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Sample records for maps reveal cosmic

  1. Cosmic string induced CMB maps

    SciTech Connect

    Landriau, M.; Shellard, E. P. S.

    2011-02-15

    We compute maps of CMB temperature fluctuations seeded by cosmic strings using high resolution simulations of cosmic strings in a Friedmann-Robertson-Walker universe. We create full-sky, 18 deg. and 3 deg. CMB maps, including the relevant string contribution at each resolution from before recombination to today. We extract the angular power spectrum from these maps, demonstrating the importance of recombination effects. We briefly discuss the probability density function of the pixel temperatures, their skewness, and kurtosis.

  2. A COSMIC MICROWAVE BACKGROUND LENSING MASS MAP AND ITS CORRELATION WITH THE COSMIC INFRARED BACKGROUND

    SciTech Connect

    Holder, G. P.; De Haan, T.; Dobbs, M. A.; Dudley, J.; Viero, M. P.; Bock, J.; Zahn, O.; Aird, K. A.; Benson, B. A.; Bhattacharya, S.; Bleem, L. E.; Carlstrom, J. E.; Chang, C. L.; Crawford, T. M.; Crites, A. T.; Brodwin, M.; Cho, H-M.; Conley, A.; George, E. M.; Halverson, N. W.; and others

    2013-07-01

    We use a temperature map of the cosmic microwave background (CMB) obtained using the South Pole Telescope at 150 GHz to construct a map of the gravitational convergence to z {approx} 1100, revealing the fluctuations in the projected mass density. This map shows individual features that are significant at the {approx}4{sigma} level, providing the first image of CMB lensing convergence. We cross-correlate this map with Herschel/SPIRE maps covering 90 deg{sup 2} at wavelengths of 500, 350, and 250 {mu}m. We show that these submillimeter (submm) wavelength maps are strongly correlated with the lensing convergence map, with detection significances in each of the three submm bands ranging from 6.7{sigma} to 8.8{sigma}. We fit the measurement of the cross power spectrum assuming a simple constant bias model and infer bias factors of b = 1.3-1.8, with a statistical uncertainty of 15%, depending on the assumed model for the redshift distribution of the dusty galaxies that are contributing to the Herschel/SPIRE maps.

  3. Spatial Statistics of Cosmic Microwave Background Maps

    NASA Astrophysics Data System (ADS)

    Szapudi, I.

    2007-11-01

    Spatial statistics in the Cosmic Microwave Background (CMB) maps are characterized by N-point correlation functions and their corresponding poly-spectra. I focus on basic statistical properties (noise, bias, optimality), and computational issues regarding two- and three-point functions, or angular power spectrum and bi-spectrum. Optimal estimators scale as D^3 for even the two-point statistics, where D is the number of data elements Even naive estimators scale scale D^N for N-point functions. I show that these daunting computational challenges can be met for present and future megapixel CMB maps with considerations about symmetries, multi-resolution techniques, and Monte Carlo methods and careful balancing of optimality, and resolution against computational resources. Once estimated, the interpretation of higher order correlation functions presents unique difficulties due to the large number of configurations: e.g., χ^2 fitting of parameters becomes non-trivial because of the large size of the corresponding covariance matrices. I show that False Discovery Rate based methods can be used for massive hypothesis testing, and I present techniques which help diagnosing and inverting covariance matrices obtained from Monte Carlo simulations.

  4. Mean maps for cosmic web structures in cosmological initial conditions

    NASA Astrophysics Data System (ADS)

    Aung, Han; Cohn, J. D.

    2016-02-01

    Haloes, filaments, sheets and voids in the cosmic web can be defined in terms of the eigenvalues of the smoothed shear tensor and a threshold λth. Using analytic methods, we construct mean maps centred on these types of structures for Gaussian random fields corresponding to cosmological initial conditions. Each map also requires a choice of shear at the origin; we consider three possibilities. We find characteristic sizes, shapes and other properties of the central objects in these mean maps and explore how these properties change with varying the threshold and smoothing scale, i.e. varying the separation of the cosmic web into different kinds of components. The mean maps become increasingly complex as the threshold λth decreases to zero. We also describe scatter around these mean maps, subtleties which can arise in their construction, and some comparisons between haloes in the maps and collapsed haloes at final times.

  5. Cosmic Pressure Fronts Mapped by Chandra

    NASA Astrophysics Data System (ADS)

    2000-03-01

    A colossal cosmic "weather system" produced by the collision of two giant clusters of galaxies has been imaged by NASA's Chandra X-ray Observatory. For the first time, the pressure fronts in the system can be traced in detail, and they show a bright, but relatively cool 50 million degree Celsius central region embedded in large elongated cloud of 70 million degree Celsius gas, all of which is roiling in a faint "atmosphere"of 100 million degree Celsius gas. "We can compare this to an intergalactic cold front," said Maxim Markevitch of the Harvard-Smithsonian Center for Astrophysics, Cambridge, Mass. and leader of the international team involved in the analysis of the observations. "A major difference is that in this case, cold means 70 million degree Celsius." The gas clouds are in the core of a galaxy cluster known as Abell 2142. The cluster is six million light years across and contains hundreds of galaxies and enough gas to make a thousand more. It is one of the most massive objects in the universe. Galaxy clusters grow to vast sizes as smaller clusters are pulled inward under the influence of gravity. They collide and merge over the course of billions of years, releasing tremendous amounts of energy that heats the cluster gas to 100 million degrees Celsius. The Chandra data provides the first detailed look at the late stages of this merger process. Previously, scientists had used the German-US Roentgensatellite to produce a broad brush picture of the cluster. The elongated shape of the bright cloud suggested that two clouds were in the process of coalescing into one, but the details remained unclear. Chandra is able to measure variations of temperature, density, and pressure with unprecedented resolution. "Now we can begin to understand the physics of these mergers, which are among the most energetic events in the universe," said Markevitch. "The pressure and density maps of the cluster show a sharp boundary that can only exist in the moving environment of a

  6. Cosmic Lens Reveals Distant Galactic Violence

    NASA Astrophysics Data System (ADS)

    2008-10-01

    By cleverly unraveling the workings of a natural cosmic lens, astronomers have gained a rare glimpse of the violent assembly of a young galaxy in the early Universe. Their new picture suggests that the galaxy has collided with another, feeding a supermassive black hole and triggering a tremendous burst of star formation. Gravitational Lens Diagram Imaging a Distant Galaxy Using a Gravitational Lens CREDIT: Bill Saxton, NRAO/AUI/NSF Click on image for details and more graphics. The astronomers used the National Science Foundation's Very Large Array (VLA) radio telescope to look at a galaxy more than 12 billion light-years from Earth, seen as it was when the Universe was only about 15 percent of its current age. Between this galaxy and Earth lies another distant galaxy, so perfectly aligned along the line of sight that its gravity bends the light and radio waves from the farther object into a circle, or "Einstein Ring." This gravitational lens made it possible for the scientists to learn details of the young, distant galaxy that would have been unobtainable otherwise. "Nature provided us with a magnifying glass to peer into the workings of a nascent galaxy, providing an exciting look at the violent, messy process of building galaxies in the early history of the Universe," said Dominik Riechers, who led this project at the Max Planck Institute for Astronomy in Germany and now is a Hubble Fellow at the California Institute of Technology (Caltech). The new picture of the distant galaxy, dubbed PSS J2322+1944, shows a massive reservoir of gas, 16,000 light-years in diameter, that contains the raw material for building new stars. A supermassive black hole is voraciously eating material, and new stars are being born at the rate of nearly 700 Suns per year. By comparison, our Milky Way Galaxy produces the equivalent of about 3-4 Suns per year. The black hole appears to be near the edge, rather than at the center, of the giant gas reservoir, indicating, the astronomers say

  7. The first cosmic ray albedo proton map of the Moon

    NASA Astrophysics Data System (ADS)

    Wilson, Jody K.; Spence, Harlan E.; Kasper, Justin; Golightly, Michael; Bern Blake, J.; Mazur, Joe E.; Townsend, Lawrence W.; Case, Anthony W.; Dixon Looper, Mark; Zeitlin, Cary; Schwadron, Nathan A.

    2012-06-01

    Neutrons emitted from the Moon are produced by the impact of galactic cosmic rays (GCRs) within the regolith. GCRs are high-energy particles capable of smashing atomic nuclei in the lunar regolith and producing a shower of energetic protons, neutrons and other subatomic particles. Secondary particles that are ejected out of the regolith become “albedo” particles. The neutron albedo has been used to study the hydrogen content of the lunar regolith, which motivates our study of albedo protons. In principle, the albedo protons should vary as a function of the input GCR source and possibly as a result of surface composition and properties. During the LRO mission, the total detection rate of albedo protons between 60 MeV and 150 MeV has been declining since 2009 in parallel with the decline in the galactic cosmic ray flux, which validates the concept of an albedo proton source. On the other hand, the average yield of albedo protons has been increasing as the galactic cosmic ray spectrum has been hardening, consistent with a disproportionately stronger modulation of lower energy GCRs as solar activity increases. We construct the first map of the normalized albedo proton emission rate from the lunar surface to look for any albedo variation that correlates with surface features. The map is consistent with a spatially uniform albedo proton yield to within statistical uncertainties.

  8. INTENSITY MAPPING OF MOLECULAR GAS DURING COSMIC REIONIZATION

    SciTech Connect

    Carilli, C. L.

    2011-04-01

    I present a simple calculation of the expected mean CO brightness temperature from the large-scale distribution of galaxies during cosmic reionization. The calculation is based on the cosmic star formation rate density required to reionize, and keep ionized, the intergalactic medium, and uses standard relationships between star formation rate, IR luminosity, and CO luminosity derived for star-forming galaxies over a wide range in redshift. I find that the mean CO brightness temperature resulting from the galaxies that could reionize the universe at z = 8 is T{sub B} {approx} 1.1(C/5)(f{sub esc}/0.1){sup -1}{mu}K, where f{sub esc} is the escape fraction of ionizing photons from the first galaxies and C is the IGM clumping factor. Intensity mapping of the CO emission from the large-scale structure of the star-forming galaxies during cosmic reionization on scales of order 10{sup 2} to 10{sup 3} deg{sup 2}, in combination with H I 21 cm imaging of the neutral IGM, will provide a comprehensive study of the earliest epoch of galaxy formation.

  9. Cosmic Microwave Background Maps from the HACME Experiment

    NASA Astrophysics Data System (ADS)

    Tegmark, Max; de Oliveira-Costa, Angélica; Staren, John W.; Meinhold, Peter R.; Lubin, Philip M.; Childers, Jeffrey D.; Figueiredo, Newton; Gaier, Todd; Lim, Mark A.; Seiffert, Michael D.; Villela, Thyrso; Wuensche, C. Alexandre

    2000-10-01

    We present cosmic microwave background (CMB) maps from the Santa Barbara HACME balloon experiment (Staren et al.), covering about 1150 square degrees split between two regions in the northern sky, near the stars γ Ursae Minoris and α Leonis, respectively. The FWHM of the beam is ~0.77d in three frequency bands centered on 39, 41, and 43 GHz. The results demonstrate that the thoroughly interconnected scan strategy employed allows efficient removal of 1/f-noise and slightly variable scan-synchronous offsets. The maps display no striping, and the noise correlations are found to be virtually isotropic, decaying on an angular scale ~1°. The noise performance of the experiment resulted in an upper limit on CMB anisotropy. However, our results demonstrate that atmospheric contamination and other systematics resulting from the circular scanning strategy can be accurately controlled and bode well for the planned follow-up experiments BEAST and ACE, since they show that even with the overly cautious assumption that 1/f-noise and offsets will be as dominant as for HACME, the problems they pose can be readily overcome with the mapmaking algorithm discussed. Our prewhitened notch-filter algorithm for destriping and offset removal is proving useful also for other balloon- and ground-based experiments whose scan strategies involve substantial interleaving, e.g., Boomerang.

  10. A map of the cosmic background radiation at 3 millimeters

    NASA Technical Reports Server (NTRS)

    Lubin, P.; Villela, T.; Epstein, G.; Smoot, G.

    1985-01-01

    Data from a series of balloon flights covering both the Northern and Southern Hemispheres, measuring the large angular scale anisotropy in the cosmic background radiation at 3.3 mm wavelength are presented. The data cover 85 percent of the sky to a limiting sensitivity of 0.7 mK per 7 deg field of view. The data show a 50-sigma (statistical error only) dipole anisotropy with an amplitude of 3.44 + or - 0.17 mK and a direction of alpha = 11.2 h + or - 0.1 h, and delta = -6.0 deg + or - 1.5 deg. A 90 percent confidence level upper limit of 0.00007 is obtained for the rms quadrupole amplitude. Flights separated by 6 months show the motion of earth around the sun. Galactic contamination is very small, with less than 0.1 mK contribution to the dipole quadrupole terms. A map of the sky has been generated from the data.

  11. Radiometer system to map the cosmic background radiation.

    PubMed

    Gorenstein, M V; Muller, R A; Smoot, G F; Tyson, J A

    1978-04-01

    We have developed a 33-GHz airborne radiometer system to map large angular scale variations in the temperature of the 3 K cosmic background radiation. A ferrite circulator switches a room-temperature mixer between two antennas pointing 60 degrees apart in the sky. In 40 min of observing, the radiometer can measure the anisotropy of the microwave background with an accuracy of +/-1 mK rms, or about 1 part in 3000 of 3 K. The apparatus is flown in a U-2 jet to 20 km altitude where 33-GHz thermal microwave emission from the atmosphere is at a low level. A second radiometer, tuned to 54 GHz near oxygen emission lines, monitors spurious signals from residual atmospheric radiation. The antennas, which have an extremely low side-lobe response of less than -65 dB past 60 degrees , reject anisotropic radiation from the earth's surface. Periodic interchange of the antenna positions and reversal of the aircraft's flight direction cancel equipment-based imbalances. The system has been operated successfully in U-2 aircraft flown from NASA-Ames at Moffett Field, CA. PMID:18699121

  12. Polarized cosmic microwave background map recovery with sparse component separation

    NASA Astrophysics Data System (ADS)

    Bobin, J.; Sureau, F.; Starck, J.-L.

    2015-11-01

    The polarization modes of the cosmological microwave background are an invaluable source of information for cosmology and a unique window to probe the energy scale of inflation. Extracting this information from microwave surveys requires distinguishing between foreground emissions and the cosmological signal, which means solving a component separation problem. Component separation techniques have been widely studied for the recovery of cosmic microwave background (CMB) temperature anisotropies, but very rarely for the polarization modes. In this case, most component separation techniques make use of second-order statistics to distinguish between the various components. More recent methods, which instead emphasize the sparsity of the components in the wavelet domain, have been shown to provide low-foreground, full-sky estimates of the CMB temperature anisotropies. Building on sparsity, we here introduce a new component separation technique dubbed the polarized generalized morphological component analysis (PolGMCA), which refines previous work to specifically work on the estimation of the polarized CMB maps: i) it benefits from a recently introduced sparsity-based mechanism to cope with partially correlated components; ii) it builds upon estimator aggregation techniques to further yield a better noise contamination/non-Gaussian foreground residual trade-off. The PolGMCA algorithm is evaluated on simulations of full-sky polarized microwave sky simulations using the Planck Sky Model (PSM). The simulations show that the proposed method achieves a precise recovery of the CMB map in polarization with low-noise and foreground contamination residuals. It provides improvements over standard methods, especially on the Galactic center, where estimating the CMB is challenging.

  13. Detecting Low-Contrast Features in the Cosmic Ray Albedo Proton Yield Map of the Moon

    NASA Astrophysics Data System (ADS)

    Wilson, J. K.; Schwadron, N.; Spence, H.; Smith, S. S.; Golightly, M. J.; Case, A. W.; Stubbs, T. J.; Blake, J. B.; Kasper, J. C.; Looper, M. D.; Mazur, J. E.; Townsend, L. W.; Zeitlin, C. J.

    2013-12-01

    High energy cosmic rays constantly bombard the lunar regolith, producing (via nuclear evaporation[1]) secondary 'albedo' or 'splash' particles like protons and neutrons, some of which escape back to space. Lunar Prospector and the Lunar Reconnaissance Orbiter (LRO), have shown that the energy distribution of albedo neutrons is modulated by the elemental composition of the lunar regolith[2-5], and by ice deposits[6] in permanently shadowed polar craters. Here we investigate an analogous phenomenon with high energy lunar albedo protons. Using the CRaTER instrument (Cosmic Ray Telescope for the Effects of Radiation) on LRO, we measure albedo protons (60 to 150 MeV) to construct a cosmic ray albedo proton map of the Moon. Our current map is a significant improvement over the proof-of-concept map of Wilson et al.[7]. In addition to using more numerous minimum ionizing GCR protons for normalization, we filter out all solar particle enhancement periods and make use of all six of CRaTER's detectors to reduce contamination from spurious non-proton events in the data stream. The average yield of albedo protons from the maria is 0.8% × 0.4% higher than the yield from the highlands. In addition there appear to be localized peaks in the albedo proton yield that are co-located with peaks in trace elemental abundances as measured by the Lunar Prospector Gamma Ray Spectrometer. More data may reveal subtler proton yield variations correlated with latitude, time of day, or the locations of permanently shadowed craters, due to the presence of water frost. Given that the most obvious features in the map have a proton yield only 2σ above average, the search for more subtle regions of enhancement or reduction in proton yield will require precise corrections for small but systematic effects of time and spacecraft altitude on the apparent proton yield. We will show the effects of these trends as well as the latest version of the albedo proton map. References: [1] Bethe (1937) Rev. Mod

  14. Portable cosmic particle detectors for subsurface density mapping

    NASA Astrophysics Data System (ADS)

    Oláh, László; Gábor Barnaföldi, Gergely; Hamar, Gergö; Surányi, Gergely; Varga, Dezsö

    2016-04-01

    Muography deduces the density length in the interior of the investigated geological object, such as a mountain or volcano by the measurement of the cosmic muon absorption along different paths through the object. If path lengths (average densities) are measured, the average density (path length) can be deduced along the muon paths. A portable, low power consumption cosmic particle tracking detector based on Close Cathode multi-wire proportional chambers [1,2] has been developed for muography based on our earlier developments and experiences at the Wigner RCP of the HAS in Budapest [3,4,5]. The newly developed tracking system consists of six layers with the sensitive area of 0.25 m2 [6]. The spatial resolution of 2 mm provides an angular resolution of 15 mrad. This instrument has been optimized for underground and outdoor measurements: it has a Raspberry pi controlled data acquisition system which includes a custom designed board with a coincidence unit and allows high level remote control, data management and analysis. The individual trigger signals, number of missed triggers, analogue signals from chambers and the temperature are recorded. The duration of data readout (dead time) is 100 microsec. The DAQ software runs on the Raspberry Pi. For standard operation, a graphical user interface has been developed, running on any remote computer with Internet connection (both of wired and wireless) to the Raspberry Pi. A temperature-controlled high-voltage power supply provides a stable and reasonable (> 95 %) tracking performance for the measurements. With total power consumption of 5W, a portable tracking detector can operate for 5 days with a standard 50 Ah battery and with gas (non flammable Ar-CO2 mixture) consumption of 0.5 liter per hour, a 10 l bottle at pressure of 150 bar is enough for four month. The portability (total weight of less than 30 kg) allowed that our tracking detectors have been applied in underground caverns for subsurface density mapping. The

  15. VLBA Movies Reveal New Details of Cosmic Jets

    NASA Astrophysics Data System (ADS)

    2008-01-01

    individual objects. "Before the VLBA was built, we were hindered in our studies of extragalactic jets by the lack of a facility that could do high-quality, regularly-spaced images showing very great detail. The VLBA's capabilities have made it a premier facility for studying these objects out to very large distances, and thus getting a large sample," Lister said. The MOJAVE observations are showing new details about the structures of magnetic fields in the jets. This is important, because magnetic fields are thought to play vital roles in the acceleration of the particles and in shaping the jets. The time-lapse movies have revealed a variety of interesting behavior in the jets. For example, the powerful radio galaxy called 3C279 emitted a bright feature that moved along a straight path for 15 years, then suddenly brightened, showed a change in its magnetic field, and sped off in a new direction. Other jets shoot successive bright features that move outward in curved paths. Some features in jets are seen to break apart. "These detailed movies of complex motions are real-world data that allow researchers to refine their computer simulations of the jets, leading to a far better understanding of the physics involved in such impressive cosmic particle accelerators," Lister said. The MOJAVE data will prove valuable for comparison with the gamma-ray information to be collected by NASA's upcoming GLAST satellite. "Using the MOJAVE data along with data from other ground-based and orbiting observatories at different wavelengths is bringing the studies of galactic jets into a new era," Lister concluded. The National Radio Astronomy Observatory is a facility of the National Science Foundation, operated under cooperative agreement by Associated Universities, Inc.

  16. Cosmic "Dig" Reveals Vestiges of the Milky Way's Building Blocks

    NASA Astrophysics Data System (ADS)

    2009-11-01

    Peering through the thick dust clouds of our galaxy's "bulge" (the myriads of stars surrounding its centre), and revealing an amazing amount of detail, a team of astronomers has unveiled an unusual mix of stars in the stellar grouping known as Terzan 5. Never observed anywhere in the bulge before, this peculiar "cocktail" of stars suggests that Terzan 5 is in fact one of the bulge's primordial building blocks, most likely the relic of a proto-galaxy that merged with the Milky Way during its very early days. "The history of the Milky Way is encoded in its oldest fragments, globular clusters and other systems of stars that have witnessed the entire evolution of our galaxy," says Francesco Ferraro from the University of Bologna, lead author of a paper appearing in this week's issue of the journal Nature. "Our study opens a new window on yet another piece of our galactic past." Like archaeologists, who dig through the dust piling up on top of the remains of past civilisations and unearth crucial pieces of the history of mankind, astronomers have been gazing through the thick layers of interstellar dust obscuring the bulge of the Milky Way and have unveiled an extraordinary cosmic relic. The target of the study is the star cluster Terzan 5. The new observations show that this object, unlike all but a few exceptional globular clusters, does not harbour stars which are all born at the same time - what astronomers call a "single population" of stars. Instead, the multitude of glowing stars in Terzan 5 formed in at least two different epochs, the earliest probably some 12 billion years ago and then again 6 billion years ago. "Only one globular cluster with such a complex history of star formation has been observed in the halo of the Milky Way: Omega Centauri," says team member Emanuele Dalessandro. "This is the first time we see this in the bulge." The galactic bulge is the most inaccessible region of our galaxy for astronomical observations: only infrared light can

  17. Giant Cosmic Lens Reveals Secrets of Distant Galaxy

    NASA Astrophysics Data System (ADS)

    2003-04-01

    Using the National Science Foundation's Very Large Array (VLA) radio telescope and helped by a gigantic cosmic lens conveniently provided by nature, an international team of astronomers has discovered that a young galaxy had a central disk of gas in which hundreds of new stars were being born every year -- at a time when the Universe was only a fraction of its current age. Artist's Conception of the Star-Forming Disk (Click on Image for Larger Version) VLA Image of PSS J2322+1944 (Click on Image for Larger Version) "This unique look into a very distant, young galaxy gives us unprecedented insight into the process that produced both tremendous numbers of stars and supermassive black holes in forming galaxies," said Chris Carilli, of the National Radio Astronomy Observatory (NRAO) in Socorro, NM, leader of the research team. "This work strongly supports the idea that the stars and the black holes formed simultaneously," he added. The research was published in the April 4 issue of Science Express. The astronomers studied a quasar called PSS J2322+1944, about 12 billion light-years from Earth. The quasar is an extremely luminous object powered by the supermassive black hole at the core of a galaxy. At the distance of this quasar, the scientists see the object as it was when the Universe was less than 2 billion years old, about 15 percent of its current age. The discovery required a huge assist from nature. To find the star-forming disk, the astronomers needed to observe natural radio emission from the carbon monoxide (CO) molecule, an important component of the gas that forms stars. However, this molecule emits radio waves at frequencies much higher than the VLA is capable of receiving. At PSS J2322+1944's distance of 12 billion light-years, however, the expansion of the Universe stretched the radio waves, reducing their frequency. CO emission at 230 GigaHertz was shifted to 45 GigaHertz, within the VLA's range. That alone was not enough. The distance that made it

  18. Construction of cosmic string induced temperature anisotropy maps with CMBFAST and statistical analysis

    NASA Astrophysics Data System (ADS)

    Simatos, N.; Perivolaropoulos, L.

    2001-01-01

    We use the publicly available code CMBFAST, as modified by Pogosian and Vachaspati, to simulate the effects of wiggly cosmic strings on the cosmic microwave background (CMB). Using the modified CMBFAST code, which takes into account vector modes and models wiggly cosmic strings by the one-scale model, we go beyond the angular power spectrum to construct CMB temperature maps with a resolution of a few degrees. The statistics of these maps are then studied using conventional and recently proposed statistical tests optimized for the detection of hidden temperature discontinuities induced by the Gott-Kaiser-Stebbins effect. We show, however, that these realistic maps cannot be distinguished in a statistically significant way from purely Gaussian maps with an identical power spectrum.

  19. NASA's Chandra Reveals Origin of Key Cosmic Explosions

    NASA Astrophysics Data System (ADS)

    2010-02-01

    WASHINGTON -- New findings from NASA's Chandra X-ray Observatory have provided a major advance in understanding a type of supernova critical for studying the dark energy that astronomers think pervades the universe. The results show mergers of two dense stellar remnants are the likely cause of many of the supernovae that have been used to measure the accelerated expansion of the universe. These supernovae, called Type Ia, serve as cosmic mile markers to measure expansion of the universe because they can be seen at large distances, and they follow a reliable pattern of brightness. However, until now, scientists have been unsure what actually causes the explosions. "These are such critical objects in understanding the universe," said Marat Gilfanov of the Max Planck Institute for Astrophysics in Germany and lead author of the study that appears in the Feb. 18 edition of the journal Nature. "It was a major embarrassment that we did not know how they worked. Now we are beginning to understand what lights the fuse of these explosions." Most scientists agree a Type Ia supernova occurs when a white dwarf star -- a collapsed remnant of an elderly star -- exceeds its weight limit, becomes unstable and explodes. Scientists have identified two main possibilities for pushing the white dwarf over the edge: two white dwarfs merging or accretion, a process in which the white dwarf pulls material from a sun-like companion star until it exceeds its weight limit. "Our results suggest the supernovae in the galaxies we studied almost all come from two white dwarfs merging," said co-author Akos Bogdan, also of Max Planck. "This is probably not what many astronomers would expect." The difference between these two scenarios may have implications for how these supernovae can be used as "standard candles" -- objects of a known brightness -- to track vast cosmic distances. Because white dwarfs can come in a range of masses, the merger of two could result in explosions that vary somewhat in

  20. VLBA Reveals Formation Region of Giant Cosmic Jet

    NASA Astrophysics Data System (ADS)

    1999-10-01

    Astronomers have gained their first glimpse of the mysterious region near a black hole at the heart of a distant galaxy, where a powerful stream of subatomic particles spewing outward at nearly the speed of light is formed into a beam, or jet, that then goes nearly straight for thousands of light-years. The astronomers used radio telescopes in Europe and the U.S., including the National Science Foundation's (NSF) Very Long Baseline Array (VLBA) to make the most detailed images ever of the center of the galaxy M87, some 50 million light-years away. "This is the first time anyone has seen the region in which a cosmic jet is formed into a narrow beam," said Bill Junor of the University of New Mexico, in Albuquerque. "We had always speculated that the jet had to be made by some mechanism relatively near the black hole, but as we looked closer and closer to the center, we kept seeing an already-formed beam. That was becoming embarrassing, because we were running out of places to put the formation mechanism that we knew had to be there." Junor, along with John Biretta and Mario Livio of the Space Telescope Science Institute, in Baltimore, MD, now have shown that M87's jet is formed within a few tenths of a light-year of the galaxy's core, presumed to be a black hole three billion times more massive than the sun. In the formation region, the jet is seen opening widely, at an angle of about 60 degrees, nearest the black hole, but is squeezed down to only 6 degrees a few light-years away. "The 60-degree angle of the inner part of M87's jet is the widest such angle yet seen in any jet in the universe," said Junor. "We found this by being able to see the jet to within a few hundredths of a light-year of the galaxy's core -- an unprecedented level of detail." The scientists reported their findings in the October 28 issue of the journal Nature. At the center of M87, material being drawn inward by the strong gravitation of the black hole is formed into a rapidly-spinning flat

  1. Recent Results from Broad-Band Intensity Mapping Measurements of Cosmic Large Scale Structure

    NASA Astrophysics Data System (ADS)

    Zemcov, Michael B.; CIBER, Herschel-SPIRE

    2016-01-01

    Intensity mapping integrates the total emission in a given spectral band over the universe's history. Tomographic measurements of cosmic structure can be performed using specific line tracers observed in narrow bands, but a wealth of information is also available from broad-band observations performed by instruments capable of capturing high-fidelity, wide-angle images of extragalactic emission. Sensitive to the continuum emission from faint and diffuse sources, these broad-band measurements provide a view on cosmic structure traced by components not readily detected in point source surveys. After accounting for measurement effects and astrophysical foregrounds, the angular power spectra of such data can be compared to predictions from models to yield powerful insights into the history of cosmic structure formation. This talk will highlight some recent measurements of large scale structure performed using broad-band intensity mapping methods that have given new insights on faint, distant, and diffuse components in the extragalactic background light.

  2. Efficient decomposition of cosmic microwave background polarization maps into pure E, pure B, and ambiguous components

    SciTech Connect

    Bunn, Emory F.

    2011-04-15

    Separation of the B component of a cosmic microwave background (CMB) polarization map from the much larger E component is an essential step in CMB polarimetry. For a map with incomplete sky coverage, this separation is necessarily hampered by the presence of ambiguous modes which could be either E or B modes. I present an efficient pixel-space algorithm for removing the ambiguous modes and separating the map into pure E and B components. The method, which works for arbitrary geometries, does not involve generating a complete basis of such modes and scales the cube of the number of pixels on the boundary of the map.

  3. Cortical cartography reveals political and physical maps.

    PubMed

    Loring, David W; Gaillard, William Davis; Bookheimer, Susan Y; Meador, Kimford J; Ojemann, Jeffrey G

    2014-05-01

    Advances in functional imaging have provided noninvasive techniques to probe brain organization of multiple constructs including language and memory. Because of high overall rates of agreements with older techniques, including Wada testing and cortical stimulation mapping (CSM), some have proposed that those approaches should be largely abandoned because of their invasiveness, and replaced with noninvasive functional imaging methods. High overall agreement, however, is based largely on concordant language lateralization in series dominated by cases of typical cerebral dominance. Advocating a universal switch from Wada testing and cortical stimulation mapping to functional magnetic resonance imaging (fMRI) or magnetoencephalography (MEG) ignores the differences in specific expertise across epilepsy centers, many of which often have greater skill with one approach rather than the other, and that Wada, CSM, fMRI, and MEG protocols vary across institutions resulting in different outcomes and reliability. Specific patient characteristics also affect whether Wada or CSM might influence surgical management, making it difficult to accept broad recommendations against currently useful clinical tools. Although the development of noninvasive techniques has diminished the frequency of more invasive approaches, advocating their use to replace Wada testing and CSM across all epilepsy surgery programs without consideration of the different skills, protocols, and expertise at any given center site is ill-advised. PMID:24815217

  4. Testing the mapping between redshift and cosmic scale factor

    NASA Astrophysics Data System (ADS)

    Wojtak, Radosław; Prada, Francisco

    2016-05-01

    The canonical redshift-scale factor relation, 1/a = 1 + z, is a key element in the standard Λ cold dark matter (ΛCDM) model of the big bang cosmology. Despite its fundamental role, this relation has not yet undergone any observational tests since Lemaître and Hubble established the expansion of the Universe. It is strictly based on the assumption of the Friedmann-Lemaître-Robertson-Walker metric describing a locally homogeneous and isotropic universe and that photons move on null geodesics of the metric. Thus any violation of this assumption, within general relativity or modified gravity, can yield a different mapping between the model redshift z = 1/a - 1 and the actually observed redshift zobs, i.e. zobs ≠ z. Here, we perform a simple test of consistency for the standard redshift-scale factor relation by determining simultaneous observational constraints on the concordance ΛCDM cosmological parameters and a generalized redshift mapping z = f(zobs). Using current baryon acoustic oscillations (BAO) and Type Ia supernova (SN) data we demonstrate that the generalized redshift mapping is strongly degenerated with dark energy. Marginalization over a class of monotonic functions f(zobs) changes substantially degeneracy between matter and dark energy density: the density parameters become anticorrelated with nearly vertical axis of degeneracy. Furthermore, we show that current SN and BAO data, analysed in a framework with the generalized redshift mapping, do not constrain dark energy unless the BAO data include the measurements from the Ly α forest of high-redshift quasars.

  5. Amplitude-Phase Analysis of Cosmic Microwave Background Maps

    NASA Astrophysics Data System (ADS)

    Novikov, D.; Naselsky, P.; Silk, J.

    We suggest the amplitude-phase analysis (APA) as a new method for the CMB image reconstruction. This method has been adopted for any kind of possible noise in the CMB observational data ( like point sources, dust emission, pixel and radiometer noise and so on). The important advantage of our scheme is that unlike other methods the phase analysis doesn't require any information about the expected CMB power spectra to subtract the noise. The only assumption we made is that the initial cosmological signal has a Gaussian nature. This method is very efficient computationally because it requires only O(Nln (N)) operations, where N is the number of pixels. Therefore, the full advantage of our scheme can be reached on very large data sets. Its efficiency has been successfully tested on simulated signals corresponding to MAP, PLANCK and RATAN-600 angular resolutions. P. Naselsky (TAC, Denmark), I. Novikov (TAC, Denmark)

  6. A FOREGROUND-CLEANED COSMIC MICROWAVE BACKGROUND MAP FROM NON-GAUSSIANITY MEASUREMENT

    SciTech Connect

    Saha, Rajib

    2011-10-01

    In this Letter, we present a new method to estimate a foreground-cleaned cosmic microwave background (CMB) map at a resolution of 1{sup 0} by minimizing the non-Gaussian properties of the cleaned map which arise dominantly due to diffuse foreground emission components from the Milky Way. We employ simple kurtosis statistic as the measure of non-Gaussian properties and perform a linear combination of five frequency maps provided by the Wilkinson Microwave Anisotropy Probe (WMAP) in its seven-year data release in such a way that the cleaned map has a minimum kurtosis which leads to a non-Gaussianity-minimized, foreground-cleaned CMB map. We validate the method by performing Monte Carlo simulations. To minimize any residual foreground contamination from the cleaned map we flag out the region near the galactic plane based upon results from simulations. Outside the masked region our new estimate of the CMB map matches well with the WMAP's Internal Linear Combination (ILC) map. A simple pseudo-C{sub l} -based CMB TT power spectrum derived from the non-Gaussianity minimized map reproduces the earlier results of WMAP's power spectrum. An important advantage of the method is that it does not introduce any negative bias in angular power spectrum in the low multipole regime, unlike usual ILC method. Comparing our results with the previously published results we argue that CMB results are robust with respect to specific foreground removal algorithms employed.

  7. Mapping Cosmic Structure Using 21-cm Hydrogen Signal at Green Bank Telescope

    NASA Astrophysics Data System (ADS)

    Voytek, Tabitha; GBT 21-cm Intensity Mapping Group

    2011-05-01

    We are using the Green Bank Telescope to make 21-cm intensity maps of cosmic structure in a 0.15 Gpc^3 box at redshift of z 1. The intensity mapping technique combines the flux from many galaxies in each pixel, allowing much greater mapping speed than the traditional redshift survey. Measurement is being made at z 1 to take advantage of a window in frequency around 700 MHz where terrestrial radio frequency interference (RFI) is currently at a minimum. This minimum is due to a reallocation of this frequency band from analog television to wide area wireless internet and public service usage. We will report progress of our attempt to detect autocorrelation of the 21-cm signal. The ultimate goal of this mapping is to use Baryon Acoustic Oscillations to provide more precise constraints to dark energy models.

  8. Simulated cosmic microwave background maps at 0.5 deg resolution: Basic results

    NASA Technical Reports Server (NTRS)

    Hinshaw, G.; Bennett, C. L.; Kogut, A.

    1995-01-01

    We have simulated full-sky maps of the cosmic microwave background (CMB) anisotropy expected from cold dark matter (CDM) models at 0.5 deg and 1.0 deg angular resolution. Statistical properties of the maps are presented as a function of sky coverage, angular resolution, and instrument noise, and the implications of these results for observability of the Doppler peak are discussed. The rms fluctuations in a map are not a particularly robust probe of the existence of a Doppler peak; however, a full correlation analysis can provide reasonable sensitivity. We find that sensitivity to the Doppler peak depends primarily on the fraction of sky covered, and only secondarily on the angular resolution and noise level. Color plates of the simulated maps are presented to illustrate the anisotropies.

  9. A Map of the Cosmic Microwave Background from the BEAST Experiment

    NASA Astrophysics Data System (ADS)

    Meinhold, Peter R.; Bersanelli, Marco; Childers, Jeffrey; Figueiredo, Newton; Gaier, Todd C.; Halevi, Doron; Huey, Gregory G.; Kangas, Miikka; Lawrence, Charles R.; Levy, Alan; Lubin, Philip M.; Malaspina, Marco; Mandolesi, Nazzareno; Marvil, Joshua; Mejía, Jorge; Natoli, Paolo; O'Dwyer, Ian; O'Neill, Hugh; Parendo, Shane; Pina, Agenor; Seiffert, Michael D.; Stebor, Nathan C.; Tello, Camilo; Villa, Fabrizio; Villela, Thyrso; Wade, Lawrence A.; Wandelt, Benjamin D.; Williams, Brian; Wuensche, Carlos Alexandre

    2005-05-01

    We present the first sky maps from the BEAST (Background Emission Anisotropy Scanning Telescope) experiment. BEAST consists of a 2.2 m off-axis Gregorian telescope fed by a cryogenic millimeter wavelength focal plane currently consisting of six Q band (40 GHz) and two Ka band (30 GHz) scalar feed horns feeding cryogenic HEMT amplifiers. Data were collected from two balloon-borne flights in 2000, followed by a lengthy ground observing campaign from the 3.8 km altitude University of California White Mountain Research Station. This paper reports the initial results from the ground-based observations. The instrument produced an annular map covering the sky over 33deg<δ<42deg. The maps cover an area of 2470 deg2 with an effective resolution of 23' FWHM at 40 GHz and 30' at 30 GHz. The map rms (smoothed to 30' and excluding Galactic foregrounds) is 57+/-5 μK (Rayleigh-Jeans) at 40 GHz. Comparison with the instrument noise and correcting for 5% atmospheric attenuation gives a cosmic signal rms contribution of 29+/-3 μK (R-J) or 30+/-3 μK relative to a Planck blackbody of 2.7 K. An estimate of the actual cosmic microwave background (CMB) sky signal requires taking into account the l space filter function of our experiment and analysis techniques, carried out in a companion paper. In addition to the robust detection of CMB anisotropies, we find a strong correlation between small portions of our maps and features in recent Hα maps. In this work we describe the data set and analysis techniques leading to the maps, including data selection, filtering, pointing reconstruction, mapmaking algorithms, and systematic effects.

  10. Peculiar high energy cosmic ray stratospheric event reveals a heavy primary origin particle above the knee region of the cosmic ray spectrum

    SciTech Connect

    Kopenkin, V.; Fujimoto, Y.

    2005-01-15

    We wish to put forward an explanation for a peculiar cosmic ray event with energy {sigma}E{sub {gamma}}{>=}2x10{sup 15} eV detected in 1975 by the balloon borne emulsion chamber experiment performed in the stratosphere, at the altitude {>=}30 km above sea level. For almost 30 years the event has been described as unusual, invoking new exotic mechanisms or models. In our opinion there is no need for an extraordinary explanation. Contrary to the widespread belief, the event gives us an example of 'unrecognized standard physics'. At the same time this event revealed a variety of features which are of considerable interest for cosmic rays, nuclear physics, and astrophysics. Here we show that the observed family is most likely to be a result of a heavy nucleus interaction with an air nucleus. In this case a primary particle would originally have been in the energy region above 'the knee' of the cosmic ray spectrum.

  11. Recombination patterns reveal information about centromere location on linkage maps.

    PubMed

    Limborg, Morten T; McKinney, Garrett J; Seeb, Lisa W; Seeb, James E

    2016-05-01

    Linkage mapping is often used to identify genes associated with phenotypic traits and for aiding genome assemblies. Still, many emerging maps do not locate centromeres - an essential component of the genomic landscape. Here, we demonstrate that for genomes with strong chiasma interference, approximate centromere placement is possible by phasing the same data used to generate linkage maps. Assuming one obligate crossover per chromosome arm, information about centromere location can be revealed by tracking the accumulated recombination frequency along linkage groups, similar to half-tetrad analyses. We validate the method on a linkage map for sockeye salmon (Oncorhynchus nerka) with known centromeric regions. Further tests suggest that the method will work well in other salmonids and other eukaryotes. However, the method performed weakly when applied to a male linkage map (rainbow trout; O. mykiss) characterized by low and unevenly distributed recombination - a general feature of male meiosis in many species. Further, a high frequency of double crossovers along chromosome arms in barley reduced resolution for locating centromeric regions on most linkage groups. Despite these limitations, our method should work well for high-density maps in species with strong recombination interference and will enrich many existing and future mapping resources. PMID:26561199

  12. Minkowski functionals used in the morphological analysis of cosmic microwave background anisotropy maps

    NASA Astrophysics Data System (ADS)

    Schmalzing, Jens; Gorski, Krzysztof M.

    1998-06-01

    We present a novel approach to quantifying the morphology of cosmic microwave background (CMB) anisotropy maps. As morphological descriptors, we use shape parameters known as Minkowski functionals. Using the mathematical framework provided by the theory of integral geometry on arbitrary curved supports, we point out the differences in their characterization and interpretation in the case of flat space. With the restrictions of real data - such as pixelization and incomplete sky coverage, to mention just a few - in mind, we derive and test unbiased estimators for all Minkowski functionals. Various examples, among them the analysis of the four-year COBE DMR data, illustrate the application of our method.

  13. Precise mapping of the magnetic field in the CMS barrel yoke using cosmic rays

    SciTech Connect

    Chatrchyan, S.; et al.,

    2010-03-01

    The CMS detector is designed around a large 4 T superconducting solenoid, enclosed in a 12000-tonne steel return yoke. A detailed map of the magnetic field is required for the accurate simulation and reconstruction of physics events in the CMS detector, not only in the inner tracking region inside the solenoid but also in the large and complex structure of the steel yoke, which is instrumented with muon chambers. Using a large sample of cosmic muon events collected by CMS in 2008, the field in the steel of the barrel yoke has been determined with a precision of 3 to 8% depending on the location.

  14. Planetary-scale wave structures of the earth's atmosphere revealed from the COSMIC observations

    NASA Astrophysics Data System (ADS)

    Anisetty, S. K. A. V. Prasad Rao; Brahmanandam, P. S.; Uma, G.; Babu, A. Narendra; Huang, Ching-Yuang; Kumar, G. Anil; Ram, S. Tulasi; Wang, Hsiao-Lan; Chu, Yen-Hsyang

    2014-02-01

    GPS radio occultation (GPS RO) method, an active satellite-to-satellite remote sensing technique, is capable of producing accurate, all-weather, round the clock, global refractive index, density, pressure, and temperature profiles of the troposphere and stratosphere. This study presents planetary-scale equatorially trapped Kelvin waves in temperature profiles retrieved using COSMIC (Constellation Observing System for Meteorology, Ionosphere, and Climate) satellites during 2006-2009 and their interactions with background atmospheric conditions. It is found that the Kelvin waves are not only associated with wave periods of higher than 10 days (slow Kelvin waves) with higher zonal wave numbers (either 1 or 2), but also possessing downward phase progression, giving evidence that the source regions of them are located at lower altitudes. A thorough verification of outgoing longwave radiation (OLR) reveals that deep convection activity has developed regularly over the Indonesian region, suggesting that the Kelvin waves are driven by the convective activity. The derived Kelvin waves show enhanced (diminished) tendencies during westward (eastward) phase of the quasi-biennial oscillation (QBO) in zonal winds, implying a mutual relation between both of them. The El Niño and Southern Oscillation (ENSO) below 18 km and the QBO features between 18 and 27 km in temperature profiles are observed during May 2006-May 2010 with the help of an adaptive data analysis technique known as Hilbert Huang Transform (HHT). Further, temperature anomalies computed using COSMIC retrieved temperatures are critically evaluated during different phases of ENSO, which has revealed interesting results and are discussed in light of available literature.

  15. REVEALING TYPE Ia SUPERNOVA PHYSICS WITH COSMIC RATES AND NUCLEAR GAMMA RAYS

    SciTech Connect

    Horiuchi, Shunsaku; Beacom, John F. E-mail: beacom@mps.ohio-state.ed

    2010-11-01

    Type Ia supernovae (SNe Ia) remain mysterious despite their central importance in cosmology and their rapidly increasing discovery rate. The progenitors of SNe Ia can be probed by the delay time between progenitor birth and explosion as SNe Ia. The explosions and progenitors of SNe Ia can be probed by MeV nuclear gamma rays emitted in the decays of radioactive nickel and cobalt into iron. We compare the cosmic star formation and SN Ia rates, finding that their different redshift evolution requires a large fraction of SNe Ia to have large delay times. A delay-time distribution of the form t {sup -}{alpha} with {alpha} = 1.0 {+-} 0.3 provides a good fit, implying that 50% of SNe Ia explode more than {approx}1 Gyr after progenitor birth. The extrapolation of the cosmic SN Ia rate to z = 0 agrees with the rate we deduce from catalogs of local SNe Ia. We investigate prospects for gamma-ray telescopes to exploit the facts that escaping gamma rays directly reveal the power source of SNe Ia and uniquely provide tomography of the expanding ejecta. We find large improvements relative to earlier studies by Gehrels et al. in 1987 and Timmes and Woosley in 1997 due to larger and more certain SN Ia rates and advances in gamma-ray detectors. The proposed Advanced Compton Telescope, with a narrow-line sensitivity {approx}60 times better than that of current satellites, would, on an annual basis, detect up to {approx}100 SNe Ia (3{sigma}) and provide revolutionary model discrimination for SNe Ia within 20 Mpc, with gamma-ray light curves measured with {approx}10{sigma} significance daily for {approx}100 days. Even more modest improvements in detector sensitivity would open a new and invaluable astronomy with frequent SN Ia gamma-ray detections.

  16. Study of cosmic rays reveals secrets of solar-terrestrial science

    NASA Astrophysics Data System (ADS)

    Jokipii, J. R.

    For many years cosmic rays provided the most important source of energetic particles for studies of subatomic physics. Today, cosmic rays are being studied as a natural phenomenon that can tell us much about both the Earth's environment in space and distant astrophysical processes. Cosmic rays are naturally occurring energetic particles—mainly ions—with kinetic energies extending from just above thermal energies to more than 1020 electron volts (eV). They constantly bombard the Earth from all directions, with more than 1018 particles having energies >1 MeV striking the top of the Earth's atmosphere each second. Figure 1 illustrates the continuous cosmic ray energy spectrum.

  17. A Flat Universe from High-Resolution Maps of the Cosmic MicrowaveBackground Radiation

    SciTech Connect

    de Bernardis, P.; Ade, P.A.R.; Bock, J.J.; Bond, J.R.; Borrill,J.; Boscaleri, A.; Coble, K.; Crill, B.P.; De Gasperis, G.; Farese, P.C.; Ferreira, P.G.; Ganga, K.; Giacometti, M.; Hivon, E.; Hristov, V.V.; Iacoangeli, A.; Jaffe, A.H.; Lange, A.E.; Martinis, L.; Masi, S.; Mason,P.; Mauskopf, P.D.; Melchiorri, A.; Miglio, L.; Montroy, T.; Netterfield,C.B.; Pascale, E.; Piacentini, F.; Pogosyan, D.; Prunet, S.; Rao, S.; Romeo, G.; Ruhl, J.E.; Scaramuzzi, F.; Sforna, D.; Vittorio, N.

    2000-04-28

    The blackbody radiation left over from the Big Bang has been transformed by the expansion of the Universe into the nearly isotropic 2.73 K Cosmic Microwave Background. Tiny inhomogeneities in the early Universe left their imprint on the microwave background in the form of small anisotropies in its temperature. These anisotropies contain information about basic cosmological parameters, particularly the total energy density and curvature of the universe. Here we report the first images of resolved structure in the microwave background anisotropies over a significant part of the sky. Maps at four frequencies clearly distinguish the microwave background from foreground emission. We compute the angular power spectrum of the microwave background, and find a peak at Legendre multipole {ell}{sub peak} = (197 {+-} 6), with an amplitude DT{sub 200} = (69 {+-} 8){mu}K. This is consistent with that expected for cold dark matter models in a flat (euclidean) Universe, as favored by standard inflationary scenarios.

  18. A flat Universe from high-resolution maps of the cosmic microwave background radiation

    PubMed

    de Bernardis P; Ade; Bock; Bond; Borrill; Boscaleri; Coble; Crill; De Gasperis G; Farese; Ferreira; Ganga; Giacometti; Hivon; Hristov; Iacoangeli; Jaffe; Lange; Martinis; Masi; Mason; Mauskopf; Melchiorri; Miglio; Montroy; Netterfield

    2000-04-27

    The blackbody radiation left over from the Big Bang has been transformed by the expansion of the Universe into the nearly isotropic 2.73 K cosmic microwave background. Tiny inhomogeneities in the early Universe left their imprint on the microwave background in the form of small anisotropies in its temperature. These anisotropies contain information about basic cosmological parameters, particularly the total energy density and curvature of the Universe. Here we report the first images of resolved structure in the microwave background anisotropies over a significant part of the sky. Maps at four frequencies clearly distinguish the microwave background from foreground emission. We compute the angular power spectrum of the microwave background, and find a peak at Legendre multipole Ipeak = (197 +/- 6), with an amplitude delta T200 = (69 +/- 8) microK. This is consistent with that expected for cold dark matter models in a flat (euclidean) Universe, as favoured by standard inflationary models. PMID:10801117

  19. Combination of hand mapping and automatic mapping to reveal the Miocene high elevation Pyrenean peneplain

    NASA Astrophysics Data System (ADS)

    Bosch, Gemma V.; Babault, Julien; Van Den Driessche, Jean

    2016-04-01

    A striking feature of the morphology of the Pyrenees is the occurrence of high-elevation, low-relief surfaces, which are interpreted as remnants of a single Miocene planation surface. Whether the original surface was uplifted or developed at high altitude is debated. This "Miocene Pyrenean peneplain" has been dissected by fluvial and glacial erosion during the Quaternary. Reworking by glacial erosion also provides new smooth surfaces such as glacial cirque floors that must not be confused with the remnants of the original planation surface. The later are convex-up landforms whereas glacial cirque floors are concave-up landforms. To reveal the Miocene high-elevation Pyrenean peneplain, we combined hand mapping and automatic mapping at the scale of the whole chain. From previous mapping in literature and from our own field work, we first perform a map of both the Miocene planation surface remnants and the Quaternary glacial cirque floors. Using Digital Elevation Models, numerical parameters were extracted from this map to characterize the two types of smooth surfaces. The slope is the parameter that helps to delimitate and differentiate the smooth surfaces from the rest of the Pyrenean topography. To distinguish between the two types of smooth surfaces we used the Topographic Index (TPI). This parameter is the difference between the elevation of a point and the mean elevation. Choosing the pertinent radius according to the scale of the landform to map, and the pertinent values interval, we can differentiate the planation surface (convex-up) from the glacial cirque floors (concave-up). A sensitivity test was performed to determine the best radius and the best interval for TPI and slope values to distinguish between the two types of smooth surfaces. Finally, we used a combination of slope values, TPI values and radius to determine automatically the high-elevation, low-relief surfaces in the entire Pyrenees. We verified in the field the presence of the newly mapped high

  20. Intensity Mapping across Cosmic Times with the Lyα Line

    NASA Astrophysics Data System (ADS)

    Pullen, Anthony R.; Doré, Olivier; Bock, Jamie

    2014-05-01

    We present a quantitative model of Lyα emission throughout cosmic history and determine the prospects for intensity mapping spatial fluctuations in the Lyα signal. Since (1) our model assumes at z > 6 the minimum star formation required to sustain reionization and (2) is based at z < 6 on a luminosity function (LF) extrapolated from the few observed bright Lyα emitters, this should be considered a lower limit. Mapping the line emission allows probes of reionization, star formation, and large-scale structure (LSS) as a function of redshift. While Lyα emission during reionization has been studied, we also predict the postreionization signal to test predictions of the intensity and motivate future intensity mapping probes of reionization. We include emission from massive dark matter halos and the intergalactic medium (IGM) in our model. We find agreement with current, measured LFs of Lyα emitters at z < 8. However, diffuse IGM emission, not associated with Lyα emitters, dominates the intensity up to z ~ 10. While our model is applicable for deep-optical or near-infrared observers like the James Webb Space Telescope, only intensity mapping will detect the diffuse IGM emission. We also construct a three-dimensional power spectrum model of the Lyα emission. Finally, we consider the prospects of an intensity mapper for measuring Lyα fluctuations while identifying interloper contamination for removal. Our results suggest that while the reionization signal is challenging, Lyα fluctuations can be an interesting new probe of LSS at late times when used in conjunction with other lines, e.g., Hα, to monitor low-redshift foreground confusion.

  1. Intensity mapping across cosmic times with the Lyα line

    SciTech Connect

    Pullen, Anthony R.; Doré, Olivier; Bock, Jamie

    2014-05-10

    We present a quantitative model of Lyα emission throughout cosmic history and determine the prospects for intensity mapping spatial fluctuations in the Lyα signal. Since (1) our model assumes at z > 6 the minimum star formation required to sustain reionization and (2) is based at z < 6 on a luminosity function (LF) extrapolated from the few observed bright Lyα emitters, this should be considered a lower limit. Mapping the line emission allows probes of reionization, star formation, and large-scale structure (LSS) as a function of redshift. While Lyα emission during reionization has been studied, we also predict the postreionization signal to test predictions of the intensity and motivate future intensity mapping probes of reionization. We include emission from massive dark matter halos and the intergalactic medium (IGM) in our model. We find agreement with current, measured LFs of Lyα emitters at z < 8. However, diffuse IGM emission, not associated with Lyα emitters, dominates the intensity up to z ∼ 10. While our model is applicable for deep-optical or near-infrared observers like the James Webb Space Telescope, only intensity mapping will detect the diffuse IGM emission. We also construct a three-dimensional power spectrum model of the Lyα emission. Finally, we consider the prospects of an intensity mapper for measuring Lyα fluctuations while identifying interloper contamination for removal. Our results suggest that while the reionization signal is challenging, Lyα fluctuations can be an interesting new probe of LSS at late times when used in conjunction with other lines, e.g., Hα, to monitor low-redshift foreground confusion.

  2. Using Wavelet Transforms to Detect Dust in Cosmic Microwave Background Maps

    NASA Astrophysics Data System (ADS)

    Rybolt, Ben; Guest, S.; Larson, G.; Bunn, E.

    2008-05-01

    A major question regarding temperature fluctuations in the cosmic microwave background (CMB) is whether or not they obey Gaussian statistics (i.e., whether they contain any additional information beyond that contained in the power spectrum). Inflation predicts that the CMB is Gaussian; future experiments will test this prediction. Dust contamination will likely be a problem for these tests, and could bias the results, as dust is known to be highly non-Gaussian. We are developing statistical test to detect dust contamination. It has previously been shown that wavelet transforms efficiently represent dust, so we compare the power of a variety of statistical tests to maps with and without wavelet transforms. Some statistics we have looked at are the skewness, linear correlations between a simulated map and a dust template, and a comparison of the mean-square signal in high-dust and low-dust regions. We have found that using a wavelet transform does not help detect dust for the skewness test, but it significantly increases the power of the mean-square test. This research is supported by grants from the National Science Foundation and the Research Corporation.

  3. Micro-spectroscopic mapping: revealing internal structures of zircon crystals

    NASA Astrophysics Data System (ADS)

    Nasdala, L.; Reiners, P. W.; Hanchar, J. M.

    2003-04-01

    Natural zircon crystals typically deviate from perfect crystallinity and ideal chemical composition. If non-ideality features are not homogeneously distributed within a crystal but show a heterogeneity pattern, this is referred to as its "internal structure". Internal structures of zircon are mostly first caused by the heterogeneous incorporation of trace elements during crystal growth. Over time, these primary patterns may become more complex after being overprinted by radioactive self-irradiation and heterogeneous alteration or recrystallization. Internal structures may provide valuable information about the origin and post-growth history of zircon crystals. Further, they need to be recognized for sound microprobe dating, for instance to avoid biased results when straddling zones of different age. Revealing internal structures has thus become an important tool in zircon research. It is mostly done by means of backscattered electrons or cathodoluminescence imaging. These two techniques are advantageous over optical microscopy in the cross-polarized mode as the volume resolution is better and simple polished mounts instead of doubly-sided sections are needed. A disadvantage, however, is that the impact of electron beam during analysis causes local structural changes. Quantitative studies of the real structure of zircon samples, such as determination of the degree of the radiation damage, is therefore tainted with potential uncertainty when being done after electron probe analysis. As an alternative, we present images of internal zircon structures generated through visible laser excitation and mapping of the Raman and photoluminescence light. Due to the time-consuming mapping procedure, such images will perhaps not be routinely used. For detailed studies, however, they may provide most valuable information. Photoluminescence maps provide, for instance, information on both the distribution of rare earth elements (band integrals) and the short-range order (band

  4. Cosmic Electromagnetic Radiation: The sky shine covers an enormous spectrum of frequencies, revealing a cosmic picture in some detail.

    PubMed

    Hafner, E M

    1964-09-18

    Within a few decades astronomy has extended the compass of its observations from the visible spectrum downward to radio waves and upward to the highest energies known to science. The major new accomplishments are in the radio and x-ray bands, and in the associated study of cosmic ray electrons. Synchrotron radiation is known to be a mechanism for radio signals; discrete x-ray sources have been found; the intensity and the charge ratio of galactic electrons are under study. Experimental results at energies above the x-ray region are less firm. The sun surely emits gamma rays at energies of about 1 Mev during flare activity, and instruments in deep space have probably recorded the general galactic glow of similar photons. Upper limits for fluxes have been set at 100 Mev and beyond. To some extent the physical processes which give rise to the extraterrestrial radiation are familiar to workers in the terrestrial laboratory. Synchrotron radiation is an example; the bremsstrahlung of electrons, the production of neutral pions in p-p collisions, and the annihilation of electron and nucleon pairs are others. Some proposed mechanisms are, and perhaps always will be, purely speculative in the sense that they are not directly observable in the laboratory. The inverse Compton effect, possibly one of the sources of a metagalactic sky glow of hard photons, is in this class. There is little chance that spontaneous creation of matter, even if it occurs in nature, can be observed on a terrestrial scale. And the extreme physical conditions proposed for neutron stars are beyond our ability to reproduce. Only through interpretation of astronomical data can we test the validity of these ideas. The many pictures of the universe given by the vast electromagnetic spectrum are essential to the synthesis of our concepts. PMID:17802004

  5. Probing the Dark Flow Signal in WMAP 9 -Year and Planck Cosmic Microwave Background Maps

    NASA Astrophysics Data System (ADS)

    Atrio-Barandela, F.; Kashlinsky, A.; Ebeling, H.; Fixsen, D. J.; Kocevski, D.

    2015-09-01

    The “dark flow” dipole is a statistically significant dipole found at the position of galaxy clusters in filtered maps of Cosmic Microwave Background (CMB) temperature anisotropies. The dipole measured in WMAP 3-, 5-, and 7- year data releases was (1) mutually consistent, (2) roughly aligned with the all-sky CMB dipole, and (3) correlated with clusters’ X-ray luminosities. We analyzed WMAP 9 -year and Planck 1st- year data releases using a catalog of 980 clusters outside of the Kp0 mask to test our earlier findings. The dipoles measured on these new data sets are fully compatible with our earlier estimates, are similar in amplitude and direction to our previous results, and are in disagreement with the results of an earlier study by the Planck Collaboration. Furthermore, in the Planck data sets dipoles are found to be independent of frequency, ruling out the thermal Sunyaev-Zeldovich as the source of the effect. In the data of both WMAP and Planck we find a clear correlation between the dipole measured at the cluster location in filtered maps and the average anisotropy on the original maps, further proving that the dipole is associated with clusters. The dipole signal is dominated by the most massive clusters, with a statistical significance that is better than 99%, slightly larger than in WMAP. Since both data sets differ in foreground contributions, instrumental noise, and other systematics, the agreement between the WMAP and Planck dipoles argues against them being due to systematic effects in either of the experiments.

  6. Synthetic protein interactions reveal a functional map of the cell

    PubMed Central

    Berry, Lisa K; Ólafsson, Guðjón; Ledesma-Fernández, Elena; Thorpe, Peter H

    2016-01-01

    To understand the function of eukaryotic cells, it is critical to understand the role of protein-protein interactions and protein localization. Currently, we do not know the importance of global protein localization nor do we understand to what extent the cell is permissive for new protein associations – a key requirement for the evolution of new protein functions. To answer this question, we fused every protein in the yeast Saccharomyces cerevisiae with a partner from each of the major cellular compartments and quantitatively assessed the effects upon growth. This analysis reveals that cells have a remarkable and unanticipated tolerance for forced protein associations, even if these associations lead to a proportion of the protein moving compartments within the cell. Furthermore, the interactions that do perturb growth provide a functional map of spatial protein regulation, identifying key regulatory complexes for the normal homeostasis of eukaryotic cells. DOI: http://dx.doi.org/10.7554/eLife.13053.001 PMID:27098839

  7. Integrative Acoustic Mapping Reveals Hudson RIver Sediment Processes an Habitats

    NASA Astrophysics Data System (ADS)

    Nitsche, F. O.; Bell, R.; Carbotte, S. M.; Ryan, W. B. F.; Slagle, A.; Chillrud, S.; Kenna, T.; Flood, R.; Ferrini, V.; Cerrato, R.; McHugh, C.; Strayer, D.

    2005-06-01

    Rivers and estuaries around the world are the focus of human settlements and activities. Needs for clean water, ecosystem preservation, commercial navigation, industrial development, and recreational access compete for the use of estuaries, and management of these resources requires a detailed understanding of estuarine morphology and sediment dynamics. This article presents an overview of the first estuary-wide study of a heavily used estuary, the Hudson River, based on high-resolution acoustic mapping of the river bottom. The integration of three high-resolution acoustic methods with extensive sampling reveals an unexpected complexity of bottom features and allows detailed classification of the benthic environment in terms of riverbed morphology, sediment type, and sedimentary processes.

  8. Distributed neural system for emotional intelligence revealed by lesion mapping

    PubMed Central

    Colom, Roberto; Grafman, Jordan

    2014-01-01

    Cognitive neuroscience has made considerable progress in understanding the neural architecture of human intelligence, identifying a broadly distributed network of frontal and parietal regions that support goal-directed, intelligent behavior. However, the contributions of this network to social and emotional aspects of intellectual function remain to be well characterized. Here we investigated the neural basis of emotional intelligence in 152 patients with focal brain injuries using voxel-based lesion-symptom mapping. Latent variable modeling was applied to obtain measures of emotional intelligence, general intelligence and personality from the Mayer, Salovey, Caruso Emotional Intelligence Test (MSCEIT), the Wechsler Adult Intelligence Scale and the Neuroticism-Extroversion-Openness Inventory, respectively. Regression analyses revealed that latent scores for measures of general intelligence and personality reliably predicted latent scores for emotional intelligence. Lesion mapping results further indicated that these convergent processes depend on a shared network of frontal, temporal and parietal brain regions. The results support an integrative framework for understanding the architecture of executive, social and emotional processes and make specific recommendations for the interpretation and application of the MSCEIT to the study of emotional intelligence in health and disease. PMID:23171618

  9. Architecture of cognitive flexibility revealed by lesion mapping

    PubMed Central

    Barbey, Aron K.; Colom, Roberto; Grafman, Jordan

    2013-01-01

    Neuroscience has made remarkable progress in understanding the architecture of human intelligence, identifying a distributed network of brain structures that support goal-directed, intelligent behavior. However, the neural foundations of cognitive flexibility and adaptive aspects of intellectual function remain to be well characterized. Here, we report a human lesion study (n = 149) that investigates the neural bases of key competencies of cognitive flexibility (i.e., mental flexibility and the fluent generation of new ideas) and systematically examine their contributions to a broad spectrum of cognitive and social processes, including psychometric intelligence (Wechsler Adult Intelligence Scale), emotional intelligence (Mayer, Salovey, Caruso Emotional Intelligence Test), and personality (Neuroticism–Extraversion–Openness Personality Inventory). Latent variable modeling was applied to obtain error-free indices of each factor, followed by voxel-based lesion-symptom mapping to elucidate their neural substrates. Regression analyses revealed that latent scores for psychometric intelligence reliably predict latent scores for cognitive flexibility (adjusted R2 = 0.94). Lesion mapping results further indicated that these convergent processes depend on a shared network of frontal, temporal, and parietal regions, including white matter association tracts, which bind these areas into an integrated system. A targeted analysis of the unique variance explained by cognitive flexibility further revealed selective damage within the right superior temporal gyrus, a region known to support insight and the recognition of novel semantic relations. The observed findings motivate an integrative framework for understanding the neural foundations of adaptive behavior, suggesting that core elements of cognitive flexibility emerge from a distributed network of brain regions that support specific competencies for human intelligence. PMID:23721727

  10. Architecture of cognitive flexibility revealed by lesion mapping.

    PubMed

    Barbey, Aron K; Colom, Roberto; Grafman, Jordan

    2013-11-15

    Neuroscience has made remarkable progress in understanding the architecture of human intelligence, identifying a distributed network of brain structures that support goal-directed, intelligent behavior. However, the neural foundations of cognitive flexibility and adaptive aspects of intellectual function remain to be well characterized. Here, we report a human lesion study (n=149) that investigates the neural bases of key competencies of cognitive flexibility (i.e., mental flexibility and the fluent generation of new ideas) and systematically examine their contributions to a broad spectrum of cognitive and social processes, including psychometric intelligence (Wechsler Adult Intelligence Scale), emotional intelligence (Mayer, Salovey, Caruso Emotional Intelligence Test), and personality (Neuroticism-Extraversion-Openness Personality Inventory). Latent variable modeling was applied to obtain error-free indices of each factor, followed by voxel-based lesion-symptom mapping to elucidate their neural substrates. Regression analyses revealed that latent scores for psychometric intelligence reliably predict latent scores for cognitive flexibility (adjusted R(2)=0.94). Lesion mapping results further indicated that these convergent processes depend on a shared network of frontal, temporal, and parietal regions, including white matter association tracts, which bind these areas into an integrated system. A targeted analysis of the unique variance explained by cognitive flexibility further revealed selective damage within the right superior temporal gyrus, a region known to support insight and the recognition of novel semantic relations. The observed findings motivate an integrative framework for understanding the neural foundations of adaptive behavior, suggesting that core elements of cognitive flexibility emerge from a distributed network of brain regions that support specific competencies for human intelligence. PMID:23721727

  11. Multiple 10Be records revealing the history of cosmic-ray variations across the Iceland Basin excursion

    NASA Astrophysics Data System (ADS)

    Horiuchi, Kazuho; Kamata, Kanae; Maejima, Shun; Sasaki, Sho; Sasaki, Nobuyoshi; Yamazaki, Toshitsugu; Fujita, Shuji; Motoyama, Hideaki; Matsuzaki, Hiroyuki

    2016-04-01

    Cosmogenic 10Be is a proxy of cosmic-ray flux, and its natural records provide vital information about the past intensity variability of the geomagnetic field and solar activity. 10Be records also serve as powerful tools for global synchronization among a variety of paleoarchives and for elucidating sedimentary processes on natural remanent magnetization acquisition. However, high-resolution (multi-decadal to multi-centennial) records of 10Be are scarce, especially those older than several tens of thousands of years. Here we present multiple high-resolution 10Be records of the Iceland Basin geomagnetic excursion interval (ca. 170-200 kyr ago) obtained from sediment cores (authigenic 10Be/9Be ratio) and an ice core (atmospheric 10Be flux). Comparing sedimentary 10Be records with relative paleointensity from the same cores, we found differences in the magnetic lock-in depth, even between adjacent cores. The 10Be-proxy records from the sediment and ice cores exhibit common characteristics: an asymmetric large-scale variation, a ∼7-kyr quasi-plateau around the maximum with a characteristic mid-term depression, and multi-millennial fluctuations in cosmic-ray flux during this interval. Minimal-synchronized and stacked 10Be records show that maximum cosmic-ray flux occurred 188.5-190.0 kyr ago and was double the present flux. A wavelet analysis of the stacked curve reveals dominant 4-kyr and secondary 8-kyr periodicities, both of which can be interpreted as intrinsic geomagnetic cycles. The wavelet spectrum of the high-resolution ice-core record shows a periodicity of 1.7 kyr and somewhat intermingled multi-centennial cycles around the maxima of 10Be, which likely represent solar cycles in this period. High-resolution 10Be records from multiple paleoarchives provide both a robust proxy record of cosmic-ray flux and a valuable tool for detailed global synchronization based on cosmic-ray variations.

  12. Identification of galaxy clusters in cosmic microwave background maps using the Sunyaev-Zel'dovich effect

    NASA Astrophysics Data System (ADS)

    Novaes, C. P.; Wuensche, C. A.

    2012-09-01

    Context. The Planck satellite was launched in 2009 by the European Space Agency to study the properties of the cosmic microwave background (CMB). An expected result of the Planck data analysis is the distinction of the various contaminants of the CMB signal. Among these contaminants is the Sunyaev-Zel'dovich (SZ) effect, which is caused by the inverse Compton scattering of CMB photons by high energy electrons in the intracluster medium of galaxy clusters. Aims: We modify a public version of the JADE (Joint Approximate Diagonalization of Eigenmatrices) algorithm, to deal with noisy data, and then use this algorithm as a tool to search for SZ clusters in two simulated datasets. Methods: The first dataset is composed of simple "homemade" simulations and the second of full sky simulations of high angular resolution, available at the LAMBDA (Legacy Archive for Microwave Background Data Analysis) website. The process of component separation can be summarized in four main steps: (1) pre-processing based on wavelet analysis, which performs an initial cleaning (denoising) of data to minimize the noise level; (2) the separation of the components (emissions) by JADE; (3) the calibration of the recovered SZ map; and (4) the identification of the positions and intensities of the clusters using the SExtractor software. Results: The results show that our JADE-based algorithm is effective in identifying the position and intensity of the SZ clusters, with the purities being higher then 90% for the extracted "catalogues". This value changes slightly according to the characteristics of noise and the number of components included in the input maps. Conclusions: The main highlight of our developed work is the effective recovery rate of SZ sources from noisy data, with no a priori assumptions. This powerful algorithm can be easily implemented and become an interesting complementary option to the "matched filter" algorithm (hereafter MF) widely used in SZ data analysis.

  13. An overview of the Cosmic Background Explorer (COBE) and its observations - New sky maps of the early universe

    NASA Technical Reports Server (NTRS)

    Smoot, George F.

    1992-01-01

    This paper discusses the three instruments aboard NASA's Cosmic Background Explorer (COBE) satellite and presents early results obtained from the first six months of observations. The three instruments (FIRAS, DMR, and DIRBE) have operated well and produced significant new results. The FIRAS measurement of the CMB spectrum supports the standard Big Bang model. The maps made from the DMR instrument measurements show a spatially smooth early universe. The maps of galactic and zodiacal emission produced by the DIRBE instrument are needed to identify the foreground emissions from extragalactic and thus to interpret its and the other COBE results in terms of events in the early universe.

  14. MADmap: A Massively Parallel Maximum-Likelihood Cosmic Microwave Background Map-Maker

    SciTech Connect

    Cantalupo, Christopher; Borrill, Julian; Jaffe, Andrew; Kisner, Theodore; Stompor, Radoslaw

    2009-06-09

    MADmap is a software application used to produce maximum-likelihood images of the sky from time-ordered data which include correlated noise, such as those gathered by Cosmic Microwave Background (CMB) experiments. It works efficiently on platforms ranging from small workstations to the most massively parallel supercomputers. Map-making is a critical step in the analysis of all CMB data sets, and the maximum-likelihood approach is the most accurate and widely applicable algorithm; however, it is a computationally challenging task. This challenge will only increase with the next generation of ground-based, balloon-borne and satellite CMB polarization experiments. The faintness of the B-mode signal that these experiments seek to measure requires them to gather enormous data sets. MADmap is already being run on up to O(1011) time samples, O(108) pixels and O(104) cores, with ongoing work to scale to the next generation of data sets and supercomputers. We describe MADmap's algorithm based around a preconditioned conjugate gradient solver, fast Fourier transforms and sparse matrix operations. We highlight MADmap's ability to address problems typically encountered in the analysis of realistic CMB data sets and describe its application to simulations of the Planck and EBEX experiments. The massively parallel and distributed implementation is detailed and scaling complexities are given for the resources required. MADmap is capable of analysing the largest data sets now being collected on computing resources currently available, and we argue that, given Moore's Law, MADmap will be capable of reducing the most massive projected data sets.

  15. Neural networks and the separation of cosmic microwave background and astrophysical signals in sky maps

    NASA Astrophysics Data System (ADS)

    Baccigalupi, C.; Bedini, L.; Burigana, C.; De Zotti, G.; Farusi, A.; Maino, D.; Maris, M.; Perrotta, F.; Salerno, E.; Toffolatti, L.; Tonazzini, A.

    2000-11-01

    We implement an independent component analysis (ICA) algorithm to separate signals of different origin in sky maps at several frequencies. Owing to its self-organizing capability, it works without prior assumptions on either the frequency dependence or the angular power spectrum of the various signals; rather, it learns directly from the input data how to identify the statistically independent components, on the assumption that all but, at most, one of the components have non-Gaussian distributions. We have applied the ICA algorithm to simulated patches of the sky at the four frequencies (30, 44, 70 and 100GHz) used by the Low Frequency Instrument of the European Space Agency's Planck satellite. Simulations include the cosmic microwave background (CMB), the synchrotron and thermal dust emissions, and extragalactic radio sources. The effects of the angular response functions of the detectors and of instrumental noise have been ignored in this first exploratory study. The ICA algorithm reconstructs the spatial distribution of each component with rms errors of about 1per cent for the CMB, and 10per cent for the much weaker Galactic components. Radio sources are almost completely recovered down to a flux limit corresponding to ~=0.7σCMB, where σCMB is the rms level of the CMB fluctuations. The signal recovered has equal quality on all scales larger than the pixel size. In addition, we show that for the strongest components (CMB and radio sources) the frequency scaling is recovered with per cent precision. Thus, algorithms of the type presented here appear to be very promising tools for component separation. On the other hand, we have been dealing here with a highly idealized situation. Work to include instrumental noise, the effect of different resolving powers at different frequencies and a more complete and realistic characterization of astrophysical foregrounds is in progress.

  16. Mapping compound cosmic telescopes containing multiple projected cluster-scale halos

    SciTech Connect

    Ammons, S. Mark; Wong, Kenneth C.; Zabludoff, Ann I.; Keeton, Charles R. E-mail: kwong@as.arizona.edu E-mail: keeton@physics.rutgers.edu

    2014-01-20

    Lines of sight with multiple projected cluster-scale gravitational lenses have high total masses and complex lens plane interactions that can boost the area of magnification, or étendue, making detection of faint background sources more likely than elsewhere. To identify these new 'compound' cosmic telescopes, we have found directions in the sky with the highest integrated mass densities, as traced by the projected concentrations of luminous red galaxies (LRGs). We use new galaxy spectroscopy to derive preliminary magnification maps for two such lines of sight with total mass exceeding ∼3 × 10{sup 15} M {sub ☉}. From 1151 MMT Hectospec spectra of galaxies down to i {sub AB} = 21.2, we identify two to three group- and cluster-scale halos in each beam. These are well traced by LRGs. The majority of the mass in beam J085007.6+360428 (0850) is contributed by Zwicky 1953, a massive cluster at z = 0.3774, whereas beam J130657.5+463219 (1306) is composed of three halos with virial masses of 6 × 10{sup 14}-2 × 10{sup 15} M {sub ☉}, one of which is A1682. The magnification maps derived from our mass models based on spectroscopy and Sloan Digital Sky Survey photometry alone display substantial étendue: the 68% confidence bands on the lens plane area with magnification exceeding 10 for a source plane of z{sub s} = 10 are [1.2, 3.8] arcmin{sup 2} for 0850 and [2.3, 6.7] arcmin{sup 2} for 1306. In deep Subaru Suprime-Cam imaging of beam 0850, we serendipitously discover a candidate multiply imaged V-dropout source at z {sub phot} = 5.03. The location of the candidate multiply imaged arcs is consistent with the critical curves for a source plane of z = 5.03 predicted by our mass model. Incorporating the position of the candidate multiply imaged galaxy as a constraint on the critical curve location in 0850 narrows the 68% confidence band on the lens plane area with μ > 10 and z{sub s} = 10 to [1.8, 4.2] arcmin{sup 2}, an étendue range comparable to that of MACS 0717

  17. Gaussian statistics of the cosmic microwave background: Correlation of temperature extrema in the COBE DMR two-year sky maps

    NASA Technical Reports Server (NTRS)

    Kogut, A.; Banday, A. J.; Bennett, C. L.; Hinshaw, G.; Lubin, P. M.; Smoot, G. F.

    1995-01-01

    We use the two-point correlation function of the extrema points (peaks and valleys) in the Cosmic Background Explorer (COBE) Differential Microwave Radiometers (DMR) 2 year sky maps as a test for non-Gaussian temperature distribution in the cosmic microwave background anisotropy. A maximum-likelihood analysis compares the DMR data to n = 1 toy models whose random-phase spherical harmonic components a(sub lm) are drawn from either Gaussian, chi-square, or log-normal parent populations. The likelihood of the 53 GHz (A+B)/2 data is greatest for the exact Gaussian model. There is less than 10% chance that the non-Gaussian models tested describe the DMR data, limited primarily by type II errors in the statistical inference. The extrema correlation function is a stronger test for this class of non-Gaussian models than topological statistics such as the genus.

  18. Maps of Dust Infrared Emission for Use in Estimation of Reddening and Cosmic Microwave Background Radiation Foregrounds

    NASA Astrophysics Data System (ADS)

    Schlegel, David J.; Finkbeiner, Douglas P.; Davis, Marc

    1998-06-01

    We present a full-sky 100 μm map that is a reprocessed composite of the COBE/DIRBE and IRAS/ISSA maps, with the zodiacal foreground and confirmed point sources removed. Before using the ISSA maps, we remove the remaining artifacts from the IRAS scan pattern. Using the DIRBE 100 and 240 μm data, we have constructed a map of the dust temperature so that the 100 μm map may be converted to a map proportional to dust column density. The dust temperature varies from 17 to 21 K, which is modest but does modify the estimate of the dust column by a factor of 5. The result of these manipulations is a map with DIRBE quality calibration and IRAS resolution. A wealth of filamentary detail is apparent on many different scales at all Galactic latitudes. In high-latitude regions, the dust map correlates well with maps of H I emission, but deviations are coherent in the sky and are especially conspicuous in regions of saturation of H I emission toward denser clouds and of formation of H2 in molecular clouds. In contrast, high-velocity H I clouds are deficient in dust emission, as expected. To generate the full-sky dust maps, we must first remove zodiacal light contamination, as well as a possible cosmic infrared background (CIB). This is done via a regression analysis of the 100 μm DIRBE map against the Leiden-Dwingeloo map of H I emission, with corrections for the zodiacal light via a suitable expansion of the DIRBE 25 μm flux. This procedure removes virtually all traces of the zodiacal foreground. For the 100 μm map no significant CIB is detected. At longer wavelengths, where the zodiacal contamination is weaker, we detect the CIB at surprisingly high flux levels of 32 +/- 13 nW m-2 sr-1 at 140 μm and of 17 +/- 4 nW m-2 sr-1 at 240 μm (95% confidence). This integrated flux ~2 times that extrapolated from optical galaxies in the Hubble Deep Field. The primary use of these maps is likely to be as a new estimator of Galactic extinction. To calibrate our maps, we assume a

  19. Astronomer's new guide to the galaxy: largest map of cold dust revealed

    NASA Astrophysics Data System (ADS)

    2009-07-01

    -wave camera on the ESO-operated APEX telescope. APEX is located at an altitude of 5100 m on the arid plateau of Chajnantor in the Chilean Andes -- a site that allows optimal viewing in the submillimetre range. The Universe is relatively unexplored at submillimetre wavelengths, as extremely dry atmospheric conditions and advanced detector technology are required for such observations. The interstellar medium -- the material between the stars -- is composed of gas and grains of cosmic dust, rather like fine sand or soot. However, the gas is mostly hydrogen and relatively difficult to detect, so astronomers often search for these dense regions by looking for the faint heat glow of the cosmic dust grains. Submillimetre light allows astronomers to see these dust clouds shining, even though they obscure our view of the Universe at visible light wavelengths. Accordingly, the ATLASGAL map includes the denser central regions of our galaxy, in the direction of the constellation of Sagittarius -- home to a supermassive black hole (ESO 46/08) -- that are otherwise hidden behind a dark shroud of dust clouds. The newly released map also reveals thousands of dense dust clumps, many never seen before, which mark the future birthplaces of massive stars. The clumps are typically a couple of light-years in size, and have masses of between ten and a few thousand times the mass of our Sun. In addition, ATLASGAL has captured images of beautiful filamentary structures and bubbles in the interstellar medium, blown by supernovae and the winds of bright stars. Some striking highlights of the map include the centre of the Milky Way, the nearby massive and dense cloud of molecular gas called Sagittarius B2, and a bubble of expanding gas called RCW120, where the interstellar medium around the bubble is collapsing and forming new stars (see ESO 40/08). "It's exciting to get our first look at ATLASGAL, and we will be increasing the size of the map over the next year to cover all of the galactic plane

  20. Ongoing cosmic ray acceleration in the supernova remnant W51C revealed with the MAGIC telescopes

    NASA Astrophysics Data System (ADS)

    Krause, J.; Reichardt, I.; Carmona, E.; Gozzini, S. R.; Jankowski, F.; MAGIC Collaboration

    2012-12-01

    The supernova remnant (SNR) W51C interacts with the molecular clouds of the star-forming region W51B, making the W51 complex one of the most promising targets to study cosmic ray acceleration. Gamma-ray emission from this region was discovered by Fermi/LAT and H.E.S.S., although its location was compatible with the SNR shell, the molecular cloud (MC) and a pulsar wind nebula (PWN) candidate. The modeling of the spectral energy distribution presented by the Fermi/LAT collaboration suggests a hadronic emission mechanism. Furthermore indications of an enhanced flux of low energy cosmic rays in the interaction region between SNR and MC have been reported based on ionization measurements in the mm regime. MAGIC conducted deep observations of W51, yielding a detection of an extended emission with more than 11 standard deviations. We extend the spectrum from the highest Fermi/LAT energies to ~5 TeV and find that it follows a single power law with an index of 2.58+/-0.07stat+/-0.22syst. We restrict the main part of the emission region to the zone where the SNR interacts with the molecular clouds. We also find a tail extending towards the PWN candidate CXO J192318.5+140305, possibly contributing up to 20% of the total flux. The broad band spectral energy distribution can be explained with a hadronic model that implies proton acceleration at least up to 50 TeV. This result, together with the morphology of the source, suggests that we observe ongoing acceleration of ions in the interaction zone between the SNR and the cloud.

  1. Genetic Analyses Reveal Functions for MAP2K3 and MAP2K6 in Mouse Testis Determination.

    PubMed

    Warr, Nick; Siggers, Pam; Carré, Gwenn-Aël; Wells, Sara; Greenfield, Andy

    2016-05-01

    Testis determination in mammals is initiated by expression of SRY in somatic cells of the embryonic gonad. Genetic analyses in the mouse have revealed a requirement for mitogen-activated protein kinase (MAPK) signaling in testis determination: targeted loss of the kinases MAP3K4 and p38 MAPK causes complete XY embryonic gonadal sex reversal. These kinases occupy positions at the top and bottom level, respectively, in the canonical three-tier MAPK-signaling cascade: MAP3K, MAP2K, MAPK. To date, no role in sex determination has been attributed to a MAP2K, although such a function is predicted to exist. Here, we report roles for the kinases MAP2K3 and MAP2K6 in testis determination. C57BL/6J (B6) embryos lacking MAP2K3 exhibited no significant abnormalities of testis development, whilst those lacking MAP2K6 exhibited a minor delay in testis determination. Compound mutants lacking three out of four functional alleles at the two loci also exhibited delayed testis determination and transient ovotestis formation as a consequence, suggestive of partially redundant roles for these kinases in testis determination. Early lethality of double-knockout embryos precludes analysis of sexual development. To reveal their roles in testis determination more clearly, we generated Map2k mutant B6 embryos using a weaker Sry allele (Sry(AKR)). Loss of Map2k3 on this highly sensitized background exacerbates ovotestis development, whilst loss of Map2k6 results in complete XY gonadal sex reversal associated with reduction of Sry expression at 11.25 days postcoitum. Our data suggest that MAP2K6 functions in mouse testis determination, via positive effects on Sry, and also indicate a minor role for MAP2K3. PMID:27009039

  2. Chandra mapping of the cosmic web converging on the virialization region of Abell 1795

    NASA Astrophysics Data System (ADS)

    Vikhlinin, Alexey

    2014-09-01

    Detailed observations of the "cosmic melting pot" in the virialization zone of rich galaxy clusters are a fairly new territory for the physics of clusters and the intergalactic medium. The first step has been taken with a deep Chandra study of A133, which has provided a uniquely detailed picture of the Cosmic Web converging onto the cluster virial radius and demonstrated that Chandra can probe to fainter surface brightness levels than any other X-ray observatory now operating. Many of the results from the A133 observation are potentially game-changers for our understanding of the virialization region and its proper modeling. We now need to follow this up with a similarly deep observation of at least one more cluster.

  3. Detecting Low-Contrast Features in the Cosmic Ray Albedo Proton Map of the Moon

    NASA Technical Reports Server (NTRS)

    Wilson, J. K.; Schwadron, N.; Spence, H. E.; Golightly, M. J.; Case, A. W.; Smith, S.; Blake, J. B.; Kasper, J.; Looper, M. D.; Mazur, J. E.; Townsend, L. W.; Zeitlin, C.; Stubbs, T. J.

    2014-01-01

    High energy cosmic rays constantly bombard the lunar regolith, producing (via nuclear evaporation) secondary 'albedo' or 'splash' particles like protons and neutrons, some of which escape back to space. Lunar Prospector and the Lunar Reconnaissance Orbiter (LRO), have shown that the energy distribution of albedo neutrons is modulated by the elemental composition of the lunar regolith, and by ice deposits in permanently shadowed polar craters. Here we investigate an analogous phenomenon with high energy ((is) approximately 100 MeV) lunar albedo protons.

  4. COSMIC MICROWAVE BACKGROUND POLARIZATION AND TEMPERATURE POWER SPECTRA ESTIMATION USING LINEAR COMBINATION OF WMAP 5 YEAR MAPS

    SciTech Connect

    Samal, Pramoda Kumar; Jain, Pankaj; Saha, Rajib; Prunet, Simon; Souradeep, Tarun

    2010-05-01

    We estimate cosmic microwave background (CMB) polarization and temperature power spectra using Wilkinson Microwave Anisotropy Probe (WMAP) 5 year foreground contaminated maps. The power spectrum is estimated by using a model-independent method, which does not utilize directly the diffuse foreground templates nor the detector noise model. The method essentially consists of two steps: (1) removal of diffuse foregrounds contamination by making linear combination of individual maps in harmonic space and (2) cross-correlation of foreground cleaned maps to minimize detector noise bias. For the temperature power spectrum we also estimate and subtract residual unresolved point source contamination in the cross-power spectrum using the point source model provided by the WMAP science team. Our TT, TE, and EE power spectra are in good agreement with the published results of the WMAP science team. We perform detailed numerical simulations to test for bias in our procedure. We find that the bias is small in almost all cases. A negative bias at low l in TT power spectrum has been pointed out in an earlier publication. We find that the bias-corrected quadrupole power (l(l + 1)C{sub l} /2{pi}) is 532 {mu}K{sup 2}, approximately 2.5 times the estimate (213.4 {mu}K{sup 2}) made by the WMAP team.

  5. Discriminating between unresolved point sources and `negative' Sunyaev-Zel'dovich clusters in cosmic microwave background maps

    NASA Astrophysics Data System (ADS)

    Rubiño-Martín, J. A.; Sunyaev, R. A.

    2003-10-01

    Clusters of galaxies produce negative features at wavelengths λ > 1.25 mm in cosmic microwave background (CMB) maps by means of the thermal Sunyaev-Zel'dovich (SZ) effect, while point radio sources produce positive peaks. This fact implies that a distribution of unresolved SZ clusters could be detected using the negative asymmetry introduced in the odd moments of the brightness map (skewness and higher), or in the probability distribution function for the fluctuations, once the map has been filtered in order to remove the contribution from primordial CMB fluctuations from large scales. This property provides a consistency check on the recent detections from CBI and BIMA experiments of an excess of power at small angular scales, in order to confirm that they are produced by a distribution of unresolved SZ clusters. However, it will require at least 1.5-2 times more observing time than detection of the corresponding power signal. This approach could also be used with the data of the planned SZ experiments (e.g. ACT, AMI, AMIBA, APEX, 8-m South Pole Telescope).

  6. Galactic Foreground Contribution to the BEAST Cosmic Microwave Background Anisotropy Maps

    NASA Astrophysics Data System (ADS)

    Mejía, Jorge; Bersanelli, Marco; Burigana, Carlo; Childers, Jeff; Figueiredo, Newton; Kangas, Miikka; Lubin, Philip; Maino, Davide; Mandolesi, Nazzareno; Marvil, Josh; Meinhold, Peter; O'Dwyer, Ian; O'Neill, Hugh; Platania, Paola; Seiffert, Michael; Stebor, Nathan; Tello, Camilo; Villela, Thyrso; Wandelt, Benjamin; Wuensche, Carlos Alexandre

    2005-05-01

    We report limits on the Galactic foreground emission contribution to the Background Emission Anisotropy Scanning Telescope (BEAST) Ka- and Q-band CMB anisotropy maps. We estimate the contribution from the cross-correlations between these maps and the foreground emission templates of an Hα map, a destriped version of the Haslam et al. 408 MHz map, and a combined 100 μm IRAS DIRBE map. Our analysis samples the BEAST ~10° declination band into 24 one-hour (R.A.) wide sectors with ~7900 pixels each, where we calculate (1) the linear correlation coefficient between the anisotropy maps and the templates; (2) the coupling constants between the specific intensity units of the templates and the antenna temperature at the BEAST frequencies; and (3) the individual foreground contributions to the BEAST anisotropy maps. The peak sector contributions of the contaminants in the Ka-band are of 56.5% free-free with a coupling constant of 8.3+/-0.4 μK R-1, and 67.4% dust with 45.0+/-2.0 μK MJy-1 sr-1. In the Q band the corresponding values are of 64.4% free-free with 4.1+/-0.2 μK R-1 and 67.5% dust with 24.0+/-1.0 μK MJy-1 sr-1. Using a lower limit of 10% in the relative uncertainty of the coupling constants, we can constrain the sector contributions of each contaminant in both maps to <20% in 21 (free-free), 19 (dust), and 22 (synchrotron) sectors. At this level, all these sectors are found outside of the |b|=14.6d region. By performing the same correlation analysis as a function of Galactic scale height, we conclude that the region within b=+/-17.5d should be removed from the BEAST maps for CMB studies in order to keep individual Galactic contributions below ~1% of the map's rms.

  7. Cosmic X-rays Reveal Evidence For New Form Of Matter

    NASA Astrophysics Data System (ADS)

    2002-04-01

    NASA's Chandra X-ray Observatory has found two stars -- one too small, one too cold -- that reveal cracks in our understanding of the structure of matter. These discoveries open a new window on nuclear physics, offering a link between the vast cosmos and its tiniest constituents. Chandra's observations of RX J1856.5-3754 and 3C58 suggest that the matter in these stars is even denser than nuclear matter found on Earth. This raises the possibility these stars are composed of pure quarks or contain crystals of sub-nuclear particles that normally have only a fleeting existence following high-energy collisions. By combining Chandra and Hubble Space Telescope data, astronomers found that RX J1856 radiates like a solid body with a temperature of 1.2 million degrees Fahrenheit (700,000 degrees Celsius) and has a diameter of about seven miles (11.3 kilometers). This size is too small to reconcile with standard models for neutron stars -- until now the most extreme form of matter known. "Taken at face value, the combined observational evidence points to a star composed not of neutrons, but of quarks in a form known as strange quark matter," said Jeremy Drake of the Harvard-Smithsonian Center for Astrophysics (CfA) in Cambridge, Mass., and lead author of a paper on RX J1856 to appear in the June 20, 2002, issue of The Astrophysical Journal. "Quarks, thought to be the fundamental constituents of nuclear particles, have never been seen outside a nucleus in Earth-bound laboratories." Observations by Chandra of 3C58 also yielded startling results. A team composed of Patrick Slane and Steven Murray, also of CfA, and David Helfand of Columbia University, New York, failed to detect the expected X-radiation from the hot surface of 3C58, a neutron star believed to have been created in an explosion witnessed by Chinese and Japanese astronomers in A.D. 1181. The team concluded that the star has a temperature of less than one million degrees Celsius, which is far below the predicted

  8. X chromosome map at 75-kb STS resolution, revealing extremes of recombination and GC content.

    PubMed

    Nagaraja, R; MacMillan, S; Kere, J; Jones, C; Griffin, S; Schmatz, M; Terrell, J; Shomaker, M; Jermak, C; Hott, C; Masisi, M; Mumm, S; Srivastava, A; Pilia, G; Featherstone, T; Mazzarella, R; Kesterson, S; McCauley, B; Railey, B; Burough, F; Nowotny, V; D'Urso, M; States, D; Brownstein, B; Schlessinger, D

    1997-03-01

    A YAC/STS map of the X chromosome has reached an inter-STS resolution of 75 kb. The map density is sufficient to provide YACs or other large-insert clones that are cross-validated as sequencing substrates across the chromosome. Marker density also permits estimates of regional gene content and a detailed comparison of genetic and physical map distances. Five regions are detected with relatively high G + C, correlated with gene richness; and a 17-Mb region with very low recombination is revealed between the Xq13.3 [XIST] and Xq21.3 XY homology loci. PMID:9074925

  9. Cosmic Flasher Reveals All!

    NASA Astrophysics Data System (ADS)

    1998-09-01

    For more information on magnetars and soft gamma-ray repeaters, see the Background Information which includes a "movie" of the flashing magnetar nebula, as seen by the VLA. Astronomers have found evidence for the most powerful magnetic field ever seen in the universe. They found it by observing a long-sought, short-lived "afterglow" of subatomic particles ejected from a magnetar -- a neutron star with a magnetic field billions of times stronger than any on Earth and 100 times stronger than any other previously known in the Universe. The afterglow is believed to be the aftermath of a massive starquake on the neutron star's surface. "And where there's smoke, there's fire, and we've seen the 'smoke' that tells us there's a magnetar out there," says Dale Frail, who used the National Science Foundation's Very Large Array (VLA) radio telescope to make the discovery. "Nature has created a unique laboratory where there are magnetic fields far stronger than anything that can be created here on Earth. As a result, the study of these objects enables us to study the effects of extraordinarily intense magnetic fields on matter," explains Dr. Morris L. Aizenman, Executive Officer in the Division of Astronomy at the National Science Foundation. Frail, an astronomer at the National Radio Astronomy Observatory (NRAO) in Socorro, New Mexico, along with Shri Kulkarni and Josh Bloom, astronomers at Caltech, discovered radio emission coming from a strange object 15,000 light-years away in our own Milky Way Galaxy. The radio emission was seen after the object experienced an outburst of gamma-rays and X-rays in late August. "This emission comes from particles ejected at nearly the speed of light from the surface of the neutron star interacting with the extremely powerful magnetic field," said Kulkarni. This is the first time this phenomenon, predicted by theorists, has been seen so clearly from a suspected magnetar. "Magnetars are expected to behave in certain ways. Astronomers have seen one type of their predicted activity previously, and now we've seen a completely different piece of evidence that says this is, in fact, a magnetar. That's exciting." Kulkarni said. The new discovery, the scientists say, will allow them to decipher further details about magnetars and their outbursts. SGR 1900+14 VLA Images of SGR 1900+14, with its short-lived radio emission turned off, left, and on, right. The radio emission comes from the interaction of subatomic particles with the magnetar's powerful magnetic field. The circles indicate the area from within which the X-ray emission of SGR 1900+14 comes. Magnetars were proposed in 1992 as a theoretical explanation for objects that repeatedly emit bursts of gamma-rays. These objects, called "soft gamma-ray repeaters," or SGRs, were identified in 1986. There still are only four of these known. They are believed to be rotating, superdense neutron stars, like pulsars, but with much stronger magnetic fields. Neutron stars are the remains of massive stars that explode as a supernova at the end of their normal lifetime. They are so dense that a thimbleful of neutron-star material would weigh 100 million tons. An ordinary pulsar emits "lighthouse beams" of radio waves that rotate with the star. When the star is oriented so that these beams sweep across the Earth, radio telescopes detect regularly-timed pulses. A magnetar is a neutron star with an extremely strong magnetic field, strong enough to rip atoms apart. In the units used by physicists, the strength of a magnetar's magnetic field is about a million billion Gauss; a refrigerator magnet has a field of about 100 Gauss. This superstrong magnetic field produces effects that distinguish magnetars from other neutron stars. First, the magnetic field is thought to act as a brake, slowing the star's rotation. The earlier discovery of pulsations several seconds apart in three SGRs indicated rotation rates slowed just as predicted by magnetar theory. Next, the magnetic field is predicted to cause "starquakes" in which the solid crust of the neutron star is cracked, releasing energy. That energy is released in two forms -- a burst of gamma-rays and X-rays and an ejection of subatomic particles at nearly the speed of light. The gamma-ray and X-ray burst lasts no more than a few minutes, while the ejected particles, interacting with the star's magnetic field, can produce detectable amounts of radio emission for several days. On August 27, the SGR called 1900+14 underwent a tremendous burst, the likes of which had not been seen since 1979. "For a number of years now, I've been routinely looking toward the region of sky where we thought this thing might be," said Frail, "hoping the magnetar would show itself." It did not disappoint; on September 3, the VLA found a new source of radio emission where one had not previously existed. The source quickly faded from view one week later. The immediate importance of this finding is that it provides a new and independent confirmation of the magnetar model. These impulsive particle "winds," predicted by theory, carry as much energy as the flashes of hard X-ray emission and are important in slowing down the spinning magnetar. This discovery also allows astronomers to pinpoint the exact location of the SGR to allow further study of the magnetar with other powerful telescopes. "Trying to find this source of gamma-rays was like nighttime sailing with a broken lighthouse; now, we're no longer in the dark, and can study the magnetar for years to come," said Bloom. In time, the free-flowing particle wind can inflate a nebula called a plerion. "This 'windbag nebula' can tell us a lot about the outflow of particles and the burst history of the object," Frail said. "In fact, studying this phenomenon can give us information about the magnetar that we can't learn any other way." The VLA is an instrument of the National Radio Astronomy Observatory, a facility of the National Science Foundation, operated under cooperative agreement by Associated Universities, Inc.

  10. Cosmic Structure and Galaxy Evolution through Intensity Mapping of Molecular Gas

    NASA Astrophysics Data System (ADS)

    Bower, Geoffrey C.; Keating, Garrett K.; Marrone, Daniel P.; YT Lee Array Team, SZA Team

    2016-01-01

    The origin and evolution of structure in the Universe is one of the major challenges of observational astronomy. How does baryonic structure trace the underlying dark matter? How have galaxies evolved to produce the present day Universe? A multi-wavelength, multi-tool approach is necessary to provide the complete story of the evolution of structure in the Universe. Intensity mapping, which relies on the ability to detect many objects at once through their integrated emission rather than direct detection of individual objects, is a critical part of this mosaic. In particular, our understanding of the molecular gas component of massive galaxies is being revolutionized by ALMA and EVLA but the population of smaller, star-forming galaxies, which provide the bulk of star formation cannot be individually probed by these instruments.In this talk, I will summarize two intensity mapping experiments to detect molecular gas through the carbon monoxide (CO) rotational transition. We have completed sensitive observations with the Sunyaev-Zel'dovic Array (SZA) telescope at a wavelength of 1 cm that are sensitive to emission at redshifts 2.3 to 3.3. The SZA experiments sets strong limits on models for the CO emission and demonstrates the ability to reject foregrounds and telescope systematics in very deep integrations. I also describe the development of an intensity mapping capability for the Y.T. Lee Array, a 13-element interferometer located on Mauna Loa. In its first phase, this project focuses on detection of CO at redshifts 2.4 - 3.0 with detection via power spectrum and cross-correlation with other surveys. The project includes a major technical upgrade, a new digital correlator and IF electronics component to be deployed in 2015/2016. The Y.T. Lee Array observations will be more sensitive and extend to larger angular scales than the SZA observations.

  11. Concept Maps in the Classroom: A New Approach to Reveal Students' Conceptual Change

    ERIC Educational Resources Information Center

    Sellmann, Daniela; Liefländer, Anne K.; Bogner, Franz X.

    2015-01-01

    When entering the classroom, adolescents already hold various conceptions on science topics. Concept maps may function as useful tools to reveal such conceptions although labor-intensive analysis often prevents application in typical classroom situations. The authors aimed to provide teachers with an appropriate approach to analyze students'…

  12. Revealing the flux: Using processed Husimi maps to visualize dynamics of bound systems and mesoscopic transport

    NASA Astrophysics Data System (ADS)

    Mason, Douglas J.; Borunda, Mario F.; Heller, Eric J.

    2015-04-01

    We elaborate upon the "processed Husimi map" representation for visualizing quantum wave functions using coherent states as a measurement of the local phase space to produce a vector field related to the probability flux. Adapted from the Husimi projection, the processed Husimi map is mathematically related to the flux operator under certain limits but offers a robust and flexible alternative since it can operate away from these limits and in systems that exhibit zero flux. The processed Husimi map is further capable of revealing the full classical dynamics underlying a quantum wave function since it reverse engineers the wave function to yield the underlying classical ray structure. We demonstrate the capabilities of processed Husimi maps on bound systems with and without electromagnetic fields, as well as on open systems on and off resonance, to examine the relationship between closed system eigenstates and mesoscopic transport.

  13. New features of global climatology revealed by satellite-derived oceanic rainfall maps

    NASA Technical Reports Server (NTRS)

    Rao, M. S. V.; Theon, J. S.

    1977-01-01

    Quantitative rainfall maps over the oceanic areas of the globe were derived from the Nimbus 5 Electrically Scanning Microwave Radiometer (ESMR) data. Analysis of satellite derived oceanic rainfall maps reveal certain distinctive characteristics of global patterns for the years 1973-74. The main ones are (1) the forking of the Intertropical Convergence Zone in the Pacific, (2) a previously unrecognized rain area in the South Atlantic, (3) the bimodal behavior of rainbelts in the Indian Ocean and (4) the large interannual variability in oceanic rainfall. These features are discussed.

  14. An Arabidopsis Transcriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors.

    PubMed

    Jin, Jinpu; He, Kun; Tang, Xing; Li, Zhe; Lv, Le; Zhao, Yi; Luo, Jingchu; Gao, Ge

    2015-07-01

    Transcription factors (TFs) play key roles in both development and stress responses. By integrating into and rewiring original systems, novel TFs contribute significantly to the evolution of transcriptional regulatory networks. Here, we report a high-confidence transcriptional regulatory map covering 388 TFs from 47 families in Arabidopsis. Systematic analysis of this map revealed the architectural heterogeneity of developmental and stress response subnetworks and identified three types of novel network motifs that are absent from unicellular organisms and essential for multicellular development. Moreover, TFs of novel families that emerged during plant landing present higher binding specificities and are preferentially wired into developmental processes and these novel network motifs. Further unveiled connection between the binding specificity and wiring preference of TFs explains the wiring preferences of novel-family TFs. These results reveal distinct functional and evolutionary features of novel TFs, suggesting a plausible mechanism for their contribution to the evolution of multicellular organisms. PMID:25750178

  15. Model-driven mapping of transcriptional networks reveals the circuitry and dynamics of virulence regulation.

    PubMed

    Maier, Ezekiel J; Haynes, Brian C; Gish, Stacey R; Wang, Zhuo A; Skowyra, Michael L; Marulli, Alyssa L; Doering, Tamara L; Brent, Michael R

    2015-05-01

    Key steps in understanding a biological process include identifying genes that are involved and determining how they are regulated. We developed a novel method for identifying transcription factors (TFs) involved in a specific process and used it to map regulation of the key virulence factor of a deadly fungus-its capsule. The map, built from expression profiles of 41 TF mutants, includes 20 TFs not previously known to regulate virulence attributes. It also reveals a hierarchy comprising executive, midlevel, and "foreman" TFs. When grouped by temporal expression pattern, these TFs explain much of the transcriptional dynamics of capsule induction. Phenotypic analysis of TF deletion mutants revealed complex relationships among virulence factors and virulence in mice. These resources and analyses provide the first integrated, systems-level view of capsule regulation and biosynthesis. Our methods dramatically improve the efficiency with which transcriptional networks can be analyzed, making genomic approaches accessible to laboratories focused on specific physiological processes. PMID:25644834

  16. Model-driven mapping of transcriptional networks reveals the circuitry and dynamics of virulence regulation

    PubMed Central

    Maier, Ezekiel J.; Haynes, Brian C.; Gish, Stacey R.; Wang, Zhuo A.; Skowyra, Michael L.; Marulli, Alyssa L.; Doering, Tamara L.; Brent, Michael R.

    2015-01-01

    Key steps in understanding a biological process include identifying genes that are involved and determining how they are regulated. We developed a novel method for identifying transcription factors (TFs) involved in a specific process and used it to map regulation of the key virulence factor of a deadly fungus—its capsule. The map, built from expression profiles of 41 TF mutants, includes 20 TFs not previously known to regulate virulence attributes. It also reveals a hierarchy comprising executive, midlevel, and “foreman” TFs. When grouped by temporal expression pattern, these TFs explain much of the transcriptional dynamics of capsule induction. Phenotypic analysis of TF deletion mutants revealed complex relationships among virulence factors and virulence in mice. These resources and analyses provide the first integrated, systems-level view of capsule regulation and biosynthesis. Our methods dramatically improve the efficiency with which transcriptional networks can be analyzed, making genomic approaches accessible to laboratories focused on specific physiological processes. PMID:25644834

  17. High-density linkage mapping revealed suppression of recombination at the sex determination locus in papaya.

    PubMed Central

    Ma, Hao; Moore, Paul H; Liu, Zhiyong; Kim, Minna S; Yu, Qingyi; Fitch, Maureen M M; Sekioka, Terry; Paterson, Andrew H; Ming, Ray

    2004-01-01

    A high-density genetic map of papaya (Carica papaya L.) was constructed using 54 F(2) plants derived from cultivars Kapoho and SunUp with 1501 markers, including 1498 amplified fragment length polymorphism (AFLP) markers, the papaya ringspot virus coat protein marker, morphological sex type, and fruit flesh color. These markers were mapped into 12 linkage groups at a LOD score of 5.0 and recombination frequency of 0.25. The 12 major linkage groups covered a total length of 3294.2 cM, with an average distance of 2.2 cM between adjacent markers. This map revealed severe suppression of recombination around the sex determination locus with a total of 225 markers cosegregating with sex types. The cytosine bases were highly methylated in this region on the basis of the distribution of methylation-sensitive and -insensitive markers. This high-density genetic map is essential for cloning of specific genes of interest such as the sex determination gene and for the integration of genetic and physical maps of papaya. PMID:15020433

  18. A cosmic web filament revealed in Lyman-α emission around a luminous high-redshift quasar.

    PubMed

    Cantalupo, Sebastiano; Arrigoni-Battaia, Fabrizio; Prochaska, J Xavier; Hennawi, Joseph F; Madau, Piero

    2014-02-01

    Simulations of structure formation in the Universe predict that galaxies are embedded in a 'cosmic web', where most baryons reside as rarefied and highly ionized gas. This material has been studied for decades in absorption against background sources, but the sparseness of these inherently one-dimensional probes preclude direct constraints on the three-dimensional morphology of the underlying web. Here we report observations of a cosmic web filament in Lyman-α emission, discovered during a survey for cosmic gas fluorescently illuminated by bright quasars at redshift z ≈ 2.3. With a linear projected size of approximately 460 physical kiloparsecs, the Lyman-α emission surrounding the radio-quiet quasar UM 287 extends well beyond the virial radius of any plausible associated dark-matter halo and therefore traces intergalactic gas. The estimated cold gas mass of the filament from the observed emission-about 10(12.0 ± 0.5)/C(1/2) solar masses, where C is the gas clumping factor-is more than ten times larger than what is typically found in cosmological simulations, suggesting that a population of intergalactic gas clumps with subkiloparsec sizes may be missing in current numerical models. PMID:24463517

  19. Comparative mapping in the Poaceae family reveals translocations in the complex polyploid genome of sugarcane

    PubMed Central

    2014-01-01

    Background The understanding of sugarcane genetics has lagged behind that of other members of the Poaceae family such as wheat, rice, barley and sorghum mainly due to the complexity, size and polyploidization of the genome. We have used the genetic map of a sugarcane cultivar to generate a consensus genetic map to increase genome coverage for comparison to the sorghum genome. We have utilized the recently developed sugarcane DArT array to increase the marker density within the genetic map. The sequence of these DArT markers plus SNP and EST-SSR markers was then used to form a bridge to the sorghum genomic sequence by BLAST alignment to start to unravel the complex genomic architecture of sugarcane. Results Comparative mapping revealed that certain sugarcane chromosomes show greater levels of synteny to sorghum than others. On a macrosyntenic level a good collinearity was observed between sugarcane and sorghum for 4 of the 8 homology groups (HGs). These 4 HGs were syntenic to four sorghum chromosomes with from 98% to 100% of these chromosomes covered by these linked markers. Four major chromosome rearrangements were identified between the other four sugarcane HGs and sorghum, two of which were condensations of chromosomes reducing the basic chromosome number of sugarcane from x = 10 to x = 8. This macro level of synteny was transferred to other members within the Poaceae family such as maize to uncover the important evolutionary relationships that exist between sugarcane and these species. Conclusions Comparative mapping of sugarcane to the sorghum genome has revealed new information on the genome structure of sugarcane which will help guide identification of important genes for use in sugarcane breeding. Furthermore of the four major chromosome rearrangements identified in this study, three were common to maize providing some evidence that chromosome reduction from a common paleo-ancestor of both maize and sugarcane was driven by the same translocation

  20. The Structure of the MAP2K MEK6 Reveals an Autoinhibitory Dimer

    SciTech Connect

    Min, Xiaoshan; Akella, Radha; He, Haixia; Humphreys, John M.; Tsutakawa, Susan E.; Lee, Seung-Jae; Tainer, John A.; Cobb, Melanie H.; Goldsmith, Elizabeth J.

    2009-07-13

    MAP2Ks are dual-specificity protein kinases functioning at the center of three-tiered MAP kinase modules. The structure of the kinase domain of the MAP2K MEK6 with phosphorylation site mimetic aspartic acid mutations (MEK6/{Delta}N/DD) has been solved at 2.3 {angstrom} resolution. The structure reveals an autoinhibited elongated ellipsoidal dimer. The enzyme adopts an inactive conformation, based upon structural queues, despite the phosphomimetic mutations. Gel filtration and small-angle X-ray scattering analysis confirm that the crystallographically observed ellipsoidal dimer is a feature of MEK6/{Delta}N/DD and full-length unphosphorylated wild-type MEK6 in solution. The interface includes the phosphate binding ribbon of each subunit, part of the activation loop, and a rare 'arginine stack' between symmetry-related arginine residues in the N-terminal lobe. The autoinhibited structure likely confers specificity on active MAP2Ks. The dimer may also serve the function in unphosphorylated MEK6 of preventing activation loop phosphorylation by inappropriate kinases.

  1. Virtual adult ears reveal the roles of acoustical factors and experience in auditory space map development

    PubMed Central

    Campbell, Robert A. A.; King, Andrew J.; Nodal, Fernando R.; Schnupp, Jan W. H.; Carlile, Simon; Doubell, Timothy P.

    2009-01-01

    Auditory neurons in the superior colliculus (SC) respond preferentially to sounds from restricted directions to form a map of auditory space. The development of this representation is shaped by sensory experience, but little is known about the relative contribution of peripheral and central factors to the emergence of adult responses. By recording from the SC of anesthetized ferrets at different age points, we show that the map matures gradually after birth; the spatial receptive fields (SRFs) become more sharply tuned and topographic order emerges by the end of the second postnatal month. Principal components analysis of the head-related transfer function revealed that the time course of map development is mirrored by the maturation of the spatial cues generated by the growing head and external ears. However, using virtual acoustic space stimuli, we show that these acoustical changes are not by themselves responsible for the emergence of SC map topography. Presenting stimuli to infant ferrets through virtual adult ears did not improve the order in the representation of sound azimuth in the SC. But using linear discriminant analysis to compare different response properties across age, we found that the SRFs of infant neurons nevertheless became more adult-like when stimuli were delivered through virtual adult ears. Hence, although the emergence of auditory topography is likely to depend on refinements in neural circuitry, maturation of the structure of the SRFs (particularly their spatial extent) can be largely accounted for by changes in the acoustics associated with growth of the head and ears. PMID:18987192

  2. Virtual adult ears reveal the roles of acoustical factors and experience in auditory space map development.

    PubMed

    Campbell, Robert A A; King, Andrew J; Nodal, Fernando R; Schnupp, Jan W H; Carlile, Simon; Doubell, Timothy P

    2008-11-01

    Auditory neurons in the superior colliculus (SC) respond preferentially to sounds from restricted directions to form a map of auditory space. The development of this representation is shaped by sensory experience, but little is known about the relative contribution of peripheral and central factors to the emergence of adult responses. By recording from the SC of anesthetized ferrets at different age points, we show that the map matures gradually after birth; the spatial receptive fields (SRFs) become more sharply tuned and topographic order emerges by the end of the second postnatal month. Principal components analysis of the head-related transfer function revealed that the time course of map development is mirrored by the maturation of the spatial cues generated by the growing head and external ears. However, using virtual acoustic space stimuli, we show that these acoustical changes are not by themselves responsible for the emergence of SC map topography. Presenting stimuli to infant ferrets through virtual adult ears did not improve the order in the representation of sound azimuth in the SC. But by using linear discriminant analysis to compare different response properties across age, we found that the SRFs of infant neurons nevertheless became more adult-like when stimuli were delivered through virtual adult ears. Hence, although the emergence of auditory topography is likely to depend on refinements in neural circuitry, maturation of the structure of the SRFs (particularly their spatial extent) can be largely accounted for by changes in the acoustics associated with growth of the head and ears. PMID:18987192

  3. Microsatellite marker based genetic linkage maps of Oreochromis aureus and O. niloticus (Cichlidae): extensive linkage group segment homologies revealed.

    PubMed

    McConnell, S K; Beynon, C; Leamon, J; Skibinski, D O

    2000-06-01

    Partial genetic linkage maps, based on microsatellite markers, were constructed for two tilapia species, Oreochromis aureus and Oreochromis niloticus using an interspecific backcross population. The linkage map for O. aureus comprised 28 markers on 10 linkage groups and covered 212.8 CM. Nine markers were mapped to four linkage groups on an O. niloticus female linkage map covering 40.6 CM. Results revealed a high degree of conservation of synteny between the linkage groups defined in O. aureus and the previously published genetic linkage map of O. niloticus. PMID:10895314

  4. Internal wave activity in the polar atmospheric regions during 2006 - 2009 revealed by COSMIC radio occultation data

    NASA Astrophysics Data System (ADS)

    Kirillovich, Ivan; Gubenko, Vladimir; Pavelyev, Alexander; Liou, Yuei-An

    The satellite mission Formosat-3/COSMIC (Constellation Observing System for Meteorology, Ionosphere and Climate) consists of six micro-satellites, and each of them has four GPS-antennas. It was launched in April 2006, orbiting around the Earth at approximately 800 km. The primary scientific goal of the mission is to demonstrate the value of near-real-time radio occultation (RO) observations in improving operational numerical weather predictions (NWP). The goal is readily shown by assimilating the measurements of atmospheric parameters into used NWP-models. These parameters include density, temperature, pressure and relative humidity fields in the atmosphere. An analysis of their geographic and seasonal distributions is necessary to the understanding of the energy and momentum transfer and the reaction of the polar atmosphere in response to global warming. This task is especially important as the Polar Regions are very sensitive to the change in global temperature and it may be a major cause of global sea level rising. In this work, a statistical analysis of the internal gravity wave (IGW) activity in polar atmospheric regions (latitudes more than 60º) using Formosat-3/COSMIC RO temperature data collected from July 2006 to March 2009 has been performed. Geographic and seasonal distributions of the IGW potential energy (wave activity indicator) in the altitude interval from 15 to 35 km have been determined and analyzed. The obtained results show that the wave activity in the polar atmosphere is strong in winter and spring. The potential energy of IGWs in spring is largest in Antarctic atmospheric region, while it is largest in winter in Arctic region. The wave potential energy increases with altitude up to 35 km in the atmosphere of both Earth’s hemispheres. In Antarctic region, internal waves with high potential energy occur in the atmosphere over the Antarctic Peninsula. In Arctic region, a high wave activity is mainly observed over North Atlantic Ocean (Iceland

  5. Optogenetic mapping of cerebellar inhibitory circuitry reveals spatially biased coordination of interneurons via electrical synapses.

    PubMed

    Kim, Jinsook; Lee, Soojung; Tsuda, Sachiko; Zhang, Xuying; Asrican, Brent; Gloss, Bernd; Feng, Guoping; Augustine, George J

    2014-06-12

    We used high-speed optogenetic mapping technology to examine the spatial organization of local inhibitory circuits formed by cerebellar interneurons. Transgenic mice expressing channelrhodopsin-2 exclusively in molecular layer interneurons allowed us to focally photostimulate these neurons, while measuring resulting responses in postsynaptic Purkinje cells. This approach revealed that interneurons converge upon Purkinje cells over a broad area and that at least seven interneurons form functional synapses with a single Purkinje cell. The number of converging interneurons was reduced by treatment with gap junction blockers, revealing that electrical synapses between interneurons contribute substantially to the spatial convergence. Remarkably, gap junction blockers affected convergence in sagittal slices, but not in coronal slices, indicating a sagittal bias in electrical coupling between interneurons. We conclude that electrical synapse networks spatially coordinate interneurons in the cerebellum and may also serve this function in other brain regions. PMID:24857665

  6. The Brain-to-Pancreatic Islet Neuronal Map Reveals Differential Glucose Regulation From Distinct Hypothalamic Regions.

    PubMed

    Rosario, Wilfredo; Singh, Inderroop; Wautlet, Arnaud; Patterson, Christa; Flak, Jonathan; Becker, Thomas C; Ali, Almas; Tamarina, Natalia; Philipson, Louis H; Enquist, Lynn W; Myers, Martin G; Rhodes, Christopher J

    2016-09-01

    The brain influences glucose homeostasis, partly by supplemental control over insulin and glucagon secretion. Without this central regulation, diabetes and its complications can ensue. Yet, the neuronal network linking to pancreatic islets has never been fully mapped. Here, we refine this map using pseudorabies virus (PRV) retrograde tracing, indicating that the pancreatic islets are innervated by efferent circuits that emanate from the hypothalamus. We found that the hypothalamic arcuate nucleus (ARC), ventromedial nucleus (VMN), and lateral hypothalamic area (LHA) significantly overlap PRV and the physiological glucose-sensing enzyme glucokinase. Then, experimentally lowering glucose sensing, specifically in the ARC, resulted in glucose intolerance due to deficient insulin secretion and no significant effect in the VMN, but in the LHA it resulted in a lowering of the glucose threshold that improved glucose tolerance and/or improved insulin sensitivity, with an exaggerated counter-regulatory response for glucagon secretion. No significant effect on insulin sensitivity or metabolic homeostasis was noted. Thus, these data reveal novel direct neuronal effects on pancreatic islets and also render a functional validation of the brain-to-islet neuronal map. They also demonstrate that distinct regions of the hypothalamus differentially control insulin and glucagon secretion, potentially in partnership to help maintain glucose homeostasis and guard against hypoglycemia. PMID:27207534

  7. Genetic Interaction Maps in Escherichia coli Reveal Functional Crosstalk among Cell Envelope Biogenesis Pathways

    PubMed Central

    Vlasblom, James; Gagarinova, Alla; Phanse, Sadhna; Graham, Chris; Yousif, Fouad; Ding, Huiming; Xiong, Xuejian; Nazarians-Armavil, Anaies; Alamgir, Md; Ali, Mehrab; Pogoutse, Oxana; Pe'er, Asaf; Arnold, Roland; Michaut, Magali; Parkinson, John; Golshani, Ashkan; Whitfield, Chris; Wodak, Shoshana J.; Moreno-Hagelsieb, Gabriel; Greenblatt, Jack F.; Emili, Andrew

    2011-01-01

    As the interface between a microbe and its environment, the bacterial cell envelope has broad biological and clinical significance. While numerous biosynthesis genes and pathways have been identified and studied in isolation, how these intersect functionally to ensure envelope integrity during adaptive responses to environmental challenge remains unclear. To this end, we performed high-density synthetic genetic screens to generate quantitative functional association maps encompassing virtually the entire cell envelope biosynthetic machinery of Escherichia coli under both auxotrophic (rich medium) and prototrophic (minimal medium) culture conditions. The differential patterns of genetic interactions detected among >235,000 digenic mutant combinations tested reveal unexpected condition-specific functional crosstalk and genetic backup mechanisms that ensure stress-resistant envelope assembly and maintenance. These networks also provide insights into the global systems connectivity and dynamic functional reorganization of a universal bacterial structure that is both broadly conserved among eubacteria (including pathogens) and an important target. PMID:22125496

  8. Genetic tracing reveals a stereotyped sensory map in the olfactory cortex

    NASA Astrophysics Data System (ADS)

    Zou, Zhihua; Horowitz, Lisa F.; Montmayeur, Jean-Pierre; Snapper, Scott; Buck, Linda B.

    2001-11-01

    The olfactory system translates myriad chemical structures into diverse odour perceptions. To gain insight into how this is accomplished, we prepared mice that coexpressed a transneuronal tracer with only one of about 1,000 different odorant receptors. The tracer travelled from nasal neurons expressing that receptor to the olfactory bulb and then to the olfactory cortex, allowing visualization of cortical neurons that receive input from a particular odorant receptor. These studies revealed a stereotyped sensory map in the olfactory cortex in which signals from a particular receptor are targeted to specific clusters of neurons. Inputs from different receptors overlap spatially and could be combined in single neurons, potentially allowing for an integration of the components of an odorant's combinatorial receptor code. Signals from the same receptor are targeted to multiple olfactory cortical areas, permitting the parallel, and perhaps differential, processing of inputs from a single receptor before delivery to the neocortex and limbic system.

  9. THREE-DIMENSIONAL DUST MAPPING REVEALS THAT ORION FORMS PART OF A LARGE RING OF DUST

    SciTech Connect

    Schlafly, E. F.; Rix, H.-W.; Martin, N. F.; Green, G.; Finkbeiner, D. P.; Burgett, W. S.; Chambers, K. C.; Kaiser, N.; Morgan, J. S.; Tonry, J. L.; Wainscoat, R. J.; Waters, C.; Draper, P. W.; Metcalfe, N.; Price, P. A.

    2015-02-01

    The Orion Molecular Complex is the nearest site of ongoing high-mass star formation, making it one of the most extensively studied molecular complexes in the Galaxy. We have developed a new technique for mapping the three-dimensional distribution of dust in the Galaxy using Pan-STARRS1 photometry. We isolate the dust at the distance to Orion using this technique, revealing a large (100 pc, 14° diameter), previously unrecognized ring of dust, which we term the ''Orion dust ring''. The ring includes Orion A and B, and is not coincident with current Hα features. The circular morphology suggests formation as an ancient bubble in the interstellar medium, though we have not been able to conclusively identify the source of the bubble. This hint at the history of Orion may have important consequences for models of high-mass star formation and triggered star formation.

  10. Proteome Mapping of Adult Zebrafish Marrow Neutrophils Reveals Partial Cross Species Conservation to Human Peripheral Neutrophils

    PubMed Central

    Singh, Sachin Kumar; Sethi, Sachin; Aravamudhan, Sriram; Krüger, Marcus; Grabher, Clemens

    2013-01-01

    Neutrophil granulocytes are pivotal cells within the first line of host defense of the innate immune system. In this study, we have used a gel-based LC-MS/MS approach to explore the proteome of primary marrow neutrophils from adult zebrafish. The identified proteins originated from all major cellular compartments. Gene ontology analysis revealed significant association of proteins with different immune-related network and pathway maps. 75% of proteins identified in neutrophils were identified in neutrophils only when compared to neutrophil-free brain tissue. Moreover, cross-species comparison with human peripheral blood neutrophils showed partial conservation of immune-related proteins between human and zebrafish. This study provides the first zebrafish neutrophil proteome and may serve as a valuable resource for an understanding of neutrophil biology and innate immunity. PMID:24019943

  11. A map of rice genome variation reveals the origin of cultivated rice.

    PubMed

    Huang, Xuehui; Kurata, Nori; Wei, Xinghua; Wang, Zi-Xuan; Wang, Ahong; Zhao, Qiang; Zhao, Yan; Liu, Kunyan; Lu, Hengyun; Li, Wenjun; Guo, Yunli; Lu, Yiqi; Zhou, Congcong; Fan, Danlin; Weng, Qijun; Zhu, Chuanrang; Huang, Tao; Zhang, Lei; Wang, Yongchun; Feng, Lei; Furuumi, Hiroyasu; Kubo, Takahiko; Miyabayashi, Toshie; Yuan, Xiaoping; Xu, Qun; Dong, Guojun; Zhan, Qilin; Li, Canyang; Fujiyama, Asao; Toyoda, Atsushi; Lu, Tingting; Feng, Qi; Qian, Qian; Li, Jiayang; Han, Bin

    2012-10-25

    Crop domestications are long-term selection experiments that have greatly advanced human civilization. The domestication of cultivated rice (Oryza sativa L.) ranks as one of the most important developments in history. However, its origins and domestication processes are controversial and have long been debated. Here we generate genome sequences from 446 geographically diverse accessions of the wild rice species Oryza rufipogon, the immediate ancestral progenitor of cultivated rice, and from 1,083 cultivated indica and japonica varieties to construct a comprehensive map of rice genome variation. In the search for signatures of selection, we identify 55 selective sweeps that have occurred during domestication. In-depth analyses of the domestication sweeps and genome-wide patterns reveal that Oryza sativa japonica rice was first domesticated from a specific population of O. rufipogon around the middle area of the Pearl River in southern China, and that Oryza sativa indica rice was subsequently developed from crosses between japonica rice and local wild rice as the initial cultivars spread into South East and South Asia. The domestication-associated traits are analysed through high-resolution genetic mapping. This study provides an important resource for rice breeding and an effective genomics approach for crop domestication research. PMID:23034647

  12. Modeling development and quantitative trait mapping reveal independent genetic modules for leaf size and shape.

    PubMed

    Baker, Robert L; Leong, Wen Fung; Brock, Marcus T; Markelz, R J Cody; Covington, Michael F; Devisetty, Upendra K; Edwards, Christine E; Maloof, Julin; Welch, Stephen; Weinig, Cynthia

    2015-10-01

    Improved predictions of fitness and yield may be obtained by characterizing the genetic controls and environmental dependencies of organismal ontogeny. Elucidating the shape of growth curves may reveal novel genetic controls that single-time-point (STP) analyses do not because, in theory, infinite numbers of growth curves can result in the same final measurement. We measured leaf lengths and widths in Brassica rapa recombinant inbred lines (RILs) throughout ontogeny. We modeled leaf growth and allometry as function valued traits (FVT), and examined genetic correlations between these traits and aspects of phenology, physiology, circadian rhythms and fitness. We used RNA-seq to construct a SNP linkage map and mapped trait quantitative trait loci (QTL). We found genetic trade-offs between leaf size and growth rate FVT and uncovered differences in genotypic and QTL correlations involving FVT vs STPs. We identified leaf shape (allometry) as a genetic module independent of length and width and identified selection on FVT parameters of development. Leaf shape is associated with venation features that affect desiccation resistance. The genetic independence of leaf shape from other leaf traits may therefore enable crop optimization in leaf shape without negative effects on traits such as size, growth rate, duration or gas exchange. PMID:26083847

  13. GWA Mapping of Anthocyanin Accumulation Reveals Balancing Selection of MYB90 in Arabidopsis thaliana

    PubMed Central

    Bac-Molenaar, Johanna A.; Fradin, Emilie F.; Rienstra, Juriaan A.; Vreugdenhil, Dick; Keurentjes, Joost J. B.

    2015-01-01

    Induction of anthocyanin accumulation by osmotic stress was assessed in 360 accessions of Arabidopsis thaliana. A wide range of natural variation, with phenotypes ranging from green to completely red/purple rosettes, was observed. A genome wide association (GWA) mapping approach revealed that sequence diversity in a small 15 kb region on chromosome 1 explained 40% of the variation observed. Sequence and expression analyses of alleles of the candidate gene MYB90 identified a causal polymorphism at amino acid (AA) position 210 of this transcription factor of the anthocyanin biosynthesis pathway. This amino acid discriminates the two most frequent alleles of MYB90. Both alleles are present in a substantial part of the population, suggesting balancing selection between these two alleles. Analysis of the geographical origin of the studied accessions suggests that the macro climate is not the driving force behind positive or negative selection for anthocyanin accumulation. An important role for local climatic conditions is, therefore, suggested. This study emphasizes that GWA mapping is a powerful approach to identify alleles that are under balancing selection pressure in nature. PMID:26588092

  14. Linkage Mapping Reveals Strong Chiasma Interference in Sockeye Salmon: Implications for Interpreting Genomic Data

    PubMed Central

    Limborg, Morten T.; Waples, Ryan K.; Allendorf, Fred W.; Seeb, James E.

    2015-01-01

    Meiotic recombination is fundamental for generating new genetic variation and for securing proper disjunction. Further, recombination plays an essential role during the rediploidization process of polyploid-origin genomes because crossovers between pairs of homeologous chromosomes retain duplicated regions. A better understanding of how recombination affects genome evolution is crucial for interpreting genomic data; unfortunately, current knowledge mainly originates from a few model species. Salmonid fishes provide a valuable system for studying the effects of recombination in nonmodel species. Salmonid females generally produce thousands of embryos, providing large families for conducting inheritance studies. Further, salmonid genomes are currently rediploidizing after a whole genome duplication and can serve as models for studying the role of homeologous crossovers on genome evolution. Here, we present a detailed interrogation of recombination patterns in sockeye salmon (Oncorhynchus nerka). First, we use RAD sequencing of haploid and diploid gynogenetic families to construct a dense linkage map that includes paralogous loci and location of centromeres. We find a nonrandom distribution of paralogs that mainly cluster in extended regions distally located on 11 different chromosomes, consistent with ongoing homeologous recombination in these regions. We also estimate the strength of interference across each chromosome; results reveal strong interference and crossovers are mostly limited to one per arm. Interference was further shown to continue across centromeres, but metacentric chromosomes generally had at least one crossover on each arm. We discuss the relevance of these findings for both mapping and population genomic studies. PMID:26384769

  15. A negative genetic interaction map in isogenic cancer cell lines reveals cancer cell vulnerabilities

    PubMed Central

    Vizeacoumar, Franco J; Arnold, Roland; Vizeacoumar, Frederick S; Chandrashekhar, Megha; Buzina, Alla; Young, Jordan T F; Kwan, Julian H M; Sayad, Azin; Mero, Patricia; Lawo, Steffen; Tanaka, Hiromasa; Brown, Kevin R; Baryshnikova, Anastasia; Mak, Anthony B; Fedyshyn, Yaroslav; Wang, Yadong; Brito, Glauber C; Kasimer, Dahlia; Makhnevych, Taras; Ketela, Troy; Datti, Alessandro; Babu, Mohan; Emili, Andrew; Pelletier, Laurence; Wrana, Jeff; Wainberg, Zev; Kim, Philip M; Rottapel, Robert; O'Brien, Catherine A; Andrews, Brenda; Boone, Charles; Moffat, Jason

    2013-01-01

    Improved efforts are necessary to define the functional product of cancer mutations currently being revealed through large-scale sequencing efforts. Using genome-scale pooled shRNA screening technology, we mapped negative genetic interactions across a set of isogenic cancer cell lines and confirmed hundreds of these interactions in orthogonal co-culture competition assays to generate a high-confidence genetic interaction network of differentially essential or differential essentiality (DiE) genes. The network uncovered examples of conserved genetic interactions, densely connected functional modules derived from comparative genomics with model systems data, functions for uncharacterized genes in the human genome and targetable vulnerabilities. Finally, we demonstrate a general applicability of DiE gene signatures in determining genetic dependencies of other non-isogenic cancer cell lines. For example, the PTEN−/− DiE genes reveal a signature that can preferentially classify PTEN-dependent genotypes across a series of non-isogenic cell lines derived from the breast, pancreas and ovarian cancers. Our reference network suggests that many cancer vulnerabilities remain to be discovered through systematic derivation of a network of differentially essential genes in an isogenic cancer cell model. PMID:24104479

  16. RNA Duplex Map in Living Cells Reveals Higher-Order Transcriptome Structure.

    PubMed

    Lu, Zhipeng; Zhang, Qiangfeng Cliff; Lee, Byron; Flynn, Ryan A; Smith, Martin A; Robinson, James T; Davidovich, Chen; Gooding, Anne R; Goodrich, Karen J; Mattick, John S; Mesirov, Jill P; Cech, Thomas R; Chang, Howard Y

    2016-05-19

    RNA has the intrinsic property to base pair, forming complex structures fundamental to its diverse functions. Here, we develop PARIS, a method based on reversible psoralen crosslinking for global mapping of RNA duplexes with near base-pair resolution in living cells. PARIS analysis in three human and mouse cell types reveals frequent long-range structures, higher-order architectures, and RNA-RNA interactions in trans across the transcriptome. PARIS determines base-pairing interactions on an individual-molecule level, revealing pervasive alternative conformations. We used PARIS-determined helices to guide phylogenetic analysis of RNA structures and discovered conserved long-range and alternative structures. XIST, a long noncoding RNA (lncRNA) essential for X chromosome inactivation, folds into evolutionarily conserved RNA structural domains that span many kilobases. XIST A-repeat forms complex inter-repeat duplexes that nucleate higher-order assembly of the key epigenetic silencing protein SPEN. PARIS is a generally applicable and versatile method that provides novel insights into the RNA structurome and interactome. VIDEO ABSTRACT. PMID:27180905

  17. Mapping replication dynamics in Trypanosoma brucei reveals a link with telomere transcription and antigenic variation

    PubMed Central

    Devlin, Rebecca; Marques, Catarina A; Paape, Daniel; Prorocic, Marko; Zurita-Leal, Andrea C; Campbell, Samantha J; Lapsley, Craig; Dickens, Nicholas; McCulloch, Richard

    2016-01-01

    Survival of Trypanosoma brucei depends upon switches in its protective Variant Surface Glycoprotein (VSG) coat by antigenic variation. VSG switching occurs by frequent homologous recombination, which is thought to require locus-specific initiation. Here, we show that a RecQ helicase, RECQ2, acts to repair DNA breaks, including in the telomeric site of VSG expression. Despite this, RECQ2 loss does not impair antigenic variation, but causes increased VSG switching by recombination, arguing against models for VSG switch initiation through direct generation of a DNA double strand break (DSB). Indeed, we show DSBs inefficiently direct recombination in the VSG expression site. By mapping genome replication dynamics, we reveal that the transcribed VSG expression site is the only telomeric site that is early replicating – a differential timing only seen in mammal-infective parasites. Specific association between VSG transcription and replication timing reveals a model for antigenic variation based on replication-derived DNA fragility. DOI: http://dx.doi.org/10.7554/eLife.12765.001 PMID:27228154

  18. High-Resolution AUV Mapping Reveals Structural Details of Submarine Inflated Lava Flows

    NASA Astrophysics Data System (ADS)

    Paduan, J.; Clague, D. A.; Caress, D. W.; Thomas, H.; Thompson, D.; Conlin, D.

    2009-12-01

    The MBARI mapping AUV D. Allan B. has now been used to map volcanic terrain at mid-ocean ridges, back-arc spreading centers, and seamounts. These include the summit caldera and upper south rift zone at Axial Volcano, the summit of Davidson Seamount, the Endeavour hydrothermal fields, the Northeast Lau Spreading Center and West Mata Volcano, and, most recently, the CoAxial, North Cleft and North Gorda historic eruption sites on the Juan de Fuca and Gorda Ridges. ROV and submersible dives at most of these sites have provided groundtruth for the textures and features revealed in the roughly 1-m resolution maps. A prominent feature in the maps from four of the sites are inflated flows that did not deflate or drain. These resemble subaerial tumuli but differ in being located on level terrain, apparently atop or very near eruptive vents instead of being in the distal portions of flows. The largest inflated flow at Axial Volcano is on the caldera floor. The main part is 500 by 300 m, and up to 30 m high, with a lobe that extends another 750 m in a sinuous path. It and two nearby, medium-sized inflated flows were first described from sidescan imagery and a submersible dive by Appelgate and Embley (Bull. Volcanol., 54, 447-458, 1992). The AUV maps show clearly the smooth, gently domed relief of the large inflated flow and its sinuous shape on the seafloor, the medium-sized nearby inflated flows, and several additional smaller ones. Particularly striking is a network of 4 to 10 m deep cracks along the crest of each inflation. The cracks occur 30 to 50 m from the margins on all sides of the wider parts of the inflated flows, and become medial cracks along the entire length of the narrow parts, which are nearly triangular in cross-section. An inflation pit 35 m in diameter has a depth equal to the surrounding lava fields. ROV Doc Ricketts dove on these flows in August 2009 and photographed the deeply cracked, uplifted, once flat-lying lineated and ropy sheet flows that form

  19. OBJECTS APPEAR SMALLER AS THEY RECEDE: HOW PROPER MOTIONS CAN DIRECTLY REVEAL THE COSMIC EXPANSION, PROVIDE GEOMETRIC DISTANCES, AND MEASURE THE HUBBLE CONSTANT

    SciTech Connect

    Darling, Jeremy

    2013-11-10

    Objects and structures gravitationally decoupled from the Hubble expansion will appear to shrink in angular size as the universe expands. Observations of extragalactic proper motions can thus directly reveal the cosmic expansion. Relatively static structures such as galaxies or galaxy clusters can potentially be used to measure the Hubble constant, and test masses in large scale structures can measure the overdensity. Since recession velocities and angular separations can be precisely measured, apparent proper motions can also provide geometric distance measurements to static structures. The apparent fractional angular compression of static objects is 15 μas yr{sup –1} in the local universe; this motion is modulated by the overdensity in dynamic expansion-decoupled structures. We use the Titov et al. quasar proper motion catalog to examine the pairwise proper motion of a sparse network of test masses. Small-separation pairs (<200 Mpc comoving) are too few to measure the expected effect, yielding an inconclusive 8.3 ± 14.9 μas yr{sup –1}. Large-separation pairs (200-1500 Mpc) show no net convergence or divergence for z < 1, –2.7 ± 3.7 μas yr{sup –1}, consistent with pure Hubble expansion and significantly inconsistent with static structures, as expected. For all pairs a 'null test' gives –0.36 ± 0.62 μas yr{sup –1}, consistent with Hubble expansion and excludes a static locus at ∼5-10σ significance for z ≅ 0.5-2.0. The observed large-separation pairs provide a reference frame for small-separation pairs that will significantly deviate from the Hubble flow. The current limitation is the number of small-separation objects with precise astrometry, but Gaia will address this and will likely detect the cosmic recession.

  20. OT2_alopezse_3: Mapping the cosmic ray ionisation rate across the Northern end of the Orion A iant molecular cloud

    NASA Astrophysics Data System (ADS)

    López-Sepulcre, A.

    2011-09-01

    Cosmic rays (CR) are ubiquitous in the Galaxy and have the important role of ionizing the dens gas of the ISM. New Herschel observations have shown the huge diagnostic power of the OH+ fundamental transition to measure the CR ionization rate in diffuse clouds. Based on previous "serendipity" observations toward OMC2-FIR4 within the KP CHESS, we discovered a tenuous foreground cloud absorbing the fundamental OH+ line. Similarly, Gupta et al. (2010) found an OH+ absorption component at a similar velocity towards Orion KL and estimated a large CR ionization rate more than 10 times larger than the average value observed in diffuse clouds . We propose here to roughly map the CR ionization rate in the direction of the OMC2 and OMC3 complex to understand its extent, nature, and, finally, the source of ionization.

  1. The anatomy of visuospatial construction revealed by lesion-symptom mapping.

    PubMed

    Biesbroek, J Matthijs; van Zandvoort, Martine J E; Kuijf, Hugo J; Weaver, Nick A; Kappelle, L Jaap; Vos, Pieter C; Velthuis, Birgitta K; Biessels, Geert Jan; Postma, Albert

    2014-09-01

    Visuospatial construction is a complex cognitive operation that is composed of a purely constructional component (visuoconstruction proper), and visuoperceptive, attentional, and decision-making components. The anatomical correlates of visuospatial construction and its cognitive subcomponents are poorly understood. The purpose of the present study was to determine the anatomical correlates of visuospatial construction by applying lesion-symptom mapping in a cohort of 111 patients with first-ever ischemic stroke. We employed the Rey-Osterrieth Complex Figure (ROCF) copy test and the Judgment of Line Orientation (JLO); both tests measure visuoperception, while only the ROCF has a constructional component. We first performed assumption-free voxel-based lesion-symptom mapping, which revealed large shared right hemispheric correlates for the ROCF and JLO in the frontal lobe, superior temporal lobe, and supramarginal gyrus. These shared anatomical correlates reflect the visuoperceptive component of the ROCF and JLO. Anatomical correlates were discordant in the right superior parietal lobule, and angular and middle occipital gyri: lesions in these regions were associated with poor performance on the ROCF, but not the JLO. Secondly, these findings were reproduced with a region of interest-based analysis that yielded a statistically significant correlation between infarct volume in the right inferior and superior parietal, angular and middle occipital cortices, and poor performance on the ROCF, but not the JLO. This discordance in anatomical correlates of the ROCF and JLO reflects the visuoconstructive component of the ROCF. These findings provide new insights in the anatomical correlates of the visuoperceptive and visuoconstructive components of the ROCF and provide evidence for a crucial role of the right inferior and superior parietal, angular and middle occipital gyri in visuoconstruction proper. PMID:25062545

  2. Cytogenomic mapping and bioinformatic mining reveal interacting brain expressed genes for intellectual disability

    PubMed Central

    2014-01-01

    Background Microarray analysis has been used as the first-tier genetic testing to detect chromosomal imbalances and copy number variants (CNVs) for pediatric patients with intellectual and developmental disabilities (ID/DD). To further investigate the candidate genes and underlying dosage-sensitive mechanisms related to ID, cytogenomic mapping of critical regions and bioinformatic mining of candidate brain-expressed genes (BEGs) and their functional interactions were performed. Critical regions of chromosomal imbalances and pathogenic CNVs were mapped by subtracting known benign CNVs from the Databases of Genomic Variants (DGV) and extracting smallest overlap regions with cases from DatabasE of Chromosomal Imbalance and Phenotype in Humans using Ensembl Resources (DECIPHER). BEGs from these critical regions were revealed by functional annotation using Database for Annotation, Visualization, and Integrated Discovery (DAVID) and by tissue expression pattern from Uniprot. Cross-region interrelations and functional networks of the BEGs were analyzed using Gene Relationships Across Implicated Loci (GRAIL) and Ingenuity Pathway Analysis (IPA). Results Of the 1,354 patients analyzed by oligonucleotide array comparative genomic hybridization (aCGH), pathogenic abnormalities were detected in 176 patients including genomic disorders in 66 patients (37.5%), subtelomeric rearrangements in 45 patients (25.6%), interstitial imbalances in 33 patients (18.8%), chromosomal structural rearrangements in 17 patients (9.7%) and aneuploidies in 15 patients (8.5%). Subtractive and extractive mapping defined 82 disjointed critical regions from the detected abnormalities. A total of 461 BEGs was generated from 73 disjointed critical regions. Enrichment of central nervous system specific genes in these regions was noted. The number of BEGs increased with the size of the regions. A list of 108 candidate BEGs with significant cross region interrelation was identified by GRAIL and five

  3. Evolution of Chromosome 6 of Solanum Species Revealed by Comparative Fluorescence in Situ Hybridization Mapping

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Comparative genome mapping is an important tool in evolutionary research. Here we demonstrate a comparative fluorescent in situ hybridization (FISH) mapping strategy. A set of 13 bacterial artificial chromosome (BAC) clones derived from potato chromosome 6 was used for FISH mapping in seven differen...

  4. A SNP based linkage map of the turkey genome reveals multiple intrachromosomal rearrangements between the Turkey and Chicken genomes

    PubMed Central

    2010-01-01

    Background The turkey (Meleagris gallopavo) is an important agricultural species that is the second largest contributor to the world's poultry meat production. The genomic resources of turkey provide turkey breeders with tools needed for the genetic improvement of commercial breeds of turkey for economically important traits. A linkage map of turkey is essential not only for the mapping of quantitative trait loci, but also as a framework to enable the assignment of sequence contigs to specific chromosomes. Comparative genomics with chicken provides insight into mechanisms of genome evolution and helps in identifying rare genomic events such as genomic rearrangements and duplications/deletions. Results Eighteen full sib families, comprising 1008 (35 F1 and 973 F2) birds, were genotyped for 775 single nucleotide polymorphisms (SNPs). Of the 775 SNPs, 570 were informative and used to construct a linkage map in turkey. The final map contains 531 markers in 28 linkage groups. The total genetic distance covered by these linkage groups is 2,324 centimorgans (cM) with the largest linkage group (81 loci) measuring 326 cM. Average marker interval for all markers across the 28 linkage groups is 4.6 cM. Comparative mapping of turkey and chicken revealed two inter-, and 57 intrachromosomal rearrangements between these two species. Conclusion Our turkey genetic map of 531 markers reveals a genome length of 2,324 cM. Our linkage map provides an improvement of previously published maps because of the more even distribution of the markers and because the map is completely based on SNP markers enabling easier and faster genotyping assays than the microsatellitemarkers used in previous linkage maps. Turkey and chicken are shown to have a highly conserved genomic structure with a relatively low number of inter-, and intrachromosomal rearrangements. PMID:21092123

  5. First-generation HapMap in Cajanus spp. reveals untapped variations in parental lines of mapping populations.

    PubMed

    Kumar, Vinay; Khan, Aamir W; Saxena, Rachit K; Garg, Vanika; Varshney, Rajeev K

    2016-08-01

    Whole genome re-sequencing (WGRS) was conducted on a panel of 20 Cajanus spp. accessions (crossing parentals of recombinant inbred lines, introgression lines, multiparent advanced generation intercross and nested association mapping population) comprising of two wild species and 18 cultivated species accessions. A total of 791.77 million paired-end reads were generated with an effective mapping depth of ~12X per accession. Analysis of WGRS data provided 5 465 676 genome-wide variations including 4 686 422 SNPs and 779 254 InDels across the accessions. Large structural variations in the form of copy number variations (2598) and presence and absence variations (970) were also identified. Additionally, 2 630 904 accession-specific variations comprising of 2 278 571 SNPs (86.6%), 166 243 deletions (6.3%) and 186 090 insertions (7.1%) were also reported. Identified polymorphic sites in this study provide the first-generation HapMap in Cajanus spp. which will be useful in mapping the genomic regions responsible for important traits. PMID:26821983

  6. Mapping of fiber quality QTLs reveals useful variation and footprints of cotton domestication using introgression lines.

    PubMed

    Zhang, Shu-Wen; Zhu, Xie-Fei; Feng, Liu-Chun; Gao, Xiang; Yang, Biao; Zhang, Tian-Zhen; Zhou, Bao-Liang

    2016-01-01

    Fiber quality improvement is a driving force for further cotton domestication and breeding. Here, QTLs for fiber quality were mapped in 115 introgression lines (ILs) first developed from two intraspecific populations of cultivated and feral cotton landraces. A total of 60 QTLs were found, which explained 2.03-16.85% of the phenotypic variance found in fiber quality traits. A total of 36 markers were associated with five fiber traits, 33 of which were found to be associated with QTLs in multiple environments. In addition, nine pairs of common QTLs were identified; namely, one pair of QTLs for fiber elongation, three pairs for fiber length, three pairs for fiber strength and two pairs for micronaire (qMICs). All common QTLs had additive effects in the same direction in both IL populations. We also found five QTL clusters, allowing cotton breeders to focus their efforts on regions of QTLs with the highest percentages of phenotypic variance. Our results also reveal footprints of domestication; for example, fourteen QTLs with positive effects were found to have remained in modern cultivars during domestication, and two negative qMICs that had never been reported before were found, suggesting that the qMICs regions may be eliminated during artificial selection. PMID:27549323

  7. Meditation effects within the hippocampal complex revealed by voxel-based morphometry and cytoarchitectonic probabilistic mapping.

    PubMed

    Luders, Eileen; Kurth, Florian; Toga, Arthur W; Narr, Katherine L; Gaser, Christian

    2013-01-01

    Scientific studies addressing anatomical variations in meditators' brains have emerged rapidly over the last few years, where significant links are most frequently reported with respect to gray matter (GM). To advance prior work, this study examined GM characteristics in a large sample of 100 subjects (50 meditators, 50 controls), where meditators have been practicing close to 20 years, on average. A standard, whole-brain voxel-based morphometry approach was applied and revealed significant meditation effects in the vicinity of the hippocampus, showing more GM in meditators than in controls as well as positive correlations with the number of years practiced. However, the hippocampal complex is regionally segregated by architecture, connectivity, and functional relevance. Thus, to establish differential effects within the hippocampal formation (cornu ammonis, fascia dentata, entorhinal cortex, subiculum) as well as the hippocampal-amygdaloid transition area, we utilized refined cytoarchitectonic probabilistic maps of (peri-) hippocampal subsections. Significant meditation effects were observed within the subiculum specifically. Since the subiculum is known to play a key role in stress regulation and meditation is an established form of stress reduction, these GM findings may reflect neuronal preservation in long-term meditators-perhaps due to an attenuated release of stress hormones and decreased neurotoxicity. PMID:23847572

  8. Metabolic connectivity mapping reveals effective connectivity in the resting human brain.

    PubMed

    Riedl, Valentin; Utz, Lukas; Castrillón, Gabriel; Grimmer, Timo; Rauschecker, Josef P; Ploner, Markus; Friston, Karl J; Drzezga, Alexander; Sorg, Christian

    2016-01-12

    Directionality of signaling among brain regions provides essential information about human cognition and disease states. Assessing such effective connectivity (EC) across brain states using functional magnetic resonance imaging (fMRI) alone has proven difficult, however. We propose a novel measure of EC, termed metabolic connectivity mapping (MCM), that integrates undirected functional connectivity (FC) with local energy metabolism from fMRI and positron emission tomography (PET) data acquired simultaneously. This method is based on the concept that most energy required for neuronal communication is consumed postsynaptically, i.e., at the target neurons. We investigated MCM and possible changes in EC within the physiological range using "eyes open" versus "eyes closed" conditions in healthy subjects. Independent of condition, MCM reliably detected stable and bidirectional communication between early and higher visual regions. Moreover, we found stable top-down signaling from a frontoparietal network including frontal eye fields. In contrast, we found additional top-down signaling from all major clusters of the salience network to early visual cortex only in the eyes open condition. MCM revealed consistent bidirectional and unidirectional signaling across the entire cortex, along with prominent changes in network interactions across two simple brain states. We propose MCM as a novel approach for inferring EC from neuronal energy metabolism that is ideally suited to study signaling hierarchies in the brain and their defects in brain disorders. PMID:26712010

  9. A genome-wide map of hyper-edited RNA reveals numerous new sites.

    PubMed

    Porath, Hagit T; Carmi, Shai; Levanon, Erez Y

    2014-01-01

    Adenosine-to-inosine editing is one of the most frequent post-transcriptional modifications, manifested as A-to-G mismatches when comparing RNA sequences with their source DNA. Recently, a number of RNA-seq data sets have been screened for the presence of A-to-G editing, and hundreds of thousands of editing sites identified. Here we show that existing screens missed the majority of sites by ignoring reads with excessive ('hyper') editing that do not easily align to the genome. We show that careful alignment and examination of the unmapped reads in RNA-seq studies reveal numerous new sites, usually many more than originally discovered, and in precisely those regions that are most heavily edited. Specifically, we discover 327,096 new editing sites in the heavily studied Illumina Human BodyMap data and more than double the number of detected sites in several published screens. We also identify thousands of new sites in mouse, rat, opossum and fly. Our results establish that hyper-editing events account for the majority of editing sites. PMID:25158696

  10. Functional brain mapping of the macaque related to spatial working memory as revealed by PET.

    PubMed

    Inoue, Masato; Mikami, Akichika; Ando, Ichiro; Tsukada, Hideo

    2004-01-01

    To define the cortical areas that subserve spatial working memory in a nonhuman primate, we measured regional cerebral blood flow (rCBF) with [(15)O]H(2)O and positron emission tomography while monkeys performed a visually guided saccade (VGS) task and an oculomotor delayed-response (ODR) task. Both Statistical Parametric Mapping and regions of interest-based analyses revealed an increase of rCBF in the area surrounding the principal sulcus (PS), the superior convexity, the anterior bank of the arcuate sulcus (AS), the lateral orbitofrontal cortex (lOFC), the frontal pole (FP), the anterior cingulate cortex (ACC), the lateral bank of the intraparietal sulcus (lIPS) and the prestriate cortex. In the prefrontal cortex (PS, superior convexity, AS, lOFC and FP), rCBF values correlated positively with ODR task performance scores. From the hippocampus, rCBF values correlated negatively with ODR task performance. From the AS, superior convexity, lOFC, FP, ACC and lIPS, rCBF values of the PS correlated positively with rCBF values and negatively with hippocampus rCBF values. These results suggest that neural circuitry in the prefrontal cortex directly contributes the spatial working memory processes and that, in spatial working memory processes, the posterior parietal cortex and hippocampus have a different role to the prefrontal cortex. PMID:14654462

  11. Mapping of fiber quality QTLs reveals useful variation and footprints of cotton domestication using introgression lines

    PubMed Central

    Zhang, Shu-Wen; Zhu, Xie-Fei; Feng, Liu-Chun; Gao, Xiang; Yang, Biao; Zhang, Tian-Zhen; Zhou, Bao-Liang

    2016-01-01

    Fiber quality improvement is a driving force for further cotton domestication and breeding. Here, QTLs for fiber quality were mapped in 115 introgression lines (ILs) first developed from two intraspecific populations of cultivated and feral cotton landraces. A total of 60 QTLs were found, which explained 2.03–16.85% of the phenotypic variance found in fiber quality traits. A total of 36 markers were associated with five fiber traits, 33 of which were found to be associated with QTLs in multiple environments. In addition, nine pairs of common QTLs were identified; namely, one pair of QTLs for fiber elongation, three pairs for fiber length, three pairs for fiber strength and two pairs for micronaire (qMICs). All common QTLs had additive effects in the same direction in both IL populations. We also found five QTL clusters, allowing cotton breeders to focus their efforts on regions of QTLs with the highest percentages of phenotypic variance. Our results also reveal footprints of domestication; for example, fourteen QTLs with positive effects were found to have remained in modern cultivars during domestication, and two negative qMICs that had never been reported before were found, suggesting that the qMICs regions may be eliminated during artificial selection. PMID:27549323

  12. A picture on the wall: innovative mapping reveals cold-water coral refuge in submarine canyon.

    PubMed

    Huvenne, Veerle A I; Tyler, Paul A; Masson, Doug G; Fisher, Elizabeth H; Hauton, Chris; Hühnerbach, Veit; Le Bas, Timothy P; Wolff, George A

    2011-01-01

    Cold-water corals are azooxanthellate species found throughout the ocean at water depths down to 5000 m. They occur in patches, reefs or large mound structures up to 380 m high, and as ecosystem engineers create important habitats for a diverse fauna. However, the majority of these habitats are now within reach of deep-sea bottom trawling. Many have been severely damaged or are under threat, despite recent protection initiatives. Here we present a cold-water coral habitat type that so far has been overlooked--quite literally--and that has received minimal impact from human activities. Vertical and overhanging cliffs in deep-sea canyons, revealed using an innovative approach to marine habitat mapping, are shown to provide the perfect substratum for extensive cold-water coral-based communities. Typical canyon-related processes, including locally enhanced internal tides and focussed downslope organic carbon transport, provide favourable environmental conditions (current regime, food input) to sustain the communities, even outside the optimal depth and density envelopes reported elsewhere in the NE Atlantic. Our findings show that deep-sea canyons can form natural refuges for faunal communities sensitive to anthropogenic disturbance, and have the potential to fulfil the crucial role of larval sources for the recolonisation of damaged sites elsewhere on the margin. PMID:22194903

  13. Metabolic connectivity mapping reveals effective connectivity in the resting human brain

    PubMed Central

    Riedl, Valentin; Utz, Lukas; Castrillón, Gabriel; Grimmer, Timo; Rauschecker, Josef P.; Drzezga, Alexander; Sorg, Christian

    2016-01-01

    Directionality of signaling among brain regions provides essential information about human cognition and disease states. Assessing such effective connectivity (EC) across brain states using functional magnetic resonance imaging (fMRI) alone has proven difficult, however. We propose a novel measure of EC, termed metabolic connectivity mapping (MCM), that integrates undirected functional connectivity (FC) with local energy metabolism from fMRI and positron emission tomography (PET) data acquired simultaneously. This method is based on the concept that most energy required for neuronal communication is consumed postsynaptically, i.e., at the target neurons. We investigated MCM and possible changes in EC within the physiological range using “eyes open” versus “eyes closed” conditions in healthy subjects. Independent of condition, MCM reliably detected stable and bidirectional communication between early and higher visual regions. Moreover, we found stable top-down signaling from a frontoparietal network including frontal eye fields. In contrast, we found additional top-down signaling from all major clusters of the salience network to early visual cortex only in the eyes open condition. MCM revealed consistent bidirectional and unidirectional signaling across the entire cortex, along with prominent changes in network interactions across two simple brain states. We propose MCM as a novel approach for inferring EC from neuronal energy metabolism that is ideally suited to study signaling hierarchies in the brain and their defects in brain disorders. PMID:26712010

  14. Genomic regions underlying agronomic traits in linseed (Linum usitatissimum L.) as revealed by association mapping.

    PubMed

    Soto-Cerda, Braulio J; Duguid, Scott; Booker, Helen; Rowland, Gordon; Diederichsen, Axel; Cloutier, Sylvie

    2014-01-01

    The extreme climate of the Canadian Prairies poses a major challenge to improve yield. Although it is possible to breed for yield per se, focusing on yield-related traits could be advantageous because of their simpler genetic architecture. The Canadian flax core collection of 390 accessions was genotyped with 464 simple sequence repeat markers, and phenotypic data for nine agronomic traits including yield, bolls per area, 1,000 seed weight, seeds per boll, start of flowering, end of flowering, plant height, plant branching, and lodging collected from up to eight environments was used for association mapping. Based on a mixed model (principal component analysis (PCA) + kinship matrix (K)), 12 significant marker-trait associations for six agronomic traits were identified. Most of the associations were stable across environments as revealed by multivariate analyses. Statistical simulation for five markers associated with 1000 seed weight indicated that the favorable alleles have additive effects. None of the modern cultivars carried the five favorable alleles and the maximum number of four observed in any accessions was mostly in breeding lines. Our results confirmed the complex genetic architecture of yield-related traits and the inherent difficulties associated with their identification while illustrating the potential for improvement through marker-assisted selection. PMID:24138336

  15. A Picture on the Wall: Innovative Mapping Reveals Cold-Water Coral Refuge in Submarine Canyon

    PubMed Central

    Huvenne, Veerle A. I.; Tyler, Paul A.; Masson, Doug G.; Fisher, Elizabeth H.; Hauton, Chris; Hühnerbach, Veit; Le Bas, Timothy P.; Wolff, George A.

    2011-01-01

    Cold-water corals are azooxanthellate species found throughout the ocean at water depths down to 5000 m. They occur in patches, reefs or large mound structures up to 380 m high, and as ecosystem engineers create important habitats for a diverse fauna. However, the majority of these habitats are now within reach of deep-sea bottom trawling. Many have been severely damaged or are under threat, despite recent protection initiatives. Here we present a cold-water coral habitat type that so far has been overlooked – quite literally – and that has received minimal impact from human activities. Vertical and overhanging cliffs in deep-sea canyons, revealed using an innovative approach to marine habitat mapping, are shown to provide the perfect substratum for extensive cold-water coral-based communities. Typical canyon-related processes, including locally enhanced internal tides and focussed downslope organic carbon transport, provide favourable environmental conditions (current regime, food input) to sustain the communities, even outside the optimal depth and density envelopes reported elsewhere in the NE Atlantic. Our findings show that deep-sea canyons can form natural refuges for faunal communities sensitive to anthropogenic disturbance, and have the potential to fulfil the crucial role of larval sources for the recolonisation of damaged sites elsewhere on the margin. PMID:22194903

  16. Cosmic Dawn

    NASA Astrophysics Data System (ADS)

    Zaldarriaga, Matias

    The following sections are included: * Rapporteur Talk by R. Ellis: Massive Black Holes: Evidence, Demographics and Cosmic Evolution * Rapporteur Talk by S. Furlanetto: The Cosmic Dawn: Theoretical Models and the Future

  17. Intensity Mapping of the History of Stellar Emission with the Cosmic Infrared Background ExpeRiment-2

    NASA Astrophysics Data System (ADS)

    Lanz, Alicia E.; Arai, Toshiaki; Battle, John; Bock, James; Cooray, Asantha R.; Hristov, Viktor; Korngut, Phillip; Lee, Dae Hee; Mason, Peter; Matsumoto, Toshio; Matsuura, Shuji; Onishi, Yosuke; Shirahata, Mai; Tsumurai, Kohji; Wada, Takehiko; Zemcov, Michael B.

    2016-01-01

    Recent measurements of the near-infrared Extragalactic Background Light (EBL) anisotropy find excess spatial power above the level predicted by known galaxy populations at large angular scales. These anisotropies trace spatial variations in integrated photon production, so measurements of EBL surface brightness fluctuations provide a complete census of the emission from stars summed over cosmic history. As a result, EBL fluctuations contain contributions from objects forming during the Epoch of Reionization (EOR), from the integrated galactic light (IGL), and faint, extended components such as intra-halo light (IHL) from stars tidally stripped from galaxies during merger events. Additional measurements with greater sensitivity, spectral range, and spectral resolution are required to disentangle these contributions.The Cosmic Infrared Background ExpeRiment 2 (CIBER-2) is an instrument optimized for the measurement of near-infrared EBL anisotropies. As the Earth's atmosphere generates time-varying near-infrared emission, CIBER-2 is launched on a sounding rocket from which it will carry out multiwavelength imaging in six spectral bands that span the visible to near-infrared. The 2.4 square degree images allow CIBER-2 to produce measurements of EBL fluctuations with high fidelity on large angular scales. The Lyman break feature from EOR sources provides a unique spectral feature which can be used to disentangle the high from the low redshift contributions to the anisotropy signal. Measurement in six independent wavebands allows detailed cross-correlation studies to constrain the source of the excess fluctuations at large angular scales. We provide an overview of the CIBER-2 instrument and explain CIBER-2 spectral feature identification and cross-correlation study methodologies.

  18. A High-Density SNP and SSR Consensus Map Reveals Segregation Distortion Regions in Wheat

    PubMed Central

    Li, Chunlian; Bai, Guihua; Chao, Shiaoman; Wang, Zhonghua

    2015-01-01

    Segregation distortion is a widespread phenomenon in plant and animal genomes and significantly affects linkage map construction and identification of quantitative trait loci (QTLs). To study segregation distortion in wheat, a high-density consensus map was constructed using single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers by merging two genetic maps developed from two recombinant-inbred line (RIL) populations, Ning7840 × Clark and Heyne × Lakin. Chromosome regions with obvious segregation distortion were identified in the map. A total of 3541 SNPs and 145 SSRs were mapped, and the map covered 3258.7 cM in genetic distance with an average interval of 0.88 cM. The number of markers that showed distorted segregation was 490 (18.5%) in the Ning7840 × Clark population and 225 (10.4%) in the Heyne × Lakin population. Most of the distorted markers (630) were mapped in the consensus map, which accounted for 17.1% of mapped markers. The majority of the distorted markers clustered in the segregation distortion regions (SDRs) on chromosomes 1B, 2A, 2B, 3A, 3B, 4B, 5A, 5B, 5D, 6B, 7A, and 7D. All of the markers in a given SDR skewed toward one of the parents, suggesting that gametophytic competition during zygote formation was most likely one of the causes for segregation distortion in the populations. PMID:26601111

  19. HST SPECTRAL MAPPING OF L/T TRANSITION BROWN DWARFS REVEALS CLOUD THICKNESS VARIATIONS

    SciTech Connect

    Apai, Daniel; Radigan, Jacqueline; Jayawardhana, Ray; Buenzli, Esther; Burrows, Adam; Reid, Iain Neill

    2013-05-10

    Most directly imaged giant exoplanets are fainter than brown dwarfs with similar spectra. To explain their relative underluminosity, unusually cloudy atmospheres have been proposed. However, with multiple parameters varying between any two objects, it remained difficult to observationally test this idea. We present a new method, sensitive time-resolved Hubble Space Telescope near-infrared spectroscopy, to study two rotating L/T transition brown dwarfs (2M2139 and SIMP0136). The observations provide spatially and spectrally resolved mapping of the cloud decks of the brown dwarfs. The data allow the study of cloud structure variations while other parameters are unchanged. We find that both brown dwarfs display variations of identical nature: J- and H-band brightness variations with minimal color and spectral changes. Our light curve models show that even the simplest surface brightness distributions require at least three elliptical spots. We show that for each source the spectral changes can be reproduced with a linear combination of only two different spectra, i.e., the entire surface is covered by two distinct types of regions. Modeling the color changes and spectral variations together reveal patchy cloud covers consisting of a spatially heterogeneous mix of low-brightness, low-temperature thick clouds and brighter, thin, and warm clouds. We show that the same thick cloud patches seen in our varying brown dwarf targets, if extended to the entire photosphere, predict near-infrared colors/magnitudes matching the range occupied by the directly imaged exoplanets that are cooler and less luminous than brown dwarfs with similar spectral types. This supports the models in which thick clouds are responsible for the near-infrared properties of these ''underluminous'' exoplanets.

  20. A microsatellite linkage map of striped bass (Morone saxatilis) reveals conserved synteny with the three-spined stickleback (Gasterosteus aculeatus).

    PubMed

    Liu, Sixin; Rexroad, Caird E; Couch, Charlene R; Cordes, Jan F; Reece, Kimberly S; Sullivan, Craig V

    2012-04-01

    The striped bass (Morone saxatilis) and its relatives (genus Morone) are of great importance to fisheries and aquaculture in North America. As part of a collaborative effort to employ molecular genetics technologies in striped bass breeding programs, we previously developed nearly 500 microsatellite markers. The objectives of this study were to construct a microsatellite linkage map of striped bass and to examine conserved synteny between striped bass and three-spined stickleback (Gasterosteus aculeatus). Of 480 microsatellite markers screened for polymorphism, 289 informative markers were identified and used to genotype two half-sib mapping families. Twenty-six linkage groups were assembled, and only two markers remain unlinked. The sex-averaged map spans 1,623.8 cM with an average marker density of 5.78 cM per marker. Among 287 striped bass microsatellite markers assigned to linkage groups, 169 (58.9%) showed homology to sequences on stickleback chromosomes or scaffolds. Comparison between the stickleback genome and the striped bass linkage map revealed conserved synteny between these two species. This is the first linkage map for any of the Morone species. This map will be useful for molecular mapping and marker-assisted selection of genes of interest in striped bass breeding programs. The conserved synteny between striped bass and stickleback will facilitate fine mapping of genome regions of interest and will serve as a new resource for comparative mapping with other Perciform fishes such as European sea bass (Dicentrarchus labrax), gilthead sea bream (Sparus aurata), and tilapia (Oreochromis ssp.). PMID:21968826

  1. Perched Lava Pond Complex on South Rift of Axial Volcano Revealed in AUV Mapping

    NASA Astrophysics Data System (ADS)

    Paduan, J. B.; Clague, D. A.; Caress, D. W.; Thomas, H. J.

    2013-12-01

    An extraordinary lava pond complex is located on Axial Volcano's distal south rift. It was discovered in EM300 multibeam bathymetry collected in 1998, and explored and sampled with ROVs Tiburon in 2005 and Doc Ricketts in 2013. It was surveyed with the MBARI Mapping AUV D. Allan B. in 2011, in a complicated mission first flying above the levees at constant depth, then skimming ~5 m over the levees at a different constant depth to survey the floors, then twice switching to constant altitude mode to map outside the ponds. The AUV navigation was adjusted using the MB-System tool mbnavadjust so that bathymetric features match in overlapping and crossing swaths. The ~1-m resolution AUV bathymetry reveals extremely rough terrain, where low-resolution EM300 data had averaged acoustic returns and obscured details of walls, floors, a breach and surrounding flows, and gives context to the ROV observations and samples. The 6 x 1.5 km pond complex has 4 large and several smaller drained ponds with rims 67 to 106 m above the floors. The combined volume before draining was 0.56 km3. The ponds overflowed to build lobate-flow levees with elongate pillows draping outer flanks, then drained, leaving lava veneer on vertical inner walls. Levee rim depths vary by only 10 m and are deeper around the southern ponds. Deep collapse-pits in the levees suggest porosity of pond walls. The eastern levee of the northeastern pond breached, draining the interconnected ponds, and fed thick, rapidly-emplaced, sheet-flows along the complex's east side. These flows travelled at least 5.5 km down-rift and have 19-33 m deep drained ponds. They extended up-rift as well, forming a 10 x 2.5 km ponded flow with level 'bathtub rings' as high as 35 m above the floor marking that flow's high-stand. Despite the breach, at least 0.066 km3 of the molten interior of the large ponds also drained back down the eruptive fissures, as the pond floors are deeper than the sill and sea floor outside the complex. Tumulus

  2. Issues of tsunami hazard maps revealed by the 2011 Tohoku tsunami

    NASA Astrophysics Data System (ADS)

    Sugimoto, M.

    2013-12-01

    Tsunami scientists are imposed responsibilities of selection for people's tsunami evacuation place after the 2011 Tohoku Tsunami in Japan. A lot of matured people died out of tsunami hazard zone based on tsunami hazard map though students made a miracle by evacuation on their own judgment in Kamaishi city. Tsunami hazard maps were based on numerical model smaller than actual magnitude 9. How can we bridge the gap between hazard map and future disasters? We have to discuss about using tsunami numerical model better enough to contribute tsunami hazard map. How do we have to improve tsunami hazard map? Tsunami hazard map should be revised included possibility of upthrust or downthrust after earthquakes and social information. Ground sank 1.14m below sea level in Ayukawa town, Tohoku. Ministry of Land, Infrastructure, Transport and Tourism's research shows around 10% people know about tsunami hazard map in Japan. However, people know about their evacuation places (buildings) through experienced drills once a year even though most people did not know about tsunami hazard map. We need wider spread of tsunami hazard with contingency of science (See the botom disaster handbook material's URL). California Emergency Management Agency (CEMA) team practically shows one good practice and solution to me. I followed their field trip in Catalina Island, California in Sep 2011. A team members are multidisciplinary specialists: A geologist, a GIS specialist, oceanographers in USC (tsunami numerical modeler) and a private company, a local policeman, a disaster manager, a local authority and so on. They check field based on their own specialties. They conduct an on-the-spot inspection of ambiguous locations between tsunami numerical model and real field conditions today. The data always become older. They pay attention not only to topographical conditions but also to social conditions: vulnerable people, elementary schools and so on. It takes a long time to check such field

  3. A Dense Linkage Map for Chinook salmon (Oncorhynchus tshawytscha) Reveals Variable Chromosomal Divergence After an Ancestral Whole Genome Duplication Event

    PubMed Central

    Brieuc, Marine S. O.; Waters, Charles D.; Seeb, James E.; Naish, Kerry A.

    2014-01-01

    Comparisons between the genomes of salmon species reveal that they underwent extensive chromosomal rearrangements following whole genome duplication that occurred in their lineage 58−63 million years ago. Extant salmonids are diploid, but occasional pairing between homeologous chromosomes exists in males. The consequences of re-diploidization can be characterized by mapping the position of duplicated loci in such species. Linkage maps are also a valuable tool for genome-wide applications such as genome-wide association studies, quantitative trait loci mapping or genome scans. Here, we investigated chromosomal evolution in Chinook salmon (Oncorhynchus tshawytscha) after genome duplication by mapping 7146 restriction-site associated DNA loci in gynogenetic haploid, gynogenetic diploid, and diploid crosses. In the process, we developed a reference database of restriction-site associated DNA loci for Chinook salmon comprising 48528 non-duplicated loci and 6409 known duplicated loci, which will facilitate locus identification and data sharing. We created a very dense linkage map anchored to all 34 chromosomes for the species, and all arms were identified through centromere mapping. The map positions of 799 duplicated loci revealed that homeologous pairs have diverged at different rates following whole genome duplication, and that degree of differentiation along arms was variable. Many of the homeologous pairs with high numbers of duplicated markers appear conserved with other salmon species, suggesting that retention of conserved homeologous pairing in some arms preceded species divergence. As chromosome arms are highly conserved across species, the major resources developed for Chinook salmon in this study are also relevant for other related species. PMID:24381192

  4. Multiscale Processes of Hurricane Sandy (2012) as Revealed by the CAMVis-MAP

    NASA Astrophysics Data System (ADS)

    Shen, B.; Li, J. F.; Cheung, S.

    2013-12-01

    In late October 2012, Storm Sandy made landfall near Brigantine, New Jersey, devastating surrounding areas and causing tremendous economic loss and hundreds of fatalities (Blake et al., 2013). An estimated damage of $50 billion made Sandy become the second costliest tropical cyclone (TC) in US history, surpassed only by Hurricane Katrina (2005). Central questions to be addressed include (1) to what extent the lead time of severe storm prediction such as Sandy can be extended (e.g., Emanuel 2012); and (2) whether and how advanced global model, supercomputing technology and numerical algorithm can help effectively illustrate the complicated physical processes that are associated with the evolution of the storms. In this study, the predictability of Sandy is addressed with a focus on short-term (or extended-range) genesis prediction as the first step toward the goal of understanding the relationship between extreme events, such as Sandy, and the current climate. The newly deployed Coupled Advanced global mesoscale Modeling (GMM) and concurrent Visualization (CAMVis) system is used for this study. We will show remarkable simulations of Hurricane Sandy with the GMM, including realistic 7-day track and intensity forecast and genesis predictions with a lead time of up to 6 days (e.g., Shen et al., 2013, GRL, submitted). We then discuss the enabling role of the high-resolution 4-D (time-X-Y-Z) visualizations in illustrating TC's transient dynamics and its interaction with tropical waves. In addition, we have finished the parallel implementation of the ensemble empirical mode decomposition (PEEMD, Cheung et al., 2013, AGU13, submitted) method that will be soon integrated into the multiscale analysis package (MAP) for the analysis of tropical weather systems such as TCs and tropical waves. While the original EEMD has previously shown superior performance in decomposition of nonlinear (local) and non-stationary data into different intrinsic modes which stay within the natural

  5. Space Telescope and Optical Reverberation Mapping Project.I. Ultraviolet Observations of the Seyfert 1 Galaxy NGC 5548 with the Cosmic Origins Spectrograph on Hubble Space Telescope

    NASA Astrophysics Data System (ADS)

    De Rosa, G.; Peterson, B. M.; Ely, J.; Kriss, G. A.; Crenshaw, D. M.; Horne, Keith; Korista, K. T.; Netzer, H.; Pogge, R. W.; Arévalo, P.; Barth, A. J.; Bentz, M. C.; Brandt, W. N.; Breeveld, A. A.; Brewer, B. J.; Dalla Bontà, E.; De Lorenzo-Cáceres, A.; Denney, K. D.; Dietrich, M.; Edelson, R.; Evans, P. A.; Fausnaugh, M. M.; Gehrels, N.; Gelbord, J. M.; Goad, M. R.; Grier, C. J.; Grupe, D.; Hall, P. B.; Kaastra, J.; Kelly, B. C.; Kennea, J. A.; Kochanek, C. S.; Lira, P.; Mathur, S.; McHardy, I. M.; Nousek, J. A.; Pancoast, A.; Papadakis, I.; Pei, L.; Schimoia, J. S.; Siegel, M.; Starkey, D.; Treu, T.; Uttley, P.; Vaughan, S.; Vestergaard, M.; Villforth, C.; Yan, H.; Young, S.; Zu, Y.

    2015-06-01

    We describe the first results from a six-month long reverberation-mapping experiment in the ultraviolet based on 171 observations of the Seyfert 1 galaxy NGC 5548 with the Cosmic Origins Spectrograph on the Hubble Space Telescope. Significant correlated variability is found in the continuum and broad emission lines, with amplitudes ranging from ˜30% to a factor of two in the emission lines and a factor of three in the continuum. The variations of all the strong emission lines lag behind those of the continuum, with He ii λ 1640 lagging behind the continuum by ˜2.5 days and Lyα λ 1215, C iv λ 1550, and Si iv λ 1400 lagging by ˜5-6 days. The relationship between the continuum and emission lines is complex. In particular, during the second half of the campaign, all emission-line lags increased by a factor of 1.3-2 and differences appear in the detailed structure of the continuum and emission-line light curves. Velocity-resolved cross-correlation analysis shows coherent structure in lag versus line of sight velocity for the emission lines; the high-velocity wings of C iv respond to continuum variations more rapidly than the line core, probably indicating higher velocity broad-line region clouds at smaller distances from the central engine. The velocity-dependent response of Lyα, however, is more complex and will require further analysis.

  6. Genome-wide mapping in a house mouse hybrid zone reveals hybrid sterility loci and Dobzhansky-Muller interactions

    PubMed Central

    Turner, Leslie M; Harr, Bettina

    2014-01-01

    Mapping hybrid defects in contact zones between incipient species can identify genomic regions contributing to reproductive isolation and reveal genetic mechanisms of speciation. The house mouse features a rare combination of sophisticated genetic tools and natural hybrid zones between subspecies. Male hybrids often show reduced fertility, a common reproductive barrier between incipient species. Laboratory crosses have identified sterility loci, but each encompasses hundreds of genes. We map genetic determinants of testis weight and testis gene expression using offspring of mice captured in a hybrid zone between M. musculus musculus and M. m. domesticus. Many generations of admixture enables high-resolution mapping of loci contributing to these sterility-related phenotypes. We identify complex interactions among sterility loci, suggesting multiple, non-independent genetic incompatibilities contribute to barriers to gene flow in the hybrid zone. DOI: http://dx.doi.org/10.7554/eLife.02504.001 PMID:25487987

  7. High Resolution Genetic Mapping by Genome Sequencing Reveals Genome Duplication and Tetraploid Genetic Structure of the Diploid Miscanthus sinensis

    PubMed Central

    Ma, Xue-Feng; Jensen, Elaine; Alexandrov, Nickolai; Troukhan, Maxim; Zhang, Liping; Thomas-Jones, Sian; Farrar, Kerrie; Clifton-Brown, John; Donnison, Iain; Swaller, Timothy; Flavell, Richard

    2012-01-01

    We have created a high-resolution linkage map of Miscanthus sinensis, using genotyping-by-sequencing (GBS), identifying all 19 linkage groups for the first time. The result is technically significant since Miscanthus has a very large and highly heterozygous genome, but has no or limited genomics information to date. The composite linkage map containing markers from both parental linkage maps is composed of 3,745 SNP markers spanning 2,396 cM on 19 linkage groups with a 0.64 cM average resolution. Comparative genomics analyses of the M. sinensis composite linkage map to the genomes of sorghum, maize, rice, and Brachypodium distachyon indicate that sorghum has the closest syntenic relationship to Miscanthus compared to other species. The comparative results revealed that each pair of the 19 M. sinensis linkages aligned to one sorghum chromosome, except for LG8, which mapped to two sorghum chromosomes (4 and 7), presumably due to a chromosome fusion event after genome duplication. The data also revealed several other chromosome rearrangements relative to sorghum, including two telomere-centromere inversions of the sorghum syntenic chromosome 7 in LG8 of M. sinensis and two paracentric inversions of sorghum syntenic chromosome 4 in LG7 and LG8 of M. sinensis. The results clearly demonstrate, for the first time, that the diploid M. sinensis is tetraploid origin consisting of two sub-genomes. This complete and high resolution composite linkage map will not only serve as a useful resource for novel QTL discoveries, but also enable informed deployment of the wealth of existing genomics resources of other species to the improvement of Miscanthus as a high biomass energy crop. In addition, it has utility as a reference for genome sequence assembly for the forthcoming whole genome sequencing of the Miscanthus genus. PMID:22439001

  8. High resolution genetic mapping by genome sequencing reveals genome duplication and tetraploid genetic structure of the diploid Miscanthus sinensis.

    PubMed

    Ma, Xue-Feng; Jensen, Elaine; Alexandrov, Nickolai; Troukhan, Maxim; Zhang, Liping; Thomas-Jones, Sian; Farrar, Kerrie; Clifton-Brown, John; Donnison, Iain; Swaller, Timothy; Flavell, Richard

    2012-01-01

    We have created a high-resolution linkage map of Miscanthus sinensis, using genotyping-by-sequencing (GBS), identifying all 19 linkage groups for the first time. The result is technically significant since Miscanthus has a very large and highly heterozygous genome, but has no or limited genomics information to date. The composite linkage map containing markers from both parental linkage maps is composed of 3,745 SNP markers spanning 2,396 cM on 19 linkage groups with a 0.64 cM average resolution. Comparative genomics analyses of the M. sinensis composite linkage map to the genomes of sorghum, maize, rice, and Brachypodium distachyon indicate that sorghum has the closest syntenic relationship to Miscanthus compared to other species. The comparative results revealed that each pair of the 19 M. sinensis linkages aligned to one sorghum chromosome, except for LG8, which mapped to two sorghum chromosomes (4 and 7), presumably due to a chromosome fusion event after genome duplication. The data also revealed several other chromosome rearrangements relative to sorghum, including two telomere-centromere inversions of the sorghum syntenic chromosome 7 in LG8 of M. sinensis and two paracentric inversions of sorghum syntenic chromosome 4 in LG7 and LG8 of M. sinensis. The results clearly demonstrate, for the first time, that the diploid M. sinensis is tetraploid origin consisting of two sub-genomes. This complete and high resolution composite linkage map will not only serve as a useful resource for novel QTL discoveries, but also enable informed deployment of the wealth of existing genomics resources of other species to the improvement of Miscanthus as a high biomass energy crop. In addition, it has utility as a reference for genome sequence assembly for the forthcoming whole genome sequencing of the Miscanthus genus. PMID:22439001

  9. Quantitative trait locus mapping reveals regions of the maize genome controlling root system architecture.

    PubMed

    Zurek, Paul R; Topp, Christopher N; Benfey, Philip N

    2015-04-01

    The quest to determine the genetic basis of root system architecture (RSA) has been greatly facilitated by recent developments in root phenotyping techniques. Methods that are accurate, high throughput, and control for environmental factors are especially attractive for quantitative trait locus mapping. Here, we describe the adaptation of a nondestructive in vivo gel-based root imaging platform for use in maize (Zea mays). We identify a large number of contrasting RSA traits among 25 founder lines of the maize nested association mapping population and locate 102 quantitative trait loci using the B73 (compact RSA)×Ki3 (exploratory RSA) mapping population. Our results suggest that a phenotypic tradeoff exists between small, compact RSA and large, exploratory RSA. PMID:25673779

  10. Quantitative Trait Locus Mapping Reveals Regions of the Maize Genome Controlling Root System Architecture1[OPEN

    PubMed Central

    Benfey, Philip N.

    2015-01-01

    The quest to determine the genetic basis of root system architecture (RSA) has been greatly facilitated by recent developments in root phenotyping techniques. Methods that are accurate, high throughput, and control for environmental factors are especially attractive for quantitative trait locus mapping. Here, we describe the adaptation of a nondestructive in vivo gel-based root imaging platform for use in maize (Zea mays). We identify a large number of contrasting RSA traits among 25 founder lines of the maize nested association mapping population and locate 102 quantitative trait loci using the B73 (compact RSA) × Ki3 (exploratory RSA) mapping population. Our results suggest that a phenotypic tradeoff exists between small, compact RSA and large, exploratory RSA. PMID:25673779

  11. Global genomic diversity of Oryza sativa varieties revealed by comparative physical mapping.

    PubMed

    Wang, Xiaoming; Kudrna, David A; Pan, Yonglong; Wang, Hao; Liu, Lin; Lin, Haiyan; Zhang, Jianwei; Song, Xiang; Goicoechea, Jose Luis; Wing, Rod A; Zhang, Qifa; Luo, Meizhong

    2014-04-01

    Bacterial artificial chromosome (BAC) physical maps embedding a large number of BAC end sequences (BESs) were generated for Oryza sativa ssp. indica varieties Minghui 63 (MH63) and Zhenshan 97 (ZS97) and were compared with the genome sequences of O. sativa spp. japonica cv. Nipponbare and O. sativa ssp. indica cv. 93-11. The comparisons exhibited substantial diversities in terms of large structural variations and small substitutions and indels. Genome-wide BAC-sized and contig-sized structural variations were detected, and the shared variations were analyzed. In the expansion regions of the Nipponbare reference sequence, in comparison to the MH63 and ZS97 physical maps, as well as to the previously constructed 93-11 physical map, the amounts and types of the repeat contents, and the outputs of gene ontology analysis, were significantly different from those of the whole genome. Using the physical maps of four wild Oryza species from OMAP (http://www.omap.org) as a control, we detected many conserved and divergent regions related to the evolution process of O. sativa. Between the BESs of MH63 and ZS97 and the two reference sequences, a total of 1532 polymorphic simple sequence repeats (SSRs), 71,383 SNPs, 1767 multiple nucleotide polymorphisms, 6340 insertions, and 9137 deletions were identified. This study provides independent whole-genome resources for intra- and intersubspecies comparisons and functional genomics studies in O. sativa. Both the comparative physical maps and the GBrowse, which integrated the QTL and molecular markers from GRAMENE (http://www.gramene.org) with our physical maps and analysis results, are open to the public through our Web site (http://gresource.hzau.edu.cn/resource/resource.html). PMID:24424778

  12. Genetic map of the human pseudoautosomal region reveals a high rate of recombination in female meiosis at the Xp telomere

    SciTech Connect

    Henke, A.; Fischer, C.; Rappold, G.A. )

    1993-12-01

    This paper describes the genetic map of the pseudoautosomal region bounded by the telomere of the short arms of the X and Y chromosomes. In males, meiotic exchange on Xp/Yp is confined to this region, leading to highly elevated recombination rates. The map was constructed using 11 pseudoautosomal probes (six of which are new) and typing individuals from 38 CEPH families. All markers have been physically mapped, thus providing the opportunity to compare genetic distance to physical distance through all intervals of the map. This comparison reveals an unexpected high rate of recombination in female meiosis between loci DXYS20 and DXYS78, within 20-80 kb from the telomere. Within this telemore-adjacent region no differences in male and female recombination rates are seen. Furthermore, data from this genetic map support the hypothesis of a linear gradient of recombination across most of the region in male meiosis and provide densely spaced anchor points for linkage studies especially in the telomeric portion of the pseudoautosomal region. 34 refs., 4 figs., 4 tabs.

  13. Homozygosity Mapping and Targeted Sanger Sequencing Reveal Genetic Defects Underlying Inherited Retinal Disease in Families from Pakistan

    PubMed Central

    Waheed, Nadia Khalida; Siddiqui, Sorath Noorani; Mustafa, Bilal; Ayub, Humaira; Ali, Liaqat; Ahmad, Shakeel; Micheal, Shazia; Hussain, Alamdar; Shah, Syed Tahir Abbas; Ali, Syeda Hafiza Benish; Ahmed, Waqas; Khan, Yar Muhammad; den Hollander, Anneke I.; Haer-Wigman, Lonneke; Collin, Rob W. J.; Khan, Muhammad Imran; Qamar, Raheel; Cremers, Frans P. M.

    2015-01-01

    Background Homozygosity mapping has facilitated the identification of the genetic causes underlying inherited diseases, particularly in consanguineous families with multiple affected individuals. This knowledge has also resulted in a mutation dataset that can be used in a cost and time effective manner to screen frequent population-specific genetic variations associated with diseases such as inherited retinal disease (IRD). Methods We genetically screened 13 families from a cohort of 81 Pakistani IRD families diagnosed with Leber congenital amaurosis (LCA), retinitis pigmentosa (RP), congenital stationary night blindness (CSNB), or cone dystrophy (CD). We employed genome-wide single nucleotide polymorphism (SNP) array analysis to identify homozygous regions shared by affected individuals and performed Sanger sequencing of IRD-associated genes located in the sizeable homozygous regions. In addition, based on population specific mutation data we performed targeted Sanger sequencing (TSS) of frequent variants in AIPL1, CEP290, CRB1, GUCY2D, LCA5, RPGRIP1 and TULP1, in probands from 28 LCA families. Results Homozygosity mapping and Sanger sequencing of IRD-associated genes revealed the underlying mutations in 10 families. TSS revealed causative variants in three families. In these 13 families four novel mutations were identified in CNGA1, CNGB1, GUCY2D, and RPGRIP1. Conclusions Homozygosity mapping and TSS revealed the underlying genetic cause in 13 IRD families, which is useful for genetic counseling as well as therapeutic interventions that are likely to become available in the near future. PMID:25775262

  14. Association Mapping in Turkish Olive Cultivars Revealed Significant Markers Related to Some Important Agronomic Traits.

    PubMed

    Kaya, Hilal Betul; Cetin, Oznur; Kaya, Hulya Sozer; Sahin, Mustafa; Sefer, Filiz; Tanyolac, Bahattin

    2016-08-01

    Olive (Olea europaea L.) is one of the most important fruit trees especially in the Mediterranean countries due to high consumption of table olive and olive oil. In olive breeding, the phenotypic traits associated to fruit are the key factors that determine productivity. Association mapping has been used in some tree species and a lot of crop plant species, and here, we perform an initial effort to detect marker-trait associations in olive tree. In the current study, a total of 96 olive genotypes, including both oil and table olive genotypes from Turkish Olive GenBank Resources, were used to examine marker-trait associations. For olive genotyping, SNP, AFLP, and SSR marker data were selected from previously published study and association analysis was performed between these markers and 5 yield-related traits. Three different approaches were used to check for false-positive results in association tests, and association results obtained from these models were compared. Using the model utilizing both population structure and relative kinship, eleven associations were significant with FDR ≤ 0.05. The largest number of significant associations was detected for fruit weight and stone weight. Our results suggested that association mapping could be an effective approach for identifying marker-trait associations in olive genotypes, without the development of mapping populations. This study shows for the first time the use of association mapping for identifying molecular markers linked to important traits in olive tree. PMID:27209034

  15. Genetic Mapping of Sulfur Assimilation Genes Reveals a QTL for Onion Bulb Pungency

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Onion exhibits wide genetic and environmental variation in bioactive organosulfur compounds that impart pungency and health benefits. A PCR-based molecular marker map that included candidate genes for sulfur assimilation was used to identify genomic regions affecting pungency in the cross 'W202A' x ...

  16. A radiation hybrid map of chromosome ID reveals synteny conservation at a wheat speciation locus.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The species cytoplasm specific (scs) genes affect nuclear-cytoplasmic interactions in interspecific hybrids. A radiation hybrid (RH) mapping population of 188 individuals was employed to refine the location of the scsae locus of Tritcum aestivum chromosome 1D. ‘Wheat Zapper’, a comparative genomic...

  17. Ultrafast Doppler reveals the mapping of cerebral vascular resistivity in neonates

    PubMed Central

    Demené, Charlie; Pernot, Mathieu; Biran, Valérie; Alison, Marianne; Fink, Mathias; Baud, Olivier; Tanter, Mickaël

    2014-01-01

    In vivo mapping of the full vasculature dynamics based on Ultrafast Doppler is showed noninvasively in the challenging case of the neonatal brain. Contrary to conventional pulsed-wave (PW) Doppler Ultrasound limited for >40 years to the estimation of vascular indices at a single location, the ultrafast frame rate (5,000 Hz) obtained using plane-wave transmissions leads to simultaneous estimation of full Doppler spectra in all pixels of wide field-of-view images within a single cardiac cycle and high sensitivity Doppler imaging. Consequently, 2D quantitative maps of the cerebro-vascular resistivity index (RI) are processed and found in agreement with local measurements obtained on large arteries of healthy neonates using conventional PW Doppler. Changes in 2D resistivity maps are monitored during recovery after therapeutic whole-body cooling of full-term neonates treated for hypoxic ischemic encephalopathy. Arterial and venous vessels are unambiguously differentiated on the basis of their distinct hemodynamics. The high spatial (250 × 250 μm2) and temporal resolution (<1 ms) of Ultrafast Doppler imaging combined with deep tissue penetration enable precise quantitative mapping of deep brain vascular dynamics and RI, which is far beyond the capabilities of any other imaging modality. PMID:24667916

  18. COMPLETE SWITCHGRASS GENETIC MAPS REVEAL SUBGENOME COLLINEARITY, PREFERENTIAL PAIRING, AND MULTILOCUS INTERACTIONS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Switchgrass (Panicum virgatum L.) is being developed as a bioenergy feedstock because it is a high-yielding perennial appropriate for marginal cropland. Switchgrass linkage maps were constructed as a step toward identification of loci underlying quality and yield using simple sequence repeat and seq...

  19. Whole-genome mapping reveals a large chromosomal inversion on Iberian Brucella suis biovar 2 strains.

    PubMed

    Ferreira, Ana Cristina; Dias, Ricardo; de Sá, Maria Inácia Corrêa; Tenreiro, Rogério

    2016-08-30

    Optical mapping is a technology able to quickly generate high resolution ordered whole-genome restriction maps of bacteria, being a proven approach to search for diversity among bacterial isolates. In this work, optical whole-genome maps were used to compare closely-related Brucella suis biovar 2 strains. This biovar is the unique isolated in domestic pigs and wild boars in Portugal and Spain and most of the strains share specific molecular characteristics establishing an Iberian clonal lineage that can be differentiated from another lineage mainly isolated in several Central European countries. We performed the BamHI whole-genome optical maps of five B. suis biovar 2 field strains, isolated from wild boars in Portugal and Spain (three from the Iberian lineage and two from the Central European one) as well as of the reference strain B. suis biovar 2 ATCC 23445 (Central European lineage, Denmark). Each strain showed a distinct, highly individual configuration of 228-231 BamHI fragments. Nevertheless, a low divergence was globally observed in chromosome II (1.6%) relatively to chromosome I (2.4%). Optical mapping also disclosed genomic events associated with B. suis strains in chromosome I, namely one indel (3.5kb) and one large inversion (944kb). By using targeted-PCR in a set of 176 B. suis strains, including all biovars and haplotypes, the indel was found to be specific of the reference strain ATCC 23445 and the large inversion was shown to be an exclusive genomic marker of the Iberian clonal lineage of biovar 2. PMID:27527786

  20. Mapping organelle motion reveals a vesicular conveyor belt spatially replenishing secretory vesicles in stimulated chromaffin cells.

    PubMed

    Maucort, Guillaume; Kasula, Ravikiran; Papadopulos, Andreas; Nieminen, Timo A; Rubinsztein-Dunlop, Halina; Meunier, Frederic A

    2014-01-01

    How neurosecretory cells spatially adjust their secretory vesicle pools to replenish those that have fused and released their hormonal content is currently unknown. Here we designed a novel set of image analyses to map the probability of tracked organelles undergoing a specific type of movement (free, caged or directed). We then applied our analysis to time-lapse z-stack confocal imaging of secretory vesicles from bovine Chromaffin cells to map the global changes in vesicle motion and directionality occurring upon secretagogue stimulation. We report a defined region abutting the cortical actin network that actively transports secretory vesicles and is dissipated by actin and microtubule depolymerizing drugs. The directionality of this "conveyor belt" towards the cell surface is activated by stimulation. Actin and microtubule networks therefore cooperatively probe the microenvironment to transport secretory vesicles to the periphery, providing a mechanism whereby cells globally adjust their vesicle pools in response to secretagogue stimulation. PMID:24489879

  1. Joint assembly and genetic mapping of the Atlantic horseshoe crab genome reveals ancient whole genome duplication

    PubMed Central

    2014-01-01

    Background Horseshoe crabs are marine arthropods with a fossil record extending back approximately 450 million years. They exhibit remarkable morphological stability over their long evolutionary history, retaining a number of ancestral arthropod traits, and are often cited as examples of “living fossils.” As arthropods, they belong to the Ecdysozoa, an ancient super-phylum whose sequenced genomes (including insects and nematodes) have thus far shown more divergence from the ancestral pattern of eumetazoan genome organization than cnidarians, deuterostomes and lophotrochozoans. However, much of ecdysozoan diversity remains unrepresented in comparative genomic analyses. Results Here we apply a new strategy of combined de novo assembly and genetic mapping to examine the chromosome-scale genome organization of the Atlantic horseshoe crab, Limulus polyphemus. We constructed a genetic linkage map of this 2.7 Gbp genome by sequencing the nuclear DNA of 34 wild-collected, full-sibling embryos and their parents at a mean redundancy of 1.1x per sample. The map includes 84,307 sequence markers grouped into 1,876 distinct genetic intervals and 5,775 candidate conserved protein coding genes. Conclusions Comparison with other metazoan genomes shows that the L. polyphemus genome preserves ancestral bilaterian linkage groups, and that a common ancestor of modern horseshoe crabs underwent one or more ancient whole genome duplications 300 million years ago, followed by extensive chromosome fusion. These results provide a counter-example to the often noted correlation between whole genome duplication and evolutionary radiations. The new, low-cost genetic mapping method for obtaining a chromosome-scale view of non-model organism genomes that we demonstrate here does not require laboratory culture, and is potentially applicable to a broad range of other species. PMID:24987520

  2. Natural speech reveals the semantic maps that tile human cerebral cortex.

    PubMed

    Huth, Alexander G; de Heer, Wendy A; Griffiths, Thomas L; Theunissen, Frédéric E; Gallant, Jack L

    2016-04-28

    The meaning of language is represented in regions of the cerebral cortex collectively known as the 'semantic system'. However, little of the semantic system has been mapped comprehensively, and the semantic selectivity of most regions is unknown. Here we systematically map semantic selectivity across the cortex using voxel-wise modelling of functional MRI (fMRI) data collected while subjects listened to hours of narrative stories. We show that the semantic system is organized into intricate patterns that seem to be consistent across individuals. We then use a novel generative model to create a detailed semantic atlas. Our results suggest that most areas within the semantic system represent information about specific semantic domains, or groups of related concepts, and our atlas shows which domains are represented in each area. This study demonstrates that data-driven methods--commonplace in studies of human neuroanatomy and functional connectivity--provide a powerful and efficient means for mapping functional representations in the brain. PMID:27121839

  3. Integrative transcriptome, proteome, phosphoproteome and genetic mapping reveals new aspects in a fiberless mutant of cotton

    PubMed Central

    Ma, Qi-Feng; Wu, Chun-Hui; Wu, Man; Pei, Wen-Feng; Li, Xing-Li; Wang, Wen-Kui; Zhang, Jinfa; Yu, Ji-Wen; Yu, Shu-Xun

    2016-01-01

    To investigate the molecular mechanisms of fiber initiation in cotton (Gossypium spp.), an integrated approach combining transcriptome, iTRAQ-based proteome and genetic mapping was taken to compare the ovules of the Xuzhou 142 wild type (WT) with its fuzzless-lintless (fl) mutant at −3 and 0 day post-anthesis. A total of 1,953 mRNAs, 187 proteins, and 131 phosphoproteins were differentially expressed (DE) between WT and fl, and the levels of transcripts and their encoded proteins and phosphoproteins were highly congruent. A functional analysis suggested that the abundance of proteins were mainly involved in amino sugar, nucleotide sugar and fatty acid metabolism, one carbon pool for folate metabolism and flavonoid biosynthesis. qRT-PCR, Western blotting, and enzymatic assays were performed to confirm the regulation of these transcripts and proteins. A molecular mapping located the lintless gene li3 in the fl mutant on chromosome 26 for the first time. A further in-silico physical mapping of DE genes with sequence variations between fl and WT identified one and four candidate genes in the li3 and n2 regions, respectively. Taken together, the transcript abundance, phosphorylation status of proteins at the fiber initiation stage and candidate genes have provided insights into regulatory processes underlying cotton fiber initiation. PMID:27075604

  4. Integrative transcriptome, proteome, phosphoproteome and genetic mapping reveals new aspects in a fiberless mutant of cotton.

    PubMed

    Ma, Qi-Feng; Wu, Chun-Hui; Wu, Man; Pei, Wen-Feng; Li, Xing-Li; Wang, Wen-Kui; Zhang, Jinfa; Yu, Ji-Wen; Yu, Shu-Xun

    2016-01-01

    To investigate the molecular mechanisms of fiber initiation in cotton (Gossypium spp.), an integrated approach combining transcriptome, iTRAQ-based proteome and genetic mapping was taken to compare the ovules of the Xuzhou 142 wild type (WT) with its fuzzless-lintless (fl) mutant at -3 and 0 day post-anthesis. A total of 1,953 mRNAs, 187 proteins, and 131 phosphoproteins were differentially expressed (DE) between WT and fl, and the levels of transcripts and their encoded proteins and phosphoproteins were highly congruent. A functional analysis suggested that the abundance of proteins were mainly involved in amino sugar, nucleotide sugar and fatty acid metabolism, one carbon pool for folate metabolism and flavonoid biosynthesis. qRT-PCR, Western blotting, and enzymatic assays were performed to confirm the regulation of these transcripts and proteins. A molecular mapping located the lintless gene li3 in the fl mutant on chromosome 26 for the first time. A further in-silico physical mapping of DE genes with sequence variations between fl and WT identified one and four candidate genes in the li3 and n2 regions, respectively. Taken together, the transcript abundance, phosphorylation status of proteins at the fiber initiation stage and candidate genes have provided insights into regulatory processes underlying cotton fiber initiation. PMID:27075604

  5. Homozygosity mapping reveals novel and known mutations in Pakistani families with inherited retinal dystrophies

    PubMed Central

    Saqib, Muhammad Arif Nadeem; Nikopoulos, Konstantinos; Ullah, Ehsan; Sher Khan, Falak; Iqbal, Jamila; Bibi, Rabia; Jarral, Afeefa; Sajid, Sundus; Nishiguchi, Koji M.; Venturini, Giulia; Ansar, Muhammad; Rivolta, Carlo

    2015-01-01

    Inherited retinal dystrophies are phenotypically and genetically heterogeneous. This extensive heterogeneity poses a challenge when performing molecular diagnosis of patients, especially in developing countries. In this study, we applied homozygosity mapping as a tool to reduce the complexity given by genetic heterogeneity and identify disease-causing variants in consanguineous Pakistani pedigrees. DNA samples from eight families with autosomal recessive retinal dystrophies were subjected to genome wide homozygosity mapping (seven by SNP arrays and one by STR markers) and genes comprised within the detected homozygous regions were analyzed by Sanger sequencing. All families displayed consistent autozygous genomic regions. Sequence analysis of candidate genes identified four previously-reported mutations in CNGB3, CNGA3, RHO, and PDE6A, as well as three novel mutations: c.2656C > T (p.L886F) in RPGRIP1, c.991G > C (p.G331R) in CNGA3, and c.413-1G > A (IVS6-1G > A) in CNGB1. This latter mutation impacted pre-mRNA splicing of CNGB1 by creating a -1 frameshift leading to a premature termination codon. In addition to better delineating the genetic landscape of inherited retinal dystrophies in Pakistan, our data confirm that combining homozygosity mapping and candidate gene sequencing is a powerful approach for mutation identification in populations where consanguineous unions are common. PMID:25943428

  6. Cosmic jets

    SciTech Connect

    Blandford, R.D.; Begelman, M.C.; Rees, M.J.

    1982-05-01

    Observations with radio telescopes have revealed that the center of many galaxies is a place of violent activity. This activity is often manifested in the production of cosmic jets. Each jet is a narrow stream of plasma that appears to squirt out of the center of a galaxy emitting radiowaves as it does so. New techniques in radio astronomy have shown how common jets are in the universe. These jets take on many different forms. The discovery of radio jets has helped in the understanding of the double structure of the majority of extragalactic radio sources. The morphology of some jets and explanations of how jets are fueled are discussed. There are many difficulties plaguing the investigation of jets. Some of these difficulties are (1) it is not known how much power the jets are radiating, (2) it is hard to tell whether a jet delieated by radio emission is identical to the region where ionized gas is flowing, and (3) what makes them. (SC)

  7. Mapping.

    ERIC Educational Resources Information Center

    Kinney, Douglas M.; McIntosh, Willard L.

    1979-01-01

    The area of geological mapping in the United States in 1978 increased greatly over that reported in 1977; state geological maps were added for California, Idaho, Nevada, and Alaska last year. (Author/BB)

  8. Cosmic impacts, cosmic catastrophes. I

    NASA Technical Reports Server (NTRS)

    Chapman, Clark R.; Morrison, David

    1989-01-01

    The discovery of cosmic impacts and their effects on the earth's surface are discussed. The manner in which the object impacts with the earth is described. The formation of crytovolcanic structures by craters is examined. Examples of cosmic debris collisions with earth, in particular the Tunguska explosion of 1908 and the Meteor Crater in Arizona, are provided.

  9. A mitochondrial-focused genetic interaction map reveals a scaffold-like complex required for inner membrane organization in mitochondria

    PubMed Central

    Hoppins, Suzanne; Collins, Sean R.; Cassidy-Stone, Ann; Hummel, Eric; DeVay, Rachel M.; Lackner, Laura L.; Westermann, Benedikt; Schuldiner, Maya

    2011-01-01

    To broadly explore mitochondrial structure and function as well as the communication of mitochondria with other cellular pathways, we constructed a quantitative, high-density genetic interaction map (the MITO-MAP) in Saccharomyces cerevisiae. The MITO-MAP provides a comprehensive view of mitochondrial function including insights into the activity of uncharacterized mitochondrial proteins and the functional connection between mitochondria and the ER. The MITO-MAP also reveals a large inner membrane–associated complex, which we term MitOS for mitochondrial organizing structure, comprised of Fcj1/Mitofilin, a conserved inner membrane protein, and five additional components. MitOS physically and functionally interacts with both outer and inner membrane components and localizes to extended structures that wrap around the inner membrane. We show that MitOS acts in concert with ATP synthase dimers to organize the inner membrane and promote normal mitochondrial morphology. We propose that MitOS acts as a conserved mitochondrial skeletal structure that differentiates regions of the inner membrane to establish the normal internal architecture of mitochondria. PMID:21987634

  10. Analysis of non-Gaussian cosmic microwave background maps based on the N-pdf. Application to Wilkinson Microwave Anisotropy Probe data

    NASA Astrophysics Data System (ADS)

    Vielva, P.; Sanz, J. L.

    2009-08-01

    We present a new method based on the N-point probability distribution function (N-pdf) to study non-Gaussianity in cosmic microwave background maps. Likelihood and Bayesian estimation are applied to a local non-linear perturbed model up to third order, characterized by a linear term which is described by a Gaussian N-pdf, and a second- and third-order terms which are proportional to the square and the cube of the linear one. We also explore a set of model selection techniques (the Akaike and the Bayesian information criteria, the minimum description length, the Bayesian evidence and the generalized likelihood ratio test) and their application to decide whether a given data set is better described by the proposed local non-Gaussian model, rather than by the standard Gaussian temperature distribution. As an application, we consider the analysis of the Wilkinson Microwave Anisotropy Probe 5-year data at a resolution of ~2°. At this angular scale (the Sachs-Wolfe regime), the non-Gaussian description proposed in this work defaults (under certain conditions) to an approximative local form of the weak non-linear coupling inflationary model previously addressed in the literature. For this particular case, we obtain an estimation for the non-linear coupling parameter of -94 < fNL < 154 at 95 per cent confidence level. Equally, model selection criteria also indicate that the Gaussian hypothesis is favoured against the particular local non-Gaussian model proposed in this work. This result is in agreement with previous findings obtained for equivalent non-Gaussian models and with different non-Gaussian estimators. However, our estimator based on the N-pdf is more efficient than previous estimators and, therefore, provides tighter constraints on the coupling parameter at degree scale.

  11. Fine mapping of the celiac disease-associated LPP locus reveals a potential functional variant

    PubMed Central

    Almeida, Rodrigo; Ricaño-Ponce, Isis; Kumar, Vinod; Deelen, Patrick; Szperl, Agata; Trynka, Gosia; Gutierrez-Achury, Javier; Kanterakis, Alexandros; Westra, Harm-Jan; Franke, Lude; Swertz, Morris A.; Platteel, Mathieu; Bilbao, Jose Ramon; Barisani, Donatella; Greco, Luigi; Mearin, Luisa; Wolters, Victorien M.; Mulder, Chris; Mazzilli, Maria Cristina; Sood, Ajit; Cukrowska, Bozena; Núñez, Concepción; Pratesi, Riccardo; Withoff, Sebo; Wijmenga, Cisca

    2014-01-01

    Using the Immunochip for genotyping, we identified 39 non-human leukocyte antigen (non-HLA) loci associated to celiac disease (CeD), an immune-mediated disease with a worldwide frequency of ∼1%. The most significant non-HLA signal mapped to the intronic region of 70 kb in the LPP gene. Our aim was to fine map and identify possible functional variants in the LPP locus. We performed a meta-analysis in a cohort of 25 169 individuals from six different populations previously genotyped using Immunochip. Imputation using data from the Genome of the Netherlands and 1000 Genomes projects, followed by meta-analysis, confirmed the strong association signal on the LPP locus (rs2030519, P = 1.79 × 10−49), without any novel associations. The conditional analysis on this top SNP-indicated association to a single common haplotype. By performing haplotype analyses in each population separately, as well as in a combined group of the four populations that reach the significant threshold after correction (P < 0.008), we narrowed down the CeD-associated region from 70 to 2.8 kb (P = 1.35 × 10−44). By intersecting regulatory data from the ENCODE project, we found a functional SNP, rs4686484 (P = 3.12 × 10−49), that maps to several B-cell enhancer elements and a highly conserved region. This SNP was also predicted to change the binding motif of the transcription factors IRF4, IRF11, Nkx2.7 and Nkx2.9, suggesting its role in transcriptional regulation. We later found significantly low levels of LPP mRNA in CeD biopsies compared with controls, thus our results suggest that rs4686484 is the functional variant in this locus, while LPP expression is decreased in CeD. PMID:24334606

  12. Revealing the Nature of Molecule-Electrode Contact in Tunneling Junctions Using Raw Data Heat Maps.

    PubMed

    Sporrer, Jacob; Chen, Jiahao; Wang, Zhengjia; Thuo, Martin M

    2015-12-17

    Mechanistic understanding of charge transport through molecular tunnel junctions requires reproducible and statistically relevant data sets. This challenge has been overcome by development of large area junctions, especially those based on liquid-metal physi-sorbed top-electrodes, such as eutectic gallium-indium. A challenge with these junctions, however, is an inability to diagnose the quality of contact between the top-electrode and the SAMs. Since tunneling currents are dependent on the distance between the two electrodes, we demonstrate that by analyzing all raw unfitted data derived from a measurement using heat-maps, one can deduce the quality of contact and other minor bias-dependent fluctuations in the charge transport behavior. We demonstrate that the use of 3D plots would be challenging to interpret, but adoption of heat maps clearly captures details on junction quality irrespective of the total size of the data set or molecules used. We propose representation of raw data, rather than reliance on statistics, as proof of quality junctions. PMID:26618717

  13. Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions.

    PubMed

    Guelen, Lars; Pagie, Ludo; Brasset, Emilie; Meuleman, Wouter; Faza, Marius B; Talhout, Wendy; Eussen, Bert H; de Klein, Annelies; Wessels, Lodewyk; de Laat, Wouter; van Steensel, Bas

    2008-06-12

    The architecture of human chromosomes in interphase nuclei is still largely unknown. Microscopy studies have indicated that specific regions of chromosomes are located in close proximity to the nuclear lamina (NL). This has led to the idea that certain genomic elements may be attached to the NL, which may contribute to the spatial organization of chromosomes inside the nucleus. However, sequences in the human genome that interact with the NL in vivo have not been identified. Here we construct a high-resolution map of the interaction sites of the entire genome with NL components in human fibroblasts. This map shows that genome-lamina interactions occur through more than 1,300 sharply defined large domains 0.1-10 megabases in size. These lamina-associated domains (LADs) are typified by low gene-expression levels, indicating that LADs represent a repressive chromatin environment. The borders of LADs are demarcated by the insulator protein CTCF, by promoters that are oriented away from LADs, or by CpG islands, suggesting possible mechanisms of LAD confinement. Taken together, these results demonstrate that the human genome is divided into large, discrete domains that are units of chromosome organization within the nucleus. PMID:18463634

  14. Interactome Mapping Reveals Important Pathways in Skeletal Muscle Development of Pigs

    PubMed Central

    Cao, Jianhua; Huang, Tinghua; Li, Xinyun; Zhao, Shuhong

    2014-01-01

    The regulatory relationship and connectivity among genes involved in myogenesis and hypertrophy of skeletal muscle in pigs still remain large challenges. Presentation of gene interactions is a potential way to understand the mechanisms of developmental events in skeletal muscle. In this study, genome-wide transcripts and miRNA profiling was determined for Landrace pigs at four time points using microarray chips. A comprehensive method integrating gene ontology annotation and interactome network mapping was conducted to analyze the biological patterns and interaction modules of muscle development events based on differentially expressed genes and miRNAs. Our results showed that in total 484 genes and 34 miRNAs were detected for the duration from embryonic stage to adult in pigs, which composed two linear expression patterns with consensus changes. Moreover, the gene ontology analysis also disclosed that there were three typical biological events i.e., microstructure assembly of sarcomere at early embryonic stage, myofibril formation at later embryonic stage and function establishments of myoblast cells at postnatal stage. The interactome mappings of different time points also found the down-regulated trend of gene expression existed across the whole duration, which brought a possibility to introduce the myogenesis related miRNAs into the interactome regulatory networks of skeletal muscle in pigs. PMID:25431924

  15. The Topography of Visuospatial Attention as Revealed by a Novel Visual Field Mapping Technique

    PubMed Central

    Brefczynski-Lewis, Julie A.; Datta, Ritobrato; Lewis, James W.; DeYoe, Edgar A.

    2009-01-01

    Previously, we and others have shown that attention can enhance visual processing in a spatially specific manner that is retinotopically mapped in the occipital cortex. However, it is difficult to appreciate the functional significance of the spatial pattern of cortical activation just by examining the brain maps. In this study, we visualize the neural representation of the “spotlight” of attention using a back-projection of attention-related brain activation onto a diagram of the visual field. In the two main experiments, we examine the topography of attentional activation in the occipital and parietal cortices. In retinotopic areas, attentional enhancement is strongest at the locations of the attended target, but also spreads to nearby locations and even weakly to restricted locations in the opposite visual field. The dispersion of attentional effects around an attended site increases with the eccentricity of the target in a manner that roughly corresponds to a constant area of spread within the cortex. When averaged across multiple observers, these patterns appear consistent with a gradient model of spatial attention. However, individual observers exhibit complex variations that are unique but reproducible. Overall, these results suggest that the topography of visual attention for each individual is composed of a common theme plus a personal variation that may reflect their own unique “attentional style.” PMID:18752412

  16. Cortical connectivity maps reveal anatomically distinct areas in the parietal cortex of the rat

    PubMed Central

    Wilber, Aaron A.; Clark, Benjamin J.; Demecha, Alexis J.; Mesina, Lilia; Vos, Jessica M.; McNaughton, Bruce L.

    2015-01-01

    A central feature of theories of spatial navigation involves the representation of spatial relationships between objects in complex environments. The parietal cortex has long been linked to the processing of spatial visual information and recent evidence from single unit recording in rodents suggests a role for this region in encoding egocentric and world-centered frames. The rat parietal cortex can be subdivided into four distinct rostral-caudal and medial-lateral regions, which includes a zone previously characterized as secondary visual cortex. At present, very little is known regarding the relative connectivity of these parietal subdivisions. Thus, we set out to map the connectivity of the entire anterior-posterior and medial-lateral span of this region. To do this we used anterograde and retrograde tracers in conjunction with open source neuronal segmentation and tracer detection tools to generate whole brain connectivity maps of parietal inputs and outputs. Our present results show that inputs to the parietal cortex varied significantly along the medial-lateral, but not the rostral-caudal axis. Specifically, retrosplenial connectivity is greater medially, but connectivity with visual cortex, though generally sparse, is more significant laterally. Finally, based on connection density, the connectivity between parietal cortex and hippocampus is indirect and likely achieved largely via dysgranular retrosplenial cortex. Thus, similar to primates, the parietal cortex of rats exhibits a difference in connectivity along the medial-lateral axis, which may represent functionally distinct areas. PMID:25601828

  17. Comparative mapping reveals quantitative trait loci that affect spawning time in coho salmon (Oncorhynchus kisutch)

    PubMed Central

    Araneda, Cristian; Díaz, Nelson F.; Gomez, Gilda; López, María Eugenia; Iturra, Patricia

    2012-01-01

    Spawning time in salmonids is a sex-limited quantitative trait that can be modified by selection. In rainbow trout (Oncorhynchus mykiss), various quantitative trait loci (QTL) that affect the expression of this trait have been discovered. In this study, we describe four microsatellite loci associated with two possible spawning time QTL regions in coho salmon (Oncorhynchus kisutch). The four loci were identified in females from two populations (early and late spawners) produced by divergent selection from the same base population. Three of the loci (OmyFGT34TUF, One2ASC and One19ASC) that were strongly associated with spawning time in coho salmon (p < 0.0002) were previously associated with QTL for the same trait in rainbow trout; a fourth loci (Oki10) with a suggestive association (p = 0.00035) mapped 10 cM from locus OmyFGT34TUF in rainbow trout. The changes in allelic frequency observed after three generations of selection were greater than expected because of genetic drift. This work shows that comparing information from closely-related species is a valid strategy for identifying QTLs for marker-assisted selection in species whose genomes are poorly characterized or lack a saturated genetic map. PMID:22888302

  18. Developmental enhancers revealed by extensive DNA methylome maps of zebrafish early embryos

    PubMed Central

    Lee, Hyung Joo; Lowdon, Rebecca F; Maricque, Brett; Zhang, Bo; Stevens, Michael; Li, Daofeng; Johnson, Stephen L; Wang, Ting

    2015-01-01

    DNA methylation undergoes dynamic changes during development and cell differentiation. Recent genome-wide studies discovered that tissue-specific differentially methylated regions (DMRs) often overlap tissue-specific distal cis-regulatory elements. However, developmental DNA methylation dynamics of the majority of the genomic CpGs outside gene promoters and CpG islands has not been extensively characterized. Here we generate and compare comprehensive DNA methylome maps of zebrafish developing embryos. From these maps we identify thousands of developmental stage-specific DMRs (dsDMR) across zebrafish developmental stages. The dsDMRs contain evolutionarily conserved sequences, are associated with developmental genes, and are marked with active enhancer histone post-translational modifications. Their methylation pattern correlates much stronger than promoter methylation with expression of putative target genes. When tested in vivo using a transgenic zebrafish assay, 20 out of 20 selected candidate dsDMRs exhibit functional enhancer activities. Our data suggest that developmental enhancers are a major target of DNA methylation changes during embryogenesis. PMID:25697895

  19. HGDP and HapMap Analysis by Ancestry Mapper Reveals Local and Global Population Relationships

    PubMed Central

    Magalhães, Tiago R.; Casey, Jillian P.; Conroy, Judith; Regan, Regina; Fitzpatrick, Darren J.; Shah, Naisha; Sobral, João; Ennis, Sean

    2012-01-01

    Knowledge of human origins, migrations, and expansions is greatly enhanced by the availability of large datasets of genetic information from different populations and by the development of bioinformatic tools used to analyze the data. We present Ancestry Mapper, which we believe improves on existing methods, for the assignment of genetic ancestry to an individual and to study the relationships between local and global populations. The principle function of the method, named Ancestry Mapper, is to give each individual analyzed a genetic identifier, made up of just 51 genetic coordinates, that corresponds to its relationship to the HGDP reference population. As a consequence, the Ancestry Mapper Id (AMid) has intrinsic biological meaning and provides a tool to measure similarity between world populations. We applied Ancestry Mapper to a dataset comprised of the HGDP and HapMap data. The results show distinctions at the continental level, while simultaneously giving details at the population level. We clustered AMids of HGDP/HapMap and observe a recapitulation of human migrations: for a small number of clusters, individuals are grouped according to continental origins; for a larger number of clusters, regional and population distinctions are evident. Calculating distances between AMids allows us to infer ancestry. The number of coordinates is expandable, increasing the power of Ancestry Mapper. An R package called Ancestry Mapper is available to apply this method to any high density genomic data set. PMID:23189146

  20. Fine-Scale Mapping of the 5q11.2 Breast Cancer Locus Reveals at Least Three Independent Risk Variants Regulating MAP3K1

    PubMed Central

    Glubb, Dylan M.; Maranian, Mel J.; Michailidou, Kyriaki; Pooley, Karen A.; Meyer, Kerstin B.; Kar, Siddhartha; Carlebur, Saskia; O’Reilly, Martin; Betts, Joshua A.; Hillman, Kristine M.; Kaufmann, Susanne; Beesley, Jonathan; Canisius, Sander; Hopper, John L.; Southey, Melissa C.; Tsimiklis, Helen; Apicella, Carmel; Schmidt, Marjanka K.; Broeks, Annegien; Hogervorst, Frans B.; van der Schoot, C. Ellen; Muir, Kenneth; Lophatananon, Artitaya; Stewart-Brown, Sarah; Siriwanarangsan, Pornthep; Fasching, Peter A.; Ruebner, Matthias; Ekici, Arif B.; Beckmann, Matthias W.; Peto, Julian; dos-Santos-Silva, Isabel; Fletcher, Olivia; Johnson, Nichola; Pharoah, Paul D.P.; Bolla, Manjeet K.; Wang, Qin; Dennis, Joe; Sawyer, Elinor J.; Tomlinson, Ian; Kerin, Michael J.; Miller, Nicola; Burwinkel, Barbara; Marme, Frederik; Yang, Rongxi; Surowy, Harald; Guénel, Pascal; Truong, Thérèse; Menegaux, Florence; Sanchez, Marie; Bojesen, Stig E.; Nordestgaard, Børge G.; Nielsen, Sune F.; Flyger, Henrik; González-Neira, Anna; Benitez, Javier; Zamora, M. Pilar; Arias Perez, Jose Ignacio; Anton-Culver, Hoda; Neuhausen, Susan L.; Brenner, Hermann; Dieffenbach, Aida Karina; Arndt, Volker; Stegmaier, Christa; Meindl, Alfons; Schmutzler, Rita K.; Brauch, Hiltrud; Ko, Yon-Dschun; Brüning, Thomas; Nevanlinna, Heli; Muranen, Taru A.; Aittomäki, Kristiina; Blomqvist, Carl; Matsuo, Keitaro; Ito, Hidemi; Iwata, Hiroji; Tanaka, Hideo; Dörk, Thilo; Bogdanova, Natalia V.; Helbig, Sonja; Lindblom, Annika; Margolin, Sara; Mannermaa, Arto; Kataja, Vesa; Kosma, Veli-Matti; Hartikainen, Jaana M.; Wu, Anna H.; Tseng, Chiu-chen; Van Den Berg, David; Stram, Daniel O.; Lambrechts, Diether; Zhao, Hui; Weltens, Caroline; van Limbergen, Erik; Chang-Claude, Jenny; Flesch-Janys, Dieter; Rudolph, Anja; Seibold, Petra; Radice, Paolo; Peterlongo, Paolo; Barile, Monica; Capra, Fabio; Couch, Fergus J.; Olson, Janet E.; Hallberg, Emily; Vachon, Celine; Giles, Graham G.; Milne, Roger L.; McLean, Catriona; Haiman, Christopher A.; Henderson, Brian E.; Schumacher, Fredrick; Le Marchand, Loic; Simard, Jacques; Goldberg, Mark S.; Labrèche, France; Dumont, Martine; Teo, Soo Hwang; Yip, Cheng Har; See, Mee-Hoong; Cornes, Belinda; Cheng, Ching-Yu; Ikram, M. Kamran; Kristensen, Vessela; Zheng, Wei; Halverson, Sandra L.; Shrubsole, Martha; Long, Jirong; Winqvist, Robert; Pylkäs, Katri; Jukkola-Vuorinen, Arja; Kauppila, Saila; Andrulis, Irene L.; Knight, Julia A.; Glendon, Gord; Tchatchou, Sandrine; Devilee, Peter; Tollenaar, Robert A.E.M.; Seynaeve, Caroline; Van Asperen, Christi J.; García-Closas, Montserrat; Figueroa, Jonine; Chanock, Stephen J.; Lissowska, Jolanta; Czene, Kamila; Klevebring, Daniel; Darabi, Hatef; Eriksson, Mikael; Hooning, Maartje J.; Hollestelle, Antoinette; Martens, John W.M.; Collée, J. Margriet; Hall, Per; Li, Jingmei; Humphreys, Keith; Shu, Xiao-Ou; Lu, Wei; Gao, Yu-Tang; Cai, Hui; Cox, Angela; Cross, Simon S.; Reed, Malcolm W.R.; Blot, William; Signorello, Lisa B.; Cai, Qiuyin; Shah, Mitul; Ghoussaini, Maya; Kang, Daehee; Choi, Ji-Yeob; Park, Sue K.; Noh, Dong-Young; Hartman, Mikael; Miao, Hui; Lim, Wei Yen; Tang, Anthony; Hamann, Ute; Torres, Diana; Jakubowska, Anna; Lubinski, Jan; Jaworska, Katarzyna; Durda, Katarzyna; Sangrajrang, Suleeporn; Gaborieau, Valerie; Brennan, Paul; McKay, James; Olswold, Curtis; Slager, Susan; Toland, Amanda E.; Yannoukakos, Drakoulis; Shen, Chen-Yang; Wu, Pei-Ei; Yu, Jyh-Cherng; Hou, Ming-Feng; Swerdlow, Anthony; Ashworth, Alan; Orr, Nick; Jones, Michael; Pita, Guillermo; Alonso, M. Rosario; Álvarez, Nuria; Herrero, Daniel; Tessier, Daniel C.; Vincent, Daniel; Bacot, Francois; Luccarini, Craig; Baynes, Caroline; Ahmed, Shahana; Healey, Catherine S.; Brown, Melissa A.; Ponder, Bruce A.J.; Chenevix-Trench, Georgia; Thompson, Deborah J.; Edwards, Stacey L.; Easton, Douglas F.; Dunning, Alison M.; French, Juliet D.

    2015-01-01

    Genome-wide association studies (GWASs) have revealed SNP rs889312 on 5q11.2 to be associated with breast cancer risk in women of European ancestry. In an attempt to identify the biologically relevant variants, we analyzed 909 genetic variants across 5q11.2 in 103,991 breast cancer individuals and control individuals from 52 studies in the Breast Cancer Association Consortium. Multiple logistic regression analyses identified three independent risk signals: the strongest associations were with 15 correlated variants (iCHAV1), where the minor allele of the best candidate, rs62355902, associated with significantly increased risks of both estrogen-receptor-positive (ER+: odds ratio [OR] = 1.24, 95% confidence interval [CI] = 1.21–1.27, ptrend = 5.7 × 10−44) and estrogen-receptor-negative (ER−: OR = 1.10, 95% CI = 1.05–1.15, ptrend = 3.0 × 10−4) tumors. After adjustment for rs62355902, we found evidence of association of a further 173 variants (iCHAV2) containing three subsets with a range of effects (the strongest was rs113317823 [pcond = 1.61 × 10−5]) and five variants composing iCHAV3 (lead rs11949391; ER+: OR = 0.90, 95% CI = 0.87–0.93, pcond = 1.4 × 10−4). Twenty-six percent of the prioritized candidate variants coincided with four putative regulatory elements that interact with the MAP3K1 promoter through chromatin looping and affect MAP3K1 promoter activity. Functional analysis indicated that the cancer risk alleles of four candidates (rs74345699 and rs62355900 [iCHAV1], rs16886397 [iCHAV2a], and rs17432750 [iCHAV3]) increased MAP3K1 transcriptional activity. Chromatin immunoprecipitation analysis revealed diminished GATA3 binding to the minor (cancer-protective) allele of rs17432750, indicating a mechanism for its action. We propose that the cancer risk alleles act to increase MAP3K1 expression in vivo and might promote breast cancer cell survival. PMID:25529635

  1. Fine-scale mapping of the 5q11.2 breast cancer locus reveals at least three independent risk variants regulating MAP3K1.

    PubMed

    Glubb, Dylan M; Maranian, Mel J; Michailidou, Kyriaki; Pooley, Karen A; Meyer, Kerstin B; Kar, Siddhartha; Carlebur, Saskia; O'Reilly, Martin; Betts, Joshua A; Hillman, Kristine M; Kaufmann, Susanne; Beesley, Jonathan; Canisius, Sander; Hopper, John L; Southey, Melissa C; Tsimiklis, Helen; Apicella, Carmel; Schmidt, Marjanka K; Broeks, Annegien; Hogervorst, Frans B; van der Schoot, C Ellen; Muir, Kenneth; Lophatananon, Artitaya; Stewart-Brown, Sarah; Siriwanarangsan, Pornthep; Fasching, Peter A; Ruebner, Matthias; Ekici, Arif B; Beckmann, Matthias W; Peto, Julian; dos-Santos-Silva, Isabel; Fletcher, Olivia; Johnson, Nichola; Pharoah, Paul D P; Bolla, Manjeet K; Wang, Qin; Dennis, Joe; Sawyer, Elinor J; Tomlinson, Ian; Kerin, Michael J; Miller, Nicola; Burwinkel, Barbara; Marme, Frederik; Yang, Rongxi; Surowy, Harald; Guénel, Pascal; Truong, Thérèse; Menegaux, Florence; Sanchez, Marie; Bojesen, Stig E; Nordestgaard, Børge G; Nielsen, Sune F; Flyger, Henrik; González-Neira, Anna; Benitez, Javier; Zamora, M Pilar; Arias Perez, Jose Ignacio; Anton-Culver, Hoda; Neuhausen, Susan L; Brenner, Hermann; Dieffenbach, Aida Karina; Arndt, Volker; Stegmaier, Christa; Meindl, Alfons; Schmutzler, Rita K; Brauch, Hiltrud; Ko, Yon-Dschun; Brüning, Thomas; Nevanlinna, Heli; Muranen, Taru A; Aittomäki, Kristiina; Blomqvist, Carl; Matsuo, Keitaro; Ito, Hidemi; Iwata, Hiroji; Tanaka, Hideo; Dörk, Thilo; Bogdanova, Natalia V; Helbig, Sonja; Lindblom, Annika; Margolin, Sara; Mannermaa, Arto; Kataja, Vesa; Kosma, Veli-Matti; Hartikainen, Jaana M; Wu, Anna H; Tseng, Chiu-chen; Van Den Berg, David; Stram, Daniel O; Lambrechts, Diether; Zhao, Hui; Weltens, Caroline; van Limbergen, Erik; Chang-Claude, Jenny; Flesch-Janys, Dieter; Rudolph, Anja; Seibold, Petra; Radice, Paolo; Peterlongo, Paolo; Barile, Monica; Capra, Fabio; Couch, Fergus J; Olson, Janet E; Hallberg, Emily; Vachon, Celine; Giles, Graham G; Milne, Roger L; McLean, Catriona; Haiman, Christopher A; Henderson, Brian E; Schumacher, Fredrick; Le Marchand, Loic; Simard, Jacques; Goldberg, Mark S; Labrèche, France; Dumont, Martine; Teo, Soo Hwang; Yip, Cheng Har; See, Mee-Hoong; Cornes, Belinda; Cheng, Ching-Yu; Ikram, M Kamran; Kristensen, Vessela; Zheng, Wei; Halverson, Sandra L; Shrubsole, Martha; Long, Jirong; Winqvist, Robert; Pylkäs, Katri; Jukkola-Vuorinen, Arja; Kauppila, Saila; Andrulis, Irene L; Knight, Julia A; Glendon, Gord; Tchatchou, Sandrine; Devilee, Peter; Tollenaar, Robert A E M; Seynaeve, Caroline; Van Asperen, Christi J; García-Closas, Montserrat; Figueroa, Jonine; Chanock, Stephen J; Lissowska, Jolanta; Czene, Kamila; Klevebring, Daniel; Darabi, Hatef; Eriksson, Mikael; Hooning, Maartje J; Hollestelle, Antoinette; Martens, John W M; Collée, J Margriet; Hall, Per; Li, Jingmei; Humphreys, Keith; Shu, Xiao-Ou; Lu, Wei; Gao, Yu-Tang; Cai, Hui; Cox, Angela; Cross, Simon S; Reed, Malcolm W R; Blot, William; Signorello, Lisa B; Cai, Qiuyin; Shah, Mitul; Ghoussaini, Maya; Kang, Daehee; Choi, Ji-Yeob; Park, Sue K; Noh, Dong-Young; Hartman, Mikael; Miao, Hui; Lim, Wei Yen; Tang, Anthony; Hamann, Ute; Torres, Diana; Jakubowska, Anna; Lubinski, Jan; Jaworska, Katarzyna; Durda, Katarzyna; Sangrajrang, Suleeporn; Gaborieau, Valerie; Brennan, Paul; McKay, James; Olswold, Curtis; Slager, Susan; Toland, Amanda E; Yannoukakos, Drakoulis; Shen, Chen-Yang; Wu, Pei-Ei; Yu, Jyh-Cherng; Hou, Ming-Feng; Swerdlow, Anthony; Ashworth, Alan; Orr, Nick; Jones, Michael; Pita, Guillermo; Alonso, M Rosario; Álvarez, Nuria; Herrero, Daniel; Tessier, Daniel C; Vincent, Daniel; Bacot, Francois; Luccarini, Craig; Baynes, Caroline; Ahmed, Shahana; Healey, Catherine S; Brown, Melissa A; Ponder, Bruce A J; Chenevix-Trench, Georgia; Thompson, Deborah J; Edwards, Stacey L; Easton, Douglas F; Dunning, Alison M; French, Juliet D

    2015-01-01

    Genome-wide association studies (GWASs) have revealed SNP rs889312 on 5q11.2 to be associated with breast cancer risk in women of European ancestry. In an attempt to identify the biologically relevant variants, we analyzed 909 genetic variants across 5q11.2 in 103,991 breast cancer individuals and control individuals from 52 studies in the Breast Cancer Association Consortium. Multiple logistic regression analyses identified three independent risk signals: the strongest associations were with 15 correlated variants (iCHAV1), where the minor allele of the best candidate, rs62355902, associated with significantly increased risks of both estrogen-receptor-positive (ER(+): odds ratio [OR] = 1.24, 95% confidence interval [CI] = 1.21-1.27, ptrend = 5.7 × 10(-44)) and estrogen-receptor-negative (ER(-): OR = 1.10, 95% CI = 1.05-1.15, ptrend = 3.0 × 10(-4)) tumors. After adjustment for rs62355902, we found evidence of association of a further 173 variants (iCHAV2) containing three subsets with a range of effects (the strongest was rs113317823 [pcond = 1.61 × 10(-5)]) and five variants composing iCHAV3 (lead rs11949391; ER(+): OR = 0.90, 95% CI = 0.87-0.93, pcond = 1.4 × 10(-4)). Twenty-six percent of the prioritized candidate variants coincided with four putative regulatory elements that interact with the MAP3K1 promoter through chromatin looping and affect MAP3K1 promoter activity. Functional analysis indicated that the cancer risk alleles of four candidates (rs74345699 and rs62355900 [iCHAV1], rs16886397 [iCHAV2a], and rs17432750 [iCHAV3]) increased MAP3K1 transcriptional activity. Chromatin immunoprecipitation analysis revealed diminished GATA3 binding to the minor (cancer-protective) allele of rs17432750, indicating a mechanism for its action. We propose that the cancer risk alleles act to increase MAP3K1 expression in vivo and might promote breast cancer cell survival. PMID:25529635

  2. Intraoperative mapping during repeat awake craniotomy reveals the functional plasticity of adult cortex.

    PubMed

    Southwell, Derek G; Hervey-Jumper, Shawn L; Perry, David W; Berger, Mitchel S

    2016-05-01

    OBJECT To avoid iatrogenic injury during the removal of intrinsic cerebral neoplasms such as gliomas, direct electrical stimulation (DES) is used to identify cortical and subcortical white matter pathways critical for language, motor, and sensory function. When a patient undergoes more than 1 brain tumor resection as in the case of tumor recurrence, the use of DES provides an unusual opportunity to examine brain plasticity in the setting of neurological disease. METHODS The authors examined 561 consecutive cases in which patients underwent DES mapping during surgery forglioma resection. "Positive" and "negative" sites-discrete cortical regions where electrical stimulation did (positive) or did not (negative) produce transient sensory, motor, or language disturbance-were identified prior to tumor resection and documented by intraoperative photography for categorization into functional maps. In this group of 561 patients, 18 were identified who underwent repeat surgery in which 1 or more stimulation sites overlapped with those tested during the initial surgery. The authors compared intraoperative sensory, motor, or language mapping results between initial and repeat surgeries, and evaluated the clinical outcomes for these patients. RESULTS A total of 117 sites were tested for sensory (7 sites, 6.0%), motor (9 sites, 7.7%), or language (101 sites, 86.3%) function during both initial and repeat surgeries. The mean interval between surgical procedures was 4.1 years. During initial surgeries, 95 (81.2%) of 117 sites were found to be negative and 22 (18.8%) of 117 sites were found to be positive. During repeat surgeries, 103 (88.0%) of 117 sites were negative and 14 (12.0%) of 117 were positive. Of the 95 sites that were negative at the initial surgery, 94 (98.9%) were also negative at the repeat surgery, while 1 (1.1%) site was found to be positive. Of the 22 sites that were initially positive, 13 (59.1%) remained positive at repeat surgery, while 9 (40.9%) had become

  3. Cosmic superstrings.

    PubMed

    Sakellariadou, Mairi

    2008-08-28

    Cosmic superstrings are expected to be formed at the end of brane inflation, within the context of brane-world cosmological models inspired from string theory. By studying the properties of cosmic superstring networks and comparing their phenomenological consequences against observational data, we aim to pin down the successful and natural inflationary model and get an insight into the stringy description of our Universe. PMID:18534932

  4. Genome-wide Mapping Reveals Conservation of Promoter DNA Methylation Following Chicken Domestication

    PubMed Central

    Li, Qinghe; Wang, Yuanyuan; Hu, Xiaoxiang; Zhao, Yaofeng; Li, Ning

    2015-01-01

    It is well-known that environment influences DNA methylation, however, the extent of heritable DNA methylation variation following animal domestication remains largely unknown. Using meDIP-chip we mapped the promoter methylomes for 23,316 genes in muscle tissues of ancestral and domestic chickens. We systematically examined the variation of promoter DNA methylation in terms of different breeds, differentially expressed genes, SNPs and genes undergo genetic selection sweeps. While considerable changes in DNA sequence and gene expression programs were prevalent, we found that the inter-strain DNA methylation patterns were highly conserved in promoter region between the wild and domestic chicken breeds. Our data suggests a global preservation of DNA methylation between the wild and domestic chicken breeds in either a genome-wide or locus-specific scale in chick muscle tissues. PMID:25735894

  5. Genome-wide DNA methylation map of human neutrophils reveals widespread inter-individual epigenetic variation

    PubMed Central

    Chatterjee, Aniruddha; Stockwell, Peter A.; Rodger, Euan J.; Duncan, Elizabeth J.; Parry, Matthew F.; Weeks, Robert J.; Morison, Ian M.

    2015-01-01

    The extent of variation in DNA methylation patterns in healthy individuals is not yet well documented. Identification of inter-individual epigenetic variation is important for understanding phenotypic variation and disease susceptibility. Using neutrophils from a cohort of healthy individuals, we generated base-resolution DNA methylation maps to document inter-individual epigenetic variation. We identified 12851 autosomal inter-individual variably methylated fragments (iVMFs). Gene promoters were the least variable, whereas gene body and upstream regions showed higher variation in DNA methylation. The iVMFs were relatively enriched in repetitive elements compared to non-iVMFs, and were associated with genome regulation and chromatin function elements. Further, variably methylated genes were disproportionately associated with regulation of transcription, responsive function and signal transduction pathways. Transcriptome analysis indicates that iVMF methylation at differentially expressed exons has a positive correlation and local effect on the inclusion of that exon in the mRNA transcript. PMID:26612583

  6. Atom Probe Tomographic Mapping Directly Reveals the Atomic Distribution of Phosphorus in Resin Embedded Ferritin

    PubMed Central

    Perea, Daniel E.; Liu, Jia; Bartrand, Jonah; Dicken, Quinten; Thevuthasan, S. Theva; Browning, Nigel D.; Evans, James E.

    2016-01-01

    Here we report the atomic-scale analysis of biological interfaces within the ferritin protein using atom probe tomography that is facilitated by an advanced specimen preparation approach. Embedding ferritin in an organic polymer resin lacking nitrogen provided chemical contrast to visualise atomic distributions and distinguish the inorganic-organic interface of the ferrihydrite mineral core and protein shell, as well as the organic-organic interface between the ferritin protein shell and embedding resin. In addition, we definitively show the atomic-scale distribution of phosphorus as being at the surface of the ferrihydrite mineral with the distribution of sodium mapped within the protein shell environment with an enhanced distribution at the mineral/protein interface. The sample preparation method is robust and can be directly extended to further enhance the study of biological, organic and inorganic nanomaterials relevant to health, energy or the environment. PMID:26924804

  7. Mapping bundles of ecosystem services reveals distinct types of multifunctionality within a Swedish landscape.

    PubMed

    Queiroz, Cibele; Meacham, Megan; Richter, Kristina; Norström, Albert V; Andersson, Erik; Norberg, Jon; Peterson, Garry

    2015-01-01

    Ecosystem services (ES) is a valuable concept to be used in the planning and management of social-ecological landscapes. However, the understanding of the determinant factors affecting the interaction between services in the form of synergies or trade-offs is still limited. We assessed the production of 16 ES across 62 municipalities in the Norrström drainage basin in Sweden. We combined GIS data with publically available information for quantifying and mapping the distribution of services. Additionally, we calculated the diversity of ES for each municipality and used correlations and k-means clustering analyses to assess the existence of ES bundles. We found five distinct types of bundles of ES spatially agglomerated in the landscape that could be explained by regional social and ecological gradients. Human-dominated landscapes were highly multifunctional in our study area and urban densely populated areas were hotspots of cultural services. PMID:25576284

  8. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping.

    PubMed

    Rao, Suhas S P; Huntley, Miriam H; Durand, Neva C; Stamenova, Elena K; Bochkov, Ivan D; Robinson, James T; Sanborn, Adrian L; Machol, Ido; Omer, Arina D; Lander, Eric S; Aiden, Erez Lieberman

    2014-12-18

    We use in situ Hi-C to probe the 3D architecture of genomes, constructing haploid and diploid maps of nine cell types. The densest, in human lymphoblastoid cells, contains 4.9 billion contacts, achieving 1 kb resolution. We find that genomes are partitioned into contact domains (median length, 185 kb), which are associated with distinct patterns of histone marks and segregate into six subcompartments. We identify ∼10,000 loops. These loops frequently link promoters and enhancers, correlate with gene activation, and show conservation across cell types and species. Loop anchors typically occur at domain boundaries and bind CTCF. CTCF sites at loop anchors occur predominantly (>90%) in a convergent orientation, with the asymmetric motifs "facing" one another. The inactive X chromosome splits into two massive domains and contains large loops anchored at CTCF-binding repeats. PMID:25497547

  9. High-resolution statistical mapping reveals gene territories in live yeast.

    PubMed

    Berger, Axel B; Cabal, Ghislain G; Fabre, Emmanuelle; Duong, Tarn; Buc, Henri; Nehrbass, Ulf; Olivo-Marin, Jean-Christophe; Gadal, Olivier; Zimmer, Christophe

    2008-12-01

    The nonrandom positioning of genes inside eukaryotic cell nuclei is implicated in central nuclear functions. However, the spatial organization of the genome remains largely uncharted, owing to limited resolution of optical microscopy, paucity of nuclear landmarks and moderate cell sampling. We developed a computational imaging approach that creates high-resolution probabilistic maps of subnuclear domains occupied by individual loci in budding yeast through automated analysis of thousands of living cells. After validation, we applied the technique to genes involved in galactose metabolism and ribosome biogenesis. We found that genomic loci are confined to 'gene territories' much smaller than the nucleus, which can be remodeled during transcriptional activation, and that the nucleolus is an important landmark for gene positioning. The technique can be used to visualize and quantify territory positions relative to each other and to nuclear landmarks, and should advance studies of nuclear architecture and function. PMID:18978785

  10. Electrostatic interaction map reveals a new binding position for tropomyosin on F-actin.

    PubMed

    Rynkiewicz, Michael J; Schott, Veronika; Orzechowski, Marek; Lehman, William; Fischer, Stefan

    2015-12-01

    Azimuthal movement of tropomyosin around the F-actin thin filament is responsible for muscle activation and relaxation. Recently a model of αα-tropomyosin, derived from molecular-mechanics and electron microscopy of different contractile states, showed that tropomyosin is rather stiff and pre-bent to present one specific face to F-actin during azimuthal transitions. However, a new model based on cryo-EM of troponin- and myosin-free filaments proposes that the interacting-face of tropomyosin can differ significantly from that in the original model. Because resolution was insufficient to assign tropomyosin side-chains, the interacting-face could not be unambiguously determined. Here, we use structural analysis and energy landscapes to further examine the proposed models. The observed bend in seven crystal structures of tropomyosin is much closer in direction and extent to the original model than to the new model. Additionally, we computed the interaction map for repositioning tropomyosin over the F-actin surface, but now extended over a much larger surface than previously (using the original interacting-face). This map shows two energy minima-one corresponding to the "blocked-state" as in the original model, and the other related by a simple 24 Å translation of tropomyosin parallel to the F-actin axis. The tropomyosin-actin complex defined by the second minimum fits perfectly into the recent cryo-EM density, without requiring any change in the interacting-face. Together, these data suggest that movement of tropomyosin between regulatory states does not require interacting-face rotation. Further, they imply that thin filament assembly may involve an interplay between initially seeded tropomyosin molecules growing from distinct binding-site regions on actin. PMID:26286845

  11. Rich RNA Structure Landscapes Revealed by Mutate-and-Map Analysis

    PubMed Central

    Cordero, Pablo; Das, Rhiju

    2015-01-01

    Landscapes exhibiting multiple secondary structures arise in natural RNA molecules that modulate gene expression, protein synthesis, and viral. We report herein that high-throughput chemical experiments can isolate an RNA’s multiple alternative secondary structures as they are stabilized by systematic mutagenesis (mutate-and-map, M2) and that a computational algorithm, REEFFIT, enables unbiased reconstruction of these states’ structures and populations. In an in silico benchmark on non-coding RNAs with complex landscapes, M2-REEFFIT recovers 95% of RNA helices present with at least 25% population while maintaining a low false discovery rate (10%) and conservative error estimates. In experimental benchmarks, M2-REEFFIT recovers the structure landscapes of a 35-nt MedLoop hairpin, a 110-nt 16S rRNA four-way junction with an excited state, a 25-nt bistable hairpin, and a 112-nt three-state adenine riboswitch with its expression platform, molecules whose characterization previously required expert mutational analysis and specialized NMR or chemical mapping experiments. With this validation, M2-REEFFIT enabled tests of whether artificial RNA sequences might exhibit complex landscapes in the absence of explicit design. An artificial flavin mononucleotide riboswitch and a randomly generated RNA sequence are found to interconvert between three or more states, including structures for which there was no design, but that could be stabilized through mutations. These results highlight the likely pervasiveness of rich landscapes with multiple secondary structures in both natural and artificial RNAs and demonstrate an automated chemical/computational route for their empirical characterization. PMID:26566145

  12. A filtering method to reveal crystalline patterns from atom probe microscopy desorption maps

    PubMed Central

    Yao, Lan

    2016-01-01

    A filtering method to reveal the crystallographic information present in Atom Probe Microscopy (APM) data is presented. The method filters atoms based on the time difference between their evaporation and the evaporation of the previous atom. Since this time difference correlates with the location and the local structure of the evaporating atoms on the surface, it can be used to reveal any crystallographic information contained within APM data. The demonstration of this method is illustrated on: • A pure Al specimen for which crystallographic poles are clearly visible on the desorption patterns easily indexed. • Three Fe-15at.% Cr datasets where crystallographic patterns are less obvious and require this filtering method. PMID:27104149

  13. Cosmic Interactions

    NASA Astrophysics Data System (ADS)

    2008-01-01

    An image based on data taken with ESO's Very Large Telescope reveals a triplet of galaxies intertwined in a cosmic dance. ESO PR Photo 02/08 ESO PR Photo 02/08 NGC 7173, 7174, and 7176 The three galaxies, catalogued as NGC 7173 (top), 7174 (bottom right) and 7176 (bottom left), are located 106 million light-years away towards the constellation of Piscis Austrinus (the 'Southern Fish'). NGC 7173 and 7176 are elliptical galaxies, while NGC 7174 is a spiral galaxy with quite disturbed dust lanes and a long, twisted tail. This seems to indicate that the two bottom galaxies - whose combined shape bears some resemblance to that of a sleeping baby - are currently interacting, with NGC 7176 providing fresh material to NGC 7174. Matter present in great quantity around the triplet's members also points to the fact that NGC 7176 and NGC 7173 have interacted in the past. Astronomers have suggested that the three galaxies will finally merge into a giant 'island universe', tens to hundreds of times as massive as our own Milky Way. ESO PR Photo 02/08 ESO PR Photo 02b/08 NGC 7173, 7174, and 7176 The triplet is part of a so-called 'Compact Group', as compiled by Canadian astronomer Paul Hickson in the early 1980s. The group, which is the 90th entry in the catalogue and is therefore known as HCG 90, actually contains four major members. One of them - NGC 7192 - lies above the trio, outside of this image, and is another peculiar spiral galaxy. Compact groups are small, relatively isolated, systems of typically four to ten galaxies in close proximity to one another. Another striking example is Robert's Quartet. Compact groups are excellent laboratories for the study of galaxy interactions and their effects, in particular the formation of stars. As the striking image reveals, there are many other galaxies in the field. Some are distant ones, while others seem to be part of the family. Studies made with other telescopes have indeed revealed that the HCG 90 group contains 16 members

  14. A RAD-Tag Genetic Map for the Platyfish (Xiphophorus maculatus) Reveals Mechanisms of Karyotype Evolution Among Teleost Fish

    PubMed Central

    Amores, Angel; Catchen, Julian; Nanda, Indrajit; Warren, Wesley; Walter, Ron; Schartl, Manfred; Postlethwait, John H.

    2014-01-01

    Mammalian genomes can vary substantially in haploid chromosome number even within a small taxon (e.g., 3–40 among deer alone); in contrast, teleost fish genomes are stable (24–25 in 58% of teleosts), but we do not yet understand the mechanisms that account for differences in karyotype stability. Among perciform teleosts, platyfish (Xiphophorus maculatus) and medaka (Oryzias latipes) both have 24 chromosome pairs, but threespine stickleback (Gasterosteus aculeatus) and green pufferfish (Tetraodon nigroviridis) have just 21 pairs. To understand the evolution of teleost genomes, we made a platyfish meiotic map containing 16,114 mapped markers scored on 267 backcross fish. We tiled genomic contigs along the map to create chromosome-length genome assemblies. Genome-wide comparisons of conserved synteny showed that platyfish and medaka karyotypes remained remarkably similar with few interchromosomal translocations but with numerous intrachromosomal rearrangements (transpositions and inversions) since their lineages diverged ∼120 million years ago. Comparative genomics with platyfish shows how reduced chromosome numbers in stickleback and green pufferfish arose by fusion of pairs of ancestral chromosomes after their lineages diverged from platyfish ∼195 million years ago. Zebrafish and human genomes provide outgroups to root observed changes. These studies identify likely genome assembly errors, characterize chromosome fusion events, distinguish lineage-independent chromosome fusions, show that the teleost genome duplication does not appear to have accelerated the rate of translocations, and reveal the stability of syntenies and gene orders in teleost chromosomes over hundreds of millions of years. PMID:24700104

  15. The mitochondrial genome map of Nelumbo nucifera reveals ancient evolutionary features

    PubMed Central

    Gui, Songtao; Wu, Zhihua; Zhang, Hongyuan; Zheng, Yinzhen; Zhu, Zhixuan; Liang, Dequan; Ding, Yi

    2016-01-01

    Nelumbo nucifera is an evolutionary relic from the Late Cretaceous period. Sequencing the N. nucifera mitochondrial genome is important for elucidating the evolutionary characteristics of basal eudicots. Here, the N. nucifera mitochondrial genome was sequenced using single molecule real-time sequencing technology (SMRT), and the mitochondrial genome map was constructed after de novo assembly and annotation. The results showed that the 524,797-bp N. nucifera mitochondrial genome has a total of 63 genes, including 40 protein-coding genes, three rRNA genes and 20 tRNA genes. Fifteen collinear gene clusters were conserved across different plant species. Approximately 700 RNA editing sites in the protein-coding genes were identified. Positively selected genes were identified with selection pressure analysis. Nineteen chloroplast-derived fragments were identified, and seven tRNAs were derived from the chloroplast. These results suggest that the N. nucifera mitochondrial genome retains evolutionarily conserved characteristics, including ancient gene content and gene clusters, high levels of RNA editing, and low levels of chloroplast-derived fragment insertions. As the first publicly available basal eudicot mitochondrial genome, the N. nucifera mitochondrial genome facilitates further analysis of the characteristics of basal eudicots and provides clues of the evolutionary trajectory from basal angiosperms to advanced eudicots. PMID:27444405

  16. Global mapping of herpesvirus-host protein complexes reveals a novel transcription strategy for late genes

    PubMed Central

    Davis, Zoe H.; Verschueren, Erik; Jang, Gwendolyn M.; Kleffman, Kevin; Johnson, Jeffrey R.; Park, Jimin; Von Dollen, John; Maher, M. Cyrus; Johnson, Tasha; Newton, William; Jäger, Stefanie; Shales, Michael; Horner, Julie; Hernandez, Ryan D.; Krogan, Nevan J.; Glaunsinger, Britt A.

    2014-01-01

    SUMMARY Mapping host-pathogen interactions has proven instrumental for understanding how viruses manipulate host machinery and how numerous cellular processes are regulated. DNA viruses such as herpesviruses have relatively large coding capacity and thus can target an extensive network of cellular proteins. To identify the host proteins hijacked by this pathogen, we systematically affinity tagged and purified all 89 proteins of Kaposi’s sarcoma-associated herpesvirus (KSHV) from human cells. Mass spectrometry of this material identified over 500 virus-host interactions. KSHV causes AIDS-associated cancers and its interaction network is enriched for proteins linked to cancer and overlaps with proteins that are also targeted by HIV-1. We found that the conserved KSHV protein ORF24 binds to RNA polymerase II and brings it to viral late promoters by mimicking and replacing cellular TATA-box-binding protein (TBP). This is required for herpesviral late gene expression, a complex and poorly understood phase of the viral lifecycle. PMID:25544563

  17. Asymmetries in Core Collapse Supernovae Revealed by Maps of Radioactive Titanium

    NASA Technical Reports Server (NTRS)

    Grefenstette, B. W.; Harrison, F. A.; Boggs, S. E.; Reynolds, S. P.; Fryer, C. L.; Madsen, K. K.; Wik, D. R.; Zoglauer, A.; Ellinger, C. I.; Alexander, D. M.; An, H.; Barret, D.; Christensen, F. E.; Craig, W. W.; Forster, K.; Giommi, P.; Hailey, C. J.; Hornstrup, A.; Kaspi, V. M.; Kitaguchi, T.; Koglin, J. E.; Mao, P. H.; Miyasaka, H.; Mori, K.; Zhang, W. W.

    2014-01-01

    Asymmetry is required by most numerical simulations of stellar core collapse explosions, however the nature differs significantly among models. The spatial distribution of radioactive Ti-44, synthesized in an exploding star near the boundary between material falling back onto the collapsing core and that ejected into the surrounding medium, directly probes the explosion1asymmetries. Cassiopeia A is a young, nearby, core-collapse remnant from which Ti-44 emission has previously been detected, but not imaged. Asymmetries in the explosion have been indirectly inferred from a high ratio of observed Ti-44 emission to that estimated from (56)Ni9, from optical light echoes, and by jet-like features seen in the X-ray and optical ejecta. Here we report on the spatial maps and spectral properties of Ti-44 in Cassiopeia A. We find the Ti-44 to be distributed non-uniformly in the un-shocked interior of the remnant. This may explain the unexpected lack of correlation between the Ti-44 and iron X-ray emission, the latter only being visible in shock heated material. The observed spatial distribution rules out symmetric explosions even with a high level of convective mixing, as well as highly asymmetric bipolar explosions resulting from a fast rotating progenitor. Instead, these observations provide strong evidence for the development of low-mode convective instabilities in core-collapse supernovae.

  18. Metabolic mapping reveals sex-dependent involvement of default mode and salience network in alexithymia.

    PubMed

    Colic, L; Demenescu, L R; Li, M; Kaufmann, J; Krause, A L; Metzger, C; Walter, M

    2016-02-01

    Alexithymia, a personality construct marked by difficulties in processing one's emotions, has been linked to the altered activity in the anterior cingulate cortex (ACC). Although longitudinal studies reported sex differences in alexithymia, what mediates them is not known. To investigate sex-specific associations of alexithymia and neuronal markers, we mapped metabolites in four brain regions involved differentially in emotion processing using a point-resolved spectroscopy MRS sequence in 3 Tesla. Both sexes showed negative correlations between alexithymia and N-acetylaspartate (NAA) in pregenual ACC (pgACC). Women showed a robust negative correlation of the joint measure of glutamate and glutamine (Glx) to NAA in posterior cingulate cortex (PCC), whereas men showed a weak positive association of Glx to NAA in dorsal ACC (dACC). Our results suggest that lowered neuronal integrity in pgACC, a region of the default mode network (DMN), might primarily account for the general difficulties in emotional processing in alexithymia. Association of alexithymia in women extends to another region in the DMN-PCC, while in men a region in the salience network (SN) was involved. These observations could be representative of sex specific regulation strategies that include diminished internal evaluation of feelings in women and cognitive emotion suppression in men. PMID:26341904

  19. Organization of the pronephric kidney revealed by large-scale gene expression mapping

    PubMed Central

    Raciti, Daniela; Reggiani, Luca; Geffers, Lars; Jiang, Qiuhong; Bacchion, Francesca; Subrizi, Astrid E; Clements, Dave; Tindal, Christopher; Davidson, Duncan R; Kaissling, Brigitte; Brändli, André W

    2008-01-01

    Background The pronephros, the simplest form of a vertebrate excretory organ, has recently become an important model of vertebrate kidney organogenesis. Here, we elucidated the nephron organization of the Xenopus pronephros and determined the similarities in segmentation with the metanephros, the adult kidney of mammals. Results We performed large-scale gene expression mapping of terminal differentiation markers to identify gene expression patterns that define distinct domains of the pronephric kidney. We analyzed the expression of over 240 genes, which included members of the solute carrier, claudin, and aquaporin gene families, as well as selected ion channels. The obtained expression patterns were deposited in the searchable European Renal Genome Project Xenopus Gene Expression Database. We found that 112 genes exhibited highly regionalized expression patterns that were adequate to define the segmental organization of the pronephric nephron. Eight functionally distinct domains were discovered that shared significant analogies in gene expression with the mammalian metanephric nephron. We therefore propose a new nomenclature, which is in line with the mammalian one. The Xenopus pronephric nephron is composed of four basic domains: proximal tubule, intermediate tubule, distal tubule, and connecting tubule. Each tubule may be further subdivided into distinct segments. Finally, we also provide compelling evidence that the expression of key genes underlying inherited renal diseases in humans has been evolutionarily conserved down to the level of the pronephric kidney. Conclusion The present study validates the Xenopus pronephros as a genuine model that may be used to elucidate the molecular basis of nephron segmentation and human renal disease. PMID:18492243

  20. Connectivity Map-based discovery of parbendazole reveals targetable human osteogenic pathway

    PubMed Central

    Brum, Andrea M.; van de Peppel, Jeroen; van der Leije, Cindy S.; Schreuders-Koedam, Marijke; Eijken, Marco; van der Eerden, Bram C. J.; van Leeuwen, Johannes P. T. M.

    2015-01-01

    Osteoporosis is a common skeletal disorder characterized by low bone mass leading to increased bone fragility and fracture susceptibility. In this study, we have identified pathways that stimulate differentiation of bone forming osteoblasts from human mesenchymal stromal cells (hMSCs). Gene expression profiling was performed in hMSCs differentiated toward osteoblasts (at 6 h). Significantly regulated genes were analyzed in silico, and the Connectivity Map (CMap) was used to identify candidate bone stimulatory compounds. The signature of parbendazole matches the expression changes observed for osteogenic hMSCs. Parbendazole stimulates osteoblast differentiation as indicated by increased alkaline phosphatase activity, mineralization, and up-regulation of bone marker genes (alkaline phosphatase/ALPL, osteopontin/SPP1, and bone sialoprotein II/IBSP) in a subset of the hMSC population resistant to the apoptotic effects of parbendazole. These osteogenic effects are independent of glucocorticoids because parbendazole does not up-regulate glucocorticoid receptor (GR) target genes and is not inhibited by the GR antagonist mifepristone. Parbendazole causes profound cytoskeletal changes including degradation of microtubules and increased focal adhesions. Stabilization of microtubules by pretreatment with Taxol inhibits osteoblast differentiation. Parbendazole up-regulates bone morphogenetic protein 2 (BMP-2) gene expression and activity. Cotreatment with the BMP-2 antagonist DMH1 limits, but does not block, parbendazole-induced mineralization. Using the CMap we have identified a previously unidentified lineage-specific, bone anabolic compound, parbendazole, which induces osteogenic differentiation through a combination of cytoskeletal changes and increased BMP-2 activity. PMID:26420877

  1. An integrative architecture for general intelligence and executive function revealed by lesion mapping

    PubMed Central

    Colom, Roberto; Solomon, Jeffrey; Krueger, Frank; Forbes, Chad; Grafman, Jordan

    2012-01-01

    Although cognitive neuroscience has made remarkable progress in understanding the involvement of the prefrontal cortex in executive control, the broader functional networks that support high-level cognition and give rise to general intelligence remain to be well characterized. Here, we investigated the neural substrates of the general factor of intelligence (g) and executive function in 182 patients with focal brain damage using voxel-based lesion–symptom mapping. The Wechsler Adult Intelligence Scale and Delis–Kaplan Executive Function System were used to derive measures of g and executive function, respectively. Impaired performance on these measures was associated with damage to a distributed network of left lateralized brain areas, including regions of frontal and parietal cortex and white matter association tracts, which bind these areas into a coordinated system. The observed findings support an integrative framework for understanding the architecture of general intelligence and executive function, supporting their reliance upon a shared fronto-parietal network for the integration and control of cognitive representations and making specific recommendations for the application of the Wechsler Adult Intelligence Scale and Delis–Kaplan Executive Function System to the study of high-level cognition in health and disease. PMID:22396393

  2. Evidence of Water Quality Degradation in Lower Mekong Basin Revealed by Self-Organizing Map

    PubMed Central

    Chea, Ratha; Grenouillet, Gaël; Lek, Sovan

    2016-01-01

    To reach a better understanding of the spatial variability of water quality in the Lower Mekong Basin (LMB), the Self-Organizing Map (SOM) was used to classify 117 monitoring sites and hotspots of pollution within the basin identified according to water quality indicators and US-EPA guidelines. Four different clusters were identified based on their similar physicochemical characteristics. The majority of sites in upper (Laos and Thailand) and middle part (Cambodia) of the basin were grouped in two clusters, considered as good quality water with high DO and low nutrient levels. The other two clusters were mostly composed of sites in Mekong delta (Vietnam) and few sites in upstream tributaries (i.e., northwestern Thailand, Tonle Sap Lake, and swamps close to Vientiane), known for moderate to poor quality of water and characterized by high nutrient and dissolved solid levels. Overall, we found that the water in the mainstream was less polluted than its tributaries; eutrophication and salinity could be key factors affecting water quality in LMB. Moreover, the seasonal variation of water quality seemed to be less marked than spatial variation occurring along the longitudinal gradient of Mekong River. Significant degradations were mainly associated with human disturbance and particularly apparent in sites distributed along the man-made canals in Vietnam delta where population growth and agricultural development are intensive. PMID:26731522

  3. Comprehensive expression map of transcription regulators in the adult zebrafish telencephalon reveals distinct neurogenic niches.

    PubMed

    Diotel, Nicolas; Rodriguez Viales, Rebecca; Armant, Olivier; März, Martin; Ferg, Marco; Rastegar, Sepand; Strähle, Uwe

    2015-06-01

    The zebrafish has become a model to study adult vertebrate neurogenesis. In particular, the adult telencephalon has been an intensely studied structure in the zebrafish brain. Differential expression of transcriptional regulators (TRs) is a key feature of development and tissue homeostasis. Here we report an expression map of 1,202 TR genes in the telencephalon of adult zebrafish. Our results are summarized in a database with search and clustering functions to identify genes expressed in particular regions of the telencephalon. We classified 562 genes into 13 distinct patterns, including genes expressed in the proliferative zone. The remaining 640 genes displayed unique and complex patterns of expression and could thus not be grouped into distinct classes. The neurogenic ventricular regions express overlapping but distinct sets of TR genes, suggesting regional differences in the neurogenic niches in the telencephalon. In summary, the small telencephalon of the zebrafish shows a remarkable complexity in TR gene expression. The adult zebrafish telencephalon has become a model to study neurogenesis. We established the expression pattern of more than 1200 transcription regulators (TR) in the adult telencephalon. The neurogenic regions express overlapping but distinct sets of TR genes suggesting regional differences in the neurogenic potential. PMID:25556858

  4. Dual-Channel Circuit Mapping Reveals Sensorimotor Convergence in the Primary Motor Cortex

    PubMed Central

    Lin, John Y.; Guo, Caiying

    2015-01-01

    Cortical cells integrate synaptic input from multiple sources, but how these different inputs are distributed across individual neurons is largely unknown. Differences in input might account for diverse responses in neighboring neurons during behavior. We present a strategy for comparing the strengths of multiple types of input onto the same neuron. We developed methods for independent dual-channel photostimulation of synaptic inputs using ChR2 together with ReaChR, a red-shifted channelrhodopsin. We used dual-channel photostimulation to probe convergence of sensory information in the mouse primary motor cortex. Input from somatosensory cortex and thalamus converges in individual neurons. Similarly, inputs from distinct somatotopic regions of the somatosensory cortex are integrated at the level of single motor cortex neurons. We next developed a ReaChR transgenic mouse under the control of both Flp- and Cre-recombinases that is an effective tool for circuit mapping. Our approach to dual-channel photostimulation enables quantitative comparison of the strengths of multiple pathways across all length scales of the brain. PMID:25762684

  5. The mitochondrial genome map of Nelumbo nucifera reveals ancient evolutionary features.

    PubMed

    Gui, Songtao; Wu, Zhihua; Zhang, Hongyuan; Zheng, Yinzhen; Zhu, Zhixuan; Liang, Dequan; Ding, Yi

    2016-01-01

    Nelumbo nucifera is an evolutionary relic from the Late Cretaceous period. Sequencing the N. nucifera mitochondrial genome is important for elucidating the evolutionary characteristics of basal eudicots. Here, the N. nucifera mitochondrial genome was sequenced using single molecule real-time sequencing technology (SMRT), and the mitochondrial genome map was constructed after de novo assembly and annotation. The results showed that the 524,797-bp N. nucifera mitochondrial genome has a total of 63 genes, including 40 protein-coding genes, three rRNA genes and 20 tRNA genes. Fifteen collinear gene clusters were conserved across different plant species. Approximately 700 RNA editing sites in the protein-coding genes were identified. Positively selected genes were identified with selection pressure analysis. Nineteen chloroplast-derived fragments were identified, and seven tRNAs were derived from the chloroplast. These results suggest that the N. nucifera mitochondrial genome retains evolutionarily conserved characteristics, including ancient gene content and gene clusters, high levels of RNA editing, and low levels of chloroplast-derived fragment insertions. As the first publicly available basal eudicot mitochondrial genome, the N. nucifera mitochondrial genome facilitates further analysis of the characteristics of basal eudicots and provides clues of the evolutionary trajectory from basal angiosperms to advanced eudicots. PMID:27444405

  6. Superresolution fluorescence mapping of single-nanoparticle catalysts reveals spatiotemporal variations in surface reactivity

    PubMed Central

    Zhang, Yuwei; Lucas, J. Matthew; Song, Ping; Beberwyck, Brandon; Fu, Qiang; Xu, Weilin; Alivisatos, A. Paul

    2015-01-01

    For the practical application of nanocatalysts, it is desirable to understand the spatiotemporal fluctuations of nanocatalytic activity at the single-nanoparticle level. Here we use time-lapsed superresolution mapping of single-molecule catalysis events on individual nanoparticles to observe time-varying changes in the spatial distribution of catalysis events on Sb-doped TiO2 nanorods and Au triangle nanoplates. Compared with the active sites on well-defined surface facets, the defects of the nanoparticle catalysts possess higher intrinsic reactivity but lower stability. Corners and ends are more reactive but also less stable than flat surfaces. Averaged over time, the most stable sites dominate the total apparent activity of single nanocatalysts. However, the active sites with higher intrinsic activity but lower stability show activity at earlier time points before deactivating. Unexpectedly, some active sites are found to recover their activity (“self-healing”) after deactivation, which is probably due to desorption of the adsorbate. Our superresolution measurement of different types of active catalytic sites, over both space and time, leads to a more comprehensive understanding of reactivity patterns and may enable the design of new and more productive heterogeneous catalysts. PMID:26150516

  7. Superresolution fluorescence mapping of single-nanoparticle catalysts reveals spatiotemporal variations in surface reactivity.

    PubMed

    Zhang, Yuwei; Lucas, J Matthew; Song, Ping; Beberwyck, Brandon; Fu, Qiang; Xu, Weilin; Alivisatos, A Paul

    2015-07-21

    For the practical application of nanocatalysts, it is desirable to understand the spatiotemporal fluctuations of nanocatalytic activity at the single-nanoparticle level. Here we use time-lapsed superresolution mapping of single-molecule catalysis events on individual nanoparticles to observe time-varying changes in the spatial distribution of catalysis events on Sb-doped TiO2 nanorods and Au triangle nanoplates. Compared with the active sites on well-defined surface facets, the defects of the nanoparticle catalysts possess higher intrinsic reactivity but lower stability. Corners and ends are more reactive but also less stable than flat surfaces. Averaged over time, the most stable sites dominate the total apparent activity of single nanocatalysts. However, the active sites with higher intrinsic activity but lower stability show activity at earlier time points before deactivating. Unexpectedly, some active sites are found to recover their activity ("self-healing") after deactivation, which is probably due to desorption of the adsorbate. Our superresolution measurement of different types of active catalytic sites, over both space and time, leads to a more comprehensive understanding of reactivity patterns and may enable the design of new and more productive heterogeneous catalysts. PMID:26150516

  8. Evidence of Water Quality Degradation in Lower Mekong Basin Revealed by Self-Organizing Map.

    PubMed

    Chea, Ratha; Grenouillet, Gaël; Lek, Sovan

    2016-01-01

    To reach a better understanding of the spatial variability of water quality in the Lower Mekong Basin (LMB), the Self-Organizing Map (SOM) was used to classify 117 monitoring sites and hotspots of pollution within the basin identified according to water quality indicators and US-EPA guidelines. Four different clusters were identified based on their similar physicochemical characteristics. The majority of sites in upper (Laos and Thailand) and middle part (Cambodia) of the basin were grouped in two clusters, considered as good quality water with high DO and low nutrient levels. The other two clusters were mostly composed of sites in Mekong delta (Vietnam) and few sites in upstream tributaries (i.e., northwestern Thailand, Tonle Sap Lake, and swamps close to Vientiane), known for moderate to poor quality of water and characterized by high nutrient and dissolved solid levels. Overall, we found that the water in the mainstream was less polluted than its tributaries; eutrophication and salinity could be key factors affecting water quality in LMB. Moreover, the seasonal variation of water quality seemed to be less marked than spatial variation occurring along the longitudinal gradient of Mekong River. Significant degradations were mainly associated with human disturbance and particularly apparent in sites distributed along the man-made canals in Vietnam delta where population growth and agricultural development are intensive. PMID:26731522

  9. 3D Magnetic Induction Maps of Nanoscale Materials Revealed by Electron Holographic Tomography

    PubMed Central

    2015-01-01

    The investigation of three-dimensional (3D) ferromagnetic nanoscale materials constitutes one of the key research areas of the current magnetism roadmap and carries great potential to impact areas such as data storage, sensing, and biomagnetism. The properties of such nanostructures are closely connected with their 3D magnetic nanostructure, making their determination highly valuable. Up to now, quantitative 3D maps providing both the internal magnetic and electric configuration of the same specimen with high spatial resolution are missing. Here, we demonstrate the quantitative 3D reconstruction of the dominant axial component of the magnetic induction and electrostatic potential within a cobalt nanowire (NW) of 100 nm in diameter with spatial resolution below 10 nm by applying electron holographic tomography. The tomogram was obtained using a dedicated TEM sample holder for acquisition, in combination with advanced alignment and tomographic reconstruction routines. The powerful approach presented here is widely applicable to a broad range of 3D magnetic nanostructures and may trigger the progress of novel spintronic nonplanar nanodevices. PMID:27182110

  10. Connectivity Map-based discovery of parbendazole reveals targetable human osteogenic pathway.

    PubMed

    Brum, Andrea M; van de Peppel, Jeroen; van der Leije, Cindy S; Schreuders-Koedam, Marijke; Eijken, Marco; van der Eerden, Bram C J; van Leeuwen, Johannes P T M

    2015-10-13

    Osteoporosis is a common skeletal disorder characterized by low bone mass leading to increased bone fragility and fracture susceptibility. In this study, we have identified pathways that stimulate differentiation of bone forming osteoblasts from human mesenchymal stromal cells (hMSCs). Gene expression profiling was performed in hMSCs differentiated toward osteoblasts (at 6 h). Significantly regulated genes were analyzed in silico, and the Connectivity Map (CMap) was used to identify candidate bone stimulatory compounds. The signature of parbendazole matches the expression changes observed for osteogenic hMSCs. Parbendazole stimulates osteoblast differentiation as indicated by increased alkaline phosphatase activity, mineralization, and up-regulation of bone marker genes (alkaline phosphatase/ALPL, osteopontin/SPP1, and bone sialoprotein II/IBSP) in a subset of the hMSC population resistant to the apoptotic effects of parbendazole. These osteogenic effects are independent of glucocorticoids because parbendazole does not up-regulate glucocorticoid receptor (GR) target genes and is not inhibited by the GR antagonist mifepristone. Parbendazole causes profound cytoskeletal changes including degradation of microtubules and increased focal adhesions. Stabilization of microtubules by pretreatment with Taxol inhibits osteoblast differentiation. Parbendazole up-regulates bone morphogenetic protein 2 (BMP-2) gene expression and activity. Cotreatment with the BMP-2 antagonist DMH1 limits, but does not block, parbendazole-induced mineralization. Using the CMap we have identified a previously unidentified lineage-specific, bone anabolic compound, parbendazole, which induces osteogenic differentiation through a combination of cytoskeletal changes and increased BMP-2 activity. PMID:26420877

  11. Genomic mapping of phosphorothioates reveals partial modification of short consensus sequences

    PubMed Central

    Cao, Bo; Chen, Chao; DeMott, Michael S.; Cheng, Qiuxiang; Clark, Tyson A.; Xiong, Xiaolin; Zheng, Xiaoqing; Butty, Vincent; Levine, Stuart S.; Yuan, George; Boitano, Matthew; Luong, Khai; Song, Yi; Zhou, Xiufen; Deng, Zixin; Turner, Stephen W.; Korlach, Jonas; You, Delin; Wang, Lianrong; Chen, Shi; Dedon, Peter C.

    2015-01-01

    Bacterial phosphorothioate (PT) DNA modifications are incorporated by Dnd proteins A-E and often function with DndF-H as a restriction-modification (R-M) system, as in Escherichia coli B7A. However, bacteria such as Vibrio cyclitrophicus FF75 lack dndF-H, which points to other PT functions. To better understand PT biology, we report two novel, orthogonal technologies to map PTs across the genomes of B7A and FF75 with >90% agreement: real-time (SMRT) sequencing and deep sequencing of iodine-induced cleavage at PT (ICDS). In B7A, we detect PT on both strands of GpsAAC/GpsTTC motifs, but with only 18% of 40,701 possible sites modified. In contrast, PT in FF75 occurs as a single-strand modification at CpsCA, again with only 14% of 160,541 sites modified. Single-molecule analysis indicates that modification could be partial at any particular genomic site even with active restriction by DndF-H, with direct interaction of modification proteins with GAAC/GTTC sites demonstrated with oligonucleotides. These results point to highly unusual target selection by PT modification proteins and rule out known R-M mechanisms. PMID:24899568

  12. Combined Linkage and Association Mapping Reveals QTL and Candidate Genes for Plant and Ear Height in Maize.

    PubMed

    Li, Xiaopeng; Zhou, Zijian; Ding, Junqiang; Wu, Yabin; Zhou, Bo; Wang, Ruixia; Ma, Jinliang; Wang, Shiwei; Zhang, Xuecai; Xia, Zongliang; Chen, Jiafa; Wu, Jianyu

    2016-01-01

    Plant height (PH) and ear height (EH) are two very important agronomic traits related to the population density and lodging in maize. In order to better understand of the genetic basis of nature variation in PH and EH, two bi-parental populations and one genome-wide association study (GWAS) population were used to map quantitative trait loci (QTL) for both traits. Phenotypic data analysis revealed a wide normal distribution and high heritability for PH and EH in the three populations, which indicated that maize height is a highly polygenic trait. A total of 21 QTL for PH and EH in three common genomic regions (bin 1.05, 5.04/05, and 6.04/05) were identified by QTL mapping in the two bi-parental populations under multiple environments. Additionally, 41 single nucleotide polymorphisms (SNPs) were identified for PH and EH by GWAS, of which 29 SNPs were located in 19 unique candidate gene regions. Most of the candidate genes were related to plant growth and development. One QTL on Chromosome 1 was further verified in a near-isogenic line (NIL) population, and GWAS identified a C2H2 zinc finger family protein that maybe the candidate gene for this QTL. These results revealed that nature variation of PH and EH are strongly controlled by multiple genes with low effect and facilitated a better understanding of the underlying mechanism of height in maize. PMID:27379126

  13. Combined Linkage and Association Mapping Reveals QTL and Candidate Genes for Plant and Ear Height in Maize

    PubMed Central

    Li, Xiaopeng; Zhou, Zijian; Ding, Junqiang; Wu, Yabin; Zhou, Bo; Wang, Ruixia; Ma, Jinliang; Wang, Shiwei; Zhang, Xuecai; Xia, Zongliang; Chen, Jiafa; Wu, Jianyu

    2016-01-01

    Plant height (PH) and ear height (EH) are two very important agronomic traits related to the population density and lodging in maize. In order to better understand of the genetic basis of nature variation in PH and EH, two bi-parental populations and one genome-wide association study (GWAS) population were used to map quantitative trait loci (QTL) for both traits. Phenotypic data analysis revealed a wide normal distribution and high heritability for PH and EH in the three populations, which indicated that maize height is a highly polygenic trait. A total of 21 QTL for PH and EH in three common genomic regions (bin 1.05, 5.04/05, and 6.04/05) were identified by QTL mapping in the two bi-parental populations under multiple environments. Additionally, 41 single nucleotide polymorphisms (SNPs) were identified for PH and EH by GWAS, of which 29 SNPs were located in 19 unique candidate gene regions. Most of the candidate genes were related to plant growth and development. One QTL on Chromosome 1 was further verified in a near-isogenic line (NIL) population, and GWAS identified a C2H2 zinc finger family protein that maybe the candidate gene for this QTL. These results revealed that nature variation of PH and EH are strongly controlled by multiple genes with low effect and facilitated a better understanding of the underlying mechanism of height in maize. PMID:27379126

  14. Multi-omics maps of cotton fibre reveal epigenetic basis for staged single-cell differentiation.

    PubMed

    Wang, Maojun; Wang, Pengcheng; Tu, Lili; Zhu, Sitao; Zhang, Lin; Li, Zhonghua; Zhang, Qinghua; Yuan, Daojun; Zhang, Xianlong

    2016-05-19

    Epigenetic modifications are highlighted for their great importance in regulating plant development, but their function associated with single-cell differentiation remains undetermined. Here, we used the cotton fibre, which is the epidermal hair on the cotton ovule, as a model to investigate the regulatory role of DNA methylation in cell differentiation. The level of CHH (H = A, T, or C) DNA methylation level was found to increase during fibre development, accompanied by a decrease in RNA-directed DNA methylation (RdDM). Examination of nucleosome positioning revealed a gradual transition from euchromatin to heterochromatin for chromatin dynamics in developing fibres, which could shape the DNA methylation landscape. The observed increase in DNA methylation in fibres, compared with other ovule tissue, was demonstrated to be mediated predominantly by an active H3K9me2-dependent pathway rather than the RdDM pathway, which was inactive. Furthermore, integrated multi-omics analyses revealed that dynamic DNA methylation played a role in the regulation of lipid biosynthesis and spatio-temporal modulation of reactive oxygen species during fibre differentiation. Our study illustrates two divergent pathways mediating a continuous increase of DNA methylation and also sheds further light on the epigenetic basis for single-cell differentiation in plants. These data and analyses are made available to the wider research community through a comprehensive web portal. PMID:27067544

  15. Multi-omics maps of cotton fibre reveal epigenetic basis for staged single-cell differentiation

    PubMed Central

    Wang, Maojun; Wang, Pengcheng; Tu, Lili; Zhu, Sitao; Zhang, Lin; Li, Zhonghua; Zhang, Qinghua; Yuan, Daojun; Zhang, Xianlong

    2016-01-01

    Epigenetic modifications are highlighted for their great importance in regulating plant development, but their function associated with single-cell differentiation remains undetermined. Here, we used the cotton fibre, which is the epidermal hair on the cotton ovule, as a model to investigate the regulatory role of DNA methylation in cell differentiation. The level of CHH (H = A, T, or C) DNA methylation level was found to increase during fibre development, accompanied by a decrease in RNA-directed DNA methylation (RdDM). Examination of nucleosome positioning revealed a gradual transition from euchromatin to heterochromatin for chromatin dynamics in developing fibres, which could shape the DNA methylation landscape. The observed increase in DNA methylation in fibres, compared with other ovule tissue, was demonstrated to be mediated predominantly by an active H3K9me2-dependent pathway rather than the RdDM pathway, which was inactive. Furthermore, integrated multi-omics analyses revealed that dynamic DNA methylation played a role in the regulation of lipid biosynthesis and spatio-temporal modulation of reactive oxygen species during fibre differentiation. Our study illustrates two divergent pathways mediating a continuous increase of DNA methylation and also sheds further light on the epigenetic basis for single-cell differentiation in plants. These data and analyses are made available to the wider research community through a comprehensive web portal. PMID:27067544

  16. COCMP Surface Current Mapping Reveals Eddy and Upwelling Jet off Cape Mendocino

    NASA Astrophysics Data System (ADS)

    Crawford, G. B.; Halle, C.; Largier, J.; Stone, S.

    2008-12-01

    Ocean surface currents are now being measured continuously over a roughly 2000 km stretch of the western US continental shelf from south of Tijuana, Mexico to the Columbia River. A long-standing gap in this coverage was finally filled on August 12, 2008, with the installation of a long-range Seasonde radar system at Shelter Cove, California (as a part of California's COCMP project). During its first three weeks of operation, this radar has revealed a large (~170 km diameter), stable, anticyclonic eddy southwest of Cape Mendocino in this poorly studied region. Upwelling-favorable winds appear to create an upwelling jet along the eastern edge of the eddy, leading to maximum daily-averaged current speeds up to 80 cm/s, and MODIS-derived chlorophyll concentrations up to 30 mg/m3 in the jet (compared to ~1 mg/m3 in the eddy center). AVHRR data reveal SST differences between the jet and the eddy center of 1.5 to 2.5 °C during these 3 weeks. These complex circulation structures modify water pathways and may interrupt nutrient delivery to locations farther south. We discuss the spatial and temporal evolution of these features.

  17. Mpath maps multi-branching single-cell trajectories revealing progenitor cell progression during development

    PubMed Central

    Chen, Jinmiao; Schlitzer, Andreas; Chakarov, Svetoslav; Ginhoux, Florent; Poidinger, Michael

    2016-01-01

    Single-cell RNA-sequencing offers unprecedented resolution of the continuum of state transition during cell differentiation and development. However, tools for constructing multi-branching cell lineages from single-cell data are limited. Here we present Mpath, an algorithm that derives multi-branching developmental trajectories using neighborhood-based cell state transitions. Applied to mouse conventional dendritic cell (cDC) progenitors, Mpath constructs multi-branching trajectories spanning from macrophage/DC progenitors through common DC progenitor to pre-dendritic cells (preDC). The Mpath-generated trajectories detect a branching event at the preDC stage revealing preDC subsets that are exclusively committed to cDC1 or cDC2 lineages. Reordering cells along cDC development reveals sequential waves of gene regulation and temporal coupling between cell cycle and cDC differentiation. Applied to human myoblasts, Mpath recapitulates the time course of myoblast differentiation and isolates a branch of non-muscle cells involved in the differentiation. Our study shows that Mpath is a useful tool for constructing cell lineages from single-cell data. PMID:27356503

  18. Mpath maps multi-branching single-cell trajectories revealing progenitor cell progression during development.

    PubMed

    Chen, Jinmiao; Schlitzer, Andreas; Chakarov, Svetoslav; Ginhoux, Florent; Poidinger, Michael

    2016-01-01

    Single-cell RNA-sequencing offers unprecedented resolution of the continuum of state transition during cell differentiation and development. However, tools for constructing multi-branching cell lineages from single-cell data are limited. Here we present Mpath, an algorithm that derives multi-branching developmental trajectories using neighborhood-based cell state transitions. Applied to mouse conventional dendritic cell (cDC) progenitors, Mpath constructs multi-branching trajectories spanning from macrophage/DC progenitors through common DC progenitor to pre-dendritic cells (preDC). The Mpath-generated trajectories detect a branching event at the preDC stage revealing preDC subsets that are exclusively committed to cDC1 or cDC2 lineages. Reordering cells along cDC development reveals sequential waves of gene regulation and temporal coupling between cell cycle and cDC differentiation. Applied to human myoblasts, Mpath recapitulates the time course of myoblast differentiation and isolates a branch of non-muscle cells involved in the differentiation. Our study shows that Mpath is a useful tool for constructing cell lineages from single-cell data. PMID:27356503

  19. Mass spectrometry reveals modularity and a complete subunit interaction map of the eukaryotic translation factor eIF3.

    PubMed

    Zhou, Min; Sandercock, Alan M; Fraser, Christopher S; Ridlova, Gabriela; Stephens, Elaine; Schenauer, Matthew R; Yokoi-Fong, Theresa; Barsky, Daniel; Leary, Julie A; Hershey, John W; Doudna, Jennifer A; Robinson, Carol V

    2008-11-25

    The eukaryotic initiation factor 3 (eIF3) plays an important role in translation initiation, acting as a docking site for several eIFs that assemble on the 40S ribosomal subunit. Here, we use mass spectrometry to probe the subunit interactions within the human eIF3 complex. Our results show that the 13-subunit complex can be maintained intact in the gas phase, enabling us to establish unambiguously its stoichiometry and its overall subunit architecture via tandem mass spectrometry and solution disruption experiments. Dissociation takes place as a function of ionic strength to form three stable modules eIF3(c:d:e:l:k), eIF3(f:h:m), and eIF3(a:b:i:g). These modules are linked by interactions between subunits eIF3b:c and eIF3c:h. We confirmed our interaction map with the homologous yeast eIF3 complex that contains the five core subunits found in the human eIF3 and supplemented our data with results from immunoprecipitation. These results, together with the 27 subcomplexes identified with increasing ionic strength, enable us to define a comprehensive interaction map for this 800-kDa species. Our interaction map allows comparison of free eIF3 with that bound to the hepatitis C virus internal ribosome entry site (HCV-IRES) RNA. We also compare our eIF3 interaction map with related complexes, containing evolutionarily conserved protein domains, and reveal the location of subunits containing RNA recognition motifs proximal to the decoding center of the 40S subunit of the ribosome. PMID:18599441

  20. Atmospheric Drivers of Greenland Surface Melt Revealed by Self-Organizing Maps

    NASA Technical Reports Server (NTRS)

    Mioduszewski, J. R.; Rennermalm, A. K.; Hammann, A.; Tedesco, M.; Noble, E. U.; Stroeve, J. C.; Mote, T. L.

    2016-01-01

    Recent acceleration in surface melt on the Greenland ice sheet (GrIS) has occurred concurrently with a rapidly warming Arctic and has been connected to persistent, anomalous atmospheric circulation patterns over Greenland. To identify synoptic setups favoring enhanced GrIS surface melt and their decadal changes, we develop a summer Arctic synoptic climatology by employing self-organizing maps. These are applied to daily 500 hPa geopotential height fields obtained from the Modern Era Retrospective Analysis for Research and Applications reanalysis, 1979-2014. Particular circulation regimes are related to meteorological conditions and GrIS surface melt estimated with outputs from the Modèle Atmosphérique Régional. Our results demonstrate that the largest positive melt anomalies occur in concert with positive height anomalies near Greenland associated with wind, temperature, and humidity patterns indicative of strong meridional transport of heat and moisture. We find an increased frequency in a 500 hPa ridge over Greenland coinciding with a 63% increase in GrIS melt between the 1979-1988 and 2005-2014 periods, with 75.0% of surface melt changes attributed to thermodynamics, 17% to dynamics, and 8.0% to a combination. We also confirm that the 2007-2012 time period has the largest dynamic forcing relative of any period but also demonstrate that increased surface energy fluxes, temperature, and moisture separate from dynamic changes contributed more to melt even during this period. This implies that GrIS surface melt is likely to continue to increase in response to an ever warmer future Arctic, regardless of future atmospheric circulation patterns.

  1. Neural organization of spoken language revealed by lesion-symptom mapping.

    PubMed

    Mirman, Daniel; Chen, Qi; Zhang, Yongsheng; Wang, Ze; Faseyitan, Olufunsho K; Coslett, H Branch; Schwartz, Myrna F

    2015-01-01

    Studies of patients with acquired cognitive deficits following brain damage and studies using contemporary neuroimaging techniques form two distinct streams of research on the neural basis of cognition. In this study, we combine high-quality structural neuroimaging analysis techniques and extensive behavioural assessment of patients with persistent acquired language deficits to study the neural basis of language. Our results reveal two major divisions within the language system-meaning versus form and recognition versus production-and their instantiation in the brain. Phonological form deficits are associated with lesions in peri-Sylvian regions, whereas semantic production and recognition deficits are associated with damage to the left anterior temporal lobe and white matter connectivity with frontal cortex, respectively. These findings provide a novel synthesis of traditional and contemporary views of the cognitive and neural architecture of language processing, emphasizing dual routes for speech processing and convergence of white matter tracts for semantic control and/or integration. PMID:25879574

  2. Whole-brain activity maps reveal stereotyped, distributed networks for visuomotor behavior

    PubMed Central

    Portugues, Ruben; Feierstein, Claudia E.; Engert, Florian; Orger, Michael B.

    2014-01-01

    Summary Most behaviors, even simple innate reflexes, are mediated by circuits of neurons spanning areas throughout the brain. However, in most cases, the distribution and dynamics of firing patterns of these neurons during behavior are not known. We imaged activity, with cellular resolution, throughout the whole brains of zebrafish performing the optokinetic response. We found a sparse, broadly distributed network that has an elaborate, but ordered, pattern, with a bilaterally symmetrical organization. Activity patterns fell into distinct clusters reflecting sensory and motor processing. By correlating neuronal responses with an array of sensory and motor variables, we find that the network can be clearly divided into distinct functional modules. Comparing aligned data from multiple fish, we find that the spatiotemporal activity dynamics and functional organization are highly stereotyped across individuals. These experiments reveal, for the first time in a vertebrate, the comprehensive functional architecture of the neural circuits underlying a sensorimotor behavior. PMID:24656252

  3. Notch2 genetic fate mapping reveals two previously unrecognized mammary epithelial lineages

    PubMed Central

    Šale, Sanja; Lafkas, Daniel; Artavanis-Tsakonas, Spyros

    2013-01-01

    Notch signalling is implicated in stem and progenitor cell fate control in numerous organs. Using conditional in vivo genetic labelling we traced the fate of cells expressing the Notch2 receptor paralogue and uncovered the existence of two previously unrecognized mammary epithelial cell lineages that we term S (Small) and L (Large). S cells appear in a bead-on-a-string formation and are embedded between the luminal and basal/myoepithelial layers in a unique reiterative pattern, whereas single or paired L cells appear among ductal and alveolar cells. Long-term lineage tracing and functional studies indicate that S and L cells regulate ipsi- and contralateral spatial placement of tertiary branches and formation of alveolar clusters. Our findings revise present models of mammary epithelial cell hierarchy, reveal a hitherto undescribed mechanism regulating branching morphogenesis and may have important implications for identification of the cell-of-origin of distinct breast cancer subtypes. PMID:23604318

  4. Conditional Epistatic Interaction Maps Reveal Global Functional Rewiring of Genome Integrity Pathways in Escherichia coli.

    PubMed

    Kumar, Ashwani; Beloglazova, Natalia; Bundalovic-Torma, Cedoljub; Phanse, Sadhna; Deineko, Viktor; Gagarinova, Alla; Musso, Gabriel; Vlasblom, James; Lemak, Sofia; Hooshyar, Mohsen; Minic, Zoran; Wagih, Omar; Mosca, Roberto; Aloy, Patrick; Golshani, Ashkan; Parkinson, John; Emili, Andrew; Yakunin, Alexander F; Babu, Mohan

    2016-01-26

    As antibiotic resistance is increasingly becoming a public health concern, an improved understanding of the bacterial DNA damage response (DDR), which is commonly targeted by antibiotics, could be of tremendous therapeutic value. Although the genetic components of the bacterial DDR have been studied extensively in isolation, how the underlying biological pathways interact functionally remains unclear. Here, we address this by performing systematic, unbiased, quantitative synthetic genetic interaction (GI) screens and uncover widespread changes in the GI network of the entire genomic integrity apparatus of Escherichia coli under standard and DNA-damaging growth conditions. The GI patterns of untreated cultures implicated two previously uncharacterized proteins (YhbQ and YqgF) as nucleases, whereas reorganization of the GI network after DNA damage revealed DDR roles for both annotated and uncharacterized genes. Analyses of pan-bacterial conservation patterns suggest that DDR mechanisms and functional relationships are near universal, highlighting a modular and highly adaptive genomic stress response. PMID:26774489

  5. Neural Organization of Spoken Language Revealed by Lesion-Symptom Mapping

    PubMed Central

    Mirman, Daniel; Chen, Qi; Zhang, Yongsheng; Wang, Ze; Faseyitan, Olufunsho K.; Coslett, H. Branch; Schwartz, Myrna F.

    2015-01-01

    Studies of patients with acquired cognitive deficits following brain damage and studies using contemporary neuroimaging techniques form two distinct streams of research on the neural basis of cognition. In this study, we combine high-quality structural neuroimaging analysis techniques and extensive behavioral assessment of patients with persistent acquired language deficits to study the neural basis of language. Our results reveal two major divisions within the language system – meaning vs. form and recognition vs. production – and their instantiation in the brain. Phonological form deficits are associated with lesions in peri-Sylvian regions, whereas semantic production and recognition deficits are associated with damage to the left anterior temporal lobe and white matter connectivity with frontal cortex, respectively. These findings provide a novel synthesis of traditional and contemporary views of the cognitive and neural architecture of language processing, emphasizing dual-routes for speech processing and convergence of white matter tracts for semantic control and/or integration. PMID:25879574

  6. A First Glimpse of Wild Lupin Karyotype Variation As Revealed by Comparative Cytogenetic Mapping

    PubMed Central

    Susek, Karolina; Bielski, Wojciech K.; Hasterok, Robert; Naganowska, Barbara; Wolko, Bogdan

    2016-01-01

    Insight into plant genomes at the cytomolecular level provides useful information about their karyotype structure, enabling inferences about taxonomic relationships and evolutionary origins. The Old World lupins (OWL) demonstrate a high level of genomic diversification involving variation in chromosome numbers (2n = 32–52), basic chromosome numbers (x = 5–7, 9, 13) and in nuclear genome size (2C DNA = 0.97–2.68 pg). Lupins comprise both crop and wild species and provide an intriguing system to study karyotype evolution. In order to investigate lupin chromosome structure, heterologous FISH was used. Sixteen BACs that had been generated as chromosome markers for the reference species, Lupinus angustifolius, were used to identify chromosomes in the wild species and explore karyotype variation. While all “single-locus” in L. angustifolius, in the wild lupins these clones proved to be “single-locus,” “single-locus” with additional signals, “repetitive” or had no detectable BAC-FISH signal. The diverse distribution of the clones in the targeted genomes suggests a complex evolution history, which possibly involved multiple chromosomal changes such as fusions/fissions and repetitive sequence amplification. Twelve BACs were sequenced and we found numerous transposable elements including DNA transposons as well as LTR and non-LTR retrotransposons with varying quantity and composition among the different lupin species. However, at this preliminary stage, no correlation was observed between the pattern of BAC-FISH signals and the repeat content in particular BACs. Here, we describe the first BAC-based chromosome-specific markers for the wild species: L. cosentinii, L. cryptanthus, L. pilosus, L. micranthus and one New World lupin, L. multiflorus. These BACs could constitute the basis for an assignment of the chromosomal and genetic maps of other lupins, e.g., L. albus and L. luteus. Moreover, we identified karyotype variation that helps illustrate the

  7. A First Glimpse of Wild Lupin Karyotype Variation As Revealed by Comparative Cytogenetic Mapping.

    PubMed

    Susek, Karolina; Bielski, Wojciech K; Hasterok, Robert; Naganowska, Barbara; Wolko, Bogdan

    2016-01-01

    Insight into plant genomes at the cytomolecular level provides useful information about their karyotype structure, enabling inferences about taxonomic relationships and evolutionary origins. The Old World lupins (OWL) demonstrate a high level of genomic diversification involving variation in chromosome numbers (2n = 32-52), basic chromosome numbers (x = 5-7, 9, 13) and in nuclear genome size (2C DNA = 0.97-2.68 pg). Lupins comprise both crop and wild species and provide an intriguing system to study karyotype evolution. In order to investigate lupin chromosome structure, heterologous FISH was used. Sixteen BACs that had been generated as chromosome markers for the reference species, Lupinus angustifolius, were used to identify chromosomes in the wild species and explore karyotype variation. While all "single-locus" in L. angustifolius, in the wild lupins these clones proved to be "single-locus," "single-locus" with additional signals, "repetitive" or had no detectable BAC-FISH signal. The diverse distribution of the clones in the targeted genomes suggests a complex evolution history, which possibly involved multiple chromosomal changes such as fusions/fissions and repetitive sequence amplification. Twelve BACs were sequenced and we found numerous transposable elements including DNA transposons as well as LTR and non-LTR retrotransposons with varying quantity and composition among the different lupin species. However, at this preliminary stage, no correlation was observed between the pattern of BAC-FISH signals and the repeat content in particular BACs. Here, we describe the first BAC-based chromosome-specific markers for the wild species: L. cosentinii, L. cryptanthus, L. pilosus, L. micranthus and one New World lupin, L. multiflorus. These BACs could constitute the basis for an assignment of the chromosomal and genetic maps of other lupins, e.g., L. albus and L. luteus. Moreover, we identified karyotype variation that helps illustrate the relationships between the

  8. Cosmic strings

    NASA Technical Reports Server (NTRS)

    Bennett, David P.

    1988-01-01

    Cosmic strings are linear topological defects which are predicted by some grand unified theories to form during a spontaneous symmetry breaking phase transition in the early universe. They are the basis for the only theories of galaxy formation aside from quantum fluctuations from inflation based on fundamental physics. In contrast to inflation, they can also be observed directly through gravitational lensing and their characterisitc microwave background anisotropy. It was recently discovered that details of cosmic string evolution are very differnt from the so-called standard model that was assumed in most of the string-induced galaxy formation calculations. Therefore, the details of galaxy formation in the cosmic string models are currently very uncertain.

  9. Cosmic strings

    SciTech Connect

    Bennett, D.P.

    1988-07-01

    Cosmic strings are linear topological defects that are predicted by some grand unified theories to form during a spontaneous symmetry breaking phase transition in the early universe. They are the basis for the only theories of galaxy formation aside from quantum fluctuations from inflation that are based on fundamental physics. In contrast to inflation, they can also be observed directly through gravitational lensing and their characteristic microwave background anistropy. It has recently been discovered by F. Bouchet and myself that details of cosmic string evolution are very different from the so-called ''standard model'' that has been assumed in most of the string induced galaxy formation calculations. Therefore, the details of galaxy formation in the cosmic string models are currently very uncertain. 29 refs., 9 figs.

  10. Enhanced transcriptome maps from multiple mouse tissues reveal evolutionary constraint in gene expression.

    PubMed

    Pervouchine, Dmitri D; Djebali, Sarah; Breschi, Alessandra; Davis, Carrie A; Barja, Pablo Prieto; Dobin, Alex; Tanzer, Andrea; Lagarde, Julien; Zaleski, Chris; See, Lei-Hoon; Fastuca, Meagan; Drenkow, Jorg; Wang, Huaien; Bussotti, Giovanni; Pei, Baikang; Balasubramanian, Suganthi; Monlong, Jean; Harmanci, Arif; Gerstein, Mark; Beer, Michael A; Notredame, Cedric; Guigó, Roderic; Gingeras, Thomas R

    2015-01-01

    Mice have been a long-standing model for human biology and disease. Here we characterize, by RNA sequencing, the transcriptional profiles of a large and heterogeneous collection of mouse tissues, augmenting the mouse transcriptome with thousands of novel transcript candidates. Comparison with transcriptome profiles in human cell lines reveals substantial conservation of transcriptional programmes, and uncovers a distinct class of genes with levels of expression that have been constrained early in vertebrate evolution. This core set of genes captures a substantial fraction of the transcriptional output of mammalian cells, and participates in basic functional and structural housekeeping processes common to all cell types. Perturbation of these constrained genes is associated with significant phenotypes including embryonic lethality and cancer. Evolutionary constraint in gene expression levels is not reflected in the conservation of the genomic sequences, but is associated with conserved epigenetic marking, as well as with characteristic post-transcriptional regulatory programme, in which sub-cellular localization and alternative splicing play comparatively large roles. PMID:25582907

  11. Deletion mapping of the potyviral helper component-proteinase reveals two regions involved in RNA binding.

    PubMed

    Urcuqui-Inchima, S; Maia, I G; Arruda, P; Haenni, A L; Bernardi, F

    2000-03-01

    The Potyvirus helper component-proteinase (HC-Pro) binds nonspecifically to single-stranded nucleic acids with a preference for RNA. To delineate the regions of the protein responsible for RNA binding, deletions were introduced into the full-length Potato potyvirus Y HC-Pro gene carried by an Escherichia coli expression vector. The corresponding proteins were expressed as fusions with the maltose-binding protein, purified, and assayed for their RNA-binding capacity. The results obtained by UV cross-linking and Northwestern blot assays demonstrated that the N- and C-terminal regions of HC-Pro are dispensable for RNA binding. They also revealed the presence of two independent RNA-binding domains (designated A and B) located in the central part of HC-Pro. Domain B appears to contain a ribonucleoprotein (RNP) motif typical of a large family of RNA-binding proteins involved in several cellular processes. The possibility that domain B consists of an RNP domain is discussed and suggests that HC-Pro could constitute the first example of a plant viral protein belonging to the RNP-containing family of proteins. PMID:10683332

  12. Substrate recruitment of γ-secretase and mechanism of clinical presenilin mutations revealed by photoaffinity mapping.

    PubMed

    Fukumori, Akio; Steiner, Harald

    2016-08-01

    Intramembrane proteases execute fundamental biological processes ranging from crucial signaling events to general membrane proteostasis. Despite the availability of structural information on these proteases, it remains unclear how these enzymes bind and recruit substrates, particularly for the Alzheimer's disease-associated γ-secretase. Systematically scanning amyloid precursor protein substrates containing a genetically inserted photocrosslinkable amino acid for binding to γ-secretase allowed us to identify residues contacting the protease. These were primarily found in the transmembrane cleavage domain of the substrate and were also present in the extramembranous domains. The N-terminal fragment of the catalytic subunit presenilin was determined as principal substrate-binding site. Clinical presenilin mutations altered substrate binding in the active site region, implying a pathogenic mechanism for familial Alzheimer's disease. Remarkably, PEN-2 was identified besides nicastrin as additional substrate-binding subunit. Probing proteolysis of crosslinked substrates revealed a mechanistic model of how these subunits interact to mediate a stepwise transfer of bound substrate to the catalytic site. We propose that sequential binding steps might be common for intramembrane proteases to sample and select cognate substrates for catalysis. PMID:27220847

  13. Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection

    PubMed Central

    Xie, Weibo; Wang, Gongwei; Yuan, Meng; Yao, Wen; Lyu, Kai; Zhao, Hu; Yang, Meng; Li, Pingbo; Zhang, Xing; Yuan, Jing; Wang, Quanxiu; Liu, Fang; Dong, Huaxia; Zhang, Lejing; Li, Xinglei; Meng, Xiangzhou; Zhang, Wan; Xiong, Lizhong; He, Yuqing; Wang, Shiping; Yu, Sibin; Xu, Caiguo; Luo, Jie; Li, Xianghua; Xiao, Jinghua; Lian, Xingming; Zhang, Qifa

    2015-01-01

    Intensive rice breeding over the past 50 y has dramatically increased productivity especially in the indica subspecies, but our knowledge of the genomic changes associated with such improvement has been limited. In this study, we analyzed low-coverage sequencing data of 1,479 rice accessions from 73 countries, including landraces and modern cultivars. We identified two major subpopulations, indica I (IndI) and indica II (IndII), in the indica subspecies, which corresponded to the two putative heterotic groups resulting from independent breeding efforts. We detected 200 regions spanning 7.8% of the rice genome that had been differentially selected between IndI and IndII, and thus referred to as breeding signatures. These regions included large numbers of known functional genes and loci associated with important agronomic traits revealed by genome-wide association studies. Grain yield was positively correlated with the number of breeding signatures in a variety, suggesting that the number of breeding signatures in a line may be useful for predicting agronomic potential and the selected loci may provide targets for rice improvement. PMID:26358652

  14. Transcriptome-wide mapping reveals reversible and dynamic N(1)-methyladenosine methylome.

    PubMed

    Li, Xiaoyu; Xiong, Xushen; Wang, Kun; Wang, Lixia; Shu, Xiaoting; Ma, Shiqing; Yi, Chengqi

    2016-05-01

    N(1)-Methyladenosine (m(1)A) is a prevalent post-transcriptional RNA modification, yet little is known about its abundance, topology and dynamics in mRNA. Here, we show that m(1)A is prevalent in Homo sapiens mRNA, which shows an m(1)A/A ratio of ∼0.02%. We develop the m(1)A-ID-seq technique, based on m(1)A immunoprecipitation and the inherent ability of m(1)A to stall reverse transcription, as a means for transcriptome-wide m(1)A profiling. m(1)A-ID-seq identifies 901 m(1)A peaks (from 600 genes) in mRNA and noncoding RNA and reveals a prominent feature, enrichment in the 5' untranslated region of mRNA transcripts, that is distinct from the pattern for N(6)-methyladenosine, the most abundant internal mammalian mRNA modification. Moreover, m(1)A in mRNA is reversible by ALKBH3, a known DNA/RNA demethylase. Lastly, we show that m(1)A methylation responds dynamically to stimuli, and we identify hundreds of stress-induced m(1)A sites. Collectively, our approaches allow comprehensive analysis of m(1)A modification and provide tools for functional studies of potential epigenetic regulation via the reversible and dynamic m(1)A methylation. PMID:26863410

  15. Superresolution Pattern Recognition Reveals the Architectural Map of the Ciliary Transition Zone

    PubMed Central

    Tony Yang, T.; Su, Jimmy; Wang, Won-Jing; Craige, Branch; Witman, George B.; Bryan Tsou, Meng-Fu; Liao, Jung-Chi

    2015-01-01

    The transition zone (TZ) of primary cilia serves as a diffusion barrier to regulate ciliogenesis and receptor localization for key signaling events such as sonic hedgehog signaling. Its gating mechanism is poorly understood due to the tiny volume accommodating a large number of ciliopathy-associated molecules. Here we performed stimulated emission depletion (STED) imaging of collective samples and recreated superresolved relative localizations of eight representative species of ciliary proteins using position averages and overlapped with representative electron microscopy (EM) images, defining an architectural foundation at the ciliary base. Upon this framework, transmembrane proteins TMEM67 and TCTN2 were accumulated at the same axial level as MKS1 and RPGRIP1L, suggesting that their regulation roles for tissue-specific ciliogenesis occur at a specific level of the TZ. CEP290 is surprisingly localized at a different axial level bridging the basal body (BB) and other TZ proteins. Upon this molecular architecture, two reservoirs of intraflagellar transport (IFT) particles, correlating with phases of ciliary growth, are present: one colocalized with the transition fibers (TFs) while the other situated beyond the distal edge of the TZ. Together, our results reveal an unprecedented structural framework of the TZ, facilitating our understanding in molecular screening and assembly at the ciliary base. PMID:26365165

  16. Enhanced transcriptome maps from multiple mouse tissues reveal evolutionary constraint in gene expression

    PubMed Central

    Pervouchine, Dmitri D.; Djebali, Sarah; Breschi, Alessandra; Davis, Carrie A.; Barja, Pablo Prieto; Dobin, Alex; Tanzer, Andrea; Lagarde, Julien; Zaleski, Chris; See, Lei-Hoon; Fastuca, Meagan; Drenkow, Jorg; Wang, Huaien; Bussotti, Giovanni; Pei, Baikang; Balasubramanian, Suganthi; Monlong, Jean; Harmanci, Arif; Gerstein, Mark; Beer, Michael A.; Notredame, Cedric; Guigó, Roderic; Gingeras, Thomas R.

    2015-01-01

    Mice have been a long-standing model for human biology and disease. Here we characterize, by RNA sequencing, the transcriptional profiles of a large and heterogeneous collection of mouse tissues, augmenting the mouse transcriptome with thousands of novel transcript candidates. Comparison with transcriptome profiles in human cell lines reveals substantial conservation of transcriptional programmes, and uncovers a distinct class of genes with levels of expression that have been constrained early in vertebrate evolution. This core set of genes captures a substantial fraction of the transcriptional output of mammalian cells, and participates in basic functional and structural housekeeping processes common to all cell types. Perturbation of these constrained genes is associated with significant phenotypes including embryonic lethality and cancer. Evolutionary constraint in gene expression levels is not reflected in the conservation of the genomic sequences, but is associated with conserved epigenetic marking, as well as with characteristic post-transcriptional regulatory programme, in which sub-cellular localization and alternative splicing play comparatively large roles. PMID:25582907

  17. Motif module map reveals enforcement of aging by continual NF-κB activity

    PubMed Central

    Adler, Adam S.; Sinha, Saurabh; Kawahara, Tiara L.A.; Zhang, Jennifer Y.; Segal, Eran; Chang, Howard Y.

    2007-01-01

    Aging is characterized by specific alterations in gene expression, but their underlying mechanisms and functional consequences are not well understood. Here we develop a systematic approach to identify combinatorial cis-regulatory motifs that drive age-dependent gene expression across different tissues and organisms. Integrated analysis of 365 microarrays spanning nine tissue types predicted fourteen motifs as major regulators of age-dependent gene expression in human and mouse. The motif most strongly associated with aging was that of the transcription factor NF-κB. Inducible genetic blockade of NF-κB for 2 wk in the epidermis of chronologically aged mice reverted the tissue characteristics and global gene expression programs to those of young mice. Age-specific NF-κB blockade and orthogonal cell cycle interventions revealed that NF-κB controls cell cycle exit and gene expression signature of aging in parallel but not sequential pathways. These results identify a conserved network of regulatory pathways underlying mammalian aging and show that NF-κB is continually required to enforce many features of aging in a tissue-specific manner. PMID:18055696

  18. “Spatial Mapping of the Neurite and Soma Proteomes Reveals a Functional Cdc42/Rac Regulatory Network”

    SciTech Connect

    Pertz, Olivier C.; Wang, Yingchun; Yang, Feng; Wang, Wei; gay, laurie J.; Gritsenko, Marina A.; Clauss, Therese RW; Anderson, David J.; Liu, Tao; Auberry, Kenneth J.; Camp, David G.; Smith, Richard D.; Klemke, Richard L.

    2008-02-12

    Neurite extension and growth cone navigation are guided by extracellular cues that control cytoskeletal rearrangements. However, understanding the complex signaling mechanisms that mediate neuritogenesis has been limited by the inability to biochemically separate the neurite and soma for spatial proteomic and bioinformatic analyses. Here, we apply global proteome profiling in combination with a novel neurite purification methodology for comparative analysis of the soma and neurite proteomes of neuroblastoma cells. The spatial relationship of 4855 proteins were mapped revealing networks of signaling proteins that control integrins, the actin cytoskeleton, and axonal guidance in the extending neurite. Bioinformatics and functional analyses revealed a spatially compartmentalized Rac/Cdc42 signaling network that operates in conjunction with multiple GEFs and GAPs to control neurite formation. Interestingly, RNA interference experiments revealed that the different GEFs and GAPs regulate specialized functions during neurite formation including neurite growth and retraction kinetics, cytoskeletal organization, and cell polarity. Our findings provide insight into the spatial organization of signaling networks that enable neuritogenesis and provide a comprehensive system-wide profile of proteins that mediate this process including those that control Rac and Cdc42 signaling.

  19. Temporal fate mapping reveals age-linked heterogeneity in naive T lymphocytes in mice

    PubMed Central

    Hogan, Thea; Gossel, Graeme; Yates, Andrew J.; Seddon, Benedict

    2015-01-01

    Understanding how our T-cell compartments are maintained requires knowledge of their population dynamics, which are typically quantified over days to weeks using the administration of labels incorporated into the DNA of dividing cells. These studies present snapshots of homeostatic dynamics and have suggested that lymphocyte populations are heterogeneous with respect to rates of division and/or death, although resolving the details of such heterogeneity is problematic. Here we present a method of studying the population dynamics of T cells in mice over timescales of months to years that reveals heterogeneity in rates of division and death with respect to the age of the host at the time of thymic export. We use the transplant conditioning drug busulfan to ablate hematopoetic stem cells in young mice but leave the peripheral lymphocyte compartments intact. Following their reconstitution with congenically labeled (donor) bone marrow, we followed the dilution of peripheral host T cells by donor-derived lymphocytes for a year after treatment. Describing these kinetics with mathematical models, we estimate rates of thymic production, division and death of naive CD4 and CD8 T cells. Population-averaged estimates of mean lifetimes are consistent with earlier studies, but we find the strongest support for a model in which both naive T-cell pools contain kinetically distinct subpopulations of older host-derived cells with self-renewing capacity that are resistant to displacement by naive donor lymphocytes. We speculate that these incumbent cells are conditioned or selected for increased fitness through homeostatic expansion into the lymphopenic neonatal environment. PMID:26607449

  20. Temporal fate mapping reveals age-linked heterogeneity in naive T lymphocytes in mice.

    PubMed

    Hogan, Thea; Gossel, Graeme; Yates, Andrew J; Seddon, Benedict

    2015-12-15

    Understanding how our T-cell compartments are maintained requires knowledge of their population dynamics, which are typically quantified over days to weeks using the administration of labels incorporated into the DNA of dividing cells. These studies present snapshots of homeostatic dynamics and have suggested that lymphocyte populations are heterogeneous with respect to rates of division and/or death, although resolving the details of such heterogeneity is problematic. Here we present a method of studying the population dynamics of T cells in mice over timescales of months to years that reveals heterogeneity in rates of division and death with respect to the age of the host at the time of thymic export. We use the transplant conditioning drug busulfan to ablate hematopoetic stem cells in young mice but leave the peripheral lymphocyte compartments intact. Following their reconstitution with congenically labeled (donor) bone marrow, we followed the dilution of peripheral host T cells by donor-derived lymphocytes for a year after treatment. Describing these kinetics with mathematical models, we estimate rates of thymic production, division and death of naive CD4 and CD8 T cells. Population-averaged estimates of mean lifetimes are consistent with earlier studies, but we find the strongest support for a model in which both naive T-cell pools contain kinetically distinct subpopulations of older host-derived cells with self-renewing capacity that are resistant to displacement by naive donor lymphocytes. We speculate that these incumbent cells are conditioned or selected for increased fitness through homeostatic expansion into the lymphopenic neonatal environment. PMID:26607449

  1. Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of human lincRNA genes

    PubMed Central

    Ma, Wenxiu; Ay, Ferhat; Lee, Choli; Gulsoy, Gunhan; Deng, Xinxian; Cook, Savannah; Hesson, Jennifer; Cavanaugh, Christopher; Ware, Carol B.; Krumm, Anton; Shendure, Jay; Blau, C. Anthony; Disteche, Christine M.; Noble, William S.; Duan, ZhiJun

    2014-01-01

    High-throughput methods based on chromosome conformation capture (3C) have greatly advanced our understanding of the three-dimensional (3D) organization of genomes but are limited in resolution by their reliance on restriction enzymes (REs). Here we describe a method called DNase Hi-C for comprehensively mapping global chromatin contacts that uses DNase I for chromatin fragmentation, leading to greatly improved efficiency and resolution compared to Hi-C. Coupling this method with DNA capture technology provides a high-throughput approach for targeted mapping of fine-scale chromatin architecture. We applied targeted DNase Hi-C to characterize the 3D organization of 998 lincRNA (long intergenic noncoding RNA) promoters in two human cell lines, thereby revealing that expression of lincRNAs is tightly controlled by complex mechanisms involving both super-enhancers and the polycomb repressive complex. Our results provide the first glimpse of a cell type-specific 3D organization of lincRNA genes. PMID:25437436

  2. Novel Sequence-Based Mapping of Recently Emerging H5NX Influenza Viruses Reveals Pandemic Vaccine Candidates

    PubMed Central

    Anderson, Christopher S.; DeDiego, Marta L.; Thakar, Juilee; Topham, David J.

    2016-01-01

    Recently, an avian influenza virus, H5NX subclade 2.3.4.4, emerged and spread to North America. This subclade has frequently reassorted, leading to multiple novel viruses capable of human infection. Four cases of human infections, three leading to death, have already occurred. Existing vaccine strains do not protect against these new viruses, raising a need to identify new vaccine candidate strains. We have developed a novel sequence-based mapping (SBM) tool capable of visualizing complex protein sequence data sets using a single intuitive map. We applied SBM on the complete set of avian H5 viruses in order to better understand hemagglutinin protein variance amongst H5 viruses and identify any patterns associated with this variation. The analysis successfully identified the original reassortments that lead to the emergence of this new subclade of H5 viruses, as well as their known unusual ability to re-assort among neuraminidase subtypes. In addition, our analysis revealed distinct clusters of 2.3.4.4 variants that would not be covered by existing strains in the H5 vaccine stockpile. The results suggest that our method may be useful for pandemic candidate vaccine virus selection. PMID:27494186

  3. Novel Sequence-Based Mapping of Recently Emerging H5NX Influenza Viruses Reveals Pandemic Vaccine Candidates.

    PubMed

    Anderson, Christopher S; DeDiego, Marta L; Thakar, Juilee; Topham, David J

    2016-01-01

    Recently, an avian influenza virus, H5NX subclade 2.3.4.4, emerged and spread to North America. This subclade has frequently reassorted, leading to multiple novel viruses capable of human infection. Four cases of human infections, three leading to death, have already occurred. Existing vaccine strains do not protect against these new viruses, raising a need to identify new vaccine candidate strains. We have developed a novel sequence-based mapping (SBM) tool capable of visualizing complex protein sequence data sets using a single intuitive map. We applied SBM on the complete set of avian H5 viruses in order to better understand hemagglutinin protein variance amongst H5 viruses and identify any patterns associated with this variation. The analysis successfully identified the original reassortments that lead to the emergence of this new subclade of H5 viruses, as well as their known unusual ability to re-assort among neuraminidase subtypes. In addition, our analysis revealed distinct clusters of 2.3.4.4 variants that would not be covered by existing strains in the H5 vaccine stockpile. The results suggest that our method may be useful for pandemic candidate vaccine virus selection. PMID:27494186

  4. Autonomous underwater vehicle (AUV) mapping reveals coral mound distribution, morphology, and oceanography in deep water of the Straits of Florida

    NASA Astrophysics Data System (ADS)

    Grasmueck, Mark; Eberli, Gregor P.; Viggiano, David A.; Correa, Thiago; Rathwell, Glenda; Luo, Jiangang

    2006-12-01

    To make progress in understanding the distribution and genesis of coral mounds in cold and dark water, maps of morphology and oceanographic conditions resolving features at the 1-10 m scale are needed. An autonomous underwater vehicle (AUV) cruising 40 m above the seafloor surveyed a 48 km2 coral mound field in 600-800 m water depth at the base of slope of Great Bahama Bank. The AUV acquired 1-3 meter resolution acoustic backscatter and bathymetry together with current vectors, salinity, and temperature. The multibeam bathymetry resolved more than 200 coral mounds reaching up to 90 m height. Mound morphology is surprisingly diverse and mound distribution follows E-W oriented off-bank ridges. Bottom currents reverse every 6 hours indicating tidal flow decoupled from the north flowing surface current. The AUV data fill the gap between low-resolution surface-based mapping and visual observations on the seafloor, revealing the dynamic environment and spatial relationships of an entire coral mound field.

  5. Cosmic Balloons

    ERIC Educational Resources Information Center

    El Abed, Mohamed

    2014-01-01

    A team of French high-school students sent a weather balloon into the upper atmosphere to recreate Viktor Hess's historical experiment that demonstrated the existence of ionizing radiation from the sky--later called cosmic radiation. This discovery earned him the Nobel Prize for Physics in 1936.

  6. Cosmic balloons

    NASA Astrophysics Data System (ADS)

    El Abed, Mohamed

    2014-11-01

    A team of French high-school students sent a weather balloon into the upper atmosphere to recreate Viktor Hess’s historical experiment that demonstrated the existence of ionizing radiation from the sky—later called cosmic radiation. This discovery earned him the Nobel Prize for Physics in 1936.

  7. Topographical Mapping of the Rainbow Trout (Oncorhynchus mykiss) Microbiome Reveals a Diverse Bacterial Community with Antifungal Properties in the Skin.

    PubMed

    Lowrey, Liam; Woodhams, Douglas C; Tacchi, Luca; Salinas, Irene

    2015-10-01

    The mucosal surfaces of wild and farmed aquatic vertebrates face the threat of many aquatic pathogens, including fungi. These surfaces are colonized by diverse symbiotic bacterial communities that may contribute to fight infection. Whereas the gut microbiome of teleosts has been extensively studied using pyrosequencing, this tool has rarely been employed to study the compositions of the bacterial communities present on other teleost mucosal surfaces. Here we provide a topographical map of the mucosal microbiome of an aquatic vertebrate, the rainbow trout (Oncorhynchus mykiss). Using 16S rRNA pyrosequencing, we revealed novel bacterial diversity at each of the five body sites sampled and showed that body site is a strong predictor of community composition. The skin exhibited the highest diversity, followed by the olfactory organ, gills, and gut. Flectobacillus was highly represented within skin and gill communities. Principal coordinate analysis and plots revealed clustering of external sites apart from internal sites. A highly diverse community was present within the epithelium, as demonstrated by confocal microscopy and pyrosequencing. Using in vitro assays, we demonstrated that two Arthrobacter sp. skin isolates, a Psychrobacter sp. strain, and a combined skin aerobic bacterial sample inhibit the growth of Saprolegnia australis and Mucor hiemalis, two important aquatic fungal pathogens. These results underscore the importance of symbiotic bacterial communities of fish and their potential role for the control of aquatic fungal diseases. PMID:26209676

  8. Topographical Mapping of the Rainbow Trout (Oncorhynchus mykiss) Microbiome Reveals a Diverse Bacterial Community with Antifungal Properties in the Skin

    PubMed Central

    Lowrey, Liam; Woodhams, Douglas C.; Tacchi, Luca

    2015-01-01

    The mucosal surfaces of wild and farmed aquatic vertebrates face the threat of many aquatic pathogens, including fungi. These surfaces are colonized by diverse symbiotic bacterial communities that may contribute to fight infection. Whereas the gut microbiome of teleosts has been extensively studied using pyrosequencing, this tool has rarely been employed to study the compositions of the bacterial communities present on other teleost mucosal surfaces. Here we provide a topographical map of the mucosal microbiome of an aquatic vertebrate, the rainbow trout (Oncorhynchus mykiss). Using 16S rRNA pyrosequencing, we revealed novel bacterial diversity at each of the five body sites sampled and showed that body site is a strong predictor of community composition. The skin exhibited the highest diversity, followed by the olfactory organ, gills, and gut. Flectobacillus was highly represented within skin and gill communities. Principal coordinate analysis and plots revealed clustering of external sites apart from internal sites. A highly diverse community was present within the epithelium, as demonstrated by confocal microscopy and pyrosequencing. Using in vitro assays, we demonstrated that two Arthrobacter sp. skin isolates, a Psychrobacter sp. strain, and a combined skin aerobic bacterial sample inhibit the growth of Saprolegnia australis and Mucor hiemalis, two important aquatic fungal pathogens. These results underscore the importance of symbiotic bacterial communities of fish and their potential role for the control of aquatic fungal diseases. PMID:26209676

  9. Cosmic jets

    NASA Technical Reports Server (NTRS)

    Rees, M. J.

    1986-01-01

    The evidence that active galactic nuclei produce collimated plasma jets is summarised. The strongest radio galaxies are probably energised by relativistic plasma jets generated by spinning black holes interacting with magnetic fields attached to infalling matter. Such objects can produce e(+)-e(-) plasma, and may be relevant to the acceleration of the highest-energy cosmic ray primaries. Small-scale counterparts of the jet phenomenon within our own galaxy are briefly reviewed.

  10. Cosmic Topology

    NASA Astrophysics Data System (ADS)

    Luminet, Jean-Pierre

    2015-08-01

    Cosmic Topology is the name given to the study of the overall shape of the universe, which involves both global topological features and more local geometrical properties such as curvature. Whether space is finite or infinite, simply-connected or multi-connected like a torus, smaller or greater than the portion of the universe that we can directly observe, are questions that refer to topology rather than curvature. A striking feature of some relativistic, multi-connected "small" universe models is to create multiples images of faraway cosmic sources. While the most recent cosmological data fit the simplest model of a zero-curvature, infinite space model, they are also consistent with compact topologies of the three homogeneous and isotropic geometries of constant curvature, such as, for instance, the spherical Poincaré Dodecahedral Space, the flat hypertorus or the hyperbolic Picard horn. After a "dark age" period, the field of Cosmic Topology has recently become one of the major concerns in cosmology, not only for theorists but also for observational astronomers, leaving open a number of unsolved issues.

  11. A study of the Ionospheric electron density profile with FORMOSAT-3/COSMIC observation data

    NASA Astrophysics Data System (ADS)

    Chou, Min-Yang; Tsai, Ho-Fang; Lin, Chi-Yen; Lee, I.-Te; Lin, Charles; Liu, Jann-Yenq

    2015-04-01

    The GPS Occultation Experiment payload onboard FORMOSAT-3/COSMIC microsatellite constellation is capable of scanning the ionospheric structure by the radio occultation (RO) technique to retrieve precise electron density profiles since 2006. Due to the success of FORMOSAT-3/COSMIC, the follow-on mission, FORMOSAT-7/COSMIC-2, is to launch 12 microsatellites in 2016 and 2018, respectively, with the Global Navigation Satellite Systems (GNSS) RO instrument onboard for tracking GPS, Galileo and/or GLONASS satellite signals and to provide more than 8,000 RO soundings per day globally. An overview of the validation of the FORMOSAT-3/COSMIC ionospheric profiling is given by means of the traditional Abel transform through bending angle and total electron content (TEC), while the ionospheric data assimilation is also applied, based on the Gauss-Markov Kalman filter with the International Reference Ionosphere model (IRI-2007) and global ionosphere map (GIM) as background model, to assimilate TEC observations from FORMOSAT-3/COSMIC. The results shows comparison of electron density profiles from Abel inversion and data assimilation. Furthermore, an observing system simulation experiment is also applied to determine the impact of FORMOSAT-7/COSMIC-2 on ionospheric weather monitoring, which reveals an opportunity on advanced study of small spatial and temporal variations in the ionosphere.

  12. A high density recombination map of the pig reveals a correlation between sex-specific recombination and GC content

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Background: The availability of a high-density SNP chip and a reference genome sequence of the pig have enabled the construction of a high-density linkage map. A high density linkage map is an essential tool for the further fine-mapping of QTL for a variety of traits in the pig and for a better und...

  13. A High-Density SNP-Based Linkage Map of the Chicken Genome Reveals Sequence Features Correlated With Recombination Rate

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The resolution of the widely used chicken consensus linkage map was highly enlarged by genotyping a total of 12,945 SNPs on the three existing mapping populations in chicken; the Wageningen (WU), East Lansing (EL) and Uppsala (UPP) mapping populations. A total of 8608 SNPs could be included on the m...

  14. Genome-Based Metabolic Mapping and 13C Flux Analysis Reveal Systematic Properties of an Oleaginous Microalga Chlorella protothecoides

    DOE PAGESBeta

    Wu, Chao; Xiong, Wei; Dai, Junbiao; Wu, Qingyu

    2014-12-15

    We report that integrated and genome-based flux balance analysis, metabolomics, and 13C-label profiling of phototrophic and heterotrophic metabolism in Chlorella protothecoides, an oleaginous green alga for biofuel. The green alga Chlorella protothecoides, capable of autotrophic and heterotrophic growth with rapid lipid synthesis, is a promising candidate for biofuel production. Based on the newly available genome knowledge of the alga, we reconstructed the compartmentalized metabolic network consisting of 272 metabolic reactions, 270 enzymes, and 461 encoding genes and simulated the growth in different cultivation conditions with flux balance analysis. Phenotype-phase plane analysis shows conditions achieving theoretical maximum of the biomass andmore » corresponding fatty acid-producing rate for phototrophic cells (the ratio of photon uptake rate to CO2 uptake rate equals 8.4) and heterotrophic ones (the glucose uptake rate to O2 consumption rate reaches 2.4), respectively. Isotope-assisted liquid chromatography-mass spectrometry/mass spectrometry reveals higher metabolite concentrations in the glycolytic pathway and the tricarboxylic acid cycle in heterotrophic cells compared with autotrophic cells. We also observed enhanced levels of ATP, nicotinamide adenine dinucleotide (phosphate), reduced, acetyl-Coenzyme A, and malonyl-Coenzyme A in heterotrophic cells consistently, consistent with a strong activity of lipid synthesis. To profile the flux map in experimental conditions, we applied nonstationary 13C metabolic flux analysis as a complementing strategy to flux balance analysis. We found that the result reveals negligible photorespiratory fluxes and a metabolically low active tricarboxylic acid cycle in phototrophic C. protothecoides. In comparison, high throughput of amphibolic reactions and the tricarboxylic acid cycle with no glyoxylate shunt activities were measured for heterotrophic cells. Lastly, taken together, the metabolic network modeling assisted

  15. Genome-based metabolic mapping and 13C flux analysis reveal systematic properties of an oleaginous microalga Chlorella protothecoides.

    PubMed

    Wu, Chao; Xiong, Wei; Dai, Junbiao; Wu, Qingyu

    2015-02-01

    Integrated and genome-based flux balance analysis, metabolomics, and (13)C-label profiling of phototrophic and heterotrophic metabolism in Chlorella protothecoides, an oleaginous green alga for biofuel. The green alga Chlorella protothecoides, capable of autotrophic and heterotrophic growth with rapid lipid synthesis, is a promising candidate for biofuel production. Based on the newly available genome knowledge of the alga, we reconstructed the compartmentalized metabolic network consisting of 272 metabolic reactions, 270 enzymes, and 461 encoding genes and simulated the growth in different cultivation conditions with flux balance analysis. Phenotype-phase plane analysis shows conditions achieving theoretical maximum of the biomass and corresponding fatty acid-producing rate for phototrophic cells (the ratio of photon uptake rate to CO2 uptake rate equals 8.4) and heterotrophic ones (the glucose uptake rate to O2 consumption rate reaches 2.4), respectively. Isotope-assisted liquid chromatography-mass spectrometry/mass spectrometry reveals higher metabolite concentrations in the glycolytic pathway and the tricarboxylic acid cycle in heterotrophic cells compared with autotrophic cells. We also observed enhanced levels of ATP, nicotinamide adenine dinucleotide (phosphate), reduced, acetyl-Coenzyme A, and malonyl-Coenzyme A in heterotrophic cells consistently, consistent with a strong activity of lipid synthesis. To profile the flux map in experimental conditions, we applied nonstationary (13)C metabolic flux analysis as a complementing strategy to flux balance analysis. The result reveals negligible photorespiratory fluxes and a metabolically low active tricarboxylic acid cycle in phototrophic C. protothecoides. In comparison, high throughput of amphibolic reactions and the tricarboxylic acid cycle with no glyoxylate shunt activities were measured for heterotrophic cells. Taken together, the metabolic network modeling assisted by experimental metabolomics and (13)C

  16. Cosmic impacts, cosmic catastrophes. II

    SciTech Connect

    Chapman, C.R.; Morrison, D. NASA, Ames Research Center, Moffett Field, CA )

    1990-02-01

    The role of extraterrestrial impacts in shaping the earth's history is discussed, arguing that cosmic impacts represent just one example of a general shift in thinking that has made the idea of catastrophes respectable in science. The origins of this view are presented and current catastrophic theory is discussed in the context of modern debate on the geological formation of the earth. Various conflicting theories are reviewed and prominent participants in the ongoing scientific controversy concerning catastrophism are introduced.

  17. Cosmic impacts, cosmic catastrophes. II

    NASA Technical Reports Server (NTRS)

    Chapman, Clark R.; Morrison, David

    1990-01-01

    The role of extraterrestrial impacts in shaping the earth's history is discussed, arguing that cosmic impacts represent just one example of a general shift in thinking that has made the idea of catastrophes respectable in science. The origins of this view are presented and current catastrophic theory is discussed in the context of modern debate on the geological formation of the earth. Various conflicting theories are reviewed and prominent participants in the ongoing scientific controversy concerning catastrophism are introduced.

  18. Genome Sequencing and Mapping Reveal Loss of Heterozygosity as a Mechanism for Rapid Adaptation in the Vegetable Pathogen Phytophthora capsici

    SciTech Connect

    Lamour, Kurt H.; Mudge, Joann; Gobena, Daniel; Hurtado-Gonzales, Oscar P.; Schmutz, Jeremy; Kuo, Alan; Miller, Neil A.; Rice, Brandon J.; Raffaele, Sylvain; Cano, Liliana M.; Bharti, Arvind K.; Donahoo, Ryan S.; Finely, Sabra; Huitema, Edgar; Hulvey, Jon; Platt, Darren; Salamov, Asaf; Savidor, Alon; Sharma, Rahul; Stam, Remco; Sotrey, Dylan; Thines, Marco; Win, Joe; Haas, Brian J.; Dinwiddie, Darrell L.; Jenkins, Jerry; Knight, James R.; Affourtit, Jason P.; Han, Cliff S.; Chertkov, Olga; Lindquist, Erika A.; Detter, Chris; Grigoriev, Igor V.; Kamoun, Sophien; Kingsmore, Stephen F.

    2012-02-07

    The oomycete vegetable pathogen Phytophthora capsici has shown remarkable adaptation to fungicides and new hosts. Like other members of this destructive genus, P. capsici has an explosive epidemiology, rapidly producing massive numbers of asexual spores on infected hosts. In addition, P. capsici can remain dormant for years as sexually recombined oospores, making it difficult to produce crops at infested sites, and allowing outcrossing populations to maintain significant genetic variation. Genome sequencing, development of a high-density genetic map, and integrative genomic or genetic characterization of P. capsici field isolates and intercross progeny revealed significant mitotic loss of heterozygosity (LOH) in diverse isolates. LOH was detected in clonally propagated field isolates and sexual progeny, cumulatively affecting >30percent of the genome. LOH altered genotypes for more than 11,000 single-nucleotide variant sites and showed a strong association with changes in mating type and pathogenicity. Overall, it appears that LOH may provide a rapid mechanism for fixing alleles and may be an important component of adaptability for P. capsici.

  19. Genome-Wide Association Mapping of Fertility Reduction upon Heat Stress Reveals Developmental Stage-Specific QTLs in Arabidopsis thaliana

    PubMed Central

    Bac-Molenaar, Johanna A.; Fradin, Emilie F.; Becker, Frank F.M.; Rienstra, Juriaan A.; van der Schoot, J.; Vreugdenhil, Dick; Keurentjes, Joost J.B.

    2015-01-01

    For crops that are grown for their fruits or seeds, elevated temperatures that occur during flowering and seed or fruit set have a stronger effect on yield than high temperatures during the vegetative stage. Even short-term exposure to heat can have a large impact on yield. In this study, we used Arabidopsis thaliana to study the effect of short-term heat exposure on flower and seed development. The impact of a single hot day (35°C) was determined in more than 250 natural accessions by measuring the lengths of the siliques along the main inflorescence. Two sensitive developmental stages were identified, one before anthesis, during male and female meiosis, and one after anthesis, during fertilization and early embryo development. In addition, we observed a correlation between flowering time and heat tolerance. Genome-wide association mapping revealed four quantitative trait loci (QTLs) strongly associated with the heat response. These QTLs were developmental stage specific, as different QTLs were detected before and after anthesis. For a number of QTLs, T-DNA insertion knockout lines could validate assigned candidate genes. Our findings show that the regulation of complex traits can be highly dependent on the developmental timing. PMID:26163573

  20. Genome sequencing and mapping reveal loss of heterozygosity as a mechanism for rapid adaptation in the vegetable pathogen Phytophthora capsici.

    PubMed

    Lamour, Kurt H; Mudge, Joann; Gobena, Daniel; Hurtado-Gonzales, Oscar P; Schmutz, Jeremy; Kuo, Alan; Miller, Neil A; Rice, Brandon J; Raffaele, Sylvain; Cano, Liliana M; Bharti, Arvind K; Donahoo, Ryan S; Finley, Sabra; Huitema, Edgar; Hulvey, Jon; Platt, Darren; Salamov, Asaf; Savidor, Alon; Sharma, Rahul; Stam, Remco; Storey, Dylan; Thines, Marco; Win, Joe; Haas, Brian J; Dinwiddie, Darrell L; Jenkins, Jerry; Knight, James R; Affourtit, Jason P; Han, Cliff S; Chertkov, Olga; Lindquist, Erika A; Detter, Chris; Grigoriev, Igor V; Kamoun, Sophien; Kingsmore, Stephen F

    2012-10-01

    The oomycete vegetable pathogen Phytophthora capsici has shown remarkable adaptation to fungicides and new hosts. Like other members of this destructive genus, P. capsici has an explosive epidemiology, rapidly producing massive numbers of asexual spores on infected hosts. In addition, P. capsici can remain dormant for years as sexually recombined oospores, making it difficult to produce crops at infested sites, and allowing outcrossing populations to maintain significant genetic variation. Genome sequencing, development of a high-density genetic map, and integrative genomic or genetic characterization of P. capsici field isolates and intercross progeny revealed significant mitotic loss of heterozygosity (LOH) in diverse isolates. LOH was detected in clonally propagated field isolates and sexual progeny, cumulatively affecting >30% of the genome. LOH altered genotypes for more than 11,000 single-nucleotide variant sites and showed a strong association with changes in mating type and pathogenicity. Overall, it appears that LOH may provide a rapid mechanism for fixing alleles and may be an important component of adaptability for P. capsici. PMID:22712506

  1. Genome sequencing and mapping reveal loss of heterozygosity as a mechanism for rapid adaptation in the vegetable pathogen Phytophthora capsici

    PubMed Central

    Lamour, Kurt H.; Mudge, Joann; Gobena, Daniel; Hurtado-Gonzales, Oscar P.; Schmutz, Jeremy; Kuo, Alan; Miller, Neil A.; Rice, Brandon J.; Raffaele, Sylvain; Cano, Liliana M.; Bharti, Arvind K.; Donahoo, Ryan S.; Finley, Sabra; Huitema, Edgar; Hulvey, Jon; Platt, Darren; Salamov, Asaf; Savidor, Alon; Sharma, Rahul; Stam, Remco; Storey, Dylan; Thines, Marco; Win, Joe; Haas, Brian J.; Dinwiddie, Darrell L.; Jenkins, Jerry; Knight, James R.; Affourtit, Jason P.; Han, Cliff S.; Chertkov, Olga; Lindquist, Erika A.; Detter, Chris; Grigoriev, Igor V.; Kamoun, Sophien; Kingsmore, Stephen F.

    2013-01-01

    The oomycete vegetable pathogen Phytophthora capsici has shown remarkable adaptation to fungicides and new hosts. Like other members of this destructive genus, P. capsici has an explosive epidemiology, rapidly producing massive numbers of asexual spores on infected hosts. In addition, P. capsici can remain dormant for years as sexually-recombined oospores, making it difficult to produce crops at infested sites, and allowing outcrossing populations to maintain significant genetic variation. Genome sequencing, development of a high-density genetic map, and integrative genomic/genetic characterization of P. capsici field isolates and intercross progeny revealed significant mitotic loss of heterozygosity (LOH) and higher levels of SNVs than those reported for humans, plants, and P. infestans. LOH was detected in clonally propagated field isolates and sexual progeny, cumulatively affecting >30% of the genome. LOH altered genotypes for more than 11,000 single nucleotide variant (SNV) sites and showed a strong association with changes in mating type and pathogenicity. Overall, it appears that LOH may provide a rapid mechanism for fixing alleles and may be an important component of adaptability for P. capsici. PMID:22712506

  2. Disease-Drug Pairs Revealed by Computational Genomic Connectivity Mapping on GBA1 Deficient, Gaucher Disease Mice

    PubMed Central

    Yuen, Tony; Iqbal, Jameel; Zhu, Ling-Ling; Sun, Li; Lin, Aiping; Zhao, Hongyu; Liu, Jun; Mistry, Pramod K.; Zaidi, Mone

    2012-01-01

    We have reported that, in addition to recapitulating the classical human Gaucher disease (GD1) phenotype, deletion of the glucocerebrosidase (GBA1) gene in mice results in the dysfunction of a diverse population of immune cells. Most of immune-related, non-classical features of GD1, including gammopathies and autoimmune diathesis, are resistant to macrophage-directed therapies. This has prompted a search for newer agents for human GD1. Here, we used high-density microarray on splenic and liver cells from affected GBA1−/− mice to establish a gene “signature”, which was then utilized to interrogate the Broad Institute database, CMAP. Computational connectivity mapping of disease and drug pairs through CMAP revealed several highly enriched, non-null, mimic and anti-mimic hits. Most notably, two compounds with anti-helminthic properties, namely albendazole and oxamniquine, were identified; these are particularly relevant for future testing as the expression of chitinases is enhanced in GD1. PMID:22588172

  3. In Vivo Mapping of Eukaryotic RNA Interactomes Reveals Principles of Higher-Order Organization and Regulation.

    PubMed

    Aw, Jong Ghut Ashley; Shen, Yang; Wilm, Andreas; Sun, Miao; Lim, Xin Ni; Boon, Kum-Loong; Tapsin, Sidika; Chan, Yun-Shen; Tan, Cheng-Peow; Sim, Adelene Y L; Zhang, Tong; Susanto, Teodorus Theo; Fu, Zhiyan; Nagarajan, Niranjan; Wan, Yue

    2016-05-19

    Identifying pairwise RNA-RNA interactions is key to understanding how RNAs fold and interact with other RNAs inside the cell. We present a high-throughput approach, sequencing of psoralen crosslinked, ligated, and selected hybrids (SPLASH), that maps pairwise RNA interactions in vivo with high sensitivity and specificity, genome-wide. Applying SPLASH to human and yeast transcriptomes revealed the diversity and dynamics of thousands of long-range intra- and intermolecular RNA-RNA interactions. Our analysis highlighted key structural features of RNA classes, including the modular organization of mRNAs, its impact on translation and decay, and the enrichment of long-range interactions in noncoding RNAs. Additionally, intermolecular mRNA interactions were organized into network clusters and were remodeled during cellular differentiation. We also identified hundreds of known and new snoRNA-rRNA binding sites, expanding our knowledge of rRNA biogenesis. These results highlight the underexplored complexity of RNA interactomes and pave the way to better understanding how RNA organization impacts biology. PMID:27184079

  4. Second-Generation Linkage Maps for the Pacific Oyster Crassostrea gigas Reveal Errors in Assembly of Genome Scaffolds

    PubMed Central

    Hedgecock, Dennis; Shin, Grace; Gracey, Andrew Y.; Den Berg, David Van; Samanta, Manoj P.

    2015-01-01

    The Pacific oyster Crassostrea gigas, a widely cultivated marine bivalve mollusc, is becoming a genetically and genomically enabled model for highly fecund marine metazoans with complex life-histories. A genome sequence is available for the Pacific oyster, as are first-generation, low-density, linkage and gene-centromere maps mostly constructed from microsatellite DNA markers. Here, higher density, second-generation, linkage maps are constructed from more than 1100 coding (exonic) single-nucleotide polymorphisms (SNPs), as well as 66 previously mapped microsatellite DNA markers, all typed in five families of Pacific oysters (nearly 172,000 genotypes). The map comprises 10 linkage groups, as expected, has an average total length of 588 cM, an average marker-spacing of 1.0 cM, and covers 86% of a genome estimated to be 616 cM. All but seven of the mapped SNPs map to 618 genome scaffolds; 260 scaffolds contain two or more mapped SNPs, but for 100 of these scaffolds (38.5%), the contained SNPs map to different linkage groups, suggesting widespread errors in scaffold assemblies. The 100 misassembled scaffolds are significantly longer than those that map to a single linkage group. On the genetic maps, marker orders and intermarker distances vary across families and mapping methods, owing to an abundance of markers segregating from only one parent, to widespread distortions of segregation ratios caused by early mortality, as previously observed for oysters, and to genotyping errors. Maps made from framework markers provide stronger support for marker orders and reasonable map lengths and are used to produce a consensus high-density linkage map containing 656 markers. PMID:26248981

  5. The goya mouse mutant reveals distinct newly identified roles for MAP3K1 in the development and survival of cochlear sensory hair cells

    PubMed Central

    Parker, Andrew; Cross, Sally H.; Jackson, Ian J.; Hardisty-Hughes, Rachel; Morse, Susan; Nicholson, George; Coghill, Emma; Bowl, Michael R.; Brown, Steve D. M.

    2015-01-01

    ABSTRACT Mitogen-activated protein kinase, MAP3K1, plays an important role in a number of cellular processes, including epithelial migration during eye organogenesis. In addition, studies in keratinocytes indicate that MAP3K1 signalling through JNK is important for actin stress fibre formation and cell migration. However, MAP3K1 can also act independently of JNK in the regulation of cell proliferation and apoptosis. We have identified a mouse mutant, goya, which exhibits the eyes-open-at-birth and microphthalmia phenotypes. In addition, these mice also have hearing loss. The goya mice carry a splice site mutation in the Map3k1 gene. We show that goya and kinase-deficient Map3k1 homozygotes initially develop supernumerary cochlear outer hair cells (OHCs) that subsequently degenerate, and a progressive profound hearing loss is observed by 9 weeks of age. Heterozygote mice also develop supernumerary OHCs, but no cellular degeneration or hearing loss is observed. MAP3K1 is expressed in a number of inner-ear cell types, including outer and inner hair cells, stria vascularis and spiral ganglion. Investigation of targets downstream of MAP3K1 identified an increase in p38 phosphorylation (Thr180/Tyr182) in multiple cochlear tissues. We also show that the extra OHCs do not arise from aberrant control of proliferation via p27KIP1. The identification of the goya mutant reveals a signalling molecule involved with hair-cell development and survival. Mammalian hair cells do not have the ability to regenerate after damage, which can lead to irreversible sensorineural hearing loss. Given the observed goya phenotype, and the many diverse cellular processes that MAP3K1 is known to act upon, further investigation of this model might help to elaborate upon the mechanisms underlying sensory hair cell specification, and pathways important for their survival. In addition, MAP3K1 is revealed as a new candidate gene for human sensorineural hearing loss. PMID:26542706

  6. One century of cosmic rays - A particle physicist's view

    NASA Astrophysics Data System (ADS)

    Sutton, Christine

    2015-12-01

    Experiments on cosmic rays and the elementary particles share a common history that dates back to the 19th century. Following the discovery of radioactivity in the 1890s, the paths of the two fields intertwined, especially during the decades after the discovery of cosmic rays. Experiments demonstrated that the primary cosmic rays are positively charged particles, while other studies of cosmic rays revealed various new sub-atomic particles, including the first antiparticle. Techniques developed in common led to the birth of neutrino astronomy in 1987 and the first observation of a cosmic γ-ray source by a ground-based cosmic-ray telescope in 1989.

  7. Techniques for Revealing 3d Hidden Archeological Features: Morphological Residual Models as Virtual-Polynomial Texture Maps

    NASA Astrophysics Data System (ADS)

    Pires, H.; Martínez Rubio, J.; Elorza Arana, A.

    2015-02-01

    The recent developments in 3D scanning technologies are not been accompanied by visualization interfaces. We are still using the same types of visual codes as when maps and drawings were made by hand. The available information in 3D scanning data sets is not being fully exploited by current visualization techniques. In this paper we present recent developments regarding the use of 3D scanning data sets for revealing invisible information from archaeological sites. These sites are affected by a common problem, decay processes, such as erosion, that never ceases its action and endangers the persistence of last vestiges of some peoples and cultures. Rock art engravings, or epigraphical inscriptions, are among the most affected by these processes because they are, due to their one nature, carved at the surface of rocks often exposed to climatic agents. The study and interpretation of these motifs and texts is strongly conditioned by the degree of conservation of the imprints left by our ancestors. Every single detail in the remaining carvings can make a huge difference in the conclusions taken by specialists. We have selected two case-studies severely affected by erosion to present the results of the on-going work dedicated to explore in new ways the information contained in 3D scanning data sets. A new method for depicting subtle morphological features in the surface of objects or sites has been developed. It allows to contrast human patterns still present at the surface but invisible to naked eye or by any other archaeological inspection technique. It was called Morphological Residual Model (MRM) because of its ability to contrast the shallowest morphological details, to which we refer as residuals, contained in the wider forms of the backdrop. Afterwards, we have simulated the process of building Polynomial Texture Maps - a widespread technique that as been contributing to archaeological studies for some years - in a 3D virtual environment using the results of MRM

  8. Methodology for Comparing Soil Maps of Different Dates with the Aim to Reveal and Describe Changes in the Soil Cover (by the Example of Soil Salinization Monitoring)

    NASA Astrophysics Data System (ADS)

    Rukhovich, D. I.; Simakova, M. S.; Kulyanitsa, A. L.; Bryzzhev, A. V.; Koroleva, P. V.; Kalinina, N. V.; Chernousenko, G. I.; Vil'chevskaya, E. V.; Dolinina, E. A.; Rukhovich, S. V.

    2016-02-01

    A methodology for comparing soil map of different dates in order to reveal changes in the soil cover is discussed. The analysis of a set of the maps of soil salinization on one of the farms in the Golodnaya Steppe region of Uzbekistan is used as an example. It is shown that traditional methods of comparing two maps developed in different years (normally, with an interval of five years and more) are low informative for the assessment of soil salinization dynamics. The suggested methodology assumes simultaneous analysis of several maps in order to reveal the trends in soil salinization. However, even in this case, the obtained results do not adequately characterize the dynamics of soil salinization on irrigated fields. It is argued that the direction of soil salinization-desalinization processes is an improper characteristic in this case. In order to understand the dynamics of soil salinization, the maps showing the dynamism of soil salinity and the maximum changes in the degree of salinity can be applied. A series of the compared maps make it possible to describe the changes in the soil cover related to salinization-desalinization processes. The high dynamism of these processes against the background of a virtually stable pool of soluble salts in the 1-m-deep soil layer is shown for the considered farm.

  9. Cosmic strings and superconducting cosmic strings

    NASA Technical Reports Server (NTRS)

    Copeland, Edmund

    1988-01-01

    The possible consequences of forming cosmic strings and superconducting cosmic strings in the early universe are discussed. Lecture 1 describes the group theoretic reasons for and the field theoretic reasons why cosmic strings can form in spontaneously broken gauge theories. Lecture 2 discusses the accretion of matter onto string loops, emphasizing the scenario with a cold dark matter dominated universe. In lecture 3 superconducting cosmic strings are discussed, as is a mechanism which leads to the formation of structure from such strings.

  10. QTL mapping reveals a two-step model for the evolutionary reduction of inner microsporangia within the asteracean genus Microseris.

    PubMed

    Gailing, O; Bachmann, K

    2003-09-01

    The reduction of inner (adaxial) pollen sacs (microsporangia, MS) as a diagnostic character for the three asteracean species, Microseris bigelovii, Microseris elegans and Microseris pygmaea, was analysed in an interspecific cross between Microseris douglasii and Microseris bigelovii with 4 MS and 2 MS, respectively, using the average number of MS per plant as a quantitative character. A previous QTL (Quantitative Trait Locus) analysis had revealed one major QTL (3B) and three modifier QTLs (3A, 4A, 7A) with epistatic effects only on the homozygous recessive 2 MS genotype of QTL 3B. Here we performed a bulked segregant analysis on four 2 MS and four 4 MS DNA-bulks with 407 EcoRI/ MseI AFLP-primer combinations each. In this way additional AFLP markers were mapped close to QTL 3B and QTL 3A. Three of them were converted to SCAR (Sequence Characterized Amplified region) markers. All markers were tested in natural populations of the disporangiate (2 MS) species M. bigelovii, M. elegans and M. pygmaea, and in different populations of tetrasporangiate (4 MS) M. douglasii. The marker distribution suggests that locus 3B mutated in a progenitor of the disporangiate species. QTL 3A has evolved in the 2 MS background of the major gene in the disporangiate species. Since M. pygmaea and M. bigelovii are the sister group to M. elegans, the 4 MS genotype for (markers of) QTL 3A in M. pygmaea populations is most likely due to a back mutation to the 4 MS state and could explain the slight instability of the 2 MS phenotype in this species. PMID:12838389

  11. Systematic mapping of WNT-FZD protein interactions reveals functional selectivity by distinct WNT-FZD pairs.

    PubMed

    Dijksterhuis, Jacomijn P; Baljinnyam, Bolormaa; Stanger, Karen; Sercan, Hakki O; Ji, Yun; Andres, Osler; Rubin, Jeffrey S; Hannoush, Rami N; Schulte, Gunnar

    2015-03-13

    The seven-transmembrane-spanning receptors of the FZD1-10 class are bound and activated by the WNT family of lipoglycoproteins, thereby inducing a complex network of signaling pathways. However, the specificity of the interaction between mammalian WNT and FZD proteins and the subsequent signaling cascade downstream of the different WNT-FZD pairs have not been systematically addressed to date. In this study, we determined the binding affinities of various WNTs for different members of the FZD family by using bio-layer interferometry and characterized their functional selectivity in a cell system. Using purified WNTs, we show that different FZD cysteine-rich domains prefer to bind to distinct WNTs with fast on-rates and slow off-rates. In a 32D cell-based system engineered to overexpress FZD2, FZD4, or FZD5, we found that WNT-3A (but not WNT-4, -5A, or -9B) activated the WNT-β-catenin pathway through FZD2/4/5 as measured by phosphorylation of LRP6 and β-catenin stabilization. Surprisingly, different WNT-FZD pairs showed differential effects on phosphorylation of DVL2 and DVL3, revealing a previously unappreciated DVL isoform selectivity by different WNT-FZD pairs in 32D cells. In summary, we present extensive mapping of WNT-FZD cysteine-rich domain interactions complemented by analysis of WNT-FZD pair functionality in a unique cell system expressing individual FZD isoforms. Differential WNT-FZD binding and selective functional readouts suggest that endogenous WNT ligands evolved with an intrinsic natural bias toward different downstream signaling pathways, a phenomenon that could be of great importance in the design of FZD-targeting drugs. PMID:25605717

  12. Using patient serum to epitope map soybean glycinins reveals common epitopes shared with many legumes and tree nuts.

    PubMed

    Saeed, Hanaa; Gagnon, Christine; Cober, Elroy; Gleddie, Steve

    2016-02-01

    Soybean consumption is increasing in many Western diets; however, recent reviews suggest that the prevalence of soy allergy can be as high as 0.5% for the general population and up to 13% for children. The immunoglobulin-E (IgE) binding of sera from six soy-sensitive adult human subjects to soybean proteins separated by 2D gel electrophoresis was studied. Synthetic peptide sets spanning the mature glycinin subunit A2 and A3 primary sequences were used to map the IgE-binding regions. Putative epitopes identified in this study were also localized on glycinin hexamer models using bioinformatics software. We identified linear IgE-binding epitopes of the major storage protein Gly m 6 by screening individual soy-sensitive patient sera. These epitopes were then further analysed by 3D in silico model localization and compared to other plant storage protein epitopes. Web-based software applications were also used to study the ability to accurately predict epitopes with mixed results. A total of nine putative IgE-binding epitopes were identified in the glycinin A3 (A3.1-A3.3) and A2 (A2.1-A2.6) subunits. Most patients' sera IgE bound to only one or two epitopes, except for one patient's serum which bound to four different A2 epitopes. Two epitopes (A3.2 and A2.4) overlapped with a previously identified epitope hot spot of 11S globulins from other plant species. Most epitopes were predicted to be exposed on the surface of the 3D model of the glycinin hexamer. Amino acid sequence alignments of soybean acidic glycinins and other plant globulins revealed one dominant epitope hot spot among the four reported hot spots. This study may be helpful for future development of soy allergy immunotherapy and diagnosis. PMID:26766775

  13. Fine mapping of type 1 diabetes regions Idd9.1 and Idd9.2 reveals genetic complexity.

    PubMed

    Hamilton-Williams, Emma E; Rainbow, Daniel B; Cheung, Jocelyn; Christensen, Mikkel; Lyons, Paul A; Peterson, Laurence B; Steward, Charles A; Sherman, Linda A; Wicker, Linda S

    2013-10-01

    Nonobese diabetic (NOD) mice congenic for C57BL/10 (B10)-derived genes in the Idd9 region of chromosome 4 are highly protected from type 1 diabetes (T1D). Idd9 has been divided into three protective subregions (Idd9.1, 9.2, and 9.3), each of which partially prevents disease. In this study we have fine-mapped the Idd9.1 and Idd9.2 regions, revealing further genetic complexity with at least two additional subregions contributing to protection from T1D. Using the NOD sequence from bacterial artificial chromosome clones of the Idd9.1 and Idd9.2 regions as well as whole-genome sequence data recently made available, sequence polymorphisms within the regions highlight a high degree of polymorphism between the NOD and B10 strains in the Idd9 regions. Among numerous candidate genes are several with immunological importance. The Idd9.1 region has been separated into Idd9.1 and Idd9.4, with Lck remaining a candidate gene within Idd9.1. One of the Idd9.2 regions contains the candidate genes Masp2 (encoding mannan-binding lectin serine peptidase 2) and Mtor (encoding mammalian target of rapamycin). From mRNA expression analyses, we have also identified several other differentially expressed candidate genes within the Idd9.1 and Idd9.2 regions. These findings highlight that multiple, relatively small genetic effects combine and interact to produce significant changes in immune tolerance and diabetes onset. PMID:23934554

  14. Systematic Mapping of WNT-FZD Protein Interactions Reveals Functional Selectivity by Distinct WNT-FZD Pairs*

    PubMed Central

    Dijksterhuis, Jacomijn P.; Baljinnyam, Bolormaa; Stanger, Karen; Sercan, Hakki O.; Ji, Yun; Andres, Osler; Rubin, Jeffrey S.; Hannoush, Rami N.; Schulte, Gunnar

    2015-01-01

    The seven-transmembrane-spanning receptors of the FZD1–10 class are bound and activated by the WNT family of lipoglycoproteins, thereby inducing a complex network of signaling pathways. However, the specificity of the interaction between mammalian WNT and FZD proteins and the subsequent signaling cascade downstream of the different WNT-FZD pairs have not been systematically addressed to date. In this study, we determined the binding affinities of various WNTs for different members of the FZD family by using bio-layer interferometry and characterized their functional selectivity in a cell system. Using purified WNTs, we show that different FZD cysteine-rich domains prefer to bind to distinct WNTs with fast on-rates and slow off-rates. In a 32D cell-based system engineered to overexpress FZD2, FZD4, or FZD5, we found that WNT-3A (but not WNT-4, -5A, or -9B) activated the WNT-β-catenin pathway through FZD2/4/5 as measured by phosphorylation of LRP6 and β-catenin stabilization. Surprisingly, different WNT-FZD pairs showed differential effects on phosphorylation of DVL2 and DVL3, revealing a previously unappreciated DVL isoform selectivity by different WNT-FZD pairs in 32D cells. In summary, we present extensive mapping of WNT-FZD cysteine-rich domain interactions complemented by analysis of WNT-FZD pair functionality in a unique cell system expressing individual FZD isoforms. Differential WNT-FZD binding and selective functional readouts suggest that endogenous WNT ligands evolved with an intrinsic natural bias toward different downstream signaling pathways, a phenomenon that could be of great importance in the design of FZD-targeting drugs. PMID:25605717

  15. A SNP Based High-Density Linkage Map of Apis cerana Reveals a High Recombination Rate Similar to Apis mellifera

    PubMed Central

    Huang, Zachary Y.; Wu, Xiao Bo; Zhu, Yong Qiang; Zheng, Hua Jun; Zeng, Zhi Jiang

    2013-01-01

    Background The Eastern honey bee, Apis cerana Fabricius, is distributed in southern and eastern Asia, from India and China to Korea and Japan and southeast to the Moluccas. This species is also widely kept for honey production besides Apis mellifera. Apis cerana is also a model organism for studying social behavior, caste determination, mating biology, sexual selection, and host-parasite interactions. Few resources are available for molecular research in this species, and a linkage map was never constructed. A linkage map is a prerequisite for quantitative trait loci mapping and for analyzing genome structure. We used the Chinese honey bee, Apis cerana cerana to construct the first linkage map in the Eastern honey bee. Results F2 workers (N = 103) were genotyped for 126,990 single nucleotide polymorphisms (SNPs). After filtering low quality and those not passing the Mendel test, we obtained 3,000 SNPs, 1,535 of these were informative and used to construct a linkage map. The preliminary map contains 19 linkage groups, we then mapped the 19 linkage groups to 16 chromosomes by comparing the markers to the genome of A. mellfiera. The final map contains 16 linkage groups with a total of 1,535 markers. The total genetic distance is 3,942.7 centimorgans (cM) with the largest linkage group (180 loci) measuring 574.5 cM. Average marker interval for all markers across the 16 linkage groups is 2.6 cM. Conclusion We constructed a high density linkage map for A. c. cerana with 1,535 markers. Because the map is based on SNP markers, it will enable easier and faster genotyping assays than randomly amplified polymorphic DNA or microsatellite based maps used in A. mellifera. PMID:24130775

  16. A genetic map in the Mimulus guttatus species complex reveals transmission ratio distortion due to heterospecific interactions.

    PubMed Central

    Fishman, L; Kelly, A J; Morgan, E; Willis, J H

    2001-01-01

    As part of a study of the genetics of floral adaptation and speciation in the Mimulus guttatus species complex, we constructed a genetic linkage map of an interspecific cross between M. guttatus and M. nasutus. We genotyped an F(2) mapping population (N = 526) at 255 AFLP, microsatellite, and gene-based markers and derived a framework map through repeated rounds of ordering and marker elimination. The final framework map consists of 174 marker loci on 14 linkage groups with a total map length of 1780 cM Kosambi. Genome length estimates (2011-2096 cM) indicate that this map provides thorough coverage of the hybrid genome, an important consideration for QTL mapping. Nearly half of the markers in the full data set (49%) and on the framework map (48%) exhibited significant transmission ratio distortion (alpha = 0.05). We localized a minimum of 11 transmission ratio distorting loci (TRDLs) throughout the genome, 9 of which generate an excess of M. guttatus alleles and a deficit of M. nasutus alleles. This pattern indicates that the transmission ratio distortion results from particular interactions between the heterospecific genomes and suggests that substantial genetic divergence has occurred between these Mimulus species. We discuss possible causes of the unequal representation of parental genomes in the F(2) generation. PMID:11779808

  17. Comparing cosmic web classifiers using information theory

    NASA Astrophysics Data System (ADS)

    Leclercq, Florent; Lavaux, Guilhem; Jasche, Jens; Wandelt, Benjamin

    2016-08-01

    We introduce a decision scheme for optimally choosing a classifier, which segments the cosmic web into different structure types (voids, sheets, filaments, and clusters). Our framework, based on information theory, accounts for the design aims of different classes of possible applications: (i) parameter inference, (ii) model selection, and (iii) prediction of new observations. As an illustration, we use cosmographic maps of web-types in the Sloan Digital Sky Survey to assess the relative performance of the classifiers T-WEB, DIVA and ORIGAMI for: (i) analyzing the morphology of the cosmic web, (ii) discriminating dark energy models, and (iii) predicting galaxy colors. Our study substantiates a data-supported connection between cosmic web analysis and information theory, and paves the path towards principled design of analysis procedures for the next generation of galaxy surveys. We have made the cosmic web maps, galaxy catalog, and analysis scripts used in this work publicly available.

  18. Genomic rearrangements and signatures of breeding in the allo-octoploid strawberry as revealed through an allele dose based SSR linkage map

    PubMed Central

    2014-01-01

    Background Breeders in the allo-octoploid strawberry currently make little use of molecular marker tools. As a first step of a QTL discovery project on fruit quality traits and resistance to soil-borne pathogens such as Phytophthora cactorum and Verticillium we built a genome-wide SSR linkage map for the cross Holiday x Korona. We used the previously published MADCE method to obtain full haplotype information for both of the parental cultivars, facilitating in-depth studies on their genomic organisation. Results The linkage map incorporates 508 segregating loci and represents each of the 28 chromosome pairs of octoploid strawberry, spanning an estimated length of 2050 cM. The sub-genomes are denoted according to their sequence divergence from F. vesca as revealed by marker performance. The map revealed high overall synteny between the sub-genomes, but also revealed two large inversions on LG2C and LG2D, of which the latter was confirmed using a separate mapping population. We discovered interesting breeding features within the parental cultivars by in-depth analysis of our haplotype data. The linkage map-derived homozygosity level of Holiday was similar to the pedigree-derived inbreeding level (33% and 29%, respectively). For Korona we found that the observed homozygosity level was over three times higher than expected from the pedigree (13% versus 3.6%). This could indicate selection pressure on genes that have favourable effects in homozygous states. The level of kinship between Holiday and Korona derived from our linkage map was 2.5 times higher than the pedigree-derived value. This large difference could be evidence of selection pressure enacted by strawberry breeders towards specific haplotypes. Conclusion The obtained SSR linkage map provides a good base for QTL discovery. It also provides the first biologically relevant basis for the discernment and notation of sub-genomes. For the first time, we revealed genomic rearrangements that were verified in a

  19. Syntenic relationships among legumes revealed using a gene-based genetic linkage map of common bean (Phaseolus vulgaris L.).

    PubMed

    McConnell, Melody; Mamidi, Sujan; Lee, Rian; Chikara, Shireen; Rossi, Monica; Papa, Roberto; McClean, Phillip

    2010-10-01

    Molecular linkage maps are an important tool for gene discovery and cloning, crop improvement, further genetic studies, studies on diversity and evolutionary history, and cross-species comparisons. Linkage maps differ in both the type of marker and type of population used. In this study, gene-based markers were used for mapping in a recombinant inbred (RI) population of Phaseolus vulgaris L. P. vulgaris, common dry bean, is an important food source, economic product, and model organism for the legumes. Gene-based markers were developed that corresponded to genes controlling mutant phenotypes in Arabidopsis thaliana, genes undergoing selection during domestication in maize, and genes that function in a biochemical pathway in A. thaliana. Sequence information, including introns and 3' UTR, was generated for over 550 genes in the two genotypes of P. vulgaris. Over 1,800 single nucleotide polymorphisms and indels were found, 300 of which were screened in the RI population. The resulting LOD 2.0 map is 1,545 cM in length and consists of 275 gene-based and previously mapped core markers. An additional 153 markers that mapped at LOD <1.0 were placed in genetic bins. By screening the parents of other mapping populations, it was determined that the markers were useful for other common Mesoamerican × Andean mapping populations. The location of the mapped genes relative to their homologs in Arabidopsis thaliana (At), Medicago truncatula (Mt), and Lotus japonicus (Lj) were determine by using a tblastx analysis with the current psedouchromosome builds for each of the species. While only short blocks of synteny were observed with At, large-scale macrosyntenic blocks were observed with Mt and Lj. By using Mt and Lj as bridging species, the syntenic relationship between the common bean and peanut was inferred. PMID:20607211

  20. Linkage mapping in the oilseed crop Jatropha curcas L. reveals a locus controlling the biosynthesis of phorbol esters which cause seed toxicity.

    PubMed

    King, Andrew J; Montes, Luis R; Clarke, Jasper G; Affleck, Julie; Li, Yi; Witsenboer, Hanneke; van der Vossen, Edwin; van der Linde, Piet; Tripathi, Yogendra; Tavares, Evanilda; Shukla, Parul; Rajasekaran, Thirunavukkarasu; van Loo, Eibertus N; Graham, Ian A

    2013-10-01

    Current efforts to grow the tropical oilseed crop Jatropha curcas L. economically are hampered by the lack of cultivars and the presence of toxic phorbol esters (PE) within the seeds of most provenances. These PE restrict the conversion of seed cake into animal feed, although naturally occurring 'nontoxic' provenances exist which produce seed lacking PE. As an important step towards the development of genetically improved varieties of J. curcas, we constructed a linkage map from four F₂ mapping populations. The consensus linkage map contains 502 codominant markers, distributed over 11 linkage groups, with a mean marker density of 1.8 cM per unique locus. Analysis of the inheritance of PE biosynthesis indicated that this is a maternally controlled dominant monogenic trait. This maternal control is due to biosynthesis of the PE occurring only within maternal tissues. The trait segregated 3 : 1 within seeds collected from F₂ plants, and QTL analysis revealed that a locus on linkage group 8 was responsible for phorbol ester biosynthesis. By taking advantage of the draft genome assemblies of J. curcas and Ricinus communis (castor), a comparative mapping approach was used to develop additional markers to fine map this mutation within 2.3 cM. The linkage map provides a framework for the dissection of agronomic traits in J. curcas, and the development of improved varieties by marker-assisted breeding. The identification of the locus responsible for PE biosynthesis means that it is now possible to rapidly breed new nontoxic varieties. PMID:23898859

  1. SNP discovery and chromosome anchoring provide the first physically-anchored hexaploid oat map and reveal synteny with model species.

    PubMed

    Oliver, Rebekah E; Tinker, Nicholas A; Lazo, Gerard R; Chao, Shiaoman; Jellen, Eric N; Carson, Martin L; Rines, Howard W; Obert, Donald E; Lutz, Joseph D; Shackelford, Irene; Korol, Abraham B; Wight, Charlene P; Gardner, Kyle M; Hattori, Jiro; Beattie, Aaron D; Bjørnstad, Åsmund; Bonman, J Michael; Jannink, Jean-Luc; Sorrells, Mark E; Brown-Guedira, Gina L; Mitchell Fetch, Jennifer W; Harrison, Stephen A; Howarth, Catherine J; Ibrahim, Amir; Kolb, Frederic L; McMullen, Michael S; Murphy, J Paul; Ohm, Herbert W; Rossnagel, Brian G; Yan, Weikai; Miclaus, Kelci J; Hiller, Jordan; Maughan, Peter J; Redman Hulse, Rachel R; Anderson, Joseph M; Islamovic, Emir; Jackson, Eric W

    2013-01-01

    A physically anchored consensus map is foundational to modern genomics research; however, construction of such a map in oat (Avena sativa L., 2n = 6x = 42) has been hindered by the size and complexity of the genome, the scarcity of robust molecular markers, and the lack of aneuploid stocks. Resources developed in this study include a modified SNP discovery method for complex genomes, a diverse set of oat SNP markers, and a novel chromosome-deficient SNP anchoring strategy. These resources were applied to build the first complete, physically-anchored consensus map of hexaploid oat. Approximately 11,000 high-confidence in silico SNPs were discovered based on nine million inter-varietal sequence reads of genomic and cDNA origin. GoldenGate genotyping of 3,072 SNP assays yielded 1,311 robust markers, of which 985 were mapped in 390 recombinant-inbred lines from six bi-parental mapping populations ranging in size from 49 to 97 progeny. The consensus map included 985 SNPs and 68 previously-published markers, resolving 21 linkage groups with a total map distance of 1,838.8 cM. Consensus linkage groups were assigned to 21 chromosomes using SNP deletion analysis of chromosome-deficient monosomic hybrid stocks. Alignments with sequenced genomes of rice and Brachypodium provide evidence for extensive conservation of genomic regions, and renewed encouragement for orthology-based genomic discovery in this important hexaploid species. These results also provide a framework for high-resolution genetic analysis in oat, and a model for marker development and map construction in other species with complex genomes and limited resources. PMID:23533580

  2. Hot Spot Cosmic Accelerators

    NASA Astrophysics Data System (ADS)

    2002-11-01

    The Universe is a violent place - as astronomers use increasingly sensitive means and methods to study the diverse processes out there, they become aware of the extraordinary forces acting in the space that surrounds us. With larger telescopes and ever-more sophisticated instruments, new information is gained about remote celestial objects and their behaviour. Among the most intriguing ones are the radio galaxies which emit prodiguous amounts of energy, in the form of fast-moving particles and intense electromagnetic radiation. One of these is known as 3C 445 ; it is located near the celestial equator within the zodiacal constellation Aquarius (The Waterman), at a distance of about 1 billion light-years. It most probably harbours a black hole at its centre, more massive than the one at the centre of our own galaxy, the Milky Way ( ESO PR 19/02 ). This galaxy was first observed from Cambridge (United Kingdom) in the 1950's and was listed as radio source no. 445 in the Third Cambridge Catalogue (1959), hence the name. Later observations revealed a strong outflow from this galaxy's active centre, visible on radio maps as two opposite plasma jets with strong synchrotron radiation ( [2]) originating from rapidly moving electrons in the associated magnetic field (image "a" in PR Photo 26/02 ). Now, a trio of European astronomers [1] have used two advanced instruments, ISAAC and FORS1 on the 8.2-m VLT ANTU telescope at the ESO Paranal Observatory (Chile) to obtain near-infrared images of these jets (images "b" and "c" in PR Photo 26/02 ). As can be clearly seen on the radio picture of 3C 445 obtained with the NRAO Very Large Array (VLA) radio facility ("a"), the plasma jets of fast particles emanating from the galaxy ram into the surrounding intergalactic medium (mostly primordial hydrogen), thereby producing two "shocks" , both at a distance of approximately 1.5 million light-years from the central galaxy and with particularly strong synchrotron emission. With a total

  3. Instantaneous and scale-versatile gourdron theory: pair momentum equation, quasi-stability concept, and statistical indeterminacy revealing masses of elementary, bio-molecular, and cosmic particles

    NASA Astrophysics Data System (ADS)

    Naitoh, Ken

    2014-04-01

    Flexible particles, including hadrons, atoms, hydrated biological molecules, cells, organs containing water, liquid fuel droplets in engines, and stars commonly break up after becoming a gourd shape rather than that of a string; this leads to cyto-fluid dynamics that can explain the proliferation, differentiation, and replication of biomolecules, onto-biology that clarifies the relationship between information, structure, and function, and the gourd theory that clarifies masses, including quark-leptons and Plank energy. The masses are related to the super-magic numbers, including the asymmetric silver ratio and symmetric yamato ratio, and reveal further mechanisms underlying symmetry breaking. This paper gives further theoretical basis and evidence, because the gourd theory reported previously is a little analogical and instinctive.

  4. Maps & minds : mapping through the ages

    USGS Publications Warehouse

    U.S. Geological Survey

    1984-01-01

    Throughout time, maps have expressed our understanding of our world. Human affairs have been influenced strongly by the quality of maps available to us at the major turning points in our history. "Maps & Minds" traces the ebb and flow of a few central ideas in the mainstream of mapping. Our expanding knowledge of our cosmic neighborhood stems largely from a small number of simple but grand ideas, vigorously pursued.

  5. Cosmic tidal reconstruction

    NASA Astrophysics Data System (ADS)

    Zhu, Hong-Ming; Pen, Ue-Li; Yu, Yu; Er, Xinzhong; Chen, Xuelei

    2016-05-01

    The gravitational coupling of a long-wavelength tidal field with small-scale density fluctuations leads to anisotropic distortions of the locally measured small-scale matter correlation function. Since the local correlation function is known to be statistically isotropic in the absence of such tidal interactions, the tidal distortions can be used to reconstruct the long-wavelength tidal field and large-scale density field in analogy with the cosmic microwave background lensing reconstruction. In this paper we present the theoretical framework of cosmic tidal reconstruction and test the reconstruction in numerical simulations. We find that the density field on large scales can be reconstructed with good accuracy and the cross-correlation coefficient between the reconstructed density field and the original density field is greater than 0.9 on large scales (k ≲0.1 h /Mpc ), with the filter scale ˜1.25 Mpc /h . This is useful in the 21 cm intensity mapping survey, where the long-wavelength radial modes are lost due to a foreground subtraction process.

  6. Level crossing analysis of cosmic microwave background radiation: a method for detecting cosmic strings

    SciTech Connect

    Movahed, M. Sadegh; Khosravi, Shahram E-mail: khosravi@ipm.ir

    2011-03-01

    In this paper we study the footprint of cosmic string as the topological defects in the very early universe on the cosmic microwave background radiation. We develop the method of level crossing analysis in the context of the well-known Kaiser-Stebbins phenomenon for exploring the signature of cosmic strings. We simulate a Gaussian map by using the best fit parameter given by WMAP-7 and then superimpose cosmic strings effects on it as an incoherent and active fluctuations. In order to investigate the capability of our method to detect the cosmic strings for the various values of tension, Gμ, a simulated pure Gaussian map is compared with that of including cosmic strings. Based on the level crossing analysis, the superimposed cosmic string with Gμ∼>4 × 10{sup −9} in the simulated map without instrumental noise and the resolution R = 1' could be detected. In the presence of anticipated instrumental noise the lower bound increases just up to Gμ∼>5.8 × 10{sup −9}.

  7. Pattern reversal visual evoked responses of V1/V2 and V5/MT as revealed by MEG combined with probabilistic cytoarchitectonic maps.

    PubMed

    Barnikol, Utako B; Amunts, Katrin; Dammers, Jürgen; Mohlberg, Hartmut; Fieseler, Thomas; Malikovic, Aleksandar; Zilles, Karl; Niedeggen, Michael; Tass, Peter A

    2006-05-15

    Pattern reversal stimulation provides an established tool for assessing the integrity of the visual pathway and for studying early visual processing. Numerous magnetoencephalographic (MEG) and electroencephalographic (EEG) studies have revealed a three-phasic waveform of the averaged pattern reversal visual evoked potential/magnetic field, with components N75(m), P100(m), and N145(m). However, the anatomical assignment of these components to distinct cortical generators is still a matter of debate, which has inter alia connected with considerable interindividual variations of the human striate and extrastriate cortex. The anatomical variability can be compensated for by means of probabilistic cytoarchitectonic maps, which are three-dimensional maps obtained by an observer-independent statistical mapping in a sample of ten postmortem brains. Transformed onto a subject's brain under consideration, these maps provide the probability with which a given voxel of the subject's brain belongs to a particular cytoarchitectonic area. We optimize the spatial selectivity of the probability maps for V1 and V2 with a probability threshold which optimizes the self- vs. cross-overlap in the population of postmortem brains used for deriving the probabilistic cytoarchitectonic maps. For the first time, we use probabilistic cytoarchitectonic maps of visual cortical areas in order to anatomically identify active cortical generators underlying pattern reversal visual evoked magnetic fields as revealed by MEG. The generators are determined with magnetic field tomography (MFT), which reconstructs the current source density in each voxel. In all seven subjects, our approach reveals generators in V1/V2 (with a greater overlap with V1) and in V5 unilaterally (right V5 in three subjects, left V5 in four subjects) and consistent time courses of their stimulus-locked activations, with three peak activations in V1/V2 (contributing to C1m/N75m, P100m, and N145m) and two peak activations in V5

  8. The Genetic Linkage Map of the Medicinal Mushroom Agaricus subrufescens Reveals Highly Conserved Macrosynteny with the Congeneric Species Agaricus bisporus.

    PubMed

    Foulongne-Oriol, Marie; Rocha de Brito, Manuela; Cabannes, Delphine; Clément, Aurélien; Spataro, Cathy; Moinard, Magalie; Dias, Eustáquio Souza; Callac, Philippe; Savoie, Jean-Michel

    2016-01-01

    Comparative linkage mapping can rapidly facilitate the transfer of genetic information from model species to orphan species. This macrosynteny analysis approach has been extensively used in plant species, but few example are available in fungi, and even fewer in mushroom crop species. Among the latter, the Agaricus genus comprises the most cultivable or potentially cultivable species. Agaricus bisporus, the button mushroom, is the model for edible and cultivable mushrooms. We have developed the first genetic linkage map for the basidiomycete A. subrufescens, an emerging mushroom crop known for its therapeutic properties and potential medicinal applications. The map includes 202 markers distributed over 16 linkage groups (LG), and covers a total length of 1701 cM, with an average marker spacing of 8.2 cM. Using 96 homologous loci, we also demonstrated the high level of macrosynteny with the genome of A. bisporus The 13 main LG of A. subrufescens were syntenic to the 13 A. bisporus chromosomes. A disrupted synteny was observed for the three remaining A. subrufescens LG. Electronic mapping of a collection of A. subrufescens expressed sequence tags on A. bisporus genome showed that the homologous loci were evenly spread, with the exception of a few local hot or cold spots of homology. Our results were discussed in the light of Agaricus species evolution process. The map provides a framework for future genetic or genomic studies of the medicinal mushroom A. subrufescens. PMID:26921302

  9. The Genetic Linkage Map of the Medicinal Mushroom Agaricus subrufescens Reveals Highly Conserved Macrosynteny with the Congeneric Species Agaricus bisporus

    PubMed Central

    Foulongne-Oriol, Marie; Rocha de Brito, Manuela; Cabannes, Delphine; Clément, Aurélien; Spataro, Cathy; Moinard, Magalie; Dias, Eustáquio Souza; Callac, Philippe; Savoie, Jean-Michel

    2016-01-01

    Comparative linkage mapping can rapidly facilitate the transfer of genetic information from model species to orphan species. This macrosynteny analysis approach has been extensively used in plant species, but few example are available in fungi, and even fewer in mushroom crop species. Among the latter, the Agaricus genus comprises the most cultivable or potentially cultivable species. Agaricus bisporus, the button mushroom, is the model for edible and cultivable mushrooms. We have developed the first genetic linkage map for the basidiomycete A. subrufescens, an emerging mushroom crop known for its therapeutic properties and potential medicinal applications. The map includes 202 markers distributed over 16 linkage groups (LG), and covers a total length of 1701 cM, with an average marker spacing of 8.2 cM. Using 96 homologous loci, we also demonstrated the high level of macrosynteny with the genome of A. bisporus. The 13 main LG of A. subrufescens were syntenic to the 13 A. bisporus chromosomes. A disrupted synteny was observed for the three remaining A. subrufescens LG. Electronic mapping of a collection of A. subrufescens expressed sequence tags on A. bisporus genome showed that the homologous loci were evenly spread, with the exception of a few local hot or cold spots of homology. Our results were discussed in the light of Agaricus species evolution process. The map provides a framework for future genetic or genomic studies of the medicinal mushroom A. subrufescens. PMID:26921302

  10. Integration of High-Resolution Physical and Genetic Map Reveals Differential Recombination Frequency between Chromosomes and the Genome Assembling Quality in Cucumber

    PubMed Central

    Cheng, Chunyan; Zhang, Zhonghua; Li, Ji; Huang, Sanwen; Chen, Jinfeng

    2013-01-01

    Cucumber is an important model crop and the first species sequenced in Cucurbitaceae family. Compared to the fast increasing genetic and genomics resources, the molecular cytogenetic researches in cucumber are still very limited, which results in directly the shortage of relation between plenty of physical sequences or genetic data and chromosome structure. We mapped twenty-three fosmids anchored by SSR markers from LG-3, the longest linkage group, and LG-4, the shortest linkage group on pachytene chromosomes 3 and 4, using uorescence in situ hybridization (FISH). Integrated molecular cytogenetic maps of chromosomes 3 and 4 were constructed. Except for three SSR markers located on heterochromatin region, the cytological order of markers was concordant with those on the linkage maps. Distinct structural differences between chromosomes 3 and 4 were revealed by the high resolution pachytene chromosomes. The extreme difference of genetic length between LG-3 and LG-4 was mainly attributed to the difference of overall recombination frequency. The significant differentiation of heterochromatin contents in chromosomes 3 and 4 might have a direct correlation with recombination frequency. Meanwhile, the uneven distribution of recombination frequency along chromosome 4 was observed, and recombination frequency of the long arm was nearly 3.5 times higher than that of the short arm. The severe suppression of recombination was exhibited in centromeric and heterochromatin domains of chromosome 4. Whereas a close correlation between the gene density and recombination frequency was observed in chromosome 4, no significant correlation was observed between them along chromosome 3. The comparison between cytogenetic and sequence maps revealed a large gap on the pericentromeric heterochromatin region of sequence map of chromosome 4. These results showed that integrated molecular cytogenetic maps can provide important information for the study of genetic and genomics in cucumber. PMID

  11. A plasma-membrane E-MAP reveals links of the eisosome with sphingolipid metabolism and endosomal trafficking

    PubMed Central

    Aguilar, Pablo S; Fröhlich, Florian; Rehman, Michael; Shales, Mike; Ulitsky, Igor; Olivera-Couto, Agustina; Braberg, Hannes; Shamir, Ron; Walter, Peter; Mann, Matthias; Ejsing, Christer S; Krogan, Nevan J; Walther, Tobias C

    2011-01-01

    The plasma membrane delimits the cell and controls material and information exchange between itself and the environment. How different plasma-membrane processes are coordinated and how the relative abundance of plasma-membrane lipids and proteins is homeostatically maintained are not yet understood. Here, we used a quantitative genetic interaction map, or E-MAP, to functionally interrogate a set of ~400 genes involved in various aspects of plasma-membrane biology, including endocytosis, signaling, lipid metabolism and eisosome function. From this E-MAP, we derived a set of 57,799 individual interactions between genes functioning in these various processes. Using triplet genetic motif analysis, we identified a new component of the eisosome, Eis1, and linked the poorly characterized gene EMP70 to endocytic and eisosome function. Finally, we implicated Rom2, a GDP/GTP exchange factor for Rho1 and Rho2, in the regulation of sphingolipid metabolism. PMID:20526336

  12. Insight Into Genomic Changes Accompanying Divergence: Genetic Linkage Maps and Synteny of Lucania goodei and L. parva Reveal a Robertsonian Fusion

    PubMed Central

    Berdan, Emma L.; Kozak, Genevieve M.; Ming, Ray; Rayburn, A. Lane; Kiehart, Ryan; Fuller, Rebecca C.

    2014-01-01

    Linkage maps are important tools in evolutionary genetics and in studies of speciation. We performed a karyotyping study and constructed high-density linkage maps for two closely related killifish species, Lucania parva and L. goodei, that differ in salinity tolerance and still hybridize in their contact zone in Florida. Using SNPs from orthologous EST contigs, we compared synteny between the two species to determine how genomic architecture has shifted with divergence. Karyotyping revealed that L. goodei possesses 24 acrocentric chromosomes (1N) whereas L. parva possesses 23 chromosomes (1N), one of which is a large metacentric chromosome. Likewise, high-density single-nucleotide polymorphism−based linkage maps indicated 24 linkage groups for L. goodei and 23 linkage groups for L. parva. Synteny mapping revealed two linkage groups in L. goodei that were highly syntenic with the largest linkage group in L. parva. Together, this evidence points to the largest linkage group in L. parva being the result of a chromosomal fusion. We further compared synteny between Lucania with the genome of a more distant teleost relative medaka (Oryzias latipes) and found good conservation of synteny at the chromosomal level. Each Lucania LG had a single best match with each medaka chromosome. These results provide the groundwork for future studies on the genetic architecture of reproductive isolation and salinity tolerance in Lucania and other Fundulidae. PMID:24898707

  13. Chemical Genetics Approach Reveals Importance of cAMP and MAP Kinase Signaling to Lipid and Carotenoid Biosynthesis in Microalgae.

    PubMed

    Choi, Yoon-E; Rhee, Jin-Kyu; Kim, Hyun-Soo; Ahn, Joon-Woo; Hwang, Hyemin; Yang, Ji-Won

    2015-05-01

    In this study, we attempted to understand signaling pathways behind lipid biosynthesis by employing a chemical genetics approach based on small molecule inhibitors. Specific signaling inhibitors of MAP kinase or modulators of cAMP signaling were selected to evaluate the functional roles of each of the key signaling pathways in three different microalgal species: Chlamydomonas reinhardtii, Chlorella vulgaris, and Haematococcus pluvialis. Our results clearly indicate that cAMP signaling pathways are indeed positively associated with microalgal lipid biosynthesis. In contrast, MAP kinase pathways in three microalgal species are all negatively implicated in both lipid and carotenoid biosynthesis. PMID:25563422

  14. Anisotropy and corotation of galactic cosmic rays.

    PubMed

    Amenomori, M; Ayabe, S; Bi, X J; Chen, D; Cui, S W; Danzengluobu; Ding, L K; Ding, X H; Feng, C F; Feng, Zhaoyang; Feng, Z Y; Gao, X Y; Geng, Q X; Guo, H W; He, H H; He, M; Hibino, K; Hotta, N; Hu, Haibing; Hu, H B; Huang, J; Huang, Q; Jia, H Y; Kajino, F; Kasahara, K; Katayose, Y; Kato, C; Kawata, K; Labaciren; Le, G M; Li, A F; Li, J Y; Lou, Y-Q; Lu, H; Lu, S L; Meng, X R; Mizutani, K; Mu, J; Munakata, K; Nagai, A; Nanjo, H; Nishizawa, M; Ohnishi, M; Ohta, I; Onuma, H; Ouchi, T; Ozawa, S; Ren, J R; Saito, T; Saito, T Y; Sakata, M; Sako, T K; Sasaki, T; Shibata, M; Shiomi, A; Shirai, T; Sugimoto, H; Takita, M; Tan, Y H; Tateyama, N; Torii, S; Tsuchiya, H; Udo, S; Wang, B; Wang, H; Wang, X; Wang, Y G; Wu, H R; Xue, L; Yamamoto, Y; Yan, C T; Yang, X C; Yasue, S; Ye, Z H; Yu, G C; Yuan, A F; Yuda, T; Zhang, H M; Zhang, J L; Zhang, N J; Zhang, X Y; Zhang, Y; Zhang, Yi; Zhaxisangzhu; Zhou, X X

    2006-10-20

    The intensity of Galactic cosmic rays is nearly isotropic because of the influence of magnetic fields in the Milky Way. Here, we present two-dimensional high-precision anisotropy measurement for energies from a few to several hundred teraelectronvolts (TeV), using the large data sample of the Tibet Air Shower Arrays. Besides revealing finer details of the known anisotropies, a new component of Galactic cosmic ray anisotropy in sidereal time is uncovered around the Cygnus region direction. For cosmic-ray energies up to a few hundred TeV, all components of anisotropies fade away, showing a corotation of Galactic cosmic rays with the local Galactic magnetic environment. These results have broad implications for a comprehensive understanding of cosmic rays, supernovae, magnetic fields, and heliospheric and Galactic dynamic environments. PMID:17053141

  15. Detecting cosmic strings in the CMB with the Canny algorithm

    SciTech Connect

    Amsel, Stephen; Brandenberger, Robert H; Berger, Joshua E-mail: jb454@cornell.edu

    2008-04-15

    Line discontinuities in cosmic microwave background anisotropy maps are a distinctive prediction of models with cosmic strings. These signatures are visible in anisotropy maps with good angular resolution and should be identifiable using edge-detection algorithms. One such algorithm is the Canny algorithm. We study the potential of this algorithm to pick out the line discontinuities generated by cosmic strings. By applying the algorithm to small-scale microwave anisotropy maps generated from theoretical models with and without cosmic strings, we find that, given an angular resolution of several minutes of arc, cosmic strings can be detected down to a limit of the mass per unit length of the string which is one order of magnitude lower than the current upper bounds.

  16. Scanning the landscape of genome architecture of non-O1 and non-O139 Vibrio cholerae by whole genome mapping reveals extensive population genetic diversity

    DOE PAGESBeta

    Chapman, Carol; Henry, Matthew; Bishop-Lilly, Kimberly A.; Awosika, Joy; Briska, Adam; Ptashkin, Ryan N.; Wagner, Trevor; Rajanna, Chythanya; Tsang, Hsinyi; Johnson, Shannon L.; et al

    2015-03-20

    Historically, cholera outbreaks have been linked to V. cholerae O1 serogroup strains or its derivatives of the O37 and O139 serogroups. A genomic study on the 2010 Haiti cholera outbreak strains highlighted the putative role of non O1/non-O139 V. cholerae in causing cholera and the lack of genomic sequences of such strains from around the world. Here we address these gaps by scanning a global collection of V. cholerae strains as a first step towards understanding the population genetic diversity and epidemic potential of non O1/non-O139 strains. Whole Genome Mapping (Optical Mapping) based bar coding produces a high resolution, orderedmore » restriction map, depicting a complete view of the unique chromosomal architecture of an organism. To assess the genomic diversity of non-O1/non-O139 V. cholerae, we applied a Whole Genome Mapping strategy on a well-defined and geographically and temporally diverse strain collection, the Sakazaki serogroup type strains. Whole Genome Map data on 91 of the 206 serogroup type strains support the hypothesis that V. cholerae has an unprecedented genetic and genomic structural diversity. Interestingly, we discovered chromosomal fusions in two unusual strains that possess a single chromosome instead of the two chromosomes usually found in V. cholerae. We also found pervasive chromosomal rearrangements such as duplications and indels in many strains. The majority of Vibrio genome sequences currently in public databases are unfinished draft sequences. The Whole Genome Mapping approach presented here enables rapid screening of large strain collections to capture genomic complexities that would not have been otherwise revealed by unfinished draft genome sequencing and thus aids in assembling and finishing draft sequences of complex genomes. Furthermore, Whole Genome Mapping allows for prediction of novel V. cholerae non-O1/non-O139 strains that may have the potential to cause future cholera outbreaks.« less

  17. Scanning the Landscape of Genome Architecture of Non-O1 and Non-O139 Vibrio cholerae by Whole Genome Mapping Reveals Extensive Population Genetic Diversity

    PubMed Central

    Awosika, Joy; Briska, Adam; Ptashkin, Ryan N.; Wagner, Trevor; Rajanna, Chythanya; Tsang, Hsinyi; Johnson, Shannon L.; Mokashi, Vishwesh P.; Chain, Patrick S. G.; Sozhamannan, Shanmuga

    2015-01-01

    Historically, cholera outbreaks have been linked to V. cholerae O1 serogroup strains or its derivatives of the O37 and O139 serogroups. A genomic study on the 2010 Haiti cholera outbreak strains highlighted the putative role of non O1/non-O139 V. cholerae in causing cholera and the lack of genomic sequences of such strains from around the world. Here we address these gaps by scanning a global collection of V. cholerae strains as a first step towards understanding the population genetic diversity and epidemic potential of non O1/non-O139 strains. Whole Genome Mapping (Optical Mapping) based bar coding produces a high resolution, ordered restriction map, depicting a complete view of the unique chromosomal architecture of an organism. To assess the genomic diversity of non-O1/non-O139 V. cholerae, we applied a Whole Genome Mapping strategy on a well-defined and geographically and temporally diverse strain collection, the Sakazaki serogroup type strains. Whole Genome Map data on 91 of the 206 serogroup type strains support the hypothesis that V. cholerae has an unprecedented genetic and genomic structural diversity. Interestingly, we discovered chromosomal fusions in two unusual strains that possess a single chromosome instead of the two chromosomes usually found in V. cholerae. We also found pervasive chromosomal rearrangements such as duplications and indels in many strains. The majority of Vibrio genome sequences currently in public databases are unfinished draft sequences. The Whole Genome Mapping approach presented here enables rapid screening of large strain collections to capture genomic complexities that would not have been otherwise revealed by unfinished draft genome sequencing and thus aids in assembling and finishing draft sequences of complex genomes. Furthermore, Whole Genome Mapping allows for prediction of novel V. cholerae non-O1/non-O139 strains that may have the potential to cause future cholera outbreaks. PMID:25794000

  18. SPACE: the SPectroscopic, All-Sky Cosmic Explorer

    NASA Technical Reports Server (NTRS)

    Cimatti, A.; Robberto, M.; Baugh, C.; Beckwith, S. W. V.; Content, R.; Daddi, E.; deLucia, G.; Garilli, B.; Guzzo, L.; Kauffmann, G.; Lehnert, M.; Maccagni, D.; Martinez-Sansigre, A.; Pasian, F.; Reid, I. N.; Rosati, P.; Salvaterra, R.; Stiavelli, M.; Wang, Y.; ZapateroOsorio, M.; Balcells, M.; Bersanelli, M.; Gardner, J.P.; Kimble, R.; Clampin, M.

    2007-01-01

    We describe the scientific motivations, the mission concept and the instrumentation of SPACE, a class-M mission proposed for concept study at the first call of the ESA Cosmic-Vision 2015-2025 planning cycle. SPACE aims at producing the largest three-dimensional evolutionary map of the Universe over the past 10 billion years by taking near-IR spectra and measuring redshifts of more than half a billion galaxies at 0 < z < 2 down to AB approximately 23 over 37r sr of the sky. In addition, SPACE will also target a smaller sky field, performing a deep spectroscopic survey of millions of galaxies to AB approximately 26 and at 2 < z < l0+. Owing to the depth, redshift range, volume coverage and quality of its spectra, SPACE will reveal with unique sensitivity most of the fundamental cosmological signatures, including the power spectrum of density fluctuations and its turnover, the baryonic acoustic oscillations imprinted when matter and radiation decoupled, the distance-luminosity relation of cosmological supernovae, the evolution of the cosmic expansion rate, the growth rate of cosmic large-scale structure, the large scale distribution of galaxies. The datasets from the SPACE mission will represent a long lasting legacy that will be data mined for many years to come.

  19. Chromosome rearrangements during domestication of cucumber as revealed from high-density genetic mapping and draft genome assembly

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cucumber is an economically important vegetable crop, but available genetic and genomics resources for cucumber are limited that hinders progress in cucumber breeding. In this study, we made significant contributions to the cucumber research community by developing a high-density genetic map for cul...

  20. The structure of pairwise correlation in mouse primary visual cortex reveals functional organization in the absence of an orientation map.

    PubMed

    Denman, Daniel J; Contreras, Diego

    2014-10-01

    Neural responses to sensory stimuli are not independent. Pairwise correlation can reduce coding efficiency, occur independent of stimulus representation, or serve as an additional channel of information, depending on the timescale of correlation and the method of decoding. Any role for correlation depends on its magnitude and structure. In sensory areas with maps, like the orientation map in primary visual cortex (V1), correlation is strongly related to the underlying functional architecture, but it is unclear whether this correlation structure is an essential feature of the system or arises from the arrangement of cells in the map. We assessed the relationship between functional architecture and pairwise correlation by measuring both synchrony and correlated spike count variability in mouse V1, which lacks an orientation map. We observed significant pairwise synchrony, which was organized by distance and relative orientation preference between cells. We also observed nonzero correlated variability in both the anesthetized (0.16) and awake states (0.18). Our results indicate that the structure of pairwise correlation is maintained in the absence of an underlying anatomical organization and may be an organizing principle of the mammalian visual system preserved by nonrandom connectivity within local networks. PMID:23689635

  1. SNP discovery and chromosome anchoring provide the first physically-anchored hexaploid oat map and reveal synteny with model species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    For the first time in many years a comprehensive genome map for cultivated oat has been constructed using a combination of single nucleotide polymorphism (SNP) markers and validated with a collection of cytogenetically defined germplasm lines. The markers were able to help distinguish the three geno...

  2. Global Anisotropies in TeV Cosmic Rays Related to the Sun's Local Galactic Environment from IBEX

    NASA Technical Reports Server (NTRS)

    Schwadron, N. A.; Adams, F. C.; Christian, E. R.; Desiati, P.; Frisch, P.; Funsten, H. O.; Jokipii, J. R.; McComas, D. J.; Moebius, E.; Zank, G. P.

    2014-01-01

    Observations with the Interstellar Boundary Explorer (IBEX) have shown enhanced energetic neutral atom (ENA) emission from a narrow, circular ribbon likely centered on the direction of the local interstellar medium (LISM) magnetic field. Here, we show that recent determinations of the local interstellar velocity, based on interstellar atom measurements with IBEX, are consistent with the interstellar modulation of high-energy (tera-electron volts, TeV) cosmic rays and diffusive propagation from supernova sources revealed in global anisotropy maps of ground-based high-energy cosmic-ray observatories (Milagro, Asg, and IceCube). Establishing a consistent local interstellar magnetic field direction using IBEX ENAs at hundreds to thousands of eV and galactic cosmic rays at tens of TeV has wide-ranging implications for the structure of our heliosphere and its interactions with the LISM, which is particularly important at the time when the Voyager spacecraft are leaving our heliosphere.

  3. Global anisotropies in TeV cosmic rays related to the Sun's local galactic environment from IBEX.

    PubMed

    Schwadron, N A; Adams, F C; Christian, E R; Desiati, P; Frisch, P; Funsten, H O; Jokipii, J R; McComas, D J; Moebius, E; Zank, G P

    2014-02-28

    Observations with the Interstellar Boundary Explorer (IBEX) have shown enhanced energetic neutral atom (ENA) emission from a narrow, circular ribbon likely centered on the direction of the local interstellar medium (LISM) magnetic field. Here, we show that recent determinations of the local interstellar velocity, based on interstellar atom measurements with IBEX, are consistent with the interstellar modulation of high-energy (tera-electron volts, TeV) cosmic rays and diffusive propagation from supernova sources revealed in global anisotropy maps of ground-based high-energy cosmic-ray observatories (Milagro, Asγ, and IceCube). Establishing a consistent local interstellar magnetic field direction using IBEX ENAs at hundreds to thousands of eV and galactic cosmic rays at tens of TeV has wide-ranging implications for the structure of our heliosphere and its interactions with the LISM, which is particularly important at the time when the Voyager spacecraft are leaving our heliosphere. PMID:24526313

  4. The COBE cosmic 3 K anisotropy experiment: A gravity wave and cosmic string probe

    NASA Technical Reports Server (NTRS)

    Bennett, Charles L.; Smoot, George F.

    1989-01-01

    Among the experiments to be carried into orbit next year, by the COBE satellite, are differential microwave radiometers. They will make sensitive all-sky maps of the temperature of the cosmic microwave background radiation at three frequencies, giving dipole, quadrupole, and higher order multipole measurements of the background radiation. The experiment will either detect, or place significant constraints on, the existence of cosmic strings and long wavelength gravity waves.

  5. COSMIC program documentation experience

    NASA Technical Reports Server (NTRS)

    Kalar, M. C.

    1970-01-01

    A brief history of COSMIC as it relates to the handling of program documentation is summarized; the items that are essential for computer program documentation are also discussed. COSMIC documentation and program standards handbook is appended.

  6. QTL mapping reveals the genetic architecture of loci affecting pre- and post-zygotic isolating barriers in Louisiana Iris

    PubMed Central

    2012-01-01

    Background Hybridization among Louisiana Irises has been well established and the genetic architecture of reproductive isolation is known to affect the potential for and the directionality of introgression between taxa. Here we use co-dominant markers to identify regions where QTL are located both within and between backcross maps to compare the genetic architecture of reproductive isolation and fitness traits across treatments and years. Results QTL mapping was used to elucidate the genetic architecture of reproductive isolation between Iris fulva and Iris brevicaulis. Homologous co-dominant EST-SSR markers scored in two backcross populations between I. fulva and I. brevicaulis were used to generate genetic linkage maps. These were used as the framework for mapping QTL associated with variation in 11 phenotypic traits likely responsible for reproductive isolation and fitness. QTL were dispersed throughout the genome, with the exception of one region of a single linkage group (LG) where QTL for flowering time, sterility, and fruit production clustered. In most cases, homologous QTL were not identified in both backcross populations, however, homologous QTL for flowering time, number of growth points per rhizome, number of nodes per inflorescence, and number of flowers per node were identified on several linkage groups. Conclusions Two different traits affecting reproductive isolation, flowering time and sterility, exhibit different genetic architectures, with numerous QTL across the Iris genome controlling flowering time and fewer, less distributed QTL affecting sterility. QTL for traits affecting fitness are largely distributed across the genome with occasional overlap, especially on LG 4, where several QTL increasing fitness and decreasing sterility cluster. Given the distribution and effect direction of QTL affecting reproductive isolation and fitness, we have predicted genomic regions where introgression may be more likely to occur (those regions associated with

  7. Mesoscale fronts as foraging habitats: composite front mapping reveals oceanographic drivers of habitat use for a pelagic seabird

    PubMed Central

    Scales, Kylie L.; Miller, Peter I.; Embling, Clare B.; Ingram, Simon N.; Pirotta, Enrico; Votier, Stephen C.

    2014-01-01

    The oceanographic drivers of marine vertebrate habitat use are poorly understood yet fundamental to our knowledge of marine ecosystem functioning. Here, we use composite front mapping and high-resolution GPS tracking to determine the significance of mesoscale oceanographic fronts as physical drivers of foraging habitat selection in northern gannets Morus bassanus. We tracked 66 breeding gannets from a Celtic Sea colony over 2 years and used residence time to identify area-restricted search (ARS) behaviour. Composite front maps identified thermal and chlorophyll-a mesoscale fronts at two different temporal scales—(i) contemporaneous fronts and (ii) seasonally persistent frontal zones. Using generalized additive models (GAMs), with generalized estimating equations (GEE-GAMs) to account for serial autocorrelation in tracking data, we found that gannets do not adjust their behaviour in response to contemporaneous fronts. However, ARS was more likely to occur within spatially predictable, seasonally persistent frontal zones (GAMs). Our results provide proof of concept that composite front mapping is a useful tool for studying the influence of oceanographic features on animal movements. Moreover, we highlight that frontal persistence is a crucial element of the formation of pelagic foraging hotspots for mobile marine vertebrates. PMID:25165595

  8. Mesoscale fronts as foraging habitats: composite front mapping reveals oceanographic drivers of habitat use for a pelagic seabird.

    PubMed

    Scales, Kylie L; Miller, Peter I; Embling, Clare B; Ingram, Simon N; Pirotta, Enrico; Votier, Stephen C

    2014-11-01

    The oceanographic drivers of marine vertebrate habitat use are poorly understood yet fundamental to our knowledge of marine ecosystem functioning. Here, we use composite front mapping and high-resolution GPS tracking to determine the significance of mesoscale oceanographic fronts as physical drivers of foraging habitat selection in northern gannets Morus bassanus. We tracked 66 breeding gannets from a Celtic Sea colony over 2 years and used residence time to identify area-restricted search (ARS) behaviour. Composite front maps identified thermal and chlorophyll-a mesoscale fronts at two different temporal scales-(i) contemporaneous fronts and (ii) seasonally persistent frontal zones. Using generalized additive models (GAMs), with generalized estimating equations (GEE-GAMs) to account for serial autocorrelation in tracking data, we found that gannets do not adjust their behaviour in response to contemporaneous fronts. However, ARS was more likely to occur within spatially predictable, seasonally persistent frontal zones (GAMs). Our results provide proof of concept that composite front mapping is a useful tool for studying the influence of oceanographic features on animal movements. Moreover, we highlight that frontal persistence is a crucial element of the formation of pelagic foraging hotspots for mobile marine vertebrates. PMID:25165595

  9. A high-resolution linkage map for the Z chromosome in chicken reveals hot spots for recombination.

    PubMed

    Wahlberg, P; Strömstedt, L; Tordoir, X; Foglio, M; Heath, S; Lechner, D; Hellström, A R; Tixier-Boichard, M; Lathrop, M; Gut, I G; Andersson, L

    2007-01-01

    A comprehensive linkage map for chicken chromosome Z was constructed as the result of a large-scale screening of single nucleotide polymorphisms (SNPs). A total of 308 SNPs were assigned to Z based on the genotype distribution among 182 birds representing several populations. A linkage map comprising 210 markers and spanning 200.9 cM was established by analyzing a small Red junglefowl/White Leghorn intercross. There was excellent agreement between the linkage map for Z and a recently released assembly of the chicken genome (May 2006). Almost all SNPs assigned to chromosome Z in the present study are on Z in the new genome assembly. The remaining 12 loci are all found on unassigned contigs that can now be assigned to Z. The average recombination rate was estimated at 2.7 cM/Mb but there was a very uneven distribution of recombination events with both cold and hot spots of recombination. The existence of one of the major hot spots of recombination, located around position 39.4 Mb, was supported by the observed pattern of linkage disequilibrium. Thirteen markers from unassigned contigs were shown to be located on chromosome W. Three of these contigs included genes that have homologues on chromosome Z. The preliminary assignment of three more genes to the gene-poor W chromosome may be important for studies on the mechanism of sex determination and dosage compensation in birds. PMID:17675841

  10. Linkage mapping in the oilseed crop Jatropha curcas L. reveals a locus controlling the biosynthesis of phorbol esters which cause seed toxicity

    PubMed Central

    King, Andrew J; Montes, Luis R; Clarke, Jasper G; Affleck, Julie; Li, Yi; Witsenboer, Hanneke; van der Vossen, Edwin; van der Linde, Piet; Tripathi, Yogendra; Tavares, Evanilda; Shukla, Parul; Rajasekaran, Thirunavukkarasu; van Loo, Eibertus N; Graham, Ian A

    2013-01-01

    Current efforts to grow the tropical oilseed crop Jatropha curcas L. economically are hampered by the lack of cultivars and the presence of toxic phorbol esters (PE) within the seeds of most provenances. These PE restrict the conversion of seed cake into animal feed, although naturally occurring ‘nontoxic’ provenances exist which produce seed lacking PE. As an important step towards the development of genetically improved varieties of J. curcas, we constructed a linkage map from four F2 mapping populations. The consensus linkage map contains 502 codominant markers, distributed over 11 linkage groups, with a mean marker density of 1.8 cM per unique locus. Analysis of the inheritance of PE biosynthesis indicated that this is a maternally controlled dominant monogenic trait. This maternal control is due to biosynthesis of the PE occurring only within maternal tissues. The trait segregated 3 : 1 within seeds collected from F2 plants, and QTL analysis revealed that a locus on linkage group 8 was responsible for phorbol ester biosynthesis. By taking advantage of the draft genome assemblies of J. curcas and Ricinus communis (castor), a comparative mapping approach was used to develop additional markers to fine map this mutation within 2.3 cM. The linkage map provides a framework for the dissection of agronomic traits in J. curcas, and the development of improved varieties by marker-assisted breeding. The identification of the locus responsible for PE biosynthesis means that it is now possible to rapidly breed new nontoxic varieties. PMID:23898859

  11. Large-scale East-Asian eQTL mapping reveals novel candidate genes for LD mapping and the genomic landscape of transcriptional effects of sequence variants.

    PubMed

    Narahara, Maiko; Higasa, Koichiro; Nakamura, Seiji; Tabara, Yasuharu; Kawaguchi, Takahisa; Ishii, Miho; Matsubara, Kenichi; Matsuda, Fumihiko; Yamada, Ryo

    2014-01-01

    Profiles of sequence variants that influence gene transcription are very important for understanding mechanisms that affect phenotypic variation and disease susceptibility. Using genotypes at 1.4 million SNPs and a comprehensive transcriptional profile of 15,454 coding genes and 6,113 lincRNA genes obtained from peripheral blood cells of 298 Japanese individuals, we mapped expression quantitative trait loci (eQTLs). We identified 3,804 cis-eQTLs (within 500 kb from target genes) and 165 trans-eQTLs (>500 kb away or on different chromosomes). Cis-eQTLs were often located in transcribed or adjacent regions of genes; among these regions, 5' untranslated regions and 5' flanking regions had the largest effects. Epigenetic evidence for regulatory potential accumulated in public databases explained the magnitude of the effects of our eQTLs. Cis-eQTLs were often located near the respective target genes, if not within genes. Large effect sizes were observed with eQTLs near target genes, and effect sizes were obviously attenuated as the eQTL distance from the gene increased. Using a very stringent significance threshold, we identified 165 large-effect trans-eQTLs. We used our eQTL map to assess 8,069 disease-associated SNPs identified in 1,436 genome-wide association studies (GWAS). We identified genes that might be truly causative, but GWAS might have failed to identify for 148 out of the GWAS-identified SNPs; for example, TUFM (P = 3.3E-48) was identified for inflammatory bowel disease (early onset); ZFP90 (P = 4.4E-34) for ulcerative colitis; and IDUA (P = 2.2E-11) for Parkinson's disease. We identified four genes (P<2.0E-14) that might be related to three diseases and two hematological traits; each expression is regulated by trans-eQTLs on a different chromosome than the gene. PMID:24956270

  12. Large-Scale East-Asian eQTL Mapping Reveals Novel Candidate Genes for LD Mapping and the Genomic Landscape of Transcriptional Effects of Sequence Variants

    PubMed Central

    Narahara, Maiko; Higasa, Koichiro; Nakamura, Seiji; Tabara, Yasuharu; Kawaguchi, Takahisa; Ishii, Miho; Matsubara, Kenichi; Matsuda, Fumihiko; Yamada, Ryo

    2014-01-01

    Profiles of sequence variants that influence gene transcription are very important for understanding mechanisms that affect phenotypic variation and disease susceptibility. Using genotypes at 1.4 million SNPs and a comprehensive transcriptional profile of 15,454 coding genes and 6,113 lincRNA genes obtained from peripheral blood cells of 298 Japanese individuals, we mapped expression quantitative trait loci (eQTLs). We identified 3,804 cis-eQTLs (within 500 kb from target genes) and 165 trans-eQTLs (>500 kb away or on different chromosomes). Cis-eQTLs were often located in transcribed or adjacent regions of genes; among these regions, 5′ untranslated regions and 5′ flanking regions had the largest effects. Epigenetic evidence for regulatory potential accumulated in public databases explained the magnitude of the effects of our eQTLs. Cis-eQTLs were often located near the respective target genes, if not within genes. Large effect sizes were observed with eQTLs near target genes, and effect sizes were obviously attenuated as the eQTL distance from the gene increased. Using a very stringent significance threshold, we identified 165 large-effect trans-eQTLs. We used our eQTL map to assess 8,069 disease-associated SNPs identified in 1,436 genome-wide association studies (GWAS). We identified genes that might be truly causative, but GWAS might have failed to identify for 148 out of the GWAS-identified SNPs; for example, TUFM (P = 3.3E-48) was identified for inflammatory bowel disease (early onset); ZFP90 (P = 4.4E-34) for ulcerative colitis; and IDUA (P = 2.2E-11) for Parkinson's disease. We identified four genes (P<2.0E-14) that might be related to three diseases and two hematological traits; each expression is regulated by trans-eQTLs on a different chromosome than the gene. PMID:24956270

  13. Searching for signatures of cosmic superstrings in the CMB

    SciTech Connect

    Danos, Rebecca J.; Brandenberger, Robert H. E-mail: rhb@physics.mcgill.ca

    2010-02-01

    Because cosmic superstrings generically form junctions and gauge theoretic strings typically do not, junctions may provide a signature to distinguish between cosmic superstrings and gauge theoretic cosmic strings. In cosmic microwave background anisotropy maps, cosmic strings lead to distinctive line discontinuities. String junctions lead to junctions in these line discontinuities. In turn, edge detection algorithms such as the Canny algorithm can be used to search for signatures of strings in anisotropy maps. We apply the Canny algorithm to simulated maps which contain the effects of cosmic strings with and without string junctions. The Canny algorithm produces edge maps. To distinguish between edge maps from string simulations with and without junctions, we examine the density distribution of edges and pixels crossed by edges. We find that in string simulations without Gaussian noise (such as produced by the dominant inflationary fluctuations) our analysis of the output data from the Canny algorithm can clearly distinguish between simulations with and without string junctions. In the presence of Gaussian noise at the level expected from the current bounds on the contribution of cosmic strings to the total power spectrum of density fluctuations, the distinction between models with and without junctions is more difficult. However, by carefully analyzing the data the models can still be differentiated.

  14. Cosmic rays from cosmic strings with condensates

    SciTech Connect

    Vachaspati, Tanmay

    2010-02-15

    We revisit the production of cosmic rays by cusps on cosmic strings. If a scalar field ('Higgs') has a linear interaction with the string world sheet, such as would occur if there is a bosonic condensate on the string, cusps on string loops emit narrow beams of very high energy Higgses which then decay to give a flux of ultrahigh energy cosmic rays. The ultrahigh energy flux and the gamma to proton ratio agree with observations if the string scale is {approx}10{sup 13} GeV. The diffuse gamma ray and proton fluxes are well below current bounds. Strings that are lighter and have linear interactions with scalars produce an excess of direct and diffuse cosmic rays and are ruled out by observations, while heavier strings ({approx}10{sup 15} GeV) are constrained by their gravitational signatures. This leaves a narrow window of parameter space for the existence of cosmic strings with bosonic condensates.

  15. Imaging the cosmic microwave background: The BEAST experiment

    NASA Astrophysics Data System (ADS)

    Natoli, P.; Bersanelli, M.; Childers, J.; Figueiredo, N.; Halevi, D.; Kangas, M.; Levy, A.; Lubin, P.; Mandolesi, N.; Meinhold, P.; Parendo, S.; Staren, J.; Villela, T.; Wuensche, C.

    2001-02-01

    We describe the Santa Barbara BEAST experiment, a balloon borne telescope to image the Cosmic Microwave Background (CMB) radiation anisotropy pattern. Some aspects of the map making pipeline are also discussed. .

  16. A physically anchored genetic map and linkage to avirulence reveals recombination suppression over the proximal region of Hessian fly chromosome A2.

    PubMed Central

    Behura, Susanta K; Valicente, Fernando H; Rider, S Dean; Shun-Chen, Ming; Jackson, Scott; Stuart, Jeffrey J

    2004-01-01

    Resistance in wheat (Triticum aestivum) to the Hessian fly (Mayetiola destructor), a major insect pest of wheat, is based on a gene-for-gene interaction. Close linkage (3 +/- 2 cM) was discovered between Hessian fly avirulence genes vH3 and vH5. Bulked segregant analysis revealed two DNA markers (28-178 and 23-201) within 10 cM of these loci and only 3 +/- 2 cM apart. However, 28-178 was located in the middle of the short arm of Hessian fly chromosome A2 whereas 23-201 was located in the middle of the long arm of chromosome A2, suggesting the presence of severe recombination suppression over its proximal region. To further test that possibility, an AFLP-based genetic map of the Hessian fly genome was constructed. Fluorescence in situ hybridization of 20 markers on the genetic map to the polytene chromosomes of the Hessian fly indicated good correspondence between the linkage groups and the four Hessian fly chromosomes. The physically anchored genetic map is the first of any gall midge species. The proximal region of mitotic chromosome A2 makes up 30% of its length but corresponded to <3% of the chromosome A2 genetic map. PMID:15166159

  17. Structural basis of FYCO1 and MAP1LC3A interaction reveals a novel binding mode for Atg8-family proteins.

    PubMed

    Cheng, Xiaofang; Wang, Yingli; Gong, Yukang; Li, Faxiang; Guo, Yujiao; Hu, Shichen; Liu, Jianping; Pan, Lifeng

    2016-08-01

    FYCO1 (FYVE and coiled-coil domain containing 1) functions as an autophagy adaptor in directly linking autophagosomes with the microtubule-based kinesin motor, and plays an essential role in the microtubule plus end-directed transport of autophagic vesicles. The specific association of FYCO1 with autophagosomes is mediated by its interaction with Atg8-family proteins decorated on the outer surface of autophagosome. However, the mechanistic basis governing the interaction between FYCO1 and Atg8-family proteins is largely unknown. Here, using biochemical and structural analyses, we demonstrated that FYCO1 contains a unique LC3-interacting region (LIR), which discriminately binds to mammalian Atg8 orthologs and preferentially binds to the MAP1LC3A and MAP1LC3B. In addition to uncovering the detailed molecular mechanism underlying the FYCO1 LIR and MAP1LC3A interaction, the determined FYCO1-LIR-MAP1LC3A complex structure also reveals a unique LIR binding mode for Atg8-family proteins, and demonstrates, first, the functional relevance of adjacent sequences C-terminal to the LIR core motif for binding to Atg8-family proteins. Taken together, our findings not only provide new mechanistic insight into FYCO1-mediated transport of autophagosomes, but also expand our understanding of the interaction modes between LIR motifs and Atg8-family proteins in general. PMID:27246247

  18. Probabilistic and single-subject retinotopic maps reveal the topographic organization of face patches in the macaque cortex.

    PubMed

    Janssens, Thomas; Zhu, Qi; Popivanov, Ivo D; Vanduffel, Wim

    2014-07-30

    Face perception is crucial to survival among social primates. It has been suggested that a group of extrastriate cortical regions responding more strongly to faces than to nonface objects is critical for face processing in primates. It is generally assumed that these regions are not retinotopically organized, as with human face-processing areas, showing foveal bias but lacking any organization with respect to polar angle. Despite many electrophysiological studies targeting monkey face patches, the retinotopic organization of these patches remains largely unclear. We have examined the relationship between cortical face patches and the topographic organization of extrastriate cortex using biologically relevant, phase-encoded retinotopic mapping stimuli in macaques. Single-subject fMRI results indicated a gradual shift from highly retinotopic to no topographic organization from posterior to anterior face patches in inferotemporal cortex. We also constructed a probabilistic retinotopic atlas of occipital and ventral extrastriate visual cortex. By comparing this probabilistic map to the locations of face patches at the group level, we showed that a previously identified posterior lateral temporal face patch (PL) is located within the posterior inferotemporal dorsal (PITd) retinotopic area. Furthermore, we identified a novel face patch posterior PL, which is located in retinotopically organized transitional area V4 (V4t). Previously published coordinates of human PITd coincide with the group-level occipital face area (OFA), according to a probabilistic map derived from a large population, implying a potential correspondence between monkey PL/PITd and human OFA/PITd. Furthermore, the monkey middle lateral temporal face patch (ML) shows consistent foveal biases but no obvious polar-angle structure. In contrast, middle fundus temporal (MF), anterior temporal and prefrontal monkey face patches lacked topographic organization. PMID:25080579

  19. Fiber tract-driven topographical mapping (FTTM) reveals microstructural relevance for interhemispheric visuomotor function in the aging brain

    PubMed Central

    Schulte, Tilman; Maddah, Mahnaz; Müller-Oehring, Eva M.; Rohlfing, Torsten; Pfefferbaum, Adolf; Sullivan, Edith V.

    2013-01-01

    We present a novel approach – DTI-based fiber tract-driven topographical mapping (FTTM) – to map and measure the influence of age on the integrity of interhemispheric fibers and challenge their selective functions with measures of interhemispheric integration of lateralized information. This approach enabled identification of spatially specific topographical maps of scalar diffusion measures and their relation to measures of visuomotor performance. Relative to younger adults, older adults showed lower fiber integrity indices in anterior than posterior callosal fibers. FTTM analysis identified a dissociation in the microstructural – function associates between age groups: in younger adults, genu fiber integrity correlated with interhemispheric transfer time, whereas in older adults, body fiber integrity was correlated with interhemispheric transfer time with topographical specificity along left-lateralized callosal fiber trajectories. Neural co-activation from redundant targets was evidenced by fMRI-derived bilateral extrastriate cortex activation in both groups, and a group difference emerged for a pontine activation cluster that was differently modulated by response hand in older than younger adults. Bilateral processing advantages in older but not younger adults further correlated with fiber integrity in transverse pontine fibers that branch into the right cerebellar cortex, thereby supporting a role for the pons in interhemispheric facilitation. In conclusion, in the face of compromised anterior callosal fibers, older adults appear to use alternative pathways to accomplish visuomotor interhemispheric information transfer and integration for lateralized processing. This shift from youthful associations may indicate recruitment of compensatory mechanisms involving medial corpus callosum fibers and subcortical pathways. PMID:23567886

  20. Change point analysis of travel routes reveals novel insights into foraging strategies and cognitive maps of wild baboons.

    PubMed

    Noser, Rahel; Byrne, Richard W

    2014-05-01

    Efficient space use is a critical challenge for animals relying on stationary resources. It is often difficult with purely observational methods to gain unambiguous insight into any ability of primates to manage and process spatial information. Investigating the visible signs of the decision processes underlying space use often leaves open important issues. We applied the change point test [Byrne et al. (2009). Anim Behav 77: 619-631], a statistical tool to objectively determine change points (CPs) in animal travel paths, to investigate to what degree directional changes in our study group's (Papio ursinus) dry season ranging were associated with important resources and prominent landmarks. One-third of directional changes were associated with fruit feeding, 1/3 with traveling, and 1/3 with dry matter feeding, travel feeding and with drinking. When directional changes were associated with traveling, the subsequent directional changes were likely to result in fruit feeding. Fruit feeding mostly occurred at the apex of the day journeys, while drinking, dry matter feeding, and travel feeding often occurred along straight travel segments. The majority of directional changes did not occur in clusters at distinctive locations, but at distances of more than 120 m apart from each other, many of them along prominent landmarks. We conclude that the CPs do not represent nodes or route bends of a network map. Rather, they represent (1) locations where the decision to turn back to their sleeping site was taken, and (2) locations next to important landmarks (changes of slope, car tracks) where slight adjustment of a movement direction was possible. We found no evidence for a Euclidean map and discuss our findings in the light of a network map representation of space. PMID:23946104

  1. Fostered and left behind alleles in peanut: interspecific QTL mapping reveals footprints of domestication and useful natural variation for breeding

    PubMed Central

    2012-01-01

    Background Polyploidy can result in genetic bottlenecks, especially for species of monophyletic origin. Cultivated peanut is an allotetraploid harbouring limited genetic diversity, likely resulting from the combined effects of its single origin and domestication. Peanut wild relatives represent an important source of novel alleles that could be used to broaden the genetic basis of the cultigen. Using an advanced backcross population developed with a synthetic amphidiploid as donor of wild alleles, under two water regimes, we conducted a detailed QTL study for several traits involved in peanut productivity and adaptation as well as domestication. Results A total of 95 QTLs were mapped in the two water treatments. About half of the QTL positive effects were associated with alleles of the wild parent and several QTLs involved in yield components were specific to the water-limited treatment. QTLs detected for the same trait mapped to non-homeologous genomic regions, suggesting differential control in subgenomes as a consequence of polyploidization. The noteworthy clustering of QTLs for traits involved in seed and pod size and in plant and pod morphology suggests, as in many crops, that a small number of loci have contributed to peanut domestication. Conclusion In our study, we have identified QTLs that differentiated cultivated peanut from its wild relatives as well as wild alleles that contributed positive variation to several traits involved in peanut productivity and adaptation. These findings offer novel opportunities for peanut improvement using wild relatives. PMID:22340522

  2. A distance-weighted interaction map reveals a previously uncharacterized layer of the Bacillus subtilis spore coat.

    PubMed

    McKenney, Peter T; Driks, Adam; Eskandarian, Haig A; Grabowski, Paul; Guberman, Jonathan; Wang, Katherine H; Gitai, Zemer; Eichenberger, Patrick

    2010-05-25

    Bacillus subtilis spores are encased in a protein assembly called the spore coat that is made up of at least 70 different proteins. Conventional electron microscopy shows the coat to be organized into two distinct layers. Because the coat is about as wide as the theoretical limit of light microscopy, quantitatively measuring the localization of individual coat proteins within the coat is challenging. We used fusions of coat proteins to green fluorescent protein to map genetic dependencies for coat assembly and to define three independent subnetworks of coat proteins. To complement the genetic data, we measured coat protein localization at subpixel resolution and integrated these two data sets to produce a distance-weighted genetic interaction map. Using these data, we predict that the coat comprises at least four spatially distinct layers, including a previously uncharacterized glycoprotein outermost layer that we name the spore crust. We found that crust assembly depends on proteins we predicted to localize to the crust. The crust may be conserved in all Bacillus spores and may play critical functions in the environment. PMID:20451384

  3. Genome-Wide Mapping of Structural Variations Reveals a Copy Number Variant That Determines Reproductive Morphology in Cucumber

    PubMed Central

    Zhang, Zhonghua; Mao, Linyong; Chen, Huiming; Bu, Fengjiao; Li, Guangcun; Sun, Jinjing; Li, Shuai; Sun, Honghe; Jiao, Chen; Blakely, Rachel; Pan, Junsong; Cai, Run; Luo, Ruibang; Van de Peer, Yves; Jacobsen, Evert; Fei, Zhangjun; Huang, Sanwen

    2015-01-01

    Structural variations (SVs) represent a major source of genetic diversity. However, the functional impact and formation mechanisms of SVs in plant genomes remain largely unexplored. Here, we report a nucleotide-resolution SV map of cucumber (Cucumis sativas) that comprises 26,788 SVs based on deep resequencing of 115 diverse accessions. The largest proportion of cucumber SVs was formed through nonhomologous end-joining rearrangements, and the occurrence of SVs is closely associated with regions of high nucleotide diversity. These SVs affect the coding regions of 1676 genes, some of which are associated with cucumber domestication. Based on the map, we discovered a copy number variation (CNV) involving four genes that defines the Female (F) locus and gives rise to gynoecious cucumber plants, which bear only female flowers and set fruit at almost every node. The CNV arose from a recent 30.2-kb duplication at a meiotically unstable region, likely via microhomology-mediated break-induced replication. The SV set provides a snapshot of structural variations in plants and will serve as an important resource for exploring genes underlying key traits and for facilitating practical breeding in cucumber. PMID:26002866

  4. Conditional independence mapping of DIGE data reveals PDIA3 protein species as key nodes associated with muscle aerobic capacity

    PubMed Central

    Burniston, Jatin G.; Kenyani, Jenna; Gray, Donna; Guadagnin, Eleonora; Jarman, Ian H.; Cobley, James N.; Cuthbertson, Daniel J.; Chen, Yi-Wen; Wastling, Jonathan M.; Lisboa, Paulo J.; Koch, Lauren G.; Britton, Steven L.

    2014-01-01

    Profiling of protein species is important because gene polymorphisms, splice variations and post-translational modifications may combine and give rise to multiple protein species that have different effects on cellular function. Two-dimensional gel electrophoresis is one of the most robust methods for differential analysis of protein species, but bioinformatic interrogation is challenging because the consequences of changes in the abundance of individual protein species on cell function are unknown and cannot be predicted. We conducted DIGE of soleus muscle from male and female rats artificially selected as either high- or low-capacity runners (HCR and LCR, respectively). In total 696 protein species were resolved and LC–MS/MS identified proteins in 337 spots. Forty protein species were differentially (P < 0.05, FDR < 10%) expressed between HCR and LCR and conditional independence mapping found distinct networks within these data, which brought insight beyond that achieved by functional annotation. Protein disulphide isomerase A3 emerged as a key node segregating with differences in aerobic capacity and unsupervised bibliometric analysis highlighted further links to signal transducer and activator of transcription 3, which were confirmed by western blotting. Thus, conditional independence mapping is a useful technique for interrogating DIGE data that is capable of highlighting latent features. PMID:24769234

  5. Genome-Wide Mapping of Structural Variations Reveals a Copy Number Variant That Determines Reproductive Morphology in Cucumber.

    PubMed

    Zhang, Zhonghua; Mao, Linyong; Chen, Huiming; Bu, Fengjiao; Li, Guangcun; Sun, Jinjing; Li, Shuai; Sun, Honghe; Jiao, Chen; Blakely, Rachel; Pan, Junsong; Cai, Run; Luo, Ruibang; Van de Peer, Yves; Jacobsen, Evert; Fei, Zhangjun; Huang, Sanwen

    2015-06-01

    Structural variations (SVs) represent a major source of genetic diversity. However, the functional impact and formation mechanisms of SVs in plant genomes remain largely unexplored. Here, we report a nucleotide-resolution SV map of cucumber (Cucumis sativas) that comprises 26,788 SVs based on deep resequencing of 115 diverse accessions. The largest proportion of cucumber SVs was formed through nonhomologous end-joining rearrangements, and the occurrence of SVs is closely associated with regions of high nucleotide diversity. These SVs affect the coding regions of 1676 genes, some of which are associated with cucumber domestication. Based on the map, we discovered a copy number variation (CNV) involving four genes that defines the Female (F) locus and gives rise to gynoecious cucumber plants, which bear only female flowers and set fruit at almost every node. The CNV arose from a recent 30.2-kb duplication at a meiotically unstable region, likely via microhomology-mediated break-induced replication. The SV set provides a snapshot of structural variations in plants and will serve as an important resource for exploring genes underlying key traits and for facilitating practical breeding in cucumber. PMID:26002866

  6. High-Resolution Sex-Specific Linkage Maps of the Mouse Reveal Polarized Distribution of Crossovers in Male Germline

    PubMed Central

    Liu, Eric Yi; Morgan, Andrew P.; Chesler, Elissa J.; Wang, Wei; Churchill, Gary A.; Pardo-Manuel de Villena, Fernando

    2014-01-01

    Since the publication of the first comprehensive linkage map for the laboratory mouse, the architecture of recombination as a basic biological process has become amenable to investigation in mammalian model organisms. Here we take advantage of high-density genotyping and the unique pedigree structure of the incipient Collaborative Cross to investigate the roles of sex and genetic background in mammalian recombination. Our results confirm the observation that map length is longer when measured through female meiosis than through male meiosis, but we find that this difference is modified by genotype at loci on both the X chromosome and the autosomes. In addition, we report a striking concentration of crossovers in the distal ends of autosomes in male meiosis that is absent in female meiosis. The presence of this pattern in both single- and double-recombinant chromosomes, combined with the absence of a corresponding asymmetry in the distribution of double-strand breaks, indicates a regulated sequence of events specific to male meiosis that is anchored by chromosome ends. This pattern is consistent with the timing of chromosome pairing and evolutionary constraints on male recombination. Finally, we identify large regions of reduced crossover frequency that together encompass 5% of the genome. Many of these “cold regions” are enriched for segmental duplications, suggesting an inverse local correlation between recombination rate and mutation rate for large copy number variants. PMID:24578350

  7. The Cosmic Ray Electron Excess

    NASA Technical Reports Server (NTRS)

    Chang, J.; Adams, J. H.; Ahn, H. S.; Bashindzhagyan, G. L.; Christl, M.; Ganel, O.; Guzik, T. G.; Isbert, J.; Kim, K. C.; Kuznetsov, E. N.; Panasyuk, M. I.; Panov, A. D.; Schmidt, W. K. H.; Seo, E. S.; Sokolskaya, N. V.; Watts, J. W.; Wefel, J. P.; Wu, J.; Zatsepin, V. I.

    2008-01-01

    This slide presentation reviews the possible sources for the apparent excess of Cosmic Ray Electrons. The presentation reviews the Advanced Thin Ionization Calorimeter (ATIC) instrument, the various parts, how cosmic ray electrons are measured, and shows graphs that review the results of the ATIC instrument measurement. A review of Cosmic Ray Electrons models is explored, along with the source candidates. Scenarios for the excess are reviewed: Supernova remnants (SNR) Pulsar Wind nebulae, or Microquasars. Each of these has some problem that mitigates the argument. The last possibility discussed is Dark Matter. The Anti-Matter Exploration and Light-nuclei Astrophysics (PAMELA) mission is to search for evidence of annihilations of dark matter particles, to search for anti-nuclei, to test cosmic-ray propagation models, and to measure electron and positron spectra. There are slides explaining the results of Pamela and how to compare these with those of the ATIC experiment. Dark matter annihilation is then reviewed, which represent two types of dark matter: Neutralinos, and kaluza-Kline (KK) particles, which are next explained. The future astrophysical measurements, those from GLAST LAT, the Alpha Magnetic Spectrometer (AMS), and HEPCAT are reviewed, in light of assisting in finding an explanation for the observed excess. Also the Compact Muon Solenoid (CMS) experiment at the Large Hadron Collider (LHC) could help by revealing if there are extra dimensions.

  8. Genome-wide Association Study and Admixture Mapping Reveal New Loci Associated with Total IgE Levels in Latinos

    PubMed Central

    Pino-Yanes, Maria; Gignoux, Christopher R.; Galanter, Joshua M.; Levin, Albert M.; Campbell, Catarina D.; Eng, Celeste; Huntsman, Scott; Nishimura, Katherine K.; Gourraud, Pierre-Antoine; Mohajeri, Kiana; O'Roak, Brian J.; Hu, Donglei; Mathias, Rasika A.; Nguyen, Elizabeth A.; Roth, Lindsey A.; Padhukasahasram, Badri; Moreno-Estrada, Andres; Sandoval, Karla; Winkler, Cheryl A.; Lurmann, Fred; Davis, Adam; Farber, Harold J.; Meade, Kelley; Avila, Pedro C.; Serebrisky, Denise; Chapela, Rocio; Ford, Jean G.; Lenoir, Michael A.; Thyne, Shannon M.; Brigino-Buenaventura, Emerita; Borrell, Luisa N.; Rodriguez-Cintron, William; Sen, Saunak; Kumar, Rajesh; Rodriguez-Santana, Jose R.; Bustamante, Carlos D.; Martinez, Fernando D.; Raby, Benjamin A.; Weiss, Scott T.; Nicolae, Dan L.; Ober, Carole; Meyers, Deborah A.; Bleecker, Eugene R.; Mack, Steven J.; Hernandez, Ryan D.; Eichler, Evan E.; Barnes, Kathleen C.; Williams, L. Keoki; Torgerson, Dara G.; Burchard, Esteban G.

    2014-01-01

    Background Immunoglobulin E (IgE) is a key mediator of allergic inflammation and is frequently elevated in allergic disorders. Objective To identify genetic variants associated with IgE levels in Latinos. Methods We performed a genome-wide association study (GWAS) and admixture mapping of total IgE levels in 3,334 Latinos from the Genes-environments & Admixture in Latino Americans (GALA II) study. Replication was evaluated in 454 Latinos, 1,564 European Americans, and 3,187 African Americans from independent studies. Results We confirmed associations of six genes identified by previous GWAS and identified a novel genome-wide significant association of a polymorphism in ZNF365 with total IgE (rs200076616, p=2.3x10−8). We next identified four admixture mapping peaks (6p21.32-p22.1, 13p22-31, 14q23.2, and 22q13.1) where local African, European, and/or Native American ancestry was significantly associated with IgE levels. The most significant peak was 6p21.32-p22.1, where Native American ancestry was associated with lower levels of IgE (p=4.95x10−8). All but 22q13.1 were replicated in an independent sample of Latinos, and two of the peaks were replicated in African Americans (6p21.32-p22.1 and 14q23.2). Fine mapping of 6p21.32-p22.1 identified six genome-wide significant single nucleotide polymorphisms in Latinos, two of which replicated in European Americans. Another SNP was peak-wide significant within 14q23.2 in African Americans (rs1741099, p=3.7x10−6), and replicated in non-African American samples (p=0.011). Conclusion We confirmed genetic associations at six genes, and identified novel associations within ZNF365, HLA-DQA1, and 14q23.2. Our results highlight the importance of studying diverse, multi-ethnic populations to uncover novel loci associated with total IgE levels. PMID:25488688

  9. Mapping of Replication Origins in the X Inactivation Center of Vole Microtus levis Reveals Extended Replication Initiation Zone

    PubMed Central

    Sherstyuk, Vladimir V.; Shevchenko, Alexander I.; Zakian, Suren M.

    2015-01-01

    DNA replication initiates at specific positions termed replication origins. Genome-wide studies of human replication origins have shown that origins are organized into replication initiation zones. However, only few replication initiation zones have been described so far. Moreover, few origins were mapped in other mammalian species besides human and mouse. Here we analyzed pattern of short nascent strands in the X inactivation center (XIC) of vole Microtus levis in fibroblasts, trophoblast stem cells, and extraembryonic endoderm stem cells and confirmed origins locations by ChIP approach. We found that replication could be initiated in a significant part of XIC. We also analyzed state of XIC chromatin in these cell types. We compared origin localization in the mouse and vole XIC. Interestingly, origins associated with gene promoters are conserved in these species. The data obtained allow us to suggest that the X inactivation center of M. levis is one extended replication initiation zone. PMID:26038842

  10. Mapping of Replication Origins in the X Inactivation Center of Vole Microtus levis Reveals Extended Replication Initiation Zone.

    PubMed

    Sherstyuk, Vladimir V; Shevchenko, Alexander I; Zakian, Suren M

    2015-01-01

    DNA replication initiates at specific positions termed replication origins. Genome-wide studies of human replication origins have shown that origins are organized into replication initiation zones. However, only few replication initiation zones have been described so far. Moreover, few origins were mapped in other mammalian species besides human and mouse. Here we analyzed pattern of short nascent strands in the X inactivation center (XIC) of vole Microtus levis in fibroblasts, trophoblast stem cells, and extraembryonic endoderm stem cells and confirmed origins locations by ChIP approach. We found that replication could be initiated in a significant part of XIC. We also analyzed state of XIC chromatin in these cell types. We compared origin localization in the mouse and vole XIC. Interestingly, origins associated with gene promoters are conserved in these species. The data obtained allow us to suggest that the X inactivation center of M. levis is one extended replication initiation zone. PMID:26038842

  11. QTL mapping of fungicide sensitivity reveals novel genes and pleiotropy with melanization in the pathogen Zymoseptoria tritici.

    PubMed

    Lendenmann, Mark H; Croll, Daniel; McDonald, Bruce A

    2015-07-01

    A major problem associated with the intensification of agriculture is the emergence of fungicide resistance. Azoles are ergosterol biosynthesis inhibitors that have been widely used in agriculture and medicine since the 1970s, leading to emergence of increasingly resistant fungal populations. The known genetic mechanisms underlying lower azole sensitivity include mutations affecting the CYP51 gene that encodes the target protein, but in many cases azole resistance is a more complex trait with an unknown genetic basis. We used quantitative trait locus (QTL) mapping to identify genes affecting azole sensitivity in two crosses of Zymoseptoria tritici, the most damaging wheat pathogen in Europe. Restriction site associated DNA sequencing (RADseq) was used to genotype 263 (cross 1) and 261 (cross 2) progeny at ∼ 8500 single nucleotide polymorphisms (SNP) and construct two dense linkage maps. Azole sensitivity was assessed using high-throughput digital image analysis of colonies growing on Petri dishes with or without the fungicide propiconazole. We identified three QTLs for azole sensitivity, including two that contained novel fungicide sensitivity genes. One of these two QTLs contained only 16 candidate genes, among which four most likely candidates were identified. The third QTL contained ERG6, encoding another protein involved in ergosterol biosynthesis. Known genes in QTLs affecting colony growth included CYP51 and PKS1, a gene affecting melanization in Z. tritici. PKS1 showed compelling evidence for pleiotropy, with a rare segregating allele that increased melanization while decreasing growth rate and propiconazole sensitivity. This study resolved the genetic architecture of an important agricultural trait and led to identification of novel genes that are likely to affect azole sensitivity in Z. tritici. It also provided insight into fitness costs associated with lowered azole sensitivity and suggests a novel fungicide mixture strategy. PMID:25979163

  12. A Complex Recombination Pattern in the Genome of Allotetraploid Brassica napus as Revealed by a High-Density Genetic Map

    PubMed Central

    Yi, Bin; Fan, Chuchuan; Edwards, David; Batley, Jacqueline; Zhou, Yongming

    2014-01-01

    Polyploidy plays a crucial role in plant evolution. Brassica napus (2n = 38, AACC), the most important oil crop in the Brassica genus, is an allotetraploid that originated through natural doubling of chromosomes after the hybridization of its progenitor species, B. rapa (2n = 20, AA) and B. oleracea (2n = 18, CC). A better understanding of the evolutionary relationship between B. napus and B. rapa, B. oleracea, as well as Arabidopsis, which has a common ancestor with these three species, will provide valuable information about the generation and evolution of allopolyploidy. Based on a high-density genetic map with single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers, we performed a comparative genomic analysis of B. napus with Arabidopsis and its progenitor species B. rapa and B. oleracea. Based on the collinear relationship of B. rapa and B. oleracea in the B. napus genetic map, the B. napus genome was found to consist of 70.1% of the skeleton components of the chromosomes of B. rapa and B. oleracea, with 17.7% of sequences derived from reciprocal translocation between homoeologous chromosomes between the A- and C-genome and 3.6% of sequences derived from reciprocal translocation between non-homologous chromosomes at both intra- and inter-genomic levels. The current study thus provides insights into the formation and evolution of the allotetraploid B. napus genome, which will allow for more accurate transfer of genomic information from B. rapa, B. oleracea and Arabidopsis to B. napus. PMID:25356735

  13. Comparative mapping of the wild perennial Glycine latifolia and soybean (G. max) reveals extensive chromosome rearrangements in the genus Glycine.

    PubMed

    Chang, Sungyul; Thurber, Carrie S; Brown, Patrick J; Hartman, Glen L; Lambert, Kris N; Domier, Leslie L

    2014-01-01

    Soybean (Glycine max L. Mer.), like many cultivated crops, has a relatively narrow genetic base and lacks diversity for some economically important traits. Glycine latifolia (Benth.) Newell & Hymowitz, one of the 26 perennial wild Glycine species related to soybean in the subgenus Glycine Willd., shows high levels of resistance to multiple soybean pathogens and pests including Alfalfa mosaic virus, Heterodera glycines Ichinohe and Sclerotinia sclerotiorum (Lib.) de Bary. However, limited information is available on the genomes of these perennial Glycine species. To generate molecular resources for gene mapping and identification, high-density linkage maps were constructed for G. latifolia using single nucleotide polymorphism (SNP) markers generated by genotyping by sequencing and evaluated in an F2 population and confirmed in an F5 population. In each population, greater than 2,300 SNP markers were selected for analysis and segregated to form 20 large linkage groups. Marker orders were similar in the F2 and F5 populations. The relationships between G. latifolia linkage groups and G. max and common bean (Phaseolus vulgaris L.) chromosomes were examined by aligning SNP-containing sequences from G. latifolia to the genome sequences of G. max and P. vulgaris. Twelve of the 20 G. latifolia linkage groups were nearly collinear with G. max chromosomes. The remaining eight G. latifolia linkage groups appeared to be products of multiple interchromosomal translocations relative to G. max. Large syntenic blocks also were observed between G. latifolia and P. vulgaris. These experiments are the first to compare genome organizations among annual and perennial Glycine species and common bean. The development of molecular resources for species closely related to G. max provides information into the evolution of genomes within the genus Glycine and tools to identify genes within perennial wild relatives of cultivated soybean that could be beneficial to soybean production. PMID

  14. Cosmic Complexity

    NASA Technical Reports Server (NTRS)

    Mather, John C.

    2012-01-01

    neutrons, liberating a little energy and creating complexity. Then, the expanding universe cooled some more, and neutrons and protons, no longer kept apart by immense temperatures, found themselves unstable and formed helium nuclei. Then, a little more cooling, and atomic nuclei and electrons were no longer kept apart, and the universe became transparent. Then a little more cooling, and the next instability began: gravitation pulled matter together across cosmic distances to form stars and galaxies. This instability is described as a "negative heat capadty" in which extracting energy from a gravitating system makes it hotter -- clearly the 2nd law of thermodynamics does not apply here! (This is the physicist's part of the answer to e e cummings' question: what is the wonder that's keeping the stars apart?) Then, the next instability is that hydrogen and helium nuclei can fuse together to release energy and make stars burn for billions of years. And then at the end of the fuel source, stars become unstable and explode and liberate the chemical elements back into space. And because of that, on planets like Earth, sustained energy flows support the development of additional instabilities and all kinds of complex patterns. Gravitational instability pulls the densest materials into the core of the Earth, leaving a thin skin of water and air, and makes the interior churn incessantly as heat flows outwards. And the heat from the sun, received mostly near the equator and flowing towards the poles, supports the complex atmospheric and oceanic circulations. And because or that, the physical Earth is full of natural chemical laboratories, concentrating elements here, mixing them there, raising and lowering temperatures, ceaselessly experimenting with uncountable events where new instabilities can arise. At least one of them was the new experiment called life. Now that we know that there are at least as many planets as there are stars, it is hard to imagine that nature's ceasess

  15. Cosmic Complexity

    NASA Technical Reports Server (NTRS)

    Mather, John C.

    2012-01-01

    neutrons, liberating a little energy and creating complexity. Then, the expanding universe cooled some more, and neutrons and protons, no longer kept apart by immense temperatures, found themselves unstable and formed helium nuclei. Then, a little more cooling, and atomic nuclei and electrons were no longer kept apart, and the universe became transparent. Then a little more cooling, and the next instability began: gravitation pulled matter together across cosmic distances to form stars and galaxies. This instability is described as a "negative heat capadty" in which extracting energy from a gravitating system makes it hotter -- clearly the 2nd law of thermodynamics does not apply here! (This is the physicist's part of the answer to e e cummings' question: what is the wonder that's keeping the stars apart?) Then, the next instability is that hydrogen and helium nuclei can fuse together to release energy and make stars burn for billions of years. And then at the end of the fuel source, stars become unstable and explode and liberate the chemical elements back into space. And because of that, on planets like Earth, sustained energy flows support the development of additional instabilities and all kinds of complex patterns. Gravitational instability pulls the densest materials into the core of the Earth, leaving a thin skin of water and air, and makes the interior churn incessantly as heat flows outwards. And the heat from the sun, received mostly near the equator and flowing towards the poles, supports the complex atmospheric and oceanic circulations. And because or that, the physical Earth is full of natural chemical laboratories, concentrating elements here, mixing them there, raising and lowering temperatures, ceaselessly experimenting with uncountable events where new instabilities can arise. At least one of them was the new experiment called life. Now that we know that there are at least as many planets as there are stars, it is hard to imagine that nature's ceasess

  16. Cosmic Inflation

    SciTech Connect

    Lincoln, Don

    2015-11-21

    In 1964, scientists discovered a faint radio hiss coming from the heavens and realized that the hiss wasn’t just noise. It was a message from eons ago; specifically the remnants of the primordial fireball, cooled to about 3 degrees above absolute zero. Subsequent research revealed that the radio hiss was the same in every direction. The temperature of the early universe was uniform to at better than a part in a hundred thousand. And this was weird. According to the prevailing theory, the two sides of the universe have never been in contact. So how could two places that had never been in contact be so similar? One possible explanation was proposed in 1979. Called inflation, the theory required that early in the history of the universe, the universe expanded faster than the speed of light. Confused? Watch this video as Fermilab’s Dr. Don Lincoln makes sense of this mind-bending idea.

  17. OT2_ymatsuda_1: The Herschel Proto-cluster Survey: SPIRE Mapping of the Nodes of the Cosmic Web at z>2

    NASA Astrophysics Data System (ADS)

    Matsuda, Y.

    2011-09-01

    We propose an experiment to search for signatures of rapid growth of galaxies and AGNs in a sample of three z>2 proto-clusters. These environments are exceptionally rare, pre-virialised regions corresponding to peaks in the matter density field, located at the nodes of large-scale (>10-Mpc) filamentary structures. They are the best candidates for the progenitors of the most massive clusters of galaxies (~10^15-Msun) today. We pay special attention to an unusual class of object, preferentially located in proto-clusters: Lyman alpha blobs (LABs) - 100-kpc scale luminous emission-line gas nebulae. Some LABs show signatures of recent galaxy-galaxy mergers/interactions, are often host to luminous continuum sources, and many have evidence of gas inflows/outflows in their emission-line morphology. A significant fraction of LABs have embedded galaxies detected at X-ray, mid-infrared, and/or sub-mm wavelengths, suggesting possible rapid growths of the galaxies and AGNs in proto-cluster regions. Are the proto-cluster systems more obscured than galaxies in the field? Are the protocluster systems growing more rapidly? By mapping these proto-clusters with SPIRE, we will: (1) measure SFRs in sub-mm (rest-frame FIR) for the galaxies and AGNs in the proto-clusters, and determine how much star formation is obscured (when compared to UV estimate) and (2) determine SSFRs for the galaxies and AGNs in the proto-clusters, and see how they compare to field galaxies at z=2-3. This program will deliver fundamental information on the growth of galaxies and super-massive black holes in the densest regions of the Universe at high-redshift, and provide valuable insight into the astrophysical processes that establish the trends linking galaxy properties and their environments.

  18. High-Density Nucleosome Occupancy Map of Human Chromosome 9p21–22 Reveals Chromatin Organization of the Type I Interferon Gene Cluster

    PubMed Central

    Freaney, Jonathan E.; Zhang, Quanwei; Yigit, Erbay; Kim, Rebecca; Widom, Jonathan; Wang, Ji-Ping

    2014-01-01

    Genome-wide investigations have dramatically increased our understanding of nucleosome positioning and the role of chromatin in gene regulation, yet some genomic regions have been poorly represented in human nucleosome maps. One such region is represented by human chromosome 9p21–22, which contains the type I interferon gene cluster that includes 16 interferon alpha genes and the single interferon beta, interferon epsilon, and interferon omega genes. A high-density nucleosome mapping strategy was used to generate locus-wide maps of the nucleosome organization of this biomedically important locus at a steady state and during a time course of infection with Sendai virus, an inducer of interferon gene expression. Detailed statistical and computational analysis illustrates that nucleosomes in this locus exhibit preferences for particular dinucleotide and oligomer DNA sequence motifs in vivo, which are similar to those reported for lower eukaryotic nucleosome–DNA interactions. These data were used to visualize the region's chromatin architecture and reveal features that are common to the organization of all the type I interferon genes, indicating a common nucleosome-mediated gene regulatory paradigm. Additionally, this study clarifies aspects of the dynamic changes that occur with the nucleosome occupying the transcriptional start site of the interferon beta gene after virus infection. PMID:24673249

  19. Linkage Maps of the dwarf and Normal Lake Whitefish (Coregonus clupeaformis) Species Complex and Their Hybrids Reveal the Genetic Architecture of Population Divergence

    PubMed Central

    Rogers, S. M.; Isabel, N.; Bernatchez, L.

    2007-01-01

    Elucidating the genetic architecture of population divergence may reveal the evolution of reproductive barriers and the genomic regions implicated in the process. We assembled genetic linkage maps for the dwarf and Normal lake whitefish species complex and their hybrids. A total of 877 AFLP loci and 30 microsatellites were positioned. The homology of mapped loci between families supported the existence of 34 linkage groups (of 40n expected) exhibiting 83% colinearity among linked loci between these two families. Classes of AFLP markers were not randomly distributed among linkage groups. Both AFLP and microsatellites exhibited deviations from Mendelian expectations, with 30.4% exhibiting significant segregation distortion across 28 linkage groups of the four linkage maps in both families (P < 0.00001). Eight loci distributed over seven homologous linkage groups were significantly distorted in both families and the level of distortion, when comparing homologous loci of the same phase between families, was correlated (Spearman R = 0.378, P = 0.0021). These results suggest that substantial divergence incurred during allopatric glacial separation and subsequent sympatric ecological specialization has resulted in several genomic regions that are no longer complementary between dwarf and Normal populations issued from different evolutionary glacial lineages. PMID:17110497

  20. Magnetic Resonance Q Mapping Reveals a Decrease in Microvessel Density in the arcAβ Mouse Model of Cerebral Amyloidosis

    PubMed Central

    Ielacqua, Giovanna D.; Schlegel, Felix; Füchtemeier, Martina; Xandry, Jael; Rudin, Markus; Klohs, Jan

    2016-01-01

    Alterations in density and morphology of the cerebral microvasculature have been reported to occur in Alzheimer's disease patients and animal models of the disease. In this study we compared magnetic resonance imaging (MRI) techniques for their utility to detect age-dependent changes of the cerebral vasculature in the arcAβ mouse model of cerebral amyloidosis. Dynamic susceptibility contrast (DSC)-MRI was performed by tracking the passage of a superparamagnetic iron oxide nanoparticle in the brain with dynamic gradient echo planar imaging (EPI). From this measurements relative cerebral blood volume [rCBV(DSC)] and relative cerebral blood flow (rCBF) were estimated. For the same animal maps of the relaxation shift index Q were computed from high resolution gradient echo and spin echo data that were acquired before and after superparamagnetic iron oxide (SPIO) nanoparticle injection. Q-values were used to derive estimates of microvessel density. The change in the relaxation rates ΔR2* obtained from pre- and post-contrast gradient echo data was used for the alternative determination of rCBV [rCBV(ΔR2*)]. Linear mixed effects modeling found no significant association between rCBV(DSC), rCBV(ΔR2*), rCBF, and Q with genotype in 13-month old mice [compared to age-matched non-transgenic littermates (NTLs)] for any of the evaluated brain regions. In 24-month old mice there was a significant association for rCBV(DSC) with genotype in the cerebral cortex, and for rCBV(ΔR2*) in the cerebral cortex and cerebellum. For rCBF there was a significant association in the cerebellum but not in other brain regions. Q-values in the olfactory bulb, cerebral cortex, striatum, hippocampus, and cerebellum in 24-month old mice were significantly associated with genotype. In those regions Q-values were reduced between 11 and 26% in arcAβ mice compared to age-matched NTLs. Vessel staining with CD31 immunohistochemistry confirmed a reduction of microvessel density in the old arcAβ mice

  1. Coding Gene SNP Mapping Reveals QTL Linked to Growth and Stress Response in Brook Charr (Salvelinus fontinalis)

    PubMed Central

    Sauvage, Christopher; Vagner, Marie; Derôme, Nicolas; Audet, Céline; Bernatchez, Louis

    2012-01-01

    Growth performance and reduced stress response are traits of major interest in fish production. Growth and stress-related quantitative trait loci (QTL) have been already identified in several salmonid species, but little effort has been devoted to charrs (genus Salvelinus). Moreover, most QTL studies to date focused on one or very few traits, and little investigation has been devoted to QTL identification for gene expression. Here, our objective was to identify QTL for 27 phenotypes related to growth and stress responses in brook charr (Salvelinus fontinalis), which is one of the most economically important freshwater aquaculture species in Canada. Phenotypes included 12 growth parameters, six blood and plasma variables, three hepatic variables, and one plasma hormone level as well as the relative expression measurements of five genes of interest linked to growth regulation. QTL analysis relied on a linkage map recently built from S. fontinalis consisting of both single-nucleotide polymorphism (SNP, n = 266) and microsatellite (n =81) markers in an F2 interstrain hybrid population (n = 171). We identified 63 growth-related QTL and four stress-related QTL across 18 of the 40 linkage groups of the brook charr linkage map. Percent variance explained, confidence interval, and allelic QTL effects also were investigated to provide insight into the genetic architecture of growth- and stress-related QTL. QTL related to growth performance and stress response that were identified could be classified into two groups: (1) a group composed of the numerous, small-effect QTL associated with some traits related to growth (i.e., weight) that may be under the control of a large number of genes or pleiotropic genes, and (2) a group of less numerous QTL associated with growth (i.e., gene expression) and with stress-related QTL that display a larger effect, suggesting that these QTL are under the control of a limited number of genes of major effect. This study represents a first step

  2. A gene expression map of the larval Xenopus laevis head reveals developmental changes underlying the evolution of new skeletal elements.

    PubMed

    Square, Tyler; Jandzik, David; Cattell, Maria; Coe, Alex; Doherty, Jacob; Medeiros, Daniel Meulemans

    2015-01-15

    The morphology of the vertebrate head skeleton is highly plastic, with the number, size, shape, and position of its components varying dramatically between groups. While this evolutionary flexibility has been key to vertebrate success, its developmental and genetic bases are poorly understood. The larval head skeleton of the frog Xenopus laevis possesses a unique combination of ancestral tetrapod features and anuran-specific novelties. We built a detailed gene expression map of the head mesenchyme in X. laevis during early larval development, focusing on transcription factor families with known functions in vertebrate head skeleton development. This map was then compared to homologous gene expression in zebrafish, mouse, and shark embryos to identify conserved and evolutionarily flexible aspects of vertebrate head skeleton development. While we observed broad conservation of gene expression between X. laevis and other gnathostomes, we also identified several divergent features that correlate to lineage-specific novelties. We noted a conspicuous change in dlx1/2 and emx2 expression in the second pharyngeal arch, presaging the differentiation of the reduced dorsal hyoid arch skeletal element typical of modern anamniote tetrapods. In the first pharyngeal arch we observed a shift in the expression of the joint inhibitor barx1, and new expression of the joint marker gdf5, shortly before skeletal differentiation. This suggests that the anuran-specific infrarostral cartilage evolved by partitioning of Meckel's cartilage with a new paired joint. Taken together, these comparisons support a model in which early patterning mechanisms divide the vertebrate head mesenchyme into a highly conserved set of skeletal precursor populations. While subtle changes in this early patterning system can affect skeletal element size, they do not appear to underlie the evolution of new joints or cartilages. In contrast, later expression of the genes that regulate skeletal element

  3. Cosmic ray antiprotons from nearby cosmic accelerators

    NASA Astrophysics Data System (ADS)

    Joshi, Jagdish C.; Gupta, Nayantara

    2015-05-01

    The antiproton flux measured by PAMELA experiment might have originated from Galactic sources of cosmic rays. These antiprotons are expected to be produced in the interactions of cosmic ray protons and nuclei with cold protons. Gamma rays are also produced in similar interactions inside some of the cosmic accelerators. We consider a few nearby supernova remnants observed by Fermi LAT. Many of them are associated with molecular clouds. Gamma rays have been detected from these sources which most likely originate in decay of neutral pions produced in hadronic interactions. The observed gamma ray fluxes from these SNRs are used to find out their contributions to the observed diffuse cosmic ray antiproton flux near the earth.

  4. Fate mapping reveals that microglia and recruited monocyte-derived macrophages are definitively distinguishable by phenotype in the retina

    PubMed Central

    O’Koren, E. G.; Mathew, R.; Saban, D. R.

    2016-01-01

    The recent paradigm shift that microglia are yolk sac-derived, not hematopoietic-derived, is reshaping our knowledge about the isolated role of microglia in CNS diseases, including degenerative conditions of the retina. However, unraveling microglial-specific functions has been hindered by phenotypic overlap of microglia with monocyte-derived macrophages. The latter are differentiated from recruited monocytes in neuroinflammation, including retina. Here we demonstrate the use of fate mapping wherein microglia and monocyte-derived cells are endogenously labeled with different fluorescent reporters. Combining this method with 12-color flow cytometry, we show that these two populations are definitively distinguishable by phenotype in retina. We prove that retinal microglia have a unique CD45lo CD11clo F4/80lo I-A/I-E− signature, conserved in the steady state and during retinal injury. The latter was observed in the widely used light-induced retinal degeneration model and corroborated in other models, including whole-body irradiation/bone-marrow transplantation. The literature contains conflicting observations about whether microglia, including in the retina, increase expression of these markers in neuroinflammation. We show that monocyte-derived macrophages have elevated expression of these surface markers, not microglia. Our resolution of such phenotypic differences may serve as a robust way to help characterize isolated roles of these cells in retinal neuroinflammation and possibly elsewhere in CNS. PMID:26856416

  5. HapMap tag-SNP analysis confirms a role for COMT in schizophrenia risk and reveals a novel association.

    PubMed

    Voisey, J; Swagell, C D; Hughes, I P; Lawford, B R; Young, R M; Morris, C P

    2012-07-01

    Catechol-O-methyl transferase (COMT) encodes an enzyme involved in the metabolism of dopamine and maps to a commonly deleted region that increases schizophrenia risk. A non-synonymous polymorphism (rs4680) in COMT has been previously found to be associated with schizophrenia and results in altered activity levels of COMT. Using a haplotype block-based gene-tagging approach we conducted an association study of seven COMT single nucleotide polymorphisms (SNPs) in 160 patients with a DSM-IV diagnosis of schizophrenia and 250 controls in an Australian population. Two polymorphisms including rs4680 and rs165774 were found to be significantly associated with schizophrenia. The rs4680 results in a Val/Met substitution but the strongest association was shown by the novel SNP, rs165774, which may still be functional even though it is located in intron five. Individuals with schizophrenia were more than twice as likely to carry the GG genotype compared to the AA genotype for both the rs165774 and rs4680 SNPs. This association was slightly improved when males were analysed separately possibly indicating a degree of sexual dimorphism. Our results confirm that COMT is a good candidate for schizophrenia risk, by replicating the association with rs4680 and identifying a novel SNP association. PMID:20934310

  6. Quantitative mapping of zinc fluxes in the mammalian egg reveals the origin of fertilization-induced zinc sparks

    DOE PAGESBeta

    Que, Emily L.; Bleher, Reiner; Duncan, Francesca E.; Kong, Betty Y.; Gleber, Sophie C.; Vogt, Stefan; Chen, Si; Garwin, Seth A.; Bayer, Amanda R.; Dravid, Vinayak P.; et al

    2014-12-15

    Fertilization of a mammalian egg induces a series of ‘zinc sparks’ that are necessary for inducing the egg-to-embryo transition. Despite the importance of these zinc efflux events little is known about their origin. To understand the molecular mechanism of the zinc spark we combined four physical approaches to resolve zinc distributions in single cells: a chemical probe for dynamic live-cell fluorescence imaging and a combination of scanning transmission electron microscopy with energy dispersive spectroscopy, X-ray fluorescence microscopy, and 3D elemental tomography for high resolution elemental mapping. Here we show that the zinc spark arises from a system of thousands ofmore » zinc-loaded vesicles, each of which contains, on average, 106 zinc atoms. These vesicles undergo dynamic movement during oocyte maturation and exocytosis at the time of fertilization. We conclude that the discovery of these vesicles and the demonstration that zinc sparks originate from them provides a quantitative framework for understanding how zinc fluxes regulate cellular processes.« less

  7. Crosslink Mapping at Amino Acid-Base Resolution Reveals the Path of Scrunched DNA in Initial Transcribing Complexes.

    PubMed

    Winkelman, Jared T; Winkelman, Bradford T; Boyce, Julian; Maloney, Michael F; Chen, Albert Y; Ross, Wilma; Gourse, Richard L

    2015-09-01

    RNA polymerase binds tightly to DNA to recognize promoters with high specificity but then releases these contacts during the initial stage of transcription. We report a site-specific crosslinking approach to map the DNA path in bacterial transcription intermediates at amino acid and nucleotide resolution. After validating the approach by showing that the DNA path in open complexes (RPO) is the same as in high-resolution X-ray structures, we define the path following substrate addition in "scrunched" complexes (RPITC). The DNA bulges that form within the transcription bubble in RPITC are positioned differently on the two strands. Our data suggest that the non-template strand bulge is extruded into solvent in complexes containing a 5-mer RNA, whereas the template strand bulge remains within the template strand tunnel, exerting stress on interactions between the β flap, β' clamp, and σ3.2. We propose that this stress contributes to σ3.2 displacement from the RNA exit channel, facilitating promoter escape. PMID:26257284

  8. Divergent whole-genome methylation maps of human and chimpanzee brains reveal epigenetic basis of human regulatory evolution.

    PubMed

    Zeng, Jia; Konopka, Genevieve; Hunt, Brendan G; Preuss, Todd M; Geschwind, Dan; Yi, Soojin V

    2012-09-01

    DNA methylation is a pervasive epigenetic DNA modification that strongly affects chromatin regulation and gene expression. To date, it remains largely unknown how patterns of DNA methylation differ between closely related species and whether such differences contribute to species-specific phenotypes. To investigate these questions, we generated nucleotide-resolution whole-genome methylation maps of the prefrontal cortex of multiple humans and chimpanzees. Levels and patterns of DNA methylation vary across individuals within species according to the age and the sex of the individuals. We also found extensive species-level divergence in patterns of DNA methylation and that hundreds of genes exhibit significantly lower levels of promoter methylation in the human brain than in the chimpanzee brain. Furthermore, we investigated the functional consequences of methylation differences in humans and chimpanzees by integrating data on gene expression generated with next-generation sequencing methods, and we found a strong relationship between differential methylation and gene expression. Finally, we found that differentially methylated genes are strikingly enriched with loci associated with neurological disorders, psychological disorders, and cancers. Our results demonstrate that differential DNA methylation might be an important molecular mechanism driving gene-expression divergence between human and chimpanzee brains and might potentially contribute to the evolution of disease vulnerabilities. Thus, comparative studies of humans and chimpanzees stand to identify key epigenomic modifications underlying the evolution of human-specific traits. PMID:22922032

  9. Development of synaptic networks in the mouse vagal pathway revealed by optical mapping with a voltage-sensitive dye.

    PubMed

    Momose-Sato, Yoko; Sato, Katsushige

    2016-07-01

    The central issue in developmental neuroscience is when and how neural synaptic networks are established and become functional within the central nervous system (CNS). Investigations of the neural network organization have been hampered because conventional electrophysiological means have some technical limitations. In this study, the multiple-site optical recording technique with a voltage-sensitive dye was employed to survey the developmental organization of the vagal system in the mouse embryo. Stimulation of the vagus nerve in E11-E14 mouse embryos elicited optical responses in areas corresponding to the vagal sensory and motor nuclei. Postsynaptic responses in the first-order sensory nucleus, the nucleus of the tractus solitarius (NTS), were identified from E11, suggesting that sensory information becomes transferred to the brain at this stage. In addition to the NTS, optical responses were identified in the rostral and contralateral brainstem regions, which corresponded to second/higher order nuclei of the vagus nerve including the parabrachial nucleus (PBN). Postsynaptic responses in the second/higher-order nuclei were detected from E12, suggesting that polysynaptic networks were functional at this stage. We discuss the results of our optical mapping, comparing them with previous findings obtained in the chick and rat embryos, and suggest some fundamental principles in the functional organization of synaptic networks in the embryonic brain. PMID:27207499

  10. Avirulence gene mapping in the Hessian fly (Mayetiola destructor) reveals a protein phosphatase 2C effector gene family.

    PubMed

    Zhao, Chaoyang; Shukle, Richard; Navarro-Escalante, Lucio; Chen, Mingshun; Richards, Stephen; Stuart, Jeffrey J

    2016-01-01

    The genetic tractability of the Hessian fly (HF, Mayetiola destructor) provides an opportunity to investigate the mechanisms insects use to induce plant gall formation. Here we demonstrate that capacity using the newly sequenced HF genome by identifying the gene (vH24) that elicits effector-triggered immunity in wheat (Triticum spp.) seedlings carrying HF resistance gene H24. vH24 was mapped within a 230-kb genomic fragment near the telomere of HF chromosome X1. That fragment contains only 21 putative genes. The best candidate vH24 gene in this region encodes a protein containing a secretion signal and a type-2 serine/threonine protein phosphatase (PP2C) domain. This gene has an H24-virulence associated insertion in its promoter that appears to silence transcription of the gene in H24-virulent larvae. Candidate vH24 is a member of a small family of genes that encode secretion signals and PP2C domains. It belongs to the fraction of genes in the HF genome previously predicted to encode effector proteins. Because PP2C proteins are not normally secreted, our results suggest that these are PP2C effectors that HF larvae inject into wheat cells to redirect, or interfere, with wheat signal transduction pathways. PMID:26439791

  11. Quantitative mapping of zinc fluxes in the mammalian egg reveals the origin of fertilization-induced zinc sparks

    SciTech Connect

    Que, Emily L.; Bleher, Reiner; Duncan, Francesca E.; Kong, Betty Y.; Gleber, Sophie C.; Vogt, Stefan; Chen, Si; Garwin, Seth A.; Bayer, Amanda R.; Dravid, Vinayak P.; Woodruff, Teresa K.; O'Halloran, Thomas V.

    2014-12-15

    Fertilization of a mammalian egg induces a series of ‘zinc sparks’ that are necessary for inducing the egg-to-embryo transition. Despite the importance of these zinc efflux events little is known about their origin. To understand the molecular mechanism of the zinc spark we combined four physical approaches to resolve zinc distributions in single cells: a chemical probe for dynamic live-cell fluorescence imaging and a combination of scanning transmission electron microscopy with energy dispersive spectroscopy, X-ray fluorescence microscopy, and 3D elemental tomography for high resolution elemental mapping. Here we show that the zinc spark arises from a system of thousands of zinc-loaded vesicles, each of which contains, on average, 106 zinc atoms. These vesicles undergo dynamic movement during oocyte maturation and exocytosis at the time of fertilization. We conclude that the discovery of these vesicles and the demonstration that zinc sparks originate from them provides a quantitative framework for understanding how zinc fluxes regulate cellular processes.

  12. Quantitative mapping of zinc fluxes in the mammalian egg reveals the origin of fertilization-induced zinc sparks

    SciTech Connect

    Que, Emily L.; Bleher, Reiner; Duncan, Francesca E.; Kong, Betty Y.; Gleber, Sophie C.; Vogt, Stefan; Chen, Si; Garwin, Seth A.; Bayer, Amanda R.; Dravid, Vinayak P.; Woodruff, Teresa K.; O'Halloran, Thomas V.

    2014-12-15

    Fertilization of a mammalian egg initiates a series of 'zinc sparks' that are necessary to induce the egg-to-embryo transition. Despite the importance of these zinc-efflux events little is known about their origin. To understand the molecular mechanism of the zinc spark we combined four physical approaches that resolve zinc distributions in single cells: a chemical probe for dynamic live-cell fluorescence imaging and a combination of scanning transmission electron microscopy with energy-dispersive spectroscopy, X-ray fluorescence microscopy and three-dimensional elemental tomography for high-resolution elemental mapping. We show that the zinc spark arises from a system of thousands of zinc-loaded vesicles, each of which contains, on average, 10(6) zinc atoms. These vesicles undergo dynamic movement during oocyte maturation and exocytosis at the time of fertilization. The discovery of these vesicles and the demonstration that zinc sparks originate from them provides a quantitative framework for understanding how zinc fluxes regulate cellular processes

  13. Quantitative mapping of zinc fluxes in the mammalian egg reveals the origin of fertilization-induced zinc sparks

    NASA Astrophysics Data System (ADS)

    Que, Emily L.; Bleher, Reiner; Duncan, Francesca E.; Kong, Betty Y.; Gleber, Sophie C.; Vogt, Stefan; Chen, Si; Garwin, Seth A.; Bayer, Amanda R.; Dravid, Vinayak P.; Woodruff, Teresa K.; O'Halloran, Thomas V.

    2015-02-01

    Fertilization of a mammalian egg initiates a series of ‘zinc sparks’ that are necessary to induce the egg-to-embryo transition. Despite the importance of these zinc-efflux events little is known about their origin. To understand the molecular mechanism of the zinc spark we combined four physical approaches that resolve zinc distributions in single cells: a chemical probe for dynamic live-cell fluorescence imaging and a combination of scanning transmission electron microscopy with energy-dispersive spectroscopy, X-ray fluorescence microscopy and three-dimensional elemental tomography for high-resolution elemental mapping. We show that the zinc spark arises from a system of thousands of zinc-loaded vesicles, each of which contains, on average, 106 zinc atoms. These vesicles undergo dynamic movement during oocyte maturation and exocytosis at the time of fertilization. The discovery of these vesicles and the demonstration that zinc sparks originate from them provides a quantitative framework for understanding how zinc fluxes regulate cellular processes.

  14. Systematic Mapping of Protein Mutational Space by Prolonged Drift Reveals the Deleterious Effects of Seemingly Neutral Mutations.

    PubMed

    Rockah-Shmuel, Liat; Tóth-Petróczy, Ágnes; Tawfik, Dan S

    2015-08-01

    Systematic mappings of the effects of protein mutations are becoming increasingly popular. Unexpectedly, these experiments often find that proteins are tolerant to most amino acid substitutions, including substitutions in positions that are highly conserved in nature. To obtain a more realistic distribution of the effects of protein mutations, we applied a laboratory drift comprising 17 rounds of random mutagenesis and selection of M.HaeIII, a DNA methyltransferase. During this drift, multiple mutations gradually accumulated. Deep sequencing of the drifted gene ensembles allowed determination of the relative effects of all possible single nucleotide mutations. Despite being averaged across many different genetic backgrounds, about 67% of all nonsynonymous, missense mutations were evidently deleterious, and an additional 16% were likely to be deleterious. In the early generations, the frequency of most deleterious mutations remained high. However, by the 17th generation, their frequency was consistently reduced, and those remaining were accepted alongside compensatory mutations. The tolerance to mutations measured in this laboratory drift correlated with sequence exchanges seen in M.HaeIII's natural orthologs. The biophysical constraints dictating purging in nature and in this laboratory drift also seemed to overlap. Our experiment therefore provides an improved method for measuring the effects of protein mutations that more closely replicates the natural evolutionary forces, and thereby a more realistic view of the mutational space of proteins. PMID:26274323

  15. Quantitative mapping of zinc fluxes in the mammalian egg reveals the origin of fertilization-induced zinc sparks

    PubMed Central

    Que, Emily L.; Bleher, Reiner; Duncan, Francesca E.; Kong, Betty Y.; Gleber, Sophie C.; Vogt, Stefan; Chen, Si; Garwin, Seth A.; Bayer, Amanda R.; Dravid, Vinayak; Woodruff, Teresa K.; O’Halloran, Thomas V.

    2015-01-01

    Fertilization of a mammalian egg induces a series of ‘zinc sparks’ that are necessary for inducing the egg-to-embryo transition. Despite the importance of these zinc efflux events little is known about their origin. To understand the molecular mechanism of the zinc spark we combined four physical approaches to resolve zinc distributions in single cells: a chemical probe for dynamic live-cell fluorescence imaging and a combination of scanning transmission electron microscopy with energy dispersive spectroscopy, X-ray fluorescence microscopy, and 3D elemental tomography for high resolution elemental mapping. We show that the zinc spark arises from a system of thousands of zinc-loaded vesicles, each of which contains, on average, 106 zinc atoms. These vesicles undergo dynamic movement during oocyte maturation and exocytosis at the time of fertilization. The discovery of these vesicles and the demonstration that zinc sparks originate from them provides a quantitative framework for understanding how zinc fluxes regulate cellular processes. PMID:25615666

  16. Fate mapping reveals that microglia and recruited monocyte-derived macrophages are definitively distinguishable by phenotype in the retina.

    PubMed

    O'Koren, E G; Mathew, R; Saban, D R

    2016-01-01

    The recent paradigm shift that microglia are yolk sac-derived, not hematopoietic-derived, is reshaping our knowledge about the isolated role of microglia in CNS diseases, including degenerative conditions of the retina. However, unraveling microglial-specific functions has been hindered by phenotypic overlap of microglia with monocyte-derived macrophages. The latter are differentiated from recruited monocytes in neuroinflammation, including retina. Here we demonstrate the use of fate mapping wherein microglia and monocyte-derived cells are endogenously labeled with different fluorescent reporters. Combining this method with 12-color flow cytometry, we show that these two populations are definitively distinguishable by phenotype in retina. We prove that retinal microglia have a unique CD45(lo) CD11c(lo) F4/80(lo) I-A/I-E(-) signature, conserved in the steady state and during retinal injury. The latter was observed in the widely used light-induced retinal degeneration model and corroborated in other models, including whole-body irradiation/bone-marrow transplantation. The literature contains conflicting observations about whether microglia, including in the retina, increase expression of these markers in neuroinflammation. We show that monocyte-derived macrophages have elevated expression of these surface markers, not microglia. Our resolution of such phenotypic differences may serve as a robust way to help characterize isolated roles of these cells in retinal neuroinflammation and possibly elsewhere in CNS. PMID:26856416

  17. Possible cosmic ray signatures in clouds?

    NASA Astrophysics Data System (ADS)

    Erlykin, A. D.; Parsons, R. D.; Wolfendale, A. W.

    2009-11-01

    The role of cosmic rays in cloud formation, by cloud condensation nuclei, is still not fully understood. Although it has been claimed by a number of authors that cosmic ray effects should be small—or even non-existent—it is still argued by others that cosmic ray effects do occur. The present work draws attention to the fact that cosmic rays do not constitute a continuous stream of particles but are characterized by occasional near-simultaneous showers of particles. Under certain circumstances, such showers should leave a signature in clouds—near vertical 'cigar-shaped clouds'—and this work describes their properties. Our own observations have revealed no such structure, but it would be valuable to have a more careful search made.

  18. Mapping the Human Platelet Lipidome Reveals Cytosolic Phospholipase A2 as a Regulator of Mitochondrial Bioenergetics during Activation.

    PubMed

    Slatter, David A; Aldrovandi, Maceler; O'Connor, Anne; Allen, Stuart M; Brasher, Christopher J; Murphy, Robert C; Mecklemann, Sven; Ravi, Saranya; Darley-Usmar, Victor; O'Donnell, Valerie B

    2016-05-10

    Human platelets acutely increase mitochondrial energy generation following stimulation. Herein, a lipidomic circuit was uncovered whereby the substrates for this are exclusively provided by cPLA2, including multiple fatty acids and oxidized species that support energy generation via β-oxidation. This indicates that acute lipid membrane remodeling is required to support energetic demands during platelet activation. Phospholipase activity is linked to energy metabolism, revealing cPLA2 as a central regulator of both lipidomics and energy flux. Using a lipidomic approach (LipidArrays), we also estimated the total number of lipids in resting, thrombin-activated, and aspirinized platelets. Significant diversity between genetically unrelated individuals and a wealth of species was revealed. Resting platelets demonstrated ∼5,600 unique species, with only ∼50% being putatively identified. Thrombin elevated ∼900 lipids >2-fold with 86% newly appearing and 45% inhibited by aspirin supplementation, indicating COX-1 is required for major activation-dependent lipidomic fluxes. Many lipids were structurally identified. With ∼50% of the lipids being absent from databases, a major opportunity for mining lipids relevant to human health and disease is presented. PMID:27133131

  19. Temporal Evolution of Volcanic Eruption, Fluvial Drainage Systems and Faulting on the Northwest Flank of Alba Patera as Revealed by Photogeological Mapping

    NASA Astrophysics Data System (ADS)

    Chowdhury, Diya

    2013-01-01

    Although Alba Patera is the largest volcano in aerial extent in the solar system (˜6.8 km high and >1000 km in radius), the geologic processes responsible for shaping its exceedingly low-angle flanks remain poorly constrained. These flanks are covered in lava flows, valleys and both radial and annular grabens. Previous attempts, limited by the resolution of the satellite images, assume that the annular grabens formed during the terminal stage of volcanic development whereas surface water flow occurred in the early stage of volcanic construction. In this study, we analyze high-resolution CTX satellite images in conjunction with digital topographic data from MOLA. Our work reveals complex cross cutting relationships between faults, drainage network development and lava flows on the northwestern flank of Alba Patera. We observe a minimum of three generations of lava flows, three generations of drainage channels and three generations of faults. Mutual and successive cross-cutting relationships between drainage channels and faults indicate that the tectonic processes responsible for creating grabens on the volcano flank operated continuously and were coeval with drainage formation. The lava flows are observed to be the oldest geomorphic features and the third generation of faults as the youngest geomorphic features in our mapped region. Crater counting indicates that the surface within the mapped region is Amazonian in age. An analysis of the crater densities reveals a decline in crater densities from the south to the north section of the mapped region. This could be attributed to resurfacing in the north due to sediments deposited by northward flowing drainage channels. Crater counting age estimates for the south section yield a result of ˜ 1.74 Ga, +/- 0.12 Ga and ˜ 1.35 Ga, +/- 0.26 Ga for the north section. Hence, the younger age estimates of the northern surface could help further constrain the age of the drainage channels and faults on the northwest flank of

  20. Observation of Anisotropy in the Galactic Cosmic Ray Arrival Directions at 400 TEV With IceCube

    NASA Technical Reports Server (NTRS)

    Abbasi, R.; Abdou, Y.; Abu-Zayyad, T.; Ackermann, M.; Adams, J.; Aguilar, J. A.; Ahlers, M.; Allen, M. M.; Altmann, D.; Andeen, K.; Auffenberg, J.; Bai, X.; Baker, M.; Barwick, S. W.; Bay, R.; Bazo, Alba, J. L.; Beattie, K.; Beatty, J. J.; Bechet, S.; Becker, J. K.; Becker, K. H.; Benabderrahmane, M. L.; Benzvi, S.; Berdermann, J.; Stamatikos, M.

    2011-01-01

    In this paper we report the first observation in the Southern hemisphere of an energy dependence in the Galactic cosmic ray anisotropy up to a few hundred TeV. This measurement was performed using cosmic ray induced muons recorded by the partially deployed IceCube observatory between May 2009 and May 2010. The data include a total of 33x l0(epx 9) muon events with a median angular resolution of approx 3 degrees. A sky map of the relative intensity in arrival direction over the Southern celestial sky is presented for cosmic ray median energies of 20 and 400 Te V. The same large-scale anisotropy observed at median energies around 20 TeV is not present at 400 TeV. Instead, the high energy skymap shows a different anisotropy structure including a deficit with a post-trial significance of -6.30 sigma. This anisotropy reveals a new feature of the Galactic cosmic ray distribution, which must be incorporated into theories of the origin and propagation of cosmic rays.

  1. Observation of an Anisotropy in the Galactic Cosmic Ray Arrival Direction at 400 TeV with IceCube

    NASA Technical Reports Server (NTRS)

    Abbasi, R.; Abdou, Y.; Abu-Zayyad, T.; Ackermann, M.; Adams, J.; Aguilar, J. A.; Ahlers, M.; Allen, M. M.; Altmann, D.; Andeen, K.; Auffenberg, J.; Bai, X.; Baker, M.; Barwick, S. W.; Bay, R.; Bazo Alba, J. L.; Beattie, K.; Beatty, J. J.; Bechet, S.; Becker, J. K.; Becker, K. H.; Benabderrahmane, M. L.; BenZvi, S.; Berdermann, J.; Stamatikos, M.

    2012-01-01

    In this paper we report the first observation in the Southern hemisphere of an energy dependence in the Galactic cosmic ray anisotropy up to a few hundred TeV. This measurement was performed using cosmic ray induced muons recorded by the partially deployed IceCube observatory between May 2009 and May 2010. The data include a total of 33 x 10(exp 9) muon events with a median angular resolution of approx. 3 degrees. A sky map of the relative intensity in arrival direction over the Southern celestial sky is presented for cosmic ray median energies of 20 and 400 TeV. The same large-scale anisotropy observed at median energies around 20 TeV is not present at 400 TeV. Instead, the high energy skymap shows a different anisotropy structure including a deficit with a post-trial significance of -6.3 sigma. This anisotropy reveals a new feature of the Galactic cosmic ray distribution, which must be incorporated into theories of the origin and propagation of cosmic rays.

  2. The influence of galactic cosmic ray on all India annual rainfall and temperature

    NASA Astrophysics Data System (ADS)

    Chaudhuri, Sutapa; Pal, Jayanti; Guhathakurta, Suchandra

    2015-02-01

    The inverse relation between galactic cosmic ray (GCR) and sunspot numbers (SSN) suggests that the increase (decrease) in GCR count is linked with low (high) solar activity. The present study attempts to reveal the influence of GCR on all India annual rainfall and temperature during the period from 1953 to 2005. The inter-annual variation depicts that during the transition from maximum to minimum count of GCR, the rainfall anomaly shows alternative variation over India. Similar variation has also been observed for maximum temperature. Implementation of Fourier analysis shows an 11 year cycle of cosmic ray and depicts an increase in GCR count in the 11 year interval during the study period. The Fourier analysis of all India annual rainfall (AIR) and temperature also shows an 11 year cycle with a decreasing trend during the 11 year interval. The inter-decadal variation shows that during high GCR count there is a possibility of decrease in rainfall and minimum temperature but an increase in maximum temperature. The seasonal correlation shows a possible proportional association between cosmic ray and rainfall during the post monsoon season. The result further depicts that the sunspot number and temperature is positively correlated during the post-monsoon season. The correlation map of rainfall and temperature shows a meager but significant correlation with cosmic ray over some parts of West and East Indian coasts.

  3. Genetic Mapping Reveals Broader Role of Vrn-H3 Gene in Root and Shoot Development beyond Heading in Barley

    PubMed Central

    Bungartz, Annemarie; Muzammil, Shumaila; P. Afsharyan, Nazanin; Léon, Jens; Naz, Ali Ahmad

    2016-01-01

    The aim of the present study was to dissect the genetic inheritance and interplay of root, shoot and heading attributes for a better understanding of these traits in crop production. For this, we utilized quantitative trait loci (QTL) and candidate gene analysis approach using a second filial (F2) population originated from a cross between spring cultivar Cheri and wild barley accession ICB181160. The F2 population comprising 182 plants was phenotyped for root dry weight (RDW), root volume (RV), root length (RL) and shoot dry weight (SDW), tiller number per plant (TIL) and days to heading (HEA). In parallel, this population was genotyped using polymerase chain reaction (PCR) based cleaved amplified polymorphic sequence (CAPS) markers distributed across the whole genome. Marker by trait analysis revealed 16 QTL for root and shoot traits localized on chromosomes 1H, 3H, 4H, 5H and 7H. The strongest and a common QTL effect for root, shoot and heading traits was identified on chromosome 7H at the putative region of Vrn-H3 gene. Later, we have established PCR based gene specific marker HvVrnH3 revealing polymorphism for early heading Vrn-H3 allele in Cheri and late heading allele vrn-H3 in ICB181160. Genotyping of these alleles revealed a clear co-segregation of early heading Vrn-H3 allele with lower root and shoot attributes, while late heading vrn-H3 allele with more TIL and higher root biomass suggesting a primary insight on the function of Vrn-H3 gene beyond flowering. Genetic interactions of vernalization genes Vrn-H3 with Vrn-H2 and Vrn-H1 also suggested the major role of Vrn-H3 alleles in determining root and shoot trait variations in barley. We believe, these data provide an opportunity for further research to test a precise significance of early heading on yield components and root associated sustainability in crops like barley and wheat. PMID:27442506

  4. Genetic Mapping Reveals Broader Role of Vrn-H3 Gene in Root and Shoot Development beyond Heading in Barley.

    PubMed

    Arifuzzaman, Md; Günal, Süleyman; Bungartz, Annemarie; Muzammil, Shumaila; P Afsharyan, Nazanin; Léon, Jens; Naz, Ali Ahmad

    2016-01-01

    The aim of the present study was to dissect the genetic inheritance and interplay of root, shoot and heading attributes for a better understanding of these traits in crop production. For this, we utilized quantitative trait loci (QTL) and candidate gene analysis approach using a second filial (F2) population originated from a cross between spring cultivar Cheri and wild barley accession ICB181160. The F2 population comprising 182 plants was phenotyped for root dry weight (RDW), root volume (RV), root length (RL) and shoot dry weight (SDW), tiller number per plant (TIL) and days to heading (HEA). In parallel, this population was genotyped using polymerase chain reaction (PCR) based cleaved amplified polymorphic sequence (CAPS) markers distributed across the whole genome. Marker by trait analysis revealed 16 QTL for root and shoot traits localized on chromosomes 1H, 3H, 4H, 5H and 7H. The strongest and a common QTL effect for root, shoot and heading traits was identified on chromosome 7H at the putative region of Vrn-H3 gene. Later, we have established PCR based gene specific marker HvVrnH3 revealing polymorphism for early heading Vrn-H3 allele in Cheri and late heading allele vrn-H3 in ICB181160. Genotyping of these alleles revealed a clear co-segregation of early heading Vrn-H3 allele with lower root and shoot attributes, while late heading vrn-H3 allele with more TIL and higher root biomass suggesting a primary insight on the function of Vrn-H3 gene beyond flowering. Genetic interactions of vernalization genes Vrn-H3 with Vrn-H2 and Vrn-H1 also suggested the major role of Vrn-H3 alleles in determining root and shoot trait variations in barley. We believe, these data provide an opportunity for further research to test a precise significance of early heading on yield components and root associated sustainability in crops like barley and wheat. PMID:27442506

  5. An eQTL mapping approach reveals that rare variants in the SEMA5A regulatory network impact autism risk

    PubMed Central

    Cheng, Ye; Quinn, Jeffrey Francis; Weiss, Lauren Anne

    2013-01-01

    To date, genome-wide single nucleotide polymorphism (SNP) and copy number variant (CNV) association studies of autism spectrum disorders (ASDs) have led to promising signals but not to easily interpretable or translatable results. Our own genome-wide association study (GWAS) showed significant association to an intergenic SNP near Semaphorin 5A (SEMA5A) and provided evidence for reduced expression of the same gene. In a novel GWAS follow-up approach, we map an expression regulatory pathway for a GWAS candidate gene, SEMA5A, in silico by using population expression and genotype data sets. We find that the SEMA5A regulatory network significantly overlaps rare autism-specific CNVs. The SEMA5A regulatory network includes previous autism candidate genes and regions, including MACROD2, A2BP1, MCPH1, MAST4, CDH8, CADM1, FOXP1, AUTS2, MBD5, 7q21, 20p, USH2A, KIRREL3, DBF4B and RELN, among others. Our results provide: (i) a novel data-derived network implicated in autism, (ii) evidence that the same pathway seeded by an initial SNP association shows association with rare genetic variation in ASDs, (iii) a potential mechanism of action and interpretation for the previous autism candidate genes and genetic variants that fall in this network, and (iv) a novel approach that can be applied to other candidate genes for complex genetic disorders. We take a step towards better understanding of the significance of SEMA5A pathways in autism that can guide interpretation of many other genetic results in ASDs. PMID:23575222

  6. Seasonal and interannual patterns of sea surface temperature in Banda Sea as revealed by self-organizing map

    NASA Astrophysics Data System (ADS)

    Iskandar, Iskhaq

    2010-05-01

    Seasonal and interannual variations of sea surface temperature (SST) in the Banda Sea are studied for the period of January 1985 through December 2007. A neural network pattern recognition approach based on self-organizing map (SOM) has been applied to monthly SST from the Advanced Very High Resolution Radiometer (AVHRR) Oceans Pathfinder. The principal conclusions of this paper are outlined as follows. There are three different patterns associated with the variations in the monsoonal winds: the southeast and northwest monsoon patterns, and the monsoon-break patterns. The southeast monsoon pattern is characterized by low SST due to the prevailing southeasterly winds that drive Ekman upwelling. The northwest monsoon pattern, on the other hand, is one of high SST distributed uniformly in space. The monsoon-break pattern is a transitional pattern between the northwest and southeast monsoon patterns, which is characterized by moderate SST patterns. On interannual time-scale, the SST variations are significantly influenced by the El Niño-Southern Oscillation (ENSO) and Indian Ocean Dipole (IOD) phenomena. Low SST is observed during El Niño and/or positive IOD events, while high SST appears during La Niña event. Low SST in the Banda Sea during positive IOD event is induced by upwelling Kelvin waves generated in the equatorial Indian Ocean which propagate along the southern coast of Sumatra and Java before entering the Banda Sea through the Lombok and Ombai Straits as well as through the Timor Passage. On the other hand, during El Niño (La Niña) events, upwelling (downwelling) Rossby waves associated with off-equatorial divergence (convergence) in response to the equatorial westerly (easterly) winds in the Pacific, partly scattered into the Indonesian archipelago which in turn induce cool (warm) SST in the Banda Sea.

  7. Can Convergent Cross Mapping Untangle Idiosyncratic Speleothem Proxy Records to Reveal the Structure of Shared Climate Forcing?

    NASA Astrophysics Data System (ADS)

    Frappier, A. E.

    2015-12-01

    Rapid growth and development of speleothem paleoclimatology has generated diverse and important new terrestrial paleoenvironmental proxy records that increasingly illuminate both the enormous potential and great complexity of cave proxy systems and speleothem data. Speleothem records commonly exhibit complex covariation patterns between proxy variables (i.e. carbon and oxygen isotopes, various trace element concentrations and ratios, stratigraphic characteristics, growth rates, etc...). Such covariation patterns frequently change sign and magnitude over time, and often show periods without significant correlation that alternate with times with strongly coupled behavior. These patterns are evident when comparing records between sites and stalagmites, and even within a single stalagmite. Instability in covariation patterns and low long-term correlations both limit our confidence in applying speleothems proxy transfer functions over long time periods. Are these complex covariation patterns meaningful or merely mirages? When two speleothem records show the same result, replication is considered by the community to be evidence that both records are highly sensitive to a common climate signal and are thus reliable proxies for that climate signal. Signals derived from a single speleothem dataset could be noise, and thus of limited value until it is validated by the replication test. Are speleothems naturally idiosyncratic and noisy? Must all speleothem records be duplicated to establish reliability? I consider whether Convergent Cross Mapping (CCM) may offer a fruitful approach to these problems. CCM is a powerful statistical tool developed in George Sugihara's lab for complex dynamical systems that tests the direction of causality and strength of forcing among multiple time-series variables. I apply CCM to speleothem timeseries records to 1) reconstruct the underlying state climate variable of interest over time (in this case, precipitation), and 2) determine the

  8. A proteome map of the zebrafish (Danio rerio) lens reveals similarities between zebrafish and mammalian crystallin expression

    PubMed Central

    Hawke, Molly; LaCava, Carrie; Prince, Courtney J.; Bellanco, Nicholas R.; Corbin, Rebecca W.

    2008-01-01

    Purpose To characterize the crystallin content of the zebrafish lens using two-dimensional gel electrophoresis (2-DE). These data will facilitate future investigations of vertebrate lens development, function, and disease. Methods Adult zebrafish lens proteins were separated by 2-DE, and the resulting spots were identified by matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS). The relative proportion of each crystallin was quantified by image analysis, and phosphospecific staining was used to identify phosphorylated α-crystallins. The proportion of each crystallin in the soluble and insoluble fraction of the lens was also determined by resolving these lens fractions separately by 2-DE. Results α-, β-, and γ-crystallins comprised 7.8, 36.0, and 47.2% of the zebrafish lens, respectively. While the α-crystallin content of the zebrafish lens is less than the amounts found in the human lens, the ratio of αA:αB crystallin is very similar. The phosphorylation pattern of zebrafish αA-crystallins was also similar to that of humans. The most abundant γ-crystallins were the diverse γMs, comprising 30.5% of the lens. Intact zebrafish crystallins were generally more common in the soluble fraction with truncated versions more common in the insoluble fraction. Conclusions While the total α- and γ-crystallin content of the zebrafish lens differs from that of humans, similarities in α-crystallin ratios and modifications and a link between crystallin truncation and insolubility suggest that the zebrafish is a suitable model for the vertebrate lens. The proteome map provided here will be of value to future studies of lens development, function, and disease. PMID:18449354

  9. Search for Cosmic Strings in Cosmic Microwave BackgroundAnisotropies

    SciTech Connect

    Jeong, E.; Smoot, GF

    2004-06-01

    We have searched the 1st-year WMAP W-Band CMB anisotropy map for evidence of cosmic strings. We have set a limit of delta = 8 pi G mu/ c2 < 8.2 times 10-6 at 95 percent CL for statistical search for a significant number of strings in the map. We also have set a limit using the uniform distribution of strings model in the WMAP data with delta = 8pi G mu/c2 < 7.34 times 10-5 at 95 percent CL. And the pattern search technique we developed here set a limit delta = 8 pi G mu/c2 < 1.54 times 10-5 at 95 percent CL.

  10. Homozygosity mapping reveals mutations of GRXCR1 as a cause of autosomal-recessive nonsyndromic hearing impairment.

    PubMed

    Schraders, Margit; Lee, Kwanghyuk; Oostrik, Jaap; Huygen, Patrick L M; Ali, Ghazanfar; Hoefsloot, Lies H; Veltman, Joris A; Cremers, Frans P M; Basit, Sulman; Ansar, Muhammad; Cremers, Cor W R J; Kunst, Henricus P M; Ahmad, Wasim; Admiraal, Ronald J C; Leal, Suzanne M; Kremer, Hannie

    2010-02-12

    We identified overlapping homozygous regions within the DFNB25 locus in two Dutch and ten Pakistani families with sensorineural autosomal-recessive nonsyndromic hearing impairment (arNSHI). Only one of the families, W98-053, was not consanguineous, and its sibship pointed toward a reduced critical region of 0.9 Mb. This region contained the GRXCR1 gene, and the orthologous mouse gene was described to be mutated in the pirouette (pi) mutant with resulting hearing loss and circling behavior. Sequence analysis of the GRXCR1 gene in hearing-impaired family members revealed splice-site mutations in two Dutch families and a missense and nonsense mutation, respectively, in two Pakistani families. The splice-site mutations are predicted to cause frameshifts and premature stop codons. In family W98-053, this could be confirmed by cDNA analysis. GRXCR1 is predicted to contain a GRX-like domain. GRX domains are involved in reversible S-glutathionylation of proteins and thereby in the modulation of activity and/or localization of these proteins. The missense mutation is located in this domain, whereas the nonsense and splice-site mutations may result in complete or partial absence of the GRX-like domain or of the complete protein. Hearing loss in patients with GRXCR1 mutations is congenital and is moderate to profound. Progression of the hearing loss was observed in family W98-053. Vestibular dysfunction was observed in some but not all affected individuals. Quantitative analysis of GRXCR1 transcripts in fetal and adult human tissues revealed a preferential expression of the gene in fetal cochlea, which may explain the nonsyndromic nature of the hearing impairment. PMID:20137778

  11. Cyclic twinning and internal defects of boron-rich nanowires revealed by three-dimensional electron diffraction mapping

    NASA Astrophysics Data System (ADS)

    Fu, Xin; Yuan, Jun

    2013-09-01

    Structural characterization of individual nanosized boron-rich nanowires has been carried out through analysing the three-dimensional (3D) electron diffraction intensity distribution. Not only can the cyclic twinning structure of these nanowires be easily determined, the new approach also reveals the heterogeneous strain relaxation within the intact nanowire, through the accurate determination of the orientation relationship between the constituent crystallites. The quantitative analysis of the fine structure in the 3D diffraction dataset indicates that this may be related to the distribution of defects such as stacking faults, microtwins and dislocations. It is envisaged that the non-destructive nature of this approach could open the way for the in situ study of the structural evolution of complex nanomaterials and polycrystalline materials in general.Structural characterization of individual nanosized boron-rich nanowires has been carried out through analysing the three-dimensional (3D) electron diffraction intensity distribution. Not only can the cyclic twinning structure of these nanowires be easily determined, the new approach also reveals the heterogeneous strain relaxation within the intact nanowire, through the accurate determination of the orientation relationship between the constituent crystallites. The quantitative analysis of the fine structure in the 3D diffraction dataset indicates that this may be related to the distribution of defects such as stacking faults, microtwins and dislocations. It is envisaged that the non-destructive nature of this approach could open the way for the in situ study of the structural evolution of complex nanomaterials and polycrystalline materials in general. Electronic supplementary information (ESI) available: Crystal structure of boron carbide, experimental geometry and diffraction pattern registration for the reconstruction of the reciprocal 3D volume, data process for 3D reciprocal volume visualization, rhombohedral

  12. The optimal cosmic epoch for precision cosmology

    SciTech Connect

    Loeb, Abraham

    2012-05-01

    The statistical uncertainty in measuring the primordial density perturbations on a given comoving scale is dictated by the number of independent regions of that scale that are accessible to an observer. This number varies with cosmic time and diminishes per Hubble volume in the distant past or future of the standard cosmological model. We show that the best constraints on the initial power spectrum of linear density perturbations are accessible (e.g. through 21-cm intensity mapping) at redshifts z ∼ 10, and that the ability to constrain the cosmological initial conditions will deteriorate quickly in our cosmic future.

  13. The cosmic history of star formation.

    PubMed

    Dunlop, James S

    2011-07-01

    Major advances in observational astronomy over the past 20 years have revolutionized our view of cosmic history, transforming our understanding of how the hot, smooth, early universe evolved into the complex and beautiful universe of stars and galaxies in which we now live. I describe how astronomers have used a range of complementary techniques to map out the rise and fall of star formation over 95% of cosmic time, back to the current observational frontier only ~500 million years after the Big Bang. PMID:21737733

  14. Cosmic Superstrings Revisited

    SciTech Connect

    Polchinski, Joseph

    2004-12-10

    It is possible that superstrings, as well as other one-dimensional branes, could have been produced in the early universe and then expanded to cosmic size today. I discuss the conditions under which this will occur, and the signatures of these strings. Such cosmic superstrings could be the brightest objects visible in gravitational wave astronomy, and might be distinguishable from gauge theory cosmic strings by their network properties.

  15. The cosmic neutrino background

    NASA Technical Reports Server (NTRS)

    Dar, Arnon

    1991-01-01

    The cosmic neutrino background is expected to consist of relic neutrinos from the big bang, of neutrinos produced during nuclear burning in stars, of neutrinos released by gravitational stellar collapse, and of neutrinos produced by cosmic ray interactions with matter and radiation in the interstellar and intergalactic medium. Formation of baryonic dark matter in the early universe, matter-antimatter annihilation in a baryonic symmetric universe, and dark matter annihilation could have also contributed significantly to the cosmic neutrino background. The purpose of this paper is to review the properties of these cosmic neutrino backgrounds, the indirect evidence for their existence, and the prospects for their detection.

  16. The Cosmic Background Explorer.

    ERIC Educational Resources Information Center

    Gulkis, Samuel; And Others

    1990-01-01

    Outlines the Cosmic Background Explorer (COBE) mission to measure celestial radiation. Describes the instruments used and experiments involving differential microwave radiometers, and a far infrared absolute spectrophotometer. (YP)

  17. Breeding signature of combining ability improvement revealed by a genomic variation map from recurrent selection population in Brassica napus

    PubMed Central

    Zhao, Xinwang; Li, Bao; Zhang, Ka; Hu, Kaining; Yi, Bin; Wen, Jing; Ma, Chaozhi; Shen, Jinxiong; Fu, Tingdong; Tu, Jinxing

    2016-01-01

    Combining ability is crucial for parent selection in crop hybrid breeding. The present investigation and results had revealed the underlying genetic factors which might contribute in adequate combining ability, further assisting in enhancing heterosis and stability. Here, we conducted a large-scale analysis of genomic variation in order to define genomic regions affecting the combining ability in recurrent selection population of rapeseed. A population of 175 individuals was genotyped with the Brassica60K SNP chip. 525 hybrids were assembled with three different testers and used to evaluate the general combining ability (GCA) in three environments. By detecting the changes of the genomic variation, we identified 376 potential genome regions, spanning 3.03% of rapeseed genome which provided QTL-level resolution on potentially selected variants. More than 96% of these regions were located in the C subgenome, indicating that C subgenome had sustained stronger selection pressure in the breeding program than the A subgenome. In addition, a high level of linkage disequilibrium in rapeseed genome was detected, suggesting that marker-assisted selection for the population improvement might be easily implemented. This study outlines the evidence for high GCA on a genomic level and provided underlying molecular mechanism for recurrent selection improvement in B. napus. PMID:27412721

  18. Overlapping representations of the neck and whiskers in the rat motor cortex revealed by mapping at different anaesthetic depths

    PubMed Central

    Tandon, Shashank; Kambi, Niranjan; Jain, Neeraj

    2008-01-01

    The primary motor cortex of mammals has an orderly representation of different body parts. Within the representation of each body part the organization is more complex, with groups of neurons representing movements of a muscle or a group of muscles. In rats, uncertainties continue to exist regarding organization of the primary motor cortex in the whisker and the neck region. Using intracortical microstimulation (ICMS) we show that movements evoked in the whisker and the neck region of the rat motor cortex are highly sensitive to the depth of anaesthesia. At light anaesthetic depth, whisker movements are readily evoked from a large medial region of the motor cortex. Lateral to this is a small region where movements of the neck are evoked. However, in animals under deep anaesthesia whisker movements cannot be evoked. Instead, neck movements are evoked from this region. The neck movement region thus becomes greatly expanded. An analysis of the threshold currents required to evoke movements at different anaesthetic depths reveals that the caudal portion of the whisker region has dual representation, of both the whisker and the neck movements. The results also underline the importance of carefully controlling the depth of anaesthesia during ICMS experiments. PMID:18093166

  19. Homozygosity mapping and targeted genomic sequencing reveal the gene responsible for cerebellar hypoplasia and quadrupedal locomotion in a consanguineous kindred

    PubMed Central

    Gulsuner, Suleyman; Tekinay, Ayse Begum; Doerschner, Katja; Boyaci, Huseyin; Bilguvar, Kaya; Unal, Hilal; Ors, Aslihan; Onat, O. Emre; Atalar, Ergin; Basak, A. Nazli; Topaloglu, Haluk; Kansu, Tulay; Tan, Meliha; Tan, Uner; Gunel, Murat; Ozcelik, Tayfun

    2011-01-01

    The biological basis for the development of the cerebro-cerebellar structures required for posture and gait in humans is poorly understood. We investigated a large consanguineous family from Turkey exhibiting an extremely rare phenotype associated with quadrupedal locomotion, mental retardation, and cerebro-cerebellar hypoplasia, linked to a 7.1-Mb region of homozygosity on chromosome 17p13.1–13.3. Diffusion weighted imaging and fiber tractography of the patients' brains revealed morphological abnormalities in the cerebellum and corpus callosum, in particular atrophy of superior, middle, and inferior peduncles of the cerebellum. Structural magnetic resonance imaging showed additional morphometric abnormalities in several cortical areas, including the corpus callosum, precentral gyrus, and Brodmann areas BA6, BA44, and BA45. Targeted sequencing of the entire homozygous region in three affected individuals and two obligate carriers uncovered a private missense mutation, WDR81 p.P856L, which cosegregated with the condition in the extended family. The mutation lies in a highly conserved region of WDR81, flanked by an N-terminal BEACH domain and C-terminal WD40 beta-propeller domains. WDR81 is predicted to be a transmembrane protein. It is highly expressed in the cerebellum and corpus callosum, in particular in the Purkinje cell layer of the cerebellum. WDR81 represents the third gene, after VLDLR and CA8, implicated in quadrupedal locomotion in humans. PMID:21885617

  20. Multi-scale perturbations of protein interactomes reveal their mechanisms of regulation, robustness and insights into genotype-phenotype maps.

    PubMed

    Filteau, Marie; Vignaud, Hélène; Rochette, Samuel; Diss, Guillaume; Chrétien, Andrée-Ève; Berger, Caroline M; Landry, Christian R

    2016-03-01

    Cellular architectures and signaling machineries are organized through protein-protein interactions (PPIs). High-throughput methods to study PPIs in yeast have opened a new perspective on the organization of the cell by allowing the study of whole protein interactomes. Recent investigations have moved from the description of this organization to the analysis of its dynamics by experimenting how protein interaction networks (PINs) are rewired in response to perturbations. Here we review studies that have used the budding yeast as an experimental system to explore these altered networks. Given the large space of possible PPIs and the diversity of potential genetic and environmental perturbations, high-throughput methods are an essential requirement to survey PIN perturbations on a large scale. Network perturbations are typically conceptualized as the removal of entire proteins (nodes), the modification of single PPIs (edges) or changes in growth conditions. These studies have revealed mechanisms of PPI regulation, PIN architectural organization, robustness and sensitivity to perturbations. Despite these major advances, there are still inherent limits to current technologies that lead to a trade-off between the number of perturbations and the number of PPIs that can be considered simultaneously. Nevertheless, as we exemplify here, targeted approaches combined with the existing resources remain extremely powerful to explore the inner organization of cells and their responses to perturbations. PMID:26476431

  1. Breeding signature of combining ability improvement revealed by a genomic variation map from recurrent selection population in Brassica napus.

    PubMed

    Zhao, Xinwang; Li, Bao; Zhang, Ka; Hu, Kaining; Yi, Bin; Wen, Jing; Ma, Chaozhi; Shen, Jinxiong; Fu, Tingdong; Tu, Jinxing

    2016-01-01

    Combining ability is crucial for parent selection in crop hybrid breeding. The present investigation and results had revealed the underlying genetic factors which might contribute in adequate combining ability, further assisting in enhancing heterosis and stability. Here, we conducted a large-scale analysis of genomic variation in order to define genomic regions affecting the combining ability in recurrent selection population of rapeseed. A population of 175 individuals was genotyped with the Brassica60K SNP chip. 525 hybrids were assembled with three different testers and used to evaluate the general combining ability (GCA) in three environments. By detecting the changes of the genomic variation, we identified 376 potential genome regions, spanning 3.03% of rapeseed genome which provided QTL-level resolution on potentially selected variants. More than 96% of these regions were located in the C subgenome, indicating that C subgenome had sustained stronger selection pressure in the breeding program than the A subgenome. In addition, a high level of linkage disequilibrium in rapeseed genome was detected, suggesting that marker-assisted selection for the population improvement might be easily implemented. This study outlines the evidence for high GCA on a genomic level and provided underlying molecular mechanism for recurrent selection improvement in B. napus. PMID:27412721

  2. Mapping physiological G protein-coupled receptor signaling pathways reveals a role for receptor phosphorylation in airway contraction

    PubMed Central

    Bradley, Sophie J.; Iglesias, Max Maza; Kong, Kok Choi; Butcher, Adrian J.; Plouffe, Bianca; Goupil, Eugénie; Bourgognon, Julie-Myrtille; Macedo-Hatch, Timothy; LeGouill, Christian; Russell, Kirsty; Laporte, Stéphane A.; König, Gabriele M.; Kostenis, Evi; Bouvier, Michel; Chung, Kian Fan; Amrani, Yassine; Tobin, Andrew B.

    2016-01-01

    G protein-coupled receptors (GPCRs) are known to initiate a plethora of signaling pathways in vitro. However, it is unclear which of these pathways are engaged to mediate physiological responses. Here, we examine the distinct roles of Gq/11-dependent signaling and receptor phosphorylation-dependent signaling in bronchial airway contraction and lung function regulated through the M3-muscarinic acetylcholine receptor (M3-mAChR). By using a genetically engineered mouse expressing a G protein-biased M3-mAChR mutant, we reveal the first evidence, to our knowledge, of a role for M3-mAChR phosphorylation in bronchial smooth muscle contraction in health and in a disease state with relevance to human asthma. Furthermore, this mouse model can be used to distinguish the physiological responses that are regulated by M3-mAChR phosphorylation (which include control of lung function) from those responses that are downstream of G protein signaling. In this way, we present an approach by which to predict the physiological/therapeutic outcome of M3-mAChR–biased ligands with important implications for drug discovery. PMID:27071102

  3. Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes

    PubMed Central

    Hillmer, Axel M.; Yao, Fei; Inaki, Koichiro; Lee, Wah Heng; Ariyaratne, Pramila N.; Teo, Audrey S.M.; Woo, Xing Yi; Zhang, Zhenshui; Zhao, Hao; Ukil, Leena; Chen, Jieqi P.; Zhu, Feng; So, Jimmy B.Y.; Salto-Tellez, Manuel; Poh, Wan Ting; Zawack, Kelson F.B.; Nagarajan, Niranjan; Gao, Song; Li, Guoliang; Kumar, Vikrant; Lim, Hui Ping J.; Sia, Yee Yen; Chan, Chee Seng; Leong, See Ting; Neo, Say Chuan; Choi, Poh Sum D.; Thoreau, Hervé; Tan, Patrick B.O.; Shahab, Atif; Ruan, Xiaoan; Bergh, Jonas; Hall, Per; Cacheux-Rataboul, Valère; Wei, Chia-Lin; Yeoh, Khay Guan; Sung, Wing-Kin; Bourque, Guillaume; Liu, Edison T.; Ruan, Yijun

    2011-01-01

    Somatic genome rearrangements are thought to play important roles in cancer development. We optimized a long-span paired-end-tag (PET) sequencing approach using 10-Kb genomic DNA inserts to study human genome structural variations (SVs). The use of a 10-Kb insert size allows the identification of breakpoints within repetitive or homology-containing regions of a few kilobases in size and results in a higher physical coverage compared with small insert libraries with the same sequencing effort. We have applied this approach to comprehensively characterize the SVs of 15 cancer and two noncancer genomes and used a filtering approach to strongly enrich for somatic SVs in the cancer genomes. Our analyses revealed that most inversions, deletions, and insertions are germ-line SVs, whereas tandem duplications, unpaired inversions, interchromosomal translocations, and complex rearrangements are over-represented among somatic rearrangements in cancer genomes. We demonstrate that the quantitative and connective nature of DNA–PET data is precise in delineating the genealogy of complex rearrangement events, we observe signatures that are compatible with breakage-fusion-bridge cycles, and we discover that large duplications are among the initial rearrangements that trigger genome instability for extensive amplification in epithelial cancers. PMID:21467267

  4. Physical Connectivity Mapping by Circular Permutation of Human Telomerase RNA Reveals New Regions Critical for Activity and Processivity.

    PubMed

    Mefford, Melissa A; Zappulla, David C

    2015-01-01

    Telomerase is a specialized ribonucleoprotein complex that extends the 3' ends of chromosomes to counteract telomere shortening. However, increased telomerase activity is associated with ∼90% of human cancers. The telomerase enzyme minimally requires an RNA (hTR) and a specialized reverse transcriptase protein (TERT) for activity in vitro. Understanding the structure-function relationships within hTR has important implications for human disease. For the first time, we have tested the physical-connectivity requirements in the 451-nucleotide hTR RNA using circular permutations, which reposition the 5' and 3' ends. Our extensive in vitro analysis identified three classes of hTR circular permutants with altered function. First, circularly permuting 3' of the template causes specific defects in repeat-addition processivity, revealing that the template recognition element found in ciliates is conserved in human telomerase RNA. Second, seven circular permutations residing within the catalytically important core and CR4/5 domains completely abolish telomerase activity, unveiling mechanistically critical portions of these domains. Third, several circular permutations between the core and CR4/5 significantly increase telomerase activity. Our extensive circular permutation results provide insights into the architecture and coordination of human telomerase RNA and highlight where the RNA could be targeted for the development of antiaging and anticancer therapeutics. PMID:26503788

  5. Anisotropy of TeV Galactic cosmic rays

    NASA Astrophysics Data System (ADS)

    Zhang, Ming; Pogorelov, Nikolai; Desiati, Paolo; DuVernois, Michael

    2016-07-01

    TeV cosmic rays are significantly deflected by the magnetic field of the heliosphere, and they gain or lose energies in heliospheric electric field that in the meantime drives the motion of plasma. These propagation mechanisms will cause the map of TeV cosmic rays seen at the Earth to look different from the map seen in the local interstellar medium without the presence of the heliosphere. We have developed a method of using Liouville's theorem to map out particle distribution function to Earth from the local interstellar medium, where we assume that the cosmic rays have small pitch-angle anisotropy harmonics up to the second order and a small uniform spatial density gradient. The amount of heliospheric distortion can be determined by tracing the trajectories of cosmic rays propagating through the heliosphere. In this paper, we apply this method to TeV cosmic ray propagation through a MHD-kinetic model of the heliosphere and try to fit observations from Tibet ASgamma and IceCube experiments. We are able to locate features in the TeV cosmic ray anisotropy that are associated with the interstellar magnetic field, hydrogen deflection plane, heliotail, and solar corona. Some of the features are also slightly affected by the solar cycle and interstellar magnetic turbulence. The results provide us powerful tools to explore large-scale heliospheric structures as well as to determine the cosmic ray distribution in the local interstellar medium.

  6. Revealing spatial distribution of soil organic carbon contents and stocks of a disturbed bog relict by in-situ NIR and apparent EC mapping

    NASA Astrophysics Data System (ADS)

    Bechtold, Michel; Tiemeyer, Bärbel; Don, Axel; Altdorff, Daniel; van der Kruk, Jan; Huisman, Johan A.

    2013-04-01

    Previous studies showed that in-situ visible near-infrared (vis-NIR) spectroscopy can overcome the limitations of conventional soil sampling. Costs can be reduced and spatial resolution enhanced when mapping field-scale variability of soil organic carbon (SOC). Detailed maps can help to improve SOC management and lead to better estimates of field-scale total carbon stocks. Knowledge of SOC field patterns may also help to reveal processes and factors controlling SOC variability. In this study, we apply in situ vis-NIR and apparent electrical conductivity (ECa) mapping to a disturbed bog relict. The major question of this application study was how field-scale in-situ vis-NIR mapping performs for a very heterogeneous area and under difficult grassland conditions and under highly-variable water content conditions. Past intensive peat cutting and deep ploughing in some areas, in combination with a high background heterogeneity of the underlying mineral sediments, have led to a high variability of SOC content (5.6 to 41.3 %), peat layer thickness (25 to 60 cm) and peat degradation states (from nearly fresh to amorphous). Using a field system developed by Veris Technologies (Salina KS, USA), we continuously collected vis-NIR spectra at 10 cm depth (measurement range: 350 nm to 2200 nm) over an area of around 12 ha with a line spacing of about 12 m. The system includes a set of discs for measuring ECa of the first 30 and 90 cm of the soil. The same area was also mapped with a non-invasive electro-magnetic induction (EMI) setup that provided ECa data of the first 25, 50 and 100 cm. For calibration and validation of the spatial data, we took 30 representative soil samples and 15 soil cores of about 90 cm depth, for which peat thickness, water content, pore water EC, bulk density (BD), as well as C and N content were determined for various depths. Preliminary results of the calibration of the NIR spectra to the near-surface SOC contents indicate good data quality despite the

  7. Mapping the Hsp90 Genetic Network Reveals Ergosterol Biosynthesis and Phosphatidylinositol-4-Kinase Signaling as Core Circuitry Governing Cellular Stress

    PubMed Central

    O’Meara, Teresa R.; Valaei, Seyedeh Fereshteh; Diezmann, Stephanie; Cowen, Leah E.

    2016-01-01

    functional capacity and new effectors governing drug resistance, morphogenesis and virulence, revealing new targets for antifungal drug development. PMID:27341673

  8. Homozygosity Mapping and Whole Exome Sequencing Reveal a Novel Homozygous COL18A1 Mutation Causing Knobloch Syndrome

    PubMed Central

    Piri, Niloofar; Nürnberg, Gudrun; Saleh-Gohari, Nasrollah; Haghighi, Amirreza; Neidhardt, John; Nürnberg, Peter; Berger, Wolfgang

    2014-01-01

    The aim of this study was to identify the genetic basis of a chorioretinal dystrophy with high myopia of unknown origin in a child of a consanguineous marriage. The proband and ten family members of Iranian ancestry participated in this study. Linkage analysis was carried out with DNA samples of the proband and her parents by using the Human SNP Array 6.0. Whole exome sequencing (WES) was performed with the patients’ DNA. Specific sequence alterations within the homozygous regions identified by whole exome sequencing were verified by Sanger sequencing. Upon genetic analysis, a novel homozygous frameshift mutation was found in exon 42 of the COL18A1 gene in the patient. Both parents were heterozygous for this sequence variation. Mutations in COL18A1 are known to cause Knobloch syndrome (KS). Retrospective analysis of clinical records of the patient revealed surgical removal of a meningocele present at birth. The clinical features shown by our patient were typical of KS with the exception of chorioretinal degeneration which is a rare manifestation. This is the first case of KS reported in a family of Iranian ancestry. We identified a novel disease-causing (deletion) mutation in the COL18A1 gene leading to a frameshift and premature stop codon in the last exon. The mutation was not present in SNP databases and was also not found in 192 control individuals. Its localization within the endostatin domain implicates a functional relevance of endostatin in KS. A combined approach of linkage analysis and WES led to a rapid identification of the disease-causing mutation even though the clinical description was not completely clear at the beginning. PMID:25392994

  9. Mapping the Hsp90 Genetic Network Reveals Ergosterol Biosynthesis and Phosphatidylinositol-4-Kinase Signaling as Core Circuitry Governing Cellular Stress.

    PubMed

    O'Meara, Teresa R; Veri, Amanda O; Polvi, Elizabeth J; Li, Xinliu; Valaei, Seyedeh Fereshteh; Diezmann, Stephanie; Cowen, Leah E

    2016-06-01

    functional capacity and new effectors governing drug resistance, morphogenesis and virulence, revealing new targets for antifungal drug development. PMID:27341673

  10. [Cosmic Microwave Background (CMB) Anisotropies

    NASA Technical Reports Server (NTRS)

    Silk, Joseph

    1998-01-01

    One of the main areas of research is the theory of cosmic microwave background (CMB) anisotropies and analysis of CMB data. Using the four year COBE data we were able to improve existing constraints on global shear and vorticity. We found that, in the flat case (which allows for greatest anisotropy), (omega/H)0 less than 10(exp -7), where omega is the vorticity and H is the Hubble constant. This is two orders of magnitude lower than the tightest, previous constraint. We have defined a new set of statistics which quantify the amount of non-Gaussianity in small field cosmic microwave background maps. By looking at the distribution of power around rings in Fourier space, and at the correlations between adjacent rings, one can identify non-Gaussian features which are masked by large scale Gaussian fluctuations. This may be particularly useful for identifying unresolved localized sources and line-like discontinuities. Levin and collaborators devised a method to determine the global geometry of the universe through observations of patterns in the hot and cold spots of the CMB. We have derived properties of the peaks (maxima) of the CMB anisotropies expected in flat and open CDM models. We represent results for angular resolutions ranging from 5 arcmin to 20 arcmin (antenna FWHM), scales that are relevant for the MAP and COBRA/SAMBA space missions and the ground-based interferometer. Results related to galaxy formation and evolution are also discussed.

  11. [Cosmic Microwave Background (CMB) Anisotropies

    NASA Astrophysics Data System (ADS)

    Silk, Joseph

    1998-01-01

    One of the main areas of research is the theory of cosmic microwave background (CMB) anisotropies and analysis of CMB data. Using the four year COBE data we were able to improve existing constraints on global shear and vorticity. We found that, in the flat case (which allows for greatest anisotropy), (omega/H)0 less than 10-7, where omega is the vorticity and H is the Hubble constant. This is two orders of magnitude lower than the tightest, previous constraint. We have defined a new set of statistics which quantify the amount of non-Gaussianity in small field cosmic microwave background maps. By looking at the distribution of power around rings in Fourier space, and at the correlations between adjacent rings, one can identify non-Gaussian features which are masked by large scale Gaussian fluctuations. This may be particularly useful for identifying unresolved localized sources and line-like discontinuities. Levin and collaborators devised a method to determine the global geometry of the universe through observations of patterns in the hot and cold spots of the CMB. We have derived properties of the peaks (maxima) of the CMB anisotropies expected in flat and open CDM models. We represent results for angular resolutions ranging from 5 arcmin to 20 arcmin (antenna FWHM), scales that are relevant for the MAP and COBRA/SAMBA space missions and the ground-based interferometer. Results related to galaxy formation and evolution are also discussed.

  12. Maria Montessori's Cosmic Vision, Cosmic Plan, and Cosmic Education

    ERIC Educational Resources Information Center

    Grazzini, Camillo

    2013-01-01

    This classic position of the breadth of Cosmic Education begins with a way of seeing the human's interaction with the world, continues on to the grandeur in scale of time and space of that vision, then brings the interdependency of life where each growing human becomes a participating adult. Mr. Grazzini confronts the laws of human nature in…

  13. Origin of the cosmic network in {Lambda}CDM: Nature vs nurture

    SciTech Connect

    Shandarin, Sergei; Habib, Salman; Heitmann, Katrin

    2010-05-15

    The large-scale structure of the Universe, as traced by the distribution of galaxies, is now being revealed by large-volume cosmological surveys. The structure is characterized by galaxies distributed along filaments, the filaments connecting in turn to form a percolating network. Our objective here is to quantitatively specify the underlying mechanisms that drive the formation of the cosmic network: By combining percolation-based analyses with N-body simulations of gravitational structure formation, we elucidate how the network has its origin in the properties of the initial density field (nature) and how its contrast is then amplified by the nonlinear mapping induced by the gravitational instability (nurture).

  14. Origin of the cosmic network in ΛCDM: Nature vs nurture

    NASA Astrophysics Data System (ADS)

    Shandarin, Sergei; Habib, Salman; Heitmann, Katrin

    2010-05-01

    The large-scale structure of the Universe, as traced by the distribution of galaxies, is now being revealed by large-volume cosmological surveys. The structure is characterized by galaxies distributed along filaments, the filaments connecting in turn to form a percolating network. Our objective here is to quantitatively specify the underlying mechanisms that drive the formation of the cosmic network: By combining percolation-based analyses with N-body simulations of gravitational structure formation, we elucidate how the network has its origin in the properties of the initial density field (nature) and how its contrast is then amplified by the nonlinear mapping induced by the gravitational instability (nurture).

  15. Laurentide Ice Sheet dynamics in the Bay of Fundy, Canada, revealed through multibeam sonar mapping of glacial landsystems

    NASA Astrophysics Data System (ADS)

    Todd, Brian J.; Shaw, John

    2012-12-01

    Recent multibeam sonar data collected in the Bay of Fundy, Canada, interpreted in conjunction with geophysical profiling and sediment sampling, reveal in unprecedented detail a suite of glacial landforms associated with the southwest margin of the Laurentide Ice Sheet. These landforms constitute four glacial landsystems. 1) Subglacial landsystem I: In southwestern Bay of Fundy, the elongated Grand Manan Basin contains ice-contact sediments of possible mid-Wisconsinan age overlain by late-Wisconsinan ice-contact sediments strongly imprinted by iceberg furrows and pits. In places, possible mid-Wisconsinan glaciomarine sediments have been eroded by late-Wisconsinan ice, creating streamlined landforms. Eroded bedrock and megafluted ice-contact sediment on the flanks of Grand Manan Basin indicate the southwest direction of topographically-steered ice. 2) Subglacial landsystem II: Along the southern margin of the Bay of Fundy, an array of drumlins, with superimposed esker complexes, was formed by glacial ice that emanated northwest from the interior of Nova Scotia and was deflected to the southwest by the ice flowing out of the Bay of Fundy to the Gulf of Maine. The esker complexes formed later when the Nova Scotia ice sheet stagnated and meltwater escaped northwest via topographic gaps. 3) Ice-marginal landsystem I: In northern Bay of Fundy, both small De Geer moraines and larger, basin-bounding moraines were created when retreating late-Wisconsinan ice became grounded in relatively shallow water. New radiocarbon ages show that the Owen Basin Moraine in this landsystem was abandoned prior to c. 14,600 14C yr BP (cal BP 17,015-17,270 [0.7], 17,286-17,405 [0.3]). 4) Ice-marginal landsystem II: This distinctive landsystem consists of numerous arcuate moraines, commonly superimposed on one another. This landsystem was formed by thin (170 m), lightly grounded ice that retreated northeast into the Bay of Fundy. The splayed pattern of the ice margin was a response to a large

  16. Searching for stringy topologies in the cosmic microwave background

    SciTech Connect

    Ben-David, Assaf; Rathaus, Ben; Itzhaki, Nissan E-mail: ben.rathaus@gmail.com

    2012-11-01

    We consider a universe with a non-classical stringy topology that has fixed points. We concentrate on the simplest example, an orbifold point, and study its observable imprints on the cosmic microwave background (CMB). We show that an orbifold preserves the Gaussian nature of the temperature fluctuations, yet modifies the angular correlation function. A direct signature of an orbifold is a single circle in the CMB that is invariant under rotation by 180°. Searching the 7-year ILC map of WMAP, we find one candidate circle with high statistical significance. However, a closer look reveals that the temperature profile does not fit an orbifold. We place a lower bound on the distance to an orbifold point at ∼ 85% of the distance to the surface of last scattering.

  17. Cortex mapping reveals regionally specific patterns of genetic and disease-specific gray-matter deficits in twins discordant for schizophrenia.

    PubMed

    Cannon, Tyrone D; Thompson, Paul M; van Erp, Theo G M; Toga, Arthur W; Poutanen, Veli-Pekka; Huttunen, Matti; Lonnqvist, Jouko; Standerskjold-Nordenstam, Carl-Gustav; Narr, Katherine L; Khaledy, Mohammad; Zoumalan, Chris I; Dail, Rajneesh; Kaprio, Jaakko

    2002-03-01

    The symptoms of schizophrenia imply disruption to brain systems supporting higher-order cognitive activity, but whether these systems are impacted differentially against a background of diffuse cortical gray-matter deficit remains ambiguous. Some unaffected first-degree relatives of schizophrenics also manifest cortical gray-matter deficits, but it is unclear whether these changes are isomorphic with those in patients, and the answer is critical to understanding the neurobiological conditions necessary for disease expression given a predisposing genotype. Here we report three-dimensional cortical surface maps (probabilistic atlases matching subjects' anatomy point by point throughout cortex) in monozygotic (MZ) and dizygotic (DZ) twins discordant for chronic schizophrenia along with demographically matched control twins. A map encoding the average differences between schizophrenia patients and their unaffected MZ co-twins revealed deficits primarily in dorsolateral prefrontal cortex, superior temporal gyrus, and superior parietal lobule. A map encoding variation associated with genetic proximity to a patient (MZ co-twins > DZ co-twins > control twins) isolated deficits primarily in polar and dorsolateral prefrontal cortex. In each case, the statistical significance was confirmed through analysis of 10,000 Monte Carlo permutations, and the remaining cortex was shown to be significantly less affected by contrast analysis. The disease-related deficits in gray matter were correlated with measures of symptom severity and cognitive dysfunction but not with duration of illness or antipsychotic drug treatment. Genetic and disease-specific influences thus affect gray matter in partially nonoverlapping areas of predominantly heteromodal association cortex, changes that may act synergistically in producing overt behavioral features of the disorder. PMID:11867725

  18. RNAi screens reveal novel metabolic regulators: RIP140, MAP4k4 and the lipid droplet associated fat specific protein (FSP) 27.

    PubMed

    Puri, V; Virbasius, J V; Guilherme, A; Czech, M P

    2008-01-01

    Adipose tissue modulates whole body metabolism and insulin sensitivity by controlling circulating lipid levels and producing molecules that can regulate fatty acid metabolism in such tissues as muscle and liver. We have developed RNA interference (RNAi) screens to identify genes in cultured adipocytes that regulate insulin signalling and key metabolic pathways. These short interfering RNA (siRNA)-based screens identified the transcriptional corepressor receptor interacting protein 140 (RIP140) (J Clin Invest 116: 125, 2006) and the mitogen-activated protein kinase (MAP4k4) (Proc Natl Acad Sci USA 103: 2087, 2006) as negative regulators of insulin-responsive hexose uptake and oxidative metabolism. Gene expression profiling revealed that RIP140 depletion upregulates the expression of clusters of genes in the pathways of glucose uptake, glycolysis, tricarboxylic acid cycle, fatty acid oxidation, mitochondrial biogenesis and oxidative phosphorylation. RIP140-null mice resist weight gain on a high-fat diet and display enhanced glucose tolerance. MAP4k4 depletion in adipocytes increases many of the RIP140-sensitive genes, increases adipogenesis and mediates some actions of tumour necrosis factor-alpha (TNF-alpha). Remarkably, another hit in our RNAi screens was fat specific protein 27 (FSP27), a highly expressed isoform of Cidea. We discovered that FSP27 unexpectedly associates specifically with lipid droplets and regulates fat storage. We conclude that RIP140, MAP4k4 and the novel lipid droplet protein FSP27 are powerful regulators of adipose tissue metabolism and are potential therapeutic targets for controlling metabolic disease. The discovery of these novel proteins validates the power of RNAi screening for discovery of new therapeutic approaches to type 2 diabetes and obesity. PMID:18171433

  19. A Gene-Based Genetic Linkage Map of the Collared Flycatcher (Ficedula albicollis) Reveals Extensive Synteny and Gene-Order Conservation During 100 Million Years of Avian Evolution

    PubMed Central

    Backström, Niclas; Karaiskou, Nikoletta; Leder, Erica H.; Gustafsson, Lars; Primmer, Craig R.; Qvarnström, Anna; Ellegren, Hans

    2008-01-01

    By taking advantage of a recently developed reference marker set for avian genome analysis we have constructed a gene-based genetic map of the collared flycatcher, an important “ecological model” for studies of life-history evolution, sexual selection, speciation, and quantitative genetics. A pedigree of 322 birds from a natural population was genotyped for 384 single nucleotide polymorphisms (SNPs) from 170 protein-coding genes and 71 microsatellites. Altogether, 147 gene markers and 64 microsatellites form 33 linkage groups with a total genetic distance of 1787 cM. Male recombination rates are, on average, 22% higher than female rates (total distance 1982 vs. 1627 cM). The ability to anchor the collared flycatcher map with the chicken genome via the gene-based SNPs revealed an extraordinary degree of both synteny and gene-order conservation during avian evolution. The great majority of chicken chromosomes correspond to a single linkage group in collared flycatchers, with only a few cases of inter- and intrachromosomal rearrangements. The rate of chromosomal diversification, fissions/fusions, and inversions combined is thus considerably lower in birds (0.05/MY) than in mammals (0.6–2.0/MY). A dearth of repeat elements, known to promote chromosomal breakage, in avian genomes may contribute to their stability. The degree of genome stability is likely to have important consequences for general evolutionary patterns and may explain, for example, the comparatively slow rate by which genetic incompatibility among lineages of birds evolves. PMID:18562642

  20. Genome-Wide Association Mapping in the Global Diversity Set Reveals New QTL Controlling Root System and Related Shoot Variation in Barley

    PubMed Central

    Reinert, Stephan; Kortz, Annika; Léon, Jens; Naz, Ali A.

    2016-01-01

    The fibrous root system is a visible sign of ecological adaptation among barley natural populations. In the present study, we utilized rich barley diversity to dissect the genetic basis of root system variation and its link with shoot attributes under well-water and drought conditions. Genome-wide association mapping of phenotype data using a dense genetic map (5892 SNP markers) revealed 17 putative QTL for root and shoot traits. Among these, at 14 loci the preeminence of exotic QTL alleles resulted in trait improvements. The most promising QTL were quantified using haplotype analysis at local and global genome levels. The strongest QTL was found on chromosome 1H which accounted for root dry weight and tiller number simultaneously. Candidate gene analysis across the targeted region detected a crucial amino acid substitution mutation in the conserved domain of a WRKY29 transcription factor among genotypes bearing major and minor QTL alleles. Similarly, the drought inducible QTL QRdw.5H (5H, 95.0 cM) seems to underlie 37 amino acid deletion and substitution mutations in the conserved domain of two related genes CBF10B and CBF10A, respectively. The identification and further characterization of these candidate genes will be essential to decipher genetics behind developmental and natural adaptation mechanisms of barley. PMID:27486472

  1. Genome-Wide Association Mapping in the Global Diversity Set Reveals New QTL Controlling Root System and Related Shoot Variation in Barley.

    PubMed

    Reinert, Stephan; Kortz, Annika; Léon, Jens; Naz, Ali A

    2016-01-01

    The fibrous root system is a visible sign of ecological adaptation among barley natural populations. In the present study, we utilized rich barley diversity to dissect the genetic basis of root system variation and its link with shoot attributes under well-water and drought conditions. Genome-wide association mapping of phenotype data using a dense genetic map (5892 SNP markers) revealed 17 putative QTL for root and shoot traits. Among these, at 14 loci the preeminence of exotic QTL alleles resulted in trait improvements. The most promising QTL were quantified using haplotype analysis at local and global genome levels. The strongest QTL was found on chromosome 1H which accounted for root dry weight and tiller number simultaneously. Candidate gene analysis across the targeted region detected a crucial amino acid substitution mutation in the conserved domain of a WRKY29 transcription factor among genotypes bearing major and minor QTL alleles. Similarly, the drought inducible QTL QRdw.5H (5H, 95.0 cM) seems to underlie 37 amino acid deletion and substitution mutations in the conserved domain of two related genes CBF10B and CBF10A, respectively. The identification and further characterization of these candidate genes will be essential to decipher genetics behind developmental and natural adaptation mechanisms of barley. PMID:27486472

  2. Cosmic ray isotopes

    NASA Technical Reports Server (NTRS)

    Stone, E. C.

    1973-01-01

    The isotopic composition of cosmic rays is studied in order to develop the relationship between cosmic rays and stellar processes. Cross section and model calculations are reported on isotopes of H, He, Be, Al and Fe. Satellite instrument measuring techniques separate only the isotopes of the lighter elements.

  3. Interactions of cosmic superstrings

    SciTech Connect

    Jackson, Mark G.; /Fermilab

    2007-06-01

    We develop methods by which cosmic superstring interactions can be studied in detail. These include the reconnection probability and emission of radiation such as gravitons or small string loops. Loop corrections to these are discussed, as well as relationships to (p; q)-strings. These tools should allow a phenomenological study of string models in anticipation of upcoming experiments sensitive to cosmic string radiation.

  4. Deepening Cosmic Education

    ERIC Educational Resources Information Center

    Leonard, Gerard

    2013-01-01

    This article is a special blend of research, theory, and practice, with clear insight into the origins of Cosmic Education and cosmic task, while recalling memories of student explorations in botany, in particular, episodes from Mr. Leonard's teaching. Mr. Leonard speaks of a storytelling curriculum that eloquently puts perspective into dimensions…

  5. Light from cosmic strings

    SciTech Connect

    Steer, Daniele A.; Vachaspati, Tanmay

    2011-02-15

    The time-dependent metric of a cosmic string leads to an effective interaction between the string and photons--the ''gravitational Aharonov-Bohm'' effect--and causes cosmic strings to emit light. We evaluate the radiation of pairs of photons from cosmic strings and find that the emission from cusps, kinks and kink-kink collisions occurs with a flat spectrum at all frequencies up to the string scale. Further, cusps emit a beam of photons, kinks emit along a curve, and the emission at a kink-kink collision is in all directions. The emission of light from cosmic strings could provide an important new observational signature of cosmic strings that is within reach of current experiments for a range of string tensions.

  6. Our Cosmic Insignificance

    PubMed Central

    Kahane, Guy

    2014-01-01

    The universe that surrounds us is vast, and we are so very small. When we reflect on the vastness of the universe, our humdrum cosmic location, and the inevitable future demise of humanity, our lives can seem utterly insignificant. Many philosophers assume that such worries about our significance reflect a banal metaethical confusion. They dismiss the very idea of cosmic significance. This, I argue, is a mistake. Worries about cosmic insignificance do not express metaethical worries about objectivity or nihilism, and we can make good sense of the idea of cosmic significance and its absence. It is also possible to explain why the vastness of the universe can make us feel insignificant. This impression does turn out to be mistaken, but not for the reasons typically assumed. In fact, we might be of immense cosmic significance—though we cannot, at this point, tell whether this is the case. PMID:25729095

  7. Xenia: A Probe of Cosmic Chemical Evolution

    NASA Technical Reports Server (NTRS)

    Kouveliotou, Chryssa; Piro, L.

    2008-01-01

    Xenia is a concept study for a medium-size astrophysical cosmology mission addressing the Cosmic Origins key objective of NASA's Science Plan. The fundamental goal of this objective is to understand the formation and evolution of structures on various scales from the early Universe to the present time (stars, galaxies and the cosmic web). Xenia will use X-and y-ray monitoring and wide field X-ray imaging and high-resolution spectroscopy to collect essential information from three major tracers of these cosmic structures: the Warm Hot Intergalactic Medium (WHIM), Galaxy Clusters and Gamma Ray Bursts (GRBs). Our goal is to trace the chemo-dynamical history of the ubiquitous warm hot diffuse baryon component in the Universe residing in cosmic filaments and clusters of galaxies up to its formation epoch (at z =0-2) and to map star formation and galaxy metal enrichment into the re-ionization era beyond z 6. The concept of Xenia (Greek for "hospitality") evolved in parallel with the Explorer of Diffuse Emission and GRB Explosions (EDGE), a mission proposed by a multinational collaboration to the ESA Cosmic Vision 2015. Xenia incorporates the European and Japanese collaborators into a U.S. led mission that builds on the scientific objectives and technological readiness of EDGE.

  8. RAD-QTL Mapping Reveals Both Genome-Level Parallelism and Different Genetic Architecture Underlying the Evolution of Body Shape in Lake Whitefish (Coregonus clupeaformis) Species Pairs

    PubMed Central

    Laporte, Martin; Rogers, Sean M.; Dion-Côté, Anne-Marie; Normandeau, Eric; Gagnaire, Pierre-Alexandre; Dalziel, Anne C.; Chebib, Jobran; Bernatchez, Louis

    2015-01-01

    Parallel changes in body shape may evolve in response to similar environmental conditions, but whether such parallel phenotypic changes share a common genetic basis is still debated. The goal of this study was to assess whether parallel phenotypic changes could be explained by genetic parallelism, multiple genetic routes, or both. We first provide evidence for parallelism in fish shape by using geometric morphometrics among 300 fish representing five species pairs of Lake Whitefish. Using a genetic map comprising 3438 restriction site−associated DNA sequencing single-nucleotide polymorphisms, we then identified quantitative trait loci underlying body shape traits in a backcross family reared in the laboratory. A total of 138 body shape quantitative trait loci were identified in this cross, thus revealing a highly polygenic architecture of body shape in Lake Whitefish. Third, we tested for evidence of genetic parallelism among independent wild populations using both a single-locus method (outlier analysis) and a polygenic approach (analysis of covariation among markers). The single-locus approach provided limited evidence for genetic parallelism. However, the polygenic analysis revealed genetic parallelism for three of the five lakes, which differed from the two other lakes. These results provide evidence for both genetic parallelism and multiple genetic routes underlying parallel phenotypic evolution in fish shape among populations occupying similar ecological niches. PMID:26002924

  9. Cosmic ray biannual variation

    NASA Technical Reports Server (NTRS)

    Attolini, M. R.; Cecchini, S.; Cinicastagnoli, G.; Galli, M.

    1985-01-01

    The study of the cosmic ray (CR) power spectrum has revealed a significant variation with a period around 2 yr that cannot be explained as a high order harmonic of the 11 yr solar cycle. Comparative study of the correlation on different time scales between CR intensity and Rz, aa, high speed streams and polar hole size has put in evidence that a high degree of coherency exists between each couple of variables at 1.58 to 1.64 yr, except between CR and Rz. On the other hand cyclic variation on a short time scale, around 26 months, has been claimed to be present in the neutrino flux. Critical tests of this hypothesis are considered and a preliminary result seems to indicate that the hypothesis of the existence of a 1.6 yr periodicity in the neutrino data during the measurement time interval, has a significance or = 99.9%. The possible origin of this variation as due to a contribution either of CR interactions in the upper atmosphere or to the solar dynamics, are discussed.

  10. Interspecific crossing and genetic mapping reveal intrinsic genomic incompatibility between two Senecio species that form a hybrid zone on Mount Etna, Sicily

    PubMed Central

    Brennan, A C; Hiscock, S J; Abbott, R J

    2014-01-01

    Studies of hybridizing species can reveal much about the genetic basis and maintenance of species divergence in the face of gene flow. Here we report a genetic segregation and linkage analysis conducted on F2 progeny of a reciprocal cross between Senecio aethnensis and S. chrysanthemifolius that form a hybrid zone on Mount Etna, Sicily, aimed at determining the genetic basis of intrinsic hybrid barriers between them. Significant transmission ratio distortion (TRD) was detected at 34 (∼27%) of 127 marker loci located in nine distinct clusters across seven of the ten linkage groups detected, indicating genomic incompatibility between the species. TRD at these loci could not be attributed entirely to post-zygotic selective loss of F2 individuals that failed to germinate or flower (16.7%). At four loci tests indicated that pre-zygotic events, such as meiotic drive in F1 parents or gametophytic selection, contributed to TRD. Additional tests revealed that cytonuclear incompatibility contributed to TRD at five loci, Bateson–Dobzhansky–Muller (BDM) incompatibilities involving epistatic interactions between loci contributed to TRD at four loci, and underdominance (heterozygote disadvantage) was a possible cause of TRD at one locus. Major chromosomal rearrangements were probably not a cause of interspecific incompatibility at the scale that could be examined with current map marker density. Intrinsic genomic incompatibility between S. aethnensis and S. chrysanthemifolius revealed by TRD across multiple genomic regions in early-generation hybrids is likely to impact the genetic structure of the natural hybrid zone on Mount Etna by limiting introgression and promoting divergence across the genome. PMID:24595365

  11. Interspecific crossing and genetic mapping reveal intrinsic genomic incompatibility between two Senecio species that form a hybrid zone on Mount Etna, Sicily.

    PubMed

    Brennan, A C; Hiscock, S J; Abbott, R J

    2014-09-01

    Studies of hybridizing species can reveal much about the genetic basis and maintenance of species divergence in the face of gene flow. Here we report a genetic segregation and linkage analysis conducted on F2 progeny of a reciprocal cross between Senecio aethnensis and S. chrysanthemifolius that form a hybrid zone on Mount Etna, Sicily, aimed at determining the genetic basis of intrinsic hybrid barriers between them. Significant transmission ratio distortion (TRD) was detected at 34 (∼27%) of 127 marker loci located in nine distinct clusters across seven of the ten linkage groups detected, indicating genomic incompatibility between the species. TRD at these loci could not be attributed entirely to post-zygotic selective loss of F2 individuals that failed to germinate or flower (16.7%). At four loci tests indicated that pre-zygotic events, such as meiotic drive in F1 parents or gametophytic selection, contributed to TRD. Additional tests revealed that cytonuclear incompatibility contributed to TRD at five loci, Bateson-Dobzhansky-Muller (BDM) incompatibilities involving epistatic interactions between loci contributed to TRD at four loci, and underdominance (heterozygote disadvantage) was a possible cause of TRD at one locus. Major chromosomal rearrangements were probably not a cause of interspecific incompatibility at the scale that could be examined with current map marker density. Intrinsic genomic incompatibility between S. aethnensis and S. chrysanthemifolius revealed by TRD across multiple genomic regions in early-generation hybrids is likely to impact the genetic structure of the natural hybrid zone on Mount Etna by limiting introgression and promoting divergence across the genome. PMID:24595365

  12. Particle acceleration in cosmic sites. Astrophysics issues in our understanding of cosmic rays

    NASA Astrophysics Data System (ADS)

    Diehl, R. L.

    2009-11-01

    Particles are accelerated in cosmic sites probably under conditions very different from those at terrestrial particle accelerator laboratories. Nevertheless, specific experiments which explore plasma conditions and stimulate particle acceleration carry significant potential to illuminate some aspects of the cosmic particle acceleration process. Here we summarize our understanding of cosmic particle acceleration, as derived from observations of the properties of cosmic ray particles, and through astronomical signatures caused by these near their sources or throughout their journey in interstellar space. We discuss the candidate-source object variety, and what has been learned about their particle-acceleration characteristics. We conclude identifying open issues as they are discussed among astrophysicists. - The cosmic ray differential intensity spectrum across energies from 1010 eV to 1021 eV reveals a rather smooth power-law spectrum. Two kinks occur at the “knee” (≃1015 eV) and at the “ankle” (≃ 3×1018 eV). It is unclear if these kinks are related to boundaries between different dominating sources, or rather related to characteristics of cosmic-ray propagation. Currently we believe that galactic sources dominate up to 1017 eV or even above, and the extragalactic origin of cosmic rays at highest energies merges rather smoothly with galactic contributions throughout the 1015-1018 eV range. Pulsars and supernova remnants are among the prime candidates for galactic cosmic-ray production, while nuclei of active galaxies are considered best candidates to produce ultrahigh-energy cosmic rays of extragalactic origin. The acceleration processes are probably related to shocks formed when matter is ejected into surrounding space from energetic sources such as supernova explosions or matter accreting onto black holes. Details of shock acceleration are complex, as relativistic particles modify the structure of the shock, and simple approximations or perturbation

  13. Eleventh European Cosmic Ray Symposium

    NASA Astrophysics Data System (ADS)

    1988-08-01

    The biannual Symposium includes all aspects of cosmic ray research. The scientific program was organized under three main headings: cosmic rays in the heliosphere, cosmic rays in the interstellar and extragalactic space, and properties of high-energy interactions as studied by cosmic rays. Selected short communications out of 114 contributed papers were indexed separately for the INIS database.

  14. Cosmic-ray astrochemistry.

    PubMed

    Indriolo, Nick; McCall, Benjamin J

    2013-10-01

    Gas-phase chemistry in the interstellar medium is driven by fast ion-molecule reactions. This, of course, demands a mechanism for ionization, and cosmic rays are the ideal candidate as they can operate throughout the majority of both diffuse and dense interstellar clouds. Aside from driving interstellar chemistry via ionization, cosmic rays also interact with the interstellar medium in ways that heat the ambient gas, produce gamma rays, and produce light element isotopes. In this paper we review the observables generated by cosmic-ray interactions with the interstellar medium, focusing primarily on the relevance to astrochemistry. PMID:23812538

  15. Supermassive cosmic string compactifications

    SciTech Connect

    Blanco-Pillado, Jose J.; Reina, Borja; Sousa, Kepa; Urrestilla, Jon E-mail: borja.reina@ehu.es E-mail: jon.urrestilla@ehu.es

    2014-06-01

    The space-time dimensions transverse to a static straight cosmic string with a sufficiently large tension (supermassive cosmic strings) are compact and typically have a singularity at a finite distance form the core. In this paper, we discuss how the presence of multiple supermassive cosmic strings in the 4d Abelian-Higgs model can induce the spontaneous compactification of the transverse space and explicitly construct solutions where the gravitational background becomes regular everywhere. We discuss the embedding of this model in N = 1 supergravity and show that some of these solutions are half-BPS, in the sense that they leave unbroken half of the supersymmetries of the model.

  16. Species relations among wild Arachis species with the A genome as revealed by FISH mapping of rDNA loci and heterochromatin detection.

    PubMed

    Robledo, G; Lavia, G I; Seijo, G

    2009-05-01

    Section Arachis of the homonymous genus includes 29 wild diploid species and two allotetraploids (A. monticola and the domesticated peanut, A. hypogaea L.). Although, three different genomes (A, B and D) have been proposed for diploid species with x = 10, they are still not well characterized. Moreover, neither the relationships among species within each genome group nor between diploids and tetraploids (AABB) are completely resolved. To tackle these issues, particularly within the A genome, in this study the rRNA genes (5S and 18S-26S) and heterochromatic bands were physically mapped using fluorescent in situ hybridization (FISH) in 13 species of Arachis. These molecular cytogenetic landmarks have allowed individual identification of a set of chromosomes and were used to construct detailed FISH-based karyotypes for each species. The bulk of the chromosome markers mapped revealed that, although the A genome species have a common karyotype structure, the species can be arranged in three groups (La Plata River Basin, Chiquitano, and Pantanal) on the basis of the variability observed in the heterochromatin and 18S-26S rRNA loci. Notably, these groups are consistent with the geographical co-distribution of the species. This coincidence is discussed on the basis of the particular reproductive traits of the species such as autogamy and geocarpy. Combined with geographic distribution of the taxa, the cytogenetic data provide evidence that A. duranensis is the most probable A genome ancestor of tetraploid species. It is expected that the groups of diploid species established, and their relation with the cultigen, may aid to rationally select wild species with agronomic traits desirable for peanut breeding programs. PMID:19234686

  17. Observational probes of cosmic acceleration

    NASA Astrophysics Data System (ADS)

    Weinberg, David H.; Mortonson, Michael J.; Eisenstein, Daniel J.; Hirata, Christopher; Riess, Adam G.; Rozo, Eduardo

    2013-09-01

    The accelerating expansion of the universe is the most surprising cosmological discovery in many decades, implying that the universe is dominated by some form of “dark energy” with exotic physical properties, or that Einstein’s theory of gravity breaks down on cosmological scales. The profound implications of cosmic acceleration have inspired ambitious efforts to understand its origin, with experiments that aim to measure the history of expansion and growth of structure with percent-level precision or higher. We review in detail the four most well established methods for making such measurements: Type Ia supernovae, baryon acoustic oscillations (BAO), weak gravitational lensing, and the abundance of galaxy clusters. We pay particular attention to the systematic uncertainties in these techniques and to strategies for controlling them at the level needed to exploit “Stage IV” dark energy facilities such as BigBOSS, LSST, Euclid, and WFIRST. We briefly review a number of other approaches including redshift-space distortions, the Alcock-Paczynski effect, and direct measurements of the Hubble constant H0. We present extensive forecasts for constraints on the dark energy equation of state and parameterized deviations from General Relativity, achievable with Stage III and Stage IV experimental programs that incorporate supernovae, BAO, weak lensing, and cosmic microwave background data. We also show the level of precision required for clusters or other methods to provide constraints competitive with those of these fiducial programs. We emphasize the value of a balanced program that employs several of the most powerful methods in combination, both to cross-check systematic uncertainties and to take advantage of complementary information. Surveys to probe cosmic acceleration produce data sets that support a wide range of scientific investigations, and they continue the longstanding astronomical tradition of mapping the universe in ever greater detail over ever

  18. The Cosmic Web in Our Own Backyard

    NASA Astrophysics Data System (ADS)

    Ibata, Rodrigo A.; Lewis, Geraint F.

    2008-01-01

    On the largest scales, matter is strung out on an intricate pattern known as the cosmic web. The tendrils of this web should reach right into our own cosmic backyard, lacing the Galactic halo with lumps of dark matter. The search for these lumps, lit up by stars that formed within them, is a major astronomical endeavor, although it has failed to find the huge expected population. Is this a dark matter crisis, or does it provide clues to the complexities of gas physics in the early universe? New technologies in the coming decade will reveal the answer.

  19. The cosmic web in our own backyard.

    PubMed

    Ibata, Rodrigo A; Lewis, Geraint F

    2008-01-01

    On the largest scales, matter is strung out on an intricate pattern known as the cosmic web. The tendrils of this web should reach right into our own cosmic backyard, lacing the Galactic halo with lumps of dark matter. The search for these lumps, lit up by stars that formed within them, is a major astronomical endeavor, although it has failed to find the huge expected population. Is this a dark matter crisis, or does it provide clues to the complexities of gas physics in the early universe? New technologies in the coming decade will reveal the answer. PMID:18174430

  20. Cosmic x ray physics

    NASA Technical Reports Server (NTRS)

    Mccammon, Dan; Cox, D. P.; Kraushaar, W. L.; Sanders, W. T.

    1990-01-01

    The annual progress report on Cosmic X Ray Physics is presented. Topics studied include: the soft x ray background, proportional counter and filter calibrations, the new sounding rocket payload: X Ray Calorimeter, and theoretical studies.

  1. Cosmic x ray physics

    NASA Technical Reports Server (NTRS)

    Mccammon, Dan; Cox, D. P.; Kraushaar, W. L.; Sanders, W. T.

    1991-01-01

    The annual progress report on Cosmic X Ray Physics for the period 1 Jan. to 31 Dec. 1990 is presented. Topics studied include: soft x ray background, new sounding rocket payload: x ray calorimeter, and theoretical studies.

  2. Getting around cosmic variance

    SciTech Connect

    Kamionkowski, M.; Loeb, A.

    1997-10-01

    Cosmic microwave background (CMB) anisotropies probe the primordial density field at the edge of the observable Universe. There is a limiting precision ({open_quotes}cosmic variance{close_quotes}) with which anisotropies can determine the amplitude of primordial mass fluctuations. This arises because the surface of last scatter (SLS) probes only a finite two-dimensional slice of the Universe. Probing other SLS{close_quote}s observed from different locations in the Universe would reduce the cosmic variance. In particular, the polarization of CMB photons scattered by the electron gas in a cluster of galaxies provides a measurement of the CMB quadrupole moment seen by the cluster. Therefore, CMB polarization measurements toward many clusters would probe the anisotropy on a variety of SLS{close_quote}s within the observable Universe, and hence reduce the cosmic-variance uncertainty. {copyright} {ital 1997} {ital The American Physical Society}

  3. A COSMIC VARIANCE COOKBOOK

    SciTech Connect

    Moster, Benjamin P.; Rix, Hans-Walter; Somerville, Rachel S.; Newman, Jeffrey A. E-mail: rix@mpia.de E-mail: janewman@pitt.edu

    2011-04-20

    Deep pencil beam surveys (<1 deg{sup 2}) are of fundamental importance for studying the high-redshift universe. However, inferences about galaxy population properties (e.g., the abundance of objects) are in practice limited by 'cosmic variance'. This is the uncertainty in observational estimates of the number density of galaxies arising from the underlying large-scale density fluctuations. This source of uncertainty can be significant, especially for surveys which cover only small areas and for massive high-redshift galaxies. Cosmic variance for a given galaxy population can be determined using predictions from cold dark matter theory and the galaxy bias. In this paper, we provide tools for experiment design and interpretation. For a given survey geometry, we present the cosmic variance of dark matter as a function of mean redshift z-bar and redshift bin size {Delta}z. Using a halo occupation model to predict galaxy clustering, we derive the galaxy bias as a function of mean redshift for galaxy samples of a given stellar mass range. In the linear regime, the cosmic variance of these galaxy samples is the product of the galaxy bias and the dark matter cosmic variance. We present a simple recipe using a fitting function to compute cosmic variance as a function of the angular dimensions of the field, z-bar , {Delta}z, and stellar mass m{sub *}. We also provide tabulated values and a software tool. The accuracy of the resulting cosmic variance estimates ({delta}{sigma}{sub v}/{sigma}{sub v}) is shown to be better than 20%. We find that for GOODS at z-bar =2 and with {Delta}z = 0.5, the relative cosmic variance of galaxies with m{sub *}>10{sup 11} M{sub sun} is {approx}38%, while it is {approx}27% for GEMS and {approx}12% for COSMOS. For galaxies of m{sub *} {approx} 10{sup 10} M{sub sun}, the relative cosmic variance is {approx}19% for GOODS, {approx}13% for GEMS, and {approx}6% for COSMOS. This implies that cosmic variance is a significant source of uncertainty at z

  4. A Cosmic Variance Cookbook

    NASA Astrophysics Data System (ADS)

    Moster, Benjamin P.; Somerville, Rachel S.; Newman, Jeffrey A.; Rix, Hans-Walter

    2011-04-01

    Deep pencil beam surveys (<1 deg2) are of fundamental importance for studying the high-redshift universe. However, inferences about galaxy population properties (e.g., the abundance of objects) are in practice limited by "cosmic variance." This is the uncertainty in observational estimates of the number density of galaxies arising from the underlying large-scale density fluctuations. This source of uncertainty can be significant, especially for surveys which cover only small areas and for massive high-redshift galaxies. Cosmic variance for a given galaxy population can be determined using predictions from cold dark matter theory and the galaxy bias. In this paper, we provide tools for experiment design and interpretation. For a given survey geometry, we present the cosmic variance of dark matter as a function of mean redshift \\bar{z} and redshift bin size Δz. Using a halo occupation model to predict galaxy clustering, we derive the galaxy bias as a function of mean redshift for galaxy samples of a given stellar mass range. In the linear regime, the cosmic variance of these galaxy samples is the product of the galaxy bias and the dark matter cosmic variance. We present a simple recipe using a fitting function to compute cosmic variance as a function of the angular dimensions of the field, \\bar{z}, Δz, and stellar mass m *. We also provide tabulated values and a software tool. The accuracy of the resulting cosmic variance estimates (δσ v /σ v ) is shown to be better than 20%. We find that for GOODS at \\bar{z}=2 and with Δz = 0.5, the relative cosmic variance of galaxies with m *>1011 M sun is ~38%, while it is ~27% for GEMS and ~12% for COSMOS. For galaxies of m * ~ 1010 M sun, the relative cosmic variance is ~19% for GOODS, ~13% for GEMS, and ~6% for COSMOS. This implies that cosmic variance is a significant source of uncertainty at \\bar{z}=2 for small fields and massive galaxies, while for larger fields and intermediate mass galaxies, cosmic variance is

  5. The Cosmic Labyrinth

    NASA Astrophysics Data System (ADS)

    Atkinson, M.

    2011-06-01

    This paper discusses the intertwined relationship between the terrestrial and celestial using the labyrinth as a metaphor referencing sources from art, gardens and Australian Indigenous culture. Including the Morning Star with the labyrinthine mortuary ritual in Arnhem Land, the cosmic plan garden at Auschwitz and Marea Atkinson's art project undertaken at the Villa Garzoni garden in Italy to create The Cosmic Labyrinth installation exhibited at Palazzo Franchetti, Venice, during the sixth conference on the Inspiration of Astronomical Phenomena.

  6. Cosmic Ray Dosimetry

    NASA Astrophysics Data System (ADS)

    Si Belkhir, F.; Attallah, R.

    2010-10-01

    Radiation levels at aircraft cruising altitudes are twenty times higher than at sea level. Thus, on average, a typical airline pilot receives a larger annual radiation dose than some one working in nuclear industry. The main source of this radiation is from galactic cosmic radiation, high energy particles generated by exploding stars within our own galaxy. In this work we study cosmic rays dosimetry at various aviation altitudes using the PARMA model.

  7. COSMIC monthly progress report

    NASA Technical Reports Server (NTRS)

    1994-01-01

    Activities of the Computer Software Management and Information Center (COSMIC) are summarized for the month of January 1994. Tables showing the current inventory of programs available from COSMIC are presented and program processing and evaluation activities are discussed. Marketing and customer service activities in this period are presented as is the progress report of NASTRAN maintenance and support. Tables of disseminations and budget summary conclude the report.

  8. Genome-Based Metabolic Mapping and 13C Flux Analysis Reveal Systematic Properties of an Oleaginous Microalga Chlorella protothecoides

    SciTech Connect

    Wu, Chao; Xiong, Wei; Dai, Junbiao; Wu, Qingyu

    2014-12-15

    We report that integrated and genome-based flux balance analysis, metabolomics, and 13C-label profiling of phototrophic and heterotrophic metabolism in Chlorella protothecoides, an oleaginous green alga for biofuel. The green alga Chlorella protothecoides, capable of autotrophic and heterotrophic growth with rapid lipid synthesis, is a promising candidate for biofuel production. Based on the newly available genome knowledge of the alga, we reconstructed the compartmentalized metabolic network consisting of 272 metabolic reactions, 270 enzymes, and 461 encoding genes and simulated the growth in different cultivation conditions with flux balance analysis. Phenotype-phase plane analysis shows conditions achieving theoretical maximum of the biomass and corresponding fatty acid-producing rate for phototrophic cells (the ratio of photon uptake rate to CO2 uptake rate equals 8.4) and heterotrophic ones (the glucose uptake rate to O2 consumption rate reaches 2.4), respectively. Isotope-assisted liquid chromatography-mass spectrometry/mass spectrometry reveals higher metabolite concentrations in the glycolytic pathway and the tricarboxylic acid cycle in heterotrophic cells compared with autotrophic cells. We also observed enhanced levels of ATP, nicotinamide adenine dinucleotide (phosphate), reduced, acetyl-Coenzyme A, and malonyl-Coenzyme A in heterotrophic cells consistently, consistent with a strong activity of lipid synthesis. To profile the flux map in experimental conditions, we applied nonstationary 13C metabolic flux analysis as a complementing strategy to flux balance analysis. We found that the result reveals negligible photorespiratory fluxes and a metabolically low active tricarboxylic acid cycle in phototrophic C. protothecoides. In comparison, high throughput of amphibolic reactions and the tricarboxylic acid cycle with no glyoxylate shunt activities were measured for heterotrophic cells. Lastly, taken together, the

  9. Genome-Based Metabolic Mapping and 13C Flux Analysis Reveal Systematic Properties of an Oleaginous Microalga Chlorella protothecoides1[OPEN

    PubMed Central

    Wu, Chao; Xiong, Wei; Dai, Junbiao; Wu, Qingyu

    2015-01-01

    Integrated and genome-based flux balance analysis, metabolomics, and 13C-label profiling of phototrophic and heterotrophic metabolism in Chlorella protothecoides, an oleaginous green alga for biofuel. The green alga Chlorella protothecoides, capable of autotrophic and heterotrophic growth with rapid lipid synthesis, is a promising candidate for biofuel production. Based on the newly available genome knowledge of the alga, we reconstructed the compartmentalized metabolic network consisting of 272 metabolic reactions, 270 enzymes, and 461 encoding genes and simulated the growth in different cultivation conditions with flux balance analysis. Phenotype-phase plane analysis shows conditions achieving theoretical maximum of the biomass and corresponding fatty acid-producing rate for phototrophic cells (the ratio of photon uptake rate to CO2 uptake rate equals 8.4) and heterotrophic ones (the glucose uptake rate to O2 consumption rate reaches 2.4), respectively. Isotope-assisted liquid chromatography-mass spectrometry/mass spectrometry reveals higher metabolite concentrations in the glycolytic pathway and the tricarboxylic acid cycle in heterotrophic cells compared with autotrophic cells. We also observed enhanced levels of ATP, nicotinamide adenine dinucleotide (phosphate), reduced, acetyl-Coenzyme A, and malonyl-Coenzyme A in heterotrophic cells consistently, consistent with a strong activity of lipid synthesis. To profile the flux map in experimental conditions, we applied nonstationary 13C metabolic flux analysis as a complementing strategy to flux balance analysis. The result reveals negligible photorespiratory fluxes and a metabolically low active tricarboxylic acid cycle in phototrophic C. protothecoides. In comparison, high throughput of amphibolic reactions and the tricarboxylic acid cycle with no glyoxylate shunt activities were measured for heterotrophic cells. Taken together, the metabolic network modeling assisted by experimental metabolomics and 13C labeling

  10. The astrobiological case for our cosmic ancestry

    NASA Astrophysics Data System (ADS)

    Wickramasinghe, Chandra

    2010-04-01

    With steadily mounting evidence that points to a cosmic origin of terrestrial life, a cultural barrier prevails against admitting that such a connection exists. Astronomy continues to reveal the presence of organic molecules and organic dust on a huge cosmic scale, amounting to a third of interstellar carbon tied up in this form. Just as the overwhelming bulk of organics on Earth stored over geological timescales are derived from the degradation of living cells, so it seems likely that interstellar organics in large measure also derive from biology. As we enter a new decade - the year 2010 - a clear pronouncement of our likely alien ancestry and of the existence of extraterrestrial life on a cosmic scale would seem to be overdue.

  11. Consistency relation for cosmic magnetic fields

    NASA Astrophysics Data System (ADS)

    Jain, Rajeev Kumar; Sloth, Martin S.

    2012-12-01

    If cosmic magnetic fields are indeed produced during inflation, they are likely to be correlated with the scalar metric perturbations that are responsible for the cosmic microwave background anisotropies and large scale structure. Within an archetypical model of inflationary magnetogenesis, we show that there exists a new simple consistency relation for the non-Gaussian cross correlation function of the scalar metric perturbation with two powers of the magnetic field in the squeezed limit where the momentum of the metric perturbation vanishes. We emphasize that such a consistency relation turns out to be extremely useful to test some recent calculations in the literature. Apart from primordial non-Gaussianity induced by the curvature perturbations, such a cross correlation might provide a new observational probe of inflation and can in principle reveal the primordial nature of cosmic magnetic fields.

  12. Polarization of Cosmic Microwave Background

    NASA Astrophysics Data System (ADS)

    Buzzelli, A.; Cabella, P.; de Gasperis, G.; Vittorio, N.

    2016-02-01

    In this work we present an extension of the ROMA map-making code for data analysis of Cosmic Microwave Background polarization, with particular attention given to the inflationary polarization B-modes. The new algorithm takes into account a possible cross- correlated noise component among the different detectors of a CMB experiment. We tested the code on the observational data of the BOOMERanG (2003) experiment and we show that we are provided with a better estimate of the power spectra, in particular the error bars of the BB spectrum are smaller up to 20% for low multipoles. We point out the general validity of the new method. A possible future application is the LSPE balloon experiment, devoted to the observation of polarization at large angular scales.

  13. Mapping the Interaction Sites between AMPA Receptors and TARPs Reveals a Role for the Receptor N-Terminal Domain in Channel Gating

    PubMed Central

    Cais, Ondrej; Herguedas, Beatriz; Krol, Karolina; Cull-Candy, Stuart G.; Farrant, Mark; Greger, Ingo H.

    2014-01-01

    Summary AMPA-type glutamate receptors (AMPARs) mediate fast neurotransmission at excitatory synapses. The extent and fidelity of postsynaptic depolarization triggered by AMPAR activation are shaped by AMPAR auxiliary subunits, including the transmembrane AMPAR regulatory proteins (TARPs). TARPs profoundly influence gating, an effect thought to be mediated by an interaction with the AMPAR ion channel and ligand binding domain (LBD). Here, we show that the distal N-terminal domain (NTD) contributes to TARP modulation. Alterations in the NTD-LBD linker result in TARP-dependent and TARP-selective changes in AMPAR gating. Using peptide arrays, we identify a TARP interaction region on the NTD and define the path of TARP contacts along the LBD surface. Moreover, we map key binding sites on the TARP itself and show that mutation of these residues mediates gating modulation. Our data reveal a TARP-dependent allosteric role for the AMPAR NTD and suggest that TARP binding triggers a drastic reorganization of the AMPAR complex. PMID:25373908

  14. Antigenic mapping of an H9N2 avian influenza virus reveals two discrete antigenic sites and a novel mechanism of immune escape

    PubMed Central

    Peacock, Thomas; Reddy, Kolli; James, Joe; Adamiak, Beata; Barclay, Wendy; Shelton, Holly; Iqbal, Munir

    2016-01-01

    H9N2 avian influenza virus is a major cause of poultry production loss across Asia leading to the wide use of vaccines. Efficacy of vaccines is often compromised due to the rapid emergence of antigenic variants. To improve the effectiveness of vaccines in the field, a better understanding of the antigenic epitopes of the major antigen, hemagglutinin, is required. To address this, a panel of nine monoclonal antibodies were generated against a contemporary Pakistani H9N2 isolate, which represents a major Asian H9N2 viral lineage. Antibodies were characterized in detail and used to select a total of 26 unique ‘escape’ mutants with substitutions across nine different amino acid residues in hemagglutinin including seven that have not been described as antigenic determinants for H9N2 viruses before. Competition assays and structural mapping revealed two novel, discrete antigenic sites “H9-A” and “H9-B”. Additionally, a second subset of escape mutants contained amino acid deletions within the hemagglutinin receptor binding site. This constitutes a novel method of escape for group 1 hemagglutinins and could represent an alternative means for H9N2 viruses to overcome vaccine induced immunity. These results will guide surveillance efforts for arising antigenic variants as well as evidence based vaccine seed selection and vaccine design. PMID:26738561

  15. Genome-Wide Mapping of Targets of Maize Histone Deacetylase HDA101 Reveals Its Function and Regulatory Mechanism during Seed Development[OPEN

    PubMed Central

    Yang, Hua; Liu, Xinye; Xin, Mingming; Du, Jinkun; Hu, Zhaorong; Peng, HuiRu; Sun, Qixin; Ni, Zhongfu; Yao, Yingyin

    2016-01-01

    Histone deacetylases (HDACs) regulate histone acetylation levels by removing the acetyl group from lysine residues. The maize (Zea mays) HDAC HDA101 influences several aspects of development, including kernel size; however, the molecular mechanism by which HDA101 affects kernel development remains unknown. In this study, we find that HDA101 regulates the expression of transfer cell-specific genes, suggesting that their misregulation may be associated with the defects in differentiation of endosperm transfer cells and smaller kernels observed in hda101 mutants. To investigate HDA101 function during the early stages of seed development, we performed genome-wide mapping of HDA101 binding sites. We observed that, like mammalian HDACs, HDA101 mainly targets highly and intermediately expressed genes. Although loss of HDA101 can induce histone hyperacetylation of its direct targets, this often does not involve variation in transcript levels. A small subset of inactive genes that must be negatively regulated during kernel development is also targeted by HDA101 and its loss leads to hyperacetylation and increased expression of these inactive genes. Finally, we report that HDA101 interacts with members of different chromatin remodeling complexes, such as NFC103/MSI1 and SNL1/SIN3-like protein corepressors. Taken together, our results reveal a complex genetic network regulated by HDA101 during seed development and provide insight into the different mechanisms of HDA101-mediated regulation of transcriptionally active and inactive genes. PMID:26908760

  16. Expression Quantitative Trait Locus Mapping across Water Availability Environments Reveals Contrasting Associations with Genomic Features in Arabidopsis[C][W][OPEN

    PubMed Central

    Lowry, David B.; Logan, Tierney L.; Santuari, Luca; Hardtke, Christian S.; Richards, James H.; DeRose-Wilson, Leah J.; McKay, John K.; Sen, Saunak; Juenger, Thomas E.

    2013-01-01

    The regulation of gene expression is crucial for an organism’s development and response to stress, and an understanding of the evolution of gene expression is of fundamental importance to basic and applied biology. To improve this understanding, we conducted expression quantitative trait locus (eQTL) mapping in the Tsu-1 (Tsushima, Japan) × Kas-1 (Kashmir, India) recombinant inbred line population of Arabidopsis thaliana across soil drying treatments. We then used genome resequencing data to evaluate whether genomic features (promoter polymorphism, recombination rate, gene length, and gene density) are associated with genes responding to the environment (E) or with genes with genetic variation (G) in gene expression in the form of eQTLs. We identified thousands of genes that responded to soil drying and hundreds of main-effect eQTLs. However, we identified very few statistically significant eQTLs that interacted with the soil drying treatment (GxE eQTL). Analysis of genome resequencing data revealed associations of several genomic features with G and E genes. In general, E genes had lower promoter diversity and local recombination rates. By contrast, genes with eQTLs (G) had significantly greater promoter diversity and were located in genomic regions with higher recombination. These results suggest that genomic architecture may play an important a role in the evolution of gene expression. PMID:24045022

  17. Genome-wide association mapping and biochemical markers reveal that seed ageing and longevity are intricately affected by genetic background and developmental and environmental conditions in barley.

    PubMed

    Nagel, Manuela; Kranner, Ilse; Neumann, Kerstin; Rolletschek, Hardy; Seal, Charlotte E; Colville, Louise; Fernández-Marín, Beatriz; Börner, Andreas

    2015-06-01

    Globally, over 7.4 million accessions of crop seeds are stored in gene banks, and conservation of genotypic variation is pivotal for breeding. We combined genetic and biochemical approaches to obtain a broad overview of factors that influence seed storability and ageing in barley (Hordeum vulgare). Seeds from a germplasm collection of 175 genotypes from four continents grown in field plots with different nutrient supply were subjected to two artificial ageing regimes. Genome-wide association mapping revealed 107 marker trait associations, and hence, genotypic effects on seed ageing. Abiotic and biotic stresses were found to affect seed longevity. To address aspects of abiotic, including oxidative, stress, two major antioxidant groups were analysed. No correlation was found between seed deterioration and the lipid-soluble tocochromanols, nor with oil, starch and protein contents. Conversely, the water-soluble glutathione and related thiols were converted to disulphides, indicating a strong shift towards more oxidizing intracellular conditions, in seeds subjected to long-term dry storage at two temperatures or to two artificial ageing treatments. The data suggest that intracellular pH and (bio)chemical processes leading to seed deterioration were influenced by the type of ageing or storage. Moreover, seed response to ageing or storage treatment appears to be significantly influenced by both maternal environment and genetic background. PMID:25328120

  18. Stratigraphic relationships and timing of the 2012 Havre submarine silicic volcanic eruption revealed by high resolution bathymetric mapping and observations by underwater vehicles.

    NASA Astrophysics Data System (ADS)

    Carey, R.; Soule, S. A.; Houghton, B. F.; White, J. D. L.; Manga, M.; Wysoczanski, R. J.; Tani, K.; McPhie, J.; Fornari, D. J.; Jutzeler, M.; Caratori Tontini, F.; Ikegami, F.; Jones, M.; Murch, A.; Fauria, K.; Mitchell, S. J.; Cahalan, R. C.; Conway, C.; McKenzie, W.

    2015-12-01

    The 2012 deep rhyolitic caldera eruption of Havre volcano in the Kermadec arc is the first historic observed submarine eruption that produced a pumice raft observed at the ocean's surface. Ship-based bathymetric surveys before and after the eruption permit the intricacies of eruption styles, products and timescales to be quantified. In 2015 we mapped this submarine volcano in unprecedented detail with two submergence vehicles in tandem, facilitating a wide and comprehensive geological survey and sampling mission. These efforts and observations show highly complex and often simultaneous eruptive behavior from more than 14 vents along two 3 km-long fissures that represent massive ruptures of the caldera walls. This survey also revealed an important role for pre- and inter-eruptive periods of mass wasting processes derived from the intrusion of magma and destablisation of caldera walls. The detailed characterization of the eruption products, and quantification of timescales provides the scientific community with the first glimpse of the nature of submarine, intermediate magnitude, deep silicic caldera eruptions and permits unanswered yet first order fundamental questions of submarine eruption and transport processes to be addressed in the decades to come.

  19. Genome-Wide Mapping of Targets of Maize Histone Deacetylase HDA101 Reveals Its Function and Regulatory Mechanism during Seed Development.

    PubMed

    Yang, Hua; Liu, Xinye; Xin, Mingming; Du, Jinkun; Hu, Zhaorong; Peng, HuiRu; Rossi, Vincenzo; Sun, Qixin; Ni, Zhongfu; Yao, Yingyin

    2016-03-01

    Histone deacetylases (HDACs) regulate histone acetylation levels by removing the acetyl group from lysine residues. The maize (Zea mays)HDACHDA101 influences several aspects of development, including kernel size; however, the molecular mechanism by which HDA101 affects kernel development remains unknown. In this study, we find that HDA101 regulates the expression of transfer cell-specific genes, suggesting that their misregulation may be associated with the defects in differentiation of endosperm transfer cells and smaller kernels observed inhda101mutants. To investigate HDA101 function during the early stages of seed development, we performed genome-wide mapping of HDA101 binding sites. We observed that, like mammalianHDACs, HDA101 mainly targets highly and intermediately expressed genes. Although loss of HDA101 can induce histone hyperacetylation of its direct targets, this often does not involve variation in transcript levels. A small subset of inactive genes that must be negatively regulated during kernel development is also targeted by HDA101 and its loss leads to hyperacetylation and increased expression of these inactive genes. Finally, we report that HDA101 interacts with members of different chromatin remodeling complexes, such as NFC103/MSI1 and SNL1/SIN3-like protein corepressors. Taken together, our results reveal a complex genetic network regulated by HDA101 during seed development and provide insight into the different mechanisms of HDA101-mediated regulation of transcriptionally active and inactive genes. PMID:26908760

  20. A Cosmic Magnifying Glass

    NASA Technical Reports Server (NTRS)

    2000-01-01

    Scanning the heavens for the first time since the successful December 1999 servicing mission, NASA's Hubble Space Telescope imaged a giant, cosmic magnifying glass, a massive cluster of galaxies called Abell 2218. This 'hefty' cluster resides in the constellation Draco, some 2 billion light-years from Earth. The cluster is so massive that its enormous gravitational field deflects light rays passing through it, much as an optical lens bends light to form an image. This phenomenon, called gravitational lensing, magnifies, brightens, and distorts images from faraway objects. The cluster's magnifying powers provides a powerful 'zoom lens' for viewing distant galaxies that could not normally be observed with the largest telescopes. The picture is dominated by spiral and elliptical galaxies. Resembling a string of tree lights, the biggest and brightest galaxies are members of the foreground cluster. Researchers are intrigued by a tiny red dot just left of top center. This dot may be an extremely remote object made visible by the cluster's magnifying powers. Further investigation is needed to confirm the object's identity. The color picture already reveals several arc-shaped features that are embedded in the cluster and cannot be easily seen in the black-and- white image. The colors in this picture yield clues to the ages, distances, and temperatures of stars, the stuff of galaxies. Blue pinpoints hot young stars. The yellow-white color of several of the galaxies represents the combined light of many stars. Red identifies cool stars, old stars, and the glow of stars in distant galaxies. This view is only possible by combining Hubble's unique image quality with the rare lensing effect provided by the magnifying cluster.

  1. Edge detection, cosmic strings and the south pole telescope

    SciTech Connect

    Stewart, Andrew; Brandenberger, Robert E-mail: rhb@physics.mcgill.ca

    2009-02-15

    We develop a method of constraining the cosmic string tension G{mu} which uses the Canny edge detection algorithm as a means of searching CMB temperature maps for the signature of the Kaiser-Stebbins effect. We test the potential of this method using high resolution, simulated CMB temperature maps. By modeling the future output from the South Pole Telescope project (including anticipated instrumental noise), we find that cosmic strings with G{mu} > 5.5 Multiplication-Sign 10{sup -8} could be detected.

  2. The Genome and Linkage Map of the Northern Pike (Esox lucius): Conserved Synteny Revealed between the Salmonid Sister Group and the Neoteleostei

    PubMed Central

    Rondeau, Eric B.; Minkley, David R.; Leong, Jong S.; Messmer, Amber M.; Jantzen, Johanna R.; von Schalburg, Kristian R.; Lemon, Craig; Bird, Nathan H.; Koop, Ben F.

    2014-01-01

    The northern pike is the most frequently studied member of the Esociformes, the closest order to the diverse and economically important Salmoniformes. The ancestor of all salmonids purportedly experienced a whole-genome duplication (WGD) event, making salmonid species ideal for studying the early impacts of genome duplication while complicating their use in wider analyses of teleost evolution. Studies suggest that the Esociformes diverged from the salmonid lineage prior to the WGD, supporting the use of northern pike as a pre-duplication outgroup. Here we present the first genome assembly, reference transcriptome and linkage map for northern pike, and evaluate the suitability of this species to provide a representative pre-duplication genome for future studies of salmonid and teleost evolution. The northern pike genome sequence is composed of 94,267 contigs (N50 = 16,909 bp) contained in 5,688 scaffolds (N50 = 700,535 bp); the total scaffolded genome size is 878 million bases. Multiple lines of evidence suggest that over 96% of the protein-coding genome is present in the genome assembly. The reference transcriptome was constructed from 13 tissues and contains 38,696 transcripts, which are accompanied by normalized expression data in all tissues. Gene-prediction analysis produced a total of 19,601 northern pike-specific gene models. The first-generation linkage map identifies 25 linkage groups, in agreement with northern pike's diploid karyotype of 2N = 50, and facilitates the placement of 46% of assembled bases onto linkage groups. Analyses reveal a high degree of conserved synteny between northern pike and other model teleost genomes. While conservation of gene order is limited to smaller syntenic blocks, the wider conservation of genome organization implies the northern pike exhibits a suitable approximation of a non-duplicated Protacanthopterygiian genome. This dataset will facilitate future studies of esocid biology and empower ongoing examinations

  3. Essential Role for the Lectin Pathway in Collagen Antibody-Induced Arthritis Revealed Through Use of Adenovirus Programming Complement Inhibitor MAp44 Expression

    PubMed Central

    Banda, Nirmal K.; Mehta, Gaurav; Kjaer, Troels R.; Takahashi, Minoru; Schaack, Jerome; Morrison, Thomas E.; Thiel, Steffen; Arend, William P.; Holers, V. Michael

    2014-01-01

    Previous studies using mannose-binding lectin (MBL) and complement C4 deficient mice have suggested that the lectin pathway (LP) is not required for the development of inflammatory arthritis in the collagen antibody-induced arthritis (CAIA) model. MBL, ficolins and collectin-11 are key LP pattern recognition molecules that associate with three serine proteases, MASP-1, MASP-2 and MASP-3, and also with two MBL-associated proteins designated sMAP and MAp44. Recent studies have shown that MAp44, an alternatively spliced product of the MASP-1/3 gene, is a competitive inhibitor of the binding of the recognition molecules to all three MASPs. In these studies we examined the effect of treatment of mice with adenovirus (Ad) programmed to express human MAp44 (AdhMAp44) on the development of CAIA. AdhMAp44 and Ad programming Green fluorescent protein (AdGFP) expression were injected intraperitoneally in C57BL/6 wild-type mice prior to the induction of CAIA. AdhMAp44 significantly reduced the clinical disease activity score (CDA) by 81% compared to mice injected with AdGFP. Similarly, histopathologic injury scores for inflammation, pannus, cartilage and bone damage, as well as C3 deposition in the cartilage and synovium, were significantly reduced by AdhMAp44 pretreatment. Mice treated with AdmMAp44, programming expression of mouse MAp44, also showed significantly decreased CDA and histopathologic injury scores. Additionally, administration of AdhMAp44 significantly diminished the severity of Ross River Virus-induced arthritis, a LP-dependent model. Our study provides conclusive evidence that an intact complement LP is essential to initiate CAIA, and that MAp44 may be an appropriate treatment for inflammatory arthritis. PMID:25070856

  4. Cosmic questions: an introduction.

    PubMed

    Primack, J R; Abrams, N E

    2001-12-01

    This introductory talk at the Cosmic Questions conference sponsored by the AAAS summarizes some earlier pictures of the universe and some pictures based on modern physics and cosmology. The uroboros (snake swallowing its tail) is an example of a traditional picture. The Biblical flat-earth picture was very different from the Greek spherical earth-centered picture, which was the standard view until the end of the Middle Ages. Many people incorrectly assume that the Newtonian picture of stars scattered through otherwise empty space is still the prevailing view. Seeing Earth from space shows the power of a new picture. The Hubble Space Telescope can see all the bright galaxies, all the way to the cosmic Dark Ages. We are at the center of cosmic spheres of time: looking outward is looking backward in time. All the matter and energy in the universe can be represented as a cosmic density pyramid. The laws of physics only allow the material objects in the universe to occupy a wedge-shaped region on a diagram of mass versus size. All sizes--from the smallest size scale, the Planck scale, to the entire visible universe--can be represented on the Cosmic Uroboros. There are interesting connections across this diagram, and the human scale lies in the middle. PMID:11797741

  5. Cosmic Ray Albedo Proton Yield Correlated with Lunar Elemental Abundances

    NASA Astrophysics Data System (ADS)

    Wilson, J. K.; Spence, H. E.; Case, A. W.; Blake, J. B.; Golightly, M. J.; Kasper, J. C.; Looper, M. D.; Mazur, J. E.; Schwadron, N. A.; Townsend, L. W.; Zeitlin, C. J.

    2012-12-01

    High energy cosmic rays constantly bombard the lunar regolith, producing secondary "albedo" or "splash" particles like protons and neutrons, some of which escape back to space. Two lunar missions, Lunar Prospector and the Lunar Reconnaissance Orbiter (LRO), have shown that the energy distribution of albedo neutrons is modulated by the elemental composition of the lunar regolith[1-4], with reduced neutron fluxes near the lunar poles being the result of collisions with hydrogen nuclei in ice deposits[5] in permanently shadowed craters. Here we investigate an analogous phenomenon with high energy (~100 MeV) lunar albedo protons. LRO has been observing the surface and environment of the Moon since June of 2009. The CRaTER instrument (Cosmic Ray Telescope for the Effects of Radiation) on LRO is designed to characterize the lunar radiation environment and its effects on simulated human tissue. CRaTER's multiple solid-state detectors can discriminate the different elements in the galactic cosmic ray (GCR) population above ~10 MeV/nucleon, and can also distinguish between primary GCR protons arriving from deep space and albedo particles propagating up from the lunar surface. We use albedo protons with energies greater than 60 MeV to construct a cosmic ray albedo proton map of the Moon. The yield of albedo protons is proportional to the rate of lunar proton detections divided by the rate of incoming GCR detections. The map accounts for time variation in the albedo particles driven by time variations in the primary GCR population, thus revealing any true spatial variation of the albedo proton yield. Our current map is a significant improvement over the proof-of-concept map of Wilson et al.[6]. In addition to including twelve more months of CRaTER data here, we use more numerous minimum ionizing GCR protons for normalization, and we make use of all six of CRaTER's detectors to reduce contamination from spurious non-proton events in the data stream. We find find that the flux

  6. Angular 21 cm power spectrum of a scaling distribution of cosmic string wakes

    SciTech Connect

    Hernández, Oscar F.; Wang, Yi; Brandenberger, Robert; Fong, José E-mail: wangyi@physics.mcgill.ca E-mail: jose.fong@ens-lyon.fr

    2011-08-01

    Cosmic string wakes lead to a large signal in 21 cm redshift maps at redshifts larger than that corresponding to reionization. Here, we compute the angular power spectrum of 21 cm radiation as predicted by a scaling distribution of cosmic strings whose wakes have undergone shock heating.

  7. A Genetic Relationship between Phosphorus Efficiency and Photosynthetic Traits in Soybean As Revealed by QTL Analysis Using a High-Density Genetic Map

    PubMed Central

    Li, Hongyan; Yang, Yuming; Zhang, Hengyou; Chu, Shanshan; Zhang, Xingguo; Yin, Dongmei; Yu, Deyue; Zhang, Dan

    2016-01-01

    Plant productivity relies on photosynthesis, and the photosynthetic process relies on phosphorus (P). The genetic basis of photosynthesis and P efficiency (PE) affecting yield has been separately characterized in various crop plants. However, the genetic relationship between PE and photosynthesis remains to be elucidated. In this study, we used a combined analysis of phenotypic correlation, linkage mapping, and expression analysis to dissect the relationship between PE and photosynthesis. We found significant phenotypic correlations between PE and photosynthetic related traits, particularly under low P stress. A total of 172 QTLs for both traits were detected and classified into 29 genomic regions. 12 (41.4%) of 29 regions were detected to be associated with both PE and photosynthetic related traits. Three major QTLs, q14-2, q15-2, and q19-2, were found to be associated with both traits and explained 6.6–58.9% of phenotypic variation. A photosynthetic-specific QTL cluster, q12-1, was detected under both normal and low P conditions, suggesting that genes responsible for this region were less effected by low P stress, and could be used in high photosynthetic efficiency breeding programs. In addition, several candidate genes with significantly differential expression upon low P stress, such as a purple acid phosphatase gene (Glyma.19G193900) within q19-2 region, were considered as promising candidates involved in regulating both soybean PE and photosynthetic capacity. Our results reveal a significant genetic relationship between PE and photosynthetic traits, and uncover several major genomic regions specific or common to these traits. The markers linked closely to these major QTLs may be used for selection of soybean varieties with improved P efficiency and photosynthetic capacity. PMID:27446154

  8. A Genetic Relationship between Phosphorus Efficiency and Photosynthetic Traits in Soybean As Revealed by QTL Analysis Using a High-Density Genetic Map.

    PubMed

    Li, Hongyan; Yang, Yuming; Zhang, Hengyou; Chu, Shanshan; Zhang, Xingguo; Yin, Dongmei; Yu, Deyue; Zhang, Dan

    2016-01-01

    Plant productivity relies on photosynthesis, and the photosynthetic process relies on phosphorus (P). The genetic basis of photosynthesis and P efficiency (PE) affecting yield has been separately characterized in various crop plants. However, the genetic relationship between PE and photosynthesis remains to be elucidated. In this study, we used a combined analysis of phenotypic correlation, linkage mapping, and expression analysis to dissect the relationship between PE and photosynthesis. We found significant phenotypic correlations between PE and photosynthetic related traits, particularly under low P stress. A total of 172 QTLs for both traits were detected and classified into 29 genomic regions. 12 (41.4%) of 29 regions were detected to be associated with both PE and photosynthetic related traits. Three major QTLs, q14-2, q15-2, and q19-2, were found to be associated with both traits and explained 6.6-58.9% of phenotypic variation. A photosynthetic-specific QTL cluster, q12-1, was detected under both normal and low P conditions, suggesting that genes responsible for this region were less effected by low P stress, and could be used in high photosynthetic efficiency breeding programs. In addition, several candidate genes with significantly differential expression upon low P stress, such as a purple acid phosphatase gene (Glyma.19G193900) within q19-2 region, were considered as promising candidates involved in regulating both soybean PE and photosynthetic capacity. Our results reveal a significant genetic relationship between PE and photosynthetic traits, and uncover several major genomic regions specific or common to these traits. The markers linked closely to these major QTLs may be used for selection of soybean varieties with improved P efficiency and photosynthetic capacity. PMID:27446154

  9. Organelle DNA rearrangement mapping reveals U-turn-like inversions as a major source of genomic instability in Arabidopsis and humans

    PubMed Central

    Zampini, Éric; Lepage, Étienne; Tremblay-Belzile, Samuel; Truche, Sébastien; Brisson, Normand

    2015-01-01

    Failure to maintain organelle genome stability has been linked to numerous phenotypes, including variegation and cytosolic male sterility (CMS) in plants, as well as cancer and neurodegenerative diseases in mammals. Here we describe a next-generation sequencing approach that precisely maps and characterizes organelle DNA rearrangements in a single genome-wide experiment. In addition to displaying global portraits of genomic instability, it surprisingly unveiled an abundance of short-range rearrangements in Arabidopsis thaliana and human organelles. Among these, short-range U-turn-like inversions reach 25% of total rearrangements in wild-type Arabidopsis plastids and 60% in human mitochondria. Furthermore, we show that replication stress correlates with the accumulation of this type of rearrangement, suggesting that U-turn-like rearrangements could be the outcome of a replication-dependent mechanism. We also show that U-turn-like rearrangements are mostly generated using microhomologies and are repressed in plastids by Whirly proteins WHY1 and WHY3. A synergistic interaction is also observed between the genes for the plastid DNA recombinase RECA1 and those encoding plastid Whirly proteins, and the triple mutant why1why3reca1 accumulates almost 60 times the WT levels of U-turn-like rearrangements. We thus propose that the process leading to U-turn-like rearrangements may constitute a RecA-independent mechanism to restart stalled forks. Our results reveal that short-range rearrangements, and especially U-turn-like rearrangements, are a major factor of genomic instability in organelles, and this raises the question of whether they could have been underestimated in diseases associated with mitochondrial dysfunction. PMID:25800675

  10. Long-Term Fate Mapping Using Conditional Lentiviral Vectors Reveals a Continuous Contribution of Radial Glia-Like Cells to Adult Hippocampal Neurogenesis in Mice

    PubMed Central

    Aelvoet, Sarah-Ann; Pascual-Brazo, Jesus; Libbrecht, Sarah; Reumers, Veerle; Gijsbers, Rik; Van den Haute, Chris; Baekelandt, Veerle

    2015-01-01

    Newborn neurons are generated throughout life in two neurogenic regions, the subventricular zone and the hippocampal dentate gyrus. Stimulation of adult neurogenesis is considered as an attractive endogenous repair mechanism to treat different neurological disorders. Although tremendous progress has been made in our understanding of adult hippocampal neurogenesis, important questions remain unanswered, regarding the identity and the behavior of neural stem cells in the dentate gyrus. We previously showed that conditional Cre-Flex lentiviral vectors can be used to label neural stem cells in the subventricular zone and to track the migration of their progeny with non-invasive bioluminescence imaging. Here, we applied these Cre-Flex lentiviral vectors to study neurogenesis in the dentate gyrus with bioluminescence imaging and histological techniques. Stereotactic injection of the Cre-Flex vectors into the dentate gyrus of transgenic Nestin-Cre mice resulted in specific labeling of the nestin-positive neural stem cells. The labeled cell population could be detected with bioluminescence imaging until 9 months post injection, but no significant increase in the number of labeled cells over time was observed with this imaging technique. Nevertheless, the specific labeling of the nestin-positive neural stem cells, combined with histological analysis at different time points, allowed detailed analysis of their neurogenic potential. This long-term fate mapping revealed that a stable pool of labeled nestin-positive neural stem cells continuously contributes to the generation of newborn neurons in the mouse brain until 9 months post injection. In conclusion, the Cre-Flex technology is a valuable tool to address remaining questions regarding neural stem cell identity and behavior in the dentate gyrus. PMID:26600383

  11. Hierarchical cosmic shear power spectrum inference

    NASA Astrophysics Data System (ADS)

    Alsing, Justin; Heavens, Alan; Jaffe, Andrew H.; Kiessling, Alina; Wandelt, Benjamin; Hoffmann, Till

    2016-02-01

    We develop a Bayesian hierarchical modelling approach for cosmic shear power spectrum inference, jointly sampling from the posterior distribution of the cosmic shear field and its (tomographic) power spectra. Inference of the shear power spectrum is a powerful intermediate product for a cosmic shear analysis, since it requires very few model assumptions and can be used to perform inference on a wide range of cosmological models a posteriori without loss of information. We show that joint posterior for the shear map and power spectrum can be sampled effectively by Gibbs sampling, iteratively drawing samples from the map and power spectrum, each conditional on the other. This approach neatly circumvents difficulties associated with complicated survey geometry and masks that plague frequentist power spectrum estimators, since the power spectrum inference provides prior information about the field in masked regions at every sampling step. We demonstrate this approach for inference of tomographic shear E-mode, B-mode and EB-cross power spectra from a simulated galaxy shear catalogue with a number of important features; galaxies distributed on the sky and in redshift with photometric redshift uncertainties, realistic random ellipticity noise for every galaxy and a complicated survey mask. The obtained posterior distributions for the tomographic power spectrum coefficients recover the underlying simulated power spectra for both E- and B-modes.

  12. Discovery of cosmic rays

    NASA Astrophysics Data System (ADS)

    Carlson, Per

    2013-02-01

    The mysterious invisible radiation that ionized air was studied a century ago by many scientists. Finally, on 7 August 1912, Victor Hess in his seventh balloon flight that year, reached an altitude of about 5000 m. With his electroscopes on board the hydrogen-filled balloon he observed that the ionization instead of decreasing with altitude increased significantly. Hess had discovered cosmic rays, a discovery that gave him the 1936 Nobel Prize in physics. When research resumed after World War I focus was on understanding the nature of the cosmic radiation. Particles or radiation? Positive or negative? Electrons, positrons or protons? Progress came using new instruments like the Geiger-Muller tube and around 1940 it was clear that cosmic rays were mostly protons.

  13. Semilocal cosmic string networks

    SciTech Connect

    Achucarro, Ana; Salmi, Petja; Urrestilla, Jon

    2007-06-15

    We report on a large-scale numerical study of networks of semilocal cosmic strings in flat space in the parameter regime in which they are perturbatively stable. We find a population of segments with an exponential length distribution and indications of a scaling network without significant loop formation. Very deep in the stability regime strings of superhorizon size grow rapidly and ''percolate'' through the box. We believe these should lead at late times to a population of infinite strings similar to topologically stable strings. However, the strings are very light; scalar gradients dominate the energy density, and the network has thus a global texturelike signature. As a result, the observational constraints, at least from the temperature power spectrum of the cosmic microwave background, on models predicting semilocal strings should be closer to those on global textures or monopoles, rather than on topologically stable gauged cosmic strings.

  14. QTL mapping in multiple populations and development stages reveals dynamic quantitative trait loci for fruit size in cucumbers of different market classes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Fruit size is an important quality trait in cucumber of different market classes. The genetic and molecular basis of fruit size variations in cucumber is not well understood. In this study, we conducted QTL mapping of fruit size in cucumber using three mapping populations developed from cross betwee...

  15. A highly recombined, high-density, eight-founder wheat MAGIC map reveals extensive segregation distortion and genomic locations of introgression segments.

    PubMed

    Gardner, Keith A; Wittern, Lukas M; Mackay, Ian J

    2016-06-01

    Multiparent Advanced Generation Intercross (MAGIC) mapping populations offer unique opportunities and challenges for marker and QTL mapping in crop species. We have constructed the first eight-parent MAGIC genetic map for wheat, comprising 18 601 SNP markers. We validated the accuracy of our map against the wheat genome sequence and found an improvement in accuracy compared to published genetic maps. Our map shows a notable increase in precision resulting from the three generations of intercrossing required to create the population. This is most pronounced in the pericentromeric regions of the chromosomes. Sixteen percent of mapped markers exhibited segregation distortion (SD) with many occurring in long (>20 cM) blocks. Some of the longest and most distorted blocks were collinear with noncentromeric high-marker-density regions of the genome, suggesting they were candidates for introgression fragments introduced into the bread wheat gene pool from other grass species. We investigated two of these linkage blocks in detail and found strong evidence that one on chromosome 4AL, showing SD against the founder Robigus, is an interspecific introgression fragment. The completed map is available from http://www.niab.com/pages/id/326/Resources. PMID:26801965

  16. T-Cell-Specific Deletion of Map3k1 Reveals the Critical Role for Mekk1 and Jnks in Cdkn1b-Dependent Proliferative Expansion.

    PubMed

    Suddason, Tesha; Anwar, Saba; Charlaftis, Nikolaos; Gallagher, Ewen

    2016-01-26

    MAPK signaling is important for T lymphocyte development, homeostasis, and effector responses. To better understand the role of Mekk1 (encoded by Map3k1) in T cells, we conditionally deleted Map3k1 in Lck(Cre/+)Map3k1(f/f) mice, and these display larger iNKT cell populations within the liver, spleen, and bone marrow. Mekk1 signaling controls splenic and liver iNKT cell expansion in response to glycolipid antigen. Lck(Cre/+)Map3k1(f/f) mice have enhanced liver damage in response to glycolipid antigen. Mekk1 regulates Jnk activation in iNKT cells and binds and transfers Lys63-linked poly-ubiquitin onto Carma1. Map3k1 is critical for the regulation of p27(Kip1) (encoded by Cdkn1b). PMID:26774476

  17. T-Cell-Specific Deletion of Map3k1 Reveals the Critical Role for Mekk1 and Jnks in Cdkn1b-Dependent Proliferative Expansion

    PubMed Central

    Suddason, Tesha; Anwar, Saba; Charlaftis, Nikolaos; Gallagher, Ewen

    2016-01-01

    Summary MAPK signaling is important for T lymphocyte development, homeostasis, and effector responses. To better understand the role of Mekk1 (encoded by Map3k1) in T cells, we conditionally deleted Map3k1 in LckCre/+Map3k1f/f mice, and these display larger iNKT cell populations within the liver, spleen, and bone marrow. Mekk1 signaling controls splenic and liver iNKT cell expansion in response to glycolipid antigen. LckCre/+Map3k1f/f mice have enhanced liver damage in response to glycolipid antigen. Mekk1 regulates Jnk activation in iNKT cells and binds and transfers Lys63-linked poly-ubiquitin onto Carma1. Map3k1 is critical for the regulation of p27Kip1 (encoded by Cdkn1b). PMID:26774476

  18. Supernova and cosmic rays

    NASA Technical Reports Server (NTRS)

    Wefel, J. P.

    1981-01-01

    A general overview of supernova astronomy is presented, followed by a discussion of the relationship between SN and galactic cosmic rays. Pre-supernova evolution is traced to core collapse, explosion, and mass ejection. The two types of SN light curves are discussed in terms of their causes, and the different nucleosynthetic processes inside SNs are reviewed. Physical events in SN remnants are discussed. The three main connections between cosmic rays and SNs, the energy requirement, the acceleration mechanism, and the detailed composition of CR, are detailed.

  19. Galactic cosmic rays

    NASA Astrophysics Data System (ADS)

    Blasi, Pasquale

    2015-12-01

    The multi-facet nature of the origin of cosmic rays is such that some of the problems currently met in our path to describing available data are due to oversimplified models of CR acceleration and transport, and others to lack of knowledge of the physical processes at work in certain conditions. On the other hand, the phenomenology of cosmic rays, as arising from better observations, is getting so rich that it makes sense to try to distinguish the problems that derive from too simple views of Nature and those that are challenging the very foundations of the existing paradigms. Here I will briefly discuss some of these issues.

  20. Heterotic cosmic strings

    SciTech Connect

    Becker, Katrin; Becker, Melanie; Krause, Axel

    2006-08-15

    We show that all three conditions for the cosmological relevance of heterotic cosmic strings, the right tension, stability and a production mechanism at the end of inflation, can be met in the strongly coupled M-theory regime. Whereas cosmic strings generated from weakly coupled heterotic strings have the well-known problems posed by Witten in 1985, we show that strings arising from M5-branes wrapped around 4-cycles (divisors) of a Calabi-Yau in heterotic M-theory compactifications solve these problems in an elegant fashion.

  1. Mapping the Heavens: Probing Cosmology with Large Surveys

    ScienceCinema

    Frieman, Joshua [Fermilab

    2009-09-01

    This talk will provide an overview of recent and on-going sky surveys, focusing on their implications for cosmology. I will place particular emphasis on the Sloan Digital Sky Survey, the most ambitious mapping of the Universe yet undertaken, showing a virtual fly-through of the survey that reveals the large-scale structure of the galaxy distribution. Recent measurements of this large-scale structure, in combination with observations of the cosmic microwave background, have provided independent evidence for a Universe dominated by dark matter and dark energy as well as insights into how galaxies and larger-scale structures formed. Future planned surveys will build on these foundations to probe the history of the cosmic expansion--and thereby the dark energy--with greater precision.

  2. High Precision Cosmology with the Cosmic Background Radiation

    NASA Astrophysics Data System (ADS)

    Farhang, Marzieh

    In this thesis we investigate the two cosmic epochs of inflation and recombination, through their imprints on the temperature and polarization anisotropies of the cosmic microwave background radiation. To probe the early universe we develop a map-based maximum-likelihood estimator to measure the amplitude of inflation-induced gravity waves, parametrized by r, from the cosmic microwave background (CMB) polarization maps. Being optimal by construction, the estimator avoids E-B mixing, a possible source of contamination in the tiny B-mode detection, the target of many current and near future CMB experiments. We explore the leakage from the E- to the B-mode of polarization by using this estimator to study the linear response of the B-mode signal at different scales to variations in the E- mode power. Similarly, for various observational cases, we probe the dependence of r measurement on the signal from different scales of E and B polarization. The estimator is used to make forecasts for Spider-like and Planck-like experimental specifications and to investigate the sky-coverage optimization of the Spider-like case. We compare the forecast errors on r to the results from a similar multipole-based estimator which, by ignoring the mode-mixing, sets a lower limit on the achievable error on r. We find that an experiment with Spider-like specifications with fsky ˜ 0:02--0:2 could place a 2sigma r ≈ 0:014 bound (˜ 95% CL), which rises to 0:02 with an ℓ-dependent foreground residual left over from an assumed efficient component separation. For the Planck-like survey, a Galaxy-masked ( fsky = 0:75) sky would give 2sigmar ≈ 0:015, rising to ≈ 0:05 with the foreground residuals. We also use a novel information-based framework to compare how different generations of CMB experiments reveal information about the early universe, through their measurements of r. We also probe the epoch of recombination by investigating possible fluctuations in the free electron fraction Xe

  3. Galactic cosmic rays and nucleosynthesis

    SciTech Connect

    Kiener, Juergen

    2010-03-01

    The nucleosynthesis of the light elements Li, Be and B by galactic cosmic rays is presented. Observations of cosmic rays and the nuclear reactions responsible for Li, Be and B nucleosynthesis are described, followed by some words on propagation. At the end, some open questions concerning galactic cosmic rays are discussed.

  4. CMB temperature bispectrum induced by cosmic strings

    SciTech Connect

    Hindmarsh, Mark; Ringeval, Christophe; Suyama, Teruaki

    2009-10-15

    The cosmic microwave background (CMB) bispectrum of the temperature anisotropies induced by a network of cosmic strings is derived for small angular scales, under the assumption that the principal cause of temperature fluctuations is the Gott-Kaiser-Stebbins effect. We provide analytical expressions for all isosceles triangle configurations in Fourier space. Their overall amplitude is amplified as the inverse cube of the angle and diverges for flat triangles. The isosceles configurations generically lead to a negative bispectrum with a power-law decay l{sup -6} for large multipole l. However, collapsed triangles are found to be associated with a positive bispectrum whereas the squeezed triangles still exhibit negative values. We then compare our analytical estimates to a direct computation of the bispectrum from a set of 300 statistically independent temperature maps obtained from Nambu-Goto cosmic string simulations in a Friedmann-Lemaitre-Robertson-Walker universe. We find good agreement for the overall amplitude, the power-law behavior, and the angle dependency of the various triangle configurations. At l{approx}500 the cosmic string Gott-Kaiser-Stebbins effect contributes approximately the same equilateral CMB bispectrum amplitude as an inflationary model with |f{sub NL}{sup loc}|{approx_equal}10{sup 3}, if the strings contribute about 10% of the temperature power spectrum at l=10. Current bounds on f{sub NL} are not derived using cosmic string bispectrum templates, and so our f{sub NL} estimate cannot be used to derive bounds on strings. However it does suggest that string bispectrum templates should be included in the search of CMB non-Gaussianities.

  5. CMB temperature bispectrum induced by cosmic strings

    NASA Astrophysics Data System (ADS)

    Hindmarsh, Mark; Ringeval, Christophe; Suyama, Teruaki

    2009-10-01

    The cosmic microwave background (CMB) bispectrum of the temperature anisotropies induced by a network of cosmic strings is derived for small angular scales, under the assumption that the principal cause of temperature fluctuations is the Gott-Kaiser-Stebbins effect. We provide analytical expressions for all isosceles triangle configurations in Fourier space. Their overall amplitude is amplified as the inverse cube of the angle and diverges for flat triangles. The isosceles configurations generically lead to a negative bispectrum with a power-law decay ℓ-6 for large multipole ℓ. However, collapsed triangles are found to be associated with a positive bispectrum whereas the squeezed triangles still exhibit negative values. We then compare our analytical estimates to a direct computation of the bispectrum from a set of 300 statistically independent temperature maps obtained from Nambu-Goto cosmic string simulations in a Friedmann-Lemaître-Robertson-Walker universe. We find good agreement for the overall amplitude, the power-law behavior, and the angle dependency of the various triangle configurations. At ℓ˜500 the cosmic string Gott-Kaiser-Stebbins effect contributes approximately the same equilateral CMB bispectrum amplitude as an inflationary model with |fNLloc|≃103, if the strings contribute about 10% of the temperature power spectrum at ℓ=10. Current bounds on fNL are not derived using cosmic string bispectrum templates, and so our fNL estimate cannot be used to derive bounds on strings. However it does suggest that string bispectrum templates should be included in the search of CMB non-Gaussianities.

  6. Searching for signatures of cosmic string wakes in 21cm redshift surveys using Minkowski Functionals

    SciTech Connect

    McDonough, Evan; Brandenberger, Robert H. E-mail: rhb@hep.physics.mcgill.ca

    2013-02-01

    Minkowski Functionals are a powerful tool for analyzing large scale structure, in particular if the distribution of matter is highly non-Gaussian, as it is in models in which cosmic strings contribute to structure formation. Here we apply Minkowski functionals to 21cm maps which arise if structure is seeded by a scaling distribution of cosmic strings embeddded in background fluctuations, and then test for the statistical significance of the cosmic string signals using the Fisher combined probability test. We find that this method allows for detection of cosmic strings with Gμ > 5 × 10{sup −8}, which would be improvement over current limits by a factor of about 3.

  7. Our Cosmic Connection

    ERIC Educational Resources Information Center

    Young, Donna L.

    2005-01-01

    To help students understand the connection that Earth and the solar system have with the cosmic cycles of stellar evolution, and to give students an appreciation of the beauty and elegance of celestial phenomena, the Chandra X-Ray Center (CXC) educational website contains a stellar evolution module that is available free to teachers. In this…

  8. Heavy cosmic strings

    SciTech Connect

    Donaire, M.; Rajantie, A.

    2006-03-15

    We argue that cosmic strings with high winding numbers generally form in first-order gauge symmetry breaking phase transitions, and we demonstrate this using computer simulations. These strings are heavier than single-winding strings and therefore more easily observable. Their cosmological evolution may also be very different.

  9. Cosmic Rays: "A Thin Rain of Charged Particles."

    ERIC Educational Resources Information Center

    Friedlander, Michael

    1990-01-01

    Discussed are balloons and electroscopes, understanding cosmic rays, cosmic ray paths, isotopes and cosmic-ray travel, sources of cosmic rays, and accelerating cosmic rays. Some of the history of the discovery and study of cosmic rays is presented. (CW)

  10. Genome-wide association study reveals genetic architecture of eating behavior in pigs and its implications for humans obesity by comparative mapping.

    PubMed

    Do, Duy Ngoc; Strathe, Anders Bjerring; Ostersen, Tage; Jensen, Just; Mark, Thomas; Kadarmideen, Haja N

    2013-01-01

    This study was aimed at identifying genomic regions controlling feeding behavior in Danish Duroc boars and its potential implications for eating behavior in humans. Data regarding individual daily feed intake (DFI), total daily time spent in feeder (TPD), number of daily visits to feeder (NVD), average duration of each visit (TPV), mean feed intake per visit (FPV) and mean feed intake rate (FR) were available for 1130 boars. All boars were genotyped using the Illumina Porcine SNP60 BeadChip. The association analyses were performed using the GenABEL package in the R program. Sixteen SNPs were found to have moderate genome-wide significance (p<5E-05) and 76 SNPs had suggestive (p<5E-04) association with feeding behavior traits. MSI2 gene on chromosome (SSC) 14 was very strongly associated with NVD. Thirty-six SNPs were located in genome regions where QTLs have previously been reported for behavior and/or feed intake traits in pigs. The regions: 64-65 Mb on SSC 1, 124-130 Mb on SSC 8, 63-68 Mb on SSC 11, 32-39 Mb and 59-60 Mb on SSC 12 harbored several signifcant SNPs. Synapse genes (GABRR2, PPP1R9B, SYT1, GABRR1, CADPS2, DLGAP2 and GOPC), dephosphorylation genes (PPM1E, DAPP1, PTPN18, PTPRZ1, PTPN4, MTMR4 and RNGTT) and positive regulation of peptide secretion genes (GHRH, NNAT and TCF7L2) were highly significantly associated with feeding behavior traits. This is the first GWAS to identify genetic variants and biological mechanisms for eating behavior in pigs and these results are important for genetic improvement of pig feed efficiency. We have also conducted pig-human comparative gene mapping to reveal key genomic regions and/or genes on the human genome that may influence eating behavior in human beings and consequently affect the development of obesity and metabolic syndrome. This is the first translational genomics study of its kind to report potential candidate genes for eating behavior in humans. PMID:23977060

  11. Cosmic Rays at Earth

    NASA Astrophysics Data System (ADS)

    Grieder, P. K. F.

    In 1912 Victor Franz Hess made the revolutionary discovery that ionizing radiation is incident upon the Earth from outer space. He showed with ground-based and balloon-borne detectors that the intensity of the radiation did not change significantly between day and night. Consequently, the sun could not be regarded as the sources of this radiation and the question of its origin remained unanswered. Today, almost one hundred years later the question of the origin of the cosmic radiation still remains a mystery. Hess' discovery has given an enormous impetus to large areas of science, in particular to physics, and has played a major role in the formation of our current understanding of universal evolution. For example, the development of new fields of research such as elementary particle physics, modern astrophysics and cosmology are direct consequences of this discovery. Over the years the field of cosmic ray research has evolved in various directions: Firstly, the field of particle physics that was initiated by the discovery of many so-called elementary particles in the cosmic radiation. There is a strong trend from the accelerator physics community to reenter the field of cosmic ray physics, now under the name of astroparticle physics. Secondly, an important branch of cosmic ray physics that has rapidly evolved in conjunction with space exploration concerns the low energy portion of the cosmic ray spectrum. Thirdly, the branch of research that is concerned with the origin, acceleration and propagation of the cosmic radiation represents a great challenge for astrophysics, astronomy and cosmology. Presently very popular fields of research have rapidly evolved, such as high-energy gamma ray and neutrino astronomy. In addition, high-energy neutrino astronomy may soon initiate as a likely spin-off neutrino tomography of the Earth and thus open a unique new branch of geophysical research of the interior of the Earth. Finally, of considerable interest are the biological

  12. Composite interval mapping and mixed models reveal QTL associated with performance and carcass traits on chicken chromosomes 1, 3, and 4.

    PubMed

    Rosario, M F; Gazaffi, R; Moura, A S A M T; Ledur, M C; Coutinho, L L; Garcia, A A F

    2014-02-01

    Interval mapping (IM) implemented in QTL Express or GridQTL is widely used, but presents some limitations, such as restriction to a fixed model, risk of mapping two QTL when there may be only one and no discrimination of two or more QTL using both cofactors located on the same and other chromosomes. These limitations were overcome with composite interval mapping (CIM). We reported QTL associated with performance and carcass traits on chicken chromosomes 1, 3, and 4 through implementation of CIM and analysis of phenotypic data using mixed models. Thirty-four microsatellite markers were used to genotype 360 F2 chickens from crosses between males from a layer line and females from a broiler line. Sixteen QTL were mapped using CIM and 14 QTL with IM. Furthermore, of those 30 QTL, six were mapped only when CIM was used: for body weight at 35 days (first and third peaks on GGA4), body weight at 41 days (GGA1B and second peak on GGA4), and weights of back and legs (both on GGA4). Three new regions had evidence for QTL presence: one on GGA1B associated with feed intake 35-41 d at 404 cM (LEI0107-ADL0183) and two on GGA4 associated with weight of back at 163 cM (LEI0076-MCW0240) and weight gain 35-41 d, feed efficiency 35-41 d and weight of legs at 241 cM (LEI0085-MCW0174). We dissected one more linked QTL on GGA4, where three QTL for BW35 and two QTL for BW41 were mapped. Therefore, these new regions mapped here need further investigations using high-density SNP to confirm these QTL and identify candidate genes associated with those traits. PMID:24288072

  13. First-generation linkage map of the gray, short-tailed opossum, Monodelphis domestica, reveals genome-wide reduction in female recombination rates.

    PubMed Central

    Samollow, Paul B; Kammerer, Candace M; Mahaney, Susan M; Schneider, Jennifer L; Westenberger, Scott J; VandeBerg, John L; Robinson, Edward S

    2004-01-01

    The gray, short-tailed opossum, Monodelphis domestica, is the most extensively used, laboratory-bred marsupial resource for basic biologic and biomedical research worldwide. To enhance the research utility of this species, we are building a linkage map, using both anonymous markers and functional gene loci, that will enable the localization of quantitative trait loci (QTL) and provide comparative information regarding the evolution of mammalian and other vertebrate genomes. The current map is composed of 83 loci distributed among eight autosomal linkage groups and the X chromosome. The autosomal linkage groups appear to encompass a very large portion of the genome, yet span a sex-average distance of only 633.0 cM, making this the most compact linkage map known among vertebrates. Most surprising, the male map is much larger than the female map (884.6 cM vs. 443.1 cM), a pattern contrary to that in eutherian mammals and other vertebrates. The finding of genome-wide reduction in female recombination in M. domestica, coupled with recombination data from two other, distantly related marsupial species, suggests that reduced female recombination might be a widespread metatherian attribute. We discuss possible explanations for reduced female recombination in marsupials as a consequence of the metatherian characteristic of determinate paternal X chromosome inactivation. PMID:15020427

  14. Population Average T2 MRI Maps Reveal Quantitative Regional Transformations in the Degenerating Rabbit Intervertebral Disc that Vary by Lumbar Level

    PubMed Central

    Martin, John T.; Collins, Christopher M.; Mauck, Robert L.; Ikuta, Kensuke; Elliott, Dawn M.; Zhang, Yeija; Anderson, D. Greg; Vaccaro, Alexander R.; Albert, Todd J.; Arlet, Vincent; Smith, Harvey E.

    2015-01-01

    Magnetic resonance imaging (MRI) with T2-weighting is routinely performed to assess intervertebral disc degeneration. Standard clinical evaluations of MR images are qualitative, however, and do not focus on region-specific alterations in the disc. Utilizing a rabbit needle puncture model, T2 mapping was performed on injured discs to develop a quantitative description of the degenerative process following puncture. To do so, an 18G needle was inserted into four discs per rabbit (L3/L4 to L6/L7) and T2 maps were generated pre- and 4 weeks post-injury. Individual T2 maps were normalized to a disc-specific coordinate system and then averaged for pre- and post-injury population composite T2 maps. We also developed a method to automatically segment the nucleus pulposus by 2-D and 3-D curve fitting routines. Puncture injury produced alterations in MR signal intensity in a region-specific manner mirroring human degeneration. Population average T2 maps provided a quantitative representation of the injury response, and identified deviations of individual degenerate discs from the pre-injury population. We found that the response to standardized injury was modest at lower lumbar levels, likely as a result of increased disc dimensions. These tools will be valuable for the quantitative characterization of disc degeneration in future clinical and pre-clinical studies. PMID:25273831

  15. Combined linkage and association mapping reveals candidates for Scmv1, a major locus involved in resistance to sugarcane mosaic virus (SCMV) in maize

    PubMed Central

    2013-01-01

    Background Sugarcane mosaic virus (SCMV) disease causes substantial losses of grain yield and forage biomass in susceptible maize cultivars. Maize resistance to SCMV is associated with two dominant genes, Scmv1 and Scmv2, which are located on the short arm of chromosome 6 and near the centromere region of chromosome 3, respectively. We combined both linkage and association mapping to identify positional candidate genes for Scmv1. Results Scmv1 was fine-mapped in a segregating population derived from near-isogenic lines and further validated and fine-mapped using two recombinant inbred line populations. The combined results assigned the Scmv1 locus to a 59.21-kb interval, and candidate genes within this region were predicted based on the publicly available B73 sequence. None of three predicted genes that are possibly involved in the disease resistance response are similar to receptor-like resistance genes. Candidate gene–based association mapping was conducted using a panel of 94 inbred lines with variable resistance to SCMV. A presence/absence variation (PAV) in the Scmv1 region and two polymorphic sites around the Zmtrx-h gene were significantly associated with SCMV resistance. Conclusion Combined linkage and association mapping pinpoints Zmtrx-h as the most likely positional candidate gene for Scmv1. These results pave the way towards cloning of Scmv1 and facilitate marker-assisted selection for potyvirus resistance in maize. PMID:24134222

  16. Surficial Geologic Mapping Using Digital Techniques Reveals Late-Phase Basin Evolution and Role of Paleoclimate, Death Valley Junction 30' × 60' Quadrangle, California and Nevada

    NASA Astrophysics Data System (ADS)

    Slate, J.; Berry, M.; Menges, C. M.

    2010-12-01

    The recently released surficial geologic map of the Death Valley Junction 30' x 60' quadrangle at 1:100,000 scale (USGS SIM 3013) was simultaneously mapped and compiled using digital photogrammetric methods. The map area covers the central part of Death Valley and adjacent mountain ranges—the Panamint Range on the west and the Funeral Mountains on the east—as well as areas east of Death Valley including some of the Amargosa Desert, the Spring Mountains, and Pahrump Valley. We mapped six alluvial units, an eolian unit, three playa or playa-related units, lacustrine beach deposits, colluvium, and marl. Interpretation of surface morphology, tone, relative height, and map pattern in air photos enabled us to differentiate among the alluvial units, which make up about 80 percent of the surficial deposits in the map area. Systematic variations in alluvial surface morphology with age permit us to map and correlate geomorphic surfaces. Surface morphology is a product of depositional and post-depositional processes. Lithologic variations across the map area influence the tone of the alluvial units. Although young alluvial units are often light-toned due to an absence or paucity of rock varnish, they may appear dark where the source rocks are dark. Lithology also influences the development of rock varnish; fine-grained or aphanitic rocks, such as quartzite or basalt, tend to become varnished more quickly than rocks such as limestone or granite. Granite commonly disaggregates to grus before becoming varnished and limestone becomes etched. Relative height (topographic position) is useful for mapping in individual drainage basins near range fronts, but basinward, especially in tectonically inactive areas, most surfaces grade to the same base level, and relative height differs little among the alluvial units. Faulting, both the magnitude and location, also affects the map pattern of alluvial units. As faulting uplifts ranges relative to the basins, streams adjust to new base

  17. On Cosmic Magnetic Fields

    NASA Astrophysics Data System (ADS)

    Florido, E.; Battaner, E.

    2010-12-01

    Magnetic fields are present in all astrophysical media. However, many models and interpretations of observations often ignore them, because magnetic fields are difficult to handle and because they produce complicated morphological features. Here we will comment on the basic intuitive properties, which even if not completely true, provide a first guiding insight on the physics of a particular astrophysical problem. These magnetic properties are not mathematically demonstrated here. How magnetic fields evolve and how they introduce dynamical effects are considered, also including a short comment on General Relativity Magnetohydrodynamics. In a second part we consider some audacious and speculative matters. They are answers to three questions: a) How draw a cube without lifting the pencil from the paper so that when the pen passes through the same side do in the same direction? B) Are MILAGRO anisotropies miraculous? C) Do cosmic magnetic lenses exist?. The last two questions deal with issues related with the interplay between magnetic fields and cosmic ray propagation.

  18. Stable Charged Cosmic Strings

    SciTech Connect

    Weigel, H.; Quandt, M.; Graham, N.

    2011-03-11

    We study the quantum stabilization of a cosmic string by a heavy fermion doublet in a reduced version of the standard model. We show that charged strings, obtained by populating fermionic bound state levels, become stable if the electroweak bosons are coupled to a fermion that is less than twice as heavy as the top quark. This result suggests that extraordinarily large fermion masses or unrealistic couplings are not required to bind a cosmic string in the standard model. Numerically we find the most favorable string profile to be a simple trough in the Higgs vacuum expectation value of radius {approx_equal}10{sup -18} m. The vacuum remains stable in our model, because neutral strings are not energetically favored.

  19. Stable charged cosmic strings.

    PubMed

    Weigel, H; Quandt, M; Graham, N

    2011-03-11

    We study the quantum stabilization of a cosmic string by a heavy fermion doublet in a reduced version of the standard model. We show that charged strings, obtained by populating fermionic bound state levels, become stable if the electroweak bosons are coupled to a fermion that is less than twice as heavy as the top quark. This result suggests that extraordinarily large fermion masses or unrealistic couplings are not required to bind a cosmic string in the standard model. Numerically we find the most favorable string profile to be a simple trough in the Higgs vacuum expectation value of radius ≈10(-18)  m. The vacuum remains stable in our model, because neutral strings are not energetically favored. PMID:21469786

  20. COSMIC monthly progress report

    NASA Technical Reports Server (NTRS)

    1994-01-01

    Activities of the Computer Software Management and Information Center (COSMIC) are summarized for the month of April 1994. Tables showing the current inventory of programs available from COSMIC are presented and program processing and evaluation activities are summarized. Five articles were prepared for publication in the NASA Tech Brief Journal. These articles (included in this report) describe the following software items: GAP 1.0 - Groove Analysis Program, Version 1.0; SUBTRANS - Subband/Transform MATLAB Functions for Image Processing; CSDM - COLD-SAT Dynamic Model; CASRE - Computer Aided Software Reliability Estimation; and XOPPS - OEL Project Planner/Scheduler Tool. Activities in the areas of marketing, customer service, benefits identification, maintenance and support, and disseminations are also described along with a budget summary.

  1. Cosmic Plasma Wakefield Acceleration

    NASA Astrophysics Data System (ADS)

    Chen, Pisin; Tajima, Toshiki; Takahashi, Yoshiyuki

    2002-10-01

    A cosmic acceleration mechanism is introduced which is based on the wakefields excited by the Alfven shocks in a relativistically flowing plasma. We show that there exists a threshold condition for transparency below which the accelerating particle is collision-free and suffers little energy loss in the plasma medium. The stochastic encounters of the random accelerating-decelerating phases results in a power-law energy spectrum: f([epsilon]) [is proportional to] 1/[epsilon]2. As an example, we discuss the possible production of super-GZK ultra high energy cosmic rays (UHECR) in the atmosphere of gamma ray bursts. The estimated event rate in our model agrees with that from UHECR observations. [copyright] 2002 American Institute of Physics

  2. Galactic cosmic ray composition

    NASA Technical Reports Server (NTRS)

    Meyer, J. P.

    1986-01-01

    An assessment is given of the galactic cosmic ray source (GCRS) elemental composition and its correlation with first ionization potential. The isotopic composition of heavy nuclei; spallation cross sections; energy spectra of primary nuclei; electrons; positrons; local galactic reference abundances; comparison of solar energetic particles and solar coronal compositions; the hydrogen; lead; nitrogen; helium; and germanium deficiency problems; and the excess of elements are among the topics covered.

  3. Carl Sagan's Cosmic Connection

    NASA Astrophysics Data System (ADS)

    Sagan, Carl; Agel, Jerome

    2000-08-01

    Foreword Freeman Dyson; Personal reflections Ann Druyan; Preface; Part I. Cosmic Perspective: 1. A transitional animal; 2. The Unicorn of Cetus; 3. A message from earth; 4. A message to earth; 5. Experiments in utopias; 6. Chauvinism; 7. Space exploration as a human enterprise I. The scientific interest; 8. Space exploration as a human enterprise II. The public interest; 9. Space exploration as a human enterprise III. The historical interest; Part II. The Solar System: 10. On teaching the first grade; 11. 'The ancient and legendary Gods of old'; 12. The Venus detective story; 13. Venus is hell; 14. Science and 'intelligence'; 15. The moons of Barsoom; 16. The mountains of Mars I. Observations from earth; 17. The mountains of Mars II. Observations from space; 18. The canals of Mars; 19. The lost pictures of Mars; 20. The Ice Age and the cauldron; 21. Beginnings and ends of the Earth; 22. Terraforming the plants; 23. The exploration and utlization of the solar system; Part III. Beyond the Solar System: 24. Some of my best friends are dolphins; 25. 'Hello, central casting? Send me twenty extraterrestrials'; 26. The cosmic connection; 27. Extraterrestrial life: an idea whose time has come; 28. Has the Earth been visited?; 29. A search strategy for detecting extraterrestrial intelligence; 30. If we succeed 31. Cables, drums, and seashells; 32. The night freight to the stars; 33. Astroengineering; 34. Twenty questions: a classification of cosmic civilisations; 35. Galactic cultural exchanges; 36. A passage to elsewhere; 37. Starfolk I. A Fable; 38. Starfolk II. A future; 39. Starfolk III. The cosmic Cheshire cats; Epilog David Morrison; Index.

  4. A Warped Cosmic String

    SciTech Connect

    Slagter, R. J.

    2010-06-23

    We present a cosmic string solution in Einstein-Yang-Mills Gauss-Bonnet theory on a warped 5 dimensional space-time conform the Randall-Sundrum-2 theory. In a simplipied model, we find an exact solutions with exponential decreasing or periodic warp function. In a more general setting, where the metric- and Yang-Mills components depend on both scales and one of the YM components resides in the bulk, we find a time dependent numerical solution.

  5. Cosmic Rays in Thunderstorms

    NASA Astrophysics Data System (ADS)

    Buitink, Stijn; Scholten, Olaf; van den Berg, Ad; Ebert, Ute

    2013-04-01

    Cosmic Rays in Thunderstorms Cosmic rays are protons and heavier nuclei that constantly bombard the Earth's atmosphere with energies spanning a vast range from 109 to 1021 eV. At typical altitudes up to 10-20 km they initiate large particle cascades, called extensive air showers, that contain millions to billions of secondary particles depending on their initial energy. These particles include electrons, positrons, hadrons and muons, and are concentrated in a compact particle front that propagates at relativistic speed. In addition, the shower leaves behind a trail of lower energy electrons from ionization of air molecules. Under thunderstorm conditions these electrons contribute to the electrical and ionization processes in the cloud. When the local electric field is strong enough the secondary electrons can create relativistic electron run-away avalanches [1] or even non-relativistic avalanches. Cosmic rays could even trigger lightning inception. Conversely, strong electric fields also influence the development of the air shower [2]. Extensive air showers emit a short (tens of nanoseconds) radio pulse due to deflection of the shower particles in the Earth's magnetic field [3]. Antenna arrays, such as AERA, LOFAR and LOPES detect these pulses in a frequency window of roughly 10-100 MHz. These systems are also sensitive to the radiation from discharges associated to thunderstorms, and provide a means to study the interaction of cosmic ray air showers and the electrical processes in thunderstorms [4]. In this presentation we discuss the involved radiation mechanisms and present analyses of thunderstorm data from air shower arrays [1] A. Gurevich et al., Phys. Lett. A 165, 463 (1992) [2] S. Buitink et al., Astropart. Phys. 33, 1 (2010) [3] H. Falcke et al., Nature 435, 313 (2005) [4] S. Buitink et al., Astron. & Astrophys. 467, 385 (2007)

  6. Cosmic ray modulation

    NASA Astrophysics Data System (ADS)

    Agarwal Mishra, Rekha; Mishra, Rajesh Kumar

    2016-07-01

    Propagation of cosmic rays to and inside the heliosphere, encounter an outward moving solar wind with cyclic magnetic field fluctuation and turbulence, causing convection and diffusion in the heliosphere. Cosmic ray counts from the ground ground-based neutron monitors at different cut of rigidity show intensity changes, which are anti-correlated with sunspot numbers. They also lose energy as they propagate towards the Earth and experience various types of modulations due to different solar activity indices. In this work, we study the first three harmonics of cosmic ray intensity on geo-magnetically quiet days over the period 1965-2014 for Beijing, Moscow and Tokyo neutron monitoring stations located at different cut off rigidity. The amplitude of first harmonic remains high for low cutoff rigidity as compared to high cutoff rigidity on quiet days. The diurnal amplitude significantly decreases during solar activity minimum years. The diurnal time of maximum significantly shifts to an earlier time as compared to the corotational direction having different cutoff rigidities. The time of maximum for first harmonic significantly shifts towards later hours and for second harmonic it shifts towards earlier hours at low cutoff rigidity station as compared to the high cut off rigidity station on quiet days. The amplitude of second/third harmonics shows a good positive correlation with solar wind velocity, while the others (i.e. amplitude and phase) have no significant correlation on quiet days. The amplitude and direction of the anisotropy on quiet days does not show any significant dependence on high-speed solar wind streams for these neutron monitoring stations of different cutoff rigidity threshold. Keywords: cosmic ray, cut off rigidity, quiet days, harmonics, amplitude, phase.

  7. FORMOSAT-3/COSMIC Mission

    NASA Astrophysics Data System (ADS)

    Cheng, F. C.; Cheng, C.

    2006-12-01

    Six identical micro-satellites of the FORMOSAT-3/COSMIC mission were successfully launched on April 14, 2006 US time. The mission is a Taiwan-US collaborative project jointly carried out by the National Space Organization (NSPO) in Taiwan and the University Corporation for Atmospheric Research (UCAR) in the United States. Each satellite carries three science payloads: a Global Positioning System (GPS) receiver which measures the amplitude and phase of GPS signals, a Tri-Band Beacon (TBB) transmitter which emits three coherent frequencies at 150 MHz, 400 MHz and 1066.7 MHz, and a Tiny Ionospheric Photometer (TIP) which measures photon emission at 135.6 nm wavelength. The FORMOSAT-3/COSMIC mission provides the first satellite constellation to obtain vertical profiles in near-real time of temperature, pressure, and water vapor in the neutral atmosphere and electron density in the ionosphere. Using the GPS radio occultation (RO) technique, the satellite constellation will take at least 2,500 measurements of vertical profiles of atmospheric air density, temperature and water vapor and ionospheric electron density every 24 hours around the globe, filling in current atmospheric data gaps over the oceans and the polar region. Combining the GPS RO data with the data from TIP and ground TBB receivers, the 3D global distribution of electron density and scintillation in the ionosphere can be obtained for space weather monitoring and modeling. Taiwan science teams are conducting an Intensive Observation Period (IOP) campaign to cross validate RO data with other observations (ground based radiosonde, weather satellites, and balloons, radars, ionosondes, etc.), and to assess the impact of FORMOSAT-3/COSMIC observations on predictions of typhoon intensity and track over eastern Asia as well as ionospheric response to storms and substorms. Highlights of early results from the FORMOSAT- 3/COSMIC mission will be presented.

  8. A cosmic superfluid phase

    NASA Technical Reports Server (NTRS)

    Gradwohl, Ben-Ami

    1991-01-01

    The universe may have undergone a superfluid-like phase during its evolution, resulting from the injection of nontopological charge into the spontaneously broken vacuum. In the presence of vortices this charge is identified with angular momentum. This leads to turbulent domains on the scale of the correlation length. By restoring the symmetry at low temperatures, the vortices dissociate and push the charges to the boundaries of these domains. The model can be scaled (phenomenologically) to very low energies, it can be incorporated in a late time phase transition and form large scale structure in the boundary layers of the correlation volumes. The novel feature of the model lies in the fact that the dark matter is endowed with coherent motion. The possibilities of identifying this flow around superfluid vortices with the observed large scale bulk motion is discussed. If this identification is possible, then the definite prediction can be made that a more extended map of peculiar velocities would have to reveal large scale circulations in the flow pattern.

  9. How to disentangle the Cosmic Web?

    NASA Astrophysics Data System (ADS)

    Shandarin, Sergei; Medvedev, Mikhail

    2015-04-01

    The Cosmic Web is a complicated highly-entangled geometrical object formed from remarkably simple - Gaussian - initial conditions. The full complexity of the Web can be fully appreciated in the six-dimensional phase space only, which study is, however, impractical due to numerous reasons. Instead, we suggest to use Lagrangian submanifold, i.e., the mapping x = x(q) , where x and q are three dimensional vectors representing Eulerian and Lagrangian coordinates. Being fully equivalent in dynamical sense to the phase space, it has the advantage of being a single valued and also metric space. In addition, we propose a new computational paradigm for the analysis of substructure of the Cosmic Web in cosmological cold dark matter (CDM) simulations. We introduce a new data-field - the flip-flop field - which carries wealth of information about the history and dynamics of the structure formation in the universe. The flip-flop (FF) field is an ordered data set in Lagrangian space representing the number of sign reversals of an elementary volume of each collisionless fluid element represented by a computational particle in a N-body simulation. This FF-field is effectively a multi-stream counter of each substructure element of the Cosmic Web. We demonstrate that the very rich subst Partially supported by DOE Grant DE-FG02-07ER54940 and NSF Grant AST-1209665.

  10. Cosmic-ray record in solar system matter

    NASA Technical Reports Server (NTRS)

    Reedy, R. C.; Arnold, J. R.; Lal, D.

    1983-01-01

    The interaction of galactic cosmic rays (GCR) and solar cosmic rays (SCR) with bodies in the solar system is discussed, and what the record of that interaction reveals about the history of the solar system is considered. The influence of the energy, charge, and mass of the particles on the interaction is addressed, showing long-term average fluxes of solar protons, predicted production rates for heavy-nuclei tracks and various radionuclides as a function of depth in lunar rock, and integral fluxes of protons emitted by solar flares. The variation of the earth's magnetic field, the gardening of the lunar surface, and the source of meteorites and cosmic dust are studied using the cosmic ray record. The time variation of GCR, SCR, and VH and VVH nuclei is discussed for both the short and the long term.

  11. The cosmic background explorer

    SciTech Connect

    Gulkis, G. ); Lubin, P.M. ); Meyer, S.S. ); Silverberg, R.F.

    1990-01-01

    Late last year the National Aeronautics and Space Administration launched its first satellite dedicated to the study of phenomena related to the origins of the universe. The satellite, called the Cosmic Background Explorer (COBE), carries three complementary detectors that will make fundamental measurements of the celestial radiation. Part of that radiation is believed to have originated in processes that occurred at the very dawn of the universe. By measuring the remnant radiation at wavelengths from one micrometer to one centimeter across the entire sky, scientists hope to be able to solve many mysteries regarding the origin and evolution of the early universe. Unfortunately, these radiative relics of the early universe are weak and veiled by local astrophysical and terrestrial sources of radiation. The wavelengths of the various cosmic components may also overlap, thereby making the understanding of the diffuse celestial radiation a challenge. Nevertheless, the COBE instruments, with their full-sky coverage, high sensitivity to a wide range of wavelengths and freedom from interference from the earth's atmosphere, will constitute for astrophysicists an observatory of unprecedented sensitivity and scope. The interesting cosmic signals will then be separated from one another and from noncosmic radiation sources by a comprehensive analysis of the data.

  12. Relativistic heavy cosmic rays

    NASA Technical Reports Server (NTRS)

    Mewaldt, R. A.; Fernandez, J. I.; Israel, M. H.; Klarmann, J.; Binns, W. R.

    1972-01-01

    During three balloon flights of a 1 sq m sr ionization chamber/Cerenkov counter detector system, measurements were made of the atmospheric attenuation, flux, and charge composition of cosmic ray nuclei with 16 is less than or = Z is less than or = 30 and rigidity greater than 4.5 GV. The attenuation mean free path in air of VH (20 less than or = Z less than or = 30) nuclei is found to be 19.7 + or - 1.6 g/sq cm, a value somewhat greater than the best previous measurement. The attenuation mean free path of iron is found to be 15.6 + or - 2.2 g/sq cm, consistent with predictions of geometric cross-section formulae. An absolute flux of VH nuclei 10 to 20% higher than earlier experiments at similar geomagnetic cutoff and level of solar activity was measured. The relative abundances of even-charged nuclei are found to be in good agreement with results of other recent high resolution counter experiments. The observed cosmic ray chemical composition implies relative abundances at the cosmic ray source of Ca/Fe = 0.12 + or - 0.04 and S/Fe = 0.14 + or - 0.05.

  13. SPACE: the spectroscopic all-sky cosmic explorer

    NASA Astrophysics Data System (ADS)

    Cimatti, A.; Robberto, M.; Baugh, C.; Beckwith, S. V. W.; Content, R.; Daddi, E.; De Lucia, G.; Garilli, B.; Guzzo, L.; Kauffmann, G.; Lehnert, M.; Maccagni, D.; Martínez-Sansigre, A.; Pasian, F.; Reid, I. N.; Rosati, P.; Salvaterra, R.; Stiavelli, M.; Wang, Y.; Zapatero Osorio, M.; Balcells, M.; Bersanelli, M.; Bertoldi, F.; Blaizot, J.; Bottini, D.; Bower, R.; Bulgarelli, A.; Burgasser, A.; Burigana, C.; Butler, R. C.; Casertano, S.; Ciardi, B.; Cirasuolo, M.; Clampin, M.; Cole, S.; Comastri, A.; Cristiani, S.; Cuby, J.-G.; Cuttaia, F.; de Rosa, A.; Sanchez, A. Diaz; di Capua, M.; Dunlop, J.; Fan, X.; Ferrara, A.; Finelli, F.; Franceschini, A.; Franx, M.; Franzetti, P.; Frenk, C.; Gardner, Jonathan P.; Gianotti, F.; Grange, R.; Gruppioni, C.; Gruppuso, A.; Hammer, F.; Hillenbrand, L.; Jacobsen, A.; Jarvis, M.; Kennicutt, R.; Kimble, R.; Kriek, M.; Kurk, J.; Kneib, J.-P.; Le Fevre, O.; Macchetto, D.; MacKenty, J.; Madau, P.; Magliocchetti, M.; Maino, D.; Mandolesi, N.; Masetti, N.; McLure, R.; Mennella, A.; Meyer, M.; Mignoli, M.; Mobasher, B.; Molinari, E.; Morgante, G.; Morris, S.; Nicastro, L.; Oliva, E.; Padovani, P.; Palazzi, E.; Paresce, F.; Perez Garrido, A.; Pian, E.; Popa, L.; Postman, M.; Pozzetti, L.; Rayner, J.; Rebolo, R.; Renzini, A.; Röttgering, H.; Schinnerer, E.; Scodeggio, M.; Saisse, M.; Shanks, T.; Shapley, A.; Sharples, R.; Shea, H.; Silk, J.; Smail, I.; Spanó, P.; Steinacker, J.; Stringhetti, L.; Szalay, A.; Tresse, L.; Trifoglio, M.; Urry, M.; Valenziano, L.; Villa, F.; Villo Perez, I.; Walter, F.; Ward, M.; White, R.; White, S.; Wright, E.; Wyse, R.; Zamorani, G.; Zacchei, A.; Zeilinger, W. W.; Zerbi, F.

    2009-03-01

    We describe the scientific motivations, the mission concept and the instrumentation of SPACE, a class-M mission proposed for concept study at the first call of the ESA Cosmic-Vision 2015-2025 planning cycle. SPACE aims to produce the largest three-dimensional evolutionary map of the Universe over the past 10 billion years by taking near-IR spectra and measuring redshifts for more than half a billion galaxies at 0 < z < 2 down to AB~23 over 3 π sr of the sky. In addition, SPACE will also target a smaller sky field, performing a deep spectroscopic survey of millions of galaxies to AB~26 and at 2 < z < 10 +. These goals are unreachable with ground-based observations due to the ≈500 times higher sky background (see e.g. Aldering, LBNL report number LBNL-51157, 2001). To achieve the main science objectives, SPACE will use a 1.5 m diameter Ritchey-Chretien telescope equipped with a set of arrays of Digital Micro-mirror Devices covering a total field of view of 0.4 deg2, and will perform large-multiplexing multi-object spectroscopy (e.g. ≈6000 targets per pointing) at a spectral resolution of R~400 as well as diffraction-limited imaging with continuous coverage from 0.8 to 1.8 μm. Owing to the depth, redshift range, volume coverage and quality of its spectra, SPACE will reveal with unique sensitivity most of the fundamental cosmological signatures, including the power spectrum of density fluctuations and its turnover. SPACE will also place high accuracy constraints on the dark energy equation of state parameter and its evolution by measuring the baryonic acoustic oscillations imprinted when matter and radiation decoupled, the distance-luminosity relation of cosmological supernovae, the evolution of the cosmic expansion rate, the growth rate of cosmic large-scale structure, and high- z galaxy clusters. The datasets from the SPACE mission will represent a long lasting legacy for the whole astronomical community whose data will be mined for many years to come.

  14. Searching for Cosmic Strings in the Cosmic Microwave Background:

    NASA Astrophysics Data System (ADS)

    Wu, Jiun-Huei Proty

    The role of cosmic defects in cosmology is entering its new phase—as a test for several fundamental physics, including unification theories and inflation. We discuss how to use the Cosmic Microwave Background (CMB) to detect cosmic strings, a type of cosmic defects, and how to use this result to constrain the underlying physics. In particular, we use the simulations for the Array for Microwave Background Anisotropy (AMiBA) to demonstrate the power of this approach. The required resolution and sensitivity in such a method are discussed, and so is the possible scientific impact.

  15. Effects of anisotropic dynamics on cosmic strings

    SciTech Connect

    Kunze, Kerstin E.

    2011-08-01

    The dynamics of cosmic strings is considered in anisotropic backgrounds. In particular, the behaviour of infinitely long straight cosmic strings and of cosmic string loops is determined. Small perturbations of a straight cosmic string are calculated. The relevance of these results is discussed with respect to the possible observational imprints of an anisotropic phase on the behaviour of a cosmic string network.

  16. Symbols of a cosmic order

    NASA Astrophysics Data System (ADS)

    Madjid, F. Hadi; Myers, John M.

    2016-10-01

    The world runs on networks over which signals communicate sequences of symbols, e.g. numerals. Examining both engineered and natural communications networks reveals an unsuspected order that depends on contact with an unpredictable entity. This order has three roots. The first is a proof within quantum theory that no evidence can ever determine its explanation, so that an agent choosing an explanation must do so unpredictably. The second root is the showing that clocks that step computers do not "tell time" but serve as self-adjusting symbol-handling agents that regulate "logically synchronized" motion in response to unpredictable disturbances. Such a clock-agent has a certain independence as well as the capacity to communicate via unpredictable symbols with other clock-agents and to adjust its own tick rate in response to that communication. The third root is the noticing of unpredictable symbol exchange in natural systems, including the transmission of symbols found in molecular biology. We introduce a symbol-handling agent as a role played in some cases by a person, for example a physicist who chooses an explanation of given experimental outcomes, and in other cases by some other biological entity, and in still other cases by an inanimate device, such as a computer-based detector used in physical measurements. While we forbear to try to explain the propensity of agents at all levels from cells to civilizations to form and operate networks of logically synchronized symbol-handling agents, we point to this propensity as an overlooked cosmic order, an order structured by the unpredictability ensuing from the proof. Appreciating the cosmic order leads to a conception of agency that replaces volition by unpredictability and reconceives the notion of objectivity in a way that makes a place for agency in the world as described by physics. Some specific implications for physics are outlined.

  17. Integrated consensus map of cultivated peanut and wild relatives reveals structures of the A and B genomes of Arachis and divergence of the legume genomes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The complex, tetraploid genome structure of peanut (Arachis hypogaea) has obstructed advances in genetics and genomics in the species. The aim of this study is to understand the genome structure of Arachis by developing a high-density integrated consensus map. Three recombinant inbred line populatio...

  18. Pervasive Sex-Linked Effects on Transcription Regulation As Revealed by Expression Quantitative Trait Loci Mapping in Lake Whitefish Species Pairs (Coregonus sp., Salmonidae)

    PubMed Central

    Derome, N.; Bougas, B.; Rogers, S. M.; Whiteley, A. R.; Labbe, A.; Laroche, J.; Bernatchez, L.

    2008-01-01

    Mapping of expression quantitative trait loci (eQTL) is a powerful means for elucidating the genetic architecture of gene regulation. Yet, eQTL mapping has not been applied toward investigating the regulation architecture of genes involved in the process of population divergence, ultimately leading to speciation events. Here, we conducted an eQTL mapping experiment to compare the genetic architecture of transcript regulation in adaptive traits, differentiating the recently evolved limnetic (dwarf) and benthic (normal) species pairs of lake whitefish. The eQTL were mapped in three data sets derived from an F1 hybrid-dwarf backcrossed family: the entire set of 66 genotyped individuals and the two sexes treated separately. We identified strikingly more eQTL in the female data set (174), compared to both male (54) and combined (33) data sets. The majority of these genes were not differentially expressed between male and female progeny of the backcross family, thus providing evidence for a strong pleiotropic sex-linked effect in transcriptomic regulation. The subtelomeric region of a linkage group segregating in females encompassed >50% of all eQTL, which exhibited the most pronounced additive effects. We also conducted a direct comparison of transcriptomic profiles between pure dwarf and normal progeny reared in controlled conditions. We detected 34 differentially expressed transcripts associated with eQTL segregating only in sex-specific data sets and mostly belonging to functional groups that differentiate dwarf and normal whitefish in natural populations. Therefore, these eQTL are not related to interindividual variation, but instead to the adaptive and historical genetic divergence between dwarf and normal whitefish. This study exemplifies how the integration of genetic and transcriptomic data offers a strong means for dissecting the functional genomic response to selection by separating mapping family-specific effects from genetic factors under selection

  19. The Origin of Cosmic Rays: What can GLAST Say?

    NASA Technical Reports Server (NTRS)

    Ormes, Jonathan F.; Digel, Seith; Moskalenko, Igor V.; Moiseev, Alexander; Williamson, Roger

    2000-01-01

    Gamma rays in the band from 30 MeV to 300 GeV, used in combination with direct measurements and with data from radio and X-ray bands, provide a powerful tool for studying the origin of Galactic cosmic rays. Gamma-ray Large Area Space Telescope (GLAST) with its fine 10-20 arcmin angular resolution will be able to map the sites of acceleration of cosmic rays and their interactions with interstellar matter, It will provide information that is necessary to study the acceleration of energetic particles in supernova shocks, their transport in the interstellar medium and penetration into molecular clouds.

  20. Polarization observations with the Cosmic Background Imager.

    PubMed

    Readhead, A C S; Myers, S T; Pearson, T J; Sievers, J L; Mason, B S; Contaldi, C R; Bond, J R; Bustos, R; Altamirano, P; Achermann, C; Bronfman, L; Carlstrom, J E; Cartwright, J K; Casassus, S; Dickinson, C; Holzapfel, W L; Kovac, J M; Leitch, E M; May, J; Padin, S; Pogosyan, D; Pospieszalski, M; Pryke, C; Reeves, R; Shepherd, M C; Torres, S

    2004-10-29

    Polarization observations of the cosmic microwave background with the Cosmic Background Imager from September 2002 to May 2004 provide a significant detection of the E-mode polarization and reveal an angular power spectrum of polarized emission showing peaks and valleys that are shifted in phase by half a cycle relative to those of the total intensity spectrum. This key agreement between the phase of the observed polari