Science.gov

Sample records for coastal strand breeding

  1. Hanging by a coastal strand: breeding system of a federally endangered morning-glory of the south-eastern Florida coast, Jacquemontia reclinata

    PubMed Central

    Pinto-Torres, Elena; Koptur, Suzanne

    2009-01-01

    Background and Aims Coastal development has led to extensive habitat destruction and the near extinction of the beach clustervine, Jacquemontia reclinata (Convolvulaceae), an endangered, perennial vine endemic to dune and coastal strand communities in south-eastern Florida. We examined the breeding system of this rare species, and observed visitors to its flowers, as part of a larger effort to document its status and facilitate its recovery. Methods Reproductively mature experimental plants were grown from seed collected from wild plants in two of the largest remaining populations. Controlled hand pollinations on potted plants were conducted to determine the level of compatibility of the species and to investigate compatibility within and between populations. Seeds from the hand pollinations were planted in soil, and they were monitored individually, recording time to seed germination (cotyledon emergence). Wild plants were observed in several of the remaining populations to determine which species visited the flowers. Key Results Hand pollination and seed planting experiments indicate that J. reclinata has a mixed mating system: flowers are able to set fruit with viable seeds with self-pollen, but outcross pollen produces significantly greater fruit and seed set than self-pollen (≥50 % for crosses vs. <25 % for self-pollinations). Visitors included a wide array of insect species, primarily of the orders Diptera, Hymenoptera and Lepidoptera. All visitors captured and examined carried J. reclinata pollen, and usually several other types of pollen. Conclusions Remnant populations of beach clustervine will have greater reproductive success not only if floral visitor populations are maintained, but also if movement of either pollen or seed takes place between populations. Restoration efforts should include provisions for the establishment and maintenance of pollinator populations. PMID:19797424

  2. Environmental gradients explain species richness and community composition of coastal breeding birds in the Baltic Sea.

    PubMed

    Nord, Maria; Forslund, Pär

    2015-01-01

    Scientifically-based systematic conservation planning for reserve design requires knowledge of species richness patterns and how these are related to environmental gradients. In this study, we explore a large inventory of coastal breeding birds, in total 48 species, sampled in 4646 1 km2 squares which covered a large archipelago in the Baltic Sea on the east coast of Sweden. We analysed how species richness (α diversity) and community composition (β diversity) of two groups of coastal breeding birds (specialists, i.e. obligate coastal breeders; generalists, i.e. facultative coastal breeders) were affected by distance to open sea, land area, shoreline length and archipelago width. The total number of species per square increased with increasing shoreline length, but increasing land area counteracted this effect in specialists. The number of specialist bird species per square increased with decreasing distance to open sea, while the opposite was true for the generalists. Differences in community composition between squares were associated with differences in land area and distance to open sea, both when considering all species pooled and each group separately. Fourteen species were nationally red-listed, and showed similar relationships to the environmental gradients as did all species, specialists and generalists. We suggest that availability of suitable breeding habitats, and probably also proximity to feeding areas, explain much of the observed spatial distributions of coastal birds in this study. Our findings have important implications for systematic conservation planning of coastal breeding birds. In particular, we provide information on where coastal breeding birds occur and which environments they seem to prefer. Small land areas with long shorelines are highly valuable both in general and for red-listed species. Thus, such areas should be prioritized for protection against human disturbance and used by management in reserve selection.

  3. Environmental Gradients Explain Species Richness and Community Composition of Coastal Breeding Birds in the Baltic Sea

    PubMed Central

    Nord, Maria; Forslund, Pär

    2015-01-01

    Scientifically-based systematic conservation planning for reserve design requires knowledge of species richness patterns and how these are related to environmental gradients. In this study, we explore a large inventory of coastal breeding birds, in total 48 species, sampled in 4646 1 km2 squares which covered a large archipelago in the Baltic Sea on the east coast of Sweden. We analysed how species richness (α diversity) and community composition (β diversity) of two groups of coastal breeding birds (specialists, i.e. obligate coastal breeders; generalists, i.e. facultative coastal breeders) were affected by distance to open sea, land area, shoreline length and archipelago width. The total number of species per square increased with increasing shoreline length, but increasing land area counteracted this effect in specialists. The number of specialist bird species per square increased with decreasing distance to open sea, while the opposite was true for the generalists. Differences in community composition between squares were associated with differences in land area and distance to open sea, both when considering all species pooled and each group separately. Fourteen species were nationally red-listed, and showed similar relationships to the environmental gradients as did all species, specialists and generalists. We suggest that availability of suitable breeding habitats, and probably also proximity to feeding areas, explain much of the observed spatial distributions of coastal birds in this study. Our findings have important implications for systematic conservation planning of coastal breeding birds. In particular, we provide information on where coastal breeding birds occur and which environments they seem to prefer. Small land areas with long shorelines are highly valuable both in general and for red-listed species. Thus, such areas should be prioritized for protection against human disturbance and used by management in reserve selection. PMID:25714432

  4. Distribution of breeding shorebirds on the Arctic Coastal Plain of Alaska

    USGS Publications Warehouse

    Johnson, J.A.; Lanctot, Richard B.; Andres, B.A.; Bart, J.R.; Brown, S.C.; Kendall, S.J.; Payer, David C.

    2007-01-01

    Available information on the distribution of breeding shorebirds across the Arctic Coastal Plain of Alaska is dated, fragmented, and limited in scope. Herein, we describe the distribution of 19 shorebird species from data gathered at 407 study plots between 1998 and 2004. This information was collected using a single-visit rapid area search technique during territory establishment and early incubation periods, a time when social displays and vocalizations make the birds highly detectable. We describe the presence or absence of each species, as well as overall numbers of species, providing a regional perspective on shorebird distribution. We compare and contrast our shorebird distribution maps to those of prior studies and describe prominent patterns of shorebird distribution. Our examination of how shorebird distribution and numbers of species varied both latitudinally and longitudinally across the Arctic Coastal Plain of Alaska indicated that most shorebird species occur more frequently in the Beaufort Coastal Plain ecoregion (i.e., closer to the coast) than in the Brooks Foothills ecoregion (i.e., farther inland). Furthermore, the occurrence of several species indicated substantial longitudinal directionality. Species richness at surveyed sites was highest in the western portion of the Beaufort Coastal Plain ecoregion. The broad-scale distribution information we present here is valuable for evaluating potential effects of human development and climate change on Arctic-breeding shorebird populations. ?? The Arctic Institute of North America.

  5. Skeletal abnormalities in humpback whales Megaptera novaeangliae stranded in the Brazilian breeding ground.

    PubMed

    Groch, Kátia R; Marcondes, Milton C C; Colosio, Adriana C; Catão-Dias, José Luiz

    2012-11-08

    Skeletal tissues of 49 humpback whales Megaptera novaeangliae that stranded between 2002 and 2011 along the Abrolhos Bank seashore and its adjacent waters in Brazil were studied. Twelve (24.5%) animals presented pathological changes in one or more bones. Degenerative changes and developmental malformations were most frequent (10.2% each), followed by inflammatory/infectious and traumatic lesions (8.2% each). Infectious diseases led to severe lesions of the caudal vertebrae of 2 whales. In one of these individuals, the lesions involved 6 caudal vertebrae, leading to ankylosis of 3 vertebrae. Degenerative changes were observed in the vertebral columns of 3 animals, involving the joints of 13 ribs of 1 individual, and in the humerus of 1 whale. Traumatic lesions, such as osseous callus in the ribs, were observed in 4 animals. In 1 whale, the rib showed severe osteomyelitis, possibly resulting from the infection of multiple fractures. Developmental abnormalities such as spina bifida on 3 cervical vertebrae of 1 whale, fusion of spinal processes on thoracic vertebrae of 1 individual and fusion of the first 2 ribs unilaterally or bilaterally in 4 animals were found. Chronic infectious conditions found in the axial skeleton may have restrained spinal mobility and had detrimental effects on the general health of the animals, contributing to stranding and death. To our knowledge, this is the first systematic study on skeletal lesions in stranded humpback whales.

  6. Estimating occurrence and detection probabilities for stream-breeding salamanders in the Gulf Coastal Plain

    USGS Publications Warehouse

    Lamb, Jennifer Y.; Waddle, J. Hardin; Qualls, Carl P.

    2017-01-01

    Large gaps exist in our knowledge of the ecology of stream-breeding plethodontid salamanders in the Gulf Coastal Plain. Data describing where these salamanders are likely to occur along environmental gradients, as well as their likelihood of detection, are important for the prevention and management of amphibian declines. We used presence/absence data from leaf litter bag surveys and a hierarchical Bayesian multispecies single-season occupancy model to estimate the occurrence of five species of plethodontids across reaches in headwater streams in the Gulf Coastal Plain. Average detection probabilities were high (range = 0.432–0.942) and unaffected by sampling covariates specific to the use of litter bags (i.e., bag submergence, sampling season, in-stream cover). Estimates of occurrence probabilities differed substantially between species (range = 0.092–0.703) and were influenced by the size of the upstream drainage area and by the maximum proportion of the reach that dried. The effects of these two factors were not equivalent across species. Our results demonstrate that hierarchical multispecies models successfully estimate occurrence parameters for both rare and common stream-breeding plethodontids. The resulting models clarify how species are distributed within stream networks, and they provide baseline values that will be useful in evaluating the conservation statuses of plethodontid species within lotic systems in the Gulf Coastal Plain.

  7. Investigating coastal erosion variability and framework geology influence along the Grand Strand, South Carolina

    NASA Astrophysics Data System (ADS)

    Dolan, Aundrea Marie

    Increasing erosional pressures along coastal systems require a better understanding of the mechanisms of natural and human-induced alterations. This is especially important in sediment-starved coastal systems where the effects from geologic framework may exert a disproportionate influence on shoreline behavior. Existing studies into geologic framework and shoreline variability are comprehensive and well documented; yet analysis into the spatial relationships between shoreline variability, lower shoreface morphodynamics, and framework in South Carolina is limited. The Grand Strand region of South Carolina has an extensive set of geophysical data, such as CHIRP seismic, sidescan sonar, borehole logs, and inner shelf cores. In addition, there is a rich suite of RTK-DGPS surveys of a shoreline contour (MHW; 0.625 m) collected monthly since 2007 to consider shoreline variability over 52 km of coastline. Calculation of various statistical parameters using the USGS Digital Shoreline Analysis System v4.2 software, including end point rate (EPR), linear regression rate (LRR) and shoreline change envelope (SCE), provides quantitative assessment of shoreline behavior. Spectral analysis is utilized to define patterns in spatial variability. In effort to target the sediment-limited lower shoreface, a multibeam survey of the region was acquired and identified sections of low relief, low backscatter cuspate-like linear scour depression features in close proximity to the depth of closure. The 6-meter contour wad digitized onto backscatter imagery and intensity values were extracted and correlated to shoreline (MHW) change throughout the study area. Chi-square analysis and correlations between geologic and physical metrics (e.g. paleochannel presence, shoreface slope, backscatter intensity) were computed to identify spatial relationships. Analyses indicate a relationship between shoreline change and backscatter intensity where deep paleochannels were present. Furthermore, power

  8. ERTS surveys a 500 km squared locust breeding site in Saudi Arabia. [Red Sea coastal plain

    NASA Technical Reports Server (NTRS)

    Pedgley, D. E.

    1974-01-01

    From September 1972 to January 1973, ERTS-1 precisely located a 500 sq km area on the Red Sea coastal plain of Saudi Arabia within which the Desert Locust (Schistocerca gregaria, Forsk.) bred successfully and produced many small swarms. Growth of vegetation shown by satellite imagery was confirmed from ground surveys and raingauge data. The experiment demonstrates the feasibility of detecting potential locust breeding sites by satellite, and shows that an operational satellite would be a powerful tool for routine survey of the 3 x 10 to the 7th power sq km invasion area of the Desert Locust in Africa and Asia, as well as of other locust species in the arid and semi-arid tropics.

  9. Predicting breeding shorebird distributions on the Arctic Coastal Plain of Alaska

    USGS Publications Warehouse

    Saalfeld, Sarah T.; Lanctot, Richard B.; Brown, Stephen C.; Saalfeld, David T.; Johnson, James A.; Andres, Brad A.; Bart, Jonathan R.

    2013-01-01

    The Arctic Coastal Plain (ACP) of Alaska is an important region for millions of migrating and nesting shorebirds. However, this region is threatened by climate change and increased human development (e.g., oil and gas production) that have the potential to greatly impact shorebird populations and breeding habitat in the near future. Because historic data on shorebird distributions in the ACP are very coarse and incomplete, we sought to develop detailed, contemporary distribution maps so that the potential impacts of climate-mediated changes and development could be ascertained. To do this, we developed and mapped habitat suitability indices for eight species of shorebirds (Black-bellied Plover [Pluvialis squatarola], American Golden-Plover [Pluvialis dominica], Semipalmated Sandpiper [Calidris pusilla], Pectoral Sandpiper [Calidris melanotos], Dunlin [Calidris alpina], Long-billed Dowitcher [Limnodromus scolopaceus], Red-necked Phalarope [Phalaropus lobatus], and Red Phalarope [Phalaropus fulicarius]) that commonly breed within the ACP of Alaska. These habitat suitability models were based on 767 plots surveyed during nine years between 1998 and 2008 (surveys were not conducted in 2003 and 2005), using single-visit rapid area searches during territory establishment and incubation (8 June, 1 July). Species specific habitat suitability indices were developed and mapped using presence-only modeling techniques (partitioned Mahalanobis distance) and landscape environmental variables. For most species, habitat suitability was greater at lower elevations (i.e., near the coast and river deltas) and lower within upland habitats. Accuracy of models was high for all species, ranging from 65 -98%. Our models predicted that the largest fraction of suitable habitat for the majority of species occurred within the National Petroleum Reserve-Alaska, with highly suitable habitat also occurring within coastal areas of the Arctic National Wildlife Refuge west to Prudhoe Bay.

  10. Accumulation pattern of organochlorine pesticides and polychlorinated biphenyls in sourthern sea otters (Enhydra lutris nereis) found stranded along coastal California, USA

    USGS Publications Warehouse

    Nakata, H.; Kannan, K.; Jing, L.; Thomas, N.J.; Tanabe, S.; Giesy, J.P.

    1998-01-01

    Concentrations of PCBs, DDTs (p,p'-DDE, p,p'-DDD and p,p'-DDT), HCHs (α-, β-, γ-isomers), chlordanes (trans-chlordane, cis-chlordane, trans-nonachlor, cis-nonachlor and oxychlordane) and HCB (hexachlorobenzene were measured in liver, kidney and brain tissues of adult southern sea otters (Enhydra lutris nereis) found stranded along coastal California, USA, during 1992–96. The contamination pattern of organochlorines in sea otters from several locations was in the order of DDTs > PCBs > > CHLs > HCHs > > HCB, whereas those from Monterey Harbor contained greater concentrations of PCBs than of DDTs. Hepatic concentrations of PCBs and DDTs were in the ranges of 58–8700 and 280–5900 ng/g, wet weight, respectively, which varied depending on the geographic location. Sea otters collected from Monterey Harbor contained the greatest concentrations of PCBs and DDTs. In general, accumulation of DDTs, CHLs and PCBs was greater in kidney than in liver, whereas that of HCHs was similar in both the tissues. The gender difference in organochlorine concentrations was less than those reported in cetaceans. The composition of DDTs, HCHs and CHLs compounds in sea otter tissues indicated no recent inputs of these compounds in coastal California. Sea otters that died from infectious diseases, neoplasia and emaciation contained higher concentrations of DDTs than those that died from trauma.

  11. Polychlorinated biphenyls, organochlorine pesticides, tris(4-chlorophenyl)methane, and tris(4-chlorophenyl)methanol in livers of small cetaceans stranded along Florida coastal waters, USA

    SciTech Connect

    Watanabe, Mafumi; Kannan, Kurunthachalam; Takahashi, Atsushi; Loganathan, B.G.; Odell, D.K.; Tanabe, Shinsuke; Giesy, J.P.

    2000-06-01

    Concentrations of polychlorinated biphenyl congeners (PCBs) and organochlorine pesticides were determined in the livers of bottlenose dolphins, Atlantic spotted dolphins, and pygmy sperm whales found stranded along the coastal waters of Florida, USA, during 1989 to 1994. The PCBs were the most predominant contaminants followed in order by DDTs, chlordanes, tris(4-chlorophenyl)methane (TCPMe), tris(4-chlorophenyl)methanol (TCPMOH), hexachlorobenzene, and hexachlorocyclohexane isomers. Among the cetaceans analyzed, organochlorine concentrations were greatest in bottlenose dolphins followed by Atlantic spotted dolphins and pygmy sperm whales. Hexa- and heptachlorobiphenyls were the predominant PCB congeners found in the livers of dolphins. Patterns of relative concentrations of PCB congeners varied among individual bottlenose dolphins. A few individuals contained predominant concentrations of octa- (CB-199, 196/201) and nonachlorobiphenyl (CB-206, 208) congeners, which suggested exposure to the highly chlorinated PCB formulation, Aroclor{reg_sign} 1268, a contaminant at a coastal site in Georgia bordering northern Florida. The estimated 2,3,7,8-tetrachlorodibenzo-p-dioxin toxic equivalents (TEQs) of coplanar PCBs in bottlenose dolphins were 170 to 18,000 pg/g, lipid weight (mean:5,400 pg/g) with mono-ortho congeners 118, 105, and 156 contributing more than 80% of the TEQs. The ratios of CB-169 to CB-126 in cetacean livers were linearly related to total PCB concentrations, which suggested a strong induction of microsomal monooxygenase enzymes in the liver. The hepatic concentrations of TCPMe and TCPMOH in bottlenose dolphins and Atlantic spotted dolphins were greater than those in the blubber of marine mammals of various regions, which suggested the presence of sources for these chemicals along the Atlantic coast of Florida.

  12. Reproductive performances and kid's mortality of pure breeds and crossed caprine genotypes in the coastal oases of southern Tunisia.

    PubMed

    Gaddour, Amor; Najari, Sghaier; Abdennebi, Mouldi; Ouni, Mabrouk

    2007-07-15

    In order to improve goat productivity in the arid regions of Tunisia, a crossing scheme of the local goat population by high performance breeds was applied under oases conditions. To cross local population, Alpine, Damascus and Murciana Granadina breeds were imported and used as paternal genotypes in several cross generation. The survey of pure breeds and crossed genotypes permitted to collect the zootechnical performances during 16 years under an intensive breeding mode. The analysis of 644 fertility, prolificacy, fecundity, abortion and sterility and kid's mortality ratio showed an important difference between the studied genotypes performances. The local goat prolificacy rate was 153% in average. The kid's mortality ratio was the highest for Alpine breed and its crossed genotypes with a ratio of 4 and 3%, respectively. The first and the second generations, the crossed Damascus x Local had a fertility of 98 and 100%, showing an important heterosis effect. Also, the reproductive performances of the imported breeds were largely lower than those of the local population. Kid's mortality and reproductive performances are largely related to the genotype adaptative potentialities.

  13. Kid's growth and dairy performances of pure breeds and crossed caprine genotypes in the coastal oases of southern Tunisia.

    PubMed

    Gaddour, Amor; Najari, Sghaier; Ouni, Mabrouk

    2007-09-01

    A data issued from 16 years performances schedule of local goat, Alpine, Damascus, Murciana and crossed groups was used to study the genotypes productive behaviour under Tunisian oases conditions. The aim is to evaluate the possibilities of local goat productivity improvement by cross breeding in intensive mode and also, to choose the better improving breed and the propice crossing level. So, data of periodic individual weighing was used to estimates kid's weight at some standard ages and dairy performances such as, daily milk average, total production by lactation and milking period of studied genetic goats groups. Statistical analysis of about 1928 kid's weights and 1923 individual goat milking shows that, the cross breeding allows to improve the growth performances since the first generation with respect to local population production. ANOVA test shows an important effect of genotypes and environment upon kid's weights (p < 0.01). The kid's weight average at birth and at 120 days age was about 3.49 and 15.78 kg, respectively. The cross breeding second generation allows the better improvement of local goat potentialities kid's weight at 120 days reaches 16.19 kg for Damascus x local genotype. The dairy production with this generation is, about 248 kg for the Alpine one, of 181 kg for Damascus and 190 kg for Murciana, is only 137 kg by lactation for the local breed.

  14. Spatial clustering of Aedes aegypti related to breeding container characteristics in Coastal Ecuador: implications for dengue control.

    PubMed

    Schafrick, Nathaniel H; Milbrath, Meghan O; Berrocal, Veronica J; Wilson, Mark L; Eisenberg, Joseph N S

    2013-10-01

    Mosquito management within households remains central to the control of dengue virus transmission. An important factor in these management decisions is the spatial clustering of Aedes aegypti. We measured spatial clustering of Ae. aegypti in the town of Borbón, Ecuador and assessed what characteristics of breeding containers influenced the clustering. We used logistic regression to assess the spatial extent of that clustering. We found strong evidence for juvenile mosquito clustering within 20 m and for adult mosquito clustering within 10 m, and stronger clustering associations for containers ≥ 40 L than those < 40 L. Aedes aegypti clusters persisted after adjusting for various container characteristics, suggesting that patterns are likely attributable to short dispersal distances rather than shared characteristics of containers in cluster areas. These findings have implications for targeting Ae. aegypti control efforts.

  15. Mapping and assessing variability in the Antarctic marginal ice zone, pack ice and coastal polynyas in two sea ice algorithms with implications on breeding success of snow petrels

    NASA Astrophysics Data System (ADS)

    Stroeve, Julienne C.; Jenouvrier, Stephanie; Campbell, G. Garrett; Barbraud, Christophe; Delord, Karine

    2016-08-01

    Sea ice variability within the marginal ice zone (MIZ) and polynyas plays an important role for phytoplankton productivity and krill abundance. Therefore, mapping their spatial extent as well as seasonal and interannual variability is essential for understanding how current and future changes in these biologically active regions may impact the Antarctic marine ecosystem. Knowledge of the distribution of MIZ, consolidated pack ice and coastal polynyas in the total Antarctic sea ice cover may also help to shed light on the factors contributing towards recent expansion of the Antarctic ice cover in some regions and contraction in others. The long-term passive microwave satellite data record provides the longest and most consistent record for assessing the proportion of the sea ice cover that is covered by each of these ice categories. However, estimates of the amount of MIZ, consolidated pack ice and polynyas depend strongly on which sea ice algorithm is used. This study uses two popular passive microwave sea ice algorithms, the NASA Team and Bootstrap, and applies the same thresholds to the sea ice concentrations to evaluate the distribution and variability in the MIZ, the consolidated pack ice and coastal polynyas. Results reveal that the seasonal cycle in the MIZ and pack ice is generally similar between both algorithms, yet the NASA Team algorithm has on average twice the MIZ and half the consolidated pack ice area as the Bootstrap algorithm. Trends also differ, with the Bootstrap algorithm suggesting statistically significant trends towards increased pack ice area and no statistically significant trends in the MIZ. The NASA Team algorithm on the other hand indicates statistically significant positive trends in the MIZ during spring. Potential coastal polynya area and amount of broken ice within the consolidated ice pack are also larger in the NASA Team algorithm. The timing of maximum polynya area may differ by as much as 5 months between algorithms. These

  16. Polychlorinated biphenyls and their hydroxylated metabolites (OH-PCBs) in the blood of toothed and baleen whales stranded along Japanese coastal waters.

    PubMed

    Nomiyama, Kei; Murata, Satoko; Kunisue, Tatsuya; Yamada, Tadasu K; Mizukawa, Hazuki; Takahashi, Shin; Tanabe, Shinsuke

    2010-05-15

    In this study, we determined the residue levels and patterns of polychlorinated biphenyls (PCBs) and hydroxylated PCBs (OH-PCBs) in the blood from eight species of toothed whales and three species of baleen whales stranded along the Japanese coast during 1999-2007. Penta- through hepta-chlorinated PCB congeners were the dominant homologue groups in all cetaceans. In contrast, specific differences in the distribution of dominant OH-PCB isomers and homologues were found among the cetacean species. In five species of toothed whales (melon-headed whale, Stejneger's beaked whale, Pacific white-sided dolphin, Blainville's beaked whale, and killer whale), the predominant homologues were OH-penta-PCBs followed by OH-tetra-PCBs and OH-tri-PCBs. The predominant homologues of finless porpoise and beluga whale were OH-penta-PCBs followed by OH-hexa-PCBs and OH-tri-PCBs. The predominant OH-PCB isomers were para-OH-PCBs such as 4OH-CB26, 4'OH-CB25/4'OH-CB26/4OH-CB31, 4OH-CB70, 4'OH-CB72, 4'OH-CB97, 4'OH-CB101/4'OH-CB120, and 4OH-CB107/4'OH-CB108 in toothed whales. In three baleen whales (common minke whale, Bryde's whale, and humpback whale) and in sperm whale (which is a toothed whale), OH-octa-PCB (4OH-CB202) was the predominant homologue group accounting for 40-80% of the total OH-PCB concentrations. The differences in concentrations and profiles of OH-PCBs may suggest species-specific diets, metabolic capability, and the transthyretin (TTR) binding specificity. These results reveal that the accumulation profiles of OH-PCBs in cetacean blood are entirely different from the profiles found in pinnipeds, polar bear, and humans.

  17. Environmental Predictors of Seabird Wrecks in a Tropical Coastal Area

    PubMed Central

    Fulgencio de Moura, Jailson; Siciliano, Salvatore

    2016-01-01

    Beached bird surveys have been widely used to monitor the impact of oil pollution in the oceans. However, separating the combined effects of oil pollution, environmental variables and methodological aspects of beach monitoring on seabird stranding patterns is a challenging task. The effects of a comprehensive set of oceanographic and climatic variables and oil pollution on seabird strandings in a tropical area of Brazil were investigated herein, using two robust and innovative methods: Generalized Linear Mixed Models and Structural Equation Modeling. We assessed strandings of four resident seabird species along 480 km of beaches divided into 11 sampling areas, between November 2010 and September 2013. We found that increasing the distance from the nearest breeding island reduce the seabird stranding events. Storm activity and biological productivity were the most important factors affecting the stranding events of brown boobies Sula leucogaster, Cabot’s terns Thalasseus acuflavidus and kelp gulls Larus dominicanus. These species are also indirectly affected by warm tropical waters, which reduce chlorophyll-a concentrations. Beach surveys are, thus, useful to investigate the mortality rates of resident species near breeding sites, where individuals are more abundant and exposed to local factors associated with at-sea mortality. In contrast, conservation actions and monitoring programs for far-ranging seabird species are needed in more distant foraging areas. Furthermore, beach monitoring programs investigating the impact of oil pollution on seabirds need to account for the effects of environmental factors on stranding patterns. The present study also demonstrated that seabirds inhabiting tropical coastal waters are sensitive to climate conditions such as adverse weather, which are expected to increase in frequency and intensity in next decades. PMID:27992578

  18. Environmental Predictors of Seabird Wrecks in a Tropical Coastal Area.

    PubMed

    Tavares, Davi Castro; Fulgencio de Moura, Jailson; Siciliano, Salvatore

    2016-01-01

    Beached bird surveys have been widely used to monitor the impact of oil pollution in the oceans. However, separating the combined effects of oil pollution, environmental variables and methodological aspects of beach monitoring on seabird stranding patterns is a challenging task. The effects of a comprehensive set of oceanographic and climatic variables and oil pollution on seabird strandings in a tropical area of Brazil were investigated herein, using two robust and innovative methods: Generalized Linear Mixed Models and Structural Equation Modeling. We assessed strandings of four resident seabird species along 480 km of beaches divided into 11 sampling areas, between November 2010 and September 2013. We found that increasing the distance from the nearest breeding island reduce the seabird stranding events. Storm activity and biological productivity were the most important factors affecting the stranding events of brown boobies Sula leucogaster, Cabot's terns Thalasseus acuflavidus and kelp gulls Larus dominicanus. These species are also indirectly affected by warm tropical waters, which reduce chlorophyll-a concentrations. Beach surveys are, thus, useful to investigate the mortality rates of resident species near breeding sites, where individuals are more abundant and exposed to local factors associated with at-sea mortality. In contrast, conservation actions and monitoring programs for far-ranging seabird species are needed in more distant foraging areas. Furthermore, beach monitoring programs investigating the impact of oil pollution on seabirds need to account for the effects of environmental factors on stranding patterns. The present study also demonstrated that seabirds inhabiting tropical coastal waters are sensitive to climate conditions such as adverse weather, which are expected to increase in frequency and intensity in next decades.

  19. Investigation of Comparative Mosquito Breeding in Dredged Material Disposal Sites Used in the Maintenance Dredging of the Atlantic Intra-Coastal Waterway in South Carolina.

    DTIC Science & Technology

    1978-01-01

    necessarily restricted to the crepuscular periods. A. soJcitanr and to a lesser extent, A. taeniorkychs will attack at anytime of day or night-even in...fully sunlit areas. 14 . Breeding habits: Mosquitoes of the floodwater group are similiar in many respects and they share the common habit of depositing...distribution of Acjco mosquito eggs on saltmarshes was correlated with vegetational type. 16. Once laid, eggs require a few days for embryonic development and

  20. Apricot Breeding

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Apricot orchard area and fruit production are increasing worldwide. Breeding programs engage in apricot development to provide new varieties to meet needs of producers and consumers. Over the last 20 years, breeders have used new techniques to assist in variety development and to increase breeding...

  1. Molecular breeding

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Use of molecular and genomic tools to assist selection of parents or progeny has become an integral part of modern cotton breeding. In this chapter, the basic components of molecular cotton breeding are described. These components include: molecular marker development, genetic and physical map const...

  2. Migratory double breeding in Neotropical migrant birds.

    PubMed

    Rohwer, Sievert; Hobson, Keith A; Rohwer, Vanya G

    2009-11-10

    Neotropical migratory songbirds typically breed in temperate regions and then travel long distances to spend the majority of the annual cycle in tropical wintering areas. Using stable-isotope methodology, we provide quantitative evidence of dual breeding ranges for 5 species of Neotropical migrants. Each is well known to have a Neotropical winter range and a breeding range in the United States and Canada. However, after their first bout of breeding in the north, many individuals migrate hundreds to thousands of kilometers south in midsummer to breed a second time during the same summer in coastal west Mexico or Baja California Sur. They then migrate further south to their final wintering areas in the Neotropics. Our discovery of dual breeding ranges in Neotropical migrants reveals a hitherto unrealized flexibility in life-history strategies for these species and underscores that demographic models and conservation plans must consider dual breeding for these migrants.

  3. Migratory double breeding in Neotropical migrant birds

    PubMed Central

    Rohwer, Sievert; Hobson, Keith A.; Rohwer, Vanya G.

    2009-01-01

    Neotropical migratory songbirds typically breed in temperate regions and then travel long distances to spend the majority of the annual cycle in tropical wintering areas. Using stable-isotope methodology, we provide quantitative evidence of dual breeding ranges for 5 species of Neotropical migrants. Each is well known to have a Neotropical winter range and a breeding range in the United States and Canada. However, after their first bout of breeding in the north, many individuals migrate hundreds to thousands of kilometers south in midsummer to breed a second time during the same summer in coastal west Mexico or Baja California Sur. They then migrate further south to their final wintering areas in the Neotropics. Our discovery of dual breeding ranges in Neotropical migrants reveals a hitherto unrealized flexibility in life-history strategies for these species and underscores that demographic models and conservation plans must consider dual breeding for these migrants. PMID:19858484

  4. Simulated Breeding

    NASA Astrophysics Data System (ADS)

    Unemi, Tatsuo

    This chapter describes a basic framework of simulated breeding, a type of interactive evolutionary computing to breed artifacts, whose origin is Blind Watchmaker by Dawkins. These methods make it easy for humans to design a complex object adapted to his/her subjective criteria, just similarly to agricultural products we have been developing over thousands of years. Starting from randomly initialized genome, the solution candidates are improved through several generations with artificial selection. The graphical user interface helps the process of breeding with techniques of multifield user interface and partial breeding. The former improves the diversity of individuals that prevents being trapped at local optimum. The latter makes it possible for the user to fix features he/she already satisfied. These methods were examined through artistic applications by the author: SBART for graphics art and SBEAT for music. Combining with a direct genome editor and exportation to another graphical or musical tool on the computer, they can be powerful tools for artistic creation. These systems may contribute to the creation of a type of new culture.

  5. Stressed Kevlar strand test

    SciTech Connect

    Golopol, H.; Clarkson, J.; Moore, R.; Hetherington, N.

    1981-09-10

    Kevlar is a polyaramid fiber used in fiber composites. In order to characterize this material, we determined the effect of time, temperature, and chemical environment on the strength retention of stressed Kevlar strands. In this work, we applied a stress load of 20% of the ultimate tensile strength (UTS). Strands were hung with a suitable weight in a closed container. Each container was then provided with its own heater and chemical environment. No significant loss of strength retention was found on these stressed strands. 4 figures, 5 tables.

  6. Patterns of Seasonal Abundance and Social Segregation in Inland and Coastal Plain Swamp Sparrows in a Delaware Tidal Marsh

    EPA Science Inventory

    The Coastal Plain Swamp Sparrow (Melospiza georgiana nigrescens, CPSS) breeds in the coastal brackish marshes of the North American Mid-Atlantic States. During the non-breeding season, coastal brackish marshes are occupied by both this subspecies and two far more widespread inte...

  7. Coastal sedimentation

    NASA Technical Reports Server (NTRS)

    Schubel, J. R.

    1980-01-01

    Several important coastal sedimentation problems are identified. Application of existing or anticipated remote sensing techniques to examine these problems is considered. Specifically, coastal fine particle sediment systems, floods and hy hurricanes and sedimentation f of coastal systems, routes and rates of sediment transport on continental shelves, and dredging and dredged material disposal are discussed.

  8. Sustainability Of Coastal Fringe Ecosystems Against Anthropogenic Chemical Stressors

    EPA Science Inventory

    Plant-dominated coastal ecosystems provide least 21 ecological services including shoreline protection, contaminant removal and nursery and breeding habitat for biota. The value of these ecological services is as great as $28000/h. These ecosystems which include intertidal wetl...

  9. Coastal Prairie

    USGS Publications Warehouse

    ,

    2000-01-01

    The coastal prairie, located along the coastal plain of southwestern Louisiana and southcentral Texas, is the southernmost tip of the tallgrass prairie ecosystem so prevalent in the Midwest. The coastal prairie ecosystem once covered as much as 3.8 million ha (9 million acres); today, more than 99% of this land has been lost to agriculture, range improvement, and urbanization. The remainder is highly fragmented and severely threatened by invasions of exotic species and urban sprawl. In Louisiana, the former 1 million ha of coastal prairie have now been reduced to about 100 ha. In Texas, only about 100,000 ha of coastal prairie remain intact.

  10. Temporal trends of perfluoroalkyl substances (PFAS) in eggs of coastal and offshore birds: Increasing PFAS levels associated with offshore bird species breeding on the Pacific coast of Canada and wintering near Asia.

    PubMed

    Miller, Aroha; Elliott, John E; Elliott, Kyle H; Lee, Sandi; Cyr, Francois

    2015-08-01

    Perfluoroalkyl substances (PFAS) such as perfluoroalkyl carboxylates (PFCAs) and perfluoroalkyl sulfonates (PFSAs) have become virtually ubiquitous throughout the environment, and, based on laboratory studies, have known toxicological consequences. Various national and international voluntary phase-outs and restrictions on these compounds have been implemented over the last 10 to 15 years. In the present study, we examine trends (1990/1991-2010/2011) in aquatic birds (ancient murrelet, Synthliboramphus antiquus [2009 only]; Leach's storm-petrels, Oceanodroma leucorhoa; rhinoceros auklets, Cerorhinca monocerata; double-crested cormorants, Phalacrocorax auritus; and great blue herons, Ardea herodias). The PFCA, PFSA, and stable isotope (δ(15) N and δ(13) C) data collected from these species from the Pacific coast of Canada, ranging over 20 to 30 years, were used to investigate temporal changes in PFAS coupled to dietary changes. Perfluorooctane sulfonic acid (PFOS), the dominant PFSA compound in all 4 species, increased and subsequently decreased in auklet and cormorant eggs in line with the manufacturing phase-out of PFOS and perfluorooctanoic acid (PFOA), but concentrations continuously increased in petrel eggs and remained largely unchanged in heron eggs. Dominant PFCA compounds varied between the offshore and coastal species, with increases seen in the offshore species and little or variable changes seen in the coastal species. Little temporal change was seen in stable isotope values, indicating that diet alone is not driving observed PFAS concentrations.

  11. Stranding Events of Kogia Whales along the Brazilian Coast

    PubMed Central

    Moura, Jailson F.; Acevedo-Trejos, Esteban; Tavares, Davi C.; Meirelles, Ana C. O.; Silva, Cristine P. N.; Oliveira, Larissa R.; Santos, Roberta A.; Wickert, Janaína C.; Machado, Rodrigo; Siciliano, Salvatore; Merico, Agostino

    2016-01-01

    The genus Kogia, which comprises only two extant species, Kogia sima and Kogia breviceps, represents one of the least known groups of cetaceans in the global ocean. In some coastal regions, however, stranding events of these species have been relatively common over the last decades. Stranding provides the opportunity to investigate the biology of these cetaceans and to explore the epidemiological aspects associated with the mortality of the organisms found on the beach. A number of disturbances (including pelagic fisheries, chemical pollution, boat strikes, and noise pollution) have been confirmed to pose a particular threat to the Kogia species. However, no study has yet investigated potential relationships between environmental conditions and stranding events. Here we analyse how a collection of environmental, physical, and biological variables, such as wind, sea surface temperature (SST), water depth, and chlorophyll-a, correlate to Kogia stranding events along the Brazilian coast. The results of our statistical analyses suggest that K. sima is more likely found in warm tropical waters, which provide an explanation for the high frequency of stranding in northeastern Brazilian coast. In contrast, K. breviceps appears to have a preference for temperate and productive waters. Wind speed results to be also an important factor for predicting Kogia strandings in Brazilian coast. Additionally, literature information in combination with our own data and analyses of stomach contents confirms that oceanic cephalopods constitute the primary nutritional source of both Kogia species. By using the available information as a qualitative proxy for habitat preference and feeding ecology, our study provides a novel and comprehensive assessment of Kogia stranding data in relation to environmental conditions along the Brazilian coast. PMID:26730951

  12. Stranding Events of Kogia Whales along the Brazilian Coast.

    PubMed

    Moura, Jailson F; Acevedo-Trejos, Esteban; Tavares, Davi C; Meirelles, Ana C O; Silva, Cristine P N; Oliveira, Larissa R; Santos, Roberta A; Wickert, Janaína C; Machado, Rodrigo; Siciliano, Salvatore; Merico, Agostino

    2016-01-01

    The genus Kogia, which comprises only two extant species, Kogia sima and Kogia breviceps, represents one of the least known groups of cetaceans in the global ocean. In some coastal regions, however, stranding events of these species have been relatively common over the last decades. Stranding provides the opportunity to investigate the biology of these cetaceans and to explore the epidemiological aspects associated with the mortality of the organisms found on the beach. A number of disturbances (including pelagic fisheries, chemical pollution, boat strikes, and noise pollution) have been confirmed to pose a particular threat to the Kogia species. However, no study has yet investigated potential relationships between environmental conditions and stranding events. Here we analyse how a collection of environmental, physical, and biological variables, such as wind, sea surface temperature (SST), water depth, and chlorophyll-a, correlate to Kogia stranding events along the Brazilian coast. The results of our statistical analyses suggest that K. sima is more likely found in warm tropical waters, which provide an explanation for the high frequency of stranding in northeastern Brazilian coast. In contrast, K. breviceps appears to have a preference for temperate and productive waters. Wind speed results to be also an important factor for predicting Kogia strandings in Brazilian coast. Additionally, literature information in combination with our own data and analyses of stomach contents confirms that oceanic cephalopods constitute the primary nutritional source of both Kogia species. By using the available information as a qualitative proxy for habitat preference and feeding ecology, our study provides a novel and comprehensive assessment of Kogia stranding data in relation to environmental conditions along the Brazilian coast.

  13. Tritium breeding in fusion reactors

    SciTech Connect

    Abdou, M.A.

    1982-10-01

    Key technological problems that influence tritium breeding in fusion blankets are reviewed. The breeding potential of candidate materials is evaluated and compared to the tritium breeding requirements. The sensitivity of tritium breeding to design and nuclear data parameters is reviewed. A framework for an integrated approach to improve tritium breeding prediction is discussed with emphasis on nuclear data requirements.

  14. Breeding and genetic diversity

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Corn breeding has been historically remarkably successful. Much research has investigated optimal breeding procedures, which are detailed here. A smaller effort has been put into identifying useful genetic resources for maize and how to best use them, but results from long-term base broadening effor...

  15. Tritium breeding materials

    SciTech Connect

    Hollenberg, G.W.; Johnson, C.E.; Abdou, M.

    1984-03-01

    Tritium breeding materials are essential to the operation of D-T fusion facilities. Both of the present options - solid ceramic breeding materials and liquid metal materials are reviewed with emphasis not only on their attractive features but also on critical materials issues which must be resolved.

  16. Sexual Reproduction and Breeding

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In the second edition of Plant Propagation Concepts and Laboratory Exercises, we have combined the first edition chapters 36: Sexual Reproduction in Angiosperms and 37: Breeding Horticultural Plants into the present single chapter Sexual Reproduction and Breeding. These topics are so closely relate...

  17. Can non-breeding be a cost of breeding dispersal?

    USGS Publications Warehouse

    Danchin, E.; Cam, E.

    2002-01-01

    Breeding habitat selection and dispersal are crucial processes that affect many components of fitness. Breeding dispersal entails costs, one of which has been neglected: dispersing animals may miss breeding opportunities because breeding dispersal requires finding a new nesting site and mate, two time- and energy-consuming activities. Dispersers are expected to be prone to non-breeding. We used the kittiwake (Rissa tridactyla) to test whether breeding dispersal influences breeding probability. Breeding probability was associated with dispersal, in that both were negatively influenced by private information (previous individual reproductive success) and public information (average reproductive success of conspecifics) about patch quality. Furthermore, the probability of skipping breeding was 1.7 times higher in birds that settled in a new patch relative to those that remained on the same patch. Finally, non-breeders that resumed breeding were 4.4 times more likely to disperse than birds that bred in successive years. Although private information may influence breeding probability directly, the link between breeding probability and public information may be indirect, through the influence of public information on breeding dispersal, non-breeding thus being a cost of dispersal. These results support the hypothesis that dispersal may result in not being able to breed. More generally, non-breeding (which can be interpreted as an extreme form of breeding failure) may reveal costs of various previous activities. Because monitoring the non-breeding portion of a population is difficult, non-breeders have been neglected in many studies of reproduction trade-offs.

  18. Classifying Saturn's F Ring Strands

    NASA Astrophysics Data System (ADS)

    Albers, Nicole; Sremcevic, M.; Esposito, L. W.; Colwell, J. E.

    2009-09-01

    The Cassini Ultraviolet Imaging Spectrograph (UVIS) High Speed Photometer (HSP) has recorded more than 113 stellar occultations by Saturn's F ring providing measurements with ring plane resolutions of a few dozen meters and better. Inner and outer F ring strands have been seen throughout the Cassini mission where they revealed themselves as non-continuous, azimuthally and temporally highly variable structures. In the light of a more accurate orbit description of the F ring core we find evidence for a ring that becomes dynamically more active as the system approaches anti-apse alignment with Prometheus. This is consistent with the observed increased strand activity. A recent strand that morphologically resembles the core is the strongest seen to date and points to the intricate relation between core and strands indicating the strands' violent creation. Using more than 150 identifications of various strands, we trace their kinematics and infer dynamical timescales and photometric properties. Implications for the dynamical evolution of the F ring will be discussed. This research was supported by the Cassini Project.

  19. Salinity tolerance of eggs of Buergeria japonica (Amphibia, Anura) inhabiting coastal areas.

    PubMed

    Haramura, Takashi

    2007-08-01

    Buergeria japonica is one of a few frogs that breed in coastal areas. To understand why this species can breed in coastal areas, I tested the salinity tolerance of eggs of B. japonica collected from a coastal area of Okinawa Island, Japan. All eggs hatched within four days after oviposition. At 0%. salinity (control), over 94% of eggs hatched normally, and even at 1 per thousand salinity over 85% of eggs hatched. Survival rate of eggs was low at 2, 3, and 4 per thousand, and no eggs hatched at 5 per thousand salinity. These results indicate that low salinity, close to pure water, is necessary for successful egg development, even for populations of B. japonica that breed in coastal areas. Future studies are necessary to examine whether females of B. japonica breeding in coastal areas select appropriate oviposition sites where the environmental salinity level is sufficiently low for eggs.

  20. Welfare in horse breeding

    PubMed Central

    Campbell, M. L. H.; Sandøe, P.

    2015-01-01

    Welfare problems related to the way horses are bred, whether by coitus or by the application of artificial reproduction techniques (ARTs), have been given no discrete consideration within the academic literature. This paper reviews the existing knowledge base about welfare issues in horse breeding and identifies areas in which data is lacking. We suggest that all methods of horse breeding are associated with potential welfare problems, but also that the judicious use of ARTs can sometimes help to address those problems. We discuss how negative welfare effects could be identified and limited and how positive welfare effects associated with breeding might be maximised. Further studies are needed to establish an evidence base about how stressful or painful various breeding procedures are for the animals involved, and what the lifetime welfare implications of ARTs are for future animal generations. PMID:25908746

  1. Cryptography with DNA binary strands.

    PubMed

    Leier, A; Richter, C; Banzhaf, W; Rauhe, H

    2000-06-01

    Biotechnological methods can be used for cryptography. Here two different cryptographic approaches based on DNA binary strands are shown. The first approach shows how DNA binary strands can be used for steganography, a technique of encryption by information hiding, to provide rapid encryption and decryption. It is shown that DNA steganography based on DNA binary strands is secure under the assumption that an interceptor has the same technological capabilities as sender and receiver of encrypted messages. The second approach shown here is based on steganography and a method of graphical subtraction of binary gel-images. It can be used to constitute a molecular checksum and can be combined with the first approach to support encryption. DNA cryptography might become of practical relevance in the context of labelling organic and inorganic materials with DNA 'barcodes'.

  2. Double stranded nucleic acid biochips

    DOEpatents

    Chernov, Boris; Golova, Julia

    2006-05-23

    This invention describes a new method of constructing double-stranded DNA (dsDNA) microarrays based on the use of pre-synthesized or natural DNA duplexes without a stem-loop structure. The complementary oligonucleotide chains are bonded together by a novel connector that includes a linker for immobilization on a matrix. A non-enzymatic method for synthesizing double-stranded nucleic acids with this novel connector enables the construction of inexpensive and robust dsDNA/dsRNA microarrays. DNA-DNA and DNA-protein interactions are investigated using the microarrays.

  3. Breeding-assisted genomics.

    PubMed

    Poland, Jesse

    2015-04-01

    The revolution of inexpensive sequencing has ushered in an unprecedented age of genomics. The promise of using this technology to accelerate plant breeding is being realized with a vision of genomics-assisted breeding that will lead to rapid genetic gain for expensive and difficult traits. The reality is now that robust phenotypic data is an increasing limiting resource to complement the current wealth of genomic information. While genomics has been hailed as the discipline to fundamentally change the scope of plant breeding, a more symbiotic relationship is likely to emerge. In the context of developing and evaluating large populations needed for functional genomics, none excel in this area more than plant breeders. While genetic studies have long relied on dedicated, well-structured populations, the resources dedicated to these populations in the context of readily available, inexpensive genotyping is making this philosophy less tractable relative to directly focusing functional genomics on material in breeding programs. Through shifting effort for basic genomic studies from dedicated structured populations, to capturing the entire scope of genetic determinants in breeding lines, we can move towards not only furthering our understanding of functional genomics in plants, but also rapidly improving crops for increased food security, availability and nutrition.

  4. 1980 breeding bird censuses

    SciTech Connect

    Raynor, G.S.

    1980-09-01

    As part of a program to characterize the plant and animal life of the Laboratory site and the surrounding region, the two breeding bird censuses originated in 1977 were continued in 1980. Coverage was below that of previous years due to illness and travel of some participants, but 11 trips were made to the BNL plot and 8 to the Westhampton plot. Each was censused by separate teams of three volunteer observers. The number of breeding species and number of territorial males on the BNL plot have progressively declined since 1977 but little change has taken place in either number of territories or species composition on the Westhampton plot.

  5. Molecular detection of Torque teno virus in different breeds of swine

    PubMed Central

    2011-01-01

    Background Torque teno virus (TTV), of the Anelloviridae family, Iotatorquevirus genus, is a non-enveloped, single-stranded, and negative sense DNA (ssDNA) virus infecting human and many domestic animals including swines. Very little information is known about the investigations of TTV prevalence in different swine breeds so far. Methods In this study, 208 serum samples collected from seven swine breeds (Rongchang pig, Chenghua pig, Zibet pig, Wild boar, Duroc, Landrace, Large Yorkshire) from two independent farms were detected to determine the prevalence of two swine TTV genogroups, TTV1 and TTV 2, by nested polymerase chain reaction methods, and to analyse prevalence difference among these breeds. Results The results showed that the prevalence of TTV in the seven breeds was 92%-100%. No significant difference (p > 0.05) in TTV infection was observed between different breeds. Interestingly, significantly higher prevalence for TTV1 in Rongchang boars (90%) and for TTV2 in Rongchang sows (95%) were detected, while co-infection rate (43.8%) was lower than other breeds. Sequence analysis showed that the homology of TTV1 and TTV2 were over 90.9% and 86.4% in these breeds, respectively. Conclusions The results indicated that TTV was widely distributed in the seven swine breeds. The prevalence of both TTV genogroups associated with swine breeds and genders. This study also respented the first description of swine TTV prevalence in different swine breeds. It was vitally necessary to further study swine TTV pathogenicity. PMID:22050715

  6. Hop Cultivars and Breeding

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Pest management decision making in hops varies among cultivars. Historically, the primary objective of hop breeding programs has been to increase the yield or characteristics associated with either bittering (high alpha-acids) or aroma (unique volatile oil profiles) cultivars. Other factors consid...

  7. Lettuce and spinach breeding

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Lettuce and spinach production is beset by numerous biotic an abiotic challenges. This report to the California Leafy Greens Research Program annual meeting provides an update by the ‘Genetic Enhancement of Lettuce, Spinach, Melon, and Related Species’ project at Salinas on the genetics and breeding...

  8. Raspberry Breeding and Genetics

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This chapter describes the origin, speciation, and history of improvement of the raspberries, Rubus section idaeobatus. The world industry in North America, Australasia, China, Europe, Eastern Europe, Africa, and South America and the breeding objectives of programs in those areas are discussed. Ger...

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

    PubMed

    Truchon, Marie-Hélène; Measures, Lena; L'Hérault, Vincent; Brêthes, Jean-Claude; Galbraith, Peter S; Harvey, Michel; Lessard, Sylvie; Starr, Michel; Lecomte, Nicolas

    2013-01-01

    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(2)adj = 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(2)adj = 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 promising

  10. Population size of snowy plovers breeding in North America

    USGS Publications Warehouse

    Thomas, Susan M.; Lyons, James E.; Andres, Brad A.; T-Smith, Elise Elliot; Palacios, Eduardo; Cavitt, John F.; Royle, J. Andrew; Fellows, Suzanne D.; Maty, Kendra; Howe, William H.; Mellink, Eric; Melvin, Stefani; Zimmerman, Tara

    2012-01-01

    Snowy Plovers (Charadrius nivosus) may be one of the rarest shorebirds in North America yet a comprehensive assessment of their abundance and distribution has not been completed. During 2007 and 2008, 557 discrete wetlands were surveyed and nine additional large wetland complexes sampled in México and the USA. From these surveys, a population of 23,555 (95% CI = 17,299 – 29,859) breeding Snowy Plovers was estimated. Combining the estimate with information from areas not surveyed, the total North American population was assessed at 25,869 (95% CI = 18,917 – 32,173). Approximately 42% of all breeding Snowy Plovers in North America resided at two sites (Great Salt Lake, Utah, and Salt Plains National Wildlife Refuge, Oklahoma), and 33% of all these were on wetlands in the Great Basin (including Great Salt Lake). Also, coastal habitats in central and southern Texas supported large numbers of breeding plovers. New breeding sites were discovered in interior deserts and highlands and along the Pacific coast of México; approximately 9% of the North American breeding population occurred in México. Because of uncertainties about effects of climate change and current stresses to breeding habitats, the species should be a management and conservation priority. Periodic monitoring should be undertaken at important sites to ensure high quality habitat is available to support the Snowy Plover population.

  11. Hyperchromicity and strand separation in bacterial DNA.

    PubMed

    FREIFELDER, D; DAVISON, P F

    1962-05-01

    Studies of the per cent of strand separation of N(14)-N(15) hybrid coli DNA heated to various temperatures in formaldehyde have shown that the process of strand separation is a function of temperature and formaldehyde concentration and is directly related to the measured hyperchromicity. No strands separate until about 75 per cent of full hyperchromicity is obtained, and even at apparently full hyperchromicity a large fraction of the strands may be held together, possibly by guanine-cytosine-rich regions.

  12. Effect of Group-Selection Opening Size on Breeding Bird Habitat Use in a Bottomland Forest

    SciTech Connect

    Moorman, C.E.; D.C. Guynn, Jr.

    2001-12-01

    Research on the effects of creating group-selection openings of various sizes on breeding birds habitat use in a bottomland hardwood forest of the Upper Coastal Plain of South Carolina. Creation of 0.5-ha group selection openings in southern bottomland forests should provide breeding habitat for some field-edge species in gaps and habitat for forest-interior species and canopy-dwelling forest-edge species between gaps provided that enough mature forest is made available.

  13. Coastal Change Along the Shore of Northeastern South Carolina: The South Carolina Coastal Erosion Study

    USGS Publications Warehouse

    Barnhardt, W. A.

    2009-01-01

    The U.S. Geological Survey, in cooperation with the South Carolina Sea Grant Consortium, conducted a 7-year, multi-disciplinary study of coastal erosion in northeastern South Carolina. The main objective was to understand the geologic and oceanographic processes that control sediment movement along the region's shoreline and thereby improve projections of coastal change. The study used high-resolution remote sensing and sampling techniques to define the geologic framework and assess historic shoreline change. Based on these findings, oceanographic-process studies and numerical modeling were carried out to determine the rates and directions of sediment transport along South Carolina's Grand Strand.

  14. Coastal Navigation Portfolio Management

    DTIC Science & Technology

    2015-02-19

    CIRP.aspx Coastal Inlets Research Program Coastal Navigation Portfolio Management The Coastal Navigatoin Portfolio Management work unit...across the vast coastal navigation portfolio of projects. The USACE maintains a vast infrastructure portfolio of deep-draft coastal entrance...the Corps needs to be able to direct resources at the navigation projects that are most critical to overall marine transportation system performance

  15. Stranded costs: Is the market paying attention?

    SciTech Connect

    Ros, A.; Domagalski, J.; O`Connor, P.R.

    1996-05-15

    This article is a discussion of the effects of the stranded costs issue on the market and book value of electric utility stocks. Mathematical models were used to determine whether stranded costs, as measured by Moody`s Investor Services and S&P, can explain variability if equity performance as expressed by the market-to-book value ratio. The models adequately explain the variances and show that increased exposure to stranded costs leads to reduced market value.

  16. Hyperchromicity and Strand Separation in Bacterial DNA

    PubMed Central

    Freifelder, David; Davison, Peter F.

    1962-01-01

    Studies of the per cent of strand separation of N14-N15 hybrid coli DNA heated to various temperatures in formaldehyde have shown that the process of strand separation is a function of temperature and formaldehyde concentration and is directly related to the measured hyperchromicity. No strands separate until about 75 per cent of full hyperchromicity is obtained, and even at apparently full hyperchromicity a large fraction of the strands may be held together, possibly by guanine-cytosine-rich regions. PMID:13894962

  17. RosBREED: Enabling Marker-Assisted Breeding In Rosaceae

    Technology Transfer Automated Retrieval System (TEKTRAN)

    RosBREED will create a national, dynamic, sustained effort in research, infrastructure establishment, training, and extension for applying marker-assisted breeding (MAB) to deliver improved plant materials more efficiently and rapidly. The Rosaceae family (including apple, peach, sweet and tart cher...

  18. Vegetation controls on the maximum size of coastal dunes

    PubMed Central

    Durán, Orencio; Moore, Laura J.

    2013-01-01

    Coastal dunes, in particular foredunes, support a resilient ecosystem and reduce coastal vulnerability to storms. In contrast to dry desert dunes, coastal dunes arise from interactions between biological and physical processes. Ecologists have traditionally addressed coastal ecosystems by assuming that they adapt to preexisting dune topography, whereas geomorphologists have studied the properties of foredunes primarily in connection to physical, not biological, factors. Here, we study foredune development using an ecomorphodynamic model that resolves the coevolution of topography and vegetation in response to both physical and ecological factors. We find that foredune growth is eventually limited by a negative feedback between wind flow and topography. As a consequence, steady-state foredunes are scale invariant, which allows us to derive scaling relations for maximum foredune height and formation time. These relations suggest that plant zonation (in particular for strand “dune-building” species) is the primary factor controlling the maximum size of foredunes and therefore the amount of sand stored in a coastal dune system. We also find that aeolian sand supply to the dunes determines the timescale of foredune formation. These results offer a potential explanation for the empirical relation between beach type and foredune size, in which large (small) foredunes are found on dissipative (reflective) beaches. Higher waves associated with dissipative beaches increase the disturbance of strand species, which shifts foredune formation landward and thus leads to larger foredunes. In this scenario, plants play a much more active role in modifying their habitat and altering coastal vulnerability than previously thought. PMID:24101481

  19. Vegetation controls on the maximum size of coastal dunes

    NASA Astrophysics Data System (ADS)

    Durán, Orencio; Moore, Laura J.

    2013-10-01

    Coastal dunes, in particular foredunes, support a resilient ecosystem and reduce coastal vulnerability to storms. In contrast to dry desert dunes, coastal dunes arise from interactions between biological and physical processes. Ecologists have traditionally addressed coastal ecosystems by assuming that they adapt to preexisting dune topography, whereas geomorphologists have studied the properties of foredunes primarily in connection to physical, not biological, factors. Here, we study foredune development using an ecomorphodynamic model that resolves the coevolution of topography and vegetation in response to both physical and ecological factors. We find that foredune growth is eventually limited by a negative feedback between wind flow and topography. As a consequence, steady-state foredunes are scale invariant, which allows us to derive scaling relations for maximum foredune height and formation time. These relations suggest that plant zonation (in particular for strand "dune-building" species) is the primary factor controlling the maximum size of foredunes and therefore the amount of sand stored in a coastal dune system. We also find that aeolian sand supply to the dunes determines the timescale of foredune formation. These results offer a potential explanation for the empirical relation between beach type and foredune size, in which large (small) foredunes are found on dissipative (reflective) beaches. Higher waves associated with dissipative beaches increase the disturbance of strand species, which shifts foredune formation landward and thus leads to larger foredunes. In this scenario, plants play a much more active role in modifying their habitat and altering coastal vulnerability than previously thought.

  20. Vegetation controls on the maximum size of coastal dunes.

    PubMed

    Durán, Orencio; Moore, Laura J

    2013-10-22

    Coastal dunes, in particular foredunes, support a resilient ecosystem and reduce coastal vulnerability to storms. In contrast to dry desert dunes, coastal dunes arise from interactions between biological and physical processes. Ecologists have traditionally addressed coastal ecosystems by assuming that they adapt to preexisting dune topography, whereas geomorphologists have studied the properties of foredunes primarily in connection to physical, not biological, factors. Here, we study foredune development using an ecomorphodynamic model that resolves the coevolution of topography and vegetation in response to both physical and ecological factors. We find that foredune growth is eventually limited by a negative feedback between wind flow and topography. As a consequence, steady-state foredunes are scale invariant, which allows us to derive scaling relations for maximum foredune height and formation time. These relations suggest that plant zonation (in particular for strand "dune-building" species) is the primary factor controlling the maximum size of foredunes and therefore the amount of sand stored in a coastal dune system. We also find that aeolian sand supply to the dunes determines the timescale of foredune formation. These results offer a potential explanation for the empirical relation between beach type and foredune size, in which large (small) foredunes are found on dissipative (reflective) beaches. Higher waves associated with dissipative beaches increase the disturbance of strand species, which shifts foredune formation landward and thus leads to larger foredunes. In this scenario, plants play a much more active role in modifying their habitat and altering coastal vulnerability than previously thought.

  1. Thermophoresis of single stranded DNA.

    PubMed

    Reineck, Philipp; Wienken, Christoph J; Braun, Dieter

    2010-01-01

    The manipulation and analysis of biomolecules in native bulk solution is highly desired; however, few methods are available. In thermophoresis, the thermal analog to electrophoresis, molecules are moved along a microscopic temperature gradient. Its theoretical foundation is still under debate, but practical applications for analytics in biology show considerable potential. Here we measured the thermophoresis of highly diluted single stranded DNA using an all-optical capillary approach. Temperature gradients were created locally by an infrared laser. The thermal depletion of oligonucleotides of between 5 and 50 bases in length were investigated by fluorescence at various salt concentrations. To a good approximation, the previously tested capacitor model describes thermophoresis: the Soret coefficient linearly depends on the Debye length and is proportional to the DNA length to the power of 0.35, dictated by the conformation-based size scaling of the diffusion coefficient. The results form the basis for quantitative DNA analytics using thermophoresis.

  2. A Biomechanical Comparison of 4-Strand and 5-Strand Anterior Cruciate Ligament Graft Constructs

    PubMed Central

    Broadhead, Matthew L.; Singla, Animesh A.; Bertollo, Nicky; Broe, David; Walsh, William R.

    2017-01-01

    Hamstring tendon autografts are used for reconstruction of the anterior cruciate ligament. This study tested the hypothesis that a 5-strand hamstring autograft construct is superior in strength to a 4-strand construct. Four-strand and 5-strand tendon grafts constructs were prepared from ovine flexor tendons and then tested in a uniaxial electromechanical load system with suspensory fixation. The 4-strand and 5-strand constructs were pre-conditioned, stress-relaxed and loaded to ultimate failure. Stress-relaxation, stiffness and ultimate load were compared using a one-way ANOVA. There were no statistical differences in stress-relaxation, initial stiffness, secondary stiffness or ultimate load between 4-strand and 5-strand split tendon graft constructs. Inconsistent failure patterns for both 4-strand and 5-strand constructs were observed. The additional strand in the 5-strand construct may be shielded from stress with additional weakness secondary to the use of suspensory fixation. The potential biological benefit of religamentization and bony integration, with more autologous tissue in the intra-articular space and bony tunnels remains unknown. PMID:28286624

  3. Postmortem investigations on winter stranded sperm whales from the coasts of Belgium and The Netherlands.

    PubMed

    Jauniaux, T; Brosens, L; Jacquinet, E; Lambrigts, D; Addink, M; Smeenk, C; Coignoul, F

    1998-01-01

    During winter 1994-95, four and three sperm whales (Physeter macrocephalus) were stranded along the Belgian and the Dutch coasts, respectively. Necropsies and tissue samplings were collected 24 hrs post mortem. Lesions on several whales included round and linear skin scars, ventral skin abrasions, acute skin ulcers, acute ulcerative stomatitides, acute to chronic external otitides, and passive visceral congestion. In addition, these sperm whales appeared to be debilitated with severe weight deficit, had blubber thickness reduction, the absence of abdominal fat, and the intestinal tracts were almost empty. Three categories of lesions and their possible relation with the stranding were evaluated. Cutaneous scars observed on the seven whales appeared to have no relation with the stranding. The poor body condition and acute integument ulcerative lesions were present before the stranding. Ventral skin abrasions and visceral passive congestion were caused by the strandings. Absence of food in the alimentary tracts, evidence of weight loss and blubber thickness reduction were compatible with an extended presence of the sperm whales in the North Sea, where adequate food is not available. This might lead to progressive weakness, predisposing the animals to secondary pathogens such as viral diseases. Finally, the coastal configuration of the southern North Sea makes it a trap for sperm whales which have entered the area during their wanderings.

  4. Unraveling the strands of Saturn's F ring

    USGS Publications Warehouse

    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.

  5. Coding capacity of complementary DNA strands.

    PubMed Central

    Casino, A; Cipollaro, M; Guerrini, A M; Mastrocinque, G; Spena, A; Scarlato, V

    1981-01-01

    A Fortran computer algorithm has been used to analyze the nucleotide sequence of several structural genes. The analysis performed on both coding and complementary DNA strands shows that whereas open reading frames shorter than 100 codons are randomly distributed on both DNA strands, open reading frames longer than 100 codons ("virtual genes") are significantly more frequent on the complementary DNA strand than on the coding one. These "virtual genes" were further investigated by looking at intron sequences, splicing points, signal sequences and by analyzing gene mutations. On the basis of this analysis coding and complementary DNA strands of several eukaryotic structural genes cannot be distinguished. In particular we suggest that the complementary DNA strand of the human epsilon-globin gene might indeed code for a protein. PMID:7015290

  6. DNA strand patterns on aluminium thin films.

    PubMed

    Khatir, Nadia Mahmoudi; Banihashemian, Seyedeh Maryam; Periasamy, Vengadesh; Majid, Wan Haliza Abd; Rahman, Saadah Abdul; Shahhosseini, Fatemeh

    2011-01-01

    A new patterning method using Deoxyribose Nucleic Acid (DNA) strands capable of producing nanogaps of less than 100 nm is proposed and investigated in this work. DNA strands from Bosenbergia rotunda were used as the fundamental element in patterning DNA on thin films of aluminium (Al) metal without the need for any lithographic techniques. The DNA strands were applied in buffer solutions onto thin films of Al on silicon (Si) and the chemical interactions between the DNA strands and Al creates nanometer scale arbitrary patterning by direct transfer of the DNA strands onto the substrate. This simple and cost-effective method can be utilized in the fabrication of various components in electronic chips for microelectronics and Nano Electronic Mechanical System (NEMS) applications in general.

  7. Modelling Toehold-Mediated RNA Strand Displacement

    PubMed Central

    Šulc, Petr; Ouldridge, Thomas E.; Romano, Flavio; Doye, Jonathan P.K.; Louis, Ard A.

    2015-01-01

    We study the thermodynamics and kinetics of an RNA toehold-mediated strand displacement reaction with a recently developed coarse-grained model of RNA. Strand displacement, during which a single strand displaces a different strand previously bound to a complementary substrate strand, is an essential mechanism in active nucleic acid nanotechnology and has also been hypothesized to occur in vivo. We study the rate of displacement reactions as a function of the length of the toehold and temperature and make two experimentally testable predictions: that the displacement is faster if the toehold is placed at the 5′ end of the substrate; and that the displacement slows down with increasing temperature for longer toeholds. PMID:25762335

  8. Modelling toehold-mediated RNA strand displacement.

    PubMed

    Šulc, Petr; Ouldridge, Thomas E; Romano, Flavio; Doye, Jonathan P K; Louis, Ard A

    2015-03-10

    We study the thermodynamics and kinetics of an RNA toehold-mediated strand displacement reaction with a recently developed coarse-grained model of RNA. Strand displacement, during which a single strand displaces a different strand previously bound to a complementary substrate strand, is an essential mechanism in active nucleic acid nanotechnology and has also been hypothesized to occur in vivo. We study the rate of displacement reactions as a function of the length of the toehold and temperature and make two experimentally testable predictions: that the displacement is faster if the toehold is placed at the 5' end of the substrate; and that the displacement slows down with increasing temperature for longer toeholds.

  9. Cause-specific temporal and spatial trends in green sea turtle strandings in the Hawaiian Archipelago (1982-2003)

    USGS Publications Warehouse

    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

  10. RosBREED: Enabling Marker-Assisted Breeding in Rosaceae

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genomics research has not yet been translated into routine practical application in breeding Rosaceae fruit crops (peach, apple, strawberry, cherry, apricot, pear, raspberry, etc.). Through dedicated efforts of many researchers worldwide, a wealth of genomics resources has accumulated, including ES...

  11. Best of Breed

    NASA Technical Reports Server (NTRS)

    Lohn, Jason

    2004-01-01

    No team of engineers, no matter how much time they took or how many bottles of cabernet they consumed, would dream up an antenna that looked like a deer antler on steroids. Yet that's what a group at NASA Ames Research Center came up with-thanks to a little help from Darwin. NASA's Space Technology 5 nanosatellites, which are scheduled to start measuring Earth's magnetosphere in late 2004, requires an antenna that can receive a wide range of frequencies regardless of the spacecraft's orientation. Rather than leave such exacting requirements in the hands of a human, the engineers decided to breed a design using genetic algorithms and 32 Linux PCs. The computers generated small antenna-constructing programs (the genotypes) and executed them to produce designs (the phenotypes). Then the designs were evaluated using an antenna simulator. The team settled on the form pictured here. You won't find this kind of antenna in any textbook, design guide, or research paper. But its innovative structure meets a challenging set of specifications. If successfully deployed, it will be the first evolved antenna to make it out of the lab and the first piece of evolved hardware ever to fly in space.

  12. Animal breeding and disease

    PubMed Central

    Nicholas, Frank W

    2005-01-01

    Single-locus disorders in domesticated animals were among the first Mendelian traits to be documented after the rediscovery of Mendelism, and to be included in early linkage maps. The use of linkage maps and (increasingly) comparative genomics has been central to the identification of the causative gene for single-locus disorders of considerable practical importance. The ‘score-card’ in domestic animals is now more than 100 disorders for which the molecular lesion has been identified and hence for which a DNA test is available. Because of the limited lifespan of any such test, a cost-effective and hence popular means of protecting the intellectual property inherent in a DNA test is not to publish the discovery. While understandable, this practice creates a disconcerting precedent. For multifactorial disorders that are scored on an all-or-none basis or into many classes, the effectiveness of control schemes could be greatly enhanced by selection on estimated breeding values for liability. Genetic variation for resistance to pathogens and parasites is ubiquitous. Selection for resistance can therefore be successful. Because of the technical and welfare challenges inherent in the requirement to expose animals to pathogens or parasites in order to be able to select for resistance, there is a very active search for DNA markers for resistance. The first practical fruits of this research were seen in 2002, with the launch of a national scrapie control programme in the UK. PMID:16048793

  13. Mutation breeding by ion implantation

    NASA Astrophysics Data System (ADS)

    Yu, Zengliang; Deng, Jianguo; He, Jianjun; Huo, Yuping; Wu, Yuejin; Wang, Xuedong; Lui, Guifu

    1991-07-01

    Ion implantation as a new mutagenic method has been used in the rice breeding program since 1986, and for mutation breeding of other crops later. It has been shown, in principle and in practice, that this method has many outstanding advantages: lower damage rate; higher mutation rate and wider mutational spectrum. Many new lines of rice with higher yield rate; broader disease resistance; shorter growing period but higher quality have been bred from ion beam induced mutants. Some of these lines have been utilized for the intersubspecies hybridization. Several new lines of cotton, wheat and other crops are now in breeding. Some biophysical effects of ion implantation for crop seeds have been studied.

  14. [Exaggerated breed characteristics in dogs].

    PubMed

    Wilting, M M; Endenburg, N

    2012-01-01

    Dutch dog owners seem to be aware of bad dog breeding practices with regard to exaggerated breed characteristics that are detrimental to the dog's welfare. Yet they do not always look for these features when buying a dog. Most dog owners think that veterinarians could have an important role in preventing these exaggerated physical traits, by providing information about these traits and taking action in their capacity as veterinarian. Articles 36 and 55 of the Dutch GWWD (animal health and welfare law) provide opportunities to act against the breeding of dogs with exaggerated genetic traits.

  15. Sex-Specific Habitat Utilization and Differential Breeding Investments in Christmas Island Frigatebirds throughout the Breeding Cycle.

    PubMed

    Hennicke, Janos C; James, David J; Weimerskirch, Henri

    2015-01-01

    In seabirds, equal bi-parental care is the rule, as it is considered crucial for raising chicks successfully because seabirds forage in an environment with unpredictable and highly variable food supply. Frigatebirds forage in poor tropical waters, yet males reduce and even stop parental care soon after chick brooding, leaving the female to provision the chick alone for an extended fledging period. Using bird-borne tracking devices, male and female Christmas Island Frigatebirds (Fregata andrewsi) were investigated during the brooding, late chick rearing and post-fledging period to examine whether sexes exhibit foraging strategies that may be linked to differential breeding investments. During brooding, males and females showed similar foraging behaviour under average marine productivity of oceanic waters close to the colony, but males shifted to more distant and more productive habitats when conditions deteriorated to continue with reduced chick provisioning. During the late chick rearing period, females progressively increased their foraging range to the more distant but productive marine areas that only males had visited during brooding. Birds spent the non-breeding period roosting in highly productive waters of the Sunda Shelf. The sex-specific utilisation of three different foraging habitats with different primary productivity (oceanic, coastal, and shelf areas) allowed for temporal and spatial segregation in the exploitation of favourable habitats which seems to enable each sex to optimise its foraging profitability. In addition, post-fledging foraging movements of females suggest a biennial breeding cycle, while limited information on males suggests the possibility of an annual breeding cycle.

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

    PubMed

    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

  17. Habitat Suitability Index Models: American eider (breeding)

    USGS Publications Warehouse

    Blumton, Arlene K.; Owen, Ray B.; Krohn, William B.

    1988-01-01

    INTRODUCTION The common eider (Somateria mollissima) consists of five subspecies; four are found in North America (Palmer 1976). Six management populations of common eiders have recently been defined in eastern Canada and the United States (Reed and Erskine 1986). The American edier (S. mollissima dresseri), of which three populations are recognized (Reed and Erskine 1986), is the southernmost subspecies and the focus of this paper. The common eider is a member of the order Anseriformes, family Anatidae, and the tribe Mergini. A seabird of the northern latitudes of the world, the common eider is the largest duck of North America, ranging in weight from 1.2 to 2.8 kg and having a total length from 53.3 to 68.6 cm (Bellrose 1980). The American subspecies averages 2.0 kg and 61.0 cm for males, and 1.5 kg and 57.0 cm for females (Bellrose 1980). The drake is distinctly patterned,, having a white back and breast and a black belly and sides. The smaller female is brown and heavily barred with dark brown. Both sexes have a leathery extension of the bill which forms a Y-shaped frontal shield that reaches almost to the eyes. Maine, which supports part of the Atlantic population of common eiders (Reed and Erskine 1986), is the only major eider breeding population in the lower 48 States. American eiders are colonial nesters and use a variety of nesting sites, but they prefer relatively small, uninhabited islands (Mendall 1976). The coastal islands of Maine, which are essential to the eider's life cycle, are increasingly subjected to recreation and development, creating potential disturbances to eider breeding colonies. During recent years, aesthetic and sporting interest in eiders has increased. Sea ducks in Maine are experiencing increased hunting pressure. Compared to hunting seasons and bag limits for inland ducks, sea duck seasons and limits are liberal (Maine Department of Inland Fisheries and Wildlife [MDIFW] 1983).

  18. Breeding gravitational lenses

    NASA Astrophysics Data System (ADS)

    Liesenborgs, J.; de Rijcke, S.; Dejonghe, H.; Bekaert, P.

    2011-03-01

    Gravitational lenses are a spectacular astrophysical phenomenon, a cosmic mirage caused by the gravitational deflection of light in which multiple images of a same background object can be seen. Their beauty is only exceeded by their usefulness, as the gravitational lens effect is a direct probe of the total mass of the deflecting object. Furthermore, since the image configuration arising from the gravitational lens effect depends on the exact gravitational potential of the deflector, it even holds the promise of learning about the distribution of the mass. In this presentation, a method for extracting the information encoded in the images and reconstructing the mass distribution is presented. Being a non-parametric method, it avoids making a priori assumptions about the shape of the mass distribution. At the core of the procedure lies a genetic algorithm, an optimization strategy inspired by Darwin's principle of ``survival of the fittest''. One only needs to specify a criterion to decide if one particular trial solution is deemed better than another, and the genetic algorithm will ``breed'' appropriate solutions to the problem. In a similar way, one can create a multi-objective genetic algorithm, capable of optimizing several fitness criteria at the same time. This provides a very flexible way to incorporate all the available information in the gravitational lens system: not only the positions and shapes of the multiple images are used, but also the so-called ``null space'', i.e. the area in which no such images can be seen. The effectiveness of this approach is illustrated using simulated data, which allows one to compare the reconstruction to the true mass distribution.

  19. Stranded superconducting cable of improved design

    NASA Technical Reports Server (NTRS)

    Brooks, J.; Laverick, C.; Lobell, G. M.; Purcell, J.

    1970-01-01

    High-current cable developed in liquid helium cooled magnets uses aluminum wire interspersed with the superconductor strands. The aluminum maintains higher electrical conductivity, is light in weight, and has low thermal capacity.

  20. DNA strand displacement system running logic programs.

    PubMed

    Rodríguez-Patón, Alfonso; Sainz de Murieta, Iñaki; Sosík, Petr

    2014-01-01

    The paper presents a DNA-based computing model which is enzyme-free and autonomous, not requiring a human intervention during the computation. The model is able to perform iterated resolution steps with logical formulae in conjunctive normal form. The implementation is based on the technique of DNA strand displacement, with each clause encoded in a separate DNA molecule. Propositions are encoded assigning a strand to each proposition p, and its complementary strand to the proposition ¬p; clauses are encoded comprising different propositions in the same strand. The model allows to run logic programs composed of Horn clauses by cascading resolution steps. The potential of the model is demonstrated also by its theoretical capability of solving SAT. The resulting SAT algorithm has a linear time complexity in the number of resolution steps, whereas its spatial complexity is exponential in the number of variables of the formula.

  1. Efficient Breeding by Genomic Mating.

    PubMed

    Akdemir, Deniz; Sánchez, Julio I

    2016-01-01

    Selection in breeding programs can be done by using phenotypes (phenotypic selection), pedigree relationship (breeding value selection) or molecular markers (marker assisted selection or genomic selection). All these methods are based on truncation selection, focusing on the best performance of parents before mating. In this article we proposed an approach to breeding, named genomic mating, which focuses on mating instead of truncation selection. Genomic mating uses information in a similar fashion to genomic selection but includes information on complementation of parents to be mated. Following the efficiency frontier surface, genomic mating uses concepts of estimated breeding values, risk (usefulness) and coefficient of ancestry to optimize mating between parents. We used a genetic algorithm to find solutions to this optimization problem and the results from our simulations comparing genomic selection, phenotypic selection and the mating approach indicate that current approach for breeding complex traits is more favorable than phenotypic and genomic selection. Genomic mating is similar to genomic selection in terms of estimating marker effects, but in genomic mating the genetic information and the estimated marker effects are used to decide which genotypes should be crossed to obtain the next breeding population.

  2. Efficient Breeding by Genomic Mating

    PubMed Central

    Akdemir, Deniz; Sánchez, Julio I.

    2016-01-01

    Selection in breeding programs can be done by using phenotypes (phenotypic selection), pedigree relationship (breeding value selection) or molecular markers (marker assisted selection or genomic selection). All these methods are based on truncation selection, focusing on the best performance of parents before mating. In this article we proposed an approach to breeding, named genomic mating, which focuses on mating instead of truncation selection. Genomic mating uses information in a similar fashion to genomic selection but includes information on complementation of parents to be mated. Following the efficiency frontier surface, genomic mating uses concepts of estimated breeding values, risk (usefulness) and coefficient of ancestry to optimize mating between parents. We used a genetic algorithm to find solutions to this optimization problem and the results from our simulations comparing genomic selection, phenotypic selection and the mating approach indicate that current approach for breeding complex traits is more favorable than phenotypic and genomic selection. Genomic mating is similar to genomic selection in terms of estimating marker effects, but in genomic mating the genetic information and the estimated marker effects are used to decide which genotypes should be crossed to obtain the next breeding population. PMID:27965707

  3. Hybrid breeding in autogamous cereals.

    PubMed

    Longin, Carl Friedrich Horst; Mühleisen, Jonathan; Maurer, Hans Peter; Zhang, Hongliang; Gowda, Manje; Reif, Jochen Christoph

    2012-10-01

    Hybrid breeding in autogamous cereals has a long history of attempts with moderate success. There is a vast amount of literature investigating the potential problems and solutions, but until now, market share of hybrids is still a niche compared to line varieties. Our aim was to summarize the status quo of hybrid breeding efforts for the autogamous cereals wheat, rice, barley, and triticale. Furthermore, the research needs for a successful hybrid breeding in autogamous cereals are intensively discussed. To our opinion, the basic requirements for a successful hybrid breeding in autogamous cereals are fulfilled. Nevertheless, optimization of the existing hybridization systems is urgently required and should be coupled with the development of clear male and female pool concepts. We present a quantitative genetic framework as a first step to compare selection gain of hybrid versus line breeding. The lack of precise empirical estimates of relevant quantitative genetic parameters, however, is currently the major bottleneck for a robust evaluation of the potential of hybrid breeding in autogamous cereals.

  4. Coastal Inlets Research Program

    DTIC Science & Technology

    2015-02-09

    FEB 2015 2. REPORT TYPE 3. DATES COVERED 00-00-2015 to 00-00-2015 4. TITLE AND SUBTITLE Coastal Inlets Research Program 5a. CONTRACT NUMBER...S) AND ADDRESS(ES) U.S. Army Engineer Research and Development Center,CIRP - The Coastal Inlets Research Program,3909 Halls Ferry Road,Vicksburg,MS...CIRP.aspx Coastal Inlets Research Program The Coastal Inlets Research Program (CIRP) is a R&D Program funded through the Operations & Maintenance

  5. Bubbles in live-stranded dolphins

    PubMed Central

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

    2012-01-01

    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. PMID:21993505

  6. Bubbles in live-stranded dolphins.

    PubMed

    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.

  7. Rock coasts and seabird breeding sites : a common optimization

    NASA Astrophysics Data System (ADS)

    Marie, Eveillard-Buchoux

    2014-05-01

    The North-West coasts of Europe support a lot of part of Northern hemisphere breeding seabirds. In that context, Scotland has a preponderant place and Brittany has southernmost limit of these species areas, for most of them. Outside the breeding season these species live mainly on the open sea and when they do visit the land to breed, they nest on a specific sites : almost all the time they breed on the rock coasts, often on seacliffs. This specific habitat are defines by geomorphological characteristics which offer special forms of the coast. The forms of rock coasts are originally and different because of several proprieties of geology, of lithology, of structures. Breeding seabird, occupying these sites, reveals, in a new light, the richness of these forms and the originals geographic location of the coastline : seabirds prefer nest in exposed coastline like rock caps, rocky points or islands. Seabirds and rock coasts are research topics in environmental geography since several years. However, these combination studies is a new approach in this field and enlargement in the heritage field allows supplement scientific approach. For example, it show that in most important touristic sites, environmental protection measures focused on landscape, habitat or bird, but much more rarely on rock coasts for these intrinsic values. Indeed, in Brittany or in Scotland, seabirds are often stars species in lot of coastal nature reserves, where they're considered like greater ecological heritage. We could see it in touristic promotion field : bird is everywhere, cliff is mostly kept in the dark, as well in leaflets as in speech visitor's guides - without, for example, as a part of this landscape. In all cases, combination of these two heritages is extremely rare. Yet, this current research illustrates the interest and the issue of development of this comparative approach seabirds / rock coasts for optimization of nature tourism and geotourism.

  8. SNP variation in ADRB3 gene reflects the breed difference of sheep populations.

    PubMed

    Wu, Jianliang; Qiao, Liying; Liu, Jianhua; Yuan, Yanan; Liu, Wenzhong

    2012-08-01

    The β3-adrenergic receptor (ADRB3), a G-protein coupled receptor, plays a major role in energy metabolism and regulation of lipolysis and homeostasis. We detect the single nucleotide polymorphism (SNP) variation in full-length sequence of ovine ADRB3 gene in 12 domestic sheep populations within four types by polymerase chain reaction-single strand conformation polymorphism and sequencing to reveal the breed difference. Twenty-two SNPs, 12 of which in the exon 1 and ten in the intron, were detected, and 12 new exonic and four new intronic SNPs were found. Most SNPs presented in Shanxi Dam Line and least ones in Dorset. The average SNP number in both meat and dual purpose for meat and wool breeds was significantly higher than general and dual purpose breeds for wool and meat. Frequency of each SNP in studied breeds or types was different. The 18C Del and 1617T Ins majorly existed in dual purpose breeds for wool and meat. The 25A Del, 119C>G and 130C>T were mostly found in the meat and dual purpose for meat and wool breeds. The 1764C>A more frequently presented in meat than in other types. The majority of variations came from within the populations as suggested by analysis of molecular variance. Close relationship presented among the Chinese and western breeds, respectively. In conclusion, SNPs of ovine ADRB3 gene can reflect the breed difference and within- and between-population variations, and to a great extent, the breed relationship.

  9. Cassava Breeding I: The Value of Breeding Value

    PubMed Central

    Ceballos, Hernán; Pérez, Juan C.; Joaqui Barandica, Orlando; Lenis, Jorge I.; Morante, Nelson; Calle, Fernando; Pino, Lizbeth; Hershey, Clair H.

    2016-01-01

    Breeding cassava relies on several selection stages (single row trial-SRT; preliminary; advanced; and uniform yield trials—UYT). This study uses data from 14 years of evaluations. From more than 20,000 genotypes initially evaluated only 114 reached the last stage. The objective was to assess how the data at SRT could be used to predict the probabilities of genotypes reaching the UYT. Phenotypic data from each genotype at SRT was integrated into the selection index (SIN) used by the cassava breeding program. Average SIN from all the progenies derived from each progenitor was then obtained. Average SIN is an approximation of the breeding value of each progenitor. Data clearly suggested that some genotypes were better progenitors than others (e.g., high number of their progenies reaching the UYT), suggesting important variation in breeding values of progenitors. However, regression of average SIN of each parental genotype on the number of their respective progenies reaching UYT resulted in a negligible coefficient of determination (r2 = 0.05). Breeding value (e.g., average SIN) at SRT was not efficient predicting which genotypes were more likely to reach the UYT stage. Number of families and progenies derived from a given progenitor were more efficient predicting the probabilities of the progeny from a given parent reaching the UYT stage. Large within-family genetic variation tends to mask the true breeding value of each progenitor. The use of partially inbred progenitors (e.g., S1 or S2 genotypes) would reduce the within-family genetic variation thus making the assessment of breeding value more accurate. Moreover, partial inbreeding of progenitors can improve the breeding value of the original (S0) parental material and sharply accelerate genetic gains. For instance, homozygous S1 genotypes for the dominant resistance to cassava mosaic disease (CMD) could be generated and selected. All gametes from these selected S1 genotypes would carry the desirable allele and

  10. Diet of canvasbacks during breeding

    USGS Publications Warehouse

    Austin, J.E.; Serie, J.R.; Noyes, J.H.

    1990-01-01

    We examined diets of canvasbacks (Aythya valisineria) breeding in southwestern Manitoba during 1977-81. Percent volume of animal foods consumed did not differ between males and females nor among prenesting, rapid follicle growth, laying, incubation, and renesting periods in females (mean = 50.1%). Tubers and shoots of fennelleaf pondweed (Potamogeton pectinatus) and midge larvae (Chironomidae) were the predominant foods, comprising on average 45% and 23% of the diet volume, respectively. Continued importance of plant foods to canvasbacks throughout reproduction contrasts with the mostly invertebrate diets of other prairie-breeding ducks, and does not fit current theories of nutritional ecology of breeding anatids (i.e., females meet the protein requirements of reproduction by consuming a high proportion of animal foods).

  11. Emperor penguins breeding on iceshelves.

    PubMed

    Fretwell, Peter T; Trathan, Phil N; Wienecke, Barbara; Kooyman, Gerald L

    2014-01-01

    We describe a new breeding behaviour discovered in emperor penguins; utilizing satellite and aerial-survey observations four emperor penguin breeding colonies have been recorded as existing on ice-shelves. Emperors have previously been considered as a sea-ice obligate species, with 44 of the 46 colonies located on sea-ice (the other two small colonies are on land). Of the colonies found on ice-shelves, two are newly discovered, and these have been recorded on shelves every season that they have been observed, the other two have been recorded both on ice-shelves and sea-ice in different breeding seasons. We conduct two analyses; the first using synthetic aperture radar data to assess why the largest of the four colonies, for which we have most data, locates sometimes on the shelf and sometimes on the sea-ice, and find that in years where the sea-ice forms late, the colony relocates onto the ice-shelf. The second analysis uses a number of environmental variables to test the habitat marginality of all emperor penguin breeding sites. We find that three of the four colonies reported in this study are in the most northerly, warmest conditions where sea-ice is often sub-optimal. The emperor penguin's reliance on sea-ice as a breeding platform coupled with recent concerns over changed sea-ice patterns consequent on regional warming, has led to their designation as "near threatened" in the IUCN red list. Current climate models predict that future loss of sea-ice around the Antarctic coastline will negatively impact emperor numbers; recent estimates suggest a halving of the population by 2052. The discovery of this new breeding behaviour at marginal sites could mitigate some of the consequences of sea-ice loss; potential benefits and whether these are permanent or temporary need to be considered and understood before further attempts are made to predict the population trajectory of this iconic species.

  12. Breeding monkeys for biomedical research

    NASA Technical Reports Server (NTRS)

    Bourne, G. H.; Golarzdebourne, M. N.; Keeling, M. E.

    1973-01-01

    Captive bred rhesus monkeys show much less pathology than wild born animals. The monkeys may be bred in cages or in an outdoor compound. Cage bred animals are not psychologically normal which makes then unsuited for some types of space related research. Compound breeding provides contact between mother and infant and an opportunity for the infants to play with their peers which are important requirements to help maintain their behavioral integrity. Offspring harvested after a year in the compound appear behaviorally normal and show little histopathology. Compound breeding is also an economical method for the rapid production of young animals. The colony can double its size about every two and a half years.

  13. Breed base representation in dairy animals of 5 breeds

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Inheritance of DNA from different dairy breeds can be determined by genotyping, just as individual ancestors such as parents, grandparents, or even great grandparents can be identified correctly in a high percentage of the cases by genotyping even if not reported or reported incorrectly in pedigrees...

  14. Cetacean Morbillivirus in Coastal Indo-Pacific Bottlenose Dolphins, Western Australia

    PubMed Central

    Duignan, Pádraig J.; Wang, Jianning; Bingham, John; Finn, Hugh; Bejder, Lars; Patterson, Anthony P.; Holyoake, Carly

    2014-01-01

    Cetacean morbillivirus (CeMV) has caused several epizootics in multiple species of cetaceans globally and is an emerging disease among cetaceans in Australia. We detected CeMV in 2 stranded coastal Indo-Pacific bottlenose dolphins (Tursiops aduncus) in Western Australia. Preliminary phylogenetic data suggest that this virus variant is divergent from known strains. PMID:24656203

  15. Cetacean morbillivirus in coastal Indo-Pacific bottlenose dolphins, Western Australia.

    PubMed

    Stephens, Nahiid; Duignan, Pádraig J; Wang, Jianning; Bingham, John; Finn, Hugh; Bejder, Lars; Patterson, Anthony P; Holyoake, Carly

    2014-04-01

    Cetacean morbillivirus (CeMV) has caused several epizootics in multiple species of cetaceans globally and is an emerging disease among cetaceans in Australia. We detected CeMV in 2 stranded coastal Indo-Pacific bottlenose dolphins (Tursiops aduncus) in Western Australia. Preliminary phylogenetic data suggest that this virus variant is divergent from known strains.

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

    PubMed

    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 (<10 mm) collected from eight coastal beaches in Guangdong Province, China. Polystyrene (PS) foams and fragments smaller than 7 mm were increasingly abundant in the smaller size classes, whereas resin pellets remained in their production sizes (∼3 mm). Microplastics (<5 mm) accounted for over 98% of the total 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.

  17. Coastal Modeling System

    DTIC Science & Technology

    2014-09-04

    Coastal Inlets Research Program Coastal Modeling System The work unit develops the Coastal Modeling System ( CMS ) and conducts basic research to...further understanding of sediment transport under mixed forcing from waves and currents. The CMS is a suite of coupled two- dimensional numerical...models for simulating waves, hydrodynamics, salinity and sediment transport, and morphology change. The CMS was identified by the USACE Hydraulics and

  18. The evolution of potato breeding

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Potato cultivars in most regions of the world are tetraploid and clonally propagated. For over a century, the breeding strategy has been phenotypic recurrent selection. However, the polyploid nature of the crop prevents breeders from eliminating deleterious alleles and assembling positive alleles fo...

  19. Breeding and propagating oakleaf hydrangeas

    Technology Transfer Automated Retrieval System (TEKTRAN)

    An oakleaf hydrangea breeding program at the U.S. National Arboretum’s worksite in McMinnville, Tenn. was started in 1996 for the purpose of developing attractive, compact oakleaf hydrangea cultivars suitable for use in small residential gardens. ‘Ruby Slippers’ and ‘Munchkin’ oakleaf hydrangeas we...

  20. USDA lettuce breeding and genetics

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The lettuce industry of California requires continued development of improved, adapted cultivars to meet new disease and insect problems, changes in the market, and changes in growing procedures. The USDA lettuce breeding and genetics project aims to incorporate valuable traits into crisphead, mixed...

  1. Conservation priorities for Ethiopian sheep breeds combining threat status, breed merits and contributions to genetic diversity

    PubMed Central

    Gizaw, Solomon; Komen, Hans; Windig, Jack J; Hanotte, Olivier; van Arendonk, Johan AM

    2008-01-01

    Prioritizing livestock breeds for conservation needs to incorporate both genetic and non-genetic aspects important for the survival of the breeds. Here, we apply a maximum-utility-strategy to prioritize 14 traditional Ethiopian sheep breeds based on their threat status, contributions to farmer livelihoods (current breed merits) and contributions to genetic diversity. Contributions of the breeds to genetic diversity were quantified using Eding's marker-estimated kinship approaches. Non-genetic aspects included threats (e.g. low population size, low preferences by farmers) and current merits (economic, ecological and cultural merits). Threat analysis identified eight of the 14 breeds as threatened. Analysis of current merits showed that sub-alpine and arid-lowland breeds contribute most to farmer livelihoods in comparison to other breeds. The highest contribution to the genetic diversity conserved was from the Simien breed. Simien showed high between-breed (low between-breed kinship = 0.04) as well as high within-breed diversity (low within-breed kinship = 0.09 and high HE = 0.73 and allelic richness = 6.83). We combined the results on threat status, current breed merits and contributions to genetic diversity to produce a ranking of the 14 breeds for conservation purposes. Our results balance the trade-offs between conserving breeds as insurance against future uncertainties and current sustainable utilization. The ranking of breeds provides a basis for conservation strategies for Ethiopian sheep and contributes to a regional or global conservation plan. PMID:18558075

  2. LRV1 viral particles in Leishmania guyanensis contain double-stranded or single-stranded RNA.

    PubMed Central

    Weeks, R; Aline, R F; Myler, P J; Stuart, K

    1992-01-01

    The 32-nm-diameter spherical viral particles found in the cytoplasm of Leishmania guyanensis CUMC1-1A sediment at 130S and have a buoyant density of approximately 1.4 g/ml in cesium chloride gradients. These particles contain a 5.3-kb double-stranded RNA, while single-stranded RNA that corresponds to the viral positive strand is associated with less-dense particles. These results suggest a conservative and sequential mode of LRV1 viral RNA replication that is exemplified by the ScV L-A virus of yeast. Images PMID:1738198

  3. METAPOPULATION STRUCTURE AND DYNAMICS OF POND BREEDING

    EPA Science Inventory

    Our review indicates that pond breeding amphibians exhibit highly variable spatial and temporal population dynamics, such that no single generalized model can realistically describe these animals. We propose that consideration of breeding pond permanence, and adaptations to pond ...

  4. NATIONAL COASTAL CONDITION REPORT III

    EPA Science Inventory

    Coastal waers in the US include estuaries, coastal wetlands, coral reefs, ,mangrove and kelp forests, seagrass meadows, and upwelling areas. Critical coastal habitats provide spawning grounds, nurseries, shelter, and food for finfish, shellfish, birds, and other wildlife. The n...

  5. Rescue Your Campus from "Stranded" Costs.

    ERIC Educational Resources Information Center

    Kadamus, David A.

    2003-01-01

    Discusses how to deal with the pressures to defer maintenance on campus buildings, including the issue of accelerated cycles of obsolescence, which "stranded" costs to avoid and to accept, and specific strategies to gain control of the physical asset portfolio. (EV)

  6. Untangling the Strands of the Fourteenth Amendment.

    ERIC Educational Resources Information Center

    Lupu, Ira C.

    1979-01-01

    Explores trends in the Court's interpretation of the libertarian and egalitarian dimensions of the Fourteenth Amendment and offers a theory of the two strands. Available from Michigan Law Review, Hutchins Hall, Ann Arbor, MI 48109; single issues $3.50. (Author/IRT)

  7. Neurobrucellosis in Stranded Dolphins, Costa Rica

    PubMed Central

    Hernández-Mora, Gabriela; González-Barrientos, Rocío; Morales, Juan-Alberto; Chaves-Olarte, Esteban; Guzmán-Verri, Caterina; Baquero-Calvo, Elías; De-Miguel, María-Jesús; Marín, Clara-María; Blasco, José-María

    2008-01-01

    Ten striped dolphins, Stenella coeruleoalba, stranded along the Costa Rican Pacific coast, had meningoencephalitis and antibodies against Brucella spp. Brucella ceti was isolated from cerebrospinal fluid of 6 dolphins and 1 fetus. S. coeruleoalba constitutes a highly susceptible host and a potential reservoir for B. ceti transmission. PMID:18760012

  8. Determination of recovery length in spiral strands

    SciTech Connect

    Raoof, M.; Kraincanic, I.

    1994-12-31

    On the offshore scene, the ever growing demands placed on moorings for conventional semi-submersible platforms, coupled with the requirements for guys to new structural forms such as compliant towers has led to the use of larger and longer ropes and spiral strands. Much emphasis has recently been placed on suitable forms of discard criteria based on the remaining fatigue life (or strength) of the spiral strands and wire ropes. It is now well established that, depending on the type of cable (strand or rope) application, the influence of broken wires on the strength of the cable is not directly equivalent to a loss of area of steel: the number and distribution of wire breaks around a cable cross-section and also along its length are both important. With sufficient friction, a broken wire will be capable of supporting its total share of the load in a relatively short length called the recovery length. The determination of recovery length for any type of steel cable, therefore, is of importance as a first step towards developing realistic guidelines for cable discard criteria. The present paper presents a theoretical model for predicting the recovery length in any layer of an axially preloaded spiral strand. Based on a series of theoretical parametric studies, a straightforward method is proposed for obtaining reasonable estimates of variations in the recovery length in any layer of a strand with changes in the lay angle. In view of the simple nature of the final results, these should prove of interest to practicing engineers. Moreover, the final recommendations should prove of some value in the context of length effects associated with axial fatigue loading of cables under laboratory conditions which has recently attracted much attention: the question here is how to determine a minimum length for test specimens whose axial fatigue life under laboratory conditions may safely be used to represent those of the much longer cables in the field.

  9. Genetic Diversity of US Sheep Breeds

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Understanding the genetic relationships between US sheep breeds is useful in developing conservation strategies and actions. A broad sampling of individual sheep from 28 breeds was performed. Breed types included: fine wool, meat types, long wool, hair, prolific, and fat tailed. Blood and semen samp...

  10. Can I compare EPD's across breeds?

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Proper comparison of the genetic merit of animals across breeds can be difficult and confusion for beef cattle producers. With the advent of a new genetic evaluation system where several breeds are evaluated in the same genetic analysis, confusion on direct comparison of animals across breeds has i...

  11. Population structure of ice-breeding seals.

    PubMed

    Davis, Corey S; Stirling, Ian; Strobeck, Curtis; Coltman, David W

    2008-07-01

    The development of population genetic structure in ice-breeding seal species is likely to be shaped by a combination of breeding habitat and life-history characteristics. Species that return to breed on predictable fast-ice locations are more likely to exhibit natal fidelity than pack-ice-breeding species, which in turn facilitates the development of genetic differentiation between subpopulations. Other aspects of life history such as geographically distinct vocalizations, female gregariousness, and the potential for polygynous breeding may also facilitate population structure. Based on these factors, we predicted that fast-ice-breeding seal species (the Weddell and ringed seal) would show elevated genetic differentiation compared to pack-ice-breeding species (the leopard, Ross, crabeater and bearded seals). We tested this prediction using microsatellite analysis to examine population structure of these six ice-breeding species. Our results did not support this prediction. While none of the Antarctic pack-ice species showed statistically significant population structure, the bearded seal of the Arctic pack ice showed strong differentiation between subpopulations. Again in contrast, the fast-ice-breeding Weddell seal of the Antarctic showed clear evidence for genetic differentiation while the ringed seal, breeding in similar habitat in the Arctic, did not. These results suggest that the development of population structure in ice-breeding phocid seals is a more complex outcome of the interplay of phylogenetic and ecological factors than can be predicted on the basis of breeding substrate and life-history characteristics.

  12. [The evaluation of breed-specific defects in dog breeds from an animal welfare viewpoint].

    PubMed

    Peyer, N; Steiger, A

    1998-01-01

    Issues of breed defects such as morphology, physiology or behaviour in pure-breed dogs, are briefly discussed. Suggestions for various kinds of improvements are made, particularly concerning legislation, analysis of pedigree to avoid undesirable breed characteristics and what breeding clubs, individual breeders, judges, future dog owners and veterinarians could and should do about these problems; these are followed by summary conclusions.

  13. Emperor Penguins Breeding on Iceshelves

    PubMed Central

    Fretwell, Peter T.; Trathan, Phil N.; Wienecke, Barbara; Kooyman, Gerald L.

    2014-01-01

    We describe a new breeding behaviour discovered in emperor penguins; utilizing satellite and aerial-survey observations four emperor penguin breeding colonies have been recorded as existing on ice-shelves. Emperors have previously been considered as a sea-ice obligate species, with 44 of the 46 colonies located on sea-ice (the other two small colonies are on land). Of the colonies found on ice-shelves, two are newly discovered, and these have been recorded on shelves every season that they have been observed, the other two have been recorded both on ice-shelves and sea-ice in different breeding seasons. We conduct two analyses; the first using synthetic aperture radar data to assess why the largest of the four colonies, for which we have most data, locates sometimes on the shelf and sometimes on the sea-ice, and find that in years where the sea-ice forms late, the colony relocates onto the ice-shelf. The second analysis uses a number of environmental variables to test the habitat marginality of all emperor penguin breeding sites. We find that three of the four colonies reported in this study are in the most northerly, warmest conditions where sea-ice is often sub-optimal. The emperor penguin’s reliance on sea-ice as a breeding platform coupled with recent concerns over changed sea-ice patterns consequent on regional warming, has led to their designation as “near threatened” in the IUCN red list. Current climate models predict that future loss of sea-ice around the Antarctic coastline will negatively impact emperor numbers; recent estimates suggest a halving of the population by 2052. The discovery of this new breeding behaviour at marginal sites could mitigate some of the consequences of sea-ice loss; potential benefits and whether these are permanent or temporary need to be considered and understood before further attempts are made to predict the population trajectory of this iconic species. PMID:24416381

  14. Endemic insular and coastal Tunisian date palm genetic diversity.

    PubMed

    Zehdi-Azouzi, Salwa; Cherif, Emira; Guenni, Karim; Abdelkrim, Ahmed Ben; Bermil, Aymen; Rhouma, Soumaya; Salah, Mohamed Ben; Santoni, Sylvain; Pintaud, Jean Christophe; Aberlenc-Bertossi, Frédérique; Hannachi, Amel Salhi

    2016-04-01

    The breeding of crop species relies on the valorisation of ancestral or wild varieties to enrich the cultivated germplasm. The Tunisian date palm genetic patrimony is being threatened by diversity loss and global climate change. We have conducted a genetic study to evaluate the potential of spontaneous coastal resources to improve the currently exploited Tunisian date palm genetic pool. Eighteen microsatellite loci of Phoenix dactylifera L. were used to compare the genetic diversity of coastal accessions from Kerkennah, Djerba, Gabès and continental date palm accessions from Tozeur. A collection of 105 date palms from the four regions was analysed. This study has provided us with an extensive understanding of the local genetic diversity and its distribution. The coastal date palm genotypes exhibit a high and specific genetic diversity. These genotypes are certainly an untapped reservoir of agronomically important genes to improve cultivated germplasm in continental date palm.

  15. NATIONAL COASTAL CONDITION REPORT

    EPA Science Inventory

    The National Coastal Condition report compiles several available data sets from different agencies and areas of the country and summarizes them to present a broad baseline picture of the condition of coastal waters. Although data sets presented in this report do not cover all coa...

  16. Resilience from coastal protection.

    PubMed

    Ewing, Lesley C

    2015-10-28

    Coastal areas are important residential, commercial and industrial areas; but coastal hazards can pose significant threats to these areas. Shoreline/coastal protection elements, both built structures such as breakwaters, seawalls and revetments, as well as natural features such as beaches, reefs and wetlands, are regular features of a coastal community and are important for community safety and development. These protection structures provide a range of resilience to coastal communities. During and after disasters, they help to minimize damages and support recovery; during non-disaster times, the values from shoreline elements shift from the narrow focus on protection. Most coastal communities have limited land and resources and few can dedicate scarce resources solely for protection. Values from shore protection can and should expand to include environmental, economic and social/cultural values. This paper discusses the key aspects of shoreline protection that influence effective community resilience and protection from disasters. This paper also presents ways that the economic, environmental and social/cultural values of shore protection can be evaluated and quantified. It presents the Coastal Community Hazard Protection Resilience (CCHPR) Index for evaluating the resilience capacity to coastal communities from various protection schemes and demonstrates the use of this Index for an urban beach in San Francisco, CA, USA.

  17. Coastal zone management

    NASA Technical Reports Server (NTRS)

    Tilton, E. L., III

    1975-01-01

    A panel of federal and state representatives concerned with coastal zone affairs discussed their problems in this area. In addition, several demonstrations of the application of remote sensing technology to coastal zone management were described. These demonstrations were performed by several agencies in a variety of geographical areas.

  18. NATIONAL COASTAL ASSESSMENT

    EPA Science Inventory

    The purpose of the National Coastal Assessment (NCA) is to estimate the status and trends of the condition of the nation's coastal resources on a state, regional and national basis. Based on NCA monitoring from 1999-2001, 100% of the nation's estuarine waters (at over 2500 locati...

  19. Ground penetrating radar study of a strand shoreline in northeastern South Carolina.

    NASA Astrophysics Data System (ADS)

    Wright, E.; Harris, M.; Correia, K.

    2008-12-01

    The 75 km long Grand Strand is the primary shoreline type of northeastern South Carolina and is forming by landward retreat of the shoreline intersecting the paleo Myrtle Beach barrier system. Previous ground penetrating radar studies have examined the geologic architecture of different stages of the regional shoreline transgression: (1) current barrier island systems to the north and south of the central Grand Strand that have transgressed across irregular Pleistocene paleo landscape but have not yet intersected the emergent Quaternary terraces, (2) shorelines with shore-parallel coastal lakes and vegetated wetlands formed at the intersection of the transgressive shoreline and the emergent terraces, and (3) coastal shorelines that are fully welded to the Pleistocene headlands. This study uses GPR to examine the pre- transgressive architecture of shorelines along the emergent paleo barrier system, in particular sections of the coastline with linear paralic wetlands that occupy lows within the paleo barrier system. Study of this pre- transgressive architecture will help to better understand the geologic development of the compound paleo Myrtle Beach barriers as well as refine geologic interpretation of the transgressing shorelines to the north and south that are currently and will be intersecting this paleo barrier system.

  20. RNA-catalysed synthesis of complementary-strand RNA

    NASA Astrophysics Data System (ADS)

    Doudna, Jennifer A.; Szostak, Jack W.

    1989-06-01

    The Tetrahymena ribozyme can splice together multiple oligonucleotides aligned on a template strand to yield a fully complementary product strand. This reaction demonstrates the feasibility of RNA-catalysed RNA replications.

  1. Non-breeding habitat preference affects ecological speciation in migratory waders

    NASA Astrophysics Data System (ADS)

    Kraaijeveld, Ken

    2008-04-01

    Models of ecological speciation predict that certain types of habitat should be more conducive to species diversification than others. In this study, I test this hypothesis in waders of the sub-order Charadrii using the number of morphological sub-species per species as an index of diversity. I classified all members of this clade as spending the non-breeding season either coastally or inland and argue that these represent fundamentally different environments. Coastal mudflats are characterised by high predictability and patchy worldwide distribution, whilst inland wetlands are widespread but unpredictable. The results show that migratory species that winter coastally are sub-divided into more sub-species than those that winter inland. This was not the case for non-migratory species. I argue that coastal environments select for more rigid migratory pathways, whilst inland wetlands favour more flexible movement patterns. Population sub-division could then result from the passive segregation of breeding sites or from the active selection for assortative mating of ecomorphs.

  2. Magnetic instabilities in Nb3Sn strands and cables

    SciTech Connect

    Kashikhim, Vadim V.; Zlobin, Alexander V.; /Fermilab

    2004-11-01

    This paper describes a model for calculation of magnetic instabilities in superconducting wires with transport current and reports results of instability simulations in Nb{sub 3}Sn strands from different manufactures. The effect of magnetic instabilities on the strand and cable performance is presented and a criterion for the maximum effective sub-element size of strands for high field magnets is formulated.

  3. Evidence for hydrophobic catalysis of DNA strand exchange.

    PubMed

    Feng, B; Westerlund, F; Nordén, B

    2015-04-30

    The catalytic role of hydrophobic co-solutes in DNA strand exchange is demonstrated by FRET kinetics. Two mechanisms that contribute to this are base stacking destabilisation and nucleation-promoted DNA strand invasion. We propose that hydrophobic catalysis is involved in the strand-exchange activity of recombination enzymes.

  4. Fish stranding in freshwater systems: sources, consequences, and mitigation.

    PubMed

    Nagrodski, Alexander; Raby, Graham D; Hasler, Caleb T; Taylor, Mark K; Cooke, Steven J

    2012-07-30

    Fish can become stranded when water levels decrease, often rapidly, as a result of anthropogenic (e.g., canal drawdown, hydropeaking, vessel wakes) and natural (e.g., floods, drought, winter ice dynamics) events. We summarize existing research on stranding of fish in freshwater, discuss the sources, consequences, and mitigation options for stranding, and report current knowledge gaps. Our literature review revealed that ∼65.5% of relevant peer-reviewed articles were found to focus on stranding associated with hydropower operations and irrigation projects. In fact, anthropogenic sources of fish stranding represented 81.8% of available literature compared to only 19.9% attributed to natural fish stranding events. While fish mortality as a result of stranding is well documented, our analysis revealed that little is known about the sublethal and long-term consequences of stranding on growth and population dynamics. Furthermore, the contribution of stranding to annual mortality rates is poorly understood as are the potential ecosystem-scale impacts. Mitigation strategies available to deal with stranding include fish salvage, ramping rate limitations, and physical habitat works (e.g., to contour substrate to minimize stranding). However, a greater knowledge of the factors that cause fish stranding would promote the development and refinement of mitigation strategies that are economically and ecologically sustainable.

  5. The Parameter of Preposition Stranding: A View from Child English

    ERIC Educational Resources Information Center

    Sugisaki, Koji; Snyder, William

    2006-01-01

    In this squib we examine the time course of children's acquisition of English to evaluate the basic insights of Kayne's (1981; 1984) proposals on preposition stranding. Kayne argued that the availability of preposition stranding (P-stranding) in English is parametrically linked to the availability of double object datives and the prepositional…

  6. Coastal Hazards: Hurricanes, Tsunamis, Coastal Erosion.

    ERIC Educational Resources Information Center

    Vandas, Steve

    1998-01-01

    Details an ocean-based lesson and provides background information on the designation of 1998 as the "Year of the Ocean" by the United Nations. Contains activities on the poster insert that can help raise student awareness of coastal-zone hazards. (DDR)

  7. A Double-Strand Elastic Rod Theory

    NASA Astrophysics Data System (ADS)

    Moakher, Maher; Maddocks, John H.

    2005-07-01

    Motivated by applications in the modeling of deformations of the DNA double helix, we construct a continuum mechanics model of two elastically interacting elastic strands. The two strands are described in terms of averaged, or macroscopic, variables plus an additional small, internal or microscopic, perturbation. We call this composite structure a birod. The balance laws for the macroscopic configuration variables of the birod can be cast in the form of a classic Cosserat rod model with coupling to the internal balance laws through the constitutive relations. The internal balance laws for the microstructure variables also take a mathematical form analogous to that for a Cosserat rod, but with coupling to the macroscopic system through terms corresponding to distributed force and couple loads.

  8. Breeding without breeding: is a complete pedigree necessary for efficient breeding?

    PubMed

    El-Kassaby, Yousry A; Cappa, Eduardo P; Liewlaksaneeyanawin, Cherdsak; Klápště, Jaroslav; Lstibůrek, Milan

    2011-01-01

    Complete pedigree information is a prerequisite for modern breeding and the ranking of parents and offspring for selection and deployment decisions. DNA fingerprinting and pedigree reconstruction can substitute for artificial matings, by allowing parentage delineation of naturally produced offspring. Here, we report on the efficacy of a breeding concept called "Breeding without Breeding" (BwB) that circumvents artificial matings, focusing instead on a subset of randomly sampled, maternally known but paternally unknown offspring to delineate their paternal parentage. We then generate the information needed to rank those offspring and their paternal parents, using a combination of complete (full-sib: FS) and incomplete (half-sib: HS) analyses of the constructed pedigrees. Using a random sample of wind-pollinated offspring from 15 females (seed donors), growing in a 41-parent western larch population, BwB is evaluated and compared to two commonly used testing methods that rely on either incomplete (maternal half-sib, open-pollinated: OP) or complete (FS) pedigree designs. BwB produced results superior to those from the incomplete design and virtually identical to those from the complete pedigree methods. The combined use of complete and incomplete pedigree information permitted evaluating all parents, both maternal and paternal, as well as all offspring, a result that could not have been accomplished with either the OP or FS methods alone. We also discuss the optimum experimental setting, in terms of the proportion of fingerprinted offspring, the size of the assembled maternal and paternal half-sib families, the role of external gene flow, and selfing, as well as the number of parents that could be realistically tested with BwB.

  9. Coastal mapping handbook

    USGS Publications Warehouse

    ,; ,; Ellis, Melvin Y.

    1978-01-01

    Passage of the Coastal Zone Management Act of 1972 focused attention on the Nation's coastal land and water areas. As plans for more effective management of the coastal zone evolved, it soon became apparent that improved maps and charts of these areas were needed. This handbook was prepared with the requirements of the entire coastal community in mind, giving greatest attention to the needs of coastal zone managers and planners at the State and local levels. Its principal objective is to provide general information and guidance; it is neither a textbook nor a technical manual, but rather a primer on coastal mapping. This handbook should help planners and managers of coastal programs to determine their mapping requirements, select the best maps and charts for their particular needs, and to deal effectively with personnel who gather data and prepare maps. The sections on "Sources of Assistance and Advice" and "Product and Data Sources" should be especially useful to all involved in mapping the coastal zone. Brief summaries of the mapping efforts of several State coastal zone management programs are included. "Future outlook" discusses anticipated progress and changes in mapping procedures and techniques. Illustrations are inserted, where appropriate, to illustrate the products and equipment discussed. Because of printing restrictions, the colors in map illustrations may vary from those in the original publication. The appendixes include substantial material which also should be of interest. In addition a glossary and an index are included to provide easy and quick access to the terms and concepts used in the text. For those interested in more technical detail than is provided in this handbook, the "Selected references" will be useful. Also, the publications of the professional societies listed in appendix 4 will provide technical information in detail.

  10. Exploring the ecological processes driving geographical patterns of breeding bird richness in British Columbia, Canada.

    PubMed

    Fitterer, Jessica L; Nelson, Trisalyn A; Coops, Nicholas C; Wulder, Michael A; Mahony, Nancy A

    2013-06-01

    British Columbia (BC), Canada, has a diverse landscape that provides breeding habitat for > 300 avian species, and the recent development of the BC Breeding Bird Atlas data set presents key information for exploring the landscape conditions which lead to biological richness. We used the volunteer-collected raw breeding bird evidence data set to analyze the effects of sampling biases on spatial distribution of observed breeding bird species and implemented regression tree analysis (Random Forests) to examine the influence of productivity, ambient energy, and habitat heterogeneity on independently measured breeding bird richness. Results indicated that total breeding species richness is correlated with total survey effort (alpha < 0.001). By stratifying species richness by survey effort, we observed that ambient energy is the top-ranked environmental predictor of breeding bird richness across BC, which, when used in combination with a number of other environmental variables, explains -40% of the variation in richness. Using our modeled relationships, we predicted breeding bird species richness in the areas of BC not presently surveyed between three and six hours. The majority of the productive Boreal Plains, the southern portion of the Taiga Plains region, the lowlands of the Southern and Central Interior, along the Rocky Mountain Trench, and the coastal areas of the Georgia Depression are predicted to have the highest categories of breeding richness (35-57 unique species). Our results support ongoing species diversity gradient research, which identifies ambient energy as an important factor influencing species diversity distributions in the Northern Hemisphere. By linking breeding bird richness to environmental data derived from remotely sensed data and systematically collected climate data, we demonstrate the potential to monitor shifts in ambient energy as a surrogate for vertebrate habitat condition affecting population levels. By analyzing the influence of

  11. Method and apparatus for testing a forward-moving strand

    DOEpatents

    Ducommun, Joel; Vulliens, Philippe

    1980-01-01

    In a method for testing a continuously forward-moving strand a light beam which passes along a plane that extends approximately perpendicularly to the longitudinal axis of the strand is introduced into the strand. The brightness value is measured on a place of the strand exterior which is distal from the light incidence place by means of at least one photoelectronic element disposed directly on the strand exterior and the measured result is evaluated in a gating circuit which is electrically connected to the photoelectronic element.

  12. Microsatellite diversity of the Nordic type of goats in relation to breed conservation: how relevant is pure ancestry?

    PubMed

    Lenstra, J A; Tigchelaar, J; Biebach, I; Hallsson, J H; Kantanen, J; Nielsen, V H; Pompanon, F; Naderi, S; Rezaei, H-R; Saether, N; Ertugrul, O; Grossen, C; Camenisch, G; Vos-Loohuis, M; van Straten, M; de Poel, E A; Windig, J; Oldenbroek, K

    2017-02-01

    In the last decades, several endangered breeds of livestock species have been re-established effectively. However, the successful revival of the Dutch and Danish Landrace goats involved crossing with exotic breeds and the ancestry of the current populations is therefore not clear. We have generated genotypes for 27 FAO-recommended microsatellites of these landraces and three phenotypically similar Nordic-type landraces and compared these breeds with central European, Mediterranean and south-west Asian goats. We found decreasing levels of genetic diversity with increasing distance from the south-west Asian domestication site with a south-east-to-north-west cline that is clearly steeper than the Mediterranean east-to-west cline. In terms of genetic diversity, the Dutch Landrace comes next to the isolated Icelandic breed, which has an extremely low diversity. The Norwegian coastal goat and the Finnish and Icelandic landraces are clearly related. It appears that by a combination of mixed origin and a population bottleneck, the Dutch and Danish Land-races are separated from the other breeds. However, the current Dutch and Danish populations with the multicoloured and long-horned appearance effectively substitute for the original breed, illustrating that for conservation of cultural heritage, the phenotype of a breed is more relevant than pure ancestry and the genetic diversity of the original breed. More in general, we propose that for conservation, the retention of genetic diversity of an original breed and of the visual phenotype by which the breed is recognized and defined needs to be considered separately.

  13. Biological consequences of strand breaks in plasmid and viral DNA.

    PubMed Central

    Schulte-Frohlinde, D.

    1987-01-01

    Some biological consequences of strand breakage in biologically active single- and double-stranded plasmid and viral DNA are examined. A double-strand break in DNA produced by restriction-endonucleases in aqueous solution is not a 100% lethal damage. The survival depends strongly on the structure of the end groups. Evidence is presented that survival is the result of a balance between degradation and repair. The enzymatically produced double-strand break (dsb) is a potentially lethal damage similar to the irradiation-produced dsb in cells. Results with double-stranded biologically active DNA treated either with gamma-rays, heat, pancrease nuclease or UV-light in aqueous solution suggest that a single-strand damage is also a potentially lethal damage. Mechanisms for conversion of single-strand damage to lethal events are discussed. PMID:3307866

  14. National Coastal Condition Assessment

    EPA Pesticide Factsheets

    The NCCA is a collaborative, statistical survey of the nation's coastal waters and the Great Lakes. It is one of four national surveys that EPA and its partners conduct to assess the condition and health of the nation's water resources.

  15. Population dynamics of king eiders breeding in northern Alaska

    USGS Publications Warehouse

    Bentzen, Rebecca L.; Powell, Abby N.

    2012-01-01

    The North American population of king eiders (Somateria spectabilis) has declined by more than 50% since the late 1970s for unknown reasons. King eiders spend most of their lives in remote areas, forcing managers to make regulatory and conservation decisions based on very little information. We incorporated available published estimates of vital rates with new estimates to build a female, stage-based matrix population model for king eiders and examine the processes underlying population dynamics of king eiders breeding at 2 sites, Teshekpuk and Kuparuk, on the coastal plain of northern Alaska and wintering around the Bering Sea (2001–2010). We predicted a decreasing population (λ = 0.981, 95% CI: 0.978–0.985), and that population growth was most sensitive to changes in adult female survival (sensitivity = 0.92). Low duckling survival may be a bottleneck to productivity (variation in ducking survival accounted for 66% of retrospective variation in λ). Adult survival was high (0.94) and invariant (σ = 0.0002, 95% CI: 0.0000–0.0007); however, catastrophic events could have a major impact and we need to consider how to mitigate and manage threats to adult survival. A hypothetical oil spill affecting breeding females in a primary spring staging area resulted in a severe population decline; although, transient population dynamics were relatively stable. However, if no catastrophic events occur, the more variable reproductive parameters (duckling and nest survival) may be more responsive to management actions.

  16. The multiple personalities of Watson and Crick strands

    PubMed Central

    2011-01-01

    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. PMID:21303550

  17. Amplification methods bias metagenomic libraries of uncultured single-stranded and double-stranded DNA viruses.

    PubMed

    Kim, Kyoung-Ho; Bae, Jin-Woo

    2011-11-01

    Investigation of viruses in the environment often requires the amplification of viral DNA before sequencing of viral metagenomes. In this study, two of the most widely used amplification methods, the linker amplified shotgun library (LASL) and multiple displacement amplification (MDA) methods, were applied to a sample from the seawater surface. Viral DNA was extracted from viruses concentrated by tangential flow filtration and amplified by these two methods. 454 pyrosequencing was used to read the metagenomic sequences from different libraries. The resulting taxonomic classifications of the viruses, their functional assignments, and assembly patterns differed substantially depending on the amplification method. Only double-stranded DNA viruses were retrieved from the LASL, whereas most sequences in the MDA library were from single-stranded DNA viruses, and double-stranded DNA viral sequences were minorities. Thus, the two amplification methods reveal different aspects of viral diversity.

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

    DOEpatents

    Gray, Joe W.; Pinkel, Daniel

    1991-01-01

    A method is provided for producing single stranded non-self-complementary nucleic acid probes, and for treating target DNA for use therewith. 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.

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

    DOEpatents

    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

  20. [Pain caused by breeding in dogs].

    PubMed

    Reetz, I C

    1997-02-01

    According to German animal protection law it is not aloud to breed animals if it has to be expected that the offspring will suffer pain caused by hereditary characters. This paper deals with those hereditary defects which are used directly or indirectly (because of linkage to other desirable traits) in dog breeding. By the patho-physiological symptoms and the genetics of selected hereditary defects recommendations are exemplified how these defects should be handled in breeding that pain can be avoided.

  1. Estimating regional landbird populations from enhanced North American Breeding Bird Surveys

    USGS Publications Warehouse

    Twedt, Daniel J.

    2015-01-01

    Estimating the size of bird populations is central to effective conservation planning and prudent management. I updated estimated regional bird populations for the East Gulf Coastal Plain of Mississippi using data from 275 North American Breeding Bird Surveys from 2009 to 2013. However, regional bird populations estimated from count surveys of breeding birds may be biased due to lack of empirical knowledge of the distance at which a species is effectively detected and the probability of detecting a species if it is present. I used data recorded within two distance classes (0–50 m and >50–400 m) and three 1-min time intervals on 130 Breeding Bird Surveys to estimate detection probability and effective detection distance for 77 species. Incorporating these empirical estimates of detection probability and detection distance resulted in estimated regional populations for these species that were markedly greater than regional populations estimated without species-specific estimates of detection parameters. Using the same Breeding Bird Survey data, I also estimated probability of site occupancy for 66 species and extrapolated this to the proportion of area occupied in the East Gulf Coastal Plain of Mississippi. I combined the area occupied with the reported range of breeding territory size for 54 species to obtain independent estimates of regional bird populations. Although the true population of these species is unknown, estimated populations that incorporated empirical estimates of detection probability and detection distance were more likely to be within the range of independently estimated, occupancy-based, regional population estimates than were population estimates that lacked empirical detection and distance information.

  2. The Breeding Bird Survey, 1966

    USGS Publications Warehouse

    Robbins, C.S.; Van Velzen, W.T.

    1967-01-01

    A Breeding Bird Survey of a large section on North America was conducted during June 1966. Cooperators ran a total of 585 Survey routes in 26 eastern States and 4 Canadian Provinces. Future coverage of established routes will enable changes in the abundance of North American breeding birds to be measured. Routes are selected at random on the basis of one-degree blocks of latitude and longitude. Each 241/2-mile route, with 3-minute stops spaced one-half mile apart, is driven by automobile. All birds heard or seen at the stops are recorded on special forms and the data are then transferred to machine punch cards. The average number of birds per route is tabulated by State, along with the total number of each species and the percent of routes and stops upon which they were recorded. Maps are presented showing the range and abundance of selected species. Also, a year-to-year comparison is made of populations of selected species on Maryland routes in 1965 and 1966.

  3. [New technology in maize breeding].

    PubMed

    Konstantinov, K; Mladenović, S; Stojkov, S; Delić, N; Gosić, S; Petrović, R; Lević, J; Denić, M

    1992-01-01

    Results obtained by several approaches in the application of Biotechnology in maize breeding are reviewed. RFLP technology in the determination of genetic variation; gene transfer by the use of different methods of gene delivery and the determination of gene integration. Three technologies for foreign gene introduction have been applied; injection of plasmid pRT100 neo into archesporial tissue before micro and macro sporogenesis, slightly modified pollen-tube pathway technology and dry seed incubation in plasmid DNA solution. NPTII gene integration was followed by dot-blot and Southern blot analysis of plant DNA of both T1 and T2 plants. Gene expression was analysed by neomycin phosphotransferase activity. Transformed plants contained the selective NPTII gene sequence in an active form. Bacterial gene integration induced several heritable changes of plant phenotype. As an important change, alteration of the flowering time has been used as a criterion for selection and plant propagation to keep transformed progeny. Besides plant genome transformation, endogenous bacteria living in different maize tissue were found. As a perspective approach for biotechnology application in maize breeding biological vaccine construction has been selected. Therefore, antagonistic effect of gram positive bacterial strains to several pathogenic fungi was investigated. Results obtained after in vivo experiments are discussed.

  4. Genomics-assisted breeding in fruit trees

    PubMed Central

    Iwata, Hiroyoshi; Minamikawa, Mai F.; Kajiya-Kanegae, Hiromi; Ishimori, Motoyuki; Hayashi, Takeshi

    2016-01-01

    Recent advancements in genomic analysis technologies have opened up new avenues to promote the efficiency of plant breeding. Novel genomics-based approaches for plant breeding and genetics research, such as genome-wide association studies (GWAS) and genomic selection (GS), are useful, especially in fruit tree breeding. The breeding of fruit trees is hindered by their long generation time, large plant size, long juvenile phase, and the necessity to wait for the physiological maturity of the plant to assess the marketable product (fruit). In this article, we describe the potential of genomics-assisted breeding, which uses these novel genomics-based approaches, to break through these barriers in conventional fruit tree breeding. We first introduce the molecular marker systems and whole-genome sequence data that are available for fruit tree breeding. Next we introduce the statistical methods for biparental linkage and quantitative trait locus (QTL) mapping as well as GWAS and GS. We then review QTL mapping, GWAS, and GS studies conducted on fruit trees. We also review novel technologies for rapid generation advancement. Finally, we note the future prospects of genomics-assisted fruit tree breeding and problems that need to be overcome in the breeding. PMID:27069395

  5. Chemical classification of cattle. 1. Breed groups.

    PubMed

    Baker, C M; Manwell, C

    1980-01-01

    From approximately 1000 papers with data on protein polymorphism in some 216 breeds of cattle, 10 polymorphic proteins were compared in means and variances of gene frequencies (arcsin p 1/2) for ten well-recognized breed groups for 196 of the breeds. The polymorphic proteins were alpha-lactalbumin, beta-lactoglobulin, caseins (alpha s1, beta and chi), serum albumin, transferrin, haemoglobin, amylase I and carbonic anhydrase II. The breed groups were North European, Pied Lowland, European Red brachyceros, Channel Island brachyceros, Upland brachyceros, primigenius-brachyceros mixed, primigenius, Indian Zebu, African Humped (with Zebu admixture), and African Humped (Sanga). The coherence within groups and the differences between groups are often impressive. Only carbonic anhydrase II fails to differentiate at least some of the major breed groups. In some cases paradoxical distributions of rare genetic variants can be explained by a more detailed inspection of breed history. The chemical data support the morphological and geographical divisions of cattle into major breed groups. There are three distinct but related brachyceros groups; for some polymorphisms the two Channel Island breeds, the Jersey and the Guernsey, are quite divergent. Although some authorities have considered the Pied Lowland as primigenius, it is a very distinct breed group.

  6. Genomics-assisted breeding in fruit trees.

    PubMed

    Iwata, Hiroyoshi; Minamikawa, Mai F; Kajiya-Kanegae, Hiromi; Ishimori, Motoyuki; Hayashi, Takeshi

    2016-01-01

    Recent advancements in genomic analysis technologies have opened up new avenues to promote the efficiency of plant breeding. Novel genomics-based approaches for plant breeding and genetics research, such as genome-wide association studies (GWAS) and genomic selection (GS), are useful, especially in fruit tree breeding. The breeding of fruit trees is hindered by their long generation time, large plant size, long juvenile phase, and the necessity to wait for the physiological maturity of the plant to assess the marketable product (fruit). In this article, we describe the potential of genomics-assisted breeding, which uses these novel genomics-based approaches, to break through these barriers in conventional fruit tree breeding. We first introduce the molecular marker systems and whole-genome sequence data that are available for fruit tree breeding. Next we introduce the statistical methods for biparental linkage and quantitative trait locus (QTL) mapping as well as GWAS and GS. We then review QTL mapping, GWAS, and GS studies conducted on fruit trees. We also review novel technologies for rapid generation advancement. Finally, we note the future prospects of genomics-assisted fruit tree breeding and problems that need to be overcome in the breeding.

  7. Differentiation among Spanish sheep breeds using microsatellites

    PubMed Central

    Arranz, Juan-José; Bayón, Yolanda; Primitivo, Fermín San

    2001-01-01

    Genetic variability at 18 microsatellites was analysed on the basis of individual genotypes in five Spanish breeds of sheep – Churra, Latxa, Castellana, Rasa-Aragonesa and Merino -, with Awassi also being studied as a reference breed. The degree of population subdivision calculated between Spanish breeds from FST diversity indices was around 7% of total variability. A high degree of reliability was obtained for individual-breed assignment from the 18 loci by using different approaches among which the Bayesian method provided to be the most efficient, with an accuracy for nine microsatellites of over 99%. Analysis of the Bayesian assignment criterion illustrated the divergence between any one breed and the others, which was highest for Awassi sheep, while no great differences were evident among the Spanish breeds. Relationships between individuals were analysed from the proportion of shared alleles. The resulting dendrogram showed a remarkable breed structure, with the highest level of clustering among members of the Spanish breeds in Latxa and the lowest in Merino sheep, the latter breed exhibiting a peculiar pattern of clustering, with animals grouped into several closely set nodes. Analysis of individual genotypes provided valuable information for understanding intra- and inter-population genetic differences and allowed for a discussion with previously reported results using populations as taxonomic units. PMID:11712973

  8. Fish genome manipulation and directional breeding.

    PubMed

    Ye, Ding; Zhu, ZuoYan; Sun, YongHua

    2015-02-01

    Aquaculture is one of the fastest developing agricultural industries worldwide. One of the most important factors for sustainable aquaculture is the development of high performing culture strains. Genome manipulation offers a powerful method to achieve rapid and directional breeding in fish. We review the history of fish breeding methods based on classical genome manipulation, including polyploidy breeding and nuclear transfer. Then, we discuss the advances and applications of fish directional breeding based on transgenic technology and recently developed genome editing technologies. These methods offer increased efficiency, precision and predictability in genetic improvement over traditional methods.

  9. The subspecific origin of the inland breeding colonies of the cormorant Phalacrocorax carbo in Britain.

    PubMed

    Winney, B J; Litton, C D; Parkin, D T; Feare, C J

    2001-01-01

    The establishment of cormorant breeding colonies inland within south-east Britain since 1981 is a matter of major conservation and pest management concern. This study was initiated to investigate the subspecific origin of two recently established breeding colonies. The analysis examined sequence variation of the control (D-loop) region of the mitochondrial genome. Samples of tissue were obtained from 334 individuals from across the species range in western Europe from both subspecies (Phalacrocorax carbo carbo and P. c. sinensis) and 84 birds from two inland breeding colonies in Britain. Single-strand conformation polymorphism (SSCP) was used to assess mitochondrial variation among samples, revealing four haplotypes. The samples from the traditional breeding colonies clustered into three distinct phylogeographic groupings: Norway-Scotland, Wales-England-Iles des Chausey and the rest of Continental Europe. These results only partly agree with the traditional subspecific taxonomic groupings and are slightly at variance with results using microsatellite DNA frequencies, and a hypothesis using results from both studies is advanced. The subspecific origin of the inland colonies was investigated using maximum likelihood and Bayesian models.

  10. Strand invasion promoted by recombination protein of coliphage

    NASA Astrophysics Data System (ADS)

    Rybalchenko, Nataliya; Golub, Efim I.; Bi, Baoyuan; Radding, Charles M.

    2004-12-01

    Studies of phage in vivo have indicated that its own recombination enzymes, protein and exonuclease, are capable of catalyzing two dissimilar pathways of homologous recombination that are widely distributed in nature: single-strand annealing and strand invasion. The former is an enzymatic splicing of overlapping ends of broken homologous DNA molecules, whereas the latter is characterized by the formation of a three-stranded synaptic intermediate and subsequent strand exchange. Previous studies in vitro have shown that protein has annealing activity, and that exonuclease, acting on branched substrates, can produce a perfect splice that requires only ligation for completion. The present study shows that protein can initiate strand invasion in vitro, as evidenced both by the formation of displacement loops (D-loops) in superhelical DNA and by strand exchange between colinear single-stranded and double-stranded molecules. Thus, protein can catalyze steps that are central to both strand annealing and strand invasion pathways of recombination. These observations add protein to a set of diverse proteins that appear to promote recognition of homology by a unitary mechanism governed by the intrinsic dynamic properties of base pairs in DNA. genetic recombination | phage λ

  11. A strand graph semantics for DNA-based computation.

    PubMed

    Petersen, Rasmus L; Lakin, Matthew R; Phillips, Andrew

    2016-06-13

    DNA nanotechnology is a promising approach for engineering computation at the nanoscale, with potential applications in biofabrication and intelligent nanomedicine. DNA strand displacement is a general strategy for implementing a broad range of nanoscale computations, including any computation that can be expressed as a chemical reaction network. Modelling and analysis of DNA strand displacement systems is an important part of the design process, prior to experimental realisation. As experimental techniques improve, it is important for modelling languages to keep pace with the complexity of structures that can be realised experimentally. In this paper we present a process calculus for modelling DNA strand displacement computations involving rich secondary structures, including DNA branches and loops. We prove that our calculus is also sufficiently expressive to model previous work on non-branching structures, and propose a mapping from our calculus to a canonical strand graph representation, in which vertices represent DNA strands, ordered sites represent domains, and edges between sites represent bonds between domains. We define interactions between strands by means of strand graph rewriting, and prove the correspondence between the process calculus and strand graph behaviours. Finally, we propose a mapping from strand graphs to an efficient implementation, which we use to perform modelling and simulation of DNA strand displacement systems with rich secondary structure.

  12. Method for producing labeled single-stranded nucleic acid probes

    DOEpatents

    Dunn, John J.; Quesada, Mark A.; Randesi, Matthew

    1999-10-19

    Disclosed is a method for the introduction of unidirectional deletions in a cloned DNA segment. More specifically, the method comprises providing a recombinant DNA construct comprising a DNA segment of interest inserted in a cloning vector, the cloning vector having an f1 endonuclease recognition sequence adjacent to the insertion site of the DNA segment of interest. The recombinant DNA construct is then contacted with the protein pII encoded by gene II of phage f1 thereby generating a single-stranded nick. The nicked DNA is then contacted with E. coli Exonuclease III thereby expanding the single-stranded nick into a single-stranded gap. The single-stranded gapped DNA is then contacted with a single-strand-specific endonuclease thereby producing a linearized DNA molecule containing a double-stranded deletion corresponding in size to the single-stranded gap. The DNA treated in this manner is then incubated with DNA ligase under conditions appropriate for ligation. Also disclosed is a method for producing single-stranded DNA probes. In this embodiment, single-stranded gapped DNA, produced as described above, is contacted with a DNA polymerase in the presence of labeled nucleotides to fill in the gap. This DNA is then linearized by digestion with a restriction enzyme which cuts outside the DNA segment of interest. The product of this digestion is then denatured to produce a labeled single-stranded nucleic acid probe.

  13. Size and retention of breeding territories of yellow-billed loons in Alaska and Canada

    USGS Publications Warehouse

    Schmutz, Joel A.; Wright, Kenneth G.; DeSorbo, Christopher R.; Fair, Jeff; Evers, David C.; Uher-Koch, Brian D.; Mulcahy, Daniel M.

    2014-01-01

    Yellow-billed Loons (Gavia adamsii) breed in lakes in the treeless Arctic and are globally rare. Like their sister taxa, the well-documented Common Loon (G. immer) of the boreal forest, Yellow-billed Loons exhibit strong territorial behavior during the breeding season. Little is known about what size territories are required, however, or how readily territories are retained from year to year. An understanding of territory dynamics and size is needed by management agencies as most of the U.S. breeding population of Yellow-billed Loons resides in the National Petroleum Reserve-Alaska where oil and gas development is expected to increase in the next few decades. Using locational data from a set of Yellow-billed Loons marked with satellite transmitters, we quantified an index of territory radius for each of three breeding populations: two in Alaska and one in Canada. The mean territory radius was 0.42 km for Yellow-billed Loons summering on lakes within the Seward Peninsula in northwest Alaska, 0.69 km for Yellow-billed Loons within the Arctic Coastal Plain of Alaska (encompasses the National Petroleum Reserve), and 0.96 km for Yellow-billed Loons within Daring Lake in mainland Canada. In this study, the mean territory radius on the Arctic Coastal Plain was about half the distance identified in stipulations for industrial development in the National Petroleum Reserve. The range in territory size among areas corresponded to a gradient in size of lakes used by Yellow-billed Loons with territories at the two Alaska sites on lakes averaging < 200 ha while territories in Canada were generally on much larger lakes. In the year after capture, 71% of Yellow-billed Loons retained territories that were held the previous year. Most Yellow-billed Loons that lost their territories wandered over a large area within 6 km of their prior territory. No Yellow-billed Loons occupied new territories, though one reacquired its prior territory after a 1-year hiatus. Retention of a territory

  14. Repair of DNA Double-Strand Breaks

    NASA Astrophysics Data System (ADS)

    Falk, Martin; Lukasova, Emilie; Kozubek, Stanislav

    The genetic information of cells continuously undergoes damage induced by intracellular processes including energy metabolism, DNA replication and transcription, and by environmental factors such as mutagenic chemicals and UV and ionizing radiation. This causes numerous DNA lesions, including double strand breaks (DSBs). Since cells cannot escape this damage or normally function with a damaged genome, several DNA repair mechanisms have evolved. Although most "single-stranded" DNA lesions are rapidly removed from DNA without permanent damage, DSBs completely break the DNA molecule, presenting a real challenge for repair mechanisms, with the highest risk among DNA lesions of incorrect repair. Hence, DSBs can have serious consequences for human health. Therefore, in this chapter, we will refer only to this type of DNA damage. In addition to the biochemical aspects of DSB repair, which have been extensively studied over a long period of time, the spatio-temporal organization of DSB induction and repair, the importance of which was recognized only recently, will be considered in terms of current knowledge and remaining questions.

  15. Why double-stranded RNA resists condensation.

    PubMed

    Tolokh, Igor S; Pabit, Suzette A; Katz, Andrea M; Chen, Yujie; Drozdetski, Aleksander; Baker, Nathan; Pollack, Lois; Onufriev, Alexey V

    2014-01-01

    The addition of small amounts of multivalent cations to solutions containing double-stranded DNA leads to inter-DNA attraction and eventual condensation. Surprisingly, the condensation is suppressed in double-stranded RNA, which carries the same negative charge as DNA, but assumes a different double helical form. Here, we combine experiment and atomistic simulations to propose a mechanism that explains the variations in condensation of short (25 base-pairs) nucleic acid (NA) duplexes, from B-like form of homopolymeric DNA, to mixed sequence DNA, to DNA:RNA hybrid, to A-like RNA. Circular dichroism measurements suggest that duplex helical geometry is not the fundamental property that ultimately determines the observed differences in condensation. Instead, these differences are governed by the spatial variation of cobalt hexammine (CoHex) binding to NA. There are two major NA-CoHex binding modes--internal and external--distinguished by the proximity of bound CoHex to the helical axis. We find a significant difference, up to 5-fold, in the fraction of ions bound to the external surfaces of the different NA constructs studied. NA condensation propensity is determined by the fraction of CoHex ions in the external binding mode.

  16. recA protein-catalyzed strand assimilation: stimulation by Escherichia coli single-stranded DNA-binding protein.

    PubMed Central

    McEntee, K; Weinstock, G M; Lehman, I R

    1980-01-01

    The single-stranded DNA-binding protein of Escherichia coli significantly alters the strand assimilation reaction catalyzed by recA protein [McEntee, K., Weinstock, G. M. & Lehman, I. R. (1979) Proc. Natl. Acad. Sci. USA 76, 2615--2619]. The binding protein (i) increases the rate and extent of strand assimilation into homologous duplex DNA, (ii) enhances the formation of a complex between recA protein and duplex DNA in the presence of homologous or heterologous single-stranded DNA, (iii) reduces the rate and extent of ATP hydrolysis catalyzed by recA protein in the presence of single-stranded DNA, (iv) reduces the high concentration of recA protein required for strand assimilation, and (v) permits detection of strand assimilation in the presence of the ATP analog, adenosine 5'-O-(O-thiotriphosphate). Single-stranded DNA-binding protein purified from a binding protein mutant (lexC) is considerably less effective than wild-type binding protein in stimulating strand assimilation, a result which suggests that single-stranded DNA-binding protein participates in general recombination in vivo. PMID:6244589

  17. Louisiana coastal ecosystem

    USGS Publications Warehouse

    ,

    2000-01-01

    Louisiana's coast and its degradation and restoration are major environmental issues being studied at the National Wetlands Research Center. Coastal ecosystems are vulnerable because of the tremendous amount of human activity that takes place along the coast. Information on ecological processes is essential to guide the development along the coast as well as to protect and restore wildlife habitat.Louisiana has about 40% of coastal wetlands in the lower 48 states; they support fish, waterfowl, and fur-bearing animals as well as unique cultures like that of the Acadians. The fish and wildlife resources of Louisiana's coast produce over $1 billion each year in revenues.But Louisiana has the highest coastal loss rate because of natural and human causes. Over the past three decades, Louisiana has lost as much as 35-40 mi2 (90-104 km2) of coastal wetlands a year.The National Wetlands Research Center is qualified to assess and monitor this ecosystem because of its proximity to the study area, a staff chosen for their expertise in the system, and a number of established partnerships with others who study the areas. The Center is often the lead group in partnerships with universities, other federal agencies, and private entities who study this ecosystem.Most of the Center's research and technology development performed for coastal wetlands are done at the Lafayette headquarters; some work is performed at the National Wetlands Research Center's project office in Baton Rouge, LA.

  18. Translocation of double strand DNA into a biological nanopore

    NASA Astrophysics Data System (ADS)

    Chatkaew, Sunita; Mlayeh, Lamia; Leonetti, Marc; Homble, Fabrice

    2009-03-01

    Translocation of double strand DNA across a unique mitochondrial biological nanopore (VDAC) is observed by an electrophysiological method. Characteristics of opened and sub-conductance states of VDAC are studied. When the applied electric potential is beyond ± 20 mV, VDAC transits to a sub-conductance state. Plasmids (circular double strand DNA) with a diameter greater than that of the channel shows the current reduction into the channel during the interaction but the state with zero-current is not observed. On the contrary, the interaction of linear double strand DNA with the channel shows the current reduction along with the zero-current state. These show the passages of linear double strand DNA across the channel and the electrostatic effect due to the surface charges of double strand DNA and channel for circular and linear double strand DNA.

  19. Strong gold atom strands formed by incorporation of carbon atoms

    NASA Astrophysics Data System (ADS)

    Oshima, Yoshifumi; Kurui, Yoshihiko; Nguyen, Huy Duy; Ono, Tomoya; Takayanagi, Kunio

    2011-07-01

    Single metal atom strands have attracted significant interest because of their unique properties, such as quantization effects and a high degree of strength. Recently it was suggested that the strength of a gold atom strand can be enhanced by the insertion of an impurity atom, but it has not been experimentally investigated. Using a transmission electron microscope under ultrahigh vacuum conditions, we observed that gold atoms were pulled out one by one from a carbon-contaminated gold (111) surface to form a long atom strand. The strand was so strong that it did not break even upon bending. Supported by first-principles calculations, the strand was found to have two carbon atoms at each gold atom interval. Our observations suggest that the carbon atoms act as a glue to form a long gold atom strand.

  20. Atomic force microscopy of single- and double-stranded DNA.

    PubMed Central

    Hansma, H G; Sinsheimer, R L; Li, M Q; Hansma, P K

    1992-01-01

    A method has been developed for imaging single-stranded DNA with the atomic force microscope (AFM). phi X174 single-stranded DNA in formaldehyde on mica can be imaged in the AFM under propanol or butanol or in air. Measured lengths of most molecules are on the order of 1 mu, although occasionally more extended molecules with lengths of 1.7 to 1.9 mu are seen. Single-stranded DNA in the AFM generally appears lumpier than double-stranded DNA, even when extended. Images of double-stranded lambda DNA in the AFM show more sharp kinks and bends than are typically observed in the electron microscope. Dense, aggregated fields of double-stranded plasmids can be converted by gentle rinsing with hot water to well spread fields. Images PMID:1386422

  1. DNA Strand Breaks, Neurodegeneration and Aging in the Brain

    PubMed Central

    Katyal, Sachin; McKinnon, Peter J.

    2013-01-01

    Defective responses to DNA single- or double-strand breaks can result in neurological disease, underscoring the critical importance of DNA repair for neural homeostasis. Human DNA repair-deficient syndromes are generally congenital, in which brain pathology reflects the consequences of developmentally incurred DNA damage. Although, it is unclear to what degree DNA strand-break repair defects in mature neural cells contributes to disease pathology. However, DNA single-strand breaks are a relatively common lesion which if not repaired can impact cells via interference with transcription. Thus, this lesion, and probably to a lesser extent DNA double strand breaks, may be particularly relevant to aging in the neural cell population. In this review we will examine the consequences of defective DNA strand break repair towards homeostasis in the brain. Further, we also consider the utility of mouse models as reagents to understand the connection between DNA strand breaks and aging in the brain. PMID:18455751

  2. Anisakid nematodes from stranded pygmy sperm whales, Kogia breviceps (Kogiidae), in three localities of the Yucatan Peninsula, Mexico.

    PubMed

    González Solíz, D; Vidal-Martínez, V M; Antochiw-Alonso, D M; Ortega-Argueta, A

    2006-10-01

    The present paper reports the presence of 3 adult and juvenile anisakid nematode species: Anisakis simplex, A. brevispiculata, and Pseudoterranova ceticola, which were recovered from the digestive tract of stranded pygmy sperm whales (Kogia breviceps) from 3 localities along the coast of the Yucatan Peninsula. The presence of these anisakid adult nematodes suggests that larval stages may occur in cephalopods or fishes used for human consumption, which represents a potential danger to public health. The occurrence of the 3 anisakid species in coastal waters of the Yucatan Peninsula represents new geographical records for Mexico.

  3. Breeding sugarcane for temperate and cold environments

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Louisiana represents one of the world’s more temperate environments where sugarcane is commercially grown. Since its inception in the 1920s, The USDA-ARS breeding program at the Sugarcane Research Laboratory in Houma, Louisiana, U.S.A. has focused on breeding varieties adapted to this unique envir...

  4. Breeding commercial sugarcane varieties for the industry

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Recent literature suggests that sugarcane breeding in the United States has reached a sugar yield plateau. If so, this could have huge implications for the future of the industry and breeding per se because yield improvement might have to be achieved through secondary, non-sugar-related traits, or t...

  5. Breeding Perspectives and Programs at East Lansing

    Technology Transfer Automated Retrieval System (TEKTRAN)

    USDA-ARS sugar beet breeding activities for both Aphanomyces resistance and CMS/O-type conversion at East Lansing reach back to the 1940’s, with variety testing activities at Michigan State University reaching back to circa 1911. Many of those contributions are well known in the sugar beet breeding ...

  6. Sugarcane Improvement Through Breeding and Biotechnology

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The advancements in sugarcane breeding and the improvement of sugarcane through biotechnology have been reviewed by a team of leading sugarcane specialists from around the world. Topics covered in the breeding section include the evolution and origin of sugarcane, early history of conventional sugar...

  7. Breed-specific dog-dandruff allergens.

    PubMed

    Lindgren, S; Belin, L; Dreborg, S; Einarsson, R; Påhlman, I

    1988-08-01

    Fifty-one patients with clinical history of dog allergy were skin prick tested with eight individual standardized dog breed-allergen preparations, one mixed breed-allergen preparation (Poodle/Alsatian), dog-serum albumin, and histamine hydrochloride, 1 mg/ml. All extracts were characterized by crossed immunoelectrophoresis and crossed radioimmunoelectrophoresis with a pool of sera from patients clinically sensitive to dog. The dog-breed extracts contained common antigens/allergens, as well as components represented only in one or two dog-breed extracts. The concentration corresponding 1000 BU/ml varied from 16 to 100 micrograms of protein per milliliter. The sensitivity of skin prick test was 67% to 88% for the various dog breed-allergen preparations, but only 18% for dog-serum albumin. Significant difference between the skin test response to different dog breed-allergen preparations indicating dog breed-specific allergens was obtained in 15% of the patients. There was no significant correlation between skin prick test results and symptoms related to a specific dog breed.

  8. Mean EPDs reported by different breeds

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Beef cattle genetic evaluations result in expected progeny differences (EPDs), which can be used to select animals for growth, productivity, carcass composition, and, most recently, economic value. Breed averages allow producers to compare the genetic value of potential breeding stock against their ...

  9. Establishing a Marine Mammal Stranding Network in the Bahamas

    DTIC Science & Technology

    2008-01-01

    Marine Mammal Stranding Network in the Bahamas Diane Elaine Claridge Bahamas Marine Mammal Research Organisation P.O. Box AB...are to establish a marine mammal stranding network in the Bahamas to better understand the conservation needs of marine mammals in the Bahamas, with...well as the biology of marine mammals . The stranding network will be structured so that it will become self-sufficient and able to continue into

  10. Genomic selection in animal breeding programs.

    PubMed

    van der Werf, Julius

    2013-01-01

    Genomic selection can have a major impact on animal breeding programs, especially where traits that are important in the breeding objective are hard to select for otherwise. Genomic selection provides more accurate estimates for breeding value earlier in the life of breeding animals, giving more selection accuracy and allowing lower generation intervals. From sheep to dairy cattle, the rates of genetic improvement could increase from 20 to 100 % and hard-to-measure traits can be improved more effectively.Reference populations for genomic selection need to be large, with thousands of animals measured for phenotype and genotype. The smaller the effective size of the breeding population, the larger the DNA segments they potentially share and the more accurate genomic prediction will be. The relative contribution of information from relatives in the reference population will be larger if the baseline accuracy is low, but such information is limited to closely related individuals and does not last over generations.

  11. Endometritis: Managing Persistent Post-Breeding Endometritis.

    PubMed

    Canisso, Igor F; Stewart, Jamie; Coutinho da Silva, Marco A

    2016-12-01

    Endometritis was rated as the third most common medical problem encountered in adult horses in North America. It is the leading cause of subfertility in broodmares and is a major contributor to economic loss in the horse breeding industry, with pregnancy rates reported to be as low as 21% in mares with severe endometritis. Endometritis may be categorized as: endometrosis (chronic degenerative endometritis), acute, chronic, active, dormant, subclinical, clinical, and persistent post-breeding. These classifications are not mutually exclusive, and mares may change categories within breeding seasons or estrous cycles or may fit in multiple classifications. This chapter will focus on discussing etiology and management strategies for mares affected by persistent post-breeding endometritis. Overall, these mares are considered subfertile but acceptable pregnancy and foaling rates can be achieved with appropriate breeding management.

  12. New progress of ITER-PF strand production in WST

    NASA Astrophysics Data System (ADS)

    Li, J. F.; Liu, W. T.; Yan, L. X.; H, J.; Gao, H. X.; Liu, J. W.; Du, S. J.; Liu, X. H.; Feng, Y.; Zhang, P. X.; Liu, S.; Li, H. W.; Niu, E. W.

    2014-05-01

    ITER Poloidal Field (PF) systems consist of 6 independent coils with different dimensions and require NbTi superconductor and copper strands. Western Superconducting Technologies Co.,Ltd.(WST) will supply PF2-5 NbTi strand for ITER, and over 14,000 km of NbTi strands have been produced in the past two years. Main performance of NbTi strands, including critical current, n value, wire diameter, Cu/non-Cu ratio, hysteresis loss and RRR are reported and analysed in this paper.

  13. Regulation of DNA Strand Displacement Using Allosteric DNA Toehold.

    PubMed

    Yang, Xiaolong; Tang, Yanan; Traynor, Sarah M; Li, Feng

    2016-10-05

    Toehold-mediated DNA strand displacement is the fundamental basis for the construction and operation of diverse DNA devices, including circuits, machines, sensors, and reconfigurable structures. Controllable activation and regulation of toeholds are critical to construct devices with multistep, autonomous, and complex behaviors. A handful of unique toehold activation mechanisms, including toehold-exchange, associative toehold, and remote toehold, have been developed and are often combined to achieve desired strand displacement behaviors and functions. Here we report an allosteric DNA toehold (A-toehold) design that allows the flexible regulation of DNA strand displacement by splitting an input strand into an A-toehold and branch migration domain. Because of its simplicity, the A-toehold mechanism can be a useful addition to the current toolbox of DNA strand displacement techniques. We demonstrated that A-toehold enabled a number of interesting functions that were previously shown using more sophisticated DNA strand displacement systems, including 1) continuously tuning the rate of strand displacement, 2) dynamic control of strand displacement reactions, and 3) selective activation of multiple strand displacement reactions. Moreover, by combining A-toehold and toehold-exchange mechanisms, we have successfully constructed a non-covalent DNA catalysis network that resembles an allosteric enzyme.

  14. Coastal Processes with Engineering Applications

    NASA Astrophysics Data System (ADS)

    Dean, Robert G.; Dalrymple, Robert A.

    2004-03-01

    The world's coastlines, dividing land from sea, are geological environments that are unique in their composition and the physical processes affecting them. At the dynamically active intersection of land and the oceans, humans have been building structures throughout history. Initially used for naval and commercial purposes, more recently recreation and tourism have increased activity in the coastal zone dramatically. Shoreline development is now causing a significant conflict with natural coastal processes. This text on coastal engineering will help the reader understand these coastal processes and develop strategies to cope effectively with shoreline erosion. The book is organized in four parts: (1) an overview of coastal engineering, using case studies to illustrate problems; (2) hydrodynamics of the coastal zone, reviewing storm surges, water waves, and low frequency motions within the nearshore and surf zone; (3) coastal responses including equilibrium beach profiles and sediment transport; (4) applications such as erosion mitigation, beach nourishment, coastal armoring, tidal inlets, and shoreline management.

  15. NATIONAL COASTAL CONDITION REPORT II

    EPA Science Inventory

    Coastal waters in the US include estuaries, coastalwetlands, coral reefs, mangrove and kep forests, seagrass meadows, and upwelling areas. Critical coastal habitats provide spawning grounds, nurseries, shelter, and food for finfish, shellfish, birds, and other wildlife. the nat...

  16. Arctic Coastal Erosion Modeling

    NASA Astrophysics Data System (ADS)

    Ravens, T. M.; Jones, B.; Zhang, J.; Tweedie, C. E.; Erikson, L. H.; Gibbs, A.; Richmond, B. M.

    2011-12-01

    A process-based coastal erosion/shoreline change model has been developed for Arctic coastal bluffs subject to niche erosion/block collapse. The model explicitly accounts for many environmental/geographic variables including: water temperature, water level, wave height, and bluff height. The model was originally developed for a small coastal segment near Drew Point, Beaufort Sea, Alaska. This coastal setting has experienced a dramatic increase in erosion since the early 2000's. The bluffs at this site are 3-4 m tall and consist of ice-wedge bounded blocks of fine-grained sediments cemented by ice-rich permafrost and capped with a thin organic layer. The bluffs are typically fronted by a narrow (~ 5 m wide) beach or none at all. During a storm surge, the sea contacts the base of the bluff and a niche is formed through thermal and mechanical erosion. The niche grows both vertically and laterally and eventually undermines the bluff, leading to block failure or collapse. The fallen block is then eroded both thermally and mechanically by waves and currents, which must occur before a new niche forming episode may begin. The model has been calibrated based on shoreline change data at Drew Point for two time periods: 1979-2002 and 2002-2007. Measured and modeled shoreline change rates were about 8 m/yr and 16 m/yr, for the earlier and later periods, respectively. In this paper, this work is extended to include modeling and measurement of coastal erosion at Drew Point on an annual basis for the period 2007-2010. In addition, the model is applied at three other Arctic coastal locations - Elson Lagoon, Cape Halkett, and Barter Island - where niche erosion/block collapse prevails.

  17. Genomic evaluation of regional dairy cattle breeds in single-breed and multibreed contexts.

    PubMed

    Jónás, D; Ducrocq, V; Fritz, S; Baur, A; Sanchez, M-P; Croiseau, P

    2017-02-01

    An important prerequisite for high prediction accuracy in genomic prediction is the availability of a large training population, which allows accurate marker effect estimation. This requirement is not fulfilled in case of regional breeds with a limited number of breeding animals. We assessed the efficiency of the current French routine genomic evaluation procedure in four regional breeds (Abondance, Tarentaise, French Simmental and Vosgienne) as well as the potential benefits when the training populations consisting of males and females of these breeds are merged to form a multibreed training population. Genomic evaluation was 5-11% more accurate than a pedigree-based BLUP in three of the four breeds, while the numerically smallest breed showed a < 1% increase in accuracy. Multibreed genomic evaluation was beneficial for two breeds (Abondance and French Simmental) with maximum gains of 5 and 8% in correlation coefficients between yield deviations and genomic estimated breeding values, when compared to the single-breed genomic evaluation results. Inflation of genomic evaluation of young candidates was also reduced. Our results indicate that genomic selection can be effective in regional breeds as well. Here, we provide empirical evidence proving that genetic distance between breeds is only one of the factors affecting the efficiency of multibreed genomic evaluation.

  18. Coastal Inlets Research Program

    DTIC Science & Technology

    2012-01-01

    US Army Corps of Engineers BUILDING STRONG® Julie Dean Rosati Program Manager Jim Walker HQ Navigation Business Line Manager Jeff Lillycrop...0.9 0.1 c VEe= 2,000,000 m3 VCe = 200,000 m3 VFe=200,000 m3 VOe=1,000,000,000 m3 Offshore Ebb Shoal Channel Flood Shoal Bay Deposition...Basin Vce ,VDe,VEe,VFe,Vye ,VOe 0.3 Coastal and Hydraulics Laboratory 4  Conduct R&D to reduce O&M costs at coastal navigation projects  Include

  19. Coastal Inlets Research Program

    DTIC Science & Technology

    2013-03-01

    e N u m b e 50 10 20 30 C u m W C u m u 00 1997 1999 2001 2003 2005 2007 2009 2011 2013** Calendar Year Coastal and Hydraulics Laboratory 4...Flow 14 Verification & Validation Cases Bouss-2D: Advanced phase -resolving wave propagation and t f ti d l Coastal and Hydraulics Laboratory 21 rans...Structures , Noyo Bay, CA Half Moon Bay, CA SWG M t d Shi Ch l TX : a agor a p anne , Galveston Bay, TX Sargent Beach, TX NAE P i t J dith H b RI

  20. Patterns of molecular genetic variation among cat breeds.

    PubMed

    Menotti-Raymond, Marilyn; David, Victor A; Pflueger, Solveig M; Lindblad-Toh, Kerstin; Wade, Claire M; O'Brien, Stephen J; Johnson, Warren E

    2008-01-01

    Genetic variation in cat breeds was assessed utilizing a panel of short tandem repeat (STR) loci genotyped in 38 cat breeds and 284 single-nucleotide polymorphisms (SNPs) genotyped in 24 breeds. Population structure in cat breeds generally reflects their recent ancestry and absence of strong breed barriers between some breeds. There is a wide range in the robustness of population definition, from breeds demonstrating high definition to breeds with as little as a third of their genetic variation partitioning into a single population. Utilizing the STRUCTURE algorithm, there was no clear demarcation of the number of population subdivisions; 16 breeds could not be resolved into independent populations, the consequence of outcrossing in established breeds to recently developed breeds with common ancestry. These 16 breeds were divided into 6 populations. Ninety-six percent of cats in a sample set of 1040 were correctly assigned to their classified breed or breed group/population. Average breed STR heterozygosities ranged from moderate (0.53; Havana, Korat) to high (0.85; Norwegian Forest Cat, Manx). Most of the variation in cat breeds was observed within a breed population (83.7%), versus 16.3% of the variation observed between populations. The hierarchical relationships of cat breeds is poorly defined as demonstrated by phylogenetic trees generated from both STR and SNP data, though phylogeographic grouping of breeds derived completely or in part from Southeast Asian ancestors was apparent.

  1. A methodology to identify stranded generation facilities and estimate stranded costs for Louisiana's electric utility industry

    NASA Astrophysics Data System (ADS)

    Cope, Robert Frank, III

    1998-12-01

    The electric utility industry in the United States is currently experiencing a new and different type of growing pain. It is the pain of having to restructure itself into a competitive business. Many industry experts are trying to explain how the nation as a whole, as well as individual states, will implement restructuring and handle its numerous "transition problems." One significant transition problem for federal and state regulators rests with determining a utility's stranded costs. Stranded generation facilities are assets which would be uneconomic in a competitive environment or costs for assets whose regulated book value is greater than market value. At issue is the methodology which will be used to estimate stranded costs. The two primary methods are known as "Top-Down" and "Bottom-Up." The "Top-Down" approach simply determines the present value of the losses in revenue as the market price for electricity changes over a period of time into the future. The problem with this approach is that it does not take into account technical issues associated with the generation and wheeling of electricity. The "Bottom-Up" approach computes the present value of specific strandable generation facilities and compares the resulting valuations with their historical costs. It is regarded as a detailed and difficult, but more precise, approach to identifying stranded assets and their associated costs. This dissertation develops a "Bottom-Up" quantitative, optimization-based approach to electric power wheeling within the state of Louisiana. It optimally evaluates all production capabilities and coordinates the movement of bulk power through transmission interconnections of competing companies in and around the state. Sensitivity analysis to this approach is performed by varying seasonal consumer demand, electric power imports, and transmission inter-connection cost parameters. Generation facility economic dispatch and transmission interconnection bulk power transfers, specific

  2. Red-throated loons (Gavia stellata) breeding in Alaska, USA, are exposed to PCBs while on their Asian wintering grounds

    USGS Publications Warehouse

    Schmutz, J.A.; Trust, K.A.; Matz, A.C.

    2009-01-01

    Red-throated loons (Gavia stellata) breeding in Alaska declined 53% during 1977-1993. We compare concentrations of environmental contaminants in red-throated loons among four nesting areas in Alaska and discuss potential ramifications of exposure on reproductive success and population trends. Eggs from the four areas had similar total polychlorinated biphenyl (PCB) concentrations, but eggs from the Arctic coastal plain had different congener profiles and greater toxic equivalents (TEQs) than eggs from elsewhere. Satellite telemetry data indicate that red-throated loons from the Arctic coastal plain in northern Alaska winter in southeast Asia, while those breeding elsewhere in Alaska winter in North America. Different wintering areas may lead to differential PCB accumulation among red-throated loon populations. For eggs from the Arctic coastal plain, TEQs were great enough to postulate PCB-associated reproductive effects in piscivores. The correlation between migration patterns and PCB profiles suggests that red-throated loons breeding in northern Alaska are exposed to PCBs while on their Asian wintering grounds.

  3. Why double-stranded RNA resists condensation

    SciTech Connect

    Tolokh, Igor S.; Pabit, Suzette; Katz, Andrea M.; Chen, Yujie; Drozdetski, Aleksander; Baker, Nathan A.; Pollack, Lois; Onufriev, Alexey

    2014-09-15

    The addition of small amounts of multivalent cations to solutions containing double-stranded DNA leads to attraction between the negatively charged helices and eventually to condensation. Surprisingly, this effect is suppressed in double-stranded RNA, which carries the same charge as the DNA, but assumes a different double helical form. However, additional characterization of short (25 base-pairs) nucleic acid (NA) duplex structures by circular dichroism shows that measured differences in condensation are not solely determined by duplex helical geometry. Here we combine experiment, theory, and atomistic simulations to propose a mechanism that connects the observed variations in condensation of short NA duplexes with the spatial variation of cobalt hexammine (CoHex) binding at the NA duplex surface. The atomistic picture that emerged showed that CoHex distributions around the NA reveals two major NA-CoHex binding modes -- internal and external -- distinguished by the proximity of bound CoHex to the helical axis. Decreasing trends in experimentally observed condensation propensity of the four studied NA duplexes (from B-like form of homopolymeric DNA, to mixed sequence DNA, to DNA:RNA hybrid, to A-like RNA) are explained by the progressive decrease of a single quantity: the fraction of CoHex ions in the external binding mode. Thus, while NA condensation depends on a complex interplay between various structural and sequence features, our coupled experimental and theoretical results suggest a new model in which a single parameter connects the NA condensation propensity with geometry and sequence dependence of CoHex binding.

  4. Toward breeding new land-sea plant hybrid species irrigable with seawater for dry regions

    PubMed Central

    Moustafa, Khaled

    2015-01-01

    A plant species growing in sea or coastal saltmarsh is greatly tolerant to high concentrations of salts, and a plant species growing in desert or dry regions is highly tolerant to drought. Breeding a new plant hybrid species from both species by means of cellular grafting, genome fusion or nuclear transfer would generate, at least in theory, a hybrid plant species that should be strongly tolerant to harsh aridity and salinity and would be potentially irrigable with seawater. Such prospective species can be used for example as a fodder, biofuel crop or stabilizer species to protect soil from wind erosion and sandy storms in dry regions. Breeding such species would change the surface of the world and help to solve major challenges of starvation, malnutrition and poverty. Here, I propose potential approaches that would be worthy of investigation toward this purpose. PMID:25806436

  5. Breeding biology of Mottled Ducks on agricultural lands in southwestern Louisiana

    USGS Publications Warehouse

    Durham, R.S.; Afton, A.D.

    2006-01-01

    Breeding biology of Anas fulvigula maculosa (Mottled Ducks) has been described in coastal marsh and associated habitats, but little information is available for agricultural habitats in Louisiana. We located nests to determine nest-initiation dates and clutch sizes during the primary breeding season (February-May) in 1999 (n = 29) and 2000 (n = 37) on agricultural lands in southwestern Louisiana. In 1999, 60% of located nests were initiated between 22 March and 10 April, whereas in 2000, only 22% of nests were initiated during the same time period. Average clutch size was 0.9 eggs smaller in 2000 than in 1999. Annual differences in reproductive parameters corresponded with extremely dry conditions caused by low rainfall before the laying period in 2000. Flooded rice fields appear to be important loafing and feeding habitat of Mottled Ducks nesting in agricultural lands, especially during drought periods when other wetland types are not available or where natural wetlands have been eliminated.

  6. Habitat Suitability Index Models: Forster's tern (breeding) - Gulf and Atlantic coasts

    USGS Publications Warehouse

    Martin, Richard P.; Zwank, Phillip J.

    1987-01-01

    The nesting range of Forster's terns hosts three allopatric breeding populations. The first and most important breeding area, in terms of the number of nes t i ng pairs, includes the western guIf coas t from the Louisiana-Mississippi border to northern Tamaulipas, Mexico (American Ornithologists' Union [AOUJ 1983). In addition, small numbers of Forster's terns have nested in Mobile County, Alabama (Imhof 1976). Although this species has not been recorded nesting in Mississippi (J. Jackson, Mississippi State University, Starkville; pers. comm.), it is observed in the coastal regions of that State every summer, and several thousand nest in adjacent Louisiana (Portnoy 1977; Clapp et ale 1983). The two largest colonies of Forster's terns documented in the literature were both in Louisiana: one of 2,750 pairs in Lake Borgne on the Louisiana-Mississippi border and one of 2,263 pairs in Calcasieu Lake (Portnoy 1977).

  7. Breeding objectives for Targhee sheep.

    PubMed

    Borg, R C; Notter, D R; Kuehn, L A; Kott, R W

    2007-11-01

    Breeding objectives were developed for Targhee sheep under rangeland production conditions. Traits considered were those for which EPD were available from the US National Sheep Improvement Program and included direct and maternal effects on 120-d weaning weight (WW and MM, respectively); yearling weight (YW); yearling fleece weight, fiber diameter, and staple length; and percent lamb crop (PLC), measured as the number of lambs born per 100 ewes lambing. A bioeconomic model was used to predict the effects of a change of 1 additive SD in EPD for each trait, holding all other traits constant at their mean, on animal performance, feed requirements, feed costs, and economic returns. Resulting economic weightings were then used to derive selection indexes. Indexes were derived separately for 3 prolificacy levels (1.41, 1.55, and 1.70 lambs/ewe lambing), 2 triplet survival levels (50 and 67%), 2 lamb pricing policies (with or without discounting of prices for heavy feeder lambs), and 3 forage cost scenarios (renting pasture, purchasing hay, or reducing flock size to accommodate increased nutrient requirements for production). Increasing PLC generally had the largest impact on profitability, although an increase in WW was equally important, with low feed costs and no discounting of prices for heavy feeder lambs. Increases in PLC were recommended at all 3 prolificacy levels, but with low triplet survival the value of increasing PLC eventually declined as the mean litter size increased to approximately 2.15 lambs/ewe lambing and above. Increasing YW (independent of WW) increased ewe maintenance costs and reduced profitability. Predicted changes in breeding values for WW and YW under index selection varied with lamb pricing policy and feed costs. With low feed costs or no discounts for heavy lambs, YW increased at a modest rate in association with increasing WW, but with high feed costs or discounting of heavy lambs, genetic trends in WW were reduced by approximately 50% to

  8. Predictive Modelling to Identify Near-Shore, Fine-Scale Seabird Distributions during the Breeding Season.

    PubMed

    Warwick-Evans, Victoria C; Atkinson, Philip W; Robinson, Leonie A; Green, Jonathan A

    2016-01-01

    During the breeding season seabirds are constrained to coastal areas and are restricted in their movements, spending much of their time in near-shore waters either loafing or foraging. However, in using these areas they may be threatened by anthropogenic activities such as fishing, watersports and coastal developments including marine renewable energy installations. Although many studies describe large scale interactions between seabirds and the environment, the drivers behind near-shore, fine-scale distributions are not well understood. For example, Alderney is an important breeding ground for many species of seabird and has a diversity of human uses of the marine environment, thus providing an ideal location to investigate the near-shore fine-scale interactions between seabirds and the environment. We used vantage point observations of seabird distribution, collected during the 2013 breeding season in order to identify and quantify some of the environmental variables affecting the near-shore, fine-scale distribution of seabirds in Alderney's coastal waters. We validate the models with observation data collected in 2014 and show that water depth, distance to the intertidal zone, and distance to the nearest seabird nest are key predictors in the distribution of Alderney's seabirds. AUC values for each species suggest that these models perform well, although the model for shags performed better than those for auks and gulls. While further unexplained underlying localised variation in the environmental conditions will undoubtedly effect the fine-scale distribution of seabirds in near-shore waters we demonstrate the potential of this approach in marine planning and decision making.

  9. Predictive Modelling to Identify Near-Shore, Fine-Scale Seabird Distributions during the Breeding Season

    PubMed Central

    Warwick-Evans, Victoria C.; Atkinson, Philip W.; Robinson, Leonie A.; Green, Jonathan A.

    2016-01-01

    During the breeding season seabirds are constrained to coastal areas and are restricted in their movements, spending much of their time in near-shore waters either loafing or foraging. However, in using these areas they may be threatened by anthropogenic activities such as fishing, watersports and coastal developments including marine renewable energy installations. Although many studies describe large scale interactions between seabirds and the environment, the drivers behind near-shore, fine-scale distributions are not well understood. For example, Alderney is an important breeding ground for many species of seabird and has a diversity of human uses of the marine environment, thus providing an ideal location to investigate the near-shore fine-scale interactions between seabirds and the environment. We used vantage point observations of seabird distribution, collected during the 2013 breeding season in order to identify and quantify some of the environmental variables affecting the near-shore, fine-scale distribution of seabirds in Alderney’s coastal waters. We validate the models with observation data collected in 2014 and show that water depth, distance to the intertidal zone, and distance to the nearest seabird nest are key predictors in the distribution of Alderney’s seabirds. AUC values for each species suggest that these models perform well, although the model for shags performed better than those for auks and gulls. While further unexplained underlying localised variation in the environmental conditions will undoubtedly effect the fine-scale distribution of seabirds in near-shore waters we demonstrate the potential of this approach in marine planning and decision making. PMID:27031616

  10. Model for Coastal Restoration

    SciTech Connect

    Thom, Ronald M.; Judd, Chaeli

    2007-07-27

    Successful restoration of wetland habitats depends on both our understanding of our system and our ability to characterize it. By developing a conceptual model, looking at different spatial scales and integrating diverse data streams: GIS datasets and NASA products, we were able to develop a dynamic model for site prioritization based on both qualitative and quantitative relationships found in the coastal environment.

  11. Neotropical coastal wetlands

    USGS Publications Warehouse

    McKee, Karen L.; Batzer, Darold P.; Baldwin, Andrew H.

    2012-01-01

    The Neotropical region, which includes the tropical Americas, is one of the world's eight biogeographic zones. It contains some of the most diverse and unique wetlands in the world, some of which are still relatively undisturbed by humans. This chapter focuses on the northern segment of the Neotropics (south Florida, the Caribbean islands, Mexico, and Central America), an area that spans a latitudinal gradient from about 7 N to 29 N and 60 W to 112 W. Examples of coastal wetlands in this realm include the Everglades (Florida, USA), Ten Thousand Islands (Florida, USA), Laguna de Terminos (Mexico), Twin Cays (Belize), and Zapata Swamp (Cuba). Coastal wetlands are dominated by mangroves, which will be emphasized here, but also include freshwater swamps and marshes, saline marshes, and seagrass beds. The aim of this chapter is to provide a broad overview of Neotropical coastal wetlands of the North American continent, with an emphasis on mangroves, since this is the dominant vegetation type and because in-depth coverage of all wetland types is impossible here. Instead, the goal is to describe the environmental settings, plant and animal communities, key ecological controls, and some conservation concerns, with specific examples. Because this book deals with wetlands of North America, this chapter excludes coastal wetlands of South America. However, much of the information is applicable to mangrove, marsh, and seagrass communities of other tropicaI regions.

  12. MANAGING COASTAL DATA

    EPA Science Inventory

    To answer broad-scale questions on environmental conditions, the Environmental Monitoring and Assessment Program (EMAP) and its partners have collected estuarine and coastal data from hundreds of stations along the coasts of the continental United States. Types of data include w...

  13. Advances in Japanese pear breeding in Japan.

    PubMed

    Saito, Toshihiro

    2016-01-01

    The Japanese pear (Pyrus pyrifolia Nakai) is one of the most widely grown fruit trees in Japan, and it has been used throughout Japan's history. The commercial production of pears increased rapidly with the successive discoveries of the chance seedling cultivars 'Chojuro' and 'Nijisseiki' around 1890, and the development of new cultivars has continued since 1915. The late-maturing, leading cultivars 'Niitaka' and 'Shinko' were released during the initial breeding stage. Furthermore, systematic breeding by the Horticultural Research Station (currently, NARO Institute of Fruit Tree Science, National Agriculture and Food Research Organization (NIFTS)) began in 1935, which mainly aimed to improve fruit quality by focusing on flesh texture and black spot disease resistance. To date, 22 cultivars have been released, including 'Kosui', 'Hosui', and 'Akizuki', which are current leading cultivars from the breeding program. Four induced mutant cultivars induced by gamma irradiation, which exhibit some resistance to black spot disease, were released from the Institute of Radiation Breeding. Among these cultivars, 'Gold Nijisseiki' has become a leading cultivar. Moreover, 'Nansui' from the Nagano prefectural institute breeding program was released, and it has also become a leading cultivar. Current breeding objectives at NIFTS mainly combine superior fruit quality with traits related to labor and cost reduction, multiple disease resistance, or self-compatibility. Regarding future breeding, marker-assisted selection for each trait, QTL analyses, genome-wide association studies, and genomic selection analyses are currently in progress.

  14. Genetic structure of European sheep breeds.

    PubMed

    Lawson Handley, L-J; Byrne, K; Santucci, F; Townsend, S; Taylor, M; Bruford, M W; Hewitt, G M

    2007-12-01

    Large-scale evaluations of genetic diversity in domestic livestock populations are necessary so that region-specific conservation measures can be implemented. We performed the first such survey in European sheep by analysing 820 individuals from 29 geographically and phenotypically diverse breeds and a closely related wild species at 23 microsatellite loci. In contrast to most other domestic species, we found evidence of widespread heterozygote deficit within breeds, even after removing loci with potentially high frequency of null alleles. This is most likely due to subdivision among flocks (Wahlund effect) and use of a small number of rams for breeding. Levels of heterozygosity were slightly higher in southern than in northern breeds, consistent with declining diversity with distance from the Near Eastern centre of domestication. Our results highlight the importance of isolation in terms of both geography and management in augmenting genetic differentiation through genetic drift, with isolated northern European breeds showing the greatest divergence and hence being obvious targets for conservation. Finally, using a Bayesian cluster analysis, we uncovered evidence of admixture between breeds, which has important implications for breed management.

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

    PubMed

    Wales, Nathan; Carøe, Christian; Sandoval-Velasco, Marcela; Gamba, Cristina; Barnett, Ross; Samaniego, José Alfredo; Madrigal, Jazmín Ramos; Orlando, Ludovic; Gilbert, M Thomas P

    2015-12-01

    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 <3% endogenous DNA, but this enrichment is less pronounced when dsDNA preparations successfully recover short endogenous DNA fragments (mean size < 70 bp). Our findings can help researchers determine when to utilize the time- and resource-intensive ssDNA library preparation method.

  16. Flow cytometry in plant breeding.

    PubMed

    Ochatt, Sergio J

    2008-07-01

    Since the first report on the flow cytometric study of plant material 35 years ago, analyzing the nuclear DNA content of field bean, an ever increasing number of applications of FCM has been developed and applied in plant science and industry, but a similar length of time elapsed before the appearance of the first complete volume devoted to FCM of plant cells. Most published information on the uses of FCM addresses various aspects of animal (including human) cell biology, thus failing to provide a pertinent substitute. FCM represents an ideal means for the analysis of both cells and subcellular particles, with a potentially large number of parameters analyzed both rapidly, simultaneously, and quantitatively, thereby furnishing statistically exploitable data and allowing for an accurate and facilitated detection of subpopulations. It is, indeed, the summation of these facts that has established FCM as an important, and sometimes essential, tool for the understanding of fundamental mechanisms and processes underlying plant growth, development, and function. In this review, special attention is paid to FCM as applied to plant cells in the context of plant breeding, and some new and less well-known uses of it for plants will be discussed.

  17. Breeding bald eagles in captivity

    USGS Publications Warehouse

    Maestrelli, J.R.; Wiemeyer, Stanley N.

    1975-01-01

    A 7-year-old female Bald Eagle from Alabama was paired with a 4-year-old Alaskan male in a large flight pen during December 1969. Both birds were free of physical defects when originally placed in the pen but the female was blind in one eye prior to the 1973 breeding season.....Nesting first occurred during 1971 when at least two eggs were laid; all but one, which showed no sign of embryonic development after being incubated for 56 days, were broken by the adult birds. Two of three eggs laid in 1972 hatched. Both young died a few days after hatching following a period of inclement weather. Three eggs were laid and hatched during 1973. Antagonism between the nestlings was observed soon after hatching and may have been responsible for the unobserved death of one nestling, two days after the third young hatched. The two remaining young were raised by the adult birds and eventually left the nest 85 days after the first egg hatched. Incubation periods for the 1972-73 clutches averaged 35 days. No renesting attempts were made by the eagles during the 3.year period.

  18. Breeding season survival and breeding incidence of female Mottled Ducks on the upper Texas gulf coast

    USGS Publications Warehouse

    Rigby, Elizabeth A.; Haukos, David A.

    2012-01-01

    Previous Mottled Duck (Anas fulvigula) studies suggested that high female breeding season survival may be caused by low nesting effort, but few breeding season estimates of survival associated with nesting effort exist on the western Gulf Coast. Here, breeding season survival (N = 40) and breeding incidence (N = 39) were estimated for female Mottled Ducks on the upper Texas coast, 2006–2008. Females were fitted with backpack radio transmitters and visually relocated every 3–4 days. Weekly survival was estimated using the Known Fate procedure of program MARK with breeding incidence estimated as the annual proportion of females observed nesting or with broods. The top-ranked survival model included a body mass covariate and held weekly female survival constant across weeks and years (SW = 0.986, SE = 0.006). When compared to survival across the entire year estimated from previous band recovery and age ratio analysis, survival rate during the breeding season did not differ. Breeding incidence was well below 100% in all years and highly variable among years (15%–63%). Breeding season survival and breeding incidence were similar to estimates obtained with implant transmitters from the mid-coast of Texas. The greatest breeding incidence for both studies occurred when drought indices indicated average environmental moisture during the breeding season. The observed combination of low breeding incidence and high breeding season survival support the hypothesis of a trade-off between the ecological cost of nesting effort and survival for Mottled Duck females. Habitat cues that trigger nesting are unknown and should be investigated.

  19. Current range of the eastern population of Painted Bunting (Passerina ciris). Part 1: Breeding

    USGS Publications Warehouse

    Sykes, P.W.; Holzman, S.

    2005-01-01

    This paper presents the current breeding range of Painted Bunting (Passerina ciris) in a series of maps and a narrative, in particular that of the eastern population, which is restricted to the states of North Carolina, South Carolina, Georgia, and Florida. Some conservation measures are recommended to protect this population. In light of the extensive habitat loss in the Outer Coastal Plain of these states, which comprise the areas of the population's greatest density, it is imperative that a consortium of diverse interests work together to provide sufficient habitats for this colorful native songbird.

  20. Breeding behavior of immature mourning doves

    USGS Publications Warehouse

    Irby, H.D.; Blankenship, L.H.

    1966-01-01

    Some immature mourning doves (Zenaidura mncroura) are capable of breeding in their first (calendar) year of life. The breeding activities of immatures observed in this study included calling, copulating, and nesting. Development of sexual structures such as cloacal papillae, oviduct openings, and gonads was also regarded as evidence of breeding potential. Immatures were identified principally by white-tipped wing coverts. Sexes were distinguished by behavioral characteristics. Males coo, perform flights, carry nest material, and attend nests during the day and females attend nests at night. Immatures were involved in at least ten nestings on two areas near Tucson, Arizona, in 1963. Five young fledged from these nests.

  1. Management and Breeding Soundness of Mature Bulls.

    PubMed

    Palmer, Colin W

    2016-07-01

    Mature bulls must be fed a balanced ration, vaccinated appropriately, and undergo a breeding soundness evaluation to ensure they meet what is required of a short, but intense breeding season. To be classified as a satisfactory potential breeder, minimum standards for physical soundness, scrotal circumference, sperm motility, and sperm morphology must be achieved using an accepted bull-breeding soundness evaluation format. Sperm production requires approximately 70 days. Heat and stress are the most common insults to spermatogenesis, causing an increase in morphologic abnormalities with obesity-associated scrotal fat accumulation being the most frequent cause of elevated testicular temperature in mature bulls.

  2. Book review: Oklahoma Breeding Bird Atlas

    USGS Publications Warehouse

    Peterjohn, Bruce G.

    2004-01-01

    The first North American breeding bird atlases were initiated during the 1970s. With atlases completed or ongoing in more than 40 U.S. states and most Canadian provinces, these projects are now familiar to professional ornithologists and amateur birders. This book provides the results of the Oklahoma Breeding Bird Atlas, the data for which were collected during 1997–2001. Its appearance less than 3 years after completing fieldwork is remarkable and everyone associated with its timely publication should be congratulated for their efforts.Review info: Oklahoma Breeding Bird Atlas. By Dan L. Reinking, 2004. ISBN: 0806136146, 528 pp.

  3. First charge breeding results at CARIBU EBIS

    SciTech Connect

    Kondrashev, S. Barcikowski, A. Dickerson, C. Ostroumov, P. N. Sharamentov, S. Vondrasek, R.; Pikin, A.

    2015-01-09

    The Electron Beam Ion Source (EBIS) developed to breed CARIBU radioactive beams at ATLAS is currently in the off-line commissioning stage. The beam commissioning is being performed using a low emittance surface ionization source producing singly-charged cesium ions. The primary goal of the off-line commissioning is the demonstration of high-efficiency charge breeding in the pulsed injection mode. An overview of the final design of the CARIBU EBIS charge breeder, the off-line commissioning installation and the first results on charge breeding of stable cesium ions are presented and discussed.

  4. Saliva of Lygus lineolaris digests double stranded ribonucleic acids

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The prospects for development of highly specific pesticides based on double stranded ribonucleic acid have been a recent focus of scientific research. Creative applications have been proposed and demonstrated. However, not all insects are sensitive to double stranded RNA (dsRNA) gene knockdown effec...

  5. 75 FR 4104 - Prestressed Concrete Steel Wire Strand From China

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-01-26

    ... COMMISSION Prestressed Concrete Steel Wire Strand From China AGENCY: United States International Trade... concrete steel wire strand, provided for in subheading 7312.10.30 of the Harmonized Tariff Schedule of the... suitable for use in prestressed concrete (both pre-tensioned and post- tensioned) applications. The...

  6. The economics of stranded investment - a two-way street

    SciTech Connect

    Cearley, R.; McKinzie, L.

    1995-11-01

    In the transition to deregulation, the risk, costs and benefits of utility assets are transferred from the customer to the investor, creating potential stranded benefits as well as stranded costs. Investors may be better or worse off depending on whether an asset`s cost is below or above market. Regulators can minimize unintended wealth transfers by compensating each potential loser in the transition. The amount of investment stranded - i.e., the portion of plant that is above market value - does seem to be a murky issue. This article sets a framework for evaluating stranded investment and traces the possible welfare effects of different policies to address it. It defines {open_quote}stranded costs,{close_quote} {open_quote}stranded investment,{close_quote} and {open_quote}stranded benefits.{close_quote} It addresses their interrelationship, and shows that the redefinition of property rights during the transition to a competitive market is what leads to stranded investment. The elimination of the utility`s exclusive franchise - i.e., its obligation to serve and customers` obligation to pay - leads to the redefinition of those property rights as they pertain to the costs, benefits and risks associated with existing utility generation. Finally, the authors address the possible welfare implications from this transition.

  7. Adcyap1 polymorphism covaries with breeding latitude in a Nearctic migratory songbird, the Wilson's warbler (Cardellina pusilla).

    PubMed

    Bazzi, Gaia; Galimberti, Andrea; Hays, Quentin R; Bruni, Ilaria; Cecere, Jacopo G; Gianfranceschi, Luca; Hobson, Keith A; Morbey, Yolanda E; Saino, Nicola; Guglielmo, Christopher G; Rubolini, Diego

    2016-05-01

    Understanding the genetic background of complex behavioral traits, showing multigenic control and extensive environmental effects, is a challenging task. Among such traits, migration is known to show a large additive genetic component. Yet, the identification of specific genes or gene regions explaining phenotypic variance in migratory behavior has received less attention. Migration ultimately depends on seasonal cycles, and polymorphism at phenological candidate genes may underlie variation in timing of migration or other aspects of migratory behavior. In this study of a Nearctic-Neotropical migratory songbird, the Wilson's warbler (Cardellina pusilla), we investigated the association between polymorphism at two phenological candidate genes, Clock and Adcyap1, and two aspects of the migratory phenotype, timing of spring migration through a stopover site and inferred latitude of the breeding destination. The breeding destination of migrating individuals was identified using feather deuterium ratio (δ (2)H), which reliably reflects breeding latitude throughout the species' western breeding range. Ninety-eight percent of the individuals were homozygous at Clock, and the rare heterozygotes did not deviate from homozygous migration phenology. Adcyap1 was highly polymorphic, and allele size was not significantly associated with migration date. However, Adcyap1 allele size significantly positively predicted the inferred breeding latitude of males but not of females. Moreover, we found a strong positive association between inferred breeding latitude and Adcyap1 allele size in long-distance migrating birds from the northern sector of the breeding range (western Canada), while this was not the case in short-distance migrating birds from the southern sector of the breeding range (coastal California). Our findings support previous evidence for a role of Adcyap1 in shaping the avian migratory phenotype, while highlighting that patterns of phenological candidate gene

  8. Coastal hazards: hurricanes, tsunamis, coastal erosion

    USGS Publications Warehouse

    Vandas, Stephen; Mersfelder, Lynne; Farrar, Frank; France, Rigoberto Guardado; Yajimovich, Oscar Efraín González; Muñoz, Aurora R.; Rivera, María del C.

    1996-01-01

    Oceans are the largest geographic feature on the surface of the Earth, covering approximately 70% of the planet's surface. As a result, oceans have a tremendous impact on the Earth, its climate, and its inhabitants. The coast or shoreline is the boundary between ocean environments and land habitats. By the year 2025, it is estimated that approximately two-thirds of the world's population will be living within 200 kilometers of a coast. In many ways, we treat the coast just like any other type of land area, as a safe and stable place to live and play. However, coastal environments are dynamic, and they constantly change in response to natural processes and to human activities.

  9. Alpha Helices Are More Robust to Mutations than Beta Strands

    PubMed Central

    Abrusán, György

    2016-01-01

    The rapidly increasing amount of data on human genetic variation has resulted in a growing demand to identify pathogenic mutations computationally, as their experimental validation is currently beyond reach. Here we show that alpha helices and beta strands differ significantly in their ability to tolerate mutations: helices can accumulate more mutations than strands without change, due to the higher numbers of inter-residue contacts in helices. This results in two patterns: a) the same number of mutations causes less structural change in helices than in strands; b) helices diverge more rapidly in sequence than strands within the same domains. Additionally, both helices and strands are significantly more robust than coils. Based on this observation we show that human missense mutations that change secondary structure are more likely to be pathogenic than those that do not. Moreover, inclusion of predicted secondary structure changes shows significant utility for improving upon state-of-the-art pathogenicity predictions. PMID:27935949

  10. Relationship between marine mammal stranding events and offshore earthquakes

    NASA Astrophysics Data System (ADS)

    Grant, Rachel; Savirina, Anna; Hoppit, Will

    2014-05-01

    The causes of marine mammal stranding events are largely unknown, but may relate to ocean currents, severe weather, anthropogenic noise pollution, and other factors. Large stranding events have been suggested to occur as a result of offshore earthquakes but there is little evidence as yet to support this hypothesis. Stranding events occur in hotspots, which are sometimes areas of high seismic activity, such as Taiwan, and other times, in areas that are removed from seismic zones, such as Cape Cod. We analyse a large and robust dataset of marine mammal stranding data collected off the coast of Washington and Oregon from 1999 to 2010, to look for statistical connections to offshore earthquakes. We looked forward, as well as backward in time from significant seismic events, to ascertain whether stranding occurrences, if connected to earthquakes, are a result of the earthquake preparation period or the earthquake itself. Possible mechanisms are discussed.

  11. Computing in mammalian cells with nucleic acid strand exchange

    PubMed Central

    Pochekailov, Sergii; Kirschman, Jonathan L.; Santangelo, Philip J.; Seelig, Georg

    2015-01-01

    DNA strand displacement has been widely used for the design of molecular circuits, motors, and sensors in cell-free settings. Recently, it has been shown that this technology can also operate in biological environments, but capabilities remain limited. Here, we look to adapt strand displacement and exchange reactions to mammalian cells and report DNA circuitry that can directly interact with a native mRNA. We began by optimizing the cellular performance of fluorescent reporters based on four-way strand exchange reactions and identified robust design principles by systematically varying the molecular structure, chemistry and delivery method. Next, we developed and tested AND and OR logic gates based on four-way strand exchange, demonstrating the feasibility of multi-input logic. Finally, we established that functional siRNA could be activated through strand exchange, and used native mRNA as programmable scaffolds for co-localizing gates and visualizing their operation with subcellular resolution. PMID:26689378

  12. Computing in mammalian cells with nucleic acid strand exchange

    NASA Astrophysics Data System (ADS)

    Groves, Benjamin; Chen, Yuan-Jyue; Zurla, Chiara; Pochekailov, Sergii; Kirschman, Jonathan L.; Santangelo, Philip J.; Seelig, Georg

    2016-03-01

    DNA strand displacement has been widely used for the design of molecular circuits, motors, and sensors in cell-free settings. Recently, it has been shown that this technology can also operate in biological environments, but capabilities remain limited. Here, we look to adapt strand displacement and exchange reactions to mammalian cells and report DNA circuitry that can directly interact with a native mRNA. We began by optimizing the cellular performance of fluorescent reporters based on four-way strand exchange reactions and identified robust design principles by systematically varying the molecular structure, chemistry and delivery method. Next, we developed and tested AND and OR logic gates based on four-way strand exchange, demonstrating the feasibility of multi-input logic. Finally, we established that functional siRNA could be activated through strand exchange, and used native mRNA as programmable scaffolds for co-localizing gates and visualizing their operation with subcellular resolution.

  13. Stranded investment, prices and privacy factor in FERC rulings

    SciTech Connect

    O`Driscoll, M.

    1993-07-16

    The Federal Energy Regulatory Commission upheld its rejection of United Illuminating Co.`s bid to recover stranded investment costs. Since UI has no wholesale customers, it is a matter best left to state regulators, FERC said. UI`s stranded investment recovery plan was part of the company`s transmission access tariff, which provides for open access transmission service at cost-based rates. FERC ordered UI to delete the stranded investment provisions, saying UI was trying to recover in its wholesale transmission rates the costs of generation facility investments that were incurred to provide service to retail customers that leave its system, reasoning that UI was seeking protection from what may be legitimate retail franchise competition, which is a state matter. UI, however, said deleting the stranded investment provision would preclude it from arguing in an individual rate filling under the transmission tariff that stranded investment costs should be borne by the wheeling customer.

  14. Dynamic DNA nanotechnology using strand-displacement reactions

    NASA Astrophysics Data System (ADS)

    Zhang, David Yu; Seelig, Georg

    2011-02-01

    The specificity and predictability of Watson-Crick base pairing make DNA a powerful and versatile material for engineering at the nanoscale. This has enabled the construction of a diverse and rapidly growing set of DNA nanostructures and nanodevices through the programmed hybridization of complementary strands. Although it had initially focused on the self-assembly of static structures, DNA nanotechnology is now also becoming increasingly attractive for engineering systems with interesting dynamic properties. Various devices, including circuits, catalytic amplifiers, autonomous molecular motors and reconfigurable nanostructures, have recently been rationally designed to use DNA strand-displacement reactions, in which two strands with partial or full complementarity hybridize, displacing in the process one or more pre-hybridized strands. This mechanism allows for the kinetic control of reaction pathways. Here, we review DNA strand-displacement-based devices, and look at how this relatively simple mechanism can lead to a surprising diversity of dynamic behaviour.

  15. Spatial and temporal patterns of stranded intertidal marine debris: is there a picture of global change?

    PubMed

    Browne, Mark Anthony; Chapman, M Gee; Thompson, Richard C; Amaral Zettler, Linda A; Jambeck, Jenna; Mallos, Nicholas J

    2015-06-16

    Floating and stranded marine debris is widespread. Increasing sea levels and altered rainfall, solar radiation, wind speed, waves, and oceanic currents associated with climatic change are likely to transfer more debris from coastal cities into marine and coastal habitats. Marine debris causes economic and ecological impacts, but understanding the scope of these requires quantitative information on spatial patterns and trends in the amounts and types of debris at a global scale. There are very few large-scale programs to measure debris, but many peer-reviewed and published scientific studies of marine debris describe local patterns. Unfortunately, methods of defining debris, sampling, and interpreting patterns in space or time vary considerably among studies, yet if data could be synthesized across studies, a global picture of the problem may be avaliable. We analyzed 104 published scientific papers on marine debris in order to determine how to evaluate this. Although many studies were well designed to answer specific questions, definitions of what constitutes marine debris, the methods used to measure, and the scale of the scope of the studies means that no general picture can emerge from this wealth of data. These problems are detailed to guide future studies and guidelines provided to enable the collection of more comparable data to better manage this growing problem.

  16. The ascent of cat breeds: genetic evaluations of breeds and worldwide random-bred populations.

    PubMed

    Lipinski, Monika J; Froenicke, Lutz; Baysac, Kathleen C; Billings, Nicholas C; Leutenegger, Christian M; Levy, Alon M; Longeri, Maria; Niini, Tirri; Ozpinar, Haydar; Slater, Margaret R; Pedersen, Niels C; Lyons, Leslie A

    2008-01-01

    The diaspora of the modern cat was traced with microsatellite markers from the presumed site of domestication to distant regions of the world. Genetic data were derived from over 1100 individuals, representing 17 random-bred populations from five continents and 22 breeds. The Mediterranean was reconfirmed to be the probable site of domestication. Genetic diversity has remained broad throughout the world, with distinct genetic clustering in the Mediterranean basin, Europe/America, Asia and Africa. However, Asian cats appeared to have separated early and expanded in relative isolation. Most breeds were derived from indigenous cats of their purported regions of origin. However, the Persian and Japanese bobtail were more aligned with European/American than with Mediterranean basin or Asian clusters. Three recently derived breeds were not distinct from their parental breeds of origin. Pure breeding was associated with a loss of genetic diversity; however, this loss did not correlate with breed popularity or age.

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

    DTIC Science & Technology

    2012-09-30

    University of Pennsylvania Philadelphia PA 19104 Kathleen Moore International Fund for Animal Welfare Yarmouth Port MA 02675 Randall Wells...stress in cetaceans . After undertaking a baseline experiment in Steller sea lions, this project will compare and contrast health, body condition, and...presence of bubbles with markers for decompression stress in mass stranded cetaceans , and compare these indices with single stranded individuals

  18. Vacuum brazing of carbon nanotube strands

    NASA Astrophysics Data System (ADS)

    Wu, Wei

    Carbon nanotubes (CNTs) discovered at 1991 have attracted great interest for applications in Nano-Electro-Mechanical-Systems (NEMS). However, the search for methods to join CNTs with metallic parts has been a worldwide challenge. Many efforts have been devoted to manipulating individual CNTs and joining them to each other. Joining processes so far attempted are premature and fall short of efficiency for joint quality evaluation. Thus, it has been found necessary to work on macro CNTs strands which are easy to handle via macro joining techniques. In this study, vacuum brazing technology has been developed for joining macro CNTs strands with Ni using a Ti-Ag-Cu alloy. The brazing mechanism has been confirmed as due to TiC formation at the CNTs/Ti-Ag-Cu interface. To evaluate this novel vacuum brazing technique for CNTs joining, the temperature effect on the brazing mechanism, microstructure and stoichiometry at joint interface needed to be understood. Firstly, the influence of temperature (from room temperature to 1000°C) on mechanical behaviour of CNTs was well examined. The ultimate tensile strength (UTS) of CNTs was measured to be a maximum at 900°C. Then, the mechanical performance of the joints was investigated from 850°C to 1000°C, and the fracture modes of the joints were identified. The UTS of joint also achieves maximum at 900°C. Below 900°C, due to little TiC formation, the bonding is weak thus leading to interfacial fracture. Above 900°C, due to much TiC formation, the bonding is strong thus resulting in CNTs fracture. Furthermore, the vacuum brazing technique was applied to join CNTs to Ni contact wires used as a lamp filament. Compared to the filament joined by Ag paste or mechanical connection, the illumination of the brazed CNTs filament was stronger. The current density of the brazed filament was superior to the Ag paste connected filament. This may represent a promising way to produce energy saving lamps.

  19. Familiar neighbors enhance breeding success in birds.

    PubMed Central

    Beletsky, L D; Orians, G H

    1989-01-01

    We tested the hypothesis that long-term familiarity with neighbors is advantageous by determining whether male red-winged blackbirds (Agelaius phoeniceus) breeding adjacent to familiar neighbors have better reproductive success than other males. Using data gathered during a 10-yr study of breeding success, we found that males with familiar neighbors fledged, on average, significantly more offspring annually than males without familiar neighbors. We also found that the same males, breeding in different years on the same territories, had significantly larger harems in the years they had familiar neighbors. Improved reproductive success was due to the males' abilities to attract more females to nest in their territories. Alternative hypotheses to explain the positive relationship between familiar neighbors and breeding success were not supported by our data. Relatively high reproductive success for breeders with long-term neighbors may provide a basis for the evolution of cooperative behavior in this and other species. PMID:2813369

  20. Economic evaluation of genomic breeding programs.

    PubMed

    König, S; Simianer, H; Willam, A

    2009-01-01

    The objective of this study was to compare a conventional dairy cattle breeding program characterized by a progeny testing scheme with different scenarios of genomic breeding programs. The ultimate economic evaluation criterion was discounted profit reflecting discounted returns minus discounted costs per cow in a balanced breeding goal of production and functionality. A deterministic approach mainly based on the gene flow method and selection index calculations was used to model a conventional progeny testing program and different scenarios of genomic breeding programs. As a novel idea, the modeling of the genomic breeding program accounted for the proportion of farmers waiting for daughter records of genotyped young bulls before using them for artificial insemination. Technical and biological coefficients for modeling were chosen to correspond to a German breeding organization. The conventional breeding program for 50 test bulls per year within a population of 100,000 cows served as a base scenario. Scenarios of genomic breeding programs considered the variation of costs for genotyping, selection intensity of cow sires, proportion of farmers waiting for daughter records of genotyped young bulls, and different accuracies of genomic indices for bulls and cows. Given that the accuracies of genomic indices are greater than 0.70, a distinct economic advantage was found for all scenarios of genomic breeding programs up to factor 2.59, mainly due to the reduction in generation intervals. Costs for genotyping were negligible when focusing on a population-wide perspective and considering additional costs for herdbook registration, milk recording, or keeping of bulls, especially if there is no need for yearly recalculation of effects of single nucleotide polymorphisms. Genomic breeding programs generated a higher discounted profit than a conventional progeny testing program for all scenarios where at least 20% of the inseminations were done by genotyped young bulls without

  1. Analysis of breed effects on semen traits in light horse, warmblood, and draught horse breeds.

    PubMed

    Gottschalk, Maren; Sieme, Harald; Martinsson, Gunilla; Distl, Ottmar

    2016-05-01

    In the present study, systematic effects on semen quality traits were investigated in 381 stallions representing 22 breeds. All stallions were used for AI either at the Lower Saxon National Stud Celle or the North Rhine-Westphalian National Stud Warendorf. A total of 71,078 fresh semen reports of the years 2001 to 2014 were edited for analysis of gel-free volume, sperm concentration, total number of sperm, progressive motility, and total number of progressively motile sperm. Breed differences were studied for warmblood and light horse breeds of both national studs (model I) and for warmblood breeds and the draught horse breed Rhenish German Coldblood from the North Rhine-Westphalian National stud (model II) using mixed model procedures. The fixed effects of age class, year, and month of semen collection had significant influences on all semen traits in both analyses. A significant influence of the horse breed was found for all semen traits but gel-free volume in both statistical models. Comparing warmblood and light horse stallions of both national studs, we observed highest sperm concentrations, total numbers of sperm, and total numbers of progressively motile sperm in Anglo-Arabian stallions. The draught horse breed Rhenish German Coldblood had the highest least squares means for gel-free volume, whereas all other investigated semen traits were significantly lower in this breed compared to the warmblood stallions under study. The variance components among stallions within breeds were significant for all semen traits and accounted for 40% to 59% of the total variance. The between-breed-variance among stallions was not significant underlining the similar size of the random stallion effect in each of the horse breeds analyzed here. In conclusion, breed and stallion are accounting for a significant proportion of the variation in semen quality.

  2. Prunus transcription factors: breeding perspectives

    PubMed Central

    Bianchi, Valmor J.; Rubio, Manuel; Trainotti, Livio; Verde, Ignazio; Bonghi, Claudio; Martínez-Gómez, Pedro

    2015-01-01

    Many plant processes depend on differential gene expression, which is generally controlled by complex proteins called transcription factors (TFs). In peach, 1533 TFs have been identified, accounting for about 5.5% of the 27,852 protein-coding genes. These TFs are the reference for the rest of the Prunus species. TF studies in Prunus have been performed on the gene expression analysis of different agronomic traits, including control of the flowering process, fruit quality, and biotic and abiotic stress resistance. These studies, using quantitative RT-PCR, have mainly been performed in peach, and to a lesser extent in other species, including almond, apricot, black cherry, Fuji cherry, Japanese apricot, plum, and sour and sweet cherry. Other tools have also been used in TF studies, including cDNA-AFLP, LC-ESI-MS, RNA, and DNA blotting or mapping. More recently, new tools assayed include microarray and high-throughput DNA sequencing (DNA-Seq) and RNA sequencing (RNA-Seq). New functional genomics opportunities include genome resequencing and the well-known synteny among Prunus genomes and transcriptomes. These new functional studies should be applied in breeding programs in the development of molecular markers. With the genome sequences available, some strategies that have been used in model systems (such as SNP genotyping assays and genotyping-by-sequencing) may be applicable in the functional analysis of Prunus TFs as well. In addition, the knowledge of the gene functions and position in the peach reference genome of the TFs represents an additional advantage. These facts could greatly facilitate the isolation of genes via QTL (quantitative trait loci) map-based cloning in the different Prunus species, following the association of these TFs with the identified QTLs using the peach reference genome. PMID:26124770

  3. [Pain caused by breeding: definition, judgment, pathogenesis].

    PubMed

    Herzog, A

    1997-02-01

    Special terms of the "German Animal Protection Law (section 11b)"and the "European Agreement for Protection of Domestic Animals" particularly "torture-breeding, genetic characteristics, well-being, soundness, pains, injuries and specific use" are commented. Examples of torture-breedings are discussed: Dog (Merle-faktor, brachycephalie, atrichosis), cat (Mans-factor, W-gene, folded-ears), birds (tuffs, ear-drops, tailesness, hypertrophy of bill-warts, abnormal position of tarsal-joints, hypertrophy of imposing behavior).

  4. Citrus breeding, genetics and genomics in Japan

    PubMed Central

    Omura, Mitsuo; Shimada, Takehiko

    2016-01-01

    Citrus is one of the most cultivated fruits in the world, and satsuma mandarin (Citrus unshiu Marc.) is a major cultivated citrus in Japan. Many excellent cultivars derived from satsuma mandarin have been released through the improvement of mandarins using a conventional breeding method. The citrus breeding program is a lengthy process owing to the long juvenility, and it is predicted that marker-assisted selection (MAS) will overcome the obstacle and improve the efficiency of conventional breeding methods. To promote citrus molecular breeding in Japan, a genetic mapping was initiated in 1987, and the experimental tools and resources necessary for citrus functional genomics have been developed in relation to the physiological analysis of satsuma mandarin. In this paper, we review the progress of citrus breeding and genome researches in Japan and report the studies on genetic mapping, expression sequence tag cataloguing, and molecular characterization of breeding characteristics, mainly in terms of the metabolism of bio-functional substances as well as factors relating to, for example, fruit quality, disease resistance, polyembryony, and flowering. PMID:27069387

  5. A double-stranded DNA rotaxane.

    PubMed

    Ackermann, Damian; Schmidt, Thorsten L; Hannam, Jeffrey S; Purohit, Chandra S; Heckel, Alexander; Famulok, Michael

    2010-06-01

    Mechanically interlocked molecules such as rotaxanes and catenanes have potential as components of molecular machinery. Rotaxanes consist of a dumb-bell-shaped molecule encircled by a macrocycle that can move unhindered along the axle, trapped by bulky stoppers. Previously, rotaxanes have been made from a variety of molecules, but not from DNA. Here, we report the design, assembly and characterization of rotaxanes in which both the dumb-bell-shaped molecule and the macrocycle are made of double-stranded DNA, and in which the axle of the dumb-bell is threaded through the macrocycle by base pairing. The assembly involves the formation of pseudorotaxanes, in which the macrocycle and the axle are locked together by hybridization. Ligation of stopper modules to the axle leads to the characteristic dumb-bell topology. When an oligonucleotide is added to release the macrocycle from the axle, the pseudorotaxanes are either converted to mechanically stable rotaxanes, or they disassemble by means of a slippage mechanism to yield a dumb-bell and a free macrocycle. Our DNA rotaxanes allow the fields of mechanically interlocked molecules and DNA nanotechnology to be combined, thus opening new possibilities for research into molecular machines and synthetic biology.

  6. A double-stranded DNA rotaxane

    NASA Astrophysics Data System (ADS)

    Ackermann, Damian; Schmidt, Thorsten L.; Hannam, Jeffrey S.; Purohit, Chandra S.; Heckel, Alexander; Famulok, Michael

    2010-06-01

    Mechanically interlocked molecules such as rotaxanes and catenanes have potential as components of molecular machinery. Rotaxanes consist of a dumb-bell-shaped molecule encircled by a macrocycle that can move unhindered along the axle, trapped by bulky stoppers. Previously, rotaxanes have been made from a variety of molecules, but not from DNA. Here, we report the design, assembly and characterization of rotaxanes in which both the dumb-bell-shaped molecule and the macrocycle are made of double-stranded DNA, and in which the axle of the dumb-bell is threaded through the macrocycle by base pairing. The assembly involves the formation of pseudorotaxanes, in which the macrocycle and the axle are locked together by hybridization. Ligation of stopper modules to the axle leads to the characteristic dumb-bell topology. When an oligonucleotide is added to release the macrocycle from the axle, the pseudorotaxanes are either converted to mechanically stable rotaxanes, or they disassemble by means of a slippage mechanism to yield a dumb-bell and a free macrocycle. Our DNA rotaxanes allow the fields of mechanically interlocked molecules and DNA nanotechnology to be combined, thus opening new possibilities for research into molecular machines and synthetic biology.

  7. Parasites in stranded cetaceans of Patagonia.

    PubMed

    Berón-Vera, Bárbara; Crespo, Enrique A; Raga, Juan A

    2008-08-01

    There is an increasing interest in parasites of marine mammals of Argentina. Here, we examined several poorly known cetaceans, i.e., 2 spectacled porpoises and 1 Burmeister's porpoise (Phocoenidae), and 1 Gray's beaked whale and 1 Cuvier's beaked whale (Ziphidae); we also updated the parasite information for 1 sperm whale (Physeteridae). These hosts strand only occasionally. We found Anisakis simplex s.l. in 2 spectacled porpoises and the Burmeister's porpoise, and recorded its distribution among the stomach chambers. Anisakis physeteris infected the sperm whale; Corynosoma cetaceum occurred in the duodenal ampulla of the Burmeister's porpoise; Corynosoma australe was found in the posterior-most region of the intestine of 1 spectacled porpoise, while another one had Tetrabothrius sp. in the anal crypts; Corynosoma bullosum and Corynosoma sp. were found in the sperm whale. The only digenean found was Pholeter gastrophilus in the Burmeister's porpoise. Merocercoids of Phyllobothrium delphini were present in the blubber of 1 spectacled porpoise, the sperm whale, and the Gray's beaked whale, while Scolex pleuronectis infected the Gray's beaked whale and 1 spectacled porpoise. No parasites were recovered from the Cuvier's beaked whale. Poor parasite-species assemblages are consistent in marine mammals of Patagonia. Given the conservation status of these hosts, the limited parasitological information gathered is valuable for conservation or management of these hosts in Patagonia.

  8. Recombination in Eukaryotic Single Stranded DNA Viruses

    PubMed Central

    Martin, Darren P.; Biagini, Philippe; Lefeuvre, Pierre; Golden, Michael; Roumagnac, Philippe; Varsani, Arvind

    2011-01-01

    Although single stranded (ss) DNA viruses that infect humans and their domesticated animals do not generally cause major diseases, the arthropod borne ssDNA viruses of plants do, and as a result seriously constrain food production in most temperate regions of the world. Besides the well known plant and animal-infecting ssDNA viruses, it has recently become apparent through metagenomic surveys of ssDNA molecules that there also exist large numbers of other diverse ssDNA viruses within almost all terrestrial and aquatic environments. The host ranges of these viruses probably span the tree of life and they are likely to be important components of global ecosystems. Various lines of evidence suggest that a pivotal evolutionary process during the generation of this global ssDNA virus diversity has probably been genetic recombination. High rates of homologous recombination, non-homologous recombination and genome component reassortment are known to occur within and between various different ssDNA virus species and we look here at the various roles that these different types of recombination may play, both in the day-to-day biology, and in the longer term evolution, of these viruses. We specifically focus on the ecological, biochemical and selective factors underlying patterns of genetic exchange detectable amongst the ssDNA viruses and discuss how these should all be considered when assessing the adaptive value of recombination during ssDNA virus evolution. PMID:21994803

  9. Recombination in eukaryotic single stranded DNA viruses.

    PubMed

    Martin, Darren P; Biagini, Philippe; Lefeuvre, Pierre; Golden, Michael; Roumagnac, Philippe; Varsani, Arvind

    2011-09-01

    Although single stranded (ss) DNA viruses that infect humans and their domesticated animals do not generally cause major diseases, the arthropod borne ssDNA viruses of plants do, and as a result seriously constrain food production in most temperate regions of the world. Besides the well known plant and animal-infecting ssDNA viruses, it has recently become apparent through metagenomic surveys of ssDNA molecules that there also exist large numbers of other diverse ssDNA viruses within almost all terrestrial and aquatic environments. The host ranges of these viruses probably span the tree of life and they are likely to be important components of global ecosystems. Various lines of evidence suggest that a pivotal evolutionary process during the generation of this global ssDNA virus diversity has probably been genetic recombination. High rates of homologous recombination, non-homologous recombination and genome component reassortment are known to occur within and between various different ssDNA virus species and we look here at the various roles that these different types of recombination may play, both in the day-to-day biology, and in the longer term evolution, of these viruses. We specifically focus on the ecological, biochemical and selective factors underlying patterns of genetic exchange detectable amongst the ssDNA viruses and discuss how these should all be considered when assessing the adaptive value of recombination during ssDNA virus evolution.

  10. Stranded costs: So what's the worry?

    SciTech Connect

    Graniere, R.J.

    1999-07-01

    This article is not concerned with the pros and cons of transforming a no-entry market into a market with unrestricted entry. The concern, instead, is with establishing the economic conditions under which stranded costs afflict the incumbents in a no-entry market undergoing a transformation to a market with unrestricted entry. What matters is an incumbent's cost structure in comparison to an entrant's cost structure. Section 1 presents a general model for a restructured electricity industry. Section 2 provides the 2 x 2 x 2 version of the model in which an incumbent and an entrant compete for the business of two customers. The intermediate bottleneck services are supplied by a regulated monopolist that does not behave anticompetitively in an effort to favor the incumbent. Section 3 contains the graphical analysis of the 2 x 2 x 2 model that is restricted to economic activity in a competitive generation market. Section 4 discusses the results of the graphical analysis that are pertinent to regulatory authorities. Section 5 sets out the conclusions derived from the analysis.

  11. Polymorphisms of KAP6, KAP7, and KAP8 genes in four Chinese sheep breeds.

    PubMed

    Liu, Y X; Shi, G Q; Wang, H X; Wan, P C; Tang, H; Yang, H; Guan, F

    2014-04-30

    High glycine-tyrosine proteins (HGTPs), also known as keratin-associated proteins (KAPs), play a key role in the major structures and mechanical properties of wool fiber. Sheep HGTPs consist of three multigene families: KAP6, KAP7, and KAP8 genes. Polymorphisms of these three genes have been proposed to have important effects on wool fiber traits. The aim of the present study was to identify polymorphisms of the KAP6, KAP7, and KAP8 genes in four sheep breeds, including Chinese Merino superfine wool sheep, Hu sheep, a Merino x Hu crossed breed, and Romney sheep. Polymerase chain reaction (PCR) product direct sequencing, PCR-single-strand conformation polymorphism, and cloned sequencing methods were used to find genetic variation and identify polymorphisms in these genes. The Mutation Surveyor v3.97 software was used to analyze the sequences. These methods revealed six different sequences of the KAP6 gene, two different sequences of the KAP7 gene, and five different sequences of the KAP8 gene. Accordingly, three (with frequencies>1%) single nucleotide polymorphisms (SNPs) of the KAP6 gene, one SNP of the KAP7 gene, and five SNPs of the KAP8 gene were detected. Interestingly, some of these sequences were present in only certain sheep breeds, thereby suggesting that these special allele sequences could be used as candidate genes of wool characteristics in further studies.

  12. Simulating decadal coastal morphodynamics

    NASA Astrophysics Data System (ADS)

    Nicholls, Robert J.; French, Jon R.; van Maanen, Barend

    2016-03-01

    Coastal geomorphic systems provide many services of key importance to humankind, including protection from flood and erosion hazards, diverse habitats and amenity values (Agardy et al., 2005; Jones et al., 2011). However, these systems are widely undergoing degradation that can be substantially attributed to the cumulative direct and indirect effects of human interference. Declining sediment inputs and throughputs are frequently a factor driving a shift towards progressive coastal erosion (Valiela, 2006; Nicholls et al., 2007). Such sediment starved systems have reduced resilience and are further threatened by human-induced climate change, not only due to accelerated sea-level rise, but also through possible shifts in wave and surge climate (Wong et al., 2014).

  13. 75 FR 27294 - Proposed Information Collection; Comment Request; Marine Mammal Stranding Report/Marine Mammal...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-14

    ... Mammal Stranding Report/Marine Mammal Rehabilitation Disposition Report AGENCY: National Oceanic and... mammal stranding report provides information on strandings so that the National Marine Fisheries Service... facilities. This information is submitted primarily by volunteer members of the marine mammal...

  14. Transgressive shoreline deposits seaward of coastal ponds along northeastern South Carolina coastline.

    NASA Astrophysics Data System (ADS)

    Wright, E.; Harris, M. S.; Pender, R.; Ball, M.

    2007-12-01

    The arcuate Long Bay coastline of northeastern South Carolina is dominated by the 75 km long Grand Strand, which is the result of landward retreat of the shoreline intersecting the paleo Myrtle Beach barrier system. As the shoreline transgresses, three stages of development have been recognized in this large coastal embayment: (1) coastal barrier island landforms north and south of the central Grand Strand that are migrating across an irregular Pleistocene paleolandscape and have not intersected emergent Quaternary paralic terraces; (2) an intermediate stage where the transgressing shoreline has created shore parallel coastal lakes and vegetated wetlands between the transgressive sediment mass and the emergent terraces; and (3) coastal segments where the transgressive shoreline is actively eroding into the emergent Pleistocene core. This study uses ground penetrating radar (GPR) and vibracore data to study the intermediate stage lake coastline. The GPR data reveals landward dipping reflectors infilling uneven topography and channels formed in the low between the irregular paleo barrier high and retreating shoreline. Study of the transgressive architecture and intersection with paleo- shoreface is important for understanding future shoreline retreat and for understanding potential storm records preserved in the infill.

  15. 50 CFR 15.24 - Permits for cooperative breeding.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 50 Wildlife and Fisheries 1 2012-10-01 2012-10-01 false Permits for cooperative breeding. 15.24... PLANTS WILD BIRD CONSERVATION ACT Permits and Approval of Cooperative Breeding Programs § 15.24 Permits for cooperative breeding. (a) Application requirements for permits for cooperative breeding....

  16. 50 CFR 15.24 - Permits for cooperative breeding.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 50 Wildlife and Fisheries 1 2013-10-01 2013-10-01 false Permits for cooperative breeding. 15.24... PLANTS WILD BIRD CONSERVATION ACT Permits and Approval of Cooperative Breeding Programs § 15.24 Permits for cooperative breeding. (a) Application requirements for permits for cooperative breeding....

  17. 50 CFR 15.24 - Permits for cooperative breeding.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 50 Wildlife and Fisheries 1 2014-10-01 2014-10-01 false Permits for cooperative breeding. 15.24... PLANTS WILD BIRD CONSERVATION ACT Permits and Approval of Cooperative Breeding Programs § 15.24 Permits for cooperative breeding. (a) Application requirements for permits for cooperative breeding....

  18. 50 CFR 15.24 - Permits for cooperative breeding.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 50 Wildlife and Fisheries 1 2011-10-01 2011-10-01 false Permits for cooperative breeding. 15.24... PLANTS WILD BIRD CONSERVATION ACT Permits and Approval of Cooperative Breeding Programs § 15.24 Permits for cooperative breeding. (a) Application requirements for permits for cooperative breeding....

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

    PubMed Central

    Roux, Simon; Solonenko, Natalie E.; Dang, Vinh T.; Poulos, Bonnie T.; Schwenck, Sarah M.; Goldsmith, Dawn B.; Coleman, Maureen L.; Breitbart, Mya

    2016-01-01

    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. PMID:28003936

  20. Proposed oil and gas exploration within the coastal plain of the Arctic National Wildlife Refuge, Alaska

    SciTech Connect

    Not Available

    1982-11-01

    The draft environmental impact statement describes the procedures and probable effects of aerial and geological surveying for oil and gas in the coastal area of Alaska's Arctic National Wildlife Refuge. The procedures provide for the protection of caribou caving areas and the avoidance of duplication in the survey activities. Temporary disturbances from seismic surveys would interfere with wildlife breeding and migration due to changes in the habitat. The Alaska National Interest Lands Conservation Act of 1980 provides the legal mandate for environmental assessment.

  1. Ultrastructural evidence for intramolecular double stranding in iota-carrageenan.

    PubMed

    Abeysekera, R M; Bergström, E T; Goodall, D M; Norton, I T; Robards, A W

    1993-10-04

    Kinetic studies of primary processes of conformational ordering in gel-forming biopolymers have suggested that a change in mechanism from intermolecular to intramolecular multistrand formation occurs on lowering the concentration of biopolymer. We report here ultrastructural observations consistent with intramolecular double stranding in a carbohydrate polymer, iota-carrageenan, by arresting this process of primary conformational ordering by an ultra-rapid freeze fixation technique. High-resolution transmission electron microscopy (TEM) revealed isolated iota-carrageenan chains showing a range of morphologies (linear, circular, and hairpin) consistent with intramolecular stranding. Control experiments in which iota-carrageenan was frozen in the disordered form revealed longer and thinner strands.

  2. Cognitive consequences of cooperative breeding in primates?

    PubMed

    Burkart, Judith Maria; van Schaik, Carel P

    2010-01-01

    Several hypotheses propose that cooperative breeding leads to increased cognitive performance, in both nonhuman and human primates, but systematic evidence for such a relationship is missing. A causal link might exist because motivational and cognitive processes necessary for the execution and coordination of helping behaviors could also favor cognitive performance in contexts not directly related to caregiving. In callitrichids, which among primates rely most strongly on cooperative breeding, these motivational and cognitive processes include attentional biases toward monitoring others, the ability to coordinate actions spatially and temporally, increased social tolerance, increased responsiveness to others' signals, and spontaneous prosociality. These processes are likely to enhance performance particularly in socio-cognitive contexts. Therefore, cooperatively breeding primates are expected to outperform their independently breeding sister taxa in socio-cognitive tasks. We evaluate this prediction by reviewing the literature and comparing cognitive performance in callitrichids with that of their sister taxa, i.e. squirrel monkeys, which are independent breeders, and capuchin monkeys, which show an intermediate breeding system. Consistent with our prediction, this review reveals that callitrichids systematically and significantly outperform their sister taxa in the socio-cognitive, but not in the non-social domain. This comparison is complemented with more qualitative evaluations of prosociality and cognitive performance in non-primate cooperative breeders, which suggest that among mammals, cooperative breeding generally produces conditions conducive to socio-cognitive performance. In the hominid lineage, however, the adoption of extensive allomaternal care presumably resulted in more pervasive cognitive consequences, because the motivational consequences of cooperative breeding was added to an ape-level cognitive system already capable of understanding simple

  3. Advances in Japanese pear breeding in Japan

    PubMed Central

    Saito, Toshihiro

    2016-01-01

    The Japanese pear (Pyrus pyrifolia Nakai) is one of the most widely grown fruit trees in Japan, and it has been used throughout Japan’s history. The commercial production of pears increased rapidly with the successive discoveries of the chance seedling cultivars ‘Chojuro’ and ‘Nijisseiki’ around 1890, and the development of new cultivars has continued since 1915. The late-maturing, leading cultivars ‘Niitaka’ and ‘Shinko’ were released during the initial breeding stage. Furthermore, systematic breeding by the Horticultural Research Station (currently, NARO Institute of Fruit Tree Science, National Agriculture and Food Research Organization (NIFTS)) began in 1935, which mainly aimed to improve fruit quality by focusing on flesh texture and black spot disease resistance. To date, 22 cultivars have been released, including ‘Kosui’, ‘Hosui’, and ‘Akizuki’, which are current leading cultivars from the breeding program. Four induced mutant cultivars induced by gamma irradiation, which exhibit some resistance to black spot disease, were released from the Institute of Radiation Breeding. Among these cultivars, ‘Gold Nijisseiki’ has become a leading cultivar. Moreover, ‘Nansui’ from the Nagano prefectural institute breeding program was released, and it has also become a leading cultivar. Current breeding objectives at NIFTS mainly combine superior fruit quality with traits related to labor and cost reduction, multiple disease resistance, or self-compatibility. Regarding future breeding, marker-assisted selection for each trait, QTL analyses, genome-wide association studies, and genomic selection analyses are currently in progress. PMID:27069390

  4. Across-breed EPD tables for the year 2016 adjusted to breed differences for birth year of 2014

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Records of progeny of 18 breeds were used to estimate differences among the breeds for birth, weaning, and yearling weight and for maternal effects of weaning weight, among 15 of the 18 breeds for carcass marbling and ribeye area and among 14 of the 18 breeds for fat depth and carcass weight. The r...

  5. Coastal Surveillance Baseline Model Development

    DTIC Science & Technology

    2015-02-27

    reconnaissance (ISR) model for coastal surveillance. The model needs to be developed in the System Toolkit (STK) software package version 10.0 (or...reconnaissance (ISR) model for coastal surveillance. The model needs to be developed in the System Toolkit (STK) software package version 10.0 (or...Catalogue STK System Toolkit TA Technical Authority DRDC CORA Task #185 Coastal Surveillance Baseline Model Development 27 February 2015 F-1 5758-001

  6. An introduction to coastal geomorphology

    SciTech Connect

    Pethick, J.S.

    1984-01-01

    This book is an introduction to wave and tidally dominated coastal forms, including beaches, cliffs, dunes, estuaries, mudflats and marshlands. The book emphasises the physical mechanisms by which this variety of landforms is produced and maintained. It introduces the energy outputs - waves, currents, tides - into the coastal 'machine', examines the way in which this energy is converted into water and sediment movement, and leads to an account of coastal landform development.

  7. Stranded pumice in the western Caribbean

    NASA Astrophysics Data System (ADS)

    Herrick, J. A.; Henton De Angelis, S.; Toscano, M. A.

    2013-12-01

    Floating and washed-up pumices have been reported by scientific expeditions along the Caribbean Sea coast of the Central American Isthmus and the northern coast of South America since at least 1947. Local coastal communities have been utilizing this resource for many years. The rounded and buffered morphology of hand specimens is consistent with water-borne transit. The volcanically active Caribbean and Central American regions provide a number of candidates for source volcanoes and eruptions. We have attempted to identify this source using samples collected from Carrie Bow Cay and Placencia Beach, Belize; Tulum Beach, Mexico; Morrosquillo Bay, Colombia; and Galeta Point, Panama. We have tracked possible transport routes through the use of river drainage and ocean current maps. The criteria for comparing the products of potential source volcanoes (including Atitlán Caldera in Guatemala and Caribbean sources such as Mt. Pelée, Martinique and Soufrière Hills, Montserrat) were developed from the whole rock major and trace element geochemistry and the compositional and textural characteristics of pumice and their constituent minerals and glasses. The largest pumice sample collected from Carrie Bow Cay, Belize, was 18.5x12 cm with the typical, rounded morphology and distinctively stretched vesicles exhibited by this pumice collection.

  8. Breeding programmes for smallholder sheep farming systems: II. Optimization of cooperative village breeding schemes.

    PubMed

    Gizaw, S; van Arendonk, J A M; Valle-Zárate, A; Haile, A; Rischkowsky, B; Dessie, T; Mwai, A O

    2014-10-01

    A simulation study was conducted to optimize a cooperative village-based sheep breeding scheme for Menz sheep of Ethiopia. Genetic gains and profits were estimated under nine levels of farmers' participation and three scenarios of controlled breeding achieved in the breeding programme, as well as under three cooperative flock sizes, ewe to ram mating ratios and durations of ram use for breeding. Under fully controlled breeding, that is, when there is no gene flow between participating (P) and non-participating (NP) flocks, profits ranged from Birr 36.9 at 90% of participation to Birr 21.3 at 10% of participation. However, genetic progress was not affected adversely. When there was gene flow from the NP to P flocks, profits declined from Birr 28.6 to Birr -3.7 as participation declined from 90 to 10%. Under the two-way gene flow model (i.e. when P and NP flocks are herded mixed in communal grazing areas), NP flocks benefited from the genetic gain achieved in the P flocks, but the benefits declined sharply when participation declined beyond 60%. Our results indicate that a cooperative breeding group can be established with as low as 600 breeding ewes mated at a ratio of 45 ewes to one ram, and the rams being used for breeding for a period of two years. This study showed that farmer cooperation is crucial to effect genetic improvement under smallholder low-input sheep farming systems.

  9. The Sub-Annual Breeding Cycle of a Tropical Seabird

    PubMed Central

    Reynolds, S. James; Martin, Graham R.; Dawson, Alistair; Wearn, Colin P.; Hughes, B. John

    2014-01-01

    Breeding periodicity allows organisms to synchronise breeding attempts with the most favourable ecological conditions under which to raise offspring. For most animal species, ecological conditions vary seasonally and usually impose an annual breeding schedule on their populations; sub-annual breeding schedules will be rare. We use a 16-year dataset of breeding attempts by a tropical seabird, the sooty tern (Onychoprion fuscatus), on Ascension Island to provide new insights about this classical example of a population of sub-annually breeding birds that was first documented in studies 60 years previously on the same island. We confirm that the breeding interval of this population has remained consistently sub-annual. By ringing >17000 birds and re-capturing a large sample of them at equivalent breeding stages in subsequent seasons, we reveal for the first time that many individual birds also consistently breed sub-annually (i.e. that sub-annual breeding is an individual as well as a population breeding strategy). Ascension Island sooty terns appear to reduce their courtship phase markedly compared with conspecifics breeding elsewhere. Our results provide rare insights into the ecological and physiological drivers of breeding periodicity, indicating that reduction of the annual cycle to just two life-history stages, breeding and moult, is a viable life-history strategy and that moult may determine the minimum time between breeding attempts. PMID:24714514

  10. The sub-annual breeding cycle of a tropical seabird.

    PubMed

    Reynolds, S James; Martin, Graham R; Dawson, Alistair; Wearn, Colin P; Hughes, B John

    2014-01-01

    Breeding periodicity allows organisms to synchronise breeding attempts with the most favourable ecological conditions under which to raise offspring. For most animal species, ecological conditions vary seasonally and usually impose an annual breeding schedule on their populations; sub-annual breeding schedules will be rare. We use a 16-year dataset of breeding attempts by a tropical seabird, the sooty tern (Onychoprion fuscatus), on Ascension Island to provide new insights about this classical example of a population of sub-annually breeding birds that was first documented in studies 60 years previously on the same island. We confirm that the breeding interval of this population has remained consistently sub-annual. By ringing >17,000 birds and re-capturing a large sample of them at equivalent breeding stages in subsequent seasons, we reveal for the first time that many individual birds also consistently breed sub-annually (i.e. that sub-annual breeding is an individual as well as a population breeding strategy). Ascension Island sooty terns appear to reduce their courtship phase markedly compared with conspecifics breeding elsewhere. Our results provide rare insights into the ecological and physiological drivers of breeding periodicity, indicating that reduction of the annual cycle to just two life-history stages, breeding and moult, is a viable life-history strategy and that moult may determine the minimum time between breeding attempts.

  11. Long-term population dynamics of breeding bird species in the German Wadden Sea area

    NASA Astrophysics Data System (ADS)

    Vauk, Gottfried; Prüter, Johannes; Hartwig, Eike

    1989-09-01

    For no other group of organisms in coastal areas are there so exact and long-term data available as there are for seabirds. Since the beginning of the 20th century, documentation of population size, especially for species breeding in colonies from the groups gulls, terns and auks, is almost complete. These species act as bio-indicators, and data on fluctuations in their population size are useful as they reflect changes in the state of the marine ecosystem. The population development of some of these seabird species (Herring Gull, Guillemot, Common, Arctic and Sandwich Tern) from the German North Sea coast, which primarily feed on fish, is given. Common to all these species is an exponential increase in numbers in recent years (1970 1985). Possible causes for this development, e.g. pressure from enemies or competitors, availability of breeding places, anthropogenic stress and mortality factors, as well as the direct and indirect anthropogenic-influenced changes in the trophic system due to the increasing eutrophication of coastal waters, are evaluated. Signs of a collapse in the stocks of seabrids resulting from environmental pollution are discussed. Consequences resulting from the ecosystem changes, such as reduction of nutrient discharge into the North Sea and the expansion of biological monitoring, are described.

  12. 1893 ROPE ROOM189380 TON ROPE MACHINEUPPER STRAND GUIDE John ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    1893 ROPE ROOM-1893-80 TON ROPE MACHINE-UPPER STRAND GUIDE - John A. Roebling's Sons Company & American Steel & Wire Company, South Broad, Clark, Elmer, Mott & Hudson Streets, Trenton, Mercer County, NJ

  13. 65. Detail view inside Manhattan anchorage of splayed cable strands. ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    65. Detail view inside Manhattan anchorage of splayed cable strands. Jet Lowe, photographer, 1982. - Brooklyn Bridge, Spanning East River between Park Row, Manhattan and Sands Street, Brooklyn, New York County, NY

  14. Establishing a Marine Mammal Stranding Network in the Bahamas

    DTIC Science & Technology

    2009-09-30

    mammal & turtle anatomy Dr Ruth Ewing, DVM, NOAA Fisheries Sample collection: The Basics Dr Charles Manire, DVM Atlantis Dolphin Cay Rescue...the Bahamas Pedro Baranda Dolphin Experience Sea turtles : species identification, strandings, and legislation Kelly Melillo Dolphin

  15. DNA nanotechnology. Programming colloidal phase transitions with DNA strand displacement.

    PubMed

    Rogers, W Benjamin; Manoharan, Vinothan N

    2015-02-06

    DNA-grafted nanoparticles have been called "programmable atom-equivalents": Like atoms, they form three-dimensional crystals, but unlike atoms, the particles themselves carry information (the sequences of the grafted strands) that can be used to "program" the equilibrium crystal structures. We show that the programmability of these colloids can be generalized to the full temperature-dependent phase diagram, not just the crystal structures themselves. We add information to the buffer in the form of soluble DNA strands designed to compete with the grafted strands through strand displacement. Using only two displacement reactions, we program phase behavior not found in atomic systems or other DNA-grafted colloids, including arbitrarily wide gas-solid coexistence, reentrant melting, and even reversible transitions between distinct crystal phases.

  16. 75 FR 8113 - Prestressed Concrete Steel Wire Strand From China

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-02-23

    ... From the Federal Register Online via the Government Publishing Office INTERNATIONAL TRADE COMMISSION 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,...

  17. 215. Dennis Hill, Photographer May 1998 DETAIL VIEW OF STRAND ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    215. Dennis Hill, Photographer May 1998 DETAIL VIEW OF STRAND SHOES AND STORM CABLE EYE BARS IN YERBA BUENA ANCHORAGE, FACING EAST. - San Francisco Oakland Bay Bridge, Spanning San Francisco Bay, San Francisco, San Francisco County, CA

  18. DNA strand exchange and RecA homologs in meiosis.

    PubMed

    Brown, M Scott; Bishop, Douglas K

    2014-12-04

    Homology search and DNA strand-exchange reactions are central to homologous recombination in meiosis. During meiosis, these processes are regulated such that the probability of choosing a homolog chromatid as recombination partner is enhanced relative to that of choosing a sister chromatid. This regulatory process occurs as homologous chromosomes pair in preparation for assembly of the synaptonemal complex. Two strand-exchange proteins, Rad51 and Dmc1, cooperate in regulated homology search and strand exchange in most organisms. Here, we summarize studies on the properties of these two proteins and their accessory factors. In addition, we review current models for the assembly of meiotic strand-exchange complexes and the possible mechanisms through which the interhomolog bias of recombination partner choice is achieved.

  19. Programmable energy landscapes for kinetic control of DNA strand displacement.

    PubMed

    Machinek, Robert R F; Ouldridge, Thomas E; Haley, Natalie E C; Bath, Jonathan; Turberfield, Andrew J

    2014-11-10

    DNA is used to construct synthetic systems that sense, actuate, move and compute. The operation of many dynamic DNA devices depends on toehold-mediated strand displacement, by which one DNA strand displaces another from a duplex. Kinetic control of strand displacement is particularly important in autonomous molecular machinery and molecular computation, in which non-equilibrium systems are controlled through rates of competing processes. Here, we introduce a new method based on the creation of mismatched base pairs as kinetic barriers to strand displacement. Reaction rate constants can be tuned across three orders of magnitude by altering the position of such a defect without significantly changing the stabilities of reactants or products. By modelling reaction free-energy landscapes, we explore the mechanistic basis of this control mechanism. We also demonstrate that oxDNA, a coarse-grained model of DNA, is capable of accurately predicting and explaining the impact of mismatches on displacement kinetics.

  20. Mass stranding of Odontoceti caused by parasitogenic eighth cranial neuropathy.

    PubMed

    Morimitsu, T; Nagai, T; Ide, M; Kawano, H; Naichuu, A; Koono, M; Ishii, A

    1987-10-01

    Hearing organs of the Odontoceti from two mass strandings in 1983 and 1986 were examined histopathologically. In the 1983 stranding, two of three pilot whales (Globicephala macrorhynchus) were necropsied and numerous Nasitrema sp. were found close to the eighth cranial nerve (nervus vistibulo cochlearis) in both animals. Patchy degeneration of the eighth cranial nerve in and out of the modiolus of the cochlea was observed. In the 1986 stranding, five of 125 false killer whales (Pseudorca crassiclens) were examined and numerous trematodes (Nasitrema gondo) were found in the tympanic cavities. Severe degeneration of the eighth cranial nerve was discovered and there were many trematode eggs in the nervous and surrounding tissues. Parasitogenic eighth neuropathy is proposed again as the cause of mass stranding of the Odontoceti.

  1. Programming colloidal phase transitions with DNA strand displacement

    NASA Astrophysics Data System (ADS)

    Rogers, William; Manoharan, Vinothan

    2014-03-01

    Specific interactions induced by transient bridging of complementary DNA strands grafted to colloidal particles can direct assembly of nanostructured materials. These interactions have been used to `program' the symmetry of novel equilibrium superlattices and could in principle enable self-assembly of prescribed structures. However, the ability to program the transitions between these equilibrium phases is currently limited: DNA-mediated attractions between particles decrease monotonically and steeply with increasing temperature, resulting only in high-temperature fluids and low-temperature solids that are inherently difficult to equilibrate. We show that by introducing free DNA strands that compete to bind with the grafted ones by strand displacement, the temperature dependence of interparticle interactions can be programmed through the base sequences of displacing strands. We use this scheme to create colloids with `designer' phase behavior such as re-entrant melting, arbitrarily wide gas-solid coexistence, and reversible transitions between different binary crystals.

  2. Coccidioidomycosis and other systemic mycoses of marine mammals stranding along the central California, USA coast: 1998-2012.

    PubMed

    Huckabone, Sara E; Gulland, Frances M D; Johnson, Suzanne M; Colegrove, Kathleen M; Dodd, Erin M; Pappagianis, Demosthenes; Dunkin, Robin C; Casper, David; Carlson, Erin L; Sykes, Jane E; Meyer, Weiland; Miller, Melissa A

    2015-04-01

    A wide range of systemic mycoses have been reported from captive and wild marine mammals from North America. Examples include regionally endemic pathogens such as Coccidioides and Blastomyces spp., and novel pathogens like Cryptococcus gattii, which appear may have been introduced to North America by humans. Stranding and necropsy data were analyzed from three marine mammal stranding and response facilities on the central California coast to assess the prevalence, host demographics, and lesion distribution of systemic mycoses affecting locally endemic marine mammals. Between 1 January 1998 and 30 June 2012, >7,000 stranded marine mammals were necropsied at the three facilities. Necropsy and histopathology records were reviewed to identify cases of locally invasive or systemic mycoses and determine the nature and distribution of fungal lesions. Forty-one animals (0.6%) exhibited cytological, culture- or histologically confirmed locally invasive or systemic mycoses: 36 had coccidioidomycosis, two had zygomycosis, two had cryptococcosis, and one was systemically infected with Scedosporium apiospermum (an Ascomycota). Infected animals included 18 California sea lions (Zalophus californianus), 20 southern sea otters (Enhydra lutris nereis), two Pacific harbor seals (Phoca vitulina richardsi), one Dall's porpoise (Phocoenoides dalli), and one northern elephant seal (Mirounga angustirostris). Coccidioidomycosis was reported from 15 sea lions, 20 sea otters, and one harbor seal, confirming that Coccidioides spp. is the most common pathogen causing systemic mycosis in marine mammals stranding along the central California coast. We also report the first confirmation of C. gattii infection in a wild marine mammal from California and the first report of coccidioidomycosis in a wild harbor seal. Awareness of these pathogenic fungi during clinical care and postmortem examination is an important part of marine mammal population health surveillance and human health protection

  3. A NATIONAL COASTAL ASSESSMENT OF COASTAL SEDIMENT CONDITION

    EPA Science Inventory

    One element of the Environmental Monitoring and Assessment Program's National Coastal Assessment is to estimate the current status, extent, changes and trends in the condition of the Nation's coastal sediments on a national basis. Based on NCA monitoring activities from 1999-2001...

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

    PubMed

    Lujan, Scott A; Williams, Jessica S; Pursell, Zachary F; Abdulovic-Cui, Amy A; Clark, Alan B; Nick McElhinny, Stephanie A; Kunkel, Thomas A

    2012-01-01

    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.

  5. Protein stabilization by introduction of cross-strand disulfides.

    PubMed

    Chakraborty, Kausik; Thakurela, Sudhir; Prajapati, Ravindra Singh; Indu, S; Ali, P Shaik Syed; Ramakrishnan, C; Varadarajan, Raghavan

    2005-11-08

    Disulfides cross-link residues in a protein that are separated in primary sequence and stabilize the protein through entropic destabilization of the unfolded state. While the removal of naturally occurring disulfides leads to protein destabilization, introduction of engineered disulfides does not always lead to significant stabilization of a protein. We have analyzed naturally occurring disulfides that span adjacent antiparallel strands of beta sheets (cross-strand disulfides). Cross-strand disulfides have recently been implicated as redox-based conformational switches in proteins such as gp120 and CD4. The propensity of these disulfides to act as conformational switches was postulated on the basis of the hypothesis that this class of disulfide is conformationally strained. In the present analysis, there was no evidence to suggest that cross-strand disulfides are more strained compared to other disulfides as assessed by their torsional energy. It was also observed that these disulfides occur solely at non-hydrogen-bonded (NHB) registered pairs of adjacent antiparallel strands and not at hydrogen-bonded (HB) positions as suggested previously. One of the half-cystines involved in cross-strand disulfide formation often occurs at an edge strand. Experimental confirmation of the stabilizing effects of such disulfides was carried out in Escherichia coli thioredoxin. Four pairs of cross-strand cysteines were introduced, two at HB and two at NHB pairs. Disulfides were formed in all four cases. However, as predicted from our analysis, disulfides at NHB positions resulted in an increase in melting temperature of 7-10 degrees C, while at HB positions there was a corresponding decrease of -7 degrees C. The reduced state of all proteins had similar stability.

  6. Direct Synthesis of Long Single-Walled Carbon Nanotube Strands

    NASA Astrophysics Data System (ADS)

    Zhu, H. W.; Xu, C. L.; Wu, D. H.; Wei, B. Q.; Vajtai, R.; Ajayan, P. M.

    2002-05-01

    In the processes that are used to produce single-walled nanotubes (electric arc, laser ablation, and chemical vapor deposition), the typical lengths of tangled nanotube bundles reach several tens of micrometers. We report that long nanotube strands, up to several centimeters in length, consisting of aligned single-walled nanotubes can be synthesized by the catalytic pyrolysis of n-hexane with an enhanced vertical floating technique. The long strands of nanotubes assemble continuously from arrays of nanotubes, which are intrinsically long.

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

    SciTech Connect

    Pozo-Yauner, Luis del; Wall, Jonathan S.; González Andrade, Martín; Sánchez-López, Rosana; Rodríguez-Ambriz, Sandra L.; Pérez Carreón, Julio I.; 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.

  8. Analysis of guanine oxidation products in double-stranded DNA and proposed guanine oxidation pathways in single-stranded, double-stranded or quadruplex DNA.

    PubMed

    Morikawa, Masayuki; Kino, Katsuhito; Oyoshi, Takanori; Suzuki, Masayo; Kobayashi, Takanobu; Miyazawa, Hiroshi

    2014-02-10

    Guanine is the most easily oxidized among the four DNA bases, and some guanine-rich sequences can form quadruplex structures. In a previous study using 6-mer DNA d(TGGGGT), which is the shortest oligomer capable of forming quadruplex structures, we demonstrated that guanine oxidation products of quadruplex DNA differ from those of single-stranded DNA. Therefore, the hotooxidation products of double-stranded DNA (dsDNA) may also differ from that of quadruplex or single-stranded DNA, with the difference likely explaining the influence of DNA structures on guanine oxidation pathways. In this study, the guanine oxidation products of the dsDNA d(TGGGGT)/d(ACCCCA) were analyzed using HPLC and electrospray ionization-mass spectrometry (ESI-MS). As a result, the oxidation products in this dsDNA were identified as 2,5-diamino-4H-imidazol-4-one (Iz), 8-oxo-7,8-dihydroguanine (8oxoG), dehydroguanidinohydantoin (Ghox), and guanidinohydantoin (Gh). The major oxidation products in dsDNA were consistent with a combination of each major oxidation product observed in single-stranded and quadruplex DNA. We previously reported that the kinds of the oxidation products in single-stranded or quadruplex DNA depend on the ease of deprotonation of the guanine radical cation (G•+) at the N1 proton. Similarly, this mechanism was also involved in dsDNA. Deprotonation in dsDNA is easier than in quadruplex DNA and more difficult in single-stranded DNA, which can explain the formation of the four oxidation products in dsDNA.

  9. Portable coastal observatories

    USGS Publications Warehouse

    Frye, Daniel; Butman, Bradford; Johnson, Mark; von der Heydt, Keith; Lerner, Steven

    2000-01-01

    Ocean observational science is in the midst of a paradigm shift from an expeditionary science centered on short research cruises and deployments of internally recording instruments to a sustained observational science where the ocean is monitored on a regular basis, much the way the atmosphere is monitored. While satellite remote sensing is one key way of meeting the challenge of real-time monitoring of large ocean regions, new technologies are required for in situ observations to measure conditions below the ocean surface and to measure ocean characteristics not observable from space. One method of making sustained observations in the coastal ocean is to install a fiber optic cable from shore to the area of interest. This approach has the advantage of providing power to offshore instruments and essentially unlimited bandwidth for data. The LEO-15 observatory offshore of New Jersey (yon Alt et al., 1997) and the planned Katama observatory offshore of Martha's Vineyard (Edson et al., 2000) use this approach. These sites, along with other cabled sites, will play an important role in coastal ocean science in the next decade. Cabled observatories, however, have two drawbacks that limit the number of sites that are likely to be installed. First, the cable and the cable installation are expensive and the shore station needed at the cable terminus is often in an environmentally sensitive area where competing interests must be resolved. Second, cabled sites are inherently limited geographically to sites within reach of the cable, so it is difficult to cover large areas of the coastal ocean.

  10. Hearing loss in stranded odontocete dolphins and whales.

    PubMed

    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

    2010-11-03

    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. A model capturing novel strand symmetries in bacterial DNA

    SciTech Connect

    Sobottka, Marcelo; Hart, Andrew G.

    2011-07-15

    Highlights: {yields} We propose a simple stochastic model to construct primitive DNA sequences. {yields} The model provide an explanation for Chargaff's second parity rule in primitive DNA sequences. {yields} The model is also used to predict a novel type of strand symmetry in primitive DNA sequences. {yields} We extend the results for bacterial DNA sequences and compare distributional properties intrinsic to the model to statistical estimates from 1049 bacterial genomes. {yields} We find out statistical evidences that the novel type of strand symmetry holds for bacterial DNA sequences. -- Abstract: Chargaff's second parity rule for short oligonucleotides states that the frequency of any short nucleotide sequence on a strand is approximately equal to the frequency of its reverse complement on the same strand. Recent studies have shown that, with the exception of organellar DNA, this parity rule generally holds for double-stranded DNA genomes and fails to hold for single-stranded genomes. While Chargaff's first parity rule is fully explained by the Watson-Crick pairing in the DNA double helix, a definitive explanation for the second parity rule has not yet been determined. In this work, we propose a model based on a hidden Markov process for approximating the distributional structure of primitive DNA sequences. Then, we use the model to provide another possible theoretical explanation for Chargaff's second parity rule, and to predict novel distributional aspects of bacterial DNA sequences.

  12. DNA Origami with Double Stranded DNA as a Unified Scaffold

    PubMed Central

    Yang, Yang; Han, Dongran; Nangreave, Jeanette; Liu, Yan; Yan, Hao

    2013-01-01

    Scaffolded DNA origami is a widely used technology for self-assembling precisely structured nanoscale objects that contain a large number of addressable features. Typical scaffolds are long, single strands of DNA (ssDNA) that are folded into distinct shapes through the action of many, short ssDNA staples that are complementary to several different domains of the scaffold. However, sources of long single stranded DNA are scarce, limiting the size and complexity of structures that can be assembled. Here we demonstrated that dsDNA scaffolds can be directly used to fabricate integrated DNA origami structures that incorporate both of the constituent ssDNA molecules. Two basic principles were employed in the design of scaffold folding paths – folding path asymmetry and periodic convergence of the two ssDNA scaffold strands. Asymmetry in the folding path minimizes unwanted complementarity between staples, and incorporating an offset between the folding paths of each ssDNA scaffold strand reduces the number of times that complementary portions of the strands are brought into close proximity with one another, both of which decrease the likelihood of dsDNA scaffold recovery. Meanwhile, the folding paths of the two ssDNA scaffold strands were designed to periodically converge to promote the assembly of a single, unified structure rather than two individual ones. Our results reveal that this basic strategy can be used to reliably assemble integrated DNA nanostructures from dsDNA scaffolds. PMID:22830653

  13. Application of strand meshes to complex aerodynamic flow fields

    NASA Astrophysics Data System (ADS)

    Katz, Aaron; Wissink, Andrew M.; Sankaran, Venkateswaran; Meakin, Robert L.; Chan, William M.

    2011-07-01

    We explore a new approach for viscous computational fluid dynamics calculations for external aerodynamics around geometrically complex bodies that incorporates nearly automatic mesh generation and efficient flow solution methods. A prismatic-like grid using "strands" is grown a short distance from the body surface to capture the viscous boundary layer, and adaptive Cartesian grids are used throughout the rest of the domain. The approach presents several advantages over established methods: nearly automatic grid generation from triangular or quadrilateral surface tessellations, very low memory overhead, automatic mesh adaptivity for time-dependent problems, and fast and efficient solvers from structured data in both the strand and Cartesian grids.The approach is evaluated for complex geometries and flow fields. We investigate the effects of strand length and strand vector smoothing to understand the effects on computed solutions. Results of three applications using the strand-adaptive Cartesian approach are given, including a NACA wing, isolated V-22 (TRAM) rotor in hover, and the DLR-F6 wing-body transport. The results from these cases show that the strand approach can successfully resolve near-body and off-body features as well as or better than established methods.

  14. Conformations of double stranded DNA: the effect of breathing bubbles

    NASA Astrophysics Data System (ADS)

    Huang, Aiqun; Bhattacharya, Aniket

    2015-03-01

    A double stranded DNA (dsDNA) is a natural semi-flexible biopolymer with persistence length ~ 50 nm, while a single stranded (ss) DNA is very flexible whose persistence length is one order of magnitude smaller (3-5 nm). Depending on the temperature and sequence, the two strands in a dsDNA can locally denature into two single strands and form bubbles along the polymer chain, i.e. dsDNA exists in the form of a combination of double strands and single strands, exhibiting a heterogeneity of bending rigidity. In our study, we adopt a coarse grained model of dsDNA developed by Kim et al. [J. Y. Kim, J. H. Jeon, and W. Sung, J. Chem. Phys. 128, 055101 2008] and further improve it by incorporating excluded volume effect and sequence heterogeneity. In this model, a dsDNA is described as two semi-flexible chains paired with each other by hydrogen bonding, the stacking interaction is designed such that the persistence length of the paired chains interpolates 3 nm and 50 nm depending on the fraction of the melted base pairs. By performing Langevin dynamics simulation we study the bubble statistics as a function of temperature and sequence and how the bubbles affect local bending rigidity and the chain conformations. We compare our results with those from WLC model.

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

    PubMed

    del Pozo-Yauner, Luis; Wall, Jonathan S; González Andrade, Martín; Sánchez-López, Rosana; Rodríguez-Ambriz, Sandra L; Pérez Carreón, Julio I; Ochoa-Leyva, Adrián; Fernández-Velasco, D Alejandro

    2014-01-10

    It has been suggested that the N-terminal strand of the light chain variable domain (V(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(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.

  16. Protein-free parallel triple-stranded DNA complex formation

    PubMed Central

    Shchyolkina, A. K.; Timofeev, E. N.; Lysov, Yu. P.; Florentiev, V. L.; Jovin, T. M.; Arndt-Jovin, D. J.

    2001-01-01

    A 14 nt DNA sequence 5′-AGAATGTGGCAAAG-3′ from the zinc finger repeat of the human KRAB zinc finger protein gene ZNF91 bearing the intercalator 2-methoxy,6-chloro,9-amino acridine (Acr) attached to the sugar–phosphate backbone in various positions has been shown to form a specific triple helix (triplex) with a 16 bp hairpin (intramolecular) or a two-stranded (intermolecular) duplex having the identical sequence in the same (parallel) orientation. Intramolecular targets with the identical sequence in the antiparallel orientation and a non-specific target sequence were tested as controls. Apparent binding constants for formation of the triplex were determined by quantitating electrophoretic band shifts. Binding of the single-stranded oligonucleotide probe sequence to the target led to an increase in the fluorescence anisotropy of acridine. The parallel orientation of the two identical sequence segments was confirmed by measurement of fluorescence resonance energy transfer between the acridine on the 5′-end of the probe strand as donor and BODIPY-Texas Red on the 3′-amino group of either strand of the target duplex as acceptor. There was full protection from OsO4-bipyridine modification of thymines in the probe strand of the triplex, in accordance with the presumed triplex formation, which excluded displacement of the homologous duplex strand by the probe–intercalator conjugate. The implications of these results for the existence of protein-independent parallel triplexes are discussed. PMID:11160932

  17. Sinking coastal cities

    NASA Astrophysics Data System (ADS)

    Erkens, Gilles; Bucx, Tom; Dam, Rien; De Lange, Ger; Lambert, John

    2014-05-01

    In many coastal and delta cities land subsidence now exceeds absolute sea level rise up to a factor of ten. Without action, parts of Jakarta, Ho Chi Minh City, Bangkok and numerous other coastal cities will sink below sea level. Land subsidence increases flood vulnerability (frequency, inundation depth and duration of floods), with floods causing major economic damage and loss of lives. In addition, differential land movement causes significant economic losses in the form of structural damage and high maintenance costs. This effects roads and transportation networks, hydraulic infrastructure - such as river embankments, sluice gates, flood barriers and pumping stations -, sewage systems, buildings and foundations. The total damage worldwide is estimated at billions of dollars annually. Excessive groundwater extraction after rapid urbanization and population growth is the main cause of severe land subsidence. In addition, coastal cities are often faced with larger natural subsidence, as they are built on thick sequences of soft soil. Because of ongoing urbanization and population growth in delta areas, in particular in coastal megacities, there is, and will be, more economic development in subsidence-prone areas. The impacts of subsidence are further exacerbated by extreme weather events (short term) and rising sea levels (long term).Consequently, detrimental impacts will increase in the near future, making it necessary to address subsidence related problems now. Subsidence is an issue that involves many policy fields, complex technical aspects and governance embedment. There is a need for an integrated approach in order to manage subsidence and to develop appropriate strategies and measures that are effective and efficient on both the short and long term. Urban (ground)water management, adaptive flood risk management and related spatial planning strategies are just examples of the options available. A major rethink is needed to deal with the 'hidden' but urgent

  18. Breeding and genetics--historical perspective.

    PubMed

    Rishell, W A

    1997-08-01

    This paper is a review of selection methods that have been used in commercial breeding of table egg stocks, broilers, and turkeys, based on the author's experience. In addition, a number of historic developments that have shaped or influenced the selection process are listed and the significance of each is discussed. The merits of mass selection are noted and compared with the multiple forms of family selection, e.g., full or half sibs, progeny testing, and recurrent methods. Each of these methods is believed to have nearly universal application in applied breeding programs being practiced today. This review concludes that a combination of individual and family selection practices aimed at improving multiple traits simultaneously is required to remain a successful supplier of breeding stock to the current commercial industry.

  19. Genetic stability in the Icelandic horse breed.

    PubMed

    Campana, M G; Stock, F; Barrett, E; Benecke, N; Barker, G W W; Seetah, K; Bower, M A

    2012-08-01

    Despite the Icelandic horse enjoying great popularity worldwide, the breed's gene pool is small. This is because of a millennium of isolation on Iceland, population crashes caused by natural disasters and selective breeding. Populations with small effective population sizes are considered to be more at risk of selection pressures such as disease and environmental change. By analysing historic and modern mitochondrial DNA sequences and nuclear coat colour genes, we examined real-time population dynamics in the Icelandic horse over the last 150 years. Despite the small gene pool of this breed, we found that the effective population size and genetic profile of the Icelandic horse have remained stable over the studied time period.

  20. Red Tide Strands South African Rock Lobsters

    NASA Technical Reports Server (NTRS)

    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

  1. Red Tide Strands South African Rock Lobsters

    NASA Technical Reports Server (NTRS)

    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

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

    DTIC Science & Technology

    2013-09-30

    Martin, V. and Arbelo, M. (2005). Gas and fat embolic syndrome involving a mass stranding of beaked whales (Family Ziphiidae) exposed to... Fraser , W. (1990). Complement activation involvement in decompression sickness of rabbits. Undersea Biomed Res. 17, 51-66.

  3. In Vivo Conversion of the Single-Stranded DNA of the Kilham Rat Virus to a Double-Stranded Form

    PubMed Central

    Salzman, Lois Ann; White, Wesley

    1973-01-01

    Kilham rat virus (KRV) contains linear, single-stranded DNA in the virion. The fate of radioactive viral DNA was followed after infection of monolayer cells. Within 60 min after infection of cells, 28 to 42% of the parental viral DNA is converted to a new form. This new DNA form is believed to be double stranded and linear on the basis of its sedimentation in neutral and alkaline sucrose gradients, elution from hydroxyapatite columns, its buoyant density in equilibrium CsCl density gradients, and appearance in the electron microscope. The double-stranded linear KRV DNA may be analogous to the replicative form of certain bacteriophages, including φX174, which contain single-stranded circular genomes. Images PMID:4347430

  4. Haploids: Constraints and opportunities in plant breeding.

    PubMed

    Dwivedi, Sangam L; Britt, Anne B; Tripathi, Leena; Sharma, Shivali; Upadhyaya, Hari D; Ortiz, Rodomiro

    2015-11-01

    The discovery of haploids in higher plants led to the use of doubled haploid (DH) technology in plant breeding. This article provides the state of the art on DH technology including the induction and identification of haploids, what factors influence haploid induction, molecular basis of microspore embryogenesis, the genetics underpinnings of haploid induction and its use in plant breeding, particularly to fix traits and unlock genetic variation. Both in vitro and in vivo methods have been used to induce haploids that are thereafter chromosome doubled to produce DH. Various heritable factors contribute to the successful induction of haploids, whose genetics is that of a quantitative trait. Genomic regions associated with in vitro and in vivo DH production were noted in various crops with the aid of DNA markers. It seems that F2 plants are the most suitable for the induction of DH lines than F1 plants. Identifying putative haploids is a key issue in haploid breeding. DH technology in Brassicas and cereals, such as barley, maize, rice, rye and wheat, has been improved and used routinely in cultivar development, while in other food staples such as pulses and root crops the technology has not reached to the stage leading to its application in plant breeding. The centromere-mediated haploid induction system has been used in Arabidopsis, but not yet in crops. Most food staples are derived from genomic resources-rich crops, including those with sequenced reference genomes. The integration of genomic resources with DH technology provides new opportunities for the improving selection methods, maximizing selection gains and accelerate cultivar development. Marker-aided breeding and DH technology have been used to improve host plant resistance in barley, rice, and wheat. Multinational seed companies are using DH technology in large-scale production of inbred lines for further development of hybrid cultivars, particularly in maize. The public sector provides support to

  5. Breeding Astyanax mexicanus through Natural Spawning.

    PubMed

    Borowsky, Richard

    2008-11-01

    INTRODUCTIONMale and female Astyanax mexicanus can be bred successfully in tanks under appropriate conditions. Females should be maintained on a diet high in fats for 10-14 d before breeding. The transfer of a male and female into clean water in a fresh tank and a change (increase) in water temperature are cues for breeding. Newly fertilized eggs may also be obtained through in vitro fertilization. Note that blind fish should never be paired with eyed fish in illuminated aquaria, because the eyed fish are aggressive and will kill even much larger blind fish. Such matings must be carried out in the dark or by using in vitro fertilization.

  6. Age-specific breeding in Emperor Geese

    USGS Publications Warehouse

    Schmutz, J.A.

    2000-01-01

    I studied the frequency with which Emperor Geese (Chen canagica) of known age were observed breeding on the Yukon-Kuskokwim Delta, Alaska. No one- or two-year old geese were observed on nests. Three-year old geese bred at a lower rate than four-year old geese. These data suggest that patterns of age-specific breeding in Emperor Geese are similar to other sympatrically nesting, large bodied geese [Greater White-fronted Geese (Anser albifrons)] but delayed relative to smaller bodied geese [Cackling Canada Geese (Branta canadensis minima) and Pacific Black Brant (B. bernicla nigricans)].

  7. NATIONAL COASTAL CONDITION REPORT IV

    EPA Science Inventory

    The National Coastal Condition Report IV (NCCR IV) is the fourth in a series of environmental assessments of U.S. coastal waters and the Great Lakes. The report includes assessments of all the nation’s estuaries in the contiguous 48 states and Puerto Rico, south-eastern Alaska, ...

  8. Sinking coastal cities

    NASA Astrophysics Data System (ADS)

    Erkens, G.; Bucx, T.; Dam, R.; de Lange, G.; Lambert, J.

    2015-11-01

    In many coastal and delta cities land subsidence now exceeds absolute sea level rise up to a factor of ten. A major cause for severe land subsidence is excessive groundwater extraction related to rapid urbanization and population growth. Without action, parts of Jakarta, Ho Chi Minh City, Bangkok and numerous other coastal cities will sink below sea level. Land subsidence increases flood vulnerability (frequency, inundation depth and duration of floods), with floods causing major economic damage and loss of lives. In addition, differential land movement causes significant economic losses in the form of structural damage and high maintenance costs for (infra)structure. The total damage worldwide is estimated at billions of dollars annually. As subsidence is often spatially variable and can be caused by multiple processes, an assessment of subsidence in delta cities needs to answer questions such as: what are the main causes? What is the current subsidence rate and what are future scenarios (and interaction with other major environmental issues)? Where are the vulnerable areas? What are the impacts and risks? How can adverse impacts be mitigated or compensated for? Who is involved and responsible to act? In this study a quick-assessment of subsidence is performed on the following mega-cities: Jakarta, Ho Chi Minh City, Dhaka, New Orleans and Bangkok. Results of these case studies will be presented and compared, and a (generic) approach how to deal with subsidence in current and future subsidence-prone areas is provided.

  9. Coastal Zone Color Scanner

    NASA Technical Reports Server (NTRS)

    Johnson, B.

    1988-01-01

    The Coastal Zone Color Scanner (CZCS) spacecraft ocean color instrument is capable of measuring and mapping global ocean surface chlorophyll concentration. It is a scanning radiometer with multiband capability. With new electronics and some mechanical, and optical re-work, it probably can be made flight worthy. Some additional components of a second flight model are also available. An engineering study and further tests are necessary to determine exactly what effort is required to properly prepare the instrument for spaceflight and the nature of interfaces to prospective spacecraft. The CZCS provides operational instrument capability for monitoring of ocean productivity and currents. It could be a simple, low cost alternative to developing new instruments for ocean color imaging. Researchers have determined that with global ocean color data they can: specify quantitatively the role of oceans in the global carbon cycle and other major biogeochemical cycles; determine the magnitude and variability of annual primary production by marine phytoplankton on a global scale; understand the fate of fluvial nutrients and their possible affect on carbon budgets; elucidate the coupling mechanism between upwelling and large scale patterns in ocean basins; answer questions concerning the large scale distribution and timing of spring blooms in the global ocean; acquire a better understanding of the processes associated with mixing along the edge of eddies, coastal currents, western boundary currents, etc., and acquire global data on marine optical properties.

  10. Estimating superpopulation size and annual probability of breeding for pond-breeding salamanders

    USGS Publications Warehouse

    Kinkead, K.E.; Otis, D.L.

    2007-01-01

    It has long been accepted that amphibians can skip breeding in any given year, and environmental conditions act as a cue for breeding. In this paper, we quantify temporary emigration or nonbreeding probability for mole and spotted salamanders (Ambystoma talpoideum and A. maculatum). We estimated that 70% of mole salamanders may skip breeding during an average rainfall year and 90% may skip during a drought year. Spotted salamanders may be more likely to breed, with only 17% avoiding the breeding pond during an average rainfall year. We illustrate how superpopulations can be estimated using temporary emigration probability estimates. The superpopulation is the total number of salamanders associated with a given breeding pond. Although most salamanders stay within a certain distance of a breeding pond for the majority of their life spans, it is difficult to determine true overall population sizes for a given site if animals are only captured during a brief time frame each year with some animals unavailable for capture at any time during a given year. ?? 2007 by The Herpetologists' League, Inc.

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

    SciTech Connect

    Poeschla, Eric

    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.

  12. C. elegans telomeres contain G-strand and C-strand overhangs that are bound by distinct proteins.

    PubMed

    Raices, Marcela; Verdun, Ramiro E; Compton, Sarah A; Haggblom, Candy I; Griffith, Jack D; Dillin, Andrew; Karlseder, Jan

    2008-03-07

    Single-strand extensions of the G strand of telomeres are known to be critical for chromosome-end protection and length regulation. Here, we report that in C. elegans, chromosome termini possess 3' G-strand overhangs as well as 5' C-strand overhangs. C tails are as abundant as G tails and are generated by a well-regulated process. These two classes of overhangs are bound by two single-stranded DNA binding proteins, CeOB1 and CeOB2, which exhibit specificity for G-rich or C-rich telomeric DNA. Strains of worms deleted for CeOB1 have elongated telomeres as well as extended G tails, whereas CeOB2 deficiency leads to telomere-length heterogeneity. Both CeOB1 and CeOB2 contain OB (oligo-saccharide/oligo-nucleotide binding) folds, which exhibit structural similarity to the second and first OB folds of the mammalian telomere binding protein hPOT1, respectively. Our results suggest that C. elegans telomere homeostasis relies on a novel mechanism that involves 5' and 3' single-stranded termini.

  13. Costs Associated with Equine Breeding in Kentucky

    NASA Astrophysics Data System (ADS)

    Walker, Cassandra L.

    There were approximately 9 million horses in the United States having a 102 billion impact on the U.S. economy (AHC, 2005). Over 1 million of those horses were involved in the breeding sector. In Kentucky, nearly 18% of the horse population have been involved in breeding. Managing an equine enterprise can be difficult, particularly given that many who undertake such endeavors do not have a background or education in business management. Kentucky Cooperative Extension has produced interactive spreadsheets to help horse owners better understand the costs associated with owning horses or managing certain equine businesses, including boarding and training operations. However, there has been little support for breeders. Therefore, the objectives of this study were to provide owners with a list of services offered for breeding and the costs associated with those services. Survey questions were created from a list of topics pertinent to equine breeding and from that list of questions, an electronic survey was created. The survey was sent via Qualtrics Survey Software to collect information on stallion and mare management costs as well as expenses related to owning and breeding. Question topics included veterinary and housing costs, management and advertising expenses, and membership fees. A total of 78 farms were selected from the 2013 breeder's listings for the Kentucky Quarter Horse Association (n = 39) and the Kentucky Thoroughbred Farm Managers' Club (n = 26), and other breed association contacts (n = 13). These farms were selected from the lists by outside individuals who were not related to the project. Participants were asked to answer all questions relevant to the farm. After the initial survey distribution, follow-up e-mails and phone calls were conducted in order to answer any questions participants might have had about the survey. Survey response rate was 32.1% (25 of 78 surveys returned). Farms in Kentucky had an average of two farm-owned and two outside

  14. Accuracy of genotype imputation in sheep breeds.

    PubMed

    Hayes, B J; Bowman, P J; Daetwyler, H D; Kijas, J W; van der Werf, J H J

    2012-02-01

    Although genomic selection offers the prospect of improving the rate of genetic gain in meat, wool and dairy sheep breeding programs, the key constraint is likely to be the cost of genotyping. Potentially, this constraint can be overcome by genotyping selection candidates for a low density (low cost) panel of SNPs with sparse genotype coverage, imputing a much higher density of SNP genotypes using a densely genotyped reference population. These imputed genotypes would then be used with a prediction equation to produce genomic estimated breeding values. In the future, it may also be desirable to impute very dense marker genotypes or even whole genome re-sequence data from moderate density SNP panels. Such a strategy could lead to an accurate prediction of genomic estimated breeding values across breeds, for example. We used genotypes from 48 640 (50K) SNPs genotyped in four sheep breeds to investigate both the accuracy of imputation of the 50K SNPs from low density SNP panels, as well as prospects for imputing very dense or whole genome re-sequence data from the 50K SNPs (by leaving out a small number of the 50K SNPs at random). Accuracy of imputation was low if the sparse panel had less than 5000 (5K) markers. Across breeds, it was clear that the accuracy of imputing from sparse marker panels to 50K was higher if the genetic diversity within a breed was lower, such that relationships among animals in that breed were higher. The accuracy of imputation from sparse genotypes to 50K genotypes was higher when the imputation was performed within breed rather than when pooling all the data, despite the fact that the pooled reference set was much larger. For Border Leicesters, Poll Dorsets and White Suffolks, 5K sparse genotypes were sufficient to impute 50K with 80% accuracy. For Merinos, the accuracy of imputing 50K from 5K was lower at 71%, despite a large number of animals with full genotypes (2215) being used as a reference. For all breeds, the relationship of

  15. 75 FR 37382 - Notice of Antidumping Duty Order: Prestressed Concrete Steel Wire Strand from the People's...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-06-29

    ... International Trade Administration Notice of Antidumping Duty Order: Prestressed Concrete Steel Wire Strand from... duty order on prestressed concrete steel wire strand (``PC strand'') from the People's Republic of... material injury to a U.S. industry. See Prestressed Concrete Steel Wire Strand from China...

  16. 75 FR 36678 - Prestressed Concrete Steel Wire Strand From China; Determinations

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-06-28

    ... COMMISSION Prestressed Concrete Steel Wire Strand From China; Determinations On the basis of the record \\1... of prestressed concrete steel wire strand (PC strand), provided for in subheading 7312.10.30 of the... (June 2010), entitled Prestressed Concrete Steel Wire Strand from China: Investigation Nos....

  17. Role of stranded gas in increasing global gas supplies

    USGS Publications Warehouse

    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.

  18. Translating Ribosomes Inhibit Poliovirus Negative-Strand RNA Synthesis

    PubMed Central

    Barton, David J.; Morasco, B. Joan; Flanegan, James B.

    1999-01-01

    Poliovirus has a single-stranded RNA genome of positive polarity that serves two essential functions at the start of the viral replication cycle in infected cells. First, it is translated to synthesize viral proteins and, second, it is copied by the viral polymerase to synthesize negative-strand RNA. We investigated these two reactions by using HeLa S10 in vitro translation-RNA replication reactions. Preinitiation RNA replication complexes were isolated from these reactions and then used to measure the sequential synthesis of negative- and positive-strand RNAs in the presence of different protein synthesis inhibitors. Puromycin was found to stimulate RNA replication overall. In contrast, RNA replication was inhibited by diphtheria toxin, cycloheximide, anisomycin, and ricin A chain. Dose-response experiments showed that precisely the same concentration of a specific drug was required to inhibit protein synthesis and to either stimulate or inhibit RNA replication. This suggested that the ability of these drugs to affect RNA replication was linked to their ability to alter the normal clearance of translating ribosomes from the input viral RNA. Consistent with this idea was the finding that the protein synthesis inhibitors had no measurable effect on positive-strand synthesis in normal RNA replication complexes. In marked contrast, negative-strand synthesis was stimulated by puromycin and was inhibited by cycloheximide. Puromycin causes polypeptide chain termination and induces the dissociation of polyribosomes from mRNA. Cycloheximide and other inhibitors of polypeptide chain elongation “freeze” ribosomes on mRNA and prevent the normal clearance of ribosomes from viral RNA templates. Therefore, it appears that the poliovirus polymerase was not able to dislodge translating ribosomes from viral RNA templates and mediate the switch from translation to negative-strand synthesis. Instead, the initiation of negative-strand synthesis appears to be coordinately regulated

  19. Multiple sensors ensure guide strand selection in human RNAi pathways.

    PubMed

    Noland, Cameron L; Doudna, Jennifer A

    2013-05-01

    Small RNAs guide RNA-induced silencing complexes (RISCs) to bind to cognate mRNA transcripts and trigger silencing of protein expression during RNA interference (RNAi) in eukaryotes. A fundamental aspect of this process is the asymmetric loading of one strand of a short interfering RNA (siRNA) or microRNA (miRNA) duplex onto RISCs for correct target recognition. Here, we use a reconstituted system to determine the extent to which the core components of the human RNAi machinery contribute to RNA guide strand selection. We show that Argonaute2 (Ago2), the endonuclease that binds directly to siRNAs and miRNAs within RISC, has intrinsic but substrate-dependent RNA strand selection capability. This activity can be enhanced substantially when Ago2 is in complex with the endonuclease Dicer and the double-stranded RNA-binding proteins (dsRBPs)-trans-activation response (TAR) RNA-binding protein (TRBP) or protein activator of PKR (PACT). The extent to which human Dicer/dsRBP complexes contribute to strand selection is dictated by specific duplex parameters such as thermodynamics, 5' nucleotide identity, and structure. Surprisingly, our results also suggest that strand selection for some miRNAs is enhanced by PACT-containing complexes but not by those containing TRBP. Furthermore, overall mRNA targeting by miRNAs is disfavored for complexes containing TRBP but not PACT. These findings demonstrate that multiple proteins collaborate to ensure optimal strand selection in humans and reveal the possibility of delineating RNAi pathways based on the presence of TRBP or PACT.

  20. Assessing Disease and Mortality among Small Cetaceans Stranded at a World Heritage Site in Southern Brazil.

    PubMed

    Domiciano, Isabela G; Domit, Camila; Broadhurst, Matt K; Koch, Mariana S; Bracarense, Ana Paula F R L

    2016-01-01

    Cetaceans are considered environmental sentinels and their health often reflects either anthropogenic or natural spatio-temporal disturbances. This study investigated the pathological findings and mortality of small cetaceans with the aim of detecting hazards and monitoring health trends in a high-biodiversity area. Between 2007 and 2012, 218 stranded cetaceans were recorded on the Paraná coast, southern Brazil. Fifty-seven (26.1%) of these animals, including 50 Sotalia guianensis, 2 Pontoporia blainvillei, 2 Stenella frontalis, 1 Stenella longirostris, 1 Tursiops truncatus and 1 Globicephala melas were necropsied and samples were collected for histopathology. Causes of death were determined in 46 of the 57 (80.7%) animals and most (30 or 65.2%) were ascribed to anthropogenic activities, including fisheries bycatch (28/30) and trauma (2/30). The remaining 16 fatalities were considered natural, and attributed to pneumonia (10/16), emaciation (3/16), septicemia (1/16), neonatal pathology (1/16) and choking via food obstruction (1/16). Irrespective of the cause, bronchointerstitial pneumonia, associated with parasitism, lymphadenitis and membranous glomerulonephritis were common findings among all fatalities. These results suggest, that while anthropogenic activities are a leading cause of cetacean strandings in Paraná, underlying pre-existing diseases may contribute towards deaths. Although the studied area is considered a biosphere reserve by UNESCO, complex anthropogenic and natural interactions might be occurring, increasing cetacean susceptibility to hazards. This study may help facilitate developing an effective conservation plan for coastal cetaceans focusing on reducing fisheries interactions, habitat degradation and pollution as mechanisms for ultimately increasing species resilience.

  1. Assessing Disease and Mortality among Small Cetaceans Stranded at a World Heritage Site in Southern Brazil

    PubMed Central

    Domiciano, Isabela G.; Domit, Camila; Broadhurst, Matt K.; Koch, Mariana S.; Bracarense, Ana Paula F. R. L.

    2016-01-01

    Cetaceans are considered environmental sentinels and their health often reflects either anthropogenic or natural spatio-temporal disturbances. This study investigated the pathological findings and mortality of small cetaceans with the aim of detecting hazards and monitoring health trends in a high-biodiversity area. Between 2007 and 2012, 218 stranded cetaceans were recorded on the Paraná coast, southern Brazil. Fifty-seven (26.1%) of these animals, including 50 Sotalia guianensis, 2 Pontoporia blainvillei, 2 Stenella frontalis, 1 Stenella longirostris, 1 Tursiops truncatus and 1 Globicephala melas were necropsied and samples were collected for histopathology. Causes of death were determined in 46 of the 57 (80.7%) animals and most (30 or 65.2%) were ascribed to anthropogenic activities, including fisheries bycatch (28/30) and trauma (2/30). The remaining 16 fatalities were considered natural, and attributed to pneumonia (10/16), emaciation (3/16), septicemia (1/16), neonatal pathology (1/16) and choking via food obstruction (1/16). Irrespective of the cause, bronchointerstitial pneumonia, associated with parasitism, lymphadenitis and membranous glomerulonephritis were common findings among all fatalities. These results suggest, that while anthropogenic activities are a leading cause of cetacean strandings in Paraná, underlying pre-existing diseases may contribute towards deaths. Although the studied area is considered a biosphere reserve by UNESCO, complex anthropogenic and natural interactions might be occurring, increasing cetacean susceptibility to hazards. This study may help facilitate developing an effective conservation plan for coastal cetaceans focusing on reducing fisheries interactions, habitat degradation and pollution as mechanisms for ultimately increasing species resilience. PMID:26871703

  2. [The application of genome editing in identification of plant gene function and crop breeding].

    PubMed

    Xiangchun, Zhou; Yongzhong, Xing

    2016-03-01

    Plant genome can be modified via current biotechnology with high specificity and excellent efficiency. Zinc finger nucleases (ZFN), transcription activator-like effector nucleases (TALEN) and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9) system are the key engineered nucleases used in the genome editing. Genome editing techniques enable gene targeted mutagenesis, gene knock-out, gene insertion or replacement at the target sites during the endogenous DNA repair process, including non-homologous end joining (NHEJ) and homologous recombination (HR), triggered by the induction of DNA double-strand break (DSB). Genome editing has been successfully applied in the genome modification of diverse plant species, such as Arabidopsis thaliana, Oryza sativa, and Nicotiana tabacum. In this review, we summarize the application of genome editing in identification of plant gene function and crop breeding. Moreover, we also discuss the improving points of genome editing in crop precision genetic improvement for further study.

  3. The excluded DNA strand is SEW important for hexameric helicase unwinding.

    PubMed

    Carney, Sean M; Trakselis, Michael A

    2016-10-01

    Helicases are proposed to unwind dsDNA primarily by translocating on one strand to sterically exclude and separate the two strands. Hexameric helicases in particular have been shown to encircle one strand while physically excluding the other strand. In this article, we will detail experimental methods used to validate specific interactions with the excluded strand on the exterior surface of hexameric helicases. Both qualitative and quantitative methods are described to identify an excluded strand interaction, determine the exterior interacting residues, and measure the dynamics of binding. The implications of exterior interactions with the nontranslocating strand are discussed and include forward unwinding stabilization, regulation of the unwinding rate, and DNA damage sensing.

  4. Development and application of biological technologies in fish genetic breeding.

    PubMed

    Xu, Kang; Duan, Wei; Xiao, Jun; Tao, Min; Zhang, Chun; Liu, Yun; Liu, ShaoJun

    2015-02-01

    Fish genetic breeding is a process that remolds heritable traits to obtain neotype and improved varieties. For the purpose of genetic improvement, researchers can select for desirable genetic traits, integrate a suite of traits from different donors, or alter the innate genetic traits of a species. These improved varieties have, in many cases, facilitated the development of the aquaculture industry by lowering costs and increasing both quality and yield. In this review, we present the pertinent literatures and summarize the biological bases and application of selection breeding technologies (containing traditional selective breeding, molecular marker-assisted breeding, genome-wide selective breeding and breeding by controlling single-sex groups), integration breeding technologies (containing cross breeding, nuclear transplantation, germline stem cells and germ cells transplantation, artificial gynogenesis, artificial androgenesis and polyploid breeding) and modification breeding technologies (represented by transgenic breeding) in fish genetic breeding. Additionally, we discuss the progress our laboratory has made in the field of chromosomal ploidy breeding of fish, including distant hybridization, gynogenesis, and androgenesis. Finally, we systematically summarize the research status and known problems associated with each technology.

  5. Rapid cyling plant breeding in citrus

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Resistance or tolerance to huanglongbing (HLB) and other important traits have been identified in several citrus types and relatives and associated markers should be identified soon. What is urgently needed in addition is an accelerated strategy for citrus variety breeding. Identification and use of...

  6. A New Breed of Environmental Film

    ERIC Educational Resources Information Center

    Malamud, Randy

    2008-01-01

    In this article, the author reports how today's environmental film festivals feature a new breed of documentary that offer nuanced narratives about intricate technologies. The author relates that the environmental films he grew up with sedately depicted the quiet sublimity of the wilderness. Today's films, the author observes, aim far beyond a…

  7. Combination solar hothouse and silkworm breeding house

    SciTech Connect

    Vardiashvili, A.B.; Muradov, M.; Kim, V.D.

    1980-01-01

    The basic arrangement is shown for a combination silkworm breeding house and solar hothouse with subsoil irrigation and accumulation of heat; it employs a semicylindrical film covering. The process of accumulation of solar heat in the subsoil pebble stores, in water-heater banks, and in the soil is described.

  8. Breeding System of Ruellia succulenta Small (Acanthaceae)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This study examines the breeding system of Ruellia succulenta (Acanthaceae), an herbaceous perennial found in the pine rockland habitat of southern Florida. Hand pollination treatments were performed on 75 plants, 25 from each of three sites. Treatments applied to test plants included: 1) control ...

  9. Marketing potential of advanced breeding clones

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The accumulation of reducing sugars during cold storage of potato tubers is a serious and costly problem for producers and processors. The degree to which cultivars accumulate reducing sugars during storage determines their processing and market potential. Cultivars or advanced breeding lines with...

  10. Impacts of the USDA basic breeding program

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The USDAs basic sugarcane breeding program began in the mid 1950s with the objective of moving genes from wild sugarcane germplasm into commercial cane. Several releases have been made from this program, but it is a very long process. To date, the pedigree of seven commercial Louisiana varieties can...

  11. Impacts of the basic breeding program

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The USDAs basic sugarcane breeding program began in the mid 1950s with the objective of moving genes from wild sugarcane germplasm into commercial cane. Several releases have been made from this program, but it is a very long process. To date, the pedigree of seven commercial Louisiana varieties ca...

  12. Linkage Drag: Implication for Plant Breeding

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Linkage drag is commonly observed in plant breeding, yet the molecular mechanisms controlling this is unclear. The Pi-ta gene, a single copy gene near the centromere region of chromosome 12, confers resistance to races of Magnaporthe oryzae that contain AVR-Pita. The Pi-ta gene in Tetep has been su...

  13. Breeding for phytonutrient content; examples from watermelon

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Breeding for high phytonutrient fruits and vegetables can be a fairly straightforward endeavor when the compounds of interest produce a visible effect or the methods for quantifying the compounds simple and inexpensive. Lycopene in tomatoes and watermelon is one such compound, since the amount of r...

  14. Biotechnology and apple breeding in Japan

    PubMed Central

    Igarashi, Megumi; Hatsuyama, Yoshimichi; Harada, Takeo; Fukasawa-Akada, Tomoko

    2016-01-01

    Apple is a fruit crop of significant economic importance, and breeders world wide continue to develop novel cultivars with improved characteristics. The lengthy juvenile period and the large field space required to grow apple populations have imposed major limitations on breeding. Various molecular biological techniques have been employed to make apple breeding easier. Transgenic technology has facilitated the development of apples with resistance to fungal or bacterial diseases, improved fruit quality, or root stocks with better rooting or dwarfing ability. DNA markers for disease resistance (scab, powdery mildew, fire-blight, Alternaria blotch) and fruit skin color have also been developed, and marker-assisted selection (MAS) has been employed in breeding programs. In the last decade, genomic sequences and chromosome maps of various cultivars have become available, allowing the development of large SNP arrays, enabling efficient QTL mapping and genomic selection (GS). In recent years, new technologies for genetic improvement, such as trans-grafting, virus vectors, and genome-editing, have emerged. Using these techniques, no foreign genes are present in the final product, and some of them show considerable promise for application to apple breeding. PMID:27069388

  15. Breed differences in behavioural development in kittens.

    PubMed

    Marchei, P; Diverio, S; Falocci, N; Fatjó, J; Ruiz-de-la-Torre, J L; Manteca, X

    2009-03-23

    Differences in behaviour of pure breed cats have been suggested but not wholly investigated. Oriental/Siamese/Abyssinian (OSA) kittens (n=43) were weekly compared with Norwegian Forest (NFO) kittens (n=39) from the 4th to the 10th week of age in a repeated Open Field Test (OFT) paradigm. Heart rate (HR) and rectal temperature (RT) before and after the test, and behavioural responses during the OFT were recorded. Behaviours registered were analysed by focal animal sampling. Significant breed differences were found; cats of the northern zones (NFO) seem to develop earlier thermoregulatory abilities. Precocious opening of eyes, higher locomotion scores and longer time spent standing, observed in OSA kittens may indicate an earlier neurological development. Inter breed differences recorded for exploration and locomotion seem to indicate coping style divergences: in the OFT challenging situation OSA kittens presented higher emotional tachycardia and performed more passively, with a faster decline in exploration and locomotion scores. NFO kittens exerted a more active behaviour as they spent more time exploring the arena and in escape attempts. Notwithstanding OSA and NFO cat selection was mainly aimed to improve divergent morphological traits, some different behavioural and physiological traits seem to have been maintained or co-selected within each breed.

  16. Breeding lettuce for fresh-cut processing

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Lettuce is increasingly consumed in fresh-cut packaged salads. New cultivars specifically bred for this use can enhance production and processing efficiency and extend shelf life. Cultivars with novel head architectures and leaf traits are being released by private and public breeding programs with ...

  17. Recent advances in peanut breeding and genetics

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Most previous advances in peanut cultivar development have been made using conventional breeding methods for self-pollinated crops. Peanut has lagged behind many other crops on use of molecular genetic technology for cultivar development in part due to lack of investment, but also because of low le...

  18. Mary Bidwell Breed: The Educator as Dean.

    ERIC Educational Resources Information Center

    Fley, Jo Ann; Jaramillo, George R.

    1979-01-01

    Mary Bidwell Breed predicted that midwestern universities would probably "pass through a stage of educational development in which the liberal arts are entirely feminized, the men are entirely commercialized." We can appreciate how close she came to pinpointing trends which did not begin to be reversed until sixty years later.…

  19. Guayule: Culture, breeding and rubber production

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Pressure on worldwide Hevea rubber supplies and other factors are renewing interest in guayule rubber. The objective of this chapter is to review recent and past research dealing with guayule production, breeding, and product development. Production research continues to show that although guayule i...

  20. New Brahman breed improvement program at STARS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    At the USDA, ARS, Subtropical Agricultural Research Station (STARS) in Brooksville, Florida we have initiated a new ambitious research project that many believe will have a positive influence on the Brahman breed. This research was developed from a meeting held at STARS that included past and prese...

  1. Traditional breeding and cultivar development (potato)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Traditional breeding allows for the genetic ‘reshuffling’ of genes and their recombination into new genotypes that may carry the desired assemblage of resistance and agronomic traits necessary for release as a new cultivar. While molecular biology techniques can be useful for improving upon a weakne...

  2. Genomics to feed a switchgrass breeding program

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Development of improved cultivars is one of three pillars, along with sustainable production and efficient conversion, required for dedicated cellulosic bioenergy crops to succeed. Breeding new cultivars is a long, slow process requiring patience, dedication, and motivation to realize gains and adva...

  3. A brief genomic history of tomato breeding

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Here we report a brief genomic history of tomato breeding by analyzing the genomes of 360 diverse accessions collected all over the world. These included 333 accessions from the red fruited clade (S. pimpinellifolium, S. l. var. cerasiforme, and S. lycopersicum) that represent various geographical o...

  4. Sinking Coastal Cities

    NASA Astrophysics Data System (ADS)

    Erkens, G.; Stuurman, R.; De Lange, G.; Bucx, T.; Lambert, J.

    2014-12-01

    In many coastal cities land subsidence now exceeds absolute sea level rise up to a factor of ten. Without action, parts of Jakarta, Ho Chi Minh City, Bangkok and numerous other coastal cities will continue to sink, even below sea level. The ever increasing industrial and domestic demand for water in these cities results in excessive groundwater extraction, causing severe subsidence. In addition, coastal cities are often faced with larger natural subsidence, as they are built on thick sequences of soft soil. The impacts of subsidence are further exacerbated by climate-induced sea level rise. Land subsidence results in two types damage: foremost it increases flood vulnerability (frequency, inundation depth and duration of floods), with floods causing major economic damage and loss of lives. Secondly, differential land movement causes significant economic losses in the form of structural damage and high maintenance costs of roads and transportation networks, sewage systems, buildings and foundations. The total damage worldwide is estimated at billions of dollars annually. To survey the extent of groundwater associated subsidence, we conducted a quick-assessment of subsidence in a series of mega-cities (Jakarta, Ho Chi Minh City, Dhaka, New Orleans and Bangkok). For each city research questions included: what are the main causes, how much is the current subsidence rate and what are predictions, where are the vulnerable areas, what are the impacts and risks, how can adverse impacts can be mitigated or compensated for, and what governmental bodies are involved and responsible to act? Using the assessment, this paper discusses subsidence modelling and measurement results from the selected cities. The focus is on the importance of delayed settlement after increases in hydraulic heads, the role of the subsurface composition for subsidence rates and best practice solutions for subsiding cities. For the latter, urban (ground)water management, adaptive flood risk management

  5. Application of Genomic Tools in Plant Breeding

    PubMed Central

    Pérez-de-Castro, A.M.; Vilanova, S.; Cañizares, J.; Pascual, L.; Blanca, J.M.; Díez, M.J.; Prohens, J.; Picó, B.

    2012-01-01

    Plant breeding has been very successful in developing improved varieties using conventional tools and methodologies. Nowadays, the availability of genomic tools and resources is leading to a new revolution of plant breeding, as they facilitate the study of the genotype and its relationship with the phenotype, in particular for complex traits. Next Generation Sequencing (NGS) technologies are allowing the mass sequencing of genomes and transcriptomes, which is producing a vast array of genomic information. The analysis of NGS data by means of bioinformatics developments allows discovering new genes and regulatory sequences and their positions, and makes available large collections of molecular markers. Genome-wide expression studies provide breeders with an understanding of the molecular basis of complex traits. Genomic approaches include TILLING and EcoTILLING, which make possible to screen mutant and germplasm collections for allelic variants in target genes. Re-sequencing of genomes is very useful for the genome-wide discovery of markers amenable for high-throughput genotyping platforms, like SSRs and SNPs, or the construction of high density genetic maps. All these tools and resources facilitate studying the genetic diversity, which is important for germplasm management, enhancement and use. Also, they allow the identification of markers linked to genes and QTLs, using a diversity of techniques like bulked segregant analysis (BSA), fine genetic mapping, or association mapping. These new markers are used for marker assisted selection, including marker assisted backcross selection, ‘breeding by design’, or new strategies, like genomic selection. In conclusion, advances in genomics are providing breeders with new tools and methodologies that allow a great leap forward in plant breeding, including the ‘superdomestication’ of crops and the genetic dissection and breeding for complex traits. PMID:23115520

  6. Breeding productivity of Smith Island black ducks

    USGS Publications Warehouse

    Haramis, G.M.; Jorde, D.G.; Olsen, G.H.; Stotts, D.B.; Harrison, M.K.; Perry, M.C.

    2002-01-01

    We investigated the breeding performance of American black ducks (Anas rubripes) on Smith Island, Chesapeake Bay, to improve our understanding of island black duck breeding ecology and to make management recommendations to enhance productivity. During 1995-96, we implanted 56 female black ducks with 20-g radio transmitters and tracked 35 of the individuals through the breeding season to locate nests, determine nest fate, and identify brood habitat. We also increased preseason banding efforts and compared capture characteristics over 12 years with those from the Deal Island Wildlife Management Area, a banding site on the mainland of Tangier Sound. A low rate of nesting (37%), lack of renesting, and poor hatching success (31%) indicated that island salt marsh habitats present a harsh environment for breeding black ducks. Black ducks located 11 of 13 nests (85%) in black needlerush (Juncus roemerianus) marsh where they were vulnerable to flooding from extreme tides and to egg predators. No nests were found on forested tree hammocks, a feature that distinguishes Smith Island from nearby South Marsh and Bloodsworth Islands. Nest predators included red foxes (Vulpes vulpes), herring gulls (Larus argentams), fish crows (Corvus ossifragus), and, potentially, Norway rats (Rattus norvegicus). Unlike mainland red foxes, foxes radio tracked on Smith Island were found to be capable swimmers and effective low marsh predators. We found shoreline meadows of widgeon grass (Ruppia maritima) to be important foraging sites for black ducks and suspected that the virtual absence of fresh water in this high salinity environment (1217+ ppt) to incur some cost in terms of growth and survival of ducklings. Preseason bandings revealed a high proportion of banded adults and a strong positive correlation in age ratios with the Deal Island banding site. This latter finding strongly suggests a negative universal effect of storm tides on nest success for Tangier Sound black ducks. Management to

  7. Proceedings of a Workshop on Antarctic Meteorite Stranding Surfaces

    NASA Technical Reports Server (NTRS)

    Cassidy, W. A. (Editor); Whillans, I. M. (Editor)

    1990-01-01

    The discovery of large numbers of meteorites on the Antarctic Ice Sheet is one of the most exciting developments in polar science in recent years. The meteorites are found on areas of ice called stranding surfaces. Because of the sudden availability of hundreds, and then thousands, of new meteorite specimens at these sites, the significance of the discovery of meteorite stranding surfaces in Antarctica had an immediate and profound impact on planetary science, but there is also in this discovery an enormous, largely unrealized potential to glaciology for records of climatic and ice sheet changes. The glaciological interest derives from the antiquity of the ice in meteorite stranding surfaces. This exposed ice covers a range of ages, probably between zero and more than 500,000 years. The Workshop on Antarctic Meteorite Stranding Surfaces was convened to explore this potential and to devise a course of action that could be recommended to granting agencies. The workshop recognized three prime functions of meteorite stranding surfaces. They provide: (1) A proxy record of climatic change (i.e., a long record of climatic change is probably preserved in the exposed ice stratigraphy); (2) A proxy record of ice volume change; and (3) A source of unique nonterrestrial material.

  8. An intercalation-locked parallel-stranded DNA tetraplex

    PubMed Central

    Tripathi, Shailesh; Zhang, Daoning; Paukstelis, Paul J.

    2015-01-01

    DNA has proved to be an excellent material for nanoscale construction because complementary DNA duplexes are programmable and structurally predictable. However, in the absence of Watson–Crick pairings, DNA can be structurally more diverse. Here, we describe the crystal structures of d(ACTCGGATGAT) and the brominated derivative, d(ACBrUCGGABrUGAT). These oligonucleotides form parallel-stranded duplexes with a crystallographically equivalent strand, resulting in the first examples of DNA crystal structures that contains four different symmetric homo base pairs. Two of the parallel-stranded duplexes are coaxially stacked in opposite directions and locked together to form a tetraplex through intercalation of the 5′-most A–A base pairs between adjacent G–G pairs in the partner duplex. The intercalation region is a new type of DNA tertiary structural motif with similarities to the i-motif. 1H–1H nuclear magnetic resonance and native gel electrophoresis confirmed the formation of a parallel-stranded duplex in solution. Finally, we modified specific nucleotide positions and added d(GAY) motifs to oligonucleotides and were readily able to obtain similar crystals. This suggests that this parallel-stranded DNA structure may be useful in the rational design of DNA crystals and nanostructures. PMID:25628357

  9. Regulation of DNA strand exchange in homologous recombination.

    PubMed

    Holthausen, J Thomas; Wyman, Claire; Kanaar, Roland

    2010-12-10

    Homologous recombination, the exchange of DNA strands between homologous DNA molecules, is involved in repair of many structural diverse DNA lesions. This versatility stems from multiple ways in which homologous DNA strands can be rearranged. At the core of homologous recombination are recombinase proteins such as RecA and RAD51 that mediate homology recognition and DNA strand exchange through formation of a dynamic nucleoprotein filament. Four stages in the life cycle of nucleoprotein filaments are filament nucleation, filament growth, homologous DNA pairing and strand exchange, and filament dissociation. Progression through this cycle requires a sequence of recombinase-DNA and recombinase protein-protein interactions coupled to ATP binding and hydrolysis. The function of recombinases is controlled by accessory proteins that allow coordination of strand exchange with other steps of homologous recombination and that tailor to the needs of specific aberrant DNA structures undergoing recombination. Accessory proteins are also able to reverse filament formation thereby guarding against inappropriate DNA rearrangements. The dynamic instability of the recombinase-DNA interactions allows both positive and negative action of accessory proteins thereby ensuring that genome maintenance by homologous recombination is not only flexible and versatile, but also accurate.

  10. Proceedings of a Workshop on Antarctic Meteorite Stranding Surfaces

    SciTech Connect

    Cassidy, W.A.; Whillans, I.M.

    1990-08-01

    The discovery of large numbers of meteorites on the Antarctic Ice Sheet is one of the most exciting developments in polar science in recent years. The meteorites are found on areas of ice called stranding surfaces. Because of the sudden availability of hundreds, and then thousands, of new meteorite specimens at these sites, the significance of the discovery of meteorite stranding surfaces in Antarctica had an immediate and profound impact on planetary science, but there is also in this discovery an enormous, largely unrealized potential to glaciology for records of climatic and ice sheet changes. The glaciological interest derives from the antiquity of the ice in meteorite stranding surfaces. This exposed ice covers a range of ages, probably between zero and more than 500,000 years. The Workshop on Antarctic Meteorite Stranding Surfaces was convened to explore this potential and to devise a course of action that could be recommended to granting agencies. The workshop recognized three prime functions of meteorite stranding surfaces. They provide: (1) A proxy record of climatic change (i.e., a long record of climatic change is probably preserved in the exposed ice stratigraphy); (2) A proxy record of ice volume change; and (3) A source of unique nonterrestrial material.

  11. Heavy ion induced double strand breaks in bacteria and bacteriophages

    NASA Astrophysics Data System (ADS)

    Micke, U.; Schäfer, M.; Anton, A.; Horneck, G.; Bücker, H.

    DNA damage induced by heavy ions in bacterial cells and bacteriophages such as Bacillus subtilis, E. coli and Bacteriophage Tl were investigated by analyzing the double strand breaks in the chromosomal DNA. This kind of lesion is considered as one of the main reasons for lethal events. To analyze double strand breaks in long molecules of DNA - up to some Mbp in length - the technique of pulse field agarose gel electrophoresis has been used. This allows the detection of one double strand break per genome. Cell lysis and DNA isolation were performed in small agarose blocks directly. This procedure secured minimum DNA destruction by shearing forces. After running a gel, the DNA was stained with ethidium bromide. The light intensity of ethidium bromide fluorescence for both the outcoming (running) DNA and the remaining intact DNA were measured by scanning. The mean number of double strand breaks was calculated by determining the quotient of these intensities. Strand break induction after heavy ion and X-ray irradiation was compared.

  12. Mass stranding of wedge-tailed shearwater chicks in Hawaii

    USGS Publications Warehouse

    Work, T.M.; Rameyer, R.A.

    1999-01-01

    Unusual numbers of wedge-tailed shearwater (Puffinus pacificus) chicks stranded on Oahu (Hawaii, USA) in 1994. Compared to healthy wedge-tailed shearwater (WTSW) chicks, stranded chicks were underweight, dehydrated, leukopenic, lymphopenic, eosinopenic, and heterophilic; some birds were toxemic and septic. Stranded chicks also were hypoglycemic and had elevated aspartate amino transferase levels. Most chicks apparently died from emaciation, dehydration, or bacteremia. Because many birds with bacteremia also had severe necrosis of the gastrointestinal (GI) mucosa associated with bacteria, we suspect the GI tract to be the source of disseminated bacterial infection. The identity of the bacteria was not confirmed. The daily number of chicks stranded was significantly related to average wind speeds, and the mortality coincided with the fledging period for WTSW. Strong southeasterly winds were a distinguishing meteorologic factor in 1994 and contributed to the distribution of stranded chicks on Oahu. More objective data on WTSW demographics would enhance future efforts to determine predisposing causes of WTSW wrecks and their effects on seabird colonies.

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

    NASA Technical Reports Server (NTRS)

    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.

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

    PubMed

    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.

  15. Hydration of single-stranded phosphodiester and phosphorothioate oligodeoxyribonucleotides.

    PubMed Central

    White, A P; Reeves, K K; Snyder, E; Farrell, J; Powell, J W; Mohan, V; Griffey, R H

    1996-01-01

    Infrared spectroscopy was used to identify hydration-sensitive structural differences between single- stranded phosphorothioate (PS) and phosphodiester (PO) oligodeoxyribonucleotides. Spectra were recorded in the mid-infrared region, 500-1800 cm-1, at relative humidities between 0 and 98%; the PS and PO spectra are substantially different. The hydration effects on spectral bands in these single-stranded oligodeoxyribonucleotides is markedly different from such behavior in double- and triple-stranded oligodeoxyribonucleotides. A strong absorption occurs at 656 cm-1 in the phosphorothioate sample which is completely absent from the PO spectra. Gravimetric measurements were carried out on one PS and one PO sample to monitor and confirm hydration. The calculated BET adsorption constants [Brunauer, S., Emmett, RH. and Teller, E. (1938) J. Am. Chem. Soc., 60, 309-319] are 1.2 and 1.4 water molecules per nucleotide in the first hydration layer of PS and PO respectively. While the gravimetric data indicate that the single-stranded oligodeoxyribonucleotides hydrate very similarly to duplex DNA, the mid-infrared conformational marker bands are strikingly different from those observed for duplex DNA. In particular, the Vas of the phosphate group (PO2) at 1222 cm-1 in the single-stranded PO spectra is independent of relative humidity. PMID:8774910

  16. Mass stranding of wedge-tailed shearwater chicks in Hawaii.

    PubMed

    Work, T M; Rameyer, R A

    1999-07-01

    Unusual numbers of wedge-tailed shearwater (Puffinus pacificus) chicks stranded on Oahu (Hawaii, USA) in 1994. Compared to healthy wedge-tailed shearwater (WTSW) chicks, stranded chicks were underweight, dehydrated, leukopenic, lymphopenic, eosinopenic, and heterophilic; some birds were toxemic and septic. Stranded chicks also were hypoglycemic and had elevated aspartate amino transferase levels. Most chicks apparently died from emaciation, dehydration, or bacteremia. Because many birds with bacteremia also had severe necrosis of the gastrointestinal (GI) mucosa associated with bacteria, we suspect the GI tract to be the source of disseminated bacterial infection. The identity of the bacteria was not confirmed. The daily number of chicks stranded was significantly related to average wind speeds, and the mortality coincided with the fledging period for WTSW. Strong southeasterly winds were a distinguishing meteorologic factor in 1994 and contributed to the distribution of stranded chicks on Oahu. More objective data on WTSW demographics would enhance future efforts to determine predisposing causes of WTSW wrecks and their effects on seabird colonies.

  17. An intercalation-locked parallel-stranded DNA tetraplex

    DOE PAGES

    Tripathi, S.; Zhang, D.; Paukstelis, P. J.

    2015-01-27

    DNA has proved to be an excellent material for nanoscale construction because complementary DNA duplexes are programmable and structurally predictable. However, in the absence of Watson–Crick pairings, DNA can be structurally more diverse. Here, we describe the crystal structures of d(ACTCGGATGAT) and the brominated derivative, d(ACBrUCGGABrUGAT). These oligonucleotides form parallel-stranded duplexes with a crystallographically equivalent strand, resulting in the first examples of DNA crystal structures that contains four different symmetric homo base pairs. Two of the parallel-stranded duplexes are coaxially stacked in opposite directions and locked together to form a tetraplex through intercalation of the 5'-most A–A base pairs betweenmore » adjacent G–G pairs in the partner duplex. The intercalation region is a new type of DNA tertiary structural motif with similarities to the i-motif. 1H–1H nuclear magnetic resonance and native gel electrophoresis confirmed the formation of a parallel-stranded duplex in solution. Finally, we modified specific nucleotide positions and added d(GAY) motifs to oligonucleotides and were readily able to obtain similar crystals. This suggests that this parallel-stranded DNA structure may be useful in the rational design of DNA crystals and nanostructures.« less

  18. An intercalation-locked parallel-stranded DNA tetraplex

    SciTech Connect

    Tripathi, S.; Zhang, D.; Paukstelis, P. J.

    2015-01-27

    DNA has proved to be an excellent material for nanoscale construction because complementary DNA duplexes are programmable and structurally predictable. However, in the absence of Watson–Crick pairings, DNA can be structurally more diverse. Here, we describe the crystal structures of d(ACTCGGATGAT) and the brominated derivative, d(ACBrUCGGABrUGAT). These oligonucleotides form parallel-stranded duplexes with a crystallographically equivalent strand, resulting in the first examples of DNA crystal structures that contains four different symmetric homo base pairs. Two of the parallel-stranded duplexes are coaxially stacked in opposite directions and locked together to form a tetraplex through intercalation of the 5'-most A–A base pairs between adjacent G–G pairs in the partner duplex. The intercalation region is a new type of DNA tertiary structural motif with similarities to the i-motif. 1H–1H nuclear magnetic resonance and native gel electrophoresis confirmed the formation of a parallel-stranded duplex in solution. Finally, we modified specific nucleotide positions and added d(GAY) motifs to oligonucleotides and were readily able to obtain similar crystals. This suggests that this parallel-stranded DNA structure may be useful in the rational design of DNA crystals and nanostructures.

  19. Oligoarginine Peptides Slow Strand Annealing and Assist Nonenzymatic RNA Replication

    PubMed Central

    Jia, Tony Z.; Fahrenbach, Albert C.; Kamat, Neha P.; Adamala, Katarzyna P.; Szostak, Jack W.

    2016-01-01

    The nonenzymatic replication of RNA is thought to have been a critical process required for the origin of life. One unsolved difficulty with nonenzymatic RNA replication is that template-directed copying of RNA results in a double-stranded product; following strand separation, rapid strand reannealing outcompetes slow nonenzymatic template copying, rendering multiple rounds of RNA replication impossible. Here we show that oligoarginine peptides slow the annealing of complementary oligoribonucleotides by up to several thousand-fold; however, short primers and activated monomers can still bind to template strands, and template-directed primer extension can still occur within a phase-separated condensed state, or coacervate. Furthermore, we show that within this phase, partial template copying occurs even in the presence of full-length complementary strands. This method for enabling further rounds of replication suggests one mechanism by which short, non-coded peptides could have enhanced early cellular fitness, potentially explaining how longer, coded peptides, i.e. proteins, came to prominence in modern biology. PMID:27657866

  20. Strand displacement synthesis by yeast DNA polymerase ε

    PubMed Central

    Ganai, Rais A.; Zhang, Xiao-Ping; Heyer, Wolf-Dietrich; Johansson, Erik

    2016-01-01

    DNA polymerase ε (Pol ε) is a replicative DNA polymerase with an associated 3′–5′ exonuclease activity. Here, we explored the capacity of Pol ε to perform strand displacement synthesis, a process that influences many DNA transactions in vivo. We found that Pol ε is unable to carry out extended strand displacement synthesis unless its 3′–5′ exonuclease activity is removed. However, the wild-type Pol ε holoenzyme efficiently displaced one nucleotide when encountering double-stranded DNA after filling a gap or nicked DNA. A flap, mimicking a D-loop or a hairpin structure, on the 5′ end of the blocking primer inhibited Pol ε from synthesizing DNA up to the fork junction. This inhibition was observed for Pol ε but not with Pol δ, RB69 gp43 or Pol η. Neither was Pol ε able to extend a D-loop in reconstitution experiments. Finally, we show that the observed strand displacement synthesis by exonuclease-deficient Pol ε is distributive. Our results suggest that Pol ε is unable to extend the invading strand in D-loops during homologous recombination or to add more than two nucleotides during long-patch base excision repair. Our results support the hypothesis that Pol ε participates in short-patch base excision repair and ribonucleotide excision repair. PMID:27325747

  1. Scenarios for coastal vulnerability assessment

    USGS Publications Warehouse

    Nicholls, Robert J.; Woodroffe, Colin D.; Burkett, Virginia; Hay, John; Wong, Poh Poh; Nurse, Leonard; Wolanski, Eric; McLusky, Donald S.

    2011-01-01

    Coastal vulnerability assessments tend to focus mainly on climate change and especially on sea-level rise. Assessment of the influence of nonclimatic environmental change or socioeconomic change is less well developed and these drivers are often completely ignored. Given that the most profound coastal changes of the twentieth century due to nonclimate drivers are likely to continue through the twenty-first century, this is a major omission. It may result in not only overstating the importance of climate change but also overlooking significant interactions of climate change and other drivers. To support the development of policies relating to climate change and coastal management, integrated assessments of climatic change in coastal areas are required, including the effects of all the relevant drivers. This chapter explores the development of scenarios (or "plausible futures") of relevant climate and nonclimate drivers that can be used for coastal analysis, with an emphasis on the nonclimate drivers. It shows the importance of analyzing the impacts of climate change and sea-level rise in a broader context of coastal change and all its drivers. This will improve the analysis of impacts, key vulnerabilities, and adaptation needs and, hence, inform climate and coastal policy. Stakeholder engagement is important in the development of scenarios, and the underlying assumptions need to be explicit, transparent, and open to scientific debate concerning their uncertainties/realism and likelihood.

  2. Simulation of charge breeding of rubidium using Monte Carlo charge breeding code and generalized ECRIS model

    SciTech Connect

    Zhao, L.; Cluggish, B.; Kim, J. S.; Pardo, R.; Vondrasek, R.

    2010-02-15

    A Monte Carlo charge breeding code (MCBC) is being developed by FAR-TECH, Inc. to model the capture and charge breeding of 1+ ion beam in an electron cyclotron resonance ion source (ECRIS) device. The ECRIS plasma is simulated using the generalized ECRIS model which has two choices of boundary settings, free boundary condition and Bohm condition. The charge state distribution of the extracted beam ions is calculated by solving the steady state ion continuity equations where the profiles of the captured ions are used as source terms. MCBC simulations of the charge breeding of Rb+ showed good agreement with recent charge breeding experiments at Argonne National Laboratory (ANL). MCBC correctly predicted the peak of highly charged ion state outputs under free boundary condition and similar charge state distribution width but a lower peak charge state under the Bohm condition. The comparisons between the simulation results and ANL experimental measurements are presented and discussed.

  3. Atlantic coastal plain

    SciTech Connect

    Libby-French, J.; Amato, R.V.

    1981-10-01

    Exploratory drilling in the Atlantic coastal plain region decreased in 1980. Seven wells were drilled, five of which were completed, for a total footage of 80,968 ft (24,679 m). Six of the wells were located in the Baltimore Canyon Trough, and one was located in the Southeast Georgia Embayment. No exploratory wells were drilled in the Georges Bank Basin or in the onshore portion of this region in 1980. Tenneco and Exxon reported gas shows in two wells in the Baltimore Canyon Trough; the remaining completed wells were reported as dry holes. No lease sales were held in 1980, but two sales are scheduled for 1981 in the Middle and South Atlantic. 1 figure, 2 tables.

  4. Coastal Research Imaging Spectrometer

    NASA Technical Reports Server (NTRS)

    2002-01-01

    The Coastal Research Imaging Spectrometer (CRIS) is an airborne remote-sensing system designed specifically for research on the physical, chemical, and biological characteristics of coastal waters. The CRIS includes a visible-light hyperspectral imaging subsystem for measuring the color of water, which contains information on the biota, sediment, and nutrient contents of the water. The CRIS also includes an infrared imaging subsystem, which provides information on the temperature of the water. The combination of measurements enables investigation of biological effects of both natural and artificial flows of water from land into the ocean, including diffuse and point-source flows that may contain biological and/or chemical pollutants. Temperature is an important element of such measurements because temperature contrasts can often be used to distinguish among flows from different sources: for example, a sewage outflow could manifest itself in spectral images as a local high-temperature anomaly.anomaly. Both the visible and infrared subsystems scan in "pushbroom" mode: that is, an aircraft carrying the system moves along a ground track, the system is aimed downward, and image data are acquired in acrosstrack linear arrays of pixels. Both subsystems operate at a frame rate of 30 Hz. The infrared and visible-light optics are adjusted so that both subsystems are aimed at the same moving swath, which has across-track angular width of 15. Data from the infrared and visible imaging subsystems are stored in the same file along with aircraft-position data acquired by a Global Positioning System receiver. The combination of the three sets of data is used to construct infrared and hyperspectral maps of scanned areas shown.

  5. Not All Mosquitoes Need Standing Water to Breed

    MedlinePlus

    ... fullstory_164604.html Not All Mosquitoes Need Standing Water to Breed: Study Many of the critters lay ... curbing mosquitoes is to eliminate pools of standing water where they might breed. But new research on ...

  6. Ecophysiological response of Adelie penguins facing an experimental increase in breeding constraints.

    PubMed

    Beaulieu, M; Spée, M; Lazin, D; Ropert-Coudert, Y; le Maho, Y; Ancel, A; Raclot, T

    2010-01-01

    Foraging strategies play a key role in breeding effort. Little is known, however, about their connection with hormonal and nutritional states, especially when breeding constraints vary. Here, we experimentally increased foraging costs and thus breeding constraints by handicapping Adélie penguins (Pygoscelis adeliae) with dummy devices representing 3-4% of the penguins' cross-sectional area. We examined food-related stress (via plasma corticosterone concentration) and nutritional state (via metabolite levels). Concurrently, we investigated the use of ecological niches via the isotopic signature of red blood cells indicating the trophic position (delta(15)N) and the spatial distribution (delta(13)C) of penguins. Handicapped birds performed approximately 70% longer foraging trips and lost approximately 60% more body mass than controls and their partners. However, corticosterone levels and the nutritional state were unchanged. The isotopic signature revealed that males and females differed in their foraging behaviour: upper trophic levels contributed more in the males' diet, who foraged in more pelagic areas. Handicapped and partner birds adopted the same strategy at sea: a shift towards higher delta(13)C values suggested that they foraged in more coastal areas than controls. This change in foraging decisions may optimize feeding time by decreasing travelling time. This may partly compensate for the presumed lower foraging efficiency of handicapped birds and for the energetic debt of their partners who had to fast approximately 70% longer on the nest. We propose that this flexible use of ecological niches may allow birds facing increased breeding constraints to avoid chronic stress and to minimize the impact on their body condition.

  7. Genetic trends and breed overlap derived from multiple-breed genetic evaluations of beef cattle for growth traits.

    PubMed

    Sullivan, P G; Wilton, J W; Miller, S P; Banks, L R

    1999-08-01

    Genetic evaluations for a multiple-breed population of beef cattle were used to estimate genetic trends for five breeds, and genetic differences and overlap among 14 breeds. Genetic evaluations studied were for direct contributions to birth weight, gain from birth to 200 and 365 d, and maternal contribution to gain from birth to 200 d. Almost all genetic trends were positive, but the magnitude of the trends varied among breeds. Trends were nonlinear between 1985 and 1995 for most breed and trait combinations. The rates of increase in genetic trends were generally higher for the lighter weight breeds, and lighter weight breeds had faster growth rate genetic trends at 1995 than the heavier breeds. Genetic trend estimates for yearling gain at 1995 were 2.46, 2.23, 1.73, 1.70, and 1.46 kg/yr for Angus, Hereford, Limousin, Charolais, and Simmental, respectively. Corresponding birth weight genetic trends were .130, .226, .049, .130, and .048 kg/yr. Mean genetic differences between breeds have been decreasing in magnitude due to these differences in genetic trends between heavier and lighter breeds. Genetic variation for the traits studied seemed to be greater within than between breeds for calves born and cows calving between 1993 and 1995. Genetic trends at 1995 suggest that ratios of within:between breed variation will increase and that across-breed genetic improvement initiatives for growth traits will become more important in the future.

  8. COASTAL 2000 MONITORING IN THE NORTHEAST

    EPA Science Inventory

    Coastal 2000 is a partnership between the U.S. Environmental Protection Agency and coastal states to develop a national coastal monitoring program. The Northeast portion of Coastal 2000 includes states from Delaware to Maine. This joint effort will provide a nationwide assessment...

  9. COASTAL 2000 MONITORING IN THE NORTHEAST

    EPA Science Inventory

    Coastal 2000 is a partnership between the U.S. Environmental Protection Agency and coastal states to develop a national coastal monitoring program. This joint effort will permit for the first time regional comparisons of coastal resource conditions. It will also provide a nationw...

  10. Coastal adaptation with ecological engineering

    NASA Astrophysics Data System (ADS)

    Cheong, So-Min; Silliman, Brian; Wong, Poh Poh; van Wesenbeeck, Bregje; Kim, Choong-Ki; Guannel, Greg

    2013-09-01

    The use of combined approaches to coastal adaptation in lieu of a single strategy, such as sea-wall construction, allows for better preparation for a highly uncertain and dynamic coastal environment. Although general principles such as mainstreaming and no- or low-regret options exist to guide coastal adaptation and provide the framework in which combined approaches operate, few have examined the interactions, synergistic effects and benefits of combined approaches to adaptation. This Perspective provides three examples of ecological engineering -- marshes, mangroves and oyster reefs -- and illustrates how the combination of ecology and engineering works.

  11. Coastal Erosion along Monterey Bay.

    DTIC Science & Technology

    1985-03-01

    RD-Al155 61@ COASTAL EROSION ALONG MONTEREY BAY(U) NAVAL1/ A8POSTGRADUATE SCHOOL MONTEREY CA A I SKLAVIDIS El AL. UNCLASSIFIED F/G 8/3 NmIIhllllllll...RESOLUTION TEST CHART NAVAL POSTGRADUATE SCHOOL Monterey, California 0 to Lfl IC)I I ~JUN 2 71985 THESIS~ COASTAL EROSION ALONG MONTEREY BAY by Anastasios I...PERIOD COVERED Master’s thesis; COASTAL EROSION ALONG MONTEREY BAY March 1985 4. PERFORMING ORG. REPORT NUMBIER 7. AUTMOR(s) 6. CONTRACT OR GRANT NUMBER(a

  12. Genetic diversity analyses reveal first insights into breed-specific selection signatures within Swiss goat breeds.

    PubMed

    Burren, A; Neuditschko, M; Signer-Hasler, H; Frischknecht, M; Reber, I; Menzi, F; Drögemüller, C; Flury, C

    2016-12-01

    We used genotype data from the caprine 50k Illumina BeadChip for the assessment of genetic diversity within and between 10 local Swiss goat breeds. Three different cluster methods allowed the goat samples to be assigned to the respective breed groups, whilst the samples of Nera Verzasca and Tessin Grey goats could not be differentiated from each other. The results of the different genetic diversity measures show that Appenzell, Toggenburg, Valais and Booted goats should be prioritized in future conservation activities. Furthermore, we examined runs of homozygosity (ROH) and compared genomic inbreeding coefficients based on ROH (FROH ) with pedigree-based inbreeding coefficients (FPED ). The linear relationship between FROH and FPED was confirmed for goats by including samples from the three main breeds (Saanen, Chamois and Toggenburg goats). FROH appears to be a suitable measure for describing levels of inbreeding in goat breeds with missing pedigree information. Finally, we derived selection signatures between the breeds. We report a total of 384 putative selection signals. The 25 most significant windows contained genes known for traits such as: coat color variation (MITF, KIT, ASIP), growth (IGF2, IGF2R, HRAS, FGFR3) and milk composition (PITX2). Several other putative genes involved in the formation of populations, which might have been selected for adaptation to the alpine environment, are highlighted. The results provide a contemporary background for the management of genetic diversity in local Swiss goat breeds.

  13. Variation in the prion protein sequence in Dutch goat breeds.

    PubMed

    Windig, J J; Hoving, R A H; Priem, J; Bossers, A; van Keulen, L J M; Langeveld, J P M

    2016-10-01

    Scrapie is a neurodegenerative disease occurring in goats and sheep. Several haplotypes of the prion protein increase resistance to scrapie infection and may be used in selective breeding to help eradicate scrapie. In this study, frequencies of the allelic variants of the PrP gene are determined for six goat breeds in the Netherlands. Overall frequencies in Dutch goats were determined from 768 brain tissue samples in 2005, 766 in 2008 and 300 in 2012, derived from random sampling for the national scrapie surveillance without knowledge of the breed. Breed specific frequencies were determined in the winter 2013/2014 by sampling 300 breeding animals from the main breeders of the different breeds. Detailed analysis of the scrapie-resistant K222 haplotype was carried out in 2014 for 220 Dutch Toggenburger goats and in 2015 for 942 goats from the Saanen derived White Goat breed. Nine haplotypes were identified in the Dutch breeds. Frequencies for non-wild type haplotypes were generally low. Exception was the K222 haplotype in the Dutch Toggenburger (29%) and the S146 haplotype in the Nubian and Boer breeds (respectively 7 and 31%). The frequency of the K222 haplotype in the Toggenburger was higher than for any other breed reported in literature, while for the White Goat breed it was with 3.1% similar to frequencies of other Saanen or Saanen derived breeds. Further evidence was found for the existence of two M142 haplotypes, M142 /S240 and M142 /P240 . Breeds vary in haplotype frequencies but frequencies of resistant genotypes are generally low and consequently selective breeding for scrapie resistance can only be slow but will benefit from animals identified in this study. The unexpectedly high frequency of the K222 haplotype in the Dutch Toggenburger underlines the need for conservation of rare breeds in order to conserve genetic diversity rare or absent in other breeds.

  14. Habitat use and movement of the endangered Arroyo Toad (Anaxyrus californicus) in coastal southern California

    USGS Publications Warehouse

    Gallegos, Elizabeth; Lyren, Lisa M.; Lovich, Robert E.; Mitrovich, Milan J.; Fisher, Robert N.

    2011-01-01

    Information on the habitat use and movement patterns of Arroyo Toads (Anaxyrus californicus) is limited. The temporal and spatial characteristics of terrestrial habitat use, especially as it relates to upland use in coastal areas of the species' range, are poorly understood. We present analyses of radiotelemetry data from 40 individual adult toads tracked at a single site in coastal southern California from March through November of 2004. We quantify adult Arroyo Toad habitat use and movements and interpret results in the context of their life history. We show concentrated activity by both male and female toads along stream terraces during and after breeding, and, although our fall sample size is low, the continued presence of adult toads in the floodplain through the late fall. Adult toads used open sandy flats with sparse vegetation. Home-range size and movement frequency varied as a function of body mass. Observed spatial patterns of movement and habitat use both during and outside of the breeding period as well as available climatological data suggest that overwintering of toads in floodplain habitats of near-coastal areas of southern California may be more common than previously considered. If adult toads are not migrating out of the floodplain at the close of the breeding season but instead overwinter on stream terraces in near-coastal areas, then current management practices that assume toad absence from floodplain habitats may be leaving adult toads over-wintering on stream terraces vulnerable to human disturbance during a time of year when Arroyo Toad mortality is potentially highest.

  15. Habitat use and movement of the endangered Arroyo Toad (Anaxyrus californicus) in coastal southern California

    USGS Publications Warehouse

    Mitrovich, M.J.; Gallegos, E.A.; Lyren, L.M.; Lovich, R.E.; Fisher, R.N.

    2011-01-01

    Information on the habitat use and movement patterns of Arroyo Toads (Anaxyrus californicus) is limited. The temporal and spatial characteristics of terrestrial habitat use, especially as it relates to upland use in coastal areas of the species' range, are poorly understood. We present analyses of radiotelemetry data from 40 individual adult toads tracked at a single site in coastal southern California from March through November of 2004. We quantify adult Arroyo Toad habitat use and movements and interpret results in the context of their life history. We show concentrated activity by both male and female toads along stream terraces during and after breeding, and, although our fall sample size is low, the continued presence of adult toads in the floodplain through the late fall. Adult toads used open sandy flats with sparse vegetation. Home-range size and movement frequency varied as a function of body mass. Observed spatial patterns of movement and habitat use both during and outside of the breeding period as well as available climatological data suggest that overwintering of toads in floodplain habitats of near-coastal areas of southern California may be more common than previously considered. If adult toads are not migrating out of the floodplain at the close of the breeding season but instead overwinter on stream terraces in near-coastal areas, then current management practices that assume toad absence from floodplain habitats may be leaving adult toads over-wintering on stream terraces vulnerable to human disturbance during a time of year when Arroyo Toad mortality is potentially highest. ?? 2011 Society for the Study of Amphibians and Reptiles.

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

    PubMed Central

    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

  17. Plant somatic hybrid cytoplasmic DNA characterization by single-strand conformation polymorphism.

    PubMed

    Olivares-Fuster, Oscar; Hernández-Garrido, María; Guerri, José; Navarro, Luis

    2007-06-01

    Unlike maternal inheritance in sexual hybridization, plant somatic hybridization allows transfer, mixing and recombination of cytoplasmic genomes. In addition to the use of somatic hybridization in plant breeding programs, application of this unique tool should lead to a better understanding of the roles played by the chloroplastic and mitochondrial genomes in determining agronomically important traits. The nucleotide sequences of cytoplasmic genomes are much more conserved than those of nuclear genomes. Cytoplasmic DNA composition in somatic hybrids is commonly elucidated either by length polymorphism analysis of restricted genome regions amplified with universal primers (PCR-RF) or by hybridization of total DNA using universal cytoplasmic probes. In this study, we demonstrate that single-stranded conformational polymorphism (SSCP) analysis is a powerful, quick and easy alternative method for cytoplasmic DNA characterization of somatic hybrids, especially for mitochondrial DNA. The technique allows detection of polymorphisms based on both size and sequence of amplified targets. Twenty-two species of the subfamily Aurantioideae were analyzed with eight universal primers (four from chloroplastic and four from mitochondrial regions). Differences in chloroplastic DNA composition were scored in 98% of all possible two-parent combinations, and different mitochondrial DNA profiles were found in 87% of them. Analysis by SSCP was also successfully used to characterize somatic hybrids and cybrids obtained by fusion of Citrus sinensis (L.) Osb. and C. excelsa Wester protoplasts.

  18. Autumn orientation behaviour of paddyfield warblers, Acrocephalus agricola, from a recently expanded breeding range on the western Black Sea coast.

    PubMed

    Zehtindjiev, Pavel; Ilieva, Mihaela; Akesson, Susanne

    2010-10-01

    The paddyfield warbler, Acrocephalus agricola, has extended its breeding range from Central Asia to the western Black Sea coast. The Balkan population offers a unique chance to test the effect of breeding range expansion on the genetically programmed migratory direction. We studied 21 paddyfield warblers at Durankulak Lake, NE Bulgaria, by recording their autumn migratory orientation in circular orientation cages. Our data show that the preferred migratory orientation is directed along a NE-SW axis. Paddyfield warblers seem to avoid direct crossing of the Black Sea by following the western coast. The mean bearing was parallel to the nearest coastline and corresponds to the direction of the historical breeding range expansion of the species. In our experiment many individuals showed south-western orientation in autumn, a course which would potentially lead the birds to exploratory movements outside the current breeding range. An axial orientation response has been often shown in circular cage tests, and can be due to factors such as coastal orientation or reverse orientation triggered by the physiological condition of some individuals. However, it might also be one of the driving mechanisms for range expansion. Hence, we can expect the future expansion of Balkan paddyfield warblers to continue towards south-west.

  19. Patterns of spatial and temporal distribution of humpback whales at the southern limit of the Southeast Pacific breeding area.

    PubMed

    Guidino, Chiara; Llapapasca, Miguel A; Silva, Sebastian; Alcorta, Belen; Pacheco, Aldo S

    2014-01-01

    Understanding the patterns of spatial and temporal distribution in threshold habitats of highly migratory and endangered species is important for understanding their habitat requirements and recovery trends. Herein, we present new data about the distribution of humpback whales (Megaptera novaeangliae) in neritic waters off the northern coast of Peru: an area that constitutes a transitional path from cold, upwelling waters to warm equatorial waters where the breeding habitat is located. Data was collected during four consecutive austral winter/spring seasons from 2010 to 2013, using whale-watching boats as platforms for research. A total of 1048 whales distributed between 487 groups were sighted. The spatial distribution of humpbacks resembled the characteristic segregation of whale groups according to their size/age class and social context in breeding habitats; mother and calf pairs were present in very shallow waters close to the coast, while dyads, trios or more whales were widely distributed from shallow to moderate depths over the continental shelf break. Sea surface temperatures (range: 18.2-25.9°C) in coastal waters were slightly colder than those closer to the oceanic realm, likely due to the influence of cold upwelled waters from the Humboldt Current system. Our results provide new evidence of the southward extension of the breeding region of humpback whales in the Southeast Pacific. Integrating this information with the knowledge from the rest of the breeding region and foraging grounds would enhance our current understanding of population dynamics and recovery trends of this species.

  20. Patterns of Spatial and Temporal Distribution of Humpback Whales at the Southern Limit of the Southeast Pacific Breeding Area

    PubMed Central

    Guidino, Chiara; Llapapasca, Miguel A.; Silva, Sebastian; Alcorta, Belen; Pacheco, Aldo S.

    2014-01-01

    Understanding the patterns of spatial and temporal distribution in threshold habitats of highly migratory and endangered species is important for understanding their habitat requirements and recovery trends. Herein, we present new data about the distribution of humpback whales (Megaptera novaeangliae) in neritic waters off the northern coast of Peru: an area that constitutes a transitional path from cold, upwelling waters to warm equatorial waters where the breeding habitat is located. Data was collected during four consecutive austral winter/spring seasons from 2010 to 2013, using whale-watching boats as platforms for research. A total of 1048 whales distributed between 487 groups were sighted. The spatial distribution of humpbacks resembled the characteristic segregation of whale groups according to their size/age class and social context in breeding habitats; mother and calf pairs were present in very shallow waters close to the coast, while dyads, trios or more whales were widely distributed from shallow to moderate depths over the continental shelf break. Sea surface temperatures (range: 18.2–25.9°C) in coastal waters were slightly colder than those closer to the oceanic realm, likely due to the influence of cold upwelled waters from the Humboldt Current system. Our results provide new evidence of the southward extension of the breeding region of humpback whales in the Southeast Pacific. Integrating this information with the knowledge from the rest of the breeding region and foraging grounds would enhance our current understanding of population dynamics and recovery trends of this species. PMID:25391137

  1. Maternal genealogical patterns of chicken breeds sampled in Europe.

    PubMed

    Lyimo, C M; Weigend, A; Msoffe, P L; Hocking, P M; Simianer, H; Weigend, S

    2015-08-01

    The aim of this study was to investigate the maternal genealogical pattern of chicken breeds sampled in Europe. Sequence polymorphisms of 1256 chickens of the hypervariable region (D-loop) of mitochondrial DNA (mtDNA) were used. Median-joining networks were constructed to establish evolutionary relationships among mtDNA haplotypes of chickens, which included a wide range of breeds with different origin and history. Chicken breeds which have had their roots in Europe for more than 3000 years were categorized by their founding regions, encompassing Mediterranean type, East European type and Northwest European type. Breeds which were introduced to Europe from Asia since the mid-19th century were classified as Asian type, and breeds based on crossbreeding between Asian breeds and European breeds were classified as Intermediate type. The last group, Game birds, included fighting birds from Asia. The classification of mtDNA haplotypes was based on Liu et al.'s (2006) nomenclature. Haplogroup E was the predominant clade among the European chicken breeds. The results showed, on average, the highest number of haplotypes, highest haplotype diversity, and highest nucleotide diversity for Asian type breeds, followed by Intermediate type chickens. East European and Northwest European breeds had lower haplotype and nucleotide diversity compared to Mediterranean, Intermediate, Game and Asian type breeds. Results of our study support earlier findings that chicken breeds sampled in Europe have their roots in the Indian subcontinent and East Asia. This is consistent with historical and archaeological evidence of chicken migration routes to Europe.

  2. Genomic predictions for crossbreds from all-breed data

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genomic predictions of transmitting ability (GPTAs) for crossbred animals were computed from marker effects of 5 dairy breeds weighted by each breed’s genomic contribution to the crossbreds. Estimates of genomic breed composition are labeled breed base representation (BBR) and are reported since May...

  3. 50 CFR 15.26 - Approval of cooperative breeding programs.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 50 Wildlife and Fisheries 1 2012-10-01 2012-10-01 false Approval of cooperative breeding programs... WILDLIFE AND PLANTS WILD BIRD CONSERVATION ACT Permits and Approval of Cooperative Breeding Programs § 15.26 Approval of cooperative breeding programs. Upon receipt of a complete application, the...

  4. 50 CFR 15.26 - Approval of cooperative breeding programs.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 50 Wildlife and Fisheries 1 2014-10-01 2014-10-01 false Approval of cooperative breeding programs... WILDLIFE AND PLANTS WILD BIRD CONSERVATION ACT Permits and Approval of Cooperative Breeding Programs § 15.26 Approval of cooperative breeding programs. Upon receipt of a complete application, the...

  5. 50 CFR 15.26 - Approval of cooperative breeding programs.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 50 Wildlife and Fisheries 1 2011-10-01 2011-10-01 false Approval of cooperative breeding programs... WILDLIFE AND PLANTS WILD BIRD CONSERVATION ACT Permits and Approval of Cooperative Breeding Programs § 15.26 Approval of cooperative breeding programs. Upon receipt of a complete application, the...

  6. 50 CFR 15.26 - Approval of cooperative breeding programs.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 50 Wildlife and Fisheries 1 2013-10-01 2013-10-01 false Approval of cooperative breeding programs... WILDLIFE AND PLANTS WILD BIRD CONSERVATION ACT Permits and Approval of Cooperative Breeding Programs § 15.26 Approval of cooperative breeding programs. Upon receipt of a complete application, the...

  7. Simultaneous binding to the tracking strand, displaced strand and the duplex of a DNA fork enhances unwinding by Dda helicase.

    PubMed

    Aarattuthodiyil, Suja; Byrd, Alicia K; Raney, Kevin D

    2014-10-01

    Interactions between helicases and the tracking strand of a DNA substrate are well-characterized; however, the role of the displaced strand is a less understood characteristic of DNA unwinding. Dda helicase exhibited greater processivity when unwinding a DNA fork compared to a ss/ds DNA junction substrate. The lag phase in the unwinding progress curve was reduced for the forked DNA compared to the ss/ds junction. Fewer kinetic steps were required to unwind the fork compared to the ss/ds junction, suggesting that binding to the fork leads to disruption of the duplex. DNA footprinting confirmed that interaction of Dda with a fork leads to two base pairs being disrupted whereas no disruption of base pairing was observed with the ss/ds junction. Neutralization of the phosphodiester backbone resulted in a DNA-footprinting pattern similar to that observed with the ss/ds junction, consistent with disruption of the interaction between Dda and the displaced strand. Several basic residues in the 1A domain which were previously proposed to bind to the incoming duplex DNA were replaced with alanines, resulting in apparent loss of interaction with the duplex. Taken together, these results suggest that Dda interaction with the tracking strand, displaced strand and duplex coordinates DNA unwinding.

  8. Mammalian Ino80 mediates double-strand break repair through its role in DNA end strand resection.

    PubMed

    Gospodinov, Anastas; Vaissiere, Thomas; Krastev, Dragomir B; Legube, Gaëlle; Anachkova, Boyka; Herceg, Zdenko

    2011-12-01

    Chromatin modifications/remodeling are important mechanisms by which cells regulate various functions through providing accessibility to chromatin DNA. Recent studies implicated INO80, a conserved chromatin-remodeling complex, in the process of DNA repair. However, the precise underlying mechanism by which this complex mediates repair in mammalian cells remains enigmatic. Here, we studied the effect of silencing of the Ino80 subunit of the complex on double-strand break repair in mammalian cells. Comet assay and homologous recombination repair reporter system analyses indicated that Ino80 is required for efficient double-strand break repair. Ino80 association with chromatin surrounding double-strand breaks suggested the direct involvement of INO80 in the repair process. Ino80 depletion impaired focal recruitment of 53BP1 but did not impede Rad51 focus formation, suggesting that Ino80 is required for the early steps of repair. Further analysis by using bromodeoxyuridine (BrdU)-labeled single-stranded DNA and replication protein A (RPA) immunofluorescent staining showed that INO80 mediates 5'-3' resection of double-strand break ends.

  9. Retroviral nucleocapsid proteins possess potent nucleic acid strand renaturation activity.

    PubMed Central

    Dib-Hajj, F.; Khan, R.; Giedroc, D. P.

    1993-01-01

    The nucleocapsid protein (NC) is the major genomic RNA binding protein that plays integral roles in the structure and replication of all animal retroviruses. In this report, select biochemical properties of recombinant Mason-Pfizer monkey virus (MPMV) and HIV-1 NCs are compared. Evidence is presented that two types of saturated Zn2 NC-polynucleotide complexes can be formed under conditions of low [NaCl] that differ in apparent site-size (n = 8 vs. n = 14). The formation of one or the other complex appears dependent on the molar ratio of NC to RNA nucleotide with the putative low site-size mode apparently predominating under conditions of protein excess. Both MPMV and HIV-1 NCs kinetically facilitate the renaturation of two complementary DNA strands, suggesting that this is a general property of retroviral NCs. NC proteins increase the second-order rate constant for renaturation of a 149-bp DNA fragment by more than four orders of magnitude over that obtained in the absence of protein at 37 degrees C. The protein-assisted rate is 100-200-fold faster than that obtained at 68 degrees C, 1 M NaCl, solution conditions considered to be optimal for strand renaturation. Provided that sufficient NC is present to coat all strands, the presence of 400-1,000-fold excess nonhomologous DNA does not greatly affect the reaction rate. The HIV-1 NC-mediated renaturation reaction functions stoichiometrically, requiring a saturated strand of DNA nucleotide:NC ratio of about 7-8, rather than 14. Under conditions of less protein, the rate acceleration is not realized. The finding of significant nucleic acid strand renaturation activity may have important implications for various events of reverse transcription particularly in initiation and cDNA strand transfer. PMID:8443601

  10. Coastal biodiversity and bioresources: variation and sustainability

    NASA Astrophysics Data System (ADS)

    Qin, Song; Liu, Zhengyi; Yu, Roger Ziye

    2016-03-01

    The 1st International Coastal Biology Congress (1st ICBC) was held in Yantai, China, in Sep. 26-30, 2014. Eighteen manuscripts of the meeting presentations were selected in this special issue. According to the four themes set in the ICBC meeting, this special issue include four sections, i.e., Coastal Biodiversity under Global Change, Adaptation and Evolution to Special Environment of Coastal Zone, Sustainable Utilization of Coastal Bioresources, and Coastal Biotechnology. Recent advances in these filed are presented.

  11. Electrodeless dielectrophoresis of single- and double-stranded DNA.

    PubMed Central

    Chou, Chia-Fu; Tegenfeldt, Jonas O; Bakajin, Olgica; Chan, Shirley S; Cox, Edward C; Darnton, Nicholas; Duke, Thomas; Austin, Robert H

    2002-01-01

    Dielectrophoretic trapping of molecules is typically carried out using metal electrodes to provide high field gradients. In this paper we demonstrate dielectrophoretic trapping using insulating constrictions at far lower frequencies than are feasible with metallic trapping structures because of water electrolysis. We demonstrate that electrodeless dielectrophoresis (EDEP) can be used for concentration and patterning of both single-strand and double-strand DNA. A possible mechanism for DNA polarization in ionic solution is discussed based on the frequency, viscosity, and field dependence of the observed trapping force. PMID:12324434

  12. Crystal structure of four-stranded Oxytricha telomeric DNA

    NASA Technical Reports Server (NTRS)

    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.

  13. DNA double-strand break repair in a cellular context.

    PubMed

    Shibata, A; Jeggo, P A

    2014-05-01

    Substantial insight into the mechanisms responding to DNA double-strand breaks has been gained from molecular, biochemical and structural approaches. Attention is now focusing on understanding the interplay between the pathways, how they interface through the cell cycle and the communication with other DNA transactions, such as replication and transcription. Understanding these aspects will facilitate an assessment of how cancer cells have modified these processes to achieve unlimited proliferative capacity and adaptability, and pave the way to identify targets suitable for therapy. Here, we briefly overview the processes responding to double-strand breaks and discuss our current understanding of their interplay in a cellular context.

  14. Apparatus and method for fabricating multi-strand superconducting cable

    DOEpatents

    Borden, Albert R.

    1986-01-01

    Multi-strand superconducting cables adapted to be used, for example, to wind a magnet is fabricated by directing wire strands inwardly from spools disposed on the perimeter of a rotating disk and wrapping them diagonally around a tapered mandrel with a flattened cross-sectional shape with a core having a wedge-shaped channel. As the cable is pulled axially, flexibly coupled wedge-shaped pieces are continuously passed through the channel in the mandrel and inserted into the cable as an internal support therefor.

  15. Partners and pathwaysrepairing a double-strand break.

    PubMed

    Haber, J E

    2000-06-01

    Double-strand chromosome breaks can arise in a number of ways, by ionizing radiation, by spontaneous chromosome breaks during DNA replication, or by the programmed action of endonucleases, such as in meiosis. Broken chromosomes can be repaired either by one of several homologous recombination mechanisms, or by a number of nonhomologous repair processes. Many of these pathways compete actively for the repair of a double-strand break. Which of these repair pathways is used appears to be regulated developmentally, genetically and during the cell cycle.

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

    SciTech Connect

    1994-12-13

    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.

  17. Interaction of DAPI with double-stranded ribonucleic acids.

    PubMed Central

    Manzini, G; Xodo, L; Barcellona, M L; Quadrifoglio, F

    1985-01-01

    The interaction of DAPI with natural and synthetic double-stranded polyribonucleotides was studied with different optical and calorimetric methods. The results were similar to those obtained previously with double-stranded polydeoxynucleotides, i.e. two interaction modes, the first of which shows high affinity for AU clusters and consequent strong fluorescence enhancement. The results suggest caution in the use of DAPI as selective fluorescent staining agent for DNA in the presence of RNA. A narrow groove binding model with hydrogen bonds between DAPI and AU pairs is proposed. An intercalation mechanism can be excluded because of the non planarity of DAPI molecule. PMID:4080554

  18. Three dimensional FEM quench simulations of superconducting strands

    SciTech Connect

    Yamada, Ryuji; Wake, Masayoshi; /KEK, Tsukuba

    2005-09-01

    The detailed phenomena in quench starting of Nb{sub 3}Sn strands are simulated in 3-D and in time using ANSYS and FEMLAB programs. The current sharing between the superconductor and copper stabilizer in strands at the beginning of a quench was studied and displayed in time. The differences in copper configuration and RRR value of copper were found to have large effect to the stability and quench propagation velocity. The MPZ theory was found to be effective for 3D multifilament situation.

  19. North Atlantic Coastal Tidal Wetlands

    EPA Science Inventory

    The book chapter provides college instructors, researchers, graduate and advanced undergraduate students, and environmental consultants interested in wetlands with foundation information on the ecology and conservation concerns of North Atlantic coastal wetlands. The book c...

  20. CLASSIFICATION FRAMEWORK FOR COASTAL SYSTEMS

    EPA Science Inventory

    U.S. Environmental Protection Agency. Classification Framework for Coastal Systems. EPA/600/R-04/061. U.S. Environmental Protection Agency, National Health and Environmental Effects Research Laboratory, Atlantic Ecology Division, Narragansett, RI, Gulf Ecology Division, Gulf Bree...

  1. Human disturbance and stage-specific habitat requirements influence snowy plover site occupancy during the breeding season

    PubMed Central

    Webber, Alyson F; Heath, Julie A; Fischer, Richard A

    2013-01-01

    Habitat use has important consequences for avian reproductive success and survival. In coastal areas with recreational activity, human disturbance may limit use of otherwise suitable habitat. Snowy plovers Charadrius nivosus have a patchy breeding distribution along the coastal areas on the Florida Panhandle, USA. Our goal was to determine the relative effects of seasonal human disturbance and habitat requirements on snowy plover habitat use. We surveyed 303 sites for snowy plovers, human disturbance, and habitat features between January and July 2009 and 2010. We made multiple visits during three different sampling periods that corresponded to snowy plover breeding: pre-breeding, incubation, and brood-rearing and used multi-season occupancy models to examine whether human disturbance, habitat features, or both influenced site occupancy, colonization (probability of transition from an unoccupied site to an occupied site), and extinction (probability of transition from an occupied site to an unoccupied site). Snowy plover site occupancy and colonization was negatively associated with human disturbance and site extinction was positively associated with human disturbance. Interdune vegetation had a negative effect on occupancy and colonization, indicating that plovers were less likely to use areas with uniform, dense vegetation among dunes. Also, dune shape, beach debris, and access to low-energy foraging areas influenced site occupancy, colonization, and extinction. Plovers used habitat based on beach characteristics that provided stage-specific resource needs; however, human disturbance was the strongest predictor of site occupancy. In addition, vegetation plantings used to enhance dune rehabilitation may negatively impact plover site occupancy. Management actions that decrease human disturbance, such as symbolic fencing and signage, may increase the amount of breeding habitat available to snowy plovers on the Florida Panhandle and in other areas with high human

  2. Africa Partnership Station: Coastal Processes

    DTIC Science & Technology

    2012-09-30

    interactions between UG and USGS included ongoing assessments of historical imagery and maps for coastal change analyses and a visit to WHOI by a UG...data, and technical training sessions. In February of 2009, Cheryl Hapke of the U.S. Geological Survey ( USGS ) and Andrew Ashton of the Woods Hole...discussions of coastal processes and the impacts of shoreline-erosion mitigation measures - Collecting ground-penetrating Radar ( GPR ) data in beach ridge

  3. 76 FR 39857 - Alaska Coastal Management Program Withdrawal From the National Coastal Management Program Under...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-07-07

    ... National Oceanic Atmospheric Administration Alaska Coastal Management Program Withdrawal From the National... Coastal Resource Management (OCRM), National Ocean Service (NOS), National Oceanic Atmospheric... withdrawal from participation in the CZMA's National Coastal Management Program. The CZMA Federal...

  4. Breeding bird response to juniper woodland expansion

    USGS Publications Warehouse

    Rosenstock, Steven S.; van Riper, Charles

    2001-01-01

    In recent times, pinyon (Pinus spp.)-juniper (Juniperus spp.) woodlands have expanded into large portions of the Southwest historically occupied by grassland vegetation. From 1997a??1998, we studied responses of breeding birds to one-seed juniper (J. monosperma) woodland expansion at 2 grassland study areas in northern Arizona. We sampled breeding birds in 3 successional stages along a grassland-woodland gradient: un-invaded grassland, grassland undergoing early stages of juniper establishment, and developing woodland. Species composition varied greatly among successional stages and was most different between endpoints of the gradient. Ground-nesting grassland species predominated in uninvaded grassland but declined dramatically as tree density increased. Tree- and cavity-nesting species increased with tree density and were most abundant in developing woodland. Restoration of juniper-invaded grasslands will benefit grassland-obligate birds and other wildlife.

  5. Breeding population inventories and measures of recruitment

    USGS Publications Warehouse

    Cowardin, L.M.; Blohm, R.J.; Batt, D.J.; Afton, A.D.; Anderson, M.G.; Ankney, C.D.; Johnson, D.H.; Kadlec, J.A.; Krapu, G.L.

    1992-01-01

    In this chapter we review the techniques used to measure two important parameters of waterfowl populations, size of breeding population and recruitment. If waterfowl are to be managed toward goals defined in terms of population sizes such as those in the recently signed North American Waterfowl Management Plan (U.S. Fish and Wildlife Service [USFWS] and Canadian Wildlife Service [CWS] 1986), there must be some measure of population size for the various species. Waterfowl managers usually measure population size during the breeding season, although for some species and in some areas winter inventories may be used. Population size is a function of natality and mortality. Other chapters in this volume deal in detail with the biology of those processes. This chapter discusses procedural aspects of measurement and reviews some of the operational systems that have been used to estimate population size and recruitment, especially in North America.

  6. Coastal Research Imaging Spectrometer

    NASA Technical Reports Server (NTRS)

    Lucey, Paul G.; Williams, Timothy; Horton, Keith A.

    2004-01-01

    The Coastal Research Imaging Spectrometer (CRIS) is an airborne remote sensing system designed specifically for research on the physical, chemical, and biological characteristics of coastal waters. The CRIS includes a visible-light hyperspectral imaging subsystem for measuring the color of water, which contains information on the biota, sediment, and nutrient contents of the water. The CRIS also includes an infrared imaging subsystem, which provides information on the temperature of the water. The combination of measurements enables investigation of biological effects of both natural and artificial flows of water from land into the ocean, including diffuse and point-source flows that may contain biological and/or chemical pollutants. Temperature is an important element of such measurements because temperature contrasts can often be used to distinguish among flows from different sources: for example, a sewage outflow could manifest itself in spectral images as a local high-temperature anomaly. Both the visible and infrared subsystems scan in pushbroom mode: that is, an aircraft carrying the system moves along a ground track, the system is aimed downward, and image data are acquired in across-track linear arrays of pixels. Both subsystems operate at a frame rate of 30 Hz. The infrared and visible-light optics are adjusted so that both subsystems are aimed at the same moving swath, which has across-track angular width of 15 . Data from the infrared and visible imaging subsystems are stored in the same file along with aircraft- position data acquired by a Global Positioning System receiver. The combination of the three sets of data is used to construct infrared and hyperspectral maps of scanned areas (see figure). The visible subsystem is based on a grating spectrograph and a rapid-readout charge-coupled-device camera. Images of the swatch are acquired in 256 spectral bands at wavelengths from 400 to 800 nm. The infrared subsystem, which is sensitive in a single

  7. A drifter for measuring water turbidity in rivers and coastal oceans.

    PubMed

    Marchant, Ross; Reading, Dean; Ridd, James; Campbell, Sean; Ridd, Peter

    2015-02-15

    A disposable instrument for measuring water turbidity in rivers and coastal oceans is described. It transmits turbidity measurements and position data via a satellite uplink to a processing server. The primary purpose of the instrument is to help document changes in sediment runoff from river catchments in North Queensland, Australia. The 'river drifter' is released into a flooded river and drifts downstream to the ocean, measuring turbidity at regular intervals. Deployment in the Herbert River showed a downstream increase in turbidity, and thus suspended sediment concentration, while for the Johnstone River there was a rapid reduction in turbidity where the river entered the sea. Potential stranding along river banks is a limitation of the instrument. However, it has proved possible for drifters to routinely collect data along 80 km of the Herbert River. One drifter deployed in the Fly River, Papua New Guinea, travelled almost 200 km before stranding.

  8. Determinants of breeding distributions of ducks

    USGS Publications Warehouse

    Johnson, D.H.; Grier, J.W.

    1988-01-01

    The settling of breeding habitat by migratory waterfowl is a topic of both theoretical and practical interest. We use the results of surveys conducted annually during 1955-81 in major breeding areas to examine the factors that affect the distributions of 10 common North American duck species. Three patterns of settling are described: homing, opportunistic, and flexible. Homing is generally more pronounced among species that use more stable (more predictable) wetlands, such as the redhead (Aythya americana), canvasback (A. valisineria), lesser scaup (A. affinis), mallard (Anas platyrhynchos), gadwall (Anas strepera), and northern shoveler (Anas clypeata). Opportunistic settling is more prevalent among species that use less stable (less predictable) wetlands, such as northern pintail (Anas acuta) and blue-winged teal (Anas discors). Flexible settling is exhibited to various degrees by most species.The 10 species are shown to fall along a natural ordination reflecting different life history characteristics. Average values of indices of r- and K-selection indicated that pintail, mallard, blue-winged teal, and shoveler have the most features associated with unstable or unpredictable environments. Gadwall, American wigeon (Anas americana), and green-winged teal (Anas crecca) were intermediate, and attributes of the diving ducks were associated with the use of stable or predictable environments.Some species--notably mallard, gadwall, blue-winged teal, redhead, and canvasback--tend to fill available breeding habitat first in the central portions of their range, and secondly in peripheral areas. Other species--American wigeon, green-winged teal, northern shoveler, northern pintail, and lesser scaup--fill their habitat in the order it is encountered during spring migration.Age and sex classes within species vary in their settling pattern. Some of this variation can be predicted from the mating systems of ducks in which breeding females, especially successful ones, have a

  9. Polybrominated diphenyl ethers in pinnipeds stranded along the southern California coast.

    PubMed

    Meng, Xiang-Zhou; Blasius, Mary Ellen; Gossett, Richard W; Maruya, Keith A

    2009-10-01

    Little to no information exists for polybrominated diphenyl ethers (PBDEs) in marine mammals frequenting the highly urbanized southern California (USA) coast. Fourteen PBDE congeners were determined by GC-ECNI-MS in blubber of pinnipeds stranded locally between 1994 and 2006. Total PBDE concentrations (SigmaPBDE) in California sea lion (n = 63) ranged from 0.04 to 33.7 microg/g wet weight (mean: 5.24 microg/g). To our knowledge, these are the highest reported PBDE levels in marine mammals to date. By comparison, mean SigmaPBDE in Pacific harbor seals (n = 9) and northern elephant seals (n = 16) were 0.96 and 0.09 microg/g, respectively. PBDEs in adult males were higher than for adult females, however, no age class differences or temporal trends were observed. As the first PBDE data reported for marine mammals in this region, the elevated levels underscore the need for additional studies on the sources, temporal trends, and potential effects of PBDEs in highly urbanized coastal zones.

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

    PubMed Central

    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 single-stranded RNA changes during exponential and stationary phases of cell growth in a fashion consistent with a viral replicative intermediate or mRNA. The single-stranded species does not appear to be polyadenylated. Images PMID:2798099

  11. Breeding ecology of the Puaiohi (Myadestes palmeri)

    USGS Publications Warehouse

    Snetsinger, T.J.; Herrmann, C.M.; Holmes, D.E.; Hayward, C.D.; Fancy, S.G.

    2005-01-01

    We studied the breeding ecology of the critically endangered Puaiohi (Myadestes palmeri), a poorly known Hawaiian thrush endemic to the island of Kauai. From 1996 through 1998, we monitored 96 active nests over the course of three breeding seasons. Mean clutch size was 2.0, and pairs produced an average of 1.5 fledglings/successful nest. Pairs renested after failure and some raised multiple broods. The mean annual reproductive effort was 2.1 nesting attempts/territory, and pairs produced a mean 1.1 fledglings/attempt. Large differences in nesting effort and productivity occurred among years, with mean number of fledglings/territory ranging from 0.4 to 4.9. Predation by owls (probably Short-eared Owls, Asia flammeus) and introduced rats (probably black rats, Rattus rattus) accounted for most nest failures. The presence of non-breeding floaters in the population and their largely unsuccessful attempts to gain territories in the study area suggest that the population is near carrying capacity. The high reproductive potential of the Puaiohi may help explain its persistence despite the species' historical rarity.

  12. Reproductive senescence in a cooperatively breeding mammal.

    PubMed

    Sharp, Stuart P; Clutton-Brock, Tim H

    2010-01-01

    1. Senescence (or 'ageing') is a widespread and important process in wild animal populations, but variation in ageing patterns within and between species is poorly understood. 2. In cooperatively breeding species, the costs of reproduction are shared between breeders and one or more helpers. The effects of ageing in breeders may therefore be moderated by the presence of helpers, but there have been very few studies of senescence patterns in natural populations of cooperative breeders. 3. Here, we use 13 years of data from a long-term study population of wild meerkats (Suricata suricatta) to investigate age-related changes in several traits known to be key components of reproductive success in females of this species. 4. Four of the six traits studied exhibited significant declines with age, indicating senescence. Litter size, the number of litters produced per year and the number of pups that survived to emergence from the natal burrow per year all increased with female age up to a peak at c. 4 years, and declined steeply thereafter; the mean pup weight at emergence in a given litter declined steadily from age zero. 5. These results provide the first evidence of reproductive senescence in a wild population of a cooperatively breeding vertebrate. Breeding success declined with age despite the sharing of reproductive costs in this species, but further study is needed to investigate whether helping affects other aspects of senescence, including survival.

  13. The development of beef breeding bulls.

    PubMed

    Engelken, T J

    2008-08-01

    Management of the bull battery will have a dramatic impact on profitability of the cow/calf enterprise. It is critical that young bulls be selected and developed to maximize longevity and productivity for the eventual buyer. Bulls must be structurally sound, healthy, and have adequate libido in order to service the required number of females. Once bulls complete their first breeding season, special care must be taken in order to ensure that they recover and regain needed body condition and pass a bull breeding soundness examination (BBSE). Mature bulls that have reached their genetic potential for growth require less intensive management, but the health program and annual BBSE cannot be overlooked. Mature bulls are also more likely to carry venereal disease and should be screened according to local disease incidence and state regulations. All bulls, regardless of age, should be observed early during the breeding season to ensure that they are physically capable of mounting and servicing females. The establishment of a complete management program, especially for young bulls, is essential to ensure that ranch resources are used efficiently, including maintenance of a high level of reproductive performance of the cow herd.

  14. Bull breeding soundness evaluation in Southern Africa.

    PubMed

    Irons, P C; Nöthling, J O; Bertschinger, H J

    2007-10-01

    The motivation for and process leading up to the publication of a new bull breeding soundness certification standard endorsed by the South African Veterinary Association is described. The veterinary certificate of bull breeding soundness and explanatory notes and minimum standards are shown. The first component of the certificate is a declaration by the veterinarian that the bull complies with the minimum standards set for examinations for the selected purpose, these being for use as a natural service sire, as a donor of semen for distribution, and for insurance purposes. This is followed by the details of the bull and owner, and a list of the recommended examinations and tests for the bull with provision for which were performed. Certificates are available in book form with the explanatory notes and minimum standards on the reverse, and a carbon copy which remains in the book. The clarity and ease of completion of the document are regarded as being positive features. Bulls are either classified as breeding sound or not, with no actual parameters indicated on the document and no certificate issued for those which do not meet the set criteria. Contact details of the parties involved are shown on the certificate to allow for communication as a means of avoiding disputes.

  15. The northeastern states' waterfowl breeding population survey

    USGS Publications Warehouse

    Heusmann, H.W.; Sauer, J.R.

    2000-01-01

    Efforts to tailor waterfowl hunting regulations to conditions in the Atlantic Flyway have been hampered by lack of information on local breeding populations. The Atlantic Flyway Council's technical section voted at its 1987 winter meeting (Atlantic Flyway Council Technical Section, Toronto, Canada) to establish a regional waterfowl breeding survey. Consequently, an annual survey was started in 1989 and further refined in 1993 using results from 1989 to 1992. During 1993-1997, annual spring surveys of more than 1,450 randomly selected 1-km2 plots, stratified by physiographic strata, were conducted in the Atlantic Flyway from New Hampshire to Virginia to estimate breeding populations of mallards (Arias platyrhynchos), American black ducks (A. rubripes), wood ducks (Aix sponsa), and Canada geese (Branta canadensis). Ground crews systematically surveyed all potential waterfowl habitat for these species in each plot. The adjusted mean mallard pair estimate over the 5-year period was 375,962 (range 310,299-415,182, mean SE 25,761) for the region surveyed. The estimate for black duck pairs was 31,1 54 (range 27,164'37,521, mean SE 4,978), and for wood duck pairs it was 240,473 (range 218,959-281,916, mean SE 25,408). Total number of Canada geese increased from 526,663 in 1993 to 892,278 in 1997. Population estimates for other species had unacceptably large standard errors.

  16. Detection of Breeding Blankets Using Antineutrinos

    NASA Astrophysics Data System (ADS)

    Cogswell, Bernadette; Huber, Patrick

    2016-03-01

    The Plutonium Management and Disposition Agreement between the United States and Russia makes arrangements for the disposal of 34 metric tons of excess weapon-grade plutonium. Under this agreement Russia plans to dispose of its excess stocks by processing the plutonium into fuel for fast breeder reactors. To meet the disposition requirements this fuel would be burned while the fast reactors are run as burners, i.e., without a natural uranium blanket that can be used to breed plutonium surrounding the core. This talk discusses the potential application of antineutrino monitoring to the verification of the presence or absence of a breeding blanket. It is found that a 36 kg antineutrino detector, exploiting coherent elastic neutrino-nucleus scattering and made of silicon, could determine the presence of a breeding blanket at a liquid sodium cooled fast reactor at the 95% confidence level within 90 days. Such a detector would be a novel non-intrusive verification tool and could present a first application of coherent elastic neutrino-nucleus scattering to a real-world challenge.

  17. The North American Breeding Bird Survey

    USGS Publications Warehouse

    Bystrak, D.; Ralph, C. John; Scott, J. Michael

    1981-01-01

    A brief history of the North American Breeding Bird Survey (BBS) and a discussion of the technique are presented. The approximately 2000 random roadside routes conducted yearly during the breeding season throughout North America produce an enormous bank of data on distribution and abundance of breeding birds with great potential use. Data on about one million total birds of 500 species per year are on computer tape to facilitate accessibility and are available to any serious investigator. The BBS includes the advantages of wide geographic coverage, sampling of most habitat types, standardization of data collection, and a relatively simple format. The Survey is limited by placement of roads (e.g., marshes and rugged mountainous areas are not well sampled), traffic noise interference in some cases and preference of some bird species for roadside habitats. These and other problems and biases of the BBS are discussed. The uniformity of the technique allows for detecting changes in populations and for creation of maps of relative abundance. Examples of each are presented.

  18. Breeding quantum error-correcting codes

    SciTech Connect

    Dong Ying; Hu Dan; Yu Sixia

    2010-02-15

    The stabilizer code, one major family of quantum error-correcting codes (QECC), is specified by the joint eigenspace of a commuting set of Pauli observables. It turns out that noncommuting sets of Pauli observables can be used to construct more efficient QECCs, such as the entanglement-assisted QECCs, which are built directly from any linear classical codes whose detailed properties are needed to determine the parameters of the resulting quantum codes. Here we propose another family of QECCs, namely, the breeding QECCs, that also employ noncommuting sets of Pauli observables and can be built from any classical additive codes, either linear or nonlinear, with the advantage that their parameters can be read off directly from the corresponding classical codes. Besides, since nonlinear codes are generally more efficient than linear codes, our breeding codes have better parameters than those codes built from linear codes. The terminology is justified by the fact that our QECCs are related to the ordinary QECCs in exactly the same way that the breeding protocols are related to the hashing protocols in the entanglement purification.

  19. Discovery, Prevalence, and Persistence of Novel Circular Single-Stranded DNA Viruses in the Ctenophores Mnemiopsis leidyi and Beroe ovata.

    PubMed

    Breitbart, Mya; Benner, Bayleigh E; Jernigan, Parker E; Rosario, Karyna; Birsa, Laura M; Harbeitner, Rachel C; Fulford, Sidney; Graham, Carina; Walters, Anna; Goldsmith, Dawn B; Berger, Stella A; Nejstgaard, Jens C

    2015-01-01

    Gelatinous zooplankton, such as ctenophores and jellyfish, are important components of marine and brackish ecosystems and play critical roles in aquatic biogeochemistry. As voracious predators of plankton, ctenophores have key positions in aquatic food webs and are often successful invaders when introduced to new areas. Gelatinous zooplankton have strong impacts on ecosystem services, particularly in coastal environments. However, little is known about the factors responsible for regulating population dynamics of gelatinous organisms, including biological interactions that may contribute to bloom demise. Ctenophores are known to contain specific bacterial communities and a variety of invertebrate parasites and symbionts; however, no previous studies have examined the presence of viruses in these organisms. Building upon recent studies demonstrating a diversity of single-stranded DNA viruses that encode a replication initiator protein (Rep) in aquatic invertebrates, this study explored the presence of circular, Rep-encoding single-stranded DNA (CRESS-DNA) viruses in the ctenophores Mnemiopsis leidyi and Beroe ovata collected from the Skidaway River Estuary and Savannah River in Georgia, USA. Using rolling circle amplification followed by restriction enzyme digestion, this study provides the first evidence of viruses in ctenophores. Investigation of four CRESS-DNA viruses over an 8-month period using PCR demonstrated temporal trends in viral prevalence and indicated that some of the viruses may persist in ctenophore populations throughout the year. Although future work needs to examine the ecological roles of these ctenophore-associated viruses, this study indicates that viral infection may play a role in population dynamics of gelatinous zooplankton.

  20. Why breed every other year? The case of albatrosses.

    PubMed

    Jouventin, Pierre; Dobson, F Stephen

    2002-09-22

    Albatrosses exhibit extremely low reproductive rates, each pair brooding only one egg and subsequent chick at a time. Furthermore, in several of the species, the majority of successful pairs breed only once every second year (termed 'biennial' breeding). Thus, on average, these latter species have an annual fecundity of about half an offspring per year, while other albatrosses produce an egg and chick every year. Using our 40-year bank of demographic data, we compared 12 species of albatrosses according to these two breeding strategies to examine potential causes of biennial breeding. Biennial breeding could be due to physiological constraints, larger animals breeding more slowly, or ecological constraints, more distant pelagic feeding trips being energetically costly, or both. We tested these hypotheses by looking for predicted associations between the duration of the rearing period, the distance to the oceanic feeding zone and breeding frequency. We also looked for associations of these variables with other life-history traits. Body size had a strong influence on the duration of the rearing period, but not on the distance that birds travelled to the feeding zone. Both the duration of the rearing period and distance to the feeding zone appeared to have direct influences on breeding frequency, as revealed by a path analysis, and thus both hypotheses to explain biennial breeding were supported. Finally, breeding frequency exhibited a strong trade-off with adult survival and age at maturity, indicating that slower breeders live through more breeding seasons, perhaps mitigating their lower annual reproductive output.

  1. Why breed every other year? The case of albatrosses.

    PubMed Central

    Jouventin, Pierre; Dobson, F Stephen

    2002-01-01

    Albatrosses exhibit extremely low reproductive rates, each pair brooding only one egg and subsequent chick at a time. Furthermore, in several of the species, the majority of successful pairs breed only once every second year (termed 'biennial' breeding). Thus, on average, these latter species have an annual fecundity of about half an offspring per year, while other albatrosses produce an egg and chick every year. Using our 40-year bank of demographic data, we compared 12 species of albatrosses according to these two breeding strategies to examine potential causes of biennial breeding. Biennial breeding could be due to physiological constraints, larger animals breeding more slowly, or ecological constraints, more distant pelagic feeding trips being energetically costly, or both. We tested these hypotheses by looking for predicted associations between the duration of the rearing period, the distance to the oceanic feeding zone and breeding frequency. We also looked for associations of these variables with other life-history traits. Body size had a strong influence on the duration of the rearing period, but not on the distance that birds travelled to the feeding zone. Both the duration of the rearing period and distance to the feeding zone appeared to have direct influences on breeding frequency, as revealed by a path analysis, and thus both hypotheses to explain biennial breeding were supported. Finally, breeding frequency exhibited a strong trade-off with adult survival and age at maturity, indicating that slower breeders live through more breeding seasons, perhaps mitigating their lower annual reproductive output. PMID:12350259

  2. The different breeding strategies of penguins: a review.

    PubMed

    Ancel, André; Beaulieu, Michaël; Gilbert, Caroline

    2013-01-01

    The 18 penguin species are exclusively and widely distributed in the Southern hemisphere, from the Equator to the Antarctic continent, and are thus submitted to various ecological constraints in their reproductive strategy. This results in a high variability in all aspects of the breeding biology of the different species. Although penguins appear primarily adapted for a marine existence, they remain dependent on land for breeding, rearing young, and moulting. Here we describe and compare the breeding cycle of all the penguin species, highlighting the characteristics of each species in terms of breeding range, population status, threats induced by environmental changes, duration of the different phases of the breeding cycle, mate fidelity, body mass, body height, egg mass and duration of egg formation. We also focus on the breeding cycle of the genus Aptenodytes, since it largely differs from the breeding cycle of most of the other penguin species.

  3. Life histories and the evolution of cooperative breeding in mammals.

    PubMed

    Lukas, Dieter; Clutton-Brock, Tim

    2012-10-07

    While the evolution of cooperative breeding systems (where non-breeding helpers participate in rearing young produced by dominant females) has been restricted to lineages with socially monogamous mating systems where coefficients of relatedness between group members are usually high, not all monogamous lineages have produced species with cooperative breeding systems, suggesting that other factors constrain the evolution of cooperative breeding. Previous studies have suggested that life-history parameters, including longevity, may constrain the evolution of cooperative breeding. Here, we show that transitions to cooperative breeding across the mammalian phylogeny have been restricted to lineages where females produce multiple offspring per birth. We find no support for effects of longevity or of other life-history parameters. We suggest that the evolution of cooperative breeding has been restricted to monogamous lineages where helpers have the potential to increase the reproductive output of breeders.

  4. Colombian Creole horse breeds: Same origin but different diversity

    PubMed Central

    Jimenez, Ligia Mercedes; Mendez, Susy; Dunner, Susana; Cañón, Javier; Cortés, Óscar

    2012-01-01

    In order to understand the genetic ancestry and mitochondrial DNA (mtDNA) diversity of current Colombian horse breeds we sequenced a 364-bp fragment of the mitocondrial DNA D-loop in 116 animals belonging to five Spanish horse breeds and the Colombian Paso Fino and Colombian Creole cattle horse breeds. Among Colombian horse breeds, haplogroup D had the highest frequency (53%), followed by haplogroups A (19%), C (8%) and F (6%). The higher frequency of haplogroup D in Colombian horse breeds supports the theory of an ancestral Iberian origin for these breeds. These results also indicate that different selective pressures among the Colombian breeds could explain the relatively higher genetic diversity found in the Colombian Creole cattle horse when compared with the Colombian Paso Fino. PMID:23271940

  5. Targeting DNA double-strand breaks with TAL effector nucleases.

    PubMed

    Christian, Michelle; Cermak, Tomas; Doyle, Erin L; Schmidt, Clarice; Zhang, Feng; Hummel, Aaron; Bogdanove, Adam J; Voytas, Daniel F

    2010-10-01

    Engineered nucleases that cleave specific DNA sequences in vivo are valuable reagents for targeted mutagenesis. Here we report a new class of sequence-specific nucleases created by fusing transcription activator-like effectors (TALEs) to the catalytic domain of the FokI endonuclease. Both native and custom TALE-nuclease fusions direct DNA double-strand breaks to specific, targeted sites.

  6. Applications of Strand-Specific in situ Hybridization

    SciTech Connect

    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.

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

    PubMed

    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.

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

    PubMed Central

    Fields, Alexander P.; Meyer, Elisabeth A.; Cohen, Adam E.

    2013-01-01

    The bending stiffness of double-stranded DNA (dsDNA) at high curvatures is fundamental to its biological activity, yet this regime has been difficult to probe experimentally, and literature results have not been consistent. We created a ‘molecular vise’ in which base-pairing interactions generated a compressive force on sub-persistence length segments of dsDNA. Short dsDNA strands (<41 base pairs) resisted this force and remained straight; longer strands became bent, a phenomenon called ‘Euler buckling’. We monitored the buckling transition via Förster Resonance Energy Transfer (FRET) between appended fluorophores. For low-to-moderate concentrations of monovalent salt (up to ∼150 mM), our results are in quantitative agreement with the worm-like chain (WLC) model of DNA elasticity, without the need to invoke any ‘kinked’ states. Greater concentrations of monovalent salts or 1 mM Mg2+ induced an apparent softening of the dsDNA, which was best accounted for by a kink in the region of highest curvature. We tested the effects of all single-nucleotide mismatches on the DNA bending. Remarkably, the propensity to kink correlated with the thermodynamic destabilization of the mismatched DNA relative the perfectly complementary strand, suggesting that the kinked state is locally melted. The molecular vise is exquisitely sensitive to the sequence-dependent linear and nonlinear elastic properties of dsDNA. PMID:23956222

  9. Solid phase sequencing of double-stranded nucleic acids

    DOEpatents

    Fu, Dong-Jing; Cantor, Charles R.; Koster, Hubert; Smith, Cassandra L.

    2002-01-01

    This invention relates to methods for detecting and sequencing of target double-stranded nucleic acid sequences, to nucleic acid probes and arrays of probes useful in these methods, and to kits and systems which contain these probes. Useful methods involve hybridizing the nucleic acids or nucleic acids which represent complementary or homologous sequences of the target to an array of nucleic acid probes. These probe comprise a single-stranded portion, an optional double-stranded portion and a variable sequence within the single-stranded portion. The molecular weights of the hybridized nucleic acids of the set can be determined by mass spectroscopy, and the sequence of the target determined from the molecular weights of the fragments. Nucleic acids whose sequences can be determined include nucleic acids in biological samples such as patient biopsies and environmental samples. Probes may be fixed to a solid support such as a hybridization chip to facilitate automated determination of molecular weights and identification of the target sequence.

  10. On the Distinction between Preposition Stranding and Orphan Prepositions

    ERIC Educational Resources Information Center

    Roberge, Yves

    2012-01-01

    Poplack, Zentz and Dion (PZD; Poplack, Zentz & Dion, 2011, this issue) examine the often unquestioned assumption that the existence of preposition stranding (PS) in Canadian French is linked to the presence of a contact situation with English in the North American context. Although this issue has been the topic of previous research from a…

  11. The Ideological "Strands" of the 5-14 Educational Narrative.

    ERIC Educational Resources Information Center

    McAllister, John

    1993-01-01

    The Scottish 5-14 master educational narrative prescribes a rigid framework for curricular policies and planning. The ideological strands of 5-14 present education as a business, promote the maintenance of a common culture, and attack teacher professionalism. Argues that the program should be seen as a means of control over the practice and…

  12. Spatial scale of local breeding habitat quality and adjustment of breeding decisions.

    PubMed

    Doligez, Blandine; Berthouly, Anne; Doligez, Damien; Tanner, Marion; Saladin, Verena; Bonfils, Danielle; Richner, Heinz

    2008-05-01

    Experimental studies provide evidence that, in spatially and temporally heterogeneous environments, individuals track variation in breeding habitat quality to adjust breeding decisions to local conditions. However, most experiments consider environmental variation at one spatial scale only, while the ability to detect the influence of a factor depends on the scale of analysis. We show that different breeding decisions by adults are based on information about habitat quality at different spatial scales. We manipulated (increased or decreased) local breeding habitat quality through food availability and parasite prevalence at a small (territory) and a large (patch) scale simultaneously in a wild population of Great Tits (Parus major). Females laid earlier in high-quality large-scale patches, but laying date did not depend on small-scale territory quality. Conversely, offspring sex ratio was higher (i.e., biased toward males) in high-quality, small-scale territories but did not depend on large-scale patch quality. Clutch size and territory occupancy probability did not depend on our experimental manipulation of habitat quality, but territories located at the edge of patches were more likely to be occupied than central territories. These results suggest that integrating different decisions taken by breeders according to environmental variation at different spatial scales is required to understand patterns of breeding strategy adjustment.

  13. Hormones and territorial behavior during breeding in snow buntings (Plectrophenax nivalis): an Arctic-breeding songbird.

    PubMed

    Romero, L M; Soma, K K; O'Reilly, K M; Suydam, R; Wingfield, J C

    1998-02-01

    We examined hormonal profiles and behavior associated with maintaining a single-purpose territory in an Arctic-breeding songbird-the snow bunting (Plectrophenax nivalis). Snow buntings differ from many other Arctic-breeding passerines by using nest cavities, an uncommon and defended resource, but not relying upon the surrounding territory for forage. Circulating levels of testosterone in males were high when territories were established and then decreased over the breeding season. LH secretion was enhanced in females while laying eggs, followed by detectable levels of estradiol during incubation. Both sexes showed equivalent corticosterone responses to the stress of being captured and held. Male snow buntings vigorously defended territories in response to a simulated territorial intrusion both when initiating breeding and when feeding young. Exogenous testosterone implants surprisingly inhibited physical aggression but enhanced singing when birds were feeding young, thus suggesting that song and physical aggression are mediated by different hormonal mechanisms at this time of year. Together, these results contrast with hormonal profiles and behavior in other Arctic-breeding passerines.

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

    PubMed Central

    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

    2015-01-01

    Objective: 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. Methods: 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). Results: 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 15th day and in 66.7% on the 30th day, making the biological tissue stronger and more resistant (p=0.095). Conclusion: 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

  15. Capture of breeding and wintering shorebirds with leg-hold noose-mats

    USGS Publications Warehouse

    Mehl, K.R.; Drake, K.L.; Page, G.W.; Sanzenbacher, Peter; Haig, Susan M.; Thompson, J.E.

    2003-01-01

    Development of effective trapping techniques is important for conservation efforts, as marking and subsequent monitoring of individuals is necessary to obtain accurate estimates of demography, movements, and habitat use. We describe a leg-hold noose-mat trap for capturing breeding and nonbreeding shorebirds. Using this method, we trapped 50 Piping Plovers (Charadrius melodus), 2258 Snowy Plovers (C. alexandrinus), 38 Killdeers (C. vociferus), and 64 Dunlins (Calidris alpina) in the western and southern United States. The trap was lightweight, making it easy to transport and set up. It was effective on unvegetated substrates at both coastal and inland sites and could be modified for a variety of habitats. Furthermore, this trap allowed researchers to target specific groups of birds including territorial individuals. Easy removal of birds from traps minimized handling time, stress, and injury

  16. Domoic acid production near California coastal upwelling zones, June 1998

    SciTech Connect

    Trainer, V L.; Adams, Nicolaus G.; Bill, Brian D.; Stehr, Carla M.; Wekell, John C.; Moeller, Peter; Busman, Mark; Woodruff, Dana L. )

    2000-01-01

    Sea lion mortalities in central California during May and June 1998 were traced to their ingestion of sardines and anchovies that had accumulated the neurotoxin domoic acid. The detection of toxin in urine, feces, and stomach contents of several sea lions represents the first proven occurrence of domoic acid transfer through the food chain to a marine mammal. The pennate diatoms, Pseudo-nitzschia multiseries and P. australis, were the dominant, toxin-producing phytoplankton constituting algal blooms near Monterey Bay, Half Moon Bay, and Oceano Dunes, areas where sea lions with neurological symptoms stranded. Toxic Pseudo-nitzschia were also found near Morrow Bay, Point Conception, Point Arguello, and Santa Barbara, demonstrating that these species were widespread along the central California coast in June 1998. Measurements of domoic acid during three cruises in early June showed the highest cellular toxin levels in P. multiseries near Point A?o Nuevo and in P. australis from Morro w Bay. Maximum cellular domoic acid levels were observed within 20 km of the coast between 0 and 5 m depth, although toxin was also measured to depths of 40 m. Hydrographic data indicated that the highest toxin levels and greatest numbers of toxic cells were positioned in water masses associated with upwelling zones near coastal headlands. Nutrient levels at these sites were less than those typically measured during periods of active upwelling, due to the 1998 El Ni?o event. The flow of cells and/or nutrients from coastal headlands into embayments where cells can multiply in a stratified environment is a possible mechanism of bloom development along the central California coast. This coupling of toxic Pseudo-nitzschia growth near upwelling zones with physical processes involved in cell transport will be understood only when long-term measurements are made at several key coastal locations, aiding in our capability to predict domoic-acid producing algal blooms.

  17. Molecular Genetics of Sex Identification, Breed Ancestry and Polydactyly in the Norwegian Lundehund Breed.

    PubMed

    Kropatsch, Regina; Melis, Claudia; Stronen, Astrid V; Jensen, Henrik; Epplen, Joerg T

    2015-01-01

    The Norwegian Lundehund breed of dog has undergone a severe loss of genetic diversity as a result of inbreeding and epizootics of canine distemper. As a consequence, the breed is extremely homogeneous and accurate sex identification is not always possible by standard screening of X-chromosomal loci. To improve our genetic understanding of the breed we genotyped 17 individuals using a genome-wide array of 170 000 single nucleotide polymorphisms (SNPs). Standard analyses based on expected homozygosity of X-chromosomal loci failed in assigning individuals to the correct sex, as determined initially by physical examination and confirmed with the Y-chromosomal marker, amelogenin. This demonstrates that identification of sex using standard SNP assays can be erroneous in highly inbred individuals.

  18. Stability of DNA-linked nanoparticle crystals: Effect of number of strands, core size, and rigidity of strand attachment

    NASA Astrophysics Data System (ADS)

    Padovan-Merhar, Olivia; Lara, Fernando Vargas; Starr, Francis W.

    2011-06-01

    Three-dimensional ordered lattices of nanoparticles (NPs) linked by DNA have potential applications in novel devices and materials, but most experimental attempts to form crystals result in amorphous packing. Here we use a coarse-grained computational model to address three factors that impact the stability of bcc and fcc crystals formed by DNA-linked NPs : (i) the number of attached strands to the NP surface, (ii) the size of the NP core, and (iii) the rigidity of the strand attachment. We find that allowing mobility in the attachment of DNA strands to the core NP can very slightly increase or decrease melting temperature TM. Larger changes to TM result from increasing the number of strands, which increases TM, or by increasing the core NP diameter, which decreases TM. Both results are consistent with experimental findings. Moreover, we show that the behavior of TM can be quantitatively described by the model introduced previously [F. Vargas Lara and F. W. Starr, Soft Matter, 7, 2085 (2011)], 10.1039/c0sm00989j.

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

    PubMed Central

    Wierer, Sebastian; Daldrop, Peter; Ud Din Ahmad, Misbha; Boos, Winfried; Drescher, Malte; Welte, Wolfram; Seidel, Ralf

    2016-01-01

    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. PMID:27214207

  20. Extraterrestrial coastal geomorphology

    NASA Astrophysics Data System (ADS)

    Parker, Timothy J.; Currey, Donald R.

    2001-04-01

    Earth is the only planet in the solar system where large amounts of liquid water have been stable at the surface throughout geologic time. This unique trait has resulted in the production of characteristic landforms and massive accumulations of aqueous sediments, as well as enabled the evolution of advanced and diverse forms of life. But while Earth is the only planet with large bodies of water on its surface today, Venus and Mars may have once had lakes or oceans as well. More exotic fluids may be stable in the outer solar system. Prior to the Voyager flybys of the outer planets during the 1970s and 1980s, the moon of Neptune, Triton, was thought to be much larger than the Voyager cameras revealed it to be, and predictions that liquid nitrogen lakes or oceans might be found were made. The moon of Saturn, Titan, however, was found to have a massive atmosphere, so the possibility remains that it may have, or may once have had, lakes or oceans of liquid hydrocarbons. The recent, high-resolution synthetic aperture radar imaging of Venus has failed to reveal any evidence of any putative clement period, but the results for Mars are much more intriguing. Herein, we briefly review work on this subject by a number of investigators, and discuss problems of identifying and recognizing martian landforms as lacustrine or marine. In addition, we present additional examples of possible martian coastal landforms. The former presence of lakes or oceans on Mars has profound implications with regard to the climate history of that planet.

  1. Patch scales in coastal ecosystems

    NASA Astrophysics Data System (ADS)

    Broitman, Bernardo R.

    Quantifying the spatial and temporal scales over which ecological processes are coupled to environmental variability is a major challenge for ecologists. Here, I assimilate patterns of oceanographic variability with ecological field studies in an attempt to quantify spatial and temporal scales of coupling. Using coastal time series of chlorophyll-a concentration from remote sensing, the first chapter examines the alongshore extent of coastal regions subject to similar temporal patterns of oceanographic variability in Western North America (WNA) and North-Central Chile (Chile). I found striking interhemispherical differences in the length of coastal sections under similar oceanographic regimes, with the Chile region showing longshore coherency over much smaller spatial scales (˜60 km) than on the coast of WNA (˜140 km). Through a spatial analysis of coastal orientation I suggest that the characteristic length scales may be traced to the geomorphologic character of the ocean margins. The second chapter examines spatial patterns of primary production through long-term means of coastal chlorophyll-a concentration and kelp (Macrocystis pyrifera) cover and explores their relationship with coastal geomorphology and sea surface temperature (SST). Spatial analyses showed a striking match in length scales around 180--250 km. Strong anticorrelations at small spatial lags and positive correlations at longer distances suggest little overlap between patches of kelp and coastal chlorophyll-a. In agreement with findings from the previous chapter, I found that coastal patches could be traced back to spatial patterns of coastal geomorphology. Through SST time series and long-term datasets of larval recruitment in Santa Cruz Island, California, the third chapter examines temporal patterns of oceanographic variability as determinants of ecological patterns. SST time series from sites experiencing low larval recruitment rates were dominated by strong temporal variability. These sites

  2. Detection of bacteriophage phi 6 minus-strand RNA and novel mRNA isoconformers synthesized in vivo and in vitro, by strand-separating agarose gels

    SciTech Connect

    Pagratis, N.; Revel, H.R. )

    1990-07-01

    Two urea-free agarose gel protocols that resolve the six individual strands of bacteriophage phi 6 dsRNA were developed and used to analyze phage RNA synthesis in vivo and in vitro. Citrate gels separate strands of the large and medium chromosomes while Tris-borate-EDTA (TBE) gels resolve the medium and small dsRNA segments. Minus strands migrate faster than plus strands on citrate gels but are retarded on TBE gels. A study of electrophoretic conditions showed that pH affects strand resolution on citrate gels, and that voltage gradient, agarose concentration, and ethidium bromide significantly alter strand migration on TBE gels. Analysis of native phi 6 RNA synthesized in vivo and in vitro showed that the large and medium message RNAs comigrate with the corresponding plus strands of denatured virion dsRNA. The small messenger RNA is exceptional. Native small mRNA was detected as three isoconformers in vivo and in vitro. The isoconformers were converted by heat denaturation to a single RNA species that comigrates with the virion s+ strand. Minus strands labeled in vivo were detected only after heat denaturation. Minus strand synthesis was detected also in heat-denatured samples from in vitro phi 6 nucleocapsid RNA polymerase reactions at pH values suboptimal for transcription.

  3. Geology of Atlantic Coastal Plain

    SciTech Connect

    Olsson, R.K.; Gohn, G.S.

    1985-01-01

    The Atlantic Coastal Plain developed landward of a hinge zone on slowly subsiding continental crust during the postrift phase of the opening of the Atlantic Ocean. Generally, a wedge of marine and non-marine sediments reaches 2000m thickness near the Atlantic Coastline. Variations in deposition along strike in the coastal plain was controlled by tectonic movement of basins and structural highs which from north to south include the Raritan Embayment, South New Jersey High, Chesapeake-Delaware Basin, Norfolk Arch, Albemarle Embayment, Cape Fear Arch, Southeast Georgia Embayment and South Florida Basin. Postrift sedimentation was initiated during late Jurassic and early Cretaceous time adjacent to the faulted hinge zone which separates thicker unstretched continental crust beneath the coastal plain from thinner stretched crust beneath the outer Atlantic margin. Continental clastic and deltaic sediments were deposited in onlapping sequence from Long Island to northern Florida. During this time carbonate deposition was initiated in the South Florida Basin. Marine deposition of terrigenous sands, silts and clays occurred along the coastal plain in late Cenomanian time. Shallow carbonate deposition continued in Florida. Transgressive and regressive marine deposition was dominant in the coastal plain during late Cretaceous and Paleogene time. Deposition during the Neogene was affected by numerous changes in sea level and consequently it is stratigraphically incomplete and irregularly distributed. Many units lack precise biostratigraphic resolution.

  4. Challenges and opportunities in genetic improvement of local livestock breeds

    PubMed Central

    Biscarini, Filippo; Nicolazzi, Ezequiel L.; Stella, Alessandra; Boettcher, Paul J.; Gandini, Gustavo

    2015-01-01

    Sufficient genetic variation in livestock populations is necessary both for adaptation to future changes in climate and consumer demand, and for continual genetic improvement of economically important traits. Unfortunately, the current trend is for reduced genetic variation, both within and across breeds. The latter occurs primarily through the loss of small, local breeds. Inferior production is a key driver for loss of small breeds, as they are replaced by high-output international transboundary breeds. Selection to improve productivity of small local breeds is therefore critical for their long term survival. The objective of this paper is to review the technology options available for the genetic improvement of small local breeds and discuss their feasibility. Most technologies have been developed for the high-input breeds and consequently are more favorably applied in that context. Nevertheless, their application in local breeds is not precluded and can yield significant benefits, especially when multiple technologies are applied in close collaboration with farmers and breeders. Breeding strategies that require cooperation and centralized decision-making, such as optimal contribution selection, may in fact be more easily implemented in small breeds. PMID:25763010

  5. Breeding implications resulting from classification of patellae luxation in dogs.

    PubMed

    van Grevenhof, E M; Hazewinkel, H A W; Heuven, H C M

    2016-08-01

    Patellar luxation (PL) is one of the major hereditary orthopaedic abnormalities observed in a variety of dog breeds. When the patellae move sideways out of the trochlear groove, this is called PL. The PL score varies between dogs from normal to very severe. Reducing the prevalence of PL by breeding could prevent surgery, thereby improve welfare. Orthopaedic specialists differentiate between normal and loose patellae, where the patellae can be moved to the edge of the trochlear groove, considering scoring loose patellae as normal in the future. Loose patellae are considered acceptable for breeding so far by the breeding organization. The aim of this study was to analyse the genetic background of PL to decide on the importance of loose patellae when breeding for healthy dogs. Data are available from two dog breeds, that is Flat-coated Retrievers (n = 3808) and Kooiker dogs (n = 794), with a total of 4602 dogs. Results show that loose patellae indicate that dogs are genetically more susceptible to develop PL because family members of the dogs with loose patellae showed more severe PL. In addition, the estimated breeding values for dogs with loose patellae indicate that breeding values of dogs with loose patellae were worse than breeding values obtained for dogs with a normal score. Given these results, it is advised to orthopaedic specialists to continue to score loose patellae as a separate class and to dog breeders to minimize the use of dogs in breeding with a genetically higher susceptibility for PL.

  6. Use of microsatellite markers to assign goats to their breeds.

    PubMed

    Aljumaah, R S; Alobre, M M; Al-Atiyat, R M

    2015-08-07

    We investigated the potential of 17 microsatellite markers for assigning Saudi goat individuals to their breeds. Three local breeds, Bishi, Jabali, and Tohami were genotyped using these markers, and Somali goats were used as a reference breed. The majority of alleles were shared between the breeds, except for some that were specific to each breed. The Garza-Williamson index was lowest in the Bishi breed, indicating that a recent bottleneck event occurred. The overall results assigned the goat individuals (based on their genotypes) to the same breeds from which they were sampled, except in a few cases. The individuals' genotypes were sufficient to provide a clear distinction between the Somali goat breed and the others. In three factorial dimensions, the results of a correspondence analysis indicated that the total variation for the first and second factors was 48.85 and 31.43%, respectively. Consequently, Jabali, Bishi, and Tohami goats were in separate groups. The Jabali goat was closely related to the Bishi goat. Somali goats were distinguished from each other and from individuals of the other three goat breeds. The markers were successful in assigning individual goats to their breeds, based on the likelihood of a given individual's genotype.

  7. Admixture and local breed marginalization threaten Algerian sheep diversity.

    PubMed

    Gaouar, Samir Bachir Souheil; Da Silva, Anne; Ciani, Elena; Kdidi, Samia; Aouissat, Miloud; Dhimi, Laziz; Lafri, Mohamed; Maftah, Abderrahman; Mehtar, Nadhira

    2015-01-01

    Due to its geo-climatic conditions, Algeria represents a biodiversity hotspot, with sheep breeds well adapted to a patchwork of extremely heterogeneous harsh habitats. The importance of this peculiar genetic reservoir increases as climate change drives the demand for new adaptations. However, the expansion of a single breed (Ouled-Djellal) which occurred in the last decades has generated a critical situation for the other breeds; some of them are being subjected to uncontrolled cross-breeding with the favored breed and/or to marginalization (effective size contraction). This study investigated genetic diversity within and among six of the nine Algerian breeds, by use of 30 microsatellite markers. Our results showed that, in spite of the census contraction experienced by most of the considered breeds, genetic diversity is still substantial (average gene diversity ranging 0.68 to 0.76) and inbreeding was not identified as a problem. However, two breeds (Rembi and Taâdmit) appeared to have lost most of their genetic originality because of intensive cross-breeding with Ouled-Djellal. Based on the above evidence, we suggest Hamra, Sidaoun, and D'man as breeds deserving the highest priority for conservation in Algeria.

  8. Admixture and Local Breed Marginalization Threaten Algerian Sheep Diversity

    PubMed Central

    Ciani, Elena; Kdidi, Samia; Aouissat, Miloud; Dhimi, Laziz; Lafri, Mohamed; Maftah, Abderrahman; Mehtar, Nadhira

    2015-01-01

    Due to its geo-climatic conditions, Algeria represents a biodiversity hotspot, with sheep breeds well adapted to a patchwork of extremely heterogeneous harsh habitats. The importance of this peculiar genetic reservoir increases as climate change drives the demand for new adaptations. However, the expansion of a single breed (Ouled-Djellal) which occurred in the last decades has generated a critical situation for the other breeds; some of them are being subjected to uncontrolled cross-breeding with the favored breed and/or to marginalization (effective size contraction). This study investigated genetic diversity within and among six of the nine Algerian breeds, by use of 30 microsatellite markers. Our results showed that, in spite of the census contraction experienced by most of the considered breeds, genetic diversity is still substantial (average gene diversity ranging 0.68 to 0.76) and inbreeding was not identified as a problem. However, two breeds (Rembi and Taâdmit) appeared to have lost most of their genetic originality because of intensive cross-breeding with Ouled-Djellal. Based on the above evidence, we suggest Hamra, Sidaoun, and D’man as breeds deserving the highest priority for conservation in Algeria. PMID:25875832

  9. Homologous recombination between single-stranded DNA and chromosomal genes in Saccharomyces cerevisiae.

    PubMed Central

    Simon, J R; Moore, P D

    1987-01-01

    Transformation of Saccharomyces cerevisiae strains was examined by using the URA3 and TRP1 genes cloned into M13 vectors in the absence of sequences capable of promoting autonomous replication. These constructs transform S. cerevisiae cells to prototrophy by homologous recombination with the resident mutant gene. Single-stranded DNA was found to transform S. cerevisiae cells at efficiencies greater than that of double-stranded DNA. No conversion of single-stranded transforming DNA into duplex forms could be detected during the transformation process, and we conclude that single-stranded DNA may participate directly in recombination with chromosomal sequences. Transformation with single-stranded DNA gave rise to both gene conversion and reciprocal exchange events. Cotransformation with competing heterologous single-stranded DNA specifically inhibited transformation by single-stranded DNA, suggesting that one of the components in the transformation-recombination process has a preferential affinity for single-stranded DNA. Images PMID:3302673

  10. 78 FR 54867 - Proposed Information Collection; Comment Request; Marine Mammal Health and Stranding Response...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-09-06

    ... National Oceanic and Atmospheric Administration Proposed Information Collection; Comment Request; Marine... AGENCY: National Oceanic and Atmospheric Administration, Commerce. ACTION: Notice. SUMMARY: The... stranding report provides information on strandings so that the National Marine Fisheries Service (NMFS)...

  11. The invariance of the total direct DNA strand break yield

    SciTech Connect

    Bernal, M. A.; Almeida, C. E. de; Sampaio, C.; Incerti, S.; Champion, C.; Nieminen, P.

    2011-07-15

    Purpose: The invariance of the total direct strand break yield when DNA is irradiated by different types of particles and energies has been reported by previous works. This study is intended to explain the physical causes of this behavior. Methods: The geant4-dna extension of the geant4 general purpose Monte Carlo simulation toolkit has been used to determine direct strand break yields induced by protons and alpha particles impacting on a B-DNA geometrical model, including five organization levels of the human genetic material. The linear energy transfer (LET) of such particles ranges from 4.8 keV/{mu}m (10 MeV protons) to about 235 keV/{mu}m (2 MeV alpha particles), at 5.225 {mu}m depth (near the center of the region of interest). Direct total, single and double strand break probabilities have been determined in a liquid water homogeneous medium with a 1.06 g/cm {sup 3} density. The energetic spectra of single strand breaks (SSB), the number of energy deposition events, and the SSB/event ratio were determined. Results: The target-hit probability was found to be independent of both the type and the energy of the incident particle, even if this latter is a secondary electron. This probability is determined by the geometrical properties of the system. The total strand break yield and the number of energy deposition events required to reach a certain absorbed dose were found nearly independent of the type and energy of the incident ion (proton or alpha). In contrast, the double strand break (DSB) yield was found strongly dependent on the LET of the incident radiation. Conclusions: The SSB generation process is homogeneous and independent of the LET of the particles involved, at least within the proton and alpha particle energy range here studied. The target-hit probability is only determined by the ratio between the total volume occupied by targets and that of the ROI where the radiation deposits its energy. The maximum separation distance between two adjacent SSBs to

  12. Genome Mapping and Molecular Breeding of Tomato

    PubMed Central

    Foolad, Majid R.

    2007-01-01

    The cultivated tomato, Lycopersicon esculentum, is the second most consumed vegetable worldwide and a well-studied crop species in terms of genetics, genomics, and breeding. It is one of the earliest crop plants for which a genetic linkage map was constructed, and currently there are several molecular maps based on crosses between the cultivated and various wild species of tomato. The high-density molecular map, developed based on an L. esculentum × L. pennellii cross, includes more than 2200 markers with an average marker distance of less than 1 cM and an average of 750 kbp per cM. Different types of molecular markers such as RFLPs, AFLPs, SSRs, CAPS, RGAs, ESTs, and COSs have been developed and mapped onto the 12 tomato chromosomes. Markers have been used extensively for identification and mapping of genes and QTLs for many biologically and agriculturally important traits and occasionally for germplasm screening, fingerprinting, and marker-assisted breeding. The utility of MAS in tomato breeding has been restricted largely due to limited marker polymorphism within the cultivated species and economical reasons. Also, when used, MAS has been employed mainly for improving simply-inherited traits and not much for improving complex traits. The latter has been due to unavailability of reliable PCR-based markers and problems with linkage drag. Efforts are being made to develop high-throughput markers with greater resolution, including SNPs. The expanding tomato EST database, which currently includes ∼214 000 sequences, the new microarray DNA chips, and the ongoing sequencing project are expected to aid development of more practical markers. Several BAC libraries have been developed that facilitate map-based cloning of genes and QTLs. Sequencing of the euchromatic portions of the tomato genome is paving the way for comparative and functional analysis of important genes and QTLs. PMID:18364989

  13. Coastal eutrophication and temperature variation

    SciTech Connect

    Ganoulis, J.; Rafailidis, S.; Bogardi, I.; Duckstein, L.; Matyasovszky, I.

    1994-12-31

    A 3-D hydroecological model has been developed to simulate the impact of climate-change-induced daily temperature variation on coastal water quality and eutrophication. Historical daily temperature time series over a thirty-year period have been used to link local meteorological variables to large-scale atmospheric circulation patterns (CPs). Then, CPs generated under a 2{times}CO{sub 2} scenario have been used to simulate climate-change-induced local daily temperature variations. Both historical and climate-change-induced temperature time series have been introduced as inputs into the hydroecological model to simulate coastal water quality and eutrophication. Subject to model validation with available data, a case study in the bay of Thessaloniki (N. Greece) indicates a risk of increasing eutrophication and oxygen depletion in coastal areas due to possible climate change.

  14. The dynamics of coastal models

    USGS Publications Warehouse

    Hearn, Clifford J.

    2008-01-01

    Coastal basins are defined as estuaries, lagoons, and embayments. This book deals with the science of coastal basins using simple models, many of which are presented in either analytical form or Microsoft Excel or MATLAB. The book introduces simple hydrodynamics and its applications, from the use of simple box and one-dimensional models to flow over coral reefs. The book also emphasizes models as a scientific tool in our understanding of coasts, and introduces the value of the most modern flexible mesh combined wave-current models. Examples from shallow basins around the world illustrate the wonders of the scientific method and the power of simple dynamics. This book is ideal for use as an advanced textbook for graduate students and as an introduction to the topic for researchers, especially those from other fields of science needing a basic understanding of the basic ideas of the dynamics of coastal basins.

  15. Management and breeding of Aotus trivirgatus.

    PubMed

    Elliott, M W; Sehgal, P K; Chalifoux, L V

    1976-12-01

    Attempts to establish successful breeding colonies of Aotus trivirgatus at this and other laboratories have largely been unsuccessful, resulting in only occasional pregnancies and a rare live birth. After the recognition of seven different karyotypes of owl monkeys, animals were paired on this basis and resulted in a marked increase in conceptions. From 1971 to 1975 only 10 pregnancies occurred but during 1975, there were 19 pregnancies. In addition to proper karyotyping, a period of acclimation and conditioning was required. Mean body measurements and weights of infants were established.

  16. Review: Towards the agroecological management of ruminants, pigs and poultry through the development of sustainable breeding programmes. II. Breeding strategies.

    PubMed

    Phocas, F; Belloc, C; Bidanel, J; Delaby, L; Dourmad, J Y; Dumont, B; Ezanno, P; Fortun-Lamothe, L; Foucras, G; Frappat, B; González-García, E; Hazard, D; Larzul, C; Lubac, S; Mignon-Grasteau, S; Moreno, C R; Tixier-Boichard, M; Brochard, M

    2016-11-01

    Agroecology uses ecological processes and local resources rather than chemical inputs to develop productive and resilient livestock and crop production systems. In this context, breeding innovations are necessary to obtain animals that are both productive and adapted to a broad range of local contexts and diversity of systems. Breeding strategies to promote agroecological systems are similar for different animal species. However, current practices differ regarding the breeding of ruminants, pigs and poultry. Ruminant breeding is still an open system where farmers continue to choose their own breeds and strategies. Conversely, pig and poultry breeding is more or less the exclusive domain of international breeding companies which supply farmers with hybrid animals. Innovations in breeding strategies must therefore be adapted to the different species. In developed countries, reorienting current breeding programmes seems to be more effective than developing programmes dedicated to agroecological systems that will struggle to be really effective because of the small size of the populations currently concerned by such systems. Particular attention needs to be paid to determining the respective usefulness of cross-breeding v. straight breeding strategies of well-adapted local breeds. While cross-breeding may offer some immediate benefits in terms of improving certain traits that enable the animals to adapt well to local environmental conditions, it may be difficult to sustain these benefits in the longer term and could also induce an important loss of genetic diversity if the initial pure-bred populations are no longer produced. As well as supporting the value of within-breed diversity, we must preserve between-breed diversity in order to maintain numerous options for adaptation to a variety of production environments and contexts. This may involve specific public policies to maintain and characterize local breeds (in terms of both phenotypes and genotypes), which could

  17. Oceanic transport of fossil dammar resin: The chemistry of coastal resinites from south Australia

    SciTech Connect

    Murray, A.P. Curtin Univ. of Technology, Perth ); Summons, R.E. ); Padley, D.; McKirdy, D.M. ); Booth, W.E. )

    1994-07-01

    Fragments of resin and fossilized resin (resinites) occasionally wash ashore along the southern Australian coast. Chemical and isotopic analyses were carried out on a suite of coastal and reference resinites to determine the likelihood of a local, as opposed to a distant, origin. All of the coastal resinites were found to contain a polymer based on the sesquiterpenoid cadinene skeleton and were markedly different from the diterpenoid resinites found in local Victorian coals. The coastal resinites closely resemble both fossil and recent dammar resin - a material associated primarily with the tropical angiosperm hardwoods of Southeast Asia, and one which has no known Australian source. Minor variations in the composition of our resinite samples are attributed to differences in their thermal history. These findings confirm the viability of long-distance oceanic transport, not only for the resinites but also for the waxy bitumens that strand along the same coastline. Analytical data on the coastal resinites also help to clarify the role of dammar resin in generating bicadinanes - a class of source and age-specific triterpanes found commonly in the Cainozoic oils and sediments of Southeast Asia.

  18. The breeding biology of lemon sharks at a tropical nursery lagoon.

    PubMed Central

    Feldheim, Kevin A; Gruber, Samuel H; Ashley, Mary V

    2002-01-01

    Surprisingly little is known about the reproductive behaviour and breeding biology of most shark species, especially in natural populations. Here, we characterize reproductive patterns and use of a natal nursery at Bimini, Bahamas by lemon sharks, Negaprion brevirostris. We systematically and exhaustively sampled young lemon sharks at Bimini annually from 1995 to 2000 and opportunistically sampled adults over the same period. Out of the 897 young sharks sampled, 119 could be assigned to five sampled mothers using microsatellite genotyping. Reproductive females showed strong philopatry to the nursery, returning to Bimini every two years to give birth. Each of these females may rely entirely on the Bimini nursery for recruitment. The protection of known nursery grounds should therefore figure prominently in conservation efforts for large coastal shark species. The reconstruction of paternal genotypes indicates that litters are sired by multiple males, and females mate with different males nearly every breeding cycle. The ubiquitous polyandry reported here raises the possibility that genetic incompatibility and post-copulatory paternity-biasing mechanisms may operate in viviparous sharks. PMID:12204125

  19. The breeding biology of lemon sharks at a tropical nursery lagoon.

    PubMed

    Feldheim, Kevin A; Gruber, Samuel H; Ashley, Mary V

    2002-08-22

    Surprisingly little is known about the reproductive behaviour and breeding biology of most shark species, especially in natural populations. Here, we characterize reproductive patterns and use of a natal nursery at Bimini, Bahamas by lemon sharks, Negaprion brevirostris. We systematically and exhaustively sampled young lemon sharks at Bimini annually from 1995 to 2000 and opportunistically sampled adults over the same period. Out of the 897 young sharks sampled, 119 could be assigned to five sampled mothers using microsatellite genotyping. Reproductive females showed strong philopatry to the nursery, returning to Bimini every two years to give birth. Each of these females may rely entirely on the Bimini nursery for recruitment. The protection of known nursery grounds should therefore figure prominently in conservation efforts for large coastal shark species. The reconstruction of paternal genotypes indicates that litters are sired by multiple males, and females mate with different males nearly every breeding cycle. The ubiquitous polyandry reported here raises the possibility that genetic incompatibility and post-copulatory paternity-biasing mechanisms may operate in viviparous sharks.

  20. National Coastal Condition Report IV Factsheet

    EPA Pesticide Factsheets

    Overall condition of the Nation’s coastal waters is fair. This rating is based on five indices of ecologicalcondition: water quality index, sediment quality index, benthic index, coastal habitat index, and fish tissue contaminants index.

  1. 75 FR 44938 - Atlantic Coastal Fisheries Cooperative Management Act Provisions; Atlantic Coastal Shark Fishery

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-07-30

    ... 0648-XX28 Atlantic Coastal Fisheries Cooperative Management Act Provisions; Atlantic Coastal Shark... cancellation of the Federal moratorium on fishing for Atlantic coastal sharks in the State waters of New Jersey... Sharks (Coastal Shark Plan). DATES: Effective July 30, 2010. ADDRESSES: Emily Menashes, Acting...

  2. Roseate Tern breeding dispersal and fidelity: Responses to two newly restored colony sites

    USGS Publications Warehouse

    Spendelow, Jeffrey A.; Monticelli, David; Nichols, James; Hines, James; Nisbet, Ian; Cormons, Grace; Hays, Helen; Hatch, Jeremy; Mostello, Carolyn

    2016-01-01

    We used 22 yr of capture–mark–reencounter (CMR) data collected from 1988 to 2009 on about 12,500 birds at what went from three to five coastal colony sites in Massachusetts, New York, and Connecticut, United States, to examine spatial and temporal variation in breeding dispersal/fidelity rates of adult Roseate Terns (Sterna dougallii). At the start of our study, Roseate Terns nested at only one site (Bird Island) in Buzzards Bay, Massachusetts, but two more sites in this bay (Ram and Penikese Islands) were subsequently recolonized and became incorporated into our CMR metapopulation study. We examined four major hypotheses about factors we thought might influence colony-site fidelity and movement rates in the restructured system. We found some evidence that colony-site fidelity remained higher at long-established sites compared with newer ones and that breeding dispersal was more likely to occur among nearby sites than distant ones. Sustained predation at Falkner Island, Connecticut, did not result in a sustained drop in fidelity rates of breeders. Patterns of breeding dispersal differed substantially at the two restored sites. The fidelity of Roseate Terns at Bird dropped quickly after nearby Ram was recolonized in 1994, and fidelity rates for Ram soon approached those for Bird. After an oil spill in Buzzards Bay in April 2003, hazing (deliberate disturbance) of the terns at Ram prior to the start of egg-laying resulted in lowering of fidelity at this site, a decrease in immigration from Bird, and recolonization of Penikese by Roseate Terns. Annual fidelity rates at Penikese increased somewhat several years after the initial recolonization, but they remained much lower there than at all the other sites throughout the study period. The sustained high annual rates of emigration from Penikese resulted in the eventual failure of the restoration effort there, and in 2013, no Roseate Terns nested at this site.

  3. 75 FR 28560 - Prestressed Concrete Steel Wire Strand From the People's Republic of China: Final Determination...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-21

    ... International Trade Administration Prestressed Concrete Steel Wire Strand From the People's Republic of China...'' section of this notice. \\1\\ See Prestressed Concrete Steel Wire Strand From the People's Republic of China...., Ltd. in the Antidumping Duty Investigation of Prestressed Concrete Steel Wire Strand From the...

  4. Folding DNA origami from a double-stranded source of scaffold

    PubMed Central

    Högberg, Björn; Liedl, Tim; Shih, William M.

    2009-01-01

    Combined heat and chemical denaturation of double-stranded DNA scaffold strands in the presence of staple strands, followed by a sudden temperature drop and then stepwise dialysis to remove the chemical denaturant, leads to self-assembly of two distinct DNA-origami structures. PMID:19566089

  5. 75 FR 32747 - Prestressed Concrete Steel Wire Strand from Mexico: Rescission of Antidumping Duty Administrative...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-06-09

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF COMMERCE INTERNATIONAL TRADE ADMINISTRATION Prestressed Concrete Steel Wire Strand from Mexico: Rescission of Antidumping... prestressed concrete steel wire strand (``PC Strand'') from Mexico for the period January 1, 2009...

  6. 7 CFR 1755.370 - RUS specification for seven wire galvanized steel strand.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 7 Agriculture 11 2014-01-01 2014-01-01 false RUS specification for seven wire galvanized steel... steel strand. (a) RUS incorporates by reference ASTM A475-78, Standard Specification for Zinc-Coated Steel Wire Strand, issued May 1978. All seven wire galvanized steel strand purchased after April 1,...

  7. 7 CFR 1755.370 - RUS specification for seven wire galvanized steel strand.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 7 Agriculture 11 2013-01-01 2013-01-01 false RUS specification for seven wire galvanized steel... steel strand. (a) RUS incorporates by reference ASTM A475-78, Standard Specification for Zinc-Coated Steel Wire Strand, issued May 1978. All seven wire galvanized steel strand purchased after April 1,...

  8. 7 CFR 1755.370 - RUS specification for seven wire galvanized steel strand.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 7 Agriculture 11 2012-01-01 2012-01-01 false RUS specification for seven wire galvanized steel... steel strand. (a) RUS incorporates by reference ASTM A475-78, Standard Specification for Zinc-Coated Steel Wire Strand, issued May 1978. All seven wire galvanized steel strand purchased after April 1,...

  9. 18 CFR 35.26 - Recovery of stranded costs by public utilities and transmitting utilities.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... requirements contract if such contract does not contain an exit fee or other explicit stranded cost provision... an exit fee or other explicit stranded cost provision, and the seller under the contract is a public... utility, and if the contract does not contain an exit fee or other explicit stranded cost provision,...

  10. 18 CFR 35.26 - Recovery of stranded costs by public utilities and transmitting utilities.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... requirements contract if such contract does not contain an exit fee or other explicit stranded cost provision... an exit fee or other explicit stranded cost provision, and the seller under the contract is a public... utility, and if the contract does not contain an exit fee or other explicit stranded cost provision,...

  11. Copper corrosion in coastal Oregon

    SciTech Connect

    Ballard, Sophie J.; Cramer, Stephen D.; Covino, Bernard S. Jr.; Holcomb, Gordon R.

    1998-01-01

    The US Department of Energy is studying the atmospheric corrosion performance of copper and other metals along the Oregon coast. Only the copper results will be presented in this paper. Atmospheric corrosion measurements of copper samples were made at seven bridges, eight coastal communities, and three inland reference sites to quantify and understand the effect of high chloride environments on the corrosion performance of copper. The materials were atmospherically exposed for 1, 2, and 3 years to examine the effects of sheltering, orientation, distance from the ocean, and coastal microclimates on the rate of corrosion and the composition of the corrosion film.

  12. Local breeds, livelihoods and livestock keepers' rights in South Asia.

    PubMed

    Köhler-Rollefson, Ilse; Rathore, H S; Mathias, E

    2009-10-01

    In South Asia, and throughout the developing world, the predominant official approach to livestock development has been improvement of production by means of upgrading local breeds via cross-breeding with exotic animals. This strategy has led to the replacement and dilution of locally adapted breeds with non-native ones. This has resulted in an alarming loss that has been estimated by the Food and Agriculture Organization of the United Nations to amount to one breed every two weeks. Based on selected case studies this paper argues that development strategies using locally adapted breeds and species are much more likely to benefit livestock keepers whilst also maintaining domestic animal diversity and bearing a smaller ecological footprint. It also analyses the rationale for "Livestock Keepers' Rights", a principle that grew out of the struggle of traditional livestock keepers to retain control over their production resources, such as grazing areas and breeding stock, in the face of unfavourable policy environments.

  13. [Molecular genetic diversity of Fujian domestic duck breeds].

    PubMed

    Li, Hui-fang; Li, Bi-chun; Ma, Yue-hui; Tang, Qing-ping; Chen, Kuan-wei; Tu, Yun-jie

    2007-02-01

    By using 28 micro-satellite markers with better polymorphism, this paper studied the genetic diversity of four Fujian provincial domestic duck breeds Jinding, Putian black, Liancheng white, and Shanma. According to the alleles frequencies, the polymorphic information content, average heterozygosity, anaqular genetic distance (DA) and Nei' s standard genetic distance (DS) for each breed were calculated. Based on DA and DS, four dendrograms were obtained by neighbor-joining (NJ) and UPGMA methods. The results showed that the average heterozygosity of the four duck breeds was 0. 5353, indicating that the protection of the genetic diversity of these breeds should be strengthened. The orders of the two types of genetic distances among the breeds were accordant, and the dendrograms were the same, reflecting that much more micro-satellite loci should be adopted to obtain more universal conclusions when the genetic diversity was analyzed. The phylogenetic relationships among the four duck breeds were in accordance with their economic types and ecological localities.

  14. Geospatial characteristics of Florida's coastal and offshore environments: Distribution of important habitats for coastal and offshore biological resources and offshore sand resources

    USGS Publications Warehouse

    Demopoulos, Amanda W.J.; Foster, Ann M.; Jones, Michal L.; Gualtieri, Daniel J.

    2011-01-01

    The Geospatial Characteristics GeoPDF of Florida's Coastal and Offshore Environments is a comprehensive collection of geospatial data describing the political boundaries and natural resources of Florida. This interactive map provides spatial information on bathymetry, sand resources, and locations of important habitats (for example, Essential Fish Habitats (EFH), nesting areas, strandings) for marine invertebrates, fish, reptiles, birds, and marine mammals. The map should be useful to coastal resource managers and others interested in marine habitats and submerged obstructions of Florida's coastal region. In particular, as oil and gas explorations continue to expand, the map can be used to explore information regarding sensitive areas and resources in the State of Florida. Users of this geospatial database will have access to synthesized information in a variety of scientific disciplines concerning Florida's coastal zone. This powerful tool provides a one-stop assembly of data that can be tailored to fit the needs of many natural resource managers. The map was originally developed to assist the Bureau of Ocean Energy Management, Regulation, and Enforcement (BOEMRE) and coastal resources managers with planning beach restoration projects. The BOEMRE uses a systematic approach in planning the development of submerged lands of the Continental Shelf seaward of Florida's territorial waters. Such development could affect the environment. BOEMRE is required to ascertain the existing physical, biological, and socioeconomic conditions of the submerged lands and estimate the impact of developing these lands. Data sources included the National Oceanic and Atmospheric Administration, BOEMRE, Florida Department of Environmental Protection, Florida Geographic Data Library, Florida Fish and Wildlife Conservation Commission, Florida Natural Areas Inventory, and the State of Florida, Bureau of Archeological Research. Federal Geographic Data Committee (FGDC) compliant metadata are

  15. Coastal Modeling System (CMS) Users Manuel

    DTIC Science & Technology

    1992-08-01

    AD-A268 830 , INSTRUCTION REPORT CERC-91-1 COASTAL MODELING SYSTEM ( CMS ) USER’S MANUAL by Mary A. Cialone, David J. Mark, Lucia W. Chou, David A...THE COASTAL MODELING SYSTEM USER’S MANUAL Supplement 1 Issued August 1992 Enclosed are additions and corrections to the Coastal Modeling System ( CMS ...COVERED1 August 1992 Supplement I to September 1991 Manual 4. TITLE AND SUBTITLE S. FUNDING NUMBERS Coastal Modeling System ( CMS ) User’s Manual WU

  16. Surface Wave Dynamics in the Coastal Zone

    DTIC Science & Technology

    2014-09-30

    heights, rip currents etc), coastal management, and help mitigate pollution hazards for humans (recreation) and coastal ecosystems . TRANSITIONS...1 Surface Wave Dynamics in the Coastal Zone Gerbrant Ph. van Vledder Department of Civil engineering and Geosciences, Delft University of...will be applicable in the coastal zone from deep water up to and including the surf zone. Our efforts will focus on analyzing high quality datasets to

  17. Reproductive characteristics of stallions during the breeding and non-breeding season in a tropical region.

    PubMed

    Leme, Denise Pereira; Papa, Frederico Ozanam; Roser, Janet F

    2012-10-01

    The objective of this study was to investigate reproductive characteristics of stallions at a tropical zone in the breeding and non-breeding seasons. The following parameters were assessed: testicular volume; semen quality; and serum concentrations of LH, FSH, and testosterone; in addition to the percentages of germ cells and proportions of germ cells/Sertoli cells by testicular cytology in stallions. Semen was collected from eight adult stallions twice a week during a 12-week period in both seasons (6 weeks before and 6 weeks after the summer and winter solstices). Jugular blood samples were collected periodically for hormone analysis by radioimmunoassay during the same periods. Testicular measures and cytological samples were taken at the end of each period. Mean concentration of testosterone was significantly higher (P = 0.04) during the breeding season and the proportion of Sertoli cells/100 germ cells in cytological smears was significantly lower during the breeding season (P = 0.0001). Effects of season were not significant either for testicular volume or for any semen parameter (P > 0.05). Seasonal changes in the mean concentrations of LH and FSH were not observed (P > 0.05). There were also no significant differences in the mean percentages of germ cell types between both seasons (P > 0.05). Lack of seasonal differences in the testicular volume and semen parameters of tropical stallions are probably due to the small variation in duration of natural light between the observed periods, slightly under 3 h.

  18. The biotron breeding system: a rapid and reliable procedure for genetic studies and breeding in rice.

    PubMed

    Ohnishi, Takayuki; Yoshino, Mihoko; Yamakawa, Hiromoto; Kinoshita, Tetsu

    2011-07-01

    Oryza sativa is widely used as a model organism for many aspects of research in monocots and cereals. However, it has certain disadvantages as a model species compared with Arabidopsis thaliana, the eudicot species most widely used in plant sciences: first, it has a long cultivation time; and second, it requires considerably more space for growth. Here, we introduce a biotron breeding system, which allows rapid and reliable rice cultivation using a well-equipped artificial environmental chamber. This system involves use of regulation of CO₂ levels, removal of tillers and embryo rescue to overcome the disadvantages of rice cultivation. The rice cultivars Nipponbare, Koshihikari, Taichung 65 and Kasalath all showed vigorous growth and sufficient seed production in the biotron breeding system with accelerated flowering time. Nipponbare, which was the earliest among these cultivars, flowered at about 50 d after sowing. The life cycle of these plants could be further shortened using an embryo rescue technique on immature seeds at 7 d after pollination, thereby avoiding the lengthy process of seed maturation. Overall, it was possible to shorten the life cycle of Nipponbare to about 2 months under the controlled conditions. Furthermore, controlled crosses, which can be difficult with conventional cultivation methods, were easy to perform as we could control the exact timing of anther dehiscence. Thus, our biotron breeding system offers a valuable new approach to genetic and breeding studies in rice.

  19. Extent of linkage disequilibrium in large breed dogs: chromosomal and breed variation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Purpose: Understanding extent of linkage disequilibrium (LD) is a crucial component for successful utilization of genome-wide association studies (GWAS). The extent of LD in the dog has been described based upon small marker sets in multiple breeds and studies. Understanding variation in LD on a per...

  20. Combining Breeding Bird Survey and distance sampling to estimate density of migrant and breeding birds

    USGS Publications Warehouse

    Somershoe, S.G.; Twedt, D.J.; Reid, B.

    2006-01-01

    We combined Breeding Bird Survey point count protocol and distance sampling to survey spring migrant and breeding birds in Vicksburg National Military Park on 33 days between March and June of 2003 and 2004. For 26 of 106 detected species, we used program DISTANCE to estimate detection probabilities and densities from 660 3-min point counts in which detections were recorded within four distance annuli. For most species, estimates of detection probability, and thereby density estimates, were improved through incorporation of the proportion of forest cover at point count locations as a covariate. Our results suggest Breeding Bird Surveys would benefit from the use of distance sampling and a quantitative characterization of habitat at point count locations. During spring migration, we estimated that the most common migrant species accounted for a population of 5000-9000 birds in Vicksburg National Military Park (636 ha). Species with average populations of 300 individuals during migration were: Blue-gray Gnatcatcher (Polioptila caerulea), Cedar Waxwing (Bombycilla cedrorum), White-eyed Vireo (Vireo griseus), Indigo Bunting (Passerina cyanea), and Ruby-crowned Kinglet (Regulus calendula). Of 56 species that bred in Vicksburg National Military Park, we estimated that the most common 18 species accounted for 8150 individuals. The six most abundant breeding species, Blue-gray Gnatcatcher, White-eyed Vireo, Summer Tanager (Piranga rubra), Northern Cardinal (Cardinalis cardinalis), Carolina Wren (Thryothorus ludovicianus), and Brown-headed Cowbird (Molothrus ater), accounted for 5800 individuals.

  1. Breeding phenology and winter activity predict subsequent breeding success in a trans-global migratory seabird.

    PubMed

    Shoji, A; Aris-Brosou, S; Culina, A; Fayet, A; Kirk, H; Padget, O; Juarez-Martinez, I; Boyle, D; Nakata, T; Perrins, C M; Guilford, T

    2015-10-01

    Inter-seasonal events are believed to connect and affect reproductive performance (RP) in animals. However, much remains unknown about such carry-over effects (COEs), in particular how behaviour patterns during highly mobile life-history stages, such as migration, affect RP. To address this question, we measured at-sea behaviour in a long-lived migratory seabird, the Manx shearwater (Puffinus puffinus) and obtained data for individual migration cycles over 5 years, by tracking with geolocator/immersion loggers, along with 6 years of RP data. We found that individual breeding and non-breeding phenology correlated with subsequent RP, with birds hyperactive during winter more likely to fail to reproduce. Furthermore, parental investment during one year influenced breeding success during the next, a COE reflecting the trade-off between current and future RP. Our results suggest that different life-history stages interact to influence RP in the next breeding season, so that behaviour patterns during winter may be important determinants of variation in subsequent fitness among individuals.

  2. To breed or not to breed: endocrine response to mercury contamination by an Arctic seabird.

    PubMed

    Tartu, Sabrina; Goutte, Aurélie; Bustamante, Paco; Angelier, Frédéric; Moe, Børge; Clément-Chastel, Céline; Bech, Claus; Gabrielsen, Geir Wing; Bustnes, Jan Ove; Chastel, Olivier

    2013-08-23

    Mercury, a ubiquitous toxic element, is known to alter expression of sex steroids and to impair reproduction across vertebrates but the mechanisms underlying these effects are not clearly identified. We examined whether contamination by mercury predicts the probability to skip reproduction in black-legged kittiwakes (Rissa tridactyla) from Svalbard. We also manipulated the endocrine system to investigate the mechanism underlying this relationship. During the pre-laying period, we injected exogenous GnRH (gonadotropin-releasing hormone) to test the ability of the pituitary to release luteinizing hormone (LH, a key hormone for the release of sex steroids and hence breeding) in relation to mercury burden. Birds that skipped reproduction had significantly higher mercury concentration in blood than breeders. Endocrine profiles of these birds also varied based on breeding status (breeders versus non-breeders), mercury contamination and sex. Specifically, in skippers (birds that did not breed), baseline LH decreased with increasing mercury concentration in males, whereas it increased in females. GnRH-induced LH levels increased with increasing mercury concentration in both sexes. These results suggest that mercury contamination may disrupt GnRH input to the pituitary. Thus, high mercury concentration could affect the ability of long-lived birds to modulate their reproductive effort (skipping or breeding) according to ongoing environmental changes in the Arctic, thereby impacting population dynamics.

  3. A decade of harbour porpoise occurrence in German waters—Analyses of aerial surveys, incidental sightings and strandings

    NASA Astrophysics Data System (ADS)

    Siebert, Ursula; Gilles, Anita; Lucke, Klaus; Ludwig, Martje; Benke, Harald; Kock, Karl-Hermann; Scheidat, Meike

    2006-07-01

    Data on the occurrence of harbour porpoises ( Phocoena phocoena) in German waters from 1988 to 2002 were collected from dedicated aerial surveys, incidental sightings and strandings. Aerial surveys conducted in 1995 and 1996 revealed a mean abundance of 4288 (in 1995) and 7356 harbour porpoises (in 1996) in the German North Sea study area. Mean abundances of harbour porpoises in the German Baltic Sea, divided into two subunits (blocks B and C), were estimated at 980 and 1830 (in 1995 and 1996 resp.) and at 601 (in 1995; there were no sightings in block C during the 1996 survey). From 1988 to 2002, 791 incidental sightings of harbour porpoise pods were reported in German and partly Danish coastal waters of the North and Baltic Seas. In the period 1990 to 2001, 996 harbour porpoises were found stranded along the German North Sea coast and 17 animals were identified as by-catch. In the same period 229 harbour porpoises were found stranded along the German Baltic Sea coast and 105 animals were incidentally taken in fisheries. The proportion of by-caught harbour porpoises was significantly larger in the Baltic Sea. Different monitoring methods are helpful for different aims and management issues: aerial surveys cover large areas in a short time and provide information on density, abundance, distributional patterns and seasonality. Incidental sighting and stranding networks provide indications of general distribution, seasonal variation in abundance, age distribution, by-catch and of areas which are important in the harbour porpoise's life cycle. Comparison of data from the North and Baltic Seas revealed a higher abundance of harbour porpoises in the North Sea than in the Baltic Sea. Altogether the data sets demonstrated a strong seasonality of harbour porpoise occurrence off the German coast with highest numbers during the summer months. Important habitats for harbour porpoises were detected west of the islands of Sylt and Amrum in the North Sea and around the Schlei

  4. Heart pathologies in dolphins stranded along the northwestern Italian coast.

    PubMed

    Scaglione, F E; Bollo, E; Pregel, P; Chiappino, L; Sereno, A; Mignone, W; Moschi, R; Garibaldi, F; Tittarelli, C; Guarda, F

    2013-11-25

    Nine striped dolphins Stenella coeruleoalba and 1 bottlenose dolphin Tursiops truncatus stranded along the Ligurian Sea coast of Italy were necropsied between February 2011 and April 2012. Macroscopic and histological findings were observed in the hearts of all animals and included saccular aneurysms of the pulmonary trunk (n = 3), cirsoid aneurysms (n = 1), right ventricular dilation (n = 1) associated with hypoplasia of the tricuspid chordae (n = 1), valvular fibrosis (n = 3), mitral leaflet thickening (n = 1), left ventricular hypertrophy (n = 1), lymphocytic myocarditis (n =1), and Lambl's excrescences (n = 4). To our best knowledge Lambl's excrescences, aneurysm of the pulmonary trunk, and cirsoid aneurysms have not previously been described in marine mammals, and some of these findings should be taken into account as possible causes of dolphin morbidity, mortality, and stranding.

  5. Single-Stranded DNA Curtains for Studying Homologous Recombination.

    PubMed

    Ma, C J; Steinfeld, J B; Greene, E C

    2017-01-01

    Homologous recombination is an important pathway involved in the repair of double-stranded DNA breaks. Genetic studies form the foundation of our knowledge on homologous recombination. Significant progress has also been made toward understanding the biochemical and biophysical properties of the proteins, complexes, and reaction intermediates involved in this essential DNA repair pathway. However, heterogeneous or transient recombination intermediates remain extremely difficult to assess through traditional ensemble methods, leaving an incomplete mechanistic picture of many steps that take place during homologous recombination. To help overcome some of these limitations, we have established DNA curtain methodologies as an experimental platform for studying homologous DNA recombination in real-time at the single-molecule level. Here, we present a detailed overview describing the preparation and use of single-stranded DNA curtains in applications related to the study of homologous DNA recombination with emphasis on recent work related to the study of the eukaryotic recombinase Rad51.

  6. Chromatin remodeling in DNA double-strand break repair.

    PubMed

    Bao, Yunhe; Shen, Xuetong

    2007-04-01

    ATP-dependent chromatin remodeling complexes use ATP hydrolysis to remodel nucleosomes and have well-established functions in transcription. However, emerging lines of evidence suggest that chromatin remodeling complexes are important players in DNA double-strand break (DSB) repair as well. The INO80 and SWI2 subfamilies of chromatin remodeling complexes have been found to be recruited to the double-strand lesions and to function directly in both homologous recombination and non-homologous end-joining, the two major conserved DSB repair pathways. Improperly repaired DSBs are implicated in cancer development in higher organisms. Understanding how chromatin remodeling complexes contribute to DSB repair should provide new insights into the mechanisms of carcinogenesis and might suggest new targets for cancer treatment.

  7. STRaND-2: Visual inspection, proximity operations & nanosatellite docking

    NASA Astrophysics Data System (ADS)

    Bridges, C. P.; Taylor, B.; Horri, N.; Underwood, C. I.; Kenyon, S.; Barrera-Ars, J.; Pryce, L.; Bird, R.

    The Surrey Training Research and Nanosatellite Demonstrator (STRaND) programme has been success in identifying and creating a leading low-cost nanosatellite programme with advanced attitude and orbit control system (AOCS) and experimental computing platforms based on smart-phone technologies. The next demonstration capabilities, that provide a challenging mission to the existing STRaND platform, is to perform visual inspection, proximity operations and nanosatellite docking. Visual inspection is to be performed using a COTS LIDAR system to estimate range and pose under 100 m. Proximity operations are controlled using a comprehensive guidance, navigation and control (GNC) loop in a polar form of the Hills Clohessy Wiltshire (HCW) frame including J2 perturbations. And finally, nanosatellite docking is performed at under 30 cm using a series of tuned magnetic coils. This paper will document the initial experiments and calculations used to qualify LIDAR components, size the mission thrust and tank requirements, and air cushion table demonstrations of the docking mechanism.

  8. HOMFLY polynomials in representation [3, 1] for 3-strand braids

    NASA Astrophysics Data System (ADS)

    Mironov, A.; Morozov, A.; Morozov, An.; Sleptsov, A.

    2016-09-01

    This paper is a new step in the project of systematic description of colored knot polynomials started in [1]. In this paper, we managed to explicitly find the inclusive Racah matrix, i.e. the whole set of mixing matrices in channels R ⊗3 -→ Q with all possible Q, for R = [3 , 1]. The calculation is made possible by the use of a newly-developed efficient highest-weight method, still it remains tedious. The result allows one to evaluate and investigate [3 , 1]-colored polynomials for arbitrary 3-strand knots, and this confirms many previous conjectures on various factorizations, universality, and differential expansions. We consider in some detail the next-to-twist-knots three-strand family ( n, -1 | 1 , -1) and deduce its colored HOMFLY. Also confirmed and clarified is the eigenvalue hypothesis for the Racah matrices, which promises to provide a shortcut to generic formulas for arbitrary representations.

  9. Scaling up digital circuit computation with DNA strand displacement cascades.

    PubMed

    Qian, Lulu; Winfree, Erik

    2011-06-03

    To construct sophisticated biochemical circuits from scratch, one needs to understand how simple the building blocks can be and how robustly such circuits can scale up. Using a simple DNA reaction mechanism based on a reversible strand displacement process, we experimentally demonstrated several digital logic circuits, culminating in a four-bit square-root circuit that comprises 130 DNA strands. These multilayer circuits include thresholding and catalysis within every logical operation to perform digital signal restoration, which enables fast and reliable function in large circuits with roughly constant switching time and linear signal propagation delays. The design naturally incorporates other crucial elements for large-scale circuitry, such as general debugging tools, parallel circuit preparation, and an abstraction hierarchy supported by an automated circuit compiler.

  10. Uncertain breeding: a short history of reproduction in monotremes.

    PubMed

    Temple-Smith, P; Grant, T

    2001-01-01

    Although much is known about the biology of monotremes, many important aspects of their reproduction remain unclear. Studies over the last century have provided valuable information on various aspects of monotreme reproduction including the structure and function of their reproductive system, breeding behaviour, sex determination and seasonality. All three living genera of monotremes have been successfully maintained in captivity, often for long periods, yet breeding has been rare and unpredictable. When breeding has occurred, however, significant gains in knowledge have ensued; for example a more accurate estimate of the gestation period of the platypus and the incubation period for the Tachyglossus egg. One of the great challenges for zoos has been to understand why breeding of monotremes is difficult to achieve. Analysis of breeding successes of platypuses and short-beaked echidnas provides some insights. The evidence suggests that although annual breeding seasons are regionally predictable, individual adult females breed unpredictably, with some showing breeding intervals of many years. The reason for this variation in individual breeding intervals may be resource-dependant, influenced by social factors or may even be genetically induced. Better knowledge of factors that influence breeding intervals may improve the success of monotreme captive breeding programmes. More certainty in captive breeding is also an important issue for enterprises wishing to trade in Australian wildlife since current legislation limits export of Australian fauna for display to at least second-generation captive-bred individuals. Given their unique evolutionary position, knowledge of reproduction in monotremes needs to be gained in advance of any future population declines so that appropriate strategies can be developed to ensure their survival.

  11. Double-Stranded Water on Stepped Platinum Surfaces

    NASA Astrophysics Data System (ADS)

    Kolb, Manuel J.; Farber, Rachael G.; Derouin, Jonathan; Badan, Cansin; Calle-Vallejo, Federico; Juurlink, Ludo B. F.; Killelea, Daniel R.; Koper, Marc T. M.

    2016-04-01

    The interaction of platinum with water plays a key role in (electro)catalysis. Herein, we describe a combined theoretical and experimental study that resolves the preferred adsorption structure of water wetting the Pt(111)-step type with adjacent (111) terraces. Double stranded lines wet the step edge forming water tetragons with dissimilar hydrogen bonds within and between the lines. Our results qualitatively explain experimental observations of water desorption and impact our thinking of solvation at the Pt electrochemical interface.

  12. RNA STRAND: The RNA Secondary Structure and Statistical Analysis Database

    PubMed Central

    Andronescu, Mirela; Bereg, Vera; Hoos, Holger H; Condon, Anne

    2008-01-01

    Background The ability to access, search and analyse secondary structures of a large set of known RNA molecules is very important for deriving improved RNA energy models, for evaluating computational predictions of RNA secondary structures and for a better understanding of RNA folding. Currently there is no database that can easily provide these capabilities for almost all RNA molecules with known secondary structures. Results In this paper we describe RNA STRAND – the RNA secondary STRucture and statistical ANalysis Database, a curated database containing known secondary structures of any type and organism. Our new database provides a wide collection of known RNA secondary structures drawn from public databases, searchable and downloadable in a common format. Comprehensive statistical information on the secondary structures in our database is provided using the RNA Secondary Structure Analyser, a new tool we have developed to analyse RNA secondary structures. The information thus obtained is valuable for understanding to which extent and with which probability certain structural motifs can appear. We outline several ways in which the data provided in RNA STRAND can facilitate research on RNA structure, including the improvement of RNA energy models and evaluation of secondary structure prediction programs. In order to keep up-to-date with new RNA secondary structure experiments, we offer the necessary tools to add solved RNA secondary structures to our database and invite researchers to contribute to RNA STRAND. Conclusion RNA STRAND is a carefully assembled database of trusted RNA secondary structures, with easy on-line tools for searching, analyzing and downloading user selected entries, and is publicly available at . PMID:18700982

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

    DTIC Science & Technology

    2005-01-01

    evidence of calicivirus infection in Atlantic marine mammals󈧨 . Poxvirus ( parapox ) skin lesions are common in stranded pinnipeds, particularly pups, and...poxvirus--a parapox virus that typically causes raised nodules on the head, neck, and flippers of infected animals-can cause painful, nodular skin...dolphin (Stenella North Pacific right whale (Eubalaena allenuata), 79, 83, 306 japonica), 79, 83, 287 Parapox . See Poxvirus Northern bottlenose whale

  14. Repair of DNA double strand breaks: in vivo biochemistry.

    PubMed

    Sugawara, Neal; Haber, James E

    2006-01-01

    Double strand breaks (DSBs) can cause damage to the genomic integrity of a cell as well as initiate genetic recombination processes. The HO and I-SceI endonucleases from budding yeast have provided a way to study these events by inducing a unique DSB in vivo under the control of a galactose-inducible promoter. The GAL::HO construct has been used extensively to study processes such as nonhomologous end joining, intra- and interchromosomal gene conversion, single strand annealing and break-induced recombination. Synchronously induced DSBs have also been important in the study of the DNA damage checkpoint, adaptation, and recovery pathways of yeast. This chapter describes methods of using GAL::HO to physically monitor the progression of events following a DSB, specifically the events leading to the switching of mating type by gene conversion of MAT using the silent donors at HML and HMR. Southern blot analysis can be used to follow the overall events in this process such as the formation of the DSB and product. Denaturing alkaline gels and slot blot techniques can be employed to follow the 5' to 3' resection of DNA starting at the DSB. After resection, the 3' tail initiates a homology search and then strand invades its homologous sequence at the donor cassette. Polymerase chain reaction is an important means to assay strand invasion and the priming of new DNA synthesis as well as the completion of gene conversion. Methods such as chromatin immunoprecipitation have provided a means to study many proteins that associate with a DSB, including not only recombination proteins, but also proteins involved in nonhomologous end joining, cell cycle arrest, chromatin remodeling, cohesin function, and mismatch repair.

  15. National Coastal Condition Report I Factsheet

    EPA Pesticide Factsheets

    The National Coastal Condition Report describes the ecological and environmental conditions in U.S. coastal waters. This first-of-its-kind Report, presents a broad baseline picture of the overall condition of U.S. coastal waters as fair to poor.

  16. National Coastal Condition Assessment Report 2010

    EPA Science Inventory

    This National Coastal Condition Assessment 2010 (NCCA 2010) is the fifth in a series of reports assessing the condition of the coastal waters of the United States, including a vast array of estuarine, Great Lakes, and coastal embayment waters. It is part of the National Aquatic R...

  17. The Breeding Bird Survey, 1967 and 1968

    USGS Publications Warehouse

    Robbins, C.S.; Van Velzen, W.T.

    1969-01-01

    In the Breeding Bird Survey of North America, cooperators ran 982 survey routes in 1967 and 1,174 in 1968. All States except Hawaii and all Canadian Provinces except Newfoundland were included. Roadside routes are selected at random within 1-degree blocks of latitude and longitude. Each 24 1/2-mile route, with 3-minute stops spaced half a mile apart, is driven by automobile. All birds heard or seen at the stops are recorded on special forms, and the data are transferred to magnetic tape for analysis. The average number of birds of each species per route is tabulated by State and Province, presenting for the first time a record of the comparative abundance of each species across the continent. The sample size is given for each species recorded. A sophisticated analysis program, here employed for the first time, is used to compute weighted mean values of the survey results for selected species at the State, stratum, regional, and continental level. The statistical significance of year-to-year changes at the 80, 90, 95, and 99 percent levels of probability are part of the computer output. An index for comparing populations of each species from year to year is established, with 1968 as the base year. Maps show the breeding range and comparative abundance of selected species.

  18. Dynamics of ovarian follicles in breeding ducks

    USGS Publications Warehouse

    Esler, Daniel N.

    1994-01-01

    I quantified ovarian rapid follicle growth (RFG) and regression of postovulatory follicles of Northern Pintails (Anas acuta), American Wigeon (A. americana), and Lesser Scaup (Aythya affinis) by a method that accounted for within-day variation in follicle size. Objective methods for identifying onset of RFG also are presented; this is crucial for accurate classification of breeding status. Duration of RFG was estimated as 4.2, 5.1, and 5.0 days for pintails, wigeon, and scaup, respectively; these are shorter than previously reported. Diameters of follicles at the beginning of RFG were estimated to be 8.2, 6.9, and 7.9 mm for pintails, wigeon, and scaup, respectively. For all species, RFG was linear, using follicle diameters, and exponential, using dry masses. Models of RFG and postovulatory follicle regression have practical value for calculating nest initiation dates, number of developing follicles, clutch size, renesting intervals, and daily energy and nutrient commitment to reproduction of collected breeding females.

  19. Nutrient reserve dynamics of breeding canvasbacks

    USGS Publications Warehouse

    Barzen, J.A.; Serie, J.R.

    1990-01-01

    We compared nutrients in reproductive and nonreproductive tissues of breeding Canvasbacks (Aythya valisineria) to assess the relative importance of endogenous reserves and exogenous foods. Fat reserves of females increased during rapid follicle growth and varied more widely in size during the early phase of this period. Females began laying with ca. 205 g of fat in reserve and lost 1.8 g of carcass fat for every 1 g of fat contained in their ovary and eggs. Females lost body mass (primarily fat) at a declining rate as incubation advanced. Protein reserves increased directly with dry oviduct mass during rapid follicle growth. This direct relationship was highly dependent upon data from 2 birds and likely biased by structural size. During laying, protein reserves did not vary with the combined mass of dry oviduct and dry egg protein. Between laying and incubation, mean protein reserves decreased by an amount equal to the protein found in 2.1 Canvasback eggs. Calcium reserves did not vary with the cumulative total of calcium deposited in eggs. Mean calcium reserve declined by the equivalent content of 1.2 eggs between laying and incubation. We believe that protein and calcium were stored in small amounts during laying, and that they were supplemented continually by exogenous sources. In contrast, fat was stored in large amounts and contributed significantly to egg production and body maintenance. Male Canvasbacks lost fat steadily--but not protein or calcium--as the breeding season progressed.

  20. Tornadic storm avoidance behavior in breeding songbirds.

    PubMed

    Streby, Henry M; Kramer, Gunnar R; Peterson, Sean M; Lehman, Justin A; Buehler, David A; Andersen, David E

    2015-01-05

    Migration is a common behavior used by animals of many taxa to occupy different habitats during different periods. Migrant birds are categorized as either facultative (i.e., those that are forced to migrate by some proximal cue, often weather) or obligate (i.e., those that migrate on a regular cycle). During migration, obligate migrants can curtail or delay flights in response to inclement weather or until favorable winds prevail, and they can temporarily reorient or reverse direction when ecological or meteorological obstacles are encountered. However, it is not known whether obligate migrants undertake facultative migrations and make large-scale movements in response to proximal cues outside of their regular migration periods. Here, we present the first documentation of obligate long-distance migrant birds undertaking a facultative migration, wherein breeding golden-winged warblers (Vermivora chrysoptera) carrying light-level geolocators performed a >1,500 km 5-day circumvention of a severe tornadic storm. The birds evacuated their breeding territories >24 hr before the arrival of the storm and atmospheric variation associated with it. The probable cue, radiating >1,000 km from tornadic storms, perceived by birds and influencing bird behavior and movements, is infrasound (i.e., sound below the range of human hearing). With the predicted increase in severity and frequency of similar storms as anthropogenic climate change progresses, understanding large-scale behavioral responses of animals to such events will be an important objective of future research.

  1. Sugars in peach fruit: a breeding perspective

    PubMed Central

    Cirilli, Marco; Bassi, Daniele; Ciacciulli, Angelo

    2016-01-01

    The last decade has been characterized by a decrease in peach (Prunus persica) fruit consumption in many countries, foremost due to unsatisfactory quality. The sugar content is one of the most important quality traits perceived by consumers, and the development of novel peach cultivars with sugar-enhanced content is a primary objective of breeding programs to revert the market inertia. Nevertheless, the progress reachable through classical phenotypic selection is limited by the narrow genetic bases of peach breeding material and by the complex quantitative nature of the trait, which is deeply affected by environmental conditions and agronomical management. The development of molecular markers applicable in MAS or MAB has become an essential strategy to boost the selection efficiency. Despite the enormous advances in ‘omics’ sciences, providing powerful tools for plant genotyping, the identification of the genetic bases of sugar-related traits is hindered by the lack of adequate phenotyping methods that are able to address strong within-plant variability. This review provides an overview of the current knowledge of the metabolic pathways and physiological mechanisms regulating sugar accumulation in peach fruit, the main advances in phenotyping approaches and genetic background, and finally addressing new research priorities and prospective for breeders. PMID:26816618

  2. Targeted Proteomics Approach for Precision Plant Breeding.

    PubMed

    Chawade, Aakash; Alexandersson, Erik; Bengtsson, Therese; Andreasson, Erik; Levander, Fredrik

    2016-02-05

    Selected reaction monitoring (SRM) is a targeted mass spectrometry technique that enables precise quantitation of hundreds of peptides in a single run. This technique provides new opportunities for multiplexed protein biomarker measurements. For precision plant breeding, DNA-based markers have been used extensively, but the potential of protein biomarkers has not been exploited. In this work, we developed an SRM marker panel with assays for 104 potato (Solanum tuberosum) peptides selected using univariate and multivariate statistics. Thereafter, using random forest classification, the prediction markers were identified for Phytopthora infestans resistance in leaves, P. infestans resistance in tubers, and plant yield in potato leaf secretome samples. The results suggest that the marker panel has the predictive potential for three traits, two of which have no commercial DNA markers so far. Furthermore, the marker panel was also tested and found to be applicable to potato clones not used during the marker development. The proposed workflow is thus a proof-of-concept for targeted proteomics as an efficient readout in accelerated breeding for complex and agronomically important traits.

  3. Breeding programs for smallholder sheep farming systems: I. Evaluation of alternative designs of breeding schemes.

    PubMed

    Gizaw, S; Rischkowsky, B; Valle-Zárate, A; Haile, A; van Arendonk, J A M; Mwai, A O; Dessie, T

    2014-10-01

    Village- and central nucleus-based schemes were simulated and evaluated for their relative bio-economic efficiencies, using Ethiopia's Menz sheep as example. The schemes were: village-based 2-tier (Scheme-1) and 1-tier (Scheme-2) cooperative village breeding schemes, dispersed village-based nuclei scheme (Scheme-3), conventional 2-tier central nucleus-based scheme (Scheme-4), and schemes linking a central nucleus and village multiplier nuclei with selection in central nucleus (Scheme-5) or in both central and village nuclei (Scheme-6). Among village-based schemes, Scheme-1 gave the highest genetic progress, while Scheme-2 was economically the most efficient with genetic gain in the breeding objective of Birr 5.6 and a profit of Birr 37.2/ewe/year. The central nucleus schemes were more efficient than the village schemes. Scheme-4 was the most efficient with genetic gain in the breeding objective of Birr 13.5 and a profit of Birr 71.2, but is operationally more difficult as it requires a very large central nucleus. The choice between village and central nucleus-based schemes would depend on local conditions (availability of infrastructure, logistics and technical knowhow and support). Linking central nucleus with village-based nuclei (Scheme-6) would be a feasible option to overcome the operational difficulties of the conventional central nucleus scheme. If a village-based breeding program is envisaged as should be the 1st step in most low-input systems, then Scheme-2 is the most efficient. To scale out to an entire Menz breed level, Scheme-3 would be recommended.

  4. Structure of the guide-strand-containing argonaute silencing complex

    SciTech Connect

    Wang, Yanli; Sheng, Gang; Juranek, Stefan; Tuschl, Thomas; Patel, Dinshaw J.

    2009-01-15

    The slicer activity of the RNA-induced silencing complex is associated with argonaute, the RNase H-like PIWI domain of which catalyses guide-strand-mediated sequence-specific cleavage of target messenger RNA. Here we report on the crystal structure of Thermus thermophilus argonaute bound to a 5'-phosphorylated 21-base DNA guide strand, thereby identifying the nucleic-acid-binding channel positioned between the PAZ- and PIWI-containing lobes, as well as the pivot-like conformational changes associated with complex formation. The bound guide strand is anchored at both of its ends, with the solvent-exposed Watson-Crick edges of stacked bases 2 to 6 positioned for nucleation with the mRNA target, whereas two critically positioned arginines lock bases 10 and 11 at the cleavage site into an unanticipated orthogonal alignment. Biochemical studies indicate that key amino acid residues at the active site and those lining the 5'-phosphate-binding pocket made up of the Mid domain are critical for cleavage activity, whereas alterations of residues lining the 2-nucleotide 3'-end-binding pocket made up of the PAZ domain show little effect.

  5. Single strand transposition at the host replication fork

    PubMed Central

    Lavatine, Laure; He, Susu; Caumont-Sarcos, Anne; Guynet, Catherine; Marty, Brigitte; Chandler, Mick; Ton-Hoang, Bao

    2016-01-01

    Members of the IS200/IS605 insertion sequence family differ fundamentally from classical IS essentially by their specific single-strand (ss) transposition mechanism, orchestrated by the Y1 transposase, TnpA, a small HuH enzyme which recognizes and processes ss DNA substrates. Transposition occurs by the ‘peel and paste’ pathway composed of two steps: precise excision of the top strand as a circular ss DNA intermediate; and subsequent integration into a specific ssDNA target. Transposition of family members was experimentally shown or suggested by in silico high-throughput analysis to be intimately coupled to the lagging strand template of the replication fork. In this study, we investigated factors involved in replication fork targeting and analysed DNA-binding properties of the transposase which can assist localization of ss DNA substrates on the replication fork. We showed that TnpA interacts with the β sliding clamp, DnaN and recognizes DNA which mimics replication fork structures. We also showed that dsDNA can facilitate TnpA targeting ssDNA substrates. We analysed the effect of Ssb and RecA proteins on TnpA activity in vitro and showed that while RecA does not show a notable effect, Ssb inhibits integration. Finally we discuss the way(s) in which integration may be directed into ssDNA at the replication fork. PMID:27466393

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

    USGS Publications Warehouse

    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.

  7. Carbon Fiber Strand Tensile Failure Dynamic Event Characterization

    NASA Technical Reports Server (NTRS)

    Johnson, Kenneth L.; Reeder, James

    2016-01-01

    There are few if any clear, visual, and detailed images of carbon fiber strand failures under tension useful for determining mechanisms, sequences of events, different types of failure modes, etc. available to researchers. This makes discussion of physics of failure difficult. It was also desired to find out whether the test article-to-test rig interface (grip) played a part in some failures. These failures have nothing to do with stress rupture failure, thus representing a source of waste for the larger 13-00912 investigation into that specific failure type. Being able to identify or mitigate any competing failure modes would improve the value of the 13-00912 test data. The beginnings of the solution to these problems lay in obtaining images of strand failures useful for understanding physics of failure and the events leading up to failure. Necessary steps include identifying imaging techniques that result in useful data, using those techniques to home in on where in a strand and when in the sequence of events one should obtain imaging data.

  8. Load monitoring in multiwire strands by interwire ultrasonic measurements

    NASA Astrophysics Data System (ADS)

    Bartoli, Ivan; Phillips, Robert; Lanza di Scalea, Francesco; Salamone, Salvatore; Coccia, Stefano; Sikorsky, Charles S.

    2008-03-01

    Nearly 90% of the bridges in California are post-tensioned box-girders. Prestressing (PS) tendons are the main load-carrying components of these and other post-tensioned structures. Despite their criticality, much research is needed to develop and deploy techniques able to provide real-time information on the level of prestress and on the presence of structural defects (e.g. corrosion and broken wires) in the PS tendons. In collaboration with Caltrans, UCSD is investigating the combination of ultrasonic guided waves and embedded sensors as an approach to provide both prestress level monitoring and defect detection capabilities in concrete-embedded PS tendons. This paper will focus on the prestress level monitoring by first discussing the behavior of ultrasonic guided waves propagating in seven-wire, 0.6-in diameter twisted strands typically used in post-tensioned concrete structures. A semi-analytical finite element analysis is used to predict modal and forced wave solutions as a function of the applied prestress level. This analysis accounts for the changing inter-wire contact as a function of applied loads. A feature shown sensitive to load levels is the inter-wire energy leakage. In order to monitor such feature, the method uses low-profile piezoelectric sensors able to probe the individual, 0.2-in wires comprising the strand. Results of load monitoring in free and embedded strands during laboratory tests will be presented.

  9. Kinetics of DNA Strand Displacement Systems with Locked Nucleic Acids.

    PubMed

    Olson, Xiaoping; Kotani, Shohei; Yurke, Bernard; Graugnard, Elton; Hughes, William L

    2017-03-30

    Locked nucleic acids (LNAs) are conformationally restricted RNA nucleotides. Their increased thermal stability and selectivity toward their complements make them well-suited for diagnostic and therapeutic applications. Although the structural and thermodynamic properties of LNA-LNA, LNA-RNA, and LNA-DNA hybridizations are known, the kinetic effects of incorporating LNA nucleotides into DNA strand displacement systems are not. Here, we thoroughly studied the strand displacement kinetics as a function of the number and position of LNA nucleotides in DNA oligonucleotides. When compared to that of an all-DNA control, with an identical sequence, the leakage rate constant was reduced more than 50-fold, to an undetectable level, and the invasion rate was preserved for a hybrid DNA/LNA system. The total performance enhancement ratio also increased more than 70-fold when calculating the ratio of the invading rate to the leakage rate constants for a hybrid system. The rational substitution of LNA nucleotides for DNA nucleotides preserves sequence space while improving the signal-to-noise ratio of strand displacement systems. Hybrid DNA/LNA systems offer great potential for high-performance chemical reaction networks that include catalyzed hairpin assemblies, hairpin chain reactions, motors, walkers, and seesaw gates.

  10. A novel bio-sensor based on DNA strand displacement.

    PubMed

    Shi, Xiaolong; Wang, Zhiyu; Deng, Chenyan; Song, Tao; Pan, Linqiang; Chen, Zhihua

    2014-01-01

    DNA strand displacement technology performs well in sensing and programming DNA segments. In this work, we construct DNA molecular systems based on DNA strand displacement performing computation of logic gates. Specifically, a class of so-called "DNA neurons" are achieved, in which a "smart" way inspired by biological neurons encoding information is developed to encode and deliver information using DNA molecules. The "DNA neuron" is bistable, that is, it can sense DNA molecules as input signals, and release "negative" or "positive" signals DNA molecules. We design intelligent DNA molecular systems that are constructed by cascading some particularly organized "DNA neurons", which could perform logic computation, including AND, OR, XOR logic gates, automatically. Both simulation results using visual DSD (DNA strand displacement) software and experimental results are obtained, which shows that the proposed systems can detect DNA signals with high sensitivity and accretion; moreover, the systems can process input signals automatically with complex nonlinear logic. The method proposed in this work may provide a new way to construct a sensitive molecular signal detection system with neurons spiking behavior in vitro, and can be used to develop intelligent molecular processing systems in vivo.

  11. Direct observation of single flexible polymers using single stranded DNA†

    PubMed Central

    Brockman, Christopher; Kim, Sun Ju

    2012-01-01

    Over the last 15 years, double stranded DNA (dsDNA) has been used as a model polymeric system for nearly all single polymer dynamics studies. However, dsDNA is a semiflexible polymer with markedly different molecular properties compared to flexible chains, including synthetic organic polymers. In this work, we report a new system for single polymer studies of flexible chains based on single stranded DNA (ssDNA). We developed a method to synthesize ssDNA for fluorescence microscopy based on rolling circle replication, which generates long strands (>65 kb) of ssDNA containing “designer” sequences, thereby preventing intramolecular base pair interactions. Polymers are synthesized to contain amine-modified bases randomly distributed along the backbone, which enables uniform labelling of polymer chains with a fluorescent dye to facilitate fluorescence microscopy and imaging. Using this approach, we synthesized ssDNA chains with long contour lengths (>30 μm) and relatively low dye loading ratios (~1 dye per 100 bases). In addition, we used epifluorescence microscopy to image single ssDNA polymer molecules stretching in flow in a microfluidic device. Overall, we anticipate that ssDNA will serve as a useful model system to probe the dynamics of polymeric materials at the molecular level. PMID:22956981

  12. High-pressure liquid-monopropellant strand combustion.

    NASA Technical Reports Server (NTRS)

    Faeth, G. M.

    1972-01-01

    Examination of the influence of dissolved gases on the state of the liquid surface during high-pressure liquid-monopropellant combustion through the use of a strand burning experiment. Liquid surface temperatures were measured, using fine-wire thermocouples, during the strand combustion of ethyl nitrate, normal propyl nitrate, and propylene glycol dinitrate at pressures up to 81 atm. These measurements were compared with the predictions of a variable-property gas-phase analysis assuming an infinite activation energy for the decomposition reaction. The state of the liquid surface was estimated using a conventional low-pressure phase equilibrium model, as well as a high-pressure version that considered the presence of dissolved combustion-product gases in the liquid phase. The high-pressure model was found to give a superior prediction of measured liquid surface temperatures. Computed total pressures required for the surface to reach its critical mixing point during strand combustion were found to be in the range from 2.15 to 4.62 times the critical pressure of the pure propellant. Computed dissolved gas concentrations at the liquid surface were in the range from 35 to 50% near the critical combustion condition.

  13. Yields of single-strand breaks in double-stranded calf thymus DNA irradiated in aqueous solution in the presence of oxygen and scavengers

    SciTech Connect

    Udovicic, Lj.; Mark, F.; Bothe, E.

    1994-11-01

    Yields of radiation-induced single-strand breaks in double-stranded calf thymus DNA have been measured as a function of OH scavenger concentration in N{sub 2}O/O{sub 2}-saturated aqueous solution. The experimental data are well represented by a theoretical model based on non-homogeneous reaction kinetics, without the need to adjust any parameter. The good agreement between experimental and theoretical data is taken as evidence that, in the presence of oxygen, the main effect of added scavengers with respect to the formation of single-strand breaks in double-stranded DNA is OH radical scavenging. 30 refs., 3 figs., 1 tab.

  14. Breeding productivity and adult survival in nongame birds

    USGS Publications Warehouse

    Martin, Thomas E.; DeSante, David F.; Paine, Charles R.; Donovan, Therese M.; Dettmers, Randy; Manolis, J.C.; Burton, K.

    1995-01-01

    Demographic data (breeding productivity and adult survival) provide the kind of early warning signal that allows detection of unhealthy populations in terms of productivity or survival problems (Martin and Guepel 1993). In addition, demographic data can help determine whether population declines are the result of low breeding productivity or low survival in migration or winter. Breeding productivity data also can help identify habitat conditions associated with successful and failed breeding attempts. Such information is critical for developing habitat- and land-management practices (Martin 1992). Here, we provide examples of the kinds of information that can be obtained by broad-scale demographic studies.

  15. Allele mining and enhanced genetic recombination for rice breeding.

    PubMed

    Leung, Hei; Raghavan, Chitra; Zhou, Bo; Oliva, Ricardo; Choi, Il Ryong; Lacorte, Vanica; Jubay, Mona Liza; Cruz, Casiana Vera; Gregorio, Glenn; Singh, Rakesh Kumar; Ulat, Victor Jun; Borja, Frances Nikki; Mauleon, Ramil; Alexandrov, Nickolai N; McNally, Kenneth L; Sackville Hamilton, Ruaraidh

    2015-12-01

    Traditional rice varieties harbour a large store of genetic diversity with potential to accelerate rice improvement. For a long time, this diversity maintained in the International Rice Genebank has not been fully used because of a lack of genome information. The publication of the first reference genome of Nipponbare by the International Rice Genome Sequencing Project (IRGSP) marked the beginning of a systematic exploration and use of rice diversity for genetic research and breeding. Since then, the Nipponbare genome has served as the reference for the assembly of many additional genomes. The recently completed 3000 Rice Genomes Project together with the public database (SNP-Seek) provides a new genomic and data resource that enables the identification of useful accessions for breeding. Using disease resistance traits as case studies, we demonstrated the power of allele mining in the 3,000 genomes for extracting accessions from the GeneBank for targeted phenotyping. Although potentially useful landraces can now be identified, their use in breeding is often hindered by unfavourable linkages. Efficient breeding designs are much needed to transfer the useful diversity to breeding. Multi-parent Advanced Generation InterCross (MAGIC) is a breeding design to produce highly recombined populations. The MAGIC approach can be used to generate pre-breeding populations with increased genotypic diversity and reduced linkage drag. Allele mining combined with a multi-parent breeding design can help convert useful diversity into breeding-ready genetic resources.

  16. A comparison of avian hematozoan epizootiology in two California coastal scrub communities

    USGS Publications Warehouse

    Super, Paul E.; van Riper, Charles

    1995-01-01

    Passerine birds within two California (USA) coastal scrub ecosystems, an island and a mainland site, were examined for hematozoa from 1984 to 1990. Island birds had a significantly lower hematozoan prevalence than mainland birds. This prevalence difference can be related to a lack of appropriate hematozoan vectors on the island. Haemoproteus spp. and Leucocytozoon spp. were the most commonly encountered hematozoa; four new species of Leucocytozoon spp. and one new Haemoproteus sp. were found in five host families. No transmission of hematozoan parasites was detected at the island site during the study. At the mainland coastal scrub site, Leucocytozoon spp. was transmitted each year while Plasmodium spp. and Haemoproteus spp. transmission varied between years. There was evidence that some species of birds acquired infections outside of their breeding season. Results of this study lend further support to the prediction of decreased disease on remote island ecosystems.

  17. Coastal Ohio Wind Project

    SciTech Connect

    Gorsevski, Peter; Afjeh, Abdollah; Jamali, Mohsin; Bingman, Verner

    2014-04-04

    The Coastal Ohio Wind Project intends to address problems that impede deployment of wind turbines in the coastal and offshore regions of Northern Ohio. The project evaluates different wind turbine designs and the potential impact of offshore turbines on migratory and resident birds by developing multidisciplinary research, which involves wildlife biology, electrical and mechanical engineering, and geospatial science. Firstly, the project conducts cost and performance studies of two- and three-blade wind turbines using a turbine design suited for the Great Lakes. The numerical studies comprised an analysis and evaluation of the annual energy production of two- and three-blade wind turbines to determine the levelized cost of energy. This task also involved wind tunnel studies of model wind turbines to quantify the wake flow field of upwind and downwind wind turbine-tower arrangements. The experimental work included a study of a scaled model of an offshore wind turbine platform in a water tunnel. The levelized cost of energy work consisted of the development and application of a cost model to predict the cost of energy produced by a wind turbine system placed offshore. The analysis found that a floating two-blade wind turbine presents the most cost effective alternative for the Great Lakes. The load effects studies showed that the two-blade wind turbine model experiences less torque under all IEC Standard design load cases considered. Other load effects did not show this trend and depending on the design load cases, the two-bladed wind turbine showed higher or lower load effects. The experimental studies of the wake were conducted using smoke flow visualization and hot wire anemometry. Flow visualization studies showed that in the downwind turbine configuration the wake flow was insensitive to the presence of the blade and was very similar to that of the tower alone. On the other hand, in the upwind turbine configuration, increasing the rotor blade angle of attack

  18. Coastal Adaptation and Ecological Engineering

    NASA Astrophysics Data System (ADS)

    Cheong, S. M.

    2014-12-01

    Ecological engineering combines ecology and engineering to sustain coastal environment and facilitate adaptation to climate change. This paper discusses how the cases of mangroves, oyster reefs, and marshes help mainstream climate change with ecosystem conservation. It demonstrates the benefits of combining strategies to combat changing climate given the financial and political constraints.

  19. Inverse Modeling of Coastal Tides

    DTIC Science & Technology

    1999-09-30

    data in the tidal band. We have concluded that understanding this discrepancy and developing assimilation methods for baroclinic tides will require...Alexandre Kurapov to develop practical assimilation methods for coastal HF radar data. REFERENCES Bennett, A.F., B.S. Chua, and L.M. Leslie, Generalized

  20. Inverse Modeling of Coastal Tides

    DTIC Science & Technology

    1998-01-01

    produced. We are also working with Profs. J. Allen and R. Miller on developing practical assimilation methods for the coastal problem. REFERENCES...40, 81--108, 1997. Egbert, G.D. and A.F. Bennett, Data assimilation methods for ocean tides, in Modern approaches to data assimilation in ocean