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

    Science.gov (United States)

    Ramírez, Oscar; Gigli, Elena; Bover, Pere; Alcover, Josep Antoni; Bertranpetit, Jaume; Castresana, Jose; Lalueza-Fox, Carles

    2009-05-22

    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. 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.

  3. Paleogenomics in a Temperate Environment: Shotgun Sequencing from an Extinct Mediterranean Caprine

    Science.gov (United States)

    Ramírez, Oscar; Gigli, Elena; Bover, Pere; Alcover, Josep Antoni; Bertranpetit, Jaume; Castresana, Jose; Lalueza-Fox, Carles

    2009-01-01

    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 ∼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. PMID:19461892

  4. Safety glasses as protection against shotgun pellets.

    Science.gov (United States)

    Robertson, D M

    1976-05-01

    I designed this experiment to determine if spectacle lenses would protect against a No. 6 shot fired from a 12-gauge shotgun over progressively longer testing distances, and compared plastics, heat-tempered glass, and chemical-tempered glass lenses of standard and industrial thicknesses. The likelihood of a spectacle lens being hit by a well-centered shot pattern at 40, 50, and 60 yards was approximately 66%, 25%, and 20%, respectively. Virtually all lenses were destroyed at a testing distance of 30 yards. At 40 yards, standard-thickness plastic and heat-tempered lenses were destroyed but the chemical-tempered lenses offered some protection. At 40 yards, all types of industrial-thickness lenses provided protection but the most protection was provided by the chemical-tempered lenses. At 50 yards, chemical-tempered lenses offered more protection than either plastic or heat-tempered lenses. Throughout the experiment, plastic lenses performed no better than heat-tempered lenses.

  5. 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

  6. Paleosol stable isotope evidence for early hominid occupation of East Asian temperate environments

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    Wang, Hongfang; Ambrose, S.H.; Liu, Chen; Follmer, L.R.

    1997-01-01

    Hominids left Africa and occupied mainland Asia by 1.8 myr ago. About 1.15 myr ago Homo erectus and an associated Stegodon-Ailuropoda fauna migrated from subtropical China across the Qinling Mountains into the temperate Loess Plateau. This migration may be an evolutionary milestone in human adaptability because it may represent the first occupation of a nontropical environment. Loess-paleosol stable isotope ratios from the last interglacial-glacial cycle provide comparative data for reconstructing the hominid paleoenvironments. The climate during Gongwangling hominid occupation about 1.15 myr ago was influenced by both Siberian-Mongolian winter and Indian summer monsoon systems characterized as a cold/cool, dry winter and warm/mild, semihumid summer and fall. The Gongwangling hominids preyed mainly on warm-climate-adapted animals such as Stegodon-Ailuropoda fauna, suggesting a warm season occupation. The stable isotope ratios also indicate that the Chenjiawo hominids occupied an environment similar to that of the Gongwangling about 650,000 yr ago. The associated fauna, with a mixture of forest and steppe, warm-and cold/cool-climate-adapted animal assemblage's, suggests a permanent occupation by this time. Thus, the reliable earliest and permanent occupation of temperate environments may have occurred 150,000 yr earlier in eastern Asia rather than in Europe. ?? 1997 University of Washington.

  7. [Shotgun injury--multiple pellets].

    Science.gov (United States)

    Hejna, P; Pleskot, J

    2009-01-01

    Both typical and less frequent features of gunshot wounds caused by shotguns are reported in the following article. The pattern of shotgun injury predominantly depends on gauge, choke, number and diameter of used pellets, muzzle-victim distance and on character of the afflicted area of the body. Characteristic ballistic properties of shotgun pellets, their wounding potential and significance in forensic patology are presented.

  8. Brain Temperature in Spontaneously Hypertensive Rats during Physical Exercise in Temperate and Warm Environments.

    Science.gov (United States)

    Drummond, Lucas Rios; Kunstetter, Ana Cançado; Vaz, Filipe Ferreira; Campos, Helton Oliveira; Andrade, André Gustavo Pereira de; Coimbra, Cândido Celso; Natali, Antônio José; Wanner, Samuel Penna; Prímola-Gomes, Thales Nicolau

    2016-01-01

    This study aimed to evaluate brain temperature (Tbrain) changes in spontaneously hypertensive rats (SHRs) subjected to two different physical exercise protocols in temperate or warm environments. We also investigated whether hypertension affects the kinetics of exercise-induced increases in Tbrain relative to the kinetics of abdominal temperature (Tabd) increases. Male 16-week-old normotensive Wistar rats (NWRs) and SHRs were implanted with an abdominal temperature sensor and a guide cannula in the frontal cortex to enable the insertion of a thermistor to measure Tbrain. Next, the animals were subjected to incremental-speed (initial speed of 10 m/min; speed was increased by 1 m/min every 3 min) or constant-speed (60% of the maximum speed) treadmill running until they were fatigued in a temperate (25°C) or warm (32°C) environment. Tbrain, Tabd and tail skin temperature were measured every min throughout the exercise trials. During incremental and constant exercise at 25°C and 32°C, the SHR group exhibited greater increases in Tbrain and Tabd relative to the NWR group. Irrespective of the environment, the heat loss threshold was attained at higher temperatures (either Tbrain or Tabd) in the SHRs. Moreover, the brain-abdominal temperature differential was lower at 32°C in the SHRs than in the NWRs during treadmill running. Overall, we conclude that SHRs exhibit enhanced brain hyperthermia during exercise and that hypertension influences the kinetics of the Tbrain relative to the Tabd increases, particularly during exercise in a warm environment.

  9. Cardiovascular drift and Vo2max during cycling and walking in a temperate environment.

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    Wingo, Jonathan E; Salaga, Laura J; Newlin, Mia K; Cureton, Kirk J

    2012-07-01

    Different muscle recruitment patterns during cycling and walking may influence the magnitude of cardiovascular drift (CV drift) during these respective modes of exercise, but whether this also influences the magnitude of reduced maximal oxygen uptake (Vo2max) associated with CV drift is unknown.This study tested the hypothesis that cycling results in greater CV drift and a greater decrement in Vo2max than walking in a temperate environment. CV drift was measured in nine recreationally active women (ages = 23 +/- 2 yr, Vo2max = 43.0 +/- 5.5 ml x kg(-1) x min(-1)) between 15 and 45 min of cycling or walking at 60% Vo2max on Separate occasions in 22 degrees C, 44% relative humidity. A graded exercise test to measure Vo2max was performed immediately after the submaximal exercise bout with no cessation of exercise. During separate trials involving each exercise mode, Vo2max was measured after 15 min of submaximal exercise so that changes in Vo2max between 15 and 45 min of exercise could be assessed between the same points in time in which CV drift occurred. Across both conditions, heart rate (HR) increased 5.4% and stroke volume (SV) decreased 11% from 15 to 45 min, but Vo2max was not significantly affected (7% reduction; 2.70 +/- 0.5 L min(-1) vs. 2.52 +/- 0.6 L min(-1)). In a temperate environment, a small CV drift corresponds to a small, non-significant decrease in Vo2max, regardless of whether the exercise performed is cycling or walking.

  10. The carbon and nitrogen ecophysiologies of two endemic tropical orchids mirrors those of their temperate relatives and the local environment.

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    Hynson, Nicole A

    2016-11-01

    Orchids are one of the most widely distributed plant families. However, current research on the ecophysiology of terrestrial orchids is biased towards temperate species. Thus, it is currently unknown whether tropical terrestrial orchids belong to similar trophic guilds as their temperate relatives. To examine the ecophysiologies of two tropical terrestrial orchids, I analysed the carbon and nitrogen stable isotope compositions and nitrogen concentrations of the Hawaiian endemics Anoectochilus sandvicensis and Liparis hawaiensis . I compared these values with those of surrounding vegetation and their temperate relatives. I found that A. sandvicensis was consistently enriched in the heavy isotope of nitrogen ( 15 N) and had higher nitrogen (N) concentrations than surrounding vegetation, and these values were even higher than those of its temperate relatives. Carbon stable isotope composition among populations of A. sandvicensis varied by island. These results point to local environment and evolutionary history determining the ecophysiology of this species. Whereas L.hawaiensis was also enriched in 15 N and had on average higher N concentrations than surrounding vegetation, these values were not significantly different from temperate relatives, indicating that evolutionary history may be a stronger predictor of this orchid species' ecophysiology than environment. I suggest that both Hawaiian species are potentially partially mycoheterotrophic.

  11. 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.

  12. Seed softening patterns of forage legumes in a temperate/subtropical environment in Uruguay

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    Javier Do Canto

    2013-03-01

    Full Text Available Few studies have been conducted in annual and perennial forage legumes to investigate the development of hardseededness and the subsequent pattern of seed softening in temperate and subtropical regions of South America. Experiments were conducted during 2007 and 2008 in central Uruguay to follow the pattern of seed softening in 35 annual and perennial forage legumes, including three native species of Uruguay and five commercial cultivars. Newly ripened seeds of each plant material were placed in mesh packets on the soil surface in mid-summer. Samples were recovered monthly for germination tests and the proportion of residual hard seeds determined. The native species Adesmia bicolor (Poir. DC., Adesmia securigerifolia Herter, and Ornithopus micranthus (Benth. Arechav., together with Ornithopus pinnatus (Mill. Druce cv. INIA Molles behaved similarly. They showed high levels of initial hard seed from 78% in A. bicolor to 99% in A. securigerifolia and O. pinnatus cv. INIA Molles in 2007; displayed pulses of seed softening, particularly in autumn, and retained moderate levels of residual hard seed for the development of a soil seed bank ranging from 15% in A. bicolor to 49% in O. micranthus. These appear to be desirable characteristics for persistence of forage legumes in subtropical grasslands, both for annual and perennial species. Trifolium repens L. and Lotus corniculatus L. produced few hard seeds, only 2% and 13% respectively were hard after 1-mo in the field and were completely soft by July placing extra reliance on their vegetative propagation for persistence. Materials of L. arenarius Brot. showed pronounced late autumn softening, while materials of L. ornithopodioides L. showed extremely high levels of hardseededness (between 96% and 100% and no softening during the evaluation period, apart from two materials that were completely soft seeded. Mediterranean forage legumes should be properly evaluated in temperate and subtropical regions as

  13. Effects of wave exposure on circulation in a temperate reef environment

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    Symonds, Graham; Zhong, Liejun; Mortimer, Nick A.

    2011-09-01

    Observations of waves and currents in a temperate reef environment off southwestern Western Australia over a period of 1 year reveal the relative importance of wind and wave forcing. During periods of low waves, linear regression analysis shows alongshore currents seaward and shoreward of the reef line are reasonably well predicted using 1% and 0.5% of the wind speed, respectively. However, shoreward of the reef line anomalously strong currents were often observed during periods of light or even opposing winds and the mean sea surface was elevated relative to offshore of the reefs. These anomalous currents and elevated sea level occur during periods of high waves and both are correlated with the root-mean-square wave height seaward of the reefs, similar to what has been observed in coral reef environments. The observations were simulated with the numerical model XBeach which includes radiation stress forcing due to the presence of the waves. The model was also used to examine the dynamics of the wave-driven flow in terms of the momentum balance. As on a coral reef, through the surf zone over the reef bottom, friction is balanced by the sum of the radiation stress gradient and pressure gradient. Away from the reefs the radiation stress gradients are small and the momentum balance is between bottom friction and pressure gradient.

  14. Growth and photosynthesis of Chlorella strains from polar, temperate and tropical freshwater environments under temperature stress

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    Lee, Kok-Keong; Lim, Phaik-Eem; Poong, Sze-Wan; Wong, Chiew-Yen; Phang, Siew-Moi; Beardall, John

    2017-09-01

    Elevated temperatures as a consequence of global warming have significant impacts on the adaptation and survival of microalgae which are important primary producers in many ecosystems. The impact of temperature on the photosynthesis of microalgae is of great interest as the primary production of algal biomass is strongly dependent on the photosynthetic rates in a dynamic environment. Here, we examine the effects of elevated temperature on Chlorella strains originating from different latitudes, namely Antarctic, Arctic, temperate and tropical regions. Chlorophyll fluorescence was used to assess the photosynthetic responses of the microalgae. Rapid light curves (RLCs) and maximum quantum yield (F v/F m) were recorded. The results showed that Chlorella originating from different latitudes portrayed different growth trends and photosynthetic performance. The Chlorella genus is eurythermal, with a broad temperature tolerance range, but with strain-specific characteristics. However, there was a large overlap between the tolerance range of the four strains due to their "eurythermal adaptivity". Changes in the photosynthetic parameters indicated temperature stress. The ability of the four strains to reactivate photosynthesis after inhibition of photosynthesis under high temperatures was also studied. The Chlorella strains were shown to recover in terms of photosynthesis and growth (measured as Chl a) when they were returned to their ambient temperatures. Polar strains showed faster recovery in their optimal temperature compared to that under the ambient temperature from which they were isolated.

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

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    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

  16. Shotgun cartridge rock breaker

    Energy Technology Data Exchange (ETDEWEB)

    Ruzzi, Peter L. (Eagan, NM); Morrell, Roger J. (Bloomington, MN)

    1995-01-01

    A rock breaker uses shotgun cartridges or other firearm ammunition as the explosive charge at the bottom of a drilled borehole. The breaker includes a heavy steel rod or bar, a gun with a firing chamber for the ammunition which screws onto the rod, a long firing pin running through a central passage in the rod, and a firing trigger mechanism at the external end of the bar which strikes the firing pin to fire the cartridge within the borehole. A tubular sleeve surround the main body of the rod and includes slits the end to allow it to expand. The rod has a conical taper at the internal end against which the end of the sleeve expands when the sleeve is forced along the rod toward the taper by a nut threaded onto the external end of the rod. As the sleeve end expands, it pushes against the borehole and holds the explosive gasses within, and also prevents the breaker from flying out of the borehole. The trigger mechanism includes a hammer with a slot and a hole for accepting a drawbar or drawpin which, when pulled by a long cord, allows the cartridge to be fired from a remote location.

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

    Directory of Open Access Journals (Sweden)

    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.

  18. 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

  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

    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...... 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. Principles of management of shotgun wounds.

    Science.gov (United States)

    Walker, M L; Poindexter, J M; Stovall, I

    1990-02-01

    As an instrument of close range combat, the shotgun has no parallel. At short distances, its destructive capacity parallels that seen from high velocity missile injury. In this study, the history of the shotgun, wound ballistics, principles of initial therapy and special management problems related to shotgun wounds of specific sites are reviewed. An analysis of pooled data on abdominal shotgun wounds is presented. A subset of patients who do not require abdominal exploration exists. Specific problems encountered in defining this subset are enumerated. Three algorithms are presented that summarize our current management approach to shotgun wounds of the torso and extremities.

  1. Shotgun metagenomics, from sampling to analysis.

    Science.gov (United States)

    Quince, Christopher; Walker, Alan W; Simpson, Jared T; Loman, Nicholas J; Segata, Nicola

    2017-09-12

    Diverse microbial communities of bacteria, archaea, viruses and single-celled eukaryotes have crucial roles in the environment and in human health. However, microbes are frequently difficult to culture in the laboratory, which can confound cataloging of members and understanding of how communities function. High-throughput sequencing technologies and a suite of computational pipelines have been combined into shotgun metagenomics methods that have transformed microbiology. Still, computational approaches to overcome the challenges that affect both assembly-based and mapping-based metagenomic profiling, particularly of high-complexity samples or environments containing organisms with limited similarity to sequenced genomes, are needed. Understanding the functions and characterizing specific strains of these communities offers biotechnological promise in therapeutic discovery and innovative ways to synthesize products using microbial factories and can pinpoint the contributions of microorganisms to planetary, animal and human health.

  2. Perfluorooctanoic acid for shotgun proteomics.

    Directory of Open Access Journals (Sweden)

    Chandra Sekhar Rao Kadiyala

    2010-12-01

    Full Text Available Here, we describe the novel use of a volatile surfactant, perfluorooctanoic acid (PFOA, for shotgun proteomics. PFOA was found to solubilize membrane proteins as effectively as sodium dodecyl sulfate (SDS. PFOA concentrations up to 0.5% (w/v did not significantly inhibit trypsin activity. The unique features of PFOA allowed us to develop a single-tube shotgun proteomics method that used all volatile chemicals that could easily be removed by evaporation prior to mass spectrometry analysis. The experimental procedures involved: 1 extraction of proteins in 2% PFOA; 2 reduction of cystine residues with triethyl phosphine and their S-alkylation with iodoethanol; 3 trypsin digestion of proteins in 0.5% PFOA; 4 removal of PFOA by evaporation; and 5 LC-MS/MS analysis of the resulting peptides. The general applicability of the method was demonstrated with the membrane preparation of photoreceptor outer segments. We identified 75 proteins from 1 µg of the tryptic peptides in a single, 1-hour, LC-MS/MS run. About 67% of the proteins identified were classified as membrane proteins. We also demonstrate that a proteolytic (18O labeling procedure can be incorporated after the PFOA removal step for quantitative proteomic experiments. The present method does not require sample clean-up devices such as solid-phase extractions and membrane filters, so no proteins/peptides are lost in any experimental steps. Thus, this single-tube shotgun proteomics method overcomes the major drawbacks of surfactant use in proteomic experiments.

  3. 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

  4. 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

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

    Directory of Open Access Journals (Sweden)

    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

  6. Association between the increase in brain temperature and physical performance at different exercise intensities and protocols in a temperate environment

    Directory of Open Access Journals (Sweden)

    A.C. Kunstetter

    2014-08-01

    Full Text Available There is evidence that brain temperature (Tbrain provides a more sensitive index than other core body temperatures in determining physical performance. However, no study has addressed whether the association between performance and increases in Tbrain in a temperate environment is dependent upon exercise intensity, and this was the primary aim of the present study. Adult male Wistar rats were subjected to constant exercise at three different speeds (18, 21, and 24 m/min until the onset of volitional fatigue. Tbrain was continuously measured by a thermistor inserted through a brain guide cannula. Exercise induced a speed-dependent increase in Tbrain, with the fastest speed associated with a higher rate of Tbrain increase. Rats subjected to constant exercise had similar Tbrain values at the time of fatigue, although a pronounced individual variability was observed (38.7-41.7°C. There were negative correlations between the rate of Tbrain increase and performance for all speeds that were studied. These results indicate that performance during constant exercise is negatively associated with the increase in Tbrain, particularly with its rate of increase. We then investigated how an incremental-speed protocol affected the association between the increase in Tbrain and performance. At volitional fatigue, Tbrain was lower during incremental exercise compared with the Tbrain resulting from constant exercise (39.3±0.3 vs 40.3±0.1°C; P<0.05, and no association between the rate of Tbrain increase and performance was observed. These findings suggest that the influence of Tbrain on performance under temperate conditions is dependent on exercise protocol.

  7. Post-clearcut dynamics of carbon, water and energy exchanges in a midlatitude temperate, deciduous broadleaf forest environment.

    Science.gov (United States)

    Williams, Christopher A; Vanderhoof, Melanie K; Khomik, Myroslava; Ghimire, Bardan

    2014-03-01

    Clearcutting and other forest disturbances perturb carbon, water, and energy balances in significant ways, with corresponding influences on Earth's climate system through biogeochemical and biogeophysical effects. Observations are needed to quantify the precise changes in these balances as they vary across diverse disturbances of different types, severities, and in various climate and ecosystem type settings. This study combines eddy covariance and micrometeorological measurements of surface-atmosphere exchanges with vegetation inventories and chamber-based estimates of soil respiration to quantify how carbon, water, and energy fluxes changed during the first 3 years following forest clearing in a temperate forest environment of the northeastern US. We observed rapid recovery with sustained increases in gross ecosystem productivity (GEP) over the first three growing seasons post-clearing, coincident with large and relatively stable net emission of CO2 because of overwhelmingly large ecosystem respiration. The rise in GEP was attributed to vegetation changes not environmental conditions (e.g., weather), but attribution to the expansion of leaf area vs. changes in vegetation composition remains unclear. Soil respiration was estimated to contribute 44% of total ecosystem respiration during summer months and coarse woody debris accounted for another 18%. Evapotranspiration also recovered rapidly and continued to rise across years with a corresponding decrease in sensible heat flux. Gross short-wave and long-wave radiative fluxes were stable across years except for strong wintertime dependence on snow covered conditions and corresponding variation in albedo. Overall, these findings underscore the highly dynamic nature of carbon and water exchanges and vegetation composition during the regrowth following a severe forest disturbance, and sheds light on both the magnitude of such changes and the underlying mechanisms with a unique example from a temperate, deciduous

  8. Association between the increase in brain temperature and physical performance at different exercise intensities and protocols in a temperate environment.

    Science.gov (United States)

    Kunstetter, A C; Wanner, S P; Madeira, L G; Wilke, C F; Rodrigues, L O C; Lima, N R V

    2014-08-01

    There is evidence that brain temperature (T brain) provides a more sensitive index than other core body temperatures in determining physical performance. However, no study has addressed whether the association between performance and increases in T brain in a temperate environment is dependent upon exercise intensity, and this was the primary aim of the present study. Adult male Wistar rats were subjected to constant exercise at three different speeds (18, 21, and 24 m/min) until the onset of volitional fatigue. T brain was continuously measured by a thermistor inserted through a brain guide cannula. Exercise induced a speed-dependent increase in T brain, with the fastest speed associated with a higher rate of T brain increase. Rats subjected to constant exercise had similar T brain values at the time of fatigue, although a pronounced individual variability was observed (38.7-41.7°C). There were negative correlations between the rate of T brain increase and performance for all speeds that were studied. These results indicate that performance during constant exercise is negatively associated with the increase in T brain, particularly with its rate of increase. We then investigated how an incremental-speed protocol affected the association between the increase in T brain and performance. At volitional fatigue, T brain was lower during incremental exercise compared with the T brain resulting from constant exercise (39.3 ± 0.3 vs 40.3 ± 0.1°C; Pbrain increase and performance was observed. These findings suggest that the influence of T brain on performance under temperate conditions is dependent on exercise protocol.

  9. 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

  10. Potential of Legume-Brassica Intercrops for Forage Production and Green Manure: Encouragements from a Temperate Southeast European Environment.

    Science.gov (United States)

    Jeromela, Ana M; Mikić, Aleksandar M; Vujić, Svetlana; Ćupina, Branko; Krstić, Đorđe; Dimitrijević, Aleksandra; Vasiljević, Sanja; Mihailović, Vojislav; Cvejić, Sandra; Miladinović, Dragana

    2017-01-01

    Legumes and brassicas have much in common: importance in agricultural history, rich biodiversity, numerous forms of use, high adaptability to diverse farming designs, and various non-food applications. Rare available resources demonstrate intercropping legumes and brassicas as beneficial to both, especially for the latter, profiting from better nitrogen nutrition. Our team aimed at designing a scheme of the intercrops of autumn- and spring-sown annual legumes with brassicas for ruminant feeding and green manure, and has carried out a set of field trials in a temperate Southeast European environment and during the past decade, aimed at assessing their potential for yields of forage dry matter and aboveground biomass nitrogen and their economic reliability via land equivalent ratio. This review provides a cross-view of the most important deliverables of our applied research, including eight annual legume crops and six brassica species, demonstrating that nearly all the intercrops were economically reliable, as well as that those involving hairy vetch, Hungarian vetch, Narbonne vetch and pea on one side, and fodder kale and rapeseed on the other, were most productive in both manners. Feeling encouraged that this pioneering study may stimulate similar analyses in other environments and that intercropping annual legume and brassicas may play a large-scale role in diverse cropping systems, our team is heading a detailed examination of various extended research.

  11. Potential of Legume–Brassica Intercrops for Forage Production and Green Manure: Encouragements from a Temperate Southeast European Environment

    Science.gov (United States)

    Jeromela, Ana M.; Mikić, Aleksandar M.; Vujić, Svetlana; Ćupina, Branko; Krstić, Đorđe; Dimitrijević, Aleksandra; Vasiljević, Sanja; Mihailović, Vojislav; Cvejić, Sandra; Miladinović, Dragana

    2017-01-01

    Legumes and brassicas have much in common: importance in agricultural history, rich biodiversity, numerous forms of use, high adaptability to diverse farming designs, and various non-food applications. Rare available resources demonstrate intercropping legumes and brassicas as beneficial to both, especially for the latter, profiting from better nitrogen nutrition. Our team aimed at designing a scheme of the intercrops of autumn- and spring-sown annual legumes with brassicas for ruminant feeding and green manure, and has carried out a set of field trials in a temperate Southeast European environment and during the past decade, aimed at assessing their potential for yields of forage dry matter and aboveground biomass nitrogen and their economic reliability via land equivalent ratio. This review provides a cross-view of the most important deliverables of our applied research, including eight annual legume crops and six brassica species, demonstrating that nearly all the intercrops were economically reliable, as well as that those involving hairy vetch, Hungarian vetch, Narbonne vetch and pea on one side, and fodder kale and rapeseed on the other, were most productive in both manners. Feeling encouraged that this pioneering study may stimulate similar analyses in other environments and that intercropping annual legume and brassicas may play a large-scale role in diverse cropping systems, our team is heading a detailed examination of various extended research. PMID:28326095

  12. Index for Characterizing Post-Fire Soil Environments in Temperate Coniferous Forests

    Directory of Open Access Journals (Sweden)

    Jonathan E. Sandquist

    2012-07-01

    Full Text Available 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 ( < 40%, and (e absence of surface organic matter (no organic matter left. We then subdivided each broad category on the basis of post-fire mineral soil colors providing a more fine-tuned post-fire soil index. We related each PFI category to characteristics such as soil temperature and duration of heating during fire, and physical, chemical, and biological responses. Classifying or describing post-fire soil conditions consistently will improve interpretations of fire effects research and facilitate communication of potential responses or outcomes (e.g., erosion potential from fires of varying severities.

  13. 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.

  14. 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

  15. 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.

  16. 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.

  17. Cryptococcus gattii infections on Vancouver Island, British Columbia, Canada: emergence of a tropical fungus in a temperate environment.

    Science.gov (United States)

    Fyfe, M; MacDougall, L; Romney, M; Starr, M; Pearce, M; Mak, S; Mithani, S; Kibsey, P

    2008-06-01

    Cryptococcus gattii causes disease among immunocompetent individuals in the tropics and subtropics. We document the appearance of C. gattii infections on Vancouver Island (VI), a temperate region, and discuss reasons for this emergence. Data on Cryptococcus hospitalizations for the calendar years 1995 through 2004 were reviewed. Viable historic isolates stored at the provincial public health laboratory between 1987 and 2000 were serotyped. Human cases were mapped by place of residence. Cryptococcosis among HIV negative individuals diagnosed on VI increased sharply after 1999. C. gattii was not detected in stored isolates prior to 1999. C. gattii cases lived in a specific biogeoclimatic zone on VI. Higher rates of illness were associated with exposure to the central region of VI. The emergence of C. gattii in a temperate region is unprecedented. Clinicians should consider C. gattii in the differential diagnosis of individuals who travelled to certain areas in British Columbia.

  18. Temper Foam

    Science.gov (United States)

    1981-01-01

    Fabricated by Expanded Rubber & Plastics Corporation, Temper Foam provides better impact protection for airplane passengers and enhances passenger comfort on long flights because it distributes body weight and pressure evenly over the entire contact area. Called a "memory foam" it matches the contour of the body pressing against it and returns to its original shape once the pressure is removed. As a shock absorber, a three-inch foam pad has the ability to absorb the impact of a 10-foot fall by an adult. Applications include seat cushioning for transportation vehicles, padding for furniture and a variety of athletic equipment medical applications including wheelchair padding, artificial limb socket lining, finger splint and hand padding for burn patients, special mattresses for the bedridden and dental stools. Production and sales rights are owned by Temper Foam, Inc. Material is manufactured under license by the Dewey and Almy Division of Grace Chemical Corporation. Distributors of the product are Kees Goebel Medical Specialties, Inc. and Alimed, Inc. They sell Temper Foam in bulk to the fabricators who trim it to shapes required by their customers.

  19. 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., forest communities globally, will remain an important challenge for ecologists in the future.

  20. TEMPERED FRACTIONAL CALCULUS

    Science.gov (United States)

    MEERSCHAERT, MARK M.; SABZIKAR, FARZAD; CHEN, JINGHUA

    2014-01-01

    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 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. PMID:26085690

  1. 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.

  2. TEMPERED FRACTIONAL CALCULUS.

    Science.gov (United States)

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

    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 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.

  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.

    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

  4. 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...

  5. 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.

  6. TEMPERED FRACTIONAL CALCULUS

    OpenAIRE

    MEERSCHAERT, MARK M.; SABZIKAR, FARZAD; 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 obs...

  7. The effect of intermediate clothing targets on shotgun ballistics.

    Science.gov (United States)

    Cail, Kenneth; Klatt, Edward

    2013-12-01

    The ballistic properties of shotgun shells are complex because of multiple projectiles fired simultaneously that interact and spread out to affect their energy relayed to a human target. Intermediate targets such as clothing can affect penetration into tissues. We studied the effect of common clothing fabrics as intermediate targets on penetration of shotgun shell pellets, using ordnance gelatin to simulate soft tissue and thin cowhide to simulate skin. A standard 12-gauge shotgun with modified choke was used with no. 8 shot ammunition. We found that protection afforded by fabrics to reduce penetration of shotgun pellets into tissues was greater at increasing distance from the muzzle beyond 40 yd (36.6 m). The thicker denim and cotton fabrics provided slightly greater protection than polyester. This study demonstrates that clothing modifies the potential wound patterns to victims of shotgun injuries.

  8. FeS Corrosion Products Formation and Hydrogen Uptake in a Sour Environment for Quenched & Tempered Steel

    Directory of Open Access Journals (Sweden)

    Elien Wallaert

    2018-01-01

    Full Text Available Surface corrosion product formation is one of the important factors affecting the corrosion rate and hydrogen uptake in a H2S environment. However, it is still unclear how the base material composition will affect the corrosion products that are generated, and consequently their impact on the corrosion rate. In this paper, corrosion product formation and the impact of the Mo content of the base material on the composition of the corrosion products and hydrogen absorption in a sour environment was investigated. The corrosion layer was composed of a double layered mackinawite (FeS1−x structure, which was enriched with molybdenum and chromium. The layers were formed via two different mechanisms, i.e., the inner layer was created via a general oxide film formation corrosion mechanism, whereas the upper layer was formed by a precipitation mechanism. The presence of this double corrosion layer had a large influence on the amount of diffusible hydrogen in the materials. This amount decreased as a function of contact time with the H2S saturated solution, while the corrosion rate of the materials shows no significant reduction. Therefore, the corrosion products are assumed to act as a physical barrier against hydrogen uptake. Mo addition caused a decrease in the maximal amount of diffusible hydrogen.

  9. 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

  10. Methods for generating shotgun and mixed shotgun/paired-end libraries for the 454 DNA sequencer.

    Science.gov (United States)

    Wiley, Graham; Macmil, Simone; Qu, Chunmei; Wang, Ping; Xing, Yanbo; White, Doug; Li, Jianfeng; White, James D; Domingo, Alexander; Roe, Bruce A

    2009-04-01

    With the introduction of massively parallel, microminiature-based instrumentation for DNA sequencing, robust, reproducible, optimized methods are needed to prepare the target DNA for analysis using these high-throughput approaches because the cost per instrument run is orders of magnitude more than for typical Sanger dideoxynucleotide sequencing on fluorescence-based capillary systems. The methods provided by the manufacturer for genome sequencing using the 454/Roche GS-20 and GS-FLX instruments are robust. However, in an effort to streamline them for automation, we have incorporated several novel changes and deleted several extraneous steps. As a result of modifying these sample preparation protocols, the number of manual manipulations has also been minimized, and the overall yields have been improved for both shotgun and mixed shotgun/paired-end libraries. (c) 2009 by John Wiley & Sons, Inc.

  11. 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

  12. Serial tempering without exchange.

    Science.gov (United States)

    Nymeyer, Hugh

    2010-09-21

    Serial tempering is a computational method that turns the temperature T (or more generally any independent λ parameter) into a dynamical variable. It is shown that, under conditions for which this variable is fast, serial tempering is equivalent to the umbrella sampling method with a single effective potential. This equivalence is demonstrated using both a small one-dimensional system and a small solvated peptide. The suggestion is then made to replace the serial tempering protocol with the equivalent umbrella sampling calculation. This approach, serial tempering without exchange (STeWiE), has the same performance as serial tempering in the limit that exchanges are frequent, is simpler to implement, and has fewer adjustable parameters than conventional serial tempering. The equivalence of serial tempering and STeWiE also provides a convenient route for estimating and optimizing the performance of serial tempering simulations and other generalized-ensemble methods.

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

    African Journals Online (AJOL)

    Analysis of pig serum proteins based on shotgun liquid chromatography-tandem mass spectrometry. Keshan Zhang, Yongjie Liu, Youjun Shang, Haixue Zheng, Jianhong Guo, Hong Tian, Ye Jin, Jijun He, Xiangtao Liu ...

  14. Blood lead concentration after a shotgun accident.

    Science.gov (United States)

    Gerhardsson, Lars; Dahlin, Lars; Knebel, Richard; Schütz, Andrejs

    2002-01-01

    In an accidental shooting, a man in his late forties was hit in his left shoulder region by about 60 lead pellets from a shotgun. He had injuries to the vessels, the clavicle, muscles, and nerves, with total paralysis of the left arm due to axonal injury. After several surgical revisions and temporary cover with split skin, reconstructive surgery was carried out 54 days after the accident. The brachial plexus was swollen, but the continuity of the nerve trunks was not broken (no neuroma present). We determined the blood lead (BPb) concentration during a follow-up period of 12 months. The BPb concentration increased considerably during the first months. Although 30 lead pellets were removed during the reconstructive surgery, the BPb concentration continued to rise, and reached a peak of 62 microg/dL (3.0 micromol/L) on day 81. Thereafter it started to decline. Twelve months after the accident, BPb had leveled off at about 30 microg/dL. At that time, muscle and sensory functions had partially recovered. The BPb concentration exceeded 30 microg/dL for 9 months, which may have influenced the recovery rate of nerve function. Subjects with a large number of lead pellets or fragments embedded in the body after shooting accidents should be followed for many years by regular determinations of BPb. To obtain a more stable basis for risk assessment, the BPb concentrations should be corrected for variations in the subject's hemoglobin concentration or erythrocyte volume fraction.

  15. 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.

  16. 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

  17. Relationships of leaf dark respiration with light environment and tissue nitrogen content in juveniles of 11 cold-temperate tree species.

    Science.gov (United States)

    Lusk, C H; Reich, P B

    2000-05-01

    It has been argued that plants adapted to low light should have lower carbon losses via dark respiration (Rd) than those not so adapted, and similarly, all species would be expected to down-regulate Rd in deep shade, because the associated advantages of high metabolic potential cannot be realized in such habitats. In order to test these hypotheses, and to explore the determinants of intraspecific variation in respiration rates, we measured Rd, leaf mass per unit area (LMA), and nitrogen content of mature foliage in juveniles of 11 cold-temperate tree species (angiosperms and conifers), growing in diverse light environments in forest understories in northern Minnesota. Among the seven angiosperm species, respiration on mass, area, and nitrogen bases showed significant negative overall relationships with shade tolerance level. Mass-based respiration rates (Rd mass ) of angiosperms as a group showed a significant positive overall relationship with an index of light availability (percentage canopy openness, %CO). Rd mass of most conifers also showed evidence of acclimation of Rd mass to light availability. LMA of all species also increased with increasing %CO, but this response was generally much stronger in angiosperms than in conifers. As a result, the response of area-based respiration (Rd area ) to %CO was dominated by ΔRd mass for conifers, and by ΔLMA for most angiosperms, i.e., functional types differed in the components of acclimation of Rd area to light availability. Among the seven angiosperm species, the relationships of leaf N on a mass basis (N mass ) with %CO were modulated by shade tolerance: negative slopes in shade-tolerant species may be related to the steep increases in LMA of these taxa along gradients of increasing light intensity, and associated dilution of N-rich, metabolically active tissue by increasing investment in leaf structural components. Although N mass was therefore an unreliable predictor of variation in Rd mass along light gradients

  18. Unsupervised statistical clustering of environmental shotgun sequences.

    Science.gov (United States)

    Kislyuk, Andrey; Bhatnagar, Srijak; Dushoff, Jonathan; Weitz, Joshua S

    2009-10-02

    The development of effective environmental shotgun sequence binning methods remains an ongoing challenge in algorithmic analysis of metagenomic data. While previous methods have focused primarily on supervised learning involving extrinsic data, a first-principles statistical model combined with a self-training fitting method has not yet been developed. We derive an unsupervised, maximum-likelihood formalism for clustering short sequences by their taxonomic origin on the basis of their k-mer distributions. The formalism is implemented using a Markov Chain Monte Carlo approach in a k-mer feature space. We introduce a space transformation that reduces the dimensionality of the feature space and a genomic fragment divergence measure that strongly correlates with the method's performance. Pairwise analysis of over 1000 completely sequenced genomes reveals that the vast majority of genomes have sufficient genomic fragment divergence to be amenable for binning using the present formalism. Using a high-performance implementation, the binner is able to classify fragments as short as 400 nt with accuracy over 90% in simulations of low-complexity communities of 2 to 10 species, given sufficient genomic fragment divergence. The method is available as an open source package called LikelyBin. An unsupervised binning method based on statistical signatures of short environmental sequences is a viable stand-alone binning method for low complexity samples. For medium and high complexity samples, we discuss the possibility of combining the current method with other methods as part of an iterative process to enhance the resolving power of sorting reads into taxonomic and/or functional bins.

  19. Unsupervised statistical clustering of environmental shotgun sequences

    Directory of Open Access Journals (Sweden)

    Bhatnagar Srijak

    2009-10-01

    Full Text Available Abstract Background The development of effective environmental shotgun sequence binning methods remains an ongoing challenge in algorithmic analysis of metagenomic data. While previous methods have focused primarily on supervised learning involving extrinsic data, a first-principles statistical model combined with a self-training fitting method has not yet been developed. Results We derive an unsupervised, maximum-likelihood formalism for clustering short sequences by their taxonomic origin on the basis of their k-mer distributions. The formalism is implemented using a Markov Chain Monte Carlo approach in a k-mer feature space. We introduce a space transformation that reduces the dimensionality of the feature space and a genomic fragment divergence measure that strongly correlates with the method's performance. Pairwise analysis of over 1000 completely sequenced genomes reveals that the vast majority of genomes have sufficient genomic fragment divergence to be amenable for binning using the present formalism. Using a high-performance implementation, the binner is able to classify fragments as short as 400 nt with accuracy over 90% in simulations of low-complexity communities of 2 to 10 species, given sufficient genomic fragment divergence. The method is available as an open source package called LikelyBin. Conclusion An unsupervised binning method based on statistical signatures of short environmental sequences is a viable stand-alone binning method for low complexity samples. For medium and high complexity samples, we discuss the possibility of combining the current method with other methods as part of an iterative process to enhance the resolving power of sorting reads into taxonomic and/or functional bins.

  20. 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.

  1. 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.

  2. Using shotgun sequence data to find active restriction enzyme genes

    Science.gov (United States)

    Zheng, Yu; Posfai, Janos; Morgan, Richard D.; Vincze, Tamas; Roberts, Richard J.

    2009-01-01

    Whole genome shotgun sequence analysis has become the standard method for beginning to determine a genome sequence. The preparation of the shotgun sequence clones is, in fact, a biological experiment. It determines which segments of the genome can be cloned into Escherichia coli and which cannot. By analyzing the complete set of sequences from such an experiment, it is possible to identify genes lethal to E. coli. Among this set are genes encoding restriction enzymes which, when active in E. coli, lead to cell death by cleaving the E. coli genome at the restriction enzyme recognition sites. By analyzing shotgun sequence data sets we show that this is a reliable method to detect active restriction enzyme genes in newly sequenced genomes, thereby facilitating functional annotation. Active restriction enzyme genes have been identified, and their activity demonstrated biochemically, in the sequenced genomes of Methanocaldococcus jannaschii, Bacillus cereus ATCC 10987 and Methylococcus capsulatus. PMID:18988632

  3. Large thoracic defect due to shotgun violation - surgical emergency management.

    Science.gov (United States)

    Rupprecht, Holger; Gaab, Katharina

    2017-01-01

    Shotgun injuries from a short distance (lethal outcome. We report about a 27-year-old patient, who was wounded on the left chest wall by a straight-cut shotgun from a short distance. In cases of this special traumatic pattern damage control measures are necessary. The measures should take place in preclinical emergency management (by the on-site emergency physician). We report about the emergency management from admission to our hospital and the following surgical treatment until discharge from the hospital.

  4. 40 CFR 426.60 - Applicability; description of the automotive glass tempering subcategory.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 29 2010-07-01 2010-07-01 false Applicability; description of the automotive glass tempering subcategory. 426.60 Section 426.60 Protection of Environment ENVIRONMENTAL... Automotive Glass Tempering Subcategory § 426.60 Applicability; description of the automotive glass tempering...

  5. Coastal Temperate Rainforest Symposium

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — The North Pacific LCC is helping sponsor the April 2012 science symposium - Coastal Temperate Rainforests: Integrating Communities, Climate Science, and Resource...

  6. How the environment, canopy structure and canopy physiological functioning influence carbon, water and energy fluxes of a temperate broad-leaved deciduous forest -- an assessment with the biophysical model CANOAK

    Energy Technology Data Exchange (ETDEWEB)

    Baldocchi, D. D.; Gu, L. [Univ. of California-Berkeley, Dept. of Environmental Science, Berkeley, CA (United States); Wilson, K. B. [NOAA. Atmospheric Turbulence and Diffusion Divison, Oak Ridge, TN (United States)

    2002-11-01

    The interaction of the environment, canopy structure and its physiological functioning in controlling and driving the exchange of carbon dioxide and water vapour between a temperate forest and the atmosphere are described. The modulation of carbon dioxide and water vapour by temporal and spatial variations in canopy structure and physiological functioning is reviewed. This review is followed by quantification of the effects of leaf dimension and thickness, vertical variations in leaf area and photosynthetic capacity, leaf clumping, leaf inclination angle stomatal conductance and weather on the annual sums of carbon dioxide and water vapour and sensible heat exchange, using the biophysical model CANOAK. The paper also attempts to estimate the amount of detail required in a model to reliably predict fluxes of carbon dioxide and water vapour. A closer coupling between detailed biophysical models like CANOAK, with modules that compute the dynamics of canopy structure is envisaged. 105 refs., 10 tabs., 3 figs.

  7. Deterministic protein inference for shotgun proteomics data provides new insights into Arabidopsis pollen development and function

    Science.gov (United States)

    Grobei, Monica A.; Qeli, Ermir; Brunner, Erich; Rehrauer, Hubert; Zhang, Runxuan; Roschitzki, Bernd; Basler, Konrad; Ahrens, Christian H.; Grossniklaus, Ueli

    2009-01-01

    Pollen, the male gametophyte of flowering plants, represents an ideal biological system to study developmental processes, such as cell polarity, tip growth, and morphogenesis. Upon hydration, the metabolically quiescent pollen rapidly switches to an active state, exhibiting extremely fast growth. This rapid switch requires relevant proteins to be stored in the mature pollen, where they have to retain functionality in a desiccated environment. Using a shotgun proteomics approach, we unambiguously identified ∼3500 proteins in Arabidopsis pollen, including 537 proteins that were not identified in genetic or transcriptomic studies. To generate this comprehensive reference data set, which extends the previously reported pollen proteome by a factor of 13, we developed a novel deterministic peptide classification scheme for protein inference. This generally applicable approach considers the gene model–protein sequence–protein accession relationships. It allowed us to classify and eliminate ambiguities inherently associated with any shotgun proteomics data set, to report a conservative list of protein identifications, and to seamlessly integrate data from previous transcriptomics studies. Manual validation of proteins unambiguously identified by a single, information-rich peptide enabled us to significantly reduce the false discovery rate, while keeping valuable identifications of shorter and lower abundant proteins. Bioinformatic analyses revealed a higher stability of pollen proteins compared to those of other tissues and implied a protein family of previously unknown function in vesicle trafficking. Interestingly, the pollen proteome is most similar to that of seeds, indicating physiological similarities between these developmentally distinct tissues. PMID:19546170

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

    Energy Technology Data Exchange (ETDEWEB)

    Huang, Eric L. [McGill University, Montreal, Quebec; Orsat, Valerie [McGill University; Shah, Manesh B [ORNL; Herndon, Elizabeth M [ORNL; Hettich, Robert {Bob} L [ORNL; Verberkmoes, Nathan C [ORNL; Lefsrud, Mark G [McGill University, Montreal, Quebec

    2012-01-01

    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.

  9. 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.

  10. Simulated Solute Tempering.

    Science.gov (United States)

    Denschlag, Robert; Lingenheil, Martin; Tavan, Paul; Mathias, Gerald

    2009-10-13

    For the enhanced conformational sampling in molecular dynamics (MD) simulations, we present "simulated solute tempering" (SST) which is an easy to implement variant of simulated tempering. SST extends conventional simulated tempering (CST) by key concepts of "replica exchange with solute tempering" (REST, Liu et al. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 13749). We have applied SST, CST, and REST to molecular dynamics (MD) simulations of an alanine octapeptide in explicit water. The weight parameters required for CST and SST are determined by two different formulas whose performance is compared. For SST only one of them yields a uniform sampling of the temperature space. Compared to CST and REST, SST provides the highest exchange probabilities between neighboring rungs in the temperature ladder. Concomitantly, SST leads to the fastest diffusion of the simulation system through the temperature space, in particular, if the "even-odd" exchange scheme is employed in SST. As a result, SST exhibits the highest sampling speed of the investigated tempering methods.

  11. 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.

  12. 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.

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

    Science.gov (United States)

    Koslicki, David; Foucart, Simon; Rosen, Gail

    2014-01-01

    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.

  14. 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

  15. Standard flow liquid chromatography for shotgun proteomics in bioenergy research

    Directory of Open Access Journals (Sweden)

    Susana M. González Fernández-Niño

    2015-04-01

    Full Text Available Over the past ten years the bioenergy and biofuels field has realized significant achievements that have encouraged many follow on efforts centered on biosynthetic production of fuel-like compounds. Key to the success of these efforts has been transformational developments in feedstock characterization and metabolic engineering of biofuel-producing microbes. Lagging far behind these advancements are analytical methods to characterize and quantify systems of interest to the bioenergy field. In particular the utilization of proteomics, while valuable for identifying novel enzymes and diagnosing problems associated with biofuel-producing microbes, is limited by a lack of robustness and limited throughput. Nano-flow liquid chromatography coupled to high-mass accuracy, high-resolution mass spectrometers has become the dominant approach for the analysis of complex proteomic samples, yet such assays still require dedicated experts for data acquisition, analysis, and instrument upkeep. The recent adoption of standard flow chromatography (ca. 0.5 mL/min for targeted proteomics has highlighted the robust nature and increased throughput of this approach for sample analysis. Consequently, we assessed the applicability of standard flow liquid chromatography for shotgun proteomics using samples from Escherichia coli and Arabidopsis thaliana, organisms commonly used as model systems for lignocellulosic biofuels research. Employing 120 minute gradients with standard flow chromatography we were able to routinely identify nearly 800 proteins from E. coli samples, while for samples from Arabidopsis over 1,000 proteins could be reliably identified. An examination of identified peptides indicated that the method was suitable for reproducible applications in shotgun proteomics. Standard flow liquid chromatography for shotgun proteomics provides a robust approach for the analysis of complex samples. To the best of our knowledge this study represents the first attempt

  16. 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]....

  17. 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...

  18. Kajian Pembuatan Cokelat Batang dengan Metode Tempering dan Tanpa Tempering

    OpenAIRE

    Eti Indarti; Normalina Arpi; Slamet Budijanto*

    2013-01-01

    This research is aimed to improve stability of milk chocolate bars by tempering process. The making of chocolate bars consisted of two formulations, namely a higher fat bar (40%) and low fat bar (21.5%).The study includes the chocolate bar preparation with and without tempering results. The melting point of milk chocolate bars that use cocoa butter tempering (L1) is higher than the milk chocolate bars that use fat without tempering (L2) for all treatments. Solid fat content (SFC) of F1 has hi...

  19. Grinder: a versatile amplicon and shotgun sequence simulator.

    Science.gov (United States)

    Angly, Florent E; Willner, Dana; Rohwer, Forest; Hugenholtz, Philip; Tyson, Gene W

    2012-07-01

    We introduce Grinder (http://sourceforge.net/projects/biogrinder/), an open-source bioinformatic tool to simulate amplicon and shotgun (genomic, metagenomic, transcriptomic and metatranscriptomic) datasets from reference sequences. This is the first tool to simulate amplicon datasets (e.g. 16S rRNA) widely used by microbial ecologists. Grinder can create sequence libraries with a specific community structure, α and β diversities and experimental biases (e.g. chimeras, gene copy number variation) for commonly used sequencing platforms. This versatility allows the creation of simple to complex read datasets necessary for hypothesis testing when developing bioinformatic software, benchmarking existing tools or designing sequence-based experiments. Grinder is particularly useful for simulating clinical or environmental microbial communities and complements the use of in vitro mock communities.

  20. Shotgun Sequencing for Microsatellite Identification in Ilex paraguariensis (Aquifoliaceae

    Directory of Open Access Journals (Sweden)

    Marlei F. Pereira

    2013-03-01

    Full Text Available Premise of the study: Ilex paraguariensis is a native tree species from Brazil, Argentina, and Paraguay that is used in the production of beverages, medicines, and cosmetics. Primers flanking microsatellites were developed to investigate genetic parameters in the species. Methods and Results: Using microsatellites cloned from an I. paraguariensis shotgun genomic library, 25 pairs of primers were designed and synthesized. Levels of polymorphism were evaluated in 24 individuals from two populations. Twenty loci were polymorphic, and an average of 4.8 and 4.5 alleles per locus were detected in the two populations, respectively. The mean observed heterozygosity was lower than the expected heterozygosity (0.54 vs. 0.60, indicating a departure from Hardy–Weinberg equilibrium and suggesting endogamy in both populations. Conclusions: The reported set of markers is highly informative and constitutes a powerful tool for the development of genetic characterization studies in I. paraguariensis.

  1. Recovery of a medieval Brucella melitensis genome using shotgun metagenomics.

    Science.gov (United States)

    Kay, Gemma L; Sergeant, Martin J; Giuffra, Valentina; Bandiera, Pasquale; Milanese, Marco; Bramanti, Barbara; Bianucci, Raffaella; Pallen, Mark J

    2014-07-15

    Shotgun metagenomics provides a powerful assumption-free approach to the recovery of pathogen genomes from contemporary and historical material. We sequenced the metagenome of a calcified nodule from the skeleton of a 14th-century middle-aged male excavated from the medieval Sardinian settlement of Geridu. We obtained 6.5-fold coverage of a Brucella melitensis genome. Sequence reads from this genome showed signatures typical of ancient or aged DNA. Despite the relatively low coverage, we were able to use information from single-nucleotide polymorphisms to place the medieval pathogen genome within a clade of B. melitensis strains that included the well-studied Ether strain and two other recent Italian isolates. We confirmed this placement using information from deletions and IS711 insertions. We conclude that metagenomics stands ready to document past and present infections, shedding light on the emergence, evolution, and spread of microbial pathogens. Importance: Infectious diseases have shaped human populations and societies throughout history. The recovery of pathogen DNA sequences from human remains provides an opportunity to identify and characterize the causes of individual and epidemic infections. By sequencing DNA extracted from medieval human remains through shotgun metagenomics, without target-specific capture or amplification, we have obtained a draft genome sequence of an ~700-year-old Brucella melitensis strain. Using a variety of bioinformatic approaches, we have shown that this historical strain is most closely related to recent strains isolated from Italy, confirming the continuity of this zoonotic infection, and even a specific lineage, in the Mediterranean region over the centuries. Copyright © 2014 Kay et al.

  2. 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...

  3. Shotgun use as high resolution seismic source; Uso de rifle como fonte sismica para alta resolucao

    Energy Technology Data Exchange (ETDEWEB)

    Antunes, Paulo de Tarso Silva; Guimaraes, Marco Antonio Gallotti [PETROBRAS, Rio de Janeiro, RJ (Brazil)

    1993-07-01

    This paper relates the performance of the 8 and 12 gauge Betsy shotgun , under different geological conditions in the Santa Fe (RN) and Camaqua (RS) regions, in Brazil. The data are presented in field seismograms, amplitude spectra and a bar graph, for evaluations of generated energy levels and frequency content. Shown are also tables of the general characteristics of the Betsy shotgun and of the data acquisition parameters, besides a picture of the shotgun. It is concluded that the shotgun is a good tool for shallow seismic reflection surveys, with advantages of being extremely lightweight, portable, of low cost and capable of producing high-frequency energy. Due to strong dependence of geological characteristics of the site, a better performance of the source was observed in the Camaqua region. (author)

  4. Shotgun Metaproteomics of the Human Distal Gut Microbiota

    Energy Technology Data Exchange (ETDEWEB)

    Verberkmoes, Nathan C [ORNL; Erickson, Alison L [ORNL; Shah, Manesh B [ORNL; Godzik, A [Burnham Institute for Medical Research, La Jolla, CA; Rosenquist, M [Swedish University of Agricultural Sciences, Upsalla, Sweden; Halfvarsson, J [Orebro University Hospital, Orebro, Sweden; Lefsrud, Mark G [McGill University, Montreal, Quebec; Apajalahti, J. [Alimetrics Ltd,; Hettich, Robert {Bob} L [ORNL; Jansson, J [Swedish University of Agricultural Sciences, Upsalla, Sweden

    2009-01-01

    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 what genes were 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 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.

  5. Shotgun Proteomics Identifies Proteins Specific for Acute Renal Transplant Rejection

    Energy Technology Data Exchange (ETDEWEB)

    Sigdel, Tara K.; Kaushal, Amit; Gritsenko, Marina A.; Norbeck, Angela D.; Qian, Weijun; Xiao, Wenzhong; Camp, David G.; Smith, Richard D.; Sarwal, Minnie M.

    2010-01-04

    Acute rejection (AR) remains the primary risk factor for renal transplant outcome; development of non-invasive diagnostic biomarkers for AR is an unmet need. We used shotgun proteomics using LC-MS/MS and ELISA to analyze a set of 92 urine samples, from patients with AR, stable grafts (STA), proteinuria (NS), and healthy controls (HC). A total of 1446 urinary proteins were identified along with a number of NS specific, renal transplantation specific and AR specific proteins. Relative abundance of identified urinary proteins was measured by protein-level spectral counts adopting a weighted fold-change statistic, assigning increased weight for more frequently observed proteins. We have identified alterations in a number of specific urinary proteins in AR, primarily relating to MHC antigens, the complement cascade and extra-cellular matrix proteins. A subset of proteins (UMOD, SERPINF1 and CD44), have been further cross-validated by ELISA in an independent set of urine samples, for significant differences in the abundance of these urinary proteins in AR. This label-free, semi-quantitative approach for sampling the urinary proteome in normal and disease states provides a robust and sensitive method for detection of urinary proteins for serial, non-invasive clinical monitoring for graft rejection after

  6. Characterizing the citrus cultivar Carrizo genome through 454 shotgun sequencing.

    Science.gov (United States)

    Belknap, William R; Wang, Yi; Huo, Naxin; Wu, Jiajie; Rockhold, David R; Gu, Yong Q; Stover, Ed

    2011-12-01

    The citrus cultivar Carrizo is the single most important rootstock to the US citrus industry and has resistance or tolerance to a number of major citrus diseases, including citrus tristeza virus, foot rot, and Huanglongbing (HLB, citrus greening). A Carrizo genomic sequence database providing approximately 3.5×genome coverage (haploid genome size approximately 367 Mb) was populated through 454 GS FLX shotgun sequencing. Analysis of the repetitive DNA fraction indicated a total interspersed repeat fraction of 36.5%. Assembly and characterization of abundant citrus Ty3/gypsy elements revealed a novel type of element containing open reading frames encoding a viral RNA-silencing suppressor protein (RNA binding protein, rbp) and a plant cytokinin riboside 5′-monophosphate phosphoribohydrolase-related protein (LONELY GUY, log). Similar gypsy elements were identified in the Populus trichocarpa genome. Gene-coding region analysis indicated that 24.4% of the nonrepetitive reads contained genic regions. The depth of genome coverage was sufficient to allow accurate assembly of constituent genes, including a putative phloem-expressed gene. The development of the Carrizo database (http://citrus.pw.usda.gov/) will contribute to characterization of agronomically significant loci and provide a publicly available genomic resource to the citrus research community.

  7. 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).

  8. 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.

  9. Shotgun proteomic analysis of porcine colostrum and mature milk.

    Science.gov (United States)

    Ogawa, Shohei; Tsukahara, Takamitsu; Nishibayashi, Ryoichiro; Nakatani, Masako; Okutani, Mie; Nakanishi, Nobuo; Ushida, Kazunari; Inoue, Ryo

    2014-04-01

    The epitheliochorial nature of the porcine placenta prevents the transfer of maternal immunity. Therefore, ingestion of the colostrum immediately after birth is crucial for neonatal piglets to acquire passive immunity from the sow. We performed a shotgun proteomic analysis of porcine milk to reveal in detail the protein composition of porcine milk. On the basis of the Swiss-Prot database, 113 and 118 proteins were identified in the porcine colostrum and mature milk, respectively, and 50 of these proteins were common to both samples. Some immune-related proteins, including interleukin-18 (IL-18), were unique to the colostrum. The IL-18 concentration in the colostrum and mature milk of four sows was measured to validate the proteomic analysis, and IL-18 was only detected in the colostrum (191.0 ± 53.9 pg/mL) and not in mature milk. In addition, some proteins involved in primary defense, such as azurocidin, which has never been detected in any other mammal's milk, were also identified in the colostrum. © 2014 Japanese Society of Animal Science.

  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. 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.

  12. Kajian Pembuatan Cokelat Batang dengan Metode Tempering dan Tanpa Tempering

    Directory of Open Access Journals (Sweden)

    Eti Indarti

    2013-02-01

    Full Text Available This research is aimed to improve stability of milk chocolate bars by tempering process. The making of chocolate bars consisted of two formulations, namely a higher fat bar (40% and low fat bar (21.5%.The study includes the chocolate bar preparation with and without tempering results. The melting point of milk chocolate bars that use cocoa butter tempering (L1 is higher than the milk chocolate bars that use fat without tempering (L2 for all treatments. Solid fat content (SFC of F1 has higher solid phase at room temperature (55-60% in all treatments compared with milk chocolate bar F2 (40-43% and chocolate produced by UKM (Malaysia 40-48 % and soccolatte 35-38% at the same temperature (350C. Blooming was not formed on the milk chocolate bars containing cocoa butter L1, while the milk chocolate bars showed blooming with L2 treatment. Keywords: chocolate bar, tempering, moulding, melting point, solid fat content, blooming

  13. 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

    Micro-organisms account for most of the Earth's biodiversity and yet remain largely unknown. The complexity and diversity of microbial communities present in clinical and environmental samples can now be robustly investigated in record times and prices thanks to recent advances in high......-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...

  14. 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...

  15. 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

  16. 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

  17. 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

  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. Large thoracic defect due to shotgun violation – surgical emergency management

    Directory of Open Access Journals (Sweden)

    Rupprecht, Holger

    2017-08-01

    Full Text Available Shotgun injuries from a short distance (<3 m may cause massive bleeding and tissue destruction. Only immediate aggressive (surgical therapy prevents lethal outcome. We report about a 27-year-old patient, who was wounded on the left chest wall by a straight-cut shotgun from a short distance. In cases of this special traumatic pattern damage control measures are necessary. The measures should take place in preclinical emergency management (by the on-site emergency physician. We report about the emergency management from admission to our hospital and the following surgical treatment until discharge from the hospital.

  20. Large thoracic defect due to shotgun violation – surgical emergency management

    Science.gov (United States)

    Rupprecht, Holger; Gaab, Katharina

    2017-01-01

    Shotgun injuries from a short distance (<3 m) may cause massive bleeding and tissue destruction. Only immediate aggressive (surgical) therapy prevents lethal outcome. We report about a 27-year-old patient, who was wounded on the left chest wall by a straight-cut shotgun from a short distance. In cases of this special traumatic pattern damage control measures are necessary. The measures should take place in preclinical emergency management (by the on-site emergency physician). We report about the emergency management from admission to our hospital and the following surgical treatment until discharge from the hospital. PMID:28868228

  1. Whole-genome shotgun optical mapping of Rhodobacter sphaeroides strain 2.4. 1 and its use for whole-genome shotgun sequence assembly

    Energy Technology Data Exchange (ETDEWEB)

    Shou, S. [Univ. Wisc.-Madison; Kvikstad, E. [Univ. Wisc.-Madison; Kile, A. [Univ. Wisc.-Madison; Severin, J. [Whole-genome shotgun optical mapping of Rhodobacter sphaeroides strain 2.4. 1 and its use for whole-genome shotgun sequence assembly; Forrest, D. [Univ. Wisc.-Madison; Runnheim, R. [Univ. Wisc.-Madison; Churas, C. [Univ. Wisc.-Madison; Hickman, J. W. [Univ. Wisc.-Madison; Mackenzie, C. [University of Texas–Houston Medical School; Choudhary, M. [University of Texas–Houston Medical School; Donohue, T. [Univ. Wisc.-Madison; Kaplan, S. [University of Texas–Houston Medical School; Schwartz, D. C. [Univ. Wisc.-Madison

    2003-09-01

    Rhodobacter sphaeroides 2.4.1 is a facultative photoheterotrophic bacterium with tremendous metabolic diversity, which has significantly contributed to our understanding of the molecular genetics of photosynthesis, photoheterotrophy, nitrogen fixation, hydrogen metabolism, carbon dioxide fixation, taxis, and tetrapyrrole biosynthesis. To further understand this remarkable bacterium, and to accelerate an ongoing sequencing project, two whole-genome restriction maps (EcoRI and HindIII) of R. sphaeroides strain 2.4.1 were constructed using shotgun optical mapping. The approach directly mapped genomic DNA by the random mapping of single molecules. The two maps were used to facilitate sequence assembly by providing an optical scaffold for high-resolution alignment and verification of sequence contigs. Our results show that such maps facilitated the closure of sequence gaps by the early detection of nascent sequence contigs during the course of the whole-genome shotgun sequencing process.

  2. Combined hybridization capture and shotgun sequencing for ancient DNA analysis of extinct wild and domestic dromedary camel.

    Science.gov (United States)

    Mohandesan, Elmira; Speller, Camilla F; Peters, Joris; Uerpmann, Hans-Peter; Uerpmann, Margarethe; De Cupere, Bea; Hofreiter, Michael; Burger, Pamela A

    2017-03-01

    The performance of hybridization capture combined with next-generation sequencing (NGS) has seen limited investigation with samples from hot and arid regions until now. We applied hybridization capture and shotgun sequencing to recover DNA sequences from bone specimens of ancient-domestic dromedary (Camelus dromedarius) and its extinct ancestor, the wild dromedary from Jordan, Syria, Turkey and the Arabian Peninsula, respectively. Our results show that hybridization capture increased the percentage of mitochondrial DNA (mtDNA) recovery by an average 187-fold and in some cases yielded virtually complete mitochondrial (mt) genomes at multifold coverage in a single capture experiment. Furthermore, we tested the effect of hybridization temperature and time by using a touchdown approach on a limited number of samples. We observed no significant difference in the number of unique dromedary mtDNA reads retrieved with the standard capture compared to the touchdown method. In total, we obtained 14 partial mitochondrial genomes from ancient-domestic dromedaries with 17-95% length coverage and 1.27-47.1-fold read depths for the covered regions. Using whole-genome shotgun sequencing, we successfully recovered endogenous dromedary nuclear DNA (nuDNA) from domestic and wild dromedary specimens with 1-1.06-fold read depths for covered regions. Our results highlight that despite recent methodological advances, obtaining ancient DNA (aDNA) from specimens recovered from hot, arid environments is still problematic. Hybridization protocols require specific optimization, and samples at the limit of DNA preservation need multiple replications of DNA extraction and hybridization capture as has been shown previously for Middle Pleistocene specimens. © 2016 The Authors. Molecular Ecology Resources Published by John Wiley & Sons Ltd.

  3. 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.

  4. 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

  5. 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

  6. 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

  7. An Optimized Shotgun Strategy for the Rapid Generation of Comprehensive Human Proteomes

    DEFF Research Database (Denmark)

    Bekker-Jensen, Dorte B; Kelstrup, Christian D; Batth, Tanveer S

    2017-01-01

    This study investigates the challenge of comprehensively cataloging the complete human proteome from a single-cell type using mass spectrometry (MS)-based shotgun proteomics. We modify a classical two-dimensional high-resolution reversed-phase peptide fractionation scheme and optimize a protocol ...

  8. Shotgun lipidomics on a LTQ Orbitrap mass spectrometer by successive switching between acquisition polarity modes

    DEFF Research Database (Denmark)

    Schuhmann, K.; Almeida, R.; Baumert, M.

    2012-01-01

    Topdown shotgun lipidomics relies on direct infusion of total lipid extracts into a high-resolution tandem mass spectrometer and implies that individual lipids are recognized by their accurately determined m/z. Lipid ionization efficiency and detection specificity strongly depend on the acquisiti...

  9. SUPER-FOCUS: a tool for agile functional analysis of shotgun metagenomic data

    NARCIS (Netherlands)

    Silva, G.G.; Green, K.T.; Dutilh, B.E.; Edwards, R.A.

    2016-01-01

    Analyzing the functional profile of a microbial community from unannotated shotgun sequencing reads is one of the important goals in metagenomics. Functional profiling has valuable applications in biological research because it identifies the abundances of the functional genes of the organisms

  10. SUPER-FOCUS: A tool for agile functional analysis of shotgun metagenomic data

    NARCIS (Netherlands)

    Silva, Genivaldo Gueiros Z; Green, Kevin T; Dutilh, Bas E; Edwards, Robert A

    2015-01-01

    Analyzing the functional profile of a microbial community from unannotated shotgun sequencing reads is one of the important goals in metagenomics. Functional profiling has valuable applications in biological research because it identifies the abundances of the functional genes of the organisms

  11. 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 i...

  12. 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

    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...

  13. 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 ...

  14. 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.

  15. Evaluation of shotgun metagenomics sequence classification methods using in silico and in vitro simulated communities.

    Science.gov (United States)

    Peabody, Michael A; Van Rossum, Thea; Lo, Raymond; Brinkman, Fiona S L

    2015-11-04

    The field of metagenomics (study of genetic material recovered directly from an environment) has grown rapidly, with many bioinformatics analysis methods being developed. To ensure appropriate use of such methods, robust comparative evaluation of their accuracy and features is needed. For taxonomic classification of sequence reads, such evaluation should include use of clade exclusion, which better evaluates a method's accuracy when identical sequences are not present in any reference database, as is common in metagenomic analysis. To date, relatively small evaluations have been performed, with evaluation approaches like clade exclusion limited to assessment of new methods by the authors of the given method. What is needed is a rigorous, independent comparison between multiple major methods, using the same in silico and in vitro test datasets, with and without approaches like clade exclusion, to better characterize accuracy under different conditions. An overview of the features of 38 bioinformatics methods is provided, evaluating accuracy with a focus on 11 programs that have reference databases that can be modified and therefore most robustly evaluated with clade exclusion. Taxonomic classification of sequence reads was evaluated using both in silico and in vitro mock bacterial communities. Clade exclusion was used at taxonomic levels from species to class-identifying how well methods perform in progressively more difficult scenarios. A wide range of variability was found in the sensitivity, precision, overall accuracy, and computational demand for the programs evaluated. In experiments where distilled water was spiked with only 11 bacterial species, frequently dozens to hundreds of species were falsely predicted by the most popular programs. The different features of each method (forces predictions or not, etc.) are summarized, and additional analysis considerations discussed. The accuracy of shotgun metagenomics classification methods varies widely. No one

  16. 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.

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

    Science.gov (United States)

    Rybak, Fanny; Depraetere, Marion; Gasc, Amandine; Le Viol, Isabelle; Pavoine, Sandrine; Sueur, Jérôme

    2015-01-01

    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. PMID:26587351

  18. 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

    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....... 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...... 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....

  19. Whole-genome shotgun sequence of phenazine-producing endophytic Streptomyces kebangsaanensis SUK12

    OpenAIRE

    Juwairiah Remali; Kok-Keong Loke; Chyan Leong Ng; Wan Mohd Aizat; John Tiong; Noraziah Mohamad Zin

    2017-01-01

    Streptomyces sp. produces bioactive compounds with a broad spectrum of activities. Streptomyces kebangsaanesis SUK12 has been identified as a novel endophytic bacteria isolated from ethnomedicinal plant Portulaca olerace, and was found to produce the phenazine class of biologically active antimicrobial metabolites. The potential use of the phenazines has led to our research interest in determining the genome sequence of Streptomyces kebangsaanensis SUK12. This Whole Genome Shotgun project has...

  20. 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....

  1. 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.

  2. SUPER-FOCUS: a tool for agile functional analysis of shotgun metagenomic data

    OpenAIRE

    Silva, Genivaldo Gueiros Z.; Green, Kevin T; Dutilh, Bas E; Edwards, Robert A

    2015-01-01

    Summary: Analyzing the functional profile of a microbial community from unannotated shotgun sequencing reads is one of the important goals in metagenomics. Functional profiling has valuable applications in biological research because it identifies the abundances of the functional genes of the organisms present in the original sample, answering the question what they can do. Currently, available tools do not scale well with increasing data volumes, which is important because both the number an...

  3. Shotgun Sequencing for Microsatellite Identification in Ilex paraguariensis (Aquifoliaceae)

    OpenAIRE

    Pereira, Marlei F.; Ciampi, Ana Y.; Inglis, Peter W.; Valderês A. Souza; Vânia C. R. Azevedo

    2013-01-01

    Premise of the study: Ilex paraguariensis is a native tree species from Brazil, Argentina, and Paraguay that is used in the production of beverages, medicines, and cosmetics. Primers flanking microsatellites were developed to investigate genetic parameters in the species. Methods and Results: Using microsatellites cloned from an I. paraguariensis shotgun genomic library, 25 pairs of primers were designed and synthesized. Levels of polymorphism were evaluated in 24 individuals from two pop...

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

    Science.gov (United States)

    Sternes, Peter R.; Lee, Danna; Kutyna, Dariusz R.

    2017-01-01

    Abstract 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. PMID:28595314

  5. 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.

  6. Large-scale 16S gene assembly using metagenomics shotgun sequences.

    Science.gov (United States)

    Zeng, Feng; Wang, Zicheng; Wang, Ying; Zhou, Jizhong; Chen, Ting

    2017-05-15

    Combining a 16S rRNA (16S) gene database with metagenomic shotgun sequences promises unbiased identification of known and novel microbes. To achieve this, we herein report reference-based ribosome assembly (RAMBL), a computational pipeline, which integrates taxonomic tree search and Dirichlet process clustering to reconstruct full-length 16S gene sequences from metagenomic sequencing data with high accuracy. By benchmarking against the synthetic and real shotgun sequences, we demonstrated that full-length 16S gene assemblies of RAMBL were a good proxy for known and putative microbes, including Candidate Phyla Radiation. We found that 30-40% of bacteria genera in the terrestrial and intestinal biomes have no closely related genome sequences. We also observed that RAMBL was able to generate a more accurate determination of environmental microbial diversity and yield better disease classification, suggesting that full-length 16S gene assemblies are a powerful alternative to marker gene set and 16S short reads. RAMBL first realizes the access to full-length 16S gene sequences in the near-terabase-scale metagenomic shotgun sequences, which markedly improve metagenomic data analysis and interpretation. RAMBL is available at https://github.com/homopolymer/RAMBL for academic use. zengfeng@xmu.edu.cn. Supplementary data are available at Bioinformatics online.

  7. In-depth proteomic analysis of boar spermatozoa through shotgun and gel-based methods.

    Science.gov (United States)

    Feugang, Jean M; Liao, Shengfa F; Willard, Scott T; Ryan, Peter L

    2018-01-18

    Mature spermatozoa contain numerous epididymal and seminal plasma proteins, which full identification through high-throughput technologies may allow for a better understanding of the sperm biology. Therefore, we conducted a global proteomic analysis of boar spermatozoa through shotgun and gel-based methodologies. The total proteins were extracted from mature spermatozoa and subjecsted to proteome analyses. Functional analyses of gene ontology representations and pathway enrichments were conducted on the shotgun dataset, followed by immunology and gene expression validations. Shotgun and gel-based approaches allowed the detection of 2728 proteins and 2123 spots, respectively. Approximately 38% and 59% of total proteins were respectively fully and partially annotated, and 3% were unknown. Gene ontology analysis indicated high proportions of proteins associated with intracellular and cytoplasm localizations, protein and nucleic acid binding, hydrolase and transferase activities, and cellular, metabolic, and regulation of biological processes. Proteins associated with phosphorylation processes and mitochondrial membranes, nucleic acid binding, and phosphate and phosphorous metabolics represented 77% of the dataset. Pathways associated with oxidative phosphorylation, citrate cycle, and extra-cellular matrix-receptor interaction were significantly enriched. Protein complex, intracellular organelle, cytoskeletal parts, fertilization and reproduction, and gap junction pathway were significantly enriched within the top 116 highly abundant proteins. Nine randomly selected protein candidates were confirmed with gel-based identification, immunofluorescence detection, and mRNA expression. This study offers an in-depth proteomic mapping of mature boar spermatozoa that will enable comparative and discovery research for the improvement of male fertility.

  8. A selective integrated tempering method.

    Science.gov (United States)

    Yang, Lijiang; Qin Gao, Yi

    2009-12-07

    In this paper, based on the integrated tempering sampling we introduce a selective integrated tempering sampling (SITS) method for the efficient conformation sampling and thermodynamics calculations for a subsystem in a large one, such as biomolecules solvated in aqueous solutions. By introducing a potential surface scaled with temperature, the sampling over the configuration space of interest (e.g., the solvated biomolecule) is selectively enhanced but the rest of the system (e.g., the solvent) stays largely unperturbed. The applications of this method to biomolecular systems allow highly efficient sampling over both energy and configuration spaces of interest. Comparing to the popular and powerful replica exchange molecular dynamics (REMD), the method presented in this paper is significantly more efficient in yielding relevant thermodynamics quantities (such as the potential of mean force for biomolecular conformational changes in aqueous solutions). It is more important that SITS but not REMD yielded results that are consistent with the traditional umbrella sampling free energy calculations when explicit solvent model is used since SITS avoids the sampling of the irrelevant phase space (such as the boiling water at high temperatures).

  9. Crenarchaeota and Euryarchaeota in temperate estuarine sediments.

    Science.gov (United States)

    Abreu, C; Jurgens, G; De Marco, P; Saano, A; Bordalo, A A

    2001-05-01

    Application of molecular techniques to ecological studies has unveiled a wide diversity of micro-organisms in natural communities, previously unknown to microbial ecologists. New lineages of Archaea were retrieved from several non-extreme environments, showing that these micro-organisms are present in a large variety of ecosystems. The aim was therefore to assess the presence and diversity of Archaea in the sediments of the river Douro estuary (Portugal), relating the results obtained to ecological data. Total DNA was extracted from sediment samples obtained from an estuary deprived of vegetation, amplified by PCR and the resulting DNA fragments cloned. The archaeal origin of the cloned inserts was checked by Southern blot, dot blot or colony blot hybridization. Recombinant plasmids were further analysed by restriction with AvaII and selected for sequencing. Phylogenetic analyses of 14 sequences revealed the presence of members of the domain Archaea. Most of the sequences could be assigned to the kingdom Crenarchaeota. Most of these sequences were closely related to those obtained from non-extreme Crenarchaeota members previously retrieved from diverse ecosystems, such as freshwater and marine environments. The presence of archaeal 16S rDNA sequences in temperate estuarine sediments emerges as a valuable contribution to the understanding of the complexity of the ecosystem.

  10. Temper Fragileness Study for RUL 2 Steel

    Directory of Open Access Journals (Sweden)

    Rodica Rădulea

    2007-10-01

    Full Text Available This paper presents an experimental study about the tenacity variation depending on the tempering temperature of the steel RUL2 grade, within q wide range of temperatures. By this analysis it is possible to study the cooling of the above mentioned heat treatment on the temper fragileness.

  11. Parallel tempering for the traveling salesman problem

    Energy Technology Data Exchange (ETDEWEB)

    Percus, Allon [Los Alamos National Laboratory; Wang, Richard [UCLA MATH DEPT; Hyman, Jeffrey [UCLA MATH DEPT; Caflisch, Russel [UCLA MATH DEPT

    2008-01-01

    We explore the potential of parallel tempering as a combinatorial optimization method, applying it to the traveling salesman problem. We compare simulation results of parallel tempering with a benchmark implementation of simulated annealing, and study how different choices of parameters affect the relative performance of the two methods. We find that a straightforward implementation of parallel tempering can outperform simulated annealing in several crucial respects. When parameters are chosen appropriately, both methods yield close approximation to the actual minimum distance for an instance with 200 nodes. However, parallel tempering yields more consistently accurate results when a series of independent simulations are performed. Our results suggest that parallel tempering might offer a simple but powerful alternative to simulated annealing for combinatorial optimization problems.

  12. 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

  13. Convergence, Consilience, and the Evolution of Temperate Deciduous Forests.

    Science.gov (United States)

    Edwards, Erika J; Chatelet, David S; Chen, Bo-Chang; Ong, Jin Yao; Tagane, Shuichiro; Kanemitsu, Hironobu; Tagawa, Kazuki; Teramoto, Kentaro; Park, Brian; Chung, Kuo-Fang; Hu, Jer-Ming; Yahara, Tetsukazu; Donoghue, Michael J

    2017-08-01

    The deciduous habit of northern temperate trees and shrubs provides one of the most obvious examples of convergent evolution, but how did it evolve? Hypotheses based on the fossil record posit that deciduousness evolved first in response to drought or darkness and preadapted certain lineages as cold climates spread. An alternative is that evergreens first established in freezing environments and later evolved the deciduous habit. We monitored phenological patterns of 20 species of Viburnum spanning tropical, lucidophyllous (subtropical montane and warm temperate), and cool temperate Asian forests. In lucidophyllous forests, all viburnums were evergreen plants that exhibited coordinated leaf flushes with the onset of the rainy season but varied greatly in the timing of leaf senescence. In contrast, deciduous species exhibited tight coordination of both flushing and senescence, and we found a perfect correlation between the deciduous habit and prolonged annual freezing. In contrast to previous stepwise hypotheses, a consilience of independent lines of evidence supports a lockstep model in which deciduousness evolved in situ, in parallel, and concurrent with a gradual cooling climate. A pervasive selective force combined with the elevated evolutionary accessibility of a particular response may explain the massive convergence of adaptive strategies that characterizes the world's biomes.

  14. 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.

  15. Screening currency notes for microbial pathogens and antibiotic resistance genes using a shotgun metagenomic approach.

    Directory of Open Access Journals (Sweden)

    Saakshi Jalali

    Full Text Available Fomites are a well-known source of microbial infections and previous studies have provided insights into the sojourning microbiome of fomites from various sources. Paper currency notes are one of the most commonly exchanged objects and its potential to transmit pathogenic organisms has been well recognized. Approaches to identify the microbiome associated with paper currency notes have been largely limited to culture dependent approaches. Subsequent studies portrayed the use of 16S ribosomal RNA based approaches which provided insights into the taxonomical distribution of the microbiome. However, recent techniques including shotgun sequencing provides resolution at gene level and enable estimation of their copy numbers in the metagenome. We investigated the microbiome of Indian paper currency notes using a shotgun metagenome sequencing approach. Metagenomic DNA isolated from samples of frequently circulated denominations of Indian currency notes were sequenced using Illumina Hiseq sequencer. Analysis of the data revealed presence of species belonging to both eukaryotic and prokaryotic genera. The taxonomic distribution at kingdom level revealed contigs mapping to eukaryota (70%, bacteria (9%, viruses and archae (~1%. We identified 78 pathogens including Staphylococcus aureus, Corynebacterium glutamicum, Enterococcus faecalis, and 75 cellulose degrading organisms including Acidothermus cellulolyticus, Cellulomonas flavigena and Ruminococcus albus. Additionally, 78 antibiotic resistance genes were identified and 18 of these were found in all the samples. Furthermore, six out of 78 pathogens harbored at least one of the 18 common antibiotic resistance genes. To the best of our knowledge, this is the first report of shotgun metagenome sequence dataset of paper currency notes, which can be useful for future applications including as bio-surveillance of exchangeable fomites for infectious agents.

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

    African Journals Online (AJOL)

    ... 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 temperature ...

  17. Whole-genome shotgun sequence of phenazine-producing endophytic Streptomyces kebangsaanensis SUK12

    Directory of Open Access Journals (Sweden)

    Juwairiah Remali

    2017-09-01

    Full Text Available Streptomyces sp. produces bioactive compounds with a broad spectrum of activities. Streptomyces kebangsaanesis SUK12 has been identified as a novel endophytic bacteria isolated from ethnomedicinal plant Portulaca olerace, and was found to produce the phenazine class of biologically active antimicrobial metabolites. The potential use of the phenazines has led to our research interest in determining the genome sequence of Streptomyces kebangsaanensis SUK12. This Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under the accession number PRJNA269542. The raw sequence data are available [https://www.ncbi.nlm.nih.gov/Traces/study/?acc=SRP105770].

  18. 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.

  19. An Optimized Shotgun Strategy for the Rapid Generation of Comprehensive Human Proteomes

    DEFF Research Database (Denmark)

    Bekker-Jensen, Dorte B; Kelstrup, Christian D; Batth, Tanveer S

    2017-01-01

    This study investigates the challenge of comprehensively cataloging the complete human proteome from a single-cell type using mass spectrometry (MS)-based shotgun proteomics. We modify a classical two-dimensional high-resolution reversed-phase peptide fractionation scheme and optimize a protocol......-coding genes). This depth is comparable with next-generation RNA sequencing and enables the identification of post-translational modifications, including ∼7,000 N-acetylation sites and ∼10,000 phosphorylation sites, without the need for enrichment. We further demonstrate the general applicability and clinical...

  20. Whole-genome shotgun sequence of phenazine-producing endophytic Streptomyces kebangsaanensis SUK12.

    Science.gov (United States)

    Remali, Juwairiah; Loke, Kok-Keong; Ng, Chyan Leong; Aizat, Wan Mohd; Tiong, John; Zin, Noraziah Mohamad

    2017-09-01

    Streptomyces sp. produces bioactive compounds with a broad spectrum of activities. Streptomyces kebangsaanesis SUK12 has been identified as a novel endophytic bacteria isolated from ethnomedicinal plant Portulaca olerace, and was found to produce the phenazine class of biologically active antimicrobial metabolites. The potential use of the phenazines has led to our research interest in determining the genome sequence of Streptomyces kebangsaanensis SUK12. This Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under the accession number PRJNA269542. The raw sequence data are available [https://www.ncbi.nlm.nih.gov/Traces/study/?acc=SRP105770].

  1. Whole genome shotgun sequence of Bacillus amyloliquefaciens TF28, a biocontrol entophytic bacterium.

    Science.gov (United States)

    Zhang, Shumei; Jiang, Wei; Li, Jing; Meng, Liqiang; Cao, Xu; Hu, Jihua; Liu, Yushuai; Chen, Jingyu; Sha, Changqing

    2016-01-01

    Bacillus amyloliquefaciens TF28 is a biocontrol endophytic bacterium that is capable of inhibition of a broad range of plant pathogenic fungi. The strain has the potential to be developed into a biocontrol agent for use in agriculture. Here we report the whole-genome shotgun sequence of the strain. The genome size of B. amyloliquefaciens TF28 is 3,987,635 bp which consists of 3754 protein-coding genes, 65 tandem repeat sequences, 47 minisatellite DNA, 2 microsatellite DNA, 63 tRNA, 7rRNA, 6 sRNA, 3 prophage and CRISPR domains.

  2. 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.

  3. A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome.

    Science.gov (United States)

    Chapman, Jarrod A; Mascher, Martin; Buluç, Aydın; Barry, Kerrie; Georganas, Evangelos; Session, Adam; Strnadova, Veronika; Jenkins, Jerry; Sehgal, Sunish; Oliker, Leonid; Schmutz, Jeremy; Yelick, Katherine A; Scholz, Uwe; Waugh, Robbie; Poland, Jesse A; Muehlbauer, Gary J; Stein, Nils; Rokhsar, Daniel S

    2015-01-31

    Polyploid species have long been thought to be recalcitrant to whole-genome assembly. By combining high-throughput sequencing, recent developments in parallel computing, and genetic mapping, we derive, de novo, a sequence assembly representing 9.1 Gbp of the highly repetitive 16 Gbp genome of hexaploid wheat, Triticum aestivum, and assign 7.1 Gb of this assembly to chromosomal locations. The genome representation and accuracy of our assembly is comparable or even exceeds that of a chromosome-by-chromosome shotgun assembly. Our assembly and mapping strategy uses only short read sequencing technology and is applicable to any species where it is possible to construct a mapping population.

  4. 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.

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

    Directory of Open Access Journals (Sweden)

    L. Henderson

    2006-12-01

    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.

  6. Comparison of sampling efficiency between simulated tempering and replica exchange

    OpenAIRE

    Zhang, Cheng; Ma, Jianpeng

    2008-01-01

    We compared the sampling efficiency of simulated tempering and replica exchange. Our results indicate that simulated tempering is superior to replica exchange if the parameters for temperature transition in simulated tempering are adjusted to be proportional to the partition function. It is shown that, in simulated tempering, the rate of traversing energy space of different temperatures is much higher than that in replica exchange, especially in the case of low tempering frequency and∕or larg...

  7. Comparison of sampling efficiency between simulated tempering and replica exchange.

    Science.gov (United States)

    Zhang, Cheng; Ma, Jianpeng

    2008-10-07

    We compared the sampling efficiency of simulated tempering and replica exchange. Our results indicate that simulated tempering is superior to replica exchange if the parameters for temperature transition in simulated tempering are adjusted to be proportional to the partition function. It is shown that, in simulated tempering, the rate of traversing energy space of different temperatures is much higher than that in replica exchange, especially in the case of low tempering frequency and/or larger temperature separations.

  8. A case of shotgun injury which occurred while an unconventional home security alarm system was being checked.

    Science.gov (United States)

    Asirdizer, Mahmut; Yavuz, Mehmet Sunay

    2009-11-20

    Installation of devices involving shotguns is rarely encountered in forensic medicine practice. In this case report, authors aimed to present an unusual and rare case of shotgun injury due to a home security alarm system and its legal assessment. An electrical technician was invited to a summer house to check a home security alarm system installed by another firm which he worked for previously. It was an unconventional home security alarm system attached to a shotgun. The technician was injured with 18 buckshot pellets (no: 4) while checking the system. The host was convicted of a possible intent to cause a life-threatening injury to the technician. We think that this verdict will set a precedent for similar cases.

  9. RiboTagger: fast and unbiased 16S/18S profiling using whole community shotgun metagenomic or metatranscriptome surveys.

    Science.gov (United States)

    Xie, Chao; Goi, Chin Lui Wesley; Huson, Daniel H; Little, Peter F R; Williams, Rohan B H

    2016-12-22

    Taxonomic profiling of microbial communities is often performed using small subunit ribosomal RNA (SSU) amplicon sequencing (16S or 18S), while environmental shotgun sequencing is often focused on functional analysis. Large shotgun datasets contain a significant number of SSU sequences and these can be exploited to perform an unbiased SSU--based taxonomic analysis. Here we present a new program called RiboTagger that identifies and extracts taxonomically informative ribotags located in a specified variable region of the SSU gene in a high-throughput fashion. RiboTagger permits fast recovery of SSU-RNA sequences from shotgun nucleic acid surveys of complex microbial communities. The program targets all three domains of life, exhibits high sensitivity and specificity and is substantially faster than comparable programs.

  10. An unusual exit wound as a result of a shotgun suicide to the head.

    Science.gov (United States)

    Kunz, S N

    2017-06-01

    The location of a gunshot entrance wound as well as the wound path trajectory are the main findings that help to determine the position from which a weapon was fired and thus distinguish firearm suicides from homicides and accidents. We present a case of a 28-year old man, who was found dead in his car. Because of an unusual position of the firearm, which was clamped into the steering wheel, and an unclear entrance/exit wound, an autopsy was performed. The deceased showed typical signs of a contact shotgun wound to the head with an entrance wound in the right temporal region and an exit wound in the midface. With the help of gunpowder attachments and a muzzle imprint at the entrance site, a wound channel from the right lower posterior part of the temporal region to the left anterior part of the mid-facial region could be reconstructed. The stellate wound in the midface was assessed as an atypical exit wound. The cause of death was a contact shotgun shot to the right temple with a consequent central regulatory failure due to extensive brain injury. The manner of death was concluded to be a suicide. Copyright © 2017 Elsevier B.V. All rights reserved.

  11. Evaluation of shotgun suicides in Konya, Turkey between 2000 and 2007.

    Science.gov (United States)

    Demirci, Serafettin; Dogan, Kamil Hakan; Deniz, Idris; Erkol, Zerrin

    2014-03-01

    The number of the suicides is increasing all around the world. In this study, the cases autopsied between 2000 and 2007 in The Konya Branch of Forensic Medicine Council were retrospectively investigated. Fifty-seven shotgun suicides were determined. The cases were evaluated in terms of their demographic characters, site of entrance wound, the type of the cartridge used, shooting distance, the place of incident, the place of death, motive for suicide, and the presence of previous suicide attempts. The most preferred site of entrance wound was the head with 34 cases (59.7%). Of 34 cases in which the entrance wound was on the head, there was indirect mandibular fracture in 16 cases (47.1%). In 11 cases (19.3%), there observed small ecchymosed abrasions on the finger surfaces, which are thought to have resulted from the trigger kicking back during triggering or the finger having been stuck between the trigger and the trigger guard. It is concluded that there is a need for a legal regulation that makes obtaining of shotguns more difficult and the people who have them are to be educated not to keep them in easily accessible places.

  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. Leveraging the complementary nature of RNA-Seq and shotgun proteomics data.

    Science.gov (United States)

    Wang, Xiaojing; Liu, Qi; Zhang, Bing

    2014-12-01

    RNA sequencing (RNA-Seq) and MS-based shotgun proteomics are powerful high-throughput technologies for identifying and quantifying RNA transcripts and proteins, respectively. With the increasing affordability of these technologies, many projects have started to apply both to the same samples to achieve a more comprehensive understanding of biological systems. A major analytical challenge for such integrative projects is how to effectively leverage the complementary nature of RNA-Seq and shotgun proteomics data. RNA-Seq provides comprehensive information on mRNA abundance, alternative splicing, nucleotide variation, and structure alteration. Sample-specific protein databases derived from RNA-Seq data can better approximate the real protein pools in cell and tissue samples and thus improve protein identification. Meanwhile, proteomics data provide essential confirmation of the validity and functional relevance of novel findings from RNA-Seq data. At the quantitative level, mRNA and protein levels are only modestly correlated, suggesting strong involvement of posttranscriptional regulation in controlling gene expression. Here, we review recent studies at the interface of RNA-Seq and proteomics data. We discuss goals, accomplishments, and challenges in RNA-Seq-based proteogenomics. We also examine the current status and future potential of parallel transcriptome and proteome quantification in revealing posttranscriptional regulatory mechanisms. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. Englacial Hydrology of Temperate Glaciers

    Science.gov (United States)

    Fountain, A. G.; Creyts, T. T.

    2015-12-01

    The englacial region of temperate glaciers is generally treated as a passive conveyor of water from the surface to the bed. Consequently, few studies have examined this region and relatively little is known. This is an important issue because englacial processes probably exert a first order control on the distribution of water to the subglacial hydraulic system. Controlling the water distribution probably controls the type of subglacial hydraulic features present and therefore sliding behavior. Certainly, englacial conduits play a major, if not primary, role in conveying water in the ablation zone. In regions of over-deepenings, areas highly crevassed, or in the accumulation zone, the importance of englacial conduits is less clear. Field studies have shown that intersecting englacial passageways in these regions are relatively common, implying that large water fluxes can drain efficiently through a network of fractures. Hypothetically, efficient drainage systems composed of englacial conduits develop in response to point input of large surface water fluxes. Where input is small and distributed, common to highly crevassed areas or the accumulation zone, water is probably routed through a network of englacial fractures. Glacier geometry may also play a role. Conduits may not develop in the over-deepened (closed basins) regions of a glacier requiring another flow pathway. That englacial fractures exist and can convey water presents a promising alternative. Measured rates of flow in fractures strongly suggest laminar conditions and a sufficient fracture density exists to accommodate the estimated water flux generated upstream by surface melt. The slow flow rates do not generate sufficient viscous heat to compensate expected rates of closure by freezing, however field observations and seismic evidence point to spontaneous fracture formation at depth that must regenerate the fracture network. It is unfortunate that englacial investigations are ignored in favor of

  15. Biotechnological efforts for preserving and enhancing temperate hardwood tree biodiversity, health, and productivity

    Science.gov (United States)

    Paula M. Pijut; Shaneka S. Lawson; Charles H. Michler

    2011-01-01

    Hardwood tree species in forest, plantation, and urban environments (temperate regions of the world) are important biological resources that play a significant role in the economy and the ecology of terrestrial ecosystems, and they have aesthetic and spiritual value. Because of these many values of hardwood tree species, preserving forest tree biodiversity through the...

  16. Landscape phenology of Wisconsin's temperate mixed forest

    Science.gov (United States)

    Liang, Liang

    This dissertation covers an intensive study of the landscape phenology of Wisconsin's temperate mixed forest. It endeavors to connect conventional plant phenology study back to its ecological complexity (from gardens/trees to the forest) and to compare field-observed phenology with remotely sensed phenology for regional to global monitoring/forecasting applications (from the forest to biomes). A new research perspective: landscape phenology (LP) is proposed in this dissertation. LP is defined as an approach to seasonal vegetation dynamics that integrates spatial patterns and temporal processes within heterogeneous environment across multiple scales. High density in situ observations, remote sensing data, and spatio-temporal analysis are employed for understanding patterns and processes within the complexity of seasonal landscape dynamics. In particular, bi-daily spring forest phenologies of multiple tree/shrub species and understory plants were observed using field protocols or digital photography; high-frequency micrometeorological measurements were used in tandem with LiDAR-based microtopography/canopy heights as well as soil condition data, to characterize microenvironments; and high-resolution, multi-temporal satellite images were employed to facilitate plant community delineation and landscape scaling. A hierarchical upscaling approach is introduced, aiming to integrate in situ phenological observations with the remotely sensed phenological measures. Primary results from this work include: a detailed account of spatio-temporal variations of spring plant phenology and their environmental drivers within a typical seasonal forest; thermal time (accumulated growing degree hours) driven linear phenological models for six forest species; a landscape-level phenological progression regime driven by antecedent weather fluctuations; a conceptual landscape phenology model that assigns phenological behaviors to levels of population, community, and ecosystem patch; and a

  17. 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.

  18. 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

  19. 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.

  20. 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.

  1. Autodeformation of Carburized Steel during Tempering

    Directory of Open Access Journals (Sweden)

    Regita BENDIKIENĖ

    2013-03-01

    Full Text Available The article analyses the results of autodeformation registered during tempering of carburized steel. Test pieces for the tests were carburized till the different depth in order to examine influence of depth of carburization on the deformation of steel during heat treatment operation. Carburization was performed on the one surface of test pieces seeking to analyze extent of acted normal stresses to autodeformation of steel. Different bending loads were applied for analyzed steel from 5 MPa to 100 MPa. Deflection of test pieces was analyzed. The obtained results proved that size and direction of deflection were affected by depth of carburization. Particular results of stretched and compressed surface examination showed different behavior of test pieces during tempering process. Test pieces, which undergo deformation at the beginning of martensitic transformation, after unloading bend further. When tempered test pieces with assimetrically carburized layer bend during hardening, its direction and extent of autodeformation depend on depth of carburization and tempering temperature. Kinetics of autodeformation (during tempering is affected by difference of volume changes in the carburized part and in the unaffected low carbon part of specimen, and similarly by decomposition of retained austenite in the carburized part.DOI: http://dx.doi.org/10.5755/j01.ms.19.1.3820

  2. 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

  3. ReAS: Recovery of ancestral sequences for transposable elements from the unassembled reads of a whole genome shotgun

    DEFF Research Database (Denmark)

    Li, Ruiqiang; Ye, Jia; Li, Songgang

    2005-01-01

    We describe an algorithm, ReAS, to recover ancestral sequences for transposable elements (TEs) from the unassembled reads of a whole genome shotgun. The main assumptions are that these TEs must exist at high copy numbers across the genome and must not be so old that they are no longer recognizable...

  4. Pigs in Sequence Space: A 0.66X Coverage Pig Genome Survey based on Shotgun Sequencing

    DEFF Research Database (Denmark)

    Wernersson, R; Schierup, Mikkel Heide; Jørgensen, Frank Grønlund

    2005-01-01

    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...

  5. 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...

  6. 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.

  7. NEW Fe-C-Mn-Si-Cr BEARING ALLOY: TEMPERING CURVES AND TEMPERED MARTENSITE EMBRITTLEMENT

    Directory of Open Access Journals (Sweden)

    José Benedito Marcomini

    2012-12-01

    Full Text Available SAE 52100 steel is not only used as a rolled raw material for bearing manufacturing but for building some rolling devices as well, such as guide rollers and straightener rollers. The purpose of this work is the characterization of a Fe-C-Mn-Si-Cr bearing alloy (SAE 52100 steel, modified with 1.74% Si by plotting the variation of quenched and tempered hardness curve (tempering curve and tempered martensite embrittlement susceptibility. The present application is based on the same idea as 300M steel regarding SAE 4340 steel. The effect of silicon on the kinetics of cementite precipitation leads to a rise in temperature of tempered martensite embrittlement. Quench and temper treatments were carried out and impact tests were performed with modified and commercial steels and the results were compared. Microstructure aspects are studied by scanning electron microscopy and x-ray diffraction analysis. The silicon alloyed steel presents great resistance to softening after tempering and no tempered martensite embrittlement.

  8. Hypohydration impairs endurance exercise performance in temperate but not cold air.

    Science.gov (United States)

    Cheuvront, Samuel N; Carter, Robert; Castellani, John W; Sawka, Michael N

    2005-11-01

    This study compared the effects of hypohydration (HYP) on endurance exercise performance in temperate and cold air environments. On four occasions, six men and two women (age = 24 +/- 6 yr, height = 170 +/- 6 cm, weight = 72.9 +/- 11.1 kg, peak O2 consumption = 48 +/- 9 ml.kg(-1).min(-1)) were exposed to 3 h of passive heat stress (45 degrees C) in the early morning with [euhydration (EUH)] or without (HYP; 3% body mass) fluid replacement. Later in the day, subjects sat in a cold (2 degrees C) or temperate (20 degrees C) environment with minimal clothing for 1 h before performing 30 min of cycle ergometry at 50% peak O2 consumption followed immediately by a 30-min performance time trial. Rectal and mean skin temperatures, heart rate, and ratings of perceived exertion measurements were made at regular intervals. Performance was assessed by the total amount of work (kJ) completed in the 30-min time trial. Skin temperature was significantly lower in the cold compared with the temperate trial, but there was no independent effect of hydration. Rectal temperature in both HYP trials was higher than EUH after 60 min of exercise, but the difference was only significant within the temperate trials (P EUH) and at 60 min within the cold trial (HYP > EUH) (P differences among trials. Total work performed during the 30-min time trial was not influenced by environment but was less (P stress per se does not.

  9. Shotgun Approach for Quantitative Imaging of Phospholipids Using Nanospray Desorption Electrospray Ionization Mass Spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Lanekoff, Ingela T.; Thomas, Mathew; Laskin, Julia

    2014-02-04

    Mass spectrometry imaging (MSI) has been extensively used for determining spatial distributions of molecules in biological samples, and there is increasing interest in using MSI for quantification. Nanospray desorption electrospray ionization, or nano-DESI, is an ambient MSI technique where a solvent is used for localized extraction of molecules followed by nanoelectrospray ionization. Doping the nano-DESI solvent with carefully selected standards enables online quantification during MSI experiments. In this proof-of-principle study, we demonstrate this quantification approach can be extended to provide shotgun-like quantification of phospholipids in thin brain tissue sections. Specifically, two phosphatidylcholine (PC) standards were added to the nano-DESI solvent for simultaneous imaging and quantification of 22 PC species observed in nano-DESI MSI. Furthermore, by combining the quantitative data obtained in the individual pixels, we demonstrate quantification of these PC species in seven different regions of a rat brain tissue section.

  10. A cross-validation scheme for machine learning algorithms in shotgun proteomics.

    Science.gov (United States)

    Granholm, Viktor; Noble, William Stafford; Käll, Lukas

    2012-01-01

    Peptides are routinely identified from mass spectrometry-based proteomics experiments by matching observed spectra to peptides derived from protein databases. The error rates of these identifications can be estimated by target-decoy analysis, which involves matching spectra to shuffled or reversed peptides. Besides estimating error rates, decoy searches can be used by semi-supervised machine learning algorithms to increase the number of confidently identified peptides. As for all machine learning algorithms, however, the results must be validated to avoid issues such as overfitting or biased learning, which would produce unreliable peptide identifications. Here, we discuss how the target-decoy method is employed in machine learning for shotgun proteomics, focusing on how the results can be validated by cross-validation, a frequently used validation scheme in machine learning. We also use simulated data to demonstrate the proposed cross-validation scheme's ability to detect overfitting.

  11. A cross-validation scheme for machine learning algorithms in shotgun proteomics

    Directory of Open Access Journals (Sweden)

    Granholm Viktor

    2012-11-01

    Full Text Available Abstract Peptides are routinely identified from mass spectrometry-based proteomics experiments by matching observed spectra to peptides derived from protein databases. The error rates of these identifications can be estimated by target-decoy analysis, which involves matching spectra to shuffled or reversed peptides. Besides estimating error rates, decoy searches can be used by semi-supervised machine learning algorithms to increase the number of confidently identified peptides. As for all machine learning algorithms, however, the results must be validated to avoid issues such as overfitting or biased learning, which would produce unreliable peptide identifications. Here, we discuss how the target-decoy method is employed in machine learning for shotgun proteomics, focusing on how the results can be validated by cross-validation, a frequently used validation scheme in machine learning. We also use simulated data to demonstrate the proposed cross-validation scheme's ability to detect overfitting.

  12. 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

  13. Polymorphic Microsatellite Loci for Virola sebifera (Myristicaceae Derived from Shotgun 454 Pyrosequencing

    Directory of Open Access Journals (Sweden)

    Na Wei

    2013-04-01

    Full Text Available Premise of the study: Polymorphic microsatellite loci were characterized in the dioecious neotropical rainforest tree Virola sebifera. The markers will be used to study ecological and genetic impacts of hunting and landscape change in this vertebrate-dispersed, insect-pollinated tree species. Methods and Results: Simple sequence repeat (SSR markers were screened from genomic libraries of South American V. sebifera obtained by shotgun 454 pyrosequencing. Primer pairs were tested on Panamanian samples (N = 42. Approximately 52% of the 61 tested SSR markers amplified, and 16% were polymorphic. Ten selected polymorphic SSR loci contained seven to 15 alleles per locus, and polymorphic information content averaged 0.694. Observed heterozygosity ranged from 0.465 to 0.905, and expected heterozygosity was between 0.477 and 0.876. Conclusions: The 10 polymorphic loci will be useful in studying gene flow and genetic structure at local and regional spatial scales in V. sebifera.

  14. Extracellular protein analysis of activated sludge and their functions in wastewater treatment plant by shotgun proteomics.

    Science.gov (United States)

    Zhang, Peng; Shen, Yu; Guo, Jin-Song; Li, Chun; Wang, Han; Chen, You-Peng; Yan, Peng; Yang, Ji-Xiang; Fang, Fang

    2015-07-10

    In this work, proteins in extracellular polymeric substances extracted from anaerobic, anoxic and aerobic sludges of wastewater treatment plant (WWTP) were analyzed to probe their origins and functions. Extracellular proteins in WWTP sludges were identified using shotgun proteomics, and 130, 108 and 114 proteins in anaerobic, anoxic and aerobic samples were classified, respectively. Most proteins originated from cell and cell part, and their most major molecular functions were catalytic activity and binding activity. The results exhibited that the main roles of extracellular proteins in activated sludges were multivalence cations and organic molecules binding, as well as in catalysis and degradation. The catalytic activity proteins were more widespread in anaerobic sludge compared with those in anoxic and aerobic sludges. The structure difference between anaerobic and aerobic sludges could be associated with their catalytic activities proteins. The results also put forward a relation between the macro characteristics of activated sludges and micro functions of extracellular proteins in biological wastewater treatment process.

  15. Noninvasive diagnosis of fetal aneuploidy by shotgun sequencing DNA from maternal blood

    Science.gov (United States)

    Fan, H. Christina; Blumenfeld, Yair J.; Chitkara, Usha; Hudgins, Louanne; Quake, Stephen R.

    2008-01-01

    We directly sequenced cell-free DNA with high-throughput shotgun sequencing technology from plasma of pregnant women, obtaining, on average, 5 million sequence tags per patient sample. This enabled us to measure the over- and underrepresentation of chromosomes from an aneuploid fetus. The sequencing approach is polymorphism-independent and therefore universally applicable for the noninvasive detection of fetal aneuploidy. Using this method, we successfully identified all nine cases of trisomy 21 (Down syndrome), two cases of trisomy 18 (Edward syndrome), and one case of trisomy 13 (Patau syndrome) in a cohort of 18 normal and aneuploid pregnancies; trisomy was detected at gestational ages as early as the 14th week. Direct sequencing also allowed us to study the characteristics of cell-free plasma DNA, and we found evidence that this DNA is enriched for sequences from nucleosomes. PMID:18838674

  16. Noninvasive diagnosis of fetal aneuploidy by shotgun sequencing DNA from maternal blood.

    Science.gov (United States)

    Fan, H Christina; Blumenfeld, Yair J; Chitkara, Usha; Hudgins, Louanne; Quake, Stephen R

    2008-10-21

    We directly sequenced cell-free DNA with high-throughput shotgun sequencing technology from plasma of pregnant women, obtaining, on average, 5 million sequence tags per patient sample. This enabled us to measure the over- and underrepresentation of chromosomes from an aneuploid fetus. The sequencing approach is polymorphism-independent and therefore universally applicable for the noninvasive detection of fetal aneuploidy. Using this method, we successfully identified all nine cases of trisomy 21 (Down syndrome), two cases of trisomy 18 (Edward syndrome), and one case of trisomy 13 (Patau syndrome) in a cohort of 18 normal and aneuploid pregnancies; trisomy was detected at gestational ages as early as the 14th week. Direct sequencing also allowed us to study the characteristics of cell-free plasma DNA, and we found evidence that this DNA is enriched for sequences from nucleosomes.

  17. What computational non-targeted mass spectrometry-based metabolomics can gain from shotgun proteomics.

    Science.gov (United States)

    Hamzeiy, Hamid; Cox, Jürgen

    2017-02-01

    Computational workflows for mass spectrometry-based shotgun proteomics and untargeted metabolomics share many steps. Despite the similarities, untargeted metabolomics is lagging behind in terms of reliable fully automated quantitative data analysis. We argue that metabolomics will strongly benefit from the adaptation of successful automated proteomics workflows to metabolomics. MaxQuant is a popular platform for proteomics data analysis and is widely considered to be superior in achieving high precursor mass accuracies through advanced nonlinear recalibration, usually leading to five to ten-fold better accuracy in complex LC-MS/MS runs. This translates to a sharp decrease in the number of peptide candidates per measured feature, thereby strongly improving the coverage of identified peptides. We argue that similar strategies can be applied to untargeted metabolomics, leading to equivalent improvements in metabolite identification. Copyright © 2016 The Author(s). Published by Elsevier Ltd.. All rights reserved.

  18. Large pore dermal microdialysis and liquid chromatography-tandem mass spectroscopy shotgun proteomic analysis

    DEFF Research Database (Denmark)

    Petersen, Lars J; Sørensen, Mette A; Codrea, Marius C

    2013-01-01

    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. ResultsResults showed variation in protein amounts and profiles for each...... of the different sampling phases. The total protein concentration was 1.7, 0.6, and 1.3mg/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...

  19. A Transnational Temperance Discourse? William Wells Brown, Creole Civilization, and Temperate Manners

    Directory of Open Access Journals (Sweden)

    Carole Lynn Stewart

    2011-03-01

    Full Text Available

    In the nineteenth century, temperance movements provided the occasion for a transnational discourse. These conversations possessed an intensity throughout Britain and the United States. In America temperance often became associated with strongly nationalistic Euro-American forms of identity and internal purity. Nonetheless, African American reformers and abolitionists bound themselves to temperance ideals in forming civil societies that would heal persons and provide communal modes of democratic freedom in the aftermath and recovery from chattel slavery. This paper explores the possibilities of temperance as a transnational discourse by considering its meaning in the life and work of the African American author and activist, William Wells Brown. Brown expressed a “creole civilization” that employed the stylistics of the trickster as a unique mode of restraint that revealed a peculiar power of passivity that was able to claim efficacy over one’s life and community. This meaning of temperance diverges from and dovetails with certain European meanings of civilization that were being forged in the nineteenth century. Brown was in conversation with temperance reformers in America, Britain, and Europe. He imagined the possible meaning of temperance in African, Egyptian, Christian, and Islamic civilizations. He speculated upon the possibility of temperance as a defining characteristic of a transnational civilization and culture that would provide spaces for the expression of democratic freedom. Brown reimagined temperance as a form of corporeal restraint that offered a direct and sacred relation to the land, space, people that appeared in between an ethnic nationalist ethos and the European imperialistic civilization.

  20. Multisystem altruistic metadynamics—Well-tempered variant

    Science.gov (United States)

    Hošek, Petr; Kříž, Pavel; Toulcová, Daniela; Spiwok, Vojtěch

    2017-03-01

    Metadynamics method has been widely used to enhance sampling in molecular simulations. Its original form suffers two major drawbacks, poor convergence in complex (especially biomolecular) systems and its serial nature. The first drawback has been addressed by introduction of a convergent variant known as well-tempered metadynamics. The second was addressed by introduction of a parallel multisystem metadynamics referred to as altruistic metadynamics. Here, we combine both approaches into well-tempered altruistic metadynamics. We provide mathematical arguments and trial simulations to show that it accurately predicts free energy surfaces.

  1. Multisystem altruistic metadynamics-Well-tempered variant.

    Science.gov (United States)

    Hošek, Petr; Kříž, Pavel; Toulcová, Daniela; Spiwok, Vojtěch

    2017-03-28

    Metadynamics method has been widely used to enhance sampling in molecular simulations. Its original form suffers two major drawbacks, poor convergence in complex (especially biomolecular) systems and its serial nature. The first drawback has been addressed by introduction of a convergent variant known as well-tempered metadynamics. The second was addressed by introduction of a parallel multisystem metadynamics referred to as altruistic metadynamics. Here, we combine both approaches into well-tempered altruistic metadynamics. We provide mathematical arguments and trial simulations to show that it accurately predicts free energy surfaces.

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

    Science.gov (United States)

    Jensen, Sara Munk; Brandl, Martin; Treusch, Alexander H; Ejsing, Christer S

    2015-03-01

    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 to characterize, for the first time, the lipid complement of the archaeon Sulfolobus islandicus. To support the identification of lipids in S. islandicus, we first compiled a database of ether lipid species previously ascribed to Archaea. Next, we analyzed the lipid complement of S. islandicus by high-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 before. This uncharacterized lipid species features two head group structures composed of a trisaccharide residue carrying an uncommon sulfono group (-SO3) and an inositol phosphate group. Both head groups are linked to a glycerol dialkyl glycerol tetraether core structure having isoprenoid chains with a total of 80 carbon atoms and 4 cyclopentane moieties. The shotgun lipidomics approach deployed here defines a novel workflow for exploratory lipid profiling of Archaea. Copyright © 2015 John Wiley & Sons, Ltd.

  3. Warm-temperate deciduous forests around the Northern Hemisphere

    National Research Council Canada - National Science Library

    Box E.O; Fujiwara K

    2015-01-01

    Warm-temperate deciduous forests are "southern", mainly oak-dominated deciduous forests, as found over the warmer southern parts of the temperate deciduous forest regions of East Asia, Europe and eastern North America...

  4. 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…

  5. Simulation of quenching and tempering of steels

    Science.gov (United States)

    Jin, Long

    An efficient simulation method, which includes microstructure, temperature and stress analysis applicable to both quenching and tempering processes, is developed and implemented using the commercial FEM package ABAQUS. This simulation encompasses phase transformations and their effects on the temperature distribution and stress/strain evolution, including the dependency of material properties on temperature and microstructure, transformation strains, latent heats and transformation plasticity. Three different multi-phase constitutive models, namely the average property model, the Voigt model and the Reuss model, have been implemented. The average property model is based on the linear mixture of material properties of different phase, while the Voigt model assumes the same strain field in all phases and the Reuss model assumes the iso-stress field. The simulation model has been applied to quenching and tempering of modified 4320 steel. Experiments of tempering and quenching on carburized circular plates of the same steel have been performed. The calculated distortion and residual stress profiles are in good agreement with corresponding measurements made in experiments and thus verifies the correctness of the model. The simulation model developed in this study is a useful design tool for quenching and tempering as well as machining of steels.

  6. 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.

  7. Patterns of genetic connectivity in invertebrates of temperate MPA networks

    Directory of Open Access Journals (Sweden)

    Patricia Marti-Puig

    2013-11-01

    Full Text Available Temperate reefs are among the most threatened marine habitats due to impacts caused by high density of human settlements, coastal development, pollution, fisheries and tourism. Networks of marine protected areas (MPAs are an important tool for ensuring long-term health and conservation of ecological processes in the marine environment. Design of the MPA network has to be based on deep understanding of spatial patterns of species distribution, and on the make-up of connectivity among populations. Most benthic invertebrates are sessile and/or sedentary in the adult phase, and their dispersal relies mainly on the gametes and/or larval behaviours. Genetic markers allow us to quantify gene flow and structuring among populations, and to infer patterns of genetic connectivity. Based on the information available in the peer reviewed literature on genetic connectivity in benthic invertebrates of temperate MPAs, we provide a comment about the gaps and the needs. Moreover, we propose a rationale to plan and optimise future studies on this topic. A conceptual framework for planning effective studies on genetic connectivity in an MPAs network is provided, including general recommendations on sampling design, key species and molecular markers to use.

  8. 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

  9. A shotgun antisense approach to the identification of novel essential genes in Pseudomonas aeruginosa.

    Science.gov (United States)

    Rusmini, Ruggero; Vecchietti, Davide; Macchi, Raffaella; Vidal-Aroca, Faustino; Bertoni, Giovanni

    2014-02-05

    Antibiotics in current use target a surprisingly small number of cellular functions: cell wall, DNA, RNA, and protein biosynthesis. Targeting of novel essential pathways is expected to play an important role in the discovery of new antibacterial agents against bacterial pathogens, such as Pseudomonas aeruginosa, that are difficult to control because of their ability to develop resistance, often multiple, to all current classes of clinical antibiotics. We aimed to identify novel essential genes in P. aeruginosa by shotgun antisense screening. This technique was developed in Staphylococcus aureus and, following a period of limited success in Gram-negative bacteria, has recently been used effectively in Escherichia coli. To also target low expressed essential genes, we included some variant steps that were expected to overcome the non-stringent regulation of the promoter carried by the expression vector used for the shotgun antisense libraries. Our antisense screenings identified 33 growth-impairing single-locus genomic inserts that allowed us to generate a list of 28 "essential-for-growth" genes: five were "classical" essential genes involved in DNA replication, transcription, translation, and cell division; seven were already reported as essential in other bacteria; and 16 were "novel" essential genes with no homologs reported to have an essential role in other bacterial species. Interestingly, the essential genes in our panel were suggested to take part in a broader range of cellular functions than those currently targeted by extant antibiotics, namely protein secretion, biosynthesis of cofactors, prosthetic groups and carriers, energy metabolism, central intermediary metabolism, transport of small molecules, translation, post-translational modification, non-ribosomal peptide synthesis, lipopolysaccharide synthesis/modification, and transcription regulation. This study also identified 43 growth-impairing inserts carrying multiple loci targeting 105 genes, of which

  10. Chemical Derivatization and Ultrahigh Resolution and Accurate Mass Spectrometry Strategies for "Shotgun" Lipidome Analysis.

    Science.gov (United States)

    Ryan, Eileen; Reid, Gavin E

    2016-09-20

    Lipids play critical structural and functional roles in the regulation of cellular homeostasis, and it is increasingly recognized that the disruption of lipid metabolism or signaling or both is associated with the onset and progression of certain metabolically linked diseases. As a result, the field of lipidomics has emerged to comprehensively identify and structurally characterize the diverse range of lipid species within a sample of interest and to quantitatively monitor their abundances under different physiological or pathological conditions. Mass spectrometry (MS) has become a critical enabling platform technology for lipidomic researchers. However, the presence of isobaric (i.e., same nominal mass) and isomeric (i.e., same exact mass) lipids within complex lipid extracts means that MS-based identification and quantification of individual lipid species remains a significant analytical challenge. Ultrahigh resolution and accurate mass spectrometry (UHRAMS) offers a convenient solution to the isobaric mass overlap problem, while a range of chromatographic separation, differential extraction, intrasource separation and selective ionization methods, or tandem mass spectrometry (MS/MS) strategies may be used to address some types of isomeric mass lipid overlaps. Alternatively, chemical derivatization strategies represent a more recent approach for the separation of lipids within complex mixtures, including for isomeric lipids. In this Account, we highlight the key components of a lipidomics workflow developed in our laboratory, whereby certain lipid classes or subclasses, namely, aminophospholipids and O-alk-1'-enyl (i.e., plasmalogen) ether-containing lipids, are shifted in mass following sequential functional group selective chemical derivatization reactions prior to "shotgun" nano-ESI-UHRAMS analysis, "targeted" MS/MS, and automated database searching. This combined derivatization and UHRAMS approach resolves both isobaric mass lipids and certain categories of

  11. Blood from a turnip: tissue origin of low-coverage shotgun sequencing libraries affects recovery of mitogenome sequences

    Science.gov (United States)

    Barker, F. Keith; Oyler-McCance, Sara; Tomback, Diana F.

    2015-01-01

    Next generation sequencing methods allow rapid, economical accumulation of data that have many applications, even at relatively low levels of genome coverage. However, the utility of shotgun sequencing data sets for specific goals may vary depending on the biological nature of the samples sequenced. We show that the ability to assemble mitogenomes from three avian samples of two different tissue types varies widely. In particular, data with coverage typical of microsatellite development efforts (∼1×) from DNA extracted from avian blood failed to cover even 50% of the mitogenome, relative to at least 500-fold coverage from muscle-derived data. Researchers should consider possible applications of their data and select the tissue source for their work accordingly. Practitioners analyzing low-coverage shotgun sequencing data (including for microsatellite locus development) should consider the potential benefits of mitogenome assembly, including internal barcode verification of species identity, mitochondrial primer development, and phylogenetics.

  12. A shotgun metagenomic method to characterise low abundant species and assign precisely taxonomy in complex microbial ecosystems

    OpenAIRE

    Abraham, Anne-Laure; Almeida, Mathieu; Pons, Nicolas; Pauvert, Charlie; Schbath, Sophie; Renault, Pierre

    2014-01-01

    A first step for a better understanding of complex microbial ecosystems, such as cheese or human gut microbiota, is the characterisation and quantification of their species composition. Once DNA is extracted from samples, two main techniques are usually used: the sequencing of evolutionary conserved genes, such as those coding for the 16S or 18S RNA or ITS, or whole genome shotgun sequencing. The first approach is widely used and provides a rapid view of the ecosystem, but often fails to prov...

  13. Shotgun Proteomic Analysis of Plasma from Dairy Cattle Suffering from Footrot: Characterization of Potential Disease-Associated Factors

    OpenAIRE

    Dongbo Sun; Hong Zhang; Donghua Guo; Anguo Sun; Hongbin Wang

    2013-01-01

    The plasma proteome of healthy dairy cattle and those with footrot was investigated using a shotgun LC-MS/MS approach. In total, 648 proteins were identified in healthy plasma samples, of which 234 were non-redundant proteins and 123 were high-confidence proteins; 712 proteins were identified from footrot plasma samples, of which 272 were non-redundant proteins and 138 were high-confidence proteins. The high-confidence proteins showed significant differences between healthy and footrot plasma...

  14. Cloning human fetal gamma globin and mouse alpha-type globin DNA: preparation and screening of shotgun collections.

    Science.gov (United States)

    Blattner, F R; Blechl, A E; Denniston-Thompson, K; Faber, H E; Richards, J E; Slightom, J L; Tucker, P W; Smithies, O

    1978-12-22

    Shotgun collections of Charon 3A bacteriophages containing Eco RI fragments of human and mouse DNA were constructed with the use of in vitro packaging. Plaques were screened by hybridization, and globin-specific clones were isolated from both human (Charon 3AHs51.1) and mouse (Charon 3AMm30.5). The fragments cloned were detected in unfractionated genomic DNA by the Southern method of hybridization.

  15. 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.

  16. Shotgun lipidomics in substantiating lipid peroxidation in redox biology: Methods and applications.

    Science.gov (United States)

    Hu, Changfeng; Wang, Miao; Han, Xianlin

    2017-08-01

    Multi-dimensional mass spectrometry-based shotgun lipidomics (MDMS-SL) has made profound advances for comprehensive analysis of cellular lipids. It represents one of the most powerful tools in analyzing lipids directly from lipid extracts of biological samples. It enables the analysis of nearly 50 lipid classes and thousands of individual lipid species with high accuracy/precision. The redox imbalance causes oxidative stress, resulting in lipid peroxidation, and alterations in lipid metabolism and homeostasis. Some lipid classes such as oxidized fatty acids, 4-hydroxyalkenal species, and plasmalogen are sensitive to oxidative stress or generated corresponding to redox imbalance. Therefore, accurate assessment of these lipid classes can provide not only the redox states, but also molecular insights into the pathogenesis of diseases. This review focuses on the advances of MDMS-SL in analysis of these lipid classes and molecular species, and summarizes their recent representative applications in biomedical/biological research. We believe that MDMS-SL can make great contributions to redox biology through substantiating the aberrant lipid metabolism, signaling, trafficking, and homeostasis under oxidative stress-related condition. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

  17. Shotgun proteomics of Xanthobacter autotrophicus Py2 reveals proteins specific to growth on propylene.

    Science.gov (United States)

    Broberg, Christopher A; Clark, Daniel D

    2010-11-01

    Coenzyme M (CoM, 2-mercaptoethanesulfonate), once thought to be exclusively produced by methanogens, is now known to be the central cofactor in the metabolism of short-chain alkenes by a variety of aerobic bacteria. There is little evidence to suggest how, and under what conditions, CoM is biosynthesized by these organisms. A shotgun proteomics approach was used to investigate CoM-dependent propylene metabolism in the Gram-negative bacterium Xanthobacter autotrophicus Py2. Cells were grown on either glucose or propylene, and the soluble proteomes were analyzed. An average of 395 proteins was identified from glucose-grown replicates, with an average of 419 identified from propylene-grown replicates. A number of linear megaplasmid (pXAUT01)-encoded proteins were found to be specifically produced by growth on propylene. These included all known to be crucial to propylene metabolism, in addition to an aldehyde dehydrogenase, a DNA-binding protein, and five putative CoM biosynthetic enzymes. This work has provided fresh insight into bacterial alkene metabolism and has generated new targets for future studies in X. autotrophicus Py2 and related CoM-dependent alkene-oxidizing bacteria.

  18. Shotgun proteomic analysis of the Mexican lime tree infected with "CandidatusPhytoplasma aurantifolia".

    Science.gov (United States)

    Monavarfeshani, Aboozar; Mirzaei, Mehdi; Sarhadi, Elham; Amirkhani, Ardeshir; Khayam Nekouei, Mojtaba; Haynes, Paul A; Mardi, Mohsen; Salekdeh, Ghasem Hosseini

    2013-02-01

    Infection of Mexican lime trees (Citrus aurantifolia L.) with the specialized bacterium "CandidatusPhytoplasma aurantifolia" causes witches' broom disease. Witches' broom disease has the potential to cause significant economic losses throughout western Asia and North Africa. We used label-free quantitative shotgun proteomics to study changes in the proteome of Mexican lime trees in response to infection by "Ca. Phytoplasma aurantifolia". Of 990 proteins present in five replicates of healthy and infected plants, the abundances of 448 proteins changed significantly in response to phytoplasma infection. Of these, 274 proteins were less abundant in infected plants than in healthy plants, and 174 proteins were more abundant in infected plants than in healthy plants. These 448 proteins were involved in stress response, metabolism, growth and development, signal transduction, photosynthesis, cell cycle, and cell wall organization. Our results suggest that proteomic changes in response to infection by phytoplasmas might support phytoplasma nutrition by promoting alterations in the host's sugar metabolism, cell wall biosynthesis, and expression of defense-related proteins. Regulation of defense-related pathways suggests that defense compounds are induced in interactions with susceptible as well as resistant hosts, with the main differences between the two interactions being the speed and intensity of the response.

  19. Microsatellite Primers for the Fungi Rhizopogon kretzerae and R. salebrosus (Rhizopogonaceae from 454 Shotgun Pyrosequencing

    Directory of Open Access Journals (Sweden)

    Lisa C. Grubisha

    2014-07-01

    Full Text Available Premise of the study: Rhizopogon kretzerae and R. salebrosus (Rhizopogonaceae are ectomycorrhizal fungi symbiotic with pines and the mycoheterotrophic plant Pterospora andromedea (Ericaceae. Microsatellite loci will allow population genetic study of fungal hosts to P. andromedea. Methods and Results: Shotgun pyrosequencing of R. kretzerae DNA resulted in primer development of 23 perfect microsatellite loci and screened across two populations each for R. kretzerae and R. salebrosus. Twelve loci were polymorphic in R. kretzerae populations, and 11 loci cross-amplified in R. salebrosus populations. For R. kretzerae and R. salebrosus, number of alleles was one to eight and one to nine, respectively, and observed heterozygosity ranged from 0.00–0.57 and 0.00–0.70, respectively. Conclusions: These are the first microsatellite loci developed for any species within Rhizopogon subgenus Amylopogon. These microsatellite loci will be used in conservation genetic studies of rare to endangered eastern populations and to compare plant and fungal population genetic structure at different hierarchical levels.

  20. 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).

  1. 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.

  2. Use of whole genome shotgun metagenomics: a practical guide for the microbiome-minded physician scientist.

    Science.gov (United States)

    Ma, Jun; Prince, Amanda; Aagaard, Kjersti M

    2014-01-01

    Whole genome shotgun sequencing (WGS) has been increasingly recognized as the most comprehensive and robust approach for metagenomics research. When compared with 16S-based metagenomics, it offers the advantage of identification of species level taxonomy and the estimation of metabolic pathway activities from human and environmental samples. Several large-scale metagenomic projects have been recently conducted or are currently underway utilizing WGS. With the generation of vast amounts of data, the bioinformatics and computational analysis of WGS results become vital for the success of a metagenomics study. However, each step in the WGS data analysis, including metagenome assembly, gene prediction, taxonomy identification, function annotation, and pathway analysis, is complicated by the shear amount of data. Algorithms and tools have been developed specifically to handle WGS-generated metagenomics data with the hope of reducing the requirement on computational time and storage space. Here, we present an overview of the current state of metagenomics through WGS sequencing, challenges frequently encountered, and up-to-date solutions. Several applications that are uniquely applicable to microbiome studies in reproductive and perinatal medicine are also discussed. Thieme Medical Publishers 333 Seventh Avenue, New York, NY 10001, USA.

  3. Genome skimming by shotgun sequencing helps resolve the phylogeny of a pantropical tree family.

    Science.gov (United States)

    Malé, Pierre-Jean G; Bardon, Léa; Besnard, Guillaume; Coissac, Eric; Delsuc, Frédéric; Engel, Julien; Lhuillier, Emeline; Scotti-Saintagne, Caroline; Tinaut, Alexandra; Chave, Jérôme

    2014-09-01

    Whole genome sequencing is helping generate robust phylogenetic hypotheses for a range of taxonomic groups that were previously recalcitrant to classical molecular phylogenetic approaches. As a case study, we performed a shallow shotgun sequencing of eight species in the tropical tree family Chrysobalanaceae to retrieve large fragments of high-copy number DNA regions and test the potential of these regions for phylogeny reconstruction. We were able to assemble the nuclear ribosomal cluster (nrDNA), the complete plastid genome (ptDNA) and a large fraction of the mitochondrial genome (mtDNA) with approximately 1000×, 450× and 120× sequencing depth respectively. The phylogenetic tree obtained with ptDNA resolved five of the seven internal nodes. In contrast, the tree obtained with mtDNA and nrDNA data were largely unresolved. This study demonstrates that genome skimming is a cost-effective approach and shows potential in plant molecular systematics within Chrysobalanaceae and other under-studied groups. © 2014 John Wiley & Sons Ltd.

  4. Quantitative Shotgun Proteomics Analysis of Rice Anther Proteins after Exposure to High Temperature

    Directory of Open Access Journals (Sweden)

    Mijeong Kim

    2015-01-01

    Full Text Available In rice, the stage of development most sensitive to high temperature stress is flowering, and exposure at this stage can result in spikelet sterility, thereby leading to significant yield losses. In this study, protein expression patterns of rice anthers from Dianxi4, a high temperature tolerant Japonica rice variety, were compared between samples exposed to high temperature and those grown in natural field conditions in Korea. Shotgun proteomics analysis of three replicate control and high-temperature-treated samples identified 3,266 nonredundant rice anther proteins (false discovery rate < 0.01. We found that high levels of ATP synthase, cupin domain-containing proteins, and pollen allergen proteins were present in rice anthers. Comparative analyses of 1,944 reproducibly expressed proteins identified 139 differentially expressed proteins, with 95 increased and 44 decreased in response to high temperature conditions. Heat shock, DnaK family, and chaperone proteins showed highly increased expression, suggesting that the high temperature tolerance of Dianxi4 is achieved by stabilization of proteins in pollen cells. Trehalose synthase was also highly increased after heat treatment, suggesting a possible role for trehalose in preventing protein denaturation through desiccation.

  5. 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.

  6. A Colorimetric Method for Monitoring Tryptic Digestion Prior to Shotgun Proteomics

    Science.gov (United States)

    Somiari, Richard I.; Renganathan, Kutralanathan; Wolfe, Steven; Somiari, Stella B.

    2014-01-01

    Tryptic digestion is an important preanalytical step in shotgun proteomics because inadequate or excessive digestion can result in a failed or incomplete experiment. Unfortunately, this step is not routinely monitored before mass spectrometry because methods available for protein digestion monitoring either are time/sample consuming or require expensive equipment. To determine if a colorimetric method (ProDM Kit) can be used to identify the extent of tryptic digestion that yields the best proteomics outcome, plasma and serum digested for 8 h and 24 h were screened with ProDM, Bioanalyzer, and LC/MS/MS, and the effect of digestion on the number of proteins identified and sequence coverage was compared. About 6% and 16% less proteins were identified when >50% of proteins were digested in plasma and serum, respectively, compared to when ~46% of proteins were digested. Average sequence coverage for albumin, haptoglobin, and serotransferrin after 2 h, 8 h, and 24 h digestion was 52%, 45%, and 45% for serum and 54%, 47%, and 42% for plasma, respectively. This paper reiterates the importance of optimizing the tryptic digestion step and demonstrates the extent to which ProDM can be used to monitor and standardize protein digestion to achieve better proteomics outcomes. PMID:24678421

  7. Bayesian Nonparametric Model for the Validation of Peptide Identification in Shotgun Proteomics*S⃞

    Science.gov (United States)

    Zhang, Jiyang; Ma, Jie; Dou, Lei; Wu, Songfeng; Qian, Xiaohong; Xie, Hongwei; Zhu, Yunping; He, Fuchu

    2009-01-01

    Tandem mass spectrometry combined with database searching allows high throughput identification of peptides in shotgun proteomics. However, validating database search results, a problem with a lot of solutions proposed, is still advancing in some aspects, such as the sensitivity, specificity, and generalizability of the validation algorithms. Here a Bayesian nonparametric (BNP) model for the validation of database search results was developed that incorporates several popular techniques in statistical learning, including the compression of feature space with a linear discriminant function, the flexible nonparametric probability density function estimation for the variable probability structure in complex problem, and the Bayesian method to calculate the posterior probability. Importantly the BNP model is compatible with the popular target-decoy database search strategy naturally. We tested the BNP model on standard proteins and real, complex sample data sets from multiple MS platforms and compared it with PeptideProphet, the cutoff-based method, and a simple nonparametric method (proposed by us previously). The performance of the BNP model was shown to be superior for all data sets searched on sensitivity and generalizability. Some high quality matches that had been filtered out by other methods were detected and assigned with high probability by the BNP model. Thus, the BNP model could be able to validate the database search results effectively and extract more information from MS/MS data. PMID:19005226

  8. SUPER-FOCUS: a tool for agile functional analysis of shotgun metagenomic data.

    Science.gov (United States)

    Silva, Genivaldo Gueiros Z; Green, Kevin T; Dutilh, Bas E; Edwards, Robert A

    2016-02-01

    Analyzing the functional profile of a microbial community from unannotated shotgun sequencing reads is one of the important goals in metagenomics. Functional profiling has valuable applications in biological research because it identifies the abundances of the functional genes of the organisms present in the original sample, answering the question what they can do. Currently, available tools do not scale well with increasing data volumes, which is important because both the number and lengths of the reads produced by sequencing platforms keep increasing. Here, we introduce SUPER-FOCUS, SUbsystems Profile by databasE Reduction using FOCUS, an agile homology-based approach using a reduced reference database to report the subsystems present in metagenomic datasets and profile their abundances. SUPER-FOCUS was tested with over 70 real metagenomes, the results showing that it accurately predicts the subsystems present in the profiled microbial communities, and is up to 1000 times faster than other tools. SUPER-FOCUS was implemented in Python, and its source code and the tool website are freely available at https://edwards.sdsu.edu/SUPERFOCUS. redwards@mail.sdsu.edu Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.

  9. 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.

  10. Shotgun mass mapping of Lactobacillus species and subspecies from caries related isolates by MALDI-MS.

    Science.gov (United States)

    Schmidt, Frank; Fiege, Thomas; Hustoft, Hanne K; Kneist, Susanne; Thiede, Bernd

    2009-04-01

    A taxonomical study of 90 isolates of lactobacilli isolated from soft and hard carious dentine of 70 deciduous molars is presented. The Lactobacillus strains were determined by shotgun mass mapping (SMM). This method based on MALDI-MS analysis of Lactobacillus isolates treated with trypsin followed by database comparison against a library of mass spectra derived from 20 reference strains. The SMM method allowed to discriminate different Lactobacillus subspecies. The method was used to analyse Lactobacillus isolates of unknown identity derived from carious dentine. Application of the SMM method to isolates from hard carious dentine revealed a nearly similar distribution of L. paracasei ss paracasei (29%), L. paracasei ss tolerans (32%) and L. casei ss rhamnosus (23%) as dominant subspecies. On the other hand, samples derived from soft carious dentine showed a clear bias only to L. paracasei ss paracasei (60%), whereas L. paracasei ss tolerans (14%) and L. casei ss rhamnosus (12%) were clear minorities. Compared to existent methods, SMM has unique potential for the analysis of Lactobacillus strains on subspecies level.

  11. 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.

  12. Shotgun proteomics and network analysis of neuroblastoma cell lines treated with curcumin.

    Science.gov (United States)

    D'Aguanno, Simona; D'Agnano, Igea; De Canio, Michele; Rossi, Claudia; Bernardini, Sergio; Federici, Giorgio; Urbani, Andrea

    2012-04-01

    Curcumin is a natural compound with recognized anti-inflammatory properties, but its anticancer activity is still object of study. We provided an unsupervised molecular investigation of the main proteome rearrangements involved in the cellular response to curcumin in a human neuroblastoma cell line sensitive to cisplatin and its resistant counterpart by a comparative proteomic approach. Shotgun analysis demonstrated that 66 proteins were differentially expressed in response to 24 h treatment with 40 μM curcumin in sensitive cells, whereas 32 proteins were significantly modulated in treated resistant cells. Functional analysis revealed that proteins involved in cellular assembly and organization, biosynthesis and glycolysis were down-regulated by curcumin treatment. Proteome changes were associated to cell cycle arrest in the G2/M phase and accumulation of polyubiquitinated proteins, also confirmed by flow cytometry and immunoblotting analysis, but not to a significant increment of reactive oxygen species production. Since the polyubiquitination of proteins influences a wide range of cellular pathways, the inhibition of the ubiquitin-proteasome system may be the main way through which curcumin performs its multi-target activity.

  13. 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.

  14. 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

  15. 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.

  16. 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

  17. 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

    that they ‘see no virtue in using climatic variables to define a [vegetation] formation type’, and then discuss problems with the climate- based global biome schemes of Holdridge (1947), Whittaker (1970), Box (1981) and Prentice et al. (1992). As our oceanic temperate forest (OTF) concept is underpinned......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...... by climatic variables, and as they suggest that it largely falls within their WTRF and cool temperate rain forest (CTRF) concepts, we take this opportunity to further discuss the relative merits of these contrasting ways of classifying vegetation cover....

  18. Eutrophication and macroalgal blooms in temperate and tropical coastal waters: nutrient enrichment experiments with Ulva spp.

    OpenAIRE

    Teichberg, Mirta; Fox, Sophia E; Olsen, Ylva S.; Valiela, Ivan; Martinetto, Paulina; Iribarne, Oscar; Muto, Elizabeti Yuriko; PETTI, MONICA A.V.; Corbisier, Tha?s N; Soto-Jim?nez, Mart?n; P?ez-Osuna, Federico; Castro, Paula; Freitas, Helena; Zitelli, Andreina; Cardinaletti, Massimo

    2010-01-01

    Receiving coastal waters and estuaries are among the most nutrient-enriched environments on earth, and one of the symptoms of the resulting eutrophication is the proliferation of opportunistic, fast-growing marine seaweeds. Here, we used a widespread macroalga often involved in blooms, Ulva spp., to investigate how supply of nitrogen (N) and phosphorus (P), the two main potential growth-limiting nutrients, influence macroalgal growth in temperate and tropical coastal waters ranging from low- ...

  19. 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. 

  20. Simulated Tempering and Swapping on Mean-Field Models

    OpenAIRE

    Bhatnagar, Nayantara; Randall, Dana

    2015-01-01

    Simulated and parallel tempering are families of Markov Chain Monte Carlo algorithms where a temperature parameter is varied during the simulation to overcome bottlenecks to convergence due to multimodality. In this work we introduce and analyze the convergence for a set of new tempering distributions which we call \\textit{entropy dampening}. For asymmetric exponential distributions and the mean field Ising model with and external field simulated tempering is known to converge slowly. We show...

  1. 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.

  2. Shotgun Metagenomic Sequencing Reveals Functional Genes and Microbiome Associated with Bovine Digital Dermatitis.

    Directory of Open Access Journals (Sweden)

    Martin Zinicola

    Full Text Available Metagenomic methods amplifying 16S ribosomal RNA genes have been used to describe the microbial diversity of healthy skin and lesion stages of bovine digital dermatitis (DD and to detect critical pathogens involved with disease pathogenesis. In this study, we characterized the microbiome and for the first time, the composition of functional genes of healthy skin (HS, active (ADD and inactive (IDD lesion stages using a whole-genome shotgun approach. Metagenomic sequences were annotated using MG-RAST pipeline. Six phyla were identified as the most abundant. Firmicutes and Actinobacteria were the predominant bacterial phyla in the microbiome of HS, while Spirochetes, Bacteroidetes and Proteobacteria were highly abundant in ADD and IDD. T. denticola-like, T. vincentii-like and T. phagedenis-like constituted the most abundant species in ADD and IDD. Recruitment plots comparing sequences from HS, ADD and IDD samples to the genomes of specific Treponema spp., supported the presence of T. denticola and T. vincentii in ADD and IDD. Comparison of the functional composition of HS to ADD and IDD identified a significant difference in genes associated with motility/chemotaxis and iron acquisition/metabolism. We also provide evidence that the microbiome of ADD and IDD compared to that of HS had significantly higher abundance of genes associated with resistance to copper and zinc, which are commonly used in footbaths to prevent and control DD. In conclusion, the results from this study provide new insights into the HS, ADD and IDD microbiomes, improve our understanding of the disease pathogenesis and generate unprecedented knowledge regarding the functional genetic composition of the digital dermatitis microbiome.

  3. Identification of carbonylated lipids from different phospholipid classes by shotgun and LC-MS lipidomics.

    Science.gov (United States)

    Ni, Zhixu; Milic, Ivana; Fedorova, Maria

    2015-07-01

    Oxidized lipids play a significant role in the pathogenesis of numerous oxidative stress-related human disorders, such as atherosclerosis, obesity, inflammation, and autoimmune diseases. Lipid peroxidation, induced by reactive oxygen and nitrogen species, yields a high variety of modified lipids. Among them, carbonylated lipid peroxidation products (oxoLPP), formed by oxidation of the fatty acid moiety yielding aldehydes or ketones (carbonyl groups), are electrophilic compounds that are able to modify nucleophilic substrates like proteins, nucleic acid, and aminophospholipids. Some carbonylated phosphatidylcholines possess even pro-inflammatory activities. However, little is known about oxoLPP derived from other phospholipid (PL) classes. Here, we present a new analytical strategy based on the mass spectrometry (MS) of PL-oxoLPP derivatized with 7-(diethylamino)coumarin-3-carbohydrazide (CHH). Shotgun MS revealed many oxoLPP derived from in vitro oxidized glycerophosphatidylglycerols (PG, 31), glycerophosphatidylcholine (PC, 23), glycerophosphatidylethanolamine (PE, 34), glycerophosphatidylserines (PS, 7), glycerophosphatidic acids (PA, 17), and phosphatidylinositiolphosphates (PIP, 6) vesicles. This data were used to optimize LipidXplorer-assisted identification, and a python-based post-processing script was developed to increase both throughput and accuracy. When applied to full lipid extracts from rat primary cardiomyocytes treated with peroxynitrite donor SIN-1, ten PL-bound oxoLPP were unambiguously identified by LC-MS, including two PC-, two PE-, one PG-, two PS-, and three PA-derived species. Some of the well-known carbonylated PC were detected, while most PL-oxoLPP were shown for the first time.

  4. 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.

  5. 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.

  6. Expansion of the Litopenaeus vannamei and Penaeus monodon peptidomes using transcriptome shotgun assembly sequence data.

    Science.gov (United States)

    Christie, Andrew E

    2014-09-15

    The shrimp Litopenaeus vannamei and Penaeus monodon are arguably the most important commercially farmed crustaceans. While expansion of their aquaculture has classically relied on improvements to rearing facilities, these options have largely been exhausted, and today a shift in focus is occurring, with increased investment in manipulating the shrimp themselves. Hormonal control is one strategy for increasing aquaculture output. However, to use it, one must first understand an animal's native hormonal systems. Here, transcriptome shotgun assembly (TSA) data were used to expand the peptidomes for L. vannamei and P. monodon. Via an established bioinformatics workflow, 41 L. vannamei and 25 P. monodon pre/preprohormone-encoding transcripts were identified, allowing for the prediction of 158 and 106 distinct peptide structures for these species, respectively. The identified peptides included isoforms of allatostatin A, B and C, as well as members the bursicon, CAPA, CCHamide, crustacean cardioactive peptide, crustacean hyperglycemic hormone, diuretic hormone 31, eclosion hormone, FLRFamide, GSEFLamide, intocin, leucokinin, molt-inhibiting hormone, myosuppressin, neuroparsin, neuropeptide F, orcokinin, orcomyotropin, pigment dispersing hormone, proctolin, red pigment concentrating hormone, RYamide, SIFamide, short neuropeptide F and tachykinin-related peptide families. While some of the predicted peptides are known L. vannamei and/or P. monodon isoforms (which vet the structures of many peptides identified previously via mass spectrometry and other means), most are described here for the first time. These data more than double the extant catalogs of L. vannamei and P. monodon peptides and provide platforms from which to launch future physiological studies of peptidergic signaling in these two commercially important species. Copyright © 2014 Elsevier Inc. All rights reserved.

  7. 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.

  8. Trichinella in arctic, subarctic and temperate regions

    DEFF Research Database (Denmark)

    Kapel, C. M O

    1997-01-01

    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......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...... populations may have epidemiological importance in relation to the recent changes in production and infrastructure in these former Soviet states....

  9. Extended Hamiltonian approach to continuous tempering.

    Science.gov (United States)

    Gobbo, Gianpaolo; Leimkuhler, Benedict J

    2015-06-01

    We introduce an enhanced sampling simulation technique based on continuous tempering, i.e., on continuously varying the temperature of the system under investigation. Our approach is mathematically straightforward, being based on an extended Hamiltonian formulation in which an auxiliary degree of freedom, determining the effective temperature, is coupled to the physical system. The physical system and its temperature evolve continuously in time according to the equations of motion derived from the extended Hamiltonian. Due to the Hamiltonian structure, it is easy to show that a particular subset of the configurations of the extended system is distributed according to the canonical ensemble for the physical system at the correct physical temperature.

  10. A temperature predictor for parallel tempering simulations.

    Science.gov (United States)

    Patriksson, Alexandra; van der Spoel, David

    2008-04-21

    An algorithm is proposed that generates a set of temperatures for use in parallel tempering simulations (also known as temperature-replica exchange molecular dynamics simulations) of proteins to obtain a desired exchange probability Pdes. The input consists of the number of protein atoms and water molecules in the system, information about the use of constraints and virtual sites and the lower temperature limits. The temperatures generated yield probabilities which are very close to Pdes (correlation 97%), independent of force field and over a wide temperature range. To facilitate its use, the algorithm has been implemented as a web server at .

  11. Land Cover Analysis of Temperate Asia

    Science.gov (United States)

    Justice, Chris

    1998-01-01

    Satellite data from the advanced very high resolution radiometer (AVHRR) instrument were used to produce a general land cover distribution of temperate Asia (referred to hence as Central Asia) from 1982, starting with the NOAA-7 satellite, and continuing through 1991, ending with the NOAA-11 satellite. Emphasis was placed upon delineating the and and semi-arid zones of Central Asia (largely Mongolia and adjacent areas), mapping broad categories of aggregated land cover, and upon studying photosynthetic capacity increases in Central Asia from 1982 to 1991.

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

    DEFF Research Database (Denmark)

    Buitenwerf, Robert

    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 ‘...

  13. Effects of initial temperature and tempering medium on thermal tempering of dental porcelains.

    Science.gov (United States)

    Hojjatie, B; Anusavice, K J

    1993-03-01

    The objective of this study was to test the hypothesis that quenching of porcelain in silicone oil rather than in compressed air will significantly increase the flexure strength by reducing the potential for crack formation during transient cooling. A secondary hypothesis to be tested is that the initial tempering temperature can be reduced significantly below the porcelain maturing temperature of 982 degrees C but well above Tg without a decrease in strength. Opaque-body porcelain disks, 16 mm in diameter and 2 mm in thickness, with a thermal contraction mismatch (delta alpha) of -1.5, 0, and +3.2 ppm/degrees C were tempered from initial temperatures of 650, 750, 850, and 982 degrees C in silicone oil with kinematic viscosities of 50, 1000, and 5000 centistokes. Porcelain disks were also subjected to three cooling procedures in air: slow cooling in a furnace (SC), free convective cooling in a laboratory bench (FC), and tempering (T) by blasting the surface of body porcelain with air. The crack size induced by a Vickers microhardness indenter was measured within one minute after crack development. For determination of the influence of initial cooling temperature on biaxial flexure strength, six body porcelain disks (delta alpha = 0) were tempered in air from initial temperatures of 650, 750, 850, and 982 degrees C. The mean crack size of specimens tempered in oil was significantly smaller (p < or = 0.001) than that of specimens that were slowly-cooled or fast-cooled in air for all thermal contraction mismatch cases.(ABSTRACT TRUNCATED AT 250 WORDS)

  14. Not-so-well-tempered neutralino

    Science.gov (United States)

    Profumo, Stefano; Stefaniak, Tim; Stephenson-Haskins, Laurel

    2017-09-01

    Light electroweakinos, the neutral and charged fermionic supersymmetric partners of the standard model SU (2 )×U (1 ) gauge bosons and of the two SU(2) Higgs doublets, are an important target for searches for new physics with the Large Hadron Collider (LHC). However, if the lightest neutralino is the dark matter, constraints from direct dark matter detection experiments rule out large swaths of the parameter space accessible to the LHC, including in large part the so-called "well-tempered" neutralinos. We focus on the minimal supersymmetric standard model (MSSM) and explore in detail which regions of parameter space are not excluded by null results from direct dark matter detection, assuming exclusive thermal production of neutralinos in the early universe, and illustrate the complementarity with current and future LHC searches for electroweak gauginos. We consider both bino-Higgsino and bino-wino "not-so-well-tempered" neutralinos, i.e. we include models where the lightest neutralino constitutes only part of the cosmological dark matter, with the consequent suppression of the constraints from direct and indirect dark matter searches.

  15. Proteomics investigation of human platelets by shotgun nUPLC-MSE and 2DE experimental strategies: a comparative study.

    Science.gov (United States)

    Finamore, Francesco; Pieroni, Luisa; Ronci, Maurizio; Marzano, Valeria; Mortera, Stefano Levi; Romano, Mario; Cortese, Claudio; Federici, Giorgio; Urbani, Andrea

    2010-06-01

    Platelets, the smallest human blood cells component, have a key role in the control of haemostasis and thrombosis but they have also been shown to be implicated in a number of different pathological states because of their involvement also in the process of inflammation end its resolution. Their peculiar anucleated morphology render the proteomics an intriguing approach to understand their biology. Given the high impact of platelet in different diseases we have started a systematic investigation of protein repertoire in controlled platelet preparation. Platelets have been extracted from blood of healthy donors (n=6) collected by venipuncture in Vacutainer. The quality of the preparation was assessed by observation and enumeration in a Bürker chamber with a conventional tissue culture microscope. To characterize human platelets proteome we analysed the pool of purified platelets combining two proteomic approaches: 2-DE separation combined with Mass Spectrometry and nanoscale ultra performances LC-MS(E) shotgun proteomics experiments. The 2D gel analysis leads an average of 1900 protein spots, after the filtering of "noise" and "false positive" spots, over 500 were selected to be eligible for further analysis given their optimal spot quality value. To perform the analysis by ion accounting shotgun proteomic approach, based on nano ultra performance liquid chromatography (nUPLC) coupled to MS(E) processing of continuum LC-MS data, the same pool of samples was subject to liquid phase tryptic digestion and the peptide obtained used for the experiments. All the data obtained were analysed using ProteinLynx GlobalServer v2.3 (PLGS, Waters). Three analytical replicates run were acquire in high/low energy modes and associated to a human protein database returning the identification of 100 distinct genes. Comparative analysis of the Gene Ontology has been performed to evaluate the differential functional representation of the molecular repertoire investigated with these two

  16. Trade-offs between seedling growth and survival in deciduous broadleaved trees in a temperate forest.

    Science.gov (United States)

    Seiwa, Kenji

    2007-03-01

    In spatially heterogeneous environments, a trade-off between seedling survival and relative growth rate may promote the coexistence of plant species. In temperate forests, however, little support for this hypothesis has been found under field conditions, as compared with shade-house experiments. Performance trade-offs were examined over a large resource gradient in a temperate hardwood forest. The relationship between seedling survival and seedling relative growth rate in mass (RGR(M)) or height (RGR(H)) was examined at three levels of canopy cover (forest understorey, FU; small gap, SG; and large gap, LG) and at two microsites within each level of canopy cover (presence or absence of leaf litter) for five deciduous broad-leaved tree species with different seed sizes. Within each species, both RGR(M) and RGR(H) usually increased with increasing light levels (in the order FU temperate forests, and that further species diversity would be promoted by increased spatial heterogeneity. The intraspecific trade-off between survival and RGR in Acer suggests that it has broad habitat requirements, whereas Betula has narrow habitat requirements and specializes in high-light environments.

  17. Combining ability of tropical and temperate inbred lines of popcorn.

    Science.gov (United States)

    da Silva, V Q R; do Amaral Júnior, A T; Gonçalves, L S A; Freitas Júnior, S P; Candido, L S; Vittorazzi, C; Moterle, L M; Vieira, R A; Scapim, C A

    2010-08-31

    In Brazil, using combining ability of popcorn genotypes to achieve superior hybrids has been unsuccessful because the local genotypes are all members of the same heterotic group. To overcome this constraint, 10 lines (P(1) to P(10)) with different adaptations to tropical or temperate edaphoclimatic environments were used to obtain 45 F(1) hybrids in a complete diallel. These hybrids and three controls were evaluated in two environments in Rio de Janeiro State. Grain yield (GY), popping expansion (PE), plant height (PH), ear height (EH), and days to silking (FL) were evaluated in randomized complete blocks with three replications. Significant differences between genotypes (P

  18. An Integrated Time-Temperature Approach for Predicting Mechanical Properties of Quenched and Tempered Steels

    OpenAIRE

    O'Connell, Corey James

    2014-01-01

    The purpose of this work was to develop a steel tempering model that is useful to the commercial heat treater. Most of the tempering models reported address isothermal conditions which are not typical of most heating methods used to perform the tempering heat treatment. In this work, a non-isothermal tempering model was developed based on the tempering response of four steel alloys. This tempering model employs the quantity resulting from the numerical integration of the time-temperature prof...

  19. The tempering quality evaluation of cocoa liquor during industrial ...

    African Journals Online (AJOL)

    The tempering quality evaluation of the crude cocoa liquor with average fat content 55.0 ± 0.3 % and an average acid value, 1.57 ± 0.34) has been established. The various parameters considered were recasting time (RT) and appearance (AP) of the tempered product on one hand and the flow (F) of the crude liquor on ...

  20. 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

  1. 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

  2. Spray mist cooling heat transfer in glass tempering process

    Science.gov (United States)

    Sozbir, Nedim; Yao, S. C.

    2017-05-01

    Energy saving is a very important issue in glass plants, especially in a glass tempering process, where very high velocity air jet impingement is applied during the cooling process of glass tempering. In fact, air compressor energy may be reduced by a spray cooling due to its high heat transfer capabilities. Presently, in this paper, both pure air and water mist spray cooling are investigated in the glass tempering process. The test results indicate that thin and low-cost tempered glass can be made by mist cooling without fracture. It is possible to find the optimal water flux and duration of mist application to achieve a desirable temperature distribution in the glass for deep penetration of the cooling front but without inducing cracking during the tempering. The use of mist cooling could give about 29 % air pressure reduction for 2-mm glass plate and 50 % reduction for both 3- and 4-mm glass plates.

  3. 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.

  4. Fragmentation of contaminant and endogenous DNA in ancient samples determined by shotgun sequencing; prospects for human palaeogenomics.

    Directory of Open Access Journals (Sweden)

    Marc García-Garcerà

    Full Text Available BACKGROUND: Despite the successful retrieval of genomes from past remains, the prospects for human palaeogenomics remain unclear because of the difficulty of distinguishing contaminant from endogenous DNA sequences. Previous sequence data generated on high-throughput sequencing platforms indicate that fragmentation of ancient DNA sequences is a characteristic trait primarily arising due to depurination processes that create abasic sites leading to DNA breaks. METHODOLOGY/PRINCIPALS FINDINGS: To investigate whether this pattern is present in ancient remains from a temperate environment, we have 454-FLX pyrosequenced different samples dated between 5,500 and 49,000 years ago: a bone from an extinct goat (Myotragus balearicus that was treated with a depurinating agent (bleach, an Iberian lynx bone not subjected to any treatment, a human Neolithic sample from Barcelona (Spain, and a Neandertal sample from the El Sidrón site (Asturias, Spain. The efficiency of retrieval of endogenous sequences is below 1% in all cases. We have used the non-human samples to identify human sequences (0.35 and 1.4%, respectively, that we positively know are contaminants. CONCLUSIONS: We observed that bleach treatment appears to create a depurination-associated fragmentation pattern in resulting contaminant sequences that is indistinguishable from previously described endogenous sequences. Furthermore, the nucleotide composition pattern observed in 5' and 3' ends of contaminant sequences is much more complex than the flat pattern previously described in some Neandertal contaminants. Although much research on samples with known contaminant histories is needed, our results suggest that endogenous and contaminant sequences cannot be distinguished by the fragmentation pattern alone.

  5. Fragmentation of contaminant and endogenous DNA in ancient samples determined by shotgun sequencing; prospects for human palaeogenomics.

    Science.gov (United States)

    García-Garcerà, Marc; Gigli, Elena; Sanchez-Quinto, Federico; Ramirez, Oscar; Calafell, Francesc; Civit, Sergi; Lalueza-Fox, Carles

    2011-01-01

    Despite the successful retrieval of genomes from past remains, the prospects for human palaeogenomics remain unclear because of the difficulty of distinguishing contaminant from endogenous DNA sequences. Previous sequence data generated on high-throughput sequencing platforms indicate that fragmentation of ancient DNA sequences is a characteristic trait primarily arising due to depurination processes that create abasic sites leading to DNA breaks. METHODOLOGY/PRINCIPALS FINDINGS: To investigate whether this pattern is present in ancient remains from a temperate environment, we have 454-FLX pyrosequenced different samples dated between 5,500 and 49,000 years ago: a bone from an extinct goat (Myotragus balearicus) that was treated with a depurinating agent (bleach), an Iberian lynx bone not subjected to any treatment, a human Neolithic sample from Barcelona (Spain), and a Neandertal sample from the El Sidrón site (Asturias, Spain). The efficiency of retrieval of endogenous sequences is below 1% in all cases. We have used the non-human samples to identify human sequences (0.35 and 1.4%, respectively), that we positively know are contaminants. We observed that bleach treatment appears to create a depurination-associated fragmentation pattern in resulting contaminant sequences that is indistinguishable from previously described endogenous sequences. Furthermore, the nucleotide composition pattern observed in 5' and 3' ends of contaminant sequences is much more complex than the flat pattern previously described in some Neandertal contaminants. Although much research on samples with known contaminant histories is needed, our results suggest that endogenous and contaminant sequences cannot be distinguished by the fragmentation pattern alone.

  6. The postman always rings twice: two cases of shotgun deaths associated with an unconventional home security alarm system.

    Science.gov (United States)

    Asirdizer, Mahmut; Turkmen, Nursel; Akan, Okan; Yavuz, Mehmet Sunay

    2014-06-01

    Injury and death cases caused by booby traps are not common in forensic medicine practice. Besides, installation of booby traps including firearms is generally for suicidal and rarely for homicidal purposes. Although few patents were described about home security alarm system that were created by firearms in the United States, 1 sample of injury with a similar unconventional mechanism of home safety system was reported by Asirdizer and Yavuz in 2009. In the published case report, the story of an electrical technician who was invited to a summer house by the homeowner to check the home security alarm system was reported. In the so-called report, he was stated to be injured by the shotgun attached to the unconventional home security alarm system while checking the system. As a result, the homeowner was convicted of a possible intent to cause a life-threatening injury to the technician.The so-called homeowner and his wife died by the same shotgun attached to the same unconventional home security alarm system 4 years on from the first event. In the present case report, we have aimed to present the findings of the crime scene and the autopsies of these unusual 2 deaths and to discuss individual and legal factors in paving the way for the deaths of 2 people.

  7. Species identification and profiling of complex microbial communities using shotgun Illumina sequencing of 16S rRNA amplicon sequences.

    Directory of Open Access Journals (Sweden)

    Swee Hoe Ong

    Full Text Available The high throughput and cost-effectiveness afforded by short-read sequencing technologies, in principle, enable researchers to perform 16S rRNA profiling of complex microbial communities at unprecedented depth and resolution. Existing Illumina sequencing protocols are, however, limited by the fraction of the 16S rRNA gene that is interrogated and therefore limit the resolution and quality of the profiling. To address this, we present the design of a novel protocol for shotgun Illumina sequencing of the bacterial 16S rRNA gene, optimized to amplify more than 90% of sequences in the Greengenes database and with the ability to distinguish nearly twice as many species-level OTUs compared to existing protocols. Using several in silico and experimental datasets, we demonstrate that despite the presence of multiple variable and conserved regions, the resulting shotgun sequences can be used to accurately quantify the constituents of complex microbial communities. The reconstruction of a significant fraction of the 16S rRNA gene also enabled high precision (>90% in species-level identification thereby opening up potential application of this approach for clinical microbial characterization.

  8. 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......-inserts using our model. In our simulated genomes of human and rice, the length distribution of repeats is different, so their optimal length distributions of clone-inserts were not the same. Thus with optimal length distribution of clone-inserts, a given genome could be assembled better at lower coverage...

  9. Temperate Ice Depth-Sounding Radar

    Science.gov (United States)

    Jara-Olivares, V. A.; Player, K.; Rodriguez-Morales, F.; Gogineni, P.

    2008-12-01

    Glaciers in several parts of the world are reported to be retreating and thinning rapidly over the last decade. Radar instruments can be used to provide a wealth of information regarding the internal and basal conditions of large and small ice masses. These instruments typically operate in the VHF and UHF regions of the electromagnetic spectrum. For temperate-ice sounding, however, the high water content produces scattering and attenuation in propagating radar waves at VHF and UHF frequencies, which significantly reduce the penetration depths. Radars operating in the HF band are better suited for systematic surveys of the thickness and sub-glacial topography of temperate-ice regions. We are developing a dual-frequency Temperate-Ice-Depth Sounding Radar (TIDSoR) that can penetrate through water pockets, thus providing more accurate measurements of temperate ice properties such as thickness and basal conditions. The radar is a light-weight, low power consumption portable system for surface-based observations in mountainous terrain or aerial surveys. TIDSoR operates at two different center frequencies: 7.7 MHz and 14 MHz, with a maximum output peak power of 20 W. The transmit waveform is a digitally generated linear frequency-modulated chirp with 1 MHz bandwidth. The radar can be installed on aircrafts such as the CReSIS UAV [1], DCH-6 (Twin Otter), or P-3 Orion for aerial surveys, where it could be supported by the airplane power system. For surface based experiments, TIDSoR can operate in a backpack configuration powered by a compact battery system. The system can also be installed on a sled towed by a motorized vehicle, in which case the power supply can be replaced by a diesel generator. The radar consists of three functional blocks: the digital section, the radio-frequency (RF) section, and the antenna, and is designed to weigh less than 2 kg, excluding the power supply. The digital section generates the transmit waveforms as well as timing and control signals

  10. 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.  

  11. 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

  12. 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.

  13. Phosphorous dynamics in a temperate intertidal estuary

    Science.gov (United States)

    Lillebø, A. I.; Neto, J. M.; Flindt, M. R.; Marques, J. C.; Pardal, M. A.

    2004-09-01

    Conservation and management of aquatic systems require detailed information of the processes that affect their functioning and development. The objectives of the present work were to describe the phosphorus dynamics during a complete tidal cycle and to quantify the relative contribution of the most common estuarine areas (e.g. seagrass beds, salt marshes, mud- and sand-flats without vegetation) to phosphorus net internal loading in a temperate intertidal estuary. Results show that phosphate efflux rates were higher during the first hours of tidal flood, and that phosphate concentrations were lowest at high tide. During tidal ebbing, ephemeral tide pools may cover a considerable percentage of the intertidal area. In these tide pools, water shallowness combined with enhanced temperatures stimulate the occurrence of high phosphate effluxes. The effluxes to the main water body during high tide contributed 57% of dissolved inorganic phosphorus and efflux during low tide contributed 43% to the net internal loading. Calculations of the phosphate net effluxes (kg P) indicate a strong contribution of the bare bottom mud-flats to the whole system internal phosphate loading, especially during the warmer periods. As a consequence of eutrophication, perennial benthic macrophytes are commonly replaced by fast-growing epiphytic macroalgae. Calculations showed that for a hypothetical intertidal estuary in a temperate region, management programs considering an eventual re-colonization of mud-flats by seagrasses or salt marsh plants may reduce the P-efflux by 13-16 kg ha -1. For example, in the small Mondego estuary, eutrophication has contributed to a reduction of the Zostera noltii meadows, leading to an increase in 190 kg of phosphorus net internal loading.

  14. Phenology of temperate trees in tropical climates

    Science.gov (United States)

    Borchert, Rolf; Robertson, Kevin; Schwartz, Mark D.; Williams-Linera, Guadalupe

    2005-09-01

    Several North American broad-leaved tree species range from the northern United States at ˜47°N to moist tropical montane forests in Mexico and Central America at 15-20°N. Along this gradient the average minimum temperatures of the coldest month (T Jan), which characterize annual variation in temperature, increase from -10 to 12°C and tree phenology changes from deciduous to leaf-exchanging or evergreen in the southern range with a year-long growing season. Between 30 and 45°N, the time of bud break is highly correlated with T Jan and bud break can be reliably predicted for the week in which mean minimum temperature rises to 7°C. Temperature-dependent deciduous phenology—and hence the validity of temperature-driven phenology models—terminates in southern North America near 30°N, where T Jan>7°C enables growth of tropical trees and cultivation of frost-sensitive citrus fruits. In tropical climates most temperate broad-leaved species exchange old for new leaves within a few weeks in January-February, i.e., their phenology becomes similar to that of tropical leaf-exchanging species. Leaf buds of the southern ecotypes of these temperate species are therefore not winter-dormant and have no chilling requirement. As in many tropical trees, bud break of Celtis, Quercus and Fagus growing in warm climates is induced in early spring by increasing daylength. In tropical climates vegetative phenology is determined mainly by leaf longevity, seasonal variation in water stress and day length. As water stress during the dry season varies widely with soil water storage, climate-driven models cannot predict tree phenology in the tropics and tropical tree phenology does not constitute a useful indicator of global warming.

  15. Interleukin-6 Induced "Acute" Phenotypic Microenvironment Promotes Th1 Anti-Tumor Immunity in Cryo-Thermal Therapy Revealed By Shotgun and Parallel Reaction Monitoring Proteomics.

    Science.gov (United States)

    Xue, Ting; Liu, Ping; Zhou, Yong; Liu, Kun; Yang, Li; Moritz, Robert L; Yan, Wei; Xu, Lisa X

    2016-01-01

    Cryo-thermal therapy has been emerged as a promising novel therapeutic strategy for advanced breast cancer, triggering higher incidence of tumor regression and enhanced remission of metastasis than routine treatments. To better understand its anti-tumor mechanism, we utilized a spontaneous metastatic mouse model and quantitative proteomics to compare N-glycoproteome changes in 94 serum samples with and without treatment. We quantified 231 highly confident N-glycosylated proteins using iTRAQ shotgun proteomics. Among them, 53 showed significantly discriminated regulatory patterns over the time course, in which the acute phase response emerged as the most enhanced pathway. The anti-tumor feature of the acute response was further investigated using parallel reaction monitoring target proteomics and flow cytometry on 23 of the 53 significant proteins. We found that cryo-thermal therapy reset the tumor chronic inflammation to an "acute" phenotype, with up-regulation of acute phase proteins including IL-6 as a key regulator. The IL-6 mediated "acute" phenotype transformed IL-4 and Treg-promoting ICOSL expression to Th1-promoting IFN-γ and IL-12 production, augmented complement system activation and CD86(+)MHCII(+) dendritic cells maturation and enhanced the proliferation of Th1 memory cells. In addition, we found an increased production of tumor progression and metastatic inhibitory proteins under such "acute" environment, favoring the anti-metastatic effect. Moreover, cryo-thermal on tumors induced the strongest "acute" response compared to cryo/hyperthermia alone or cryo-thermal on healthy tissues, accompanying by the most pronounced anti-tumor immunological effect. In summary, we demonstrated that cryo-thermal therapy induced, IL-6 mediated "acute" microenvironment shifted the tumor chronic microenvironment from Th2 immunosuppressive and pro-tumorigenic to Th1 immunostimulatory and tumoricidal state. Moreover, the magnitude of "acute" and "danger" signals play a key

  16. 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.

  17. The effect of tempering temperature on pitting corrosion resistance of 420 stainless steels

    Energy Technology Data Exchange (ETDEWEB)

    Anwar, Moch Syaiful, E-mail: moch026@lipi.go.id; Prifiharni, Siska, E-mail: sisk002@lipi.go.id; Mabruri, Efendi, E-mail: effe004@lipi.go.id [Research Center for Metallurgy and Materials – Indonesian Institute of Sciences (LIPI) Kawasan PUSPIPTEK Building 470 – South of Tangerang – Banten – 15314 (Indonesia)

    2016-04-19

    The AISI Type 420 stainless steels are commonly used to steam generators, mixer blades, etc. These stainless steels are most prone to pitting in dissolved Cl{sup −} containing environments. In this paper, the effect of tempering temperature on pitting corrosion resistance of AISI Type 420 stainless steels was studied. The AISI Type 420 stainless steels specimens were heat treated at the temperature of 1050°C for 1 hour to reach austenite stabilization and then quench in the oil. After that, the specimens were tempered at the temperature of 150, 250, 350 and 450°C for 30 minutes and then air cooled to the room temperature. The electrochemical potentiodynamic polarization test was conducted at 3.5% sodium chloride solution to evaluate corrosion rate and pitting corrosion behaviour. The Scanning Electron Microscope (SEM), Energy Dispersive X-Ray Spectroscopy (EDS) were used to evaluate the pitting corrosion product. The result have shown that highest pitting potential was found in the sample tempered at 250°C and corrosion pits were found to initiate preferentially around chromium carbides.

  18. The effect of tempering temperature on pitting corrosion resistance of 420 stainless steels

    Science.gov (United States)

    Anwar, Moch. Syaiful; Prifiharni, Siska; Mabruri, Efendi

    2016-04-01

    The AISI Type 420 stainless steels are commonly used to steam generators, mixer blades, etc. These stainless steels are most prone to pitting in dissolved Cl- containing environments. In this paper, the effect of tempering temperature on pitting corrosion resistance of AISI Type 420 stainless steels was studied. The AISI Type 420 stainless steels specimens were heat treated at the temperature of 1050°C for 1 hour to reach austenite stabilization and then quench in the oil. After that, the specimens were tempered at the temperature of 150, 250, 350 and 450°C for 30 minutes and then air cooled to the room temperature. The electrochemical potentiodynamic polarization test was conducted at 3.5% sodium chloride solution to evaluate corrosion rate and pitting corrosion behaviour. The Scanning Electron Microscope (SEM), Energy Dispersive X-Ray Spectroscopy (EDS) were used to evaluate the pitting corrosion product. The result have shown that highest pitting potential was found in the sample tempered at 250°C and corrosion pits were found to initiate preferentially around chromium carbides.

  19. Independent Demographic Responses to Climate Change among Temperate and Tropical Milksnakes (Colubridae: Genus Lampropeltis).

    Science.gov (United States)

    Ruane, Sara; Torres-Carvajal, Omar; Burbrink, Frank T

    2015-01-01

    The effects of Late Quaternary climate change have been examined for many temperate New World taxa, but the impact of Pleistocene glacial cycles on Neotropical taxa is less well understood, specifically with respect to changes in population demography. Here, we examine historical demographic trends for six species of milksnake with representatives in both the temperate and tropical Americas to determine if species share responses to climate change as a taxon or by area (i.e., temperate versus tropical environments). Using a multilocus dataset, we test for the demographic signature of population expansion and decline using non-genealogical summary statistics, as well as coalescent-based methods. In addition, we determine whether range sizes are correlated with effective population sizes for milksnakes. Results indicate that there are no identifiable trends with respect to demographic response based on location, and that species responded to changing climates independently, with tropical taxa showing greater instability. There is also no correlation between range size and effective population size, with the largest population size belonging to the species with the smallest geographic distribution. Our study highlights the importance of not generalizing the demographic histories of taxa by region and further illustrates that the New World tropics may not have been a stable refuge during the Pleistocene.

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

    DEFF Research Database (Denmark)

    Schneider, Jens; Hilcken, Jonas; Aronen, Antti

    2016-01-01

    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......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...

  1. 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....

  2. 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...

  3. 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

  4. Error and efficiency of simulated tempering simulations.

    Science.gov (United States)

    Rosta, Edina; Hummer, Gerhard

    2010-01-21

    We derive simple analytical expressions for the error and computational efficiency of simulated tempering (ST) simulations. The theory applies to the important case of systems whose dynamics at long times is dominated by the slow interconversion between two metastable states. An extension to the multistate case is described. We show that the relative gain in efficiency of ST simulations over regular molecular dynamics (MD) or Monte Carlo (MC) simulations is given by the ratio of their reactive fluxes, i.e., the number of transitions between the two states summed over all ST temperatures divided by the number of transitions at the single temperature of the MD or MC simulation. This relation for the efficiency is derived for the limit in which changes in the ST temperature are fast compared to the two-state transitions. In this limit, ST is most efficient. Our expression for the maximum efficiency gain of ST simulations is essentially identical to the corresponding expression derived by us for replica exchange MD and MC simulations [E. Rosta and G. Hummer, J. Chem. Phys. 131, 165102 (2009)] on a different route. We find quantitative agreement between predicted and observed efficiency gains in a test against ST and replica exchange MC simulations of a two-dimensional Ising model. Based on the efficiency formula, we provide recommendations for the optimal choice of ST simulation parameters, in particular, the range and number of temperatures, and the frequency of attempted temperature changes.

  5. 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.

  6. Enhanced SDC-assisted digestion coupled with lipid chromatography-tandem mass spectrometry for shotgun analysis of membrane proteome.

    Science.gov (United States)

    Lin, Yong; Wang, Kunbo; Liu, Zhonghua; Lin, Haiyan; Yu, Lijun

    2015-10-01

    Despite the biological importance of membrane proteins, their analysis has lagged behind that of soluble proteins and still presents a great challenge mainly because of their highly hydrophobic nature and low abundance. Sodium deoxycholate (SDC)-assisted digestion strategy has been introduced in our previous papers, which cleverly circumvents many of the challenges in shotgun membrane proteomics. However, it is associated with significant sample loss due to the slightly weaker extraction/solubilization ability of 1% SDC. In this study, an enhanced SDC-assisted digestion method (ESDC method) was developed that incorporates the almost strongest ability of SDC with a high concentration (5%) to lyse membrane and extract/solubilize hydrophobic membrane proteins, and then dilution to 1% for more efficient digestion. The comparative study using rat liver membrane-enriched sample showed that, compared with previous SDC-assisted method and the "universal" filter-aided sample preparation (FASP) method, the ESDC method not only increased the identified number of total proteins, membrane proteins, hydrophobic proteins, integral membrane proteins (IMPs) and IMPs with more than 5 transmembrane domains (TMDs) by an average of 10.8%, 13.2%, 17.8%, 17.9% and 52.9%, respectively, but also enhanced the identified number of total peptides and hydrophobic peptides by averagely 12.5% and 14.2%. These results demonstrated that the ESDC method provides a substantial improvement in the recovery and identification of membrane proteins, especially those with high hydrophobicity and multiple TMDs, and thereby displaying more potential for shotgun membrane proteomics. Copyright © 2015 Elsevier B.V. All rights reserved.

  7. 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.

  8. 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.

  9. 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.

  10. Dung beetle communities: a neotropical-north temperate comparison.

    Science.gov (United States)

    Radtke, Meghan G; Fonseca, Cláudio R V da; Williamson, G Bruce

    2010-01-01

    Dung beetle communities have been compared across north temperate latitudes. Tropical dung beetle communities appear to be more diverse based on studies using different methodologies. Here, we present results from a standardized sampling protocol used to compare dung beetle communities across five neotropical forests in Brazil and Ecuador and two warm, north temperate forests in Mississippi and Louisiana. Species richness in the tropical forests was three to seven times higher than the temperate forests, as would be expected by studies of other taxa across tropical and temperate latitudes. Average body size in the temperate forests was larger than the tropical forests, as predicted by Bergmann's rule. Dung beetle abundance and volume per trap-day were generally higher in Ecuador than Brazil, and higher in Mississippi than Louisiana, but there were no tropical-temperate differences. Species rank-abundance curves were similar within countries and between countries. Rank-volume distributions indicated a smaller range of beetle body sizes in Ecuador versus Brazil or the USA. Community similarity was high within countries and low between countries. Community differences between Brazil and Ecuador sites may be explained by differences in productivity based on geological age of the soils.

  11. Predicting the response of a temperate forest ecosystem to atmospheric CO[sub 2] increase

    Energy Technology Data Exchange (ETDEWEB)

    Bazzaz, F.A.

    1993-01-01

    This report summarizes the second year of research progress. Included are progress reports for the following studies: the responses of temperate forest tree to 3 years of exposure to elevated carbon dioxide, and high and low nutrient and light levels; pot-size limitations in carbon dioxide studies, interactive effects of carbon dioxide and soil moisture availability on tree seedling's tissue water relations, growth, and niche characteristics; individual versus population responses to elevated carbon dioxide levels in two species of annual weeds; and the development of gypsy moth larvae raised on gray and yellow birth foliage grown in ambient and elevated carbon dioxide environments.

  12. Stumbling across the Same Phage: Comparative Genomics of Widespread Temperate Phages Infecting the Fish Pathogen Vibrio anguillarum

    Directory of Open Access Journals (Sweden)

    Panos G. Kalatzis

    2017-05-01

    Full Text Available Nineteen Vibrio anguillarum-specific temperate bacteriophages isolated across Europe and Chile from aquaculture and environmental sites were genome sequenced and analyzed for host range, morphology and life cycle characteristics. The phages were classified as Siphoviridae with genome sizes between 46,006 and 54,201 bp. All 19 phages showed high genetic similarity, and 13 phages were genetically identical. Apart from sporadically distributed single nucleotide polymorphisms (SNPs, genetic diversifications were located in three variable regions (VR1, VR2 and VR3 in six of the phage genomes. Identification of specific genes, such as N6-adenine methyltransferase and lambda like repressor, as well as the presence of a tRNAArg, suggested a both mutualistic and parasitic interaction between phages and hosts. During short term phage exposure experiments, 28% of a V. anguillarum host population was lysogenized by the temperate phages and a genomic analysis of a collection of 31 virulent V. anguillarum showed that the isolated phages were present as prophages in >50% of the strains covering large geographical distances. Further, phage sequences were widely distributed among CRISPR-Cas arrays of publicly available sequenced Vibrios. The observed distribution of these specific temperate Vibriophages across large geographical scales may be explained by efficient dispersal of phages and bacteria in the marine environment combined with a mutualistic interaction between temperate phages and their hosts which selects for co-existence rather than arms race dynamics.

  13. Hallauer's Tusón: a decade of selection for tropical-to-temperate phenological adaptation in maize.

    Science.gov (United States)

    Teixeira, J E C; Weldekidan, T; de Leon, N; Flint-Garcia, S; Holland, J B; Lauter, N; Murray, S C; Xu, W; Hessel, D A; Kleintop, A E; Hawk, J A; Hallauer, A; Wisser, R J

    2015-02-01

    Crop species exhibit an astounding capacity for environmental adaptation, but genetic bottlenecks resulting from intense selection for adaptation and productivity can lead to a genetically vulnerable crop. Improving the genetic resiliency of temperate maize depends upon the use of tropical germplasm, which harbors a rich source of natural allelic diversity. Here, the adaptation process was studied in a tropical maize population subjected to 10 recurrent generations of directional selection for early flowering in a single temperate environment in Iowa, USA. We evaluated the response to this selection across a geographical range spanning from 43.05° (WI) to 18.00° (PR) latitude. The capacity for an all-tropical maize population to become adapted to a temperate environment was revealed in a marked fashion: on average, families from generation 10 flowered 20 days earlier than families in generation 0, with a nine-day separation between the latest generation 10 family and the earliest generation 0 family. Results suggest that adaptation was primarily due to selection on genetic main effects tailored to temperature-dependent plasticity in flowering time. Genotype-by-environment interactions represented a relatively small component of the phenotypic variation in flowering time, but were sufficient to produce a signature of localized adaptation that radiated latitudinally, in partial association with daylength and temperature, from the original location of selection. Furthermore, the original population exhibited a maladaptive syndrome including excessive ear and plant heights along with later flowering; this was reduced in frequency by selection for flowering time.

  14. Kinship analyses identify fish dispersal events on a temperate coastline.

    Science.gov (United States)

    Schunter, C; Pascual, M; Garza, J C; Raventos, N; Macpherson, E

    2014-06-22

    Connectivity is crucial for the persistence and resilience of marine species, the establishment of networks of marine protected areas and the delineation of fishery management units. In the marine environment, understanding connectivity is still a major challenge, due to the technical difficulties of tracking larvae. Recently, parentage analysis has provided a means to address this question effectively. To be effective, this method requires limited adult movement and extensive sampling of parents, which is often not possible for marine species. An alternative approach that is less sensitive to constraints in parental movement and sampling could be the reconstruction of sibships. Here, we directly measure connectivity and larval dispersal in a temperate marine ecosystem through both analytical approaches. We use data from 178 single nucleotide polymorphism markers to perform parentage and sibship reconstruction of the black-faced blenny (Tripterygion delaisi) from an open coastline in the Mediterranean Sea. Parentage analysis revealed a decrease in dispersal success in the focal area over 1 km distance and approximately 6.5% of the juveniles were identified as self-recruits. Sibship reconstruction analysis found that, in general, full siblings did not recruit together to the same location, and that the largest distance between recruitment locations was much higher (11.5 km) than found for parent-offspring pairs (1.2 km). Direct measurements of dispersal are essential to understanding connectivity patterns in different marine habitats, and show the degree of self-replenishment and sustainability of populations of marine organisms. We demonstrate that sibship reconstruction allows direct measurements of dispersal and family structure in marine species while being more easily applied in those species for which the collection of the parental population is difficult or unfeasible.

  15. Effects of 28 days of resistance exercise and consuming a commercially available pre-workout supplement, NO-Shotgun(R), on body composition, muscle strength and mass, markers of satellite cell activation, and clinical safety markers in males.

    Science.gov (United States)

    Shelmadine, Brian; Cooke, Matt; Buford, Thomas; Hudson, Geoffrey; Redd, Liz; Leutholtz, Brian; Willoughby, Darryn S

    2009-08-05

    This study determined the effects of 28 days of heavy resistance exercise combined with the nutritional supplement, NO-Shotgun(R), on body composition, muscle strength and mass, markers of satellite cell activation, and clinical safety markers. Eighteen non-resistance-trained males participated in a resistance training program (3 x 10-RM) 4 times/wk for 28 days while also ingesting 27 g/day of placebo (PL) or NO-Shotgun(R) (NO) 30 min prior to exercise. Data were analyzed with separate 2 x 2 ANOVA and t-tests (p 0.05). When combined with heavy resistance training for 28 days, NO-Shotgun(R) is not associated with any negative side effects, nor does it abnormally impact any of the clinical chemistry markers. Rather, NO-Shotgun(R) effectively increases muscle strength and mass, myofibrillar protein content, and increases the content of markers indicative of satellite cell activation.

  16. Shotgun sequencing of Yersinia enterocolitica strain W22703 (biotype 2, serotype O:9: genomic evidence for oscillation between invertebrates and mammals

    Directory of Open Access Journals (Sweden)

    Starke Mandy

    2011-03-01

    Full Text Available Abstract Background Yersinia enterocolitica strains responsible for mild gastroenteritis in humans are very diverse with respect to their metabolic and virulence properties. Strain W22703 (biotype 2, serotype O:9 was recently identified to possess nematocidal and insecticidal activity. To better understand the relationship between pathogenicity towards insects and humans, we compared the W22703 genome with that of the highly pathogenic strain 8081 (biotype1B; serotype O:8, the only Y. enterocolitica strain sequenced so far. Results We used whole-genome shotgun data to assemble, annotate and analyse the sequence of strain W22703. Numerous factors assumed to contribute to enteric survival and pathogenesis, among them osmoregulated periplasmic glucan, hydrogenases, cobalamin-dependent pathways, iron uptake systems and the Yersinia genome island 1 (YGI-1 involved in tight adherence were identified to be common to the 8081 and W22703 genomes. However, sets of ~550 genes revealed to be specific for each of them in comparison to the other strain. The plasticity zone (PZ of 142 kb in the W22703 genome carries an ancient flagellar cluster Flg-2 of ~40 kb, but it lacks the pathogenicity island YAPIYe, the secretion system ysa and yts1, and other virulence determinants of the 8081 PZ. Its composition underlines the prominent variability of this genome region and demonstrates its contribution to the higher pathogenicity of biotype 1B strains with respect to W22703. A novel type three secretion system of mosaic structure was found in the genome of W22703 that is absent in the sequenced strains of the human pathogenic Yersinia species, but conserved in the genomes of the apathogenic species. We identified several regions of differences in W22703 that mainly code for transporters, regulators, metabolic pathways, and defence factors. Conclusion The W22703 sequence analysis revealed a genome composition distinct from other pathogenic Yersinia enterocolitica

  17. MUMAL2: Improving sensitivity in shotgun proteomics using cost sensitive artificial neural networks and a threshold selector algorithm.

    Science.gov (United States)

    Cerqueira, Fabio Ribeiro; Ricardo, Adilson Mendes; de Paiva Oliveira, Alcione; Graber, Armin; Baumgartner, Christian

    2016-12-15

    This work presents a machine learning strategy to increase sensitivity in tandem mass spectrometry (MS/MS) data analysis for peptide/protein identification. MS/MS yields thousands of spectra in a single run which are then interpreted by software. Most of these computer programs use a protein database to match peptide sequences to the observed spectra. The peptide-spectrum matches (PSMs) must also be assessed by computational tools since manual evaluation is not practicable. The target-decoy database strategy is largely used for error estimation in PSM assessment. However, in general, that strategy does not account for sensitivity. In a previous study, we proposed the method MUMAL that applies an artificial neural network to effectively generate a model to classify PSMs using decoy hits with increased sensitivity. Nevertheless, the present approach shows that the sensitivity can be further improved with the use of a cost matrix associated with the learning algorithm. We also demonstrate that using a threshold selector algorithm for probability adjustment leads to more coherent probability values assigned to the PSMs. Our new approach, termed MUMAL2, provides a two-fold contribution to shotgun proteomics. First, the increase in the number of correctly interpreted spectra in the peptide level augments the chance of identifying more proteins. Second, the more appropriate PSM probability values that are produced by the threshold selector algorithm impact the protein inference stage performed by programs that take probabilities into account, such as ProteinProphet. Our experiments demonstrate that MUMAL2 reached around 15% of improvement in sensitivity compared to the best current method. Furthermore, the area under the ROC curve obtained was 0.93, demonstrating that the probabilities generated by our model are in fact appropriate. Finally, Venn diagrams comparing MUMAL2 with the best current method show that the number of exclusive peptides found by our method was

  18. Hail resistance of solar collectors with tempered glass covers

    Science.gov (United States)

    Lof, G. O. G.; French, R. R.

    1980-01-01

    The resistance of solar collectors glazed with 3 mm of tempered glass to hailstones of up to 10 cm in diameter and 0.5 kg in weight which fell on Fort Collins, Colorado is discussed. Of the ten solar heating systems directly in the hailpath with tempered glass covers, seven were undamaged, two lost one collector panel each, and a 700-panel collector had seven broken covers, amounting to a total breakage of nine panels out of 956, approximately 1%. In addition, one system with nontempered glass covers suffered two glass punctures in a 26-panel collector. It is concluded that the risk of hail damage to commercial solar collectors glazed with 3-mm tempered glass is negligibly small, and greatly exceeded by the risk of hail damage to the roofs of buildings and automobiles or to fiberglass-reinforced polyester sheets used as collector glazings.

  19. 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.

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

    OpenAIRE

    G. Golański

    2008-01-01

    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 temperin...

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

    Science.gov (United States)

    Fonvielle, J A; Reynaud, S; Jacquet, S; LeBerre, B; Ferrier-Pages, C

    2015-01-01

    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.

  2. 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.

  3. A high-throughput de novo sequencing approach for shotgun proteomics using high-resolution tandem mass spectrometry

    Directory of Open Access Journals (Sweden)

    Banfield Jillian F

    2010-03-01

    Full Text Available Abstract Background High-resolution tandem mass spectra can now be readily acquired with hybrid instruments, such as LTQ-Orbitrap and LTQ-FT, in high-throughput shotgun proteomics workflows. The improved spectral quality enables more accurate de novo sequencing for identification of post-translational modifications and amino acid polymorphisms. Results In this study, a new de novo sequencing algorithm, called Vonode, has been developed specifically for analysis of such high-resolution tandem mass spectra. To fully exploit the high mass accuracy of these spectra, a unique scoring system is proposed to evaluate sequence tags based primarily on mass accuracy information of fragment ions. Consensus sequence tags were inferred for 11,422 spectra with an average peptide length of 5.5 residues from a total of 40,297 input spectra acquired in a 24-hour proteomics measurement of Rhodopseudomonas palustris. The accuracy of inferred consensus sequence tags was 84%. According to our comparison, the performance of Vonode was shown to be superior to the PepNovo v2.0 algorithm, in terms of the number of de novo sequenced spectra and the sequencing accuracy. Conclusions Here, we improved de novo sequencing performance by developing a new algorithm specifically for high-resolution tandem mass spectral data. The Vonode algorithm is freely available for download at http://compbio.ornl.gov/Vonode.

  4. Characterization of the stromatolite microbiome from Little Darby Island, The Bahamas using predictive and whole shotgun metagenomic analysis.

    Science.gov (United States)

    Casaburi, Giorgio; Duscher, Alexandrea A; Reid, R Pamela; Foster, Jamie S

    2016-05-01

    Modern stromatolites represent ideal ecosystems to understand the biological processes required for the precipitation of carbonate due to their long evolutionary history and occurrence in a wide range of habitats. However, most of the prior molecular work on stromatolites has focused on understanding the taxonomic complexity and not fully elucidating the functional capabilities of these systems. Here, we begin to characterize the microbiome associated with stromatolites of Little Darby Island, The Bahamas using predictive metagenomics of the 16S rRNA gene coupled with direct whole shotgun sequencing. The metagenomic analysis of the Little Darby stromatolites revealed many shared taxa and core pathways associated with biologically induced carbonate precipitation, suggesting functional convergence within Bahamian stromatolites. A comparison of the Little Darby stromatolites with other lithifying microbial ecosystems also revealed that although factors, such as geographic location and salinity, do drive some differences within the population, there are extensive similarities within the microbial populations. These results suggest that for stromatolite formation, 'who' is in the community is not as critical as metabolic activities and environmental interactions. Together, these analyses help improve our understanding of the similarities among lithifying ecosystems and provide an important first step in characterizing the shared microbiome of modern stromatolites. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

  5. Shotgun Quantitative Proteomic Analysis of Proteins Responding to Drought Stress in Brassica rapa L. (Inbred Line “Chiifu”

    Directory of Open Access Journals (Sweden)

    Soon-Wook Kwon

    2016-01-01

    Full Text Available Through a comparative shotgun quantitative proteomics analysis in Brassica rapa (inbred line Chiifu, total of 3,009 nonredundant proteins were identified with a false discovery rate of 0.01 in 3-week-old plants subjected to dehydration treatment for 0, 24, and 48 h, plants subjected to drought stress. Ribulose-bisphosphate carboxylases, chlorophyll a/b-binding protein, and light harvesting complex in photosystem II were highly abundant proteins in the leaves and accounted for 9%, 2%, and 4%, respectively, of the total identified proteins. Comparative analysis of the treatments enabled detection of 440 differentially expressed proteins during dehydration. The results of clustering analysis, gene ontology (GO enrichment analysis, and analysis of composite expression profiles of functional categories for the differentially expressed proteins indicated that drought stress reduced the levels of proteins associated with photosynthesis and increased the levels of proteins involved in catabolic processes and stress responses. We observed enhanced expression of many proteins involved in osmotic stress responses and proteins with antioxidant activities. Based on previously reported molecular functions, we propose that the following five differentially expressed proteins could provide target genes for engineering drought resistance in plants: annexin, phospholipase D delta, sDNA-binding transcriptional regulator, auxin-responsive GH3 family protein, and TRAF-like family protein.

  6. Shotgun proteomic monitoring of Clostridium acetobutylicum during stationary phase of butanol fermentation using xylose and comparison with the exponential phase

    Energy Technology Data Exchange (ETDEWEB)

    Sivagnanam, Kumaran [McGill University, Montreal, Quebec; Raghavan, Vijaya G. S. [McGill University, Montreal, Quebec; Shah, Manesh B [ORNL; Hettich, Robert {Bob} L [ORNL; Verberkmoes, Nathan C [ORNL; Lefsrud, Mark G [McGill University, Montreal, Quebec

    2012-01-01

    Economically viable production of solvents through acetone butanol ethanol (ABE) fermentation requires a detailed understanding of Clostridium acetobutylicum. This study focuses on the proteomic profiling of C. acetobutylicum ATCC 824 from the stationary phase of ABE fermentation using xylose and compares with the exponential growth by shotgun proteomics approach. Comparative proteomic analysis revealed 22.9% of the C. acetobutylicum genome and 18.6% was found to be common in both exponential and stationary phases. The proteomic profile of C. acetobutylicum changed during the ABE fermentation such that 17 proteins were significantly differentially expressed between the two phases. Specifically, the expression of five proteins namely, CAC2873, CAP0164, CAP0165, CAC3298, and CAC1742 involved in the solvent production pathway were found to be significantly lower in the stationary phase compared to the exponential growth. Similarly, the expression of fucose isomerase (CAC2610), xylulose kinase (CAC2612), and a putative uncharacterized protein (CAC2611) involved in the xylose utilization pathway were also significantly lower in the stationary phase. These findings provide an insight into the metabolic behavior of C. acetobutylicum between different phases of ABE fermentation using xylose.

  7. 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.

  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. Tracking the sources of blood meals of parasitic arthropods using shotgun proteomics and unidentified tandem mass spectral libraries.

    Science.gov (United States)

    Önder, Özlem; Shao, Wenguang; Lam, Henry; Brisson, Dustin

    2014-04-01

    Identifying the species on which hematophagous arthropods feed is crucial for studying the factors that affect pathogen distributions and that can aid public health. Here we describe a protocol to identify the species a parasitic arthropod has previously fed upon by identifying the source of the remnants of a previous blood meal via shotgun proteomics and spectral matching. The protocol is a nontargeted approach that uses the entire detected blood proteome for source identification; it does not require a priori knowledge of genome or protein sequences. Instead, reference spectral libraries are compiled from the blood of multiple host species by using SpectraST, which takes ∼4 d; the identification of the species from which a previous blood meal of a hematophagous arthropod was taken is achieved with spectral matching against the reference spectral libraries, which takes approximately another 4 d. This method is robust against random degradation of the blood meal and can identify unknown blood remnants months after the feeding event.

  10. 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.

  11. Shotgun redox proteomics: identification and quantitation of carbonylated proteins in the UVB-resistant marine bacterium, Photobacterium angustum S14.

    Directory of Open Access Journals (Sweden)

    Sabine Matallana-Surget

    Full Text Available UVB oxidizes proteins through the generation of reactive oxygen species. One consequence of UVB irradiation is carbonylation, the irreversible formation of a carbonyl group on proline, lysine, arginine or threonine residues. In this study, redox proteomics was performed to identify carbonylated proteins in the UVB resistant marine bacterium Photobacterium angustum. Mass-spectrometry was performed with either biotin-labeled or dinitrophenylhydrazide (DNPH derivatized proteins. The DNPH redox proteomics method enabled the identification of 62 carbonylated proteins (5% of 1221 identified proteins in cells exposed to UVB or darkness. Eleven carbonylated proteins were quantified and the UVB/dark abundance ratio was determined at both the protein and peptide levels. As a result we determined which functional classes of proteins were carbonylated, which residues were preferentially modified, and what the implications of the carbonylation were for protein function. As the first large scale, shotgun redox proteomics analysis examining carbonylation to be performed on bacteria, our study provides a new level of understanding about the effects of UVB on cellular proteins, and provides a methodology for advancing studies in other biological systems.

  12. Shotgun redox proteomics: identification and quantitation of carbonylated proteins in the UVB-resistant marine bacterium, Photobacterium angustum S14.

    Science.gov (United States)

    Matallana-Surget, Sabine; Cavicchioli, Ricardo; Fauconnier, Charles; Wattiez, Ruddy; Leroy, Baptiste; Joux, Fabien; Raftery, Mark J; Lebaron, Philippe

    2013-01-01

    UVB oxidizes proteins through the generation of reactive oxygen species. One consequence of UVB irradiation is carbonylation, the irreversible formation of a carbonyl group on proline, lysine, arginine or threonine residues. In this study, redox proteomics was performed to identify carbonylated proteins in the UVB resistant marine bacterium Photobacterium angustum. Mass-spectrometry was performed with either biotin-labeled or dinitrophenylhydrazide (DNPH) derivatized proteins. The DNPH redox proteomics method enabled the identification of 62 carbonylated proteins (5% of 1221 identified proteins) in cells exposed to UVB or darkness. Eleven carbonylated proteins were quantified and the UVB/dark abundance ratio was determined at both the protein and peptide levels. As a result we determined which functional classes of proteins were carbonylated, which residues were preferentially modified, and what the implications of the carbonylation were for protein function. As the first large scale, shotgun redox proteomics analysis examining carbonylation to be performed on bacteria, our study provides a new level of understanding about the effects of UVB on cellular proteins, and provides a methodology for advancing studies in other biological systems.

  13. A multidimensional liquid chromatography-tandem mass spectrometry platform to improve protein identification in high-throughput shotgun proteomics.

    Science.gov (United States)

    Capriotti, Anna Laura; Cavaliere, Chiara; Cavazzini, Alberto; Gasparrini, Francesco; Pierri, Giuseppe; Piovesana, Susy; Laganà, Aldo

    2017-05-19

    A new on-line multidimensional system for sequential trapping and individual elution and separation of peptides based on their molecular weight is described. By sequentially using two chemically different trapping columns, a polymethacrylate monolith and a packed C18 one, peptides from complex samples can be on-line trapped and divided into two fractions, containing respectively mainly medium-large peptides and smaller peptides. Then, by means of two switching valves working in parallel, the two fractions were individually separated by reversed phase chromatography. The whole gradient consisted of two subgradients, with the first one dedicated to the separation of smaller peptides and the second one to the separation of larger peptides. Such configuration allowed to identify up to 1476 proteins in a standard E. coli tryptic digest, with improved performance, increased average sequence coverage and reduced single unique peptide identifications compared to a conventional shotgun proteomics configuration comprising only the C18 trapping column and the analytical column. Copyright © 2017 Elsevier B.V. All rights reserved.

  14. 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...

  15. 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

  16. The investigation of applicability of the Hollomon-Jaffe equation on tempering the HSLA steel

    OpenAIRE

    A. Patarić; Mihailović, M.; Z. Gulišija; Z. Janjušević

    2009-01-01

    High strength low-alloyed (HSLA) Cr-Mn-Si steels belong to a group of steels that can reach their full mechanical properties after quenching and tempering. Those properties depend both on the temperature and time of tempering. Knowing the tempering parameters, it is possible to reach the desired properties of the treated steel. Some results on investigating the Hollomon-Jaffe equation (in parametric form) application for tempering of HSLA steel, are shown in this paper. The experiments were p...

  17. 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).

  18. 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.

  19. A note on the water budget of temperate glaciers

    NARCIS (Netherlands)

    Oerlemans, J.

    2013-01-01

    In this note, the total dissipative melting in temperate glaciers is studied. The analysis is based on the notion that the dissipation is determined by the loss of potential energy due to the downward motion of mass (ice, snow, meltwater and rain). A mathematical formulation of the dissipation is

  20. Effect of climate change on temperate forest ecosystems

    NARCIS (Netherlands)

    Brolsma, R.J.|info:eu-repo/dai/nl/304847364

    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

  1. Dry kiln schedules for commercial woods : temperate and tropical

    Science.gov (United States)

    R. Sidney Boone; Charles J. Kozlik; Paul J. Bois; Eugene M. Wengert

    1988-01-01

    This report contains suggested dry kiln schedules for over 500 commercial woods, both temperate and tropical. Kiln schedules are completely assembled and written out for easy use. Schedules for several thicknesses and specialty products (e.g. squares, handle stock, gunstock blanks) are given for many species. The majority of the schedules are from the world literature...

  2. ballistic performance of a quenched and tempered steel against ...

    African Journals Online (AJOL)

    eobe

    Author, Tel: +234-805-671-5551. BALLISTIC PERFORMANCE OF A QUENCHED AND TEMPERED STEEL. AGAINST 7.62MM CALIBRE. AGAINST 7.62MM CALIBRE PROJECTILE. PROJECTILE. PROJECTILE. O. M. Sanusi1 and J. O. Akindapo2. 1RESEARCH AND DEVELOPMENT CENTRE, DEFENCE INDUSTRIES ...

  3. 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...

  4. Mixed livestock grazing in diverse temperate and semi-arid ...

    African Journals Online (AJOL)

    Concerns for product quality, uniformity and continuity and for animal welfare will increasingly drive production processes. In this paper, the potential of mixed grazing for higher output of quality animal products, within these constraints, is assessed under both temperate and semi-arid conditions. Complementary ...

  5. Conservation importance of early post-disturbance temperate forests

    Science.gov (United States)

    Charles Kwit; David I. King; Beverly Collins; Mark E. Swanson

    2014-01-01

    The early post-disturbance stage of temperate forest succession (also referred to as 'early-seral' or 'early-successional' forest) has been the subject of interest and debate. Often thought of as an ephemeral (and often disorganized) state of eventual closed-canopy systems, its direct and immediate role in conservation traditionally has been ignored...

  6. 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...

  7. Temperate non-breeding surveys - a key to shorebird conservation

    Science.gov (United States)

    Sue Thomas

    2005-01-01

    Completion of the United States and Canadian shorebird conservation plans recently identified and prioritized shorebird monitoring, management, and conservation needs in the Western Hemisphere. We present an emerging approach to monitor shorebird use of temperate non-breeding areas under the Program for Regional and International Shorebird Monitoring (PRISM). This...

  8. Tempered Water Lower Port Connector Structural Analysis Verification

    Energy Technology Data Exchange (ETDEWEB)

    CREA, B.A.

    2000-05-05

    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.

  9. Late Glacial and Holocene Paleoliminology of two temperate lakes ...

    Indian Academy of Sciences (India)

    The stable carbon isotope (13C) and elemental C/N ratios in Total Organic Carbon (TOC) extracted from radiometrically dated cores from two Midwestern USA lakes were determined to investigate the factors that control these values in temperate lakes. The range of 13C values ( -26 to -32%) and C/N ratios (mean value ...

  10. Temperate forest dynamics and carbon storage: A 26-year case ...

    African Journals Online (AJOL)

    Temperate forests are globally important carbon stores that are, in the face of recent improvements in their conservation, likely to increase their storage capacity in the future. Despite this, these ecosystems are poorly understood, especially over longer time periods. To remedy this and to better understand these important ...

  11. Effect of tempering after cryogenic treatment of tungsten carbide ...

    Indian Academy of Sciences (India)

    Cryogenic treatment is a recent advancement in the field of machining to improve the properties of cutting tool materials. Tungsten carbide is the most commonly used cutting tool material in the industry and the technique can also be extended to it. Although the importance of tempering after cryogenic treatment has been ...

  12. 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

  13. Silviculture for restoration of degraded temperate and boreal forests

    Science.gov (United States)

    John A. Stanturf; Palle Madsen; Emile S. Gardiner

    2004-01-01

    Throughout the temperate and boreal zones, human intervention has influenced landscapes and forests for millennia. The degree of human disturbance has only been constrained by the technology and resources available to different cultures and by time since initial habitation. Humans have influenced forests by regulating populations of browsers, clearing for agriculture,...

  14. Testosterone, territorial response, and song in seasonally breeding tropical and temperate stonechats.

    Science.gov (United States)

    Apfelbeck, Beate; Mortega, Kim G; Flinks, Heiner; Illera, Juan Carlos; Helm, Barbara

    2017-04-17

    Testosterone facilitates physiological, morphological, and behavioral changes required for breeding in male vertebrates. However, testosterone concentrations and the link between its seasonal changes and those in reproductive behaviors vary greatly among species. To better understand the impact of tropical and temperate environments and life history factors on this variation, we have compared testosterone, territorial behavior and song performance across sequential stages of the breeding season in males of 16 closely related taxa of East African tropical and West European temperate stonechats (Saxicola spp), which all breed during a short breeding season, but differ in migratory behavior, seasonal territory-acquisition and pace of life. We found that generally, the profiles of testosterone and territorial behavior were similar across latitudes. African stonechats with a slow pace of life had equally high peak testosterone concentrations and responded as aggressively to an intruder as European stonechats with a fast pace of life. However, song performance at the beginning of the breeding season was lower in African than in European stonechats. The differences in song performance were not associated with variation in testosterone levels between tropical and temperate stonechats. The results suggest a very similar role for testosterone as a mediator of high intensity territorial aggression during the fertile period of females in tropical and temperate stonechats, which all are highly seasonal, locally synchronous breeders. A potential explanation may be high risk of extra-pair copulations which has been associated with synchronous breeding. Interestingly, an association was not consistent for song performance. Our data suggest that song performance can be disassociated from peak testosterone levels depending on its role in breeding behavior. Despite similar testosterone levels, European males, which early in the breeding season acquire territories and mates, showed

  15. Ecophysiological roles of abaxial anthocyanins in a perennial understorey herb from temperate deciduous forests.

    Science.gov (United States)

    Fernández-Marín, Beatriz; Esteban, Raquel; Míguez, Fátima; Artetxe, Unai; Castañeda, Verónica; Pintó-Marijuan, Marta; Becerril, José María; García-Plazaola, José Ignacio

    2015-04-28

    Accumulation of abaxial anthocyanins is an intriguing leaf trait particularly common among deeply shaded understorey plants of tropical and temperate forests whose ecological significance is still not properly understood. To shed light on it, possible ecophysiological roles of abaxial anthocyanins were tested in the perennial understorey herb of temperate deciduous forests Saxifraga hirsuta, chosen as a model species due to the coexistence of green and anthocyanic leaves and the presence of an easily removable lower anthocyanic epidermis. Anthocyanins accumulated during autumn, which temporally matched the overstorey leaf fall. Patterns of development of abaxial anthocyanins and direct measurements of photochemical efficiency under monochromatic light were not consistent with a photoprotective hypothesis. Enhancement of light capture also seemed unlikely since the back-scattering of red light towards the lower mesophyll was negligible. Seed germination was similar under acyanic and anthocyanic leaves. A relevant consequence of abaxial anthocyanins was the dramatic reduction of light transmission through the leaf. The dark environment generated underneath the Saxifraga canopy was enhanced by the horizontal repositioning of leaves, which occurs in parallel with reddening. This might play a role in biotic interactions by inhibiting vital processes of competitors, which may be of especial importance in spring before the overstorey leaves sprout. Published by Oxford University Press on behalf of the Annals of Botany Company.

  16. 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.

  17. Significant N₂ fixation by heterotrophs, photoheterotrophs and heterocystous cyanobacteria in two temperate estuaries.

    Science.gov (United States)

    Bentzon-Tilia, Mikkel; Traving, Sachia J; Mantikci, Mustafa; Knudsen-Leerbeck, Helle; Hansen, Jørgen L S; Markager, Stiig; Riemann, Lasse

    2015-02-01

    Nitrogen (N) fixation is fueling planktonic production in a multitude of aquatic environments. In meso- and poly-haline estuaries, however, the contribution of N by pelagic N₂ fixation is believed to be insignificant due to the high input of N from land and the presumed absence of active N₂-fixing organisms. Here we report N₂ fixation rates, nifH gene composition and nifH gene transcript abundance for key diazotrophic groups over 1 year in two contrasting, temperate, estuarine systems: Roskilde Fjord (RF) and the Great Belt (GB) strait. Annual pelagic N₂ fixation rates averaged 17 and 61 mmol N m(-2) per year at the two sites, respectively. In RF, N₂ fixation was mainly accompanied by transcripts related to heterotrophic (for example, Pseudomonas sp.) and photoheterotrophic bacteria (for example, unicellular diazotrophic cyanobacteria group A). In the GB, the first of two N₂ fixation peaks coincided with a similar nifH-expressing community as in RF, whereas the second peak was synchronous with increased nifH expression by an array of diazotrophs, including heterotrophic organisms as well as the heterocystous cyanobacterium Anabaena. Thus, we show for the first time that significant planktonic N₂ fixation takes place in mesohaline, temperate estuaries and that the importance of heterotrophic, photoheterotrophic and photosynthetic diazotrophs is clearly variable in space and time.

  18. Significant N2 fixation by heterotrophs, photoheterotrophs and heterocystous cyanobacteria in two temperate estuaries

    Science.gov (United States)

    Bentzon-Tilia, Mikkel; Traving, Sachia J; Mantikci, Mustafa; Knudsen-Leerbeck, Helle; Hansen, Jørgen LS; Markager, Stiig; Riemann, Lasse

    2015-01-01

    Nitrogen (N) fixation is fueling planktonic production in a multitude of aquatic environments. In meso- and poly-haline estuaries, however, the contribution of N by pelagic N2 fixation is believed to be insignificant due to the high input of N from land and the presumed absence of active N2-fixing organisms. Here we report N2 fixation rates, nifH gene composition and nifH gene transcript abundance for key diazotrophic groups over 1 year in two contrasting, temperate, estuarine systems: Roskilde Fjord (RF) and the Great Belt (GB) strait. Annual pelagic N2 fixation rates averaged 17 and 61 mmol N m−2 per year at the two sites, respectively. In RF, N2 fixation was mainly accompanied by transcripts related to heterotrophic (for example, Pseudomonas sp.) and photoheterotrophic bacteria (for example, unicellular diazotrophic cyanobacteria group A). In the GB, the first of two N2 fixation peaks coincided with a similar nifH-expressing community as in RF, whereas the second peak was synchronous with increased nifH expression by an array of diazotrophs, including heterotrophic organisms as well as the heterocystous cyanobacterium Anabaena. Thus, we show for the first time that significant planktonic N2 fixation takes place in mesohaline, temperate estuaries and that the importance of heterotrophic, photoheterotrophic and photosynthetic diazotrophs is clearly variable in space and time. PMID:25026373

  19. 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

  20. 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

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

    Science.gov (United States)

    Dsouza, Melissa; Taylor, Michael W; Turner, Susan J; Aislabie, Jackie

    2014-01-01

    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 investigations into

  2. Processing shotgun proteomics data on the Amazon cloud with the trans-proteomic pipeline.

    Science.gov (United States)

    Slagel, Joseph; Mendoza, Luis; Shteynberg, David; Deutsch, Eric W; Moritz, Robert L

    2015-02-01

    Cloud computing, where scalable, on-demand compute cycles and storage are available as a service, has the potential to accelerate mass spectrometry-based proteomics research by providing simple, expandable, and affordable large-scale computing to all laboratories regardless of location or information technology expertise. We present new cloud computing functionality for the Trans-Proteomic Pipeline, a free and open-source suite of tools for the processing and analysis of tandem mass spectrometry datasets. Enabled with Amazon Web Services cloud computing, the Trans-Proteomic Pipeline now accesses large scale computing resources, limited only by the available Amazon Web Services infrastructure, for all users. The Trans-Proteomic Pipeline runs in an environment fully hosted on Amazon Web Services, where all software and data reside on cloud resources to tackle large search studies. In addition, it can also be run on a local computer with computationally intensive tasks launched onto the Amazon Elastic Compute Cloud service to greatly decrease analysis times. We describe the new Trans-Proteomic Pipeline cloud service components, compare the relative performance and costs of various Elastic Compute Cloud service instance types, and present on-line tutorials that enable users to learn how to deploy cloud computing technology rapidly with the Trans-Proteomic Pipeline. We provide tools for estimating the necessary computing resources and costs given the scale of a job and demonstrate the use of cloud enabled Trans-Proteomic Pipeline by performing over 1100 tandem mass spectrometry files through four proteomic search engines in 9 h and at a very low cost. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  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. 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.

  5. Shotgun metagenomic analysis of metabolic diversity and microbial community structure in experimental vernal pools subjected to nitrate pulse.

    Science.gov (United States)

    Carrino-Kyker, Sarah R; Smemo, Kurt A; Burke, David J

    2013-04-10

    Human activities have greatly increased nitrogen (N) levels in natural habitats through atmospheric N deposition and nutrient leaching, which can have large effects on N cycling and other ecosystem processes. Because of the significant role microorganisms play in N cycling, high inputs of nitrogenous compounds, such as nitrate (NO3-), into natural ecosystems could have cascading effects on microbial community structure and the metabolic processes that microbes perform. To investigate the multiple effects of NO3- pollution on microbial communities, we created two shotgun metagenomes from vernal pool microcosms that were either enriched with a solution of 10 mg NO3--N (+NO3-) or received distilled water as a control (-N). After only 20 hours of exposure to NO3-, the initial microbial community had shifted toward one containing a higher proportional abundance of stress tolerance and fermentation environmental gene tags (EGTs). Surprisingly, we found no changes to N metabolism EGTs, even though large shifts in denitrification rates were seen between the +NO3- and -N microcosms. Thus, in the absence of NO3- addition, it is plausible that the microbes used other respiratory pathways for energy. Respiratory pathways involving iron may have been particularly important in our -N microcosms, since iron acquisition EGTs were proportionally higher in the -N metagenome. Additionally, we noted a proportional increase in Acidobacteria and Alphaproteobacteria EGTs in response to NO3- addition. These community shifts in were not evident with TRFLP, suggesting that metagenomic analyses may detect fine-scale changes not possible with community profiling techniques. Our results suggest that the vernal pool microbial communities profiled here may rely on their metabolic plasticity for growth and survival when certain resources are limiting. The creation of these metagenomes also highlights how little is known about the effects of NO3- pollution on microbial communities, and the

  6. Shotgun Proteomics Identifies Serum Fibronectin as a Candidate Diagnostic Biomarker for Inclusion in Future Multiplex Tests for Ectopic Pregnancy

    Science.gov (United States)

    Brown, Jeremy K.; Lauer, Katarina B.; Ironmonger, Emily L.; Inglis, Neil F.; Bourne, Tom H.; Critchley, Hilary O. D.; Horne, Andrew W.

    2013-01-01

    Ectopic pregnancy (EP) is difficult to diagnose early and accurately. Women often present at emergency departments in early pregnancy with a ‘pregnancy of unknown location’ (PUL), and diagnosis and exclusion of EP is challenging due to a lack of reliable biomarkers. The objective of this study was to identify novel diagnostic biomarkers for EP. Shotgun proteomics, incorporating combinatorial-ligand library pre-fractionation, was used to interrogate pooled sera (n = 40) from women undergoing surgery for EP, termination of viable intrauterine pregnancy and management of non-viable intrauterine pregnancy. Western blot was used to validate results in individual sera. ELISAs were developed to interrogate sera from women with PUL (n = 120). Sera were collected at time of first symptomatic presentation and categorized according to pregnancy outcome. The main outcome measures were differences between groups and area under the receiver operating curve (ROC). Proteomics identified six biomarker candidates. Western blot detected significant differences in levels of two of these candidates. ELISA of sera from second cohort revealed that these differences were only significant for one of these candidates, fibronectin. ROC analysis of ability of fibronectin to discriminate EP from other pregnancy outcomes suggested that fibronectin has diagnostic potential (ROC 0.6439; 95% CI 0.5090 to 0.7788; P>0.05), becoming significant when ‘ambiguous’ medically managed PUL excluded from analysis (ROC 0.6538; 95% CI 0.5158 to 0.7918; P<0.05). Fibronectin may make a useful adjunct to future multiplex EP diagnostic tests. PMID:23826180

  7. Phage-Induced Expression of CRISPR-Associated Proteins is Revealed by Shotgun Proteomics in Streptococcus thermophilus

    Energy Technology Data Exchange (ETDEWEB)

    Young, Jacque C [ORNL; Dill, Brian [ORNL; Pan, Chongle [ORNL; Hettich, Robert {Bob} L [ORNL; Banfield, Jillian F. [University of California, Berkeley; Shah, Manesh B [ORNL; Fremaux, Christophe [Danisco France SAS; Horvath, Philippe [Danisco France SAS; Barrangou, Rodolphe [Danisco USA; Verberkmoes, Nathan C [ORNL

    2012-01-01

    The CRISPR/Cas system, comprised of clustered regularly interspaced short palindromic repeats along with their associated (Cas) proteins, protects bacteria and archaea from viral predation and invading nucleic acids. While the mechanism of action for this acquired immunity is currently under investigation, the response of Cas protein expression to phage infection has yet to be elucidated. In this study, we employed shotgun proteomics to measure the global proteome expression in a model system for studying the CRISPR/Cas response: infection of S. thermophilus DGCC7710 with phage 2972. Host and viral proteins were simultaneously measured following inoculation at two different multiplicities of infection and across various time points using two-dimensional liquid chromatography tandem mass spectroscopy. Thirty-seven out of forty predicted viral proteins were detected, including all proteins of the structural virome and viral effector proteins. In total, 1,013 of 2,079 predicted S. thermophilus proteins were detected, facilitating the monitoring of host protein synthesis changes in response to virus infection. Importantly, Cas proteins from all four CRISPR loci in the S. thermophilus DGCC7710 genome were detected, including loci previously thought to be inactive. Many Cas proteins were found to be constitutively expressed, but several demonstrated increased abundance during peak infection, including the Cas9 proteins from the CRISPR1 and CRISPR3 loci, which are key players in the interference phase of the CRISPR/Cas response. Altogether, these results provide novel insights into the proteomic response of S. thermophilus, specifically CRISPR-associated proteins, upon phage 2972 infection.

  8. Deciphering upper respiratory tract microbiota complexity in healthy calves and calves that develop respiratory disease using shotgun metagenomics.

    Science.gov (United States)

    Gaeta, Natália C; Lima, Svetlana F; Teixeira, Andre G; Ganda, Erika K; Oikonomou, Georgios; Gregory, Lilian; Bicalho, Rodrigo C

    2017-02-01

    Bovine respiratory disease (BRD) is a multifactorial disorder responsible for severe economic losses in dairy and feedlot herds. Advances in next-generation sequencing mean that microbial communities in clinical samples, including non-culturable bacteria, can be characterized. Our aim was to evaluate the microbiota of the upper respiratory tract of healthy calves and calves with BRD using whole-genome sequencing (shotgun metagenomics). We performed deep nasopharyngeal swabs on 16 Holstein heifer calves (10 healthy and 6 diagnosed with BRD during the study) at 14 and 28 d of life in 1 dairy herd near Ithaca, New York. Total DNA was extracted, and whole-genome sequencing was performed using the MiSeq Illumina platform (Illumina Inc., San Diego, CA). Samples included 5 predominant phyla: Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes, and Tenericutes. At the genus level, we observed differences between groups for Pseudomonas spp. At the species level, Mannheimia haemolytica was the most abundant bacterium detected. We detected significant differences between groups of calves in the relative abundance of Pseudomonas fluorescens. Pasteurella multocida was among the 20 most abundant species, and Moraxella catarrhalis, commonly associated with pneumonia in humans, was detected in all groups. Analysis of resistance to antibiotics and compounds profiling revealed differences in cobalt-zinc-cadmium resistance. Further research to elucidate the role of Moraxella catarrhalis in BRD is warranted. Genes that were resistant to cobalt-zinc-cadmium, observed mostly in calves with BRD, might be associated with difficulties in antibiotic treatment. Copyright © 2017 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

  9. Shotgun label-free proteomic analysis of clubroot (Plasmodiophora brassicae resistance conferred by the gene Rcr1 in Brassica rapa

    Directory of Open Access Journals (Sweden)

    Tao Song

    2016-07-01

    Full Text Available Clubroot, caused by the plasmodiophorid pathogen Plasmodiophora brassicae, is one of the most serious diseases on Brassica crops worldwide and a major threat to canola production in western Canada. Host resistance is the key strategy for clubroot management on canola. Several clubroot resistance (CR genes have been identified, but the mechanisms associated with these CR genes are poorly understood. In the current study, a label-free shotgun proteomic approach was used to profile and compare the proteomes of B. rapa carrying and not carrying the CR gene Rcr1 upon P. brassicae infection. A total of 527 differentially accumulated proteins (DAPs were identified between the resistant and susceptible samples, and functional annotation of these DAPs indicates that the perception of P. brassicae and activation of defense responses is triggered via an unique signaling pathway distinct from common modes of recognition receptors reported with many other plant-pathogen interactions; this pathway appears to act in a calcium-independent manner through a not-well defined cascade of mitogen-activated protein kinases and may require the ubiquitin-26S proteasome related to abiotic stresses, especially the cold-stress tolerance. Both up-regulation of defense-related and down-regulation of pathogenicity-related metabolism were observed in plants carrying Rcr1, and these functions may all contribute to the clubroot resistance mediated by this CR gene. These results, combined with those of transcriptomic analysis reported earlier, improved our understanding of molecular mechanisms associated with Rcr1 and clubroot resistance at large, and identified candidate metabolites or pathways for further confirmation of specific resistance mechanisms. Deploying CR genes with different modes of action may help improve the durability of clubroot resistance.

  10. 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

  11. Dynamic and temporal assessment of human dried blood spot MS/MSALL shotgun lipidomics analysis.

    Science.gov (United States)

    Gao, Fei; McDaniel, Justice; Chen, Emily Y; Rockwell, Hannah E; Drolet, Jeremy; Vishnudas, Vivek K; Tolstikov, Vladimir; Sarangarajan, Rangaprasad; Narain, Niven R; Kiebish, Michael A

    2017-01-01

    Real-time and dynamic assessment of an individual's lipid homeostatic state in blood is complicated due to the need to collect samples in a clinical environment. In the context of precision medicine and population health, tools that facilitate sample collection and empower the individual to participate in the process are necessary to complement advanced bioanalytical analysis. The dried blood spot (DBS) methodology via finger prick or heel prick is a minimally invasive sample collection method that allows the relative ease and low cost of sample collection as well as transport. However, it has yet to be integrated into broad scale personalized lipidomic analysis. Therefore, in this study we report the development of a novel DBS high resolution MS/MSALL lipidomics workflow. In this report we compared lipidomic analysis of four types of blood sample collection methods (DBS, venous whole blood, serum, and plasma) across several parameters, which include lipidomics coverage of each matrix and the effects of temperature and time on the coverage and stability of different lipid classes and molecular species. The novel DBS-MS/MSALL lipidomics platform developed in this report was then applied to examine postprandial effects on the blood lipidome and further to explore the temporal fluctuation of the lipidome across hours and days. More than 1,200 lipid molecular species from a single DBS sample were identified and quantified. The lipidomics profile of the DBS samples is comparable to whole blood matrix. DBS-MS/MSALL lipidomic analysis in postprandial experiments revealed significant alterations in triacylglyceride species. Temporal analysis of the lipidome at various times in the day and across days identified several lipid species that fluctuate as a function of time, and a subset of lipid species were identified to be significantly altered across hours within a day and within successive days of the week. A novel DBS-MS/MSALL lipidomics method has been established for

  12. 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

  13. Limits to diffusive O2 transport: flow, form, and function in nudibranch egg masses from temperate and polar regions.

    Directory of Open Access Journals (Sweden)

    Amy L Moran

    Full Text Available BACKGROUND: Many aquatic animals enclose embryos in gelatinous masses, and these embryos rely on diffusion to supply oxygen. Mass structure plays an important role in limiting or facilitating O2 supply, but external factors such as temperature and photosynthesis can play important roles as well. Other external factors are less well understood. METHODOLOGY/PRINCIPAL FINDINGS: We first explored the effects of water flow on O2 levels inside nudibranch embryo masses and compared the effects of flow on masses from temperate and polar regions. Water flow (still vs. vigorously bubbled had a strong effect on central O2 levels in all masses; in still water, masses were considerably more hypoxic than in bubbled water. This effect was stronger in temperate than in polar masses, likely due to the increased metabolic demand and O2 consumption of temperate masses. Second, we made what are to our knowledge the first measurements of O2 in invertebrate masses in the field. Consistent with laboratory experiments, O2 in Antarctic masses was high in masses in situ, suggesting that boundary-layer effects do not substantially limit O2 supply to polar embryos in the field. CONCLUSIONS/SIGNIFICANCE: All else being equal, boundary layers are more likely to depress O2 in masses in temperate or tropical regions; thus, selection on parents to choose high-flow sites for mass deposition is likely greater in warm water. Because of the large number of variables affecting diffusive O2 supply to embryos in their natural environment, field observations are necessary to test hypotheses generated from laboratory experiments and mathematical modeling.

  14. 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

    OpenAIRE

    Palma, Álvaro T.; F. PATRICIO OJEDA

    2002-01-01

    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 tha...

  15. Shotgun analysis of membrane proteomes by an improved SDS-assisted sample preparation method coupled with liquid chromatography-tandem mass spectrometry.

    Science.gov (United States)

    Lin, Yong; Jiang, Huajun; Yan, Yujun; Peng, Bin; Chen, Jinhua; Lin, Haiyan; Liu, Zhonghua

    2012-12-12

    Analysis of the membrane proteins, particularly the integral membrane proteins, is limited by the inherent membrane hydrophobicity. Sodium dodecyl sulfate (SDS) is one of the most efficient reagents used for the extraction of membrane proteins, but its presence in samples interferes with LC-MS-based proteomic analyses because it affects RP-LC separations and electrospray ionization. In this paper, we present an improved sample preparation strategy based on SDS-assisted digestion and peptide-level SDS-removal using an optimized potassium dodecyl sulfate (KDS) precipitation method (SSDP method) for shotgun analysis of the membrane proteome. This method utilizes a high concentration of SDS (1.0%) to lyse the membranes and to solubilize the hydrophobic membrane proteins, resulting in a more complete protein digestion in the diluted SDS buffer (0.1% SDS), and a high efficiency of SDS removal and peptide recovery by the optimized KDS precipitation for protein identification. The SSDP method provides evidence that proteins can be efficiently digested, and the SDS can be decreased to 95% peptide recovery. Compared to other sample preparation methods commonly used in shotgun membrane proteomics, the newly developed method not only increased the identified number of the total proteins, membrane proteins and integral membrane proteins by an average of 33.1%, 37.2% and 40.5%, respectively, but also leading to the identification of highest number of matching peptides. All the results showed that the method yielded better recovery and reliability in the identification of the proteins especially the highly hydrophobic integral membrane proteins, and thus providing a promising tool for the shotgun analysis of membrane proteome. Copyright © 2012 Elsevier B.V. All rights reserved.

  16. 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.

  17. 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.

  18. Bifurcation dynamics of the tempered fractional Langevin equation.

    Science.gov (United States)

    Zeng, Caibin; Yang, Qigui; Chen, YangQuan

    2016-08-01

    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.

  19. 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.

  20. Generalized Langevin equation with tempered memory kernel

    Science.gov (United States)

    Liemert, André; Sandev, Trifce; Kantz, Holger

    2017-01-01

    We study a generalized Langevin equation for a free particle in presence of a truncated power-law and Mittag-Leffler memory kernel. It is shown that in presence of truncation, the particle from subdiffusive behavior in the short time limit, turns to normal diffusion in the long time limit. The case of harmonic oscillator is considered as well, and the relaxation functions and the normalized displacement correlation function are represented in an exact form. By considering external time-dependent periodic force we obtain resonant behavior even in case of a free particle due to the influence of the environment on the particle movement. Additionally, the double-peak phenomenon in the imaginary part of the complex susceptibility is observed. It is obtained that the truncation parameter has a huge influence on the behavior of these quantities, and it is shown how the truncation parameter changes the critical frequencies. The normalized displacement correlation function for a fractional generalized Langevin equation is investigated as well. All the results are exact and given in terms of the three parameter Mittag-Leffler function and the Prabhakar generalized integral operator, which in the kernel contains a three parameter Mittag-Leffler function. Such kind of truncated Langevin equation motion can be of high relevance for the description of lateral diffusion of lipids and proteins in cell membranes.

  1. Linking energetics and overwintering in temperate insects.

    Science.gov (United States)

    Sinclair, Brent J

    2015-12-01

    Overwintering insects cannot feed, and energy they take into winter must therefore fuel energy demands during autumn, overwintering, warm periods prior to resumption of development in spring, and subsequent activity. Insects primarily consume lipids during winter, but may also use carbohydrate and proteins as fuel. Because they are ectotherms, the metabolic rate of insects is temperature-dependent, and the curvilinear nature of the metabolic rate-temperature relationship means that warm temperatures are disproportionately important to overwinter energy use. This energy use may be reduced physiologically, by reducing the slope or elevation of the metabolic rate-temperature relationship, or because of threshold changes, such as metabolic suppression upon freezing. Insects may also choose microhabitats or life history stages that reduce the impact of overwinter energy drain. There is considerable capacity for overwinter energy drain to affect insect survival and performance both directly (via starvation) or indirectly (for example, through a trade-off with cryoprotection), but this has not been well-explored. Likewise, the impact of overwinter energy drain on growing-season performance is not well understood. I conclude that overwinter energetics provides a useful lens through which to link physiology and ecology and winter and summer in studies of insect responses to their environment. Copyright © 2014 Elsevier Ltd. All rights reserved.

  2. Tropical fishes dominate temperate reef fish communities within western Japan.

    Science.gov (United States)

    Nakamura, Yohei; Feary, David A; Kanda, Masaru; Yamaoka, Kosaku

    2013-01-01

    Climate change is resulting in rapid poleward shifts in the geographical distribution of tropical and subtropical fish species. We can expect that such range shifts are likely to be limited by species-specific resource requirements, with temperate rocky reefs potentially lacking a range of settlement substrates or specific dietary components important in structuring the settlement and success of tropical and subtropical fish species. We examined the importance of resource use in structuring the distribution patterns of range shifting tropical and subtropical fishes, comparing this with resident temperate fish species within western Japan (Tosa Bay); the abundance, diversity, size class, functional structure and latitudinal range of reef fishes utilizing both coral reef and adjacent rocky reef habitat were quantified over a 2 year period (2008-2010). This region has undergone rapid poleward expansion of reef-building corals in response to increasing coastal water temperatures, and forms one of the global hotspots for rapid coastal changes. Despite the temperate latitude surveyed (33°N, 133°E) the fish assemblage was both numerically, and in terms of richness, dominated by tropical fishes. Such tropical faunal dominance was apparent within both coral, and rocky reef habitats. The size structure of the assemblage suggested that a relatively large number of tropical species are overwintering within both coral and rocky habitats, with a subset of these species being potentially reproductively active. The relatively high abundance and richness of tropical species with obligate associations with live coral resources (i.e., obligate corallivores) shows that this region holds the most well developed temperate-located tropical fish fauna globally. We argue that future tropicalisation of the fish fauna in western Japan, associated with increasing coral habitat development and reported increasing shifts in coastal water temperatures, may have considerable positive economic

  3. Increase in forest growth: new evidences from temperate forests

    Directory of Open Access Journals (Sweden)

    Lingua E

    2010-07-01

    Full Text Available A paper recently published on PNAS provides a new evidence for an increase in forest growth in temperate forests. The possible causes of this process are discussed. The results show a relation between this change in tree growth with the increase in atmospheric CO2 concentration, temperature, and length of growth season. A better understanding of the specific mechanisms involved and the assessment of the consequences on the current and future global changes are needed.

  4. Tropical Fishes Dominate Temperate Reef Fish Communities within Western Japan

    OpenAIRE

    Yohei Nakamura; Feary, David A.; Masaru Kanda; Kosaku Yamaoka

    2013-01-01

    Climate change is resulting in rapid poleward shifts in the geographical distribution of tropical and subtropical fish species. We can expect that such range shifts are likely to be limited by species-specific resource requirements, with temperate rocky reefs potentially lacking a range of settlement substrates or specific dietary components important in structuring the settlement and success of tropical and subtropical fish species. We examined the importance of resource use in structuring t...

  5. 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

  6. The Research and Application of Webpage Temper-proofing System

    OpenAIRE

    Wang Yongquan; Wu Beihua

    2012-01-01

    With the sharp increase of hacking attacks over the last couple of years, web application security has become a key concern. The attack to websites, especially the explosion of webpage interpolating incidents has becomeone of the most serious problems of it. In this paper, the system adopts Web server core embedded technology to imbed tamper detection module and application protection module into the Web server, define correspondingstrategies for temper-proofing, and realize the real-time m...

  7. Computer simulation of quenched and tempered steel properties

    OpenAIRE

    B. Smoljan; D. Iljkić; Novak, H.

    2011-01-01

    Purpose: The algorithm of estimation of mechanical properties based on steel hardness has been established.Design/methodology/approach: Numerical modelling of hardness distribution in as-quenched steel specimen was performed by involving the results of simple experimental test, i.e., Jominy-test. Hardness of quenched and tempered steel has been expressed as function of maximal hardness of actual steel and hardness of actual steel with 50% of martensite in microstructure, according to the time...

  8. Small Sample Sizes Yield Biased Allometric Equations in Temperate Forests

    OpenAIRE

    Duncanson, L.; Rourke, O.; Dubayah, R.

    2015-01-01

    Accurate quantification of forest carbon stocks is required for constraining the global carbon cycle and its impacts on climate. The accuracies of forest biomass maps are inherently dependent on the accuracy of the field biomass estimates used to calibrate models, which are generated with allometric equations. Here, we provide a quantitative assessment of the sensitivity of allometric parameters to sample size in temperate forests, focusing on the allometric relationship between tree height a...

  9. Indirect effects of sea otter recovery on temperate reef fish

    OpenAIRE

    Silberg, Joshua Neal

    2015-01-01

    The loss or recovery of apex predators can have profound positive or negative ecological and socio-economic impacts. Effects of predator depletion or recovery are frequently accompanied by time lags, which are often context-dependent. In temperate rocky reef ecosystems, sea otters (Enhydra lutris) trigger a cascade of direct and indirect effects driving transitions between kelp-depleted and kelp-dominated states. We quantified the indirect effects of sea otter recovery on copper rockfish (Seb...

  10. Tropical fishes dominate temperate reef fish communities within western Japan.

    Directory of Open Access Journals (Sweden)

    Yohei Nakamura

    Full Text Available Climate change is resulting in rapid poleward shifts in the geographical distribution of tropical and subtropical fish species. We can expect that such range shifts are likely to be limited by species-specific resource requirements, with temperate rocky reefs potentially lacking a range of settlement substrates or specific dietary components important in structuring the settlement and success of tropical and subtropical fish species. We examined the importance of resource use in structuring the distribution patterns of range shifting tropical and subtropical fishes, comparing this with resident temperate fish species within western Japan (Tosa Bay; the abundance, diversity, size class, functional structure and latitudinal range of reef fishes utilizing both coral reef and adjacent rocky reef habitat were quantified over a 2 year period (2008-2010. This region has undergone rapid poleward expansion of reef-building corals in response to increasing coastal water temperatures, and forms one of the global hotspots for rapid coastal changes. Despite the temperate latitude surveyed (33°N, 133°E the fish assemblage was both numerically, and in terms of richness, dominated by tropical fishes. Such tropical faunal dominance was apparent within both coral, and rocky reef habitats. The size structure of the assemblage suggested that a relatively large number of tropical species are overwintering within both coral and rocky habitats, with a subset of these species being potentially reproductively active. The relatively high abundance and richness of tropical species with obligate associations with live coral resources (i.e., obligate corallivores shows that this region holds the most well developed temperate-located tropical fish fauna globally. We argue that future tropicalisation of the fish fauna in western Japan, associated with increasing coral habitat development and reported increasing shifts in coastal water temperatures, may have considerable

  11. 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

  12. The Effects of Test Temperature, Temper, and Alloyed Copper on the Hydrogen-Controlled Crack Growth Rate of an Al-Zn-Mg-(Cu) Alloy

    Energy Technology Data Exchange (ETDEWEB)

    G.A. Young, Jr.; J.R. Scully

    2000-09-17

    The hydrogen embrittlement controlled stage II crack growth rate of AA 7050 (6.09 wt.% Zn, 2.14 wt% Mg, 2.19 wt.% Cu) was investigated as a function of temper and alloyed copper level in a humid air environment at various temperatures. Three tempers representing the underaged, peak aged, and overaged conditions were tested in 90% relative humidity (RH) air at temperatures between 25 and 90 C. At all test temperatures, an increased degree of aging (from underaged to overaged) produced slower stage II crack growth rates. The stage II crack growth rate of each alloy and temper displayed Arrhenius-type temperature dependence with activation energies between 58 and 99 kJ/mol. For both the normal copper and low copper alloys, the fracture path was predominantly intergranular at all test temperatures (25-90 C) in each temper investigated. Comparison of the stage II crack growth rates for normal (2.19 wt.%) and low (0.06 wt.%) copper alloys in the peak aged and overaged tempers showed the beneficial effect of copper additions on stage II crack growth rate in humid air. In the 2.19 wt.% copper alloy, the significant decrease ({approx} 10 times at 25 C) in stage II crack growth rate upon overaging is attributed to an increase in the apparent activation energy for crack growth. IN the 0.06 wt.% copper alloy, overaging did not increase the activation energy for crack growth but did lower the pre-exponential factor, {nu}{sub 0}, resulting in a modest ({approx} 2.5 times at 25 C) decrease in crack growth rate. These results indicate that alloyed copper and thermal aging affect the kinetic factors that govern stage II crack growth rate. Overaged, copper bearing alloys are not intrinsically immune to hydrogen environment assisted cracking but are more resistant due to an increased apparent activation energy for stage II crack growth.

  13. 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.

  14. Winter climate change: a critical factor for temperate vegetation performance.

    Science.gov (United States)

    Kreyling, Juergen

    2010-07-01

    Winter ecological processes are important drivers of vegetation and ecosystem functioning in temperate ecosystems. There, winter conditions are subject to rapid climate change. The potential loss of a longer-lasting snow cover with implications to other plant-related climate parameters and overwintering strategies make the temperate zone particularly vulnerable to winter climate change. A formalized literature search in the ISI Web of Science shows that plant related research on the effects of winter climate change is generally underrepresented. Temperate regions in particular are rarely studied in this respect, although the few existing studies imply strong effects of winter climate change on species ranges, species compositions, phenology, or frost injury. The generally positive effect of warming on plant survival and production may be counteracted by effects such as an increased frost injury of roots and shoots, an increased insect pest risk, or a disrupted synchrony between plants and pollinators. Based on the literature study, gaps in current knowledge are discussed. Understanding the relative effects of interacting climate parameters, as well as a stronger consideration of shortterm events and variability of climatic conditions is urgent. With respect to plant response, it would be particularly worthwhile to account for hidden players such as pathogens, pollinators, herbivores, or fungal partners in mycorrhization.

  15. Frontiers in alley cropping: Transformative solutions for temperate agriculture.

    Science.gov (United States)

    Wolz, Kevin J; Lovell, Sarah T; Branham, Bruce E; Eddy, William C; Keeley, Keefe; Revord, Ronald S; Wander, Michelle M; Yang, Wendy H; DeLucia, Evan H

    2017-12-08

    Annual row crops dominate agriculture around the world and have considerable negative environmental impacts, including significant greenhouse gas emissions. Transformative land-use solutions are necessary to mitigate climate change and restore critical ecosystem services. Alley cropping (AC)-the integration of trees with crops-is an agroforestry practice that has been studied as a transformative, multifunctional land-use solution. In the temperate zone, AC has strong potential for climate change mitigation through direct emissions reductions and increases in land-use efficiency via overyielding compared to trees and crops grown separately. In addition, AC provides climate change adaptation potential and ecological benefits by buffering alley crops to weather extremes, diversifying income to hedge financial risk, increasing biodiversity, reducing soil erosion, and improving nutrient- and water-use efficiency. The scope of temperate AC research and application has been largely limited to simple systems that combine one timber tree species with an annual grain. We propose two frontiers in temperate AC that expand this scope and could transform its climate-related benefits: (i) diversification via woody polyculture and (ii) expanded use of tree crops for food and fodder. While AC is ready now for implementation on marginal lands, we discuss key considerations that could enhance the scalability of the two proposed frontiers and catalyze widespread adoption. © 2017 John Wiley & Sons Ltd.

  16. 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.

  17. Sliding mode controllers for a tempered glass furnace.

    Science.gov (United States)

    Almutairi, Naif B; Zribi, Mohamed

    2016-01-01

    This paper investigates the design of two sliding mode controllers (SMCs) applied to a tempered glass furnace system. The main objective of the proposed controllers is to regulate the glass plate temperature, the upper-wall temperature and the lower-wall temperature in the furnace to a common desired temperature. The first controller is a conventional sliding mode controller. The key step in the design of this controller is the introduction of a nonlinear transformation that maps the dynamic model of the tempered glass furnace into the generalized controller canonical form; this step facilitates the design of the sliding mode controller. The second controller is based on a state-dependent coefficient (SDC) factorization of the tempered glass furnace dynamic model. Using an SDC factorization, a simplified sliding mode controller is designed. The simulation results indicate that the two proposed control schemes work very well. Moreover, the robustness of the control schemes to changes in the system's parameters as well as to disturbances is investigated. In addition, a comparison of the proposed control schemes with a fuzzy PID controller is performed; the results show that the proposed SDC-based sliding mode controller gave better results. Copyright © 2015 ISA. Published by Elsevier Ltd. All rights reserved.

  18. Predicting the response of a temperate forest ecosystem to atmospheric CO{sub 2} increase. Annual report, 1992--1993

    Energy Technology Data Exchange (ETDEWEB)

    Bazzaz, F.A.

    1993-03-01

    This report summarizes the second year of research progress. Included are progress reports for the following studies: the responses of temperate forest tree to 3 years of exposure to elevated carbon dioxide, and high and low nutrient and light levels; pot-size limitations in carbon dioxide studies, interactive effects of carbon dioxide and soil moisture availability on tree seedling`s tissue water relations, growth, and niche characteristics; individual versus population responses to elevated carbon dioxide levels in two species of annual weeds; and the development of gypsy moth larvae raised on gray and yellow birth foliage grown in ambient and elevated carbon dioxide environments.

  19. 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.

  20. 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

  1. Integrated SDS removal and peptide separation by strong-cation exchange liquid chromatography for SDS-assisted shotgun proteome analysis.

    Science.gov (United States)

    Sun, Difei; Wang, Nan; Li, Liang

    2012-02-03

    We report an improved shotgun method for analyzing proteomic samples containing sodium dodecyl sulfate (SDS). This method is based on the use of strong-cation exchange (SCX) liquid chromatography (LC) for SDS removal that can be integrated with peptide separation as the first dimension of the two-dimensional LC tandem mass spectrometry workflow. To optimize the performance of SDS removal, various experimental conditions, including the concentrations of chemical reagents and salts in the sample, the SDS concentration, and the SCX mobile phase composition, were investigated. It was found that a peptide recovery rate of about 90% could be achieved while removing SDS efficiently. One key finding was that, by increasing the SDS concentration to a certain level (0.5%) in the digested peptide sample, the sample recovery rate could be increased. The peptide recovery rate of BSA digests was found to be 90.6 ± 1.0% (n = 3), and SDS in the SCX fractions collected was not detectable by pyrolysis GC-MS, i.e., below the detection limit of 0.00006% for the undesalted SCX fractions. The peptide recovery rates were found to be 90.9% ± 2.7 (n = 3) and 89.5% ± 0.5% (n = 3) for the digests of the membrane-protein-enriched fractions of E. coli cell lysates and the MCF-7 breast cancer cell line, respectively. Compared to the methods that use acid-labile surfactants, such as RapiGest and PPS, for the MCF-7 membrane fraction sample, the SDS method identified, on average (n = 3), more peptides (∼5%) and proteins (∼16%) than the RapiGest method, while the RapiGest method identified more peptides (∼21%) and proteins (∼7%) from the E. coli membrane fraction than the SDS method. In both cases, the two methods identified more peptides and proteins than the PPS method. Since SCX is widely used as the first dimension of 2D-LC MS/MS, integration of SDS removal with peptide separation in SCX does not add any extra steps to the sample handling process. We demonstrated the application of

  2. Characterization of the Gut Microbial Community of Obese Patients Following a Weight-Loss Intervention Using Whole Metagenome Shotgun Sequencing.

    Directory of Open Access Journals (Sweden)

    Sandrine Louis

    Full Text Available Cross-sectional studies suggested that obesity is promoted by the gut microbiota. However, longitudinal data on taxonomic and functional changes in the gut microbiota of obese patients are scarce. The aim of this work is to study microbiota changes in the course of weight loss therapy and the following year in obese individuals with or without co-morbidities, and to asses a possible predictive value of the gut microbiota with regard to weight loss maintenance.Sixteen adult patients, who followed a 52-week weight-loss program comprising low calorie diet, exercise and behavioral therapy, were selected according to their weight-loss course. Over two years, anthropometric and metabolic parameters were assessed and microbiota from stool samples was functionally and taxonomically analyzed using DNA shotgun sequencing.Overall the microbiota responded to the dietetic and lifestyle intervention but tended to return to the initial situation both at the taxonomical and functional level at the end of the intervention after one year, except for an increase in Akkermansia abundance which remained stable over two years (12.7x103 counts, 95%CI: 322-25100 at month 0; 141x103 counts, 95%CI: 49-233x103 at month 24; p = 0.005. The Firmicutes/Bacteroidetes ratio was higher in obese subjects with metabolic syndrome (0.64, 95%CI: 0.34-0.95 than in the "healthy obese" (0.27, 95%CI: 0.08-0.45, p = 0.04. Participants, who succeeded in losing their weight consistently over the two years, had at baseline a microbiota enriched in Alistipes, Pseudoflavonifractor and enzymes of the oxidative phosphorylation pathway compared to patients who were less successful in weight reduction.Successful weight reduction in the obese is accompanied with increased Akkermansia numbers in feces. Metabolic co-morbidities are associated with a higher Firmicutes/Bacteroidetes ratio. Most interestingly, microbiota differences might allow discrimination between successful and unsuccessful weight

  3. Genomic methods and microbiological technologies for profiling novel and extreme environments for the extreme microbiome project (XMP)

    OpenAIRE

    Tighe, S; Afshinnekoo, E; Rock, TM; McGrath, K; Alexander, N; McIntyre, A; Ahsanuddins, S; Bezdan, D; Green, SJ; Joye, S; Johnson, SS; Baldwin, DA; Bivens, N; Ajami, N; Carmical, JR

    2017-01-01

    © 2017, Association of Biomolecular Resource Facilities. All rights reserved. The Extreme Microbiome Project (XMP) is a project launched by the Association of Biomolecular Resource Facilities Metagenomics Research Group (ABRF MGRG) that focuses on whole genome shotgun sequencing of extreme and unique environments using a wide variety of biomolecular techniques. The goals are multifaceted, including development and refinement of new techniques for the following: 1) the detection and characteri...

  4. 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.

  5. $\\mu$-tempered metadynamics: Artifact independent convergence times for wide hills

    CERN Document Server

    Dickson, Bradley M

    2015-01-01

    Recent analysis of well-tempered metadynamics (WTmetaD) showed that it converges without mollification artifacts in the bias potential. Here we explore how metadynamics heals mollification artifacts, how healing impacts convergence time, and whether alternative temperings may be used to improve efficiency. We introduce "$\\mu$-tempered" metadynamics as a simple tempering scheme, inspired by a related mollified adaptive biasing potential (mABP), that results in artifact independent convergence of the free energy estimate. We use a toy model to examine the role of artifacts in WTmetaD and solvated alanine dipeptide to compare the well-tempered and $\\mu$-tempered frameworks demonstrating fast convergence for hill widths as large as $60^{\\circ}$ for $\\mu$TmetaD.

  6. Dilatometric and hardness analysis of C45 steel tempering with different heating-up rates

    Directory of Open Access Journals (Sweden)

    A. Kulawik

    2012-01-01

    Full Text Available Modelling of technological processes of heat treatment or welding, involving multiple heat source transitions, requires considering the phenomenon of tempering. In work have been presented results of dilatometric research of hardened C45 steel subjected to tempering. The analysis of the influence of heating rate at the kinetic determined from dilatometric curves has been made. There have also been estimated quantities of transformation expansions and thermal expansion coefficients of hardening and tempering structures (austenite, ferrite, pearlite, martensite and sorbite. The analysis of tempering time influence on the hardness of tempered steel has been made. Functions associating hardness with tempering time (rate of heating-up in technological processes based on short-timed action of a heat source (eg. laser treatment have been suggested.

  7. 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.

  8. 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.

  9. Seedlings of temperate rainforest conifer and angiosperm trees differ in leaf area display.

    Science.gov (United States)

    Lusk, Christopher H; Pérez-Millaqueo, Manuel M; Saldaña, Alfredo; Burns, Bruce R; Laughlin, Daniel C; Falster, Daniel S

    2012-07-01

    The contemporary relegation of conifers mainly to cold or infertile sites has been ascribed to low competitive ability, as a result of the hydraulic inefficiency of tracheids and their seedlings' initial dependence on small foliage areas. Here it is hypothesized that, in temperate rainforests, the larger leaves of angiosperms also reduce self-shading and thus enable display of larger effective foliage areas than the numerous small leaves of conifers. This hypothesis was tested using 3-D modelling of plant architecture and structural equation modelling to compare self-shading and light interception potential of seedlings of six conifers and 12 angiosperm trees from temperate rainforests. The ratio of displayed leaf area to plant mass (LAR(d)) was used to indicate plant light interception potential: LAR(d) is the product of specific leaf area, leaf mass fraction, self-shading and leaf angle. Angiosperm seedlings self-shaded less than conifers, mainly because of differences in leaf number (more than leaf size), and on average their LAR(d) was about twice that of conifers. Although specific leaf area was the most pervasive influence on LAR(d), differences in self-shading also significantly influenced LAR(d) of large seedlings. The ability to deploy foliage in relatively few, large leaves is advantageous in minimizing self-shading and enhancing seedling light interception potential per unit of plant biomass. This study adds significantly to evidence that vegetative traits may be at least as important as reproductive innovations in explaining the success of angiosperms in productive environments where vegetation is structured by light competition.

  10. Fate and Trophic Transfer of Rare Earth Elements in Temperate Lake Food Webs.

    Science.gov (United States)

    Amyot, Marc; Clayden, Meredith G; MacMillan, Gwyneth A; Perron, Tania; Arscott-Gauvin, Alexandre

    2017-06-06

    Many mining projects targeting rare earth elements (REE) are in development in North America, but the background concentrations and trophic transfer of these elements in natural environments have not been well characterized. We sampled abiotic and food web components in 14 Canadian temperate lakes unaffected by mines to assess the natural ecosystem fate of REE. Individual REE and total REE concentrations (sum of individual element concentrations, ΣREE) were strongly related with each other throughout different components of lake food webs. Dissolved organic carbon and dissolved oxygen in the water column, as well as ΣREE in sediments, were identified as potential drivers of aqueous ΣREE. Log10 of median bioaccumulation factors ranged from 1.3, 3.7, 4.0, and 4.4 L/kg (wet weight) for fish muscle, zooplankton, predatory invertebrates, and nonpredatory invertebrates, respectively. [ΣREE] in fish, benthic macroinvertebrates, and zooplankton declined as a function of their trophic position, as determined by functional feeding groups and isotopic signatures of nitrogen (δ15N), indicating that REE were subject to trophic dilution. Low concentrations of REE in freshwater fish muscle compared to their potential invertebrate prey suggest that fish fillet consumption is unlikely to be a significant source of REE to humans in areas unperturbed by mining activities. However, other fish predators (e.g., piscivorous birds and mammals) may accumulate REE from whole fish as they are more concentrated than muscle. Overall, this study provides key information on the baseline concentrations and trophic patterns for REE in freshwater temperate lakes in Quebec, Canada.

  11. Off-season uptake of nitrogen in temperate heath vegetation

    DEFF Research Database (Denmark)

    Andresen, Louise C.; Michelsen, Anders

    2005-01-01

    , and the graminoids Carex arenaria and Deschampsia flexuosa, showed high root uptake of both forms of nitrogen, both 1 day after labelling and after a month, in species specific temporal patterns. Plant uptake of 13C was not significant, providing no further evidence of intact uptake of glycine. Translocation....... The winter temperatures were similar to those of an average winter in the northern temperate region of Europe, with only few days of soil temperatures below zero or above 5 degrees C. The vegetation, consisting of the evergreen dwarf shrub Calluna vulgaris, the deciduous dwarf shrub Salix arenaria...

  12. Net ecosystem carbon exchange of a dry temperate eucalypt forest

    Science.gov (United States)

    Hinko-Najera, Nina; Isaac, Peter; Beringer, Jason; van Gorsel, Eva; Ewenz, Cacilia; McHugh, Ian; Exbrayat, Jean-François; Livesley, Stephen J.; Arndt, Stefan K.

    2017-08-01

    Forest ecosystems play a crucial role in the global carbon cycle by sequestering a considerable fraction of anthropogenic CO2, thereby contributing to climate change mitigation. However, there is a gap in our understanding about the carbon dynamics of eucalypt (broadleaf evergreen) forests in temperate climates, which might differ from temperate evergreen coniferous or deciduous broadleaved forests given their fundamental differences in physiology, phenology and growth dynamics. To address this gap we undertook a 3-year study (2010-2012) of eddy covariance measurements in a dry temperate eucalypt forest in southeastern Australia. We determined the annual net carbon balance and investigated the temporal (seasonal and inter-annual) variability in and environmental controls of net ecosystem carbon exchange (NEE), gross primary productivity (GPP) and ecosystem respiration (ER). The forest was a large and constant carbon sink throughout the study period, even in winter, with an overall mean NEE of -1234 ± 109 (SE) g C m-2 yr-1. Estimated annual ER was similar for 2010 and 2011 but decreased in 2012 ranging from 1603 to 1346 g C m-2 yr-1, whereas GPP showed no significant inter-annual variability, with a mean annual estimate of 2728 ± 39 g C m-2 yr-1. All ecosystem carbon fluxes had a pronounced seasonality, with GPP being greatest during spring and summer and ER being highest during summer, whereas peaks in NEE occurred in early spring and again in summer. High NEE in spring was likely caused by a delayed increase in ER due to low temperatures. A strong seasonal pattern in environmental controls of daytime and night-time NEE was revealed. Daytime NEE was equally explained by incoming solar radiation and air temperature, whereas air temperature was the main environmental driver of night-time NEE. The forest experienced unusual above-average annual rainfall during the first 2 years of this 3-year period so that soil water content remained relatively high and the forest

  13. 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...

  14. Transport in the spatially tempered, fractional Fokker-Planck equation

    Science.gov (United States)

    Kullberg, A.; del-Castillo-Negrete, D.

    2012-06-01

    A study of truncated Lévy flights in super-diffusive transport in the presence of an external potential is presented. The study is based on the spatially tempered, fractional Fokker-Planck (TFFP) equation in which the fractional diffusion operator is replaced by a tempered fractional diffusion (TFD) operator. We focus on harmonic (quadratic) potentials and periodic potentials with broken spatial symmetry. The main objective is to study the dependence of the steady-state probability density function (PDF), and the current (in the case of periodic potentials) on the level of tempering, λ, and on the order of the fractional derivative in space, α. An expansion of the TFD operator for large λ is presented, and the corresponding equation for the coarse grained PDF is obtained. The steady-state PDF solution of the TFFP equation for a harmonic potential is computed numerically. In the limit λ → ∞, the PDF approaches the expected Boltzmann distribution. However, nontrivial departures from this distribution are observed for finite (λ > 0) truncations, and α ≠ 2. In the study of periodic potentials, we use two complementary numerical methods: a finite-difference scheme based on the Grunwald-Letnikov discretization of the truncated fractional derivatives and a Fourier-based spectral method. In the limit λ → ∞, the PDFs converges to the Boltzmann distribution and the current vanishes. However, for α ≠ 2, the PDF deviates from the Boltzmann distribution and a finite non-equilibrium ratchet current appears for any λ > 0. The current is observed to converge exponentially in time to the steady-state value. The steady-state current exhibits algebraical decay with λ, as J ˜ λ-ζ, for α ⩾ 1.75. However, for α ⩽ 1.5, the steady-state current decays exponentially with λ, as J ˜ e-ξλ. In the presence of an asymmetry in the TFD operator, the tempering can lead to a current reversal. A detailed numerical study is presented on the dependence of the

  15. Transport in the spatially tempered, fractional Fokker-Planck equation

    Energy Technology Data Exchange (ETDEWEB)

    Kullberg, A. [University of California, Los Angeles; Del-Castillo-Negrete, Diego B [ORNL

    2012-01-01

    A study of truncated Levy flights in super-diffusive transport in the presence of an external potential is presented. The study is based on the spatially tempered, fractional Fokker-Planck (TFFP) equation in which the fractional diffusion operator is replaced by a tempered fractional diffusion (TFD) operator. We focus on harmonic (quadratic) potentials and periodic potentials with broken spatial symmetry. The main objective is to study the dependence of the steady-state probability density function (PDF), and the current (in the case of periodic potentials) on the level of tempering, lambda, and on the order of the fractional derivative in space, alpha. An expansion of the TFD operator for large lambda is presented, and the corresponding equation for the coarse grained PDF is obtained. The steady-state PDF solution of the TFFP equation for a harmonic potential is computed numerically. In the limit lambda -> infinity, the PDF approaches the expected Boltzmann distribution. However, nontrivial departures from this distribution are observed for finite (lambda > 0) truncations, and alpha not equal 2. In the study of periodic potentials, we use two complementary numerical methods: a finite-difference scheme based on the Grunwald-Letnikov discretization of the truncated fractional derivatives and a Fourier-based spectral method. In the limit lambda -> infinity, the PDFs converges to the Boltzmann distribution and the current vanishes. However, for alpha not equal 2, the PDF deviates from the Boltzmann distribution and a finite non-equilibrium ratchet current appears for any lambda > 0. The current is observed to converge exponentially in time to the steady-state value. The steady-state current exhibits algebraical decay with lambda, as J similar to lambda(-zeta), for alpha >= 1.75. However, for alpha <= 1.5, the steady-state current decays exponentially with lambda, as J similar to e(-xi lambda). In the presence of an asymmetry in the TFD operator, the tempering can lead

  16. Net ecosystem carbon exchange of a dry temperate eucalypt forest

    Directory of Open Access Journals (Sweden)

    N. Hinko-Najera

    2017-08-01

    Full Text Available Forest ecosystems play a crucial role in the global carbon cycle by sequestering a considerable fraction of anthropogenic CO2, thereby contributing to climate change mitigation. However, there is a gap in our understanding about the carbon dynamics of eucalypt (broadleaf evergreen forests in temperate climates, which might differ from temperate evergreen coniferous or deciduous broadleaved forests given their fundamental differences in physiology, phenology and growth dynamics. To address this gap we undertook a 3-year study (2010–2012 of eddy covariance measurements in a dry temperate eucalypt forest in southeastern Australia. We determined the annual net carbon balance and investigated the temporal (seasonal and inter-annual variability in and environmental controls of net ecosystem carbon exchange (NEE, gross primary productivity (GPP and ecosystem respiration (ER. The forest was a large and constant carbon sink throughout the study period, even in winter, with an overall mean NEE of −1234 ± 109 (SE g C m−2 yr−1. Estimated annual ER was similar for 2010 and 2011 but decreased in 2012 ranging from 1603 to 1346 g C m−2 yr−1, whereas GPP showed no significant inter-annual variability, with a mean annual estimate of 2728 ± 39 g C m−2 yr−1. All ecosystem carbon fluxes had a pronounced seasonality, with GPP being greatest during spring and summer and ER being highest during summer, whereas peaks in NEE occurred in early spring and again in summer. High NEE in spring was likely caused by a delayed increase in ER due to low temperatures. A strong seasonal pattern in environmental controls of daytime and night-time NEE was revealed. Daytime NEE was equally explained by incoming solar radiation and air temperature, whereas air temperature was the main environmental driver of night-time NEE. The forest experienced unusual above-average annual rainfall during the first 2 years of this 3-year period so

  17. Tempered fractional Feynman-Kac equation: Theory and examples.

    Science.gov (United States)

    Wu, Xiaochao; Deng, Weihua; Barkai, Eli

    2016-03-01

    Functionals of Brownian and non-Brownian motions have diverse applications and attracted a lot of interest among scientists. This paper focuses on deriving the forward and backward fractional Feynman-Kac equations describing the distribution of the functionals of the space and time-tempered anomalous diffusion, belonging to the continuous time random walk class. Several examples of the functionals are explicitly treated, including the occupation time in half-space, the first passage time, the maximal displacement, the fluctuations of the occupation fraction, and the fluctuations of the time-averaged position.

  18. 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

  19. Genetic and Morphological Diversity of Temperate and Tropical Isolates of Phytophthora capsici.

    Science.gov (United States)

    Bowers, J H; Martin, F N; Tooley, P W; Luz, E D M N

    2007-04-01

    ABSTRACT Phytophthora capsici is a diverse species causing disease on a broad range of both temperate and tropical plants. In this study, we used cultural characteristics, amplified fragment length polymorphism (AFLP), and DNA sequence analyses of the ribosomal internal transcribed spacer (ITS) region and mitochondrial cytochrome oxidase II (cox II) genes to characterize temperate and tropical isolates from a wide range of host species. All but one temperate isolate grew at 35 degrees C, while all tropical isolates did not. All but two tropical isolates formed chlamydospores, while temperate isolates did not. There was strong bootstrap support for separation of temperate and tropical isolates using AFLP analysis; however, the temperate isolates appeared as a subgroup within the observed variation of the tropical isolates. The majority of temperate isolates clustered within a single clade with low variation regardless of host or geographical origin, while the tropical isolates were more variable and grouped into three distinct clades. Two clades of tropical isolates grouped together and were affiliated closely with the temperate isolates, while the third tropical clade was more distantly related. Phylogenetic analysis of the ITS regions resulted in similar groupings and variation within and between the temperate and tropical isolates as with the AFLP results. Sequence divergence among isolates and clades was low, with more variation within the tropical isolates than within the temperate isolates. Analysis of other species revealed shorter branch lengths separating temperate and tropical isolates than were observed in comparisons among other phylogenetically closely related species in the genus. Analysis of cox II sequence data was less clear. Although the temperate and tropical isolates grouped together apart from other species, there was no bootstrap support for separating these isolates. Restriction fragment length polymorphism (RFLP) analysis of the ITS regions

  20. Fruiting and flushing phenology in Asian tropical and temperate forests: implications for primate ecology.

    Science.gov (United States)

    Hanya, Goro; Tsuji, Yamato; Grueter, Cyril C

    2013-04-01

    In order to understand the ecological adaptations of primates to survive in temperate forests, we need to know the general patterns of plant phenology in temperate and tropical forests. Comparative analyses have been employed to investigate general trends in the seasonality and abundance of fruit and young leaves in tropical and temperate forests. Previous studies have shown that (1) fruit fall biomass in temperate forest is lower than in tropical forest, (2) non-fleshy species, in particular acorns, comprise the majority of the fruit biomass in temperate forest, (3) the duration of the fruiting season is shorter in temperate forest, and (4) the fruiting peak occurs in autumn in most temperate forests. Through our comparative analyses of the fruiting and flushing phenology between Asian temperate and tropical forests, we revealed that (1) fruiting is more annually periodic (the pattern in one year is similar to that seen in the next year) in temperate forest in terms of the number of fruiting species or trees, (2) there is no consistent difference in interannual variations in fruiting between temperate and tropical forests, although some oak-dominated temperate forests exhibit extremely large interannual variations in fruiting, (3) the timing of the flushing peak is predictable (in spring and early summer), and (4) the duration of the flushing season is shorter. The flushing season in temperate forests (17-28 % of that in tropical forests) was quite limited, even compared to the fruiting season (68 %). These results imply that temperate primates need to survive a long period of scarcity of young leaves and fruits, but the timing is predictable. Therefore, a dependence on low-quality foods, such as mature leaves, buds, bark, and lichens, would be indispensable for temperate primates. Due to the high predictability of the timing of fruiting and flushing in temperate forests, fat accumulation during the fruit-abundant period and fat metabolization during the

  1. 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).

  2. Responses of temperate forest productivity to insect and pathogen disturbances

    Science.gov (United States)

    Flower, C. E.; Gonzalez-Meler, M. A.

    2014-12-01

    Climate forcing factors have been documented to directly (e.g. CO2 fertilization) or indirectly (e.g. temperature and vapor pressure deficit) affect net primary productivity (NPP) of forests. Climate variations can also affect the vulnerability of forests to pests and pathogens, causing diffuse or widespread mortality. The introduction of novel pests is causing rapid mortality of targeted species with undetermined effects on forest productivity: NPP could decrease or increase depending on the severity (proportion of basal area impacted) and species diversity. We attempted to document the impact of diffuse mortality caused by insect outbreaks on North American temperate forests through synthesis of literature. Despite the large number of studies (>500) only a few (12) documented NPP in a systematic manner. The magnitude of insect and pathogen disturbance was larger in western than eastern forests due to the redundancy and functional diversity of temperate deciduous and mixed deciduous forests. Recovery from disturbance was more rapid from diffuse short duration defoliation events relative to the long lasting impacts of wood boring insects. Forest resilience may decrease as insect disturbance increases, particularly with generalist invasive pests that target a variety of species. We conclude that these biotic interactions, particularly when caused by invasive pests, impose biological forcing to forest NPP at similar magnitude and time scales than climate forcing.

  3. Parallel Tempering for sampling and optimization in seismic inverse problems

    Science.gov (United States)

    Sambridge, Malcolm

    2013-04-01

    The field of seismology is rich with inverse problems. Seismologists are constantly seeking new ways to use seismic waveforms, and data products derived from them, to constrain subsurface structure in the form of Earth properties in 1-, 2- and 3 dimensions, as well as seismic sources in space and time. Every approach has its limitations and a virtual smorgasbord of methods exist, and have been applied over thirty years, with varying degrees of success. In this presentation we discuss a new class of approach. Parallel Tempering (PT) is a technique originating in the field of computational statistics that is finding increasing success for probabilistic sampling problems in astro and quantum physics, and more recently ocean acoustics but appears to be virtually unknown in the solid earth geosciences. In seismology two classes of inference approach are common for nonlinear inverse problems, Bayesian (probabilistic) sampling and optimization. Parallel Tempering can be applied to both situations and is related to better known methods such as Simulated Annealing and Metropolis Sampling. PT is distinguished as it has a theoretical basis for being superior to both. PT is best viewed as a `meta' algorithm. In a sense wrapping around existing optimization or Bayesian sampling methods to facilitate more robust performance (optimization) and more rapid exploration of parameter space (sampling). PT has generated much interest across the physical sciences with encouraging results emerging. This presentation will describe the basic ideas, and present results of implementations on seismic waveform inversion for both sampling and optimization.

  4. 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.

  5. Restoration of a temperate reef: Effects on the fish community

    DEFF Research Database (Denmark)

    Støttrup, Josianne; Stenberg, Claus; Dahl, Karsten

    2014-01-01

    The extraction of large boulders from coastal reefs for construction of harbours and coastal protection has led to habitat degradation for local fish populations through the destruction of cavernous reefs and changes in macroalgal cover resulting from a loss of substrate. The temperate reef at Læ....... The findings highlight the importance of reef habitats for fish communities and the need for their protection......The extraction of large boulders from coastal reefs for construction of harbours and coastal protection has led to habitat degradation for local fish populations through the destruction of cavernous reefs and changes in macroalgal cover resulting from a loss of substrate. The temperate reef at Læsø...... Trindel in Kattegat, Denmark, has now been re-established with the aim of restoring the reef’s historical structure and function. The effects of the restoration on the local fish community are reported here. Fishing surveys using gillnets and fyke nets were conducted before the restoration (2007) and four...

  6. 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.

  7. 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

  8. Evaluation of tropically adapted straightbred and crossbred cattle: postweaning gain and feed efficiency when finished in a temperate climate.

    Science.gov (United States)

    Coleman, S W; Chase, C C; Phillips, W A; Riley, D G; Olson, T A

    2012-06-01

    Beef cows in the subtropical USA must be adapted to the stressors of the environment, typically supplied by using Brahman (Br) breeding. Calves produced in the region, however, are usually grown and finished in more temperate regions, and have a perceived reputation for poor ADG and feed efficiency during finishing. Compromised fertility and carcass quality often associated with the Br have increased interest in tropically adapted Bos taurus breed types. The objective of this study was to evaluate 3 breeds [An = Angus (Bos taurus, temperate); Br (B. indicus, tropical); and Ro = Romosinuano (B. taurus, tropical)] and all possible crosses during various segments of post-weaning growth, and for feed efficiency during the finishing phase. Steer calves (n = 473) born over 3 yr were weaned in late September, backgrounded for at least 21 d (BKG), shipped 2,025 km to El Reno, OK, in October, fed a preconditioning diet for 28 d (RCV), grazed wheat (Triticum aestivum L.) pasture from November to May (WHT), finished on a conventional feedlot diet (FIN), and serially harvested after approximately 95, 125, and 150 d on feed. Body weight and ADG during each segment were tested using a mixed model that included calf age at weaning, year (Y), breed of sire (SB), breed of dam (DB), and interactions. In addition, winter treatment (continuous wheat or reduced grazing of wheat with supplement) was included for the wheat and feedlot phases. Sire within SB × SB [and pen (barn × year) for feedlot phase] were considered random. The SB × DB interaction was significant for all traits (P residual feed intake. No heterosis was evident. These data show that in temperate zones, winter is the period when productivity of tropically adapted cattle is compromised.

  9. Effect of tempering temperature on microstructure and mechanical properties of high boron white cast iron

    Directory of Open Access Journals (Sweden)

    Liu Zhongli

    2012-11-01

    Full Text Available The effect of different tempering temperatures on the microstructure and mechanical properties of air-quenched high boron white cast iron was studied. The results indicate that the high boron white cast iron comprises dendritic matrix and inter-dendritic M2B boride; and the matrix comprises martensite and pearlite. After quenching in the air, the matrix is changed into lath martensite; but only 1-μm-size second phase exists in the matrix. After tempering, another second phase of several tens of nanometers is found in the matrix, and the size and quantity increase with an increase in tempering temperature. The two kinds of second precipitation phase with different sizes in the matrix have the same chemical formula, but their forming stages are different. The precipitation phase with larger size forms during the austenitizing process, while the precipitation phase with smaller size forms during the tempering process. When tempered at different temperatures after quenching, the hardness decreases with an increase in the tempering temperature, but it increases a little at 450 ℃ due to the precipitation strengthening effect of the second phase, and it decreases greatly due to the martensite decomposition above 450 ℃. The impact toughness increases a little when tempered below 300 ℃, but it then decreases continuously owing to the increase in size and quantity of the secondary precipitate above 300 ℃. Considered comprehensively, the optimum tempering temperature is suggested at 300 ℃ to obtain a good combination of hardness and toughness.

  10. Investigation of carbon segregation during low temperature tempering in a medium carbon steel

    Energy Technology Data Exchange (ETDEWEB)

    Xiao, Y. [State Key Lab of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240 (China); Collaborative Innovation Center for Advanced Ship and Deep-Sea Exploration, Shanghai 200240 (China); Li, W., E-mail: weilee@sjtu.edu.cn [Collaborative Innovation Center for Advanced Ship and Deep-Sea Exploration, Shanghai 200240 (China); Zhao, H.S.; Lu, X.W. [State Key Lab of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240 (China); Jin, X.J., E-mail: jin@sjtu.edu.cn [State Key Lab of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240 (China); Collaborative Innovation Center for Advanced Ship and Deep-Sea Exploration, Shanghai 200240 (China)

    2016-07-15

    Low temperature tempering is important in improving the mechanical properties of steels. In this study, the thermoelectric power method was employed to investigate carbon segregation during low temperature tempering ranging from 110 °C to 170 °C of a medium carbon alloyed steel, combined with micro-hardness, transmission electron microscopy and atom probe tomography. Evolution of carbon dissolution from martensite and segregation to grain boundaries/interfaces and dislocations were investigated for different tempering conditions. Carbon concentration variation was quantified from 0.33 wt.% in quenching sample to 0.15 wt.% after long time tempering. The kinetic of carbon diffusion during tempering process was discussed through Johnson-Mehl-Avrami equation. - Highlights: • The thermoelectric power (TEP) was employed to investigate the low temperature tempering of a medium carbon alloyed steel. • Evolution of carbon dissolution was investigated for different tempering conditions. • Carbon concentration variation was quantified from 0.33 wt.% in quenching sample to 0.15 wt.% after long time tempering.

  11. Simulated-tempering replica-exchange method for the multidimensional version.

    Science.gov (United States)

    Mitsutake, Ayori

    2009-09-07

    In this article, the general formulation of the multidimensional simulated-tempering replica-exchange method is described. In previous works, the one-dimensional replica-exchange simulated-tempering and simulated-tempering replica-exchange methods were developed. For the former method, the weight factor of the one-dimensional simulated tempering is determined by a short replica-exchange simulation and multiple-histogram reweighing techniques. For the latter method, the production run is a replica-exchange simulation with a few replicas not in the canonical ensembles but in the simulated-tempering ensembles which cover wide ranges of temperature. Recently, the general formulation of the multidimensional replica-exchange simulated tempering was presented. In this article, the extension of the simulated-tempering replica-exchange method for the multidimensional version is given. As an example of applications of the algorithm, a two-dimensional replica-exchange simulation and two simulated-tempering replica-exchange simulations have been performed. Here, an alpha-helical peptide system with a model solvent has been used for the applications.

  12. Influence of heating rate on sorbitic transformation temperature of tempering C45 steel

    Directory of Open Access Journals (Sweden)

    A. Kulawik

    2011-04-01

    Full Text Available In this paper the analysis of speed heating influence on sorbitic transormation temperature of tempering C45 steel is presented. On thebasis of dilatometric research, functions associating heating time with initial and final temperature of sorbitic transformation have beendetermined as well as the size structural (γ and thermal (α expansion coefficients of quenching and tempering structures have beenestimated.

  13. The investigation of applicability of the Hollomon-Jaffe equation on tempering the HSLA steel

    Directory of Open Access Journals (Sweden)

    A. Patarić

    2009-09-01

    Full Text Available High strength low-alloyed (HSLA Cr-Mn-Si steels belong to a group of steels that can reach their full mechanical properties after quenching and tempering. Those properties depend both on the temperature and time of tempering. Knowing the tempering parameters, it is possible to reach the desired properties of the treated steel. Some results on investigating the Hollomon-Jaffe equation (in parametric form application for tempering of HSLA steel, are shown in this paper. The experiments were performed in real production conditions, using a standard material. The quenching was performed at 870 C, the heating period was always 30 min, with subsequent cooling into the oil bath. The tempering was carried out in temperature range from 480 to 680 C, while tempering time varied from 15 min to 24 h. The degree of tempering is referred through the hardness values changing. The experimental results have shown a pretty well agreement to tempering parameters, included in Hollomon- -Jaffe equation, for this kind of HSLA steel.

  14. On microstructure and performance of tempered high-boron high-speed steel roll

    Directory of Open Access Journals (Sweden)

    Fu Hanguang

    2012-08-01

    Full Text Available Influences of the tempering temperature on the microstructure, mechanical property and wear resistance of High-Boron High Speed Steel (HBHSS roll materials were investigated by means of optical microscopy, scanning electron microscopy (SEM, X-ray diffraction, hardness measurement, impact tester, tensile tester and pin abrasion tester. The results show that the as-cast structure of HBHSS consists of a great amount of martensite and M2(B,C and a few retained austenites and M23(B,C6. After solution treated at 1,050 °C and followed by oil cooling, the amount of M23(B,C6 carbo-borides in quenched HBHSS increases obviously and the macrohardness of the quenched HBHSS is 66 HRC, which is very close to the 65.8 HRC of as-cast HBHSS. On the whole, the hardness of HBHSS alloy shows a trend of slight decrease with increasing tempering temperature when tempered below 500 °C. While when above 500 °C, the hardness increases slightly as the tempering temperature increases and reaches a peak at 525 °C and then decreases obviously. The impact toughness of HBHSS has a tendency to increase as the tempering temperature increases. Tempering can improve the tensile strength and elongation of HBHSS, but a higher tempering temperature causes a slight decrease in both tensile strength and elongation. Excellent wear resistance can be obtained by tempering at 500 to 550 °C.

  15. 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 ...

  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. 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 Several 14C dates have been obtained from the fibre temper in cooking bowls made by the forbears of the Zeekoe River Bushmen (Basarwa), South Africa. Although the temper appears to be burned grass, the Q (13) C values do not match those of local C4...

  18. 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.

  19. Exercise in a hot environment influences plasma anti-inflammatory and antioxidant status in well-trained athletes.

    Science.gov (United States)

    Sureda, Antoni; Mestre-Alfaro, Antonia; Banquells, Montserrat; Riera, Joan; Drobnic, Franchek; Camps, Jordi; Joven, Jorge; Tur, Josep A; Pons, Antoni

    2015-01-01

    Exercise in thermally stressful environmental conditions can enhance oxidative stress. We sought to measure the plasma antioxidant defenses and cytokine response together with oxidative damage post-exercise in a temperate versus a hot environment. The plasma concentrations of vasoactive endothelin-1 and vascular angiogenic growth factor were also evaluated. Male athletes (n=9) volunteered to participate. The athletes randomly performed two bouts of treadmill exercise of 45min at 75-80% of maximal oxygen uptake in a climatic-controlled chamber under two different conditions: temperate environment (10-12°C, 40-55% humidity) and hot, humid environment (30-32°C, 75-78% humidity). Venous blood samples were obtained immediately pre- and post-bout and on recovery after 2h. Serum glucose, malondialdehyde and lactate concentrations were significantly increased post-exercise in hot but maintained in the temperate environment; these post-exercise values were significantly higher after exercise in hot than in temperate. Urinary 8-hydroxy-2'-deoxyguanosine concentration, plasma phosphocreatine kinase and catalase activities, creatinine and monocyte chemoattractant protein-1, and interleukin-6 significantly increased post-exercise in hot but maintained in temperate environment. The post-exercise circulating values of antioxidant enzyme paraoxonase-1 and endothelin were significantly higher in the hot than in temperate environment. Exercise in a hot and humid environment resulted in mild hyperthermia with elevated perceived exertion and thermal stress. Hyperthermic environment induced hyperglycemia, lactatecidemia and more cellular and oxidative damage than exercise in a temperate environment but also induced a post-exercise antioxidant and anti-inflammatory response in plasma. These results suggest that environmental temperature needs to be taken into account when evaluating exercise-related oxidative stress and inflammation. Copyright © 2014 Elsevier Ltd. All rights reserved.

  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...... utilization capacity could not be directly linked to the community dynamics. The overall importance of dissolved organic matter (DOM) parameters in the LASSO models indicate that bacterioplankton respond to the present substrate landscape, with a particular importance of nitrogenous DOM. The identification...

  1. 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...

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

    Science.gov (United States)

    2010-01-01

    during rearing and is considered a susceptible strain; preliminary tests with pyre- thrum and permethrin in bottle bioassays cause death in #15 min...prior to the applications to attach them to the posts. The sentinel cages were cylindrical paper food containers (8.5 cm wide 3 4.5 cm deep; Neptune...M, Wheeler S, Gutierrez A, Gomsi D, Reisen WK. 2007a. Evaluation of pyrethrin and permethrin ground ultra-low volume applications for adult Culex

  3. Ultraviolet radiation and primary productivity in temperate aquatic environments of Patagonia (Argentina)

    NARCIS (Netherlands)

    Villafañe, Virginia

    2004-01-01

    Numerous studies carried out since the discovery of the ozone “hole” over the Antarctic continent have motivated photobiological research to determine the potential effects of increased solar ultraviolet radiation – UV-B (280-315 nm) on organisms and ecosystems. Since then, the amount of literature

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

    Science.gov (United States)

    1993-02-01

    sweet at altitude, so foods that are too sweet at sea level may taste better at altitude Suggested snacks are raisins and other dried fruits, yogurt ...loss of 1/2 to 1 pound per week is recommended for safe weight loss. .< * Choose a Diet Low in Fat, Saturated Fat, Lis_ and Cholesterol - In general, to...eat a diet 1-5 24 ---R3 low in fat, saturated fat, and cholesterol : 1) Eat plenty of vegetables, fruits, and grain prducts, 2) Choose lean meats, fish

  5. Nutrition for Health and Performance, 2000: Nutritional Guidance for Military Operations in Temperate and Extreme Environments.

    Science.gov (United States)

    1999-12-01

    Diet Low in Fat, Saturated Fat, and Cholesterol - In general, to eat a diet low in fat, saturated fat, and cholesterol : 1) Eat plenty of vegetables...important to consume adequate amounts. If a person is intolerant of fluid milk, cheese and yogurt can often be substituted. Another possibility is...servings you choose from each group. Figure 1. A Guide to Daily Food Choices Fats, Oils, & Sweets USE SPARINGLY Milk, Yogurt , & Cheese Group 2

  6. Herbivory on temperate rainforest seedlings in sun and shade: resistance, tolerance and habitat distribution.

    Directory of Open Access Journals (Sweden)

    Cristian Salgado-Luarte

    Full Text Available Differential herbivory and/or differential plant resistance or tolerance in sun and shade environments may influence plant distribution along the light gradient. Embothrium coccineum is one of the few light-demanding tree species in the temperate rainforest of southern South America, and seedlings are frequently attacked by insects and snails. Herbivory may contribute to the exclusion of E. coccineum from the shade if 1 herbivory pressure is greater in the shade, which in turn can result from shade plants being less resistant or from habitat preferences of herbivores, and/or 2 consequences of damage are more detrimental in the shade, i.e., shade plants are less tolerant. We tested this in a field study with naturally established seedlings in treefall gaps (sun and forest understory (shade in a temperate rainforest of southern Chile. Seedlings growing in the sun sustained nearly 40% more herbivore damage and displayed half of the specific leaf area than those growing in the shade. A palatability test showed that a generalist snail consumed ten times more leaf area when fed on shade leaves compared to sun leaves, i.e., plant resistance was greater in sun-grown seedlings. Herbivore abundance (total biomass was two-fold greater in treefall gaps compared to the forest understory. Undamaged seedlings survived better and showed a slightly higher growth rate in the sun. Whereas simulated herbivory in the shade decreased seedling survival and growth by 34% and 19%, respectively, damaged and undamaged seedlings showed similar survival and growth in the sun. Leaf tissue lost to herbivores in the shade appears to be too expensive to replace under the limiting light conditions of forest understory. Following evaluations of herbivore abundance and plant resistance and tolerance in contrasting light environments, we have shown how herbivory on a light-demanding tree species may contribute to its exclusion from shade sites. Thus, in the shaded forest understory

  7. Root Branching Is a Leading Root Trait of the Plant Economics Spectrum in Temperate Trees.

    Science.gov (United States)

    Liese, Rebecca; Alings, Katrin; Meier, Ina C

    2017-01-01

    Global vegetation models use conceived relationships between functional traits to simulate ecosystem responses to environmental change. In this context, the concept of the leaf economics spectrum (LES) suggests coordinated leaf trait variation, and separates species which invest resources into short-lived leaves with a high expected energy return rate from species with longer-lived leaves and slower energy return. While it has been assumed that being fast (acquisitive) or slow (conservative) is a general feature for all organ systems, the translation of the LES into a root economics spectrum (RES) for tree species has been hitherto inconclusive. This may be partly due to the assumption that the bulk of tree fine roots have similar uptake functions as leaves, despite the heterogeneity of their environments and resources. In this study we investigated well-established functional leaf and stature traits as well as a high number of fine root traits (14 traits split by different root orders) of 13 dominant or subdominant temperate tree species of Central Europe, representing two phylogenetic groups (gymnosperms and angiosperms) and two mycorrhizal associations (arbuscular and ectomycorrhizal). We found reflected variation in leaf and lower-order root traits in some (surface areas and C:N) but not all (N content and longevity) traits central to the LES. Accordingly, the LES was not mirrored belowground. We identified significant phylogenetic signal in morphological lower-order root traits, i.e., in root tissue density, root diameter, and specific root length. By contrast, root architecture (root branching) was influenced by the mycorrhizal association type which developed independent from phylogeny of the host tree. In structural equation models we show that root branching significantly influences both belowground (direct influence on root C:N) and aboveground (indirect influences on specific leaf area and leaf longevity) traits which relate to resource investment and

  8. Temper Outbursts in Paediatric Obsessive-Compulsive Disorder and Their Association with Depressed Mood and Treatment Outcome

    Science.gov (United States)

    Krebs, Georgina; Bolhuis, Koen; Heyman, Isobel; Mataix-Cols, David; Turner, Cynthia; Stringaris, Argyris

    2013-01-01

    Background: Temper outbursts in youth with obsessive-compulsive disorder (OCD) are a common source of concern, but remain poorly understood. This study examined a set of hypotheses related to: (a) the prevalence of temper outbursts in paediatric OCD, (b) the associations of temper outbursts with OCD severity and depressive symptoms; and (c) the…

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

    Science.gov (United States)

    Steward, Grieg F; Preston, Christina M

    2011-06-09

    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. We purified viruses from approximately one cubic meter of seawater collected from 200 m depth in Monterey Bay, CA. DNA was extracted from the virus fraction, sheared, and cloned with no prior amplification into a plasmid vector and propagated in E. coli to produce the MBv200m library. Random clones were sequenced by the Sanger method. Sequences were assembled then compared to sequences in GenBank and to other viral metagenomic libraries using BLAST analyses. Only 26% of the 881 sequences remaining after assembly had significant (E≤0.001) BLAST hits to sequences in the GenBank nr database, with most being matches to bacteria (15%) and viruses (8%). When BLAST analysis included environmental sequences, 74% of sequences in the MBv200m library had a significant match. Most of these hits (70%) were to microbial metagenome sequences and only 0.7% were to sequences from viral metagenomes. Of the 121 sequences with a significant hit to a known virus, 94% matched bacteriophages (Families Podo-, Sipho-, and Myoviridae) and 6% matched viruses of eukaryotes in the Family Phycodnaviridae (5 sequences) or the Mimivirus (2 sequences). The largest percentages of hits to viral genes of known function were to those involved in DNA modification (25%) or structural genes (17%). Based on reciprocal BLAST analyses, the MBv200m library appeared to be most similar to viral metagenomes from two other bays and least similar to a viral metagenome from the Arctic Ocean. Direct cloning of DNA from diverse marine viruses was feasible and resulted in a distribution of virus types and functional genes at depth that differed in detail

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

    Directory of Open Access Journals (Sweden)

    Preston Christina M

    2011-06-01

    Full Text Available 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 Monterey Bay, CA. DNA was extracted from the virus fraction, sheared, and cloned with no prior amplification into a plasmid vector and propagated in E. coli to produce the MBv200m library. Random clones were sequenced by the Sanger method. Sequences were assembled then compared to sequences in GenBank and to other viral metagenomic libraries using BLAST analyses. Results Only 26% of the 881 sequences remaining after assembly had significant (E ≤ 0.001 BLAST hits to sequences in the GenBank nr database, with most being matches to bacteria (15% and viruses (8%. When BLAST analysis included environmental sequences, 74% of sequences in the MBv200m library had a significant match. Most of these hits (70% were to microbial metagenome sequences and only 0.7% were to sequences from viral metagenomes. Of the 121 sequences with a significant hit to a known virus, 94% matched bacteriophages (Families Podo-, Sipho-, and Myoviridae and 6% matched viruses of eukaryotes in the Family Phycodnaviridae (5 sequences or the Mimivirus (2 sequences. The largest percentages of hits to viral genes of known function were to those involved in DNA modification (25% or structural genes (17%. Based on reciprocal BLAST analyses, the MBv200m library appeared to be most similar to viral metagenomes from two other bays and least similar to a viral metagenome from the Arctic Ocean. Conclusions Direct cloning of DNA from diverse marine viruses was feasible and resulted in a distribution of virus

  11. Eye injury after jellyfish sting in temperate Australia.

    Science.gov (United States)

    Winkel, Kenneth D; Hawdon, Gabrielle M; Ashby, Karen; Ozanne-Smith, Joan

    2002-01-01

    Although jellyfish stings are an uncommon medical problem in temperate Australia, significant morbidity can occur, particularly in association with infestations of large numbers of jellyfish in public swimming areas. We report a case of a jellyfish sting-related eye injury, probably caused by the "hair" jellyfish (Cyanea capillata) from southeast Australia. The patient, a 54-year-old man, was stung while swimming without goggles in a jellyfish-infested bay. He experienced severe pain in his right eye, requiring narcotic analgesia, and had decreased visual acuity associated with right-sided facial swelling. Although usually brief and self-limiting, eye injuries after jellyfish stings should be assessed and treated as early as possible to reduce the risk of longer term sequelae. Water safety campaigns should incorporate information on the prevention and early treatment of such stings.

  12. Ecosystem respiration depends strongly on photosynthesis in a temperate heath

    DEFF Research Database (Denmark)

    Larsen, Klaus Steenberg; Ibrom, A.; Beier, C.

    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...... respiration from October to March was 22% and 30% of annual flux, respectively, suggesting that both cold-season carbon gain and loss were important in the annual carbon cycle of the ecosystem. Model fit of R-E of a classic, first-order exponential equation related to temperature ( second year; R-2 = 0......) of 2.5 by the modified model. The model introduces R-photo, which describes the part of respiration being tightly coupled to the photosynthetic rate. It makes up 5% of the assimilated carbon dioxide flux at 0 degrees C and 35% at 20 degrees C implying a high sensitivity of respiration to photosynthesis...

  13. Temperance, alcohol, and the American evangelical: a reassessment.

    Science.gov (United States)

    Warner, Jessica

    2009-07-01

    Abstinence from alcohol is a way of life for many American evangelicals, with rates of abstention running at over 70% among some Pentecostal denominations. This paper examines the religious beliefs that, historically, have supported teetotalism. The most notable of these is Christian perfection, a doctrine that originated in 18th-century England, that was then radicalized in America in the early 19th century. Abstinence from alcohol is highest among denominations that make Christian perfection the cornerstone of their teachings, and lowest among those that discount human agency. The paper also argues that 19th-century American evangelicals were by no means committed uniformly to temperance as a way of life, and that this was especially true of the various Methodist churches.

  14. The effects of climate stability on northern temperate forests

    DEFF Research Database (Denmark)

    Ma, Ziyu

    2016-01-01

    refugia have served as both museums and cradles for old and new species, respectively. Moreover, comparing gymnosperm to angiosperm trees in North America, I found that gymnosperm phylogenetic diversity patterns were more linked to historical than to current climate. However, I also documented effects......Life's display of diversity and evolutionary histories is intertwined with climate on Earth. In this Ph.D. study, I explored the influence of both the past and ongoing climate change on forest trees north of the tropics using large geospatial data sets. Phylogenetic structure of species assemblage....... The evolutionary relationship among species is known as phylogeny. Tree diversity was mapped using a phylogenetic supertree, covering species in the temperate forests of North America, Europe, and China. I found that Quaternary climate fluctuations limited phylogenetic endemism, which quantified unique...

  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

    2015-10-06

    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. Evolution of Thermal Reaction Norms in Seasonally Varying Environments.

    Science.gov (United States)

    Amarasekare, Priyanga; Johnson, Christopher

    2017-03-01

    Thermal reaction norms of ectotherms exhibit a distinctive latitudinal pattern: the temperature at which performance is maximized coincides with the mean habitat temperature in tropical ectotherms but exceeds the mean temperature in temperate ectotherms. We hypothesize, on the basis of Jensen's inequality, that this pattern is driven by latitudinal variation in seasonal temperature fluctuations. We test this hypothesis with an eco-evolutionary model that integrates the quantitative genetics of reaction norm evolution with stage-structured population dynamics, which we parameterize with data from insects. We find that thermal optima of temperate and Mediterranean species evolve to exceed the mean habitat temperature if seasonal fluctuations are strong, while the thermal optimum of tropical species evolves to coincide with the mean habitat temperature if fluctuations are weak. Importantly, ecological dynamics can impose a constraint on reaction norm evolution. Tropical species cannot tolerate an increase in seasonal fluctuations at the high mean habitat temperature it experiences, while the temperate species cannot tolerate a reduction in seasonal fluctuations if the mean temperature is higher. In both cases, stochastic extinction during periods of low abundances precludes adaptation to a novel thermal environment. Our findings suggest a potential directionality in colonization success. Tropical ectotherms, because of their high thermal optima, can successfully colonize temperate habitats, while temperate ectotherms, because of their low optima, are less successful in colonizing tropical habitats.

  17. Comparative genomics and transduction potential of Enterococcus faecalis temperate bacteriophages.

    Science.gov (United States)

    Yasmin, Azra; Kenny, John G; Shankar, Jayendra; Darby, Alistair C; Hall, Neil; Edwards, Clive; Horsburgh, Malcolm J

    2010-02-01

    To determine the relative importance of temperate bacteriophage in the horizontal gene transfer of fitness and virulence determinants of Enterococcus faecalis, a panel of 47 bacteremia isolates were treated with the inducing agents mitomycin C, norfloxacin, and UV radiation. Thirty-four phages were purified from culture supernatants and discriminated using pulsed-field gel electrophoresis (PFGE) and restriction mapping. From these analyses the genomes of eight representative phages were pyrosequenced, revealing four distinct groups of phages. Three groups of phages, PhiFL1 to 3, were found to be sequence related, with PhiFL1A to C and PhiFL2A and B sharing the greatest identity (87 to 88%), while PhiFL3A and B share 37 to 41% identity with PhiFL1 and 2. PhiFL4A shares 3 to 12% identity with the phages PhiFL1 to 3. The PhiFL3A and B phages possess a high DNA sequence identity with the morphogenesis and lysis modules of Lactococcus lactis subsp. cremoris prophages. Homologs of the Streptococcus mitis platelet binding phage tail proteins, PblA and PblB, are encoded on each sequenced E. faecalis phage. Few other phage genes encoding potential virulence functions were identified, and there was little evidence of carriage of lysogenic conversion genes distal to endolysin, as has been observed with genomes of many temperate phages from the opportunist pathogens Staphylococcus aureus and Streptococcus pyogenes. E. faecalis JH2-2 lysogens were generated using the eight phages, and these were examined for their relative fitness in Galleria mellonella. Several lysogens exhibited different effects upon survival of G. mellonella compared to their isogenic parent. The eight phages were tested for their ability to package host DNA, and three were shown to be very effective for generalized transduction of naive host cells of the laboratory strains OG1RF and JH2-2.

  18. Ice duration drives winter nitrate accumulation in north temperate lakes

    Science.gov (United States)

    Powers, Steven M; Labou, Stephanie G.; Baulch, Helen M.; Hunt, Randall J.; Lottig, Noah R.; Hampton, Stephanie E.; Stanley, Emily H.

    2017-01-01

    The duration of winter ice cover on lakes varies substantially with climate variability, and has decreased over the last several decades in many temperate lakes. However, little is known of how changes in seasonal ice cover may affect biogeochemical processes under ice. We examined winter nitrogen (N) dynamics under ice using a 30+ yr dataset from five oligotrophic/mesotrophic north temperate lakes to determine how changes in inorganic N species varied with ice duration. Nitrate accumulated during winter and was strongly related to the number of days since ice-on. Exogenous inputs accounted for less than 3% of nitrate accumulation in four of the five lakes, suggesting a paramount role of nitrification in regulating N transformation and the timing of chemical conditions under ice. Winter nitrate accumulation rates ranged from 0.15 μg N L−1 d−1 to 2.7 μg N L−1 d−1 (0.011–0.19 μM d−1), and the mean for intermediate depths was 0.94 μg N L−1 d−1(0.067 μM d−1). Given that winters with shorter ice duration (< 120 d) have become more frequent in these lakes since the late 1990s, peak winter nitrate concentrations and cumulative nitrate production under ice may be declining. As ice extent and duration change, the physical and chemical conditions supporting life will shift. This research suggests we may expect changes in the form and amount of inorganic N, and altered dissolved nitrogen : phosphorus ratios, in lakes during winters with shorter ice duration.

  19. Selective Sorption of Dissolved Organic Carbon Compounds by Temperate Soils

    Science.gov (United States)

    Jagadamma, Sindhu; Mayes, Melanie A.; Phillips, Jana R.

    2012-01-01

    Background Physico-chemical sorption onto soil minerals is one of the major processes of dissolved organic carbon (OC) stabilization in deeper soils. The interaction of DOC on soil solids is related to the reactivity of soil minerals, the chemistry of sorbate functional groups, and the stability of sorbate to microbial degradation. This study was conducted to examine the sorption of diverse OC compounds (D-glucose, L-alanine, oxalic acid, salicylic acid, and sinapyl alcohol) on temperate climate soil orders (Mollisols, Ultisols and Alfisols). Methodology Equilibrium batch experiments were conducted using 0–100 mg C L−1 at a solid-solution ratio of 1∶60 for 48 hrs on natural soils and on soils sterilized by γ-irradiation. The maximum sorption capacity, Qmax and binding coefficient, k were calculated by fitting to the Langmuir model. Results Ultisols appeared to sorb more glucose, alanine, and salicylic acid than did Alfisols or Mollisols and the isotherms followed a non-linear pattern (higher k). Sterile experiments revealed that glucose and alanine were both readily degraded and/or incorporated into microbial biomass because the observed Qmax under sterile conditions decreased by 22–46% for glucose and 17–77% for alanine as compared to non-sterile conditions. Mollisols, in contrast, more readily reacted with oxalic acid (Qmax of 886 mg kg−1) and sinapyl alcohol (Qmax of 2031 mg kg−1), and no degradation was observed. The reactivity of Alfisols to DOC was intermediate to that of Ultisols and Mollisols, and degradation followed similar patterns as for Ultisols. Conclusion This study demonstrated that three common temperate soil orders experienced differential sorption and degradation of simple OC compounds, indicating that sorbate chemistry plays a significant role in the sorptive stabilization of DOC. PMID:23209742

  20. 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. 

  1. 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.

  2. A comparison of conventional and radio frequency tempering of beef meats: Effects on product temperature distribution.

    Science.gov (United States)

    Farag, K W; Lyng, J G; Morgan, D J; Cronin, D A

    2008-10-01

    This study aimed to develop radio frequency (RF) pilot-scale protocols for tempering beef meat blends (4kg blocks) to achieve average temperatures between -2 and -5°C. Post-tempering temperature distribution in these blocks was compared to products tempered by conventional methods. The optimum RF power-time combination for tempering lean and 50:50 lean:fat mixtures to the target range was 500W for 11min which produced respective means of -3.6°C (s.d. 1.1) and -3.4°C (s.d. 1.5). In contrast, 400W for 11min was optimum for fat (mean -4.9°C, s.d. 2.1). This study shows the principal advantages of RF over conventional tempering as an approximate 30 fold tempering time reduction and a greater uniformity of end point temperature distribution under the conditions employed. Furthermore, power consumption was reduced approximately ninefold with RF compared to conventional tempering. More uniform temperature distribution was achieved in samples that were comminuted to a greater extent.

  3. Characteristics of the Transformation of Retained Austenite in Tempered Austempered Ductile Iron

    Science.gov (United States)

    Wang, Bingxu; Barber, Gary; Sun, Xichen; Shaw, Michael; Seaton, Phil

    2017-05-01

    Controlling the amount of retained austenite is a concern in austempered ductile iron formation. Retained austenite has a strong influence on austempered ductile iron properties, such as hardness and wear resistance. In this research, the characteristics of the transformation of retained austenite were investigated as a function of the number of tempering cycles. The hardness of the austempered ductile iron samples was measured, and the specific amount of retained austenite was analyzed by x-ray diffraction (XRD). Wear tests were conducted on a ball-on-flat sliding fixture. The tempering process was found to have no effect on the hardness of the austempered ductile iron samples. This may be due to retained austenite being partially converted into brittle quenched martensite during the tempering process. However, tougher tempered martensite was also formed from existing martensite. The two effects seemed to offset each other, and no significant differences occurred in overall hardness. XRD analysis showed that under the same austempering temperature and holding time, the amount of retained austenite decreased with additional tempering cycles. Also, with the same holding time and tempering cycles, less retained austenite was contained in the matrix at higher austempering temperatures. This was due to more high carbon content austenite and needle-like ferrite being present in the austempered ductile iron matrix. In addition, tempered austempered ductile iron exhibited significantly higher wear resistance as compared to traditionally treated ductile iron.

  4. Temper outbursts in Prader-Willi syndrome: causes, behavioural and emotional sequence and responses by carers.

    Science.gov (United States)

    Tunnicliffe, P; Woodcock, K; Bull, L; Oliver, C; Penhallow, J

    2014-02-01

    Temper outbursts are common in Prader-Willi syndrome but rarely described in detail. This study investigated the phenomenology of temper outbursts in terms of antecedents, sequence of behaviours and emotions and intervention strategies used. A semi-structured interview about temper outbursts was conducted with the main carers of seven children (9.5 to 16.7 years) and seven adults (24.7 to 47.10 years) with Prader-Willi syndrome (10 male, 4 female). Reliability and validity of the interview results was established. Various setting events increased and reduced the likelihood of temper outbursts. The most common antecedent was a change to routine or expectation. There were marked similarities in the sequence of behaviours and emotions during temper outbursts, with anger rising quickly followed by expressions of remorse and distress at the end of an outburst. The sequence of behaviours and emotions within outbursts was similar to that described in temper tantrums in typical development. Cognitive and emotional processes are likely to be important in the understanding of temper outbursts with implications for early intervention. © 2013 The Authors. Journal of Intellectual Disability Research © 2013 John Wiley & Sons Ltd, MENCAP & IASSIDD.

  5. Atom Probe Tomography Examination of Carbon Redistribution in Quenched and Tempered 4340 Steel

    Energy Technology Data Exchange (ETDEWEB)

    Clarke, Amy J. [Los Alamos National Laboratory; Miller, Michael K. [ORNL; Alexander, David J. [Los Alamos National Laboratory; Field, Robert D. [Los Alamos National Laboratory; Clarke, Kester D. [Los Alamos National Laboratory

    2012-08-07

    Quenching and tempering produces a wide range of mechanical properties in medium carbon, low alloyed steels - Study fragmentation behavior as a function of heat-treatment. Subtle microstructural changes accompany the mechanical property changes that result from quenching and tempering - Characterize the location and distribution of carbon and alloying elements in the microstructure using atom probe tomography (APT). Perform complementary transmission electron microscopy (TEM). Tempering influences the mechanical properties and fragmentation of quenched 4340 (hemi-shaped samples). APT revealed carbon-enriched features that contain a maximum of {approx}12-14 at.% carbon after quenching to RT (the level of carbon is perhaps associated with the extent of autotempering). TEM confirmed the presence of twinned martensite and indicates {var_epsilon} ({eta}) transition carbides after oil quenching to RT. Tempering at 325 C resulted in carbon-enriched plates (> 25 at.% C) with no significant element partitioning (transition carbides?). Tempering at 450 C and 575 C resulted in cementite ({approx} 25 at.% C) during late stage tempering; Cr, Mn, Mo partitioned to cementite and Si partitioned to ferrite. Tempering at 575 C resulted in P segregation at cementite interfaces and the formation of Cottrell atmospheres.

  6. Forest ecosystems of temperate climatic regions: from ancient use to climate change.

    Science.gov (United States)

    Gilliam, Frank S

    2016-12-01

    871 I. 871 II. 874 III. 875 IV. 878 V. 882 884 References 884 SUMMARY: Humans have long utilized resources from all forest biomes, but the most indelible anthropogenic signature has been the expanse of human populations in temperate forests. The purpose of this review is to bring into focus the diverse forests of the temperate region of the biosphere, including those of hardwood, conifer and mixed dominance, with a particular emphasis on crucial challenges for the future of these forested areas. Implicit in the term 'temperate' is that the predominant climate of these forest regions has distinct cyclic, seasonal changes involving periods of growth and dormancy. The specific temporal patterns of seasonal change, however, display an impressive variability among temperate forest regions. In addition to the more apparent current anthropogenic disturbances of temperate forests, such as forest management and conversion to agriculture, human alteration of temperate forests is actually an ancient phenomenon, going as far back as 7000 yr before present (bp). As deep-seated as these past legacies are for temperate forests, all current and future perturbations, including timber harvesting, excess nitrogen deposition, altered species' phenologies, and increasing frequency of drought and fire, must be viewed through the lens of climate change. © 2016 The Author. New Phytologist © 2016 New Phytologist Trust.

  7. Effect of tempering methods on quality changes of pork loin frozen by cryogenic immersion.

    Science.gov (United States)

    Choi, Eun Ji; Park, Hae Woong; Chung, Young Bae; Park, Sung Hoon; Kim, Jin Se; Chun, Ho Hyun

    2017-02-01

    The quality characteristics of pork loin frozen by cryogenic immersion were examined, such as the drip loss, cooking loss, water holding capacity, moisture content, protein solubility, lipid and protein oxidation, color, and microstructure, and compared after different tempering methods: radio frequency (27.12MHz), water immersion, forced-air convection, and microwave tempering. Forced-air tempering was the most time-consuming process, whereas electromagnetic energy methods (radio frequency and microwave) were the shortest. The tempering rate of radio frequency at 400W was 5 and 94 times greater than that obtained with water immersion and forced-air tempering, respectively. The drip loss, water holding capacity, moisture content, color, and microstructure of pork samples all declined as a result of microwave tempering. By contrast, the least degree of changes in the drip loss, microstructure, and color of the pork loin samples was obtained with radio frequency tempering, suggesting its potential application in providing rapid defrosting without quality deterioration in the frozen meat industry. Copyright © 2016 Elsevier Ltd. All rights reserved.

  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. 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.

  10. 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.

  11. Seasonal patterns of the insect community structure in urban rain pools of temperate Argentina.

    Science.gov (United States)

    Fontanarrosa, M Soledad; Collantes, Marta B; Bachmann, Axel O

    2009-01-01

    Temporary aquatic environments are widespread in the world, and although there are considerable regional differences in their type and method of formation they have many physical, chemical and biological properties in common. With the aim to increase knowledge of urban temporary pool fauna, the objectives of this work were to assess the seasonal patterns of species composition, richness, and diversity of the aquatic insect community inhabiting rain pools in urban temperate Argentina, and to identify the environmental variables associated to these patterns. Four temporary pools of an urban green space in Buenos Aires City were studied throughout a 1-year period. Eleven flood cycles with very varied hydroperiods and dry periods, mainly associated with rainfall, were identified. Insect species richness in these temporary urban pools, 86 taxa were documented, was found to be within the range reported for wild temporary water bodies of other regions of the world. The present results provide evidence for the existence of a clear link between habitat and community variability. Hydroperiod and seasonality were the main environmental factors involved in structuring the insect communities of the studied water bodies. Urban pools in green spaces have the potential to act to its dwellers like corridors through the urban matrix. Taking into account these characteristics and their accessibility, urban temporary pools can be considered as promising habitats for the study of ecological processes involving the insect community.

  12. Practically Efficient and Robust Free Energy Calculations: Double-Integration Orthogonal Space Tempering.

    Science.gov (United States)

    Zheng, Lianqing; Yang, Wei

    2012-03-13

    The orthogonal space random walk (OSRW) method, which enables synchronous acceleration of the motions of a focused region and its coupled environment, was recently introduced to enhance sampling for free energy simulations. In the present work, the OSRW algorithm is generalized to be the orthogonal space tempering (OST) method via the introduction of the orthogonal space sampling temperature. Moreover, a double-integration recursion method is developed to enable practically efficient and robust OST free energy calculations, and the algorithm is augmented by a novel θ-dynamics approach to realize both the uniform sampling of order parameter spaces and rigorous end point constraints. In the present work, the double-integration OST method is employed to perform alchemical free energy simulations, specifically to calculate the free energy difference between benzyl phosphonate and difluorobenzyl phosphonate in aqueous solution, to estimate the solvation free energy of the octanol molecule, and to predict the nontrivial Barnase-Barstar binding affinity change induced by the Barnase N58A mutation. As demonstrated in these model studies, the DI-OST method can robustly enable practically efficient free energy predictions, particularly when strongly coupled slow environmental transitions are involved.

  13. Seasonal variation in the antifouling defence of the temperate brown alga Fucus vesiculosus.

    Science.gov (United States)

    Saha, Mahasweta; Wahl, Martin

    2013-01-01

    The important role of marine epibiotic biofilms in the interactions of the host with its environment has been acknowledged recently. Previous studies with the temperate brown macroalga Fucus vesiculosus have identified polar and non-polar compounds recovered from the algal surface that have the potential to control such biofilms. Furthermore, both the fouling pressure and the composition of the epibiotic bacterial communities on this macroalga varied seasonally. The extent to which this reflects a seasonal fluctuation of the fouling control mechanisms of the host is, however, unexplored in an ecological context. The present study investigated seasonal variation in the anti-settlement activity of surface extracts of F. vesiculosus against eight biofilm-forming bacteria isolated from rockweed-dominated habitats, including replication of two populations from two geographically distant sites. The anti-settlement activity at both sites was found to vary temporally, reaching a peak in summer/autumn. Anti-settlement activity also showed a consistent and strong difference between sites throughout the year. This study is the first to report temporal variation of antifouling defence originating from ecologically relevant surface-associated compounds.

  14. Shift in colonial reproductive strategy associated with a tropical-temperate gradient in Rhytidoponera ants.

    Science.gov (United States)

    Molet, Mathieu; Van Baalen, Minus; Peeters, Christian

    2008-07-01

    Offspring quality and quantity are subject to a trade-off. Depending on species, ant colonies can produce either numerous winged queens that start new colonies alone (independent colony foundation [ICF]) or one propagule consisting of reproductives helped by workers (fission). Some species do both. In the Rhytidoponera impressa group, colonies with winged queens use ICF, whereas colonies with mated workers use fission. We assessed the effect of latitude and environment on colonial reproduction by collecting 79 colonies along the Australian east coast. A population dynamical model predicted that from tropical north to temperate south, seasonal fluctuations and harsher conditions should lead to a decrease in ICF success (-48%), making fission a suitable alternative. Yet, our empirical data showed that ICF persists at a higher rate than expected, presumably because it allows aerial dispersal, unlike fission. Investigation of colony demography and measurement of lean and fat weights in virgin winged queens and workers showed that, from north to south, colonies increase quality of queens relative to workers (+50%) at the cost of quantity (-86%). This modification limits the decrease in ICF success (-34%). A tremendous range of offspring phenotypes associated with quality-quantity trade-offs make ants competitive in diverse habitats.

  15. Seasonal Patterns of the Insect Community Structure in Urban Rain Pools of Temperate Argentina

    Science.gov (United States)

    Fontanarrosa, M. Soledad; Collantes, Marta B.; Bachmann, Axel O.

    2009-01-01

    Temporary aquatic environments are widespread in the world, and although there are considerable regional differences in their type and method of formation they have many physical, chemical and biological properties in common. With the aim to increase knowledge of urban temporary pool fauna, the objectives of this work were to assess the seasonal patterns of species composition, richness, and diversity of the aquatic insect community inhabiting rain pools in urban temperate Argentina, and to identify the environmental variables associated to these patterns. Four temporary pools of an urban green space in Buenos Aires City were studied throughout a 1-year period. Eleven flood cycles with very varied hydroperiods and dry periods, mainly associated with rainfall, were identified. Insect species richness in these temporary urban pools, 86 taxa were documented, was found to be within the range reported for wild temporary water bodies of other regions of the world. The present results provide evidence for the existence of a clear link between habitat and community variability. Hydroperiod and seasonality were the main environmental factors involved in structuring the insect communities of the studied water bodies. Urban pools in green spaces have the potential to act to its dwellers like corridors through the urban matrix. Taking into account these characteristics and their accessibility, urban temporary pools can be considered as promising habitats for the study of ecological processes involving the insect community. PMID:19611261

  16. 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

  17. Seasonal determinations of algal virus decay rates reveal overwintering in a temperate freshwater pond.

    Science.gov (United States)

    Long, Andrew M; Short, Steven M

    2016-07-01

    To address questions about algal virus persistence (i.e., continued existence) in the environment, rates of decay of infectivity for two viruses that infect Chlorella-like algae, ATCV-1 and CVM-1, and a virus that infects the prymnesiophyte Chrysochromulina parva, CpV-BQ1, were estimated from in situ incubations in a temperate, seasonally frozen pond. A series of experiments were conducted to estimate rates of decay of infectivity in all four seasons with incubations lasting 21 days in spring, summer and autumn, and 126 days in winter. Decay rates observed across this study were relatively low compared with previous estimates obtained for other algal viruses, and ranged from 0.012 to 11% h(-1). Overall, the virus CpV-BQ1 decayed most rapidly whereas ATCV-1 decayed most slowly, but for all viruses the highest decay rates were observed during the summer and the lowest were observed during the winter. Furthermore, the winter incubations revealed the ability of each virus to overwinter under ice as ATCV-1, CVM-1 and CpV-BQ1 retained up to 48%, 19% and 9% of their infectivity after 126 days, respectively. The observed resilience of algal viruses in a seasonally frozen freshwater pond provides a mechanism that can support the maintenance of viral seed banks in nature. However, the high rates of decay observed in the summer demonstrate that virus survival and therefore environmental persistence can be subject to seasonal bottlenecks.

  18. Cold resistance depends on acclimation and behavioral caste in a temperate ant

    Science.gov (United States)

    Modlmeier, Andreas P.; Pamminger, Tobias; Foitzik, Susanne; Scharf, Inon

    2012-10-01

    Adjusting to low temperatures is important for animals living in cold environments. We studied the chill-coma recovery time in temperate ant workers ( Temnothorax nylanderi) from colonies collected in autumn and spring in Germany. We experimentally acclimated these ant colonies to cold temperatures followed by warm temperatures. As expected, cold-acclimated workers recovered faster from freezing temperatures, but subsequent heat acclimation did not change the short recovery times observed after cold acclimation. Hence, either heat acclimation improves cold tolerance, possibly as a general response to stress, or at least it does not negate enhanced cold tolerance following cold acclimation. Colonies collected in spring showed similar cold tolerance levels to cold-acclimated colonies in the laboratory. Next, we compared the chill-coma recovery time of different worker castes and found that exterior workers recovered faster than interior workers. This difference may be related to their more frequent exposure to cold, higher activity level, or distinct physiology. Interior workers were also heavier and showed a higher gaster-to-head ratio and thorax ratio compared to exterior workers. An obvious difference between exterior and interior workers is activity level, but we found no link between activity and cold tolerance. This suggests that physiology rather than behavioral differences could cause the increased cold tolerance of exterior workers. Our study reveals the importance of acclimation for cold tolerance under natural and standardized conditions and demonstrates differences in cold tolerance and body dimensions in monomorphic behavioral castes of an ant.

  19. A constant entropy increase model for the selection of parallel tempering ensembles.

    Science.gov (United States)

    Sabo, Dubravko; Meuwly, Markus; Freeman, David L; Doll, J D

    2008-05-07

    The present paper explores a simple approach to the question of parallel tempering temperature selection. We argue that to optimize the performance of parallel tempering it is reasonable to require that the increase in entropy between successive temperatures be uniform over the entire ensemble. An estimate of the system's heat capacity, obtained either from experiment, a preliminary simulation, or a suitable physical model, thus provides a means for generating the desired tempering ensemble. Applications to the two-dimensional Ising problem indicate that the resulting method is effective, simple to implement, and robust with respect to its sensitivity to the quality of the underlying heat capacity model.

  20. From multidimensional replica-exchange method to multidimensional multicanonical algorithm and simulated tempering.

    Science.gov (United States)

    Mitsutake, Ayori; Okamoto, Yuko

    2009-04-01

    We discuss multidimensional generalizations of multicanonical algorithm, simulated tempering, and replica-exchange method. We generalize the original potential-energy function E0 by adding any physical quantity V of interest as a new energy term with a coupling constant lambda. We then perform a multidimensional multicanonical simulation where a random walk in E0 and V spaces is realized. We can alternately perform a multidimensional simulated-tempering simulation where a random walk in temperature T and parameter lambda is realized. The results of the multidimensional replica-exchange simulations can be used to determine the weight factors for these multidimensional multicanonical and simulated-tempering simulations.

  1. Evolution of compressive strains in retained austenite during sub-zero Celsius martensite formation and tempering

    DEFF Research Database (Denmark)

    Villa, Matteo; Pantleon, Karen; Somers, Marcel A. J.

    2014-01-01

    tempering. Furthermore, it is demonstrated that sub-zero Celsius treatment after tempering leads to compressive strain in austenite. Finally, it is reported that no compressive strain builds up in austenite when the martensite formation occurs below a certain critical temperature.......; (ii) to measure the evolution of the lattice strain in retained austenite; and (iii) to identify the different stages of tempering. This work shows for the first time that the compressive strains built up in austenite upon martensite formation during sub-zero Celsius treatment are retained after...

  2. 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.

  3. 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

  4. The toxic benthic dinoflagellates of the genus Ostreopsis in temperate areas: a review

    Directory of Open Access Journals (Sweden)

    Stefano Accoroni

    2016-04-01

    Full Text Available The genus Ostreopsis includes species largely distributed from tropical to temperate marine areas worldwide. Among the nine species of the genus, O. siamensis, O. mascarenensis, O. lenticularis and O. cf. ovata can produce toxins of the palytoxin group. In the last decade Ostreopsis cf. ovata and O. cf. siamensis originated intense blooms in all the rocky Mediterranean Sea coastal areas, typically during summer-late summer. The correct identification of Ostreopsis species in field samples is often problematic as Ostreopsis species are morphologically plastic and hardly discriminable under light microscopy and, therefore, molecular analyses are required. Ostreopsis blooms are often associated with noxious effects on health of both humans and benthic marine organisms mainly carried by aerosol and direct contact with seawater. Environmental factors have been shown to affect toxin content of Ostreopsis which generally produces more toxins per cell when growing under suboptimal conditions. O. cf. ovata is able to produce both temporary and resting cysts. In particular, the resting cysts are able to germinate in laboratory conditions for as long as 5 months after their formation at 25°C, but not at 21°C; the presence of a temperature threshold affecting cyst germination in the laboratory suggests that temperature represents a key factor for Ostreopsis cf. ovata bloom onset in natural environments as well. Several studies conducted to assess the role of abiotic factors (mainly hydrodynamics, water temperature and nutrients on the bloom dynamics, revealed that the synergic effects of hydrodynamics, temperature and N:P ratios would lead the Ostreopsis blooms in temperate areas. Ostreopsis abundances showed a significant decrease with depth, likely related to light availability, although there are conflicting data about the relationship between light intensity and Ostreopsis growth in experimental conditions. The relationship between Ostreopsis blooms

  5. Environmental Controls and Management Effects on Ecosystem Carbon Exchange in Two Grazed Temperate Grasslands

    Science.gov (United States)

    Ni Choncubhair, O.; Humphreys, J.; Lanigan, G.

    2013-12-01

    Temperate grasslands constitute over 30% of the Earth's naturally-occurring biomes and make an important contribution towards the partial mitigation of anthropogenic greenhouse gas emissions by terrestrial ecosystems. Accumulation of carbon (C) in grassland systems predominantly takes place in below-ground repositories, enhanced by the presence of a stable soil environment with low carbon turnover rates, active rhizodeposition and high levels of residue and organic inputs. However, this C sequestration is strongly influenced by soil characteristics and climatic variables. Furthermore, in managed pasture systems, carbon exchange across the soil-atmosphere boundary is additionally affected by management activities, such as biomass removal, grazing events and the deposition or application of organic amendments. These biotic and abiotic factors contribute greatly towards the large uncertainty associated with the carbon balance of grassland ecosystems and demand further analysis. In the present study, the controls and drivers of carbon dynamics in two rotationally-grazed grasslands in Ireland were examined. The sites experience similar temperate climatic regimes but differ in soil texture classification and stocking rate. Eddy covariance measurements of net ecosystem exchange of carbon were complemented by regular assessment of standing biomass, leaf cover, harvest exports and organic amendment inputs. Our study showed that mild weather conditions and an extended growing season sustained net C accumulation at both sites for at least ten months of the year. Despite differing soil drainage characteristics, winter fluxes of net carbon exchange and its component fluxes, gross photosynthesis and ecosystem respiration, were highly comparable between the two sites. Management practices during the active growing season exerted a strong influence on both the direction and the rate of C exchange in the grassland systems, with a strong dependence, however, on the timing and

  6. Carbon density and distribution of six Chinese temperate forests.

    Science.gov (United States)

    Zhang, QuanZhi; Wang, ChuanKuan

    2010-07-01

    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 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 of C allocation patterns in a specific forest is jointly influenced by vegetation type, management history, and local water and nutrient availability. The study provides important data for developing and validating C cycling models for

  7. Shotgun proteomic analysis of tiger milk mushroom (Lignosus rhinocerotis) and the isolation of a cytotoxic fungal serine protease from its sclerotium.

    Science.gov (United States)

    Yap, Hui-Yeng Y; Fung, Shin-Yee; Ng, Szu-Ting; Tan, Chon-Seng; Tan, Nget-Hong

    2015-11-04

    The sclerotium of Lignosus rhinocerotis (Cooke) Ryvarden (tiger milk mushroom) has been traditionally used as a complementary and alternative medicine for cancer treatment by the local communities of Southeast Asia. Despite the continuous research interest in its antiproliferative activity, the identity of the bioactive compound(s) responsible has yet to be determined. This study aims to bridge the gap in existing research literature by using proteomics approach for investigation of the nature of the anticancer substance of L. rhinocerotis. To elucidate the proteome of L. rhinocerotis TM02 sclerotium by protein mass spectrometry and to further isolate and identify the cytotoxic component(s) bearing anticancer potential. The proteome of L. rhinocerotis sclerotium was analyzed by label-free quantitative shotgun proteomics, using 1D-SDS-PAGE coupled with nano-ESI-LC-MS/MS based on the availability of its genome-sequence database. The cytotoxicity of L. rhinocerotis sclerotial extracts against human breast adenocarcinoma cells (MCF7) were assessed by MTT cytotoxicity assay prior to successive purification steps by a combination of gel filtration chromatography, ammonium sulfate precipitation, and anion exchange chromatography. Bioactive compound(s) in the extracts was identified by shotgun proteomics and N-terminal protein sequencing. Several proteins with interesting biological activities including lectins, fungal immunomodulatory proteins, and several antioxidant proteins were identified from the proteome of L. rhinocerotis. A cytotoxic protein fraction (termed F5) which was partially purified from its sclerotial cold water extract F5 shows two distinct bands of 31 and 36 kDa in reducing SDS-PAGE and exhibited potent selective cytotoxicity against MCF7 cells with IC50 value of 3.00 ± 1.01 μg/ml. Both bands were identified to be serine protease by LC-MS/MS analysis. Phenylmethylsulfonyl fluoride, a specific serine protease inhibitor, inhibited both the proteolytic

  8. 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

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

    Science.gov (United States)

    Doughty, Emma L; Sergeant, Martin J; Adetifa, Ifedayo; Antonio, Martin; Pallen, Mark J

    2014-01-01

    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 strains. We have

  10. 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

    2017-08-25

    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

  11. Contrasting Propagation of Natural Calls of Two Anuran Species from the South American Temperate Forest

    National Research Council Canada - National Science Library

    Penna, Mario; Moreno-Gómez, Felipe N

    2015-01-01

    .... emiliopugini in the austral temperate forest where they communicate and breed syntopically. The calls of E. calcaratus have higher frequency components and lower amplitude relative to calls of E...

  12. Impacts of convection schemes on simulating tropical-temperate troughs over southern Africa

    CSIR Research Space (South Africa)

    Tozuka, T

    2013-03-01

    Full Text Available This study examines southern African summer rainfall and tropical temperate troughs (TTTs) simulated with three versions of an atmospheric general circulation model differing only in the convection scheme. All three versions provide realistic...

  13. Climate change reduces extent of temperate drylands and intensifies drought in deep soils

    Science.gov (United States)

    Schlaepfer, Daniel R.; Bradford, John B.; Lauenroth, William K.; Munson, Seth M.; Tietjen, Britta; Hall, Sonia A.; Wilson, Scott D.; Duniway, Michael C.; Jia, Gensuo; Pyke, David A.; Lkhagva, Ariuntsetseg; Jamiyansharav, Khishigbayar

    2017-01-01

    Drylands cover 40% of the global terrestrial surface and provide important ecosystem services. While drylands as a whole are expected to increase in extent and aridity in coming decades, temperature and precipitation forecasts vary by latitude and geographic region suggesting different trajectories for tropical, subtropical, and temperate drylands. Uncertainty in the future of tropical and subtropical drylands is well constrained, whereas soil moisture and ecological droughts, which drive vegetation productivity and composition, remain poorly understood in temperate drylands. Here we show that, over the twenty first century, temperate drylands may contract by a third, primarily converting to subtropical drylands, and that deep soil layers could be increasingly dry during the growing season. These changes imply major shifts in vegetation and ecosystem service delivery. Our results illustrate the importance of appropriate drought measures and, as a global study that focuses on temperate drylands, highlight a distinct fate for these highly populated areas.

  14. Genomic estimation of complex traits reveals ancient maize adaptation to temperate North America.

    Science.gov (United States)

    Swarts, Kelly; Gutaker, Rafal M; Benz, Bruce; Blake, Michael; Bukowski, Robert; Holland, James; Kruse-Peeples, Melissa; Lepak, Nicholas; Prim, Lynda; Romay, M Cinta; Ross-Ibarra, Jeffrey; Sanchez-Gonzalez, Jose de Jesus; Schmidt, Chris; Schuenemann, Verena J; Krause, Johannes; Matson, R G; Weigel, Detlef; Buckler, Edward S; Burbano, Hernán A

    2017-08-04

    By 4000 years ago, people had introduced maize to the southwestern United States; full agriculture was established quickly in the lowland deserts but delayed in the temperate highlands for 2000 years. We test if the earliest upland maize was adapted for early flowering, a characteristic of modern temperate maize. We sequenced fifteen 1900-year-old maize cobs from Turkey Pen Shelter in the temperate Southwest. Indirectly validated genomic models predicted that Turkey Pen maize was marginally adapted with respect to flowering, as well as short, tillering, and segregating for yellow kernel color. Temperate adaptation drove modern population differentiation and was selected in situ from ancient standing variation. Validated prediction of polygenic traits improves our understanding of ancient phenotypes and the dynamics of environmental adaptation. Copyright © 2017 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

  15. Molecular control of seasonal flowering in rice, arabidopsis and temperate cereals.

    Science.gov (United States)

    Shrestha, Roshi; Gómez-Ariza, Jorge; Brambilla, Vittoria; Fornara, Fabio

    2014-11-01

    Rice (Oryza sativa) and Arabidopsis thaliana have been widely used as model systems to understand how plants control flowering time in response to photoperiod and cold exposure. Extensive research has resulted in the isolation of several regulatory genes involved in flowering and for them to be organized into a molecular network responsive to environmental cues. When plants are exposed to favourable conditions, the network activates expression of florigenic proteins that are transported to the shoot apical meristem where they drive developmental reprogramming of a population of meristematic cells. Several regulatory factors are evolutionarily conserved between rice and arabidopsis. However, other pathways have evolved independently and confer specific characteristics to flowering responses. This review summarizes recent knowledge on the molecular mechanisms regulating daylength perception and flowering time control in arabidopsis and rice. Similarities and differences are discussed between the regulatory networks of the two species and they are compared with the regulatory networks of temperate cereals, which are evolutionarily more similar to rice but have evolved in regions where exposure to low temperatures is crucial to confer competence to flower. Finally, the role of flowering time genes in expansion of rice cultivation to Northern latitudes is discussed. Understanding the mechanisms involved in photoperiodic flowering and comparing the regulatory networks of dicots and monocots has revealed how plants respond to environmental cues and adapt to seasonal changes. The molecular architecture of such regulation shows striking similarities across diverse species. However, integration of specific pathways on a basal scheme is essential for adaptation to different environments. Artificial manipulation of flowering time by means of natural genetic resources is essential for expanding the cultivation of cereals across different environments. © The Author 2014

  16. Carbonyl sulfide exchange in a temperate loblolly pine forest grown under ambient and elevated CO2

    Directory of Open Access Journals (Sweden)

    B. C. Sive

    2010-01-01

    Full Text Available Vegetation, soil and ecosystem level carbonyl sulfide (COS exchange was observed at Duke Forest, a temperate loblolly pine forest, grown under ambient (Ring 1, R1 and elevated (Ring 2, R2 CO2. During calm meteorological conditions, ambient COS mixing ratios at the top of the forest canopy followed a distinct diurnal pattern in both CO2 growth regimes, with maximum COS mixing ratios during the day (R1=380±4 pptv and R2=373±3 pptv, daytime mean ± standard error and minimums at night (R1=340±6 pptv and R2=346±5 pptv, nighttime mean ± standard error reflecting a significant nighttime sink. Nocturnal vegetative uptake (−11 to −21 pmol m−2s−1, negative values indicate uptake from the atmosphere dominated nighttime net ecosystem COS flux estimates (−10 to −30 pmol m−2s−1 in both CO2 regimes. In comparison, soil uptake (−0.8 to −1.7 pmol m−2 s−1 was a minor component of net ecosystem COS flux. In both CO2 regimes, loblolly pine trees exhibited substantial COS consumption overnight (50% of daytime rates that was independent of CO2 assimilation. This suggests current estimates of the global vegetative COS sink, which assume that COS and CO2 are consumed simultaneously, may need to be reevaluated. Ambient COS mixing ratios, species specific diurnal patterns of stomatal conductance, temperature and canopy position were the major factors influencing the vegetative COS flux at the branch level. While variability in branch level vegetative COS consumption measurements in ambient and enhanced CO2 environments could not be attributed to CO2 enrichment effects, estimates of net ecosystem COS flux based on ambient canopy mixing ratio measurements suggest less nighttime uptake of COS in R2, the CO2 enriched environment.

  17. 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

  18. Genotypic and phenotypic variation as stress adaptations in temperate tree species: a review of several case studies.

    Science.gov (United States)

    Abrams, Marc D.

    1994-01-01

    Species that occupy large geographic ranges or a variety of habitats within a limited area deal with contrasting environmental conditions by genotypic and phenotypic variation. My students and I have studied these forms of ecophysiological variation in temperate tree species in eastern North America by means of a series of field and greenhouse experiments, including controlled studies with Cercis canadensis L., Fraxinus pennsylvanica Marsh., Acer rubrum L., Prunus serotina Ehrh. and Quercus rubra L., in relation to drought stress. These studies have included measurements of gas exchange, tissue water relations and leaf morphology, and have identified genotypic variation at the biome and individual community levels. Xeric genotypes generally had higher net photosynthesis and leaf conductance and lower osmotic and water potentials at incipient wilting than mesic genotypes during drought. Xeric genotypes also produced leaves with greater thickness, leaf mass per area and stomatal density and smaller area than the mesic genotypes, suggesting general coordination among leaf morphology, gas exchange and tissue water relations. Leaf phenotypic plasticity to different light environments occurred in virtually every study species, which represented a wide array of ecological tolerances. In a study of interactions of genotypes with environment, shade plants, but not sun plants, exhibited osmotic adjustment during drought and shade plants had smaller reductions in photosynthesis with decreasing leaf water potential. In that study, sun, but not shade, plants had significant genotypic differences in leaf structure, but with certain variables phenotypic variation exceeded genotype variation. Thus, genotypic variation was not expressed in all phenotypes, and phenotypes responded differentially to stress. Overall, these studies indicate the importance of genotypic and phenotypic variation as stress adaptations in temperate tree species among both distant and nearby sites of

  19. In the Valley of the Moon: Enclosure, Temperance, and the American War on John Barleycorn

    OpenAIRE

    Worley, Zita Marie

    2015-01-01

    The history of temperance and prohibition has long been constructed as either a rural backlash against modernity or a defining feature of middle-class culture. Early scholarship inaccurately denounced prohibition as a consequence of rural discontent in an increasingly urban immigrant America. More recent scholarship has relocated temperance in middle-class culture and politics, often to the neglect of the agrarian sector. Using an exploration of the production of space, this dissertation reex...

  20. EFFECTS OF AUSTENITIZATION ON STRUCTURE FORMATION СHROMO-MOLYBDENUM-VANADIUM STEEL AFTER HIGH TEMPERING

    Directory of Open Access Journals (Sweden)

    V. A. Lutsenko

    2017-01-01

    Full Text Available Influence of austenitization temperature of chrome-molybdenum-vanadium steel on structure formation at the softening heat treatment is studied. It is shown that the decline of the austenitization temperature promotes to reduce the micro-hardness values due to the intensification of spheroidizing of pearlite after the overcooling and high tempering. Increasing the austenitization temperature leads to formation of an uneven structure after tempering.

  1. Origin of the enhanced hardness of a tempered high-nitrogen martensitic steel

    Energy Technology Data Exchange (ETDEWEB)

    Ojima, M. [National Institute for Materials Science, 1-2-1 Sengen, Tsukuba 305-0047 (Japan); Graduate School of Science and Engineering, Ibaraki University, Nakanarusawa 316-8511, Hitachi (Japan); Ohnuma, M. [National Institute for Materials Science, 1-2-1 Sengen, Tsukuba 305-0047 (Japan)], E-mail: OHNUMA.Masato@nims.go.jp; Suzuki, J. [Japan Atomic Energy Agency, Tokai 319-1195 (Japan); Ueta, S.; Narita, S.; Shimizu, T. [Research and Development Center, Daido Steel Co., Ltd., 2-30 Daido-cho, Minami-ku, Nagoya (Japan); Tomota, Y. [Graduate School of Science and Engineering, Ibaraki University, Nakanarusawa 316-8511, Hitachi (Japan)

    2008-08-15

    The tempering process of a high-nitrogen martensitic stainless steel has been studied using small-angle neutron and X-ray scattering. The formation of an extremely fine nitrogen-enriched region has been confirmed for the first time in the tempering stage where the hardness starts to increase. After reaching peak hardness, the size of the N-enriched regions increases and their shape is anisotropic, which is typical for coherent precipitates.

  2. 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.

  3. Biodiversity of Chironomidae at the North Temperate Lakes LTER Site

    Science.gov (United States)

    Berg, M. B.; Olson, S.; Hayford, B.; Gresens, S. E.; Kennedy, J.; Bouchard, R. W.; Ferrington, L. C.

    2005-05-01

    The National Science Foundation has established a network of Long Term Ecological Research (LTER) sites to enhance research at large spatial scales, extended temporal scales, and to facilitate intersite comparisons of system structure and processes. Present knowledge of Chironomidae community structure at LTER sites is insufficient to accomplish these goals. Our project objectives are to determine species composition of Chironomidae in a wide variety of aquatic habitats at LTERs, describe all undescribed species/life stage associations, determine the temporal seasonality of emergence and develop a data base of species by habitat and emergence times. Our methods include light trapping and sweep netting for adults, dip-netting and hand-picking wood/aquatic vegetation for larvae, collecting surface-floating pupal exuviae, and rearing to associate life stages. Our initial focus on the North Temperate Lakes LTER in Wisconsin and has documented 80 genera (representing > 125 species, including 18 undescribed species and/or unknown life stages) from 11 lakes, 5 streams and 2 bogs. Taxa include species with larvae that are: epiphytic, endophytic, xylophagic, phoretic on mollusks or other aquatic insects, specialized to feed on freshwater sponges, predators of black fly pupae, and those occurring in hyporheic zones, marginal semi-aquatic habitats or terrestrial soils.

  4. Responses of temperate forest productivity to insect and pathogen disturbances.

    Science.gov (United States)

    Flower, Charles E; Gonzalez-Meler, Miquel A

    2015-01-01

    Pest and pathogen disturbances are ubiquitous across forest ecosystems, impacting their species composition, structure, and function. Whereas severe abiotic disturbances (e.g., clear-cutting and fire) largely reset successional trajectories, pest and pathogen disturbances cause diffuse mortality, driving forests into nonanalogous system states. Biotic perturbations that disrupt forest carbon dynamics either reduce or enhance net primary production (NPP) and carbon storage, depending on pathogen type. Relative to defoliators, wood borers and invasive pests have the largest negative impact on NPP and the longest recovery time. Forest diversity is an important contributing factor to productivity: NPP is neutral, marginally enhanced, or reduced in high-diversity stands in which a small portion of the canopy is affected (temperate deciduous or mixed forests) but very negative in low-diversity stands in which a large portion of the canopy is affected (western US forests). Pests and pathogens reduce forest structural and functional redundancy, affecting their resilience to future climate change or new outbreaks. Therefore, pests and pathogens can be considered biotic forcing agents capable of causing consequences of similar magnitude to climate forcing factors.

  5. Generalized simulated tempering for exploring strong phase transitions.

    Science.gov (United States)

    Kim, Jaegil; Straub, John E

    2010-10-21

    An extension of the simulation tempering algorithm is proposed. It is shown to be particularly suited to the exploration of first-order phase transition systems characterized by the backbending or S-loop in the statistical temperature or a microcanonical caloric curve. A guided Markov process in an auxiliary parameter space systematically combines a set of parametrized Tsallis-weight ensemble simulations, which are targeted to transform unstable or metastable energy states of canonical ensembles into stable ones and smoothly join ordered and disordered phases across phase transition regions via a succession of unimodal energy distributions. The inverse mapping between the sampling weight and the effective temperature enables an optimal selection of relevant Tsallis-weight parameters. A semianalytic expression for the biasing weight in parameter space is adaptively updated "on the fly" during the simulation to achieve rapid convergence. Accelerated tunneling transitions with a comprehensive sampling for phase-coexistent states are explicitly demonstrated in systems subject to strong hysteresis including Potts and Ising spin models and a 147 atom Lennard-Jones cluster.

  6. Silicon pools in human impacted soils of temperate zones

    Science.gov (United States)

    Vandevenne, F. I.; Barão, L.; Ronchi, B.; Govers, G.; Meire, P.; Kelly, E. F.; Struyf, E.

    2015-09-01

    Besides well-known effects of climate and parent material on silicate weathering the role of land use change as a driver in the global silicon cycle is not well known. Changes in vegetation cover have altered reservoirs of silicon and carbon in plants and soils. This has potential consequences for plant-Si availability, agricultural yields, and coastal eutrophication, as Si is a beneficial element for many crop plants and an essential nutrient for diatom growth. We here examined the role of sustained and intensive land use and human disturbance on silicon (Si) pool distribution in soils with similar climatological and bulk mineralogical characteristics. We show that land use impacts both biogenic and nonbiogenic Si pools. While biogenic Si strongly decreases along the land use change gradient (from forest to croplands), pedogenic silica fractions (e.g. pedogenic clays) increase in topsoils with a long duration of cultivation and soil disturbance. Our results suggest that nonbiogenic Si pools might compensate for the loss of reactive biogenic silicon in temperate zones.

  7. 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.

  8. 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...

  9. 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

    2017-02-02

    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.

  10. 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.

  11. 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.

  12. Response of a temperate demersal fish community to global warming

    Science.gov (United States)

    Punzón, A.; Serrano, A.; Sánchez, F.; Velasco, F.; Preciado, I.; González-Irusta, J. M.; López-López, L.

    2016-09-01

    Changes in the distribution of the demersal fish species have been identified in north-European Atlantic waters. The consequence of these changes has been a northward shift of the distribution limits and changes in richness. In this study a notable increase in demersal fish species richness per sampling station was detected in the southern Bay of Biscay. This rise was due to an increase in frequency of occurrence and abundance of the majority of fish species in the area (53% from the total species). A fisheries relate explanation was discarded because the mismatch between the changes in the fishing effort and the augment in frequency of occurrence and abundance. On the contrary, these changes are in agreement with expected response under the increasing temperature of the sea observed over the last three decades, associated to global warming. These changes were positively correlated with an increase in temperature of intermediate waters in the study area. In addition, some of these species showed a notable western displacements of the Centre of Gravity in the study area, which would be expected if temperate water species would be favoured by an increase in water temperature. Our results are consistent with studies in the North Sea, where many of these species showing widened distribution limits towards north. The analysis of the results shows that the studied ecosystem, the Bay of Biscay is under a meridionalization process. On the other hand, only one tropicalization event (Lepidotrigla dieuzeidei), was recorded, maybe due to the conservative restrictions applied in species selection.

  13. Disequilibrium Chemistry and Photochemical Hazes in Temperate Jupiter Atmospheres

    Science.gov (United States)

    Gao, Peter; Zahnle, Kevin; Marley, Mark; Morley, Caroline

    2018-01-01

    Probing the chemical composition and aerosol content of "temperate Jupiters" - young, Jupiter-like worlds with effective temperatures between 400 and 800 K with no direct analogues in our own Solar System - may be possible with the James Webb Space Telescope and its direct imaging capabilities. The relatively low temperatures of these exoplanets, as compared to hot Jupiters, means that disequilibrium processes such as eddy mixing and photochemistry could play a dominant role in determining the composition of their atmospheres. In this work we use a photochemical model and a cloud microphysics model to investigate the impact of disequilibrium processes. We find that the resulting model atmospheres may be significantly different from one predicted by equilibrium chemistry. For example, upward transport of CO from depth leads to the formation of large amounts of CO2, such that observed CO2 abundances may not scale with metallicity the same way as in equilibrium models. In addition, formation of sulfur hazes from H2S loss could lead to UV heating of the atmosphere, and increased albedos at red-optical wavelengths. Our results show that disequilibrium models may be necessary to interpret future observations of these cool objects.

  14. Soil variations on hillslopes in humid temperate climates

    Science.gov (United States)

    John Gerrard, A.

    1990-09-01

    Considerable insight into the nature and causes of soil variations on hillslopes has been provided by studies which have incorporated both pedological and geomorphological concepts into their methodology. Even so, there is still a great deal of uncertainty concerning the relationships between soils and landforms. This paper attempts to outline the conceptual and methodological issues involved in such a synthesis by examining the nature of soil variation on specific examples of landscapes in humid temperate climates. It has not been possible to examine soils across the whole of this region but soil-landform relationships on the Chalk of southeast England, the granite uplands of Dartmoor and in the Wyre Forest of England have been used to examine a number of well-established principles. One of these principles is that many landscapes possess slopes with easily identifiable toposequences. The hillslopes analysed have shown that relationships do exist between soils and landforms but the idea that many slopes are integrated along their entire length is not necessarily true. Individual components of slopes possess soil characteristics that appear to be related to the morphological nature of those components but the slopes, as a whole, do not possess integrated soil systems. Different parts of the slope appear to act independently. This questions the validity of employing traditional concepts such as that of the catena in soil-landform relationships.

  15. 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.

  16. Small Sample Sizes Yield Biased Allometric Equations in Temperate Forests

    Science.gov (United States)

    Duncanson, L.; Rourke, O.; Dubayah, R.

    2015-11-01

    Accurate quantification of forest carbon stocks is required for constraining the global carbon cycle and its impacts on climate. The accuracies of forest biomass maps are inherently dependent on the accuracy of the field biomass estimates used to calibrate models, which are generated with allometric equations. Here, we provide a quantitative assessment of the sensitivity of allometric parameters to sample size in temperate forests, focusing on the allometric relationship between tree height and crown radius. We use LiDAR remote sensing to isolate between 10,000 to more than 1,000,000 tree height and crown radius measurements per site in six U.S. forests. We find that fitted allometric parameters are highly sensitive to sample size, producing systematic overestimates of height. We extend our analysis to biomass through the application of empirical relationships from the literature, and show that given the small sample sizes used in common allometric equations for biomass, the average site-level biomass bias is ~+70% with a standard deviation of 71%, ranging from -4% to +193%. These findings underscore the importance of increasing the sample sizes used for allometric equation generation.

  17. High abundance of Crenarchaeota in a temperate acidic forest soil.

    Science.gov (United States)

    Kemnitz, Dana; Kolb, Steffen; Conrad, Ralf

    2007-06-01

    The objective of the study was to elucidate the depth distribution and community composition of Archaea in a temperate acidic forest soil. Numbers of Archaea and Bacteria were measured in the upper 18 cm of the soil, and soil cores were sampled on two separate occasions using quantitative PCR targeting 16S rRNA genes. Maximum numbers of Archaea were 0.6-3.8 x 10(8) 16S rRNA genes per gram of dry soil. Numbers of Bacteria were generally higher, but Archaea always accounted for a high percentage of the total gene numbers (12-38%). The archaeal community structure was analysed by the construction of clone libraries and by terminal restriction length polymorphism (T-RFLP) using the same Archaea-specific primers. With the reverse primer labelled, T-RFLP analysis led to the detection of four T-RFs. Three had lengths of 83, 185 and 218 bp and corresponded to uncultured Crenarchaeota. One (447 bp) was assigned to Thermoplasmales. Labelling of the forward primer allowed further separation of the T-RF into Crenarchaeota Group I.1c and Group I.1b, and indicated that Crenarchaeota of the Group I.1c were the predominant 16S rRNA genotype (Crenarchaeota Group I.1c participated in ammonia oxidation or had another phenotype.

  18. 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.

    2014-01-01

    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. PMID:24966312

  19. 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.

  20. Effect of Temper Condition on the Corrosion and Fatigue Performance of AA2219 Aluminum Alloy

    Science.gov (United States)

    Ghosh, Rahul; Venugopal, A.; Rao, G. Sudarshan; Ramesh Narayanan, P.; Pant, Bhanu; Cherian, Roy M.

    2018-01-01

    The effect of temper condition and corrosion on the fatigue behavior of alloy AA2219 has been investigated in different temper conditions (T87 and T851). Corrosion testing was performed by exposing the tensile specimens to 3.5% NaCl solution for different time periods, and the corrosion damage was quantified using a 3D profilometer. The exposure-tested specimens were subjected for fatigue testing at different stress levels, and the reduction in fatigue life was measured along with detailed fracture morphology variations. The results indicated that the alloy in both tempers suffers localized corrosion damage and the measured corrosion depth was 120 and 1200 µm, respectively, for T87 and T851 conditions. The loss in fatigue strength was found to be high for T851 (67%) when compared to that of T87 temper condition (58%) for a pre-corrosion time of 15 days. In both cases, fatigue crack initiation is associated with corrosion pits, which act as stress raisers. However, the crack propagation was predominantly transgranular for T87 and a mixed transgranular and intergranular fracture in the case of T851 temper condition. This was shown to be due to the heterogeneous microstructure due to the thermomechanical working and the delay in quench time imposed on the alloy forging in T851 temper condition. The findings in this paper present useful information for the selection of appropriate heat treatment condition to facilitate control of the corrosion behavior which is of great significance for their fatigue performance.

  1. Expansion of corals on temperate reefs: direct and indirect effects of marine heatwaves

    Science.gov (United States)

    Tuckett, C. A.; de Bettignies, T.; Fromont, J.; Wernberg, T.

    2017-09-01

    Globally, many temperate marine communities have experienced significant temperature increases over recent decades in the form of gradual warming and heatwaves. As a result, these communities are shifting towards increasingly subtropical and tropical species compositions. Expanding coral populations have been reported from several temperate reef ecosystems along warming coastlines; these changes have been attributed to direct effects of gradual warming over decades. In contrast, increases in coral populations following shorter-term extreme warming events have rarely been documented. In this study, we compared coral populations on 17 temperate reefs in Western Australia before (2005/06) and after (2013) multiple marine heatwaves (2010-2012) affected the entire coastline. We hypothesised that coral communities would expand and change as a consequence of increasing local populations and recruitment of warm-affinity species. We found differences in coral community structure over time, driven primarily by a fourfold increase of one local species, Plesiastrea versipora, rather than recruitment of warm-affinity species. Coral populations became strongly dominated by small size classes, indicative of recent increased recruitment or recruit survival. These changes were likely facilitated by competitive release of corals from dominant temperate seaweeds, which perished during the heatwaves, rather than driven by direct temperature effects. Overall, as corals are inherently warm-water taxa not commonly associated with seaweed-dominated temperate reefs, these findings are consistent with a net tropicalisation. Our study draws attention to processes other than gradual warming that also influence the trajectory of temperate reefs in a changing ocean.

  2. Tempering behavior of a low nitrogen boron-added 9%Cr steel

    Energy Technology Data Exchange (ETDEWEB)

    Fedorova, I., E-mail: irfe@mek.dtu.dk [Belgorod State University, 308015 Belgorod (Russian Federation); Max-Planck-Institut fur Eisenforschung GmbH, 40237 Dusseldorf (Germany); Kostka, A. [Max-Planck-Institut fur Eisenforschung GmbH, 40237 Dusseldorf (Germany); Institut fur Werkstoffe, Ruhr-Universitat Bochum, 44801 Bochum (Germany); Tkachev, E.; Belyakov, A.; Kaibyshev, R. [Belgorod State University, 308015 Belgorod (Russian Federation)

    2016-04-26

    The effect of tempering temperature on microstructure and mechanical properties was studied in a low-nitrogen, high-boron, 9%Cr steel. After normalizing and low-temperature tempering, cementite platelets precipitated within the martensitic matrix. This phase transformation has no distinct effect on mechanical properties. After tempering at 500 °C, M{sub 23}C{sub 6} carbides appeared in the form of layers and particles with irregular shapes along the high-angle boundaries. Approximately, 6% of the retained austenite was observed after normalizing, which reduced to 2% after tempering at 550 °C. This is accompanied by reduction in toughness from 40 J/cm{sup 2} to 8.5 J/cm{sup 2}. Further increase of the tempering temperature led to spheroidization and coagulation of M{sub 23}C{sub 6} particles that is followed by a significant increase in toughness to 250 J/cm{sup 2} at 750 °C. Three-phase separations of M(C,N) carbonitrides to particles enriched with V, Nb and Ti were detected after high-temperature tempering.

  3. 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.

  4. Prophage Provide a Safe Haven for Adaptive Exploration in Temperate Viruses.

    Science.gov (United States)

    Wahl, Lindi M; Pattenden, Tyler

    2017-05-01

    Prophage sequences constitute a substantial fraction of the temperate virus gene pool. Although subject to mutational decay, prophage sequences can also be an important source of adaptive mutations for these viral populations. Here we develop a life-history model for temperate viruses, including both the virulent (lytic) and the temperate phases of the life cycle. We then examine the survival of mutations that increase fitness during the lytic phase (attachment rate, burst size), increase fitness in the temperate phase (increasing host survival), or affect transitions between the two phases (integration or induction probability). We find that beneficial mutations are much more likely to survive, ultimately, if they first occur in the prophage state. This conclusion applies even to traits that are only expressed during the lytic phase, and arises due to the substantially lower variance in the offspring distribution during the temperate cycle. This observation, however, is balanced by the fact that many more mutations can be generated during lytic replication. Overall we predict that the prophage state provides a refuge, relatively shielded from genetic drift, in which temperate viruses can explore possible adaptive steps. Copyright © 2017 by the Genetics Society of America.

  5. 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.

  6. Comparative Shotgun Proteomic Analysis of Wastewater-Cultured Microalgae: Nitrogen Sensing and Carbon Fixation for Growth and Nutrient Removal in Chlamydomonas reinhardtii.

    Science.gov (United States)

    Patel, Anil K; Huang, Eric L; Low-Décarie, Etienne; Lefsrud, Mark G

    2015-08-07

    Chlamydomonas reinhardtii was batch-cultured for 12 days under continuous illumination to investigate nitrogen uptake and metabolic responses to wastewater processing. Our approach compared two conditions: (1) artificial wastewater containing nitrate and ammonia and (2) nutrient-sufficient control containing nitrate as sole form of nitrogen. Treatments did not differ in final biomass; however, comparison of group proteomes revealed significant differences. Label-free shotgun proteomic analysis identified 2358 proteins, of which 92 were significantly differentially abundant. Wastewater cells showed higher relative abundances of photosynthetic antenna proteins, enzymes related to carbon fixation, and biosynthesis of amino acids and secondary metabolites. Control cells showed higher abundances of enzymes and proteins related to nitrogen metabolism and assimilation, synthesis and utilization of starch, amino acid recycling, evidence of oxidative stress, and little lipid biosynthesis. This study of the eukaryotic microalgal proteome response to nitrogen source, availability, and switching highlights tightly controlled pathways essential to the maintenance of culture health and productivity in concert with light absorption and carbon assimilation. Enriched pathways in artificial wastewater, notably, photosynthetic carbon fixation and biosynthesis of plant hormones, and those in nitrate only control, most notably, nitrogen, amino acid, and starch metabolism, represent potential targets for genetic improvement requiring targeted elucidation.

  7. Quantitative shotgun proteomics reveals extensive changes to the proteome of the orbitofrontal cortex in rats that are hyperactive following withdrawal from a high sugar diet.

    Science.gov (United States)

    Franklin, Jane L; Mirzaei, Mehdi; Wearne, Travis A; Sauer, Melanie K; Homewood, Judi; Goodchild, Ann K; Haynes, Paul A; Cornish, Jennifer L

    2016-02-01

    In most Westernized societies, there has been an alarming increase in the consumption of sugar-sweetened drinks. For many adults these drinks represent a substantial proportion of their total daily caloric intake. Here we investigated whether extended exposure to sugar changes behavior and protein expression in the orbitofrontal cortex (OFC). Male adult Sprague-Dawley rats (n = 8 per group) were treated for 26 days with either water or a 10% sucrose solution. Locomotor behavior was measured on the first and last day of treatment, then 1 week after treatment. Following the 1-week period free from treatment, sucrose treated rats were significantly more active than the control. Two hours following final behavioral testing, brains were rapidly removed and prepared for proteomic analysis of the OFC. Label free quantitative shotgun proteomic analyses of three rats from each group found 290 proteins were differentially expressed in the sucrose treated group when compared to the control group. Major changes in the proteome were seen in proteins related to energy metabolism, mitochondrial function and the cellular response to stress. This research does not seek to suggest that sugar will cause specific neurological disorders, however similar changes in proteins have been seen in neurological disorders such as Alzheimer's disease, Parkinson's disease and schizophrenia. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. BuildSummary: using a group-based approach to improve the sensitivity of peptide/protein identification in shotgun proteomics.

    Science.gov (United States)

    Sheng, Quanhu; Dai, Jie; Wu, Yibo; Tang, Haixu; Zeng, Rong

    2012-03-02

    The target-decoy database search strategy is widely accepted as a standard method for estimating the false discovery rate (FDR) of peptide identification, based on which peptide-spectrum matches (PSMs) from the target database are filtered. To improve the sensitivity of protein identification given a fixed accuracy (frequently defined by a protein FDR threshold), a postprocessing procedure is often used that integrates results from different peptide search engines that had assayed the same data set. In this work, we show that PSMs that are grouped by the precursor charge, the number of missed internal cleavage sites, the modification state, and the numbers of protease termini and that the proteins grouped by their unique peptide count should be filtered separately according to the given FDR. We also develop an iterative procedure to filter the PSMs and proteins simultaneously, according to the given FDR. Finally, we present a general framework to integrate the results from different peptide search engines using the same FDR threshold. Our method was tested with several shotgun proteomics data sets that were acquired by multiple LC/MS instruments from two different biological samples. The results showed a satisfactory performance. We implemented the method in a user-friendly software package called BuildSummary, which can be downloaded for free from http://www.proteomics.ac.cn/software/proteomicstools/index.htm as part of the software suite ProteomicsTools.

  9. Adaptive Discriminant Function Analysis and Re-ranking of MS/MS Database Search Results for Improved Peptide Identification in Shotgun Proteomics

    Science.gov (United States)

    Ding, Ying; Choi, Hyungwon; Nesvizhskii, Alexey I.

    2013-01-01

    Robust statistical validation of peptide identifications obtained by tandem mass spectrometry and sequence database searching is an important task in shotgun proteomics. PeptideProphet is a commonly used computational tool that computes confidence measures for peptide identifications. In this paper, we investigate several limitations of the PeptideProphet modeling approach, including the use of fixed coefficients in computing the discriminant search score and selection of the top scoring peptide assignment per spectrum only. To address these limitations, we describe an adaptive method in which a new discriminant function is learned from the data in an iterative fashion. We extend the modeling framework to go beyond the top scoring peptide assignment per spectrum. We also investigate the effect of clustering the spectra according to their spectrum quality score followed by cluster-specific mixture modeling. The analysis is carried out using data acquired from a mixture of purified proteins on four different types of mass spectrometers, as well as using a complex human serum dataset. A special emphasis is placed on the analysis of data generated on high mass accuracy instruments. PMID:18788775

  10. 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.

  11. 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

  12. 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

  13. 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.

  14. Prey type and foraging ecology of Sanderlings Calidris alba in different climate zones: are tropical areas more favourable than temperate sites?

    Science.gov (United States)

    Ntiamoa-Baidu, Yaa; Piersma, Theunis; Reneerkens, Jeroen

    2015-01-01

    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. PMID:26290790

  15. 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.

  16. Invasion of Nostocales (cyanobacteria to subtropical and temperate freshwater lakes – Physiological, regional and global driving forces

    Directory of Open Access Journals (Sweden)

    Assaf eSukenik

    2012-03-01

    Full Text Available Similarly to the increased number of studies on invasive plants and animals in terrestrial and aquatic ecosystems, many reports were recently published on the invasion of Nostocales (cyanobacteria to freshwater environments worldwide. Invasion and proliferation of Nostocales in new habitats have the potential to significantly alter the structure of native community and to modify ecosystem functioning. But most importantly, they influence the water quality due to a variety of toxic compounds that some species produce. Therefore a special attention was given to the invasion and persistence of toxic cyanobacteria in many aquatic ecosystems. Here we summarize the currently published records on the invasion of two Nostocales genera, Cylindrospermopsis and Aphanizomenon, to lakes and water reservoirs in subtropical and temperate zones. These invading species possess traits thought to be common to many invasive organisms: high growth rate, high resource utilization efficiency and overall superior competitive abilities over native species when local conditions vary. Assuming that dispersion routes of cyanobacteria have not been changed much in recent decades, their recent establishment and proliferation in new habitats indicate changes in the environment under which they can exploit their physiological advantage over the native phytoplankton population. In many cases global warming was identified as the major driving force for the invasion of Nostocales. Due to this uncontrollable trend, invasive Nostocales species are expected to maintain their presence in new habitats and further expand to new environments. In other cases regional changes in nutrient loads and in biotic conditions were attributed to the invasion events

  17. EFFECTS OF TEMPERING AND PWHT ON MICROSTRUCTURES AND MECHANICAL PROPERTIES OF SA508 GR.4N STEEL

    OpenAIRE

    Lee, Ki-Hyoung; JHUNG, MYUNG JO; Kim, Min-Chul; Lee, Bong-Sang

    2014-01-01

    Presented in this study are the variations of microstructures and mechanical properties with tempering and Post-Weld Heat Treatment (PWHT) conditions for SA508 Gr.4N steel used as Reactor Pressure Vessel (RPV) material. The blocks of model alloy were austenitized at the conventional temperature of 880 °C, then tempered and post-weld heat treated at four different conditions. The hardness and yield strength decrease with increased tempering and PWHT temperatures, but impact toughness is signif...