzel & Adelung, 1996, The suitability of oiled Guillemots (Uria aalge) as monitoring organisms for geographical comparisons of trace element contaminants. Archives of Environmental Contamination and Toxicology, 31, 368-377), influences both the metal concentration and its binding to metallothioneins (MT): the lower the condition index, the more emaciated the animals, and the higher the total Cu concentration and the concentration of Cu bound to MT. In less robust individuals, our results suggest that Cu could displace Zn from MT, rendering the Zn ions available to induce a new MT synthesis. Sex-related effects also emerged as significantly higher hepatic MT as well as Cu- and Zn-MT concentrations were found in emaciated male guillemots compared to females. In both organs, Cd concentrations remained low and typically demonstrated an age-dependent renal accumulation, with no noticeable effect of the condition index. As a whole, these results suggest that, for guillemots found stranded at the Belgian coast. Cu binding to hepatic and renal MT could function as a protective mechanism, rendering the metal ions unavailable to exert any cytotoxic activity.

  5. Prostate brachytherapy postimplant dosimetry: Seed orientation and the impact of dosimetric anisotropy in stranded implants

    International Nuclear Information System (INIS)

    Chng, Nicholas; Spadinger, Ingrid; Rasoda, Rosey; Morris, W. James; Salcudean, Septimiu

    2012-01-01

    Purpose: In postimplant dosimetry for prostate brachytherapy, dose is commonly calculated using the TG-43 1D formalism, because seed orientations are difficult to determine from CT images, the current standard for the procedure. However, the orientation of stranded seeds soon after implantation is predictable, as these seeds tend to maintain their relative spacing, and orient themselves along the implant trajectory. The aim of this study was to develop a method for determining seed orientations from reconstructed strand trajectories, and to use this information to investigate the dosimetric impact of applying the TG-43 2D formalism to clinical postimplant analysis. Methods: Using in-house software, the preplan to postimplant seed correspondence was determined for a cohort of 30 patients during routine day-0 CT-based postimplant dosimetry. All patients were implanted with stranded-seed trains. Spline curves were fit to each set of seeds composing a strand, with the requirement that the distance along the spline between seeds be equal to the seed spacing within the strand. The orientations of the seeds were estimated by the tangents to the spline at each seed centroid. Dose distributions were then determined using the 1D and 2D TG-43 formalisms. These were compared using the TG-137 recommended dose metrics for the prostate, prostatic urethra, and rectum. Results: Seven hundred and sixty one strands were analyzed in total. Defining the z-axis to be cranial-positive and the x-axis to be left-lateral positive in the CT coordinate system, the average seed had an inclination of 21 deg. ± 10 deg. and an azimuth of -81 deg. ± 57 deg. These values correspond to the average strand rising anteriorly from apex to base, approximately parallel to the midsagittal plane. Clinically minor but statistically significant differences in dose metrics were noted. Compared to the 2D calculation, the 1D calculation underestimated prostate V100 by 1.1% and D90 by 2.3 Gy, while

  6. Induction of DNA double-strand breaks by ionizing radiation of different quality and their relevance for cell inactivation

    International Nuclear Information System (INIS)

    Kampf, G.

    1988-01-01

    By investigation of the production of DNA strand breaks and of DNA release from the nuclear membrane complex in Chinese hamster cells using different radiation qualities from 1 to 360 keV/μm, partly also under hypoxic conditions, and by relating the results to the induction of chromosome aberrations and to cell inactivation it has become possible to find connections between the induction of molecular lesions and the expression of this damage on the cellular level. From the studies follows that DNA pieces are cut off from the nuclear membrane complex by DNA double-strand breaks (DSB). The share and size of the released pieces depends on radiation dose and quality as well as on the oxygen conditions. The lesions can partly be repaired. In connection with the DSB rates the results of the DNA release studies led to the conclusion that the DNA in the cells must be organized in superstructure units (MASSUs) with a DNA mass of about 2 x 10 9 g/mol, which are associated to the nuclear membrane in attachment points. The numerical relations show that for a 37% survival probability about 90 DSB per genome are required with sparsely ionizing radiation; this number declines to about 40 by use of more densely ionizing radiation up to 150 keV/μm, and increases again with further rise of the ionization density. Hence, for cell inactivation not simply a certain number of DSB per cell is required but rather seems their cooperation within a small structure section of the DNA to be relevant. These critical structures are with high probability the MASSUs. An irrepairable release of DNA from such a structure unit can bring about a chromosome break detectable in the metaphase and finally lead to cell inactivation. DSB turned out to be the essential lethal events in bacteria as well. The relatively small differences to the eukaryotic cells in the position of the maximum of radiation sensitivity on the LET scale and in the lesion sensitivity towards DSB let suggest that a common critical

  7. Metallographic autopsies of full-scale ITER prototype cable-in-conduit conductors after full cyclic testing in SULTAN: II. Significant reduction of strand movement and strand damage in short twist pitch CICCs

    International Nuclear Information System (INIS)

    Sanabria, Carlos; Lee, Peter J; Starch, William; Larbalestier, David C; Devred, Arnaud

    2015-01-01

    Prototype cable-in-conduit-conductors (CICCs) destined for use in the toroidal field and central solenoid coils of the ITER experimental fusion reactor underwent severe cyclic loading in the SULTAN facility. Their autopsies revealed significant and permanent transverse strand migration due to the large Lorentz forces of the SULTAN test. The movement resulted in a 3%–7% void fraction increase on the low pressure (LP) side of the longer twist pitch CICCs. However, short twist pitch conductors exhibited less than 1% void fraction increase in the LP side, as well as a complete absence of the Nb 3 Sn filament fractures observed in the longer twist pitch conductors. We report here a detailed strand-to-cable analysis of short and longer ‘baseline’ twist pitch CICCs. It was found that the use of internal tin (IT) strands in the longer ‘baseline’ twist pitch CICCs can be beneficial possibly because of their superior stiffness—which better resist strand movement—while the use of bronze process strands showed more movement and poorer cyclic test performance. This was not the case for the short twist pitch CICC. Such conductor design seems to work well with both strand types. But it was found that despite the absence of filament fractures, the short twist pitch CICC made from the IT strands studied here developed severe strand distortion during cabling which resulted in diffusion barrier breaks and Sn contamination of the Cu stabilizer during the heat treatment. Conversely, the short twist pitch CICC made from bronze process strands preserved diffusion barrier integrity. (paper)

  8. Late Quaternary slip history of the Mill Creek strand of the San Andreas fault in San Gorgonio Pass, southern California: The role of a subsidiary left-lateral fault in strand switching

    Science.gov (United States)

    Kendrick, Katherine J.; Matti, Jonathan; Mahan, Shannon

    2015-01-01

    The fault history of the Mill Creek strand of the San Andreas fault (SAF) in the San Gorgonio Pass region, along with the reconstructed geomorphology surrounding this fault strand, reveals the important role of the left-lateral Pinto Mountain fault in the regional fault strand switching. The Mill Creek strand has 7.1–8.7 km total slip. Following this displacement, the Pinto Mountain fault offset the Mill Creek strand 1–1.25 km, as SAF slip transferred to the San Bernardino, Banning, and Garnet Hill strands. An alluvial complex within the Mission Creek watershed can be linked to palinspastic reconstruction of drainage segments to constrain slip history of the Mill Creek strand. We investigated surface remnants through detailed geologic mapping, morphometric and stratigraphic analysis, geochronology, and pedogenic analysis. The degree of soil development constrains the duration of surface stability when correlated to other regional, independently dated pedons. This correlation indicates that the oldest surfaces are significantly older than 500 ka. Luminescence dates of 106 ka and 95 ka from (respectively) 5 and 4 m beneath a younger fan surface are consistent with age estimates based on soil-profile development. Offset of the Mill Creek strand by the Pinto Mountain fault suggests a short-term slip rate of ∼10–12.5 mm/yr for the Pinto Mountain fault, and a lower long-term slip rate. Uplift of the Yucaipa Ridge block during the period of Mill Creek strand activity is consistent with thermochronologic modeled uplift estimates.

  9. Association of Shiny White Blotches and Strands With Nonpigmented Basal Cell Carcinoma

    Science.gov (United States)

    Navarrete-Dechent, Cristián; Bajaj, Shirin; Marchetti, Michael A.; Rabinovitz, Harold; Dusza, Stephen W.; Marghoob, Ashfaq A.

    2016-01-01

    IMPORTANCE Basal cell carcinoma (BCC) is the most common type of skin cancer and is usually nonpigmented. Shiny white structures (SWSs) are frequently present in BCC. OBJECTIVE To determine the diagnostic accuracy of various morphologies of SWSs for diagnosis of nonpigmented BCC. DESIGN, SETTING, AND PARTICIPANTS Nonpigmented skin tumors, determined clinically and dermoscopically, were identified from a database of lesions consecutively biopsied over a 3-year period (January 2, 2009, to December 31, 2012) from a single dermatology practice. Data analysis was conducted from October 9, 2014, to November 15, 2015. Investigators blinded to histopathologic diagnosis evaluated the polarized dermoscopic images for the presence of SWSs, which were categorized as blotches, strands, short white lines, and rosettes. Measures of diagnostic accuracy for BCC were estimated. Participants included 2375 patients from a dermatologic clinic in Plantation, Florida. Review of the medical records identified 2891 biopsied skin lesions; 457 of these were nonpigmented neoplasms. MAIN OUTCOMES AND MEASURES Diagnosis of BCC with dermoscopy compared with all other diagnoses combined was the primary outcome; the secondary outcome was diagnosis of BCC compared with amelanotic melanoma. We calculated diagnostic accuracy measured as odds ratios (ORs), sensitivity, and specificity of shiny white blotches and/or strands for the diagnosis of BCC. RESULTS Of the 457 nonpigmented neoplasms evaluated, 287 (62.8%) were BCCs, 106 (23.2%) were squamous cell carcinoma, 39 (8.5%) were lichen planus–like keratosis, 21 (4.6%) were melanomas, and 4 (0.9%) were nevi. The prevalence of SWSs was 49.0% (n = 224). In multivariate analysis (reported as OR [95% CI]) controlling for age, sex, and anatomical location, the presence of any SWS was associated with a diagnosis of BCC (2.3 [1.5–3.6]; P < .001). Blotches (6.3 [3.6–10.9]; P < .001), strands (4.9 [2.9–8.4]; P < .001), and blotches and strands together

  10. Yield of radiation-induced DNA single-strand breaks in Escherichia coli and superinfecting phage lambda at different dose rates. Repair of strand breaks in different buffers

    International Nuclear Information System (INIS)

    Boye, E.; Johansen, I.; Brustad, T.

    1976-01-01

    Cells of E. coli K-12 strain AB 1886 were irradiated in oxygenated phosphate buffered saline at 2 0 C with electrons from a 4-MeV linear accelerator. The yield of DNA single-strand breaks was determined as a function of the dose rate between 2.5 and 21,000 krad/min. For dose rates over 100 krad/min the yield was found to be constant. Below 10 krad/min the yield of breaks decreases drastically. This is explained by rejoining of breaks during irradiation. Twenty percent of the breaks induced by acute exposure are repaired within 3 min at 2 0 C. Superinfecting phage lambda DNA is repaired at the same rate as chromosomal DNA. In contrast to the results obtained with phosphate-buffered saline, an increase in the number of breaks after irradiation is observed when the bacteria are suspended in tris buffer. It is suggested that buffers of low ionic strength facilitate the leakage through the membrane of a small-molecular-weight component(s) necessary for DNA strand rejoining

  11. Structural chromosome abnormalities, increased DNA strand breaks and DNA strand break repair deficiency in dermal fibroblasts from old female human donors

    Science.gov (United States)

    Kalfalah, Faiza; Seggewiß, Sabine; Walter, Regina; Tigges, Julia; Moreno-Villanueva, María; Bürkle, Alexander; Ohse, Sebastian; Busch, Hauke; Boerries, Melanie; Hildebrandt, Barbara; Royer-Pokora, Brigitte; Boege, Fritz

    2015-01-01

    Dermal fibroblasts provide a paradigmatic model of cellular adaptation to long-term exogenous stress and ageing processes driven thereby. Here we addressed whether fibroblast ageing analysed ex vivo entails genome instability. Dermal fibroblasts from human female donors aged 20–67 years were studied in primary culture at low population doubling. Under these conditions, the incidence of replicative senescence and rates of age-correlated telomere shortening were insignificant. Genome-wide gene expression analysis revealed age-related impairment of mitosis, telomere and chromosome maintenance and induction of genes associated with DNA repair and non-homologous end-joining, most notably XRCC4 and ligase 4. We observed an age-correlated drop in proliferative capacity and age-correlated increases in heterochromatin marks, structural chromosome abnormalities (deletions, translocations and chromatid breaks), DNA strand breaks and histone H2AX-phosphorylation. In a third of the cells from old and middle-aged donors repair of X-ray induced DNA strand breaks was impaired despite up-regulation of DNA repair genes. The distinct phenotype of genome instability, increased heterochromatinisation and (in 30% of the cases futile) up-regulation of DNA repair genes was stably maintained over several cell passages indicating that it represents a feature of geroconversion that is distinct from cellular senescence, as it does not encompass a block of proliferation. PMID:25678531

  12. Probing Enhanced Double-Strand Break Formation at Abasic Sites within Clustered Lesions in Nucleosome Core Particles.

    Science.gov (United States)

    Banerjee, Samya; Chakraborty, Supratim; Jacinto, Marco Paolo; Paul, Michael D; Balster, Morgan V; Greenberg, Marc M

    2017-01-10

    DNA is rapidly cleaved under mild alkaline conditions at apyrimidinic/apurinic sites, but the half-life is several weeks in phosphate buffer (pH 7.5). However, abasic sites are ∼100-fold more reactive within nucleosome core particles (NCPs). Histone proteins catalyze the strand scission, and at superhelical location 1.5, the histone H4 tail is largely responsible for the accelerated cleavage. The rate constant for strand scission at an abasic site is enhanced further in a nucleosome core particle when it is part of a bistranded lesion containing a proximal strand break. Cleavage of this form results in a highly deleterious double-strand break. This acceleration is dependent upon the position of the abasic lesion in the NCP and its structure. The enhancement in cleavage rate at an apurinic/apyrimidinic site rapidly drops off as the distance between the strand break and abasic site increases and is negligible once the two forms of damage are separated by 7 bp. However, the enhancement of the rate of double-strand break formation increases when the size of the gap is increased from one to two nucleotides. In contrast, the cleavage rate enhancement at 2-deoxyribonolactone within bistranded lesions is more modest, and it is similar in free DNA and nucleosome core particles. We postulate that the enhanced rate of double-strand break formation at bistranded lesions containing apurinic/apyrimidinic sites within nucleosome core particles is a general phenomenon and is due to increased DNA flexibility.

  13. Association of neighboring β-strands of outer membrane protein A in lipid bilayers revealed by site-directed fluorescence quenching

    NARCIS (Netherlands)

    Kleinschmidt, J.H.; Bulieris, P.V.; Qu, J.; Dogterom, M.; den Blaauwen, T.

    2011-01-01

    We present a detailed study on the formation of neighboring β-strands during the folding of a monomeric integral membrane protein of the β-barrel type. β-Strand and β-barrel formations were investigated for the eight-stranded transmembrane domain of outer membrane protein A (OmpA) with

  14. Review of thirty-two years of toothed whale strandings in Santa Catarina, southern Brazil (Cetacea: Odontoceti

    Directory of Open Access Journals (Sweden)

    Thaís dos S. Vianna

    Full Text Available ABSTRACT Marine mammal strandings provide valuable insights into local biodiversity. Strandings can be caused by both natural and anthropogenic factors. In the state of Santa Catarina, Southern Brazil, organized marine mammal collections started in the 1980s through opportunistic and non-systematic collection efforts, representing a record of over 30 years of marine biodiversity. This study aimed to perform a preliminary review of 32 years of stranding records within this region. The secondary aim was to elucidate the stranding dynamics of the three most commonly recorded species. A total of 460 records were obtained, representing 17 species of odontocetes. The species registered most frequently were the franciscana, Pontoporia blainvillei (Gervais & d' Orbigny, 1844 (n = 173, bottlenose dolphin, Tursiops truncatus (Montagu, 1821 (n = 100, and Guiana dolphin Sotalia guianensis (Van Bénéden, 1864 (n = 97. Most of the stranding records were observed in the second half of the year during the austral winter and spring. The apparent causes of death could not be determined for most of the specimens due to carcass decomposition. For the specimens in which the apparent cause of death could be determined, 27% of the strandings were compatible with anthropogenic interactions. While the focus of this study was a preliminary assessment of stranding data obtained through opportunistic collection, it is evident that future systematic monitoring efforts and stable networks of collaborators will generate more reliable coastal biodiversity inventories and will allow the knowledge of population dynamics of marine mammal species. In particular, for threatened and vulnerable species, or species with poor natural history data, strandings are a fundamental tool for the understanding of marine biodiversity. Ideally, future more refined analyses of stranding data should be used to inform conservation and management policies and to elucidate the biology and ecology of

  15. Tissue heavy metal concentrations of stranded California sea lions (Zalophus californianus) in Southern California

    Energy Technology Data Exchange (ETDEWEB)

    Harper, Erin R. [SeaWorld San Diego, 500 SeaWorld Drive, San Diego, CA 92109 (United States)]. E-mail: erin-harper@hotmail.com; St Leger, Judy A. [SeaWorld San Diego, 500 SeaWorld Drive, San Diego, CA 92109 (United States); Westberg, Jody A. [SeaWorld San Diego, 500 SeaWorld Drive, San Diego, CA 92109 (United States); Mazzaro, Lisa [Mystic Aquarium and Institute for Exploration, 55 Coogan Blvd, Mystic, CT 06355 (United States); Schmitt, Todd [SeaWorld San Diego, 500 SeaWorld Drive, San Diego, CA 92109 (United States); Reidarson, Tom H. [SeaWorld San Diego, 500 SeaWorld Drive, San Diego, CA 92109 (United States); Tucker, Melinda [SeaWorld San Diego, 500 SeaWorld Drive, San Diego, CA 92109 (United States); Cross, Dee H. [SeaWorld San Diego, 500 SeaWorld Drive, San Diego, CA 92109 (United States); Puschner, Birgit [California Animal Health and Food Safety Laboratory System, School of Veterinary Medicine, University of California at Davis, One Shields Avenue, Davis, CA 95616 (United States)

    2007-06-15

    Concentrations of nine heavy metals (As, Cd, Cu, Fe, Hg, Pb, Mn, Mo and Zn) were determined in the hepatic and renal tissues of 80 stranded California sea lions (Zalophus californianus). Significant age-dependant increases were observed in liver and kidney concentrations of cadmium and mercury, and renal zinc concentrations. Hepatic iron concentrations were significantly higher in females than males. Animals with suspected domoic acid associated pathological findings had significantly higher concentrations of liver and kidney cadmium; and significantly higher liver mercury concentrations when compared to animals classified with infectious disease or traumatic mortality. Significantly higher hepatic burdens of molybdenum and zinc were found in animals that died from infectious diseases. This is the largest study of tissue heavy metal concentrations in California sea lions to date. These data demonstrate how passive monitoring of stranded animals can provide insight into environmental impacts on marine mammals. - Tissue heavy metal concentrations are valuable in population and environmental monitoring.

  16. Crosslinks rather than strand breaks determine access to ancient DNA sequences from frozen sediments

    DEFF Research Database (Denmark)

    Hansen, Anders Johannes; Mitchell, D.L.; Wiuf, C.

    2006-01-01

    Diagenesis was studied in DNA obtained from Siberian permafrost (permanently frozen soil) ranging from 10 to 400 thousand years in age. Despite optimal preservation conditions, we found the sedimentary DNA to be severely modified by interstrand crosslinks, single and double stranded breaks......, and freely exposed sugar, phosphate, and hydroxyl groups. Intriguingly, interstrand crosslinks were found to accumulate about hundred times faster than single stranded breaks, suggesting that crosslinking rather than depurination is the primary limiting factor for ancient DNA amplification under frozen...... conditions. The results question the reliability of the commonly used models relying on depurination kinetics for predicting the long-term survival of DNA under permafrost conditions and suggest that new strategies for repair of ancient DNA must be considered if the yield of amplifiable DNA from permafrost...

  17. Anchoring device enabling relaxation of a multi-strand prestressing cable

    International Nuclear Information System (INIS)

    1979-01-01

    Anchoring device, in a concrete structure, for a multi-strand prestressing cable, enabling the cable to be stressed or relaxed, comprising: (a) an axisymmetrical block, fitted with channels to enable the cable strands to be stressed and anchored through this block, (b) a duct with its opening splayed to a diameter greater than that of the block over a length corresponding to the stretching of the cable when being stressed, (c) a round bearing plate on the concrete around the expanded hole of the duct and (d) at least one intermediate removable bearing piece coming between the edge of the block and the internal edge of the plate. The removable parts are crown sectors of which the opposite bearing faces of each are slanted with respect to the centre line of the block and orientated in the same direction so as to transmit the cable stress at an angle from the block to the edge of the bearing plate [fr

  18. Sites of termination of in vitro DNA synthesis on psoralen phototreated single-stranded templates

    International Nuclear Information System (INIS)

    Piette, J.; Hearst, J.

    1985-01-01

    Single-stranded DNA has been photochemically induced to react with 4'-hydroxymethyl-4,5',8-trimethylpsoralen (HMT) and used as substrate for DNA replication with E. coli DNA polymerase I large fragment. By using the dideoxy sequencing procedure, it is possible to map the termination sites on the template photoreacted with HMT. These sites occur at the nucleotides preceding each thymine residue (and a few cytosine residues), emphasizing the fact that in a single-stranded stretch of DNA, HMT reacts with each thymine residue without any specificity regarding the flanking base sequence of the thymine residues. In addition, termination of DNA synthesis due to psoralen-adducted thymine is not influenced by the efficiency of the 3'-5' exonuclease proof-reading activity of the DNA polymerase. (author)

  19. Introduction of Nonlinear Properties Into Hierachical Models of Nb3Sn Strands

    International Nuclear Information System (INIS)

    Collins, B.; Krishnan, J.; Arbelaez, D.; Ferracin, P.; Prestemon, S.O.; Godeke, A.; Dietderich, D.R.; Zohdi, T.I.

    2011-01-01

    The development of computational models representing Rutherford cable formation and deformation is necessary to investigate the strain state in the superconducting filaments in Nb 3 Sn magnets. The wide variety of length scales within accelerator magnets suggests usage of a hierarchical structure within the model. As part of an ongoing investigation at LBNL, a three-dimensional simplified nonlinear multiscale model is developed as a way to extend previous linear elastic versions. The inclusion of plasticity models into the problem formulation allows an improved representation of strand behavior compared to the linear elastic model. This formulation is applied to a single Nb 3 Sn strand to find its effective properties as well as the strain state in the conductor under loading.

  20. Sequence-specific RNA Photocleavage by Single-stranded DNA in Presence of Riboflavin

    Science.gov (United States)

    Zhao, Yongyun; Chen, Gangyi; Yuan, Yi; Li, Na; Dong, Juan; Huang, Xin; Cui, Xin; Tang, Zhuo

    2015-10-01

    Constant efforts have been made to develop new method to realize sequence-specific RNA degradation, which could cause inhibition of the expression of targeted gene. Herein, by using an unmodified short DNA oligonucleotide for sequence recognition and endogenic small molecue, vitamin B2 (riboflavin) as photosensitizer, we report a simple strategy to realize the sequence-specific photocleavage of targeted RNA. The DNA strand is complimentary to the target sequence to form DNA/RNA duplex containing a G•U wobble in the middle. The cleavage reaction goes through oxidative elimination mechanism at the nucleoside downstream of U of the G•U wobble in duplex to obtain unnatural RNA terminal, and the whole process is under tight control by using light as switch, which means the cleavage could be carried out according to specific spatial and temporal requirements. The biocompatibility of this method makes the DNA strand in combination with riboflavin a promising molecular tool for RNA manipulation.