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Sample records for temperate environment shotgun

  1. Paleogenomics in a temperate environment: shotgun sequencing from an extinct Mediterranean caprine.

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    Oscar Ramírez

    Full Text Available BACKGROUND: Numerous endemic mammals, including dwarf elephants, goats, hippos and deers, evolved in isolation in the Mediterranean islands during the Pliocene and Pleistocene. Most of them subsequently became extinct during the Holocene. Recently developed high-throughput sequencing technologies could provide a unique tool for retrieving genomic data from these extinct species, making it possible to study their evolutionary history and the genetic bases underlying their particular, sometimes unique, adaptations. METHODOLOGY/PRINCIPALS FINDINGS: A DNA extraction of a approximately 6,000 year-old bone sample from an extinct caprine (Myotragus balearicus from the Balearic Islands in the Western Mediterranean, has been subjected to shotgun sequencing with the GS FLX 454 platform. Only 0.27% of the resulting sequences, identified from alignments with the cow genome and comprising 15,832 nucleotides, with an average length of 60 nucleotides, proved to be endogenous. CONCLUSIONS: A phylogenetic tree generated with Myotragus sequences and those from other artiodactyls displays an identical topology to that generated from mitochondrial DNA data. Despite being in an unfavourable thermal environment, which explains the low yield of endogenous sequences, our study demonstrates that it is possible to obtain genomic data from extinct species from temperate regions.

  2. Staying cool: preadaptation to temperate climates required for colonising tropical alpine-like environments

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    Berit Gehrke

    2018-04-01

    Full Text Available Plant species tend to retain their ancestral ecology, responding to temporal, geographic and climatic changes by tracking suitable habitats rather than adapting to novel conditions. Nevertheless, transitions into different environments or biomes still seem to be common. Especially intriguing are the tropical alpine-like areas found on only the highest mountainous regions surrounded by tropical environments. Tropical mountains are hotspots of biodiversity, often with striking degrees of endemism at higher elevations. On these mountains, steep environmental gradients and high habitat heterogeneity within small spaces coincide with astounding species diversity of great conservation value. The analysis presented here shows that the importance of in situ speciation in tropical alpine-like areas has been underestimated. Additionally and contrary to widely held opinion, the impact of dispersal from other regions with alpine-like environments is relatively minor compared to that of immigration from other biomes with a temperate (but not alpine-like climate. This suggests that establishment in tropical alpine-like regions is favoured by preadaptation to a temperate, especially aseasonal, freezing regime such as the cool temperate climate regions in the Tropics. Furthermore, emigration out of an alpine-like environment is generally rare, suggesting that alpine-like environments – at least tropical ones – are species sinks.

  3. Shotgun protein sequencing.

    Energy Technology Data Exchange (ETDEWEB)

    Faulon, Jean-Loup Michel; Heffelfinger, Grant S.

    2009-06-01

    A novel experimental and computational technique based on multiple enzymatic digestion of a protein or protein mixture that reconstructs protein sequences from sequences of overlapping peptides is described in this SAND report. This approach, analogous to shotgun sequencing of DNA, is to be used to sequence alternative spliced proteins, to identify post-translational modifications, and to sequence genetically engineered proteins.

  4. Whole-Genome Shotgun Sequence of the Keratinolytic Bacterium Lysobacter sp. A03, Isolated from the Antarctic Environment

    OpenAIRE

    Pereira, Jamile Queiroz; Ambrosini, Adriana; Sant?Anna, Fernando Hayashi; Tadra-Sfeir, Michele; Faoro, Helisson; Pedrosa, F?bio Oliveira; Souza, Emanuel Maltempi; Brandelli, Adriano; Passaglia, Luciane M. P.

    2015-01-01

    Lysobacter sp. strain A03 is a protease-producing bacterium isolated from decomposing-penguin feathers collected in the Antarctic environment. This strain has the ability to degrade keratin at low temperatures. The A03 genome sequence provides the possibility of finding new genes with biotechnological potential to better understand its cold-adaptation mechanism and survival in cold environments.

  5. Whole-Genome Shotgun Sequence of the Keratinolytic Bacterium Lysobacter sp. A03, Isolated from the Antarctic Environment.

    Science.gov (United States)

    Pereira, Jamile Queiroz; Ambrosini, Adriana; Sant'Anna, Fernando Hayashi; Tadra-Sfeir, Michele; Faoro, Helisson; Pedrosa, Fábio Oliveira; Souza, Emanuel Maltempi; Brandelli, Adriano; Passaglia, Luciane M P

    2015-04-02

    Lysobacter sp. strain A03 is a protease-producing bacterium isolated from decomposing-penguin feathers collected in the Antarctic environment. This strain has the ability to degrade keratin at low temperatures. The A03 genome sequence provides the possibility of finding new genes with biotechnological potential to better understand its cold-adaptation mechanism and survival in cold environments. Copyright © 2015 Pereira et al.

  6. Physical exercise performance in temperate and warm environments is decreased by an impaired arterial baroreflex.

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    Washington Pires

    Full Text Available The present study aimed to investigate whether running performance in different environments is dependent on intact arterial baroreceptor reflexes. We also assessed the exercise-induced cardiovascular and thermoregulatory responses in animals lacking arterial baroafferent signals. To accomplish these goals, male Wistar rats were subjected to sinoaortic denervation (SAD or sham surgery (SHAM and had a catheter implanted into the ascending aorta to record arterial pressure and a telemetry sensor implanted in the abdominal cavity to record core temperature. After recovering from these surgeries, the animals were subjected to constant- or incremental-speed exercises performed until the voluntary interruption of effort under temperate (25° C and warm (35° C conditions. During the constant-speed exercises, the running time until the rats were fatigued was shorter in SAD rats in both environments. Although the core temperature was not significantly different between the groups, tail skin temperature was higher in SAD rats under temperate conditions. The denervated rats also displayed exaggerated increases in blood pressure and double product compared with the SHAM rats; in particular, in the warm environment, these exaggerated cardiovascular responses in the SAD rats persisted until they were fatigued. These SAD-mediated changes occurred in parallel with increased variability in the very low and low components of the systolic arterial pressure power spectrum. The running performance was also affected by SAD during the incremental-speed exercises, with the maximal speed attained being decreased by approximately 20% in both environments. Furthermore, at the maximal power output tolerated during the incremental exercises, the mean arterial pressure, heart rate and double product were exaggerated in the SAD relative to SHAM rats. In conclusion, the chronic absence of the arterial baroafferents accelerates exercise fatigue in temperate and warm

  7. Shotgun metagenomic data streams: surfing without fear

    Energy Technology Data Exchange (ETDEWEB)

    Berendzen, Joel R [Los Alamos National Laboratory

    2010-12-06

    Timely information about bio-threat prevalence, consequence, propagation, attribution, and mitigation is needed to support decision-making, both routinely and in a crisis. One DNA sequencer can stream 25 Gbp of information per day, but sampling strategies and analysis techniques are needed to turn raw sequencing power into actionable knowledge. Shotgun metagenomics can enable biosurveillance at the level of a single city, hospital, or airplane. Metagenomics characterizes viruses and bacteria from complex environments such as soil, air filters, or sewage. Unlike targeted-primer-based sequencing, shotgun methods are not blind to sequences that are truly novel, and they can measure absolute prevalence. Shotgun metagenomic sampling can be non-invasive, efficient, and inexpensive while being informative. We have developed analysis techniques for shotgun metagenomic sequencing that rely upon phylogenetic signature patterns. They work by indexing local sequence patterns in a manner similar to web search engines. Our methods are laptop-fast and favorable scaling properties ensure they will be sustainable as sequencing methods grow. We show examples of application to soil metagenomic samples.

  8. Playing by the rules? Phenotypic adaptation to temperate environments in an American marsupial

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    Harrigan, Ryan J.; Wayne, Robert K.

    2018-01-01

    Phenotypic variation along environmental gradients can provide evidence suggesting local adaptation has shaped observed morphological disparities. These differences, in traits such as body and extremity size, as well as skin and coat pigmentation, may affect the overall fitness of individuals in their environments. The Virginia opossum (Didelphis virginiana) is a marsupial that shows phenotypic variation across its range, one that has recently expanded into temperate environments. It is unknown, however, whether the variation observed in the species fits adaptive ecogeographic patterns, or if phenotypic change is associated with any environmental factors. Using phenotypic measurements of over 300 museum specimens of Virginia opossum, collected throughout its distribution range, we applied regression analysis to determine if phenotypes change along a latitudinal gradient. Then, using predictors from remote-sensing databases and a random forest algorithm, we tested environmental models to find the most important variables driving the phenotypic variation. We found that despite the recent expansion into temperate environments, the phenotypic variation in the Virginia opossum follows a latitudinal gradient fitting three adaptive ecogeographic patterns codified under Bergmann’s, Allen’s and Gloger’s rules. Temperature seasonality was an important predictor of body size variation, with larger opossums occurring at high latitudes with more seasonal environments. Annual mean temperature predicted important variation in extremity size, with smaller extremities found in northern populations. Finally, we found that precipitation and temperature seasonality as well as low temperatures were strong environmental predictors of skin and coat pigmentation variation; darker opossums are distributed at low latitudes in warmer environments with higher precipitation seasonality. These results indicate that the adaptive mechanisms underlying the variation in body size, extremity

  9. Playing by the rules? Phenotypic adaptation to temperate environments in an American marsupial

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    Sergio F. Nigenda-Morales

    2018-03-01

    Full Text Available Phenotypic variation along environmental gradients can provide evidence suggesting local adaptation has shaped observed morphological disparities. These differences, in traits such as body and extremity size, as well as skin and coat pigmentation, may affect the overall fitness of individuals in their environments. The Virginia opossum (Didelphis virginiana is a marsupial that shows phenotypic variation across its range, one that has recently expanded into temperate environments. It is unknown, however, whether the variation observed in the species fits adaptive ecogeographic patterns, or if phenotypic change is associated with any environmental factors. Using phenotypic measurements of over 300 museum specimens of Virginia opossum, collected throughout its distribution range, we applied regression analysis to determine if phenotypes change along a latitudinal gradient. Then, using predictors from remote-sensing databases and a random forest algorithm, we tested environmental models to find the most important variables driving the phenotypic variation. We found that despite the recent expansion into temperate environments, the phenotypic variation in the Virginia opossum follows a latitudinal gradient fitting three adaptive ecogeographic patterns codified under Bergmann’s, Allen’s and Gloger’s rules. Temperature seasonality was an important predictor of body size variation, with larger opossums occurring at high latitudes with more seasonal environments. Annual mean temperature predicted important variation in extremity size, with smaller extremities found in northern populations. Finally, we found that precipitation and temperature seasonality as well as low temperatures were strong environmental predictors of skin and coat pigmentation variation; darker opossums are distributed at low latitudes in warmer environments with higher precipitation seasonality. These results indicate that the adaptive mechanisms underlying the variation in

  10. Airborne Laser Scanning to support forest resource management under alpine, temperate and Mediterranean environments in Italy

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    Piermaria Corona

    2012-03-01

    Full Text Available This paper aims to provide general considerations, in the form of a scientific review, with reference to selected experiences of ALS applications under alpine, temperate and Mediterranean environments in Italy as case studies. In Italy, the use of ALS data have been mainly focused on the stratification of forest stands and the estimation of their timber volume and biomass at local scale. Potential for ALS data exploitation concerns their integration in forest inventories on large territories, their usage for silvicultural systems detection and their use for the estimation of fuel load in forest and pre-forest stands. Multitemporal ALS may even be suitable to support the assessment of current annual volume increment and the harvesting rates.

  11. Comparative growth analysis of cool- and warm-season grasses in a cool-temperate environment

    International Nuclear Information System (INIS)

    Belesky, D.P.; Fedders, J.M.

    1995-01-01

    Using both cool-season (C3) and warm-season (C4) species is a viable means of optimizing herbage productivity over varying climatic conditions in temperate environments. Despite well-documented differences in water, N, and radiation use, no consistent evidence demonstrates productivity differences among C3 and C4 perennial grass species under identical management. A field study was conducted to determine relative growth rates (RGR), nitrogen productivity (NP), and mean radiation productivity (RP) (dry matter production as a function of incident radiation) of cool- and warm-season grasses managed identically. Results were used to identify management practices thd could lead to optimal productivity in combinations or mixtures of cool- and warm-season grasses. Dry matter yields of warm-season grasses equaled or surpassed those of cool-season grasses, despite a 40% shorter growth interval. Certain cool- and warm-season grasses appear to be suitable for use in mixtures, based on distribution of herbage production; however, actual compatibility may be altered by defoliation management. Relative growth rates varied among years and were about 40% lower for canopies clipped to a 10-cm residue height each time 20-cm of growth accumulated compared with other treatments. The RGR of warm-season grasses was twice that of cool-season grasses Nitrogen productivity (g DM g-1 N d -1) and mean radiation productivity (g DM MJ-1) for warm-season grasses was also more than twice that of cool-season grasses. Radiation productivity of cool-season grasses was dependent on N, while this was not always the case for warm-season grasses. The superior production capability of certain warm-season compared with cool-season grasses in a cool-temperate environment can be sustained under a range of defoliation treatments and demonstrates suitability for use in frequently defoliated situations

  12. The geology of selected peat-forming environments in temperate and tropical latitudes

    Science.gov (United States)

    Cameron, C.C.; Palmer, C.A.; Esterle, J.S.

    1990-01-01

    We studied peat in several geologic and climatic settings: (1) a glaciated terrain in cold-temperate Maine and Minnesota, U.S.A.; (2) an island in a temperate maritime climate in the Atlantic Ocean off the coast of Maine, U.S.A., where sea level is rising rapidly and changing the environment of peat accumulation; (3) swamps along the warm-temperate U.S. Atlantic and Gulf Coastal Plains, where sea level has changed often, thus creating sites for accumulation; and (4) in a tropical climate along the coast of Sarawak, Malaysia, and the delta of the Batang Hari River, Sumatra, Indonesia (Figs. 1 and 2). With the exception of the deposits on the Atlantic and Gulf Coastal Plains, most of the deposits described are domed bogs in which peat accumulation continued above the surface of the surrounding soil. The bogs of the U.S. Atlantic and Gulf Coastal Plains have almost level surfaces. All domed bogs are not entirely ombrotrophic (watered only from precipitation); multidomed bogs that rise from irregular or hilly surfaces may be crossed by streams that supply water to the bogs. The geologic processes or organic sedimentation, namely terrestrialization and paludification, are similar in all peat deposits considered here. Differences in geomorphology affecting the quantity and that quality of peat that has ash contents of less than 25%, which are desirable for commercial purposes, depend chiefly on: (1) high humidity, which is favorable to luxuriant growth of peat-forming vegetation; (2) a depositional setting that permits extensive accumulation relatively free from inorganic contamination from sea water and streams and from dust and volcanic ash; and (3) a stable regional water table that controls the rate of decomposition under aerobic conditions and protects the deposit against the ravages of fire. Differences in peat textures are due to the type of vegetation and to the degree of decomposition. The rate of decomposition is largely the result of the amount of oxidation

  13. The geology, botany and chemistry of selected peat-forming environments from temperate and tropical latitudes

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    Cameron, C.C.; Esterle, J.S.; Palmer, C.A.

    1989-01-01

    Peat has been studied in several geologic settings: (1) glaciated terrain in cold temperate Maine and Minnesota, U.S.A.; (2) an island in the Atlantic Ocean off the coast of Maine, where sea level is rising; (3) the warm temperate U.S. Atlantic and Gulf Coastal Plains, where sea level has changed often; and (4) the tropical coast of Sarawak, Malaysia, and the tropical delta of the Batang Hari River, Sumatra, Indonesia. Most of these deposits are domed (ombrotrophic or partly ombrotrophic) bogs in which peat accumulation continued above the surface of the surrounding soil. However, the bogs of the U.S. Atlantic and Gulf Coastal Plains are comparatively not as domed, and many have almost level surfaces. In some bogs, aquatic or semi-aquatic plant materials accumulated, replaced water in the depressions, and formed a surface on which marsh or swamp vegetation could subsequently live, die, and accumulate. In others, the plant materials accumulated initially on level silt or sand surfaces supporting marshes or swamps. As the peat dome formed, plants growing on it changed from luxuriant ones near the base of the dome, where nutrients were brought into the bog by surface and ground water, to stunted ones at the top of the dome, where the raised bogs are fed by nutrient-poor precipitation. The physical and chemical changes that take place in the sequence of environments from the pond stage of deposit development, through the grassy marsh stage, through the forested swamp stage, and finally through the heath dome stage can be measured in terms of acidity and ash, volatile matter, carbon, hydrogen, nitrogen, sulfur and oxygen contents, as well as in the kind and distribution of trace elements. The organic and inorganic contents of the deposits relate to geomorphology, and geomorphology relates to their settings. As models of coal formation, some domed peat deposits may help in solving problems of distribution and character of ancient coal beds. But clearly not all peat

  14. The testicular cycle of captive Tupinambis merianae lizards in a temperate environment

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    Noriega, Teresa

    2002-08-01

    phenomenon, characterized by a short spring sexual activity. This work examines the testicular changes that occur during the reproductive cycle of Tupinambis merianae specimens raised in a temperate environment. The involvement of the kidney sexual portion as a secondary sexual gland is also considered. In autumn and winter, the testicle exhibits a discontinuous gametogenesis. Spermacytogenesis takes place in autumn, giving rise to a precocious abortive spermiogenesis which concludes at cool months. At early spring, the gonad restarts its spermiogenetic activity attaining promptly a peak of maximal growth and abundant sperm production. The testicular climax occurs shortly after hibernation and coincides with a mating period of about a month (October. At that period, the quite enlarged epididymis is lined with a cylindrical epithelium and contains large sperm masses. Simultaneously, the sexual portions of kidney tubules display hypertrophic columnar cells filled with large PAS (+ cytoplasmic granules. Soon, the reproductive activity ceases and makes way for a phase of gonadal involution which extends through the rest of spring and summer (November-February, indicating the existence of a single reproductive event per year. The observations are discussed in connection with climate factors and biological features of the group.

  15. Interactions between sire family and production environment (temperate vs. tropical) on performance and thermoregulation responses in growing pigs.

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    Rosé, R; Gilbert, H; Loyau, T; Giorgi, M; Billon, Y; Riquet, J; Renaudeau, D; Gourdine, J-L

    2017-11-01

    The aim of this study was to evaluate the effect of 2 climatic environments (temperate [TEMP] vs. tropical humid [TROP]) on production and thermoregulation traits in growing pigs. A backcross design involving Large White (LW; heat sensitive) and Creole (CR; heat tolerant) pigs was studied. The same 10 F LW × CR boars were mated with related LW sows in each environment. A total of 1,298 backcross pigs ( = 634 pigs from 11 batches for the TEMP environment and = 664 pigs from 12 batches for the TROP environment) were phenotyped on BW (every 15 d from wk 11 to 23 of age), voluntary feed intake (ADFI, from wk 11 to 23), backfat thickness (BFT; at wk 19 and 23), skin temperature (ST; at wk 19 and 23), and rectal temperature (RT; at wk 19, 21, and 23). The feed conversion ratio was computed for the whole test period (11 to 23 wk). The calculation of the temperature-humidity index showed an average difference of 2.4°C between the TEMP and TROP environments. The ADG and ADFI were higher in the TEMP environment than in the TROP environment (834 vs. 754 g/d and 2.20 vs. 1.80 kg/d, respectively; environment than in the TEMP environment (35.9 vs. 34.8°C for ST and 39.5 vs. 39.3°C for RT, respectively; environment interactions ( environment interaction and to detect QTL related to heat tolerance.

  16. Comparison of atmosphere/aquatic environment concentration ratio of volatile chlorinated hydrocarbons between temperate regions and Antarctica.

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    Zoccolillo, Lelio; Amendola, Luca; Insogna, Susanna

    2009-09-01

    For the purpose of understanding the transport and deposition mechanisms and the air-water distribution of some volatile chlorinated hydrocarbons (VCHCs), their atmosphere/aquatic environment concentration ratio was evaluated. In addition, for the purpose of differentiating VCHC behaviour in a temperate climate from its behaviour in a polar climate, the atmosphere/aquatic environment concentration ratio evaluated in matrices from temperate zones was compared with the concentration ratio evaluated in Antarctic matrices. In order to perform air samplings also at rigid Antarctic temperatures, the sampling apparatus, consisting of a diaphragm pump and canisters, was suitably modified. Chloroform, 1,1,1-trichloroethane, tetrachloromethane, 1,1,2-trichloroethylene and tetrachloroethylene were measured in air, water and snow using specific techniques composed of a purpose-made cryofocusing-trap-injector (for air samples) and a modified purge-and-trap injector (for aqueous samples) coupled to a gas chromatograph with mass spectrometric detection operating in selected ion monitoring mode. The VCHCs were retrieved in all the investigated matrices, both Italian and Antarctic, with concentrations varying from tens to thousands of ng m(-3) in air and from digits to hundreds of ng kg(-1) in water and snow. The atmosphere/aquatic environment concentration ratios were always found to be lower than 1. In particular, the Italian air/water concentration ratios were smaller than the Antarctic ones, by reason of the higher atmospheric photochemical activity in temperate zones. On the other hand, the Antarctic air/snow concentration ratios proved to be largely in favour of snow with respect to the Italian ratios, thus corroborating the hypothesis of a more efficient VCHC deposition mechanism and accumulation on Antarctic snow.

  17. Ovarian changes during the reproductive cycle of the Tupinambis merianae lizard raised in a temperate environment

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    Manes, Mario E.

    2007-03-01

    Full Text Available El ciclo reproductor de hembras de Tupinambis merianae criadas en ambiente templado consiste de tres fases gonadales: previtelogénica, vitelogénica y postovulatoria o lútea. Durante la fase previtelogénica, que ocupa gran parte del verano, el otoño e invierno, los ovarios son pequeños, pesan menos de 4 g y contienen solamente folículos no vitelogénicos, los cuales se desarrollan lentamente a partir de los nidos germinales, alcanzando unos 5 mm de diámetro. Debido a una maduración gonadal asincrónica entre ambos sexos, las cópulas acontecen cuando los ovarios son aún previtelogénicos. Luego sobreviene una corta e intensa vitelogénesis, durante la cual los folículos crecen uniformemente incrementando unas 6 veces su diámetro (cerca de 30 mm, mientras que la masa ovárica total alcanza unos 400 g. El proceso culmina entre los 15 y 20 días, con una ovulación generalizada y la subsiguiente oviposición. Como consecuencia, los ovarios postovulatorios aparecen reducidos a unos 5 g, con una superficie casi enteramente cubierta de cicatrices foliculares, las cuales pronto desarrollan cuerpos lúteos. La detención del ciclo ovárico, con atresia folicular previtelogénica masiva, como resultado del aislamiento de las hembras, permite concluir sobre la existencia de estímulos sexuales promotores de la vitelogénesis. The reproductive cycle of Tupinambis merianae females raised in a temperate environment consists of three gonadal phases: previtellogenic, vitellogenic and postovulatory or luteal phases. During the previtellogenic phase, which takes great part of the summer, autumn and winter, the ovaries are small, weigh less than 4 g, and contain only nonvitellogenic follicles, which develop slowly from germinal beds, until they are almost 5 mm diameter. Due to an asynchronous gonadal maturation in both sexes, matings occur when ovaries are still previtellogenic. Then comes a short and intense vitellogenesis, during which follicles grow

  18. Suicide with Shotgun: A Case Report

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    Ali Yildirim

    2011-03-01

    Full Text Available Suicide appears to be a major public health problem in our country and all over the World. Suicide methods will vary between the various communities the most common types of suicides are hanging, using chemicals and using firearms (pistol, shotgun. Connected with easy availability of shotguns suicide cases with using shotgun is significantly increasing in recent years. In our study, suicide with a shotgun, are evaluated in terms of shooting range and its features, originate, area of suicide, crime scene, sex and age. [J Contemp Med 2011; 1(1.000: 29-34

  19. Coupling bacterioplankton populations and environment to community function in coastal temperate waters

    DEFF Research Database (Denmark)

    Traving, S. J.; Bentzon-Tilia, Mikkel; Knudsen-Leerbeck, H.

    2016-01-01

    drivers of bacterioplankton community functions, taking into account the variability in community composition and environmental conditions over seasons, in two contrasting coastal systems. A Least Absolute Shrinkage and Selection Operator (LASSO) analysis of the biological and chemical data obtained from...... surface waters over a full year indicated that specific bacterial populations were linked to measured functions. Namely, Synechococcus (Cyanobacteria) was strongly correlated with protease activity. Both function and community composition showed seasonal variation. However, the pattern of substrate...... of common drivers of bacterioplankton community functions in two different systems indicates that the drivers may be of broader relevance in coastal temperate waters....

  20. Growth performance of commercial temperate mushrooms Agaricus bisporus and Hypsizygus sp. under local environment

    International Nuclear Information System (INIS)

    Rosnani Abdul Rashid; Mat Rasol Awang; Hassan Hamdani Hassan Mutaat; Mohd Meswan Maskom

    2010-01-01

    To date, the Malaysian mushroom industry focuses on only seven species of mushroom for commercial purpose. To expand and further develop the mushroom industry, new mushroom species should be introduced into our local market. Temperate mushrooms are possible to be cultivated commercially in Malaysia but the optimisation of growth performance for high quality spawn and high mushroom yield need to be studied. In the present study the growth performance of mycelia of Agaricus bisporus and Hypsizygus sp. on culture media and substrates were investigated. Four types of culture media, viz. Potato Dextrose Agar (PDA), Nutrient Agar (NA), Malt Yeast Extract (MYE) and Complete Yeast Media (CYM) were used to determine the suitable culturing media for mycelial growth. The mycelia were inoculated on oil palm empty fruit bunch (EFB) and sawdust substrate and incubated at room temperature and in a low temperature in incubation room (10 - 12 degree Celsius). From the observation, Agaricus bisporus grew better on Malt Yeast Extract (MYE) medium with a growth rate of 0.306 cm/ day. Complete Yeast Media (CYM) was found more suitable for Hypsizygus sp. with a growth rate of 1.049 cm/ day. The linear growth rate of mycelium as measured on the surface of mushroom bag of Agaricus bisporus on EFB incubated at room temperature was 0.4364 cm/ day and cool temperature was 0.055 cm/ day. For Hypsizygus sp. the linear growth rate of the mycelium was 2.11 cm/ day. The linear growth of Hypsizygus sp. on sawdust substrate incubated in cool temperature was 1.4 cm/ day. (author)

  1. Antibiotic resistant Pseudomonas spp. in the aquatic environment: A prevalence study under tropical and temperate climate conditions.

    Science.gov (United States)

    Devarajan, Naresh; Köhler, Thilo; Sivalingam, Periyasamy; van Delden, Christian; Mulaji, Crispin K; Mpiana, Pius T; Ibelings, Bastiaan W; Poté, John

    2017-05-15

    Microbial populations which are resistant to antibiotics are an emerging environmental concern with potentially serious implications for public health. Thus, there is a growing concern in exploring the occurrence of antibiotic resistance in the environment with no limitations to the factors that contribute to their emergence. The aquatic environment is considered to be a hot-spot for the acquisition and spread of antibiotic resistance due to pollution with emerging contaminants derived from anthropogenic activities. In this study, we report on the isolation and characterization of 141 Pseudomonas spp. from aquatic sediments receiving partially (un)treated hospital and communal effluents from three distinct geographical locations: Democratic Republic of the Congo (DRC), India (IN), and Switzerland (CH). P. putida (42%) and P. aeruginosa (39%) were the dominant Pseudomonas species. The highest frequency of antibiotic resistance against eight anti-pseudomonas agents was found among IN isolates (35-60%), followed by DRC (18-50%) and CH (12-54%). CTX-M was the most frequent β-lactamase found in CH (47% of isolates), while VIM-1 was dominant in isolates from DRC (61%) and IN (29%). NDM-1 was found in 29% of the total IN isolates and surprisingly also in 6% of CH isolates. Chromosomally-encoded efflux mechanisms were overexpressed in P. aeruginosa isolates from all three geographic locations. In vitro conjugative transfers of antibiotic resistance plasmids occurred more frequently under tropical temperatures (30 and 37 °C) than under temperate conditions (10 °C). The presence of Extended Spectrum β-lactamases (ESBLs) and Metallo β-lactamases (MBLs) in the isolates from environmental samples has important implications for humans who depend on public water supply and sanitation facilities. To our knowledge, this is the first study to demonstrate a comparison between treated/untreated effluents from urban and hospital settings as a source of microbial resistance

  2. Time-Dependent Effects of Acute Exercise on University Students’ Cognitive Performance in Temperate and Cold Environments

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    Ling-Yu Ji

    2017-07-01

    Full Text Available Background: Few studies have examined the acute exercise-induced changes in cognitive performance in different thermal environments and the time course effects.Objective: Investigate the time-dependent effects of acute exercise on university students’ processing speed, working memory and cognitive flexibility in temperate and cold environments.Method: Twenty male university students (age 23.5 ± 2.0 years with moderate physical activity level participated in a repeated-measures within-subjects design. Processing speed, working memory and cognitive flexibility were assessed using CogState test battery at baseline (BASE, followed by a 45-min rest (REST, immediately after (EX and 30 min after (POST-EX 30-min moderate-intensity treadmill running in both temperate (TEMP; 25°C and cold (COLD; 10°C environments. Mean skin temperature (MST and thermal sensation (TS were also recorded. Two-way repeated measures ANOVA was performed to analyze each variable. Spearman’s rho was used to identify the correlations between MST, TS and cognitive performance.Results: Reaction time (RT of processing speed and working memory decreased immediately after exercise in both conditions (processing speed: p = 0.003; working memory: p = 0.007. The facilitating effects on processing speed disappeared within 30 min after exercise in TEMP (p = 0.163 and COLD (p = 0.667, while improvements on working memory remained 30 min after exercise in TEMP (p = 0.047, but not in COLD (p = 0.663. Though RT of cognitive flexibility reduced in both conditions (p = 0.003, no significance was found between EX and REST (p = 0.135. Increased MST and TS were significantly associated with reductions in processing speed RT (MST: r = -0.341, p < 0.001; TS: r = -0.262, p = 0.001 and working memory RT (MST: r = -0.282, p < 0.001; TS: r = -0.2229, p = 0.005, and improvements in working memory accuracy (MST: r = 0.249, p = 0.002; TS: r = 0.255, p = 0.001.Conclusion: The results demonstrate

  3. Spring molybdenum enrichment in scallop shells: a potential tracer of diatom productivity in coastal temperate environments (Brittany, NW France)?

    Science.gov (United States)

    Barats, A.; Amouroux, D.; Pécheyran, C.; Chauvaud, L.; Thébault, J.; Donard, O. F. X.

    2009-08-01

    Skeletal molybdenum/calcium ([Mo]/[Ca])shell ratios were recently examined in bivalves. These ratios were determined by quantitative LA-ICP-MS analyses every third daily striae (i.e. a temporal resolution of 3 days) in 36 flat valves of the Great Scallop shells Pecten maximus (2-year old; 3 shells/year) collected in temperate coastal environments of Western Europe (42 to 49° N). Variations of ([Mo]/[Ca])shell ratio were significant and reproducible for scallops from a same population, from different years (1998-2004) and from different coastal temperate locations. ([Mo]/[Ca])shell exhibits typical profiles characterized by a background content, below the method detection limit (<0.003 μmol/mol) for most of the shell growth period, which is punctuated by a significant transient enrichment (0.031-2.1 μmol/mol) mainly occurring from May to June. The Bay of Brest (France) was especially investigated because of long term observations on scallop communities, environmental variables, and high resolution analyses of dissolved Mo in bottom seawater in 2000. In 2000, dissolved Mo exhibited significant increasing concentration just preceding a maximum of ([Mo]/[Ca])shell ratio. The environmental conditions preceding ([Mo]/[Ca])shell maximum events, both in 2000 and over the 7-year survey indicates a direct influence of the scallop environmental conditions at the sediment water interface subsequent to the intense and periodic spring bloom event. Spring maxima of ([Mo]/[Ca])shell ratio were found to be specifically related to the dynamic of spring diatom blooms and to the extent of the subsequent silicate depletion. ([Mo]/[Ca])shell records reveal thus unexpected biogeochemical routes of Mo, potentially related to coastal spring productivity.

  4. Index for characterizing post-fire soil environments in temperate coniferous forests

    Science.gov (United States)

    Theresa B. Jain; David S. Pilliod; Russell T. Graham; Leigh B. Lentile; Jonathan E. Sandquist

    2012-01-01

    Many scientists and managers have an interest in describing the environment following a fire to understand the effects on soil productivity, vegetation growth, and wildlife habitat, but little research has focused on the scientific rationale for classifying the post-fire environment. We developed an empirically-grounded soil post-fire index (PFI) based on available...

  5. Seagrasses under threat: Understanding the resilience of temperate seagrass meadows in a changing environment

    NARCIS (Netherlands)

    Soissons, L.M.

    2017-01-01

    Despite being highly valuable ecosystems, seagrass meadows are threatened worldwide, mostly by human activities. In order to preserve seagrass meadows from collapse, we need to better understand their resilience in a changing environment. By means of various

  6. "Shotgunning" as an illicit drug smoking practice.

    Science.gov (United States)

    Perlman, D C; Perkins, M P; Paone, D; Kochems, L; Salomon, N; Friedmann, P; Des Jarlais, D C

    1997-01-01

    There has been a rise in illicit drug smoking in the United States. "Shotgunning" drugs (or "doing a shotgun") refers to the practice of inhaling smoke and then exhaling it into another individual's mouth, a practice with the potential for the efficient transmission of respiratory pathogens. Three hundred fifty-four drug users (239 from a syringe exchange and 115 from a drug detoxification program) were interviewed about shotgunning and screened for tuberculosis (TB). Fifty-nine (17%; 95% CI 12.9%-20.9%) reported shotgunning while smoking crack cocaine (68%), marijuana (41%), or heroin (2%). In multivariate analysis, age alcohol to intoxication (OR 2.2, 95% CI 1.1-4.3), having engaged in high-risk sex (OR 2.6, 95% CI 1.04-6.7), and crack use (OR 6.0, 95% CI 3.0-12) were independently associated with shotgunning. Shotgunning is a frequent drug smoking practice with the potential to transmit respiratory pathogens, underscoring the need for education of drug users about the risks of specific drug use practices, and the ongoing need for TB control among active drug users.

  7. Shotgun Proteomics and Biomarker Discovery

    Directory of Open Access Journals (Sweden)

    W. Hayes McDonald

    2002-01-01

    Full Text Available Coupling large-scale sequencing projects with the amino acid sequence information that can be gleaned from tandem mass spectrometry (MS/MS has made it much easier to analyze complex mixtures of proteins. The limits of this “shotgun” approach, in which the protein mixture is proteolytically digested before separation, can be further expanded by separating the resulting mixture of peptides prior to MS/MS analysis. Both single dimensional high pressure liquid chromatography (LC and multidimensional LC (LC/LC can be directly interfaced with the mass spectrometer to allow for automated collection of tremendous quantities of data. While there is no single technique that addresses all proteomic challenges, the shotgun approaches, especially LC/LC-MS/MS-based techniques such as MudPIT (multidimensional protein identification technology, show advantages over gel-based techniques in speed, sensitivity, scope of analysis, and dynamic range. Advances in the ability to quantitate differences between samples and to detect for an array of post-translational modifications allow for the discovery of classes of protein biomarkers that were previously unassailable.

  8. Index for characterizing post-fire soil environments in temperate coniferous forests

    Science.gov (United States)

    Jain, Theresa B.; Pilliod, David S.; Graham, Russell T.; Lentile, Leigh B.; Sandquist, Jonathan E.

    2012-01-01

    Many scientists and managers have an interest in describing the environment following a fire to understand the effects on soil productivity, vegetation growth, and wildlife habitat, but little research has focused on the scientific rationale for classifying the post-fire environment. We developed an empirically-grounded soil post-fire index (PFI) based on available science and ecological thresholds. Using over 50 literature sources, we identified a minimum of five broad categories of post-fire outcomes: (a) unburned, (b) abundant surface organic matter ( > 85% surface organic matter), (c) moderate amount of surface organic matter ( ≥ 40 through 85%), (d) small amounts of surface organic matter ( communication of potential responses or outcomes (e.g., erosion potential) from fires of varying severities.

  9. Spring molybdenum enrichment in scallop shells: a potential tracer of diatom productivity in temperate coastal environments (Brittany, NW France)

    Science.gov (United States)

    Barats, A.; Amouroux, D.; Pécheyran, C.; Chauvaud, L.; Thébault, J.; Donard, O. F. X.

    2010-01-01

    Skeletal molybdenum/calcium ([Mo]/[Ca])shell ratios were examined in shells of the Great Scallop Pecten maximus collected in temperate coastal environments of Western Europe (42 to 49° N). These ratios were determined by quantitative LA-ICP-MS analyses of daily striae taken every third day (i.e. a temporal resolution of 3 days) in 36 flat valves (2-years old; 3 shells/year). Variations of ([Mo]/[Ca])shell ratios were significant and reproducible for scallops from the same population, from different years (1998-2004) and temperate coastal locations (NW France). The [Mo]/[Ca])shell ratios exhibit typical profiles characterized by a background content, below the detection limit for this method (<0.003 μmol/mol) for most of the shell growth period, which is punctuated by a significant transient enrichment (0.031-2.1 μmol/mol) mainly occurring from May to June. The Bay of Brest (France) was investigated in particular because of its long term observations on scallop communities, environmental variables, and high resolution analyses of dissolved Mo in bottom seawater in 2000. In 2000, dissolved Mo exhibited a significant increase in concentration just preceding the maximum ([Mo]/[Ca])shell ratio. Both the intense monitoring survey in 2000 and over the 7-year period indicates that the ([Mo]/[Ca])shell maximum is directly influenced by spring changes of environmental conditions at the sediment water interface (SWI), occurring subsequent to the intense and periodic spring bloom. Spring maxima of ([Mo]/[Ca])shell ratios are closely correlated to the extent of silicic acid and nitrate depletion in seawater between winter and late spring (r2=0.878 and 0.780, p<0.05, n=6) that reflects diatom uptake and productivity in the Bay of Brest. The Mo inputs in bottom waters and subsequent shell enrichment are thus suggested to be directly or indirectly influenced by such biogenic material input at the SWI. The [Mo]/[Ca])shell records thus reveal unexpected biogeochemical cycles of

  10. Atmospheric mixing ratios of methyl ethyl ketone (2-butanone in tropical, boreal, temperate and marine environments

    Directory of Open Access Journals (Sweden)

    A. M. Yáñez-Serrano

    2016-09-01

    Full Text Available Methyl ethyl ketone (MEK enters the atmosphere following direct emission from vegetation and anthropogenic activities, as well as being produced by the gas-phase oxidation of volatile organic compounds (VOCs such as n-butane. This study presents the first overview of ambient MEK measurements at six different locations, characteristic of forested, urban and marine environments. In order to understand better the occurrence and behaviour of MEK in the atmosphere, we analyse diel cycles of MEK mixing ratios, vertical profiles, ecosystem flux data, and HYSPLIT back trajectories, and compare with co-measured VOCs. MEK measurements were primarily conducted with proton-transfer-reaction mass spectrometer (PTR-MS instruments. Results from the sites under biogenic influence demonstrate that vegetation is an important source of MEK. The diel cycle of MEK follows that of ambient temperature and the forest structure plays an important role in air mixing. At such sites, a high correlation of MEK with acetone was observed (e.g. r2 = 0.96 for the SMEAR Estonia site in a remote hemiboreal forest in Tartumaa, Estonia, and r2 = 0.89 at the ATTO pristine tropical rainforest site in central Amazonia. Under polluted conditions, we observed strongly enhanced MEK mixing ratios. Overall, the MEK mixing ratios and flux data presented here indicate that both biogenic and anthropogenic sources contribute to its occurrence in the global atmosphere.

  11. Forest impacts on snow accumulation and ablation across an elevation gradient in a temperate montane environment

    Science.gov (United States)

    Roth, Travis R.; Nolin, Anne W.

    2017-11-01

    Forest cover modifies snow accumulation and ablation rates via canopy interception and changes in sub-canopy energy balance processes. However, the ways in which snowpacks are affected by forest canopy processes vary depending on climatic, topographic and forest characteristics. Here we present results from a 4-year study of snow-forest interactions in the Oregon Cascades. We continuously monitored snow and meteorological variables at paired forested and open sites at three elevations representing the Low, Mid, and High seasonal snow zones in the study region. On a monthly to bi-weekly basis, we surveyed snow depth and snow water equivalent across 900 m transects connecting the forested and open pairs of sites. Our results show that relative to nearby open areas, the dense, relatively warm forests at Low and Mid sites impede snow accumulation via canopy snow interception and increase sub-canopy snowpack energy inputs via longwave radiation. Compared with the Forest sites, snowpacks are deeper and last longer in the Open site at the Low and Mid sites (4-26 and 11-33 days, respectively). However, we see the opposite relationship at the relatively colder High sites, with the Forest site maintaining snow longer into the spring by 15-29 days relative to the nearby Open site. Canopy interception efficiency (CIE) values at the Low and Mid Forest sites averaged 79 and 76 % of the total event snowfall, whereas CIE was 31 % at the lower density High Forest site. At all elevations, longwave radiation in forested environments appears to be the primary energy component due to the maritime climate and forest presence, accounting for 93, 92, and 47 % of total energy inputs to the snowpack at the Low, Mid, and High Forest sites, respectively. Higher wind speeds in the High Open site significantly increase turbulent energy exchanges and snow sublimation. Lower wind speeds in the High Forest site create preferential snowfall deposition. These results show the importance of

  12. An automatic approach for rice mapping in temperate region using time series of MODIS imagery: first results for Mediterranean environment

    Science.gov (United States)

    Boschetti, M.; Nelson, A.; Manfrom, G.; Brivio, P. A.

    2012-04-01

    Timely and accurate information on crop typology and status are required to support suitable action to better manage agriculture production and reduce food insecurity. More specifically, regional crop masking and phenological information are important inputs for spatialized crop growth models for yield forecasting systems. Digital cartographic data available at global/regional scale, such as GLC2000, GLOBCOVER or MODIS land cover products (MOD12), are often not adequate for this crop modeling application. For this reason, there is a need to develop and test methods that can provide such information for specific cropsusing automated classification techniques.. In this framework we focused our analysis on the rice cultivation area detection due to the importance of this crop. Rice is a staple food for half of the world's population (FAO 2004). Over 90% of the world's rice is produced and consumed in Asia and the region is home to 70% of the world's poor, most of whom depend on rice for their livelihoods andor food security. Several initiatives are being promoted at the international level to provide maps of rice cultivated areas in South and South East Asia using different approaches available in literature for rice mapping in tropical regions. We contribute to these efforts by proposing an automatic method to detect rice cultivated areas in temperate regions exploiting MODIS 8-Day composite of Surface Reflectance at 500m spatial resolution (MOD09A1product). Temperate rice is cultivated worldwide in more than 20 countries covering around 16M ha for a total production of about 65M tons of paddy per year. The proposed method is based on a common approach available in literature that first identifies flood condition that can be related to rice agronomic practice and then checks for vegetation growth. The method presents innovative aspects related both to the flood detection, exploiting Short Wave Infrared spectral information, and to the crop grow monitoring analyzing

  13. 24-h Fluid Kinetics and Perception of Sweat Losses Following a 1-h Run in a Temperate Environment

    Directory of Open Access Journals (Sweden)

    Eric K. O'Neal

    2013-12-01

    Full Text Available This study examined 24-h post-run hydration status and sweat loss estimation accuracy in college age runners (men = 12, women = 8 after completing a 1-h self-paced outdoor run (wet bulb globe temperature = 19.9 ± 3.0 °C. Sweat losses (1353 ± 422 mL; 1.9% ± 0.5% of body mass were significantly greater (p < 0.001 than perceived losses (686 ± 586 mL. Cumulative fluid consumption equaled 3876 ± 1133 mL (218 ± 178 mL during with 37% of fluid ingested lost through urine voids (1450 ± 678 mL. Fluid balance based on intake and urine production equaled +554 ± 669 mL at 12 h and +1186 ± 735 mL at 24 h. Most runners reported euhydrated (pre-run urine specific gravity (USG = 1.018 ± 0.008 with no changes (p = 0.33 at hours 12 or 24 when both genders were included. However, USG was higher (p = 0.004 at 12 h post-run for men (1.025 ± 0.0070 vs. 1.014 ± 0.007, who consumed 171% ± 40% of sweat losses at 12 h vs. 268% ± 88% for women. Most runners do not need intervention concerning between bout hydration needs in temperate environments. However, repeated USG measurements were able to identify runners who greatly under or over consumed fluid during recovery. Practitioners can use multiple USG assessments as cheap method to detect runners who need to modify their hydration strategies and should promote assessment of sweat losses by change in body mass, as runners had poor perception of sweat losses.

  14. Temper Tantrums

    Science.gov (United States)

    ... Nine Steps to More Effective Parenting How Can Parents Discipline Without Spanking? Delayed Speech or Language Development Talking to Your Child's Preschool Teacher Your Child's Habits Separation Anxiety Breath-Holding Spells Train Your Temper View ...

  15. Shotgun approaches to gait analysis : insights & limitations

    NARCIS (Netherlands)

    Kaptein, Ronald G.; Wezenberg, Daphne; IJmker, Trienke; Houdijk, Han; Beek, Peter J.; Lamoth, Claudine J. C.; Daffertshofer, Andreas

    2014-01-01

    Background: Identifying features for gait classification is a formidable problem. The number of candidate measures is legion. This calls for proper, objective criteria when ranking their relevance. Methods: Following a shotgun approach we determined a plenitude of kinematic and physiological gait

  16. Entrance, exit, and reentrance of one shot with a shotgun

    DEFF Research Database (Denmark)

    Gulmann, C; Hougen, H P

    1999-01-01

    The case being reported is one of a homicidal shotgun fatality with an unusual wound pattern. A 34-year-old man was shot at close range with a 12-gauge shotgun armed with No. 5 birdshot ammunition. The shot entered the left axillary region, exited through the left infraclavicular region, and ther......The case being reported is one of a homicidal shotgun fatality with an unusual wound pattern. A 34-year-old man was shot at close range with a 12-gauge shotgun armed with No. 5 birdshot ammunition. The shot entered the left axillary region, exited through the left infraclavicular region...

  17. Tempered fractional calculus

    Energy Technology Data Exchange (ETDEWEB)

    Sabzikar, Farzad, E-mail: sabzika2@stt.msu.edu [Department of Statistics and Probability, Michigan State University, East Lansing, MI 48823 (United States); Meerschaert, Mark M., E-mail: mcubed@stt.msu.edu [Department of Statistics and Probability, Michigan State University, East Lansing, MI 48823 (United States); Chen, Jinghua, E-mail: cjhdzdz@163.com [School of Sciences, Jimei University, Xiamen, Fujian, 361021 (China)

    2015-07-15

    Fractional derivatives and integrals are convolutions with a power law. Multiplying by an exponential factor leads to tempered fractional derivatives and integrals. Tempered fractional diffusion equations, where the usual second derivative in space is replaced by a tempered fractional derivative, govern the limits of random walk models with an exponentially tempered power law jump distribution. The limiting tempered stable probability densities exhibit semi-heavy tails, which are commonly observed in finance. Tempered power law waiting times lead to tempered fractional time derivatives, which have proven useful in geophysics. The tempered fractional derivative or integral of a Brownian motion, called a tempered fractional Brownian motion, can exhibit semi-long range dependence. The increments of this process, called tempered fractional Gaussian noise, provide a useful new stochastic model for wind speed data. A tempered fractional difference forms the basis for numerical methods to solve tempered fractional diffusion equations, and it also provides a useful new correlation model in time series.

  18. Tempered fractional calculus

    Science.gov (United States)

    Sabzikar, Farzad; Meerschaert, Mark M.; Chen, Jinghua

    2015-07-01

    Fractional derivatives and integrals are convolutions with a power law. Multiplying by an exponential factor leads to tempered fractional derivatives and integrals. Tempered fractional diffusion equations, where the usual second derivative in space is replaced by a tempered fractional derivative, govern the limits of random walk models with an exponentially tempered power law jump distribution. The limiting tempered stable probability densities exhibit semi-heavy tails, which are commonly observed in finance. Tempered power law waiting times lead to tempered fractional time derivatives, which have proven useful in geophysics. The tempered fractional derivative or integral of a Brownian motion, called a tempered fractional Brownian motion, can exhibit semi-long range dependence. The increments of this process, called tempered fractional Gaussian noise, provide a useful new stochastic model for wind speed data. A tempered fractional difference forms the basis for numerical methods to solve tempered fractional diffusion equations, and it also provides a useful new correlation model in time series.

  19. Tempered fractional calculus

    International Nuclear Information System (INIS)

    Sabzikar, Farzad; Meerschaert, Mark M.; Chen, Jinghua

    2015-01-01

    Fractional derivatives and integrals are convolutions with a power law. Multiplying by an exponential factor leads to tempered fractional derivatives and integrals. Tempered fractional diffusion equations, where the usual second derivative in space is replaced by a tempered fractional derivative, govern the limits of random walk models with an exponentially tempered power law jump distribution. The limiting tempered stable probability densities exhibit semi-heavy tails, which are commonly observed in finance. Tempered power law waiting times lead to tempered fractional time derivatives, which have proven useful in geophysics. The tempered fractional derivative or integral of a Brownian motion, called a tempered fractional Brownian motion, can exhibit semi-long range dependence. The increments of this process, called tempered fractional Gaussian noise, provide a useful new stochastic model for wind speed data. A tempered fractional difference forms the basis for numerical methods to solve tempered fractional diffusion equations, and it also provides a useful new correlation model in time series

  20. Evaluation of heat stress effects on production traits and somatic cell score of Holsteins in a temperate environment.

    Science.gov (United States)

    Hammami, H; Bormann, J; M'hamdi, N; Montaldo, H H; Gengler, N

    2013-03-01

    This study was aimed to evaluate the degree of thermal stress exhibited by Holsteins under a continental temperate climate. Milk, fat, protein, and somatic cell count test-day records collected between 2000 and 2011 from 23,963 cows in 604 herds were combined with meteorological data from 14 public weather stations in Luxembourg. Daily values of 6 different thermal indices (TI) weighted in term of temperature, relative humidity, solar radiation, and wind speed were calculated by averaging hourly TI over 24h. Heat stress thresholds were first identified by a broken-line regression model. Regression models were thereafter applied to quantify milk production losses due to heat stress. The tipping points at which milk and protein yields declined were effectively identified. For fat yield, no valid threshold was identified for any of the studied TI. Daily fat yields tended to decrease steadily with increasing values of TI. Daily somatic cell score patterns were marked by increased values at both lowest and highest TI ranges, with a more pronounced reaction to cold stress for apparent temperature indices. Thresholds differed between TI and traits. For production traits, they ranged from 62 (TI(1)) to 80 (TI(3)) for temperature-humidity indices (THI) and from 16 (TI(5)) to 20 (TI(6)) for apparent temperature indices. Corresponding somatic cell score thresholds were higher and ranged from 66 (TI(1)) to 82 (TI(3)) and from 20 (TI(5)) to 23 (TI(6)), respectively. The largest milk decline per unit of mild, moderate, and extreme heat stress levels of 0.164, 0.356, and 0.955 kg, respectively, was observed when using the conventional THI (TI(1)). The highest yearly milk, fat, and protein losses of 54, 5.7, and 4.2 kg, respectively, were detected by TI(2), the THI index that is adjusted for wind speed and solar radiation. The latter index could be considered as the best indicator of heat stress to be used for forecast and herd management in a first step in temperate regions under

  1. Species associations structured by environment and land-use history promote beta-diversity in a temperate forest.

    Science.gov (United States)

    Murphy, Stephen J; Audino, Livia D; Whitacre, James; Eck, Jenalle L; Wenzel, John W; Queenborough, Simon A; Comita, Liza S

    2015-03-01

    Patterns of diversity and community composition in forests are controlled by a combination of environmental factors, historical events, and stochastic or neutral mechanisms. Each of these processes has been linked to forest community assembly, but their combined contributions to alpha and beta-diversity in forests has not been well explored. Here we use variance partitioning to analyze approximately 40,000 individual trees of 49 species, collected within 137 ha of sampling area spread across a 900-ha temperate deciduous forest reserve in Pennsylvania to ask (1) To what extent is site-to-site variation in species richness and community composition of a temperate forest explained by measured environmental gradients and by spatial descriptors (used here to estimate dispersal-assembly or unmeasured, spatially structured processes)? (2) How does the incorporation of land-use history information increase the importance attributed to deterministic community assembly? and (3) How do the distributions and abundances of individual species within the community correlate with these factors? Environmental variables (i.e., topography, soils, and distance to stream), spatial descriptors (i.e., spatial eigenvectors derived from Cartesian coordinates), and land-use history variables (i.e., land-use type and intensity, forest age, and distance to road), explained about half of the variation in both species richness and community composition. Spatial descriptors explained the most variation, followed by measured environmental variables and then by land- use history. Individual species revealed variable responses to each of these sets of predictor variables. Several species were associated with stream habitats, and others were strictly delimited across opposing north- and south-facing slopes. Several species were also associated with areas that experienced recent (i.e., indicate that deterministic factors, including environmental and land-use history variables, are important drivers

  2. Interactive Effects of Temperature and UV Radiation on Photosynthesis of Chlorella Strains from Polar, Temperate and Tropical Environments: Differential Impacts on Damage and Repair

    Science.gov (United States)

    Wong, Chiew-Yen; Teoh, Ming-Li; Phang, Siew-Moi; Lim, Phaik-Eem; Beardall, John

    2015-01-01

    Global warming and ozone depletion, and the resulting increase of ultraviolet radiation (UVR), have far-reaching impacts on biota, especially affecting the algae that form the basis of the food webs in aquatic ecosystems. The aim of the present study was to investigate the interactive effects of temperature and UVR by comparing the photosynthetic responses of similar taxa of Chlorella from Antarctic (Chlorella UMACC 237), temperate (Chlorella vulgaris UMACC 248) and tropical (Chlorella vulgaris UMACC 001) environments. The cultures were exposed to three different treatments: photosynthetically active radiation (PAR; 400–700 nm), PAR plus ultraviolet-A (320–400 nm) radiation (PAR + UV-A) and PAR plus UV-A and ultraviolet-B (280–320 nm) radiation (PAR + UV-A + UV-B) for one hour in incubators set at different temperatures. The Antarctic Chlorella was exposed to 4, 14 and 20°C. The temperate Chlorella was exposed to 11, 18 and 25°C while the tropical Chlorella was exposed to 24, 28 and 30°C. A pulse-amplitude modulated (PAM) fluorometer was used to assess the photosynthetic response of microalgae. Parameters such as the photoadaptive index (Ek) and light harvesting efficiency (α) were determined from rapid light curves. The damage (k) and repair (r) rates were calculated from the decrease in ΦPSIIeff over time during exposure response curves where cells were exposed to the various combinations of PAR and UVR, and fitting the data to the Kok model. The results showed that UV-A caused much lower inhibition than UV-B in photosynthesis in all Chlorella isolates. The three isolates of Chlorella from different regions showed different trends in their photosynthesis responses under the combined effects of UVR (PAR + UV-A + UV-B) and temperature. In accordance with the noted strain-specific characteristics, we can conclude that the repair (r) mechanisms at higher temperatures were not sufficient to overcome damage caused by UVR in the Antarctic Chlorella strain

  3. Interactive Effects of Temperature and UV Radiation on Photosynthesis of Chlorella Strains from Polar, Temperate and Tropical Environments: Differential Impacts on Damage and Repair.

    Directory of Open Access Journals (Sweden)

    Chiew-Yen Wong

    Full Text Available Global warming and ozone depletion, and the resulting increase of ultraviolet radiation (UVR, have far-reaching impacts on biota, especially affecting the algae that form the basis of the food webs in aquatic ecosystems. The aim of the present study was to investigate the interactive effects of temperature and UVR by comparing the photosynthetic responses of similar taxa of Chlorella from Antarctic (Chlorella UMACC 237, temperate (Chlorella vulgaris UMACC 248 and tropical (Chlorella vulgaris UMACC 001 environments. The cultures were exposed to three different treatments: photosynthetically active radiation (PAR; 400-700 nm, PAR plus ultraviolet-A (320-400 nm radiation (PAR + UV-A and PAR plus UV-A and ultraviolet-B (280-320 nm radiation (PAR + UV-A + UV-B for one hour in incubators set at different temperatures. The Antarctic Chlorella was exposed to 4, 14 and 20°C. The temperate Chlorella was exposed to 11, 18 and 25°C while the tropical Chlorella was exposed to 24, 28 and 30°C. A pulse-amplitude modulated (PAM fluorometer was used to assess the photosynthetic response of microalgae. Parameters such as the photoadaptive index (Ek and light harvesting efficiency (α were determined from rapid light curves. The damage (k and repair (r rates were calculated from the decrease in ΦPSIIeff over time during exposure response curves where cells were exposed to the various combinations of PAR and UVR, and fitting the data to the Kok model. The results showed that UV-A caused much lower inhibition than UV-B in photosynthesis in all Chlorella isolates. The three isolates of Chlorella from different regions showed different trends in their photosynthesis responses under the combined effects of UVR (PAR + UV-A + UV-B and temperature. In accordance with the noted strain-specific characteristics, we can conclude that the repair (r mechanisms at higher temperatures were not sufficient to overcome damage caused by UVR in the Antarctic Chlorella strain

  4. Performance comparison of dwarf laying hens segregating for the naked neck gene in temperate and subtropical environments

    Directory of Open Access Journals (Sweden)

    Bordas André

    2009-01-01

    Full Text Available Abstract This study compares laying performances between two environments of dwarf laying hen lines segregating for the naked neck mutation (NA locus, a selected dwarf line of brown-egg layers and its control line. Layers with one of the three genotypes at the NA locus were produced from 11 sires from the control line and 12 sires from the selected line. Two hatches produced 216 adult hens in Taiwan and 297 hens in France. Genetic parameters for laying traits were estimated in each environment and the ranking of sire breeding values was compared between environments. Laying performance was lower, and mortality was higher in Taiwan than in France. The line by environment interaction was highly significant for body weight at 16 weeks, clutch length and egg number, with or without Box-Cox transformation. The selected line was more sensitive to environmental change but in Taiwan it could maintain a higher egg number than the control line. Estimated heritability values in the selected line were higher in France than in Taiwan, but not for all the traits in the control line. The rank correlations between sire breeding values were low within the selected line and slightly higher in the control line. A few sire families showed a good ranking in both environments, suggesting that some families may adapt better to environmental change.

  5. OTU analysis using metagenomic shotgun sequencing data.

    Directory of Open Access Journals (Sweden)

    Xiaolin Hao

    Full Text Available Because of technological limitations, the primer and amplification biases in targeted sequencing of 16S rRNA genes have veiled the true microbial diversity underlying environmental samples. However, the protocol of metagenomic shotgun sequencing provides 16S rRNA gene fragment data with natural immunity against the biases raised during priming and thus the potential of uncovering the true structure of microbial community by giving more accurate predictions of operational taxonomic units (OTUs. Nonetheless, the lack of statistically rigorous comparison between 16S rRNA gene fragments and other data types makes it difficult to interpret previously reported results using 16S rRNA gene fragments. Therefore, in the present work, we established a standard analysis pipeline that would help confirm if the differences in the data are true or are just due to potential technical bias. This pipeline is built by using simulated data to find optimal mapping and OTU prediction methods. The comparison between simulated datasets revealed a relationship between 16S rRNA gene fragments and full-length 16S rRNA sequences that a 16S rRNA gene fragment having a length >150 bp provides the same accuracy as a full-length 16S rRNA sequence using our proposed pipeline, which could serve as a good starting point for experimental design and making the comparison between 16S rRNA gene fragment-based and targeted 16S rRNA sequencing-based surveys possible.

  6. A comparative assessment of heavy metal accumulation in soft parts and byssus of mussels from subarctic, temperate, subtropical and tropical marine environments

    International Nuclear Information System (INIS)

    Szefer, P.; Fowler, S.W.; Ikuta, K.; Osuna, F. Paez; Ali, A.A.; Kim, B.-S.; Fernandes, H.M.; Belzunce, M.-J.; Guterstam, B.; Kunzendorf, H.; Wolowicz, M.; Hummel, H.; Deslous-Paoli, M.

    2006-01-01

    Existing data on metal concentrations in mussels from subarctic, temperate, subtropical and tropical waters were analyzed using multivariate statistics in order to assess regional variations in metal contamination. Potential errors were reduced by only analyzing data from surveys that employed the same protocols, analytical methodologies and analysts. Factor analysis demonstrated that mussels inhabiting extremely contaminated areas (e.g. from Japanese and Swedish metallurgy sources) could be separated from mussels from other contaminated areas, and that metals such as Cd, Pb, Cu and Zn could be used to identify heavily contaminated samples while Co, Fe, Cr and Ni concentrations were good markers for exposure to inputs from different industrial sources. Furthermore byssus, like soft tissue, selectively and sensitively reflects variations of certain metal concentrations in ambient waters and thus serves as a reliable biomonitor for these contaminants in a variety of coastal and estuarine areas. - Byssus of mytilids, like soft tissues can be used as efficient biomonitor for heavy metals in the marine environment

  7. A comparative assessment of heavy metal accumulation in soft parts and byssus of mussels from subarctic, temperate, subtropical and tropical marine environments

    Energy Technology Data Exchange (ETDEWEB)

    Szefer, P. [Department of Food Sciences, Medical University of Gdansk, Al. Gen. J. Hallera 107, PL 80-416 Gdansk (Poland)]. E-mail: pszef@amg.gda.pl; Fowler, S.W. [IAEA Marine Environment Laboratory, 4 Quai Antoine 1er, MC-98000 (Monaco); Ikuta, K. [Laboratory of Aquatic Environment and Ecology, Department of Fisheries, Faculty of Agriculture, Miyazaki University, 889-21 Miyazaki (Japan); Osuna, F. Paez [Institute of Marine Sciences and Limnology, Mazatlan Station, National Autonomous University of Mexico, Mazatlan 82000, Sinaloa (Mexico); Ali, A.A. [Faculty of Science, Arts and Education, University of Aden, PO Box 6014, Khormaksar, Aden (Yemen); Kim, B.-S. [School of Earth and Environmental Science, Seoul National University, 56-1 Shillimdong, 151-742 (Korea, Republic of); Fernandes, H.M. [Instituto de Radioprotecao e Dosimetria, Cz. Postal 37 750 - CEP: 22642-970, Rio de Janeiro (Brazil); Belzunce, M.-J. [Instituto Tecnnologico Pesquero y Alimentario, Dpto de Oceanografia y Medio Ambiente Marino, Herrera Kaia, Portualdea z/g, 20110 Pasaia (Gipuzkoa) (Spain); Guterstam, B. [Stensund Ecological Center, 61991 Trosa, Sweden and Global Water Partnership Secretariat, Hantverkargatan 5, SE-112 21 Stockholm (Sweden); Kunzendorf, H. [Gamma Dating Center (GDC), Institute of Geography, University of Copenhagen, Oster Voldgage 10 DK-1350 Copenhagen K (Denmark); Wolowicz, M. [Laboratory of Estuarine Ecology, Institute of Oceanography, University of Gdansk, Al. Pilsudskiego 46, 81-378, Gdynia (Poland); Hummel, H. [Centre for Estuarine and Marine Ecology, Netherlands Institute of Ecology, Korringaweg 7, 4401 NT Yerseke (Netherlands); Deslous-Paoli, M. [IFREMER, Unite Ecologie Conchylicole, 1, rue Jean Vilar, 34200 Sete (France)

    2006-01-15

    Existing data on metal concentrations in mussels from subarctic, temperate, subtropical and tropical waters were analyzed using multivariate statistics in order to assess regional variations in metal contamination. Potential errors were reduced by only analyzing data from surveys that employed the same protocols, analytical methodologies and analysts. Factor analysis demonstrated that mussels inhabiting extremely contaminated areas (e.g. from Japanese and Swedish metallurgy sources) could be separated from mussels from other contaminated areas, and that metals such as Cd, Pb, Cu and Zn could be used to identify heavily contaminated samples while Co, Fe, Cr and Ni concentrations were good markers for exposure to inputs from different industrial sources. Furthermore byssus, like soft tissue, selectively and sensitively reflects variations of certain metal concentrations in ambient waters and thus serves as a reliable biomonitor for these contaminants in a variety of coastal and estuarine areas. - Byssus of mytilids, like soft tissues can be used as efficient biomonitor for heavy metals in the marine environment.

  8. GO Explorer: A gene-ontology tool to aid in the interpretation of shotgun proteomics data

    Directory of Open Access Journals (Sweden)

    Domont Gilberto B

    2009-02-01

    Full Text Available Abstract Background Spectral counting is a shotgun proteomics approach comprising the identification and relative quantitation of thousands of proteins in complex mixtures. However, this strategy generates bewildering amounts of data whose biological interpretation is a challenge. Results Here we present a new algorithm, termed GO Explorer (GOEx, that leverages the gene ontology (GO to aid in the interpretation of proteomic data. GOEx stands out because it combines data from protein fold changes with GO over-representation statistics to help draw conclusions. Moreover, it is tightly integrated within the PatternLab for Proteomics project and, thus, lies within a complete computational environment that provides parsers and pattern recognition tools designed for spectral counting. GOEx offers three independent methods to query data: an interactive directed acyclic graph, a specialist mode where key words can be searched, and an automatic search. Its usefulness is demonstrated by applying it to help interpret the effects of perillyl alcohol, a natural chemotherapeutic agent, on glioblastoma multiform cell lines (A172. We used a new multi-surfactant shotgun proteomic strategy and identified more than 2600 proteins; GOEx pinpointed key sets of differentially expressed proteins related to cell cycle, alcohol catabolism, the Ras pathway, apoptosis, and stress response, to name a few. Conclusion GOEx facilitates organism-specific studies by leveraging GO and providing a rich graphical user interface. It is a simple to use tool, specialized for biologists who wish to analyze spectral counting data from shotgun proteomics. GOEx is available at http://pcarvalho.com/patternlab.

  9. GO Explorer: A gene-ontology tool to aid in the interpretation of shotgun proteomics data.

    Science.gov (United States)

    Carvalho, Paulo C; Fischer, Juliana Sg; Chen, Emily I; Domont, Gilberto B; Carvalho, Maria Gc; Degrave, Wim M; Yates, John R; Barbosa, Valmir C

    2009-02-24

    Spectral counting is a shotgun proteomics approach comprising the identification and relative quantitation of thousands of proteins in complex mixtures. However, this strategy generates bewildering amounts of data whose biological interpretation is a challenge. Here we present a new algorithm, termed GO Explorer (GOEx), that leverages the gene ontology (GO) to aid in the interpretation of proteomic data. GOEx stands out because it combines data from protein fold changes with GO over-representation statistics to help draw conclusions. Moreover, it is tightly integrated within the PatternLab for Proteomics project and, thus, lies within a complete computational environment that provides parsers and pattern recognition tools designed for spectral counting. GOEx offers three independent methods to query data: an interactive directed acyclic graph, a specialist mode where key words can be searched, and an automatic search. Its usefulness is demonstrated by applying it to help interpret the effects of perillyl alcohol, a natural chemotherapeutic agent, on glioblastoma multiform cell lines (A172). We used a new multi-surfactant shotgun proteomic strategy and identified more than 2600 proteins; GOEx pinpointed key sets of differentially expressed proteins related to cell cycle, alcohol catabolism, the Ras pathway, apoptosis, and stress response, to name a few. GOEx facilitates organism-specific studies by leveraging GO and providing a rich graphical user interface. It is a simple to use tool, specialized for biologists who wish to analyze spectral counting data from shotgun proteomics. GOEx is available at http://pcarvalho.com/patternlab.

  10. Shotgun pyrosequencing metagenomic analyses of dusts from swine confinement and grain facilities.

    Science.gov (United States)

    Boissy, Robert J; Romberger, Debra J; Roughead, William A; Weissenburger-Moser, Lisa; Poole, Jill A; LeVan, Tricia D

    2014-01-01

    Inhalation of agricultural dusts causes inflammatory reactions and symptoms such as headache, fever, and malaise, which can progress to chronic airway inflammation and associated diseases, e.g. asthma, chronic bronchitis, chronic obstructive pulmonary disease, and hypersensitivity pneumonitis. Although in many agricultural environments feed particles are the major constituent of these dusts, the inflammatory responses that they provoke are likely attributable to particle-associated bacteria, archaebacteria, fungi, and viruses. In this study, we performed shotgun pyrosequencing metagenomic analyses of DNA from dusts from swine confinement facilities or grain elevators, with comparisons to dusts from pet-free households. DNA sequence alignment showed that 19% or 62% of shotgun pyrosequencing metagenomic DNA sequence reads from swine facility or household dusts, respectively, were of swine or human origin, respectively. In contrast only 2% of such reads from grain elevator dust were of mammalian origin. These metagenomic shotgun reads of mammalian origin were excluded from our analyses of agricultural dust microbiota. The ten most prevalent bacterial taxa identified in swine facility compared to grain elevator or household dust were comprised of 75%, 16%, and 42% gram-positive organisms, respectively. Four of the top five swine facility dust genera were assignable (Clostridium, Lactobacillus, Ruminococcus, and Eubacterium, ranging from 4% to 19% relative abundance). The relative abundances of these four genera were lower in dust from grain elevators or pet-free households. These analyses also highlighted the predominance in swine facility dust of Firmicutes (70%) at the phylum level, Clostridia (44%) at the Class level, and Clostridiales at the Order level (41%). In summary, shotgun pyrosequencing metagenomic analyses of agricultural dusts show that they differ qualitatively and quantitatively at the level of microbial taxa present, and that the bioinformatic analyses

  11. Shotgun pyrosequencing metagenomic analyses of dusts from swine confinement and grain facilities.

    Directory of Open Access Journals (Sweden)

    Robert J Boissy

    Full Text Available Inhalation of agricultural dusts causes inflammatory reactions and symptoms such as headache, fever, and malaise, which can progress to chronic airway inflammation and associated diseases, e.g. asthma, chronic bronchitis, chronic obstructive pulmonary disease, and hypersensitivity pneumonitis. Although in many agricultural environments feed particles are the major constituent of these dusts, the inflammatory responses that they provoke are likely attributable to particle-associated bacteria, archaebacteria, fungi, and viruses. In this study, we performed shotgun pyrosequencing metagenomic analyses of DNA from dusts from swine confinement facilities or grain elevators, with comparisons to dusts from pet-free households. DNA sequence alignment showed that 19% or 62% of shotgun pyrosequencing metagenomic DNA sequence reads from swine facility or household dusts, respectively, were of swine or human origin, respectively. In contrast only 2% of such reads from grain elevator dust were of mammalian origin. These metagenomic shotgun reads of mammalian origin were excluded from our analyses of agricultural dust microbiota. The ten most prevalent bacterial taxa identified in swine facility compared to grain elevator or household dust were comprised of 75%, 16%, and 42% gram-positive organisms, respectively. Four of the top five swine facility dust genera were assignable (Clostridium, Lactobacillus, Ruminococcus, and Eubacterium, ranging from 4% to 19% relative abundance. The relative abundances of these four genera were lower in dust from grain elevators or pet-free households. These analyses also highlighted the predominance in swine facility dust of Firmicutes (70% at the phylum level, Clostridia (44% at the Class level, and Clostridiales at the Order level (41%. In summary, shotgun pyrosequencing metagenomic analyses of agricultural dusts show that they differ qualitatively and quantitatively at the level of microbial taxa present, and that the

  12. Effects of Wintering Environment and Parasite-Pathogen Interactions on Honey Bee Colony Loss in North Temperate Regions.

    Directory of Open Access Journals (Sweden)

    Suresh D Desai

    Full Text Available Extreme winter losses of honey bee colonies are a major threat to beekeeping but the combinations of factors underlying colony loss remain debatable. We monitored colonies in two environments (colonies wintered indoors or outdoors and characterized the effects of two parasitic mites, seven viruses, and Nosema on honey bee colony mortality and population loss over winter. Samples were collected from two locations within hives in fall, mid-winter and spring of 2009/2010. Although fall parasite and pathogen loads were similar in outdoor and indoor-wintered colonies, the outdoor-wintered colonies had greater relative reductions in bee population score over winter. Seasonal patterns in deformed wing virus (DWV, black queen cell virus (BQCV, and Nosema level also differed with the wintering environment. DWV and Nosema levels decreased over winter for indoor-wintered colonies but BQCV did not. Both BQCV and Nosema concentration increased over winter in outdoor-wintered colonies. The mean abundance of Varroa decreased and concentration of Sacbrood virus (SBV, Kashmir bee virus (KBV, and Chronic bee paralysis virus (CBPV increased over winter but seasonal patterns were not affected by wintering method. For most viruses, either entrance or brood area samples were reasonable predictors of colony virus load but there were significant season*sample location interactions for Nosema and BQCV, indicating that care must be taken when selecting samples from a single location. For Nosema spp., the fall entrance samples were better predictors of future infestation levels than were fall brood area samples. For indoor-wintered colonies, Israeli acute paralysis virus IAPV concentration was negatively correlated with spring population size. For outdoor-wintered hives, spring Varroa abundance and DWV concentration were positively correlated with bee loss and negatively correlated with spring population size. Multivariate analyses for fall collected samples indicated

  13. Forest impacts on snow accumulation and ablation across an elevation gradient in a temperate montane environment

    Directory of Open Access Journals (Sweden)

    T. R. Roth

    2017-11-01

    Full Text Available Forest cover modifies snow accumulation and ablation rates via canopy interception and changes in sub-canopy energy balance processes. However, the ways in which snowpacks are affected by forest canopy processes vary depending on climatic, topographic and forest characteristics. Here we present results from a 4-year study of snow–forest interactions in the Oregon Cascades. We continuously monitored snow and meteorological variables at paired forested and open sites at three elevations representing the Low, Mid, and High seasonal snow zones in the study region. On a monthly to bi-weekly basis, we surveyed snow depth and snow water equivalent across 900 m transects connecting the forested and open pairs of sites. Our results show that relative to nearby open areas, the dense, relatively warm forests at Low and Mid sites impede snow accumulation via canopy snow interception and increase sub-canopy snowpack energy inputs via longwave radiation. Compared with the Forest sites, snowpacks are deeper and last longer in the Open site at the Low and Mid sites (4–26 and 11–33 days, respectively. However, we see the opposite relationship at the relatively colder High sites, with the Forest site maintaining snow longer into the spring by 15–29 days relative to the nearby Open site. Canopy interception efficiency (CIE values at the Low and Mid Forest sites averaged 79 and 76 % of the total event snowfall, whereas CIE was 31 % at the lower density High Forest site. At all elevations, longwave radiation in forested environments appears to be the primary energy component due to the maritime climate and forest presence, accounting for 93, 92, and 47 % of total energy inputs to the snowpack at the Low, Mid, and High Forest sites, respectively. Higher wind speeds in the High Open site significantly increase turbulent energy exchanges and snow sublimation. Lower wind speeds in the High Forest site create preferential snowfall deposition. These

  14. Novel advances in shotgun lipidomics for biology and medicine.

    Science.gov (United States)

    Wang, Miao; Wang, Chunyan; Han, Rowland H; Han, Xianlin

    2016-01-01

    The field of lipidomics, as coined in 2003, has made profound advances and been rapidly expanded. The mass spectrometry-based strategies of this analytical methodology-oriented research discipline for lipid analysis are largely fallen into three categories: direct infusion-based shotgun lipidomics, liquid chromatography-mass spectrometry-based platforms, and matrix-assisted laser desorption/ionization mass spectrometry-based approaches (particularly in imagining lipid distribution in tissues or cells). This review focuses on shotgun lipidomics. After briefly introducing its fundamentals, the major materials of this article cover its recent advances. These include the novel methods of lipid extraction, novel shotgun lipidomics strategies for identification and quantification of previously hardly accessible lipid classes and molecular species including isomers, and novel tools for processing and interpretation of lipidomics data. Representative applications of advanced shotgun lipidomics for biological and biomedical research are also presented in this review. We believe that with these novel advances in shotgun lipidomics, this approach for lipid analysis should become more comprehensive and high throughput, thereby greatly accelerating the lipidomics field to substantiate the aberrant lipid metabolism, signaling, trafficking, and homeostasis under pathological conditions and their underpinning biochemical mechanisms. Copyright © 2015 Elsevier B.V. All rights reserved.

  15. Whole genome shotgun sequencing of Indian strains of Streptococcus agalactiae

    Directory of Open Access Journals (Sweden)

    Balaji Veeraraghavan

    2017-12-01

    Full Text Available Group B streptococcus is known as a leading cause of neonatal infections in developing countries. The present study describes the whole genome shotgun sequences of four Group B Streptococcus (GBS isolates. Molecular data on clonality is lacking for GBS in India. The present genome report will add important information on the scarce genome data of GBS and will help in deriving comparative genome studies of GBS isolates at global level. This Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under the accession numbers NHPL00000000 – NHPO00000000.

  16. Analysis of pig serum proteins based on shotgun liquid ...

    African Journals Online (AJOL)

    Recent advances in proteomics technologies have opened up significant opportunities for future applications. We used shotgun liquid chromatography, coupled with tandem mass spectrometry (LC-MS/MS) to determine the proteome profile of healthy pig serum. Samples of venous blood were collected and subjected to ...

  17. The Need for Temperance

    Directory of Open Access Journals (Sweden)

    Karl Inge Tangen

    2015-11-01

    Full Text Available This article explores how temperance as a virtue relates to organizational leadership. The study begins with a short survey of classical Greek and Christian notions of temperance before proceeding to ex-plore temperance in relation to self-leadership, visionary and strategic leadership, and relational lead-ership. The final part of the article offers reflections on how temperance might be cultivated from a theological perspective. Temperance is understood not only as sound thinking but also as embodied self-control and active patience. On the level of self-leadership, it is argued that temperance enables the leader to establish forms of integrity that protect the leader’s self from chaos and destruction. Moreover, temperance may also nurture focused visionary leadership that accepts ethical limits and has an eye to the common good. The study also suggests that organizations should cultivate a culture of strategic discipline that is capable of realizing such visions. On the interpersonal level, temperance is viewed as critical in terms of enabling leaders to treat co-workers with respect and wisdom and han-dle conflict with consideration. Finally, is argued that that the cultivation of temperance is not a one-way street from the inside to the outside or a subordination of feelings to reason but rather a very complex process that includes interpersonal humility, finds vision in an encounter with the good, and yet remains a personal responsibility.

  18. metaBIT, an integrative and automated metagenomic pipeline for analysing microbial profiles from high-throughput sequencing shotgun data

    DEFF Research Database (Denmark)

    Louvel, Guillaume; Der Sarkissian, Clio; Hanghøj, Kristian Ebbesen

    2016-01-01

    -throughput DNA sequencing (HTS). Here, we develop metaBIT, an open-source computational pipeline automatizing routine microbial profiling of shotgun HTS data. Customizable by the user at different stringency levels, it performs robust taxonomy-based assignment and relative abundance calculation of microbial taxa......, as well as cross-sample statistical analyses of microbial diversity distributions. We demonstrate the versatility of metaBIT within a range of published HTS data sets sampled from the environment (soil and seawater) and the human body (skin and gut), but also from archaeological specimens. We present......-friendly profiling of the microbial DNA present in HTS shotgun data sets. The applications of metaBIT are vast, from monitoring of laboratory errors and contaminations, to the reconstruction of past and present microbiota, and the detection of candidate species, including pathogens....

  19. Bioinformatics for whole-genome shotgun sequencing of microbial communities.

    Directory of Open Access Journals (Sweden)

    Kevin Chen

    2005-07-01

    Full Text Available The application of whole-genome shotgun sequencing to microbial communities represents a major development in metagenomics, the study of uncultured microbes via the tools of modern genomic analysis. In the past year, whole-genome shotgun sequencing projects of prokaryotic communities from an acid mine biofilm, the Sargasso Sea, Minnesota farm soil, three deep-sea whale falls, and deep-sea sediments have been reported, adding to previously published work on viral communities from marine and fecal samples. The interpretation of this new kind of data poses a wide variety of exciting and difficult bioinformatics problems. The aim of this review is to introduce the bioinformatics community to this emerging field by surveying existing techniques and promising new approaches for several of the most interesting of these computational problems.

  20. The temporal analysis of yeast exponential phase using shotgun proteomics as a fermentation monitoring technique.

    Science.gov (United States)

    Huang, Eric L; Orsat, Valérie; Shah, Manesh B; Hettich, Robert L; VerBerkmoes, Nathan C; Lefsrud, Mark G

    2012-09-18

    System biology and bioprocess technology can be better understood using shotgun proteomics as a monitoring system during the fermentation. We demonstrated a shotgun proteomic method to monitor the temporal yeast proteome in early, middle and late exponential phases. Our study identified a total of 1389 proteins combining all 2D-LC-MS/MS runs. The temporal Saccharomyces cerevisiae proteome was enriched with proteolysis, radical detoxification, translation, one-carbon metabolism, glycolysis and TCA cycle. Heat shock proteins and proteins associated with oxidative stress response were found throughout the exponential phase. The most abundant proteins observed were translation elongation factors, ribosomal proteins, chaperones and glycolytic enzymes. The high abundance of the H-protein of the glycine decarboxylase complex (Gcv3p) indicated the availability of glycine in the environment. We observed differentially expressed proteins and the induced proteins at mid-exponential phase were involved in ribosome biogenesis, mitochondria DNA binding/replication and transcriptional activator. Induction of tryptophan synthase (Trp5p) indicated the abundance of tryptophan during the fermentation. As fermentation progressed toward late exponential phase, a decrease in cell proliferation was implied from the repression of ribosomal proteins, transcription coactivators, methionine aminopeptidase and translation-associated proteins. Copyright © 2012 Elsevier B.V. All rights reserved.

  1. Microbial Community Profiling of Human Saliva Using Shotgun Metagenomic Sequencing

    OpenAIRE

    Hasan, Nur A.; Young, Brian A.; Minard-Smith, Angela T.; Saeed, Kelly; Li, Huai; Heizer, Esley M.; McMillan, Nancy J.; Isom, Richard; Abdullah, Abdul Shakur; Bornman, Daniel M.; Faith, Seth A.; Choi, Seon Young; Dickens, Michael L.; Cebula, Thomas A.; Colwell, Rita R.

    2014-01-01

    Human saliva is clinically informative of both oral and general health. Since next generation shotgun sequencing (NGS) is now widely used to identify and quantify bacteria, we investigated the bacterial flora of saliva microbiomes of two healthy volunteers and five datasets from the Human Microbiome Project, along with a control dataset containing short NGS reads from bacterial species representative of the bacterial flora of human saliva. GENIUS, a system designed to identify and quantify ba...

  2. WGSQuikr: fast whole-genome shotgun metagenomic classification.

    Directory of Open Access Journals (Sweden)

    David Koslicki

    Full Text Available With the decrease in cost and increase in output of whole-genome shotgun technologies, many metagenomic studies are utilizing this approach in lieu of the more traditional 16S rRNA amplicon technique. Due to the large number of relatively short reads output from whole-genome shotgun technologies, there is a need for fast and accurate short-read OTU classifiers. While there are relatively fast and accurate algorithms available, such as MetaPhlAn, MetaPhyler, PhyloPythiaS, and PhymmBL, these algorithms still classify samples in a read-by-read fashion and so execution times can range from hours to days on large datasets. We introduce WGSQuikr, a reconstruction method which can compute a vector of taxonomic assignments and their proportions in the sample with remarkable speed and accuracy. We demonstrate on simulated data that WGSQuikr is typically more accurate and up to an order of magnitude faster than the aforementioned classification algorithms. We also verify the utility of WGSQuikr on real biological data in the form of a mock community. WGSQuikr is a Whole-Genome Shotgun QUadratic, Iterative, K-mer based Reconstruction method which extends the previously introduced 16S rRNA-based algorithm Quikr. A MATLAB implementation of WGSQuikr is available at: http://sourceforge.net/projects/wgsquikr.

  3. Shotgun microbial profiling of fossil remains

    DEFF Research Database (Denmark)

    Der Sarkissian, Clio; Ermini, Luca; Jónsson, Hákon

    2014-01-01

    the specimen of interest, but instead reflect environmental organisms that colonized the specimen after death. Here, we characterize the microbial diversity recovered from seven c. 200- to 13 000-year-old horse bones collected from northern Siberia. We use a robust, taxonomy-based assignment approach...... to identify the microorganisms present in ancient DNA extracts and quantify their relative abundance. Our results suggest that molecular preservation niches exist within ancient samples that can potentially be used to characterize the environments from which the remains are recovered. In addition, microbial...... community profiling of the seven specimens revealed site-specific environmental signatures. These microbial communities appear to comprise mainly organisms that colonized the fossils recently. Our approach significantly extends the amount of useful data that can be recovered from ancient specimens using...

  4. PAnalyzer: A software tool for protein inference in shotgun proteomics

    Directory of Open Access Journals (Sweden)

    Prieto Gorka

    2012-11-01

    Full Text Available Abstract Background Protein inference from peptide identifications in shotgun proteomics must deal with ambiguities that arise due to the presence of peptides shared between different proteins, which is common in higher eukaryotes. Recently data independent acquisition (DIA approaches have emerged as an alternative to the traditional data dependent acquisition (DDA in shotgun proteomics experiments. MSE is the term used to name one of the DIA approaches used in QTOF instruments. MSE data require specialized software to process acquired spectra and to perform peptide and protein identifications. However the software available at the moment does not group the identified proteins in a transparent way by taking into account peptide evidence categories. Furthermore the inspection, comparison and report of the obtained results require tedious manual intervention. Here we report a software tool to address these limitations for MSE data. Results In this paper we present PAnalyzer, a software tool focused on the protein inference process of shotgun proteomics. Our approach considers all the identified proteins and groups them when necessary indicating their confidence using different evidence categories. PAnalyzer can read protein identification files in the XML output format of the ProteinLynx Global Server (PLGS software provided by Waters Corporation for their MSE data, and also in the mzIdentML format recently standardized by HUPO-PSI. Multiple files can also be read simultaneously and are considered as technical replicates. Results are saved to CSV, HTML and mzIdentML (in the case of a single mzIdentML input file files. An MSE analysis of a real sample is presented to compare the results of PAnalyzer and ProteinLynx Global Server. Conclusions We present a software tool to deal with the ambiguities that arise in the protein inference process. Key contributions are support for MSE data analysis by ProteinLynx Global Server and technical replicates

  5. Identification of meat products by shotgun spectral matching

    DEFF Research Database (Denmark)

    Ohana, D.; Dalebout, H.; Marissen, R. J.

    2016-01-01

    A new method, based on shotgun spectral matching of peptide tandem mass spectra, was successfully applied to the identification of different food species. The method was demonstrated to work on raw as well as processed samples from 16 mammalian and 10 bird species by counting spectral matches...... to spectral libraries in a reference database with one spectral library per species. A phylogenetic tree could also be constructed directly from the spectra. Nearly all samples could be correctly identified at the species level, and 100% at the genus level. The method does not use any genomic information...

  6. Shotgun lipidomic analysis of chemically sulfated sterols compromises analytical sensitivity

    DEFF Research Database (Denmark)

    Casanovas, Albert; Hannibal-Bach, Hans Kristian; Jensen, Ole Nørregaard

    2014-01-01

    Shotgun lipidomics affords comprehensive and quantitative analysis of lipid species in cells and tissues at high-throughput [1 5]. The methodology is based on direct infusion of lipid extracts by electrospray ionization (ESI) combined with tandem mass spectrometry (MS/MS) and/or high resolution F...... low ionization efficiency in ESI [7]. For this reason, chemical derivatization procedures including acetylation [8] or sulfation [9] are commonly implemented to facilitate ionization, detection and quantification of sterols for global lipidome analysis [1-3, 10]....

  7. Environment vs. Plant Ontogeny: Arthropod Herbivory Patterns on European Beech Leaves along the Vertical Gradient of Temperate Forests in Central Germany

    Directory of Open Access Journals (Sweden)

    Stephanie Stiegel

    2018-01-01

    Full Text Available Environmental and leaf trait effects on herbivory are supposed to vary among different feeding guilds. Herbivores also show variability in their preferences for plant ontogenetic stages. Along the vertical forest gradient, environmental conditions change, and trees represent juvenile and adult individuals in the understorey and canopy, respectively. This study was conducted in ten forests sites in Central Germany for the enrichment of canopy research in temperate forests. Arthropod herbivory of different feeding traces was surveyed on leaves of Fagus sylvatica Linnaeus (European beech; Fagaceae in three strata. Effects of microclimate, leaf traits, and plant ontogenetic stage were analyzed as determining parameters for herbivory. The highest herbivory was caused by exophagous feeding traces. Herbivore attack levels varied along the vertical forest gradient for most feeding traces with distinct patterns. If differences of herbivory levels were present, they only occurred between juvenile and adult F. sylvatica individuals, but not between the lower and upper canopy. In contrast, differences of microclimate and important leaf traits were present between the lower and upper canopy. In conclusion, the plant ontogenetic stage had a stronger effect on herbivory than microclimate or leaf traits along the vertical forest gradient.

  8. Plastic litter from shotgun ammunition on Danish coastlines - Amounts and provenance.

    Science.gov (United States)

    Kanstrup, Niels; Balsby, Thorsten J S

    2018-06-01

    Plastic litter in the marine environment is a major global issue. Discarded plastic shotgun ammunition shells and discharged wads are an unwelcome addition and feature among the top ten litter items found on reference beaches in Denmark. To understand this problem, its scale and origins, collections were made by volunteers along Danish coastal shorelines. In all 3669 plastic ammunition items were collected at 68 sites along 44.6 km of shoreline. The collected items were scored for characteristic variables such as gauge and length, shot type, and the legibility of text, the erosion, and the presence of metallic components. Scores for characteristics were related to the site, area, and season and possible influences discussed. The prevalence of collected plastic shotgun litter ranges from zero to 41 items per 100 m with an average of 3.7 items per 100 m. Most ammunition litter on Danish coasts originates from hunting on Danish coastal waterbodies, but a small amount may come from further afield. North Sea coasts are the most distinctive suggesting the possible contribution of long distance drift as well as the likelihood that such litter can persist in marine habitats for decades. The pathway from initial discard to eventual wash-up and collection depends on the physical properties of plastic components, marine tides and currents, coastal topography and shoreline vegetation. Judging from the disintegration of the cartridge and the wear and decomposition of components, we conclude that there is a substantial supply of polluting plastic ammunition materials that has and will accumulate. These plastic items pose a hazard to marine ecosystems and wash up on coasts for many years to come. We recommend that responsible managers, hunters and ammunition manufacturers will take action now to reduce the problem and, thereby, protect ecosystems, wildlife and the sustainability of hunting. Copyright © 2018 Elsevier Ltd. All rights reserved.

  9. Diversity of thermophiles in a Malaysian hot spring determined using 16S rRNA and shotgun metagenome sequencing.

    Science.gov (United States)

    Chan, Chia Sing; Chan, Kok-Gan; Tay, Yea-Ling; Chua, Yi-Heng; Goh, Kian Mau

    2015-01-01

    The Sungai Klah (SK) hot spring is the second hottest geothermal spring in Malaysia. This hot spring is a shallow, 150-m-long, fast-flowing stream, with temperatures varying from 50 to 110°C and a pH range of 7.0-9.0. Hidden within a wooded area, the SK hot spring is continually fed by plant litter, resulting in a relatively high degree of total organic content (TOC). In this study, a sample taken from the middle of the stream was analyzed at the 16S rRNA V3-V4 region by amplicon metagenome sequencing. Over 35 phyla were detected by analyzing the 16S rRNA data. Firmicutes and Proteobacteria represented approximately 57% of the microbiome. Approximately 70% of the detected thermophiles were strict anaerobes; however, Hydrogenobacter spp., obligate chemolithotrophic thermophiles, represented one of the major taxa. Several thermophilic photosynthetic microorganisms and acidothermophiles were also detected. Most of the phyla identified by 16S rRNA were also found using the shotgun metagenome approaches. The carbon, sulfur, and nitrogen metabolism within the SK hot spring community were evaluated by shotgun metagenome sequencing, and the data revealed diversity in terms of metabolic activity and dynamics. This hot spring has a rich diversified phylogenetic community partly due to its natural environment (plant litter, high TOC, and a shallow stream) and geochemical parameters (broad temperature and pH range). It is speculated that symbiotic relationships occur between the members of the community.

  10. Microbial community profiling of human saliva using shotgun metagenomic sequencing.

    Directory of Open Access Journals (Sweden)

    Nur A Hasan

    Full Text Available Human saliva is clinically informative of both oral and general health. Since next generation shotgun sequencing (NGS is now widely used to identify and quantify bacteria, we investigated the bacterial flora of saliva microbiomes of two healthy volunteers and five datasets from the Human Microbiome Project, along with a control dataset containing short NGS reads from bacterial species representative of the bacterial flora of human saliva. GENIUS, a system designed to identify and quantify bacterial species using unassembled short NGS reads was used to identify the bacterial species comprising the microbiomes of the saliva samples and datasets. Results, achieved within minutes and at greater than 90% accuracy, showed more than 175 bacterial species comprised the bacterial flora of human saliva, including bacteria known to be commensal human flora but also Haemophilus influenzae, Neisseria meningitidis, Streptococcus pneumoniae, and Gamma proteobacteria. Basic Local Alignment Search Tool (BLASTn analysis in parallel, reported ca. five times more species than those actually comprising the in silico sample. Both GENIUS and BLAST analyses of saliva samples identified major genera comprising the bacterial flora of saliva, but GENIUS provided a more precise description of species composition, identifying to strain in most cases and delivered results at least 10,000 times faster. Therefore, GENIUS offers a facile and accurate system for identification and quantification of bacterial species and/or strains in metagenomic samples.

  11. Genomic V exons from whole genome shotgun data in reptiles.

    Science.gov (United States)

    Olivieri, D N; von Haeften, B; Sánchez-Espinel, C; Faro, J; Gambón-Deza, F

    2014-08-01

    Reptiles and mammals diverged over 300 million years ago, creating two parallel evolutionary lineages amongst terrestrial vertebrates. In reptiles, two main evolutionary lines emerged: one gave rise to Squamata, while the other gave rise to Testudines, Crocodylia, and Aves. In this study, we determined the genomic variable (V) exons from whole genome shotgun sequencing (WGS) data in reptiles corresponding to the three main immunoglobulin (IG) loci and the four main T cell receptor (TR) loci. We show that Squamata lack the TRG and TRD genes, and snakes lack the IGKV genes. In representative species of Testudines and Crocodylia, the seven major IG and TR loci are maintained. As in mammals, genes of the IG loci can be grouped into well-defined IMGT clans through a multi-species phylogenetic analysis. We show that the reptilian IGHV and IGLV genes are distributed amongst the established mammalian clans, while their IGKV genes are found within a single clan, nearly exclusive from the mammalian sequences. The reptilian and mammalian TRAV genes cluster into six common evolutionary clades (since IMGT clans have not been defined for TR). In contrast, the reptilian TRBV genes cluster into three clades, which have few mammalian members. In this locus, the V exon sequences from mammals appear to have undergone different evolutionary diversification processes that occurred outside these shared reptilian clans. These sequences can be obtained in a freely available public repository (http://vgenerepertoire.org).

  12. Shotgun metaproteomics of the human distal gut microbiota

    Energy Technology Data Exchange (ETDEWEB)

    VerBerkmoes, N.C.; Russell, A.L.; Shah, M.; Godzik, A.; Rosenquist, M.; Halfvarsson, J.; Lefsrud, M.G.; Apajalahti, J.; Tysk, C.; Hettich, R.L.; Jansson, Janet K.

    2008-10-15

    The human gut contains a dense, complex and diverse microbial community, comprising the gut microbiome. Metagenomics has recently revealed the composition of genes in the gut microbiome, but provides no direct information about which genes are expressed or functioning. Therefore, our goal was to develop a novel approach to directly identify microbial proteins in fecal samples to gain information about the genes expressed and about key microbial functions in the human gut. We used a non-targeted, shotgun mass spectrometry-based whole community proteomics, or metaproteomics, approach for the first deep proteome measurements of thousands of proteins in human fecal samples, thus demonstrating this approach on the most complex sample type to date. The resulting metaproteomes had a skewed distribution relative to the metagenome, with more proteins for translation, energy production and carbohydrate metabolism when compared to what was earlier predicted from metagenomics. Human proteins, including antimicrobial peptides, were also identified, providing a non-targeted glimpse of the host response to the microbiota. Several unknown proteins represented previously undescribed microbial pathways or host immune responses, revealing a novel complex interplay between the human host and its associated microbes.

  13. Shotgun proteomics reveals physiological response to ocean acidification in Crassostrea gigas.

    Science.gov (United States)

    Timmins-Schiffman, Emma; Coffey, William D; Hua, Wilber; Nunn, Brook L; Dickinson, Gary H; Roberts, Steven B

    2014-11-03

    Ocean acidification as a result of increased anthropogenic CO2 emissions is occurring in marine and estuarine environments worldwide. The coastal ocean experiences additional daily and seasonal fluctuations in pH that can be lower than projected end-of-century open ocean pH reductions. In order to assess the impact of ocean acidification on marine invertebrates, Pacific oysters (Crassostrea gigas) were exposed to one of four different p CO2 levels for four weeks: 400 μatm (pH 8.0), 800 μatm (pH 7.7), 1000 μatm (pH 7.6), or 2800 μatm (pH 7.3). At the end of the four week exposure period, oysters in all four p CO2 environments deposited new shell, but growth rate was not different among the treatments. However, micromechanical properties of the new shell were compromised by elevated p CO2. Elevated p CO2 affected neither whole body fatty acid composition, nor glycogen content, nor mortality rate associated with acute heat shock. Shotgun proteomics revealed that several physiological pathways were significantly affected by ocean acidification, including antioxidant response, carbohydrate metabolism, and transcription and translation. Additionally, the proteomic response to a second stress differed with p CO2, with numerous processes significantly affected by mechanical stimulation at high versus low p CO2 (all proteomics data are available in the ProteomeXchange under the identifier PXD000835). Oyster physiology is significantly altered by exposure to elevated p CO2, indicating changes in energy resource use. This is especially apparent in the assessment of the effects of p CO2 on the proteomic response to a second stress. The altered stress response illustrates that ocean acidification may impact how oysters respond to other changes in their environment. These data contribute to an integrative view of the effects of ocean acidification on oysters as well as physiological trade-offs during environmental stress.

  14. A framework for intelligent data acquisition and real-time database searching for shotgun proteomics.

    Science.gov (United States)

    Graumann, Johannes; Scheltema, Richard A; Zhang, Yong; Cox, Jürgen; Mann, Matthias

    2012-03-01

    In the analysis of complex peptide mixtures by MS-based proteomics, many more peptides elute at any given time than can be identified and quantified by the mass spectrometer. This makes it desirable to optimally allocate peptide sequencing and narrow mass range quantification events. In computer science, intelligent agents are frequently used to make autonomous decisions in complex environments. Here we develop and describe a framework for intelligent data acquisition and real-time database searching and showcase selected examples. The intelligent agent is implemented in the MaxQuant computational proteomics environment, termed MaxQuant Real-Time. It analyzes data as it is acquired on the mass spectrometer, constructs isotope patterns and SILAC pair information as well as controls MS and tandem MS events based on real-time and prior MS data or external knowledge. Re-implementing a top10 method in the intelligent agent yields similar performance to the data dependent methods running on the mass spectrometer itself. We demonstrate the capabilities of MaxQuant Real-Time by creating a real-time search engine capable of identifying peptides "on-the-fly" within 30 ms, well within the time constraints of a shotgun fragmentation "topN" method. The agent can focus sequencing events onto peptides of specific interest, such as those originating from a specific gene ontology (GO) term, or peptides that are likely modified versions of already identified peptides. Finally, we demonstrate enhanced quantification of SILAC pairs whose ratios were poorly defined in survey spectra. MaxQuant Real-Time is flexible and can be applied to a large number of scenarios that would benefit from intelligent, directed data acquisition. Our framework should be especially useful for new instrument types, such as the quadrupole-Orbitrap, that are currently becoming available.

  15. MUMAL: Multivariate analysis in shotgun proteomics using machine learning techniques

    Directory of Open Access Journals (Sweden)

    Cerqueira Fabio R

    2012-10-01

    Full Text Available Abstract Background The shotgun strategy (liquid chromatography coupled with tandem mass spectrometry is widely applied for identification of proteins in complex mixtures. This method gives rise to thousands of spectra in a single run, which are interpreted by computational tools. Such tools normally use a protein database from which peptide sequences are extracted for matching with experimentally derived mass spectral data. After the database search, the correctness of obtained peptide-spectrum matches (PSMs needs to be evaluated also by algorithms, as a manual curation of these huge datasets would be impractical. The target-decoy database strategy is largely used to perform spectrum evaluation. Nonetheless, this method has been applied without considering sensitivity, i.e., only error estimation is taken into account. A recently proposed method termed MUDE treats the target-decoy analysis as an optimization problem, where sensitivity is maximized. This method demonstrates a significant increase in the retrieved number of PSMs for a fixed error rate. However, the MUDE model is constructed in such a way that linear decision boundaries are established to separate correct from incorrect PSMs. Besides, the described heuristic for solving the optimization problem has to be executed many times to achieve a significant augmentation in sensitivity. Results Here, we propose a new method, termed MUMAL, for PSM assessment that is based on machine learning techniques. Our method can establish nonlinear decision boundaries, leading to a higher chance to retrieve more true positives. Furthermore, we need few iterations to achieve high sensitivities, strikingly shortening the running time of the whole process. Experiments show that our method achieves a considerably higher number of PSMs compared with standard tools such as MUDE, PeptideProphet, and typical target-decoy approaches. Conclusion Our approach not only enhances the computational performance, and

  16. High-throughput shotgun lipidomics by quadrupole time-of-flight mass spectrometry

    DEFF Research Database (Denmark)

    Ståhlman, Marcus; Ejsing, Christer S.; Tarasov, Kirill

    2009-01-01

    Technological advances in mass spectrometry and meticulous method development have produced several shotgun lipidomic approaches capable of characterizing lipid species by direct analysis of total lipid extracts. Shotgun lipidomics by hybrid quadrupole time-of-flight mass spectrometry allows...... the absolute quantification of hundreds of molecular glycerophospholipid species, glycerolipid species, sphingolipid species and sterol lipids. Future applications in clinical cohort studies demand detailed lipid molecule information and the application of high-throughput lipidomics platforms. In this review...... we describe a novel high-throughput shotgun lipidomic platform based on 96-well robot-assisted lipid extraction, automated sample infusion by mircofluidic-based nanoelectrospray ionization, and quantitative multiple precursor ion scanning analysis on a quadrupole time-of-flight mass spectrometer...

  17. Shotgun proteomics of plant plasma membrane and microdomain proteins using nano-LC-MS/MS.

    Science.gov (United States)

    Takahashi, Daisuke; Li, Bin; Nakayama, Takato; Kawamura, Yukio; Uemura, Matsuo

    2014-01-01

    Shotgun proteomics allows the comprehensive analysis of proteins extracted from plant cells, subcellular organelles, and membranes. Previously, two-dimensional gel electrophoresis-based proteomics was used for mass spectrometric analysis of plasma membrane proteins. In order to get comprehensive proteome profiles of the plasma membrane including highly hydrophobic proteins with a number of transmembrane domains, a mass spectrometry-based shotgun proteomics method using nano-LC-MS/MS for proteins from the plasma membrane proteins and plasma membrane microdomain fraction is described. The results obtained are easily applicable to label-free protein semiquantification.

  18. Diversity of thermophiles in a Malaysian hot spring determined using 16S rRNA and shotgun metagenome sequencing

    Directory of Open Access Journals (Sweden)

    Chia Sing eChan

    2015-03-01

    Full Text Available The Sungai Klah (SK hot spring is the second hottest geothermal spring in Malaysia. This hot spring is a shallow, 150-meter-long, fast-flowing stream, with temperatures varying from 50 to 110°C and a pH range of 7.0 to 9.0. Hidden within a wooded area, the SK hot spring is continually fed by plant litter, resulting in a relatively high degree of total organic content (TOC. In this study, a sample taken from the middle of the stream was analyzed at the 16S rRNA V3−V4 region by amplicon metagenome sequencing. Over 35 phyla were detected by analyzing the 16S rRNA data. Firmicutes and Proteobacteria represented approximately 57% of the microbiome. Approximately 70% of the detected thermophiles were strict anaerobes; however, Hydrogenobacter spp., obligate chemolithotrophic thermophiles, represented one of the major taxa. Several thermophilic photosynthetic microorganisms and acidothermophiles were also detected. Most of the phyla identified by 16S rRNA were also found using the shotgun metagenome approaches. The carbon, sulfur, and nitrogen metabolism within the SK hot spring community were evaluated by shotgun metagenome sequencing, and the data revealed diversity in terms of metabolic activity and dynamics. This hot spring has a rich diversified phylogenetic community partly due to its natural environment (plant litter, high TOC, and a shallow stream and geochemical parameters (broad temperature and pH range. It is speculated that symbiotic relationships occur between the members of the community.

  19. Survey of bacterial diversity in chronic wounds using Pyrosequencing, DGGE, and full ribosome shotgun sequencing

    Directory of Open Access Journals (Sweden)

    Wolcott Benjamin M

    2008-03-01

    Full Text Available Abstract Background Chronic wound pathogenic biofilms are host-pathogen environments that colonize and exist as a cohabitation of many bacterial species. These bacterial populations cooperate to promote their own survival and the chronic nature of the infection. Few studies have performed extensive surveys of the bacterial populations that occur within different types of chronic wound biofilms. The use of 3 separate16S-based molecular amplifications followed by pyrosequencing, shotgun Sanger sequencing, and denaturing gradient gel electrophoresis were utilized to survey the major populations of bacteria that occur in the pathogenic biofilms of three types of chronic wound types: diabetic foot ulcers (D, venous leg ulcers (V, and pressure ulcers (P. Results There are specific major populations of bacteria that were evident in the biofilms of all chronic wound types, including Staphylococcus, Pseudomonas, Peptoniphilus, Enterobacter, Stenotrophomonas, Finegoldia, and Serratia spp. Each of the wound types reveals marked differences in bacterial populations, such as pressure ulcers in which 62% of the populations were identified as obligate anaerobes. There were also populations of bacteria that were identified but not recognized as wound pathogens, such as Abiotrophia para-adiacens and Rhodopseudomonas spp. Results of molecular analyses were also compared to those obtained using traditional culture-based diagnostics. Only in one wound type did culture methods correctly identify the primary bacterial population indicating the need for improved diagnostic methods. Conclusion If clinicians can gain a better understanding of the wound's microbiota, it will give them a greater understanding of the wound's ecology and will allow them to better manage healing of the wound improving the prognosis of patients. This research highlights the necessity to begin evaluating, studying, and treating chronic wound pathogenic biofilms as multi-species entities in

  20. Time-temperature equivalence in Martensite tempering

    Energy Technology Data Exchange (ETDEWEB)

    Hackenberg, Robert E. [Los Alamos National Laboratory; Thomas, Grant A. [CSM; Speer, John G. [CSM; Matlock, David K. [CSM; Krauss, George [CSM

    2008-06-16

    The relationship between time and temperature is of great consequence in many materials-related processes including the tempering of martensite. In 1945, Hollomon and Jaffe quantified the 'degree of tempering' as a function of both tempering time, t, and tempering temperature, T, using the expression, T(log t + c). Here, c is thought to be a material constant and appears to decrease linearly with increasing carbon content. The Hollomon-Jaffe tempering parameter is frequently cited in the literature. This work reviews the original derivation of the tempering parameter concept, and presents the use of the characteristics diffusion distance as an alternative time-temperature relationship during martensite tempering. During the tempering of martensite, interstitial carbon atoms diffuse to form carbides. In addition, austenite decomposes, dislocations and grain boundaries rearrange, associated with iron self diffusion. Since these are all diffusional processes, it is reasonable to expect the degree of tempering to relate to the extent of diffusion.

  1. Enhanced detection method for corneal protein identification using shotgun proteomics

    Directory of Open Access Journals (Sweden)

    Schlager John J

    2009-06-01

    Full Text Available Abstract Background The cornea is a specialized transparent connective tissue responsible for the majority of light refraction and image focus for the retina. There are three main layers of the cornea: the epithelium that is exposed and acts as a protective barrier for the eye, the center stroma consisting of parallel collagen fibrils that refract light, and the endothelium that is responsible for hydration of the cornea from the aqueous humor. Normal cornea is an immunologically privileged tissue devoid of blood vessels, but injury can produce a loss of these conditions causing invasion of other processes that degrade the homeostatic properties resulting in a decrease in the amount of light refracted onto the retina. Determining a measure and drift of phenotypic cornea state from normal to an injured or diseased state requires knowledge of the existing protein signature within the tissue. In the study of corneal proteins, proteomics procedures have typically involved the pulverization of the entire cornea prior to analysis. Separation of the epithelium and endothelium from the core stroma and performing separate shotgun proteomics using liquid chromatography/mass spectrometry results in identification of many more proteins than previously employed methods using complete pulverized cornea. Results Rabbit corneas were purchased, the epithelium and endothelium regions were removed, proteins processed and separately analyzed using liquid chromatography/mass spectrometry. Proteins identified from separate layers were compared against results from complete corneal samples. Protein digests were separated using a six hour liquid chromatographic gradient and ion-trap mass spectrometry used for detection of eluted peptide fractions. The SEQUEST database search results were filtered to allow only proteins with match probabilities of equal or better than 10-3 and peptides with a probability of 10-2 or less with at least two unique peptides isolated within

  2. A common framework for greenhouse gas assessment protocols in temperate agroforestry systems: Connecting via GRACEnet

    Science.gov (United States)

    Agroforestry systems offer many ecosystem benefits, but such systems have previously been marginalized in temperate environments due to overriding economic goals and perceived management complexity. In view of adaptation to a changing climate, agroforestry systems offer advantages that require quan...

  3. Understanding seagrass resilience in temperate systems: the importance of timing of the disturbance

    NARCIS (Netherlands)

    Soissons, L.M.; Li, B.; Han, Q.; van Katwijk, M.M.; Ysebaert, T.; Herman, P.M.J.; Bouma, T.J.

    2016-01-01

    Temperate seagrass meadows form valuable ecosystems in coastal environments and present a distinctseasonal growth. They are threatened by an increasing amount of stressors, potentially affecting theircapacity to recover from disturbances. We hypothesized that their resilience to disturbances is

  4. Understanding seagrass resilience in temperate systems: the importance of timing of the disturbance

    NARCIS (Netherlands)

    Soissons, L.M.; Li, B.Q.; Han, Q.Y.; Katwijk, M.M. van; Ysebaert, T.; Herman, P.M.J.; Bouma, T.J.

    2016-01-01

    Temperate seagrass meadows form valuable ecosystems in coastal environments and present a distinct seasonal growth. They are threatened by an increasing amount of stressors, potentially affecting their capacity to recover from disturbances. We hypothesized that their resilience to disturbances is

  5. Studies on growth and age of bivalves from temperate and tropical estuarine ecosystems

    Digital Repository Service at National Institute of Oceanography (India)

    Parulekar, A.H.

    Comparison of growth progression and age composition of Abra alba and Nuculana minuta from temperate estuarine ecosystem with Meretrix casta and Paphia malabarica from tropical estuarine environment, revealed that the annual growth rate in tropical...

  6. Tempered stable laws as random walk limits

    OpenAIRE

    Chakrabarty, Arijit; Meerschaert, Mark M.

    2010-01-01

    Stable laws can be tempered by modifying the L\\'evy measure to cool the probability of large jumps. Tempered stable laws retain their signature power law behavior at infinity, and infinite divisibility. This paper develops random walk models that converge to a tempered stable law under a triangular array scheme. Since tempered stable laws and processes are useful in statistical physics, these random walk models can provide a basic physical model for the underlying physical phenomena.

  7. Diversity and abundance of photosynthetic sponges in temperate Western Australia

    Directory of Open Access Journals (Sweden)

    Brümmer Franz

    2009-02-01

    Full Text Available Abstract Background Photosynthetic sponges are important components of reef ecosystems around the world, but are poorly understood. It is often assumed that temperate regions have low diversity and abundance of photosynthetic sponges, but to date no studies have investigated this question. The aim of this study was to compare the percentages of photosynthetic sponges in temperate Western Australia (WA with previously published data on tropical regions, and to determine the abundance and diversity of these associations in a range of temperate environments. Results We sampled sponges on 5 m belt transects to determine the percentage of photosynthetic sponges and identified at least one representative of each group of symbionts using 16S rDNA sequencing together with microscopy techniques. Our results demonstrate that photosynthetic sponges are abundant in temperate WA, with an average of 63% of sponge individuals hosting high levels of photosynthetic symbionts and 11% with low to medium levels. These percentages of photosynthetic sponges are comparable to those found on tropical reefs and may have important implications for ecosystem function on temperate reefs in other areas of the world. A diverse range of symbionts sometimes occurred within a small geographic area, including the three "big" cyanobacterial clades, Oscillatoria spongeliae, "Candidatus Synechococcus spongiarum" and Synechocystis species, and it appears that these clades all occur in a wide range of sponges. Additionally, spongin-permeating red algae occurred in at least 7 sponge species. This study provides the first investigation of the molecular phylogeny of rhodophyte symbionts in sponges. Conclusion Photosynthetic sponges are abundant and diverse in temperate WA, with comparable percentages of photosynthetic to non-photosynthetic sponges to tropical zones. It appears that there are three common generalist clades of cyanobacterial symbionts of sponges which occur in a wide

  8. MULTI-DIMENSIONAL MASS SPECTROMETRY-BASED SHOTGUN LIPIDOMICS AND NOVEL STRATEGIES FOR LIPIDOMIC ANALYSES

    Science.gov (United States)

    Han, Xianlin; Yang, Kui; Gross, Richard W.

    2011-01-01

    Since our last comprehensive review on multi-dimensional mass spectrometry-based shotgun lipidomics (Mass Spectrom. Rev. 24 (2005), 367), many new developments in the field of lipidomics have occurred. These developments include new strategies and refinements for shotgun lipidomic approaches that use direct infusion, including novel fragmentation strategies, identification of multiple new informative dimensions for mass spectrometric interrogation, and the development of new bioinformatic approaches for enhanced identification and quantitation of the individual molecular constituents that comprise each cell’s lipidome. Concurrently, advances in liquid chromatography-based platforms and novel strategies for quantitative matrix-assisted laser desorption/ionization mass spectrometry for lipidomic analyses have been developed. Through the synergistic use of this repertoire of new mass spectrometric approaches, the power and scope of lipidomics has been greatly expanded to accelerate progress toward the comprehensive understanding of the pleiotropic roles of lipids in biological systems. PMID:21755525

  9. In-Depth Analysis of Exoproteomes from Marine Bacteria by Shotgun Liquid Chromatography-Tandem Mass Spectrometry: the Ruegeria pomeroyi DSS-3 Case-Study

    Directory of Open Access Journals (Sweden)

    Jean Armengaud

    2010-07-01

    Full Text Available Microorganisms secrete into their extracellular environment numerous compounds that are required for their survival. Many of these compounds could be of great interest for biotechnology applications and their genes used in synthetic biology design. The secreted proteins and the components of the translocation systems themselves can be scrutinized in-depth by the most recent proteomic tools. While the secretomes of pathogens are well-documented, those of non-pathogens remain largely to be established. Here, we present the analysis of the exoproteome from the marine bacterium Ruegeria pomeroyi DSS-3 grown in standard laboratory conditions. We used a shotgun approach consisting of trypsin digestion of the exoproteome, and identification of the resulting peptides by liquid chromatography coupled to tandem mass spectrometry. Three different proteins that have domains homologous to those observed in RTX toxins were uncovered and were semi-quantified as the most abundantly secreted proteins. One of these proteins clearly stands out from the catalogue, representing over half of the total exoproteome. We also listed many soluble proteins related to ABC and TRAP transporters implied in the uptake of nutrients. The Ruegeria pomeroyi DSS-3 case-study illustrates the power of the shotgun nano-LC-MS/MS strategy to decipher the exoproteome from marine bacteria and to contribute to environmental proteomics.

  10. The genome of flax (Linum usitatissimum) assembled de novo from short shotgun sequence reads

    DEFF Research Database (Denmark)

    Wang, Zhiwen; Hobson, Neil; Galindo, Leonardo

    2012-01-01

    Flax (Linum usitatissimum) is an ancient crop that is widely cultivated as a source of fiber, oil and medicinally relevant compounds. To accelerate crop improvement, we performed whole-genome shotgun sequencing of the nuclear genome of flax. Seven paired-end libraries ranging in size from 300 bp...... these results show that de novo assembly, based solely on whole-genome shotgun short-sequence reads, is an efficient means of obtaining nearly complete genome sequence information for some plant species....

  11. A high-throughput shotgun mutagenesis approach to mapping B-cell antibody epitopes.

    Science.gov (United States)

    Davidson, Edgar; Doranz, Benjamin J

    2014-09-01

    Characterizing the binding sites of monoclonal antibodies (mAbs) on protein targets, their 'epitopes', can aid in the discovery and development of new therapeutics, diagnostics and vaccines. However, the speed of epitope mapping techniques has not kept pace with the increasingly large numbers of mAbs being isolated. Obtaining detailed epitope maps for functionally relevant antibodies can be challenging, particularly for conformational epitopes on structurally complex proteins. To enable rapid epitope mapping, we developed a high-throughput strategy, shotgun mutagenesis, that enables the identification of both linear and conformational epitopes in a fraction of the time required by conventional approaches. Shotgun mutagenesis epitope mapping is based on large-scale mutagenesis and rapid cellular testing of natively folded proteins. Hundreds of mutant plasmids are individually cloned, arrayed in 384-well microplates, expressed within human cells, and tested for mAb reactivity. Residues are identified as a component of a mAb epitope if their mutation (e.g. to alanine) does not support candidate mAb binding but does support that of other conformational mAbs or allows full protein function. Shotgun mutagenesis is particularly suited for studying structurally complex proteins because targets are expressed in their native form directly within human cells. Shotgun mutagenesis has been used to delineate hundreds of epitopes on a variety of proteins, including G protein-coupled receptor and viral envelope proteins. The epitopes mapped on dengue virus prM/E represent one of the largest collections of epitope information for any viral protein, and results are being used to design better vaccines and drugs. © 2014 John Wiley & Sons Ltd.

  12. The genome of flax (Linum usitatissimum) assembled de novo from short shotgun sequence reads.

    Science.gov (United States)

    Wang, Zhiwen; Hobson, Neil; Galindo, Leonardo; Zhu, Shilin; Shi, Daihu; McDill, Joshua; Yang, Linfeng; Hawkins, Simon; Neutelings, Godfrey; Datla, Raju; Lambert, Georgina; Galbraith, David W; Grassa, Christopher J; Geraldes, Armando; Cronk, Quentin C; Cullis, Christopher; Dash, Prasanta K; Kumar, Polumetla A; Cloutier, Sylvie; Sharpe, Andrew G; Wong, Gane K-S; Wang, Jun; Deyholos, Michael K

    2012-11-01

    Flax (Linum usitatissimum) is an ancient crop that is widely cultivated as a source of fiber, oil and medicinally relevant compounds. To accelerate crop improvement, we performed whole-genome shotgun sequencing of the nuclear genome of flax. Seven paired-end libraries ranging in size from 300 bp to 10 kb were sequenced using an Illumina genome analyzer. A de novo assembly, comprised exclusively of deep-coverage (approximately 94× raw, approximately 69× filtered) short-sequence reads (44-100 bp), produced a set of scaffolds with N(50) =694 kb, including contigs with N(50)=20.1 kb. The contig assembly contained 302 Mb of non-redundant sequence representing an estimated 81% genome coverage. Up to 96% of published flax ESTs aligned to the whole-genome shotgun scaffolds. However, comparisons with independently sequenced BACs and fosmids showed some mis-assembly of regions at the genome scale. A total of 43384 protein-coding genes were predicted in the whole-genome shotgun assembly, and up to 93% of published flax ESTs, and 86% of A. thaliana genes aligned to these predicted genes, indicating excellent coverage and accuracy at the gene level. Analysis of the synonymous substitution rates (K(s) ) observed within duplicate gene pairs was consistent with a recent (5-9 MYA) whole-genome duplication in flax. Within the predicted proteome, we observed enrichment of many conserved domains (Pfam-A) that may contribute to the unique properties of this crop, including agglutinin proteins. Together these results show that de novo assembly, based solely on whole-genome shotgun short-sequence reads, is an efficient means of obtaining nearly complete genome sequence information for some plant species. © 2012 The Authors. The Plant Journal © 2012 Blackwell Publishing Ltd.

  13. Global analysis of the yeast lipidome by quantitative shotgun mass spectrometry

    DEFF Research Database (Denmark)

    Ejsing, Christer S.; Sampaio, Julio L; Surendranath, Vineeth

    2009-01-01

    95% coverage of the yeast lipidome achieved with 125-fold improvement in sensitivity compared with previous approaches. Comparative lipidomics demonstrated that growth temperature and defects in lipid biosynthesis induce ripple effects throughout the molecular composition of the yeast lipidome....... This work serves as a resource for molecular characterization of eukaryotic lipidomes, and establishes shotgun lipidomics as a powerful platform for complementing biochemical studies and other systems-level approaches....

  14. A Novel Prosthetic Joint Infection Pathogen, Mycoplasma salivarium, Identified by Metagenomic Shotgun Sequencing.

    Science.gov (United States)

    Thoendel, Matthew; Jeraldo, Patricio; Greenwood-Quaintance, Kerryl E; Chia, Nicholas; Abdel, Matthew P; Steckelberg, James M; Osmon, Douglas R; Patel, Robin

    2017-07-15

    Defining the microbial etiology of culture-negative prosthetic joint infection (PJI) can be challenging. Metagenomic shotgun sequencing is a new tool to identify organisms undetected by conventional methods. We present a case where metagenomics was used to identify Mycoplasma salivarium as a novel PJI pathogen in a patient with hypogammaglobulinemia. © The Author 2017. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail: journals.permissions@oup.com.

  15. A combined meta-barcoding and shotgun metagenomic analysis of spontaneous wine fermentation.

    Science.gov (United States)

    Sternes, Peter R; Lee, Danna; Kutyna, Dariusz R; Borneman, Anthony R

    2017-07-01

    Wine is a complex beverage, comprising hundreds of metabolites produced through the action of yeasts and bacteria in fermenting grape must. Commercially, there is now a growing trend away from using wine yeast (Saccharomyces) starter cultures, toward the historic practice of uninoculated or "wild" fermentation, where the yeasts and bacteria associated with the grapes and/or winery perform the fermentation. It is the varied metabolic contributions of these numerous non-Saccharomyces species that are thought to impart complexity and desirable taste and aroma attributes to wild ferments in comparison to their inoculated counterparts. To map the microflora of spontaneous fermentation, metagenomic techniques were employed to characterize and monitor the progression of fungal species in 5 different wild fermentations. Both amplicon-based ribosomal DNA internal transcribed spacer (ITS) phylotyping and shotgun metagenomics were used to assess community structure across different stages of fermentation. While providing a sensitive and highly accurate means of characterizing the wine microbiome, the shotgun metagenomic data also uncovered a significant overabundance bias in the ITS phylotyping abundance estimations for the common non-Saccharomyces wine yeast genus Metschnikowia. By identifying biases such as that observed for Metschnikowia, abundance measurements from future ITS phylotyping datasets can be corrected to provide more accurate species representation. Ultimately, as more shotgun metagenomic and single-strain de novo assemblies for key wine species become available, the accuracy of both ITS-amplicon and shotgun studies will greatly increase, providing a powerful methodology for deciphering the influence of the microbial community on the wine flavor and aroma. © The Authors 2017. Published by Oxford University Press.

  16. Midpregnancy Marriage and Divorce: Why the Death of Shotgun Marriage Has Been Greatly Exaggerated.

    Science.gov (United States)

    Gibson-Davis, Christina M; Ananat, Elizabeth O; Gassman-Pines, Anna

    2016-12-01

    Conventional wisdom holds that births following the colloquially termed "shotgun marriage"-that is, births to parents who married between conception and the birth-are nearing obsolescence. To investigate trends in shotgun marriage, we matched North Carolina administrative data on nearly 800,000 first births among white and black mothers to marriage and divorce records. We found that among married births, midpregnancy-married births (our preferred term for shotgun-married births) have been relatively stable at about 10 % over the past quarter-century while increasing substantially for vulnerable population subgroups. In 2012, among black and white less-educated and younger women, midpregnancy-married births accounted for approximately 20 % to 25 % of married first births. The increasing representation of midpregnancy-married births among married births raises concerns about well-being among at-risk families because midpregnancy marriages may be quite fragile. Our analysis revealed, however, that midpregnancy marriages were more likely to dissolve only among more advantaged groups. Of those groups considered to be most at risk of divorce-namely, black women with lower levels of education and who were younger-midpregnancy marriages had the same or lower likelihood of divorce as preconception marriages. Our results suggest an overlooked resiliency in a type of marriage that has only increased in salience.

  17. Shotgun Wedding: Interagency Transformation for the 21st Century Security Environment

    National Research Council Canada - National Science Library

    Gibler, Michael L

    2008-01-01

    .... Equally present are the numerous statements and studies by governmental bodies, military leadership, non-partisan think tanks, academia and political elites who believe the current National Security...

  18. Environment

    DEFF Research Database (Denmark)

    Valentini, Chiara

    2017-01-01

    The term environment refers to the internal and external context in which organizations operate. For some scholars, environment is defined as an arrangement of political, economic, social and cultural factors existing in a given context that have an impact on organizational processes and structures....... For others, environment is a generic term describing a large variety of stakeholders and how these interact and act upon organizations. Organizations and their environment are mutually interdependent and organizational communications are highly affected by the environment. This entry examines the origin...... and development of organization-environment interdependence, the nature of the concept of environment and its relevance for communication scholarships and activities....

  19. On choice of tempered steels

    International Nuclear Information System (INIS)

    Govorov, A.A.; Pan'shin, I.F.; Rakhmanov, V.I.

    1978-01-01

    For the purpose of developing a graphical method for choosing structural steels, a change in the propagation work of a crack and in the critical temperature of brittleness of 40, 40Kh, 40KhN, and 40KhNM steels, was examined depending on the hardness after hardening and tempering. A diagram enabling to choose the grade of steel for making an article of known dimensions according to the preset values of its mechanical properties has been plotted. The developed selection scheme takes into account the hardenability of steels and the influence of the hardness after thermal treatment on the cold-shortness of steel

  20. First description of underwater acoustic diversity in three temperate ponds

    Directory of Open Access Journals (Sweden)

    Camille Desjonquères

    2015-11-01

    Full Text Available The past decade has produced an increased ecological interest in sonic environments, or soundscapes. However, despite this rise in interest and technological improvements that allow for long-term acoustic surveys in various environments, some habitats’ soundscapes remain to be explored. Ponds, and more generally freshwater habitats, are one of these acoustically unexplored environments. Here we undertook the first long term acoustic monitoring of three temperate ponds in France. By aural and visual inspection of a selection of recordings, we identified 48 different sound types, and according to the rarefaction curves we calculated, more sound types are likely present in one of the three ponds. The richness of sound types varied significantly across ponds. Surprisingly, there was no pond-to-pond daily consistency of sound type richness variation; each pond had its own daily patterns of activity. We also explored the possibility of using six acoustic diversity indices to conduct rapid biodiversity assessments in temperate ponds. We found that all indices were sensitive to the background noise as estimated through correlations with the signal-to-noise ratio (SNR. However, we determined that the AR index could be a good candidate to measure acoustic diversities using partial correlations with the SNR as a control variable. Yet, research is still required to automatically compute the SNR in order to apply this index on a large data set of recordings. The results showed that these three temperate ponds host a high level of acoustic diversity in which the soundscapes were variable not only between but also within the ponds. The sources producing this diversity of sounds and the drivers of difference in daily song type richness variation both require further investigation. Such research would yield insights into the biodiversity and ecology of temperate ponds.

  1. Sorption of pesticides in tropical and temperate soils from Australia and the Philippines.

    Science.gov (United States)

    Oliver, Danielle P; Kookana, Rai S; Quintana, Belen

    2005-08-10

    The sorption behavior of diuron, imidacloprid, and thiacloprid was investigated using 22 soils collected in triplicate from temperate environments in Australia and tropical environments in Australia and the Philippines. Within the temperate environment in Australia, the soils were selected from a range of land uses. The average KOC values (L/kg) for imidacloprid were 326, 322, and 336; for thiacloprid, the values were 915, 743, and 842; and for diuron, the values were 579, 536, and 618 for the Ord (tropical), Mt. Lofty (temperate), and Philippines (tropical) soils, respectively. For all soils, the sorption coefficients decreased in the following order: thiacloprid > diuron > imidacloprid. There were no significant differences in sorption behavior between the tropical soils from the Philippines and the temperate soils from Australia. Sorption was also not significantly related with soil characteristics, namely, organic carbon (OC) content, clay content, and pH, for any of the three chemicals studied. When the data were sorted into separate land uses, the sorption of all three chemicals was highly correlated (P soils from the Philippines. Sorption coefficients for all three chemicals were highly correlated with OC in temperate, native soils only when one extreme value was removed. The relationships between sorption of all three chemicals and OC in temperate, pasture soils were best described by a polynomial. Sorption coefficients for imidacloprid and thiacloprid determined in the temperate pasture soils remained fairly consistent as the OC content increased from 3.3 to 5.3%, indicating that, although the total OC in the pasture soils was increasing, the component of OC involved with sorption of these two compounds may have been remaining constant. This study demonstrated that the origin of the soils (i.e., temperate vs tropical) had no significant effect on the sorption behavior, but in some cases, land use significantly affected the sorption behavior of the three

  2. RePS: a sequence assembler that masks exact repeats identified from the shotgun data

    DEFF Research Database (Denmark)

    Wang, Jun; Wong, Gane Ka-Shu; Ni, Peixiang

    2002-01-01

    We describe a sequence assembler, RePS (repeat-masked Phrap with scaffolding), that explicitly identifies exact 20mer repeats from the shotgun data and removes them prior to the assembly. The established software is used to compute meaningful error probabilities for each base. Clone......-end-pairing information is used to construct scaffolds that order and orient the contigs. We show with real data for human and rice that reasonable assemblies are possible even at coverages of only 4x to 6x, despite having up to 42.2% in exact repeats. Udgivelsesdato: 2002-May...

  3. Tandem Mass Spectrum Sequencing: An Alternative to Database Search Engines in Shotgun Proteomics.

    Science.gov (United States)

    Muth, Thilo; Rapp, Erdmann; Berven, Frode S; Barsnes, Harald; Vaudel, Marc

    2016-01-01

    Protein identification via database searches has become the gold standard in mass spectrometry based shotgun proteomics. However, as the quality of tandem mass spectra improves, direct mass spectrum sequencing gains interest as a database-independent alternative. In this chapter, the general principle of this so-called de novo sequencing is introduced along with pitfalls and challenges of the technique. The main tools available are presented with a focus on user friendly open source software which can be directly applied in everyday proteomic workflows.

  4. HOMICIDE BY CERVICAL SPINAL CORD GUNSHOT INJURY WITH SHOTGUN FIRE PELLETS: CASE REPORT

    Directory of Open Access Journals (Sweden)

    Dana Turliuc, Serban Turliuc, Iustin Mihailov, Andrei Cucu, Gabriel Dumitrescu,Claudia Costea

    2015-10-01

    Full Text Available This case present a rare forensic case of cervical spinal gunshot injury of a female by her husband, a professional hunter, during a family fight with a shotgun fire pellets. The gunshot destroyed completely the cervical spinal cord, without injury to the neck vessels and organs and with the patient survival for seven days. We discuss notions of judicial ballistics, assessment of the patient with spinal cord gunshot injury and therapeutic strategies. Even if cervical spine gunshot injuries are most of the times lethal for majority of patients, the surviving patients need the coordination of a multidisciplinary surgical team to ensure the optimal functional prognostic.

  5. Population genetic analysis of shotgun assemblies of genomic sequences from multiple individuals

    DEFF Research Database (Denmark)

    Hellmann, Ines; Mang, Yuan; Gu, Zhiping

    2008-01-01

    We introduce a simple, broadly applicable method for obtaining estimates of nucleotide diversity from genomic shotgun sequencing data. The method takes into account the special nature of these data: random sampling of genomic segments from one or more individuals and a relatively high error rate...... for individual reads. Applying this method to data from the Celera human genome sequencing and SNP discovery project, we obtain estimates of nucleotide diversity in windows spanning the human genome and show that the diversity to divergence ratio is reduced in regions of low recombination. Furthermore, we show...

  6. Testing for functional convergence of temperate rainforest tree assemblages in Chile and New Zealand

    NARCIS (Netherlands)

    Lusk, C.H.; Jimenez-Castillo, M.; Aragón, R.; Easdale, T.A.; Poorter, L.; Hinojosa, L.F.; Mason, N.W.H.W.H.

    2016-01-01

    An important tenet of biogeography and comparative ecology is that disjunct assemblages in similar physical environments are functionally more similar to each other than to assemblages from other environments. Temperate rainforests in South America, New Zealand and Australia share certain

  7. New temperable solar coatings: Tempsol

    Science.gov (United States)

    Demiryont, Hulya

    2001-11-01

    This paper deals with the large area deposition and coating properties of the thermo-stable (temperable/bendable) solar coating material, CuO, and some new optical coating systems comprising CuO films for architectural and automotive/transportation applications. The CuO solar coating is combined with other coating layers, for example, an anti-reflection film, a reflection film, a coloration coating layer, etc., which are also thermo-stable. The film systems are developed at the research laboratory by D.C. Magnetron reactive sputtering process. The new developed technologies then transferred to the production line. Product performances are compared before and after heat treatment of the coating systems. Performance tables and other physical properties, including optical parameters, mechanical and environmental stability, storage properties, etc., are also presented for this new product series.

  8. Organization and evolution of primate centromeric DNA from whole-genome shotgun sequence data.

    Directory of Open Access Journals (Sweden)

    Can Alkan

    2007-09-01

    Full Text Available The major DNA constituent of primate centromeres is alpha satellite DNA. As much as 2%-5% of sequence generated as part of primate genome sequencing projects consists of this material, which is fragmented or not assembled as part of published genome sequences due to its highly repetitive nature. Here, we develop computational methods to rapidly recover and categorize alpha-satellite sequences from previously uncharacterized whole-genome shotgun sequence data. We present an algorithm to computationally predict potential higher-order array structure based on paired-end sequence data and then experimentally validate its organization and distribution by experimental analyses. Using whole-genome shotgun data from the human, chimpanzee, and macaque genomes, we examine the phylogenetic relationship of these sequences and provide further support for a model for their evolution and mutation over the last 25 million years. Our results confirm fundamental differences in the dispersal and evolution of centromeric satellites in the Old World monkey and ape lineages of evolution.

  9. Defining Diagnostic Biomarkers Using Shotgun Proteomics and MALDI-TOF Mass Spectrometry.

    Science.gov (United States)

    Armengaud, Jean

    2017-01-01

    Whole-cell MALDI-TOF has become a robust and widely used tool to quickly identify any pathogen. In addition to being routinely used in hospitals, it is also useful for low cost dereplication in large scale screening procedures of new environmental isolates for environmental biotechnology or taxonomical applications. Here, I describe how specific biomarkers can be defined using shotgun proteomics and whole-cell MALDI-TOF mass spectrometry. Based on MALDI-TOF spectra recorded on a given set of pathogens with internal calibrants, m/z values of interest are extracted. The proteins which contribute to these peaks are deduced from label-free shotgun proteomics measurements carried out on the same sample. Quantitative information based on the spectral count approach allows ranking the most probable candidates. Proteogenomic approaches help to define whether these proteins give the same m/z values along the whole taxon under consideration or result in heterogeneous lists. These specific biomarkers nicely complement conventional profiling approaches and may help to better define groups of organisms, for example at the subspecies level.

  10. Shotgun glycomics of pig lung identifies natural endogenous receptors for influenza viruses.

    Science.gov (United States)

    Byrd-Leotis, Lauren; Liu, Renpeng; Bradley, Konrad C; Lasanajak, Yi; Cummings, Sandra F; Song, Xuezheng; Heimburg-Molinaro, Jamie; Galloway, Summer E; Culhane, Marie R; Smith, David F; Steinhauer, David A; Cummings, Richard D

    2014-06-03

    Influenza viruses bind to host cell surface glycans containing terminal sialic acids, but as studies on influenza binding become more sophisticated, it is becoming evident that although sialic acid may be necessary, it is not sufficient for productive binding. To better define endogenous glycans that serve as viral receptors, we have explored glycan recognition in the pig lung, because influenza is broadly disseminated in swine, and swine have been postulated as an intermediary host for the emergence of pandemic strains. For these studies, we used the technology of "shotgun glycomics" to identify natural receptor glycans. The total released N- and O-glycans from pig lung glycoproteins and glycolipid-derived glycans were fluorescently tagged and separated by multidimensional HPLC, and individual glycans were covalently printed to generate pig lung shotgun glycan microarrays. All viruses tested interacted with one or more sialylated N-glycans but not O-glycans or glycolipid-derived glycans, and each virus demonstrated novel and unexpected differences in endogenous N-glycan recognition. The results illustrate the repertoire of specific, endogenous N-glycans of pig lung glycoproteins for virus recognition and offer a new direction for studying endogenous glycan functions in viral pathogenesis.

  11. Automated and Accurate Estimation of Gene Family Abundance from Shotgun Metagenomes.

    Directory of Open Access Journals (Sweden)

    Stephen Nayfach

    2015-11-01

    Full Text Available Shotgun metagenomic DNA sequencing is a widely applicable tool for characterizing the functions that are encoded by microbial communities. Several bioinformatic tools can be used to functionally annotate metagenomes, allowing researchers to draw inferences about the functional potential of the community and to identify putative functional biomarkers. However, little is known about how decisions made during annotation affect the reliability of the results. Here, we use statistical simulations to rigorously assess how to optimize annotation accuracy and speed, given parameters of the input data like read length and library size. We identify best practices in metagenome annotation and use them to guide the development of the Shotgun Metagenome Annotation Pipeline (ShotMAP. ShotMAP is an analytically flexible, end-to-end annotation pipeline that can be implemented either on a local computer or a cloud compute cluster. We use ShotMAP to assess how different annotation databases impact the interpretation of how marine metagenome and metatranscriptome functional capacity changes across seasons. We also apply ShotMAP to data obtained from a clinical microbiome investigation of inflammatory bowel disease. This analysis finds that gut microbiota collected from Crohn's disease patients are functionally distinct from gut microbiota collected from either ulcerative colitis patients or healthy controls, with differential abundance of metabolic pathways related to host-microbiome interactions that may serve as putative biomarkers of disease.

  12. Organization and evolution of primate centromeric DNA from whole-genome shotgun sequence data.

    Science.gov (United States)

    Alkan, Can; Ventura, Mario; Archidiacono, Nicoletta; Rocchi, Mariano; Sahinalp, S Cenk; Eichler, Evan E

    2007-09-01

    The major DNA constituent of primate centromeres is alpha satellite DNA. As much as 2%-5% of sequence generated as part of primate genome sequencing projects consists of this material, which is fragmented or not assembled as part of published genome sequences due to its highly repetitive nature. Here, we develop computational methods to rapidly recover and categorize alpha-satellite sequences from previously uncharacterized whole-genome shotgun sequence data. We present an algorithm to computationally predict potential higher-order array structure based on paired-end sequence data and then experimentally validate its organization and distribution by experimental analyses. Using whole-genome shotgun data from the human, chimpanzee, and macaque genomes, we examine the phylogenetic relationship of these sequences and provide further support for a model for their evolution and mutation over the last 25 million years. Our results confirm fundamental differences in the dispersal and evolution of centromeric satellites in the Old World monkey and ape lineages of evolution.

  13. Comparative visual ecophysiology of mid-Atlantic temperate reef fishes

    Directory of Open Access Journals (Sweden)

    Andrij Z. Horodysky

    2013-11-01

    The absolute light sensitivities, temporal properties, and spectral sensitivities of the visual systems of three mid-Atlantic temperate reef fishes (Atlantic spadefish [Ephippidae: Chaetodipterus faber], tautog [Labridae: Tautoga onitis], and black sea bass [Serranidae: Centropristis striata] were studied via electroretinography (ERG. Pelagic Atlantic spadefish exhibited higher temporal resolution but a narrower dynamic range than the two more demersal foragers. The higher luminous sensitivities of tautog and black sea bass were similar to other benthic and demersal coastal mid-Atlantic fishes. Flicker fusion frequency experiments revealed significant interspecific differences at maximum intensities that correlated with lifestyle and habitat. Spectral responses of the three species spanned 400–610 nm, with high likelihood of cone dichromacy providing the basis for color and contrast discrimination. Significant day-night differences in spectral responses were evident in spadefish and black sea bass but not tautog, a labrid with characteristic structure-associated nocturnal torpor. Atlantic spadefish responded to a wider range of wavelengths than did deeper-dwelling tautog or black sea bass. Collectively, these results suggest that temperate reef-associated fishes are well-adapted to their gradient of brighter to dimmer photoclimates, representative of their unique ecologies and life histories. Continuing anthropogenic degradation of water quality in coastal environments, at a pace faster than the evolution of visual systems, may however impede visual foraging and reproductive signaling in temperate reef fishes.

  14. The Effect of Tempering on Strength Properties and Seed Coat ...

    African Journals Online (AJOL)

    The effect of tempering on seed coat adhesion strength and mechanical strength of sorghum and millet grain kernels was investigated at different tempering durations. Tempering reduced the kernel breaking strength and had significant effect on seed coat adhesion strength. Tempering the grain for 60 minutes at ambient ...

  15. Comparisons of invasive plants in southern Africa originating from southern temperate, northern temperate and tropical regions

    Directory of Open Access Journals (Sweden)

    L. Henderson

    2006-08-01

    Full Text Available A subset of invasive alien plant species in southern Africa was analysed in terms of their history of introduction, rate of spread, countries/region of origin, taxonomy, growth forms, cultivated uses, weed status and current distribution in southern Africa, and comparisons made of those originating from south of the tropic of Capricorn, north of the tropic of Cancer and from the tropics. The subset of 233 species, belonging to 58 families, includes all important declared species and some potentially important species. Almost as many species originate from temperate regions (112 as from the tropics (121. Most southern temperate species came from Australia (28/36, most tropical species from tropical America (92/121 and most northern temperate species from Europe (including the Mediterranean and Asia (58/76. Transformers account for 33% of  all species. More transformers are of tropical origin (36 than of northern temperate (24 and southern temperate origin (18. However. 50% of southern temperate species are transformers, compared to 32% of northern temperate and 29% of tropical species. Southern temperate transformer species are mainly woody trees and shrubs that were established on a grand scale as silvicultural crops, barriers (hedges, windbreaks and screens and cover/binders. Most aquatics, herbs, climbers and succulent shrubs an. trom the tropics. Ornamentals are the single largest category of plants from all three regions, the tropics having contributed twice as many species as temperate regions.

  16. Large pore dermal microdialysis and liquid chromatography-tandem mass spectroscopy shotgun proteomic analysis: a feasibility study

    DEFF Research Database (Denmark)

    Petersen, Lars J.; Sorensen, Mette A.; Codrea, Marius C.

    2013-01-01

    Background/AimsThe purpose of the present pilot study was to investigate the feasibility of combining large pore dermal microdialysis with shotgun proteomic analysis in human skin. MethodsDialysate was recovered from human skin by 2000 kDa microdialysis membranes from one subject at three different...

  17. High-content screening of yeast mutant libraries by shotgun lipidomics

    DEFF Research Database (Denmark)

    Tarasov, Kirill; Stefanko, Adam; Casanovas, Albert

    2014-01-01

    To identify proteins with a functional role in lipid metabolism and homeostasis we designed a high-throughput platform for high-content lipidomic screening of yeast mutant libraries. To this end, we combined culturing and lipid extraction in 96-well format, automated direct infusion...... factor KAR4 precipitated distinct lipid metabolic phenotypes. These results demonstrate that the high-throughput shotgun lipidomics platform is a valid and complementary proxy for high-content screening of yeast mutant libraries....... nanoelectrospray ionization, high-resolution Orbitrap mass spectrometry, and a dedicated data processing framework to support lipid phenotyping across hundreds of Saccharomyces cerevisiae mutants. Our novel approach revealed that the absence of genes with unknown function YBR141C and YJR015W, and the transcription...

  18. Analysis of secretome of breast cancer cell line with an optimized semi-shotgun method

    International Nuclear Information System (INIS)

    Tang Xiaorong; Yao Ling; Chen Keying; Hu Xiaofang; Xu Lisa; Fan Chunhai

    2009-01-01

    Secretome, the totality of secreted proteins, is viewed as a promising pool of candidate cancer biomarkers. Simple and reliable methods for identifying secreted proteins are highly desired. We used an optimized semi-shotgun liquid chromatography followed by tandem mass spectrometry (LC-MS/MS) method to analyze the secretome of breast cancer cell line MDA-MB-231. A total of 464 proteins were identified. About 63% of the proteins were classified as secreted proteins, including many promising breast cancer biomarkers, which were thought to be correlated with tumorigenesis, tumor development and metastasis. These results suggest that the optimized method may be a powerful strategy for cell line secretome profiling, and can be used to find potential cancer biomarkers with great clinical significance. (authors)

  19. Shotgun metagenomics of 250 adult twins reveals genetic and environmental impacts on the gut microbiome

    DEFF Research Database (Denmark)

    Xie, Hailiang; Guo, Ruijin; Zhong, Huanzi

    2016-01-01

    The gut microbiota has been typically viewed as an environmental factor for human health. Twins are well suited for investigating the concordance of their gut microbiomes and decomposing genetic and environmental influences. However, existing twin studies utilizing metagenomic shotgun sequencing...... have included only a few samples. Here, we sequenced fecal samples from 250 adult twins in the TwinsUK registry and constructed a comprehensive gut microbial reference gene catalog. We demonstrate heritability of many microbial taxa and functional modules in the gut microbiome, including those...... associated with diseases. Moreover, we identified 8 million SNPs in the gut microbiome and observe a high similarity in microbiome SNPs between twins that slowly decreases after decades of living apart. The results shed new light on the genetic and environmental influences on the composition and function...

  20. Structural characterization of ether lipids from the archaeon Sulfolobus islandicus by high-resolution shotgun lipidomics

    DEFF Research Database (Denmark)

    Jensen, Sara Munk; Brandl, Martin; Treusch, Alexander H

    2015-01-01

    The molecular structures, biosynthetic pathways and physiological functions of membrane lipids produced by organisms in the domain Archaea are poorly characterized as compared with that of counterparts in Bacteria and Eukaryota. Here we report on the use of high-resolution shotgun lipidomics......-resolution Fourier transform mass spectrometry using an ion trap-orbitrap mass spectrometer. This analysis identified five clusters of molecular ions that matched ether lipids in the database with sub-ppm mass accuracy. To structurally characterize and validate the identities of the potential lipid species, we...... performed structural analysis using multistage activation on the ion trap-orbitrap instrument as well as tandem mass analysis using a quadrupole time-of-flight machine. Our analysis identified four ether lipid species previously reported in Archaea, and one ether lipid species that had not been described...

  1. Fine-scale variation in meiotic recombination in Mimulus inferred from population shotgun sequencing

    Energy Technology Data Exchange (ETDEWEB)

    Hellsten, Uffe [USDOE Joint Genome Inst., Walnut Creek, CA (United States); Wright, Kevin M. [Harvard Univ., Cambridge, MA (United States); Jenkins, Jerry [USDOE Joint Genome Inst., Walnut Creek, CA (United States); HudsonAlpha Inst. of Biotechnology, Huntsville, AL (United States); Shu, Shengqiang [USDOE Joint Genome Inst., Walnut Creek, CA (United States); Yuan, Yao-Wu [Univ. of Connecticut, Storrs, CT (United States); Wessler, Susan R. [Univ. of California, Riverside, CA (United States); Schmutz, Jeremy [USDOE Joint Genome Inst., Walnut Creek, CA (United States); HudsonAlpha Inst. of Biotechnology, Huntsville, AL (United States); Willis, John H. [Duke Univ., Durham, NC (United States); Rokhsar, Daniel S. [USDOE Joint Genome Inst., Walnut Creek, CA (United States); Univ. of California, Berkeley, CA (United States)

    2013-11-13

    Meiotic recombination rates can vary widely across genomes, with hotspots of intense activity interspersed among cold regions. In yeast, hotspots tend to occur in promoter regions of genes, whereas in humans and mice hotspots are largely defined by binding sites of the PRDM9 protein. To investigate the detailed recombination pattern in a flowering plant we use shotgun resequencing of a wild population of the monkeyflower Mimulus guttatus to precisely locate over 400,000 boundaries of historic crossovers or gene conversion tracts. Their distribution defines some 13,000 hotspots of varying strengths, interspersed with cold regions of undetectably low recombination. Average recombination rates peak near starts of genes and fall off sharply, exhibiting polarity. Within genes, recombination tracts are more likely to terminate in exons than in introns. The general pattern is similar to that observed in yeast, as well as in PRDM9-knockout mice, suggesting that recombination initiation described here in Mimulus may reflect ancient and conserved eukaryotic mechanisms

  2. A statistical approach designed for finding mathematically defined repeats in shotgun data and determining the length distribution of clone-inserts

    DEFF Research Database (Denmark)

    Zhong, Lan; Zhang, Kunlin; Huang, Xiangang

    2003-01-01

    that repeats of different copy number have different probabilities of appearance in shotgun data, so based on this principle, we constructed a statistical model and inferred criteria for mathematically defined repeats (MDRs) at different shotgun coverages. According to these criteria, we developed software...... MDRmasker to identify and mask MDRs in shotgun data. With repeats masked prior to assembly, the speed of assembly was increased with lower error probability. In addition, clone-insert size affect the accuracy of repeat assembly and scaffold construction, we also designed length distribution of clone...

  3. Cellular metabolic rate is influenced by life-history traits in tropical and temperate birds.

    Science.gov (United States)

    Jimenez, Ana Gabriela; Van Brocklyn, James; Wortman, Matthew; Williams, Joseph B

    2014-01-01

    In general, tropical birds have a "slow pace of life," lower rates of whole-animal metabolism and higher survival rates, than temperate species. A fundamental challenge facing physiological ecologists is the understanding of how variation in life-history at the whole-organism level might be linked to cellular function. Because tropical birds have lower rates of whole-animal metabolism, we hypothesized that cells from tropical species would also have lower rates of cellular metabolism than cells from temperate species of similar body size and common phylogenetic history. We cultured primary dermal fibroblasts from 17 tropical and 17 temperate phylogenetically-paired species of birds in a common nutritive and thermal environment and then examined basal, uncoupled, and non-mitochondrial cellular O2 consumption (OCR), proton leak, and anaerobic glycolysis (extracellular acidification rates [ECAR]), using an XF24 Seahorse Analyzer. We found that multiple measures of metabolism in cells from tropical birds were significantly lower than their temperate counterparts. Basal and uncoupled cellular metabolism were 29% and 35% lower in cells from tropical birds, respectively, a decrease closely aligned with differences in whole-animal metabolism between tropical and temperate birds. Proton leak was significantly lower in cells from tropical birds compared with cells from temperate birds. Our results offer compelling evidence that whole-animal metabolism is linked to cellular respiration as a function of an animal's life-history evolution. These findings are consistent with the idea that natural selection has uniquely fashioned cells of long-lived tropical bird species to have lower rates of metabolism than cells from shorter-lived temperate species.

  4. Cellular metabolic rate is influenced by life-history traits in tropical and temperate birds.

    Directory of Open Access Journals (Sweden)

    Ana Gabriela Jimenez

    Full Text Available In general, tropical birds have a "slow pace of life," lower rates of whole-animal metabolism and higher survival rates, than temperate species. A fundamental challenge facing physiological ecologists is the understanding of how variation in life-history at the whole-organism level might be linked to cellular function. Because tropical birds have lower rates of whole-animal metabolism, we hypothesized that cells from tropical species would also have lower rates of cellular metabolism than cells from temperate species of similar body size and common phylogenetic history. We cultured primary dermal fibroblasts from 17 tropical and 17 temperate phylogenetically-paired species of birds in a common nutritive and thermal environment and then examined basal, uncoupled, and non-mitochondrial cellular O2 consumption (OCR, proton leak, and anaerobic glycolysis (extracellular acidification rates [ECAR], using an XF24 Seahorse Analyzer. We found that multiple measures of metabolism in cells from tropical birds were significantly lower than their temperate counterparts. Basal and uncoupled cellular metabolism were 29% and 35% lower in cells from tropical birds, respectively, a decrease closely aligned with differences in whole-animal metabolism between tropical and temperate birds. Proton leak was significantly lower in cells from tropical birds compared with cells from temperate birds. Our results offer compelling evidence that whole-animal metabolism is linked to cellular respiration as a function of an animal's life-history evolution. These findings are consistent with the idea that natural selection has uniquely fashioned cells of long-lived tropical bird species to have lower rates of metabolism than cells from shorter-lived temperate species.

  5. Cellular Metabolic Rate Is Influenced by Life-History Traits in Tropical and Temperate Birds

    Science.gov (United States)

    Jimenez, Ana Gabriela; Van Brocklyn, James; Wortman, Matthew; Williams, Joseph B.

    2014-01-01

    In general, tropical birds have a “slow pace of life,” lower rates of whole-animal metabolism and higher survival rates, than temperate species. A fundamental challenge facing physiological ecologists is the understanding of how variation in life-history at the whole-organism level might be linked to cellular function. Because tropical birds have lower rates of whole-animal metabolism, we hypothesized that cells from tropical species would also have lower rates of cellular metabolism than cells from temperate species of similar body size and common phylogenetic history. We cultured primary dermal fibroblasts from 17 tropical and 17 temperate phylogenetically-paired species of birds in a common nutritive and thermal environment and then examined basal, uncoupled, and non-mitochondrial cellular O2 consumption (OCR), proton leak, and anaerobic glycolysis (extracellular acidification rates [ECAR]), using an XF24 Seahorse Analyzer. We found that multiple measures of metabolism in cells from tropical birds were significantly lower than their temperate counterparts. Basal and uncoupled cellular metabolism were 29% and 35% lower in cells from tropical birds, respectively, a decrease closely aligned with differences in whole-animal metabolism between tropical and temperate birds. Proton leak was significantly lower in cells from tropical birds compared with cells from temperate birds. Our results offer compelling evidence that whole-animal metabolism is linked to cellular respiration as a function of an animal’s life-history evolution. These findings are consistent with the idea that natural selection has uniquely fashioned cells of long-lived tropical bird species to have lower rates of metabolism than cells from shorter-lived temperate species. PMID:24498080

  6. Comparative life history of the south temperate Cape Penduline Tit (Anthoscopus minutus) and north temperate Remizidae species

    Science.gov (United States)

    Lloyd, Penn; Frauenknecht, Bernhard D.; du Plessis, Morné A.; Martin, Thomas E.

    2017-01-01

    We studied the breeding biology of the south temperate Cape Penduline Tit (Anthoscopus minutus) in order to compare its life history traits with those of related north temperate members of the family Remizidae, namely the Eurasian Penduline Tit (Remiz pendulinus) and the Verdin (Auriparus flaviceps). We used this comparison to test key predictions of three hypotheses thought to explain latitudinal variation in life histories among bird species—the seasonality and food limitation hypothesis, nest predation hypothesis and adult mortality hypothesis. Contrary to the general pattern of smaller clutch size and lower adult mortality among south-temperate birds living in less seasonal environments, the Cape Penduline Tit has a clutch size larger than that of the Verdin and similar to that of the Eurasian Penduline Tit, and higher adult mortality than both of the other two species. The most notable difference between the Cape Penduline Tit and the two other species is in parental behavioural strategy, with the former exhibiting bi-parental care at all stages of nesting together with facultative cooperative breeding, whereas the Eurasian Penduline Tit has uni-parental care and the Verdin has a combination of female-only incubation but bi-parental nestling care. Consequently, in comparison to the other two species, the Cape Penduline Tit exhibits greater nest attentiveness during incubation, a similar per-nestling feeding rate and greater post-fledging survival. Its relatively large clutch size, high parental investment and associated high adult mortality in a less seasonal environment are consistent with key predictions of the adult mortality hypothesis but not with key predictions of the seasonality and food limitation hypothesis in explaining life history variation among Remizidae species. These results add to a growing body of evidence of the importance of age-specific mortality in shaping life history evolution.

  7. Environment

    International Nuclear Information System (INIS)

    McIntyre, A.D.; Turnbull, R.G.H.

    1992-01-01

    The development of the hydrocarbon resources of the North Sea has resulted in both offshore and onshore environmental repercussions, involving the existing physical attributes of the sea and seabed, the coastline and adjoining land. The social and economic repercussions of the industry were equally widespread. The dramatic and speedy impact of the exploration and exploitation of the northern North Sea resources in the early 1970s, on the physical resources of Scotland was quickly realised together with the concern that any environmental and social damage to the physical and social fabric should be kept to a minimum. To this end, a wide range of research and other activities by central and local government, and other interested agencies was undertaken to extend existing knowledge on the marine and terrestrial environments that might be affected by the oil and gas industry. The outcome of these activities is summarized in this paper. The topics covered include a survey of the marine ecosystems of the North Sea, the fishing industry, the impact of oil pollution on seabirds and fish stocks, the ecology of the Scottish coastline and the impact of the petroleum industry on a selection of particular sites. (author)

  8. First Temperate Exoplanet Sized Up

    Science.gov (United States)

    2010-03-01

    Combining observations from the CoRoT satellite and the ESO HARPS instrument, astronomers have discovered the first "normal" exoplanet that can be studied in great detail. Designated Corot-9b, the planet regularly passes in front of a star similar to the Sun located 1500 light-years away from Earth towards the constellation of Serpens (the Snake). "This is a normal, temperate exoplanet just like dozens we already know, but this is the first whose properties we can study in depth," says Claire Moutou, who is part of the international team of 60 astronomers that made the discovery. "It is bound to become a Rosetta stone in exoplanet research." "Corot-9b is the first exoplanet that really does resemble planets in our solar system," adds lead author Hans Deeg. "It has the size of Jupiter and an orbit similar to that of Mercury." "Like our own giant planets, Jupiter and Saturn, the planet is mostly made of hydrogen and helium," says team member Tristan Guillot, "and it may contain up to 20 Earth masses of other elements, including water and rock at high temperatures and pressures." Corot-9b passes in front of its host star every 95 days, as seen from Earth [1]. This "transit" lasts for about 8 hours, and provides astronomers with much additional information on the planet. This is fortunate as the gas giant shares many features with the majority of exoplanets discovered so far [2]. "Our analysis has provided more information on Corot-9b than for other exoplanets of the same type," says co-author Didier Queloz. "It may open up a new field of research to understand the atmospheres of moderate- and low-temperature planets, and in particular a completely new window in our understanding of low-temperature chemistry." More than 400 exoplanets have been discovered so far, 70 of them through the transit method. Corot-9b is special in that its distance from its host star is about ten times larger than that of any planet previously discovered by this method. And unlike all such

  9. Tempering of Low-Temperature Bainite

    Science.gov (United States)

    Peet, Mathew J.; Babu, Sudarsanam Suresh; Miller, Mike K.; Bhadeshia, H. K. D. H.

    2017-07-01

    Electron microscopy, X-ray diffraction, and atom probe tomography have been used to identify the changes which occur during the tempering of a carbide-free bainitic steel transformed at 473 K (200 °C). Partitioning of solute between ferrite and thin-films of retained austenite was observed on tempering at 673 K (400 °C) for 30 minutes. After tempering at 673 K (400 °C) and 773 K (500 °C) for 30 minutes, cementite was observed in the form of nanometre scale precipitates. Proximity histograms showed that the partitioning of solutes other than silicon from the cementite was slight at 673 K (400 °C) and more obvious at 773 K (500 °C). In both cases, the nanometre scale carbides are greatly depleted in silicon.

  10. Well-Tempered Metadynamics Converges Asymptotically

    Science.gov (United States)

    Dama, James F.; Parrinello, Michele; Voth, Gregory A.

    2014-06-01

    Metadynamics is a versatile and capable enhanced sampling method for the computational study of soft matter materials and biomolecular systems. However, over a decade of application and several attempts to give this adaptive umbrella sampling method a firm theoretical grounding prove that a rigorous convergence analysis is elusive. This Letter describes such an analysis, demonstrating that well-tempered metadynamics converges to the final state it was designed to reach and, therefore, that the simple formulas currently used to interpret the final converged state of tempered metadynamics are correct and exact. The results do not rely on any assumption that the collective variable dynamics are effectively Brownian or any idealizations of the hill deposition function; instead, they suggest new, more permissive criteria for the method to be well behaved. The results apply to tempered metadynamics with or without adaptive Gaussians or boundary corrections and whether the bias is stored approximately on a grid or exactly.

  11. PatternLab for proteomics: a tool for differential shotgun proteomics

    Directory of Open Access Journals (Sweden)

    Yates John R

    2008-07-01

    Full Text Available Abstract Background A goal of proteomics is to distinguish between states of a biological system by identifying protein expression differences. Liu et al. demonstrated a method to perform semi-relative protein quantitation in shotgun proteomics data by correlating the number of tandem mass spectra obtained for each protein, or "spectral count", with its abundance in a mixture; however, two issues have remained open: how to normalize spectral counting data and how to efficiently pinpoint differences between profiles. Moreover, Chen et al. recently showed how to increase the number of identified proteins in shotgun proteomics by analyzing samples with different MS-compatible detergents while performing proteolytic digestion. The latter introduced new challenges as seen from the data analysis perspective, since replicate readings are not acquired. Results To address the open issues above, we present a program termed PatternLab for proteomics. This program implements existing strategies and adds two new methods to pinpoint differences in protein profiles. The first method, ACFold, addresses experiments with less than three replicates from each state or having assays acquired by different protocols as described by Chen et al. ACFold uses a combined criterion based on expression fold changes, the AC test, and the false-discovery rate, and can supply a "bird's-eye view" of differentially expressed proteins. The other method addresses experimental designs having multiple readings from each state and is referred to as nSVM (natural support vector machine because of its roots in evolutionary computing and in statistical learning theory. Our observations suggest that nSVM's niche comprises projects that select a minimum set of proteins for classification purposes; for example, the development of an early detection kit for a given pathology. We demonstrate the effectiveness of each method on experimental data and confront them with existing strategies

  12. Nonoperative Management of Multiple Penetrating Cardiac and Colon Wounds from a Shotgun: A Case Report and Literature Review

    OpenAIRE

    Jaramillo, Paula M.; Montoya, Jaime A.; Mejia, David A.; Pereira Warr, Salin

    2018-01-01

    Introduction. Surgery for cardiac trauma is considered fatal and for wounds of the colon by associated sepsis is normally considered; however, conservative management of many traumatic lesions of different injured organs has progressed over the years. Presentation of the Case. A 65-year-old male patient presented with multiple shotgun wounds on the left upper limb, thorax, and abdomen. On evaluation, he was hemodynamically stable with normal sinus rhythm and normal blood pressure, no dyspnea,...

  13. Use of Metagenomic Shotgun Sequencing Technology To Detect Foodborne Pathogens within the Microbiome of the Beef Production Chain

    OpenAIRE

    Yang, Xiang; Noyes, Noelle R.; Doster, Enrique; Martin, Jennifer N.; Linke, Lyndsey M.; Magnuson, Roberta J.; Yang, Hua; Geornaras, Ifigenia; Woerner, Dale R.; Jones, Kenneth L.; Ruiz, Jaime; Boucher, Christina; Morley, Paul S.; Belk, Keith E.

    2016-01-01

    Foodborne illnesses associated with pathogenic bacteria are a global public health and economic challenge. The diversity of microorganisms (pathogenic and nonpathogenic) that exists within the food and meat industries complicates efforts to understand pathogen ecology. Further, little is known about the interaction of pathogens within the microbiome throughout the meat production chain. Here, a metagenomic approach and shotgun sequencing technology were used as tools to detect pathogenic bact...

  14. Identification of antimicrobial resistance genes in multidrug-resistant clinical Bacteroides fragilis isolates by whole genome shotgun sequencing

    DEFF Research Database (Denmark)

    Sydenham, Thomas Vognbjerg; Sóki, József; Hasman, Henrik

    2015-01-01

    Bacteroides fragilis constitutes the most frequent anaerobic bacterium causing bacteremia in humans. The genetic background for antimicrobial resistance in B. fragilis is diverse with some genes requiring insertion sequence (IS) elements inserted upstream for increased expression. To evaluate whole...... genome shotgun sequencing as a method for predicting antimicrobial resistance properties, one meropenem resistant and five multidrug-resistant blood culture isolates were sequenced and antimicrobial resistance genes and IS elements identified using ResFinder 2.1 (http...

  15. Nitrogen Deposition Effects on Soil Carbon Dynamics in Temperate Forests

    DEFF Research Database (Denmark)

    Ginzburg Ozeri, Shimon

    Soils contain the largest fraction of terrestrial carbon (C). Understanding the factors regulating the decomposition and storage of soil organic matter (SOM) is essential for predictions of the C sink strength of the terrestrial environment in the light of global change. Elevated long-term nitrog...... implications for modelling the carbon sink-strength of temperate forests under global change.......Soils contain the largest fraction of terrestrial carbon (C). Understanding the factors regulating the decomposition and storage of soil organic matter (SOM) is essential for predictions of the C sink strength of the terrestrial environment in the light of global change. Elevated long-term nitrogen...... (N) deposition into forest ecosystems has been increasing globally and was hypothesized to raise soil organic C (SOC) stocks by increasing forest productivity and by reducing SOM decomposition. Yet, these effects of N deposition on forest SOC stocks are uncertain and largely based on observations...

  16. Improvement of a sample preparation method assisted by sodium deoxycholate for mass-spectrometry-based shotgun membrane proteomics.

    Science.gov (United States)

    Lin, Yong; Lin, Haiyan; Liu, Zhonghua; Wang, Kunbo; Yan, Yujun

    2014-11-01

    In current shotgun-proteomics-based biological discovery, the identification of membrane proteins is a challenge. This is especially true for integral membrane proteins due to their highly hydrophobic nature and low abundance. Thus, much effort has been directed at sample preparation strategies such as use of detergents, chaotropes, and organic solvents. We previously described a sample preparation method for shotgun membrane proteomics, the sodium deoxycholate assisted method, which cleverly circumvents many of the challenges associated with traditional sample preparation methods. However, the method is associated with significant sample loss due to the slightly weaker extraction/solubilization ability of sodium deoxycholate when it is used at relatively low concentrations such as 1%. Hence, we present an enhanced sodium deoxycholate sample preparation strategy that first uses a high concentration of sodium deoxycholate (5%) to lyse membranes and extract/solubilize hydrophobic membrane proteins, and then dilutes the detergent to 1% for a more efficient digestion. We then applied the improved method to shotgun analysis of proteins from rat liver membrane enriched fraction. Compared with other representative sample preparation strategies including our previous sodium deoxycholate assisted method, the enhanced sodium deoxycholate method exhibited superior sensitivity, coverage, and reliability for the identification of membrane proteins particularly those with high hydrophobicity and/or multiple transmembrane domains. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. Large pore dermal microdialysis and liquid chromatography-tandem mass spectroscopy shotgun proteomic analysis: a feasibility study.

    Science.gov (United States)

    Petersen, Lars J; Sørensen, Mette A; Codrea, Marius C; Zacho, Helle D; Bendixen, Emøke

    2013-11-01

    The purpose of the present pilot study was to investigate the feasibility of combining large pore dermal microdialysis with shotgun proteomic analysis in human skin. Dialysate was recovered from human skin by 2000 kDa microdialysis membranes from one subject at three different phases of the study; trauma due to implantation of the dialysis device, a post implantation steady-state period, and after induction of vasodilatation and plasma extravasation. For shotgun proteomics, the proteins were extracted and digested with trypsin. Peptides were separated by capillary and nanoflow HPLC systems, followed by tandem mass spectrometry (MS/MS) on a Quadrupole-TOF hybrid instrument. The MS/MS spectra were merged and mapped to a human target protein database to achieve peptide identification and protein inference. Results showed variation in protein amounts and profiles for each of the different sampling phases. The total protein concentration was 1.7, 0.6, and 1.3 mg/mL during the three phases, respectively. A total of 158 different proteins were identified. Immunoglobulins and the major classes of plasma proteins, including proteases, coagulation factors, apolipoproteins, albumins, and complement factors, make up the major load of proteins in all three test conditions. Shotgun proteomics allowed the identification of more than 150 proteins in microdialysis samples from human skin. This highlights the opportunities of LC-MS/MS to study the complex molecular interactions in the skin. © 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  18. Comparative study of label and label-free techniques using shotgun proteomics for relative protein quantification.

    Science.gov (United States)

    Sjödin, Marcus O D; Wetterhall, Magnus; Kultima, Kim; Artemenko, Konstantin

    2013-06-01

    The analytical performance of three different strategies, iTRAQ (isobaric tag for relative and absolute quantification), dimethyl labeling (DML) and label free (LF) for relative protein quantification using shotgun proteomics have been evaluated. The methods have been explored using samples containing (i) Bovine proteins in known ratios and (ii) Bovine proteins in known ratios spiked into Escherichia coli. The latter case mimics the actual conditions in a typical biological sample with a few differentially expressed proteins and a bulk of proteins with unchanged ratios. Additionally, the evaluation was performed on both QStar and LTQ-FTICR mass spectrometers. LF LTQ-FTICR was found to have the highest proteome coverage while the highest accuracy based on the artificially regulated proteins was found for DML LTQ-FTICR (54%). A varying linearity (k: 0.55-1.16, r(2): 0.61-0.96) was shown for all methods within selected dynamic ranges. All methods were found to consistently underestimate Bovine protein ratios when matrix proteins were added. However, LF LTQ-FTICR was more tolerant toward a compression effect. A single peptide was demonstrated to be sufficient for a reliable quantification using iTRAQ. A ranking system utilizing several parameters important for quantitative proteomics demonstrated that the overall performance of the five different methods was; DML LTQ-FTICR>iTRAQ QStar>LF LTQ-FTICR>DML QStar>LF QStar. Copyright © 2013 Elsevier B.V. All rights reserved.

  19. Comparative evaluation of seven commercial products for human serum enrichment/depletion by shotgun proteomics.

    Science.gov (United States)

    Pisanu, Salvatore; Biosa, Grazia; Carcangiu, Laura; Uzzau, Sergio; Pagnozzi, Daniela

    2018-08-01

    Seven commercial products for human serum depletion/enrichment were tested and compared by shotgun proteomics. Methods were based on four different capturing agents: antibodies (Qproteome Albumin/IgG Depletion kit, ProteoPrep Immunoaffinity Albumin and IgG Depletion Kit, Top 2 Abundant Protein Depletion Spin Columns, and Top 12 Abundant Protein Depletion Spin Columns), specific ligands (Albumin/IgG Removal), mixture of antibodies and ligands (Albumin and IgG Depletion SpinTrap), and combinatorial peptide ligand libraries (ProteoMiner beads), respectively. All procedures, to a greater or lesser extent, allowed an increase of identified proteins. ProteoMiner beads provided the highest number of proteins; Albumin and IgG Depletion SpinTrap and ProteoPrep Immunoaffinity Albumin and IgG Depletion Kit resulted the most efficient in albumin removal; Top 2 and Top 12 Abundant Protein Depletion Spin Columns decreased the overall immunoglobulin levels more than other procedures, whereas specifically gamma immunoglobulins were mostly removed by Albumin and IgG Depletion SpinTrap, ProteoPrep Immunoaffinity Albumin and IgG Depletion Kit, and Top 2 Abundant Protein Depletion Spin Columns. Albumin/IgG Removal, a resin bound to a mixture of protein A and Cibacron Blue, behaved less efficiently than the other products. Copyright © 2018 Elsevier B.V. All rights reserved.

  20. Iatrogenic artefacts attributable to traditional cupping therapy in a shotgun fatality.

    Science.gov (United States)

    Cavlak, Mehmet; Özkök, Alper; Sarı, Serhat; Dursun, Ahmet; Akar, Taner; Karapirli, Mustafa; Demirel, Birol

    2015-10-01

    Cupping is a traditional treatment method that has been used for thousands of years to diminish pain, restore appetite and improve digestion, remove tendency to faint or remove 'bad blood' from the body. The suction of the cup is created by fire or mechanical devices. This procedure may result in circular erythema, petechiae, purpura, ecchymosis, burns and may be mistaken for trauma-related ecchymosis or livor mortis. Forty-year-old male was died by shotgun injuries in the same day of the wounding. Circular ecchymoses were observed on the forehead, within the scalp of occipital region, the back of the neck, and on the back. They were defined as ecchymoses in the first examination made by a general practitioner. In the external examination during the legal autopsy superficial incisions were observed on the circular ecchymoses. The shape, localization and color of and the characteristics of incisions on the circular lesions were concluded to be caused by the dry cupping therapy and wet cupping therapy procedures. These lesions and their formation mechanisms should be well-known by the forensic medical examiners and the other medical personnel involved in the forensic medical examination. Copyright © 2015 Elsevier Ltd and Faculty of Forensic and Legal Medicine. All rights reserved.

  1. Uncertainty estimation of predictions of peptides' chromatographic retention times in shotgun proteomics.

    Science.gov (United States)

    Maboudi Afkham, Heydar; Qiu, Xuanbin; The, Matthew; Käll, Lukas

    2017-02-15

    Liquid chromatography is frequently used as a means to reduce the complexity of peptide-mixtures in shotgun proteomics. For such systems, the time when a peptide is released from a chromatography column and registered in the mass spectrometer is referred to as the peptide's retention time . Using heuristics or machine learning techniques, previous studies have demonstrated that it is possible to predict the retention time of a peptide from its amino acid sequence. In this paper, we are applying Gaussian Process Regression to the feature representation of a previously described predictor E lude . Using this framework, we demonstrate that it is possible to estimate the uncertainty of the prediction made by the model. Here we show how this uncertainty relates to the actual error of the prediction. In our experiments, we observe a strong correlation between the estimated uncertainty provided by Gaussian Process Regression and the actual prediction error. This relation provides us with new means for assessment of the predictions. We demonstrate how a subset of the peptides can be selected with lower prediction error compared to the whole set. We also demonstrate how such predicted standard deviations can be used for designing adaptive windowing strategies. lukas.kall@scilifelab.se. Our software and the data used in our experiments is publicly available and can be downloaded from https://github.com/statisticalbiotechnology/GPTime . © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

  2. IdentiPy: an extensible search engine for protein identification in shotgun proteomics.

    Science.gov (United States)

    Levitsky, Lev I; Ivanov, Mark V; Lobas, Anna A; Bubis, Julia A; Tarasova, Irina A; Solovyeva, Elizaveta M; Pridatchenko, Marina L; Gorshkov, Mikhail V

    2018-04-23

    We present an open-source, extensible search engine for shotgun proteomics. Implemented in Python programming language, IdentiPy shows competitive processing speed and sensitivity compared with the state-of-the-art search engines. It is equipped with a user-friendly web interface, IdentiPy Server, enabling the use of a single server installation accessed from multiple workstations. Using a simplified version of X!Tandem scoring algorithm and its novel ``auto-tune'' feature, IdentiPy outperforms the popular alternatives on high-resolution data sets. Auto-tune adjusts the search parameters for the particular data set, resulting in improved search efficiency and simplifying the user experience. IdentiPy with the auto-tune feature shows higher sensitivity compared with the evaluated search engines. IdentiPy Server has built-in post-processing and protein inference procedures and provides graphic visualization of the statistical properties of the data set and the search results. It is open-source and can be freely extended to use third-party scoring functions or processing algorithms, and allows customization of the search workflow for specialized applications.

  3. MaRaCluster: A Fragment Rarity Metric for Clustering Fragment Spectra in Shotgun Proteomics.

    Science.gov (United States)

    The, Matthew; Käll, Lukas

    2016-03-04

    Shotgun proteomics experiments generate large amounts of fragment spectra as primary data, normally with high redundancy between and within experiments. Here, we have devised a clustering technique to identify fragment spectra stemming from the same species of peptide. This is a powerful alternative method to traditional search engines for analyzing spectra, specifically useful for larger scale mass spectrometry studies. As an aid in this process, we propose a distance calculation relying on the rarity of experimental fragment peaks, following the intuition that peaks shared by only a few spectra offer more evidence than peaks shared by a large number of spectra. We used this distance calculation and a complete-linkage scheme to cluster data from a recent large-scale mass spectrometry-based study. The clusterings produced by our method have up to 40% more identified peptides for their consensus spectra compared to those produced by the previous state-of-the-art method. We see that our method would advance the construction of spectral libraries as well as serve as a tool for mining large sets of fragment spectra. The source code and Ubuntu binary packages are available at https://github.com/statisticalbiotechnology/maracluster (under an Apache 2.0 license).

  4. Cloud CPFP: a shotgun proteomics data analysis pipeline using cloud and high performance computing.

    Science.gov (United States)

    Trudgian, David C; Mirzaei, Hamid

    2012-12-07

    We have extended the functionality of the Central Proteomics Facilities Pipeline (CPFP) to allow use of remote cloud and high performance computing (HPC) resources for shotgun proteomics data processing. CPFP has been modified to include modular local and remote scheduling for data processing jobs. The pipeline can now be run on a single PC or server, a local cluster, a remote HPC cluster, and/or the Amazon Web Services (AWS) cloud. We provide public images that allow easy deployment of CPFP in its entirety in the AWS cloud. This significantly reduces the effort necessary to use the software, and allows proteomics laboratories to pay for compute time ad hoc, rather than obtaining and maintaining expensive local server clusters. Alternatively the Amazon cloud can be used to increase the throughput of a local installation of CPFP as necessary. We demonstrate that cloud CPFP allows users to process data at higher speed than local installations but with similar cost and lower staff requirements. In addition to the computational improvements, the web interface to CPFP is simplified, and other functionalities are enhanced. The software is under active development at two leading institutions and continues to be released under an open-source license at http://cpfp.sourceforge.net.

  5. Structural Analysis of Unsaturated Glycosphingolipids Using Shotgun Ozone-Induced Dissociation Mass Spectrometry

    Science.gov (United States)

    Barrientos, Rodell C.; Vu, Ngoc; Zhang, Qibin

    2017-08-01

    Glycosphingolipids are essential biomolecules widely distributed across biological kingdoms yet remain relatively underexplored owing to both compositional and structural complexity. While the glycan head group has been the subject of most studies, there is paucity of reports on the lipid moiety, particularly the location of unsaturation. In this paper, ozone-induced dissociation mass spectrometry (OzID-MS) implemented in a traveling wave-based quadrupole time-of-flight (Q-ToF) mass spectrometer was applied to study unsaturated glycosphingolipids using shotgun approach. Resulting high resolution mass spectra facilitated the unambiguous identification of diagnostic OzID product ions. Using [M+Na]+ adducts of authentic standards, we observed that the long chain base and fatty acyl unsaturation had distinct reactivity with ozone. The reactivity of unsaturation in the fatty acyl chain was about 8-fold higher than that in the long chain base, which enables their straightforward differentiation. Influence of the head group, fatty acyl hydroxylation, and length of fatty acyl chain on the oxidative cleavage of double bonds was also observed. Application of this technique to bovine brain galactocerebrosides revealed co-isolated isobaric and regioisomeric species, which otherwise would be incompletely identified using contemporary collision-induced dissociation (CID) alone. These results highlight the potential of OzID-MS in glycosphingolipids research, which not only provides complementary structural information to existing CID technique but also facilitates de novo structural determination of these complex biomolecules. [Figure not available: see fulltext.

  6. Shotgun proteomic analytical approach for studying proteins adsorbed onto liposome surface

    KAUST Repository

    Capriotti, Anna Laura

    2011-07-02

    The knowledge about the interaction between plasma proteins and nanocarriers employed for in vivo delivery is fundamental to understand their biodistribution. Protein adsorption onto nanoparticle surface (protein corona) is strongly affected by vector surface characteristics. In general, the primary interaction is thought to be electrostatic, thus surface charge of carrier is supposed to play a central role in protein adsorption. Because protein corona composition can be critical in modifying the interactive surface that is recognized by cells, characterizing its formation onto lipid particles may serve as a fundamental predictive model for the in vivo efficiency of a lipidic vector. In the present work, protein coronas adsorbed onto three differently charged cationic liposome formulations were compared by a shotgun proteomic approach based on nano-liquid chromatography-high-resolution mass spectrometry. About 130 proteins were identified in each corona, with only small differences between the different cationic liposome formulations. However, this study could be useful for the future controlled design of colloidal drug carriers and possibly in the controlled creation of biocompatible surfaces of other devices that come into contact with proteins into body fluids. © 2011 Springer-Verlag.

  7. A Facies Model for Temperate Continental Glaciers.

    Science.gov (United States)

    Ashley, Gail Mowry

    1987-01-01

    Discusses the presence and dynamics of continental glaciers in the domination of the physical processes of erosion and deposition in the mid-latitudes during the Pleistocene period. Describes the use of a sedimentary facies model as a guide to recognizing ancient temperate continental glacial deposits. (TW)

  8. The Temperance Movement and Social Work

    Science.gov (United States)

    Murdach, Allison D.

    2009-01-01

    This article examines a forgotten episode in social work history: the involvement of the profession in the temperance movement in the late 19th and early 20th centuries. Though some notable social workers such as Jane Addams, Robert A. Woods, and Representative Jeannette Rankin (the first woman elected to the U.S. Congress), championed the…

  9. Intensity of Urban Heat Islands in Tropical and Temperate Climates

    Directory of Open Access Journals (Sweden)

    Margarete Cristiane de Costa Trindade Amorim

    2017-12-01

    Full Text Available Nowadays, most of the Earth’s population lives in urban areas. The replacement of vegetation by buildings and the general soil sealing, associated with human activity, lead to a rise in cities temperature, resulting in the formation of urban heat islands. This article aims to evaluate the intensity and the hourly maintenance of the atmospheric heat islands in two climates: one tropical (Presidente Prudente, Brazil and one temperate (Rennes, France throughout 2016. For this, air temperature and hourly averages were measured and calculated using both a HOBO datalogger (U23-002—protected under the same RS3 brand and weather stations Davis Vantage PRO 2. The daily evolution of the heat islands presented characteristics that varied according to the hours and seasons of the year. For both Rennes and Presidente Prudente, the largest magnitudes occurred overnight, being more greatly expressed in the tropical environment and during the driest months (winter in the tropical city and summer in the temperate one. The variability of synoptic conditions from one month to another also leads to a great heterogeneity of UHI intensity throughout the year.

  10. Estimating Green Water Footprints in a Temperate Environment

    Directory of Open Access Journals (Sweden)

    Tim Hess

    2010-07-01

    Full Text Available The “green” water footprint (GWF of a product is often considered less important than the “blue” water footprint (BWF as “green” water generally has a low, or even negligible, opportunity cost. However, when considering food, fibre and tree products, is not only a useful indicator of the total appropriation of a natural resource, but from a methodological perspective, blue water footprints are frequently estimated as the residual after green water is subtracted from total crop water use. In most published studies, green water use (ETgreen has been estimated from the FAO CROPWAT model using the USDA method for effective rainfall. In this study, four methods for the estimation of the ETgreen of pasture were compared. Two were based on effective rainfall estimated from monthly rainfall and potential evapotranspiration, and two were based on a simulated water balance using long-term daily, or average monthly, weather data from 11 stations in England. The results show that the effective rainfall methods significantly underestimate the annual ETgreen in all cases, as they do not adequately account for the depletion of stored soil water during the summer. A simplified model, based on annual rainfall and reference evapotranspiration (ETo has been tested and used to map the average annual ETgreen of pasture in England.

  11. RNA shotgun metagenomic sequencing of northern California (USA mosquitoes uncovers viruses, bacteria, and fungi

    Directory of Open Access Journals (Sweden)

    James Angus eChandler

    2015-03-01

    Full Text Available Mosquitoes, most often recognized for the microbial agents of disease they may carry, harbor diverse microbial communities that include viruses, bacteria, and fungi, collectively called the microbiota. The composition of the microbiota can directly and indirectly affect disease transmission through microbial interactions that could be revealed by its characterization in natural populations of mosquitoes. Furthermore, the use of shotgun metagenomic sequencing (SMS approaches could allow the discovery of unknown members of the microbiota. In this study, we use RNA SMS to characterize the microbiota of seven individual mosquitoes (species include Culex pipiens, Culiseta incidens, and Ochlerotatus sierrensis collected from a variety of habitats in California, USA. Sequencing was performed on the Illumina HiSeq platform and the resulting sequences were quality-checked and assembled into contigs using the A5 pipeline. Sequences related to single stranded RNA viruses of the Bunyaviridae and Rhabdoviridae were uncovered, along with an unclassified genus of double-stranded RNA viruses. Phylogenetic analysis finds that in all three cases, the closest relatives of the identified viral sequences are other mosquito-associated viruses, suggesting widespread host-group specificity among disparate viral taxa. Interestingly, we identified a Narnavirus of fungi, also reported elsewhere in mosquitoes, that potentially demonstrates a nested host-parasite association between virus, fungi, and mosquito. Sequences related to 8 bacterial families and 13 fungal families were found across the seven samples. Bacillus and Escherichia/Shigella were identified in all samples and Wolbachia was identified in all Cx. pipiens samples, while no single fungal genus was found in more than two samples. This study exemplifies the utility of RNA SMS in the characterization of the natural microbiota of mosquitoes and, in particular, the value of identifying all microbes associated with

  12. An inventory of the Aspergillus niger secretome by combining in silico predictions with shotgun proteomics data

    Directory of Open Access Journals (Sweden)

    Martens-Uzunova Elena S

    2010-10-01

    Full Text Available Abstract Background The ecological niche occupied by a fungal species, its pathogenicity and its usefulness as a microbial cell factory to a large degree depends on its secretome. Protein secretion usually requires the presence of a N-terminal signal peptide (SP and by scanning for this feature using available highly accurate SP-prediction tools, the fraction of potentially secreted proteins can be directly predicted. However, prediction of a SP does not guarantee that the protein is actually secreted and current in silico prediction methods suffer from gene-model errors introduced during genome annotation. Results A majority rule based classifier that also evaluates signal peptide predictions from the best homologs of three neighbouring Aspergillus species was developed to create an improved list of potential signal peptide containing proteins encoded by the Aspergillus niger genome. As a complement to these in silico predictions, the secretome associated with growth and upon carbon source depletion was determined using a shotgun proteomics approach. Overall, some 200 proteins with a predicted signal peptide were identified to be secreted proteins. Concordant changes in the secretome state were observed as a response to changes in growth/culture conditions. Additionally, two proteins secreted via a non-classical route operating in A. niger were identified. Conclusions We were able to improve the in silico inventory of A. niger secretory proteins by combining different gene-model predictions from neighbouring Aspergilli and thereby avoiding prediction conflicts associated with inaccurate gene-models. The expected accuracy of signal peptide prediction for proteins that lack homologous sequences in the proteomes of related species is 85%. An experimental validation of the predicted proteome confirmed in silico predictions.

  13. An inventory of the Aspergillus niger secretome by combining in silico predictions with shotgun proteomics data.

    Science.gov (United States)

    Braaksma, Machtelt; Martens-Uzunova, Elena S; Punt, Peter J; Schaap, Peter J

    2010-10-19

    The ecological niche occupied by a fungal species, its pathogenicity and its usefulness as a microbial cell factory to a large degree depends on its secretome. Protein secretion usually requires the presence of a N-terminal signal peptide (SP) and by scanning for this feature using available highly accurate SP-prediction tools, the fraction of potentially secreted proteins can be directly predicted. However, prediction of a SP does not guarantee that the protein is actually secreted and current in silico prediction methods suffer from gene-model errors introduced during genome annotation. A majority rule based classifier that also evaluates signal peptide predictions from the best homologs of three neighbouring Aspergillus species was developed to create an improved list of potential signal peptide containing proteins encoded by the Aspergillus niger genome. As a complement to these in silico predictions, the secretome associated with growth and upon carbon source depletion was determined using a shotgun proteomics approach. Overall, some 200 proteins with a predicted signal peptide were identified to be secreted proteins. Concordant changes in the secretome state were observed as a response to changes in growth/culture conditions. Additionally, two proteins secreted via a non-classical route operating in A. niger were identified. We were able to improve the in silico inventory of A. niger secretory proteins by combining different gene-model predictions from neighbouring Aspergilli and thereby avoiding prediction conflicts associated with inaccurate gene-models. The expected accuracy of signal peptide prediction for proteins that lack homologous sequences in the proteomes of related species is 85%. An experimental validation of the predicted proteome confirmed in silico predictions.

  14. Sex differences in shotgun proteome analyses for chronic oral intake of cadmium in mice.

    Directory of Open Access Journals (Sweden)

    Yoshiharu Yamanobe

    Full Text Available Environmental diseases related to cadmium exposure primarily develop owing to industrial wastewater pollution and/or contaminated food. In regions with high cadmium exposure in Japan, cadmium accumulation occurs primarily in the kidneys of individuals who are exposed to the metal. In contrast, in the itai-itai disease outbreak that occurred in the Jinzu River basin in Toyama Prefecture in Japan, cadmium primarily accumulated in the liver. On the other hand, high concentration of cadmium caused renal tubular disorder and osteomalacia (multiple bone fracture, probably resulting from the renal tubular dysfunction and additional pathology. In this study, we aimed to establish a mouse model of chronic cadmium intake. We administered cadmium-containing drinking water (32 mg/l to female and male mice ad libitum for 11 weeks. Metal analysis using inductively coupled plasma mass spectrometry revealed that cadmium accumulated in the kidneys (927 x 10 + 185 ng/g in females and 661 x 10 + 101 ng/g in males, liver (397 x 10 + 199 ng/g in females and 238 x 10 + 652 ng/g in males, and thyroid gland (293 + 93.7 ng/g in females and 129 + 72.7 ng/g in males of mice. Female mice showed higher cadmium accumulation in the kidney, liver, and thyroid gland than males did (p = 0.00345, p = 0.00213, and p = 0.0331, respectively. Shotgun proteome analyses after chronic oral administration of cadmium revealed that protein levels of glutathione S-transferase Mu2, Mu4, and Mu7 decreased in the liver, and those of A1 and A2 decreased in the kidneys in both female and male mice.

  15. Microbiological profile of chicken carcasses: A comparative analysis using shotgun metagenomic sequencing

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    Alessandra De Cesare

    2018-04-01

    Full Text Available In the last few years metagenomic and 16S rRNA sequencing have completly changed the microbiological investigations of food products. In this preliminary study, the microbiological profile of chicken carcasses collected from animals fed with different diets were tested by using shotgun metagenomic sequencing. A total of 15 carcasses have been collected at the slaughetrhouse at the end of the refrigeration tunnel from chickens reared for 35 days and fed with a control diet (n=5, a diet supplemented with 1500 FTU/kg of commercial phytase (n=5 and a diet supplemented with 1500 FTU/kg of commercial phytase and 3g/kg of inositol (n=5. Ten grams of neck and breast skin were obtained from each carcass and submited to total DNA extraction by using the DNeasy Blood & Tissue Kit (Qiagen. Sequencing libraries have been prepared by using the Nextera XT DNA Library Preparation Kit (Illumina and sequenced in a HiScanSQ (Illumina at 100 bp in paired ends. A number of sequences ranging between 5 and 9 million was obtained for each sample. Sequence analysis showed that Proteobacteria and Firmicutes represented more than 98% of whole bacterial populations associated to carcass skin in all groups but their abundances were different between groups. Moraxellaceae and other degradative bacteria showed a significantly higher abundance in the control compared to the treated groups. Furthermore, Clostridium perfringens showed a relative frequency of abundance significantly higher in the group fed with phytase and Salmonella enterica in the group fed with phytase plus inositol. The results of this preliminary study showed that metagenome sequencing is suitable to investigate and monitor carcass microbiota in order to detect specific pathogenic and/or degradative populations.

  16. A linear programming model for protein inference problem in shotgun proteomics.

    Science.gov (United States)

    Huang, Ting; He, Zengyou

    2012-11-15

    Assembling peptides identified from tandem mass spectra into a list of proteins, referred to as protein inference, is an important issue in shotgun proteomics. The objective of protein inference is to find a subset of proteins that are truly present in the sample. Although many methods have been proposed for protein inference, several issues such as peptide degeneracy still remain unsolved. In this article, we present a linear programming model for protein inference. In this model, we use a transformation of the joint probability that each peptide/protein pair is present in the sample as the variable. Then, both the peptide probability and protein probability can be expressed as a formula in terms of the linear combination of these variables. Based on this simple fact, the protein inference problem is formulated as an optimization problem: minimize the number of proteins with non-zero probabilities under the constraint that the difference between the calculated peptide probability and the peptide probability generated from peptide identification algorithms should be less than some threshold. This model addresses the peptide degeneracy issue by forcing some joint probability variables involving degenerate peptides to be zero in a rigorous manner. The corresponding inference algorithm is named as ProteinLP. We test the performance of ProteinLP on six datasets. Experimental results show that our method is competitive with the state-of-the-art protein inference algorithms. The source code of our algorithm is available at: https://sourceforge.net/projects/prolp/. zyhe@dlut.edu.cn. Supplementary data are available at Bioinformatics Online.

  17. Trichinella in arctic, subarctic and temperate regions

    DEFF Research Database (Denmark)

    Kapel, C. M O

    1997-01-01

    The transmission and occurrence of Trichinella spp according to the zoogeography of different climatic conditions, socioeconomy and human activity are discussed. Comparing arctic, subarctic and temperate regions, it appears that the species of Trichinella present, the composition of the fauna...... and the human activity are all very important interacting factors affecting epidemiology. In Greenland, where only sylvatic trichinellosis is present, the high prevalence in wildlife appears closely connected with polar bear hunting. In the Scandinavian countries, the prevalence of both sylvatic and domestic...

  18. World temperate fruit production: characteristics and challenges

    Directory of Open Access Journals (Sweden)

    Jorge B. Retamales

    2011-10-01

    Full Text Available In the last 30 years world population has increased 70% but per capita global fruit consumption is only 20% higher. Even though tropical and temperate fruit have similar contributions to the 50 kg/person/year of US consumption of fresh fruit, in the last 30 years this has been slightly greater for temperate fruit. Within fruit consumption, the largest expansion has been for organic fruit which increased more than 50% in the 2002-2006 period. The largest expansion of area planted in the 1996-2006 has been for kiwi (29% and blueberries (20%, while apples (-24% and sour cherries (-13% have had the largest reductions. Nearly 50% of the total global volume of fruit is produced by 5 countries: China, USA, Brazil, Italy and Spain. The main producer (China accounts for 23% of the total. While the main exporters are Spain, USA and Italy, the main importers are Germany, Russia and UK. Demands for the industry have evolved towards quality, food safety and traceability. The industry faces higher productions costs (labor, energy, agrichemicals. The retailers are moving towards consolidation while the customers are changing preferences (food for health. In this context there is greater pressure on growers, processors and retailers. Emerging issues are labor supply, climate change, water availability and sustainability. Recent developments in precision agriculture, molecular biology, phenomics, crop modelling and post harvest physiology should increase yields and quality, and reduce costs for temperate fruit production around the world.

  19. Assessment of Soil Organic Carbon Stock of Temperate Coniferous Forests in Northern Kashmir

    Directory of Open Access Journals (Sweden)

    Davood A. Dar

    2015-02-01

    Full Text Available  Soil organic carbon (SOC estimation in temperate forests of the Himalaya is important to estimate their contribution to regional, national and global carbon stocks. Physico chemical properties of soil were quantified to assess soil organic carbon density (SOC and SOC CO2 mitigation density at two soil depths (0-10 and 10-20 cms under temperate forest in the Northern region of Kashmir Himalayas India. The results indicate that conductance, moisture content, organic carbon and organic matter were significantly higher while as pH and bulk density were lower at Gulmarg forest site. SOC % was ranging from 2.31± 0.96 at Gulmarg meadow site to 2.31 ± 0.26 in Gulmarg forest site. SOC stocks in these temperate forests were from 36.39 ±15.40 to 50.09 ± 15.51 Mg C ha-1. The present study reveals that natural vegetation is the main contributor of soil quality as it maintained the soil organic carbon stock. In addition, organic matter is an important indicator of soil quality and environmental parameters such as soil moisture and soil biological activity change soil carbon sequestration potential in temperate forest ecosystems.DOI: http://dx.doi.org/10.3126/ije.v4i1.12186International Journal of Environment Volume-4, Issue-1, Dec-Feb 2014/15; page: 161-178

  20. Thermal biology of the sub-polar-temperate estuarine crab Hemigrapsus crenulatus (Crustacea: Decapoda: Varunidae).

    Science.gov (United States)

    Cumillaf, Juan P; Blanc, Johnny; Paschke, Kurt; Gebauer, Paulina; Díaz, Fernando; Re, Denisse; Chimal, María E; Vásquez, Jorge; Rosas, Carlos

    2016-02-15

    Optimum temperatures can be measured through aerobic scope, preferred temperatures or growth. A complete thermal window, including optimum, transition (Pejus) and critical temperatures (CT), can be described if preferred temperatures and CT are defined. The crustacean Hemigrapsus crenulatus was used as a model species to evaluate the effect of acclimation temperature on: (i) thermal preference and width of thermal window, (ii) respiratory metabolism, and (iii) haemolymph proteins. Dependant on acclimation temperature, preferred temperature was between 11.8°C and 25.2°C while CT was found between a minimum of 2.7°C (CTmin) and a maximum of 35.9°C (CTmax). These data and data from tropical and temperate crustaceans were compared to examine the association between environmental temperature and thermal tolerance. Temperate species have a CTmax limit around 35°C that corresponded with the low CTmax limit of tropical species (34-36°C). Tropical species showed a CTmin limit around 9°C similar to the maximum CTmin of temperate species (5-6°C). The maximum CTmin of deep sea species that occur in cold environments (2.5°C) matched the low CTmin values (3.2°C) of temperate species. Results also indicate that the energy required to activate the enzyme complex (Ei) involved in respiratory metabolism of ectotherms changes along the latitudinal gradient of temperature. © 2016. Published by The Company of Biologists Ltd.

  1. Thermal biology of the sub-polar–temperate estuarine crab Hemigrapsus crenulatus (Crustacea: Decapoda: Varunidae)

    Science.gov (United States)

    Cumillaf, Juan P.; Blanc, Johnny; Paschke, Kurt; Gebauer, Paulina; Díaz, Fernando; Re, Denisse; Chimal, María E.; Vásquez, Jorge; Rosas, Carlos

    2016-01-01

    ABSTRACT Optimum temperatures can be measured through aerobic scope, preferred temperatures or growth. A complete thermal window, including optimum, transition (Pejus) and critical temperatures (CT), can be described if preferred temperatures and CT are defined. The crustacean Hemigrapsus crenulatus was used as a model species to evaluate the effect of acclimation temperature on: (i) thermal preference and width of thermal window, (ii) respiratory metabolism, and (iii) haemolymph proteins. Dependant on acclimation temperature, preferred temperature was between 11.8°C and 25.2°C while CT was found between a minimum of 2.7°C (CTmin) and a maximum of 35.9°C (CTmax). These data and data from tropical and temperate crustaceans were compared to examine the association between environmental temperature and thermal tolerance. Temperate species have a CTmax limit around 35°C that corresponded with the low CTmax limit of tropical species (34–36°C). Tropical species showed a CTmin limit around 9°C similar to the maximum CTmin of temperate species (5–6°C). The maximum CTmin of deep sea species that occur in cold environments (2.5°C) matched the low CTmin values (3.2°C) of temperate species. Results also indicate that the energy required to activate the enzyme complex (Ei) involved in respiratory metabolism of ectotherms changes along the latitudinal gradient of temperature. PMID:26879464

  2. Thermal biology of the sub-polar–temperate estuarine crab Hemigrapsus crenulatus (Crustacea: Decapoda: Varunidae

    Directory of Open Access Journals (Sweden)

    Juan P. Cumillaf

    2016-03-01

    Full Text Available Optimum temperatures can be measured through aerobic scope, preferred temperatures or growth. A complete thermal window, including optimum, transition (Pejus and critical temperatures (CT, can be described if preferred temperatures and CT are defined. The crustacean Hemigrapsus crenulatus was used as a model species to evaluate the effect of acclimation temperature on: (i thermal preference and width of thermal window, (ii respiratory metabolism, and (iii haemolymph proteins. Dependant on acclimation temperature, preferred temperature was between 11.8°C and 25.2°C while CT was found between a minimum of 2.7°C (CTmin and a maximum of 35.9°C (CTmax. These data and data from tropical and temperate crustaceans were compared to examine the association between environmental temperature and thermal tolerance. Temperate species have a CTmax limit around 35°C that corresponded with the low CTmax limit of tropical species (34–36°C. Tropical species showed a CTmin limit around 9°C similar to the maximum CTmin of temperate species (5–6°C. The maximum CTmin of deep sea species that occur in cold environments (2.5°C matched the low CTmin values (3.2°C of temperate species. Results also indicate that the energy required to activate the enzyme complex (Ei involved in respiratory metabolism of ectotherms changes along the latitudinal gradient of temperature.

  3. Revisiting Notechis scutatus venom: on shotgun proteomics and neutralization by the "bivalent" Sea Snake Antivenom.

    Science.gov (United States)

    Tan, Choo Hock; Tan, Kae Yi; Tan, Nget Hong

    2016-07-20

    Recent advances in proteomics enable deep profiling of the compositional details of snake venoms for improved understanding on envenomation pathophysiology and immunological neutralization. In this study, the venom of Australian tiger snake (Notechis scutatus) was trypsin-digested in solution and subjected to nano-ESI-LCMS/MS. Applying a relative quantitative proteomic approach, the findings revealed a proteome comprising 42 toxin subtypes clustered into 12 protein families. Phospholipases A2 constitute the most abundant toxins (74.5% of total venom proteins) followed by Kunitz serine protease inhibitors (6.9%), snake venom serine proteases (5.9%), alpha-neurotoxins (5.6%) and several toxins of lower abundance. The proteome correlates with N. scutatus envenoming effects including pre-synaptic and post-synaptic neurotoxicity and consumptive coagulopathy. The venom is highly lethal in mice (intravenous median lethal dose=0.09μg/g). BioCSL Sea Snake Antivenom, raised against the venoms of beaked sea snake (Hydrophis schistosus) and N. scutatus (added for enhanced immunogenicity), neutralized the lethal effect of N. scutatus venom (potency=2.95mg/ml) much more effectively than the targeted H.schistosus venom (potency=0.48mg/ml). The combined venom immunogen may have improved the neutralization against phospholipases A2 which are abundant in both venoms, but not short-neurotoxins which are predominant only in H. schistosus venom. A shotgun proteomic approach adopted in this study revealed the compositional details of the venom of common tiger snake from Australia, Notechis scutatus. The proteomic findings provided additional information on the relative abundances of toxins and the detection of proteins of minor expression unreported previously. The potent lethal effect of the venom was neutralized by bioCSL Sea Snake Antivenom, an anticipated finding due to the fact that the Sea Snake Antivenom is actually bivalent in nature, being raised against a mix of venoms of the

  4. A label-free quantitative shotgun proteomics analysis of rice grain development

    Directory of Open Access Journals (Sweden)

    Koh Hee-Jong

    2011-09-01

    Full Text Available Abstract Background Although a great deal of rice proteomic research has been conducted, there are relatively few studies specifically addressing the rice grain proteome. The existing rice grain proteomic researches have focused on the identification of differentially expressed proteins or monitoring protein expression patterns during grain filling stages. Results Proteins were extracted from rice grains 10, 20, and 30 days after flowering, as well as from fully mature grains. By merging all of the identified proteins in this study, we identified 4,172 non-redundant proteins with a wide range of molecular weights (from 5.2 kDa to 611 kDa and pI values (from pH 2.9 to pH 12.6. A Genome Ontology category enrichment analysis for the 4,172 proteins revealed that 52 categories were enriched, including the carbohydrate metabolic process, transport, localization, lipid metabolic process, and secondary metabolic process. The relative abundances of the 1,784 reproducibly identified proteins were compared to detect 484 differentially expressed proteins during rice grain development. Clustering analysis and Genome Ontology category enrichment analysis revealed that proteins involved in the metabolic process were enriched through all stages of development, suggesting that proteome changes occurred even in the desiccation phase. Interestingly, enrichments of proteins involved in protein folding were detected in the desiccation phase and in fully mature grain. Conclusion This is the first report conducting comprehensive identification of rice grain proteins. With a label free shotgun proteomic approach, we identified large number of rice grain proteins and compared the expression patterns of reproducibly identified proteins during rice grain development. Clustering analysis, Genome Ontology category enrichment analysis, and the analysis of composite expression profiles revealed dynamic changes of metabolisms during rice grain development. Interestingly, we

  5. PENGARUH VARIASI SUHU PADA PROSES SELF TEMPERING DAN VARIASI WAKTU TAHAN PADA PROSES TEMPERING TERHADAP SIFAT MEKANIS BAJA AISI 4140

    Directory of Open Access Journals (Sweden)

    Sunardi Sunardi

    2016-07-01

    Full Text Available Tujuan penelitian ini adalah untuk mengetahui sifat mekanis pada baja AISI 4140 dengan proses tempering dengan variasi waktu tahan dan variasi suhu pada proses self tempering. Material terlebih dahulu dipanaskan pada suhu 850°C, di tahan dengan waktu 14 dan 28 menit, media pendinginan adalah Oli SAE 20. Pada proses tempering baja dipanaskan kembali dengan suhu 200°C di tahan dengan waktu 30 dan 120 menit. Sedangkan untuk proses self tempering, baja di panaskan pada suhu 850°C di tahan dengan waktu 14 dan 28 menit kemudian didinginkan, suhu yang harus dicapai pada pendinginan adalah 200°C, 400°C dan 600°C. Proses tempering dengan variasi waktu tahan mempunyai nilai kekerasan terbesar 50,1 HRC dengan waktu tahan 120 menit, sedangkan nilai kekerasan terbesar pada proses self tempering dengan variasi suhu adalah 29,68 HRC pada suhu 200°C. Nilai ketangguhan terbesar pada saat proses tempering adalah 0,341 (J/mm2 dengan waktu tahan 120 menit, sedangkan pada saat proses self tempering ketangguhan terbesar pada suhu 600°C dengan nilai 0,375 (J/mm2. Laju korosi terbesar pada saat tempering adalah 0,055 (mpy dengan waktu tahan 30 menit, sedangkan pada saat proses self tempering laju korosi terbesar pada suhu 400°C dengan nilai 0,0388 (mpy. 

  6. Choosing the best plant for the job: a cost-effective assay to prescreen ancient plant remains destined for shotgun sequencing.

    Directory of Open Access Journals (Sweden)

    Nathan Wales

    Full Text Available DNA extracted from ancient plant remains almost always contains a mixture of endogenous (that is, derived from the plant and exogenous (derived from other sources DNA. The exogenous 'contaminant' DNA, chiefly derived from microorganisms, presents significant problems for shotgun sequencing. In some samples, more than 90% of the recovered sequences are exogenous, providing limited data relevant to the sample. However, other samples have far less contamination and subsequently yield much more useful data via shotgun sequencing. Given the investment required for high-throughput sequencing, whenever multiple samples are available, it is most economical to sequence the least contaminated sample. We present an assay based on quantitative real-time PCR which estimates the relative amounts of fungal and bacterial DNA in a sample in comparison to the endogenous plant DNA. Given a collection of contextually-similar ancient plant samples, this low cost assay aids in selecting the best sample for shotgun sequencing.

  7. Corrosion fatigue in nitrocarburized quenched and tempered steels

    Science.gov (United States)

    Khani, M. Karim; Dengel, D.

    1996-05-01

    In order to investigate the fatigue strength and fracture mechanism of salt bath nitrocarburized steels, specimens of the steels SAE 4135 and SAE 4140, in a quenched and tempered state, and additionally in a salt bath nitrocarburized and oxidizing cooled state as well as in a polished (after the oxidizing cooling) and renewed oxidized state, were subjected to comparative rotating bending fatigue tests in inert oil and 5 pct NaCl solution. In addition, some of the quenched and tempered specimens of SAE 4135 material were provided with an approximately 50-μm-thick electroless Ni-P layer, in order to compare corrosion fatigue behavior between the Ni-P layer and the nitride layers. Long-life corrosion fatigue tests of SAE 4135 material were carried out under small stresses in the long-life range up to 108 cycles with a test frequency of 100 Hz. Fatigue tests of SAE 4140 material were carried out in the range of finite life (low-cycle range) with a test frequency of 13 Hz. The results show that the 5 pct NaCl environment drastically reduced fatigue life, but nitrocarburizing plus oxidation treatment was found to improve the corrosion fatigue life over that of untreated and Ni-P coated specimens. The beneficial effect of nitrocarburizing followed by oxidation treatment on cor-rosion fatigue life results from the protection rendered by the compound layer by means of a well-sealed oxide layer, whereby the pores present in the compound layer fill up with oxides. The role of inclusions in initiating fatigue cracks was investigated. It was found that under corrosion fatigue conditions, the fatigue cracks started at cavities along the interfaces of MnS inclusions and matrix in the case of quenched and tempered specimens. The nitrocarburized specimens, however, showed a superposition of pitting corrosion and corrosion fatigue in which pores and nonmetallic inclusions in the compound layer play a predominant role concerning the formation of pits in the substrate.

  8. Data on xylem sap proteins from Mn- and Fe-deficient tomato plants obtained using shotgun proteomics.

    Science.gov (United States)

    Ceballos-Laita, Laura; Gutierrez-Carbonell, Elain; Takahashi, Daisuke; Abadía, Anunciación; Uemura, Matsuo; Abadía, Javier; López-Millán, Ana Flor

    2018-04-01

    This article contains consolidated proteomic data obtained from xylem sap collected from tomato plants grown in Fe- and Mn-sufficient control, as well as Fe-deficient and Mn-deficient conditions. Data presented here cover proteins identified and quantified by shotgun proteomics and Progenesis LC-MS analyses: proteins identified with at least two peptides and showing changes statistically significant (ANOVA; p ≤ 0.05) and above a biologically relevant selected threshold (fold ≥ 2) between treatments are listed. The comparison between Fe-deficient, Mn-deficient and control xylem sap samples using a multivariate statistical data analysis (Principal Component Analysis, PCA) is also included. Data included in this article are discussed in depth in the research article entitled "Effects of Fe and Mn deficiencies on the protein profiles of tomato ( Solanum lycopersicum) xylem sap as revealed by shotgun analyses" [1]. This dataset is made available to support the cited study as well to extend analyses at a later stage.

  9. Parallel tempering in full QCD with Wilson fermions

    International Nuclear Information System (INIS)

    Ilgenfritz, E.-M.; Kerler, W.; Mueller-Preussker, M.; Stueben, H.

    2002-01-01

    We study the performance of QCD simulations with dynamical Wilson fermions by combining the hybrid Monte Carlo algorithm with parallel tempering on 10 4 and 12 4 lattices. In order to compare tempered with standard simulations, covariance matrices between subensembles have to be formulated and evaluated using the general properties of autocorrelations of the parallel tempering algorithm. We find that rendering the hopping parameter κ dynamical does not lead to an essential improvement. We point out possible reasons for this observation and discuss more suitable ways of applying parallel tempering to QCD

  10. Seasonality of temperate forest photosynthesis and daytime respiration.

    Science.gov (United States)

    Wehr, R; Munger, J W; McManus, J B; Nelson, D D; Zahniser, M S; Davidson, E A; Wofsy, S C; Saleska, S R

    2016-06-30

    Terrestrial ecosystems currently offset one-quarter of anthropogenic carbon dioxide (CO2) emissions because of a slight imbalance between global terrestrial photosynthesis and respiration. Understanding what controls these two biological fluxes is therefore crucial to predicting climate change. Yet there is no way of directly measuring the photosynthesis or daytime respiration of a whole ecosystem of interacting organisms; instead, these fluxes are generally inferred from measurements of net ecosystem-atmosphere CO2 exchange (NEE), in a way that is based on assumed ecosystem-scale responses to the environment. The consequent view of temperate deciduous forests (an important CO2 sink) is that, first, ecosystem respiration is greater during the day than at night; and second, ecosystem photosynthetic light-use efficiency peaks after leaf expansion in spring and then declines, presumably because of leaf ageing or water stress. This view has underlain the development of terrestrial biosphere models used in climate prediction and of remote sensing indices of global biosphere productivity. Here, we use new isotopic instrumentation to determine ecosystem photosynthesis and daytime respiration in a temperate deciduous forest over a three-year period. We find that ecosystem respiration is lower during the day than at night-the first robust evidence of the inhibition of leaf respiration by light at the ecosystem scale. Because they do not capture this effect, standard approaches overestimate ecosystem photosynthesis and daytime respiration in the first half of the growing season at our site, and inaccurately portray ecosystem photosynthetic light-use efficiency. These findings revise our understanding of forest-atmosphere carbon exchange, and provide a basis for investigating how leaf-level physiological dynamics manifest at the canopy scale in other ecosystems.

  11. Marine Biodiversity in Temperate Western Australia: Multi-Taxon Surveys of Minden and Roe Reefs

    Directory of Open Access Journals (Sweden)

    Zoe Richards

    2016-03-01

    Full Text Available A growing body of evidence indicates that temperate marine ecosystems are being tropicalised due to the poleward extension of tropical species. Such climate mediated changes in species distribution patterns have the potential to profoundly alter temperate communities, as this advance can serve to push temperate taxa, many of which are southern Australian endemics, southward. These changes can lead to cascading effects for the biodiversity and function of coastal ecosystems, including contraction of ranges/habitats of sensitive cool water species. Hence there is growing concern for the future of Australia’s temperate marine biodiversity. Here we examine the diversity and abundance of marine flora and fauna at two reefs near Perth’s metropolitan area—Minden Reef and Roe Reef. We report the presence of 427 species of marine flora and fauna from eight taxon groups occurring in the Perth metropolitan area; at least three species of which appear to be new to science. Our data also extends the known range of 15 species, and in numerous instances, thousands of kilometres south from the Kimberley or Pilbara and verifies that tropicalisation of reef communities in the Perth metropolitan area is occurring. We report the presence of 24 species endemic to south-west Australia that may be at risk of range contractions with continued ocean warming. The results of these surveys add to our knowledge of local nearshore marine environments in the Perth metropolitan area and support the growing body of evidence that indicates a diverse and regionally significant marine fauna occurs in temperate Western Australia. Regular, repeated survey work across seasons is important in order to thoroughly document the status of marine biodiversity in this significant transition zone.

  12. Biophysical processes leading to the ingress of temperate fish larvae into estuarine nursery areas: A review

    Science.gov (United States)

    Teodósio, Maria Alexandra; Paris, Claire B.; Wolanski, Eric; Morais, Pedro

    2016-12-01

    A series of complementary hypotheses have been proposed to explain the recruitment of marine and temperate pelagic fish larvae originated from pelagic eggs in coastal environments. In this review, we propose a new and complementary hypothesis describing the biophysical processes intervening in the recruitment of temperate fish larvae into estuaries. This new hypothesis, the Sense Acuity And Behavioral (SAAB) hypothesis, recognizes that recruitment is unlikely if the larvae drift passively with the water currents, and that successful recruitment requires the sense acuity of temperate fish larvae and their behavioral response to the estuarine cues present in coastal areas. We propose that temperate fish larvae use a hierarchy of sensory cues (odor, sound, visual and geomagnetic cues) to detect estuarine nursery areas and to aid during navigation towards these areas. The sensorial acuity increases along ontogeny, which coincides with increased swimming capabilities. The swimming strategies of post-flexion larvae differ from offshore areas to the tidal zone. In offshore areas, innate behavior might lead larvae towards the coast guided by a sun compass or by the earth's geomagnetic field. In areas under limited influence of estuarine plumes (either in energetic nearshore areas or offshore), post-flexion larvae display a searching swimming behavior for estuarine disconnected patches (infotaxis strategy). After finding an estuarine plume, larvae may swim along the increasing cue concentration to ingress into the estuary. Here, larvae exhibit a rheotaxis behavior and avoid displacement by longshore currents by keeping bearing during navigation. When larvae reach the vicinity of an estuary, merging diel rhythms with feeding and predator avoidance strategies with tidally induced movements is essential to increase their chances of estuarine ingress. A fish larva recruitment model developed for the Ria Formosa lagoon supports the general framework of the SAAB hypothesis. In

  13. Oceanic temperate forest versus warm temperate rainforest: a reply to Grubb et al. (2017)

    DEFF Research Database (Denmark)

    McGlone, Matt S.; Buitenwerf, Robert; Richardson, Sarah J.

    2017-01-01

    Grubb et al. (2017) point out that we (McGlone et al. 2016) erroneously stated that the definition of warm temperate rain forest (WTRF; Grubb et al. 2013) was based in part on climatic criteria. We apologise: their text made clear that this was not the case. However, they go on to say that they ‘...

  14. Adhesion and wear properties of boro-tempered ductile iron

    International Nuclear Information System (INIS)

    Kayali, Yusuf; Yalcin, Yilmaz; Taktak, Suekrue

    2011-01-01

    Highlights: → In this study, the wear and adhesion properties of BDI were investigated. → Boro-tempering process under several heat treatment conditions was examined. → Optical microscope, SEM and XRD analysis were carried out to investigate the microstructure. → It was observed that boro-tempering process improves micro-hardness and wear properties of ductile irons. -- Abstract: In this study, adhesion and wear properties of boro-tempered ductile iron (BDI) were investigated. Boro-tempering was carried out on two stage processes i.e. boronizing and tempering. At the first stage, ductile iron samples were boronized by using pack process at 900 o C for 1, 3, and 5 h and then, secondly tempered at 250, 300, 350, and 400 o C for 1 h. X-ray diffraction (XRD) analysis of boro-tempered samples showed that FeB and Fe 2 B phases were found on the surface of the samples. The Daimler-Benz Rockwell-C adhesion test was used to assess the adhesion of boride layer. Test result showed that adhesion decreased with increasing boriding time and increased with increasing tempering temperature. Dry sliding wear tests of these samples were performed against Al 2 O 3 ball at a constant sliding speed and loads of 5 and 10 N. Wear tests indicated that boro-tempering heat treatment increased wear resistance of ductile iron. In addition, it was found that while wear rate of boro-tempered samples decreased with increasing boriding time, there is no significant affect of tempering temperature on wear rate.

  15. Hardness of H13 Tool Steel After Non-isothermal Tempering

    Science.gov (United States)

    Nelson, E.; Kohli, A.; Poirier, D. R.

    2018-04-01

    A direct method to calculate the tempering response of a tool steel (H13) that exhibits secondary hardening is presented. Based on the traditional method of presenting tempering response in terms of isothermal tempering, we show that the tempering response for a steel undergoing a non-isothermal tempering schedule can be predicted. Experiments comprised (1) isothermal tempering, (2) non-isothermal tempering pertaining to a relatively slow heating to process-temperature and (3) fast-heating cycles that are relevant to tempering by induction heating. After establishing the tempering response of the steel under simple isothermal conditions, the tempering response can be applied to non-isothermal tempering by using a numerical method to calculate the tempering parameter. Calculated results are verified by the experiments.

  16. Temperate radiations and dying embers of a tropical past: the diversification of Viburnum.

    Science.gov (United States)

    Spriggs, Elizabeth L; Clement, Wendy L; Sweeney, Patrick W; Madriñán, Santiago; Edwards, Erika J; Donoghue, Michael J

    2015-07-01

    We used a near-complete phylogeny for the angiosperm clade Viburnum to assess lineage diversification rates, and to examine possible morphological and ecological factors driving radiations. Maximum-likelihood and Bayesian approaches identified shifts in diversification rate and possible links to character evolution. We inferred the ancestral environment for Viburnum and changes in diversification dynamics associated with subsequent biome shifts. Viburnum probably diversified in tropical forests of Southeast Asia in the Eocene, with three subsequent radiations in temperate clades during the Miocene. Four traits (purple fruits, extrafloral nectaries, bud scales and toothed leaves) were statistically associated with higher rates of diversification. However, we argue that these traits are unlikely to be driving diversification directly. Instead, two radiations were associated with the occupation of mountainous regions and a third with repeated shifts between colder and warmer temperate forests. Early-branching depauperate lineages imply that the rare lowland tropical species are 'dying embers' of once more diverse lineages; net diversification rates in Viburnum likely decreased in these tropical environments after the Oligocene. We suggest that 'taxon pulse' dynamics might characterize other temperate plant lineages. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

  17. Dry matter intake and digestibility of temperate pastures ...

    African Journals Online (AJOL)

    The aim of this study was to evaluate the effect of sorghum grain supplementation on total and forage dry matter (DM) intake and digestibility of wethers and heifers consuming temperate pasture. Twenty four Corriedale x Milchschaf wethers and 24 crossbred heifers fed temperate pasture were non-supplemented or ...

  18. Simulation of Residual Stresses at Holes in Tempered Glass

    DEFF Research Database (Denmark)

    Nielsen, Jens Henrik; Olesen, John Forbes; Poulsen, Peter Noe

    2010-01-01

    This work presents a full 3D numerical study of the residual stresses in tempered (toughened) glass near holes using Narayanaswamy’s model for the tempering process. It is the objective of the paper to elucidate the influence on the minimal residual compressive stresses at holes from variations in...

  19. Effects of Fe and Mn deficiencies on the protein profiles of tomato (Solanum lycopersicum) xylem sap as revealed by shotgun analyses

    Science.gov (United States)

    The aim of this work was to study the effects of Fe and Mn deficiencies on the xylem sap proteome of tomato using a shotgun proteomic approach, with the final goal of elucidating plant response mechanisms to these stresses. This approach yielded 643 proteins reliably identified and quantified with 7...

  20. Using Growing Self-Organising Maps to Improve the Binning Process in Environmental Whole-Genome Shotgun Sequencing

    Science.gov (United States)

    Chan, Chon-Kit Kenneth; Hsu, Arthur L.; Tang, Sen-Lin; Halgamuge, Saman K.

    2008-01-01

    Metagenomic projects using whole-genome shotgun (WGS) sequencing produces many unassembled DNA sequences and small contigs. The step of clustering these sequences, based on biological and molecular features, is called binning. A reported strategy for binning that combines oligonucleotide frequency and self-organising maps (SOM) shows high potential. We improve this strategy by identifying suitable training features, implementing a better clustering algorithm, and defining quantitative measures for assessing results. We investigated the suitability of each of di-, tri-, tetra-, and pentanucleotide frequencies. The results show that dinucleotide frequency is not a sufficiently strong signature for binning 10 kb long DNA sequences, compared to the other three. Furthermore, we observed that increased order of oligonucleotide frequency may deteriorate the assignment result in some cases, which indicates the possible existence of optimal species-specific oligonucleotide frequency. We replaced SOM with growing self-organising map (GSOM) where comparable results are obtained while gaining 7%–15% speed improvement. PMID:18288261

  1. Application of whole genome shotgun sequencing for detection and characterization of genetically modified organisms and derived products.

    Science.gov (United States)

    Holst-Jensen, Arne; Spilsberg, Bjørn; Arulandhu, Alfred J; Kok, Esther; Shi, Jianxin; Zel, Jana

    2016-07-01

    The emergence of high-throughput, massive or next-generation sequencing technologies has created a completely new foundation for molecular analyses. Various selective enrichment processes are commonly applied to facilitate detection of predefined (known) targets. Such approaches, however, inevitably introduce a bias and are prone to miss unknown targets. Here we review the application of high-throughput sequencing technologies and the preparation of fit-for-purpose whole genome shotgun sequencing libraries for the detection and characterization of genetically modified and derived products. The potential impact of these new sequencing technologies for the characterization, breeding selection, risk assessment, and traceability of genetically modified organisms and genetically modified products is yet to be fully acknowledged. The published literature is reviewed, and the prospects for future developments and use of the new sequencing technologies for these purposes are discussed.

  2. Use of Metagenomic Shotgun Sequencing Technology To Detect Foodborne Pathogens within the Microbiome of the Beef Production Chain.

    Science.gov (United States)

    Yang, Xiang; Noyes, Noelle R; Doster, Enrique; Martin, Jennifer N; Linke, Lyndsey M; Magnuson, Roberta J; Yang, Hua; Geornaras, Ifigenia; Woerner, Dale R; Jones, Kenneth L; Ruiz, Jaime; Boucher, Christina; Morley, Paul S; Belk, Keith E

    2016-04-01

    Foodborne illnesses associated with pathogenic bacteria are a global public health and economic challenge. The diversity of microorganisms (pathogenic and nonpathogenic) that exists within the food and meat industries complicates efforts to understand pathogen ecology. Further, little is known about the interaction of pathogens within the microbiome throughout the meat production chain. Here, a metagenomic approach and shotgun sequencing technology were used as tools to detect pathogenic bacteria in environmental samples collected from the same groups of cattle at different longitudinal processing steps of the beef production chain: cattle entry to feedlot, exit from feedlot, cattle transport trucks, abattoir holding pens, and the end of the fabrication system. The log read counts classified as pathogens per million reads for Salmonella enterica,Listeria monocytogenes,Escherichia coli,Staphylococcus aureus, Clostridium spp. (C. botulinum and C. perfringens), and Campylobacter spp. (C. jejuni,C. coli, and C. fetus) decreased over subsequential processing steps. Furthermore, the normalized read counts for S. enterica,E. coli, and C. botulinumwere greater in the final product than at the feedlots, indicating that the proportion of these bacteria increased (the effect on absolute numbers was unknown) within the remaining microbiome. From an ecological perspective, data indicated that shotgun metagenomics can be used to evaluate not only the microbiome but also shifts in pathogen populations during beef production. Nonetheless, there were several challenges in this analysis approach, one of the main ones being the identification of the specific pathogen from which the sequence reads originated, which makes this approach impractical for use in pathogen identification for regulatory and confirmation purposes. Copyright © 2016 Yang et al.

  3. Pigs in sequence space: A 0.66X coverage pig genome survey based on shotgun sequencing

    Directory of Open Access Journals (Sweden)

    Li Wei

    2005-05-01

    Full Text Available Abstract Background Comparative whole genome analysis of Mammalia can benefit from the addition of more species. The pig is an obvious choice due to its economic and medical importance as well as its evolutionary position in the artiodactyls. Results We have generated ~3.84 million shotgun sequences (0.66X coverage from the pig genome. The data are hereby released (NCBI Trace repository with center name "SDJVP", and project name "Sino-Danish Pig Genome Project" together with an initial evolutionary analysis. The non-repetitive fraction of the sequences was aligned to the UCSC human-mouse alignment and the resulting three-species alignments were annotated using the human genome annotation. Ultra-conserved elements and miRNAs were identified. The results show that for each of these types of orthologous data, pig is much closer to human than mouse is. Purifying selection has been more efficient in pig compared to human, but not as efficient as in mouse, and pig seems to have an isochore structure most similar to the structure in human. Conclusion The addition of the pig to the set of species sequenced at low coverage adds to the understanding of selective pressures that have acted on the human genome by bisecting the evolutionary branch between human and mouse with the mouse branch being approximately 3 times as long as the human branch. Additionally, the joint alignment of the shot-gun sequences to the human-mouse alignment offers the investigator a rapid way to defining specific regions for analysis and resequencing.

  4. Proteomic analysis of protein interactions between Eimeria maxima sporozoites and chicken jejunal epithelial cells by shotgun LC-MS/MS.

    Science.gov (United States)

    Huang, Jingwei; Liu, Tingqi; Li, Ke; Song, Xiaokai; Yan, Ruofeng; Xu, Lixin; Li, Xiangrui

    2018-04-04

    Eimeria maxima initiates infection by invading the jejunal epithelial cells of chicken. However, the proteins involved in invasion remain unknown. The research of the molecules that participate in the interactions between E. maxima sporozoites and host target cells will fill a gap in our understanding of the invasion system of this parasitic pathogen. In the present study, chicken jejunal epithelial cells were isolated and cultured in vitro. Western blot was employed to analyze the soluble proteins of E. maxima sporozoites that bound to chicken jejunal epithelial cells. Co-immunoprecipitation (co-IP) assay was used to separate the E. maxima proteins that bound to chicken jejunal epithelial cells. Shotgun LC-MS/MS technique was used for proteomics identification and Gene Ontology was employed for the bioinformatics analysis. The results of Western blot analysis showed that four proteins bands from jejunal epithelial cells co-cultured with soluble proteins of E. maxima sporozoites were recognized by the positive sera, with molecular weights of 70, 90, 95 and 130 kDa. The co-IP dilutions were analyzed by shotgun LC-MS/MS. A total of 204 proteins were identified in the E. maxima protein database using the MASCOT search engine. Thirty-five proteins including microneme protein 3 and 7 had more than two unique peptide counts and were annotated using Gene Ontology for molecular function, biological process and cellular localization. The results revealed that of the 35 annotated peptides, 22 (62.86%) were associated with binding activity and 15 (42.86%) were involved in catalytic activity. Our findings provide an insight into the interaction between E. maxima and the corresponding host cells and it is important for the understanding of molecular mechanisms underlying E. maxima invasion.

  5. Comparative shotgun proteomic analysis of wild and domesticated Opuntia spp. species shows a metabolic adaptation through domestication.

    Science.gov (United States)

    Pichereaux, Carole; Hernández-Domínguez, Eric E; Santos-Diaz, Maria Del Socorro; Reyes-Agüero, Antonio; Astello-García, Marizel; Guéraud, Françoise; Negre-Salvayre, Anne; Schiltz, Odile; Rossignol, Michel; Barba de la Rosa, Ana Paulina

    2016-06-30

    The Opuntia genus is widely distributed in America, but the highest richness of wild species are found in Mexico, as well as the most domesticated Opuntia ficus-indica, which is the most domesticated species and an important crop in agricultural economies of arid and semiarid areas worldwide. During domestication process, the Opuntia morphological characteristics were favored, such as less and smaller spines in cladodes and less seeds in fruits, but changes at molecular level are almost unknown. To obtain more insights about the Opuntia molecular changes through domestication, a shotgun proteomic analysis and database-dependent searches by homology was carried out. >1000 protein species were identified and by using a label-free quantitation method, the Opuntia proteomes were compared in order to identify differentially accumulated proteins among wild and domesticated species. Most of the changes were observed in glucose, secondary, and 1C metabolism, which correlate with the observed protein, fiber and phenolic compounds accumulation in Opuntia cladodes. Regulatory proteins, ribosomal proteins, and proteins related with response to stress were also observed in differential accumulation. These results provide new valuable data that will help to the understanding of the molecular changes of Opuntia species through domestication. Opuntia species are well adapted to dry and warm conditions in arid and semiarid regions worldwide, and they are highly productive plants showing considerable promises as an alternative food source. However, there is a gap regarding Opuntia molecular mechanisms that enable them to grow in extreme environmental conditions and how the domestication processes has changed them. In the present study, a shotgun analysis was carried out to characterize the proteomes of five Opuntia species selected by its domestication degree. Our results will help to a better understanding of proteomic features underlying the selection and specialization under

  6. Dams release methane even in temperate zoned

    International Nuclear Information System (INIS)

    Lemarchand, F.

    2010-01-01

    The Wohlen lake (near Bern) is a retaining dam built 90 years ago that has undergone a campaign to measure the quantity of methane released. The campaign lasted 1 year and the result was unexpected: 0.15 g/m 2 *day which one of the highest release rates in temperate zones. This result is all the more stunning since water stays only 2 days in average in the reservoir and that the drowned area is not important. In fact the river Aar that feeds the lake is loaded with organic matter coming from humane activities: agriculture and 3 sewage plants. This organic matter decays in the lake releasing methane. (A.C.)

  7. Moist temperate forest butterflies of western Bhutan

    Directory of Open Access Journals (Sweden)

    Arun P. Singh

    2016-03-01

    Full Text Available Random surveys were carried out in moist temperate forests (1,860–3,116 m around Bunakha Village and Dochula Pass, near Thimphu in western Bhutan, recording 65 species of butterflies.  Of these, 11 species, viz., Straightwing Blue Orthomiella pontis pontis Elwes, Slate Royal Maneca bhotea bhotea Moore, Dull Green Hairstreak Esakiozephyrus icana Moore, Yellow Woodbrown Lethe nicetas Hewitson, Small Silverfork Zophoessa jalaurida elwesi Moore, Scarce Labyrinth, Neope pulahina (Evans, Chumbi Wall Chonala masoni Elwes, Pale Hockeystick Sailer Neptis manasa manasa Moore and White Commodore Parasarpa dudu dudu Westwood, are restricted to the eastern Himalaya, northeastern India and Myanmar.  Two other species, Tawny Mime Chiasa agestor agestor (Gray and Himalayan Spotted Flat Celaenorrhinus munda Moore have been only rarely recorded from Bhutan and a few individuals of the rare Bhutan Glory Bhutanitis lidderdalei Atkinson were also recorded near Bunakha.  

  8. Study on tempering behaviour of AISI 410 stainless steel

    International Nuclear Information System (INIS)

    Chakraborty, Gopa; Das, C.R.; Albert, S.K.; Bhaduri, A.K.; Thomas Paul, V.; Panneerselvam, G.; Dasgupta, Arup

    2015-01-01

    Martensitic stainless steels find extensive applications due to their optimum combination of strength, hardness and wear-resistance in tempered condition. However, this class of steels is susceptible to embrittlement during tempering if it is carried out in a specific temperature range resulting in significant reduction in toughness. Embrittlement of as-normalised AISI 410 martensitic stainless steel, subjected to tempering treatment in the temperature range of 673–923 K was studied using Charpy impact tests followed by metallurgical investigations using field emission scanning electron and transmission electron microscopes. Carbides precipitated during tempering were extracted by electrochemical dissolution of the matrix and identified by X-ray diffraction. Studies indicated that temper embrittlement is highest when the steel is tempered at 823 K. Mostly iron rich carbides are present in the steel subjected to tempering at low temperatures of around 723 K, whereas chromium rich carbides (M 23 C 6 ) dominate precipitation at high temperature tempering. The range 773–823 K is the transition temperature range for the precipitates, with both Fe 2 C and M 23 C 6 types of carbides coexisting in the material. The nucleation of Fe 2 C within the martensite lath, during low temperature tempering, has a definite role in the embrittlement of this steel. Embrittlement is not observed at high temperature tempering because of precipitation of M 23 C 6 carbides, instead of Fe 2 C, preferentially along the lath and prior austenite boundaries. Segregation of S and P, which is widely reported as one of the causes for temper embrittlement, could not be detected in the material even through Auger electron spectroscopy studies. - Highlights: • Tempering behaviour of AISI 410 steel is studied within 673–923 K temperature range. • Temperature regime of maximum embrittlement is identified as 773–848 K. • Results show that type of carbide precipitation varies with

  9. Study on tempering behaviour of AISI 410 stainless steel

    Energy Technology Data Exchange (ETDEWEB)

    Chakraborty, Gopa, E-mail: gopa_mjs@igcar.gov.in [Metallurgy & Materials Group, Indira Gandhi Center for Atomic Research, Kalpakkam 603102 (India); Das, C.R.; Albert, S.K.; Bhaduri, A.K.; Thomas Paul, V. [Metallurgy & Materials Group, Indira Gandhi Center for Atomic Research, Kalpakkam 603102 (India); Panneerselvam, G. [Chemistry Group, Indira Gandhi Center for Atomic Research, Kalpakkam 603102 (India); Dasgupta, Arup [Metallurgy & Materials Group, Indira Gandhi Center for Atomic Research, Kalpakkam 603102 (India)

    2015-02-15

    Martensitic stainless steels find extensive applications due to their optimum combination of strength, hardness and wear-resistance in tempered condition. However, this class of steels is susceptible to embrittlement during tempering if it is carried out in a specific temperature range resulting in significant reduction in toughness. Embrittlement of as-normalised AISI 410 martensitic stainless steel, subjected to tempering treatment in the temperature range of 673–923 K was studied using Charpy impact tests followed by metallurgical investigations using field emission scanning electron and transmission electron microscopes. Carbides precipitated during tempering were extracted by electrochemical dissolution of the matrix and identified by X-ray diffraction. Studies indicated that temper embrittlement is highest when the steel is tempered at 823 K. Mostly iron rich carbides are present in the steel subjected to tempering at low temperatures of around 723 K, whereas chromium rich carbides (M{sub 23}C{sub 6}) dominate precipitation at high temperature tempering. The range 773–823 K is the transition temperature range for the precipitates, with both Fe{sub 2}C and M{sub 23}C{sub 6} types of carbides coexisting in the material. The nucleation of Fe{sub 2}C within the martensite lath, during low temperature tempering, has a definite role in the embrittlement of this steel. Embrittlement is not observed at high temperature tempering because of precipitation of M{sub 23}C{sub 6} carbides, instead of Fe{sub 2}C, preferentially along the lath and prior austenite boundaries. Segregation of S and P, which is widely reported as one of the causes for temper embrittlement, could not be detected in the material even through Auger electron spectroscopy studies. - Highlights: • Tempering behaviour of AISI 410 steel is studied within 673–923 K temperature range. • Temperature regime of maximum embrittlement is identified as 773–848 K. • Results show that type of

  10. Forecasting cyanobacteria dominance in Canadian temperate lakes.

    Science.gov (United States)

    Persaud, Anurani D; Paterson, Andrew M; Dillon, Peter J; Winter, Jennifer G; Palmer, Michelle; Somers, Keith M

    2015-03-15

    Predictive models based on broad scale, spatial surveys typically identify nutrients and climate as the most important predictors of cyanobacteria abundance; however these models generally have low predictive power because at smaller geographic scales numerous other factors may be equally or more important. At the lake level, for example, the ability to forecast cyanobacteria dominance is of tremendous value to lake managers as they can use such models to communicate exposure risks associated with recreational and drinking water use, and possible exposure to algal toxins, in advance of bloom occurrence. We used detailed algal, limnological and meteorological data from two temperate lakes in south-central Ontario, Canada to determine the factors that are closely linked to cyanobacteria dominance, and to develop easy to use models to forecast cyanobacteria biovolume. For Brandy Lake (BL), the strongest and most parsimonious model for forecasting % cyanobacteria biovolume (% CB) included water column stability, hypolimnetic TP, and % cyanobacteria biovolume two weeks prior. For Three Mile Lake (TML), the best model for forecasting % CB included water column stability, hypolimnetic TP concentration, and 7-d mean wind speed. The models for forecasting % CB in BL and TML are fundamentally different in their lag periods (BL = lag 1 model and TML = lag 2 model) and in some predictor variables despite the close proximity of the study lakes. We speculate that three main factors (nutrient concentrations, water transparency and lake morphometry) may have contributed to differences in the models developed, and may account for variation observed in models derived from large spatial surveys. Our results illustrate that while forecast models can be developed to determine when cyanobacteria will dominate within two temperate lakes, the models require detailed, lake-specific calibration to be effective as risk-management tools. Copyright © 2015 Elsevier Ltd. All rights reserved.

  11. Shotgun proteomics of Aspergillus niger microsomes upon D-xylose induction

    NARCIS (Netherlands)

    Ferreira de Oliveira, J.M.P.; Passel, van M.W.J.; Schaap, P.J.; Graaff, de L.H.

    2010-01-01

    Protein secretion plays an eminent role in cell maintenance and adaptation to the extracellular environment of microorganisms. Although protein secretion is an extremely efficient process in filamentous fungi, the mechanisms underlying protein secretion have remained largely uncharacterized in these

  12. Physiological underpinnings associated with differences in pace of life and metabolic rate in north temperate and neotropical birds.

    Science.gov (United States)

    Jimenez, Ana Gabriela; Cooper-Mullin, Clara; Calhoon, Elisabeth A; Williams, Joseph B

    2014-07-01

    Animal life-history traits fall within limited ecological space with animals that have high reproductive rates having short lives, a continuum referred to as a "slow-fast" life-history axis. Animals of the same body mass at the slow end of the life-history continuum are characterized by low annual reproductive output and low mortality rate, such as is found in many tropical birds, whereas at the fast end, rates of reproduction and mortality are high, as in temperate birds. These differences in life-history traits are thought to result from trade-offs between investment in reproduction or self-maintenance as mediated by the biotic and abiotic environment. Thus, tropical and temperate birds provide a unique system to examine physiological consequences of life-history trade-offs at opposing ends of the "pace of life" spectrum. We have explored the implications of these trade-offs at several levels of physiological organization including whole-animal, organ systems, and cells. Tropical birds tend to have higher survival, slower growth, lower rates of whole-animal basal metabolic rate and peak metabolic rate, and smaller metabolically active organs compared with temperate birds. At the cellular level, primary dermal fibroblasts from tropical birds tend to have lower cellular metabolic rates and appear to be more resistant to oxidative cell stress than those of temperate birds. However, at the subcellular level, lipid peroxidation rates, a measure of the ability of lipid molecules within the cell membranes to thwart the propagation of oxidative damage, appear not to be different between tropical and temperate species. Nevertheless, lipids in mitochondrial membranes of tropical birds tend to have increased concentrations of plasmalogens (phospholipids with antioxidant properties), and decreased concentrations of cardiolipin (a complex phospholipid in the electron transport chain) compared with temperate birds.

  13. Stress relaxation in tempered glass caused by heat soak testing

    DEFF Research Database (Denmark)

    Schneider, Jens; Hilcken, Jonas; Aronen, Antti

    2016-01-01

    Heat soak testing of tempered glass is a thermal process required after the tempering process itself to bring glasses of commercial soda-lime-silica-glass to failure that are contaminated with nickel sulphide inclusions, diameter 50 mm to 500 mm typically. Thus, the tests avoid a so-called "spont...... of commercial soda-lime-silica glass, it causes stress relaxation in tempered glass and the fracture pattern of the glass changes accordingly, especially thin glasses are affected. Based on the Tool-Narayanaswamy-Model, this paper comprises the theoretical background of the stress...

  14. Drilling in tempered glass – modelling and experiments

    DEFF Research Database (Denmark)

    Nielsen, Jens Henrik

    The present paper reports experimentally and numerically obtained results for the process of drilling in tempered glass. The experimental results are drilling depths on the edge in 19mm tempered glass with a known residual stress state measured by a scattered light polariscope. The experiments have...... been modelled using a state-of-the-art model and compared with satisfying result to the performed experiments. The numerical model has been used for a parametric study, investigating the redistribution of residual stresses during the process of drilling. This is done for investigating the possibility...... of applying forces in such holes and thereby being able to mechanically assemble tempered glass without the need of drilling holes before the tempering process. The paper is the result of currently ongoing research and the results should be treated as so....

  15. Analysis of a viral metagenomic library from 200 m depth in Monterey Bay, California constructed by direct shotgun cloning

    OpenAIRE

    Preston Christina M; Steward Grieg F

    2011-01-01

    Abstract Background Viruses have a profound influence on both the ecology and evolution of marine plankton, but the genetic diversity of viral assemblages, particularly those in deeper ocean waters, remains poorly described. Here we report on the construction and analysis of a viral metagenome prepared from below the euphotic zone in a temperate, eutrophic bay of coastal California. Methods We purified viruses from approximately one cubic meter of seawater collected from 200m depth in Montere...

  16. Hot wire TIG temper bead welding for nuclear repairs

    International Nuclear Information System (INIS)

    Lambert, J.A.; Gilston, P.F.

    1989-08-01

    A preliminary assessment has been carried out to determine the suitability of the hot wire tungsten inert gas (TIG) welding process for the repair of thick section, ferritic steel nuclear pressure vessels. The objective has been to identify a hot wire TIG temper bead procedure, suitable for repairs without post weld heat treatment. This procedure involves depositing two weld layers with carefully selected welding parameters such that overlapping thermal cycles produce a refined and tempered heat affected zone, HAZ, microstructure. (author)

  17. The tempered polymerization of human neuroserpin.

    Directory of Open Access Journals (Sweden)

    Rosina Noto

    Full Text Available Neuroserpin, a member of the serpin protein superfamily, is an inhibitor of proteolytic activity that is involved in pathologies such as ischemia, Alzheimer's disease, and Familial Encephalopathy with Neuroserpin Inclusion Bodies (FENIB. The latter belongs to a class of conformational diseases, known as serpinopathies, which are related to the aberrant polymerization of serpin mutants. Neuroserpin is known to polymerize, even in its wild type form, under thermal stress. Here, we study the mechanism of neuroserpin polymerization over a wide range of temperatures by different techniques. Our experiments show how the onset of polymerization is dependent on the formation of an intermediate monomeric conformer, which then associates with a native monomer to yield a dimeric species. After the formation of small polymers, the aggregation proceeds via monomer addition as well as polymer-polymer association. No further secondary mechanism takes place up to very high temperatures, thus resulting in the formation of neuroserpin linear polymeric chains. Most interesting, the overall aggregation is tuned by the co-occurrence of monomer inactivation (i.e. the formation of latent neuroserpin and by a mechanism of fragmentation. The polymerization kinetics exhibit a unique modulation of the average mass and size of polymers, which might suggest synchronization among the different processes involved. Thus, fragmentation would control and temper the aggregation process, instead of enhancing it, as typically observed (e.g. for amyloid fibrillation.

  18. Influence of tempering temperature on mechanical properties of cast steels

    Directory of Open Access Journals (Sweden)

    G. Golański

    2008-12-01

    Full Text Available The paper presents results of research on the influence of tempering temperature on structure and mechanical properties of bainite hardened cast steel: G21CrMoV4 – 6 (L21HMF and G17CrMoV5 – 10 (L17HMF. Investigated cast steels were taken out from internal frames of steam turbines serviced for long time at elevated temperatures. Tempering of the investigated cast steel was carried out within the temperature range of 690 ÷ 730 C (G21CrMoV4 – 6 and 700 ÷ 740 C (G17CrMoV5 – 10. After tempering the cast steels were characterized by a structure of tempered lower bainite with numerous precipitations of carbides. Performed research of mechanical properties has shown that high temperatures of tempering of bainitic structure do not cause decrease of mechanical properties beneath the required minimum.oo It has also been proved that high-temperature tempering (>720 oC ensures high impact energy at the 20% decrease of mechanical properties.

  19. Study of the effects of austenitizing and tempering heat treatments on the alloy HT-9

    International Nuclear Information System (INIS)

    Redmon, J.W.

    1982-01-01

    This paper investigates the potential use of the ferritic alloy Sandvik HT-9 (12 Cr - 1 Mo) as an alternative to stainless steels used in high-neutron-fluence environments. The neutron radiation influences embrittlement where the impact-energy versus test-temperature curve is seen displaced to the right. As a result, commercially effective solutioning and tempering processes are needed to suppress this effect in the pre-irradiated condition. The effects of austenitizing treatments on the impact energy of HT-9 were identified. 18 figures, 6 tables

  20. Shotgun metagenomic data on the human stool samples to characterize shifts of the gut microbial profile after the Helicobacter pylori eradication therapy

    Directory of Open Access Journals (Sweden)

    Eugenia A. Boulygina

    2017-10-01

    Full Text Available The shotgun sequencing data presented in this report are related to the research article named “Gut microbiome shotgun sequencing in assessment of microbial community changes associated with H. pylori eradication therapy” (Khusnutdinova et al., 2016 [1]. Typically, the H. pylori eradication protocol includes a prolonged two-week use of the broad-spectrum antibiotics. The presented data on the whole-genome sequencing of the total DNA from stool samples of patients before the start of the eradication, immediately after eradication and several weeks after the end of treatment could help to profile the gut microbiota both taxonomically and functionally. The presented data together with those described in Glushchenko et al. (2017 [2] allow researchers to characterize the metagenomic profiles in which the use of antibiotics could result in dramatic changes in the intestinal microbiota composition. We perform 15 gut metagenomes from 5 patients with H. pylori infection, obtained through the shotgun sequencing on the SOLiD 5500 W platform. Raw reads are deposited in the ENA under project ID PRJEB21338.

  1. Application of the whole-transcriptome shotgun sequencing approach to the study of Philadelphia-positive acute lymphoblastic leukemia

    International Nuclear Information System (INIS)

    Iacobucci, I; Ferrarini, A; Sazzini, M; Giacomelli, E; Lonetti, A; Xumerle, L; Ferrari, A; Papayannidis, C; Malerba, G; Luiselli, D; Boattini, A; Garagnani, P; Vitale, A; Soverini, S; Pane, F; Baccarani, M; Delledonne, M; Martinelli, G

    2012-01-01

    Although the pathogenesis of BCR–ABL1-positive acute lymphoblastic leukemia (ALL) is mainly related to the expression of the BCR–ABL1 fusion transcript, additional cooperating genetic lesions are supposed to be involved in its development and progression. Therefore, in an attempt to investigate the complex landscape of mutations, changes in expression profiles and alternative splicing (AS) events that can be observed in such disease, the leukemia transcriptome of a BCR–ABL1-positive ALL patient at diagnosis and at relapse was sequenced using a whole-transcriptome shotgun sequencing (RNA-Seq) approach. A total of 13.9 and 15.8 million sequence reads was generated from de novo and relapsed samples, respectively, and aligned to the human genome reference sequence. This led to the identification of five validated missense mutations in genes involved in metabolic processes (DPEP1, TMEM46), transport (MVP), cell cycle regulation (ABL1) and catalytic activity (CTSZ), two of which resulted in acquired relapse variants. In all, 6390 and 4671 putative AS events were also detected, as well as expression levels for 18 315 and 18 795 genes, 28% of which were differentially expressed in the two disease phases. These data demonstrate that RNA-Seq is a suitable approach for identifying a wide spectrum of genetic alterations potentially involved in ALL

  2. Seasonal changes in the communities of photosynthetic picoeukaryotes in Ofunato Bay as revealed by shotgun metagenomic sequencing

    KAUST Repository

    Rashid, Jonaira

    2018-04-30

    Small photosynthetic eukaryotes play important roles in oceanic food webs in coastal regions. We investigated seasonal changes in the communities of photosynthetic picoeukaryotes (PPEs) of the class Mamiellophyceae, including the genera Bathycoccus, Micromonas and Ostreococcus, in Ofunato Bay, which is located in northeastern Japan and faces the Pacific Ocean. The abundances of PPEs were assessed over a period of one year in 2015 at three sampling stations, KSt. 1 (innermost bay area), KSt. 2 (middle bay area) and KSt. 3 (bay entrance area) at depths of 1 m (KSt. 1, KSt. 2 and KSt. 3), 8 m (KSt. 1) or 10 m (KSt. 2 and KSt. 3) by employing MiSeq shotgun metagenomic sequencing. The total abundances of Bathycoccus, Ostreococcus and Micromonas were in the ranges of 42–49%, 35–49% and 13–17%, respectively. Considering all assayed sampling stations and depths, seasonal changes revealed high abundances of PPEs during the winter and summer and low abundances during late winter to early spring and late summer to early autumn. Bathycoccus was most abundant in the winter, and Ostreococcus showed a high abundance during the summer. Another genus, Micromonas, was relatively low in abundance throughout the study period. Taken together with previously suggested blooming periods of phytoplankton, as revealed by chlorophyll a concentrations in Ofunato Bay during spring and late autumn, these results for PPEs suggest that greater phytoplankton blooming has a negative influence on the seasonal occurrences of PPEs in the bay.

  3. Streamlined Membrane Proteome Preparation for Shotgun Proteomics Analysis with Triton X-100 Cloud Point Extraction and Nanodiamond Solid Phase Extraction

    Directory of Open Access Journals (Sweden)

    Minh D. Pham

    2016-05-01

    Full Text Available While mass spectrometry (MS plays a key role in proteomics research, characterization of membrane proteins (MP by MS has been a challenging task because of the presence of a host of interfering chemicals in the hydrophobic protein extraction process, and the low protease digestion efficiency. We report a sample preparation protocol, two-phase separation with Triton X-100, induced by NaCl, with coomassie blue added for visualizing the detergent-rich phase, which streamlines MP preparation for SDS-PAGE analysis of intact MP and shot-gun proteomic analyses. MP solubilized in the detergent-rich milieu were then sequentially extracted and fractionated by surface-oxidized nanodiamond (ND at three pHs. The high MP affinity of ND enabled extensive washes for removal of salts, detergents, lipids, and other impurities to ensure uncompromised ensuing purposes, notably enhanced proteolytic digestion and down-stream mass spectrometric (MS analyses. Starting with a typical membranous cellular lysate fraction harvested with centrifugation/ultracentrifugation, MP purities of 70%, based on number (not weight of proteins identified by MS, was achieved; the weight-based purity can be expected to be much higher.

  4. Analysis of lipid experiments (ALEX: a software framework for analysis of high-resolution shotgun lipidomics data.

    Directory of Open Access Journals (Sweden)

    Peter Husen

    Full Text Available Global lipidomics analysis across large sample sizes produces high-content datasets that require dedicated software tools supporting lipid identification and quantification, efficient data management and lipidome visualization. Here we present a novel software-based platform for streamlined data processing, management and visualization of shotgun lipidomics data acquired using high-resolution Orbitrap mass spectrometry. The platform features the ALEX framework designed for automated identification and export of lipid species intensity directly from proprietary mass spectral data files, and an auxiliary workflow using database exploration tools for integration of sample information, computation of lipid abundance and lipidome visualization. A key feature of the platform is the organization of lipidomics data in "database table format" which provides the user with an unsurpassed flexibility for rapid lipidome navigation using selected features within the dataset. To demonstrate the efficacy of the platform, we present a comparative neurolipidomics study of cerebellum, hippocampus and somatosensory barrel cortex (S1BF from wild-type and knockout mice devoid of the putative lipid phosphate phosphatase PRG-1 (plasticity related gene-1. The presented framework is generic, extendable to processing and integration of other lipidomic data structures, can be interfaced with post-processing protocols supporting statistical testing and multivariate analysis, and can serve as an avenue for disseminating lipidomics data within the scientific community. The ALEX software is available at www.msLipidomics.info.

  5. Analysis of lipid experiments (ALEX): a software framework for analysis of high-resolution shotgun lipidomics data.

    Science.gov (United States)

    Husen, Peter; Tarasov, Kirill; Katafiasz, Maciej; Sokol, Elena; Vogt, Johannes; Baumgart, Jan; Nitsch, Robert; Ekroos, Kim; Ejsing, Christer S

    2013-01-01

    Global lipidomics analysis across large sample sizes produces high-content datasets that require dedicated software tools supporting lipid identification and quantification, efficient data management and lipidome visualization. Here we present a novel software-based platform for streamlined data processing, management and visualization of shotgun lipidomics data acquired using high-resolution Orbitrap mass spectrometry. The platform features the ALEX framework designed for automated identification and export of lipid species intensity directly from proprietary mass spectral data files, and an auxiliary workflow using database exploration tools for integration of sample information, computation of lipid abundance and lipidome visualization. A key feature of the platform is the organization of lipidomics data in "database table format" which provides the user with an unsurpassed flexibility for rapid lipidome navigation using selected features within the dataset. To demonstrate the efficacy of the platform, we present a comparative neurolipidomics study of cerebellum, hippocampus and somatosensory barrel cortex (S1BF) from wild-type and knockout mice devoid of the putative lipid phosphate phosphatase PRG-1 (plasticity related gene-1). The presented framework is generic, extendable to processing and integration of other lipidomic data structures, can be interfaced with post-processing protocols supporting statistical testing and multivariate analysis, and can serve as an avenue for disseminating lipidomics data within the scientific community. The ALEX software is available at www.msLipidomics.info.

  6. Seasonal changes in the communities of photosynthetic picoeukaryotes in Ofunato Bay as revealed by shotgun metagenomic sequencing

    KAUST Repository

    Rashid, Jonaira; Kobiyama, Atsushi; Reza, Md. Shaheed; Yamada, Yuichiro; Ikeda, Yuri; Ikeda, Daisuke; Mizusawa, Nanami; Ikeo, Kazuho; Sato, Shigeru; Ogata, Takehiko; Kudo, Toshiaki; Kaga, Shinnosuke; Watanabe, Shiho; Naiki, Kimiaki; Kaga, Yoshimasa; Mineta, Katsuhiko; Bajic, Vladimir B.; Gojobori, Takashi; Watabe, Shugo

    2018-01-01

    Small photosynthetic eukaryotes play important roles in oceanic food webs in coastal regions. We investigated seasonal changes in the communities of photosynthetic picoeukaryotes (PPEs) of the class Mamiellophyceae, including the genera Bathycoccus, Micromonas and Ostreococcus, in Ofunato Bay, which is located in northeastern Japan and faces the Pacific Ocean. The abundances of PPEs were assessed over a period of one year in 2015 at three sampling stations, KSt. 1 (innermost bay area), KSt. 2 (middle bay area) and KSt. 3 (bay entrance area) at depths of 1 m (KSt. 1, KSt. 2 and KSt. 3), 8 m (KSt. 1) or 10 m (KSt. 2 and KSt. 3) by employing MiSeq shotgun metagenomic sequencing. The total abundances of Bathycoccus, Ostreococcus and Micromonas were in the ranges of 42–49%, 35–49% and 13–17%, respectively. Considering all assayed sampling stations and depths, seasonal changes revealed high abundances of PPEs during the winter and summer and low abundances during late winter to early spring and late summer to early autumn. Bathycoccus was most abundant in the winter, and Ostreococcus showed a high abundance during the summer. Another genus, Micromonas, was relatively low in abundance throughout the study period. Taken together with previously suggested blooming periods of phytoplankton, as revealed by chlorophyll a concentrations in Ofunato Bay during spring and late autumn, these results for PPEs suggest that greater phytoplankton blooming has a negative influence on the seasonal occurrences of PPEs in the bay.

  7. Discovering and differentiating new and emerging clonal populations of Chlamydia trachomatis with a novel shotgun cell culture harvest assay.

    Science.gov (United States)

    Somboonna, Naraporn; Mead, Sally; Liu, Jessica; Dean, Deborah

    2008-03-01

    Chlamydia trachomatis is the leading cause of preventable blindness and bacterial sexually transmitted diseases worldwide. Plaque assays have been used to clonally segregate laboratory-adapted C. trachomatis strains from mixed infections, but no assays have been reported to segregate clones from recent clinical samples. We developed a novel shotgun cell culture harvest assay for this purpose because we found that recent clinical samples do not form plaques. Clones were strain-typed by using outer membrane protein A and 16S rRNA sequences. Surprisingly, ocular trachoma reference strain A/SA-1 contained clones of Chlamydophila abortus. C. abortus primarily infects ruminants and pigs and has never been identified in populations where trachoma is endemic. Three clonal variants of reference strain Ba/Apache-2 were also identified. Our findings reflect the importance of clonal isolation in identifying constituents of mixed infections containing new or emerging strains and of viable clones for research to more fully understand the dynamics of in vivo strain-mixing, evolution, and disease pathogenesis.

  8. Nonoperative Management of Multiple Penetrating Cardiac and Colon Wounds from a Shotgun: A Case Report and Literature Review

    Directory of Open Access Journals (Sweden)

    Paula M. Jaramillo

    2018-01-01

    Full Text Available Introduction. Surgery for cardiac trauma is considered fatal and for wounds of the colon by associated sepsis is normally considered; however, conservative management of many traumatic lesions of different injured organs has progressed over the years. Presentation of the Case. A 65-year-old male patient presented with multiple shotgun wounds on the left upper limb, thorax, and abdomen. On evaluation, he was hemodynamically stable with normal sinus rhythm and normal blood pressure, no dyspnea, or abdominal pain. Computed tomography (CT scan of the chest shows hematoma around the aorta without injury to the blood vessel wall with an intramyocardial projectile without pericardial effusion. CT scan of the abdomen showed pellets in the transverse colon and descending colon endoluminal without extravasation of contrast medium or intra-abdominal fluid. The patient remains hemodynamically stable, and nonsurgical procedure was established. Discussion. Patients with asymptomatic intramyocardial projectiles can be safely managed without surgery. Nonsurgical management is only possible in asymptomatic patients with trauma of the colon through close surveillance and with very selective patients since standard management is surgery. Conclusion. Nonsurgical management of cardiac trauma, as well as colon penetrating trauma, can be performed in carefully selected patients with proper clinical follow-up, imaging, and laboratory studies.

  9. Initial characterization of the large genome of the salamander Ambystoma mexicanum using shotgun and laser capture chromosome sequencing.

    Science.gov (United States)

    Keinath, Melissa C; Timoshevskiy, Vladimir A; Timoshevskaya, Nataliya Y; Tsonis, Panagiotis A; Voss, S Randal; Smith, Jeramiah J

    2015-11-10

    Vertebrates exhibit substantial diversity in genome size, and some of the largest genomes exist in species that uniquely inform diverse areas of basic and biomedical research. For example, the salamander Ambystoma mexicanum (the Mexican axolotl) is a model organism for studies of regeneration, development and genome evolution, yet its genome is ~10× larger than the human genome. As part of a hierarchical approach toward improving genome resources for the species, we generated 600 Gb of shotgun sequence data and developed methods for sequencing individual laser-captured chromosomes. Based on these data, we estimate that the A. mexicanum genome is ~32 Gb. Notably, as much as 19 Gb of the A. mexicanum genome can potentially be considered single copy, which presumably reflects the evolutionary diversification of mobile elements that accumulated during an ancient episode of genome expansion. Chromosome-targeted sequencing permitted the development of assemblies within the constraints of modern computational platforms, allowed us to place 2062 genes on the two smallest A. mexicanum chromosomes and resolves key events in the history of vertebrate genome evolution. Our analyses show that the capture and sequencing of individual chromosomes is likely to provide valuable information for the systematic sequencing, assembly and scaffolding of large genomes.

  10. Shotgun proteomics deciphered age/division of labor-related functional specification of three honeybee (Apis mellifera L.) exocrine glands.

    Science.gov (United States)

    Fujita, Toshiyuki; Kozuka-Hata, Hiroko; Hori, Yutaro; Takeuchi, Jun; Kubo, Takeo; Oyama, Masaaki

    2018-01-01

    The honeybee (Apis mellifera L.) uses various chemical signals produced by the worker exocrine glands to maintain the functioning of its colony. The roles of worker postcerebral glands (PcGs), thoracic glands (TGs), and mandibular glands (MGs) and the functional changes they undergo according to the division of labor from nursing to foraging are not as well studied. To comprehensively characterize the molecular roles of these glands in workers and their changes according to the division of labor of workers, we analyzed the proteomes of PcGs, TGs, and MGs from nurse bees and foragers using shotgun proteomics technology. We identified approximately 2000 proteins from each of the nurse bee or forager glands and highlighted the features of these glands at the molecular level by semiquantitative enrichment analyses of frequently detected, gland-selective, and labor-selective proteins. First, we found the high potential to produce lipids in PcGs and MGs, suggesting their relation to pheromone production. Second, we also found the proton pumps abundant in TGs and propose some transporters possibly related to the saliva production. Finally, our data unveiled candidate enzymes involved in labor-dependent acid production in MGs.

  11. Immune indexes of larks from desert and temperate regions show weak associations with life history but stronger links to environmental variation in microbial abundance

    NARCIS (Netherlands)

    Horrocks, N.P.C.; Hegemann, A.; Matson, K.D.; Hine, K.; Jaquier, S.; Shobrak, M.; Williams, J.B.; Tinbergen, J.M.; Tieleman, B.I.

    2012-01-01

    Immune defense may vary as a result of trade-offs with other life-history traits or in parallel with variation in antigen levels in the environment. We studied lark species (Alaudidae) in the Arabian Desert and temperate Netherlands to test opposing predictions from these two hypotheses. Based on

  12. Immune Indexes of Larks from Desert and Temperate Regions Show Weak Associations with Life History but Stronger Links to Environmental Variation in Microbial Abundance

    NARCIS (Netherlands)

    Horrocks, Nicholas P. C.; Hegemann, Arne; Matson, Kevin D.; Hine, Kathryn; Jaquier, Sophie; Shobrak, Mohammed; Williams, Joseph B.; Tinbergen, Joost M.; Tieleman, B. Irene

    2012-01-01

    Immune defense may vary as a result of trade-offs with other life-history traits or in parallel with variation in antigen levels in the environment. We studied lark species (Alaudidae) in the Arabian Desert and temperate Netherlands to test opposing predictions from these two hypotheses. Based on

  13. P-MartCancer–Interactive Online Software to Enable Analysis of Shotgun Cancer Proteomic Datasets

    Energy Technology Data Exchange (ETDEWEB)

    Webb-Robertson, Bobbie-Jo M.; Bramer, Lisa M.; Jensen, Jeffrey L.; Kobold, Markus A.; Stratton, Kelly G.; White, Amanda M.; Rodland, Karin D.

    2017-10-31

    P-MartCancer is a new interactive web-based software environment that enables biomedical and biological scientists to perform in-depth analyses of global proteomics data without requiring direct interaction with the data or with statistical software. P-MartCancer offers a series of statistical modules associated with quality assessment, peptide and protein statistics, protein quantification and exploratory data analyses driven by the user via customized workflows and interactive visualization. Currently, P-MartCancer offers access to multiple cancer proteomic datasets generated through the Clinical Proteomics Tumor Analysis Consortium (CPTAC) at the peptide, gene and protein levels. P-MartCancer is deployed using Azure technologies (http://pmart.labworks.org/cptac.html), the web-service is alternatively available via Docker Hub (https://hub.docker.com/r/pnnl/pmart-web/) and many statistical functions can be utilized directly from an R package available on GitHub (https://github.com/pmartR).

  14. P-MartCancer-Interactive Online Software to Enable Analysis of Shotgun Cancer Proteomic Datasets.

    Science.gov (United States)

    Webb-Robertson, Bobbie-Jo M; Bramer, Lisa M; Jensen, Jeffrey L; Kobold, Markus A; Stratton, Kelly G; White, Amanda M; Rodland, Karin D

    2017-11-01

    P-MartCancer is an interactive web-based software environment that enables statistical analyses of peptide or protein data, quantitated from mass spectrometry-based global proteomics experiments, without requiring in-depth knowledge of statistical programming. P-MartCancer offers a series of statistical modules associated with quality assessment, peptide and protein statistics, protein quantification, and exploratory data analyses driven by the user via customized workflows and interactive visualization. Currently, P-MartCancer offers access and the capability to analyze multiple cancer proteomic datasets generated through the Clinical Proteomics Tumor Analysis Consortium at the peptide, gene, and protein levels. P-MartCancer is deployed as a web service (https://pmart.labworks.org/cptac.html), alternatively available via Docker Hub (https://hub.docker.com/r/pnnl/pmart-web/). Cancer Res; 77(21); e47-50. ©2017 AACR . ©2017 American Association for Cancer Research.

  15. Evolution of Microsatellite Loci of Tropical and Temperate Anguilla Eels

    Directory of Open Access Journals (Sweden)

    Mei-Chen Tseng

    2012-04-01

    Full Text Available Anguilla eels are divided into temperate and tropical eels, based on their major distributions. The present study collected two temperate eels, Anguilla japonica and Anguilla anguilla, and two tropical eels, Anguilla marmorata and Anguilla bicolor pacifica, to examine two questions: do temperate and tropical Anguilla eels have different genetic polymorphic patterns?; and do temperate Anguilla japonica and Anguilla anguilla have a closer relationship to each other than to tropical eels? In total, 274 sequences were cloned and sequenced from six conserved microsatellite loci to examine polymorphic patterns of these four catadromous eels. Different mutational events, including substitutions, and repeat-unit deletions and insertions, appeared in major regions, while different point mutations were observed in flanking regions. The results implied that parallel patterns of microsatellite sequences occurred within both tropical and temperate freshwater eels. Consensus flanking sequences of six homologous loci from each of the four species were constructed. Genetic distances ranged from 0.044 (Anguilla bicolor pacifica vs. Anguilla marmorata to 0.061 (Anguilla marmorata vs. Anguilla anguilla. The tree topology suggests the hypothesis of Anguilla japonica and Anguilla anguilla being a sister group must be rejected.

  16. Effects of tempering on internal friction of carbon steels

    International Nuclear Information System (INIS)

    Hoyos, J.J.; Ghilarducci, A.A.; Salva, H.R.; Chaves, C.A.; Velez, J.M.

    2011-01-01

    Research highlights: → Time tempering dependent microstructure of two steels is studied by internal friction. → Internal friction indicates the interactions of dislocations with carbon and carbides. → Internal friction detects the first stage of tempering. → Precipitation hardening is detected by the decrease in the background. - Abstract: Two steels containing 0.626 and 0.71 wt.% carbon have been studied to determine the effects of tempering on the microstructure and the internal friction. The steels were annealed at 1093 K, quenched into water and tempered for 60 min at 423 K, 573 K and 723 K. The increase of the tempering time diminishes the martensite tetragonality due to the redistribution of carbon atoms from octahedrical interstitial sites to dislocations. Internal friction spectrum is decomposed into five peaks and an exponential background, which are attributed to the carbide precipitation and the dislocation relaxation process. Simultaneous presence of peaks P1 and P2 indicates the interaction of dislocations with the segregated carbon and carbide precipitate.

  17. Early stages of formation and dispersal of the temperate flora in the Boreal region

    International Nuclear Information System (INIS)

    Budantsev, L.Y.

    1992-01-01

    The thesis of this review is that the composition of a flora can be understood only as a process, or separate stage, in the context of migration in time and space of various floristic assemblages and their isolation, as induced by transformation of continental and ocean shapes, changes in climate, and the environment as a whole. Thus the formation of geofloras of the past was influenced by gradually changing environments that determined the spread, patterning, and spatial differentiation of floras and their evolution. Parallel to the more commonly-seen names of eras-Paleozoic, Mesozoic, and Cenozoic-we can speak of the Paleophytic, Mesophytic, and Cenophytic eras. Eras defined in these two ways (by faunistic or by floristic criteria) do not completely coincide. Generally, changes in the flora have, necessarily, preceded changes in the fauna. It is the Cenophytic with which this review is mostly concerned, the era of Angiosperm dominance. The movement of early subtropical and warm temperate floras in the Early Cenophytic, followed by temperate or even boreal floras, as the climate changes, is traced in detail

  18. Shotgun Proteomics of Aspergillus niger Microsomes upon d-Xylose Induction▿ †

    Science.gov (United States)

    de Oliveira, José Miguel P. Ferreira; van Passel, Mark W. J.; Schaap, Peter J.; de Graaff, Leo H.

    2010-01-01

    Protein secretion plays an eminent role in cell maintenance and adaptation to the extracellular environment of microorganisms. Although protein secretion is an extremely efficient process in filamentous fungi, the mechanisms underlying protein secretion have remained largely uncharacterized in these organisms. In this study, we analyzed the effects of the d-xylose induction of cellulase and hemicellulase enzyme secretion on the protein composition of secretory organelles in Aspergillus niger. We aimed to systematically identify the components involved in the secretion of these enzymes via mass spectrometry of enriched subcellular microsomal fractions. Under each condition, fractions enriched for secretory organelles were processed for tandem mass spectrometry, resulting in the identification of peptides that originate from 1,081 proteins, 254 of which—many of them hypothetical proteins—were predicted to play direct roles in the secretory pathway. d-Xylose induction led to an increase in specific small GTPases known to be associated with polarized growth, exocytosis, and endocytosis. Moreover, the endoplasmic-reticulum-associated degradation (ERAD) components Cdc48 and all 14 of the 20S proteasomal subunits were recruited to the secretory organelles. In conclusion, induction of extracellular enzymes results in specific changes in the secretory subproteome of A. niger, and the most prominent change found in this study was the recruitment of the 20S proteasomal subunits to the secretory organelles. PMID:20453123

  19. Shotgun proteomics of Aspergillus niger microsomes upon D-xylose induction.

    Science.gov (United States)

    Ferreira de Oliveira, José Miguel P; van Passel, Mark W J; Schaap, Peter J; de Graaff, Leo H

    2010-07-01

    Protein secretion plays an eminent role in cell maintenance and adaptation to the extracellular environment of microorganisms. Although protein secretion is an extremely efficient process in filamentous fungi, the mechanisms underlying protein secretion have remained largely uncharacterized in these organisms. In this study, we analyzed the effects of the d-xylose induction of cellulase and hemicellulase enzyme secretion on the protein composition of secretory organelles in Aspergillus niger. We aimed to systematically identify the components involved in the secretion of these enzymes via mass spectrometry of enriched subcellular microsomal fractions. Under each condition, fractions enriched for secretory organelles were processed for tandem mass spectrometry, resulting in the identification of peptides that originate from 1,081 proteins, 254 of which-many of them hypothetical proteins-were predicted to play direct roles in the secretory pathway. d-Xylose induction led to an increase in specific small GTPases known to be associated with polarized growth, exocytosis, and endocytosis. Moreover, the endoplasmic-reticulum-associated degradation (ERAD) components Cdc48 and all 14 of the 20S proteasomal subunits were recruited to the secretory organelles. In conclusion, induction of extracellular enzymes results in specific changes in the secretory subproteome of A. niger, and the most prominent change found in this study was the recruitment of the 20S proteasomal subunits to the secretory organelles.

  20. Radiation processing of temperate fruits of Kashmir valley

    International Nuclear Information System (INIS)

    Hussain, Peerzada R.; Meena, Raghuveer S.; Dar, Mohd A.; Wani, Ali M.

    2011-01-01

    Kashmir valley is famous for its temperate horticulture. Main temperate fruits grown commercially in the valley include apple, pear, peach, plum, cherry, strawberry and apricot. These fruits being perishable and susceptible to microbial spoilage, have a short shelf-life. The short shelf-life in an impediment in their transportation and marketing and results in huge losses. Study was carried out at NRL, Srinagar to investigate the effect of gamma irradiation on the keeping quality of most of these fruits. The effect of gamma irradiation alone and in combination with other techniques like controlled low temperature storage, edible polysaccharide coating and calcium chloride treatment was studied in detail. The results revealed that there is a great potential for the use of radiation in extending the storage life of most of the temperate fruits produced in the valley of Kashmir. (author)

  1. Tempered stable distributions stochastic models for multiscale processes

    CERN Document Server

    Grabchak, Michael

    2015-01-01

    This brief is concerned with tempered stable distributions and their associated Levy processes. It is a good text for researchers interested in learning about tempered stable distributions.  A tempered stable distribution is one which takes a stable distribution and modifies its tails to make them lighter. The motivation for this class comes from the fact that infinite variance stable distributions appear to provide a good fit to data in a variety of situations, but the extremely heavy tails of these models are not realistic for most real world applications. The idea of using distributions that modify the tails of stable models to make them lighter seems to have originated in the influential paper of Mantegna and Stanley (1994). Since then, these distributions have been extended and generalized in a variety of ways. They have been applied to a wide variety of areas including mathematical finance, biostatistics,computer science, and physics.

  2. Resistance to small plastic strains during martensite tempering under tension

    Energy Technology Data Exchange (ETDEWEB)

    Zabil' skij, V.V.; Sarrak, V.I. (AN SSSR, Sverdlovsk. Inst. Fiziki Metallov)

    1982-11-01

    The mechanism of plastic deformation of martensite of a series of hardened steels (N18, 20KhG, 50KhFA and others) during tempering under tension and the role of residual internal microstresses and phase transformations are studied. It is shown that martensite low resistance to small plastic deformations during tempering under tension which is usually associated with phase transformations depends as well on the level of residual internal microstresses in the martensite structure. The decrease of resistance to deformation in the course of the decomposition of a solid solution is due to weakening of martensitic matrix because of carbon departure from the solid solution and carbide coarsening. An assumption is made that martensite plastic deformation during tempering under tension is realized at the expense of the directed microplastic deformation in the regions of higher concentration of internal stresses.

  3. Unbiased RNA Shotgun Metagenomics in Social and Solitary Wild Bees Detects Associations with Eukaryote Parasites and New Viruses.

    Directory of Open Access Journals (Sweden)

    Karel Schoonvaere

    Full Text Available The diversity of eukaryote organisms and viruses associated with wild bees remains poorly characterized in contrast to the well-documented pathosphere of the western honey bee, Apis mellifera. Using a deliberate RNA shotgun metagenomic sequencing strategy in combination with a dedicated bioinformatics workflow, we identified the (micro-organisms and viruses associated with two bumble bee hosts, Bombus terrestris and Bombus pascuorum, and two solitary bee hosts, Osmia cornuta and Andrena vaga. Ion Torrent semiconductor sequencing generated approximately 3.8 million high quality reads. The most significant eukaryote associations were two protozoan, Apicystis bombi and Crithidia bombi, and one nematode parasite Sphaerularia bombi in bumble bees. The trypanosome protozoan C. bombi was also found in the solitary bee O. cornuta. Next to the identification of three honey bee viruses Black queen cell virus, Sacbrood virus and Varroa destructor virus-1 and four plant viruses, we describe two novel RNA viruses Scaldis River bee virus (SRBV and Ganda bee virus (GABV based on their partial genomic sequences. The novel viruses belong to the class of negative-sense RNA viruses, SRBV is related to the order Mononegavirales whereas GABV is related to the family Bunyaviridae. The potential biological role of both viruses in bees is discussed in the context of recent advances in the field of arthropod viruses. Further, fragmentary sequence evidence for other undescribed viruses is presented, among which a nudivirus in O. cornuta and an unclassified virus related to Chronic bee paralysis virus in B. terrestris. Our findings extend the current knowledge of wild bee parasites in general and addsto the growing evidence of unexplored arthropod viruses in valuable insects.

  4. Characterization of Foodborne Strains of Staphylococcus aureus by Shotgun Proteomics: Functional Networks, Virulence Factors and Species-Specific Peptide Biomarkers

    Science.gov (United States)

    Carrera, Mónica; Böhme, Karola; Gallardo, José M.; Barros-Velázquez, Jorge; Cañas, Benito; Calo-Mata, Pilar

    2017-01-01

    In the present work, we applied a shotgun proteomics approach for the fast and easy characterization of 20 different foodborne strains of Staphylococcus aureus (S. aureus), one of the most recognized foodborne pathogenic bacteria. A total of 644 non-redundant proteins were identified and analyzed via an easy and rapid protein sample preparation procedure. The results allowed the differentiation of several proteome datasets from the different strains (common, accessory, and unique datasets), which were used to determine relevant functional pathways and differentiate the strains into different Euclidean hierarchical clusters. Moreover, a predicted protein-protein interaction network of the foodborne S. aureus strains was created. The whole confidence network contains 77 nodes and 769 interactions. Most of the identified proteins were surface-associated proteins that were related to pathways and networks of energy, lipid metabolism and virulence. Twenty-seven virulence factors were identified, and most of them corresponded to autolysins, N-acetylmuramoyl-L-alanine amidases, phenol-soluble modulins, extracellular fibrinogen-binding proteins and virulence factor EsxA. Potential species-specific peptide biomarkers were screened. Twenty-one species-specific peptide biomarkers, belonging to eight different proteins (nickel-ABC transporter, N-acetylmuramoyl-L-alanine amidase, autolysin, clumping factor A, gram-positive signal peptide YSIRK, cysteine protease/staphopain, transcriptional regulator MarR, and transcriptional regulator Sar-A), were proposed to identify S. aureus. These results constitute the first major dataset of peptides and proteins of foodborne S. aureus strains. This repository may be useful for further studies, for the development of new therapeutic treatments for S. aureus food intoxications and for microbial source-tracking in foodstuffs. PMID:29312172

  5. Prediction of the neuropeptidomes of members of the Astacidea (Crustacea, Decapoda) using publicly accessible transcriptome shotgun assembly (TSA) sequence data.

    Science.gov (United States)

    Christie, Andrew E; Chi, Megan

    2015-12-01

    The decapod infraorder Astacidea is comprised of clawed lobsters and freshwater crayfish. Due to their economic importance and their use as models for investigating neurochemical signaling, much work has focused on elucidating their neurochemistry, particularly their peptidergic systems. Interestingly, no astacidean has been the subject of large-scale peptidomic analysis via in silico transcriptome mining, this despite growing transcriptomic resources for members of this taxon. Here, the publicly accessible astacidean transcriptome shotgun assembly data were mined for putative peptide-encoding transcripts; these sequences were used to predict the structures of mature neuropeptides. One hundred seventy-six distinct peptides were predicted for Procambarus clarkii, including isoforms of adipokinetic hormone-corazonin-like peptide (ACP), allatostatin A (AST-A), allatostatin B, allatostatin C (AST-C) bursicon α, bursicon β, CCHamide, crustacean hyperglycemic hormone (CHH)/ion transport peptide (ITP), diuretic hormone 31 (DH31), eclosion hormone (EH), FMRFamide-like peptide, GSEFLamide, intocin, leucokinin, neuroparsin, neuropeptide F, pigment dispersing hormone, pyrokinin, RYamide, short neuropeptide F (sNPF), SIFamide, sulfakinin and tachykinin-related peptide (TRP). Forty-six distinct peptides, including isoforms of AST-A, AST-C, bursicon α, CCHamide, CHH/ITP, DH31, EH, intocin, myosuppressin, neuroparsin, red pigment concentrating hormone, sNPF and TRP, were predicted for Pontastacus leptodactylus, with a bursicon β and a neuroparsin predicted for Cherax quadricarinatus. The identification of ACP is the first from a decapod, while the predictions of CCHamide, EH, GSEFLamide, intocin, neuroparsin and RYamide are firsts for the Astacidea. Collectively, these data greatly expand the catalog of known astacidean neuropeptides and provide a foundation for functional studies of peptidergic signaling in members of this decapod infraorder. Copyright © 2015 Elsevier Inc

  6. Unbiased RNA Shotgun Metagenomics in Social and Solitary Wild Bees Detects Associations with Eukaryote Parasites and New Viruses.

    Science.gov (United States)

    Schoonvaere, Karel; De Smet, Lina; Smagghe, Guy; Vierstraete, Andy; Braeckman, Bart P; de Graaf, Dirk C

    2016-01-01

    The diversity of eukaryote organisms and viruses associated with wild bees remains poorly characterized in contrast to the well-documented pathosphere of the western honey bee, Apis mellifera. Using a deliberate RNA shotgun metagenomic sequencing strategy in combination with a dedicated bioinformatics workflow, we identified the (micro-)organisms and viruses associated with two bumble bee hosts, Bombus terrestris and Bombus pascuorum, and two solitary bee hosts, Osmia cornuta and Andrena vaga. Ion Torrent semiconductor sequencing generated approximately 3.8 million high quality reads. The most significant eukaryote associations were two protozoan, Apicystis bombi and Crithidia bombi, and one nematode parasite Sphaerularia bombi in bumble bees. The trypanosome protozoan C. bombi was also found in the solitary bee O. cornuta. Next to the identification of three honey bee viruses Black queen cell virus, Sacbrood virus and Varroa destructor virus-1 and four plant viruses, we describe two novel RNA viruses Scaldis River bee virus (SRBV) and Ganda bee virus (GABV) based on their partial genomic sequences. The novel viruses belong to the class of negative-sense RNA viruses, SRBV is related to the order Mononegavirales whereas GABV is related to the family Bunyaviridae. The potential biological role of both viruses in bees is discussed in the context of recent advances in the field of arthropod viruses. Further, fragmentary sequence evidence for other undescribed viruses is presented, among which a nudivirus in O. cornuta and an unclassified virus related to Chronic bee paralysis virus in B. terrestris. Our findings extend the current knowledge of wild bee parasites in general and addsto the growing evidence of unexplored arthropod viruses in valuable insects.

  7. Ultra low carbon bainitic (ULCB) steels after quenching and tempering

    International Nuclear Information System (INIS)

    Lis, A.K.; Lis, J.; Kolan, C.; Jeziorski, L.

    1998-01-01

    The mechanical and Charpy V impact strength properties of new advanced ultra low carbon bainitic (ULBC) steels after water quenching and tempering (WQT) have been investigated. Their chemical compositions are given. The nine continuous cooling transformation diagrams (CCT) of the new ULCB steel grades have been established. The CCT diagrams for ULCB N i steels containing 9% Ni - grade 10N9 and 5% Ni - grade HN5MVNb are given. The comparison between CCT diagrams of 3.5%Ni + 1.5%Cu containing steels grade HSLA 100 and HN3MCu is shown. The effect of the increase in carbon and titanium contents in the chemical composition of ULCB M n steels 04G3Ti, 06G3Ti and 09G3Ti on the kinetics of phase transformations during continuous cooling is presented by the shifting CCT diagrams. The Charpy V impact strength and brittle fracture occurence curves are shown. The effect of tempering temperature on tensile properties of WQT HN3MCu steel is shown and Charpy V impact strength curves after different tempering conditions are shown. The optimum tempering temperatures region of HN3MCu steel for high Charpy V impact toughness at law temperatures - 80 o C(193 K) and -120 o C(153 K) is estimated. The effect of tempering temperature on mechanical properties of HN5MVNb steel is given. The low temperature impact Charpy V toughness of HN5MVNb steel is shown. The optimum range of tempering temperature during 1 hour for high toughness of WQT HN5MVNb steel is given. HN3MCu and HN5MVNb steels after WQT have high yield strength YS≥690 MPa and high Charpy V impact toughness KV≥80 J at -100 o C (173K) and KCV≥50 J/cm 2 at - 120 o C (153K) so they may be used for cryogenic applications

  8. Baseline and stress-induced levels of corticosterone in male and female Afrotropical and European temperate stonechats during breeding.

    Science.gov (United States)

    Apfelbeck, Beate; Helm, Barbara; Illera, Juan Carlos; Mortega, Kim G; Smiddy, Patrick; Evans, Neil P

    2017-05-22

    demanding activities in males and females and reflects investment into reproduction. Low parental workload was associated with lower post-capture (baseline) CORT as expected for a slow pace of life in tropical species. On a finer resolution, however, this tropical-temperate contrast did not generally hold. Post-capture (baseline) CORT was higher during mating stages in particular in tropical males, possibly to support the energetic needs of mate-guarding. Counter to predictions based on life history theory, our data do not confirm the hypothesis that long-lived tropical populations have higher stress-induced CORT concentrations than short-lived temperate populations. Instead, in the predator-rich tropical environments of African stonechats, a dampened stress response during parental stages may increase survival probabilities of young. Overall our data further support an association between life history and baseline CORT, but challenge the role of stress-induced CORT as a mediator of tropical-temperate variation in life history.

  9. Uptake and Persistence of Homologous and Heterologous Zooxanthellae in the Temperate Sea Anemone Cereus pedunculatus (Pennant).

    Science.gov (United States)

    Davy, S K; Lucas, I A N; Turner, J R

    1997-04-01

    The uptake and persistence of symbiotic dinoflagellates (zooxanthellae) were measured in the temperate sea anemone Cereus pedunculatus (Pennant). Aposymbiotic specimens of C. pedunculatus were inoculated with zooxanthellae freshly isolated from a range of temperate and subtropical Anthozoa. Each inoculate consisted of zooxanthellae from a single host species and was either homologous (zooxanthellae from a host of the same species as the one being inoculated) or heterologous (from a host of a different species than the one being inoculated). The densities of zooxanthellae in host tissues were determined at regular intervals. C. pedunculatus took up homologous and heterologous zooxanthellae to similar degrees, except for zooxanthellae from the temperate Anthopleura ballii, which were taken up to a lesser extent. The densities of all zooxanthellae declined between 4 hours and 4 days after uptake, indicating that zooxanthellae were expelled, digested, or both during this period. The densities of all zooxanthellae increased between 2 and 8 weeks after inoculation, indicating zooxanthella growth. Over the entire 8-week period after uptake, densities of homologous zooxanthellae were always greater than those of heterologous zooxanthellae. Between 8 and 36 weeks after infection, densities of homologous zooxanthellae declined markedly and densities of some heterologous zooxanthellae increased further, resulting in homologous and heterologous zooxanthella densities being the same at 36 weeks. These densities were the same as those in naturally infected C. pedunculatus of similar size. The results suggest that zooxanthellae from a range of host species and environments can establish symbioses with C. pedunculatus and that, over long periods under laboratory conditions, heterologous zooxanthellae may populate C. pedunculatus to the same extent as homologous zooxanthellae.

  10. First Evidence of an Important Organic Matter Trophic Pathway between Temperate Corals and Pelagic Microbial Communities.

    Directory of Open Access Journals (Sweden)

    J A Fonvielle

    Full Text Available Mucus, i.e., particulate and dissolved organic matter (POM, DOM released by corals, acts as an important energy carrier in tropical ecosystems, but little is known on its ecological role in temperate environments. This study assessed POM and DOM production by the temperate coral Cladocora caespitosa under different environmental conditions. The subsequent enzymatic degradation, growth of prokaryotes and virus-like particles (VLPs as well as changes in the structure of the prokaryotic communities were also monitored. C. caespitosa produced an important quantity of mucus, which varied according to the environmental conditions (from 37.8 to 67.75 nmol carbon h-1 cm-2, but remained higher or comparable to productions observed in tropical corals. It has an important nutritional value, as highlighted by the high content in dissolved nitrogen (50% to 90% of the organic matter released. Organic matter was rapidly degraded by prokaryotes' enzymatic activities, and due to its nitrogen content, aminopeptidase activity was 500 fold higher than the α-glucosidase activity. Prokaryotes, as well as VLPs, presented a rapid growth in the mucus, with prokaryote production rates as high as 0.31 μg h-1 L-1. Changes in bacterial and archaeal communities were observed in the ageing mucus and between mucus and the water column, suggesting a clear impact of mucus on microorganism diversity. Overall, our results show that the organic matter released by temperate corals, such as C. caespitosa, which can form reef structures in the Mediterranean Sea, stimulates microbial activity and thereby functions as a significant carbon and nitrogen supplier to the microbial loop.

  11. SWFSC/MMTD/CCE: Leatherback Use of Temperate Habitat (LUTH) 2008

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Leatherback Use of Temperate Habitat (LUTH) survey is an ecosystem assessment of temperate foraging habitats of endangered leatherback turtles off the coast of...

  12. Direct dating and identity of fiber temper in pre-contact Bushman (Masarwa) pottery

    CSIR Research Space (South Africa)

    Bollong, CA

    1993-01-01

    Full Text Available , ashed grass, or absorbed blood. Visual characteristics rule out the possibility of animal dung temper. Blood and fat residues absorbed by grass temper could be the combined cause of anomalous Q (13) C and high P values....

  13. Global analysis of threat status reveals higher extinction risk in tropical than in temperate bird sister species

    Directory of Open Access Journals (Sweden)

    Reif Jiří

    2016-06-01

    Full Text Available Given increasing pressures upon biodiversity, identification of species’ traits related to elevated extinction risk is useful for more efficient allocation of limited resources for nature conservation. Despite its need, such a global analysis was lacking in the case of birds. Therefore, we performed this exercise for avian sister species using information about their global extinction risk from IUCN Red List. We focused on 113 pairs of sister species, each containing a threatened and an unthreatened species to factor out the effects of common evolutionary history on the revealed relationship. We collected data on five traits with expected relationships to species’ extinction risk based on previous studies performed at regional or national levels: breeding habitat (recognizing forest, grassland, wetland and oceanic species, latitudinal range position (temperate and tropics species, migration strategy (migratory and resident species, diet (carnivorous, insectivorous, herbivorous and omnivorous species and body mass. We related the extinction risk using IUCN threat level categories to species’ traits using generalised linear mixed effects models expecting lower risk for forest, temperate, omnivorous and smaller-bodied species. Our expectation was confirmed only in the case of latitudinal range position, as we revealed higher threat level for tropical than for temperate species. This relationship was robust to different methods of threat level expression and cannot be explained by a simple association of high bird species richness with the tropical zone. Instead, it seems that tropical species are more threatened because of their intrinsic characteristics such as slow life histories, adaptations to stable environments and small geographic ranges. These characteristics are obviously disadvantageous in conditions of current human-induced environmental perturbations. Moreover, given the absence of habitat effects, our study indicates that such

  14. Elucidation of taste- and odor-producing bacteria and toxigenic cyanobacteria in a Midwestern drinking water supply reservoir by shotgun metagenomics analysis

    Science.gov (United States)

    Otten, Timothy; Graham, Jennifer L.; Harris, Theodore D.; Dreher, Theo

    2016-01-01

    While commonplace in clinical settings, DNA-based assays for identification or enumeration of drinking water pathogens and other biological contaminants remain widely unadopted by the monitoring community. In this study, shotgun metagenomics was used to identify taste-and-odor producers and toxin-producing cyanobacteria over a 2-year period in a drinking water reservoir. The sequencing data implicated several cyanobacteria, including Anabaena spp.,Microcystis spp., and an unresolved member of the order Oscillatoriales as the likely principal producers of geosmin, microcystin, and 2-methylisoborneol (MIB), respectively. To further demonstrate this, quantitative PCR (qPCR) assays targeting geosmin-producing Anabaena and microcystin-producing Microcystis were utilized, and these data were fitted using generalized linear models and compared with routine monitoring data, including microscopic cell counts, sonde-based physicochemical analyses, and assays of all inorganic and organic nitrogen and phosphorus forms and fractions. The qPCR assays explained the greatest variation in observed geosmin (adjusted R2 = 0.71) and microcystin (adjusted R2 = 0.84) concentrations over the study period, highlighting their potential for routine monitoring applications. The origin of the monoterpene cyclase required for MIB biosynthesis was putatively linked to a periphytic cyanobacterial mat attached to the concrete drinking water inflow structure. We conclude that shotgun metagenomics can be used to identify microbial agents involved in water quality deterioration and to guide PCR assay selection or design for routine monitoring purposes. Finally, we offer estimates of microbial diversity and metagenomic coverage of our data sets for reference to others wishing to apply shotgun metagenomics to other lacustrine systems.

  15. Elucidation of Taste- and Odor-Producing Bacteria and Toxigenic Cyanobacteria in a Midwestern Drinking Water Supply Reservoir by Shotgun Metagenomic Analysis.

    Science.gov (United States)

    Otten, Timothy G; Graham, Jennifer L; Harris, Theodore D; Dreher, Theo W

    2016-09-01

    While commonplace in clinical settings, DNA-based assays for identification or enumeration of drinking water pathogens and other biological contaminants remain widely unadopted by the monitoring community. In this study, shotgun metagenomics was used to identify taste-and-odor producers and toxin-producing cyanobacteria over a 2-year period in a drinking water reservoir. The sequencing data implicated several cyanobacteria, including Anabaena spp., Microcystis spp., and an unresolved member of the order Oscillatoriales as the likely principal producers of geosmin, microcystin, and 2-methylisoborneol (MIB), respectively. To further demonstrate this, quantitative PCR (qPCR) assays targeting geosmin-producing Anabaena and microcystin-producing Microcystis were utilized, and these data were fitted using generalized linear models and compared with routine monitoring data, including microscopic cell counts, sonde-based physicochemical analyses, and assays of all inorganic and organic nitrogen and phosphorus forms and fractions. The qPCR assays explained the greatest variation in observed geosmin (adjusted R(2) = 0.71) and microcystin (adjusted R(2) = 0.84) concentrations over the study period, highlighting their potential for routine monitoring applications. The origin of the monoterpene cyclase required for MIB biosynthesis was putatively linked to a periphytic cyanobacterial mat attached to the concrete drinking water inflow structure. We conclude that shotgun metagenomics can be used to identify microbial agents involved in water quality deterioration and to guide PCR assay selection or design for routine monitoring purposes. Finally, we offer estimates of microbial diversity and metagenomic coverage of our data sets for reference to others wishing to apply shotgun metagenomics to other lacustrine systems. Cyanobacterial toxins and microbial taste-and-odor compounds are a growing concern for drinking water utilities reliant upon surface water resources. Specific

  16. Tempered fractional time series model for turbulence in geophysical flows

    Science.gov (United States)

    Meerschaert, Mark M.; Sabzikar, Farzad; Phanikumar, Mantha S.; Zeleke, Aklilu

    2014-09-01

    We propose a new time series model for velocity data in turbulent flows. The new model employs tempered fractional calculus to extend the classical 5/3 spectral model of Kolmogorov. Application to wind speed and water velocity in a large lake are presented, to demonstrate the practical utility of the model.

  17. Tempered fractional time series model for turbulence in geophysical flows

    International Nuclear Information System (INIS)

    Meerschaert, Mark M; Sabzikar, Farzad; Phanikumar, Mantha S; Zeleke, Aklilu

    2014-01-01

    We propose a new time series model for velocity data in turbulent flows. The new model employs tempered fractional calculus to extend the classical 5/3 spectral model of Kolmogorov. Application to wind speed and water velocity in a large lake are presented, to demonstrate the practical utility of the model. (paper)

  18. Joint measurement of risk aversion, prudence, and temperance

    NARCIS (Netherlands)

    Ebert, S.; Wiesen, D.

    Risk aversion—but also the higher-order risk preferences of prudence and temperance—are fundamental concepts in the study of economic decision making. We propose a method to jointly measure the intensity of risk aversion, prudence, and temperance. Our theoretical approach is to define risk

  19. The Fracture Process of Tempered Soda-Lime-Silica Glass

    DEFF Research Database (Denmark)

    Nielsen, Jens Henrik; Olesen, John Forbes; Stang, Henrik

    2009-01-01

    This work presents experimental observations of the characteristic fracture process of tempered glass. Square specimens with a side length of 300 mm, various thicknesses and a residual stress state characterized by photoelastic measurements were used. Fracture was initiated using a 2.5 mm diamond...

  20. Tempered orbital energies and the potential curve within a molecule

    International Nuclear Information System (INIS)

    Anno, T.; Sakai, Y.

    1979-01-01

    It is shown that the sum of the tempered orbital energies behaves much the same way as does the some of the Hartree--Fock orbital energies. The H 2 moluecule in its minimum basis set description is chosen as an example and comparison of orbital energies is carried out

  1. Significance of rate of work hardening in tempered martensite embrittlement

    International Nuclear Information System (INIS)

    Pietikainen, J.

    1995-01-01

    The main explanations for tempered martensite embrittlement are based on the effects of impurities and cementite precipitation on the prior austenite grain boundaries. There are some studies where the rate of work hardening is proposed as a potential reason for the brittleness. One steel was studied by means of a specially developed precision torsional testing device. The test steel had a high Si and Ni content so ε carbide and Fe 3 C appear in quite different tempering temperature ranges. The M S temperature is low enough so that self tempering does not occur. With the testing device it was possible to obtain the true stress - true strain curves to very high deformations. The minimum toughness was always associated with the minimum of rate of work hardening. The change of deformed steel volume before the loss of mechanical stability is proposed as at least one reason for tempered martensite embrittlement. The reasons for the minimum of the rate of work hardening are considered. (orig.)

  2. Tempered Water Lower Port Connector Structural Analysis Verification

    International Nuclear Information System (INIS)

    CREA, B.A.

    2000-01-01

    Structural analysis of the lower port connection of the Tempered Water System of the Cold Vacuum Drying Facility was performed. Subsequent detailed design changes to enhance operability resulted in the need to re-evaluate the bases of the original analysis to verify its continued validity. This evaluation is contained in Appendix A of this report. The original evaluation is contained in Appendix B

  3. Effects of temperate agriculture on neotropical migrant landbirds

    Science.gov (United States)

    Nicholas L. Rodenhouse; Louis B. Best; Raymond J. O' Connor; Eric K. Bollinger

    1993-01-01

    The ecology of Neotropical migrant landbirds in temperate farmland is reviewed to develop management recommendations for the conservation of migrants. Migrants constitute about 71% of bird species using farmland and 86% of bird species nesting there. The number and abundances of Neotropical migrants using farmland are greatest in uncultivated edges with trees and...

  4. Effect of climate change on temperate forest ecosystems

    NARCIS (Netherlands)

    Brolsma, R.J.

    2010-01-01

    In temperate climates groundwater can have a strong effect on vegetation, because it can influence the spatio-temporal distribution of soil moisture and therefore water and oxygen stress of vegetation. Current IPCC climate projections based on CO2 emission scenarios show a global temperature rise

  5. Solid-wood production from temperate eucalypt plantations: a ...

    African Journals Online (AJOL)

    Since 1988, there has been a major focus in Tasmania on research for the management of temperate eucalypt plantations for solid wood. This coincided with the formal transfer of large areas of native forest that had previously been part of the production forest estate into reserves, a decision that triggered the establishment ...

  6. Groundwater flow modelling of periods with temperate climate conditions - Forsmark

    Energy Technology Data Exchange (ETDEWEB)

    Joyce, Steven; Simpson, Trevor; Hartley, Lee; Applegate, David; Hoek, Jaap; Jackson, Peter; Swan, David (Serco Technical Consulting Services (United Kingdom)); Marsic, Niko (Kemakta Konsult AB (Sweden)); Follin, Sven (SF GeoLogic AB (Sweden))

    2010-11-15

    As a part of the license application for a final repository for spent nuclear fuel at Forsmark, the Swedish Nuclear Fuel and Waste Management Company (SKB) has undertaken a series of groundwater flow modelling studies. These represent time periods with different climate conditions and the simulations carried out contribute to the overall evaluation of the repository design and long-term radiological safety. This report concerns the modelling of a repository at the Forsmark site during temperate conditions; i.e. from post-closure and throughout the temperate period up until the receding shoreline leaves the modelling domain at around 12,000 AD. The collation and implementation of onsite hydrogeological and hydrogeochemical data from previous reports are used in the construction of a hydrogeological base case (reference case conceptualisation) and then in an examination of various areas of uncertainty within the current understanding by a series of model variants. The hydrogeological base case models at three different scales, 'repository', 'site' and 'regional', make use of continuous porous medium (CPM), equivalent continuous porous medium (ECPM) and discrete fracture network (DFN) models. The use of hydrogeological models allow for the investigation of the groundwater flow from a deep disposal facility to the biosphere and for the calculation of performance measures that will provide an input to the site performance assessment. The focus of the study described in this report has been to perform numerical simulations of the hydrogeological system from post-closure and throughout the temperate period. Besides providing quantitative results for the immediate temperate period following post-closure, these results are also intended to give a qualitative indication of the evolution of the groundwater system during future temperate periods within an ongoing cycle of glacial/inter-glacial events

  7. The effectiveness of common thermo-regulatory behaviours in a cool temperate grasshopper.

    Science.gov (United States)

    Harris, Rebecca M B; McQuillan, Peter; Hughes, Lesley

    2015-08-01

    Behavioural thermoregulation has the potential to alleviate the short-term impacts of climate change on some small ectotherms, without the need for changes to species distributions or genetic adaptation. We illustrate this by measuring the effect of behaviour in a cool temperate species of grasshopper (Phaulacridium vittatum) over a range of spatial and temporal scales in laboratory and natural field experiments. Microhabitat selection at the site scale was tested in free-ranging grasshoppers and related to changing thermal quality over a daily period. Artificial warming experiments were then used to measure the temperature at which common thermoregulatory behaviours are initiated and the subsequent reductions in body temperature. Behavioural means such as timing of activity, choice of substrates with optimum surface temperatures, shade seeking and postural adjustments (e.g. stilting, vertical orientation) were found to be highly effective at maintaining preferred body temperature. The maximum voluntarily tolerated temperature (MVT) was determined to be 44°C±0.4°C, indicating the upper bounds of thermal flexibility in this species. Behavioural thermoregulation effectively enables small ectotherms to regulate exposure to changing environmental temperatures and utilize the spatially and temporally heterogeneous environments they occupy. Species such as the wingless grasshopper, although adapted to cool temperate conditions, are likely to be well equipped to respond successfully to coarse scale climate change. Copyright © 2015 Elsevier Ltd. All rights reserved.

  8. Using Ecophysiology to Improve Farm Efficiency: Application in Temperate Dairy Grazing Systems

    Directory of Open Access Journals (Sweden)

    David F. Chapman

    2016-04-01

    Full Text Available Information on the physiological ecology of grass-dominant pastures has made a substantial contribution to the development of practices that optimise the amount of feed harvested by grazing animals in temperate livestock systems. However, the contribution of ecophysiology is often under-stated, and the need for further research in this field is sometimes questioned. The challenge for ecophysiolgists, therefore, is to demonstrate how ecophysiological knowledge can help solve significant problems looming for grassland farming in temperate regions while also removing constraints to improved productivity from grazed pastures. To do this, ecophysiological research needs to align more closely with related disciplines, particularly genetics/genomics, agronomy, and farming systems, including systems modelling. This review considers how ecophysiological information has contributed to the development of grazing management practices in the New Zealand dairy industry, an industry that is generally regarded as a world leader in the efficiency with which pasture is grown and utilised for animal production. Even so, there are clear opportunities for further gains in pasture utilisation through the refinement of grazing management practices and the harnessing of those practices to improved pasture plant cultivars with phenotypes that facilitate greater grazing efficiency. Meanwhile, sub-optimal persistence of new pastures continues to constrain productivity in some environments. The underlying plant and population processes associated with this have not been clearly defined. Ecophysiological information, placed in the context of trait identification, grounded in well-designed agronomic studies and linked to plant improvements programmes, is required to address this.

  9. Adaptive root foraging strategies along a boreal-temperate forest gradient.

    Science.gov (United States)

    Ostonen, Ivika; Truu, Marika; Helmisaari, Heljä-Sisko; Lukac, Martin; Borken, Werner; Vanguelova, Elena; Godbold, Douglas L; Lõhmus, Krista; Zang, Ulrich; Tedersoo, Leho; Preem, Jens-Konrad; Rosenvald, Katrin; Aosaar, Jürgen; Armolaitis, Kęstutis; Frey, Jane; Kabral, Naima; Kukumägi, Mai; Leppälammi-Kujansuu, Jaana; Lindroos, Antti-Jussi; Merilä, Päivi; Napa, Ülle; Nöjd, Pekka; Parts, Kaarin; Uri, Veiko; Varik, Mats; Truu, Jaak

    2017-08-01

    The tree root-mycorhizosphere plays a key role in resource uptake, but also in the adaptation of forests to changing environments. The adaptive foraging mechanisms of ectomycorrhizal (EcM) and fine roots of Picea abies, Pinus sylvestris and Betula pendula were evaluated along a gradient from temperate to subarctic boreal forest (38 sites between latitudes 48°N and 69°N) in Europe. Variables describing tree resource uptake structures and processes (absorptive fine root biomass and morphology, nitrogen (N) concentration in absorptive roots, extramatrical mycelium (EMM) biomass, community structure of root-associated EcM fungi, soil and rhizosphere bacteria) were used to analyse relationships between root system functional traits and climate, soil and stand characteristics. Absorptive fine root biomass per stand basal area increased significantly from temperate to boreal forests, coinciding with longer and thinner root tips with higher tissue density, smaller EMM biomass per root length and a shift in soil microbial community structure. The soil carbon (C) : N ratio was found to explain most of the variability in absorptive fine root and EMM biomass, root tissue density, N concentration and rhizosphere bacterial community structure. We suggest a concept of absorptive fine root foraging strategies involving both qualitative and quantitative changes in the root-mycorrhiza-bacteria continuum along climate and soil C : N gradients. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

  10. Transposon fingerprinting using low coverage whole genome shotgun sequencing in cacao (Theobroma cacao L.) and related species.

    Science.gov (United States)

    Sveinsson, Saemundur; Gill, Navdeep; Kane, Nolan C; Cronk, Quentin

    2013-07-24

    Transposable elements (TEs) and other repetitive elements are a large and dynamically evolving part of eukaryotic genomes, especially in plants where they can account for a significant proportion of genome size. Their dynamic nature gives them the potential for use in identifying and characterizing crop germplasm. However, their repetitive nature makes them challenging to study using conventional methods of molecular biology. Next generation sequencing and new computational tools have greatly facilitated the investigation of TE variation within species and among closely related species. (i) We generated low-coverage Illumina whole genome shotgun sequencing reads for multiple individuals of cacao (Theobroma cacao) and related species. These reads were analysed using both an alignment/mapping approach and a de novo (graph based clustering) approach. (ii) A standard set of ultra-conserved orthologous sequences (UCOS) standardized TE data between samples and provided phylogenetic information on the relatedness of samples. (iii) The mapping approach proved highly effective within the reference species but underestimated TE abundance in interspecific comparisons relative to the de novo methods. (iv) Individual T. cacao accessions have unique patterns of TE abundance indicating that the TE composition of the genome is evolving actively within this species. (v) LTR/Gypsy elements are the most abundant, comprising c.10% of the genome. (vi) Within T. cacao the retroelement families show an order of magnitude greater sequence variability than the DNA transposon families. (vii) Theobroma grandiflorum has a similar TE composition to T. cacao, but the related genus Herrania is rather different, with LTRs making up a lower proportion of the genome, perhaps because of a massive presence (c. 20%) of distinctive low complexity satellite-like repeats in this genome. (i) Short read alignment/mapping to reference TE contigs provides a simple and effective method of investigating

  11. Genome-based comparative analyses of Antarctic and temperate species of Paenibacillus.

    Directory of Open Access Journals (Sweden)

    Melissa Dsouza

    Full Text Available Antarctic soils represent a unique environment characterised by extremes of temperature, salinity, elevated UV radiation, low nutrient and low water content. Despite the harshness of this environment, members of 15 bacterial phyla have been identified in soils of the Ross Sea Region (RSR. However, the survival mechanisms and ecological roles of these phyla are largely unknown. The aim of this study was to investigate whether strains of Paenibacillus darwinianus owe their resilience to substantial genomic changes. For this, genome-based comparative analyses were performed on three P. darwinianus strains, isolated from gamma-irradiated RSR soils, together with nine temperate, soil-dwelling Paenibacillus spp. The genome of each strain was sequenced to over 1,000-fold coverage, then assembled into contigs totalling approximately 3 Mbp per genome. Based on the occurrence of essential, single-copy genes, genome completeness was estimated at approximately 88%. Genome analysis revealed between 3,043-3,091 protein-coding sequences (CDSs, primarily associated with two-component systems, sigma factors, transporters, sporulation and genes induced by cold-shock, oxidative and osmotic stresses. These comparative analyses provide an insight into the metabolic potential of P. darwinianus, revealing potential adaptive mechanisms for survival in Antarctic soils. However, a large proportion of these mechanisms were also identified in temperate Paenibacillus spp., suggesting that these mechanisms are beneficial for growth and survival in a range of soil environments. These analyses have also revealed that the P. darwinianus genomes contain significantly fewer CDSs and have a lower paralogous content. Notwithstanding the incompleteness of the assemblies, the large differences in genome sizes, determined by the number of genes in paralogous clusters and the CDS content, are indicative of genome content scaling. Finally, these sequences are a resource for further

  12. Acoustic Shotgun System

    Science.gov (United States)

    2009-09-16

    dispersing a plurality of relatively small, supercavitating projectiles in the water over a wide spatial field at long ranges from an underwater gun...or surface gun. (2) Description of the Prior Art [0004] One major technical challenge related to employing supercavitating projectiles against...accordingly is more limited. [0005] A second problem common to supercavitating projectiles is the configuration of the projectile itself. The primary

  13. Source-pathway-receptor investigation of the fate of trace elements derived from shotgun pellets discharged in terrestrial ecosystems managed for game shooting

    International Nuclear Information System (INIS)

    Sneddon, Jennifer; Clemente, Rafael; Riby, Philip; Lepp, Nicholas W.

    2009-01-01

    Spent shotgun pellets may contaminate terrestrial ecosystems. We examined the fate of elements originating from shotgun pellets in pasture and woodland ecosystems. Two source-receptor pathways: i) soil-soil pore water-plant and ii) whole earthworm/worm gut contents - washed and unwashed small mammal hair were investigated. Concentrations of Pb and associated contaminants were higher in soils from shot areas than controls. Arsenic and lead concentrations were positively correlated in soils, soil pore water and associated biota. Element concentrations in biota were below statutory levels in all locations. Bioavailability of lead to small mammals, based on concentrations in washed body hair was low. Lead movement from soil water to higher trophic levels was minor compared to lead adsorbed onto body surfaces. Lead was concentrated in earthworm gut and some plants. Results indicate that managed game shooting presents minimal risk in terms of element transfer to soils and their associated biota. - Source-receptor pathway analysis of a managed game shooting site showed no environmental risk of trace element transfer.

  14. Source-pathway-receptor investigation of the fate of trace elements derived from shotgun pellets discharged in terrestrial ecosystems managed for game shooting

    Energy Technology Data Exchange (ETDEWEB)

    Sneddon, Jennifer [School of Natural Sciences and Psychology, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF (United Kingdom); Clemente, Rafael, E-mail: rclemente@cebas.csic.e [School of Natural Sciences and Psychology, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF (United Kingdom); Riby, Philip [School of Pharmacy and Chemistry, Liverpool John Moores University, Liverpool L3 3AF (United Kingdom); Lepp, Nicholas W., E-mail: n.w.lepp@ljmu.ac.u [School of Natural Sciences and Psychology, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF (United Kingdom)

    2009-10-15

    Spent shotgun pellets may contaminate terrestrial ecosystems. We examined the fate of elements originating from shotgun pellets in pasture and woodland ecosystems. Two source-receptor pathways: i) soil-soil pore water-plant and ii) whole earthworm/worm gut contents - washed and unwashed small mammal hair were investigated. Concentrations of Pb and associated contaminants were higher in soils from shot areas than controls. Arsenic and lead concentrations were positively correlated in soils, soil pore water and associated biota. Element concentrations in biota were below statutory levels in all locations. Bioavailability of lead to small mammals, based on concentrations in washed body hair was low. Lead movement from soil water to higher trophic levels was minor compared to lead adsorbed onto body surfaces. Lead was concentrated in earthworm gut and some plants. Results indicate that managed game shooting presents minimal risk in terms of element transfer to soils and their associated biota. - Source-receptor pathway analysis of a managed game shooting site showed no environmental risk of trace element transfer.

  15. Protein identification and quantification from riverbank grape, Vitis riparia: Comparing SDS-PAGE and FASP-GPF techniques for shotgun proteomic analysis.

    Science.gov (United States)

    George, Iniga S; Fennell, Anne Y; Haynes, Paul A

    2015-09-01

    Protein sample preparation optimisation is critical for establishing reproducible high throughput proteomic analysis. In this study, two different fractionation sample preparation techniques (in-gel digestion and in-solution digestion) for shotgun proteomics were used to quantitatively compare proteins identified in Vitis riparia leaf samples. The total number of proteins and peptides identified were compared between filter aided sample preparation (FASP) coupled with gas phase fractionation (GPF) and SDS-PAGE methods. There was a 24% increase in the total number of reproducibly identified proteins when FASP-GPF was used. FASP-GPF is more reproducible, less expensive and a better method than SDS-PAGE for shotgun proteomics of grapevine samples as it significantly increases protein identification across biological replicates. Total peptide and protein information from the two fractionation techniques is available in PRIDE with the identifier PXD001399 (http://proteomecentral.proteomexchange.org/dataset/PXD001399). © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. The amount of parenchyma and living fibers affects storage of nonstructural carbohydrates in young stems and roots of temperate trees.

    Science.gov (United States)

    Plavcová, Lenka; Hoch, Günter; Morris, Hugh; Ghiasi, Sara; Jansen, Steven

    2016-04-01

    Concentrations of nonstructural carbohydrates (NSCs) are used as proxies for the net carbon balance of trees and as indicators of carbon starvation resulting from environmental stress. Woody organs are the largest NSC-storing compartments in forest ecosystems; therefore, it is essential to understand the factors that affect the size of this important storage pool. In wood, NSC are predominantly deposited in ray and axial parenchyma (RAP); however, direct links between nutrient storage and RAP anatomy have not yet been established. Here, we tested whether the NSC storage capacity of wood is influenced by the amount of RAP. We measured NSC concentrations and RAP fractions in root and stem sapwood of 12 temperate species sampled at the onset of winter dormancy and in stem sapwood of four tropical trees growing in an evergreen lowland rainforest. The patterns of starch distribution were visualized by staining with Lugol's solution. The concentration of NSCs in sapwood of temperate trees scales tightly with the amount of RAP and living fibers (LFs), with almost all RAP and LFs being densely packed with starch grains. In contrast, the tropical species had lower NSC concentrations despite their higher RAP and LFs fraction and had considerable interspecific differences in starch distribution. The differences in RAP and LFs abundance affect the ability of sapwood to store NSC in temperate trees, whereas a more diverse set of functions of RAP might be pronounced in species growing in a tropical environment with little seasonality. © 2016 Botanical Society of America.

  17. Herbivores modify selection on plant functional traits in a temperate rainforest understory.

    Science.gov (United States)

    Salgado-Luarte, Cristian; Gianoli, Ernesto

    2012-08-01

    There is limited evidence regarding the adaptive value of plant functional traits in contrasting light environments. It has been suggested that changes in these traits in response to light availability can increase herbivore susceptibility. We tested the adaptive value of plant functional traits linked with carbon gain in contrasting light environments and also evaluated whether herbivores can modify selection on these traits in each light environment. In a temperate rainforest, we examined phenotypic selection on functional traits in seedlings of the pioneer tree Aristotelia chilensis growing in sun (canopy gap) and shade (forest understory) and subjected to either natural herbivory or herbivore exclusion. We found differential selection on functional traits depending on light environment. In sun, there was positive directional selection on photosynthetic rate and relative growth rate (RGR), indicating that selection favors competitive ability in a high-resource environment. Seedlings with high specific leaf area (SLA) and intermediate RGR were selected in shade, suggesting that light capture and conservative resource use are favored in the understory. Herbivores reduced the strength of positive directional selection acting on SLA in shade. We provide the first demonstration that natural herbivory rates can change the strength of selection on plant ecophysiological traits, that is, attributes whose main function is resource uptake. Research addressing the evolution of shade tolerance should incorporate the selective role of herbivores.

  18. Vibrio vulnificus phage PV94 is closely related to temperate phages of V. cholerae and other Vibrio species.

    Directory of Open Access Journals (Sweden)

    Mark Pryshliak

    Full Text Available BACKGROUND: Vibrio vulnificus is an important pathogen which can cause serious infections in humans. Yet, there is limited knowledge on its virulence factors and the question whether temperate phages might be involved in pathogenicity, as is the case with V. cholerae. Thus far, only two phages (SSP002 and VvAW1 infecting V. vulnificus have been genetically characterized. These phages were isolated from the environment and are not related to Vibrio cholerae phages. The lack of information on temperate V. vulnificus phages prompted us to isolate those phages from lysogenic strains and to compare them with phages of other Vibrio species. RESULTS: In this study the temperate phage PV94 was isolated from a V. vulnificus biotype 1 strain by mitomycin C induction. PV94 is a myovirus whose genome is a linear double-stranded DNA of 33,828 bp with 5'-protruding ends. Sequence analysis of PV94 revealed a modular organization of the genome. The left half of the genome comprising the immunity region and genes for the integrase, terminase and replication proteins shows similarites to V. cholerae kappa phages whereas the right half containing genes for structural proteins is closely related to a prophage residing in V. furnissii NCTC 11218. CONCLUSION: We present the first genomic sequence of a temperate phage isolated from a human V. vulnificus isolate. The sequence analysis of the PV94 genome demonstrates the wide distribution of closely related prophages in various Vibrio species. Moreover, the mosaicism of the PV94 genome indicates a high degree of horizontal genetic exchange within the genus Vibrio, by which V. vulnificus might acquire virulence-associated genes from other species.

  19. Ocean cleaning stations under a changing climate: biological responses of tropical and temperate fish-cleaner shrimp to global warming.

    Science.gov (United States)

    Rosa, Rui; Lopes, Ana Rita; Pimentel, Marta; Faleiro, Filipa; Baptista, Miguel; Trübenbach, Katja; Narciso, Luis; Dionísio, Gisela; Pegado, Maria Rita; Repolho, Tiago; Calado, Ricardo; Diniz, Mário

    2014-10-01

    Cleaning symbioses play an important role in the health of certain coastal marine communities. These interspecific associations often occur at specific sites (cleaning stations) where a cleaner organism (commonly a fish or shrimp) removes ectoparasites/damaged tissue from a 'client' (a larger cooperating fish). At present, the potential impact of climate change on the fitness of cleaner organisms remains unknown. This study investigated the physiological and biochemical responses of tropical (Lysmata amboinensis) and temperate (L. seticaudata) cleaner shrimp to global warming. Specifically, thermal limits (CTMax), metabolic rates, thermal sensitivity, heat shock response (HSR), lipid peroxidation [malondialdehyde (MDA) concentration], lactate levels, antioxidant (GST, SOD and catalase) and digestive enzyme activities (trypsin and alkaline phosphatase) at current and warming (+3 °C) temperature conditions. In contrast to the temperate species, CTMax values decreased significantly from current (24-27 °C) to warming temperature conditions (30 °C) for the tropical shrimp, where metabolic thermal sensitivity was affected and the HSR was significantly reduced. MDA levels in tropical shrimp increased dramatically, indicating extreme cellular lipid peroxidation, which was not observed in the temperate shrimp. Lactate levels, GST and SOD activities were significantly enhanced within the muscle tissue of the tropical species. Digestive enzyme activities in the hepatopancreas of both species were significantly decreased by warmer temperatures. Our data suggest that the tropical cleaner shrimp will be more vulnerable to global warming than the temperate Lysmata seticaudata; the latter evolved in a relatively unstable environment with seasonal thermal variations that may have conferred greater adaptive plasticity. Thus, tropical cleaning symbioses may be challenged at a greater degree by warming-related anthropogenic forcing, with potential cascading effects on the health

  20. Bifurcation dynamics of the tempered fractional Langevin equation

    Energy Technology Data Exchange (ETDEWEB)

    Zeng, Caibin, E-mail: macbzeng@scut.edu.cn; Yang, Qigui, E-mail: qgyang@scut.edu.cn [School of Mathematics, South China University of Technology, Guangzhou 510640 (China); Chen, YangQuan, E-mail: ychen53@ucmerced.edu [MESA LAB, School of Engineering, University of California, Merced, 5200 N. Lake Road, Merced, California 95343 (United States)

    2016-08-15

    Tempered fractional processes offer a useful extension for turbulence to include low frequencies. In this paper, we investigate the stochastic phenomenological bifurcation, or stochastic P-bifurcation, of the Langevin equation perturbed by tempered fractional Brownian motion. However, most standard tools from the well-studied framework of random dynamical systems cannot be applied to systems driven by non-Markovian noise, so it is desirable to construct possible approaches in a non-Markovian framework. We first derive the spectral density function of the considered system based on the generalized Parseval's formula and the Wiener-Khinchin theorem. Then we show that it enjoys interesting and diverse bifurcation phenomena exchanging between or among explosive-like, unimodal, and bimodal kurtosis. Therefore, our procedures in this paper are not merely comparable in scope to the existing theory of Markovian systems but also provide a possible approach to discern P-bifurcation dynamics in the non-Markovian settings.

  1. Linking Well-Tempered Metadynamics Simulations with Experiments

    Science.gov (United States)

    Barducci, Alessandro; Bonomi, Massimiliano; Parrinello, Michele

    2010-01-01

    Abstract Linking experiments with the atomistic resolution provided by molecular dynamics simulations can shed light on the structure and dynamics of protein-disordered states. The sampling limitations of classical molecular dynamics can be overcome using metadynamics, which is based on the introduction of a history-dependent bias on a small number of suitably chosen collective variables. Even if such bias distorts the probability distribution of the other degrees of freedom, the equilibrium Boltzmann distribution can be reconstructed using a recently developed reweighting algorithm. Quantitative comparison with experimental data is thus possible. Here we show the potential of this combined approach by characterizing the conformational ensemble explored by a 13-residue helix-forming peptide by means of a well-tempered metadynamics/parallel tempering approach and comparing the reconstructed nuclear magnetic resonance scalar couplings with experimental data. PMID:20441734

  2. Reversible temper brittleness on tensile tests at room temperature

    International Nuclear Information System (INIS)

    Quadros, N.F. de; Cabral, U.Q.

    1976-01-01

    Tensile tests were carried out on unnotched test pieces at room temperature and three strain rates: 2,5x10 -4 , 2,5x10 -3 and 1,0x10 -2 s -1 in a low alloy No-Cr-Mo steel to observe the variation in its mechanical properties with the occurrence of reversible temper brittleness. The brittle samples showed a sensitivity of 50 0 C in a 48 hour heat treatment at 500 0 C. The tests showed that at the strain rate of 2,5x10 -4 s -1 there are statistically significant differences between the elongations of the material in the brittle and the nonbrittle and regenerated states. A short review of reversible temper brittleness is given and a theory suggested for the mechanism [pt

  3. The tempered stable process with infinitely divisible inverse subordinators

    International Nuclear Information System (INIS)

    Wyłomańska, Agnieszka

    2013-01-01

    In the last decade processes driven by inverse subordinators have become extremely popular. They have been used in many different applications, especially for data with observable constant time periods. However, the classical model, i.e. the subordinated Brownian motion, can be inappropriate for the description of observed phenomena that exhibit behavior not adequate for Gaussian systems. Therefore, in this paper we extend the classical approach and replace the Brownian motion by the tempered stable process. Moreover, on the other hand, as an extension of the classical model, we analyze the general class of inverse subordinators. We examine the main properties of the tempered stable process driven by inverse subordinators from the infinitely divisible class of distributions. We show the fractional Fokker–Planck equation of the examined process and the asymptotic behavior of the mean square displacement for two cases of subordinators. Additionally, we examine how an external force can influence the examined characteristics. (paper)

  4. Effect of tempering on corrosion resistance of cast aluminium bronzes

    International Nuclear Information System (INIS)

    Aaltonen, P.; Klemetti, K.; Haenninen, H.

    1985-01-01

    The subject of this study is corrosion resistance of aluminium bronzes, which are copper base alloys containing aluminium up to 12% with additions of nickel, iron and manganese. The main conclutions that can be drawn are: (1) The dealloying corrosion resistance of nickel-aluminium bronze is much better than that of aluminium bronze with iron and manganese additions, but it is not immune; (2) The dealloying corrosion resistance of aluminium bronzes can be improved by appropiate heat treatments. The best properties were obtained by temperering between 600 and 800 deg C, depending on the initial microstructure; (3) In crevice conditions, where local acidification can occur, dealloying of aluminium bronzes is a consequence of the preferential attack of aluminium-rich phases. By appropriate tempering, a uniform distribution of aluminium-rich phases is obtained and the continous path for selective corrosion is not formed

  5. Interspecific variation in total phenolic content in temperate brown algae

    Directory of Open Access Journals (Sweden)

    Anna Maria Mannino

    2017-09-01

    Full Text Available Marine algae synthesize secondary metabolites such as polyphenols that function as defense and protection mechanisms. Among brown algae, Fucales and Dictyotales (Phaeophyceae contain the highest levels of phenolic compounds, mainly phlorotannins, that play multiple roles. Four temperate brown algae (Cystoseira amentacea, Cystoseira compressa, Dictyopteris polypodioides and Padina pavonica were studied for total phenolic contents. Total phenolic content was determined colorimetrically with the Folin-Ciocalteu reagent. Significant differences in total phenolic content were observed between leathery and sheetlike algae and also within each morphological group. Among the four species, the sheet-like alga D. polypodioides, living in the upper infralittoral zone, showed the highest concentration of phenolic compounds. These results are in agreement with the hypothesis that total phenolic content in temperate brown algae is influenced by a combination of several factors, such as growth form, depth, and exposition to solar radiation.

  6. Hurricane Impacts to Tropical and Temperate Forest Landscapes

    OpenAIRE

    Boose, Emery Robert; Foster, David Russell; Fluet, Marcheterre

    1994-01-01

    Hurricanes represent an important natural disturbance process to tropical and temperate forests in many coastal areas of the world. The complex patterns of damage created in forests by hurricane winds result from the interaction of meteorological, physiographic, and biotic factors on a range of spatial scales. To improve our understanding of these factors and of the role of catastrophic hurricane wind as a disturbance process, we take an integrative approach. A simple meteorological model (HU...

  7. Groundwater flow modelling of periods with temperate climate conditions - Laxemar

    International Nuclear Information System (INIS)

    Joyce, Steven; Simpson, Trevor; Hartley, Lee; Applegate, David; Hoek, Jaap; Jackson, Peter; Roberts, David; Swan, David; Gylling, Bjoern; Marsic, Niko; Rhen, Ingvar

    2010-12-01

    As a part of the license application for a final repository for spent nuclear fuel at Forsmark, the Swedish Nuclear Fuel and Waste Management Company (SKB) has undertaken a series of groundwater flow modelling studies. These represent time periods with different hydraulic conditions and the simulations carried out contribute to the overall evaluation of the repository design and long-term radiological safety. This report concerns the modelling of a repository at the Laxemar-Simpevarp site during temperate climate conditions as a comparison to corresponding modelling carried out for Forsmark /Joyce et al. 2010/. The collation and implementation of onsite hydrogeological and hydrogeochemical data from previous reports are used in the construction of a Hydrogeological base case (reference case conceptualisation) and then an examination of various areas of uncertainty within the current understanding by a series of model variants. The Hydrogeological base case models at three different scales, 'repository', 'site' and 'regional' make use of a discrete fracture network (DFN) and equivalent continuous porous medium (ECPM) models. The use of hydrogeological models allow for the investigation of the groundwater flow from a deep disposal facility to the biosphere and for the calculation of performance measures that will provide an input to the site performance assessment. The focus of the study described in this report has been to perform numerical simulations of the hydrogeological system from post-closure and throughout the temperate period up until the receding shoreline leaves the modelling domain at around 15,000 AD. Besides providing quantitative results for the immediate temperate period following post-closure, these results are also intended to give a qualitative indication of the evolution of the groundwater system during future temperate periods within an ongoing cycle of glacial/inter-glacial events

  8. Groundwater flow modelling of periods with temperate climate conditions - Laxemar

    Energy Technology Data Exchange (ETDEWEB)

    Joyce, Steven; Simpson, Trevor; Hartley, Lee; Applegate, David; Hoek, Jaap; Jackson, Peter; Roberts, David; Swan, David (Serco Technical Consulting Services (United Kingdom)); Gylling, Bjoern; Marsic, Niko (Kemakta Konsult AB, Stockholm (Sweden)); Rhen, Ingvar (SWECO Environment AB, Falun (Sweden))

    2010-12-15

    As a part of the license application for a final repository for spent nuclear fuel at Forsmark, the Swedish Nuclear Fuel and Waste Management Company (SKB) has undertaken a series of groundwater flow modelling studies. These represent time periods with different hydraulic conditions and the simulations carried out contribute to the overall evaluation of the repository design and long-term radiological safety. This report concerns the modelling of a repository at the Laxemar-Simpevarp site during temperate climate conditions as a comparison to corresponding modelling carried out for Forsmark /Joyce et al. 2010/. The collation and implementation of onsite hydrogeological and hydrogeochemical data from previous reports are used in the construction of a Hydrogeological base case (reference case conceptualisation) and then an examination of various areas of uncertainty within the current understanding by a series of model variants. The Hydrogeological base case models at three different scales, 'repository', 'site' and 'regional' make use of a discrete fracture network (DFN) and equivalent continuous porous medium (ECPM) models. The use of hydrogeological models allow for the investigation of the groundwater flow from a deep disposal facility to the biosphere and for the calculation of performance measures that will provide an input to the site performance assessment. The focus of the study described in this report has been to perform numerical simulations of the hydrogeological system from post-closure and throughout the temperate period up until the receding shoreline leaves the modelling domain at around 15,000 AD. Besides providing quantitative results for the immediate temperate period following post-closure, these results are also intended to give a qualitative indication of the evolution of the groundwater system during future temperate periods within an ongoing cycle of glacial/inter-glacial events

  9. Efficient assignment of the temperature set for Parallel Tempering

    International Nuclear Information System (INIS)

    Guidetti, M.; Rolando, V.; Tripiccione, R.

    2012-01-01

    We propose a simple algorithm able to identify a set of temperatures for a Parallel Tempering Monte Carlo simulation, that maximizes the probability that the configurations drift across all temperature values, from the coldest to the hottest ones, and vice versa. The proposed algorithm starts from data gathered from relatively short Monte Carlo simulations and is straightforward to implement. We assess its effectiveness on a test case simulation of an Edwards–Anderson spin glass on a lattice of 12 3 sites.

  10. Diagenesis of polymineralic temperate limestones in a cyclothemic sedimentary succession, eastern North Island, New Zealand

    International Nuclear Information System (INIS)

    Haywick, D.W.

    2004-01-01

    Temperate carbonate petrofacies (calcarenite and coquina) in the Pliocene-Pleistocene Petane Group of eastern North Island, New Zealand, are dominated by aragonite faunas consisting primarily of bivalves and gastropods. Unlike calcite-dominated temperate limestones, these polymineralic carbonates have undergone extensive early diagenetic alteration including extensive calcite cementation induced by aragonite dissolution. Marine cementation (type 1: pore-lining, bladed calcite) was isolated to biogenic pores. It predated glauconite and may have been precipitated as low-magnesium calcite, possibly in marine phreatic environments during sea-level transgressions. Four phases of calcite cement with varying but definitive degrees of meteoric influence occur in the Petane Group. Type 2 (ferroan scalenohedral calcite) was the initial pore-filling cement and precipitated from reduced pore fluids in a phreatic environment, possibly during or soon after the transition from marine to meteoric diagenesis. Type 3 (moderately ferroan drusy) calcite and type 4 (non-ferroan drusy) calcite were sequentially precipitated during meteoric conditions from pore waters that changed from reducing to oxidising. Type 5 (sinter) cements comprise several forms precipitated during vadose meteoric diagenesis, the final meteoric phase of alteration in the Petane Group. Ferroan calcite cementation of silt matrix in coquina limestones overlain by terrigenous silt (type 6: matrix cement) probably occurred simultaneously with type 2/3 pore-filling phases. A similar ferroan to moderately ferroan to non-ferroan suite of drusy calcite cements also lithified concretions in non-carbonate (siliciclastic sand) facies in the Petane Group, but only after the onset of compaction. Extensive skeletal diagenesis (stabilisation of magnesium calcite allochems, dissolution/recrystallisation of aragonite) occurred during type 3 and 4 cementation phases. Diagenesis in the Petane Group was stratigraphically influenced

  11. Grain boundary diffusion in terms of the tempered fractional calculus

    Energy Technology Data Exchange (ETDEWEB)

    Sibatov, R.T., E-mail: ren_sib@bk.ru [Ulyanovsk State University, 432017, 42 Leo Tolstoy str., Ulyanovsk (Russian Federation); Svetukhin, V.V. [Ulyanovsk State University, 432017, 42 Leo Tolstoy str., Ulyanovsk (Russian Federation); Institute of Nanotechnology and Microelectronics of the Russian Academy of Sciences, 115487, 18 Nagatinskaya str., Moscow (Russian Federation)

    2017-06-28

    Mathematical treatment of grain-boundary diffusion based on the model first proposed by Fisher is usually formulated in terms of normal diffusion equations in a two-component nonhomogeneous medium. On the other hand, fractional equations of anomalous diffusion proved themselves to be useful in description of grain-boundary diffusion phenomena. Moreover, the most important propagation regime predicted by Fisher's model demonstrates subdiffusive behavior. However, the direct link between fractional approach and the Fisher model and its modifications has not found yet. Here, we fill this gap and show that solution of fractional subdiffusion equation offers general properties of classical solutions obtained by Whipple and Suzuoka. The tempered fractional approach is a convenient tool for studying precipitation in granular materials as the tempered subdiffusion limited process. - Highlights: • The link connected fractional diffusion approach and Fisher's model of grain-boundary diffusion is derived. • The subdiffusion exponent of grain-boundary diffusion can differ from 1/2. • Nucleation in granular materials is modeled by the process limited by tempered subdiffusion.

  12. Biochar boosts tropical but not temperate crop yields

    Science.gov (United States)

    Jeffery, Simon; Abalos, Diego; Prodana, Marija; Catarina Bastos, Ana; van Groenigen, Jan Willem; Hungate, Bruce A.; Verheijen, Frank

    2017-05-01

    Applying biochar to soil is thought to have multiple benefits, from helping mitigate climate change [1, 2], to managing waste [3] to conserving soil [4]. Biochar is also widely assumed to boost crop yield [5, 6], but there is controversy regarding the extent and cause of any yield benefit [7]. Here we use a global-scale meta-analysis to show that biochar has, on average, no effect on crop yield in temperate latitudes, yet elicits a 25% average increase in yield in the tropics. In the tropics, biochar increased yield through liming and fertilization, consistent with the low soil pH, low fertility, and low fertilizer inputs typical of arable tropical soils. We also found that, in tropical soils, high-nutrient biochar inputs stimulated yield substantially more than low-nutrient biochar, further supporting the role of nutrient fertilization in the observed yield stimulation. In contrast, arable soils in temperate regions are moderate in pH, higher in fertility, and generally receive higher fertilizer inputs, leaving little room for additional benefits from biochar. Our findings demonstrate that the yield-stimulating effects of biochar are not universal, but may especially benefit agriculture in low-nutrient, acidic soils in the tropics. Biochar management in temperate zones should focus on potential non-yield benefits such as lime and fertilizer cost savings, greenhouse gas emissions control, and other ecosystem services.

  13. Grain boundary diffusion in terms of the tempered fractional calculus

    International Nuclear Information System (INIS)

    Sibatov, R.T.; Svetukhin, V.V.

    2017-01-01

    Mathematical treatment of grain-boundary diffusion based on the model first proposed by Fisher is usually formulated in terms of normal diffusion equations in a two-component nonhomogeneous medium. On the other hand, fractional equations of anomalous diffusion proved themselves to be useful in description of grain-boundary diffusion phenomena. Moreover, the most important propagation regime predicted by Fisher's model demonstrates subdiffusive behavior. However, the direct link between fractional approach and the Fisher model and its modifications has not found yet. Here, we fill this gap and show that solution of fractional subdiffusion equation offers general properties of classical solutions obtained by Whipple and Suzuoka. The tempered fractional approach is a convenient tool for studying precipitation in granular materials as the tempered subdiffusion limited process. - Highlights: • The link connected fractional diffusion approach and Fisher's model of grain-boundary diffusion is derived. • The subdiffusion exponent of grain-boundary diffusion can differ from 1/2. • Nucleation in granular materials is modeled by the process limited by tempered subdiffusion.

  14. Carbon sequestration in managed temperate coniferous forests under climate change

    Science.gov (United States)

    Dymond, Caren C.; Beukema, Sarah; Nitschke, Craig R.; Coates, K. David; Scheller, Robert M.

    2016-03-01

    Management of temperate forests has the potential to increase carbon sinks and mitigate climate change. However, those opportunities may be confounded by negative climate change impacts. We therefore need a better understanding of climate change alterations to temperate forest carbon dynamics before developing mitigation strategies. The purpose of this project was to investigate the interactions of species composition, fire, management, and climate change in the Copper-Pine Creek valley, a temperate coniferous forest with a wide range of growing conditions. To do so, we used the LANDIS-II modelling framework including the new Forest Carbon Succession extension to simulate forest ecosystems under four different productivity scenarios, with and without climate change effects, until 2050. Significantly, the new extension allowed us to calculate the net sector productivity, a carbon accounting metric that integrates aboveground and belowground carbon dynamics, disturbances, and the eventual fate of forest products. The model output was validated against literature values. The results implied that the species optimum growing conditions relative to current and future conditions strongly influenced future carbon dynamics. Warmer growing conditions led to increased carbon sinks and storage in the colder and wetter ecoregions but not necessarily in the others. Climate change impacts varied among species and site conditions, and this indicates that both of these components need to be taken into account when considering climate change mitigation activities and adaptive management. The introduction of a new carbon indicator, net sector productivity, promises to be useful in assessing management effectiveness and mitigation activities.

  15. The possibility of tribopair lifetime extending by welding of quenched and tempered stainless steel with quenched and tempered carbon steel

    Directory of Open Access Journals (Sweden)

    V. Marušić

    2015-04-01

    Full Text Available In the conditions of tribocorrosion wear, extending of parts lifetime could be achieved by using stainless steel,which is hardened to sufficiently high hardness. In the tribosystem bolt/ bushing shell/link plate of the bucket elevator transporter conveyor machine, the previously quenched and tempered martensitic stainless steel for bolts is hardened at ≈47 HRC and welded with the quenched and tempered high yield carbon steel for bolts. Additional material, based on Cr-Ni-Mo (18/8/6 is used. The microstructure and hardness of welded samples are tested. On the tensile tester, resistance of the welded joint is tested with a simulated experiment. Dimensional control of worn tribosystem elements was performed after six months of service.

  16. Spent nuclear fuel project cold vacuum drying facility tempered water and tempered water cooling system design description

    International Nuclear Information System (INIS)

    IRWIN, J.J.

    1998-01-01

    This document provides the System Design Description (SDD) for the Cold Vacuum Drying Facility (CVDF) Tempered Water (TW) and Tempered Water Cooling (TWC) System . The SDD was developed in conjunction with HNF-SD-SNF-SAR-002, Safety Analysis Report for the Cold Vacuum Drying Facility, Phase 2, Supporting Installation of Processing Systems (Garvin 1998), The HNF-SD-SNF-DRD-O02, 1998, Cold Vacuum Drying Facility Design Requirements, and the CVDF Design Summary Report. The SDD contains general descriptions of the TW and TWC equipment, the system functions, requirements and interfaces. The SDD provides references for design and fabrication details, operation sequences and maintenance. This SOD has been developed for the SNFP Operations Organization and shall be updated, expanded, and revised in accordance with future design, construction and startup phases of the CVDF until the CVDF final ORR is approved

  17. Prediction of hardness in pieces of quenched and tempered steel

    International Nuclear Information System (INIS)

    Yanzon, Rodolfo Carlos; Rodriguez, Augusto; Sanchez, Arlington Ricardo

    2006-01-01

    This presentation describes the first stage of a work plan to obtain a simple software, for predicting properties at certain points of a quenched and tempered piece. In this first stage, this prediction is limited to cylindrical pieces made with steels whose chemical composition is within a certain range. The methodology basically consists of obtaining , from experimental data, a mathematical tool able to predict the hardness value, for Jominy test piece ends made with this type of steel. This meant beginning with the analysis of the usual forms of theoretical calculation of Jominy curves of quenched samples, which resulted in a proposal to modify the Just equation. Two different mathematical methods were then developed, that could predict hardness values in tempered Jominy test pieces. One, based on the determination of polynomic equations, that reproduces the loss of hardness at points along the test piece, base on the quenching value and as a function of the tempering temperature. The other one, which uses the lineal multidimensional interpolation method, because of its ease of application, has been selected as the mathematical tool to use in the software under development. At this stage of the work, the relationship between the points on the piece and those on the Jominy test pieces is carried out by the Lamont method and the representative variable of the temperature/time combination for the tempering process itself, is obtained with software based on the Hollomon and Jaffe expression. Data is needed to define: a) chemical composition and grain size of the steel used, b) diameter of the piece, c) 'H G ' severity of the quenching medium d) temperature and time of the tempering. The work's second stage continued with the addition of hardness values measured in Jominy test pieces made with other steels. The chemical composition and grain size data of each steel introduced are converted by the software into one more variable, using the concept of ideal critical

  18. The tropicalization of temperate marine ecosystems: climate-mediated changes in herbivory and community phase shifts

    Science.gov (United States)

    Vergés, Adriana; Steinberg, Peter D.; Hay, Mark E.; Poore, Alistair G. B.; Campbell, Alexandra H.; Ballesteros, Enric; Heck, Kenneth L.; Booth, David J.; Coleman, Melinda A.; Feary, David A.; Figueira, Will; Langlois, Tim; Marzinelli, Ezequiel M.; Mizerek, Toni; Mumby, Peter J.; Nakamura, Yohei; Roughan, Moninya; van Sebille, Erik; Gupta, Alex Sen; Smale, Dan A.; Tomas, Fiona; Wernberg, Thomas; Wilson, Shaun K.

    2014-01-01

    Climate-driven changes in biotic interactions can profoundly alter ecological communities, particularly when they impact foundation species. In marine systems, changes in herbivory and the consequent loss of dominant habitat forming species can result in dramatic community phase shifts, such as from coral to macroalgal dominance when tropical fish herbivory decreases, and from algal forests to ‘barrens’ when temperate urchin grazing increases. Here, we propose a novel phase-shift away from macroalgal dominance caused by tropical herbivores extending their range into temperate regions. We argue that this phase shift is facilitated by poleward-flowing boundary currents that are creating ocean warming hotspots around the globe, enabling the range expansion of tropical species and increasing their grazing rates in temperate areas. Overgrazing of temperate macroalgae by tropical herbivorous fishes has already occurred in Japan and the Mediterranean. Emerging evidence suggests similar phenomena are occurring in other temperate regions, with increasing occurrence of tropical fishes on temperate reefs. PMID:25009065

  19. An investigation on high temperature fatigue properties of tempered nuclear-grade deposited weld metals

    Science.gov (United States)

    Cao, X. Y.; Zhu, P.; Yong, Q.; Liu, T. G.; Lu, Y. H.; Zhao, J. C.; Jiang, Y.; Shoji, T.

    2018-02-01

    Effect of tempering on low cycle fatigue (LCF) behaviors of nuclear-grade deposited weld metal was investigated, and The LCF tests were performed at 350 °C with strain amplitudes ranging from 0.2% to 0.6%. The results showed that at a low strain amplitude, deposited weld metal tempered for 1 h had a high fatigue resistance due to high yield strength, while at a high strain amplitude, the one tempered for 24 h had a superior fatigue resistance due to high ductility. Deposited weld metal tempered for 1 h exhibited cyclic hardening at the tested strain amplitudes. Deposited weld metal tempered for 24 h exhibited cyclic hardening at a low strain amplitude but cyclic softening at a high strain amplitude. Existence and decomposition of martensite-austenite (M-A) islands as well as dislocations activities contributed to fatigue property discrepancy among the two tempered deposited weld metal.

  20. Development of 13 microsatellites for Gunnison Sage-grouse (Centrocercus minimus) using next-generation shotgun sequencing and their utility in Greater Sage-grouse (Centrocercus urophasianus)

    Science.gov (United States)

    Fike, Jennifer A.; Oyler-McCance, Sara J.; Zimmerman, Shawna J; Castoe, Todd A.

    2015-01-01

    Gunnison Sage-grouse are an obligate sagebrush species that has experienced significant population declines and has been proposed for listing under the U.S. Endangered Species Act. In order to examine levels of connectivity among Gunnison Sage-grouse leks, we identified 13 novel microsatellite loci though next-generation shotgun sequencing, and tested them on the closely related Greater Sage-grouse. The number of alleles per locus ranged from 2 to 12. No loci were found to be linked, although 2 loci revealed significant departures from Hardy–Weinberg equilibrium or evidence of null alleles. While these microsatellites were designed for Gunnison Sage-grouse, they also work well for Greater Sage-grouse and could be used for numerous genetic questions including landscape and population genetics.

  1. Effect of Tempering and Baking on the Charpy Impact Energy of Hydrogen-Charged 4340 Steel

    Science.gov (United States)

    Mori, K.; Lee, E. W.; Frazier, W. E.; Niji, K.; Battel, G.; Tran, A.; Iriarte, E.; Perez, O.; Ruiz, H.; Choi, T.; Stoyanov, P.; Ogren, J.; Alrashaid, J.; Es-Said, O. S.

    2015-01-01

    Tempered AISI 4340 steel was hydrogen charged and tested for impact energy. It was found that samples tempered above 468 °C (875 °F) and subjected to hydrogen charging exhibited lower impact energy values when compared to uncharged samples. No significant difference between charged and uncharged samples tempered below 468 °C (875 °F) was observed. Neither exposure nor bake time had any significant effect on impact energy within the tested ranges.

  2. On the evolution of Cu-Ni-rich bridges of Alnico alloys with tempering

    Energy Technology Data Exchange (ETDEWEB)

    Fan, M. [Department of Materials Science and Engineering, North Carolina State University, Campus Box 7907, Raleigh, NC 27695-7907 (United States); Liu, Y. [Department of Materials Science and Engineering, North Carolina State University, Campus Box 7907, Raleigh, NC 27695-7907 (United States); Analytical Instrumentation Facility, North Carolina State University, Raleigh, NC 27695 (United States); Jha, Rajesh; Dulikravich, George S. [Departments of Mechanical and Materials Engineering, MAIDROC, Florida International University, EC3462, 10555 West Flagler Street, Miami, FL 33174 (United States); Schwartz, J.; Koch, C.C. [Department of Materials Science and Engineering, North Carolina State University, Campus Box 7907, Raleigh, NC 27695-7907 (United States)

    2016-12-15

    Tempering is a critical step in Alnico alloy processing, yet the effects of tempering on microstructure have not been well studied. Here we report these effects, and in particular the effects on the Cu-Ni bridges. Energy-dispersive X-ray spectroscopy (EDS) maps and line scans show that tempering changes the elemental distribution in the Cu-Ni bridges, but not the morphology and distribution of Cu-bridges. The Cu concentration in the Cu-Ni bridges increases after tempering while other element concentrations decrease, especially Ni and Al. Furthermore, tempering sharpens the Cu bridge boundaries. These effects are primarily related to the large 2C{sub 44}/(C{sub 11}−C{sub 12}) ratio for Cu, largest of all elements in Alnico. In addition, the Ni-Cu loops around the α{sub 1} phases become inconspicuous with tempering. The diffusion of Fe and Co to the α{sub 1} phase during tempering, which increases the difference of saturation magnetization between the α{sub 1} and α{sub 2} phases, is observed by EDS. In summary, α{sub 1}, α{sub 2} and Cu-bridges are concentrated with their major elements during tempering which improves the magnetic properties. The formation of these features formed through elemental diffusion is discussed via energy theories. - Highlights: • Tempering changes the elemental distribution in the Cu-Ni bridges, but not morphology. • Cu concentration in the Cu-Ni bridges increases after tempering while others decrease. • These effects are related to the large 2C{sub 44}/(C{sub 11}−C{sub 12}) ratio for Cu. • The Ni-Cu loops around the α{sub 1} phases become inconspicuous with tempering. • The diffusion of Fe and Co to the α{sub 1} phase during tempering is observed by EDS.

  3. Method to Predict Tempering of Steels Under Non-isothermal Conditions

    Science.gov (United States)

    Poirier, D. R.; Kohli, A.

    2017-05-01

    A common way of representing the tempering responses of steels is with a "tempering parameter" that includes the effect of temperature and time on hardness after hardening. Such functions, usually in graphical form, are available for many steels and have been applied for isothermal tempering. In this article, we demonstrate that the method can be extended to non-isothermal conditions. Controlled heating experiments were done on three grades in order to verify the method.

  4. Time-dependent temper embrittlement of reactor pressure vessel steel: Correlation between microstructural evolution and mechanical properties during tempering at 650 °C

    Energy Technology Data Exchange (ETDEWEB)

    Li, Chuanwei; Han, Lizhan; Yan, Guanghua; Liu, Qingdong; Luo, Xiaomeng; Gu, Jianfeng, E-mail: gujf@sjtu.edu.cn

    2016-11-15

    The microstructural evolution of reactor pressure vessel (RPV) steel and its effect on the mechanical properties during tempering at 650 °C were studied to reveal the time-dependent toughness and temper embrittlement. The results show that the toughening of the material should be attributed to the decomposition of the martensite/austenite constituents and uniform distribution of carbides. When the tempering duration was 5 h, the strength of the investigated steel decreased to strike a balance with the material impact toughness that reached a plateau. As the tempering duration was further increased, the material strength was slightly reduced but the material impact toughness deteriorated drastically. This time-dependent temper embrittlement is different from traditional temper embrittlement, and it can be partly attributed to the softening of the matrix and the broadening of the ferrite laths. Moreover, the dimensions and distribution of the grain carbides are the most important factors of the impact toughness. - Highlights: • The fracture mechanism of reactor pressure vessel (RPV) steels under impact load was investigated. • The Charpy V-notch impact test and the hinge model were employed for the study. • Grain boundary carbides play a key role in the impact toughness and fracture toughness. • The dependence of the deterioration of impact toughness on tempering time was analyzed for the first time.

  5. Prevalence and genetic variability of Plesiomonas shigelloides in temperate climate surface waters of the Pannonian Plain

    Directory of Open Access Journals (Sweden)

    Petrušić Milivoje

    2018-01-01

    Full Text Available Plesiomonas shigelloides, a Gram-negative bacterium and the causative agent of intestinal diseases and extraintestinal infections in humans and animals, is most frequently found in aquatic environments in tropical or subtropical areas. The present study was designed to establish the prevalence and genetic variability of P. shigelloides in surface waters (lakes, rivers, ponds, inlets and canals located in a temperate climate zone, namely the Pannonian Plain of the northern part of Serbia and southern part of Hungary. The strains were isolated directly by plating samples on inositol-brilliant green-bile agar with neutral red or phenol red as indicators. Our results indicate that phenol red effectively facilitates differentiation of P. shigelloides from other bacteria. A number of samples were enriched using alkaline peptone water broth, peptone inositolbile broth and tetrathionate broth. The recovery of the isolates was more successful with the first medium. Out of a total of 51 water samples collected from 28 different locations, 22 samples (43.1% were found positive for P. shigelloides. Among the 37 isolated strains, 34 were from lakes (Šatrinci, Ludaš, Panonija, Krivaja, Pecs, Kapetanski rit, Pavlovci, Kovacsszenaja, Dobrodol, Vranjaš, Borkovac, Hermann Otto, Sot, Šelevrenac, Zobnatica, Palić, Orfui, Jarkovci, Čonoplja and 3 were from rivers (Danube, Sava. The strains were identified by phenotypic characteristic or by the VITEK2 system and confirmed by PCR using 23S rRNA species-specific oligos. The strains showed a high genetic variability, displaying a variety of RAPD profiles. Our results reveal for the first time a high prevalence of genetically diverse P. shigelloides populations in surface waters located in the temperate climate of central and southeastern Europe. [Project of the Serbian Ministry of Education, Science and Technological Development, Grant no. OI 172058

  6. Nitrous oxide production from temperate and tropical oyster species in response to nutrient loading

    Science.gov (United States)

    Chan, H.; Garate, M.; Moseman-Valtierra, S.

    2016-02-01

    Anthropogenic pollution, such as nitrogen (N), has the potential to increase greenhouse gas (GHG) emissions in marine ecosystems. Some organisms can be used as important biological indicators for GHG emissions to their environment based on their feeding habits. With large inputs of these anthropogenic pollutants, emissions of nitrous oxide (N2O), a potent GHG, can be potentially increased from temperate invertebrates, though not much is known about tropical invertebrates. Thus, we compared N2O emissions in response to N additions from the temperate oyster species Crassostrea virginica and compared it to a tropical species, Isognomon alatus, found in Puerto Rico. Oysters were exposed to two seawater treatments: (1) no nutrient addition (control) and (2) 100µM ammonium nitrate. Each treatment had 4-5 replicates. Measurements for dissolved N2O and nutrients were taken at the start of the incubation and then at two, four, and five hours by collecting water samples of each tank. Dissolved N2O concentrations were analyzed using gas chromatography. We hypothesized that the N addition treatment would produce more N2O for both Rhode Island and Puerto Rico. We found that there was no significant difference between the control and N enriched treatments for C. virginica over the short timespan, although the N enriched treatment did have a steady trend in increasing in N2O concentration over time. Further analysis is needed for the I. alatus, though we expect an increase in N2O emissions due to warmer water temperatures, which might enhance microbial metabolism and production of N2O. This differs from work previously done in a long-term experiment on C. virginica, which showed that N2O significantly in the N enriched treatment over 28-days. Our study shows that short-term pulses of N may not potentially increase N2O emissions, though further analysis is needed for longer-term exposures.

  7. Nematode spatial and ecological patterns from tropical and temperate rainforests.

    Directory of Open Access Journals (Sweden)

    Dorota L Porazinska

    Full Text Available Large scale diversity patterns are well established for terrestrial macrobiota (e.g. plants and vertebrates, but not for microscopic organisms (e.g. nematodes. Due to small size, high abundance, and extensive dispersal, microbiota are assumed to exhibit cosmopolitan distributions with no biogeographical patterns. This assumption has been extrapolated from local spatial scale studies of a few taxonomic groups utilizing morphological approaches. Recent molecularly-based studies, however, suggest something quite opposite. Nematodes are the most abundant metazoans on earth, but their diversity patterns are largely unknown. We conducted a survey of nematode diversity within three vertical strata (soil, litter, and canopy of rainforests at two contrasting latitudes in the North American meridian (temperate: the Olympic National Forest, WA, U.S.A and tropical: La Selva Biological Station, Costa Rica using standardized sampling designs and sample processing protocols. To describe nematode diversity, we applied an ecometagenetic approach using 454 pyrosequencing. We observed that: 1 nematode communities were unique without even a single common species between the two rainforests, 2 nematode communities were unique among habitats in both rainforests, 3 total species richness was 300% more in the tropical than in the temperate rainforest, 4 80% of the species in the temperate rainforest resided in the soil, whereas only 20% in the tropics, 5 more than 90% of identified species were novel. Overall, our data provided no support for cosmopolitanism at both local (habitats and large (rainforests spatial scales. In addition, our data indicated that biogeographical patterns typical of macrobiota also exist for microbiota.

  8. Nematode Spatial and Ecological Patterns from Tropical and Temperate Rainforests

    Science.gov (United States)

    Porazinska, Dorota L.; Giblin-Davis, Robin M.; Powers, Thomas O.; Thomas, W. Kelley

    2012-01-01

    Large scale diversity patterns are well established for terrestrial macrobiota (e.g. plants and vertebrates), but not for microscopic organisms (e.g. nematodes). Due to small size, high abundance, and extensive dispersal, microbiota are assumed to exhibit cosmopolitan distributions with no biogeographical patterns. This assumption has been extrapolated from local spatial scale studies of a few taxonomic groups utilizing morphological approaches. Recent molecularly-based studies, however, suggest something quite opposite. Nematodes are the most abundant metazoans on earth, but their diversity patterns are largely unknown. We conducted a survey of nematode diversity within three vertical strata (soil, litter, and canopy) of rainforests at two contrasting latitudes in the North American meridian (temperate: the Olympic National Forest, WA, U.S.A and tropical: La Selva Biological Station, Costa Rica) using standardized sampling designs and sample processing protocols. To describe nematode diversity, we applied an ecometagenetic approach using 454 pyrosequencing. We observed that: 1) nematode communities were unique without even a single common species between the two rainforests, 2) nematode communities were unique among habitats in both rainforests, 3) total species richness was 300% more in the tropical than in the temperate rainforest, 4) 80% of the species in the temperate rainforest resided in the soil, whereas only 20% in the tropics, 5) more than 90% of identified species were novel. Overall, our data provided no support for cosmopolitanism at both local (habitats) and large (rainforests) spatial scales. In addition, our data indicated that biogeographical patterns typical of macrobiota also exist for microbiota. PMID:22984536

  9. Joints in Tempered Glass Using Glass Dowel Discs

    DEFF Research Database (Denmark)

    Nielsen, Jens Henrik; Poulsen, Peter Noe

    One of the major reasons for using glass in structures is its transparency; however, traditional mechanical joints such as friction joints and steel dowel pinned connections are compromising the transparency. The present paper describes a novel joint which is practically maintaining the complete...... transparency of the glass. This is achieved by using a dowel disc made entirely of tempered glass. The concept of the joint is proved by pilot tests and numerical models. From the work it is seen that the load-carrying capacity of such a connection is similar to what is found for traditionally in-plane loaded...

  10. Beneficial Effects of Temperate Forage Legumes that Contain Condensed Tannins

    Directory of Open Access Journals (Sweden)

    Jennifer W. MacAdam

    2015-07-01

    Full Text Available The two temperate forage legumes containing condensed tannins (CT that promote ruminant production are birdsfoot trefoil (Lotus corniculatus L.; BFT and sainfoin (Onobrychis viciifolia Scop.; SF. Both are well-adapted to the cool-temperate climate and alkaline soils of the Mountain West USA. Condensed tannins comprise a diverse family of bioactive chemicals with multiple beneficial functions for ruminants, including suppression of internal parasites and enteric methane. Birdsfoot trefoil contains 10 to 40 g·CT·kg−1 dry matter (DM, while SF contains 30 to 80 g·CT·kg−1 DM. Our studies have focused on these two plant species and have demonstrated consistently elevated rates of gain for beef calves grazing both BFT and SF. Novel results from our BFT research include carcass dressing percentages and consumer sensory evaluations equivalent to feedlot-finished steers and significantly greater than grass-finished steers, but with omega-3 fatty acid concentrations equal to grass-finished beef. We have further demonstrated that ruminants fed BFT or SF will consume more endophyte-infected tall fescue (Schedonorus arundinaceus (Schreb. Dumort. forage or seed than ruminants fed a non-CT forage legume. There is great potential value for sustainable livestock production in the use of highly digestible, nitrogen-fixing legumes containing tannins demonstrated to improve ruminant productivity.

  11. Chilling and heat requirements for flowering in temperate fruit trees.

    Science.gov (United States)

    Guo, Liang; Dai, Junhu; Ranjitkar, Sailesh; Yu, Haiying; Xu, Jianchu; Luedeling, Eike

    2014-08-01

    Climate change has affected the rates of chilling and heat accumulation, which are vital for flowering and production, in temperate fruit trees, but few studies have been conducted in the cold-winter climates of East Asia. To evaluate tree responses to variation in chill and heat accumulation rates, partial least squares regression was used to correlate first flowering dates of chestnut (Castanea mollissima Blume) and jujube (Zizyphus jujube Mill.) in Beijing, China, with daily chill and heat accumulation between 1963 and 2008. The Dynamic Model and the Growing Degree Hour Model were used to convert daily records of minimum and maximum temperature into horticulturally meaningful metrics. Regression analyses identified the chilling and forcing periods for chestnut and jujube. The forcing periods started when half the chilling requirements were fulfilled. Over the past 50 years, heat accumulation during tree dormancy increased significantly, while chill accumulation remained relatively stable for both species. Heat accumulation was the main driver of bloom timing, with effects of variation in chill accumulation negligible in Beijing’s cold-winter climate. It does not seem likely that reductions in chill will have a major effect on the studied species in Beijing in the near future. Such problems are much more likely for trees grown in locations that are substantially warmer than their native habitats, such as temperate species in the subtropics and tropics.

  12. Chilling and heat requirements for flowering in temperate fruit trees

    Science.gov (United States)

    Guo, Liang; Dai, Junhu; Ranjitkar, Sailesh; Yu, Haiying; Xu, Jianchu; Luedeling, Eike

    2014-08-01

    Climate change has affected the rates of chilling and heat accumulation, which are vital for flowering and production, in temperate fruit trees, but few studies have been conducted in the cold-winter climates of East Asia. To evaluate tree responses to variation in chill and heat accumulation rates, partial least squares regression was used to correlate first flowering dates of chestnut ( Castanea mollissima Blume) and jujube ( Zizyphus jujube Mill.) in Beijing, China, with daily chill and heat accumulation between 1963 and 2008. The Dynamic Model and the Growing Degree Hour Model were used to convert daily records of minimum and maximum temperature into horticulturally meaningful metrics. Regression analyses identified the chilling and forcing periods for chestnut and jujube. The forcing periods started when half the chilling requirements were fulfilled. Over the past 50 years, heat accumulation during tree dormancy increased significantly, while chill accumulation remained relatively stable for both species. Heat accumulation was the main driver of bloom timing, with effects of variation in chill accumulation negligible in Beijing's cold-winter climate. It does not seem likely that reductions in chill will have a major effect on the studied species in Beijing in the near future. Such problems are much more likely for trees grown in locations that are substantially warmer than their native habitats, such as temperate species in the subtropics and tropics.

  13. Nitrous oxide emission reduction in temperate biochar-amended soils

    Science.gov (United States)

    Felber, R.; Hüppi, R.; Leifeld, J.; Neftel, A.

    2012-01-01

    Biochar, a pyrolysis product of organic residues, is an amendment for agricultural soils to improve soil fertility, sequester CO2 and reduce greenhouse gas (GHG) emissions. In highly weathered tropical soils laboratory incubations of soil-biochar mixtures revealed substantial reductions for nitrous oxide (N2O) and carbon dioxide (CO2). In contrast, evidence is scarce for temperate soils. In a three-factorial laboratory incubation experiment two different temperate agricultural soils were amended with green waste and coffee grounds biochar. N2O and CO2 emissions were measured at the beginning and end of a three month incubation. The experiments were conducted under three different conditions (no additional nutrients, glucose addition, and nitrate and glucose addition) representing different field conditions. We found mean N2O emission reductions of 60 % compared to soils without addition of biochar. The reduction depended on biochar type and soil type as well as on the age of the samples. CO2 emissions were slightly reduced, too. NO3- but not NH4+ concentrations were significantly reduced shortly after biochar incorporation. Despite the highly significant suppression of N2O emissions biochar effects should not be transferred one-to-one to field conditions but need to be tested accordingly.

  14. Temperate marine protected area provides recruitment subsidies to local fisheries.

    Science.gov (United States)

    Le Port, A; Montgomery, J C; Smith, A N H; Croucher, A E; McLeod, I M; Lavery, S D

    2017-10-25

    The utility of marine protected areas (MPAs) as a means of protecting exploited species and conserving biodiversity within MPA boundaries is supported by strong empirical evidence. However, the potential contribution of MPAs to fished populations beyond their boundaries is still highly controversial; empirical measures are scarce and modelling studies have produced a range of predictions, including both positive and negative effects. Using a combination of genetic parentage and relatedness analysis, we measured larval subsidies to local fisheries replenishment for Australasian snapper ( Chrysophrys auratus : Sparidae) from a small (5.2 km 2 ), well-established, temperate, coastal MPA in northern New Zealand. Adult snapper within the MPA contributed an estimated 10.6% (95% CI: 5.5-18.1%) of newly settled juveniles to surrounding areas (approx. 400 km 2 ), with no decreasing trend in contributions up to 40 km away. Biophysical modelling of larval dispersal matched experimental data, showing larvae produced inside the MPA dispersed over a comparable distance. These results demonstrate that temperate MPAs have the potential to provide recruitment subsidies at magnitudes and spatial scales relevant to fisheries management. The validated biophysical model provides a cost-efficient opportunity to generalize these findings to other locations and climate conditions, and potentially informs the design of MPA networks for enhancing fisheries management. © 2017 The Author(s).

  15. Abundance, distribution and feeding patterns of a temperate reef fish in subtidal environments of the Chilean coast: the importance of understory algal turf Abundancia, distribución y patrones alimentarios de un pez de arrecifes templados en ambientes submareales de la costa de Chile: la importancia de la capa de algas del subdosel

    Directory of Open Access Journals (Sweden)

    ÁLVARO T. PALMA

    2002-03-01

    Full Text Available Cheilodactylus variegatus is an abundant carnivorous demersal reef fish that lives in the shallow subtidal of the north-central Chilean coast. Characteristically, these environments are dominated by kelp forests of Lessonia trabeculata. This species preys on a great variety of benthic invertebrates, and shows particularly high consumption rates on amphipod crustaceans. In our study, two widely separated populations of C. variegatus were considered (central and northern Chile. Individuals that form part of these populations show considerable differences in their distribution, abundance and trophic behavior. In the northern zone, the species is abundant and both juveniles and adults are distributed along the whole bathymetric gradient. This contrasts with populations found in central Chile, which are more sparse and lack juveniles. The distribution and abundance patterns appear to be influenced mainly by the great abundance of diverse understory macroalgae in the northern subtidal, which harbors a large number of invertebrates, especially amphipods. In contrast, the understory algal abundance of the central zone is much lower, and does not show a direct relationship with the lesser abundance of amphipods. In general, C. variegatus maintains a high consumption rate on amphipods throughout its ontogeny but it includes several other prey items in later ontogenetic stages. The different understory algal assemblages, and their associated fauna, are likely to be the main factors influencing the patterns of abundance and distribution observed between these two geographically distinct fish populationsCheilodactylus variegatus es un pez demersal abundante que habita el submareal somero de la costa norte y central de Chile. Es característico de estos ambientes el estar dominados por praderas del alga Lessonia trabeculata. Esta especie incorpora en su dieta una variada gama de invertebrados bentónicos, mostrando una tasa particularmente alta de consumo de

  16. 46 CFR 54.25-25 - Welding of quenched and tempered steels (modifies UHT-82).

    Science.gov (United States)

    2010-10-01

    ... 46 Shipping 2 2010-10-01 2010-10-01 false Welding of quenched and tempered steels (modifies UHT-82... ENGINEERING PRESSURE VESSELS Construction With Carbon, Alloy, and Heat Treated Steels § 54.25-25 Welding of quenched and tempered steels (modifies UHT-82). (a) The qualification of welding procedures, welders, and...

  17. Rumen pH and NH3-N concentration of sheep fed temperate ...

    African Journals Online (AJOL)

    The aim of this study was to evaluate the effect of sorghum grain supplementation on ruminal pH and NH. 3-N concentration of wethers consuming a fresh temperate pasture (Lotus corniculatus) in metabolism cages. Sixteen Corriedale x Milchschaf wethers were fed temperate pastures ad libitum and were ...

  18. Effects of contrasting omnivorous fish on submerged macrophyte biomass in temperate lakes: a mesocosm experiment

    NARCIS (Netherlands)

    Dorenbosch, M.; Bakker, E.S.

    2012-01-01

    1.Freshwater fish can affect aquatic vegetation directly by consuming macrophytes or indirectly by changing water quality. However, most fish in the temperate climate zone have an omnivorous diet. The impact of fish as aquatic herbivores in temperate climates therefore remains unclear and depends on

  19. The effects of boro-tempering heat treatment on microstructural properties of ductile iron

    International Nuclear Information System (INIS)

    Kayali, Yusuf; Yalcin, Yilmaz

    2011-01-01

    In this study, the effects of boro-tempering heat treatment on microstructural properties of ductile iron were investigated. Test samples with dimensions of 10 x 10 x 55 mm were boronized at 900 o C for 1, 3 and 5 h and then tempered at four different temperatures (250, 300, 350 and 450 o C) for 1 h. Both optical microscopy and scanning electron microscopy were used to reveal the microstructural details of coating and matrix of boro-tempered ductile iron. X-ray diffraction was used to determine the constituents of the coating layer. The boride layer formed on the surface of boro-tempered ductile cast iron is tooth shape form and consisted of FeB and Fe 2 B phases. The thickness of boride layer increases as the boronizing time increases and tempering temperature decreases. Tempering temperature is more effective than boronizing time on the matrix structure. Boro-tempering heat treatment reduces the formation of lower and upper ausferritic matrix temperature according to classical austempering. This causes formation of upper ausferritic matrix in the sample when tempered at 300 o C. This is in contrast to general case which is the formation of lower ausferritic matrix via austempering at this temperature.

  20. The longevity of broadleaf deciduous trees in Northern Hemisphere temperate forests: insights from tree-ring series

    Directory of Open Access Journals (Sweden)

    Alfredo eDi Filippo

    2015-05-01

    Full Text Available Understanding the factors controlling the expression of longevity in trees is still an outstanding challenge for tree biologists and forest ecologists. We gathered tree-ring data and literature for broadleaf deciduous (BD temperate trees growing in closed-canopy old-growth forests in the Northern Hemisphere to explore the role of geographic patterns, climate variability, and growth rates on longevity. Our pan-continental analysis, covering 32 species from 12 genera, showed that 300-400 years can be considered a baseline threshold for maximum tree lifespan in many temperate deciduous forests. Maximum age varies greatly in relation to environmental features, even within the same species. Tree longevity is generally promoted by reduced growth rates across large genetic differences and environmental gradients. We argue that slower growth rates, and the associated smaller size, provide trees with an advantage against biotic and abiotic disturbance agents, supporting the idea that size, not age, is the main constraint to tree longevity. The oldest trees were living most of their life in subordinate canopy conditions and/or within primary forests in cool temperate environments and outside major storm tracks. Very old trees are thus characterized by slow growth and often live in forests with harsh site conditions and infrequent disturbance events that kill much of the trees. Temperature inversely controls the expression of longevity in mesophilous species (Fagus spp., but its role in Quercus spp. is more complex and warrants further research in disturbance ecology. Biological, ecological and historical drivers must be considered to understand the constraints imposed to longevity within different forest landscapes.

  1. Endemic shrubs in temperate arid and semiarid regions of northern China and their potentials for rangeland restoration.

    Science.gov (United States)

    Chu, Jianmin; Yang, Hongxiao; Lu, Qi; Zhang, Xiaoyan

    2015-06-03

    Some endemic shrubs in arid and semiarid ecosystems are in danger of extinction, and yet they can play useful roles in maintaining or restoring these ecosystems, thus practical efforts are needed to conserve them. The shrubs Amygdalus pedunculata Pall., Amygdalus mongolica (Maxim.) Ricker and Ammopiptanthus mongolicus (Maxim. ex Kom.) Cheng f. are endemic species in arid and semiarid regions of northern China, where rangeland desertification is pronounced due to chronic overgrazing. In this study, we tested the hypothesis that these endemic shrubs have developed adaptations to arid and semiarid environments and could play critical roles as nurse species to initiate the process of rangeland recovery. Based on careful vegetation surveys, we analysed the niches of these species in relation to precipitation, temperature and habitats. All sampling plots were categorized by these endemics and sorted by the non-metric multidimensional scaling method. Species ratios of each life form and species co-occurrence rates with the endemics were also evaluated. Annual average temperature and annual precipitation were found to be the key factors determining vegetation diversity and distributions. Amygdalus pedunculata prefers low hills and sandy land in temperate semiarid regions. Amygdalus mongolica prefers gravel deserts of temperate semiarid regions. Ammopiptanthus mongolicus prefers sandy land of temperate arid regions. Communities of A. pedunculata have the highest diversity and the largest ratios of long-lived grass species, whereas those of A. mongolicus have the lowest diversity but the largest ratios of shrub species. Communities of A. mongolica are a transition between the first two community types. These findings demonstrate that our focal endemic shrubs have evolved adaptations to arid and semiarid conditions, thus they can be nurse plants to stabilize sand ground for vegetation restoration. We suggest that land managers begin using these shrub species to restore

  2. Investigation on tempering of granular bainite in an offshore platform steel

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, Yanlei; Jia, Tao; Zhang, Xiangjun [The State Key Laboratory of Rolling and Automation, Northeastern University, P.O. Box 105, No. 11, Lane 3, Wenhua Road, HePing District, Shenyang 110819 (China); Liu, Zhenyu, E-mail: zyliu@mail.neu.edu.cn [The State Key Laboratory of Rolling and Automation, Northeastern University, P.O. Box 105, No. 11, Lane 3, Wenhua Road, HePing District, Shenyang 110819 (China); Misra, R.D.K. [Department of Metallurgical and Materials Engineering, University of Texas at El Paso, 500 W. University Avenue, El Paso, TX 79968-0521 (United States)

    2015-02-25

    Granular bainite, where M-A constituents dispersed in bainitic ferrite matrix usually presents at the half thickness region in thermo-mechanically processed heavy gauge offshore platform steel. In the present work, the decomposition of M-A constituents during tempering at 600 °C was firstly revealed by transmission electron microscopy (TEM) analysis, which primarily involves the precipitation of cementite, recovery and recrystallization of highly dislocated ferrite matrix. Then, the effect of tempering on mechanical properties was investigated by tempering at different temperature for 60 min. Results indicated that, at tempering temperature of 500–600 °C, large quantity of micro-alloying carbides precipitated and partially compensated the loss of strength mainly due to the decomposition of M-A constituents. Compared with the as-rolled state, the decomposition of M-A constituents and softening of bainitic ferrite matrix after tempering have resulted in higher density of microvoids and substantial plastic deformation before impact failure.

  3. Wear behavior of tempered and borided tool steels under various conditions

    International Nuclear Information System (INIS)

    Al-Haidary, T. J.; Faleh, M. N.

    2000-01-01

    . Tool steel 61CrV5, 50 NiCr13 and X1000Cr MoV51 were used in the first stage of this investigation. They have been treated as follows: boriding, boriding and tempering and hardening and tempering. The wear tests were conducted under fixed conditions (150 N/mm 2 , 0.48m/sec) with and without lubricant. The wear rate and coefficient of friction of 61Cr Si V5 steel have been studied in the second stage hoping to find the influence of working conditions on these parameters and then to compare these results with the case of hardening and tempering which is the usual case in the actual working field. The study gives a good indication about the improvement achieved in boriding and tempering cases (∼ 30%) as compared with hardening tempering cases in dry sliding conditions -∼5% with lubricating ones. (authors). 13 refs., 19 figs., 1 table

  4. Quantitative consideration for the tempering effect during multi-pass thermal cycle in HAZ of low-alloy steel

    International Nuclear Information System (INIS)

    Yu, Lina; Nakabayashi, Yuma; Saida, Kazuyoshi; Mochizuki, Masahito; Nishimoto, Kazutoshi; Kameyama, Masashi; Hirano, Shinro; Chigusa, Naoki

    2011-01-01

    A new Thermal Cycle Tempering Parameter (TCTP) to deal with the tempering effect during multi-pass thermal cycles has been proposed by extending Larson-Miller parameter (LMP). Experimental result revealed that the hardness in synthetic HAZ of the low alloy steel subjected to multi tempering thermal cycles has a good linear relationship with TCTP. By using this relationship, the hardness of the low-alloy steel reheated with tempering thermal cycles can be predicted when the original hardness is known. (author)

  5. Light requirements of Australian tropical vs. cool-temperate rainforest tree species show different relationships with seedling growth and functional traits.

    Science.gov (United States)

    Lusk, Christopher H; Kelly, Jeff W G; Gleason, Sean M

    2013-03-01

    A trade-off between shade tolerance and growth in high light is thought to underlie the temporal dynamics of humid forests. On the other hand, it has been suggested that tree species sorting on temperature gradients involves a trade-off between growth rate and cold resistance. Little is known about how these two major trade-offs interact. Seedlings of Australian tropical and cool-temperate rainforest trees were grown in glasshouse environments to compare growth versus shade-tolerance trade-offs in these two assemblages. Biomass distribution, photosynthetic capacity and vessel diameters were measured in order to examine the functional correlates of species differences in light requirements and growth rate. Species light requirements were assessed by field estimation of the light compensation point for stem growth. Light-demanding and shade-tolerant tropical species differed markedly in relative growth rates (RGR), but this trend was less evident among temperate species. This pattern was paralleled by biomass distribution data: specific leaf area (SLA) and leaf area ratio (LAR) of tropical species were significantly positively correlated with compensation points, but not those of cool-temperate species. The relatively slow growth and small SLA and LAR of Tasmanian light-demanders were associated with narrow vessels and low potential sapwood conductivity. The conservative xylem traits, small LAR and modest RGR of Tasmanian light-demanders are consistent with selection for resistance to freeze-thaw embolism, at the expense of growth rate. Whereas competition for light favours rapid growth in light-demanding trees native to environments with warm, frost-free growing seasons, frost resistance may be an equally important determinant of the fitness of light-demanders in cool-temperate rainforest, as seedlings establishing in large openings are exposed to sub-zero temperatures that can occur throughout most of the year.

  6. Effects of Fe and Mn deficiencies on the protein profiles of tomato (Solanum lycopersicum) xylem sap as revealed by shotgun analyses.

    Science.gov (United States)

    Ceballos-Laita, Laura; Gutierrez-Carbonell, Elain; Takahashi, Daisuke; Abadía, Anunciación; Uemura, Matsuo; Abadía, Javier; López-Millán, Ana Flor

    2018-01-06

    The aim of this work was to study the effects of Fe and Mn deficiencies on the xylem sap proteome of tomato using a shotgun proteomic approach, with the final goal of elucidating plant response mechanisms to these stresses. This approach yielded 643 proteins reliably identified and quantified with 70% of them predicted as secretory. Iron and Mn deficiencies caused statistically significant and biologically relevant abundance changes in 119 and 118 xylem sap proteins, respectively. In both deficiencies, metabolic pathways most affected were protein metabolism, stress/oxidoreductases and cell wall modifications. First, results suggest that Fe deficiency elicited more stress responses than Mn deficiency, based on the changes in oxidative and proteolytic enzymes. Second, both nutrient deficiencies affect the secondary cell wall metabolism, with changes in Fe deficiency occurring via peroxidase activity, and in Mn deficiency involving peroxidase, Cu-oxidase and fasciclin-like arabinogalactan proteins. Third, the primary cell wall metabolism was affected by both nutrient deficiencies, with changes following opposite directions as judged from the abundances of several glycoside-hydrolases with endo-glycolytic activities and pectin esterases. Fourth, signaling pathways via xylem involving CLE and/or lipids as well as changes in phosphorylation and N-glycosylation also play a role in the responses to these stresses. Biological significance In spite of being essential for the delivery of nutrients to the shoots, our knowledge of xylem responses to nutrient deficiencies is very limited. The present work applies a shotgun proteomic approach to unravel the effects of Fe and Mn deficiencies on the xylem sap proteome. Overall, Fe deficiency seems to elicit more stress in the xylem sap proteome than Mn deficiency, based on the changes measured in proteolytic and oxido-reductase proteins, whereas both nutrients exert modifications in the composition of the primary and secondary

  7. Culture-independent detection and characterisation of Mycobacterium tuberculosis and M. africanum in sputum samples using shotgun metagenomics on a benchtop sequencer

    Directory of Open Access Journals (Sweden)

    Emma L. Doughty

    2014-09-01

    Full Text Available Tuberculosis remains a major global health problem. Laboratory diagnostic methods that allow effective, early detection of cases are central to management of tuberculosis in the individual patient and in the community. Since the 1880s, laboratory diagnosis of tuberculosis has relied primarily on microscopy and culture. However, microscopy fails to provide species- or lineage-level identification and culture-based workflows for diagnosis of tuberculosis remain complex, expensive, slow, technically demanding and poorly able to handle mixed infections. We therefore explored the potential of shotgun metagenomics, sequencing of DNA from samples without culture or target-specific amplification or capture, to detect and characterise strains from the Mycobacterium tuberculosis complex in smear-positive sputum samples obtained from The Gambia in West Africa. Eight smear- and culture-positive sputum samples were investigated using a differential-lysis protocol followed by a kit-based DNA extraction method, with sequencing performed on a benchtop sequencing instrument, the Illumina MiSeq. The number of sequence reads in each sputum-derived metagenome ranged from 989,442 to 2,818,238. The proportion of reads in each metagenome mapping against the human genome ranged from 20% to 99%. We were able to detect sequences from the M. tuberculosis complex in all eight samples, with coverage of the H37Rv reference genome ranging from 0.002X to 0.7X. By analysing the distribution of large sequence polymorphisms (deletions and the locations of the insertion element IS6110 and single nucleotide polymorphisms (SNPs, we were able to assign seven of eight metagenome-derived genomes to a species and lineage within the M. tuberculosis complex. Two metagenome-derived mycobacterial genomes were assigned to M. africanum, a species largely confined to West Africa; the others that could be assigned belonged to lineages T, H or LAM within the clade of “modern” M. tuberculosis

  8. Microevolution of European temperate oaks in response to environmental changes.

    Science.gov (United States)

    Kremer, Antoine

    2016-01-01

    This review reconstructs microevolutionary processes that allowed long-lived species as temperate oaks (Quercus petraea and Q. robur) to cope with climate change since the last glacial maximum, by assembling insights from complementary synchronic and allochronic approaches. Paleobotanical and genetic investigations show that oaks migrated at larger velocities than expected, thanks to long-distance rare events and most likely human interferences. Hybridization was a key mechanism accelerating migration and enhancing species succession. Common garden experiments and genome wide association studies demonstrated that diversifying selection across large environmental gradients contributed to rapid local adaptation. Finally the review explores how lessons taken from past evolutionary scenarios may help to predict future responses of oaks to ongoing climate change. Copyright © 2016. Published by Elsevier SAS.

  9. Temperance internationalism: Guy Hayler and the World Prohibition Federation.

    Science.gov (United States)

    Fahey, David M

    2006-01-01

    The World Prohibition Federation, organized in 1909, and the International Record, published from 1917 to 1968, sought to internationalize the temperance movement by collecting and disseminating anti-drink news from around the globe. The Federation was based in London, and most of its activities were English-speakers. A British reformer named Guy Hayler served as its honorary president for thirty years and edited the "International Record" until his death in 1943. The Federation emphasized that prohibitionists comprised a moral community, united regardless of race, religion, nationality, or politics. Poorly funded, the Federation had difficulty competing with the World League against Alcoholism after the Anti-Saloon League of America organized this rival propaganda society in 1919.

  10. Influence of titanium on the tempering structure of austenitic steels

    International Nuclear Information System (INIS)

    Ghuezaiel, M.J.

    1985-10-01

    The microstructure of titanium-stabilized and initially deformed (approximately 20%) austenitic stainless steels used in structures of fast neutrons reactors has been studied after one hour duration annealings (500 0 C) by X-ray diffraction, optical microscopy, microhardness and transmission electron microscopy. The studied alloys were either of industrial type CND 17-13 (0.23 to 0.45 wt% Ti) or pure steels (18% Cr, 14% Ni, 0 or 0.3 wt% Ti). During tempering, the pure steels presented some restauration before recristallization. In the industrial steels, only recristallization occurred, and this only in the most deformed steel. Precipitation does not occur in the titanium-free pure steel. In industrial steels, many intermetallic phases are formed when recristallization starts [fr

  11. Temporal flexibility of reproduction in temperate-breeding dabbling ducks

    Science.gov (United States)

    Krapu, Gary L.

    2000-01-01

    I compared nesting intervals during three consecutive years in five species of temperate-nesting dabbling ducks (Mallard [Anas platyrhynchos], Northern Pintail [Anas acuta], Northern Shoveler [Anas clypeata], Blue-winged Teal [Anas discors], Gadwall [Anas strepera]) and assessed whether differences existed in timing of refractoriness. Most nesting by females of all five species ended by the summer solstice. Nesting ended earliest for Northern Shovelers and Northern Pintails and latest for Gadwalls. Some Mallards, Blue-winged Teal, and Gadwalls continued to nest into mid- and late summer, whereas Northern Shovelers and Northern pintails did not. Mallards, Blue-winged Teal, and Gadwalls accounted for 99% (81 of 82) of flightless broods resulting from nests initiated during mid- or late summer in North Dakota and 98% (58 of 59) of flightless juveniles shot on or after 1 October by a random sample of duck hunters from across the United States. Early cessation of breeding by Northern Shovelers may have evolved in response to the species' limited flexibility in diet. Photorefractory mechanisms that limit most breeding to spring presumably evolved in response to severe constraints on reproductive success when nesting continued through summer(e.g. mortality of late-hatched young and molting females due to low temperatures). Interspecific differences in photosensitivity may account for variation in timing of cessation of nesting in late spring, but controlled experiments are needed to assess the possible role of non-photic influences. My results suggest that the refractory mechanisms controlling length of the breeding in temperate-nesting dabbling ducks are more varied and complex than previously thought, with non-photic influences (e.g. water conditions, food availability, food quality) having a larger role than indicated by earlier research.

  12. Influence of tempering on mechanical properties of ferritic martensitic steels

    International Nuclear Information System (INIS)

    Chun, Y. B.; Han, C. H.; Choi, B. K.; Lee, D. W.; Kim, T. K.; Jeong, Y. H.; Cho, S.

    2012-01-01

    In the mid-1980s research programs for development of low activation materials began. This is based on the US Nuclear Regulatory Commission Guidelines (10CFR part 61) that were developed to reduce long-lived radioactive isotopes, which allows nuclear reactor waste to be disposed of by shallow land burial when removed from service. Development of low activation materials is also key issue in nuclear fusion systems, as the structural components can became radioactive due to nuclear transmutation caused by exposure to high dose neutron irradiation. Reduced-activation ferritic martensitic (RAFM) steels have been developed in the leading countries in nuclear fusion technology, and are now being considered as primary candidate material for the test blanket module (TBM) in the international thermonuclear experiment reactor (ITER). RAFM steels developed so far (e.g., EUROFER 97 and F82H) meet the requirement for structural application in the ITER. However, if such alloys are used in the DEMO or commercial fusion reactor is still unclear, as the reactors are designed to operate under much severe conditions (i.e., higher outlet coolant temperature and neutron fluences). Such harsh operating conditions lead to development of RAFM steels with better creep and irradiation resistances. Mechanical properties of RAFM steels are strongly affected by microstructural features including the distribution, size and type of precipitates, dislocation density and grain size. For a given composition, such microstructural characteristics are determined mainly by thermo-mechanical process employed to fabricate the final product, and accordingly a final heat treatment, i.e., tempering is the key step to control the microstructure and mechanical properties. In the present work, we investigated mechanical properties of the RAFM steels with a particular attention being paid to effects of tempering on impact and creep properties

  13. Social implications of residential demand response in cool temperate climates

    International Nuclear Information System (INIS)

    Darby, Sarah J.; McKenna, Eoghan

    2012-01-01

    Residential electrical demand response (DR) offers the prospect of reducing the environmental impact of electricity use, and also the supply costs. However, the relatively small loads and numerous actors imply a large effort: response ratio. Residential DR may be an essential part of future smart grids, but how viable is it in the short to medium term? This paper reviews some DR concepts, then evaluates the propositions that households in cool temperate climates will be in a position to contribute to grid flexibility within the next decade, and that that they will allow some automated load control. Examples of demand response from around the world are discussed in order to assess the main considerations for cool climates. Different tariff types and forms of control are assessed in terms of what is being asked of electricity users, with a focus on real-time pricing and direct load control in energy systems with increasingly distributed resources. The literature points to the significance of thermal loads, supply mix, demand-side infrastructure, market regulation, and the framing of risks and opportunities associated with DR. In concentrating on social aspects of residential demand response, the paper complements the body of work on technical and economic potential. - Highlights: ► Demand response implies major change in governance of electricity systems. ► Households in cool temperate climates can be flexible, mainly with thermal loads. ► DR requires simple tariffs, appropriate enabling technology, education, and feedback. ► Need to test consumer acceptance of DR in specific conditions. ► Introduce tariffs with technologies e.g., TOU tariff plus DLC with electric vehicles.

  14. Reduced germination success of temperate grassland seeds sown in dung: consequences for post-dispersal seed fate.

    Science.gov (United States)

    Milotić, T; Hoffmann, M

    2016-11-01

    Endozoochory is one of the main drivers shaping temperate grassland communities by maintaining plant populations of its constituents and enabling plants to colonize new habitats. Successful endozoochorous dispersal implies that seeds not only get consumed and survive the digestive tract but are also able to develop into viable seedlings in a dung environment. We experimentally assessed the germination probability and timing of 15 annual and perennial temperate European grassland species in cattle and horse dung and in different climatic conditions (greenhouse and outdoor conditions). Interspecific variation in germinability and germination timing are found, while life strategy had only an effect on germination timing. We found adverse effects of both cattle and horse dung on the germination characteristics of all tested grassland species, but the effects of cattle dung were more pronounced. In comparison with the control treatment, fewer seeds emerged in dung and more time was needed to germinate. Also, germination metrics clearly differed between the artificial greenhouse and outdoor conditions, with generally a lower germinability in outdoor conditions. According to our results, a large cost seems to be associated with endozoochorous dispersal in this stage of the life cycle, as seed dispersal effectiveness strongly depends on the quality of the deposition site with a lowered survival and germination probability when seeds are deposited in dung. © 2016 German Botanical Society and The Royal Botanical Society of the Netherlands.

  15. Time-scales of hydrological forcing on the geochemistry and bacterial community structure of temperate peat soils

    Science.gov (United States)

    Nunes, Flavia L. D.; Aquilina, Luc; De Ridder, Jo; Francez, André-Jean; Quaiser, Achim; Caudal, Jean-Pierre; Vandenkoornhuyse, Philippe; Dufresne, Alexis

    2015-10-01

    Peatlands are an important global carbon reservoir. The continued accumulation of carbon in peatlands depends on the persistence of anoxic conditions, in part induced by water saturation, which prevents oxidation of organic matter, and slows down decomposition. Here we investigate how and over what time scales the hydrological regime impacts the geochemistry and the bacterial community structure of temperate peat soils. Peat cores from two sites having contrasting groundwater budgets were subjected to four controlled drought-rewetting cycles. Pore water geochemistry and metagenomic profiling of bacterial communities showed that frequent water table drawdown induced lower concentrations of dissolved carbon, higher concentrations of sulfate and iron and reduced bacterial richness and diversity in the peat soil and water. Short-term drought cycles (3-9 day frequency) resulted in different communities from continuously saturated environments. Furthermore, the site that has more frequently experienced water table drawdown during the last two decades presented the most striking shifts in bacterial community structure, altering biogeochemical functioning of peat soils. Our results suggest that the increase in frequency and duration of drought conditions under changing climatic conditions or water resource use can induce profound changes in bacterial communities, with potentially severe consequences for carbon storage in temperate peatlands.

  16. Northward migrating trees establish in treefall gaps at the northern limit of the temperate-boreal ecotone, Ontario, Canada.

    Science.gov (United States)

    Leithead, Mark D; Anand, Madhur; Silva, Lucas C R

    2010-12-01

    Climate change is expected to promote migration of species. In ecotones, areas of ecological tension, disturbances may provide opportunities for some migrating species to establish in otherwise competitive environments. The size of and time since disturbance may determine the establishment ability of these species. We investigated gap dynamics of an old-growth red pine (Pinus resinosa Sol. ex Aiton) forest in the Great Lakes-St. Lawrence forest in northern Ontario, Canada, a transition zone between temperate and boreal forest. We investigated the effects of gaps of different sizes and ages on tree species abundance and basal area. Our results show that tree species from the temperate forest further south, such as red maple (Acer rubrum L.), red oak (Quercus rubra L.), and white pine (Pinus strobus L.), establish more often in large, old gaps; however, tree species that have more northern distributions, such as black spruce (Picea mariana Mill.), paper birch (Betula papyrifera Marsh.), and red pine show no difference in establishment ability with gap size or age. These differences in composition could not be attributed to autogenic succession. We conclude that treefall gaps in this forest facilitate the establishment of northward migrating species, potentially providing a pathway for future forest migration in response to recent changes in climate.

  17. Nutrition for Health and Performance: Nutritional Guidance for Military Operations in Temperate and Extreme Environments

    Science.gov (United States)

    1993-02-01

    oatmeal, Cream of Wheat, Cheerios, Chex, etc.) juices (liquid or powders) instant mashed potatoes or rice Cup of Noodles Ramen Fruit Newtons (fig, apple...juices and sugar-sweetened beverage base fruits (dried, canned, or fresh), instant mashed potatoes, rice, couscous, noodles , MRE and T ration cakes...easy-to-tolerate foods that might appeal to soldiers suffering from AMS include Cream of Wheat or oatmeal, instant mashed potatoes, instant rice

  18. Disappearance and Compressibility of Buried Pine Wood in a Warm Temperate Soil Environment.

    Science.gov (United States)

    Gholz, H L; Krazynski, L M; Volk, B G

    1991-02-01

    The rate of disappearance of buried pine wood in Florida was found to be 15%/yr.As consumption by microorganisms and termites proceeded, the wood also became more compressible. After only 5 yr, consumption and compression could account for 60-70% loss of original volume of wood under pavement near the surface of an embankment. This large volume loss occurring in a relatively short time period may be responsible for many surface deformations in pavements and weaknesses in other embankments where wood may occur as a contaminant. © 1991 by the Ecological Society of America.

  19. Building organic matter of long-term sugarcane soils in a temperate environment

    Science.gov (United States)

    Mineral soils with a history of sugarcane monoculture cropping contain less soil organic matter (-35%), and plant macro- and micronutrients, including N (-20%), K (-26%), S (-7%), Ca (-8%), B (-33%), Zn (-88%), Mn (-29%), and Cu (-26%), than adjacent non-cultivated soils. Harvesting sugarcane ‘green...

  20. Coupling bacterioplankton populations and environment to community function in coastal temperate waters

    DEFF Research Database (Denmark)

    Traving, S. J.; Bentzon-Tilia, Mikkel; Knudsen-Leerbeck, H.

    2016-01-01

    Bacterioplankton play a key role in marine waters facilitating processes important for carbon cycling. However, the influence of specific bacterial populations and environmental conditions on bacterioplankton community performance remains unclear. The aim of the present study was to identify...... drivers of bacterioplankton community functions, taking into account the variability in community composition and environmental conditions over seasons, in two contrasting coastal systems. A Least Absolute Shrinkage and Selection Operator (LASSO) analysis of the biological and chemical data obtained from...... surface waters over a full year indicated that specific bacterial populations were linked to measured functions. Namely, Synechococcus (Cyanobacteria) was strongly correlated with protease activity. Both function and community composition showed seasonal variation. However, the pattern of substrate...

  1. Handbook of parameter values for the prediction of radionuclide transfer in temperate environments

    International Nuclear Information System (INIS)

    1994-01-01

    This Handbook has been prepared in response to a widely expressed interest in having a convenient and authoritative reference for radionuclide transfer parameter values used in biospheric assessment models. It draws on data from North America and Europe, much of which was collected through projects of the International Union of Radioecologists (IUR) and the Commission of European Communities (CEC) over the last decade. It is intended to supplement existing IAEA publications on environmental assessment methodology, primarily Generic Models and Parameters for Assessing the Environmental Transfer of Radionuclides from Routine Releases, IAEA Safety Series No. 57 (1982). 219 refs, 3 figs, 32 tabs

  2. Evaluation of ULV and Thermal Fog Mosquito Control Applications in Temperate and Desert Environments

    Science.gov (United States)

    Ultra low volume (ULV) and thermal fog aerosol dispersals of pesticides have been used against mosquitoes and other insects for half a century. Although each spray technology has advantages and disadvantages, only 7 studies have been identified that directly compare their performance in the field. U...

  3. Airborne laser scanning for forested landslides investigation in temperate and tropical environments

    NARCIS (Netherlands)

    Razak, K.A.

    2014-01-01

    Landslide hazard and risk have increased over the last decades and pose a significant threat to modern society. Despite remarkable efforts of compiling and updating landslide maps at regional, national or global scales, the number of landslide events is often underestimated, especially in forested

  4. The Cytotoxicity Mechanism of 6-Shogaol-Treated HeLa Human Cervical Cancer Cells Revealed by Label-Free Shotgun Proteomics and Bioinformatics Analysis

    Directory of Open Access Journals (Sweden)

    Qun Liu

    2012-01-01

    Full Text Available Cervical cancer is one of the most common cancers among women in the world. 6-Shogaol is a natural compound isolated from the rhizome of ginger (Zingiber officinale. In this paper, we demonstrated that 6-shogaol induced apoptosis and G2/M phase arrest in human cervical cancer HeLa cells. Endoplasmic reticulum stress and mitochondrial pathway were involved in 6-shogaol-mediated apoptosis. Proteomic analysis based on label-free strategy by liquid chromatography chip quadrupole time-of-flight mass spectrometry was subsequently proposed to identify, in a non-target-biased manner, the molecular changes in cellular proteins in response to 6-shogaol treatment. A total of 287 proteins were differentially expressed in response to 24 h treatment with 15 μM 6-shogaol in HeLa cells. Significantly changed proteins were subjected to functional pathway analysis by multiple analyzing software. Ingenuity pathway analysis (IPA suggested that 14-3-3 signaling is a predominant canonical pathway involved in networks which may be significantly associated with the process of apoptosis and G2/M cell cycle arrest induced by 6-shogaol. In conclusion, this work developed an unbiased protein analysis strategy by shotgun proteomics and bioinformatics analysis. Data observed provide a comprehensive analysis of the 6-shogaol-treated HeLa cell proteome and reveal protein alterations that are associated with its anticancer mechanism.

  5. A Shotgun Proteomic Approach Reveals That Fe Deficiency Causes Marked Changes in the Protein Profiles of Plasma Membrane and Detergent-Resistant Microdomain Preparations from Beta vulgaris Roots.

    Science.gov (United States)

    Gutierrez-Carbonell, Elain; Takahashi, Daisuke; Lüthje, Sabine; González-Reyes, José Antonio; Mongrand, Sébastien; Contreras-Moreira, Bruno; Abadía, Anunciación; Uemura, Matsuo; Abadía, Javier; López-Millán, Ana Flor

    2016-08-05

    In the present study we have used label-free shotgun proteomic analysis to examine the effects of Fe deficiency on the protein profiles of highly pure sugar beet root plasma membrane (PM) preparations and detergent-resistant membranes (DRMs), the latter as an approach to study microdomains. Altogether, 545 proteins were detected, with 52 and 68 of them changing significantly with Fe deficiency in PM and DRM, respectively. Functional categorization of these proteins showed that signaling and general and vesicle-related transport accounted for approximately 50% of the differences in both PM and DRM, indicating that from a qualitative point of view changes induced by Fe deficiency are similar in both preparations. Results indicate that Fe deficiency has an impact in phosphorylation processes at the PM level and highlight the involvement of signaling proteins, especially those from the 14-3-3 family. Lipid profiling revealed Fe-deficiency-induced decreases in phosphatidic acid derivatives, which may impair vesicle formation, in agreement with the decreases measured in proteins related to intracellular trafficking and secretion. The modifications induced by Fe deficiency in the relative enrichment of proteins in DRMs revealed the existence of a group of cytoplasmic proteins that appears to be more attached to the PM in conditions of Fe deficiency.

  6. Retrospective Identification of Herpes Simplex 2 Virus-Associated Acute Liver Failure in an Immunocompetent Patient Detected Using Whole Transcriptome Shotgun Sequencing.

    Science.gov (United States)

    Ono, Atsushi; Hayes, C Nelson; Akamatsu, Sakura; Imamura, Michio; Aikata, Hiroshi; Chayama, Kazuaki

    2017-01-01

    Acute liver failure (ALF) is a severe condition in which liver function rapidly deteriorates in individuals without prior history of liver disease. While most cases result from acetaminophen overdose or viral hepatitis, in up to a third of patients, no clear cause can be identified. Liver transplantation has greatly reduced mortality among these patients, but 40% of patients recover without liver transplantation. Therefore, there is an urgent need for rapid determination of the etiology of acute liver failure. In this case report, we present a case of herpes simplex 2 virus- (HSV-) associated ALF in an immunocompetent patient. The patient recovered without LT, but the presence of HSV was not suspected at the time, precluding more effective treatment with acyclovir. To determine the etiology, stored blood samples were analyzed using whole transcriptome shotgun sequencing followed by mapping to a panel of viral reference sequences. The presence of HSV-DNA in blood samples at the time of admission was confirmed using real-time polymerase chain reaction, and, at the time of discharge, HSV-DNA levels had decreased by a factor of 10 6 . Conclusions. In ALF cases of undetermined etiology, uncommon causes should be considered, especially those for which an effective treatment is available.

  7. Retrospective Identification of Herpes Simplex 2 Virus-Associated Acute Liver Failure in an Immunocompetent Patient Detected Using Whole Transcriptome Shotgun Sequencing

    Directory of Open Access Journals (Sweden)

    Atsushi Ono

    2017-01-01

    Full Text Available Acute liver failure (ALF is a severe condition in which liver function rapidly deteriorates in individuals without prior history of liver disease. While most cases result from acetaminophen overdose or viral hepatitis, in up to a third of patients, no clear cause can be identified. Liver transplantation has greatly reduced mortality among these patients, but 40% of patients recover without liver transplantation. Therefore, there is an urgent need for rapid determination of the etiology of acute liver failure. In this case report, we present a case of herpes simplex 2 virus- (HSV- associated ALF in an immunocompetent patient. The patient recovered without LT, but the presence of HSV was not suspected at the time, precluding more effective treatment with acyclovir. To determine the etiology, stored blood samples were analyzed using whole transcriptome shotgun sequencing followed by mapping to a panel of viral reference sequences. The presence of HSV-DNA in blood samples at the time of admission was confirmed using real-time polymerase chain reaction, and, at the time of discharge, HSV-DNA levels had decreased by a factor of 106. Conclusions. In ALF cases of undetermined etiology, uncommon causes should be considered, especially those for which an effective treatment is available.

  8. Effect of tempering upon the tensile properties of a nanostructured bainitic steel

    Energy Technology Data Exchange (ETDEWEB)

    Hasan, H.S. [University of Technology, Baghdad (Iraq); Peet, M.J., E-mail: mjp54@cam.ac.uk [Department of Materials Science and Metallurgy, 27 Charles Babbage Road, Cambridge CB3 0FS (United Kingdom); Avettand-Fènoël, M-N. [Unité Matériaux Et Transformations (UMET) UMR CNRS 8207, Université, Lille 1, 59655 Villeneuve D' ASCQ (France); Bhadeshia, H.K.D.H. [Department of Materials Science and Metallurgy, 27 Charles Babbage Road, Cambridge CB3 0FS (United Kingdom)

    2014-10-06

    The tensile properties of a nanostructured carbide-free bainitic steel formed at 200–250 °C are compared against those after tempering sufficiently to remove the retained austenite. Although significant ductility is observed following tempering, a comparison of tempered and untempered samples shows that it is in fact reduced when a comparison is made at identical strength. The shape of the stress–strain curves shows clear evidence that the capacity for work hardening is reduced with the loss of austenite. The nanostructure of the steel transformed at 250 °C is examined by transmission electron microscopy, to compare the as-transformed to the tempered structure. In this case after tempering at 500 °C the energy absorbed during the tensile test is lower, due to the lower strength. Reduction of strength is caused by the slight coarsening of the bainite plates, and lower dislocation density after tempering. Considering the formation of carbide particles in high strength steel, impressive ductility is exhibited even in the tempered condition.

  9. Effect of tempering upon the tensile properties of a nanostructured bainitic steel

    International Nuclear Information System (INIS)

    Hasan, H.S.; Peet, M.J.; Avettand-Fènoël, M-N.; Bhadeshia, H.K.D.H.

    2014-01-01

    The tensile properties of a nanostructured carbide-free bainitic steel formed at 200–250 °C are compared against those after tempering sufficiently to remove the retained austenite. Although significant ductility is observed following tempering, a comparison of tempered and untempered samples shows that it is in fact reduced when a comparison is made at identical strength. The shape of the stress–strain curves shows clear evidence that the capacity for work hardening is reduced with the loss of austenite. The nanostructure of the steel transformed at 250 °C is examined by transmission electron microscopy, to compare the as-transformed to the tempered structure. In this case after tempering at 500 °C the energy absorbed during the tensile test is lower, due to the lower strength. Reduction of strength is caused by the slight coarsening of the bainite plates, and lower dislocation density after tempering. Considering the formation of carbide particles in high strength steel, impressive ductility is exhibited even in the tempered condition

  10. DETERMINATION OF THE OPTIMAL TEMPERING TEMPERATURE IN HARD FACING OF THE FORGING DIES

    Directory of Open Access Journals (Sweden)

    Milan Mutavdžić

    2012-06-01

    Full Text Available Here is analyzed selection of the optimal technology for heat treatment during the reparation of the damaged forging dies. Those tools are manufactured from alloyed tool steels for operation at elevated temperatures. Those steels are prone to self-hardening, so in reparatory hard-facing they must be preheated, additionally heated and tempered. During the tempering, in temperature interval 500-600°C, a secondary increase of hardness and decrease of impact toughness occurs, the so-called reversible tempering brittleness. Here is shown that it can be avoided by application of metallurgical and technological measures. Metallurgical measures assume adequate selection of steels. Since the considered steels are per se prone to tempering brittleness, we conducted experimental investigations to define the technological measures to avoid it. Tests on models were conducted: tempering from different temperatures, slow heating and cooling in still air. Hardness measurements showed that at 520°C, the secondary increase of hardness occurs, with drop of the impact toughness. Additional hard-facing tests included samples tempered at various regimes. Samples were prepared for mechanical and metallographic investigations. Results presented illustrate influence of additional heat treatment on structure, hardness and mechanical properties of the hard-faced layers. This enabled establishing the possibility of avoiding the tempering brittleness through technological measures.

  11. Determination of the optimal tempering temperature in hard facing of the forging dies

    Directory of Open Access Journals (Sweden)

    Milan Mutavdžić

    2012-05-01

    Full Text Available Here is analyzed selection of the optimal technology for heat treatment during the reparation of the damaged forging dies. Those tools are manufactured from alloyed tool steels for operation at elevated temperatures. Those steels are prone to self-hardening, so in reparatory hard-facing they must be preheated, additionally heated and tempered. During the tempering, in temperature interval 500-600°C, a secondary increase of hardness and decrease of impact toughness occurs, the so-called reversible tempering brittleness. Here is shown that it can be avoided by application of metallurgical and technological measures. Metallurgical measures assume adequate selection of steels. Since the considered steels are per se prone to tempering brittleness, we conducted experimental investigations to define the technological measures to avoid it. Tests on models were conducted: tempering from different temperatures, slow heating and cooling in still air. Hardness measurements showed that at 520°C, the secondary increase of hardness occurs, with drop of the impact toughness. Additional hard-facing tests included samples tempered at various regimes. Samples were prepared for mechanical and metallographic investigations. Results presented illustrate influence of additional heat treatment on structure, hardness and mechanical properties of the hard-faced layers. This enabled establishing the possibility of avoiding the tempering brittleness through technological measures. 

  12. Effect of tempering on the microstructure and mechanical properties of a medium carbon bainitic steel

    Energy Technology Data Exchange (ETDEWEB)

    Kang, J. [State Key Laboratory of Metastable Materials Science and Technology, Yanshan University, Qinhuangdao 066004 (China); Zhang, F.C., E-mail: zfc@ysu.edu.cn [State Key Laboratory of Metastable Materials Science and Technology, Yanshan University, Qinhuangdao 066004 (China); National Engineering Research Center for Equipment and Technology of Cold Strip Rolling, Yanshan University, Qinhuangdao 066004 (China); Yang, X.W. [State Key Laboratory of Metastable Materials Science and Technology, Yanshan University, Qinhuangdao 066004 (China); Lv, B. [College of Environmental and Chemical Engineering, Yanshan University, Qinhuangdao 066004 (China); Wu, K.M. [International Research Institute for Steel Technology, Wuhan University of Science and Technology, Wuhan 430081 (China); Materials Science and Metallurgy, University of Cambridge, Cambridge CB2 3QZ (United Kingdom)

    2017-02-16

    The effect of tempering on the microstructure and mechanical properties of a medium carbon bainitic steel has been investigated through optical microscopy, electron back-scattered diffraction, transmission electron microscopy and X-ray diffraction analyses. A nano-level microstructure containing plate-like bainitic ferrite and film-like retained austenite is obtained by isothermal transformation at Ms+10 °C followed by tempering within 240–450 °C. Results show that the sample tempered at 340 °C occupies the optimal balance of strength and toughness by maintaining a certain level of plasticity; samples tempered at 320 °C and 360 °C with low and high yield ratio come second. The microstructure of the steel is not sensitive to tempering temperatures before 360 °C. When the temperature is increased to 450 °C, the significantly coarsened bainitic ferrite plate and the occurrence of a small quantity of carbide precipitation account for its low toughness. The amount of retained austenite increases with the tempering temperature before 400 °C, followed by decreasing with further increase in the temperature. This behavior is related to the competition between retained austenite further transforming into bainite and decomposing into carbide during tempering.

  13. Effect of microalloying elements on microstructure and properties of quenched and tempered constructional steel

    Science.gov (United States)

    Ma, Qingshen; Huang, Leqing; Di, Guobiao; Wang, Yanfeng; Yang, Yongda; Ma, Changwen

    2017-09-01

    The effects of microalloying elements Nb, V and Ti on microstructure and properties of quenched and tempered steel were studied. Results showed that the addition of microalloying elements led to the formation of bainite and increased strength, while the austenization and ferrite transformation temperature was barely affected, i.e. 10°C. Microalloying elements shortened the incubation time for bainite transformation by refinement of austenite grain, and decreased the hardenability by forming carbides and therefore reducing the carbon content of super-cooled austenite. Either of them promoted the bainite transformation. The better tempering stability was ascribed to the as hot-rolled bainite microstructure and secondary carbide precipitation during tempering.

  14. Internal strains after recovery of hardness in tempered martensitic steels for fusion reactors

    Science.gov (United States)

    Brunelli, L.; Gondi, P.; Montanari, R.; Coppola, R.

    1991-03-01

    After tempering, with recovery of hardness, MANET steels present internal strains; these residual strains increase with quenching rate prior to tempering, and they remain after prolonged tempering times. On account of their persistence, after thermal treatments which lead to low dislocation and sub-boundary densities, the possibility has been considered that the high swelling resistance of MANET is connected with these centres of strain, probably connected with the formation, in ferrite, of Cr-enriched and contiguous Cr-depleted zones which may act as sinks for interstitials. Comparative observations on the internal strain behaviour of cold worked 316L stainless steel appear consistent with this possibility.

  15. On the tempered martensite embrittlement in AISI 4140 low alloy steel

    Energy Technology Data Exchange (ETDEWEB)

    Darwish, F.A. (Dept. of Materials Science and Metallurgy, Catholic Univ., Rio de Janeiro, RJ (Brazil)); Pereira, L.C.; Gatts, C. (Dept. of Metallurgy and Materials Engineering, Federal Univ., Rio de Janeiro, RJ (Brazil)); Graca, M.L. (Materials Div., Technical Aerospace Center, Sao Jose dos Campos, SP (Brazil))

    1991-02-01

    In the present investigation the Auger electron spectroscopy (AES) technique was used to determine local carbon and phosphorus concentrations on the fracture surfaces of as-quenched and quenched-and-tempered (at 350deg C) AISI 4140 steel specimens austenitized at low and high temperatures. The AES results were rationalized to conclude that, although carbide growth as well as phosphorus segregation are expected to contribute to tempered martensite embrittlement, carbide precipitation on prior austenite grain boundaries during tempering is seen to be the microstructural change directly responsible for the occurrence of the referred embrittlement phenomenon. (orig.).

  16. Effect of tempering time on the ballistic performance of a high strength armour steel

    OpenAIRE

    Jena, Pradipta Kumar; Senthil P., Ponguru; K., Siva Kumar

    2016-01-01

    The investigation describes and analyses the effect of tempering time on the mechanical and ballistic performance of a high strength armour steel. The steel is subjected to tempering at 300 °C for 2, 24 and 48 h. A marginal variation in strength and hardness is observed with increase in tempering time, whereas ductility and Charpy impact values are found to be decreasing. Ballistic performance of the samples are evaluated by impacting 7.62 mm and 12.7 mm armour piercing projectiles at 0° angl...

  17. Comparative assessment of single and joint effects of diuron and Irgarol 1051 on Arctic and temperate microalgae using chlorophyll a fluorescence imaging

    KAUST Repository

    Kottuparambil, Sreejith

    2017-02-06

    Ship groundings and ice-breakers can cause pollution of the polar environment with antifouling biocides such as diuron and Irgarol 1051. The present study used pulse amplitude modulated fluorometry to compare single and joint toxicities of diuron and Irgarol 1051 on two freshwater taxa of microalgae (Chlorella and Chlamydomonas) originating from Arctic and temperate regions. 30min acute toxicity tests using chlorophyll a (Chl a) fluorescence revealed that Arctic strains of microalgae were more sensitive to herbicides than their temperate counterparts. Diuron and Irgarol 1051 had equal toxicities in the Arctic species, while Irgarol 1051 was more toxic (EC50=5.55–14.70μgL−1) than diuron (EC50=12.90–>40μgL−1) in the temperate species. Toxicity assessment of various mixtures of diuron and Irgarol 1051 revealed antagonistic, additive, and synergistic effects. Our data suggest that herbicides can adversely affect photosynthesis in Arctic microalgae at relatively low levels, and their impact can increase under complex mixture conditions.

  18. Comparative assessment of single and joint effects of diuron and Irgarol 1051 on Arctic and temperate microalgae using chlorophyll a fluorescence imaging

    KAUST Repository

    Kottuparambil, Sreejith; Brown, Murray T.; Park, Jihae; Choi, Soyeon; Lee, Hojun; Choi, Han-Gu; Depuydt, Stephen; Han, Taejun

    2017-01-01

    Ship groundings and ice-breakers can cause pollution of the polar environment with antifouling biocides such as diuron and Irgarol 1051. The present study used pulse amplitude modulated fluorometry to compare single and joint toxicities of diuron and Irgarol 1051 on two freshwater taxa of microalgae (Chlorella and Chlamydomonas) originating from Arctic and temperate regions. 30min acute toxicity tests using chlorophyll a (Chl a) fluorescence revealed that Arctic strains of microalgae were more sensitive to herbicides than their temperate counterparts. Diuron and Irgarol 1051 had equal toxicities in the Arctic species, while Irgarol 1051 was more toxic (EC50=5.55–14.70μgL−1) than diuron (EC50=12.90–>40μgL−1) in the temperate species. Toxicity assessment of various mixtures of diuron and Irgarol 1051 revealed antagonistic, additive, and synergistic effects. Our data suggest that herbicides can adversely affect photosynthesis in Arctic microalgae at relatively low levels, and their impact can increase under complex mixture conditions.

  19. Classification of Snowfall Events and Their Effect on Canopy Interception Efficiency in a Temperate Montane Forest.

    Science.gov (United States)

    Roth, T. R.; Nolin, A. W.

    2015-12-01

    Forest canopies intercept as much as 60% of snowfall in maritime environments, while processes of sublimation and melt can reduce the amount of snow transferred from the canopy to the ground. This research examines canopy interception efficiency (CIE) as a function of forest and event-scale snowfall characteristics. We use a 4-year dataset of continuous meteorological measurements and monthly snow surveys from the Forest Elevation Snow Transect (ForEST) network that has forested and open sites at three elevations spanning the rain-snow transition zone to the upper seasonal snow zone. Over 150 individual storms were classified by forest and storm type characteristics (e.g. forest density, vegetation type, air temperature, snowfall amount, storm duration, wind speed, and storm direction). The between-site comparisons showed that, as expected, CIE was highest for the lower elevation (warmer) sites with higher forest density compared with the higher elevation sites where storm temperatures were colder, trees were smaller and forests were less dense. Within-site comparisons based on storm type show that this classification system can be used to predict CIE.Our results suggest that the coupling of forest type and storm type information can improve estimates of canopy interception. Understanding the effects of temperature and storm type in temperate montane forests is also valuable for future estimates of canopy interception under a warming climate.

  20. Fish and phytoplankton exhibit contrasting temporal species abundance patterns in a dynamic north temperate lake.

    Directory of Open Access Journals (Sweden)

    Gretchen J A Hansen

    Full Text Available Temporal patterns of species abundance, although less well-studied than spatial patterns, provide valuable insight to the processes governing community assembly. We compared temporal abundance distributions of two communities, phytoplankton and fish, in a north temperate lake. We used both 17 years of observed relative abundance data as well as resampled data from Monte Carlo simulations to account for the possible effects of non-detection of rare species. Similar to what has been found in other communities, phytoplankton and fish species that appeared more frequently were generally more abundant than rare species. However, neither community exhibited two distinct groups of "core" (common occurrence and high abundance and "occasional" (rare occurrence and low abundance species. Both observed and resampled data show that the phytoplankton community was dominated by occasional species appearing in only one year that exhibited large variation in their abundances, while the fish community was dominated by core species occurring in all 17 years at high abundances. We hypothesize that the life-history traits that enable phytoplankton to persist in highly dynamic environments may result in communities dominated by occasional species capable of reaching high abundances when conditions allow. Conversely, longer turnover times and broad environmental tolerances of fish may result in communities dominated by core species structured primarily by competitive interactions.

  1. Facilitation between woody and herbaceous plants that associate with arbuscular mycorrhizal fungi in temperate European forests.

    Science.gov (United States)

    Veresoglou, Stavros D; Wulf, Monika; Rillig, Matthias C

    2017-02-01

    In late-successional environments, low in available nutrient such as the forest understory, herbaceous plant individuals depend strongly on their mycorrhizal associates for survival. We tested whether in temperate European forests arbuscular mycorrhizal (AM) woody plants might facilitate the establishment of AM herbaceous plants in agreement with the mycorrhizal mediation hypothesis. We used a dataset spanning over 400 vegetation plots in the Weser-Elbe region (northwest Germany). Mycorrhizal status information was obtained from published resources, and Ellenberg indicator values were used to infer environmental data. We carried out tests for both relative richness and relative abundance of herbaceous plants. We found that the subset of herbaceous individuals that associated with AM profited when there was a high cover of AM woody plants. These relationships were retained when we accounted for environmental filtering effects using path analysis. Our findings build on the existing literature highlighting the prominent role of mycorrhiza as a coexistence mechanism in plant communities. From a nature conservation point of view, it may be possible to promote functional diversity in the forest understory through introducing AM woody trees in stands when absent.

  2. Fish and Phytoplankton Exhibit Contrasting Temporal Species Abundance Patterns in a Dynamic North Temperate Lake

    Science.gov (United States)

    Hansen, Gretchen J. A.; Carey, Cayelan C.

    2015-01-01

    Temporal patterns of species abundance, although less well-studied than spatial patterns, provide valuable insight to the processes governing community assembly. We compared temporal abundance distributions of two communities, phytoplankton and fish, in a north temperate lake. We used both 17 years of observed relative abundance data as well as resampled data from Monte Carlo simulations to account for the possible effects of non-detection of rare species. Similar to what has been found in other communities, phytoplankton and fish species that appeared more frequently were generally more abundant than rare species. However, neither community exhibited two distinct groups of “core” (common occurrence and high abundance) and “occasional” (rare occurrence and low abundance) species. Both observed and resampled data show that the phytoplankton community was dominated by occasional species appearing in only one year that exhibited large variation in their abundances, while the fish community was dominated by core species occurring in all 17 years at high abundances. We hypothesize that the life-history traits that enable phytoplankton to persist in highly dynamic environments may result in communities dominated by occasional species capable of reaching high abundances when conditions allow. Conversely, longer turnover times and broad environmental tolerances of fish may result in communities dominated by core species structured primarily by competitive interactions. PMID:25651399

  3. Synchrotron micro-diffraction analysis of the microstructure of cryogenically treated high performance tool steels prior to and after tempering

    Energy Technology Data Exchange (ETDEWEB)

    Xu, N.; Cavallaro, G.P. [Applied Centre for Structural and Synchrotron Studies, Mawson Lakes Blvd, University of South Australia, Mawson Lakes, South Australia 5095 (Australia); Gerson, A.R., E-mail: Andrea.Gerson@unisa.edu.au [Applied Centre for Structural and Synchrotron Studies, Mawson Lakes Blvd, University of South Australia, Mawson Lakes, South Australia 5095 (Australia)

    2010-10-15

    The phase transformation and strain changes within cryogenically (-196 deg. C) treated high performance tool steels (AISI H13) before and after tempering have been examined using both laboratory XRD and synchrotron micro-diffraction. The martensitic unit cell was found to have very low tetragonality as expected for low carbon steel. Tempering resulted in the diffusion of excess carbon out of the martensite phase and consequent unit cell shrinkage. In addition on tempering the martensite became more homogeneous as compared to the same samples prior to tempering. For cryogenically treated samples, the effect was most pronounced for the rapidly cooled sample which was the least homogenous sample prior to tempering but was the most homogenous sample after tempering. This suggests that the considerable degree of disorder resulting from rapid cryogenic cooling results in the beneficial release of micro-stresses on tempering thus possibly resulting in the improved wear resistance and durability observed for cryogenically treated tool steels.

  4. Synchrotron micro-diffraction analysis of the microstructure of cryogenically treated high performance tool steels prior to and after tempering

    International Nuclear Information System (INIS)

    Xu, N.; Cavallaro, G.P.; Gerson, A.R.

    2010-01-01

    The phase transformation and strain changes within cryogenically (-196 deg. C) treated high performance tool steels (AISI H13) before and after tempering have been examined using both laboratory XRD and synchrotron micro-diffraction. The martensitic unit cell was found to have very low tetragonality as expected for low carbon steel. Tempering resulted in the diffusion of excess carbon out of the martensite phase and consequent unit cell shrinkage. In addition on tempering the martensite became more homogeneous as compared to the same samples prior to tempering. For cryogenically treated samples, the effect was most pronounced for the rapidly cooled sample which was the least homogenous sample prior to tempering but was the most homogenous sample after tempering. This suggests that the considerable degree of disorder resulting from rapid cryogenic cooling results in the beneficial release of micro-stresses on tempering thus possibly resulting in the improved wear resistance and durability observed for cryogenically treated tool steels.

  5. Carbon and Water Exchanges in a Chronosequence of Temperate White Pine Forest

    Science.gov (United States)

    Arain, M.; Restrepo, N.; Pejam, M.; Khomik, M.

    2003-12-01

    Quantification of carbon sink or source strengths of temperate forest ecosystems, growing in northern mid-latitudes, is essential to resolve uncertainties in carbon balance of the world's terrestrial ecosystems. Long-term flux measurements are needed to quantify seasonal and annual variability of carbon and water exchanges from these ecosystems and to relate the variability to environmental and physiological factors. Such long-term measurements are of particular interest for different stand developmental stages. An understanding of environmental control factors is necessary to improve predictive capabilities of terrestrial carbon and water cycles. A long-term year-round measurement program has been initiated to observe energy, water vapour, and carbon dioxide fluxes in a chronosequence of white pine (Pinus Strobus) forests in southeastern Canada. White pine is an important species in the North American landscape because of its ability to adapt to dry environments. White pine efficiently grows on coarse and sandy soils, where other deciduous and conifer species cannot survive. Generally, it is the first woody species to flourish after disturbances such as fire and clearing. The climate at the study site is temperate, with a mean annual temperature of 8 degree C and a mean annual precipitation of about 800 mm. The growing season is one of the longest in Canada, with at least 150 frost-free days. Measurements at the site began in June 2002 and are continuing at present. Flux measurements at the 60 year old stand are being made using a close-path eddy covariance (EC) system, while fluxes at the three younger stands (30, 15 and 1 year old) are being measured over 10 to 20 day periods using a roving open-path EC system Soil respiration is being measured every 2-weeks across 50-m transects at all four sites using a mobile chamber system (LI-COR 6400). The mature stand was a sink of carbon with annual NEP value of 140 g C m-2 from June 2002 to May 2003. Gross ecosystem

  6. Consequences and potential problems of operating room outbursts and temper tantrums by surgeons.

    Science.gov (United States)

    Jacobs, George B; Wille, Rosanne L

    2012-01-01

    Anecdotal tales of colorful temper tantrums and outbursts by surgeons directed at operating room nurses and at times other health care providers, like residents and fellows, are part of the history of surgery and include not only verbal abuse but also instrument throwing and real harassment. Our Editor-in-Chief, Dr. Nancy Epstein, has made the literature review of "Are there truly any risks and consequences when spine surgeons mistreat their predominantly female OR nursing staff/colleagues, and what can we do about it?," an assigned topic for members of the editorial board as part of a new category entitled Ethical Note for our journal. This is a topic long overdue and I chose to research it. There is no medical literature to review dealing with nurse abuse. To research this topic, one has to involve business, industry, educational institutions, compliance standards and practices, and existing state and federal laws. I asked Dr. Rosanne Wille to co-author this paper since, as the former Dean of Nursing and then Provost and Senior Vice President for Academic Affairs at a major higher educational institution, she had personal experience with compliance regulations and both sexual harassment and employment discrimination complaints, to make this review meaningful. A review of the existing business practices and both state and federal laws strongly suggests that although there has not been any specific legal complaint that is part of the public record, any surgeon who chooses to act out his or her frustration and nervous energy demands by abusing co-workers on the health care team, and in this case specifically operating room personnel, is taking a chance of making legal history with financial outcomes which only an actual trial can predict or determine. Even more serious outcomes of an out-of-control temper tantrum and disruptive behavior can terminate, after multiple hearings and appeals, in adverse decisions affecting hospital privileges. Surgeons who abuse other

  7. Crown-To-Rhizosphere Carbon Transfer In A Temperate Mixed Forest

    Science.gov (United States)

    Siegwolf, R. T.; Steinmann, K.; Saurer, M.; Koerner, C.

    2005-12-01

    -scale forest girdling shows that current photosynthesis drives soil respiration. Nature, 411 (6839): 789-792. Pepin, S and Koerner C (2002). Web-FACE: a new canopy free-air CO2 enrichment system for tall trees in mature forests. Oecologia 133(1): 1-9. Janssens IA et al (2001) Productivity overshadows temperature in determining soil and ecosystem respiration across European forests. Global Change Biol 7:269-278 Malhi Y, Baldocchi DD, Jarvis PG (1999) The carbon balance of tropical, temperate and boreal forests. Plant Cell Environ 22:715-740 Koerner C, Asshoff R., Bignucolo O, Haettenschwiler S., Keel SG., Pela'ez-Riedl S., Pepin S, Siegwolf RTW., Zotz G. (2005). Carbon Flux and Growth in Mature Deciduous Forest Trees Exposed to Elevated CO2. Science, Vol. 309/Nr. 5739, pp. 1360-1362. Steinmann K., Siegwolf RTW, Saurer M., Koerner C. (2004) Carbon fluxes to the soil in a mature temperate forest assessed by 13C isotope tracing. Oecologia 141: 489-501

  8. Seasonal pattern of anthropogenic salinization in temperate forested headwater streams.

    Science.gov (United States)

    Timpano, Anthony J; Zipper, Carl E; Soucek, David J; Schoenholtz, Stephen H

    2018-04-15

    Salinization of freshwaters by human activities is of growing concern globally. Consequences of salt pollution include adverse effects to aquatic biodiversity, ecosystem function, human health, and ecosystem services. In headwater streams of the temperate forests of eastern USA, elevated specific conductance (SC), a surrogate measurement for the major dissolved ions composing salinity, has been linked to decreased diversity of aquatic insects. However, such linkages have typically been based on limited numbers of SC measurements that do not quantify intra-annual variation. Effective management of salinization requires tools to accurately monitor and predict salinity while accounting for temporal variability. Toward that end, high-frequency SC data were collected within the central Appalachian coalfield over 4 years at 25 forested headwater streams spanning a gradient of salinity. A sinusoidal periodic function was used to model the annual cycle of SC, averaged across years and streams. The resultant model revealed that, on average, salinity deviated approximately ±20% from annual mean levels across all years and streams, with minimum SC occurring in late winter and peak SC occurring in late summer. The pattern was evident in headwater streams influenced by surface coal mining, unmined headwater reference streams with low salinity, and larger-order salinized rivers draining the study area. The pattern was strongly responsive to varying seasonal dilution as driven by catchment evapotranspiration, an effect that was amplified slightly in unmined catchments with greater relative forest cover. Evaluation of alternative sampling intervals indicated that discrete sampling can approximate the model performance afforded by high-frequency data but model error increases rapidly as discrete sampling intervals exceed 30 days. This study demonstrates that intra-annual variation of salinity in temperate forested headwater streams of Appalachia USA follows a natural seasonal

  9. In Situ Study of Phase Transformations during Non-Isothermal Tempering of Bainitic and Martensitic Microstructures

    Directory of Open Access Journals (Sweden)

    S. Hesamodin Talebi

    2017-09-01

    Full Text Available Phase transformations during non-isothermal tempering of bainitic or martensitic microstructures obtained after quenching of a medium-carbon low-alloy steel was studied. The microstructures correspond to different locations of an as-quenched large-sized forged ingot used as a die material in the automotive industry. High-resolution dilatometry experiments were conducted to simulate the heat treatment process, as well as to investigate different phenomena occurring during non-isothermal tempering. The microstructures were characterized using optical and scanning electron microscopy. Dilatometry analyses demonstrated that tempering behavior varied significantly from bainitic to martensitic microstructures. Retained austenite, which exists between bainitic ferrite sheaves, decomposes to lower bainite causing a remarkable volume increase. It was found that this decomposition finishes below 386 °C. By contrast, martensite tempering was accompanied with a volume decrease due to the decomposition of medium-carbon martensite to low carbon martensite and carbides.

  10. Analysis of mechanical properties of steel 1045 plasma nitriding: with and without tempering

    International Nuclear Information System (INIS)

    Machado, N.T.B.; Passos, M.L.M. dos; Riani, J.C.; Recco, A.A.C.

    2014-01-01

    The purpose of this study was to evaluate the possibility of tempering during the nitriding of AISI 1045 steel. The objective was to evaluate the possibility of eliminating this phase, with the nitriding properties remaining unaltered. For this, three parameter samples were compared: quenched, tempered and nitrided for 2h; quenching and nitrided for 2h and quenching and nitrided for 4h. The analysis techniques used for characterizing the samples before and after nitriding were optical microscopy, hardness Rockwell C (HRC), scanning electron microscopy (SEM), X-ray diffraction (XRD). Results showed that phase γ is the most favorable of all parameters tested. The hardness assays showed that samples with different initial hardness (with and without tempering) and even nitriding time showed similar mechanical properties. This fact suggests that the tempering process occurred parallel to the nitriding process. (author)

  11. Evolutionary and ecological differentiation in the pantropical to warm-temperate seaweed Digenea simplex (Rhodophyta)

    NARCIS (Netherlands)

    Pakker, H; Klerk, H; vanCampen, JH; Olsen, JL; Breeman, AM

    Genetic differentiation among geographic isolates of the pantropical to warm-temperate red alga Digenea simplex (Wulfen) C. Agardh was investigated using random amplified polymorphic DNA (RAPD) markers, crossing studies, and temperature tolerances experiments. Eleven isolates representing

  12. Can Detectability Analysis Improve the Utility of Point Counts for Temperate Forest Raptors?

    Science.gov (United States)

    Temperate forest breeding raptors are poorly represented in typical point count surveys because these birds are cryptic and typically breed at low densities. In recent years, many new methods for estimating detectability during point counts have been developed, including distanc...

  13. Comparison of the segregation behavior between tempered martensite and tempered bainite in Ni-Cr-Mo high strength low alloy RPV steel

    Energy Technology Data Exchange (ETDEWEB)

    Park, Sang Gyu; Kim, Min Chul; Kim, Hyung Jun; Lee, Bong Sang [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

    2012-05-15

    SA508 Gr.4N Ni-Cr-Mo low alloy steel has an superior fracture toughness and strength, compared to commercial Mn-Mo-Ni low alloy RPV steel SA508 Gr.3. Higher strength and fracture toughness of low alloy steels could be obtained by adding Ni and Cr. So several were performed on researches on SA508 Gr.4N low alloy steel for a RPV application. The operation temperature and term of a reactor pressure vessel is more than 300 .deg. C and over 40 years. Therefore, in order to apply the SA508 Gr.4N low alloy steel for a reactor pressure vessel, the resistance of thermal embrittlement in the high temperature range including temper embrittlement is required. S. Raoul reported that the susceptibility to temper embrittlement was increasing a function of the cooling rate in SA533 steel, which suggests the martensitic microstructures resulting from increased cooling rates are more susceptible to temper embrittlement. However, this result has not been proved yet. So the comparison of temper embrittlement behavior was made between martensitic microstructure and bainitic microstructure with a viewpoint of boundary features in SA508 Gr.4N, which have mixture of tempered bainite/martensite. We have compared temper embrittlement behaviors of SA508 Gr.4N low alloy steel with changing volume fraction of martensite. The mechanical properties of these low alloy steels were evaluated after a long-term heat treatment. Then, the the segregated boundaries were observed and segregation behavior was analyzed by AES. In order to compare the misorientation distributions of model alloys, grain boundary structures were measured with EBSD

  14. Nitrogen acquisition by plants and microorganisms in a temperate grassland.

    Science.gov (United States)

    Liu, Qianyuan; Qiao, Na; Xu, Xingliang; Xin, Xiaoping; Han, Jessie Yc; Tian, Yuqiang; Ouyang, Hua; Kuzyakov, Yakov

    2016-03-10

    Nitrogen (N) limitation is common in most terrestrial ecosystems, often leading to strong competition between microorganisms and plants. The mechanisms of niche differentiation to reduce this competition remain unclear. Short-term (15)N experiments with NH4(+), NO3(-), and glycine were conducted in July, August and September in a temperate grassland to evaluate the chemical, spatial and temporal niche differentiation by competition between plants and microorganisms for N. Microorganisms preferred NH4(+) and NO3(-), while plants preferred NO3(-). Both plants and microorganisms acquired more N in August and September than in July. The soil depth had no significant effects on microbial uptake, but significantly affected plant N uptake. Plants acquired 67% of their N from the 0-5 cm soil layer and 33% from the 5-15 cm layer. The amount of N taken up by microorganisms was at least seven times than plants. Although microorganisms efficiently compete for N with plants, the competition is alleviated through chemical partitioning mainly in deeper soil layer. In the upper soil layer, neither chemical nor temporal niche separation is realized leading to strong competition between plants and microorganisms that modifies N dynamics in grasslands.

  15. Synchronous dynamics of zooplankton competitors prevail in temperate lake ecosystems.

    Science.gov (United States)

    Vasseur, David A; Fox, Jeremy W; Gonzalez, Andrew; Adrian, Rita; Beisner, Beatrix E; Helmus, Matthew R; Johnson, Catherine; Kratina, Pavel; Kremer, Colin; de Mazancourt, Claire; Miller, Elizabeth; Nelson, William A; Paterson, Michael; Rusak, James A; Shurin, Jonathan B; Steiner, Christopher F

    2014-08-07

    Although competing species are expected to exhibit compensatory dynamics (negative temporal covariation), empirical work has demonstrated that competitive communities often exhibit synchronous dynamics (positive temporal covariation). This has led to the suggestion that environmental forcing dominates species dynamics; however, synchronous and compensatory dynamics may appear at different length scales and/or at different times, making it challenging to identify their relative importance. We compiled 58 long-term datasets of zooplankton abundance in north-temperate and sub-tropical lakes and used wavelet analysis to quantify general patterns in the times and scales at which synchronous/compensatory dynamics dominated zooplankton communities in different regions and across the entire dataset. Synchronous dynamics were far more prevalent at all scales and times and were ubiquitous at the annual scale. Although we found compensatory dynamics in approximately 14% of all combinations of time period/scale/lake, there were no consistent scales or time periods during which compensatory dynamics were apparent across different regions. Our results suggest that the processes driving compensatory dynamics may be local in their extent, while those generating synchronous dynamics operate at much larger scales. This highlights an important gap in our understanding of the interaction between environmental and biotic forces that structure communities. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

  16. Soil Respiration in Semiarid Temperate Grasslands under Various Land Management.

    Directory of Open Access Journals (Sweden)

    Zhen Wang

    Full Text Available Soil respiration, a major component of the global carbon cycle, is significantly influenced by land management practices. Grasslands are potentially a major sink for carbon, but can also be a source. Here, we investigated the potential effect of land management (grazing, clipping, and ungrazed enclosures on soil respiration in the semiarid grassland of northern China. Our results showed the mean soil respiration was significantly higher under enclosures (2.17 μmol.m(-2.s(-1 and clipping (2.06 μmol.m(-2.s(-1 than under grazing (1.65 μmol.m-(2.s(-1 over the three growing seasons. The high rates of soil respiration under enclosure and clipping were associated with the higher belowground net primary productivity (BNPP. Our analyses indicated that soil respiration was primarily related to BNPP under grazing, to soil water content under clipping. Using structural equation models, we found that soil water content, aboveground net primary productivity (ANPP and BNPP regulated soil respiration, with soil water content as the predominant factor. Our findings highlight that management-induced changes in abiotic (soil temperature and soil water content and biotic (ANPP and BNPP factors regulate soil respiration in the semiarid temperate grassland of northern China.

  17. Seasonal sediment dynamics shape temperate bedrock reef communities

    Science.gov (United States)

    Figurski, Jared D.; Freiwald, Jan; Lonhart, Steve I.; Storlazzi, Curt

    2016-01-01

    Mobilized seafloor sediment can impact benthic reef communities through burial, scour, and turbidity. These processes are ubiquitous in coastal oceans and, through their influence on the survival, fitness, and interactions of species, can alter the structure and function of benthic communities. In northern Monterey Bay, California, USA, as much as 30% of the seafloor is buried or exposed seasonally, making this an ideal location to test how subtidal temperate rocky reef communities vary in the presence and absence of chronic sediment-based disturbances. Designated dynamic plots were naturally inundated by sediment in summer (50 to 100% cover) and swept clean in winter, whereas designated stable plots remained free of sediment during our study. Multivariate analyses indicated significant differences in the structure of sessile and mobile communities between dynamic and stable reef habitats. For sessile species, community structure in disturbed plots was less variable in space and time than in stable plots due to the maintenance of an early successional state. In contrast, community structure of mobile species varied more in disturbed plots than in stable plots, reflecting how mobile species distribute in response to sediment dynamics. Some species were found only in these disturbed areas, suggesting that the spatial mosaic of disturbance could increase regional diversity. We discuss how the relative ability of species to tolerate disturbance at different life history stages and their ability to colonize habitat translate into community-level differences among habitats, and how this response varies between mobile and sessile communities.

  18. Winter habitat occurrence patterns of temperate migrant birds in Belize

    Science.gov (United States)

    Dawson, D.K.; Robbins, C.S.; Sauer, J.R.

    1992-01-01

    We used mist nets and point counts to sample bird populations in 61 sites in Belize during January-March of 1987-1991. Sites were classified as forest, second growth, woody agricultural crops (citrus, mango, cacao, and cashew), or non-woody agricultural crops (rice and sugar cane). We evaluated patterns of occurence of wintering temperate migrant bird species in these habitats. Mist net captures of 22 of 31 migrant species differed significantly among habitats. Of these, 13 species were captured more frequently in the agricultural habitats. American Redstart (Setophaga ruticilla), Black-and-white Warbler (Mniotilta varia), and Magnolia Warbler (Dendroica magnolia) were among the species captured most frequently in woody agricultural habitats; captures of Common Yellowthroat (Geothlypis trichas), Indigo Bunting (Passerina cyanea), and Northern (lcterus galbula) and Orchard orioles (I. spur/anus) were highest in the non-woody agricultural sites. We relate these occurrence patterns to trends in breeding populations in North America. While count data provide a wide picture of winter habitat distribution of migrants, more intensive work is necessary to assess temporal and geographic variation of migrant bird use of agricultural habitats.

  19. Ecosystem respiration depends strongly on photosynthesis in a temperate heath

    DEFF Research Database (Denmark)

    Larsen, Klaus Steenberg; Ibrom, Andreas; Beier, Claus

    2007-01-01

    We measured net ecosystem CO2 flux (F-n) and ecosystem respiration (R-E), and estimated gross ecosystem photosynthesis (P-g) by difference, for two years in a temperate heath ecosystem using a chamber method. The exchange rates of carbon were high and of similar magnitude as for productive forest...... ecosystems with a net ecosystem carbon gain during the second year of 293 +/- 11 g C m(-2) year(-1) showing that the carbon sink strength of heather-dominated ecosystems may be considerable when C. vulgaris is in the building phase of its life cycle. The estimated gross ecosystem photosynthesis and ecosystem.......65) was improved when the P-g rate was incorporated into the model (second year; R-2 = 0.79), suggesting that daytime R-E increased with increasing photosynthesis. Furthermore, the temperature sensitivity of R-E decreased from apparent Q(10) values of 3.3 to 3.9 by the classic equation to a more realistic Q(10...

  20. Reasons to temper enthusiasm about open access nursing journals.

    Science.gov (United States)

    de Jong, Gideon

    2017-04-01

    Open access is a relatively new phenomenon within nursing science. Several papers from various nursing journals have been published recently on the disadvantages of the traditional model of purchasing proprietary fee-based databases to access scholarly information. Just few nursing scholars are less optimistic about the possible benefits of open access nursing journals. A critical reflection on the merits and pitfalls of open access journals along insights from the literature and personal opinion. Two arguments are discussed, providing justification for tempering enthusiasm about open access journals. First, only research groups with sufficient financial resources can publish in open access journals. Second, open access has conflicting incentives, where the aim is to expand production at the expense of publishing quality articles; a business model that fits well into a neoliberal discourse. There are valid reasons to criticise the traditional publishers for the excessive costs of a single article, therefore preventing the dissemination of scholarly nursing information. On the contrary, the business model of open access publishers is no less imbued with the neoliberal tendency of lining the pockets.

  1. Soil Respiration in Semiarid Temperate Grasslands under Various Land Management.

    Science.gov (United States)

    Wang, Zhen; Ji, Lei; Hou, Xiangyang; Schellenberg, Michael P

    2016-01-01

    Soil respiration, a major component of the global carbon cycle, is significantly influenced by land management practices. Grasslands are potentially a major sink for carbon, but can also be a source. Here, we investigated the potential effect of land management (grazing, clipping, and ungrazed enclosures) on soil respiration in the semiarid grassland of northern China. Our results showed the mean soil respiration was significantly higher under enclosures (2.17 μmol.m(-2).s(-1)) and clipping (2.06 μmol.m(-2).s(-1)) than under grazing (1.65 μmol.m-(2).s(-1)) over the three growing seasons. The high rates of soil respiration under enclosure and clipping were associated with the higher belowground net primary productivity (BNPP). Our analyses indicated that soil respiration was primarily related to BNPP under grazing, to soil water content under clipping. Using structural equation models, we found that soil water content, aboveground net primary productivity (ANPP) and BNPP regulated soil respiration, with soil water content as the predominant factor. Our findings highlight that management-induced changes in abiotic (soil temperature and soil water content) and biotic (ANPP and BNPP) factors regulate soil respiration in the semiarid temperate grassland of northern China.

  2. Mercury emission from a temperate lake during autumn turnover

    International Nuclear Information System (INIS)

    Wollenberg, Jennifer L.; Peters, Stephen C.

    2009-01-01

    Lakes in temperate regions stratify during summer and winter months, creating distinct layers of water differentiated by their physical and chemical characteristics. When lakes mix in autumn and spring, mercury cycling may be affected by the chemical changes that occur during mixing. Sampling was conducted in Lake Lacawac, Eastern Pennsylvania, USA, throughout the autumn of 2007 to characterize changes in emission of gaseous elemental mercury (Hg 0 ) from the lake surface and dissolved mercury profiles in the water column during mixing. Water chemistry and weather parameters were also measured, including dissolved organic carbon (DOC), iron, and solar radiation which have been shown to interact with mercury species. Results indicate that emission of Hg 0 from the lake to the atmosphere during turnover was controlled both by solar radiation and by surface water mercury concentration. As autumn turnover progressed through the months of October and November, higher mercury concentration water from the hypolimnion mixed with epilimnetic water, increasing mercury concentration in epilimnetic waters. Dissolved absorbance was significantly correlated with mercury concentrations and with iron, but DOC concentrations were essentially constant throughout the study period and did not exhibit a relationship with either dissolved mercury concentrations or emission rates. Positive correlations between dissolved mercury and iron and manganese also suggest a role for these elements in mercury transport within the lake, but iron and manganese did not demonstrate a relationship with emission rates. This research indicates that consideration of seasonal processes in lakes is important when evaluating mercury cycling in aquatic systems

  3. Growth mindset tempers the effects of poverty on academic achievement.

    Science.gov (United States)

    Claro, Susana; Paunesku, David; Dweck, Carol S

    2016-08-02

    Two largely separate bodies of empirical research have shown that academic achievement is influenced by structural factors, such as socioeconomic background, and psychological factors, such as students' beliefs about their abilities. In this research, we use a nationwide sample of high school students from Chile to investigate how these factors interact on a systemic level. Confirming prior research, we find that family income is a strong predictor of achievement. Extending prior research, we find that a growth mindset (the belief that intelligence is not fixed and can be developed) is a comparably strong predictor of achievement and that it exhibits a positive relationship with achievement across all of the socioeconomic strata in the country. Furthermore, we find that students from lower-income families were less likely to hold a growth mindset than their wealthier peers, but those who did hold a growth mindset were appreciably buffered against the deleterious effects of poverty on achievement: students in the lowest 10th percentile of family income who exhibited a growth mindset showed academic performance as high as that of fixed mindset students from the 80th income percentile. These results suggest that students' mindsets may temper or exacerbate the effects of economic disadvantage on a systemic level.

  4. Elevation alters ecosystem properties across temperate treelines globally

    Science.gov (United States)

    Mayor, Jordan R.; Sanders, Nathan J.; Classen, Aimée T.; Bardgett, Richard D.; Clément, Jean-Christophe; Fajardo, Alex; Lavorel, Sandra; Sundqvist, Maja K.; Bahn, Michael; Chisholm, Chelsea; Cieraad, Ellen; Gedalof, Ze'Ev; Grigulis, Karl; Kudo, Gaku; Oberski, Daniel L.; Wardle, David A.

    2017-01-01

    Temperature is a primary driver of the distribution of biodiversity as well as of ecosystem boundaries. Declining temperature with increasing elevation in montane systems has long been recognized as a major factor shaping plant community biodiversity, metabolic processes, and ecosystem dynamics. Elevational gradients, as thermoclines, also enable prediction of long-term ecological responses to climate warming. One of the most striking manifestations of increasing elevation is the abrupt transitions from forest to treeless alpine tundra. However, whether there are globally consistent above- and belowground responses to these transitions remains an open question. To disentangle the direct and indirect effects of temperature on ecosystem properties, here we evaluate replicate treeline ecotones in seven temperate regions of the world. We find that declining temperatures with increasing elevation did not affect tree leaf nutrient concentrations, but did reduce ground-layer community-weighted plant nitrogen, leading to the strong stoichiometric convergence of ground-layer plant community nitrogen to phosphorus ratios across all regions. Further, elevation-driven changes in plant nutrients were associated with changes in soil organic matter content and quality (carbon to nitrogen ratios) and microbial properties. Combined, our identification of direct and indirect temperature controls over plant communities and soil properties in seven contrasting regions suggests that future warming may disrupt the functional properties of montane ecosystems, particularly where plant community reorganization outpaces treeline advance.

  5. Shotgun proteomics reveals specific modulated protein patterns in tears of patients with primary open angle glaucoma naïve to therapy.

    Science.gov (United States)

    Pieragostino, Damiana; Agnifili, Luca; Fasanella, Vincenzo; D'Aguanno, Simona; Mastropasqua, Rodolfo; Di Ilio, Carmine; Sacchetta, Paolo; Urbani, Andrea; Del Boccio, Piero

    2013-06-01

    Primary open angle glaucoma (POAG) is one of the main causes of irreversible blindness worldwide. The pathogenesis of POAG is still unclear. Alteration and sclerosis of trabecular meshwork with changes in aqueous humor molecular composition seem to play the key role. Increased intraocular pressure is widely known to be the main risk factor for the onset and progression of the disease. Unfortunately, the early diagnosis of POAG still remains the main challenge. In order to provide insight into the patho-physiology of glaucoma, here we report a shotgun proteomics approach to tears of patients with POAG naïve to therapy. Our proteomics results showed 27 differential tear proteins in POAG vs. CTRL comparison (25 up regulated proteins in the POAG group and two unique proteins in the CTRL group), 16 of which were associated with inflammatory response, free radical scavenging, cell-to-cell signaling and interaction. Overall the protein modulation shown in POAG tears proves the involvement of biochemical networks linked to inflammation. Among all regulated proteins, a sub-group of 12 up-regulated proteins in naïve POAG patients were found to be down-regulated in medically controlled POAG patients treated with prostanoid analogues (PGA), as reported in our previous work (i.e., lipocalin-1, lysozyme C, lactotransferrin, proline-rich-protein 4, prolactin-inducible protein, zinc-alpha-2-glycoprotein, polymeric immunoglobulin receptor, cystatin S, Ig kappa chain C region, Ig alpha-2 chain C region, immunoglobulin J chain, Ig alpha-1 chain C region). In summary, our findings indicate that the POAG tears protein expression is a mixture of increased inflammatory proteins that could be potential biomarkers of the disease, and their regulation may be involved in the mechanism by which PGA are able to decrease the intraocular pressure in glaucoma patients.

  6. Development of a Schistosoma mansoni shotgun O-glycan microarray and application to the discovery of new antigenic schistosome glycan motifs.

    Science.gov (United States)

    van Diepen, Angela; van der Plas, Arend-Jan; Kozak, Radoslaw P; Royle, Louise; Dunne, David W; Hokke, Cornelis H

    2015-06-01

    Upon infection with Schistosoma, antibody responses are mounted that are largely directed against glycans. Over the last few years significant progress has been made in characterising the antigenic properties of N-glycans of Schistosoma mansoni. Despite also being abundantly expressed by schistosomes, much less is understood about O-glycans and antibody responses to these have not yet been systematically analysed. Antibody binding to schistosome glycans can be analysed efficiently and quantitatively using glycan microarrays, but O-glycan array construction and exploration is lagging behind because no universal O-glycanase is available, and release of O-glycans has been dependent on chemical methods. Recently, a modified hydrazinolysis method has been developed that allows the release of O-glycans with free reducing termini and limited degradation, and we applied this method to obtain O-glycans from different S. mansoni life stages. Two-dimensional HPLC separation of 2-aminobenzoic acid-labelled O-glycans generated 362 O-glycan-containing fractions that were printed on an epoxide-modified glass slide, thereby generating the first shotgun O-glycan microarray containing naturally occurring schistosome O-glycans. Monoclonal antibodies and mass spectrometry showed that the O-glycan microarray contains well-known antigenic glycan motifs as well as numerous other, potentially novel, antibody targets. Incubations of the microarrays with sera from Schistosoma-infected humans showed substantial antibody responses to O-glycans in addition to those observed to the previously investigated N- and glycosphingolipid glycans. This underlines the importance of the inclusion of these often schistosome-specific O-glycans in glycan antigen studies and indicates that O-glycans contain novel antigenic motifs that have potential for use in diagnostic methods and studies aiming at the discovery of vaccine targets. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights

  7. Membrane phospholipid composition may contribute to exceptional longevity of the naked mole-rat (Heterocephalus glaber): a comparative study using shotgun lipidomics.

    Science.gov (United States)

    Mitchell, Todd W; Buffenstein, Rochelle; Hulbert, A J

    2007-11-01

    Phospholipids containing highly polyunsaturated fatty acids are particularly prone to peroxidation and membrane composition may therefore influence longevity. Phospholipid molecules, in particular those containing docosahexaenoic acid (DHA), from the skeletal muscle, heart, liver and liver mitochondria were identified and quantified using mass-spectrometry shotgun lipidomics in two similar-sized rodents that show an approximately 9-fold difference in maximum lifespan. The naked mole rat is the longest-living rodent known with a maximum lifespan of >28 years. Total phospholipid distribution is similar in tissues of both species; DHA is only found in phosphatidylcholines (PC), phosphatidylethanolamines (PE) and phosphatidylserines (PS), and DHA is relatively more concentrated in PE than PC. Naked mole-rats have fewer molecular species of both PC and PE than do mice. DHA-containing phospholipids represent 27-57% of all phospholipids in mice but only 2-6% in naked mole-rats. Furthermore, while mice have small amounts of di-polyunsaturated PC and PE, these are lacking in naked mole-rats. Vinyl ether-linked phospholipids (plasmalogens) are higher in naked mole-rat tissues than in mice. The lower level of DHA-containing phospholipids suggests a lower susceptibility to peroxidative damage in membranes of naked mole-rats compared to mice. Whereas the high level of plasmalogens might enhance membrane antioxidant protection in naked mole-rats compared to mice. Both characteristics possibly contribute to the exceptional longevity of naked mole-rats and may indicate a special role for peroxisomes in this extended longevity.

  8. Shot-gun proteome and transcriptome mapping of the jujube floral organ and identification of a pollen-specific S-locus F-box gene

    Directory of Open Access Journals (Sweden)

    Ruihong Chen

    2017-07-01

    Full Text Available The flower is a plant reproductive organ that forms part of the fruit produced as the flowering season ends. While the number and identity of proteins expressed in a jujube (Ziziphus jujuba Mill. flower is currently unknown, integrative proteomic and transcriptomic analyses provide a systematic strategy of characterizing the floral biology of plants. We conducted a shotgun proteomic analysis on jujube flowers by using a filter-aided sample preparation tryptic digestion, followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS. In addition, transcriptomics analyses were performed on HiSeq2000 sequencers. In total, 7,853 proteins were identified accounting for nearly 30% of the ‘Junzao’ gene models (27,443. Genes identified in proteome generally showed higher RPKM (reads per kilobase per million mapped reads values than undetected genes. Gene ontology categories showed that ribosomes and intracellular organelles were the most dominant classes and accounted for 17.0% and 14.0% of the proteome mass, respectively. The top-ranking proteins with iBAQ >1010 included non-specific lipid transfer proteins, histones, actin-related proteins, fructose-bisphosphate aldolase, Bet v I type allergens, etc. In addition, we identified one pollen-specificity S-locus F-box-like gene located on the same chromosome as the S-RNase gene. Both of these may activate the behaviour of gametophyte self-incompatibility in jujube. These results reflected the protein profile features of jujube flowers and contributes new information important to the jujube breeding system.

  9. Deep Illumina-based shotgun sequencing reveals dietary effects on the structure and function of the fecal microbiome of growing kittens.

    Directory of Open Access Journals (Sweden)

    Oliver Deusch

    Full Text Available Previously, we demonstrated that dietary protein:carbohydrate ratio dramatically affects the fecal microbial taxonomic structure of kittens using targeted 16S gene sequencing. The present study, using the same fecal samples, applied deep Illumina shotgun sequencing to identify the diet-associated functional potential and analyze taxonomic changes of the feline fecal microbiome.Fecal samples from kittens fed one of two diets differing in protein and carbohydrate content (high-protein, low-carbohydrate, HPLC; and moderate-protein, moderate-carbohydrate, MPMC were collected at 8, 12 and 16 weeks of age (n = 6 per group. A total of 345.3 gigabases of sequence were generated from 36 samples, with 99.75% of annotated sequences identified as bacterial. At the genus level, 26% and 39% of reads were annotated for HPLC- and MPMC-fed kittens, with HPLC-fed cats showing greater species richness and microbial diversity. Two phyla, ten families and fifteen genera were responsible for more than 80% of the sequences at each taxonomic level for both diet groups, consistent with the previous taxonomic study. Significantly different abundances between diet groups were observed for 324 genera (56% of all genera identified demonstrating widespread diet-induced changes in microbial taxonomic structure. Diversity was not affected over time. Functional analysis identified 2,013 putative enzyme function groups were different (p<0.000007 between the two dietary groups and were associated to 194 pathways, which formed five discrete clusters based on average relative abundance. Of those, ten contained more (p<0.022 enzyme functions with significant diet effects than expected by chance. Six pathways were related to amino acid biosynthesis and metabolism linking changes in dietary protein with functional differences of the gut microbiome.These data indicate that feline feces-derived microbiomes have large structural and functional differences relating to the dietary

  10. Quantifying the effects of tempering on individual phase properties of DP980 steel with nanoindentation

    Energy Technology Data Exchange (ETDEWEB)

    Cheng, G.; Zhang, F.; Ruimi, A.; Field, D. P.; Sun, X.

    2016-06-01

    We conduct a series of thermal and mechanical testing on a commercial dual phase (DP) 980 steel in order to quantify the effects of tempering on its individual phase properties. Tempering treatment is conducted at 250 °C and 400 °C for 60 minutes each. Ferrite and martensite grains are distinguished using electron backscatter diffraction (EBSD) and scanning probe microscopy (SPM), and the martensite volume fractions (MVF) are determined based on the image quality (IQ) map. Multi-scale indentation tests combined with a newly developed inverse method are used to obtain the individual phase flow properties in each tempered DP980 sample. The results show that, i) tempering significantly reduces martensite yield strength, while it only slightly reduces the ferrite yield strength; ii) tempering temperature has a more significant influence on the work hardening exponent of ferrite than that of martensite; iii) the elastic modulus of martensite is consistently higher than that of ferrite. As a validation, a simple rule of mixtures is used to verify the above-predicted individual phase flow stresses with the experimentally obtained overall true stress vs. true strain curves. The methodology and the corresponding results shown in this study can help guide the selection of tempering parameters in optimizing the mechanical properties of DP steels for their intended applications.

  11. Influence of Mo addition on the tempered properties of 13Cr martensitic stainless steel

    International Nuclear Information System (INIS)

    Jung, Byong Ho; Ahn, Yong Sik

    1998-01-01

    In order to investigate the effect of Mo addition on the mechanical properties of 13Cr-0.2C martensitic stainless steel, tensile test and Charpy V-notch test were performed after tempering at the temperature range of 200∼700 .deg. C following austenitizing at 1100 .deg. C. The yield strength and hardness of the steel were increased with the increase of Mo content at all tempering conditions, because Mo causes retardation of precipitation and coarsening of carbides and solid solution strengthening of matrix. Except 500 .deg. C of tempering temperature, the Charpy impact energy was significantly increased with Mo content and showed the highest value at 1.5 wt% addition. The increase of impact energy of the steel containing Mo is thought to be caused by δ-ferrite formed in the tempered martensitic matrix. At 500 .deg. C tempering, Charpy impact energy was decreased drastically due to temper embrittlement and it was not possible to prevent it even though Mo was added up to 1.5 wt%

  12. A Novel Methods for Fracture Toughness Evaluation of Tool Steels with Post-Tempering Cryogenic Treatment

    Directory of Open Access Journals (Sweden)

    Ramona Sola

    2017-02-01

    Full Text Available Cryogenic treatments are usually carried out immediately after quenching, but their use can be extended to post tempering in order to improve their fracture toughness. This research paper focuses on the influence of post-tempering cryogenic treatment on the microstructure and mechanical properties of tempered AISI M2, AISI D2, and X105CrCoMo18 steels. The aforementioned steels have been analysed after tempering and tempering + cryogenic treatment with scanning electron microscopy, X-ray diffraction for residual stress measurements, and micro- and nano-indentation to determine Young’s modulus and plasticity factor measurement. Besides the improvement of toughness, a further aim of the present work is the investigation of the pertinence of a novel technique for characterizing the fracture toughness via scratch experiments on cryogenically-treated steels. Results show that the application of post-tempering cryogenic treatment on AISI M2, AISI D2, and X105CrCoMo18 steels induce precipitation of fine and homogeneously dispersed sub-micrometric carbides which do not alter hardness and Young’s modulus values, but reduce residual stresses and increase fracture toughness. Finally, scratch test proved to be an alternative simple technique to determine the fracture toughness of cryogenically treated steels.

  13. Mechanism of Secondary Hardening in Rapid Tempering of Dual-Phase Steel

    Science.gov (United States)

    Saha, Dulal Chandra; Nayak, Sashank S.; Biro, Elliot; Gerlich, Adrian P.; Zhou, Y.

    2014-12-01

    Dual-phase steel with ferrite-martensite-bainite microstructure exhibited secondary hardening in the subcritical heat affected zone during fiber laser welding. Rapid isothermal tempering conducted in a Gleeble simulator also indicated occurrence of secondary hardening at 773 K (500 °C), as confirmed by plotting the tempered hardness against the Holloman-Jaffe parameter. Isothermally tempered specimens were characterized by analytic transmission electron microscopy and high-angle annular dark-field imaging. The cementite (Fe3C) and TiC located in the bainite phase of DP steel decomposed upon rapid tempering to form needle-shaped Mo2C (aspect ratio ranging from 10 to 25) and plate-shaped M4C3 carbides giving rise to secondary hardening. Precipitation of these thermodynamically stable and coherent carbides promoted the hardening phenomenon. However, complex carbides were only seen in the tempered bainite and were not detected in the tempered martensite. The martensite phase decomposed into ferrite and spherical Fe3C, and interlath-retained austenite decomposed into ferrite and elongated carbide.

  14. Tempering of Mn and Mn-Si-V dual-phase steels

    Science.gov (United States)

    Speich, G. R.; Schwoeble, A. J.; Huffman, G. P.

    1983-06-01

    Changes in the yield behavior, strength, and ductility of a Mn and a Mn-Si-V d11Al-phase (ferrite-martensite) steel were investigated after tempering one hour at 200 to 600 °C. The change in yield behavior was complex in both steels with the yield strength first increasing and then decreasing as the tempering temperature was increased. This complex behavior is attributed to a combination of factors including carbon segregation to dislocations, a return of discontinuous yielding, and the relief of resid11Al stresses. In contrast, the tensile strength decreased continuously as the tempering temperature was increased in a manner that could be predicted from the change in hardness of the martensite phase using a simple composite strengthening model. The initial tensile ductility (total elongation) of the Mn-Si-V steel was much greater than that of the Mn steel. However, upon tempering up to 400 °C, the ductility of the Mn-Si-V decreased whereas that of the Mn steel increased. As a result, both steels had similar ductilities after tempering at 400 °C or higher temperatures. These results are attributed to the larger amounts of retained austenite in the Mn-Si-V steel (9 pct) compared to the Mn steel (3 pct) and its contribution to tensile ductility by transforming to martensite during plastic straining. Upon tempering at 400 °C, the retained austenite decomposes to bainite and its contribution to tensile ductility is eliminated.

  15. Fledgling survival increases with development time and adult survival across north and south temperate zones

    Science.gov (United States)

    Lloyd, Penn; Martin, Thomas E.

    2016-01-01

    Slow life histories are characterized by high adult survival and few offspring, which are thought to allow increased investment per offspring to increase juvenile survival. Consistent with this pattern, south temperate zone birds are commonly longer-lived and have fewer young than north temperate zone species. However, comparative analyses of juvenile survival, including during the first few weeks of the post-fledging period when most juvenile mortality occurs, are largely lacking. We combined our measurements of fledgling survival for eight passerines in South Africa with estimates from published studies of 57 north and south temperate zone songbird species to test three predictions: (1) fledgling survival increases with length of development time in the nest; (2) fledgling survival increases with adult survival and reduced brood size controlled for development time; and (3) south temperate zone species, with their higher adult survival and smaller brood sizes, exhibit higher fledgling survival than north temperate zone species controlled for development time. We found that fledgling survival was higher among south temperate zone species and generally increased with development time and adult survival within and between latitudinal regions. Clutch size did not explain additional variation, but was confounded with adult survival. Given the importance of age-specific mortality to life history evolution, understanding the causes of these geographical patterns of mortality is important.

  16. Anthropogenic impact on amorphous silica pools in temperate soils

    Directory of Open Access Journals (Sweden)

    W. Clymans

    2011-08-01

    Full Text Available Human land use changes perturb biogeochemical silica (Si cycling in terrestrial ecosystems. This directly affects Si mobilisation and Si storage and influences Si export from the continents, although the magnitude of the impact is unknown. A major reason for our lack of understanding is that very little information exists on how land use affects amorphous silica (ASi storage in soils. We have quantified and compared total alkali-extracted (PSia and easily soluble (PSie Si pools at four sites along a gradient of anthropogenic disturbance in southern Sweden. Land use clearly affects ASi pools and their distribution. Total PSia and PSie for a continuous forested site at Siggaboda Nature Reserve (66 900 ± 22 800 kg SiO2 ha−1 and 952 ± 16 kg SiO2 ha−1 are significantly higher than disturbed land use types from the Råshult Culture Reserve including arable land (28 800 ± 7200 kg SiO2 ha−1 and 239 ± 91 kg SiO2 ha−1, pasture sites (27 300 ± 5980 kg SiO2 ha−1 and 370 ± 129 kg SiO2 ha−1 and grazed forest (23 600 ± 6370 kg SiO2 ha−1 and 346 ± 123 kg SiO2 ha−1. Vertical PSia and PSie profiles show significant (p < 0.05 variation among the sites. These differences in size and distribution are interpreted as the long-term effect of reduced ASi replenishment, as well as changes in ecosystem specific pedogenic processes and increased mobilisation of the PSia in disturbed soils. We have also made a first, though rough, estimate of the magnitude of change in temperate continental ASi pools due to human disturbance. Assuming that our data are representative, we estimate that total ASi storage in soils has declined by ca. 10 % since the onset of agricultural development (3000 BCE

  17. Carbon density and distribution of six Chinese temperate forests

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    Quantifying forest carbon(C) storage and distribution is important for forest C cycling studies and terrestrial ecosystem modeling.Forest inventory and allometric approaches were used to measure C density and allocation in six representative temperate forests of similar stand age(42-59 years old) and growing under the same climate in northeastern China.The forests were an aspen-birch forest,a hardwood forest,a Korean pine plantation,a Dahurian larch plantation,a mixed deciduous forest,and a Mongolian oak forest.There were no significant differences in the C densities of ecosystem components(except for detritus) although the six forests had varying vegetation compositions and site conditions.However,the differences were significant when the C pools were normalized against stand basal area.The total ecosystem C density varied from 186.9 tC hm-2 to 349.2 tC hm-2 across the forests.The C densities of vegetation,detritus,and soil ranged from 86.3-122.7 tC hm-2,6.5-10.5 tC hm-2,and 93.7-220.1 tC hm-2,respectively,which accounted for 39.7% ± 7.1%(mean ± SD),3.3% ± 1.1%,and 57.0% ± 7.9% of the total C densities,respectively.The overstory C pool accounted for > 99% of the total vegetation C pool.The foliage biomass,small root(diameter < 5mm) biomass,root-shoot ratio,and small root to foliage biomass ratio varied from 2.08-4.72 tC hm-2,0.95-3.24 tC hm-2,22.0%-28.3%,and 34.5%-122.2%,respectively.The Korean pine plantation had the lowest foliage production efficiency(total biomass/foliage biomass:22.6 g g-1) among the six forests,while the Dahurian larch plantation had the highest small root production efficiency(total biomass/small root biomass:124.7 g g-1).The small root C density decreased with soil depth for all forests except for the Mongolian oak forest,in which the small roots tended to be vertically distributed downwards.The C density of coarse woody debris was significantly less in the two plantations than in the four naturally regenerated forests.The variability

  18. Transfer parameter values in temperate forest ecosystems: a review

    International Nuclear Information System (INIS)

    Calmon, Philippe; Thiry, Yves; Zibold, Gregor; Rantavaara, Aino; Fesenko, Sergei

    2009-01-01

    activity reduction, quantified as an ecological half-life, reflect the soil and pasture conditions at individual locations. Forests in temperate and boreal regions differ with respect to soil type and vegetation, and a faster decline of muscle activity concentrations in deer occurs in the temperate zone. However, in wild boar the caesium activity concentration shows no decline because of its special feeding habits. In the late phase, i.e. at least a few months since the external radionuclide contamination on feed plants has been removed, a T ag value of 0.01 m 2 kg -1 (fresh weight) is common for 137 Cs in the muscles of adult moose and terrestrial birds living in boreal forests, and 0.03 m 2 kg -1 (fresh weight) for arctic hare. Radiocaesium concentrations in reindeer muscle in winter may exceed the summer content by a factor of more than two, the mean T ag values for winter ranging from 0.02 to 0.8 m 2 kg -1 (fresh weight), and in summer from 0.04 to 0.4 m 2 kg -1 . The highest values are found in the year of initial contamination, followed by a gradual reduction. In waterfowl a relatively fast decline in uptake of 137 Cs has been found, with T ag values changing from 0.01 to 0.002 m 2 kg -1 (fresh weight) in the three years after the contaminating event, the rate being determined by the dynamics of 137 Cs in aquatic ecosystems.

  19. Transfer parameter values in temperate forest ecosystems: a review

    Energy Technology Data Exchange (ETDEWEB)

    Calmon, Philippe [Department of Radioecology, Institute of Radioprotection and Nuclear Safety, CE Cadarache, BP 3, 13115 Saint Paul-les-Durance Cedex (France)], E-mail: philippe.calmon@irsn.fr; Thiry, Yves [Biosphere Impact Studies, Belgian Nuclear Research Center (SCK.CEN, Foundation of Public Utility), 2400 Mol (Belgium); Zibold, Gregor [Hochschule Ravensburg-Weingarten, University of Applied Sciences, 88250 Weingarten (Germany); Rantavaara, Aino [Research and Environmental Surveillance, Radiation and Nuclear Safety Authority (STUK), BP 14, FIN-00881 Helsinki (Finland); Fesenko, Sergei [International Atomic Energy Agency (IAEA), 1400 Vienna (Austria)

    2009-09-15

    of radioactive caesium to game animals and reindeer and the rate of activity reduction, quantified as an ecological half-life, reflect the soil and pasture conditions at individual locations. Forests in temperate and boreal regions differ with respect to soil type and vegetation, and a faster decline of muscle activity concentrations in deer occurs in the temperate zone. However, in wild boar the caesium activity concentration shows no decline because of its special feeding habits. In the late phase, i.e. at least a few months since the external radionuclide contamination on feed plants has been removed, a T{sub ag} value of 0.01 m{sup 2} kg{sup -1} (fresh weight) is common for {sup 137}Cs in the muscles of adult moose and terrestrial birds living in boreal forests, and 0.03 m{sup 2} kg{sup -1} (fresh weight) for arctic hare. Radiocaesium concentrations in reindeer muscle in winter may exceed the summer content by a factor of more than two, the mean T{sub ag} values for winter ranging from 0.02 to 0.8 m{sup 2} kg{sup -1} (fresh weight), and in summer from 0.04 to 0.4 m{sup 2} kg{sup -1}. The highest values are found in the year of initial contamination, followed by a gradual reduction. In waterfowl a relatively fast decline in uptake of {sup 137}Cs has been found, with T{sub ag} values changing from 0.01 to 0.002 m{sup 2} kg{sup -1} (fresh weight) in the three years after the contaminating event, the rate being determined by the dynamics of {sup 137}Cs in aquatic ecosystems.

  20. Are all temperate lakes eutrophying in a warmer world?

    Science.gov (United States)

    Paltsev, A.; Creed, I. F.

    2017-12-01

    Freshwater lakes are at risk of eutrophication due to climate change and intensification of human activities on the planet. In relatively undisturbed areas of the temperate forest biome, lakes are "sentinels" of the effects of rising temperatures. We hypothesise that rising temperatures are driving a shift from nutrient-poor oligotrophic states to nutrient-rich eutrophic states. To test this hypothesis, we examined a time series of satellite based chlorophyll-a (a proxy of algal biomass) of 12,000+ lakes over 30 years in the Canadian portion of the Laurentian Great Lakes basin. From the time series, non-stationary trends (detected by Mann-Kendall analysis) and stationary cycles (revealed through Morlet wavelet analysis) were removed, and the standard deviation (SD) of the remaining residuals was used as an indicator of lake stability. Four classes of lake stability were identified: (1) stable (SD is consistently low); (2) destabilizing (SD increases over time); (3) unstable (SD is consistently high); and (4) stabilizing lakes (SD decreases over time). Stable lakes were either oligotrophic or eutrophic indicating the presence of two stable states in the region. Destabilizing lakes were shifting from oligotrophic to lakes with a higher trophic status (indicating eutrophication), unstable lakes were mostly mesotrophic, and stabilizing lakes were shifting from eutrophic to the lakes with lower trophic status (indicating oligotrophication). In contrast to common expectations, while many lakes (2142) were shifting from oligotrophic to eutrophic states, more lakes (3199) were showing the opposite trend and shifting from eutrophic to oligotrophic states. This finding reveals a complexity of lake responses to rising temperatures and the need to improve understanding of why some lakes shift while others do not. Future work is focused on exploring the interactive effects of global, regional, and local drivers of lake trophic states.

  1. Production of fermentables and biomass by six temperate fuelcrops

    Energy Technology Data Exchange (ETDEWEB)

    Parrish, D.J.; Gammon, T.C.; Graves, B.

    1985-12-01

    Several potential fuelcrops have been studied individually, but relatively little work has been done to compare the various temperate species in side-by-side trials. The production has been examined of readily fermentable carbohydrates and biomass by six fuelcrop candidates: grain sorghum (Sorghum bicolor), Jerusalem articoke (Helianthus tuberosus), maize (Zea Mays), sugarbeet (Beta vulgaris), sweet potato (Ipomoea batatas) and sweet sorghum (Sorghum bicolor). A randomized complete block design with four replicates was employed at each of three locations that were somewhat diverse in soil type, elevation, growing season length, and 1980 rainfall distribution. Fermentables in the harvestable dry matter were determined colorimetrically following dilute acid plus enzymatic hydrolysis. Overall, sugarbeet was the most prolific producer of fermentables (7.4 Mg/ha); Jerusalem artichoke (5.8 Mg/ha), maize (4.8 Mg/ha) and sweet sorghum stems (5.8 Mg/ha) were statistically equivalent, while sweet potato (4.0 Mg/ha) and grain sorghum (3.8 Mg/ha) were less productive than the other candidates. The crops performed somewhat differently at each location, but the most striking site-specific differences were seen at the site with the coarsest textured soil and driest season. At that location, maize produced the least fermentables (0.6 Mg/ha). Biomass production generally reflected either the amount of time each species was actively growing or limiations to growth associated with drought. No general recommendations are made concerning a preferred temperature fuelcrop. Based on the studies, however, maize may not always be the fuelcrop of choice; others, especially sugarbeet and sweet sorghum (when harvested for grain also), may be superior to maize in productivity of fermentable substrates. 6 tabs., 13 refs.

  2. Analysis of ecological thresholds in a temperate forest undergoing dieback.

    Directory of Open Access Journals (Sweden)

    Philip Martin

    Full Text Available Positive feedbacks in drivers of degradation can cause threshold responses in natural ecosystems. Though threshold responses have received much attention in studies of aquatic ecosystems, they have been neglected in terrestrial systems, such as forests, where the long time-scales required for monitoring have impeded research. In this study we explored the role of positive feedbacks in a temperate forest that has been monitored for 50 years and is undergoing dieback, largely as a result of death of the canopy dominant species (Fagus sylvatica, beech. Statistical analyses showed strong non-linear losses in basal area for some plots, while others showed relatively gradual change. Beech seedling density was positively related to canopy openness, but a similar relationship was not observed for saplings, suggesting a feedback whereby mortality in areas with high canopy openness was elevated. We combined this observation with empirical data on size- and growth-mediated mortality of trees to produce an individual-based model of forest dynamics. We used this model to simulate changes in the structure of the forest over 100 years under scenarios with different juvenile and mature mortality probabilities, as well as a positive feedback between seedling and mature tree mortality. This model produced declines in forest basal area when critical juvenile and mature mortality probabilities were exceeded. Feedbacks in juvenile mortality caused a greater reduction in basal area relative to scenarios with no feedback. Non-linear, concave declines of basal area occurred only when mature tree mortality was 3-5 times higher than rates observed in the field. Our results indicate that the longevity of trees may help to buffer forests against environmental change and that the maintenance of old, large trees may aid the resilience of forest stands. In addition, our work suggests that dieback of forests may be avoidable providing pressures on mature and juvenile trees do

  3. Radiation budget changes with dry forest clearing in temperate Argentina.

    Science.gov (United States)

    Houspanossian, Javier; Nosetto, Marcelo; Jobbágy, Esteban G

    2013-04-01

    Land cover changes may affect climate and the energy balance of the Earth through their influence on the greenhouse gas composition of the atmosphere (biogeochemical effects) but also through shifts in the physical properties of the land surface (biophysical effects). We explored how the radiation budget changes following the replacement of temperate dry forests by crops in central semiarid Argentina and quantified the biophysical radiative forcing of this transformation. For this purpose, we computed the albedo and surface temperature for a 7-year period (2003-2009) from MODIS imagery at 70 paired sites occupied by native forests and crops and calculated the radiation budget at the tropopause and surface levels using a columnar radiation model parameterized with satellite data. Mean annual black-sky albedo and diurnal surface temperature were 50% and 2.5 °C higher in croplands than in dry forests. These contrasts increased the outgoing shortwave energy flux at the top of the atmosphere in croplands by a quarter (58.4 vs. 45.9 W m(-2) ) which, together with a slight increase in the outgoing longwave flux, yielded a net cooling of -14 W m(-2) . This biophysical cooling effect would be equivalent to a reduction in atmospheric CO2 of 22 Mg C ha(-1) , which involves approximately a quarter to a half of the typical carbon emissions that accompany deforestation in these ecosystems. We showed that the replacement of dry forests by crops in central Argentina has strong biophysical effects on the energy budget which could counterbalance the biogeochemical effects of deforestation. Underestimating or ignoring these biophysical consequences of land-use changes on climate will certainly curtail the effectiveness of many warming mitigation actions, particularly in semiarid regions where high radiation load and smaller active carbon pools would increase the relative importance of biophysical forcing. © 2012 Blackwell Publishing Ltd.

  4. Microstructural, mechanical and electrochemical behaviour of a 7017 Al–Zn–Mg alloy of different tempers

    Energy Technology Data Exchange (ETDEWEB)

    Rout, Prasanta Kumar, E-mail: prasantonnet55@yahoo.com; Ghosh, M.M.; Ghosh, K.S., E-mail: ksghosh2001@yahoo.co.uk

    2015-06-15

    The aim of the investigation is to assess the microstructural features and associated physical, mechanical and electrochemical properties of a 7017 Al–Zn–Mg alloy of various tempers. A 7017 Al–Zn–Mg alloy was subjected to different ageing schedules to produce under-(T4), peak-(T6), over-(T7) and highly over-aged tempers. Optical microscopy, hardness measurement, electrical conductivity measurement, tensile testing and SEM fractographs, differential scanning calorimetry (DSC), transmission electron microscopy (TEM), and electrochemical polarization studies have been used to characterize the alloy tempers. Hardness measurement and tensile testing showed the characteristic age hardening phenomenon of aluminium alloys. Optical and TEM micrographs have revealed the variation in size of matrix strengthening η′ (MgZn{sub 2}) and also the size and distribution of grain boundary η (MgZn{sub 2}) precipitate with ageing time. DSC thermograms exhibiting exothermic and endothermic peaks indicated the characteristic solid state reaction sequence of the 7017 alloy. Potentiodynamic polarization study of the 7017 alloy of various tempers in 3.5 wt.% NaCl solution at near neutral pH showed typical active metal dissolution behaviour, but at pH 12 an active–passive–transpassive transition behaviour has been observed. - Graphical abstract: TEM micrograph of the 7017 aluminium alloy of various tempers (a, b) under aged (T4), (c, d) peak aged (T6), (e, f) over aged (T7) and (g, h) highly over-aged. Display Omitted - Highlights: • 7017 Al-Zn-Mg alloy was subjected to different artificial ageing treatments. • Characterization of 7017 alloy tempers by hardness, tensile, DSC, TEM and electrochemical behaviour. • Structure-properties relationship of the 7017 Al-Zn-Mg alloy of various tempers.

  5. Importance of adaptation and genotype × environment interactions in tropical beef breeding systems.

    Science.gov (United States)

    Burrow, H M

    2012-05-01

    This paper examines the relative importance of productive and adaptive traits in beef breeding systems based on Bos taurus and tropically adapted breeds across temperate and (sub)tropical environments. In the (sub)tropics, differences that exist between breeds in temperate environments are masked by the effects of environmental stressors. Hence in tropical environments, breeds are best categorised into breed types to compare their performance across environments. Because of the presence of environmental stressors, there are more sources of genetic variation in tropical breeding programmes. It is therefore necessary to examine the genetic basis of productive and adaptive traits for breeding programmes in those environments. This paper reviews the heritabilities and genetic relationships between economically important productive and adaptive traits relevant to (sub)tropical breeding programmes. It is concluded that it is possible to simultaneously genetically improve productive and adaptive traits in tropically adapted breeds of beef cattle grazed in tropical environments without serious detrimental consequences for either adaptation or production. However, breed-specific parameters are required for genetic evaluations. The paper also reviews the magnitude of genotype × environment (G × E) interactions impacting on production and adaptation of cattle, where 'genotype' is defined as breed (within a crossbreeding system), sire within breed (in a within-breed selection programme) or associations between economically important traits and single nucleotide polymorphisms (SNPs - within a marker-assisted selection programme). It is concluded that re-ranking of breeds across environments is best managed by the use of the breed type(s) best suited to the particular production environment. Re-ranking of sires across environments is apparent in poorly adapted breed types across extreme tropical and temperate environments or where breeding animals are selected in a temperate

  6. Effects of 28 days of resistance exercise and consuming a commercially available pre-workout supplement, NO-Shotgun®, on body composition, muscle strength and mass, markers of satellite cell activation, and clinical safety markers in males

    Directory of Open Access Journals (Sweden)

    Leutholtz Brian

    2009-08-01

    Full Text Available Abstract Purpose This study determined the effects of 28 days of heavy resistance exercise combined with the nutritional supplement, NO-Shotgun®, on body composition, muscle strength and mass, markers of satellite cell activation, and clinical safety markers. Methods Eighteen non-resistance-trained males participated in a resistance training program (3 × 10-RM 4 times/wk for 28 days while also ingesting 27 g/day of placebo (PL or NO-Shotgun® (NO 30 min prior to exercise. Data were analyzed with separate 2 × 2 ANOVA and t-tests (p Results Total body mass was increased in both groups (p = 0.001, but without any significant increases in total body water (p = 0.77. No significant changes occurred with fat mass (p = 0.62; however fat-free mass did increase with training (p = 0.001, and NO was significantly greater than PL (p = 0.001. Bench press strength for NO was significantly greater than PL (p = 0.003. Myofibrillar protein increased with training (p = 0.001, with NO being significantly greater than PL (p = 0.019. Serum IGF-1 (p = 0.046 and HGF (p = 0.06 were significantly increased with training and for NO HGF was greater than PL (p = 0.002. Muscle phosphorylated c-met was increased with training for both groups (p = 0.019. Total DNA was increased in both groups (p = 0.006, while NO was significantly greater than PL (p = 0.038. For DNA/protein, PL was decreased and NO was not changed (p = 0.014. All of the myogenic regulatory factors were increased with training; however, NO was shown to be significantly greater than PL for Myo-D (p = 0.008 and MRF-4 (p = 0.022. No significant differences were located for any of the whole blood and serum clinical chemistry markers (p > 0.05. Conclusion When combined with heavy resistance training for 28 days, NO-Shotgun® is not associated with any negative side effects, nor does it abnormally impact any of the clinical chemistry markers. Rather, NO-Shotgun® effectively increases muscle strength and mass

  7. Prey type and foraging ecology of Sanderlings Calidris alba in different climate zones: are tropical areas more favourable than temperate sites?

    Directory of Open Access Journals (Sweden)

    Kirsten Grond

    2015-08-01

    Full Text Available Sanderlings (Calidris alba are long-distance migratory shorebirds with a non-breeding range that spans temperate and tropical coastal habitats. Breeding in the High Arctic combined with non-breeding seasons in the tropics necessitate long migrations, which are energetically demanding. On an annual basis, the higher energy expenditures during migration might pay off if food availability in the tropics is higher than at temperate latitudes. We compared foraging behaviour of birds at a north temperate and a tropical non-breeding site in the Netherlands and Ghana, respectively. In both cases the birds used similar habitats (open beaches, and experienced similar periods of daylight, which enabled us to compare food abundance and availability, and behavioural time budgets and food intake. During the non-breeding season, Sanderlings in the Netherlands spent 79% of their day foraging; in Ghana birds spent only 38% of the daytime period foraging and the largest proportion of their time resting (58%. The main prey item in the Netherlands was the soft-bodied polychaete Scolelepis squamata, while Sanderlings in Ghana fed almost exclusively on the bivalve Donax pulchellus, which they swallowed whole and crushed internally. Average availability of polychaete worms in the Netherlands was 7.4 g ash free dry mass (AFDM m−2, which was one tenth of the 77.1 g AFDM m−2 estimated for the beach in Ghana. In the tropical environment of Ghana the Sanderlings combined relatively low energy requirements with high prey intake rates (1.64 mg opposed to 0.13 mg AFDM s−1 for Ghana and the Netherlands respectively. Although this may suggest that the Ghana beaches are the most favourable environment, processing the hard-shelled bivalve (D. pulchellus which is the staple food could be costly. The large amount of daytime spent resting in Ghana may be indicative of the time needed to process the shell fragments, rather than indicate rest.

  8. Wave exposure as a predictor of benthic habitat distribution on high energy temperate reefs

    Directory of Open Access Journals (Sweden)

    Alex eRattray

    2015-02-01

    Full Text Available The new found ability to measure physical attributes of the marine environment at high resolution across broad spatial scales has driven the rapid evolution of benthic habitat mapping as a field in its own right. Improvement of the resolution and ecological validity of seafloor habitat distribution models has, for the most part, paralleled developments in new generations of acoustic survey tools such as multibeam echosounders. While sonar methods have been well demonstrated to provide useful proxies of the relatively static geophysical patterns that reflect distribution of benthic species and assemblages, the spatially and temporally variable influence of hydrodynamic energy on habitat distribution have been less well studied. Here we investigate the role of wave exposure on patterns of distribution of near-shore benthic habitats. A high resolution spectral wave model was developed for a 624 km2 site along Cape Otway, a major coastal feature of western Victoria, Australia. Comparison of habitat classifications implemented using the Random Forests algorithm established that significantly more accurate estimations of habitat distribution were obtained by including a fine-scale numerical wave model, extended to the seabed using linear wave theory, than by using depth and seafloor morphology information alone. Variable importance measures and map interpretation indicated that the spatial variation in wave induced bottom orbital velocity was most influential in discriminating habitat the classes containing canopy forming kelp Ecklonia radiata, a foundation kelp species that affects biodiversity and ecological functioning on shallow reefs across temperate Australasia. We demonstrate that hydrodynamic models reflecting key environmental drivers on wave exposed coastlines are important in accurately defining distributions of benthic habitats.

  9. Silviculture and biology of short-rotation woody crops in temperate regions: Then and now

    Energy Technology Data Exchange (ETDEWEB)

    Dickmann, Donald I. [Department of Forestry, Michigan State University, East Lansing, MI 48824-1222 (United States)

    2006-08-15

    Although its roots are in antiquity, the current concept of short-rotation woody crops (SRWC) for fiber and energy evolved scientifically from pioneering tree breeding work begun in the early 20th century. A natural outgrowth of this work was the culture of fast-growing trees on rotations of 1-15 years. Close-spaced tree culture received further impetus with the introduction of the 'silage sycamore' concept in the southeastern US in the mid-1960s and the OPEC oil embargo in 1973, leading to statistically designed trials at numerous locations in North America, Europe, and Scandinavia. Early silvicultural research focused on spacing and species trials, propagation methods, site preparation, weed management, nutrition, growth, and yield. Because these trials were based on small plots, and the importance of pest depredations or site variation were not fully recognized, early biomass yield predictions tended to be overly optimistic. Soon physiologists and ecologists began to unravel the biological characteristics of SRWC plantations and their responses to environment. Knowledge of the influence and diversity of pests-insects, diseases, and animals-provided a necessary reality check. Many hardwood tree species and a few conifers have been evaluated over the years for SRWC in temperate regions of the world. Clones of Populus and Salix, however, became the dominant plantation material because of their inherently rapid growth and ease of propagation by hardwood cuttings. Among conifers, loblolly pine (Pinus taeda) also shows promise. Because genetic variation is readily exploitable in the dominant SRWC taxa, strongly focused breeding programs began to provide highly productive genotypes and seed sources in the last decades of the 20th century. A new plateau, with significant practical potential, was reached in the late 20th century when biotechnological methods were applied to tree taxa. Recently, the DNA in the Populus genome was sequenced. Thus, the few current

  10. Chlorophyll fluorescence tracks seasonal variations of photosynthesis from leaf to canopy in a temperate forest.

    Science.gov (United States)

    Yang, Hualei; Yang, Xi; Zhang, Yongguang; Heskel, Mary A; Lu, Xiaoliang; Munger, J William; Sun, Shucun; Tang, Jianwu

    2017-07-01

    Accurate estimation of terrestrial gross primary productivity (GPP) remains a challenge despite its importance in the global carbon cycle. Chlorophyll fluorescence (ChlF) has been recently adopted to understand photosynthesis and its response to the environment, particularly with remote sensing data. However, it remains unclear how ChlF and photosynthesis are linked at different spatial scales across the growing season. We examined seasonal relationships between ChlF and photosynthesis at the leaf, canopy, and ecosystem scales and explored how leaf-level ChlF was linked with canopy-scale solar-induced chlorophyll fluorescence (SIF) in a temperate deciduous forest at Harvard Forest, Massachusetts, USA. Our results show that ChlF captured the seasonal variations of photosynthesis with significant linear relationships between ChlF and photosynthesis across the growing season over different spatial scales (R 2  = 0.73, 0.77, and 0.86 at leaf, canopy, and satellite scales, respectively; P chlorophyll content (R 2  = 0.65 for canopy GPP SIF and chlorophyll content; P < 0.0001), leaf area index (LAI) (R 2  = 0.35 for canopy GPP SIF and LAI; P < 0.0001), and normalized difference vegetation index (NDVI) (R 2  = 0.36 for canopy GPP SIF and NDVI; P < 0.0001). Our results suggest that ChlF can be a powerful tool to track photosynthetic rates at leaf, canopy, and ecosystem scales. © 2016 John Wiley & Sons Ltd.

  11. Climbing plants in a temperate rainforest understorey: searching for high light or coping with deep shade?

    Science.gov (United States)

    Valladares, Fernando; Gianoli, Ernesto; Saldaña, Alfredo

    2011-08-01

    While the climbing habit allows vines to reach well-lit canopy areas with a minimum investment in support biomass, many of them have to survive under the dim understorey light during certain stages of their life cycle. But, if the growth/survival trade-off widely reported for trees hold for climbing plants, they cannot maximize both light-interception efficiency and shade avoidance (i.e. escaping from the understorey). The seven most important woody climbers occurring in a Chilean temperate evergreen rainforest were studied with the hypothesis that light-capture efficiency of climbers would be positively associated with their abundance in the understorey. Species abundance in the understorey was quantified from their relative frequency and density in field plots, the light environment was quantified by hemispherical photography, the photosynthetic response to light was measured with portable gas-exchange analyser, and the whole shoot light-interception efficiency and carbon gain was estimated with the 3-D computer model Y-plant. Species differed in specific leaf area, leaf mass fraction, above ground leaf area ratio, light-interception efficiency and potential carbon gain. Abundance of species in the understorey was related to whole shoot features but not to leaf level features such as specific leaf area. Potential carbon gain was inversely related to light-interception efficiency. Mutual shading among leaves within a shoot was very low (<20 %). The abundance of climbing plants in this southern rainforest understorey was directly related to their capacity to intercept light efficiently but not to their potential carbon gain. The most abundant climbers in this ecosystem match well with a shade-tolerance syndrome in contrast to the pioneer-like nature of climbers observed in tropical studies. The climbers studied seem to sacrifice high-light searching for coping with the dim understorey light.

  12. Impacts of climate change on paddy rice yield in a temperate climate.

    Science.gov (United States)

    Kim, Han-Yong; Ko, Jonghan; Kang, Suchel; Tenhunen, John

    2013-02-01

    The crop simulation model is a suitable tool for evaluating the potential impacts of climate change on crop production and on the environment. This study investigates the effects of climate change on paddy rice production in the temperate climate regions under the East Asian monsoon system using the CERES-Rice 4.0 crop simulation model. This model was first calibrated and validated for crop production under elevated CO2 and various temperature conditions. Data were obtained from experiments performed using a temperature gradient field chamber (TGFC) with a CO2 enrichment system installed at Chonnam National University in Gwangju, Korea in 2009 and 2010. Based on the empirical calibration and validation, the model was applied to deliver a simulated forecast of paddy rice production for the region, as well as for the other Japonica rice growing regions in East Asia, projecting for years 2050 and 2100. In these climate change projection simulations in Gwangju, Korea, the yield increases (+12.6 and + 22.0%) due to CO2 elevation were adjusted according to temperature increases showing variation dependent upon the cultivars, which resulted in significant yield decreases (-22.1% and -35.0%). The projected yields were determined to increase as latitude increases due to reduced temperature effects, showing the highest increase for any of the study locations (+24%) in Harbin, China. It appears that the potential negative impact on crop production may be mediated by appropriate cultivar selection and cultivation changes such as alteration of the planting date. Results reported in this study using the CERES-Rice 4.0 model demonstrate the promising potential for its further application in simulating the impacts of climate change on rice production from a local to a regional scale under the monsoon climate system. © 2012 Blackwell Publishing Ltd.

  13. Bioavailable dissolved and particulate organic carbon flux from coastal temperate rainforest watersheds

    Science.gov (United States)

    Fellman, J.; Hood, E. W.; D'Amore, D. V.; Moll, A.

    2017-12-01

    Coastal temperate rainforest (CTR) watersheds of southeast Alaska have dense soil carbon stocks ( 300 Mg C ha-1) and high specific discharge (1.5-7 m yr-1) driven by frontal storms from the Gulf of Alaska. As a result, dissolved organic carbon (DOC) fluxes from Alaskan CTR watersheds are estimated to exceed 2 Tg yr-1; however, little is known about the export of particulate organic carbon (POC). The magnitude and bioavailability of this land-to-ocean flux of terrigenous organic matter ultimately determines how much metabolic energy is translocated to downstream and coastal marine ecosystems in this region. We sampled streamwater weekly from May through October from four watersheds of varying landcover (gradient of wetland to glacial coverage) to investigate changes in the concentration and flux of DOC and POC exported to the coastal ocean. We also used headspace analysis of CO2 following 14 day laboratory incubations to determine the flux of bioavailable DOC and POC exported from CTR watersheds. Across all sites, bioavailable DOC concentrations ranged from 0.2 to 1.9 mg L-1 but were on average 0.6 mg L-1. For POC, bioavailable concentrations ranged from below detection to 0.3 mg L-1 but were on average 0.1 mg L-1. The concentration, flux and bioavailability of DOC was higher than for POC highlighting the potential importance of DOC as a metabolic subsidy to downstream and coastal environments. Ratios of DOC to POC decreased during high flow events because the increase in POC concentrations with discharge exceeds that for DOC. Overall, our findings suggest that projected increases in precipitation and storm intensity will drive changes in the speciation, magnitude and bioavailability of the organic carbon flux from CTR watersheds.

  14. Quantitative assessments of water-use efficiency in Temperate Eurasian Steppe along an aridity gradient.

    Directory of Open Access Journals (Sweden)

    Yizhao Chen

    Full Text Available Water-use efficiency (WUE, defined as the ratio of net primary productivity (NPP to evapotranspiration (ET, is an important indicator to represent the trade-off pattern between vegetation productivity and water consumption. Its dynamics under climate change are important to ecohydrology and ecosystem management, especially in the drylands. In this study, we modified and used a late version of Boreal Ecosystem Productivity Simulator (BEPS, to quantify the WUE in the typical dryland ecosystems, Temperate Eurasian Steppe (TES. The Aridity Index (AI was used to specify the terrestrial water availability condition. The regional results showed that during the period of 1999-2008, the WUE has a clear decreasing trend in the spatial distribution from arid to humid areas. The highest annual average WUE was in dry and semi-humid sub-region (DSH with 0.88 gC mm-1 and the lowest was in arid sub-region (AR with 0.22 gC mm-1. A two-stage pattern of WUE was found in TES. That is, WUE would enhance with lower aridity stress, but decline under the humid environment. Over 65% of the region exhibited increasing WUE. This enhancement, however, could not indicate that the grasslands were getting better because the NPP even slightly decreased. It was mainly attributed to the reduction of ET over 70% of the region, which is closely related to the rainfall decrease. The results also suggested a similar negative spatial correlation between the WUE and the mean annual precipitation (MAP at the driest and the most humid ends. This regional pattern reflected the different roles of water in regulating the terrestrial ecosystems under different aridity levels. This study could facilitate the understanding of the interactions between terrestrial carbon and water cycles, and thus contribute to a sustainable management of nature resources in the dryland ecosystems.

  15. Quantitative assessments of water-use efficiency in Temperate Eurasian Steppe along an aridity gradient.

    Science.gov (United States)

    Chen, Yizhao; Li, Jianlong; Ju, Weimin; Ruan, Honghua; Qin, Zhihao; Huang, Yiye; Jeelani, Nasreen; Padarian, José; Propastin, Pavel

    2017-01-01

    Water-use efficiency (WUE), defined as the ratio of net primary productivity (NPP) to evapotranspiration (ET), is an important indicator to represent the trade-off pattern between vegetation productivity and water consumption. Its dynamics under climate change are important to ecohydrology and ecosystem management, especially in the drylands. In this study, we modified and used a late version of Boreal Ecosystem Productivity Simulator (BEPS), to quantify the WUE in the typical dryland ecosystems, Temperate Eurasian Steppe (TES). The Aridity Index (AI) was used to specify the terrestrial water availability condition. The regional results showed that during the period of 1999-2008, the WUE has a clear decreasing trend in the spatial distribution from arid to humid areas. The highest annual average WUE was in dry and semi-humid sub-region (DSH) with 0.88 gC mm-1 and the lowest was in arid sub-region (AR) with 0.22 gC mm-1. A two-stage pattern of WUE was found in TES. That is, WUE would enhance with lower aridity stress, but decline under the humid environment. Over 65% of the region exhibited increasing WUE. This enhancement, however, could not indicate that the grasslands were getting better because the NPP even slightly decreased. It was mainly attributed to the reduction of ET over 70% of the region, which is closely related to the rainfall decrease. The results also suggested a similar negative spatial correlation between the WUE and the mean annual precipitation (MAP) at the driest and the most humid ends. This regional pattern reflected the different roles of water in regulating the terrestrial ecosystems under different aridity levels. This study could facilitate the understanding of the interactions between terrestrial carbon and water cycles, and thus contribute to a sustainable management of nature resources in the dryland ecosystems.

  16. Temporal assemblage turnovers of intertidal foraminiferal communities from tropical (SE Caribbean) and temperate (NE England and SW Spain) regions

    Science.gov (United States)

    Costelloe, Ashleigh; Wilson, Brent; Horton, Benjamin P.; Hayek, Lee-Ann C.

    2018-05-01

    This is the first quantitative study of temporal assemblage turnovers of the relationships between intertidal foraminifera. Time series datasets collected from tropical Caroni Swamp and Claxton Bay (Trinidad, SE Caribbean) and temperate Cowpen Marsh (NE England, U.K.) and Bay of Cadiz (SW Spain) were used. The assemblage turnover index (ATI) examined species interrelationships through comparisons of monthly or biweekly species proportional abundances over one or two years. Species contributing to major assemblage turnovers (ATI > x + σ) were identified using the conditioned on-boundary index (CoBI). Foraminiferal species are heterogeneously distributed within the sediment; multiple sample stations at a study location cumulatively represent the foraminiferal metacommunity and clusters represent foraminiferal assemblages. The ATI and CoBI were applied to the proportional abundances of live specimens recorded for the metacommunity and assemblages at each location. At Caroni Swamp and Claxton Bay, major assemblage turnovers were driven by the most abundant species and the majority coincided with seasonal change or the arrival of the seasonal Orinoco plume in the Gulf of Paria. Seasonal turnovers of the foraminiferal metacommunities at temperate Cowpen Marsh and Bay of Cádiz occurred during the summer and winter. Major assemblage turnovers in the upper Cowpen Marsh occurred in the summer, and the lower marsh in the winter. Foraminiferans are useful bioindicators for monitoring the health of coastal environments. Understanding foraminiferal population dynamics will allow cyclical changes to be differentiated from abrupt and persistent changes, which are related to anthropogenic disturbances or long-term climate change. The ATI and CoBI are useful indices for quantitatively exploring relationships of foraminiferal populations over time.

  17. Re-annotation of the physical map of Glycine max for polyploid-like regions by BAC end sequence driven whole genome shotgun read assembly

    Directory of Open Access Journals (Sweden)

    Shultz Jeffry

    2008-07-01

    Full Text Available Abstract Background Many of the world's most important food crops have either polyploid genomes or homeologous regions derived from segmental shuffling following polyploid formation. The soybean (Glycine max genome has been shown to be composed of approximately four thousand short interspersed homeologous regions with 1, 2 or 4 copies per haploid genome by RFLP analysis, microsatellite anchors to BACs and by contigs formed from BAC fingerprints. Despite these similar regions,, the genome has been sequenced by whole genome shotgun sequence (WGS. Here the aim was to use BAC end sequences (BES derived from three minimum tile paths (MTP to examine the extent and homogeneity of polyploid-like regions within contigs and the extent of correlation between the polyploid-like regions inferred from fingerprinting and the polyploid-like sequences inferred from WGS matches. Results Results show that when sequence divergence was 1–10%, the copy number of homeologous regions could be identified from sequence variation in WGS reads overlapping BES. Homeolog sequence variants (HSVs were single nucleotide polymorphisms (SNPs; 89% and single nucleotide indels (SNIs 10%. Larger indels were rare but present (1%. Simulations that had predicted fingerprints of homeologous regions could be separated when divergence exceeded 2% were shown to be false. We show that a 5–10% sequence divergence is necessary to separate homeologs by fingerprinting. BES compared to WGS traces showed polyploid-like regions with less than 1% sequence divergence exist at 2.3% of the locations assayed. Conclusion The use of HSVs like SNPs and SNIs to characterize BACs wil improve contig building methods. The implications for bioinformatic and functional annotation of polyploid and paleopolyploid genomes show that a combined approach of BAC fingerprint based physical maps, WGS sequence and HSV-based partitioning of BAC clones from homeologous regions to separate contigs will allow reliable de

  18. Reference of Temperature and Time during tempering process for non-stoichiometric FTO films

    Science.gov (United States)

    Yang, J. K.; Liang, B.; Zhao, M. J.; Gao, Y.; Zhang, F. C.; Zhao, H. L.

    2015-10-01

    In order to enhance the mechanical strength of Low-E glass, Fluorine-doped tin oxide (FTO) films have to be tempered at high temperatures together with glass substrates. The effects of tempering temperature (600 °C ~ 720 °C) and time (150 s ~ 300 s) on the structural and electrical properties of FTO films were investigated. The results show all the films consist of non-stoichiometric, polycrystalline SnO2 without detectable amounts of fluoride. 700 °C and 260 s may be the critical tempering temperature and time, respectively. FTO films tempered at 700 °C for 260 s possesses the resistivity of 7.54 × 10-4 Ω•cm, the average transmittance in 400 ~ 800 nm of ~80%, and the calculated emissivity of 0.38. Hall mobility of FTO films tempered in this proper condition is mainly limited by the ionized impurity scattering. The value of [O]/[Sn] at the film surface is much higher than the stoichiometric value of 2.0 of pure crystalline SnO2.

  19. Effect of land use change on methane oxidation in temperate forest and grassland soils

    Energy Technology Data Exchange (ETDEWEB)

    Ojima, D.S.; Valentine, D.W.; Mosier, A.R.; Parton, W.J.; Schimel, D.S. (Colorado State University, Fort Collins, CO (USA). Natural Resources Ecology Lab.)

    Evidence is accumulating that land use changes and other human activity during the past 100 to 200 years have contributed to decreased CH[sub 4] oxidation in the soil. Increased N additions to temperate forest soils in the northeastern United States decreased CH[sub 4] uptake by 30 to 60%, and increased N fertilization and conversion to cropland in temperate grasslands decreased CH[sub 4] uptake by 30 to 75%. Using these data, a series of calculations were made to estimate the impact of land use and management changes which have altered soil, the CH[sub 4] sink in temperate forest and grassland ecosystems. As the atmospheric mixing ratio of CH[sub 4] has increased during the past 150 y, the temperate CH[sub 4] sink has risen from approximately 8 Tg y[sup -1] to 27 Tg y[sup -1], assuming no loss of land cover to cropland conversion. The net effect of intensive land cover changes and extensive chronic disturbance (i.e., increased atmospheric N deposition) to these ecosystems have resulted in about 30% reduction in the CH[sub 4] budget even more as atmospheric CH[sub 4] concentrations increase and as a result of further disturbance to other biomes. Without accounting for this approximately 20 Tg y[sup -1] temperate soil sink, the atmospheric CH[sub 4] concentration would be increasing about 1.5 times the current rate. 39 refs., 2 figs., 1 tab.

  20. Methane Ebullition in Temperate Hydropower Reservoirs and Implications for US Policy on Greenhouse Gas Emissions.

    Science.gov (United States)

    Miller, Benjamin L; Arntzen, Evan V; Goldman, Amy E; Richmond, Marshall C

    2017-10-01

    The United States is home to 2198 dams actively used for hydropower production. With the December 2015 consensus adoption of the United Nations Framework Convention on Climate Change Paris Agreement, it is important to accurately quantify anthropogenic greenhouse gas emissions. Methane ebullition, or methane bubbles originating from river or lake sediments, has been shown to account for nearly all methane emissions from tropical hydropower reservoirs to the atmosphere. However, distinct ebullitive methane fluxes have been studied in comparatively few temperate hydropower reservoirs globally. This study measures ebullitive and diffusive methane fluxes from two eastern Washington reservoirs, and synthesizes existing studies of methane ebullition in temperate, boreal, and tropical hydropower reservoirs. Ebullition comprises nearly all methane emissions (>97%) from this study's two eastern Washington hydropower reservoirs to the atmosphere. Summer methane ebullition from these reservoirs was higher than ebullition in six southeastern U.S. hydropower reservoirs, however it was similar to temperate reservoirs in other parts of the world. Our literature synthesis suggests that methane ebullition from temperate hydropower reservoirs can be seasonally elevated compared to tropical climates, however annual emissions are likely to be higher within tropical climates, emphasizing the possible range of methane ebullition fluxes and the need for the further study of temperate reservoirs. Possible future changes to the Intergovernmental Panel on Climate Change and UNFCCC guidelines for national greenhouse gas inventories highlights the need for accurate assessment of reservoir emissions.

  1. Methane Ebullition in Temperate Hydropower Reservoirs and Implications for US Policy on Greenhouse Gas Emissions

    Science.gov (United States)

    Miller, Benjamin L.; Arntzen, Evan V.; Goldman, Amy E.; Richmond, Marshall C.

    2017-10-01

    The United States is home to 2198 dams actively used for hydropower production. With the December 2015 consensus adoption of the United Nations Framework Convention on Climate Change Paris Agreement, it is important to accurately quantify anthropogenic greenhouse gas emissions. Methane ebullition, or methane bubbles originating from river or lake sediments, has been shown to account for nearly all methane emissions from tropical hydropower reservoirs to the atmosphere. However, distinct ebullitive methane fluxes have been studied in comparatively few temperate hydropower reservoirs globally. This study measures ebullitive and diffusive methane fluxes from two eastern Washington reservoirs, and synthesizes existing studies of methane ebullition in temperate, boreal, and tropical hydropower reservoirs. Ebullition comprises nearly all methane emissions (>97%) from this study's two eastern Washington hydropower reservoirs to the atmosphere. Summer methane ebullition from these reservoirs was higher than ebullition in six southeastern U.S. hydropower reservoirs, however it was similar to temperate reservoirs in other parts of the world. Our literature synthesis suggests that methane ebullition from temperate hydropower reservoirs can be seasonally elevated compared to tropical climates, however annual emissions are likely to be higher within tropical climates, emphasizing the possible range of methane ebullition fluxes and the need for the further study of temperate reservoirs. Possible future changes to the Intergovernmental Panel on Climate Change and UNFCCC guidelines for national greenhouse gas inventories highlights the need for accurate assessment of reservoir emissions.

  2. Appropriate welding conditions of temper bead weld repair for SQV2A pressure vessel steel

    International Nuclear Information System (INIS)

    Mizuno, R.; Matsuda, F.; Brziak, P.; Lomozik, M.

    2004-01-01

    Temper bead welding technique is one of the most important repair welding methods for large structures for which it is difficult to perform the specified post weld heat treatment. In this study, appropriate temper bead welding conditions to improve the characteristics of heat affected zone (HAZ) are studied using pressure vessel steel SQV2A corresponding to ASTM A533 Type B Class 1. Thermal/mechanical simulator is employed to give specimens welding thermal cycles from single to quadruple cycle. Charpy absorbed energy and hardness of simulated CGHAZ by first cycle were degraded as compared with base metal. Improvability of these degradations by subsequent cycles is discussed and appropriate temper bead thermal cycles are clarified. When the peak temperature lower than Ac1 and near Ac1 in the second thermal cycle is applied to CGAHZ by first thermal cycle, the characteristics of CGHAZ improve enough. When the other peak temperatures (that is, higher than Ac1) in the second thermal cycle are applied to the CGHAZ, third or more thermal cycle temper bead process should be applied to improve the properties. Appropriate weld condition ranges are selected based on the above results. The validity of the selected ranges is verified by the temper bead welding test. (orig.)

  3. The Kinetics of Phase Transformations During Tempering in Laser Melted High Chromium Cast Steel

    Science.gov (United States)

    Li, M. Y.; Wang, Y.; Han, B.

    2012-06-01

    The precipitation of secondary carbides in the laser melted high chromium cast steels during tempering at 300-650 °C for 2 h in air furnace was characterized and the present phases was identified, by using transmission electron microscopy. Laser melted high chromium cast steel consists of austenitic dendrites and interdendritic M23C6 carbides. The austenite has such a strong tempering stability that it remains unchanged at temperature below 400 °C and the secondary hardening phenomenon starts from 450 °C to the maximum value of 672 HV at 560 °C. After tempering at 450 °C fine M23C6 carbides precipitate from the supersaturated austenite preferentially. In addition, the dislocation lines and slip bands still exist inside the austenite. While tempering at temperature below 560 °C, the secondary hardening simultaneously results from the martensite phase transformation and the precipitation of carbides as well as dislocation strengthening within a refined microstructure. Moreover, the formation of the ferrite matrix and large quality of coarse lamellar M3C carbides when the samples were tempered at 650 °C contributes to the decrease of hardness.

  4. Multiyear greenhouse gas balances at a rewetted temperate peatland.

    Science.gov (United States)

    Wilson, David; Farrell, Catherine A; Fallon, David; Moser, Gerald; Müller, Christoph; Renou-Wilson, Florence

    2016-12-01

    Drained peat soils are a significant source of greenhouse gas (GHG) emissions to the atmosphere. Rewetting these soils is considered an important climate change mitigation tool to reduce emissions and create suitable conditions for carbon sequestration. Long-term monitoring is essential to capture interannual variations in GHG emissions and associated environmental variables and to reduce the uncertainty linked with GHG emission factor calculations. In this study, we present GHG balances: carbon dioxide (CO 2 ), methane (CH 4 ) and nitrous oxide (N 2 O) calculated for a 5-year period at a rewetted industrial cutaway peatland in Ireland (rewetted 7 years prior to the start of the study); and compare the results with an adjacent drained area (2-year data set), and with ten long-term data sets from intact (i.e. undrained) peatlands in temperate and boreal regions. In the rewetted site, CO 2 exchange (or net ecosystem exchange (NEE)) was strongly influenced by ecosystem respiration (R eco ) rather than gross primary production (GPP). CH 4 emissions were related to soil temperature and either water table level or plant biomass. N 2 O emissions were not detected in either drained or rewetted sites. Rewetting reduced CO 2 emissions in unvegetated areas by approximately 50%. When upscaled to the ecosystem level, the emission factors (calculated as 5-year mean of annual balances) for the rewetted site were (±SD) -104 ± 80 g CO 2 -C m -2  yr -1 (i.e. CO 2 sink) and 9 ± 2 g CH 4 -C m -2  yr -1 (i.e. CH 4 source). Nearly a decade after rewetting, the GHG balance (100-year global warming potential) had reduced noticeably (i.e. less warming) in comparison with the drained site but was still higher than comparative intact sites. Our results indicate that rewetted sites may be more sensitive to interannual changes in weather conditions than their more resilient intact counterparts and may switch from an annual CO 2 sink to a source if triggered by slightly drier

  5. Bed-Deformation Experiments Beneath a Temperate Glacier

    Science.gov (United States)

    Iverson, N. R.; Hooyer, T. S.; Fischer, U. H.; Cohen, D.; Jackson, M.; Moore, P. L.; Lappegard, G.; Kohler, J.

    2002-12-01

    Fast flow of glaciers and genesis of glacial landforms are commonly attributed to shear deformation of subglacial sediment. Although models of this process abound, data gathered subglacially on the kinematics and mechanics of such deformation are difficult to interpret. Major difficulties stem from the necessity of either measuring deformation near glacier margins, where conditions may be abnormal, or at the bottoms of boreholes, where the scope of instrumentation is limited, drilling disturbs sediment, and local boundary conditions are poorly known. A different approach is possible at the Svartisen Subglacial Laboratory, where tunnels melted in the ice provide temporary human access to the bed of Engabreen, a temperate outlet glacier of the Svartisen Ice Cap in Norway. A trough (2 m x 1.5 m x 0.5 m deep) was blasted in the rock bed, where the glacier is 220 m thick and sliding at 0.1-0.2 m/d. During two spring field seasons, this trough was filled with 2.5 tons of simulated till. Instruments in the till recorded shear (tiltmeters), volume change, total normal stress, and pore-water pressure as ice moved across the till surface. Pore pressure was brought to near the total normal stress by feeding water to the base of the till with a high-pressure pump, operated in a rock tunnel 4 m below the bed surface. Results illustrate some fundamental aspects of bed deformation. Permanent shear deformation requires low effective normal stress and hence high pore-water pressure, owing to the frictional nature of till. Shear strain generally increases upward in the bed toward the glacier sole, consistent with previous measurements beneath thinner ice at glacier margins. At low effective normal stresses, ice sometimes decouples from underlying till. Overall, bed deformation accounts for 10-35 % of basal motion, although this range excludes shear in the uppermost 0.05 m of till where shear was not measured. Pump tests with durations ranging from seconds to hours highlight the need

  6. Survival rates of birds of tropical and temperate forests: will the dogma survive?

    Science.gov (United States)

    Karr, J.R.; Nichols, J.D.; Klimkiewicz, M.K.; Brawn, J.D.

    1990-01-01

    Survival rates of tropical forest birds are widely assumed to be high relative to the survival rates of temperate forest birds. Much life-history theory is based on this assumption despite the lack of empirical data to support it. We provide the first detailed comparison of survival rates of tropical and temperate forest birds based on extensive data bases and modern capture-recapture models. We find no support for the conventional wisdom. Because clutch size is only one component of reproductive rate, the frequently assumed, simple association between clutch size and adult survival rates should not necessarily be expected. Our results emphasize the need to consider components of fecundity in addition to clutch size when comparing the life histories of tropical and temperate birds and suggest similar considerations in the development of vertebrate life-history theory.

  7. Microstructural characteristics of steel rebar submitted to the process of self - tempering

    International Nuclear Information System (INIS)

    Barreto, M.F.O.

    2014-01-01

    Every day the construction industry seeks new alternatives to maximize use of the materials provided new tools for structural design of the new techniques in welding rods. In this sense, this work proposes to study the mechanical properties of steel rebar self-tempering for civil construction, choosing the bars from 6.3 to 25.4 mm in diameter for the study. The cooling process of rebar, after rolling, known as self-tempering produces a rebar with excellent mechanical properties and low cost to the plant, they put the rebar shall be composed of concentric layers with different mechanical properties among themselves. To study the influence of these layers on the mechanical behavior of rebar microstructural characterization was made by means of electron microscopy analysis of transmitted light and scanning of all samples. From the results it was found that only the bars 20 and 25mm diameter had a heat treatment for self-tempering relevant. (author)

  8. Evaluation of temper embrittlement of martensitic and ferritic-martensitic steels by acoustic emission

    International Nuclear Information System (INIS)

    Lu, Yusho; Takahashi, Hideaki; Shoji, Tetsuo

    1987-01-01

    Martensitic (HT-9) and ferritic-martensitic steels (9Cr-2Mo) are considered as fusion first wall materials. In this investigation in order to understand the sensitivity of temper embrittlement in these steels under actual service condition, fracture toughness testing was made by use of acoustic emission technique. The temper embrittlement was characterized in terms of fracture toughness. The fracture toughness of these steels under 500 deg C, 100 hrs, and 1000 hrs heat treatment was decreased and their changes in micro-fracture process have been observed. The fracture toughness changes by temper embrittlement was discussed by the characteristic of AE, AE spectrum analysis and fractographic investigation. The relation between micro-fracture processes and AE has been clarified. (author)

  9. Quantifying the effects of tempering on individual phase properties of DP980 steel with nanoindentation

    Energy Technology Data Exchange (ETDEWEB)

    Cheng, G. [Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, P.O. Box 999, Richland, WA (United States); Zhang, F. [School of Mechanical and Materials Engineering, Washington State University, Pullman, WA (United States); Ruimi, A. [Department of Mechanical Engineering, Texas A& M University, Doha (Qatar); Field, D.P. [School of Mechanical and Materials Engineering, Washington State University, Pullman, WA (United States); Sun, X., E-mail: xin.sun@pnnl.gov [Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, P.O. Box 999, Richland, WA (United States)

    2016-06-14

    Tempering treatment is conducted on a commercial dual phase (DP) 980 steel at 250 °C and 400 °C for 60 min each. Ferrite and martensite grains are distinguished using electron backscatter diffraction (EBSD) and scanning probe microscopy (SPM), and the martensite volume fractions (MVF) are determined based on the image quality (IQ) map. Indentation tests combined with a newly developed inverse method are used to obtain the individual phase flow properties in each sample. The results show that, i) tempering significantly reduces martensite yield strength, while it slightly reduces the ferrite yield strength; ii) tempering temperature has a more significant influence on the work hardening exponent of ferrite than that of martensite. As a validation, a simple rule-of-mixtures is used to verify the above-predicted individual phase flow stresses with the experimentally obtained overall true stress vs. true strain curves.

  10. Testing the correlation of fragmented pollen records of the middle and late Pleistocene temperate stages

    DEFF Research Database (Denmark)

    Kuneš, Petr; Odgaard, Bent Vad

    Quaternary temperate stages have long been described based on changing pollen abundances of various tree taxa in lacustrine sediments. Later, attempts have been made to assign such biostratigraphic units to distinct marine isotope stages (MIS). Existing continuous chronosequences from Southern...... records depends on site-to-site correlations. This comparison has often been performed on a visual basis, lacking clearly defined protocols and statements of underlying assumptions. Here I test the correlation of well and poorly known pollen records of the middle- and late-Pleistocene temperate stages...... from Northern-Central Europe and evaluate the usefulness of several numerical techniques. TWINSPAN analysis identifies groups of temperate stages based on presence/absence of their indicative taxa and may be useful for distinguishing between older and younger interglacials. Site-to-site sequence...

  11. Electromagnetic nondestructive evaluation of tempering process in AISI D2 tool steel

    Science.gov (United States)

    Kahrobaee, Saeed; Kashefi, Mehrdad

    2015-05-01

    The present paper investigates the potential of using eddy current technique as a reliable nondestructive tool to detect microstructural changes during the different stages of tempering treatment in AISI D2 tool steel. Five stages occur in tempering of the steel: precipitation of ɛ carbides, formation of cementite, retained austenite decomposition, secondary hardening effect and spheroidization of carbides. These stages were characterized by destructive methods, including dilatometry, differential scanning calorimetry, X-ray diffraction, scanning electron microscopic observations, and hardness measurements. The microstructural changes alter the electrical resistivity/magnetic saturation, which, in turn, influence the eddy current signals. Two EC parameters, induced voltage sensed by pickup coil and impedance point detected by excitation coil, were evaluated as a function of tempering temperature to characterize the microstructural features, nondestructively. The study revealed that a good correlation exists between the EC parameters and the microstructural changes.

  12. Investigation of the self tempering effect of martensite by means of atom probe tomography

    International Nuclear Information System (INIS)

    Sackl, Stephanie; Clemens, Helmut; Primig, Sophie

    2015-01-01

    Self-tempering effects can be observed in steels with relatively high martensite start temperatures. After the formation of the first martensitic laths, carbon is able to diffuse in these laths during cooling, which can be attributed to sufficiently high temperatures. This effect cannot be observed in laths formed at lower temperatures. In steels containing up to 0.2 m.-% carbon, up to 90 % of the carbon atoms in the martensite segregate to dislocations during quenching. Due to its atomic resolution and sensitivity with respect to light elements, atom probe tomography is very well suited for the investigation of this phenomenon. In this study, the self-tempering effect in a quenched and tempered steel 42CrMo4 with a martensite start temperature of 310 C is investigated by means of atom probe tomography.

  13. Resonant behavior of the generalized Langevin system with tempered Mittag–Leffler memory kernel

    Science.gov (United States)

    Chen, Yao; Wang, Xudong; Deng, Weihua

    2018-05-01

    The generalized Langevin equation describes anomalous dynamics. Noise is not only the origin of uncertainty but also plays a positive role in helping to detect signals with information, termed stochastic resonance (SR). This paper analyzes the anomalous resonant behaviors of the generalized Langevin system with a multiplicative dichotomous noise and an internal tempered Mittag–Leffler noise. For a system with a fluctuating harmonic potential, we obtain the exact expressions of several types of SR such as the first moment, the amplitude and autocorrelation function for the output signal as well as the signal–noise ratio. We analyze the influence of the tempering parameter and memory exponent on the bona fide SR and the general SR. Moreover, it is detected that the critical memory exponent changes regularly with the increase of the tempering parameter. Almost all the theoretical results are validated by numerical simulations.

  14. Remaining stress-state and strain-energy in tempered glass fragments

    DEFF Research Database (Denmark)

    Nielsen, Jens Henrik

    2016-01-01

    to the fragmentation process and some authors e.g. Barsom (J Am Ceram Soc 51(2):75, 1968), Gulati (Glass processing days, Tamglass Engineering Oy, Tampere, 1997), Warren (Fractography of glasses and ceramics IV, Alfred University, Alfred, 2001) and Tandon and Glass (Fracture mechanics of ceramics—active materials......When tempered glass breaks, it shatters into relatively small pieces depending on the residual stress state in the glass. This has been known for centuries and is currently used in standards for classifying whether a piece of glass is tempered or not. However, the process of fragmentation...... is complex and only a few, relatively simple, models have been suggested for predicting the fragment size. The full theoretical explanation is still to be found and this work aims at providing another brick to the puzzle. The strain-energy present in tempered glass is obviously contributing...

  15. Tempering response to different morphologies of martensite in tensile deformation of dual-phase steel

    International Nuclear Information System (INIS)

    Ahmad, E.; Manzoor, T.; Sarwar, M.; Arif, M.; Hussain, N.

    2011-01-01

    A low alloy steel containing 0.2% C was heat treated with three cycles of heat treatments with the aim to acquire different morphologies of martensite in dual phase microstructure. Microscopic examination revealed that the morphologies consisting of grain boundary growth, scattered laths and bulk form of martensite were obtained. These morphologies have their distinct patterns of distribution in the matrix (ferrite). In tensile properties observations the dual phase steel with bulk morphology of martensite showed minimum of ductility but high tensile strength as compared to other two morphologies. This may be due to poor alignments of bulk martensite particles along tensile axes during deformation. Tempering was employed with various holding times at 550 deg. C to induce ductility in the heat treated material. The tempering progressively increased the ductility by increasing holding time. However, tempering response to strengths and ductilities was different to all three morphologies of martensite. (author)

  16. Localization and Ballistic Diffusion for the Tempered Fractional Brownian-Langevin Motion

    Science.gov (United States)

    Chen, Yao; Wang, Xudong; Deng, Weihua

    2017-10-01

    This paper discusses the tempered fractional Brownian motion (tfBm), its ergodicity, and the derivation of the corresponding Fokker-Planck equation. Then we introduce the generalized Langevin equation with the tempered fractional Gaussian noise for a free particle, called tempered fractional Langevin equation (tfLe). While the tfBm displays localization diffusion for the long time limit and for the short time its mean squared displacement (MSD) has the asymptotic form t^{2H}, we show that the asymptotic form of the MSD of the tfLe transits from t^2 (ballistic diffusion for short time) to t^{2-2H}, and then to t^2 (again ballistic diffusion for long time). On the other hand, the overdamped tfLe has the transition of the diffusion type from t^{2-2H} to t^2 (ballistic diffusion). The tfLe with harmonic potential is also considered.

  17. T6 and T78 tempers of AA6065 alloy: a quantitative TEM study

    Energy Technology Data Exchange (ETDEWEB)

    Tanaka, M.; Warner, T. [Compagnie de Produits Chimiques et Electrometallurgiques Pechiney, Centre de Recherches de Voreppe, 38 (France)

    2000-07-01

    Quantitative transmission electron microscopy is used to characterize the microstructure of an industrial Al-Mg-Si-Cu alloy (AA6056) in a state (T78 temper) desensitized to intergranular corrosion in comparison with the peak aged state (T6 temper). Analysis of dark-field images and of zero-loss filtered selected-area-diffraction patterns, along with EDX spectroscopy, indicates an advanced precipitation of the quaternary phase containing Si and Cu in the T78-tempered alloy compared to the T6 one. This supports the current theory of the desensitization of AA6056 alloy. However, the application of EDX analysis to provide direct evidence of the chemical composition variation in the solid solution across the grain boundary appears less satisfactory. (orig.)

  18. Plasmodium vivax populations revisited: mitochondrial genomes of temperate strains in Asia suggest ancient population expansion

    Directory of Open Access Journals (Sweden)

    Miao Miao

    2012-02-01

    Full Text Available Abstract Background Plasmodium vivax is the most widely distributed human malaria parasite outside of Africa, and its range extends well into the temperate zones. Previous studies provided evidence for vivax population differentiation, but temperate vivax parasites were not well represented in these analyses. Here we address this deficit by using complete mitochondrial (mt genome sequences to elucidate the broad genetic diversity and population structure of P. vivax from temperate regions in East and Southeast Asia. Results From the complete mtDNA sequences of 99 clinical samples collected in China, Myanmar and Korea, a total of 30 different haplotypes were identified from 26 polymorphic sites. Significant differentiation between different East and Southeast Asian parasite populations was observed except for the comparison between populations from Korea and southern China. Haplotype patterns and structure diversity analysis showed coexistence of two different groups in East Asia, which were genetically related to the Southeast Asian population and Myanmar population, respectively. The demographic history of P. vivax, examined using neutrality tests and mismatch distribution analyses, revealed population expansion events across the entire P. vivax range and the Myanmar population. Bayesian skyline analysis further supported the occurrence of ancient P. vivax population expansion. Conclusions This study provided further resolution of the population structure and evolution of P. vivax, especially in temperate/warm-temperate endemic areas of Asia. The results revealed divergence of the P. vivax populations in temperate regions of China and Korea from other populations. Multiple analyses confirmed ancient population expansion of this parasite. The extensive genetic diversity of the P. vivax populations is consistent with phenotypic plasticity of the parasites, which has implications for malaria control.

  19. Tempering Behavior of TiC-Reinforced SKD11 Steel Matrix Composite

    Science.gov (United States)

    Hwang, Ji-In; Kim, Seong Hoon; Heo, Yoon-Uk; Kim, Dae Ha; Hwang, Keum-Cheol; Suh, Dong-Woo

    2018-03-01

    TiC-reinforced SKD11 steel matrix composite, fabricated by a pressure infiltration casting, undergoes monotonic decrease in hardness as tempering temperature increases. Element mappings by TEM-EDS and thermodynamic calculation indicate that remarkable redistribution of V between the reinforcement and the steel matrix occurs by partial dissolution and re-precipitation of MC carbides upon casting process. The absence of secondary hardening is led by the enrichment of V in the reinforcement that reduces the V content in the steel matrix; this reduction in V content makes the precipitation of fine VC sluggish during the tempering.

  20. X-ray residual stress analysis on machined and tempered HPSN-ceramics

    Energy Technology Data Exchange (ETDEWEB)

    Immelmann, S.; Welle, E.; Reimers, W. [Hahn-Meitner-Institut Berlin GmbH (Germany)

    1997-11-15

    The residual stress state induced by grinding and tempering of hot pressed silicon nitride (HPSN) samples is studied by X-ray diffraction. The results reveal that the residual stress values at the surface of the samples as well as their gradient within the penetration depth of the X-rays depend on the sintering aid and thus, on the glassy phase content of the HPSN. Tempering of the ground HPSN reduces the residual stress values due to microplastic deformation, whereas an oxidation of the glassy phase leads to the formation of compressive residual stresses. (orig.) 35 refs.

  1. Use of the integration elements encoded by the temperate lactococcal bacteriophage TP901-1

    DEFF Research Database (Denmark)

    Brøndsted, Lone; Hammer, Karin

    1999-01-01

    Previously we showed that only one phage-expressed protein (Orf1), a 425-bp region upstream of the orf1 gene (presumably encoding a promoter), and the attP region are necessary and also sufficient for integration of the bacteriophage TP901-1 genome into the chromosome of Lactococcus lactis subsp......P region seem to be necessary for site-specific integration of the temperate bacteriophage TP901-1. By use of the integrative elements (attP and orf1) expressed by the temperate lactococcal bacteriophage TP901-1, a system for obtaining stable chromosomal single-copy transcriptional fusions in L. lactis...

  2. Effect of tempering on microstructure and tensile properties of niobium modified martensitic 9Cr heat resistant steel

    Energy Technology Data Exchange (ETDEWEB)

    Mandal, A., E-mail: anupmetal@gmail.com; Bandyopadhay, T.K.

    2015-01-03

    The effect of tempering on the microstructure of niobium modified 8.8 wt% chromium steel has been evaluated. Steel has been prepared using the conventional melting and casting route. Homogenization and forging is done at 1100 °C. Dilatometric study shows that the Ac{sub 1}, Ac{sub 3} and M{sub s} temperatures are 800, 855, and 131 °C, respectively. Initial cast and forged microstructures consist of martensite/ferrite. The samples are subsequently tempered at 500–800 °C for various intervals of time (1–5 h). The microstructure of the tempered sample is analyzed using optical microscopy, scanning electron microscopy, and X-ray diffraction. High Resolution Transmission Electron Microscopy (HRTEM) is used to identify the precipitate. Nanometer-sized precipitates (50–200 nm) are observed after tempering at 700 °C for 1 h. Niobium rich MC type carbide precipitates and chromium rich M{sub 23}C{sub 6} type precipitates are observed after tempering at 700 °C. Tensile strength decreases with increasing tempering temperature. Maximum tensile strength of 920 MPa is observed after tempering at 700 °C and maximum elongation of ∼11% is observed after tempering at 750 °C.

  3. Effect of tempering temperature on microstructure and sliding wear property of laser quenched 4Cr13 steel

    NARCIS (Netherlands)

    Ouyang, J.H.; Pei, Y.T.; Li, X.D.; Lei, T.C.

    1994-01-01

    4Cr13 martensite stainless steel was quenched by a CO2 laser and tempered for 2 h at different temperatures in the range 200 °C to 550 °C. The microstructure of treated layer was observed by SEM, XRD and TEM. Tempering leads to the decomposition of a large number of retained austenites in laser

  4. Immune indexes of larks from desert and temperate regions show weak associations with life history but stronger links to environmental variation in microbial abundance.

    Science.gov (United States)

    Horrocks, Nicholas P C; Hegemann, Arne; Matson, Kevin D; Hine, Kathryn; Jaquier, Sophie; Shobrak, Mohammed; Williams, Joseph B; Tinbergen, Joost M; Tieleman, B Irene

    2012-01-01

    Immune defense may vary as a result of trade-offs with other life-history traits or in parallel with variation in antigen levels in the environment. We studied lark species (Alaudidae) in the Arabian Desert and temperate Netherlands to test opposing predictions from these two hypotheses. Based on their slower pace of life, the trade-off hypothesis predicts relatively stronger immune defenses in desert larks compared with temperate larks. However, as predicted by the antigen exposure hypothesis, reduced microbial abundances in deserts should result in desert-living larks having relatively weaker immune defenses. We quantified host-independent and host-dependent microbial abundances of culturable microbes in ambient air and from the surfaces of birds. We measured components of immunity by quantifying concentrations of the acute-phase protein haptoglobin, natural antibody-mediated agglutination titers, complement-mediated lysis titers, and the microbicidal ability of whole blood. Desert-living larks were exposed to significantly lower concentrations of airborne microbes than temperate larks, and densities of some bird-associated microbes were also lower in desert species. Haptoglobin concentrations and lysis titers were also significantly lower in desert-living larks, but other immune indexes did not differ. Thus, contrary to the trade-off hypothesis, we found little evidence that a slow pace of life predicted increased immunological investment. In contrast, and in support of the antigen exposure hypothesis, associations between microbial exposure and some immune indexes were apparent. Measures of antigen exposure, including assessment of host-independent and host-dependent microbial assemblages, can provide novel insights into the mechanisms underlying immunological variation.

  5. Effect of quenching and tempering process on sulfide stress cracking susceptibility in API-5CT-C110 casing steel

    Energy Technology Data Exchange (ETDEWEB)

    Liu, M.; Wang, C.H.; Dai, Y.C.; Li, X.; Cao, G.H. [State Key Laboratory of Advanced Special Steel & Shanghai Key Laboratory of Advanced Ferrometallurgy & School of Materials Science and Engineering, Shanghai University, 149 Yanchang Road, Shanghai 200072 (China); Russell, A.M. [Division of Materials Science and Engineering, Ames Laboratory of the U.S.D.O.E., and Department of Materials Science and Engineering, Iowa State University, Ames, IA 50011-2300 (United States); Liu, Y.H.; Dong, X.M. [Tube & Pipe Department, Baosteel Research Institute, Baoshan Iron & Steel Co., Ltd, Shanghai 201900 (China); Zhang, Z.H., E-mail: zhzhang@baosteel.com [Tube & Pipe Department, Baosteel Research Institute, Baoshan Iron & Steel Co., Ltd, Shanghai 201900 (China)

    2017-03-14

    Three quenching and tempering processes performed on API-5CT-C110 casing steel produced tempered martensite structures and similar mechanical properties but distinct sulfide stress cracking (SSC) behavior as evaluated by Double Cantilever Beam (DCB) testing. An as-quenched specimen tempered at 690 °C for two hours showed superior SSC behavior compared to another specimen tempered at 715 °C for one hour. The latter contained a larger fraction of low-angle boundaries (LABs) and higher values of kernel average misorientation (KAM) than those in the former. Moreover, one more quenching and tempering on the former specimen would produce better SSC resistance with a decrease in the fraction of LABs and the values of KAM. Since dislocations trap hydrogen more strongly than grain boundaries, the specimen with higher KAM values, as well as higher dislocation density, would trap more hydrogen atoms and lead to greater SSC.

  6. Extreme Arthropods: Exploring Evolutionary Adaptations to Polar and Temperate Deserts

    Science.gov (United States)

    Sandro, Luke; Constible, Juanita M.; Lee, Richard E., Jr.

    2007-01-01

    In this activity, Namib and Antarctic arthropods are used to illustrate several important biological principles. Among these are the key ideas that form follows function and that the environment drives evolution. In addition, students will discover that the climates of the Namib Desert and the Antarctic Peninsula are similar in several ways, and…

  7. IoT enabled aquatic drone for environment monitoring

    OpenAIRE

    Matos, João Ricardo Baptista de

    2016-01-01

    This thesis presents a platform that tackles environment monitoring by using air and water quality sensors to provide data for the user to know what is happening in that surveilled area. The hardware is incorporated in a sensing module in order to be used with an Unmanned Surface Vehicle (USV). It presents a monitoring system based on Raspberry Pi platform and a multichannel sensing module associated with water quality and air quality measurement parameters. Thus, the temper...

  8. The northern flying squirrel as an indicator species of temperate rain forest: test of an hypothesis.

    Science.gov (United States)

    Winston P. Smith; Scott M. Gende; Jeffrey V. Nichols

    2005-01-01

    Management indicator species (MIS) often are selected because their life history and demographics are thought to reflect a suite of ecosystem conditions that are too difficult or costly to measure directly. The northern flying squirrel (Glaucomys sabrinus) has been proposed as an MIS of temperate rain forest of southeastern Alaska based on previous...

  9. Restoration of a boulder reef in temperate waters: Strategy, methodology and lessons learnt

    DEFF Research Database (Denmark)

    Støttrup, Josianne Gatt; Dahl, Karsten; Niemann, Sanne

    2017-01-01

    Anthropogenic impacts on marine habitats are a global problem, particularly in coastal areas. While boulder reefs in temperate waters hold high biomass and biodiversity, and may be unable to recover from anthropogenic stressors without restoration efforts, little is known about how to restore and...

  10. Characterization of Nanometric-Sized Carbides Formed During Tempering of Carbide-Steel Cermets

    Directory of Open Access Journals (Sweden)

    Matus K.

    2016-06-01

    Full Text Available The aim of this article of this paper is to present issues related to characterization of nanometric-sized carbides, nitrides and/or carbonitrides formed during tempering of carbide-steel cermets. Closer examination of those materials is important because of hardness growth of carbide-steel cermet after tempering. The results obtained during research show that the upswing of hardness is significantly higher than for high-speed steels. Another interesting fact is the displacement of secondary hardness effect observed for this material to a higher tempering temperature range. Determined influence of the atmosphere in the sintering process on precipitations formed during tempering of carbide-steel cermets. So far examination of carbidesteel cermet produced by powder injection moulding was carried out mainly in the scanning electron microscope. A proper description of nanosized particles is both important and difficult as achievements of nanoscience and nanotechnology confirm the significant influence of nanocrystalline particles on material properties even if its mass fraction is undetectable by standard methods. The following research studies have been carried out using transmission electron microscopy, mainly selected area electron diffraction and energy dispersive spectroscopy. The obtained results and computer simulations comparison were made.

  11. Modification of Low-Alloy Steel Surface by High-Temperature Gas Nitriding Plus Tempering

    Science.gov (United States)

    Jiao, Dongling; Li, Minsong; Ding, Hongzhen; Qiu, Wanqi; Luo, Chengping

    2018-02-01

    The low-alloy steel was nitrided in a pure NH3 gas atmosphere at 640 660 °C for 2 h, i.e., high-temperature gas nitriding (HTGN), followed by tempering at 225 °C, which can produce a high property surface coating without brittle compound (white) layer. The steel was also plasma nitriding for comparison. The composition, microstructure and microhardness of the nitrided and tempered specimens were examined, and their tribological behavior investigated. The results showed that the as-gas-nitrided layer consisted of a white layer composed of FeN0.095 phase (nitrided austenite) and a diffusional zone underneath the white layer. After tempering, the white layer was decomposed to a nano-sized (α-Fe + γ'-Fe4N + retained austenite) bainitic microstructure with a high hardness of 1150HV/25 g. Wear test results showed that the wear resistance and wear coefficient yielded by the complex HTGN plus tempering were considerably higher and lower, respectively, than those produced by the conventional plasma nitriding.

  12. Effect of microstructure on the susceptibility of a 533 steel to temper embrittlement

    International Nuclear Information System (INIS)

    Raoul, S.; Marini, B.; Pineau, A.

    1998-01-01

    In ferritic steels, brittle fracture usually occurs at low temperature by cleavage. However the segregation of impurities (P, As, Sn etc..) along prior γ grain boundaries can change the brittle fracture mode from transgranular to intergranular. In quenched and tempered steels, this segregation is associated with what is called the temper-embrittlement phenomenon. The main objective of the present study is to investigate the influence of the as-quenched microstructure (lower bainite or martensite) on the susceptibility of a low alloy steel (A533 cl.1) to temper-embrittlement. Dilatometric tests were performed to determine the continous-cooling-transformation (CCT) diagram of the material and to measure the critical cooling rate (V c ) for a martensitic quench. Then subsized Charpy V-notched specimens were given various cooling rates from the austenitization temperature to obtain a wide range of as-quenched microstructures, including martensite and bainite. These specimens were subsequently given a heat treatment to develop temper embrittlement and tested to measure the V-notch fracture toughness at -50 C. The fracture surfaces were examined by SEM. It is shown that martensitic microstructures are more susceptible to intergranular embrittlement than bainitic microstructures. These observed microstructural influences are briefly discussed. (orig.)

  13. Finite Element Implementation of a Glass Tempering Model in Three Dimensions

    DEFF Research Database (Denmark)

    Nielsen, Jens Henrik; Olesen, John Forbes; Poulsen, Peter Noe

    2010-01-01

    The present paper develops and validates a 3D model for the simulation of glass tempering. It is assembled from well-known models of temperature dependent viscoelasticity and structural relaxation and predicts both transient and steady-state stresses in complex 3D glass geometries. The theory and...

  14. Effect of microstructure on the susceptibility of a 533 steel to temper embrittlement

    Energy Technology Data Exchange (ETDEWEB)

    Raoul, S.; Marini, B. [CEA Centre d`Etudes Nucleaires de Saclay, 91 - Gif-sur-Yvette (France). Service de Recherches Metallurgiques Appliquees; Pineau, A. [CNRS, Evry (France). Centre de Materiaux

    1998-11-01

    In ferritic steels, brittle fracture usually occurs at low temperature by cleavage. However the segregation of impurities (P, As, Sn etc..) along prior {gamma} grain boundaries can change the brittle fracture mode from transgranular to intergranular. In quenched and tempered steels, this segregation is associated with what is called the temper-embrittlement phenomenon. The main objective of the present study is to investigate the influence of the as-quenched microstructure (lower bainite or martensite) on the susceptibility of a low alloy steel (A533 cl.1) to temper-embrittlement. Dilatometric tests were performed to determine the continous-cooling-transformation (CCT) diagram of the material and to measure the critical cooling rate (V{sub c}) for a martensitic quench. Then subsized Charpy V-notched specimens were given various cooling rates from the austenitization temperature to obtain a wide range of as-quenched microstructures, including martensite and bainite. These specimens were subsequently given a heat treatment to develop temper embrittlement and tested to measure the V-notch fracture toughness at -50 C. The fracture surfaces were examined by SEM. It is shown that martensitic microstructures are more susceptible to intergranular embrittlement than bainitic microstructures. These observed microstructural influences are briefly discussed. (orig.) 11 refs.

  15. Forest dynamics in the temperate rainforests of Alaska: from individual tree to regional scales

    Science.gov (United States)

    Tara M. Barrett

    2015-01-01

    Analysis of remeasurement data from 1079 Forest Inventory and Analysis (FIA) plots revealed multi-scale change occurring in the temperate rainforests of southeast Alaska. In the western half of the region, including Prince William Sound, aboveground live tree biomass and carbon are increasing at a rate of 8 ( ± 2 ) percent per decade, driven by an increase in Sitka...

  16. Ecological correlates of flying squirrel microhabitat use and density in temperate rainforests of southeastern Alaska

    Science.gov (United States)

    Winston P. Smith; Scott M. Gende; Jeffrey V. Nichols

    2004-01-01

    We studied habitat relations of the Prince of Wales flying squirrel (Glaucomys sabrinus griseifrons), an endemic of the temperate, coniferous rainforest of southeastern Alaska, because of concerns over population viability from extensive clear-cut logging in the region. We used stepwise logistic regression to examine relationships between...

  17. Preparation and characterization of tempered tungsten layers on single crystalline silicon

    International Nuclear Information System (INIS)

    Nitzsche, K.; Knedlik, C.; Tippmann, H.; Spiess, L.; Harman, R.; Vanek, O.; Tvarozek, V.

    1984-01-01

    Tungsten layers have been deposited on single crystalline silicon by sputtering and characterized by measurements of the sheet resistance by a linear four point method and the van der Pauw method. The influence of tempering under argon on the resistance has been studied. By means of the RBS spectroscopy it was found that the increase in the specific resistance is caused by interdiffusion

  18. The effect of prior tempering on cryogenic treatment to reduce retained austenite

    International Nuclear Information System (INIS)

    Stratton, Paul

    2010-01-01

    The consensus view is that a high carbon case gives gears the best overall properties provided that there is no carbide network and that the retained austenite has been reduced below 20% by cryogenic treatment. This view is effectively enshrined in the SAE AMS 2759/7 standard. The cryogenic treatment usually takes place immediately after the quench to avoid austenite stabilisation. However, for some parts with complex geometries that might crack during the treatment, a short low temperature temper is carried out first. Little is known on how this temper affects the subsequent cryogenic treatment. Three carburizing steels used extensively in the aerospace industry were carburized to produce high retained austenite levels in the case using two different, but typical carburizing cycles. The retained austenite was determined by XRD before and after cryogenic treatment carried out in accordance with the standard and compared with that obtained when an intermediate temper was used. This study shows that for three typical carburizing steels, carburized using typical cycles, the efficacy of the cryogenic treatment is reduced only slightly after the temper, and not enough to be industrially significant. (author)

  19. Griswold Tempered Water Flow Regulator Valves Used as Anti-Siphon Valves

    International Nuclear Information System (INIS)

    MISKA, C.

    2000-01-01

    FCV-1*22 and 1*23 are Griswold constant flow regulators used as anti-siphon valves in the tempered water system, they fail closed but valve cartridge orifice allows minimum flow to prevent loss of water from the MCO/CASK annulus

  20. Feed efficiency of tropically adapted cattle when fed in winter or spring in a temperate location

    Science.gov (United States)

    Earlier work has shown that young, tropically adapted cattle do not gain as rapidly as temperately adapted cattle during the winter in OK. The objective for this study was to determine if efficiency of gains was also impacted in tropically adapted cattle and if efficiency is consistent in different...

  1. Reinforced glass beams composed of annealed, heat-strengthened and fully tempered glass

    NARCIS (Netherlands)

    Louter, P.C.; Belis, J.L.I.F.; Bos, F.P.; Veer, F.A.

    Annealed, heat-strengthened and fully tempered SG-laminated reinforced glass beam specimens were subjected to four-point bending tests to investigate the effects of glass type on their structural response. During the test the beams showed linear elastic response until initial glass failure, followed

  2. Elevated carbon dioxide and ozone alter productivity and ecosystem carbon content in northern temperate forests

    Science.gov (United States)

    Alan F. Talhelm; Kurt S. Pregitzer; Mark E. Kubiske; Donald R. Zak; Courtney E. Campany; Andrew J. Burton; Richard E. Dickson; George R. Hendrey; J. G. Isebrands; Keith F. Lewin; John Nagy; David F. Karnosky

    2014-01-01

    Three young northern temperate forest communities in the north-central United States were exposed to factorial combinations of elevated carbon dioxide (CO2) and tropospheric ozone (O3) for 11 years. Here, we report results from an extensive sampling of plant biomass and soil conducted at the conclusion of the experiment...

  3. Human impact on open temperate woodlands during the middle Holocene in Central Europe

    Czech Academy of Sciences Publication Activity Database

    Jamrichová, Eva; Hédl, Radim; Kolář, Jan; Tóth, P.; Bobek, Přemysl; Hajnalová, M.; Procházka, J.; Kadlec, Jaroslav; Szabó, Péter

    2017-01-01

    Roč. 245, OCT 2017 (2017), s. 55-68 ISSN 0034-6667 EU Projects: European Commission(XE) 278065 - LONGWOOD Institutional support: RVO:67985939 ; RVO:67985530 Keywords : temperate oakwoods * Quercus * human impact Subject RIV: EH - Ecology, Behaviour; DE - Earth Magnetism, Geodesy, Geography (GFU-E) OBOR OECD: Ecology; Physical geography (GFU-E) Impact factor: 1.817, year: 2016

  4. Detrital carbon pools in temperate forests: magnitude and potential for landscape-scale assessment

    Science.gov (United States)

    John Bradford; Peter Weishampel; Marie-Louise Smith; Randall Kolka; Richard A. Birdsey; Scott V. Ollinger; Michael G. Ryan

    2009-01-01

    Reliably estimating carbon storage and cycling in detrital biomass is an obstacle to carbon accounting. We examined carbon pools and fluxes in three small temperate forest landscapes to assess the magnitude of carbon stored in detrital biomass and determine whether detrital carbon storage is related to stand structural properties (leaf area, aboveground biomass,...

  5. Soil quality indicators of a mature alley-cropping agroforestry system in temperate North America

    Science.gov (United States)

    Although agroforestry practices are believed to improve soil quality, reports on long-term effects of alley cropping on soils within agroforestry in the temperate zone are limited. The objective of this study was to examine effects of management, landscape, and soil depth of an established agrofores...

  6. Soil quality differences in a mature alley cropping system in temperate North America

    Science.gov (United States)

    Alley cropping in agroforestry practices has been shown to improve soil quality, however information on long-term effects (>10 years) of alley cropping on soils in the temperate zone is very limited. The objective of this study was to examine effects of management, landscape, and soil depth on soil...

  7. Detrimental Influence of Invasive Earthworms on North American Cold-Temperate Forest Soils

    Science.gov (United States)

    Enerson, Isabel

    2012-01-01

    The topic of invasive earthworms is a timely concern that goes against many preconceived notions regarding the positive benefits of all worms. In the cold-temperate forests of North America invasive worms are threatening forest ecosystems, due to the changes they create in the soil, including decreases in C:N ratios and leaf litter, disruption of…

  8. Interannual, seasonal, and retrospective analysis of the methane and carbon dioxide budgets of a temperate peatland

    Science.gov (United States)

    D.M. Olson; T.J. Griffis; A. Noormets; R. Kolka; J. Chen

    2013-01-01

    Three years (2009-2011) of near-continuous methane (CH4) and carbon dioxide (CO2) fluxes were measured with the eddy covariance (EC) technique at a temperate peatland located within the Marcell Experimental Forest, in northern Minnesota, USA. The peatland was a net source of CH4 and a net sink of CO...

  9. Hardness prediction of HAZ in temper bead welding by non-consistent layer technique

    International Nuclear Information System (INIS)

    Yu, Lina; Saida, Kazuyoshi; Mochizuki, Masahito; Kameyama, Masashi; Chigusa, Naoki; Nishimoto, Kazutoshi

    2014-01-01

    Based on the experimentally obtained hardness database, the neural network-based hardness prediction system of heat affect zone (HAZ) in temper bead welding by Consistent Layer (CSL) technique has been constructed by the authors. However in practical operation, CSL technique is sometimes difficult to perform because of difficulty of the precise heat input controlling, and in such case non-CSL techniques are mainly used in the actual repair process. Therefore in the present study, the neural network-based hardness prediction system of HAZ in temper bead welding by non-CSL techniques has been constructed through thermal cycle simplification, from the view of engineering. The hardness distribution in HAZ with non-CSL techniques was calculated based on the thermal cycles numerically obtained by finite element method. The experimental result has shown that the predicted hardness is in good accordance with the measured ones. It follows that the currently proposed method is effective for estimating the tempering effect during temper bead welding by non-CSL techniques. (author)

  10. Electromagnetic nondestructive evaluation of tempering process in AISI D2 tool steel

    International Nuclear Information System (INIS)

    Kahrobaee, Saeed; Kashefi, Mehrdad

    2015-01-01

    The present paper investigates the potential of using eddy current technique as a reliable nondestructive tool to detect microstructural changes during the different stages of tempering treatment in AISI D2 tool steel. Five stages occur in tempering of the steel: precipitation of ε carbides, formation of cementite, retained austenite decomposition, secondary hardening effect and spheroidization of carbides. These stages were characterized by destructive methods, including dilatometry, differential scanning calorimetry, X-ray diffraction, scanning electron microscopic observations, and hardness measurements. The microstructural changes alter the electrical resistivity/magnetic saturation, which, in turn, influence the eddy current signals. Two EC parameters, induced voltage sensed by pickup coil and impedance point detected by excitation coil, were evaluated as a function of tempering temperature to characterize the microstructural features, nondestructively. The study revealed that a good correlation exists between the EC parameters and the microstructural changes. - Highlights: • D2 steel parts were tempered at 200-650 °C to produce various microstructures. • Precipitation of ε and Fe 3 C carbides and spheroidization of carbides were detected. • Retained austenite decomposition and secondary hardening effect were determined. • Variations of electrical resistivity (ρ) and magnetic saturation (Bs) were studied. • Combined effects of ρ and Bs on the EC outputs were evaluated

  11. Electromagnetic nondestructive evaluation of tempering process in AISI D2 tool steel

    Energy Technology Data Exchange (ETDEWEB)

    Kahrobaee, Saeed, E-mail: saeed.kahrobaee@yahoo.com; Kashefi, Mehrdad, E-mail: m-kashefi@um.ac.ir

    2015-05-15

    The present paper investigates the potential of using eddy current technique as a reliable nondestructive tool to detect microstructural changes during the different stages of tempering treatment in AISI D2 tool steel. Five stages occur in tempering of the steel: precipitation of ε carbides, formation of cementite, retained austenite decomposition, secondary hardening effect and spheroidization of carbides. These stages were characterized by destructive methods, including dilatometry, differential scanning calorimetry, X-ray diffraction, scanning electron microscopic observations, and hardness measurements. The microstructural changes alter the electrical resistivity/magnetic saturation, which, in turn, influence the eddy current signals. Two EC parameters, induced voltage sensed by pickup coil and impedance point detected by excitation coil, were evaluated as a function of tempering temperature to characterize the microstructural features, nondestructively. The study revealed that a good correlation exists between the EC parameters and the microstructural changes. - Highlights: • D2 steel parts were tempered at 200-650 °C to produce various microstructures. • Precipitation of ε and Fe{sub 3}C carbides and spheroidization of carbides were detected. • Retained austenite decomposition and secondary hardening effect were determined. • Variations of electrical resistivity (ρ) and magnetic saturation (Bs) were studied. • Combined effects of ρ and Bs on the EC outputs were evaluated.

  12. Evapotranspiration and soil moisture dynamics in a temperate grassland ecosystem in Inner Mongolia China

    Science.gov (United States)

    L. Hao; Ge Sun; Yongqiang Liu; G. S. Zhou; J. H.   Wan;  L. B. Zhang; J. L. Niu; Y. H. Sang;  J. J He

    2015-01-01

    Precipitation, evapotranspiration (ET), and soil moisture are the key controls for the productivity and functioning of temperate grassland ecosystems in Inner Mongolia, northern China. Quantifying the soil moisture dynamics and water balances in the grasslands is essential to sustainable grassland management under global climate change. We...

  13. Cold in the common garden: comparative low-temperature tolerance of boreal and temperate conifer foliage

    Science.gov (United States)

    G. Richard Strimbeck; Trygve D. Kjellsen; Paul G. Schaberg; Paula F. Murakami

    2007-01-01

    Because they maintain green foliage throughout the winter season, evergreen conifers may face special physiological challenges in a warming world. We assessed the midwinter low-temperature (LT) tolerance of foliage from eight temperate and boreal species in each of the genera Abies, Picea, and Pinus growing in an arboretum in...

  14. Effects of seasonal variation of photosynthetic capacity on the carbon fluxes of a temperate deciduous forest

    Science.gov (United States)

    David Medvigy; Su-Jong Jeong; Kenneth L. Clark; Nicholas S. Skowronski; Karina V. R. Schäfer

    2013-01-01

    Seasonal variation in photosynthetic capacity is an important part of the overall seasonal variability of temperate deciduous forests. However, it has only recently been introduced in a few terrestrial biosphere models, and many models still do not include it. The biases that result from this omission are not well understood. In this study, we use the Ecosystem...

  15. Temperature dependence of UV radiation effects in Arctic and temperate isolates of three red macrophytes

    NARCIS (Netherlands)

    van de Poll, W.H.; Eggert, A.; Buma, A.G.J.; Breeman, Arno

    The temperature dependence of UV effects was studied for Arctic and temperate isolates of the red macrophytes Palmaria palmata, Coccotylus truncatus and Phycodrys rubens. The effects of daily repeated artificial ultraviolet B and A radiation (UVBR: 280-320 nm, UVAR: 320-400 nm) treatments were

  16. Ecological anachronisms in the recruitment of temperate light-demanding tree species in wooded pastures

    NARCIS (Netherlands)

    Bakker, ES; Olff, H; Vandenberghe, C; De Maeyer, K; Smit, R; Gleichman, JM; Vera, FWM

    1. Light-demanding trees and thorny shrubs in temperate plant communities may reflect adaptations to now-extinct large grazers, such as aurochs and tarpans, rendering these adaptations ecological anachronisms. 2. We explored the ecological functions of plant traits of Quercus robur and Prunus

  17. Strain-tempering of low carbon martensite steel wire by rapid heating

    International Nuclear Information System (INIS)

    Torisaka, Yasunori; Kihara, Junji

    1978-01-01

    In the production of prestressed concrete steel wires, a series of the cold drawing-patenting process are performed to improve the strength. In order to reduce cyclic process, the low carbon martensite steel wire which can be produced only by the process of hot rolling and direct quench has been investigated as strain-tempering material. When strain-tempering is performed on the low carbon martensite steel wire, stress relaxation (Re%) increases and mechanical properties such as total elongation, reduction of area, ultimate tensile strength and proof stress decrease remarkably by annealing. In order to shorten the heating time, the authors performed on the steel wire the strain-tempering with a heating time of 1.0 s using direct electrical resistance heating and examined the effects of rapid heating on the stress relaxation and the mechanical properties. Stress relaxation decreases without impairment of the mechanical properties up to a strain-tempering temperature of 573 K. Re(%) after 10.8 ks is 0% at the testing temperature 301 K, 0.49% at 363 K and 1.39% at 433 K. (auth.)

  18. On the Nature of Internal Interfaces in Tempered Martensite Ferritic Steels

    Czech Academy of Sciences Publication Activity Database

    Dronhofer, A.; Pešička, J.; Dlouhý, Antonín; Eggeler, G.

    2003-01-01

    Roč. 94, č. 5 (2003), s. 511-520 ISSN 0044-3093 R&D Projects: GA ČR GA106/99/1172 Institutional research plan: CEZ:AV0Z2041904 Keywords : Tempered martensite ferritic steels * martensite variants * orientation imaging Subject RIV: JG - Metallurgy Impact factor: 0.637, year: 2003

  19. Parallel continuous simulated tempering and its applications in large-scale molecular simulations

    Energy Technology Data Exchange (ETDEWEB)

    Zang, Tianwu; Yu, Linglin; Zhang, Chong [Applied Physics Program and Department of Bioengineering, Rice University, Houston, Texas 77005 (United States); Ma, Jianpeng, E-mail: jpma@bcm.tmc.edu [Applied Physics Program and Department of Bioengineering, Rice University, Houston, Texas 77005 (United States); Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, BCM-125, Houston, Texas 77030 (United States)

    2014-07-28

    In this paper, we introduce a parallel continuous simulated tempering (PCST) method for enhanced sampling in studying large complex systems. It mainly inherits the continuous simulated tempering (CST) method in our previous studies [C. Zhang and J. Ma, J. Chem. Phys. 130, 194112 (2009); C. Zhang and J. Ma, J. Chem. Phys. 132, 244101 (2010)], while adopts the spirit of parallel tempering (PT), or replica exchange method, by employing multiple copies with different temperature distributions. Differing from conventional PT methods, despite the large stride of total temperature range, the PCST method requires very few copies of simulations, typically 2–3 copies, yet it is still capable of maintaining a high rate of exchange between neighboring copies. Furthermore, in PCST method, the size of the system does not dramatically affect the number of copy needed because the exchange rate is independent of total potential energy, thus providing an enormous advantage over conventional PT methods in studying very large systems. The sampling efficiency of PCST was tested in two-dimensional Ising model, Lennard-Jones liquid and all-atom folding simulation of a small globular protein trp-cage in explicit solvent. The results demonstrate that the PCST method significantly improves sampling efficiency compared with other methods and it is particularly effective in simulating systems with long relaxation time or correlation time. We expect the PCST method to be a good alternative to parallel tempering methods in simulating large systems such as phase transition and dynamics of macromolecules in explicit solvent.

  20. Solar Radiation Disinfection of Drinking Water at Temperate Latitudes: Inactivation rates for an optimized reactor configuration

    Science.gov (United States)

    Solar radiation-driven inactivation of bacteria, virus and protozoan pathogen models was quantified in simulated drinking water at a temperate latitude (34°S). The water was seeded with Enterococcus faecalis, Clostridium sporogenes spores, and P22 bacteriophage, each at ca 1 x 10...

  1. Numerical simulation of tropical-temperate troughs over Southern Africa using the CSU RAMS model

    CSIR Research Space (South Africa)

    Van den Heever, SC

    1997-08-01

    Full Text Available ) and the wet (1981) late summer case studies has been examined. Model simulations reveal that the tropical-temperate troughs form when an upper westerly wave coincides with an easterly, wave or depression in lower levels. These systems occur preferentially over...

  2. Mechanisms of nitrogen deposition effects on temperate forest lichens and trees

    Science.gov (United States)

    Therese S. Carter; Christopher M. Clark; Mark E. Fenn; Sarah Jovan; Steven S. Perakis; Jennifer Riddell; Paul G. Schaberg; Tara L. Greaver; Meredith G. Hastings

    2017-01-01

    We review the mechanisms of deleterious nitrogen (N) deposition impacts on temperate forests, with a particular focus on trees and lichens. Elevated anthropogenic N deposition to forests has varied effects on individual organisms depending on characteristics both of the N inputs (form, timing, amount) and of the organisms (ecology, physiology) involved. Improved...

  3. A conceptual framework for predicting temperate ecosystem sensitivity to human impacts on fire regimes

    Science.gov (United States)

    D. B. McWethy; P. E. Higuera; C. Whitlock; T. T. Veblen; D. M. J. S. Bowman; G. J. Cary; S. G. Haberle; R. E. Keane; B. D. Maxwell; M. S. McGlone; G. L. W. Perry; J. M. Wilmshurst

    2013-01-01

    The increased incidence of large fires around much of the world in recent decades raises questions about human and non-human drivers of fire and the likelihood of increased fire activity in the future. The purpose of this paper is to outline a conceptual framework for examining where human-set fires and feedbacks are likely to be most pronounced in temperate forests...

  4. Influence of tempering on mechanical strains in Mo2Si films

    International Nuclear Information System (INIS)

    Zscheile, H.D.

    1984-01-01

    Amorphous or crystalline MoSi 2 films on (111) silicon wafers, deposited by DC triode sputtering, showed compressive stress. Tensile stress was found in the same films formed by dual electron beam evaporation. By isochronous tempering in the temperature range of 300 to 1270 K the compressive stress of the sputtered films was converted into tensile stress

  5. Estimating Janka hardness from specific gravity for tropical and temperate species

    Science.gov (United States)

    Michael C. Wiemann; David W. Green

    2007-01-01

    Using mean values for basic (green) specific gravity and Janka side hardness for individual species obtained from the world literature, regression equations were developed to predict side hardness from specific gravity. Statistical and graphical methods showed that the hardness–specific gravity relationship is the same for tropical and temperate hardwoods, but that the...

  6. Drivers of temporal changes in temperate forest plant diversity vary across spatial scales

    Czech Academy of Sciences Publication Activity Database

    Bernhardt-Römermann, M.; Baeten, L.; Craven, D.; De Frenne, P.; Hédl, Radim; Lenoir, J.; Bert, D.; Brunet, J.; Chudomelová, Markéta; Decocq, G.; Dierschke, H.; Dirnböck, T.; Dörfler, I.; Heinken, T.; Hermy, M.; Hommel, P.; Jaroszewicz, B.; Keczynski, A.; Kelly, D. L.; Kirkby, K.J.; Kopecký, Martin; Macek, Martin; Máliš, F.; Mirtl, M.; Mitchell, F. J. G.; Naaf, T.; Newman, M.; Peterken, G.; Petřík, Petr; Schmidt, W.; Standovár, T.; Tóth, Z.; Van Calster, H.; Verstraeten, G.; Vladovič, J.; Vild, Ondřej; Wulf, M.; Verheyen, K.

    2015-01-01

    Roč. 21, č. 10 (2015), s. 3726-3737 ISSN 1354-1013 R&D Projects: GA MŠk(CZ) EE2.3.20.0267 EU Projects: European Commission(XE) 278065 - LONGWOOD Institutional support: RVO:67985939 Keywords : temperate forest * long-term change * herbaceous layer Subject RIV: EF - Botanics Impact factor: 8.444, year: 2015

  7. Arthropod vertical stratification in temperate deciduous forests: Implications for conservation oriented management

    Science.gov (United States)

    Ulyshen Michael

    2011-01-01

    Studies on the vertical distribution patterns of arthropods in temperate deciduous forests reveal highly stratified (i.e., unevenly vertically distributed) communities. These patterns are determined by multiple factors acting simultaneously, including: (1) time (forest age, season, time of day); (2) forest structure (height, vertical foliage complexity, plant surface...

  8. Suitability of close-to-nature silviculture for adapting temperate European forests to climate change

    NARCIS (Netherlands)

    Brang, P.; Spathelf, P.; Larsen, J.B.; Bauhus, J.; Boncina, A.; Mohren, G.M.J.

    2014-01-01

    In many parts of Europe, close-to-nature silviculture (CNS) has been widely advocated as being the best approach for managing forests to cope with future climate change. In this review, we identify and evaluate six principles for enhancing the adaptive capacity of European temperate forests in a

  9. RECONSTRUCTING THE EVOLUTIONARY HISTORY OF THE FOREST FUNGAL PATHOGEN, ARMILLARIA MELLEA, IN A TEMPERATE WORLDWIDE POPULATIONS

    Science.gov (United States)

    The forest pathogen Armillaria mellea s.s. (Basidiomycota, Physalacriaceae) is among the most significant forest pathogens causing root rot in northern temperate forest trees worldwide. Phylogenetic reconstructions for A. mellea show distinct European, Asian and North American lineages. The North Am...

  10. Seed dispersal by fishes in tropical and temperate fresh waters: The growing evidence

    NARCIS (Netherlands)

    Horn, M.H.; Correa, S.B.; Parolin, P.; Pollux, B.J.A.; Anderson, J.T.; Lucas, C.; Widmann, P.; Tjiu, A.; Galetti, M.; Goulding, M.

    2011-01-01

    Fruit-eating by fishes represents an ancient (perhaps Paleozoic) interaction increasingly regarded as important for seed dispersal (ichthyochory) in tropical and temperate ecosystems. Most of the more than 275 known frugivorous species belong to the mainly Neotropical Characiformes (pacus, piranhas)

  11. Substrate and nutrient limitation of ammonia-oxidizing bacteria and archaea in temperate forest soil

    Science.gov (United States)

    J.S. Norman; J.E. Barrett

    2014-01-01

    Ammonia-oxidizing microbes control the rate-limiting step of nitrification, a critical ecosystem process, which affects retention and mobility of nitrogen in soil ecosystems. This study investigated substrate (NH4þ) and nutrient (K and P) limitation of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in temperate forest soils at Coweeta Hydrologic...

  12. Planetesimal Formation in the Warm, Inner Disk: Experiments with Tempered Dust

    Energy Technology Data Exchange (ETDEWEB)

    De Beule, Caroline; Landers, Joachim; Salamon, Soma; Wende, Heiko; Wurm, Gerhard, E-mail: gerhard.wurm@uni-due.de [Faculty of Physics, University of Duisburg-Essen, Lotharstr. 1, D-47057 Duisburg (Germany)

    2017-03-01

    It is an open question how elevated temperatures in the inner parts of protoplanetary disks influence the formation of planetesimals. We approach this problem here by studying the tensile strength of granular beds with dust samples tempered at different temperatures. We find via laboratory experiments that tempering at increasing temperatures is correlated with an increase in cohesive forces. We studied dust samples of palagonite (JSC Mars-1a) which were tempered for up to 200 hr at temperatures between 600 and 1200 K, and measured the relative tensile strengths of highly porous dust layers once the samples cooled to room temperature. Tempering increases the tensile strength from 800 K upwards. This change is accompanied by mineral transformations, the formation of iron oxide crystallites as analyzed by Mössbauer spectroscopy, changes in the number size distribution, and the morphology of the surface visible as cracks in larger grains. These results suggest a difference in the collisional evolution toward larger bodies with increasing temperature as collisional growth is fundamentally based on cohesion. While high temperatures might also increase sticking (not studied here), compositional evolution will already enhance the cohesion and the possibility of growing larger aggregates on the way toward planetesimals. This might lead to a preferred in situ formation of inner planets and explain the observed presence of dense inner planetary systems.

  13. Drought enhances symbiotic dinitrogen fixation and competitive ability of a temperate forest tree

    Science.gov (United States)

    Nina Wurzburger; Chelcy Ford Miniat

    2013-01-01

    General circulation models project more intense and frequent droughts over the next century, but many questions remain about how terrestrial ecosystems will respond. Of particular importance, is to understand how drought will alter the species composition of regenerating temperate forests wherein symbiotic dinitrogen (N2)- fixing plants play a...

  14. Mechanisms promoting higher growth rate in arctic than in temperate shorebirds

    NARCIS (Netherlands)

    Schekkerman, H.; Tulp, I.Y.M.; Piersma, T.; Visser, G.H.

    2003-01-01

    We compared prefledging growth, energy expenditure, and time budgets in the arctic-breeding red knot (Calidris canutus) to those in temperate shorebirds, to investigate how arctic chicks achieve a high growth rate despite energetic difficulties associated with precocial development in a cold

  15. Simple model for daily evaporation from fallow tilled soil under spring conditions in a temperate climate.

    NARCIS (Netherlands)

    Boesten, J.J.T.I.; Stroosnijder, L.

    1986-01-01

    A simple parametric model is presented to estimate daily evaporation from fallow tilled soil under spring conditions in a temperate climate. In this model, cumulative actual evaporation during a drying cycle is directly proportional to the square root of cumulative potential evaporation. The model

  16. Mechanisms promoting higher growth rate in arctic than in temperate shorebirds

    NARCIS (Netherlands)

    Schekkerman, H; Tulp, Ingrid; Piersma, T.; Visser, G.H.

    We compared prefledging growth, energy expenditure, and time budgets in the arctic-breeding red knot (Calidris canutus) to those in temperate shorebirds, to investigate how arctic chicks achieve a high growth rate despite energetic difficulties associated with precocial development in a cold

  17. Heat stress in cows at pasture and benefit of shade in a temperate climate region

    Science.gov (United States)

    Veissier, Isabelle; Van laer, Eva; Palme, Rupert; Moons, Christel P. H.; Ampe, Bart; Sonck, Bart; Andanson, Stéphane; Tuyttens, Frank A. M.

    2017-11-01

    Under temperate climates, cattle are often at pasture in summer and are not necessarily provided with shade. We aimed at evaluating in a temperate region (Belgium) to what extent cattle may suffer from heat stress (measured through body temperature, respiration rate and panting score, cortisol or its metabolites in milk, and feces on hot days) and at assessing the potential benefits of shade. During the summer of 2012, 20 cows were kept on pasture without access to shade. During the summer of 2011, ten cows had access to shade (young trees with shade cloth hung between them), whereas ten cows had no access. Climatic conditions were quantified by the Heat Load Index (HLI). In animals without access to shade respiration rates, panting scores, rectal temperatures, and milk cortisol concentrations increased as HLI increased in both 2011 and 2012. Fecal cortisol metabolites varied with HLI in 2011 only. When cattle had access to shade, their use of shade increased as the HLI increased. This effect was more pronounced during the last part of the summer, possibly due to better acquaintance with the shade construction. In this case, shade use increased to 65% at the highest HLI (79). Shade tempered the effects on respiration, rectal temperature, and fecal cortisol metabolites. Milk cortisol was not influenced by HLI for cows using shade for > 10% of the day. Therefore, even in temperate areas, cattle may suffer from heat when they are at pasture in summer and providing shade can reduce such stress.

  18. The marine radiocarbon bomb pulse across the temperate North Atlantic: a compilation of Delta

    NARCIS (Netherlands)

    Scourse, J.D.; Wanamaker jr., A.D.; Weidman, C.; Heinemeier, J.; Reimer, P.J.; Butler, P.G.; Witbaard, R.; Richardson, C.A.

    2012-01-01

    Marine radiocarbon bomb-pulse time histories of annually resolved archives from temperate regions have been underexploited. We present here series of Delta C-14 excess from known-age annual increments of the long-lived bivalve mollusk Arctica islandica from 4 sites across the coastal North Atlantic

  19. Modeling complex effects of multiple environmental stresses on carbon dynamics of Mid-Atlantic temperate forests

    Science.gov (United States)

    Yude Pan; Richard Birdsey; John Hom; Kevin McCullough

    2007-01-01

    We used our GIS variant of the PnET-CN model to investigate changes of forest carbon stocks and fluxes in Mid-Atlantic temperate forests over the last century (1900-2000). Forests in this region are affected by multiple environmental changes including climate, atmospheric CO2 concentration, N deposition and tropospheric ozone, and extensive land disturbances. Our...

  20. Temperate and virulent Lactobacillus delbrueckii bacteriophages: comparison of their thermal and chemical resistance.

    Science.gov (United States)

    Ebrecht, Ana C; Guglielmotti, Daniela M; Tremmel, Gustavo; Reinheimer, Jorge A; Suárez, Viviana B

    2010-06-01

    The aim of this work was to study the efficiency of diverse chemical and thermal treatments usually used in dairy industries to control the number of virulent and temperate Lactobacillus delbrueckii bacteriophages. Two temperate (Cb1/204 and Cb1/342) and three virulent (BYM, YAB and Ib3) phages were studied. The thermal treatments applied were: 63 degrees C for 30 min (low temperature--long time, LTLT), 72 degrees C for 15 s (high temperature--short time, HTST), 82 degrees C for 5 min (milk destined to yogurt elaboration) and 90 degrees C for 15 min (FIL-IDF). The chemical agents studied were: sodium hypochlorite, ethanol, isopropanol, peracetic acid, biocides A (quaternary ammonium chloride), B (hydrogen peroxide, peracetic acid and peroctanoic acid), C (alkaline chloride foam), D (p-toluensulfonchloroamide, sodium salt) and E (ethoxylated nonylphenol and phosphoric acid). The kinetics of inactivation were drew and T(99) (time necessary to eliminate the 99% of phage particles) calculated. Results obtained showed that temperate phages revealed lower resistance than the virulent ones to the treatment temperatures. Biocides A, C, E and peracetic acid showed a notable efficiency to inactivate high concentrations of temperate and virulent L. delbrueckii phages. Biocide B evidenced, in general, a good capacity to eliminate the phage particles. Particularly for this biocide virulent phage Ib3 showed the highest resistance in comparison to the rest of temperate and virulent ones. On the contrary, biocide D and isopropanol presented a very low capacity to inactivate all phages studied. The efficiency of ethanol and hypochlorite was variable depending to the phages considered. These results allow a better knowledge and give useful information to outline more effective treatments to reduce the phage infections in dairy plants. 2009 Elsevier Ltd. All rights reserved.

  1. Effect of tempering temperature on the microstructure and mechanical properties of a reactor pressure vessel steel

    Energy Technology Data Exchange (ETDEWEB)

    Li, C.W.; Han, L.Z.; Luo, X.M.; Liu, Q.D.; Gu, J.F., E-mail: gujf@sjtu.edu.cn

    2016-08-15

    The microstructure and mechanical properties of reactor pressure vessel (RPV) steel were investigated after tempering at different temperatures ranging from 580 to 700 °C for 5 h. With increasing tempering temperature, the impact toughness, which is qualified by Charpy V-notch total absorbed energy, initially increases from 142 to 252 J, and then decreases to 47 J, with a maximum value at 650 °C, while the ultimate tensile strength varies in exactly the opposite direction. Comparing the microstructure and fracture surfaces of different specimens, the variations in toughness and strength with the tempering temperature were generally attributed to the softening of the bainitic ferrite, the agminated Fe{sub 3}C carbides that resulted from decomposition of martensite/austenite (M/A) constituents, the precipitation of Mo{sub 2}C carbides, and the newly formed M/A constituents at the grain boundaries. Finally, the correlation between the impact toughness and the volume fraction of the M/A constituents was established, and the fracture mechanisms for the different tempering conditions are explained. - Highlights: • The dependence of the deterioration of impact toughness on tempering temperature has been analysed. • The instrumented Charpy V-notch impact test has been employed to study the fracture mechanism. • The influence of M/A constituents on different fracture mechanisms based on the hinge model has been demonstrated. • A correlation between the mechanical properties and the amount of M/A constituents has been established.

  2. A comparison of PCB bioaccumulation factors between an arctic and a temperate marine food web.

    Science.gov (United States)

    Sobek, Anna; McLachlan, Michael S; Borgå, Katrine; Asplund, Lillemor; Lundstedt-Enkel, Katrin; Polder, Anuschka; Gustafsson, Orjan

    2010-06-01

    To test how environmental conditions in the Arctic and the resulting ecological adaptations affect accumulation of persistent organic pollutants (POPs) in the marine food web, bioaccumulation of four polychlorinated biphenyls (PCBs) in an arctic (Barents Sea 77 degrees N-82 degrees N) and a temperate marine (Baltic Sea 54 degrees N-62 degrees N) food web were compared. Three different trophic levels were studied (zooplankton, fish, and seal), representing the span from first-level consumer to top predator. Previously published high-quality data on PCB water concentrations in the two areas were used for calculation of bioaccumulation factors (BAF). BAF was calculated as the ratio of the PCB concentration in the organism ([PCB](org); pg/kg lipid) to the dissolved water concentration (C(w); pg/L). The BAF(Arctic):BAF(Temperate) ratios were above 1 for all four PCB congeners in zooplankton (6.4-13.8) and planktivorous fish (2.9-5.0)), whereas the ratios were below 1 in seal. The mean ratio between arctic and temperate BAFs for all trophic levels and congeners (BAF(Arcti):BAF(Temperate)) was 4.8. When the data were corrected for the seawater temperature difference between the two ecosystems, the ratio was 2.0. We conclude that bioaccumulation differences caused by ecological or physiological adaptations of organisms between the two ecosystems were well within a water concentration variability of 50%. Further, our data support the hypothesis that lower seawater temperature lead to a thermodynamically favoured passive partitioning to organic matrices and thus elevated ambient BAFs in the Arctic compared to the Baltic Sea. This would imply that bioaccumulation in the Arctic may be described in the same way as bioaccumulation in temperate regions, e.g. by the use of mechanistic models parameterised for the Arctic. Copyright (c) 2010. Published by Elsevier B.V.

  3. Temperate bacterial viruses as double-edged swords in bacterial warfare.

    Science.gov (United States)

    Gama, João Alves; Reis, Ana Maria; Domingues, Iolanda; Mendes-Soares, Helena; Matos, Ana Margarida; Dionisio, Francisco

    2013-01-01

    It has been argued that bacterial cells may use their temperate viruses as biological weapons. For instance, a few bacterial cells among a population of lysogenic cells could release the virus and kill susceptible non-lysogenic competitors, while their clone mates would be immune. Because viruses replicate inside their victims upon infection, this process would amplify their number in the arena. Sometimes, however, temperate viruses spare recipient cells from death by establishing themselves in a dormant state inside cells. This phenomenon is called lysogenization and, for some viruses such as the λ virus, the probability of lysogenization increases with the multiplicity of infection. Therefore, the amplification of viruses leads to conflicting predictions about the efficacy of temperate viruses as biological weapons: amplification can increase the relative advantage of clone mates of lysogens but also the likelihood of saving susceptible cells from death, because the probability of lysogenization is higher. To test the usefulness of viruses as biological weapons, we performed competition experiments between lysogenic Escherichia coli cells carrying the λ virus and susceptible λ-free E. coli cells, either in a structured or unstructured habitat. In structured and sometimes in unstructured habitats, the λ virus qualitatively behaved as a "replicating toxin". However, such toxic effect of λ viruses ceased after a few days of competition. This was due to the fact that many of initially susceptible cells became lysogenic. Massive lysogenization of susceptible cells occurred precisely under the conditions where the amplification of the virus was substantial. From then on, these cells and their descendants became immune to the λ virus. In conclusion, if at short term bacterial cells may use temperate viruses as biological weapons, after a few days only the classical view of temperate bacterial viruses as parasitic agents prevails.

  4. Temperate bacterial viruses as double-edged swords in bacterial warfare.

    Directory of Open Access Journals (Sweden)

    João Alves Gama

    Full Text Available It has been argued that bacterial cells may use their temperate viruses as biological weapons. For instance, a few bacterial cells among a population of lysogenic cells could release the virus and kill susceptible non-lysogenic competitors, while their clone mates would be immune. Because viruses replicate inside their victims upon infection, this process would amplify their number in the arena. Sometimes, however, temperate viruses spare recipient cells from death by establishing themselves in a dormant state inside cells. This phenomenon is called lysogenization and, for some viruses such as the λ virus, the probability of lysogenization increases with the multiplicity of infection. Therefore, the amplification of viruses leads to conflicting predictions about the efficacy of temperate viruses as biological weapons: amplification can increase the relative advantage of clone mates of lysogens but also the likelihood of saving susceptible cells from death, because the probability of lysogenization is higher. To test the usefulness of viruses as biological weapons, we performed competition experiments between lysogenic Escherichia coli cells carrying the λ virus and susceptible λ-free E. coli cells, either in a structured or unstructured habitat. In structured and sometimes in unstructured habitats, the λ virus qualitatively behaved as a "replicating toxin". However, such toxic effect of λ viruses ceased after a few days of competition. This was due to the fact that many of initially susceptible cells became lysogenic. Massive lysogenization of susceptible cells occurred precisely under the conditions where the amplification of the virus was substantial. From then on, these cells and their descendants became immune to the λ virus. In conclusion, if at short term bacterial cells may use temperate viruses as biological weapons, after a few days only the classical view of temperate bacterial viruses as parasitic agents prevails.

  5. Differences in muscle fiber size and associated energetic costs in phylogenetically paired tropical and temperate birds.

    Science.gov (United States)

    Jimenez, Ana Gabriela; Williams, Joseph B

    2014-01-01

    Tropical and temperate birds provide a unique system to examine mechanistic consequences of life-history trade-offs at opposing ends of the pace-of-life spectrum; tropical birds tend to have a slow pace of life whereas temperate birds the opposite. Birds in the tropics have a lower whole-animal basal metabolic rate and peak metabolic rate, lower rates of reproduction, and longer survival than birds in temperate regions. Although skeletal muscle has a relatively low tissue-specific metabolism at rest, it makes up the largest fraction of body mass and therefore contributes more to basal metabolism than any other tissue. A principal property of muscle cells that influences their rate of metabolism is fiber size. The optimal fiber size hypothesis attempts to link whole-animal basal metabolic rate to the cost of maintaining muscle mass by stating that larger fibers may be metabolically cheaper to maintain since the surface area∶volume ratio (SA∶V) is reduced compared with smaller fibers and thus the amount of area to transport ions is also reduced. Because tropical birds have a reduced whole-organism metabolism, we hypothesized that they would have larger muscle fibers than temperate birds, given that larger muscle fibers have reduced energy demand from membrane Na(+)-K(+) pumps. Alternatively, smaller muscle fibers could result in a lower capacity for shivering and exercise. To test this idea, we examined muscle fiber size and Na(+)-K(+)-ATPase activity in 16 phylogenetically paired species of tropical and temperate birds. We found that 3 of the 16 paired comparisons indicated that tropical birds had significantly larger fibers, contrary to our hypothesis. Our data show that SA∶V is proportional to Na(+)-K(+)-ATPase activity in muscles of birds.

  6. Role of temperate zone forests in the world carbon cycle: problem definition and research needs

    Energy Technology Data Exchange (ETDEWEB)

    Armentano, T.V.; Hett, J. (eds.)

    1979-01-01

    The proceedings of a workshop on carbon uptake and losses from temperate zone forests are presented. The goals of the workshop were to analyze existing data on growth and utilization of the temperate zone forest carbon pool and to identify further research needs in relation to the role of temperate forests in the global carbon cycle. Total standing stock and growth recovery transients were examined for most of the temperate region over a period from pre-settlement times to the present, with emphasis on the last three decades. Because of data availability, certain regions and topics were covered more in detail than others. Forest inventory data from most of the commercial timberlands of the north temperate zone suggest these forests have functioned over the past several decades as an annual sink for about 10/sup 9/ metric tons of carbon. Thus, net growth of these forests has withdrawn carbon from the atmosphere at a rate equivalent, approximately, to 50% of the annual rise in atmospheric carbon. Various data inadequacies make this estimate probably no more precise than plus or minus half of the value. Analysis of growth and vegetation changes in New England and the southeastern United States shows that forest biomass has partly recovered since extensive clearing took place in the 18th and 19th centuries. This regrowth represents a net withdrawal of carbon (carbon sink) from the atmosphere in recent decades, although the difference in pool size between present and original forests means that, in the longer term, the two regions have functioned as carbon sources.

  7. Strategies for Constraining the Atmospheres of Temperate Terrestrial Planets with JWST

    Science.gov (United States)

    Batalha, Natasha E.; Lewis, Nikole K.; Line, Michael R.; Valenti, Jeff; Stevenson, Kevin

    2018-04-01

    The Transiting Exoplanet Survey Satellite (TESS) is expected to discover dozens of temperate terrestrial planets orbiting M-dwarfs with atmospheres that could be followed up with the James Webb Space Telescope (JWST). Currently, the TRAPPIST-1 system serves as a benchmark for determining the feasibility and resources required to yield atmospheric constraints. We assess these questions and leverage an information content analysis to determine observing strategies for yielding high-precision spectroscopy in transmission and emission. Our goal is to guide observing strategies of temperate terrestrial planets in preparation for the early JWST cycles. First, we explore JWST’s current capabilities and expected spectral precision for targets near the saturation limits of specific modes. In doing so, we highlight the enhanced capabilities of high-efficiency readout patterns that are being considered for implementation in Cycle 2. We propose a partial saturation strategy to increase the achievable precision of JWST's NIRSpec Prism. We show that JWST has the potential to detect the dominant absorbing gas in the atmospheres of temperate terrestrial planets by the 10th transit using transmission spectroscopy techniques in the near-infrared (NIR). We also show that stacking ⪆10 transmission spectroscopy observations is unlikely to yield significant improvements in determining atmospheric composition. For emission spectroscopy, we show that the MIRI Low Resolution Spectroscopy (LRS) is unlikely to provide robust constraints on the atmospheric composition of temperate terrestrial planets. Higher-precision emission spectroscopy at wavelengths longward of those accessible to MIRI LRS, as proposed in the Origins Space Telescope concept, could help improve the constraints on molecular abundances of temperate terrestrial planets orbiting M-dwarfs.

  8. A comparison of PCB bioaccumulation factors between an arctic and a temperate marine food web

    International Nuclear Information System (INIS)

    Sobek, Anna; McLachlan, Michael S.; Borga, Katrine; Asplund, Lillemor; Lundstedt-Enkel, Katrin; Polder, Anuschka; Gustafsson, Orjan

    2010-01-01

    To test how environmental conditions in the Arctic and the resulting ecological adaptations affect accumulation of persistent organic pollutants (POPs) in the marine food web, bioaccumulation of four polychlorinated biphenyls (PCBs) in an arctic (Barents Sea 77 o N-82 o N) and a temperate marine (Baltic Sea 54 o N-62 o N) food web were compared. Three different trophic levels were studied (zooplankton, fish, and seal), representing the span from first-level consumer to top predator. Previously published high-quality data on PCB water concentrations in the two areas were used for calculation of bioaccumulation factors (BAF). BAF was calculated as the ratio of the PCB concentration in the organism ([PCB] org ; pg/kg lipid) to the dissolved water concentration (C w ; pg/L). The BAF Arctic :BAF Temperate ratios were above 1 for all four PCB congeners in zooplankton (6.4-13.8) and planktivorous fish (2.9-5.0)), whereas the ratios were below 1 in seal. The mean ratio between arctic and temperate BAFs for all trophic levels and congeners (BAF Arcti :BAF Temperate ) was 4.8. When the data were corrected for the seawater temperature difference between the two ecosystems, the ratio was 2.0. We conclude that bioaccumulation differences caused by ecological or physiological adaptations of organisms between the two ecosystems were well within a water concentration variability of 50%. Further, our data support the hypothesis that lower seawater temperature lead to a thermodynamically favoured passive partitioning to organic matrices and thus elevated ambient BAFs in the Arctic compared to the Baltic Sea. This would imply that bioaccumulation in the Arctic may be described in the same way as bioaccumulation in temperate regions, e.g. by the use of mechanistic models parameterised for the Arctic.

  9. Weeds as a source for human consumption. A comparison between tropical and temperate Latin America

    Directory of Open Access Journals (Sweden)

    Martha Díaz-Betancourt

    1999-09-01

    Full Text Available Weeds abound in urban and agricultural environments. Depending on region and site, up to 66% of weed species are edible, and may constitute an additional food source for humans. Based on 400 samples, ¼ m² each, collected in tropical areas (e.g., roadsides, urban vacant lots, streets, sugar cane and coffee plantations in Coatepec, Mexico, average figures of edible fresh biomass vary between 1277 and 3582 kg/ha. A similar survey performed in a temperate area (739 samples in Bariloche, Argentina showed mean values between 287 and 2939 kg/ha. A total of 43 species were sampled in Coatepec and 32 species in Bariloche. The general means were 2.1 and 1.3 tons/ha, respectively. At a greater geographic scale, a comparison between Mexican and Argentine weeds shows that, proportionately, the food parts vary a little between regions. In general, from higher to lower, the order of uses goes from leaves, seeds, roots, fruits, herbals, flowers and condiments. Edible roots (including bulbs and rhizomes appear to be more common among perennials than among annuals.Las malezas abundan en ambientes urbanos y rurales. Según la región y lugar, hasta el 66% de las especies de malezas pueden ser comestibles y constituir un recurso alimentario adicional para el ser humano. Sobre la base de 400 muestras de ¼ m² cada una, recolectadas en áreas tropicales (rutas, terrenos baldíos, calles y plantaciones en Coatepec, México el promedio de la biomasa en peso fresco varió entre 1 277 y 3 582 kg/ha. Un muestreo similar en un área templada (739 muestras en Bariloche, Argentina arrojó valores medios entre 287 y 2 939 kg/ha. En total se registraron 43 especies en Coatepec y 32 especies en Bariloche. La media general (total fue de 2.1 y 1.3 ton/ha, respectivamente. A una escala geográfica mayor, una comparación entre las malezas mexicanas y argentinas no mostró mayores variaciones regionales en cuanto a qué partes u órganos son los comestibles. En ambos lugares, el

  10. Thermotolerance and responses to short duration heat stress in tropical and temperate species

    Science.gov (United States)

    Marias, D.; Meinzer, F. C.; Still, C. J.

    2017-12-01

    Temperature and heat waves are predicted to increase throughout the 21st century in both tropical and temperate regions. Tropical species are vulnerable to heat stress because of the higher radiation load and the narrower distribution of temperatures typically experienced compared to extratropical species. Germinant seedlings are also vulnerable to heat stress because they inhabit the boundary layer close to the soil surface where intense heating occurs. We quantified the effect of leaf age and heat stress duration (45 min, 90 min) on leaf thermotolerance and whole plant physiological responses to heat stress in Coffea arabica (COAR) saplings. We also evaluated leaf thermotolerance and whole plant responses to heat stress of seedlings in two populations each of Pinus ponderosa (PIPO) and Pseudotsuga menziesii (PSME) from contrasting climates. Thermotolerance of detached leaves/needles was evaluated using chlorophyll fluorescence (FV/FM, FO) and electrolyte leakage. After exposure of whole plants to a simulated heat wave in a growth chamber, we monitored FV/FM, photosynthesis (A), stomatal conductance (gs), non-structural carbohydrates (NSCs), and carbon isotope ratios (δ13C). In COAR, thermotolerance and rate of recovery increased with leaf age. Following heat treatment, reductions in A and gs led to reduced intrinsic water use efficiency (iWUE) and increased leaf temperatures. NSC results suggested that starch was converted to sugars for recovery from heat stress and phloem transport was inhibited. Plants failed to flower in both heat stress duration treatments. In PIPO and PSME, heat treatment induced significant reductions in FV/FM and A. NSC results suggested that starch was converted to glucose + fructose to aid recovery from heat-induced damage. Populations from drier sites had greater δ13C values than those from wetter sites, consistent with higher iWUE of populations from drier climates. Thermotolerance and heat stress responses appeared to be

  11. Patterns and multi-scale drivers of phytoplankton species richness in temperate peri-urban lakes

    Energy Technology Data Exchange (ETDEWEB)

    Catherine, Arnaud, E-mail: arnocat@mnhn.fr [UMR7245 MCAM MNHN-CNRS, Muséum National d' Histoire Naturelle, CC 39, 12 rue Buffon, F-75231 Paris, Cedex 05 (France); Selma, Maloufi, E-mail: maloufi@mnhn.fr [UMR7245 MCAM MNHN-CNRS, Muséum National d' Histoire Naturelle, CC 39, 12 rue Buffon, F-75231 Paris, Cedex 05 (France); Mouillot, David, E-mail: david.mouillot@univ-montp2.fr [UMR 9190 MARBEC UM2-CNRS-IRD-UM1-IFREMER, CC 93, Place Eugène Bataillon, Université de Montpellier 2, F-34095 Montpellier (France); Troussellier, Marc, E-mail: troussel@univ-montp2.fr [UMR 9190 MARBEC UM2-CNRS-IRD-UM1-IFREMER, CC 93, Place Eugène Bataillon, Université de Montpellier 2, F-34095 Montpellier (France); Bernard, Cécile, E-mail: cbernard@mnhn.fr [UMR7245 MCAM MNHN-CNRS, Muséum National d' Histoire Naturelle, CC 39, 12 rue Buffon, F-75231 Paris, Cedex 05 (France)

    2016-07-15

    Local species richness (SR) is a key characteristic affecting ecosystem functioning. Yet, the mechanisms regulating phytoplankton diversity in freshwater ecosystems are not fully understood, especially in peri-urban environments where anthropogenic pressures strongly impact the quality of aquatic ecosystems. To address this issue, we sampled the phytoplankton communities of 50 lakes in the Paris area (France) characterized by a large gradient of physico-chemical and catchment-scale characteristics. We used large phytoplankton datasets to describe phytoplankton diversity patterns and applied a machine-learning algorithm to test the degree to which species richness patterns are potentially controlled by environmental factors. Selected environmental factors were studied at two scales: the lake-scale (e.g. nutrients concentrations, water temperature, lake depth) and the catchment-scale (e.g. catchment, landscape and climate variables). Then, we used a variance partitioning approach to evaluate the interaction between lake-scale and catchment-scale variables in explaining local species richness. Finally, we analysed the residuals of predictive models to identify potential vectors of improvement of phytoplankton species richness predictive models. Lake-scale and catchment-scale drivers provided similar predictive accuracy of local species richness (R{sup 2} = 0.458 and 0.424, respectively). Both models suggested that seasonal temperature variations and nutrient supply strongly modulate local species richness. Integrating lake- and catchment-scale predictors in a single predictive model did not provide increased predictive accuracy; therefore suggesting that the catchment-scale model probably explains observed species richness variations through the impact of catchment-scale variables on in-lake water quality characteristics. Models based on catchment characteristics, which include simple and easy to obtain variables, provide a meaningful way of predicting phytoplankton

  12. Patterns and multi-scale drivers of phytoplankton species richness in temperate peri-urban lakes

    International Nuclear Information System (INIS)

    Catherine, Arnaud; Selma, Maloufi; Mouillot, David; Troussellier, Marc; Bernard, Cécile

    2016-01-01

    Local species richness (SR) is a key characteristic affecting ecosystem functioning. Yet, the mechanisms regulating phytoplankton diversity in freshwater ecosystems are not fully understood, especially in peri-urban environments where anthropogenic pressures strongly impact the quality of aquatic ecosystems. To address this issue, we sampled the phytoplankton communities of 50 lakes in the Paris area (France) characterized by a large gradient of physico-chemical and catchment-scale characteristics. We used large phytoplankton datasets to describe phytoplankton diversity patterns and applied a machine-learning algorithm to test the degree to which species richness patterns are potentially controlled by environmental factors. Selected environmental factors were studied at two scales: the lake-scale (e.g. nutrients concentrations, water temperature, lake depth) and the catchment-scale (e.g. catchment, landscape and climate variables). Then, we used a variance partitioning approach to evaluate the interaction between lake-scale and catchment-scale variables in explaining local species richness. Finally, we analysed the residuals of predictive models to identify potential vectors of improvement of phytoplankton species richness predictive models. Lake-scale and catchment-scale drivers provided similar predictive accuracy of local species richness (R"2 = 0.458 and 0.424, respectively). Both models suggested that seasonal temperature variations and nutrient supply strongly modulate local species richness. Integrating lake- and catchment-scale predictors in a single predictive model did not provide increased predictive accuracy; therefore suggesting that the catchment-scale model probably explains observed species richness variations through the impact of catchment-scale variables on in-lake water quality characteristics. Models based on catchment characteristics, which include simple and easy to obtain variables, provide a meaningful way of predicting phytoplankton

  13. Additive and Synergistic Impacts of Fishing and Warming on the Growth of a Temperate Marine Fish

    Science.gov (United States)

    Morrongiello, J.

    2016-02-01

    Fishing and climate change are having profound impacts on the trajectory and variability of marine populations. However, despite the wealth of work undertaken in marine environments on the causes of longer-term biological change, the effects of these two drivers have traditionally been considered in isolation or just additively. Such an approach obviously overlooks the potential for significant synergistic or antagonistic interactions between fishing and climate to occur. Indeed, it is increasingly becoming acknowledged that the direction and magnitude of biological responses to natural environmental variation and climate change can be mediated by other anthropogenic disturbances such as fishing, and vice versa. Somatic growth is an ideal candidate with which to explore the impacts of fishing and environmental variability due to its strong biological relevance and its heightened sensitivity to natural and anthropogenic drivers. I developed 19-year growth biochronologies (1980-1999) for three south-east Australian populations of a site-attached temperate reef fish, purple wrasse (Notolabrus fucicola) using individual-based growth information naturally archived in otoliths. A commercial wrasse fishery began in the early 1990s; before this there was negligible recreational or commercial fishing. The growth of older fish was proportionally higher and that of the youngest fish proportionally lower after the onset of commercial fishing; 2-year olds grew 7.4% slower, but 5-year-olds grew 10.3% and 10-year-olds 26% faster in the latter period. These results are consistent with a density dependent response to harvesting. Average growth rates across all ages increased by 6.6%.oC-1, reflecting either a direct or indirect temperature effect in this global marine 'hotspot'. Finally, the distribution of individual thermal reaction norms significantly changed post fishing, showing that fishing and temperature can have a synergetic impact on marine populations via within

  14. Effect of twice quenching and tempering on the mechanical properties and microstructures of SCRAM steel for fusion application

    Energy Technology Data Exchange (ETDEWEB)

    Xiong Xuesong; Yang Feng; Zou Xingrong [State Key Laboratory of Mould Technology, Institute of Materials Science and Engineering, Huazhong University of Science and Technology, Wuhan 430074 (China); Suo Jinping, E-mail: jpsuo@yahoo.com.cn [State Key Laboratory of Mould Technology, Institute of Materials Science and Engineering, Huazhong University of Science and Technology, Wuhan 430074 (China)

    2012-11-15

    The effect of twice quenching and tempering on the mechanical properties and microstructures of SCRAM steel was investigated. The results from tensile tests showed that whether twice quenching and tempering processes(1253 K/0.5 h/W.C(water cool) + 1033 K/2 h/A.C(air cool) + 1233 K/0.5 h/W.C + 1033 K/2 h/A.C named after 2Q and 2TI, and 1253 K/0.5 h/W.C + 1033 K/2 h/A.C + 1233 K/0.5 h/W.C + 1013 K/2 h/A.C named after 2Q and 2TII)increased strength of steel or not depended largely on the second tempering temperature compared to quenching and tempering process(1253 K/0.5 h/W.C + 1033 K/2 h/A.C named after 1Q and 1T). Charpy V-notch impact tests indicated that twice quenching and tempering processes reduced the ductile brittle transition temperature (DBTT). Microstructure inspection revealed that the prior austenitic grain size and martensite lath width were refined after twice quenching and tempering treatments. Precipitate growth was inhibited by a slight decrease of the second tempering temperature from 1033 to 1013 K. The finer average size of precipitates is considered to be the main possible reason for the higher strength and lower DBTT of 2Q and 2TII compared with 2Q and 2TI.

  15. AUTOMATION OF GLASS TEMPERING FURNACE BY USING PLC

    Directory of Open Access Journals (Sweden)

    Abdullah BÜYÜKYILDIZ

    2007-02-01

    Full Text Available In this study, a furnace which is used for observation of environments under high temperature, and also used for manufacturing of glasses which are resisted to high temperature has been designed and implemented. Automation of this system has been done by using PLC. Operating parameters of furnace such as materials entering, the furnace, the local temperature control of furnace, cooling control and materials outing have been sensed with Hall Effect Sensor. Furthermore, the observation of parameters of furnace on screen has been provided with SCADA software. Obtained products have been shown the system works successfully.

  16. Feeding ecology of Rhabdosargus holubi (family Sparidae) in multiple vegetated refugia of selected warm temperate estuaries in South Africa

    Science.gov (United States)

    Nel, L.; Strydom, N. A.; Perissinotto, R.; Adams, J. B.; Lemley, D. A.

    2017-10-01

    Estuarine marine-dependent species, such as Rhabdosargus holubi, depend greatly on structured sheltered environments and important feeding areas provided by estuaries. In this study, we investigate the ecological feeding niches of the estuarine marine-dependent sparid, R. holubi, by using conventional stomach contents and stable isotope methods (δ13C and δ15N signatures). The study has been carried out in five temperate estuaries in order to understand how fish feed in multiple intertidal vegetated habitats. These habitats included the submerged seagrass, Zostera capensis, and both previously unexplored small intertidal cord grass, Spartina maritima, and the common reed, Phragmites australis. The diet varied amongst habitats, estuaries and fish sizes and data consistently confirmed their omnivorous diet relating to ontogenetic niche shifts. Stomach contents revealed the importance of benthic prey within both the S. maritima and P. australis habitats in the absence of large intertidal vegetation, available during low tides. Similarly, isotopic mixing models showed that R. holubi from these habitats have a greater isotopic niche compared to the Z. capensis habitat, due to their limited availability during the falling tide, suggesting migration between available habitats. Stable isotopes confirmed that R. holubi actively feeds on the epiphytic algae (especially diatoms) covering the leaves and stalks of plant matter, as supported by Bayesian mixing models. These findings add to the current knowledge regarding habitat partitioning in multiple aquatic vegetation types critical to fish ecology and the effective management and conservation of estuaries.

  17. Evolution of the miR5200-FLOWERING LOCUS T flowering time regulon in the temperate grass subfamily Pooideae.

    Science.gov (United States)

    McKeown, Meghan; Schubert, Marian; Preston, Jill C; Fjellheim, Siri

    2017-09-01

    Flowering time is a carefully regulated trait controlled primarily through the action of the central genetic regulator, FLOWERING LOCUS T (FT). Recently it was demonstrated that a microRNA, miR5200, targets the end of the second exon of FT under short-day photoperiods in the grass subfamily Pooideae, thus preventing FT transcripts from reaching threshold levels under non-inductive conditions. Pooideae are an interesting group in that they rapidly diversified from the tropics into the northern temperate region during a major global cooling event spanning the Eocene-Oligocene transition. We hypothesize that miR5200 photoperiod-sensitive regulation of Pooideae flowering time networks assisted their transition into northern seasonal environments. Here, we test predictions derived from this hypothesis that miR5200, originally found in bread wheat and later identified in Brachypodium distachyon, (1) was present in the genome of the Pooideae common ancestor, (2) is transcriptionally regulated by photoperiod, and (3) is negatively correlated with FT transcript abundance, indicative of miR5200 regulating FT. Our results demonstrate that miR5200 did evolve at or around the base of Pooideae, but only acquired photoperiod-regulated transcription within the Brachypodium lineage. Based on expression profiles and previous data, we posit that the progenitor of miR5200 was co-regulated with FT by an unknown mechanism. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

  18. The role of clothing in thermal comfort: how people dress in a temperate and humid climate in Brazil

    Directory of Open Access Journals (Sweden)

    Renata De Vecchi

    Full Text Available Abstract Thermal insulation from clothing is one of the most important input variables used to predict the thermal comfort of a building's occupants. This paper investigates the clothing pattern in buildings with different configurations located in a temperate and humid climate in Brazil. Occupants of two kinds of buildings (three offices and two university classrooms assessed their thermal environment through 'right-here-right-now' questionnaires, while at the same time indoor climatic measurements were carried out in situ (air temperature and radiant temperature, air speed and humidity. A total of 5,036 votes from 1,161 occupants were collected. Results suggest that the clothing values adopted by occupants inside buildings were influenced by: 1 climate and seasons of the year; 2 different configurations and indoor thermal conditions; and 3 occupants' age and gender. Significant intergenerational and gender differences were found, which might be explained by differences in metabolic rates and fashion. The results also indicate that there is a great opportunity to exceed the clothing interval of the thermal comfort zones proposed by international standards such as ASHRAE 55 (2013 - 0.5 to 1.0 clo - and thereby save energy from cooling and heating systems, without compromising the occupants' indoor thermal comfort.

  19. „WELL TEMPERED " VAT - BETWEEN THEORY AND PRACTICE

    Directory of Open Access Journals (Sweden)

    SĂLCEANU ALEXANDRU

    2014-05-01

    Full Text Available VAT represents an indirect tax due to the state budget that includes all phases of the economic circuit, namely manufacturing, services and distribution, up to sales to final consumers. VAT collection is done fractionally, according to the value added at each stage of the economic circuit. Introduced in our country in 1993, VAT has been continuously improved and since Romania has been a member of the European Union (EU since 2007, WATT has been harmonized with the European Community directives. Today, Romania encounters serious difficulties in collecting the VAT, being atop of the countries with tax arrears. This is why it is required a more effective collaboration between the parliament, which adopts laws, the government, that implements and business environment, where the added value is obtained, in order to achieve a more efficient and robust VAT system against fraud that can contribute to fiscal consolidation by increasing public budget revenues.

  20. Fighting alcoholism among railway workers in the light of early 20th Century Polish-language temperance publications

    Directory of Open Access Journals (Sweden)

    Izabela Krasińska

    2016-12-01

    Discussion and conclusions: The Polish-language temperance periodicals provide, among other things, valuable information referring to as yet unknown though essential problem of fighting alcoholism among railway workers in Europe, USA and the Polish territories of the Three Partitions.