Science.gov

Sample records for maps reveal cosmic

  1. Mapping the Cosmic Dawn

    NASA Astrophysics Data System (ADS)

    Furlanetto, Steven

    The following sections are included: * A Brief History of Our Universe: From Soup to Galaxies * The Hidden Cosmic Dawn * The Solution: Flipping Spins * The Spin-Flip Transition as an Astronomical Tool * Foiled!: Early Cosmology with the Spin-Flip Transition * Spin-Flip Radiation Holds the Key to Observing the Cosmic Dawn * The Spin-Flip Background: The First Stars * The Spin-Flip Background: The First Black Holes * The Spin-Flip Background: The Epoch of Reionization * FM Radio Antennae as Cosmic Observatories * Piles and Tiles of Antennae: Mapping the Spin-Flip Background * Mountains to Scale: Challenges to Observing the Spin-Flip Background * Sound and Fury, Signifying Statistics * An Explosion of Telescopes * Dreams for the Future * An Unfinished Story

  2. 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

  3. Topological analysis of COBE-DMR cosmic microwave background maps

    NASA Astrophysics Data System (ADS)

    Torres, Sergio

    1994-03-01

    Geometric characteristics of random fields are exploited to test the consistency of density perturbation model spectra with Cosmic Background Explorer (COBE) data. These cosmic microwave background (CMB) maps are analyzed using the number of anisotropy hot spots and their boundary curvature. CMB maps which account for instrumental effects and sky coverage are Monte Carlo generated. These simulations show that a scale-invariant Harrison-Zeldovich primordial Gaussian density fluctuation spectrum is consistent with the data. The CMB fluctuation coherence angle, based on boundary curvature, gives a spectral index n = 1.2 +/- 0.3.

  4. 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

  5. Mapping of cosmic radiation dose in Croatia.

    PubMed

    Poje, M; Vuković, B; Radolić, V; Miklavčić, I; Faj, D; Varga Pajtler, M; Planinić, J

    2012-01-01

    The Earth is continually bombarded by high-energy particles coming from the outer space and the sun. These particles, termed cosmic radiation, interact with nuclei of atmospheric constituents and decrease in intensity with depth in the atmosphere. Measurements of photon and gamma radiation, performed with a Radiameter at 1 m above the ground, indicated dose rates of 50-100 nSv/h. The neutron dose rate was measured with the CR-39 track etch detector calibrated by the CERN-EU high-energy Reference Field (CERF) facility. Correlation between neutron dose rates and altitudes at 36 sites was examined in order to obtain a significant positive correlation coefficient; the resulting linear regression enabled estimation of a neutron dose at particular altitude. The measured neutron dose rate in Osijek (altitude of 89 m, latitude of 45.31° N) was 110 nSv/h.

  6. Footprints of Loop I on Cosmic Microwave Background maps

    SciTech Connect

    Hausegger, Sebastian von; Liu, Hao; Sarkar, Subir; Mertsch, Philipp E-mail: liuhao@nbi.dk E-mail: s.sarkar@physics.ox.ac.uk

    2016-03-01

    Cosmology has made enormous progress through studies of the cosmic microwave background, however the subtle signals being now sought such as B-mode polarisation due to primordial gravitational waves are increasingly hard to disentangle from residual Galactic foregrounds in the derived CMB maps. We revisit our finding that on large angular scales there are traces of the nearby old supernova remnant Loop I in the WMAP 9-year map of the CMB and confirm this with the new SMICA map from the Planck satellite.

  7. Extragalactic sources in Cosmic Microwave Background maps

    SciTech Connect

    Zotti, G. De; Castex, G.; González-Nuevo, J.; Cai, Z.-Y.; Delabrouille, J.; Herranz, D.; Bonavera, L.; Serjeant, S.; Bilicki, M.; Andreani, P. E-mail: gcastex@sissa.it E-mail: marcos.lopez.caniego@sciops.esa.int; and others

    2015-06-01

    We discuss the potential of a next generation space-borne CMB experiment for studies of extragalactic sources with reference to COrE+, a project submitted to ESA in response to the call for a Medium-size mission (M4). We consider three possible options for the telescope size: 1 m, 1.5 m and 2 m (although the last option is probably impractical, given the M4 boundary conditions). The proposed instrument will be far more sensitive than Planck and will have a diffraction-limited angular resolution. These properties imply that even the 1 m telescope option will perform substantially better than Planck for studies of extragalactic sources. The source detection limits as a function of frequency have been estimated by means of realistic simulations taking into account all the relevant foregrounds. Predictions for the various classes of extragalactic sources are based on up-to-date models. The most significant improvements over Planck results are presented for each option. COrE+ will provide much larger samples of truly local star-forming galaxies (by about a factor of 8 for the 1 m telescope, of 17 for 1.5 m, of 30 for 2 m), making possible analyses of the properties of galaxies (luminosity functions, dust mass functions, star formation rate functions, dust temperature distributions, etc.) across the Hubble sequence. Even more interestingly, COrE+ will detect, at |b| > 30°, thousands of strongly gravitationally lensed galaxies (about 2,000, 6,000 and 13,000 for the 1 m, 1.5 m and 2 m options, respectively). Such large samples are of extraordinary astrophysical and cosmological value in many fields. Moreover, COrE+ high frequency maps will be optimally suited to pick up proto-clusters of dusty galaxies, i.e. to investigate the evolution of large scale structure at larger redshifts than can be reached by other means. Thanks to its high sensitivity COrE+ will also yield a spectacular advance in the blind detection of extragalactic sources in polarization: we expect that

  8. Magnetic Visions: Mapping Cosmic Magnetism with LOFAR and SKA

    NASA Astrophysics Data System (ADS)

    Beck, R.

    2009-08-01

    The origin of magnetic fields in the Universe is an open problem in astrophysics and fundamental physics. ``Cosmic Magnetism'' has been accepted as Key Science Project both for the Low Frequency Array (LOFAR, under construction) and the planned Square Kilometre Array (SKA). At low frequencies LOFAR and SKA will allow to map the structure of weak magnetic fields in the outer regions and halos of galaxies, in galaxy clusters and in the Milky Way. High-resolution polarization observations at high frequencies with the SKA will trace magnetic fields in the disks and central regions of galaxies in unprecedented detail. All-sky surveys of Faraday rotation measures (RM) towards polarized background sources will be used to model the structure and strength of the magnetic fields in the Milky Way, the interstellar medium of galaxies and the intergalactic medium. The new method of ``RM Synthesis'', applied to spectro-polarimetric data cubes, will separate RM components from different distances and allow 3-D ``Faraday tomography''. Magnetic fields in distant galaxies and clusters and in intergalactic filaments will be searched for by deep imaging of weak synchrotron emission and of RM towards background sources. This will open a new era in the observation of cosmic magnetic fields.

  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. Radiometer system to map the cosmic background radiation

    NASA Technical Reports Server (NTRS)

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

    1978-01-01

    A 33-GHz airborne radiometer system has been developed 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 deg apart in the sky. In 40 min of observing, the radiometer can measure the anisotropy of the microwave background with an accuracy of plus or minus 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 deg, 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, Calif.

  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.

  12. 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.

  13. 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.

  14. 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

  15. 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

  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. Cosmic X-ray Flashes Reveal Their Distance

    NASA Astrophysics Data System (ADS)

    2003-09-01

    Astronomers using X-ray, radio, and optical telescopes have announced a big leap in solving the origin of mysterious objects known as X-ray flashes (XRFs) by finding that they originate from blue star forming galaxies. This discovery of the cosmic distance scale effectively ends the widely-held speculation that XRFs are the death-cries from stars exploding in the infant universe. X-ray flashes resemble a lower energy and longer-duration version of a gamma-ray burst, an energetic explosion thought to signal the death of a massive star. The properties of XRFs led to speculation that they were gamma-ray bursts that occurred less than a few billion years after the Big Bang, and whose light had been subsequently weakened and time-stretched by the expansion of the universe. "Now that the very distant origin has been ruled out, X-ray flashes could be due to exploding massive stars, just like gamma-ray bursts" explained Dr. Joshua Bloom at the Harvard-Smithsonian Center for Astrophysics in Cambridge, Mass., lead author on the paper announcing the results to be published in The Astrophysical Journal. Bloom continued: "But the explosion from an X-ray flash would need to contain less matter or less energy than a typical gamma-ray burst. Alternatively, X-ray flashes could be gamma-ray bursts viewed off-axis." These results are being discussed at the "30th Anniversary of the Discovery of Gamma-ray Bursts" conference currently being held in Sante Fe, New Mexico. The location of the sources studied by Bloom's group required a careful coordination of NASA's Chandra X-ray Observatory and Hubble Space Telescope, along with the National Radio Astronomy Observatory's Very Large Array (VLA) in Socorro, New Mexico. Chandra and the VLA provided a precise location of the fading X-ray and radio "afterglow" of two X-ray flashes known as XRF 011030 and XRF 020427. The Hubble Space Telescope was used to identify and study galaxies at these locations and estimate their distances to between

  18. 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

  19. Making cosmic microwave background temperature and polarization maps with MADAM

    NASA Astrophysics Data System (ADS)

    Keihänen, E.; Keskitalo, R.; Kurki-Suonio, H.; Poutanen, T.; Sirviö, A.-S.

    2010-02-01

    MADAM is a CMB map-making code, designed to make temperature and polarization maps of time-ordered data of total power experiments like Planck. The algorithm is based on the destriping technique, but it also makes use of known noise properties in the form of a noise prior. The method in its early form was presented in an earlier work by Keihänen et al. (2005, MNRAS, 360, 390). In this paper we present an update of the method, extended to non-averaged data, and include polarization. In this method the baseline length is a freely adjustable parameter, and destriping can be performed at a different map resolution than that of the final maps. We show results obtained with simulated data. This study is related to Planck LFI activities.

  20. 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)

  1. 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.

  2. 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.

  3. Language plasticity revealed by electroencephalogram mapping.

    PubMed

    Foz, Flávia B; Lucchini, Fábio L P; Palimieri, Samanta; Rocha, Armando F; Rodella, Ednilson C; Rondó, Andrea G; Cardoso, Marly B; Ramazzini, Patrícia B; Leite, Claudia C

    2002-02-01

    Reasoning is the result of the computations made by intelligent systems, for instance those in the brain. It is not an abstract concept because calculations performed by computations are very concrete transactions among the different central processing unit components. Entropy measurements are proposed here to disclose the plasticity of the cerebral processing associated with language comprehension in video game playing. It is also assumed that entropy may be evaluated from the correlation coefficients obtained for the game event-related activity calculated for the different electroencephalogram derivations in the 10/20 system. The brain mapping derived from these entropy measurements clearly demonstrates the reallocation of speech functions to right brain areas when the classic left language circuits are damaged during prenatal life.

  4. 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.

  5. 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.

  6. 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.

  7. Optimal cosmic microwave background map-making in the presence of cross-correlated noise

    NASA Astrophysics Data System (ADS)

    de Gasperis, G.; Buzzelli, A.; Cabella, P.; de Bernardis, P.; Vittorio, N.

    2016-08-01

    Aims: We present an extension of the ROMA map-making algorithm for the generation of optimal cosmic microwave background polarization maps. The new code allows for a possible cross-correlated noise component among the detectors of a CMB experiment. A promising application is the forthcoming LSPE balloon-borne experiment, which is devoted to the accurate observation of CMB polarization at large angular scales. Methods: We generalized the noise covariance matrix in time domain to account for all the off-diagonal terms due to the detector cross-talk. Hence, we performed preliminary forecasts of the LSPE-SWIPE instrument. Results: We found that considering the noise cross-correlation among the detectors results in a more realistic estimate of the angular power spectra. In particular, the extended ROMA algorithm has provided a considerable reduction of the spectra error bars. We expect that this improvement could be crucial in constraining the B-mode polarization at the largest scales.

  8. Revealing the z ~ 2.5 Cosmic Web with 3D Lyα Forest Tomography: a Deformation Tensor Approach

    NASA Astrophysics Data System (ADS)

    Lee, Khee-Gan; White, Martin

    2016-11-01

    Studies of cosmological objects should take into account their positions within the cosmic web of large-scale structure. Unfortunately, the cosmic web has only been extensively mapped at low redshifts (z\\lt 1), using galaxy redshifts as tracers of the underlying density field. At z\\gt 1, the required galaxy densities are inaccessible for the foreseeable future, but 3D reconstructions of Lyα forest absorption in closely separated background QSOs and star-forming galaxies already offer a detailed window into z˜ 2-3 large-scale structure. We quantify the utility of such maps for studying the cosmic web by using realistic z = 2.5 Lyα forest simulations matched to observational properties of upcoming surveys. A deformation tensor-based analysis is used to classify voids, sheets, filaments, and nodes in the flux, which are compared to those determined from the underlying dark matter (DM) field. We find an extremely good correspondence, with 70% of the volume in the flux maps correctly classified relative to the DM web, and 99% classified to within one eigenvalue. This compares favorably to the performance of galaxy-based classifiers with even the highest galaxy densities from low-redshift surveys. We find that narrow survey geometries can degrade the recovery of the cosmic web unless the survey is ≳ 60 {h}-1 {Mpc} or ≳ 1 deg on the sky. We also examine halo abundances as a function of the cosmic web, and find a clear dependence as a function of flux overdensity, but little explicit dependence on the cosmic web. These methods will provide a new window on cosmological environments of galaxies at this very special time in galaxy formation, “high noon,” and on overall properties of cosmological structures at this epoch.

  9. Mapping the Cosmic Web with the largest all-sky surveys

    NASA Astrophysics Data System (ADS)

    Bilicki, Maciej; Peacock, John A.; Jarrett, Thomas H.; Cluver, Michelle E.; Steward, Louise

    2016-10-01

    Our view of the low-redshift Cosmic Web has been revolutionized by galaxy redshift surveys such as 6dFGS, SDSS and 2MRS. However, the trade-off between depth and angular coverage limits a systematic three-dimensional account of the entire sky beyond the Local Volume (z < 0.05). In order to reliably map the Universe to cosmologically significant depths over the full celestial sphere, one must draw on multiwavelength datasets and state-of-the-art photometric redshift techniques. We have undertaken a dedicated program of cross-matching the largest photometric all-sky surveys - 2MASS, WISE and SuperCOSMOS - to obtain accurate redshift estimates of millions of galaxies. The first outcome of these efforts - the 2MASS Photometric Redshift catalog (2MPZ, Bilicki et al. 2014a) - has been publicly released and includes almost 1 million galaxies with a mean redshift of z=0.08. Here we summarize how this catalog was constructed and how using the WISE mid-infrared sample together with SuperCOSMOS optical data allows us to push to redshift shells of z~ 0.2 -0.3 on unprecedented angular scales. Our catalogs, with ~ 20 million sources in total, provide access to cosmological volumes crucial for studies of local galaxy flows (clustering dipole, bulk flow) and cross-correlations with the cosmic microwave background such as the integrated Sachs-Wolfe effect or lensing studies.

  10. Maps of random walks on complex networks reveal community structure.

    PubMed

    Rosvall, Martin; Bergstrom, Carl T

    2008-01-29

    To comprehend the multipartite organization of large-scale biological and social systems, we introduce an information theoretic approach that reveals community structure in weighted and directed networks. We use the probability flow of random walks on a network as a proxy for information flows in the real system and decompose the network into modules by compressing a description of the probability flow. The result is a map that both simplifies and highlights the regularities in the structure and their relationships. We illustrate the method by making a map of scientific communication as captured in the citation patterns of >6,000 journals. We discover a multicentric organization with fields that vary dramatically in size and degree of integration into the network of science. Along the backbone of the network-including physics, chemistry, molecular biology, and medicine-information flows bidirectionally, but the map reveals a directional pattern of citation from the applied fields to the basic sciences.

  11. 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.

  12. 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.

  13. 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.

  14. Robust likelihoods for inflationary gravitational waves from maps of cosmic microwave background polarization

    NASA Astrophysics Data System (ADS)

    Switzer, Eric R.; Watts, Duncan J.

    2016-09-01

    The B -mode polarization of the cosmic microwave background provides a unique window into tensor perturbations from inflationary gravitational waves. Survey effects complicate the estimation and description of the power spectrum on the largest angular scales. The pixel-space likelihood yields parameter distributions without the power spectrum as an intermediate step, but it does not have the large suite of tests available to power spectral methods. Searches for primordial B -modes must rigorously reject and rule out contamination. Many forms of contamination vary or are uncorrelated across epochs, frequencies, surveys, or other data treatment subsets. The cross power and the power spectrum of the difference of subset maps provide approaches to reject and isolate excess variance. We develop an analogous joint pixel-space likelihood. Contamination not modeled in the likelihood produces parameter-dependent bias and complicates the interpretation of the difference map. We describe a null test that consistently weights the difference map. Excess variance should either be explicitly modeled in the covariance or be removed through reprocessing the data.

  15. 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.

  16. PROBING THE DARK FLOW SIGNAL IN WMAP 9 -YEAR AND PLANCK COSMIC MICROWAVE BACKGROUND MAPS

    SciTech Connect

    Atrio-Barandela, F.; Kashlinsky, A.; Ebeling, H.; Fixsen, D. J.; Kocevski, D. E-mail: Alexander.Kashlinsky@nasa.gov E-mail: Dale.Fixsen@nasa.gov

    2015-09-10

    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.

  17. Accelerating the cosmic microwave background map-making procedure through preconditioning

    NASA Astrophysics Data System (ADS)

    Szydlarski, M.; Grigori, L.; Stompor, R.

    2014-12-01

    Estimation of the sky signal from sequences of time ordered data is one of the key steps in cosmic microwave background (CMB) data analysis, commonly referred to as the map-making problem. Some of the most popular and general methods proposed for this problem involve solving generalised least-squares (GLS) equations with non-diagonal noise weights given by a block-diagonal matrix with Toeplitz blocks. In this work, we study new map-making solvers potentially suitable for applications to the largest anticipated data sets. They are based on iterative conjugate gradient (CG) approaches enhanced with novel, parallel, two-level preconditioners. We apply the proposed solvers to examples of simulated non-polarised and polarised CMB observations and a set of idealised scanning strategies with sky coverage ranging from a nearly full sky down to small sky patches. We discuss their implementation for massively parallel computational platforms and their performance for a broad range of parameters that characterise the simulated data sets in detail. We find that our best new solver can outperform carefully optimised standard solvers used today by a factor of as much as five in terms of the convergence rate and a factor of up to four in terms of the time to solution, without significantly increasing the memory consumption and the volume of inter-processor communication. The performance of the new algorithms is also found to be more stable and robust and less dependent on specific characteristics of the analysed data set. We therefore conclude that the proposed approaches are well suited to address successfully challenges posed by new and forthcoming CMB data sets.

  18. 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.

  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. 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.

  1. 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.

  2. 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

  3. Mapping Compound Cosmic Telescopes Containing Multiple Projected Cluster-scale Halos

    NASA Astrophysics Data System (ADS)

    Ammons, S. Mark; Wong, Kenneth C.; Zabludoff, Ann I.; Keeton, Charles R.

    2014-01-01

    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 × 1015 M ⊙. From 1151 MMT Hectospec spectra of galaxies down to i 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 × 1014-2 × 1015 M ⊙, 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 zs = 10 are [1.2, 3.8] arcmin2 for 0850 and [2.3, 6.7] arcmin2 for 1306. In deep Subaru Suprime-Cam imaging of beam 0850, we serendipitously discover a candidate multiply imaged V-dropout source at z 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 zs = 10 to [1.8, 4.2] arcmin2, an étendue range comparable to that of MACS 0717+3745 and El Gordo, two of the most powerful single cluster lenses known

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

    PubMed

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

    2014-03-01

    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.

  5. 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.

  6. 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.

  7. Revealing W51C as a Cosmic Ray Source Using Fermi-LAT Data

    NASA Astrophysics Data System (ADS)

    Jogler, T.; Funk, S.

    2016-01-01

    Supernova remnants (SNRs) are commonly believed to be the primary sources of Galactic cosmic rays. Despite intensive study of the non-thermal emission of many SNRs the identification of the accelerated particle type relies heavily on assumptions of ambient-medium parameters that are only loosely constrained. Compelling evidence of hadronic acceleration can be provided by detecting a strong roll-off in the secondary γ-ray spectrum below the {π }0 production threshold energy of about 135 MeV, the so called “pion bump.” Here we use five years of Fermi-Large Area Telescope data to study the spectrum above 60 MeV of the middle-aged SNR W51C. A clear break in the power-law γ-ray spectrum at {E}{{break}}=290+/- 20 {{MeV}} is detected with 9σ significance and we show that this break is most likely associated with the energy production threshold of {π }0mesons. A high-energy break in the γ-ray spectrum at about 2.7 GeV is found with 7.5σ significance. The spectral index at energies beyond this second break is {{{Γ }}}2={2.52}-0.07+0.06 and closely matches the spectral index derived by the MAGIC Collaboration above 75 GeV. Therefore our analysis provides strong evidence to explain the γ-ray spectrum of W51C by a single particle population of protons with a momentum spectrum best described by a broken power law with break momentum {p}{{break}}∼ 80 {{G}}{{e}}{{V}}/c. W51C is the third middle-aged SNR that displays compelling evidence for cosmic-ray acceleration and thus strengthens the case of SNRs as the main source of Galactic cosmic rays.

  8. 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

  9. Cosmic ray heavy ion LET mapping for aluminum, silicon, and tissue targets

    NASA Technical Reports Server (NTRS)

    Stassinopoulos, E. G.; Barth, J. M.; Jordan, T. M.

    1987-01-01

    Linear energy transfer (LET) values in aluminum, silicon, and tissue targets have been calculated for 31 galactic cosmic ray ion species in eight different units. The values are described for single event upset (SEU) effect assessments or radiobiological evaluations. The data are presented in graphical and tabular form.

  10. Genome-wide Mapping of Drug-DNA Interactions in Cells with COSMIC (Crosslinking of Small Molecules to Isolate Chromatin)

    PubMed Central

    Erwin, Graham S.; Grieshop, Matthew P.; Bhimsaria, Devesh; Eguchi, Asuka; Rodríguez-Martínez, José A.; Ansari, Aseem Z.

    2016-01-01

    The genome is the target of some of the most effective chemotherapeutics, but most of these drugs lack DNA sequence specificity, which leads to dose-limiting toxicity and many adverse side effects. Targeting the genome with sequence-specific small molecules may enable molecules with increased therapeutic index and fewer off-target effects. N-methylpyrrole/N-methylimidazole polyamides are molecules that can be rationally designed to target specific DNA sequences with exquisite precision. And unlike most natural transcription factors, polyamides can bind to methylated and chromatinized DNA without a loss in affinity. The sequence specificity of polyamides has been extensively studied in vitro with cognate site identification (CSI) and with traditional biochemical and biophysical approaches, but the study of polyamide binding to genomic targets in cells remains elusive. Here we report a method, the crosslinking of small molecules to isolate chromatin (COSMIC), that identifies polyamide binding sites across the genome. COSMIC is similar to chromatin immunoprecipitation (ChIP), but differs in two important ways: (1) a photocrosslinker is employed to enable selective, temporally-controlled capture of polyamide binding events, and (2) the biotin affinity handle is used to purify polyamide–DNA conjugates under semi-denaturing conditions to decrease DNA that is non-covalently bound. COSMIC is a general strategy that can be used to reveal the genome-wide binding events of polyamides and other genome-targeting chemotherapeutic agents. PMID:26863565

  11. Genome-wide Mapping of Drug-DNA Interactions in Cells with COSMIC (Crosslinking of Small Molecules to Isolate Chromatin).

    PubMed

    Erwin, Graham S; Grieshop, Matthew P; Bhimsaria, Devesh; Eguchi, Asuka; Rodríguez-Martínez, José A; Ansari, Aseem Z

    2016-01-20

    The genome is the target of some of the most effective chemotherapeutics, but most of these drugs lack DNA sequence specificity, which leads to dose-limiting toxicity and many adverse side effects. Targeting the genome with sequence-specific small molecules may enable molecules with increased therapeutic index and fewer off-target effects. N-methylpyrrole/N-methylimidazole polyamides are molecules that can be rationally designed to target specific DNA sequences with exquisite precision. And unlike most natural transcription factors, polyamides can bind to methylated and chromatinized DNA without a loss in affinity. The sequence specificity of polyamides has been extensively studied in vitro with cognate site identification (CSI) and with traditional biochemical and biophysical approaches, but the study of polyamide binding to genomic targets in cells remains elusive. Here we report a method, the crosslinking of small molecules to isolate chromatin (COSMIC), that identifies polyamide binding sites across the genome. COSMIC is similar to chromatin immunoprecipitation (ChIP), but differs in two important ways: (1) a photocrosslinker is employed to enable selective, temporally-controlled capture of polyamide binding events, and (2) the biotin affinity handle is used to purify polyamide-DNA conjugates under semi-denaturing conditions to decrease DNA that is non-covalently bound. COSMIC is a general strategy that can be used to reveal the genome-wide binding events of polyamides and other genome-targeting chemotherapeutic agents.

  12. 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.

  13. 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.

  14. 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

  15. 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.

  16. Measuring cosmic velocities with 21 cm intensity mapping and galaxy redshift survey cross-correlation dipoles

    NASA Astrophysics Data System (ADS)

    Hall, Alex; Bonvin, Camille

    2017-02-01

    We investigate the feasibility of measuring the effects of peculiar velocities in large-scale structure using the dipole of the redshift-space cross-correlation function. We combine number counts of galaxies with brightness-temperature fluctuations from 21 cm intensity mapping, demonstrating that the dipole may be measured at modest significance (≲2 σ ) by combining the upcoming radio survey Canadian Hydrogen Intensity Mapping Experiment with the future redshift surveys of Dark Energy Spectroscopic Instrument (DESI) and Euclid. More significant measurements (≲10 σ ) will be possible by combining intensity maps from the Square Kilometre Array (SKA) with these of DESI or Euclid, and an even higher significance measurement (≲100 σ ) may be made by combining observables completely internally to the SKA. We account for effects such as contamination by wide-angle terms, interferometer noise and beams in the intensity maps, nonlinear enhancements to the power spectrum, stacking multiple populations, sensitivity to the magnification slope, and the possibility that number counts and intensity maps probe the same tracers. We also derive a new expression for the covariance matrix of multitracer redshift-space correlation function estimators with arbitrary orientation weights, which may be useful for upcoming surveys aiming at measuring redshift-space clustering with multiple tracers.

  17. Active Interaction Mapping Reveals the Hierarchical Organization of Autophagy.

    PubMed

    Kramer, Michael H; Farré, Jean-Claude; Mitra, Koyel; Yu, Michael Ku; Ono, Keiichiro; Demchak, Barry; Licon, Katherine; Flagg, Mitchell; Balakrishnan, Rama; Cherry, J Michael; Subramani, Suresh; Ideker, Trey

    2017-02-16

    We have developed a general progressive procedure, Active Interaction Mapping, to guide assembly of the hierarchy of functions encoding any biological system. Using this process, we assemble an ontology of functions comprising autophagy, a central recycling process implicated in numerous diseases. A first-generation model, built from existing gene networks in Saccharomyces, captures most known autophagy components in broad relation to vesicle transport, cell cycle, and stress response. Systematic analysis identifies synthetic-lethal interactions as most informative for further experiments; consequently, we saturate the model with 156,364 such measurements across autophagy-activating conditions. These targeted interactions provide more information about autophagy than all previous datasets, producing a second-generation ontology of 220 functions. Approximately half are previously unknown; we confirm roles for Gyp1 at the phagophore-assembly site, Atg24 in cargo engulfment, Atg26 in cytoplasm-to-vacuole targeting, and Ssd1, Did4, and others in selective and non-selective autophagy. The procedure and autophagy hierarchy are at http://atgo.ucsd.edu/.

  18. 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

  19. Linkage mapping reveals sex-dimorphic map distances in a passerine bird

    PubMed Central

    Hansson, Bengt; Åkesson, Mikael; Slate, Jon; Pemberton, Josephine M

    2005-01-01

    Linkage maps are lacking for many highly influential model organisms in evolutionary research, including all passerine birds. Consequently, their full potential as research models is severely hampered. Here, we provide a partial linkage map and give novel estimates of sex-specific recombination rates in a passerine bird, the great reed warbler (Acrocephalus arundinaceus). Linkage analysis of genotypic data at 51 autosomal microsatellites and seven markers on the Z-chromosome (one of the sex chromosomes) from an extended pedigree resulted in 12 linkage groups with 2–8 loci. A striking feature of the map was the pronounced sex-dimorphism: males had a substantially lower recombination rate than females, which resulted in a suppressed autosomal map in males (sum of linkage groups: 110.2 cM) compared to females (237.2 cM; female/male map ratio: 2.15). The sex-specific recombination rates will facilitate the building of a denser linkage map and cast light on hypotheses about sex-specific recombination rates. PMID:16191642

  20. 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.

  1. Conservation and rewiring of functional modules revealed by an epistasis map in fission yeast.

    PubMed

    Roguev, Assen; Bandyopadhyay, Sourav; Zofall, Martin; Zhang, Ke; Fischer, Tamas; Collins, Sean R; Qu, Hongjing; Shales, Michael; Park, Han-Oh; Hayles, Jacqueline; Hoe, Kwang-Lae; Kim, Dong-Uk; Ideker, Trey; Grewal, Shiv I; Weissman, Jonathan S; Krogan, Nevan J

    2008-10-17

    An epistasis map (E-MAP) was constructed in the fission yeast, Schizosaccharomyces pombe, by systematically measuring the phenotypes associated with pairs of mutations. This high-density, quantitative genetic interaction map focused on various aspects of chromosome function, including transcription regulation and DNA repair/replication. The E-MAP uncovered a previously unidentified component of the RNA interference (RNAi) machinery (rsh1) and linked the RNAi pathway to several other biological processes. Comparison of the S. pombe E-MAP to an analogous genetic map from the budding yeast revealed that, whereas negative interactions were conserved between genes involved in similar biological processes, positive interactions and overall genetic profiles between pairs of genes coding for physically associated proteins were even more conserved. Hence, conservation occurs at the level of the functional module (protein complex), but the genetic cross talk between modules can differ substantially.

  2. 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

    2014-02-06

    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.

  3. 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.

  4. 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'…

  5. 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.

  6. 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.

  7. 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

  8. Comparative mapping reveals autosomal origin of sex chromosome in octoploid Fragaria virginiana.

    PubMed

    Spigler, Rachel B; Lewers, Kim S; Johnson, Anna L; Ashman, Tia-Lynn

    2010-01-01

    Recent evolution of separate sexes in flowering plants provides unparalleled opportunities for understanding the early stages of sex chromosome evolution, including their origin from autosomes. Moreover, the transition from combined to separate sexes can be associated with speciation via polyploidization in angiosperms, suggesting that genome doubling/merger may facilitate sterility mutations required for sex chromosome formation. To gain insight into the origin of sex chromosomes in a polyploid plant, we doubled the simple sequence repeat (SSR) density and increased genome coverage in a genetic map of octoploid Fragaria virginiana, a species purported to have a "proto-sex" chromosome, where limited recombination occurs between 2 linked "loci" carrying the male- and female-sterility mutations. Incorporation of almost 3 times the number of SSR markers into the current map facilitated complete characterization of the F. virginiana proto-sex chromosome, revealing its largely autosomal nature and the location of the sex-determining region toward the distal end. Furthermore, extensive synteny between our genetic map and a map involving diploid hermaphroditic congeners allowed assignment of linkage groups to homeologous groups, identification of the proto-sex chromosome's autosomal homoeolog, and detection of a putative rearrangement near the sex-determining region. Fine mapping and additional comparative work will shed light on the intriguing possibility that rearrangements during polyploidization were involved in the evolution of sex chromosomes in Fragaria.

  9. 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

  10. 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.

  11. Genetic mapping of sulfur assimilation genes reveals a QTL for onion bulb pungency.

    PubMed

    McCallum, John; Pither-Joyce, Meeghan; Shaw, Martin; Kenel, Fernand; Davis, Sheree; Butler, Ruth; Scheffer, John; Jakse, Jernej; Havey, Michael J

    2007-03-01

    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 'Texas Grano 438'. Linkage mapping revealed that genes encoding plastidic ferredoxin-sulfite reductase (SiR) and plastidic ATP sulfurylase (ATPS) are closely linked (1-2 cM) on chromosome 3. Inbred F(3) families derived from the F(2 )population used to construct the genetic map were grown in replicated trials in two environments and bulb pungency was evaluated as pyruvic acid or lachrymatory factor. Broad-sense heritability of pungency was estimated to be 0.78-0.80. QTL analysis revealed significant associations of both pungency and bulb soluble solids content with marker intervals on chromosomes 3 and 5, which have previously been reported to condition pleiotropic effects on bulb carbohydrate composition. Highly significant associations (LOD 3.7-8.7) were observed between ATPS and SiR Loci and bulb pungency but not with bulb solids content. This association was confirmed in two larger, independently derived F(2) families from the same cross. Single-locus models suggested that the partially dominant locus associated with these candidate genes controls 30-50% of genetic variation in pungency in these pedigrees. These markers may provide a practical means to select for lower pungency without correlated selection for lowered solids.

  12. High-Throughput Phenotyping and QTL Mapping Reveals the Genetic Architecture of Maize Plant Growth.

    PubMed

    Zhang, Xuehai; Huang, Chenglong; Wu, Di; Qiao, Feng; Li, Wenqiang; Duan, Lingfeng; Wang, Ke; Xiao, Yingjie; Chen, Guoxing; Liu, Qian; Xiong, Lizhong; Yang, Wanneng; Yan, Jianbing

    2017-03-01

    With increasing demand for novel traits in crop breeding, the plant research community faces the challenge of quantitatively analyzing the structure and function of large numbers of plants. A clear goal of high-throughput phenotyping is to bridge the gap between genomics and phenomics. In this study, we quantified 106 traits from a maize (Zea mays) recombinant inbred line population (n = 167) across 16 developmental stages using the automatic phenotyping platform. Quantitative trait locus (QTL) mapping with a high-density genetic linkage map, including 2,496 recombinant bins, was used to uncover the genetic basis of these complex agronomic traits, and 988 QTLs have been identified for all investigated traits, including three QTL hotspots. Biomass accumulation and final yield were predicted using a combination of dissected traits in the early growth stage. These results reveal the dynamic genetic architecture of maize plant growth and enhance ideotype-based maize breeding and prediction.

  13. A Consensus Map in Cultivated Hexaploid Oat Reveals Conserved Grass Synteny with Substantial Subgenome Rearrangement.

    PubMed

    Chaffin, Ashley S; Huang, Yung-Fen; Smith, Scott; Bekele, Wubishet A; Babiker, Ebrahiem; Gnanesh, Belaghihalli N; Foresman, Bradley J; Blanchard, Steven G; Jay, Jeremy J; Reid, Robert W; Wight, Charlene P; Chao, Shiaoman; Oliver, Rebekah; Islamovic, Emir; Kolb, Frederic L; McCartney, Curt; Mitchell Fetch, Jennifer W; Beattie, Aaron D; Bjørnstad, Åsmund; Bonman, J Michael; Langdon, Tim; Howarth, Catherine J; Brouwer, Cory R; Jellen, Eric N; Klos, Kathy Esvelt; Poland, Jesse A; Hsieh, Tzung-Fu; Brown, Ryan; Jackson, Eric; Schlueter, Jessica A; Tinker, Nicholas A

    2016-07-01

    Hexaploid oat ( L., 2 = 6 = 42) is a member of the Poaceae family and has a large genome (∼12.5 Gb) containing 21 chromosome pairs from three ancestral genomes. Physical rearrangements among parental genomes have hindered the development of linkage maps in this species. The objective of this work was to develop a single high-density consensus linkage map that is representative of the majority of commonly grown oat varieties. Data from a cDNA-derived single-nucleotide polymorphism (SNP) array and genotyping-by-sequencing (GBS) were collected from the progeny of 12 biparental recombinant inbred line populations derived from 19 parents representing oat germplasm cultivated primarily in North America. Linkage groups from all mapping populations were compared to identify 21 clusters of conserved collinearity. Linkage groups within each cluster were then merged into 21 consensus chromosomes, generating a framework consensus map of 7202 markers spanning 2843 cM. An additional 9678 markers were placed on this map with a lower degree of certainty. Assignment to physical chromosomes with high confidence was made for nine chromosomes. Comparison of homeologous regions among oat chromosomes and matches to orthologous regions of rice ( L.) reveal that the hexaploid oat genome has been highly rearranged relative to its ancestral diploid genomes as a result of frequent translocations among chromosomes. Heterogeneous chromosome rearrangements among populations were also evident, probably accounting for the failure of some linkage groups to match the consensus. This work contributes to a further understanding of the organization and evolution of hexaploid grass genomes.

  14. Mapping the electrophysiological marker of sleep depth reveals skill maturation in children and adolescents.

    PubMed

    Kurth, Salome; Ringli, Maya; Lebourgeois, Monique K; Geiger, Anja; Buchmann, Andreas; Jenni, Oskar G; Huber, Reto

    2012-11-01

    Electroencephalographically (EEG) recorded slow wave activity (SWA, 1-4.5Hz), reflecting the depth of sleep, is suggested to play a crucial role in synaptic plasticity. Mapping of SWA by means of high-density EEG reveals that cortical regions showing signs of maturational changes (structural and behavioral) during childhood and adolescence exhibit more SWA. Moreover, the maturation of specific skills is predicted by the topographical distribution of SWA. Thus, SWA topography may serve as a promising neuroimaging tool with prognostic potential. Finally, our data suggest that deep sleep SWA in humans is involved in cortical development that optimizes performance.

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

    PubMed

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

    2016-05-26

    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.

  16. 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.

  17. Thermal Evolution of a Failed Flux Rope Eruption Revealed by Temperature Maps

    NASA Astrophysics Data System (ADS)

    Song, H.; Zhang, J.; CHEN, Y.

    2013-12-01

    Flux rope is generally considered to be the fundamental magnetic configuration of a coronal mass ejection (CME). Recent observations suggest that hot channel or blob structures during the eruptions be the direct observational manifestation of flux ropes. In this study, we report our analysis of thermal evolution of a failed solar eruption with an apparent flux rope embedded. The thermal structure of the eruption is revealed through differential emission measure (DEM) analysis technique, which shows detailed temperature maps in both high spatial resolution and high temperature resolution based on SDO/AIA observations. Our results show that the flux rope exists in the corona before the eruption, and its temperature can quickly rise to over 10 MK within one minute of the eruption. The correlation study between the flux rope temperature and the soft x-ray flux suggests that the flux rope should be heated through the direct thermal energy release of magnetic reconnection. Further, we study the kinematic evolution process of the flux rope, in an effort to find the physical mechanism that prevents the magnetic rope eruption to become a full coronal mass ejection. This kind of study using temperature maps might reveal where and when magnetic reconnection takes place during solar eruptions.

  18. Volcanic Features in the Northwestern Hawaiian Islands Revealed by SWATH Mapping

    NASA Astrophysics Data System (ADS)

    Smith, J. R.; Miller, J.; Evans, B. K.; Johnson, P.; Weirich, J. B.

    2003-12-01

    The Northwestern Hawaiian Islands Coral Reef Ecosystem Reserve (NWHICRER) has only recently been established, and has already caused an infusion of interest and funds for studies to assess what is there to preserve and how best to do it. The Northwestern chain stretches over 2200 km to the northwest of the 775 km-long Main Hawaiian Islands (MHI). The MHI have only in recent years been systematically mapped with modern multibeam swath sonar systems and the work is not yet complete. With these southeastern islands being the population center, it is easy to imagine the lack of coverage along the Northwestern chain where no one lives except those stationed at remote outposts for scientific study. Manned and robotic submersible studies and limited multibeam mapping have been carried out by the Hawaii Undersea Research Lab every year in the NWHICRER for the past several years though focused on relatively shallow water biological sites. In late 2002, the first dedicated exploratory multibeam mapping expedition took place aboard the new University of Hawaii SWATH ship R/V Kilo Moana. While the primary mission was shallow mapping on carbonate platforms in support of the NWHICRER boundaries, a large amount of data were collected over the deeper volcanic foundations of the atolls. These surveys revealed dramatic rift zones on the same scale as those in the MHI, sea level terraces, submarine canyons cutting through the platforms with debris chutes continuing down to base of the islands, additional submarine landslide scars and debris fields in more detail than the USGS GLORIA sidescan program of the previous decade, and previously unmapped seamounts with some likely resulting from Hawaiian hot spot activity while others formed during creation of the Pacific Plate. A diving program is planned on many of these features in late 2003 and preliminary results will be presented.

  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. 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.

  1. High-Resolution Transcriptome Maps Reveal Strain-Specific Regulatory Features of Multiple Campylobacter jejuni Isolates

    PubMed Central

    Förstner, Konrad U.; Heidrich, Nadja; Reinhardt, Richard; Nieselt, Kay; Sharma, Cynthia M.

    2013-01-01

    Campylobacter jejuni is currently the leading cause of bacterial gastroenteritis in humans. Comparison of multiple Campylobacter strains revealed a high genetic and phenotypic diversity. However, little is known about differences in transcriptome organization, gene expression, and small RNA (sRNA) repertoires. Here we present the first comparative primary transcriptome analysis based on the differential RNA–seq (dRNA–seq) of four C. jejuni isolates. Our approach includes a novel, generic method for the automated annotation of transcriptional start sites (TSS), which allowed us to provide genome-wide promoter maps in the analyzed strains. These global TSS maps are refined through the integration of a SuperGenome approach that allows for a comparative TSS annotation by mapping RNA–seq data of multiple strains into a common coordinate system derived from a whole-genome alignment. Considering the steadily increasing amount of RNA–seq studies, our automated TSS annotation will not only facilitate transcriptome annotation for a wider range of pro- and eukaryotes but can also be adapted for the analysis among different growth or stress conditions. Our comparative dRNA–seq analysis revealed conservation of most TSS, but also single-nucleotide-polymorphisms (SNP) in promoter regions, which lead to strain-specific transcriptional output. Furthermore, we identified strain-specific sRNA repertoires that could contribute to differential gene regulation among strains. In addition, we identified a novel minimal CRISPR-system in Campylobacter of the type-II CRISPR subtype, which relies on the host factor RNase III and a trans-encoded sRNA for maturation of crRNAs. This minimal system of Campylobacter, which seems active in only some strains, employs a unique maturation pathway, since the crRNAs are transcribed from individual promoters in the upstream repeats and thereby minimize the requirements for the maturation machinery. Overall, our study provides new insights into

  2. Comparative organization of cattle chromosome 5 revealed by comparative mapping by annotation and sequence similarity and radiation hybrid mapping.

    PubMed

    Ozawa, A; Band, M R; Larson, J H; Donovan, J; Green, C A; Womack, J E; Lewin, H A

    2000-04-11

    A whole genome cattle-hamster radiation hybrid cell panel was used to construct a map of 54 markers located on bovine chromosome 5 (BTA5). Of the 54 markers, 34 are microsatellites selected from the cattle linkage map and 20 are genes. Among the 20 mapped genes, 10 are new assignments that were made by using the comparative mapping by annotation and sequence similarity strategy. A LOD-3 radiation hybrid framework map consisting of 21 markers was constructed. The relatively low retention frequency of markers on this chromosome (19%) prevented unambiguous ordering of the other 33 markers. The length of the map is 398.7 cR, corresponding to a ratio of approximately 2.8 cR(5,000)/cM. Type I genes were binned for comparison of gene order among cattle, humans, and mice. Multiple internal rearrangements within conserved syntenic groups were apparent upon comparison of gene order on BTA5 and HSA12 and HSA22. A similarly high number of rearrangements were observed between BTA5 and MMU6, MMU10, and MMU15. The detailed comparative map of BTA5 should facilitate identification of genes affecting economically important traits that have been mapped to this chromosome and should contribute to our understanding of mammalian chromosome evolution.

  3. 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.

  4. 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.

  5. 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.

  6. Comprehensive polyadenylation site maps in yeast and human reveal pervasive alternative polyadenylation.

    PubMed

    Ozsolak, Fatih; Kapranov, Philipp; Foissac, Sylvain; Kim, Sang Woo; Fishilevich, Elane; Monaghan, A Paula; John, Bino; Milos, Patrice M

    2010-12-10

    The emerging discoveries on the link between polyadenylation and disease states underline the need to fully characterize genome-wide polyadenylation states. Here, we report comprehensive maps of global polyadenylation events in human and yeast generated using refinements to the Direct RNA Sequencing technology. This direct approach provides a quantitative view of genome-wide polyadenylation states in a strand-specific manner and requires only attomole RNA quantities. The polyadenylation profiles revealed an abundance of unannotated polyadenylation sites, alternative polyadenylation patterns, and regulatory element-associated poly(A)(+) RNAs. We observed differences in sequence composition surrounding canonical and noncanonical human polyadenylation sites, suggesting novel noncoding RNA-specific polyadenylation mechanisms in humans. Furthermore, we observed the correlation level between sense and antisense transcripts to depend on gene expression levels, supporting the view that overlapping transcription from opposite strands may play a regulatory role. Our data provide a comprehensive view of the polyadenylation state and overlapping transcription.

  7. Cosmic wabi-sabi: Tell-tale morphological imperfections in impact crater shapes revealed by numerical analysis

    NASA Astrophysics Data System (ADS)

    Tabares-Rodenas, Pascual; Ormö, Jens; King, David T.

    2013-09-01

    Geomorphological features result from a combination of factors such as material strength, structure, and the forces of nature. An impact crater is a good example. In an ideally simple situation (e.g., a vertical impact of a spherical object into a homogeneous target), the resulting crater will obtain a perfectly circular shape. Any deviation from the perfect circle can reveal important information about the cratering process, target properties, and even the surficial environment in which the impact occurred (e.g. the presence of an atmosphere). However, irregularities in the crater shape are not always obvious. What appears to be a perfect circle may hide subtle information undetectable to the naked eye. Here we present a new method of numerical aspect classification that allows even the slightest morphological irregularities to be detected. Our method is based on a numerical analysis of dip directions of segments within a digital terrain model (DTM) of the crater rim. We show the successful application of our method on a crater with well-known polygonal shape (Meteor Crater, USA) as well as two apparently circular Martian impact craters. Our Crater Aspect Classification (CAC) can be applied on any other micro- to mega-scale structures for which a DTM can be produced, thus allowing applications to fields of science and technology within and beyond the scope of geomorphology.

  8. 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

  9. A comprehensive excitatory input map of the striatum reveals novel functional organization

    PubMed Central

    Hunnicutt, Barbara J; Jongbloets, Bart C; Birdsong, William T; Gertz, Katrina J; Zhong, Haining; Mao, Tianyi

    2016-01-01

    The striatum integrates excitatory inputs from the cortex and the thalamus to control diverse functions. Although the striatum is thought to consist of sensorimotor, associative and limbic domains, their precise demarcations and whether additional functional subdivisions exist remain unclear. How striatal inputs are differentially segregated into each domain is also poorly understood. This study presents a comprehensive map of the excitatory inputs to the mouse striatum. The input patterns reveal boundaries between the known striatal domains. The most posterior striatum likely represents the 4th functional subdivision, and the dorsomedial striatum integrates highly heterogeneous, multimodal inputs. The complete thalamo-cortico-striatal loop is also presented, which reveals that the thalamic subregions innervated by the basal ganglia preferentially interconnect with motor-related cortical areas. Optogenetic experiments show the subregion-specific heterogeneity in the synaptic properties of striatal inputs from both the cortex and the thalamus. This projectome will guide functional studies investigating diverse striatal functions. DOI: http://dx.doi.org/10.7554/eLife.19103.001 PMID:27892854

  10. 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

  11. 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.

  12. 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.

  13. 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.

  14. 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

  15. 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

  16. Comparative analysis and functional mapping of SACS mutations reveal novel insights into sacsin repeated architecture.

    PubMed

    Romano, Alessandro; Tessa, Alessandra; Barca, Amilcare; Fattori, Fabiana; de Leva, Maria Fulvia; Terracciano, Alessandra; Storelli, Carlo; Santorelli, Filippo Maria; Verri, Tiziano

    2013-03-01

    Autosomal recessive spastic ataxia of Charlevoix-Saguenay (ARSACS) is a neurological disease with mutations in SACS, encoding sacsin, a multidomain protein of 4,579 amino acids. The large size of SACS and its translated protein has hindered biochemical analysis of ARSACS, and how mutant sacsins lead to disease remains largely unknown. Three repeated sequences, called sacsin repeating region (SRR) supradomains, have been recognized, which contribute to sacsin chaperone-like activity. We found that the three SRRs are much larger (≥1,100 residues) than previously described, and organized in discrete subrepeats. We named the large repeated regions Sacsin Internal RePeaTs (SIRPT1, SIRPT2, and SIRPT3) and the subrepeats sr1, sr2, sr3, and srX. Comparative analysis of vertebrate sacsins in combination with fine positional mapping of a set of human mutations revealed that sr1, sr2, sr3, and srX are functional. Notably, the position of the pathogenic mutations in sr1, sr2, sr3, and srX appeared to be related to the severity of the clinical phenotype, as assessed by defining a severity scoring system. Our results suggest that the relative position of mutations in subrepeats will variably influence sacsin dysfunction. The characterization of the specific role of each repeated region will help in developing a comprehensive and integrated pathophysiological model of function for sacsin.

  17. The complete fragmentation history of a strombolian eruption revealed using new bomb mapping method

    NASA Astrophysics Data System (ADS)

    Colò, L.; Gurioli, L.; Harris, A. J.; Houghton, B. F.; Ripepe, M.

    2010-12-01

    During June 2008, a multidisciplinary experiment was deployed at Stromboli volcano (Aeolian Islands, Italy). Our aim was to better define the magma fragmentation associated with the mildly explosive activity for which Stromboli is famous and to improve our ability to place Stromboli in a granulometric classification of explosion products. Four tarps were deployed just below the rim of Stromboli’s SW crater to collect ash, lapilli and scoria from a single explosive event. Clasts landing on the tarps burnt holes in the plastic, effectively creating a map for the clast distribution across each area. These “maps” could be paired with geophysical data, such as seismic tremor, infrasonic pressure and thermal images, for the same events. After retrieval, digital photo mosaics were created for each tarp. The images were processed to obtain scoria size distributions based on the size of the holes left by scoriae. The scoria size distribution followed a power law revealing that the magma fragmentation process was not random, but was controlled by a single mechanism. In addition, the distributions must be the result of a single explosion, or derived from multiple explosions with identical mechanisms. Small scoria clasts that remained stuck to the tarps were measured and weighed, allowing us to obtain a reliable weight-area relationship. Using this relationship, cumulative area-distribution data were converted in cumulative mass data with the aim of obtaining mass balances.

  18. 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

  19. Neural correlates of apathy revealed by lesion mapping in participants with traumatic brain injuries.

    PubMed

    Knutson, Kristine M; Monte, Olga Dal; Raymont, Vanessa; Wassermann, Eric M; Krueger, Frank; Grafman, Jordan

    2014-03-01

    Apathy, common in neurological disorders, is defined as disinterest and loss of motivation, with a reduction in self-initiated activity. Research in diseased populations has shown that apathy is associated with variations in the volume of brain regions such as the anterior cingulate and the frontal lobes. The goal of this study was to determine the neural signatures of apathy in people with penetrating traumatic brain injuries (pTBIs), as to our knowledge, these have not been studied in this sample. We studied 176 male Vietnam War veterans with pTBIs using voxel-based lesion-symptom mapping (VLSM) and apathy scores from the UCLA Neuropsychiatric Inventory (NPI), a structured inventory of symptoms completed by a caregiver. Our results revealed that increased apathy symptoms were associated with brain damage in limbic and cortical areas of the left hemisphere including the anterior cingulate, inferior, middle, and superior frontal regions, insula, and supplementary motor area. Our results are consistent with the literature, and extend them to people with focal pTBI. Apathy is a significant symptom since it can reduce participation of the patient in family and other social interactions, and diminish affective decision-making.

  20. 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.

  1. Bayesian Mapping Reveals That Attention Boosts Neural Responses to Predicted and Unpredicted Stimuli.

    PubMed

    Garrido, Marta I; Rowe, Elise G; Halász, Veronika; Mattingley, Jason B

    2017-04-10

    Predictive coding posits that the human brain continually monitors the environment for regularities and detects inconsistencies. It is unclear, however, what effect attention has on expectation processes, as there have been relatively few studies and the results of these have yielded contradictory findings. Here, we employed Bayesian model comparison to adjudicate between 2 alternative computational models. The "Opposition" model states that attention boosts neural responses equally to predicted and unpredicted stimuli, whereas the "Interaction" model assumes that attentional boosting of neural signals depends on the level of predictability. We designed a novel, audiospatial attention task that orthogonally manipulated attention and prediction by playing oddball sequences in either the attended or unattended ear. We observed sensory prediction error responses, with electroencephalography, across all attentional manipulations. Crucially, posterior probability maps revealed that, overall, the Opposition model better explained scalp and source data, suggesting that attention boosts responses to predicted and unpredicted stimuli equally. Furthermore, Dynamic Causal Modeling showed that these Opposition effects were expressed in plastic changes within the mismatch negativity network. Our findings provide empirical evidence for a computational model of the opposing interplay of attention and expectation in the brain.

  2. 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.

  3. Association Mapping Reveals Genetic Loci Associated with Important Agronomic Traits in Lentinula edodes, Shiitake Mushroom

    PubMed Central

    Li, Chuang; Gong, Wenbing; Zhang, Lin; Yang, Zhiquan; Nong, Wenyan; Bian, Yinbing; Kwan, Hoi-Shan; Cheung, Man-Kit; Xiao, Yang

    2017-01-01

    Association mapping is a robust approach for the detection of quantitative trait loci (QTLs). Here, by genotyping 297 genome-wide molecular markers of 89 Lentinula edodes cultivars in China, the genetic diversity, population structure and genetic loci associated with 11 agronomic traits were examined. A total of 873 alleles were detected in the tested strains with a mean of 2.939 alleles per locus, and the Shannon's information index was 0.734. Population structure analysis revealed two robustly differentiated groups among the Chinese L. edodes cultivars (FST = 0.247). Using the mixed linear model, a total of 43 markers were detected to be significantly associated with four traits. The number of markers associated with traits ranged from 9 to 26, and the phenotypic variations explained by each marker varied from 12.07% to 31.32%. Apart from five previously reported markers, the remaining 38 markers were newly reported here. Twenty-one markers were identified as simultaneously linked to two to four traits, and five markers were associated with the same traits in cultivation tests performed in two consecutive years. The 43 traits-associated markers were related to 97 genes, and 24 of them were related to 10 traits-associated markers detected in both years or identified previously, 13 of which had a >2-fold expression change between the mycelium and primordium stages. Our study has provided candidate markers for marker-assisted selection (MAS) and useful clues for understanding the genetic architecture of agronomic traits in the shiitake mushroom. PMID:28261189

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

    Recent acceleration in summer surface melt on the Greenland ice sheet (GrIS) has occurred concurrently with a rapidly warming Arctic and has been connected to persistent, anomalous circulation patterns over Greenland. To identify patterns that favor enhanced GrIS surface melt and their decadal changes, we first develop a summer Arctic synoptic climatology by employing a nonlinear classification technique known as the self organizing map (SOM). This is applied to daily JJA sea level pressure (SLP) and 500 hPa geopotential height fields obtained from the Modern Era Retrospective Analysis for Research and Applications (MERRA) reanalysis product from 1979 to 2014. Model output from Modèle Atmosphérique Régional (MAR) is used to relate meteorological conditions and subsequent Greenland surface melt anomalies to particular circulation regimes. Results demonstrate that circulation patterns featuring positive SLP anomalies from Greenland to the Beaufort Sea support the largest positive surface melt anomalies, particularly over western Greenland. These patterns facilitate strong meridional transport of heat and moisture, contrasted by a dominant zonal flow across the North Atlantic during periods of low surface melt. Additionally, composites of energy balance components reveal that melt events are favored under clear conditions generating positive shortwave radiation anomalies rather than increased downwelling longwave radiation occurring with increased cloud cover. Sea surface temperature anomalies suggest that there may be a linkage between surface melt and recent sea ice loss around Greenland, though a causal relationship is not established. We assess decadal shifts in the SOM nodes, finding an increased frequency of upper level patterns favoring higher 500 hPa geopotential heights primarily over Greenland. The observed increases in GrIS melt through the time period coincides with this shift in SOM node frequency.

  5. The Nature of Genetic Variation for Complex Traits Revealed by GWAS and Regional Heritability Mapping Analyses

    PubMed Central

    Caballero, Armando; Tenesa, Albert; Keightley, Peter D.

    2015-01-01

    We use computer simulations to investigate the amount of genetic variation for complex traits that can be revealed by single-SNP genome-wide association studies (GWAS) or regional heritability mapping (RHM) analyses based on full genome sequence data or SNP chips. We model a large population subject to mutation, recombination, selection, and drift, assuming a pleiotropic model of mutations sampled from a bivariate distribution of effects of mutations on a quantitative trait and fitness. The pleiotropic model investigated, in contrast to previous models, implies that common mutations of large effect are responsible for most of the genetic variation for quantitative traits, except when the trait is fitness itself. We show that GWAS applied to the full sequence increases the number of QTL detected by as much as 50% compared to the number found with SNP chips but only modestly increases the amount of additive genetic variance explained. Even with full sequence data, the total amount of additive variance explained is generally below 50%. Using RHM on the full sequence data, a slightly larger number of QTL are detected than by GWAS if the same probability threshold is assumed, but these QTL explain a slightly smaller amount of genetic variance. Our results also suggest that most of the missing heritability is due to the inability to detect variants of moderate effect (∼0.03–0.3 phenotypic SDs) segregating at substantial frequencies. Very rare variants, which are more difficult to detect by GWAS, are expected to contribute little genetic variation, so their eventual detection is less relevant for resolving the missing heritability problem. PMID:26482794

  6. 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.

  7. 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.).

  8. An integrated linkage map reveals candidate genes underlying adaptive variation in Chinook salmon (Oncorhynchus tshawytscha).

    PubMed

    McKinney, G J; Seeb, L W; Larson, W A; Gomez-Uchida, D; Limborg, M T; Brieuc, M S O; Everett, M V; Naish, K A; Waples, R K; Seeb, J E

    2016-05-01

    Salmonids are an important cultural and ecological resource exhibiting near worldwide distribution between their native and introduced range. Previous research has generated linkage maps and genomic resources for several species as well as genome assemblies for two species. We first leveraged improvements in mapping and genotyping methods to create a dense linkage map for Chinook salmon Oncorhynchus tshawytscha by assembling family data from different sources. We successfully mapped 14 620 SNP loci including 2336 paralogs in subtelomeric regions. This improved map was then used as a foundation to integrate genomic resources for gene annotation and population genomic analyses. We anchored a total of 286 scaffolds from the Atlantic salmon genome to the linkage map to provide a framework for the placement 11 728 Chinook salmon ESTs. Previously identified thermotolerance QTL were found to colocalize with several candidate genes including HSP70, a gene known to be involved in thermal response, as well as its inhibitor. Multiple regions of the genome with elevated divergence between populations were also identified, and annotation of ESTs in these regions identified candidate genes for fitness related traits such as stress response, growth and behaviour. Collectively, these results demonstrate the utility of combining genomic resources with linkage maps to enhance evolutionary inferences.

  9. Salmonid Chromosome Evolution as Revealed by a Novel Method for Comparing RADseq Linkage Maps

    PubMed Central

    Gosselin, Thierry; Normandeau, Eric; Lamothe, Manuel; Isabel, Nathalie; Audet, Céline; Bernatchez, Louis

    2016-01-01

    Whole genome duplication (WGD) can provide material for evolutionary innovation. Family Salmonidae is ideal for studying the effects of WGD as the ancestral salmonid underwent WGD relatively recently, ∼65 Ma, then rediploidized and diversified. Extensive synteny between homologous chromosome arms occurs in extant salmonids, but each species has both conserved and unique chromosome arm fusions and fissions. Assembly of large, outbred eukaryotic genomes can be difficult, but structural rearrangements within such taxa can be investigated using linkage maps. RAD sequencing provides unprecedented ability to generate high-density linkage maps for nonmodel species, but can result in low numbers of homologous markers between species due to phylogenetic distance or differences in library preparation. Here, we generate a high-density linkage map (3,826 markers) for the Salvelinus genera (Brook Charr S. fontinalis), and then identify corresponding chromosome arms among the other available salmonid high-density linkage maps, including six species of Oncorhynchus, and one species for each of Salmo, Coregonus, and the nonduplicated sister group for the salmonids, Northern Pike Esox lucius for identifying post-duplicated homeologs. To facilitate this process, we developed MapComp to identify identical and proximate (i.e. nearby) markers between linkage maps using a reference genome of a related species as an intermediate, increasing the number of comparable markers between linkage maps by 5-fold. This enabled a characterization of the most likely history of retained chromosomal rearrangements post-WGD, and several conserved chromosomal inversions. Analyses of RADseq-based linkage maps from other taxa will also benefit from MapComp, available at: https://github.com/enormandeau/mapcomp/ PMID:28173098

  10. 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

  11. 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

  12. The Double-Reduction Landscape in Tetraploid Potato as Revealed by a High-Density Linkage Map.

    PubMed

    Bourke, Peter M; Voorrips, Roeland E; Visser, Richard G F; Maliepaard, Chris

    2015-11-01

    The creation of genetic linkage maps in polyploid species has been a long-standing problem for which various approaches have been proposed. In the case of autopolyploids, a commonly used simplification is that random bivalents form during meiosis. This leads to relatively straightforward estimation of recombination frequencies using maximum likelihood, from which a genetic map can be derived. However, autopolyploids such as tetraploid potato (Solanum tuberosum L.) may exhibit additional features, such as double reduction, not normally encountered in diploid or allopolyploid species. In this study, we produced a high-density linkage map of tetraploid potato and used it to identify regions of double reduction in a biparental mapping population. The frequency of multivalents required to produce this degree of double reduction was determined through simulation. We also determined the effect that multivalents or preferential pairing between homologous chromosomes has on linkage mapping. Low levels of multivalents or preferential pairing do not adversely affect map construction when highly informative marker types and phases are used. We reveal the double-reduction landscape in tetraploid potato, clearly showing that this phenomenon increases with distance from the centromeres.

  13. 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

  14. On the Bispectrum of Cosmic String Seeded CMB Fluctuations

    NASA Astrophysics Data System (ADS)

    Landriau, M.

    2013-07-01

    I compute the bispectrum of maps of cosmic microwave background (CMB) fluctuations seeded by cosmic strings from large to 30 arcminute scales. Examining the distribution of triangle configurations and comparing with Gaussian realizations with the same power spectrum, I conclude that the CMB bispectrum cannot pick up the mild non-Gaussianity present in the maps and thus that it cannot characterize cosmic string induced non-Gaussianity produced in the regimes probed by these maps.

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

    PubMed

    Turner, Leslie M; Harr, Bettina

    2014-12-09

    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.

  16. 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

  17. 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.

  18. 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.

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

    PubMed Central

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

    2016-01-01

    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 modeling of fMRI data collected while subjects listened to hours of narrative stories. We show that the semantic system is organized into intricate patterns that appear 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

  20. Chaotic Electrical Excitation in the Rat Atrium Revealed by Optical Mapping Studies

    NASA Astrophysics Data System (ADS)

    Sakai, Tetsuro; Kamino, Kohtaro

    Spatiotemporal patterns of chaotic electrical excitation-waves in isolated rat atrial preparations were mapped by multiple-site optical recording methods using a multi-element photodiode array together with a fast merocyanine-rhodanine voltage-sensitive dye. Tachycardia-like excitation was evoked by electrical stimulation, then maps of the excitation spread patterns were constructed. In these maps, event-to-event variations are always observed. The event-to-event variations seem to result from the physiologically trivial difference(s) in the initial conditions. This nature of "complex system" strongly supports the idea that tachycardia-like excitation is an example of the functional "self organizing systems". Although, at the present stage, it is quite difficult to analyze this phenomenon quantitatively, we consider the tachycardia-like excitation observed here as the "physiology-specific attractor".

  1. Comprehensive mapping of long-range interactions reveals folding principles of the human genome.

    PubMed

    Lieberman-Aiden, Erez; van Berkum, Nynke L; Williams, Louise; Imakaev, Maxim; Ragoczy, Tobias; Telling, Agnes; Amit, Ido; Lajoie, Bryan R; Sabo, Peter J; Dorschner, Michael O; Sandstrom, Richard; Bernstein, Bradley; Bender, M A; Groudine, Mark; Gnirke, Andreas; Stamatoyannopoulos, John; Mirny, Leonid A; Lander, Eric S; Dekker, Job

    2009-10-09

    We describe Hi-C, a method that probes the three-dimensional architecture of whole genomes by coupling proximity-based ligation with massively parallel sequencing. We constructed spatial proximity maps of the human genome with Hi-C at a resolution of 1 megabase. These maps confirm the presence of chromosome territories and the spatial proximity of small, gene-rich chromosomes. We identified an additional level of genome organization that is characterized by the spatial segregation of open and closed chromatin to form two genome-wide compartments. At the megabase scale, the chromatin conformation is consistent with a fractal globule, a knot-free, polymer conformation that enables maximally dense packing while preserving the ability to easily fold and unfold any genomic locus. The fractal globule is distinct from the more commonly used globular equilibrium model. Our results demonstrate the power of Hi-C to map the dynamic conformations of whole genomes.

  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.

  3. 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.

  4. Mapping Human Cortical Areas in vivo Based on Myelin Content as Revealed by T1- and T2-weighted MRI

    PubMed Central

    Glasser, Matthew F.; Van Essen, David C.

    2011-01-01

    Non-invasively mapping the layout of cortical areas in humans is a continuing challenge for neuroscience. We present a new method of mapping cortical areas based on myelin content as revealed by T1-weighted (T1w) and T2-weighted (T2w) MRI. The method is generalizable across different 3T scanners and pulse sequences. We use the ratio of T1w/T2w image intensities to eliminate the MR-related image intensity bias and enhance the contrast to noise ratio for myelin. Data from each subject was mapped to the cortical surface and aligned across individuals using surface-based registration. The spatial gradient of the group average myelin map provides an observer-independent measure of sharp transitions in myelin content across the surface—i.e. putative cortical areal borders. We found excellent agreement between the gradients of the myelin maps and the gradients of published probabilistic cytoarchitectonically defined cortical areas that were registered to the same surface-based atlas. For other cortical regions, we used published anatomical and functional information to make putative identifications of dozens of cortical areas or candidate areas. In general, primary and early unimodal association cortices are heavily myelinated and higher, multi-modal, association cortices are more lightly myelinated, but there are notable exceptions in the literature that are confirmed by our results. The overall pattern in the myelin maps also has important correlations with the developmental onset of subcortical white matter myelination, evolutionary cortical areal expansion in humans compared to macaques, postnatal cortical expansion in humans, and maps of neuronal density in non-human primates. PMID:21832190

  5. 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...

  6. A Primary Linkage Map of the Porcine Genome Reveals a Low Rate of Genetic Recombination

    PubMed Central

    Ellegren, H.; Chowdhary, B. P.; Johansson, M.; Marklund, L.; Fredholm, M.; Gustavsson, I.; Andersson, L.

    1994-01-01

    A comprehensive genetic linkage map of the porcine genome has been developed by typing 128 genetic markers in a cross between the European Wild Boar and a domestic breed (Large White). The marker set includes 68 polymerase chain reaction-formatted microsatellites, 60 anchored reference markers informative for comparative mapping and 47 markers which have been physically assigned by in situ hybridization. Novel multipoint assignments are provided for 54 of the markers. The map covers about 1800 cM, and the average spacing between markers is 11 cM. We used the map data to estimate the genome size in pigs, thereby addressing the total recombination distance in a third mammalian species. A sex-average genome length of 1873 +/- 139 cM was obtained by comparing the recombinational and physical distances in defined regions of the genome. This is strikingly different from the length of the human genome (3800-4000 cM) and is more similar to the mouse estimate (1600 cM). The recombination rate in females was significantly higher than in males. PMID:7982563

  7. 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.

  8. 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.

  9. 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

  10. Comparative mapping reveals partial conservation of synteny at the apomixis locus in Paspalum spp.

    PubMed

    Pupilli, F; Martinez, E J; Busti, A; Calderini, O; Quarin, C L; Arcioni, S

    2004-01-01

    In plants, gametophytic apomixis is a form of asexual reproduction that leads to the formation of seed-derived offspring that are genetically identical to the mother plant. A common set of RFLP markers, including five rice anchor markers previously shown to be linked to apomixis in Paspalum simplex, were used to detect linkage with apomixis in P. notatum and P. malacophyllum. A comparative map of the region around the apomixis locus was constructed for the three Paspalum species, and compared to the rice map. The locus that controls apomixis in P. simplex was almost completely conserved in the closely related species P. malacophyllum, whereas it was only partially represented in the distantly related species P. notatum. Although strong synteny of markers was noted between this locus and a portion of rice chromosome 12 in both P. simplex and P. malacophyllum, the same locus in P. notatum was localized to a hybrid chromosome which carries markers that map to rice chromosomes 2 and 12. All three Paspalum species showed recombination suppression at the apomixis locus; in the case of P. notatum, this might be due to a heterozygosity for a translocation that most probably negatively interferes with chromosomal pairing near the locus. A common set of markers that show linkage with apomixis in all three Paspalum species define a portion of the apomixis-controlling locus that is likely to contain genes critical for apomictic reproduction.

  11. Comparative physical mapping reveals features of microsynteny between Glycine max, Medicago truncatula, and Arabidopsis thaliana.

    PubMed

    Yan, H H; Mudge, J; Kim, D-J; Shoemaker, R C; Cook, D R; Young, N D

    2004-02-01

    To gain insight into genomic relationships between soybean (Glycine max) and Medicago truncatula, eight groups of bacterial artificial chromosome (BAC) contigs, together spanning 2.60 million base pairs (Mb) in G. max and 1.56 Mb in M. truncatula, were compared through high-resolution physical mapping combined with sequence and hybridization analysis of low-copy BAC ends. Cross-hybridization among G. max and M. truncatula contigs uncovered microsynteny in six of the contig groups and extensive microsynteny in three. Between G. max homoeologous (within genome duplicate) contigs, 85% of coding and 75% of noncoding sequences were conserved at the level of cross-hybridization. By contrast, only 29% of sequences were conserved between G. max and M. truncatula, and some kilobase-scale rearrangements were also observed. Detailed restriction maps were constructed for 11 contigs from the three highly microsyntenic groups, and these maps suggested that sequence order was highly conserved between G. max duplicates and generally conserved between G. max and M. truncatula. One instance of homoeologous BAC contigs in M. truncatula was also observed and examined in detail. A sequence similarity search against the Arabidopsis thaliana genome sequence identified up to three microsyntenic regions in A. thaliana for each of two of the legume BAC contig groups. Together, these results confirm previous predictions of one recent genome-wide duplication in G. max and suggest that M. truncatula also experienced ancient large-scale genome duplications.

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

    PubMed

    Hoppins, Suzanne; Collins, Sean R; Cassidy-Stone, Ann; Hummel, Eric; Devay, Rachel M; Lackner, Laura L; Westermann, Benedikt; Schuldiner, Maya; Weissman, Jonathan S; Nunnari, Jodi

    2011-10-17

    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.

  13. Genome-wide mapping of transcription factor binding reveals developmental process integration and a fresh look at evolutionary dynamics.

    PubMed

    Yant, Levi

    2012-02-01

    How does evolution forge adaptive responses? Are many changes required or few? Just how complex are the transcriptional networks that control development? Diverse questions like these are being newly addressed by next-generation sequencing-based techniques. Facilitating a mechanistic understanding, these approaches reveal the direct in vivo interactions between transcription factors and their physical targets, combined with genome-scale readouts to comprehensively map adaptive gene regulatory networks (GRNs). Here I focus on pioneering work from the last 3 years that has leveraged these data to investigate diverse aspects of GRN circuitry controlling the reproductive transition in plants. These approaches have revealed surprising new functions for long-investigated key players in developmental programs and laid bare the basis for pleiotropy in many others, suggesting widespread process integration at the transcriptional level. Evolutionary questions begged by the recent deluge of GRN mapping data are being assessed anew, both by emerging work outside Arabidopsis thaliana and novel analyses within. These studies have swiftly exposed the distinctive power and adaptability of genome-wide GRN mapping and illustrate that this unique data type holds tremendous promise for plant biology.

  14. Demonstration of Cosmic Microwave Background Delensing Using the Cosmic Infrared Background

    NASA Astrophysics Data System (ADS)

    Larsen, Patricia; Challinor, Anthony; Sherwin, Blake D.; Mak, Daisy

    2016-10-01

    Delensing is an increasingly important technique to reverse the gravitational lensing of the cosmic microwave background (CMB) and thus reveal primordial signals the lensing may obscure. We present a first demonstration of delensing on Planck temperature maps using the cosmic infrared background (CIB). Reversing the lensing deflections in Planck CMB temperature maps using a linear combination of the 545 and 857 GHz maps as a lensing tracer, we find that the lensing effects in the temperature power spectrum are reduced in a manner consistent with theoretical expectations. In particular, the characteristic sharpening of the acoustic peaks of the temperature power spectrum resulting from successful delensing is detected at a significance of 16 σ , with an amplitude of Adelens=1.12 ±0.07 relative to the expected value of unity. This first demonstration on data of CIB delensing, and of delensing techniques in general, is significant because lensing removal will soon be essential for achieving high-precision constraints on inflationary B -mode polarization.

  15. Demonstration of Cosmic Microwave Background Delensing Using the Cosmic Infrared Background.

    PubMed

    Larsen, Patricia; Challinor, Anthony; Sherwin, Blake D; Mak, Daisy

    2016-10-07

    Delensing is an increasingly important technique to reverse the gravitational lensing of the cosmic microwave background (CMB) and thus reveal primordial signals the lensing may obscure. We present a first demonstration of delensing on Planck temperature maps using the cosmic infrared background (CIB). Reversing the lensing deflections in Planck CMB temperature maps using a linear combination of the 545 and 857 GHz maps as a lensing tracer, we find that the lensing effects in the temperature power spectrum are reduced in a manner consistent with theoretical expectations. In particular, the characteristic sharpening of the acoustic peaks of the temperature power spectrum resulting from successful delensing is detected at a significance of 16σ, with an amplitude of A_{delens}=1.12±0.07 relative to the expected value of unity. This first demonstration on data of CIB delensing, and of delensing techniques in general, is significant because lensing removal will soon be essential for achieving high-precision constraints on inflationary B-mode polarization.

  16. Chemical map of Schizosaccharomyces pombe reveals species-specific features in nucleosome positioning.

    PubMed

    Moyle-Heyrman, Georgette; Zaichuk, Tetiana; Xi, Liqun; Zhang, Quanwei; Uhlenbeck, Olke C; Holmgren, Robert; Widom, Jonathan; Wang, Ji-Ping

    2013-12-10

    Using a recently developed chemical approach, we have generated a genome-wide map of nucleosomes in vivo in Schizosaccharomyces pombe (S. pombe) at base pair resolution. The shorter linker length previously identified in S. pombe is due to a preponderance of nucleosomes separated by ∼4/5 bp, placing nucleosomes on opposite faces of the DNA. The periodic dinucleotide feature thought to position nucleosomes is equally strong in exons as in introns, demonstrating that nucleosome positioning information can be superimposed on coding information. Unlike the case in Saccharomyces cerevisiae, A/T-rich sequences are enriched in S. pombe nucleosomes, particularly at ±20 bp around the dyad. This difference in nucleosome binding preference gives rise to a major distinction downstream of the transcription start site, where nucleosome phasing is highly predictable by A/T frequency in S. pombe but not in S. cerevisiae, suggesting that the genomes and DNA binding preferences of nucleosomes have coevolved in different species. The poly (dA-dT) tracts affect but do not deplete nucleosomes in S. pombe, and they prefer special rotational positions within the nucleosome, with longer tracts enriched in the 10- to 30-bp region from the dyad. S. pombe does not have a well-defined nucleosome-depleted region immediately upstream of most transcription start sites; instead, the -1 nucleosome is positioned with the expected spacing relative to the +1 nucleosome, and its occupancy is negatively correlated with gene expression. Although there is generally very good agreement between nucleosome maps generated by chemical cleavage and micrococcal nuclease digestion, the chemical map shows consistently higher nucleosome occupancy on DNA with high A/T content.

  17. THE GALACTIC {sup 26}AL EMISSION MAP AS REVEALED BY INTEGRAL SPI

    SciTech Connect

    Bouchet, Laurent; Jourdain, Elisabeth; Roques, Jean-Pierre

    2015-03-10

    Diffuse emission is often challenging since it is undetectable by most instruments, which are generally dedicated to point-source studies. The {sup 26}Al emission is a good illustration: the only available {sup 26}Al map to date has been released, more than 15 yr ago, thanks to the COMPTEL instrument. However, at the present time, the SPI spectrometer aboard the International Gamma-Ray Astrophysics Laboratory mission offers a unique opportunity to enrich this first result. In this paper, 2 × 10{sup 8} s of data accumulated between 2003 and 2013 are used to perform a dedicated analysis, aiming to deeply investigate the spatial morphology of the {sup 26}Al emission. The data are first compared with several sky maps based on observations at various wavelengths to model the {sup 26}Al distribution throughout the Galaxy. For most of the distribution models, the inner Galaxy flux is compatible with a value of 3.3 × 10{sup −4} photons cm{sup −2} s{sup −1}, while the preferred template maps correspond to young stellar components such as core-collapse supernovae (SNe), Wolf–Rayet stars, and massive AGB stars. To get more details about this emission, an image reconstruction is performed using an algorithm based on the maximum-entropy method. In addition to the inner Galaxy emission, several excesses suggest that some sites of emission are linked to the spiral arm structure. Lastly, an estimation of the {sup 60}Fe line flux, assuming a spatial distribution similar to {sup 26}Al line emission, results in a {sup 60}Fe-to-{sup 26}Al ratio around 0.14, which agrees with the most recent studies and with the SN explosion model predictions.

  18. The Galactic 26Al Emission Map as Revealed by INTEGRAL SPI

    NASA Astrophysics Data System (ADS)

    Bouchet, Laurent; Jourdain, Elisabeth; Roques, Jean-Pierre

    2015-03-01

    Diffuse emission is often challenging since it is undetectable by most instruments, which are generally dedicated to point-source studies. The 26Al emission is a good illustration: the only available 26Al map to date has been released, more than 15 yr ago, thanks to the COMPTEL instrument. However, at the present time, the SPI spectrometer aboard the International Gamma-Ray Astrophysics Laboratory mission offers a unique opportunity to enrich this first result. In this paper, 2 × 108 s of data accumulated between 2003 and 2013 are used to perform a dedicated analysis, aiming to deeply investigate the spatial morphology of the 26Al emission. The data are first compared with several sky maps based on observations at various wavelengths to model the 26Al distribution throughout the Galaxy. For most of the distribution models, the inner Galaxy flux is compatible with a value of 3.3 × 10-4 photons cm-2 s-1, while the preferred template maps correspond to young stellar components such as core-collapse supernovae (SNe), Wolf-Rayet stars, and massive AGB stars. To get more details about this emission, an image reconstruction is performed using an algorithm based on the maximum-entropy method. In addition to the inner Galaxy emission, several excesses suggest that some sites of emission are linked to the spiral arm structure. Lastly, an estimation of the 60Fe line flux, assuming a spatial distribution similar to 26Al line emission, results in a 60Fe-to-26Al ratio around 0.14, which agrees with the most recent studies and with the SN explosion model predictions.

  19. Spatial Variations of PAH Properties in M17SW Revealed by Spitzer/IRS Spectral Mapping

    NASA Astrophysics Data System (ADS)

    Yamagishi, M.; Kaneda, H.; Ishihara, D.; Oyabu, S.; Suzuki, T.; Onaka, T.; Nagayama, T.; Umemoto, T.; Minamidani, T.; Nishimura, A.; Matsuo, M.; Fujita, S.; Tsuda, Y.; Kohno, M.; Ohashi, S.

    2016-12-01

    We present Spitzer/IRS mid-infrared spectral maps of the Galactic star-forming region M17 as well as IRSF/SIRIUS Brγ and Nobeyama 45 m/FOREST 13CO (J = 1-0) maps. The spectra show prominent features due to polycyclic aromatic hydrocarbons (PAHs) at wavelengths of 6.2, 7.7, 8.6, 11.3, 12.0, 12.7, 13.5, and 14.2 μm. We find that the PAH emission features are bright in the region between the H ii region traced by Brγ and the molecular cloud traced by 13CO, supporting that the PAH emission originates mostly from photo-dissociation regions. Based on the spatially resolved Spitzer/IRS maps, we examine spatial variations of the PAH properties in detail. As a result, we find that the interband ratio of PAH 7.7 μm/PAH 11.3 μm varies locally near M17SW, but rather independently of the distance from the OB stars in M17, suggesting that the degree of PAH ionization is mainly controlled by local conditions rather than the global UV environments determined by the OB stars in M17. We also find that the interband ratios of the PAH 12.0 μm, 12.7 μm, 13.5 μm, and 14.2 μm features to the PAH 11.3 μm feature are high near the M17 center, which suggests structural changes of PAHs through processing due to intense UV radiation, producing abundant edgy irregular PAHs near the M17 center.

  20. High-Throughput Phenotyping and QTL Mapping Reveals the Genetic Architecture of Maize Plant Growth1[OPEN

    PubMed Central

    Huang, Chenglong; Wu, Di; Qiao, Feng; Li, Wenqiang; Duan, Lingfeng; Wang, Ke; Xiao, Yingjie; Chen, Guoxing; Liu, Qian; Yang, Wanneng

    2017-01-01

    With increasing demand for novel traits in crop breeding, the plant research community faces the challenge of quantitatively analyzing the structure and function of large numbers of plants. A clear goal of high-throughput phenotyping is to bridge the gap between genomics and phenomics. In this study, we quantified 106 traits from a maize (Zea mays) recombinant inbred line population (n = 167) across 16 developmental stages using the automatic phenotyping platform. Quantitative trait locus (QTL) mapping with a high-density genetic linkage map, including 2,496 recombinant bins, was used to uncover the genetic basis of these complex agronomic traits, and 988 QTLs have been identified for all investigated traits, including three QTL hotspots. Biomass accumulation and final yield were predicted using a combination of dissected traits in the early growth stage. These results reveal the dynamic genetic architecture of maize plant growth and enhance ideotype-based maize breeding and prediction. PMID:28153923

  1. Active chromatin domains are defined by acetylation islands revealed by genome-wide mapping.

    PubMed

    Roh, Tae-Young; Cuddapah, Suresh; Zhao, Keji

    2005-03-01

    The identity and developmental potential of a human cell is specified by its epigenome that is largely defined by patterns of chromatin modifications including histone acetylation. Here we report high-resolution genome-wide mapping of diacetylation of histone H3 at Lys 9 and Lys 14 in resting and activated human T cells by genome-wide mapping technique (GMAT). Our data show that high levels of the H3 acetylation are detected in gene-rich regions. The chromatin accessibility and gene expression of a genetic domain is correlated with hyperacetylation of promoters and other regulatory elements but not with generally elevated acetylation of the entire domain. Islands of acetylation are identified in the intergenic and transcribed regions. The locations of the 46,813 acetylation islands identified in this study are significantly correlated with conserved noncoding sequences (CNSs) and many of them are colocalized with known regulatory elements in T cells. TCR signaling induces 4045 new acetylation loci that may mediate the global chromatin remodeling and gene activation. We propose that the acetylation islands are epigenetic marks that allow prediction of functional regulatory elements.

  2. Active chromatin domains are defined by acetylation islands revealed by genome-wide mapping

    PubMed Central

    Roh, Tae-Young; Cuddapah, Suresh; Zhao, Keji

    2005-01-01

    The identity and developmental potential of a human cell is specified by its epigenome that is largely defined by patterns of chromatin modifications including histone acetylation. Here we report high-resolution genome-wide mapping of diacetylation of histone H3 at Lys 9 and Lys 14 in resting and activated human T cells by genome-wide mapping technique (GMAT). Our data show that high levels of the H3 acetylation are detected in gene-rich regions. The chromatin accessibility and gene expression of a genetic domain is correlated with hyperacetylation of promoters and other regulatory elements but not with generally elevated acetylation of the entire domain. Islands of acetylation are identified in the intergenic and transcribed regions. The locations of the 46,813 acetylation islands identified in this study are significantly correlated with conserved noncoding sequences (CNSs) and many of them are colocalized with known regulatory elements in T cells. TCR signaling induces 4045 new acetylation loci that may mediate the global chromatin remodeling and gene activation. We propose that the acetylation islands are epigenetic marks that allow prediction of functional regulatory elements. PMID:15706033

  3. HGDP and HapMap analysis by Ancestry Mapper reveals local and global population relationships.

    PubMed

    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.

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

    PubMed

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

    2014-01-01

    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.

  5. 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

  6. 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

  7. Extensive conservation of sex chromosome organization between cat and human revealed by parallel radiation hybrid mapping.

    PubMed

    Murphy, W J; Sun, S; Chen, Z Q; Pecon-Slattery, J; O'Brien, S J

    1999-12-01

    A radiation hybrid (RH)-derived physical map of 25 markers on the feline X chromosome (including 19 Type I coding loci and 6 Type II microsatellite markers) was compared to homologous marker order on the human and mouse X chromosome maps. Complete conservation of synteny and marker order was observed between feline and human X chromosomes, whereas the same markers identified a minimum of seven rearranged syntenic segments between mouse and cat/human X chromosome marker order. Within the blocks, the feline, human, and mouse marker order was strongly conserved. Similarly, Y chromosome locus order was remarkably conserved between cat and human Y chromosomes, with only one marker (SMCY) position rearranged between the species. Tight linkage and a conserved gene order for a segment encoding three genes, DFFRY-DBY-UTY in human, mouse, and cat Y chromosomes, coupled with demonstrated deletion effects of these genes on reproductive impairment in both human and mouse, implicates the region as critical for Y-mediated sperm production.

  8. 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.

  9. 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

    2015-01-08

    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.

  10. 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

  11. 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

  12. 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

  13. Increasing water vapor transport to the Greenland Ice Sheet revealed using self-organizing maps

    NASA Astrophysics Data System (ADS)

    Mattingly, Kyle S.; Ramseyer, Craig A.; Rosen, Joshua J.; Mote, Thomas L.; Muthyala, Rohi

    2016-09-01

    The Greenland Ice Sheet (GrIS) has been losing mass in recent decades, with an acceleration in mass loss since 2000. In this study, we apply a self-organizing map classification to integrated vapor transport data from the ERA-Interim reanalysis to determine if these GrIS mass loss trends are linked to increases in moisture transport to Greenland. We find that "moist" days (i.e., days featuring anomalously intense water vapor transport to Greenland) were significantly more common during 2000-2015 compared to 1979-1994. Furthermore, the two most intense GrIS melt seasons during the last 36 years were either preceded by a record percentage of moist winter days (2010) or occurred during a summer with a record frequency of moist days (2012). We hypothesize that moisture transport events alter the GrIS energy budget by increasing downwelling longwave radiation and turbulent fluxes of sensible and latent energy.

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

    PubMed

    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

    2015-01-22

    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.

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

    PubMed

    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.

  16. 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.

  17. A RAD-tag genetic map for the platyfish (Xiphophorus maculatus) reveals mechanisms of karyotype evolution among teleost fish.

    PubMed

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

    2014-06-01

    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.

  18. 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

  19. High-resolution spatiotemporal strain mapping reveals non-uniform deformation in micropatterned elastomers

    NASA Astrophysics Data System (ADS)

    Aksoy, B.; Rehman, A.; Bayraktar, H.; Alaca, B. E.

    2017-04-01

    overcome this challenge and provides a displacement measurement resolution of 116 nm and a strain resolution of 0.04% over a gage length of 300 µm. Similarly, the ability to capture inhomogeneities is demonstrated by mapping strain around a thru-hole. The robustness of the technique is also evaluated, where no appreciable change in strain measurement is observed despite the significant variations imposed on the measurement mesh. The proposed approach introduces critical improvements for the determination of displacement and strain gradients in elastomers regarding the real-time nature of strain mapping with a microscale spatial resolution.

  20. 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

  1. 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.

  2. Quantitative interaction mapping reveals an extended UBX domain in ASPL that disrupts functional p97 hexamers

    PubMed Central

    Arumughan, Anup; Roske, Yvette; Barth, Carolin; Forero, Laura Lleras; Bravo-Rodriguez, Kenny; Redel, Alexandra; Kostova, Simona; McShane, Erik; Opitz, Robert; Faelber, Katja; Rau, Kirstin; Mielke, Thorsten; Daumke, Oliver; Selbach, Matthias; Sanchez-Garcia, Elsa; Rocks, Oliver; Panáková, Daniela; Heinemann, Udo; Wanker, Erich E.

    2016-01-01

    Interaction mapping is a powerful strategy to elucidate the biological function of protein assemblies and their regulators. Here, we report the generation of a quantitative interaction network, directly linking 14 human proteins to the AAA+ ATPase p97, an essential hexameric protein with multiple cellular functions. We show that the high-affinity interacting protein ASPL efficiently promotes p97 hexamer disassembly, resulting in the formation of stable p97:ASPL heterotetramers. High-resolution structural and biochemical studies indicate that an extended UBX domain (eUBX) in ASPL is critical for p97 hexamer disassembly and facilitates the assembly of p97:ASPL heterotetramers. This spontaneous process is accompanied by a reorientation of the D2 ATPase domain in p97 and a loss of its activity. Finally, we demonstrate that overproduction of ASPL disrupts p97 hexamer function in ERAD and that engineered eUBX polypeptides can induce cell death, providing a rationale for developing anti-cancer polypeptide inhibitors that may target p97 activity. PMID:27762274

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

    PubMed Central

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

    2016-01-01

    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

  4. Fate mapping reveals origins and dynamics of monocytes and tissue macrophages under homeostasis

    PubMed Central

    Yona, Simon; Kim, Ki-Wook; Wolf, Yochai; Mildner, Alexander; Varol, Diana; Breker, Michal; Strauss-Ayali, Dalit; Viukov, Sergey; Guilliams, Martin; Misharin, Alexander; Hume, David A.; Perlman, Harris; Malissen, Bernard; Zelzer, Elazar; Jung, Steffen

    2013-01-01

    SUMMARY Mononuclear phagocytes, including monocytes, macrophages and dendritic cells, contribute to tissue integrity, as well as innate and adaptive immune defense. Emerging evidence for labour division indicates that manipulation of these cells could bear therapeutic potential. However, specific ontogenies of individual populations and the overall functional organisation of the cellular network are not well-defined. Here we report a fate mapping study of the murine monocyte and macrophage compartment taking advantage of constitutive and conditional CX3CR1 promoter-driven Cre recombinase expression. We have demonstrated that major tissue resident macrophage populations, including liver Kupffer cells, lung alveolar, splenic and peritoneal macrophages, are established prior to birth and maintain themselves subsequently during adulthood independent of replenishment by blood monocytes. Furthermore, we have established that the short-lived Ly6C+ monocytes constitute obligatory steady state precursors of blood-resident Ly6C− cells and that the abundance of Ly6C+ blood monocytes dynamically controls the circulation life span of their progeny. PMID:23273845

  5. 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.

  6. 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

  7. 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

  8. Comprehensive Expression Map of Transcription Regulators in the Adult Zebrafish Telencephalon Reveals Distinct Neurogenic Niches

    PubMed Central

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

    2015-01-01

    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. J. Comp. Neurol. 523:1202–1221, 2015. © 2015 Wiley Periodicals, Inc. PMID:25556858

  9. Genome-Scale Mapping of Escherichia coli σ54 Reveals Widespread, Conserved Intragenic Binding

    PubMed Central

    Bonocora, Richard P.; Smith, Carol; Lapierre, Pascal; Wade, Joseph T.

    2015-01-01

    Bacterial RNA polymerases must associate with a σ factor to bind promoter DNA and initiate transcription. There are two families of σ factor: the σ70 family and the σ54 family. Members of the σ54 family are distinct in their ability to bind promoter DNA sequences, in the context of RNA polymerase holoenzyme, in a transcriptionally inactive state. Here, we map the genome-wide association of Escherichia coli σ54, the archetypal member of the σ54 family. Thus, we vastly expand the list of known σ54 binding sites to 135. Moreover, we estimate that there are more than 250 σ54 sites in total. Strikingly, the majority of σ54 binding sites are located inside genes. The location and orientation of intragenic σ54 binding sites is non-random, and many intragenic σ54 binding sites are conserved. We conclude that many intragenic σ54 binding sites are likely to be functional. Consistent with this assertion, we identify three conserved, intragenic σ54 promoters that drive transcription of mRNAs with unusually long 5ʹ UTRs. PMID:26425847

  10. 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

  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. 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

  13. Revealing the cerebral regions and networks mediating vulnerability to depression: oxidative metabolism mapping of rat brain.

    PubMed

    Harro, Jaanus; Kanarik, Margus; Kaart, Tanel; Matrov, Denis; Kõiv, Kadri; Mällo, Tanel; Del Río, Joaquin; Tordera, Rosa M; Ramirez, Maria J

    2014-07-01

    The large variety of available animal models has revealed much on the neurobiology of depression, but each model appears as specific to a significant extent, and distinction between stress response, pathogenesis of depression and underlying vulnerability is difficult to make. Evidence from epidemiological studies suggests that depression occurs in biologically predisposed subjects under impact of adverse life events. We applied the diathesis-stress concept to reveal brain regions and functional networks that mediate vulnerability to depression and response to chronic stress by collapsing data on cerebral long term neuronal activity as measured by cytochrome c oxidase histochemistry in distinct animal models. Rats were rendered vulnerable to depression either by partial serotonergic lesion or by maternal deprivation, or selected for a vulnerable phenotype (low positive affect, low novelty-related activity or high hedonic response). Environmental adversity was brought about by applying chronic variable stress or chronic social defeat. Several brain regions, most significantly median raphe, habenula, retrosplenial cortex and reticular thalamus, were universally implicated in long-term metabolic stress response, vulnerability to depression, or both. Vulnerability was associated with higher oxidative metabolism levels as compared to resilience to chronic stress. Chronic stress, in contrast, had three distinct patterns of effect on oxidative metabolism in vulnerable vs. resilient animals. In general, associations between regional activities in several brain circuits were strongest in vulnerable animals, and chronic stress disrupted this interrelatedness. These findings highlight networks that underlie resilience to stress, and the distinct response to stress that occurs in vulnerable subjects.

  14. 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.

  15. 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.

  16. Ambient gas influence on electrospray potential as revealed by potential mapping within the electrospray capillary.

    PubMed

    Pozniak, Boguslaw P; Cole, Richard B

    2007-05-01

    The effect of ambient gas on potentials inside the electrospray (ES) capillary was investigated. Potential measurements and differential electrospray emitter potential (DEEP) maps were obtained with the help of a small, movable, disklike platinum wire electrode inserted into the ES capillary. Typical solvents used for electrospray mass spectrometry such as methanol and mixtures of methanol-water and chloroform/methanol have been tested. It was found that oxygen is readily adsorbed from the surrounding ambient gas into the spraying liquid. Following adsorption, it resides in, or near to, the Taylor cone, thereby affecting the electrochemical potential near the ES capillary exit, as well as the character of the inherent electrochemical reactions occurring during the ES process. The potentials measured in an air environment with reactive oxygen present are contrasted against those obtained in an inert nitrogen environment. The kinetics of oxygen admission have been found to be quite fast, i.e., occurring in a matter of seconds, but it takes far longer to purge the system of oxygen by changing the ambient atmosphere to nitrogen. The oxygen effect is present in negative and positive ion modes of ES, but the total ES current is not affected by the change of ambient gas. The magnitude of the oxygen effect owing to ambient air was compared to the effect caused by initially dissolving oxygen in the solution prior to the start of ES; it was found that the presence of oxygen in the ambient gas has a far greater consequence. These results indicate that the presence of reactive gases, such as molecular oxygen, in the region of the ES emitter may have unintended secondary effects on the ES process prior to mass spectrometric analysis.

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

    PubMed

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

    2014-03-19

    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 systematically reveal the functional architecture of neural circuits underlying a sensorimotor behavior in a vertebrate brain.

  18. High-resolution mapping of protein concentration reveals principles of proteome architecture and adaptation.

    PubMed

    Levy, Emmanuel D; Kowarzyk, Jacqueline; Michnick, Stephen W

    2014-05-22

    A single yeast cell contains a hundred million protein molecules. How these proteins are organized to orchestrate living processes is a central question in biology. To probe this organization in vivo, we measured the local concentration of proteins based on the strength of their nonspecific interactions with a neutral reporter protein. We first used a cytosolic reporter and measured local concentrations for ~2,000 proteins in S. cerevisiae, with accuracy comparable to that of mass spectrometry. Localizing the reporter to membranes specifically increased the local concentration measured for membrane proteins. Comparing the concentrations measured by both reporters revealed that encounter frequencies between proteins are primarily dictated by their abundances. However, to change these encounter frequencies and restructure the proteome, as in adaptation, we find that changes in localization have more impact than changes in abundance. These results highlight how protein abundance and localization contribute to proteome organization and reorganization.

  19. 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

  20. Mapping of Gene Expression Reveals CYP27A1 as a Susceptibility Gene for Sporadic ALS

    PubMed Central

    van Rheenen, Wouter; Franke, Lude; Jansen, Ritsert C.; van Es, Michael A.; van Vught, Paul W. J.; Blauw, Hylke M.; Groen, Ewout J. N.; Horvath, Steve; Estrada, Karol; Rivadeneira, Fernando; Hofman, Albert; Uitterlinden, Andre G.; Robberecht, Wim; Andersen, Peter M.; Melki, Judith; Meininger, Vincent; Hardiman, Orla; Landers, John E.; Brown, Robert H.; Shatunov, Aleksey; Shaw, Christopher E.; Leigh, P. Nigel; Al-Chalabi, Ammar; Ophoff, Roel A.

    2012-01-01

    Amyotrophic lateral sclerosis (ALS) is a progressive, neurodegenerative disease characterized by loss of upper and lower motor neurons. ALS is considered to be a complex trait and genome-wide association studies (GWAS) have implicated a few susceptibility loci. However, many more causal loci remain to be discovered. Since it has been shown that genetic variants associated with complex traits are more likely to be eQTLs than frequency-matched variants from GWAS platforms, we conducted a two-stage genome-wide screening for eQTLs associated with ALS. In addition, we applied an eQTL analysis to finemap association loci. Expression profiles using peripheral blood of 323 sporadic ALS patients and 413 controls were mapped to genome-wide genotyping data. Subsequently, data from a two-stage GWAS (3,568 patients and 10,163 controls) were used to prioritize eQTLs identified in the first stage (162 ALS, 207 controls). These prioritized eQTLs were carried forward to the second sample with both gene-expression and genotyping data (161 ALS, 206 controls). Replicated eQTL SNPs were then tested for association in the second-stage GWAS data to find SNPs associated with disease, that survived correction for multiple testing. We thus identified twelve cis eQTLs with nominally significant associations in the second-stage GWAS data. Eight SNP-transcript pairs of highest significance (lowest p = 1.27×10−51) withstood multiple-testing correction in the second stage and modulated CYP27A1 gene expression. Additionally, we show that C9orf72 appears to be the only gene in the 9p21.2 locus that is regulated in cis, showing the potential of this approach in identifying causative genes in association loci in ALS. This study has identified candidate genes for sporadic ALS, most notably CYP27A1. Mutations in CYP27A1 are causal to cerebrotendinous xanthomatosis which can present as a clinical mimic of ALS with progressive upper motor neuron loss, making it a plausible susceptibility gene for

  1. 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

  2. Cosmic Catastrophes

    NASA Astrophysics Data System (ADS)

    Wheeler, J. Craig

    2000-07-01

    In this tour de force of the ultimate and extreme in astrophysics, renowned astrophysicist and author J. Craig Wheeler takes us on a breathtaking journey to supernovae, black holes, gamma-ray bursts and adventures in hyperspace. This is no far-fetched science fiction tale, but an enthusiastic exploration of ideas at the cutting edge of current astrophysics. Wheeler follows the tortuous life of a star from birth to evolution and death, and goes on to consider the complete collapse of a star into a black hole, worm-hole time machines, the possible birth of baby bubble universes, and the prospect of a revolutionary view of space and time in a ten-dimensional string theory. Along the way he offers evidence that suggests the Universe is accelerating and describes recent developments in understanding gamma-ray bursts--perhaps the most catastrophic cosmic events of all. With the use of lucid analogies, simple language and crystal-clear cartoons, Cosmic Catastrophes makes accessible some of the most exciting and mind-bending objects and ideas in the Universe. J. Craig Wheeler is currently Samuel T. and Fern Yanagisawa Regents Professor of Astronomy at the University of Texas at Austin and Vice President of the American Astronomical Society as of 1999.

  3. 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.

  4. 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

  5. Phosphorylation site mapping of soluble proteins: bioinformatical filtering reveals potential plastidic phosphoproteins in Arabidopsis thaliana.

    PubMed

    Lohrig, Katharina; Müller, Bernd; Davydova, Joulia; Leister, Dario; Wolters, Dirk Andreas

    2009-04-01

    Protein phosphorylation is a major mode of regulation of metabolism, gene expression, and cell architecture. A combination of phosphopeptide enrichment strategies based on TiO(2) and IMAC in addition to our MudPIT strategy revealed the detection of 181 phosphorylation sites which are located on 125 potentially plastidic proteins predicted by GoMiner, TargetP/Predotar in Arabidopsis thaliana. In our study phosphorylation on serine is favored over threonine and this in turn over phosphorylation on tyrosine residues, showing a percentage of 67.4% to 24.3% to 8.3% for pS:pT:pY. Four phosphorylated residues (S208, Y239, T246 and T330), identified by our approach have been fitted to the structure of the activated form of spinach RuBisCO, which are located in close proximity to the substrate binding site for ribulosebisphosphate. Potentially, these phosphorylation sites exert a direct influence on the catalytic activity of the enzyme. Such examples show nicely the value of the presented mass spectrometric dataset for further biochemical applications, since alternative mutation analysis often turns out to be unsuccessful, caused by mutations in essential proteins which result in lethal phenotypes.

  6. Global Mapping of the Inc-Human Interactome Reveals that Retromer Restricts Chlamydia Infection.

    PubMed

    Mirrashidi, Kathleen M; Elwell, Cherilyn A; Verschueren, Erik; Johnson, Jeffrey R; Frando, Andrew; Von Dollen, John; Rosenberg, Oren; Gulbahce, Natali; Jang, Gwendolyn; Johnson, Tasha; Jäger, Stefanie; Gopalakrishnan, Anusha M; Sherry, Jessica; Dunn, Joe Dan; Olive, Andrew; Penn, Bennett; Shales, Michael; Cox, Jeffery S; Starnbach, Michael N; Derre, Isabelle; Valdivia, Raphael; Krogan, Nevan J; Engel, Joanne

    2015-07-08

    Chlamydia trachomatis is a leading cause of genital and ocular infections for which no vaccine exists. Upon entry into host cells, C. trachomatis resides within a membrane-bound compartment—the inclusion—and secretes inclusion membrane proteins (Incs) that are thought to modulate the host-bacterium interface. To expand our understanding of Inc function(s), we subjected putative C. trachomatis Incs to affinity purification-mass spectroscopy (AP-MS). We identified Inc-human interactions for 38/58 Incs with enrichment in host processes consistent with Chlamydia's intracellular life cycle. There is significant overlap between Inc targets and viral proteins, suggesting common pathogenic mechanisms among obligate intracellular microbes. IncE binds to sorting nexins (SNXs) 5/6, components of the retromer, which relocalizes SNX5/6 to the inclusion membrane and augments inclusion membrane tubulation. Depletion of retromer components enhances progeny production, revealing that retromer restricts Chlamydia infection. This study demonstrates the value of proteomics in unveiling host-pathogen interactions in genetically challenging microbes.

  7. Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions.

    PubMed

    Chu, Ci; Qu, Kun; Zhong, Franklin L; Artandi, Steven E; Chang, Howard Y

    2011-11-18

    Long noncoding RNAs (lncRNAs) are key regulators of chromatin state, yet the nature and sites of RNA-chromatin interaction are mostly unknown. Here we introduce Chromatin Isolation by RNA Purification (ChIRP), where tiling oligonucleotides retrieve specific lncRNAs with bound protein and DNA sequences, which are enumerated by deep sequencing. ChIRP-seq of three lncRNAs reveal that RNA occupancy sites in the genome are focal, sequence-specific, and numerous. Drosophila roX2 RNA occupies male X-linked gene bodies with increasing tendency toward the 3' end, peaking at CES sites. Human telomerase RNA TERC occupies telomeres and Wnt pathway genes. HOTAIR lncRNA preferentially occupies a GA-rich DNA motif to nucleate broad domains of Polycomb occupancy and histone H3 lysine 27 trimethylation. HOTAIR occupancy occurs independently of EZH2, suggesting the order of RNA guidance of Polycomb occupancy. ChIRP-seq is generally applicable to illuminate the intersection of RNA and chromatin with newfound precision genome wide.

  8. “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.

  9. Mapping evaporative water loss in desert passerines reveals an expanding threat of lethal dehydration.

    PubMed

    Albright, Thomas P; Mutiibwa, Denis; Gerson, Alexander R; Smith, Eric Krabbe; Talbot, William A; O'Neill, Jacqueline J; McKechnie, Andrew E; Wolf, Blair O

    2017-02-28

    Extreme high environmental temperatures produce a variety of consequences for wildlife, including mass die-offs. Heat waves are increasing in frequency, intensity, and extent, and are projected to increase further under climate change. However, the spatial and temporal dynamics of die-off risk are poorly understood. Here, we examine the effects of heat waves on evaporative water loss (EWL) and survival in five desert passerine birds across the southwestern United States using a combination of physiological data, mechanistically informed models, and hourly geospatial temperature data. We ask how rates of EWL vary with temperature across species; how frequently, over what areas, and how rapidly lethal dehydration occurs; how EWL and die-off risk vary with body mass; and how die-off risk is affected by climate warming. We find that smaller-bodied passerines are subject to higher rates of mass-specific EWL than larger-bodied counterparts and thus encounter potentially lethal conditions much more frequently, over shorter daily intervals, and over larger geographic areas. Warming by 4 °C greatly expands the extent, frequency, and intensity of dehydration risk, and introduces new threats for larger passerine birds, particularly those with limited geographic ranges. Our models reveal that increasing air temperatures and heat wave occurrence will potentially have important impacts on the water balance, daily activity, and geographic distribution of arid-zone birds. Impacts may be exacerbated by chronic effects and interactions with other environmental changes. This work underscores the importance of acute risks of high temperatures, particularly for small-bodied species, and suggests conservation of thermal refugia and water sources.

  10. Observation of TeV-Energy Cosmic-Ray Anisotropy with the HAWC Observatory

    NASA Astrophysics Data System (ADS)

    Fiorino, Daniel W.

    Over the past two decades, ground-based measurements of the arrival directions of TeV cosmic rays have revealed an unexpected anisotropy. Multiple detectors have recorded fluxes above all-sky averages to high statistical significance for features at large (about 180°) and small (about 5°) angular sizes. Likely sources of high-energy cosmic rays are no closer than about 100 pc, about 100,000 Larmor radii for a TeV proton in typical interstellar magnetic fields of order several microGauss. This thesis outlines methods to search for signals in cosmic-ray arrival directions on data from the High-Altitude Water Cherenkov (HAWC) Observatory -- an extended air shower detector array in Puebla, Mexico, sensitive to gamma rays and cosmic rays at TeV energies. The detector is currently under construction, but data acquisition with the partially deployed detector started in 2013. An analysis of the cosmic-ray arrival direction distribution based on 86 billion events recorded between June 2013 and July 2014 shows anisotropy at the 10. (-4) level on angular scales of about 10°. The HAWC cosmic-raysky map exhibits three regions of significantly enhanced cosmic-ray flux; two of these regions were first reported by the Milagro experiment. A third region coincides with an excess recently reported by the ARGO-YBJ experiment. An angular power spectrum analysis of the sky shows that all terms up to l=15 contribute significantly to the excesses. Large angular scales (>60°) are also considered, but the results are still preliminary as they are contaminated with non-sidereal signals which cancel for integer years of continuous data. An analysis of the cosmic-ray Moon shadow is shown to demonstrate the angular resolution and energy scale of the data set and to evaluate part of the analysis technique.

  11. In-depth mapping of the mouse brain N-glycoproteome reveals widespread N-glycosylation of diverse brain proteins

    PubMed Central

    Fang, Pan; Wang, Xin-jian; Xue, Yu; Liu, Ming-qi; Zeng, Wen-feng; Zhang, Yang; Zhang, Lei; Gao, Xing; Yan, Guo-quan; Yao, Jun; Shen, Hua-li; Yang, Peng-yuan

    2016-01-01

    N-glycosylation is one of the most prominent and abundant posttranslational modifications of proteins. It is estimated that over 50% of mammalian proteins undergo glycosylation. However, the analysis of N-glycoproteins has been limited by the available analytical technology. In this study, we comprehensively mapped the N-glycosylation sites in the mouse brain proteome by combining complementary methods, which included seven protease treatments, four enrichment techniques and two fractionation strategies. Altogether, 13492 N-glycopeptides containing 8386 N-glycosylation sites on 3982 proteins were identified. After evaluating the performance of the above methods, we proposed a simple and efficient workflow for large-scale N-glycosylation site mapping. The optimized workflow yielded 80% of the initially identified N-glycosylation sites with considerably less effort. Analysis of the identified N-glycoproteins revealed that many of the mouse brain proteins are N-glycosylated, including those proteins in critical pathways for nervous system development and neurological disease. Additionally, several important biomarkers of various diseases were found to be N-glycosylated. These data confirm that N-glycosylation is important in both physiological and pathological processes in the brain, and provide useful details about numerous N-glycosylation sites in brain proteins. PMID:27259237

  12. 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

  13. 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.

  14. Cosmic plasma

    NASA Technical Reports Server (NTRS)

    Alfven, H.

    1981-01-01

    Attention is given to experimental and theoretical approaches to plasma physics, plasma phenomena in laboratory and space, field and particle aspects of plasmas, the present state of the classical theory, boundary conditions and circuit dependence, and cosmology. Electric currents in space plasmas are considered, taking into account dualism in physics, particle-related phenomena in plasma physics, magnetic field lines, filaments, local plasma properties and the circuit, electric double layers, field-aligned currents as 'cables', an expanding circuit, different types of plasma regions, the cellular structure of space, and the fine structure of active plasma regions. Other topics discussed are related to circuits, the theory of cosmic plasmas, the origin of the solar system, the coexistence of matter and antimatter, annihilation as a source of energy, the Hubble expansion in a Euclidean space, and a model for the evolution of the Metagalaxy.

  15. Disentangling the Cosmic Web with Lagrangian Submanifold

    NASA Astrophysics Data System (ADS)

    Shandarin, Sergei F.; Medvedev, Mikhail V.

    2016-10-01

    The Cosmic Web is a complicated highly-entangled geometrical object. Remarkably it has formed from practically Gaussian initial conditions, which may be regarded as the simplest departure from exactly uniform universe in purely deterministic mapping. The full complexity of the web is revealed neither in configuration no velocity spaces considered separately. It can be fully appreciated only in six-dimensional (6D) phase space. However, studies of the phase space is complicated by the fact that every projection of it on a three-dimensional (3D) space is multivalued and contained caustics. In addition phase space is not a metric space that complicates studies of geometry. We suggest to use Lagrangian submanifold i.e., x = x(q), where both x and q are 3D vectors instead of the phase space for studies the complexity of cosmic web in cosmological N-body dark matter simulations. Being fully equivalent in dynamical sense to the phase space it has an advantage of being a single valued and also metric space.

  16. 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

  17. Physics of the Cosmic Microwave Background Radiation

    NASA Astrophysics Data System (ADS)

    Wands, David; Piattella, Oliver F.; Casarini, Luciano

    The cosmic microwave background (CMB) radiation provides a remarkable window onto the early universe, revealing its composition and structure. In these lectures we review and discuss the physics underlying the main features of the CMB.

  18. BLAST: CORRELATIONS IN THE COSMIC FAR-INFRARED BACKGROUND AT 250, 350, AND 500 mum REVEAL CLUSTERING OF STAR-FORMING GALAXIES

    SciTech Connect

    Viero, Marco P.; Martin, Peter G.; Netterfield, Calvin B.; Ade, Peter A. R.; Griffin, Matthew; Hargrave, Peter C.; Mauskopf, Philip; Moncelsi, Lorenzo; Pascale, Enzo; Bock, James J.; Chapin, Edward L.; Halpern, Mark; Marsden, Gaelen; Devlin, Mark J.; Klein, Jeff; Gundersen, Joshua O.; Hughes, David H.; MacTavish, Carrie J.; Negrello, Mattia; Olmi, Luca

    2009-12-20

    We detect correlations in the cosmic far-infrared background due to the clustering of star-forming galaxies in observations made with the Balloon-borne Large Aperture Submillimeter Telescope, at 250, 350, and 500 mum. We perform jackknife and other tests to confirm the reality of the signal. The measured correlations are well fitted by a power law over scales of 5'-25', with DELTAI/I = 15.1% +- 1.7%. We adopt a specific model for submillimeter sources in which the contribution to clustering comes from sources in the redshift ranges 1.3 <= z <= 2.2, 1.5 <= z <= 2.7, and 1.7 <= z <= 3.2, at 250, 350, and 500 mum, respectively. With these distributions, our measurement of the power spectrum, P(k{sub t}heta), corresponds to linear bias parameters, b = 3.8 +- 0.6, 3.9 +- 0.6, and 4.4 +- 0.7, respectively. We further interpret the results in terms of the halo model, and find that at the smaller scales, the simplest halo model fails to fit our results. One way to improve the fit is to increase the radius at which dark matter halos are artificially truncated in the model, which is equivalent to having some star-forming galaxies at z >= 1 located in the outskirts of groups and clusters. In the context of this model, we find a minimum halo mass required to host a galaxy is log(M{sub min}/M{sub sun}) = 11.5{sup +0.4}{sub -0.1}, and we derive effective biases b{sub eff} = 2.2 +- 0.2, 2.4 +- 0.2, and 2.6 +- 0.2, and effective masses log(M{sub eff}/M{sub odot})=12.9+-0.3, 12.8 +- 0.2, and 12.7 +- 0.2, at 250, 350 and 500 mum, corresponding to spatial correlation lengths of r{sub 0} = 4.9, 5.0, and 5.2+-0.7 h{sup -1}Mpc, respectively. Finally, we discuss implications for clustering measurement strategies with Herschel and Planck.

  19. 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

  20. 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}.

  1. The temporal-spatial dynamics of feature maps during monocular deprivation revealed by chronic imaging and self-organization model simulation.

    PubMed

    Tong, Lei; Xie, Yang; Yu, Hongbo

    2016-12-17

    Experiments on the adult visual cortex of cats, ferrets and monkeys have revealed organized spatial relationships between multiple feature maps which can also be reproduced by the Kohonen and elastic net self-organization models. However, attempts to apply these models to simulate the temporal kinetics of monocular deprivation (MD) during the critical period, and their effects on the spatial arrangement of feature maps, have led to conflicting results. In this study, we performed MD and chronic imaging in the ferret visual cortex during the critical period of ocular dominance (OD) plasticity. We also used the Kohonen model to simulate the effects of MD on OD and orientation map development. Both the experiments and simulations demonstrated two general parameter-insensitive findings. Specifically, our first finding demonstrated that the OD index shift resulting from MD, and its subsequent recovery during binocular vision (BV), were both nonlinear, with a significantly stronger shift occurring during the initial period. Meanwhile, spatial reorganization of feature maps led to globally unchanged but locally shifted map patterns. In detail, we found that the periodicity of OD and orientation maps remained unchanged during, and after, deprivation. Relationships between OD and orientation maps remained similar but were significantly weakened due to OD border shifts. These results indicate that orthogonal gradient relationships between maps may be preset and are only mildly modifiable during the critical period. The Kohonen model was able to reproduce these experimental results, hence its role is further extended to the description of cortical feature map dynamics during development.

  2. Large-Scale Structure of the Molecular Gas in Taurus Revealed by High Linear Dynamic Range Spectral Line Mapping

    NASA Astrophysics Data System (ADS)

    Goldsmith, Paul F.; Heyer, Mark; Narayanan, Gopal; Snell, Ronald; Li, Di; Brunt, Chris

    2008-06-01

    We report the results of a 100 deg2 survey of the Taurus molecular cloud region in 12CO and 13CO J = 1→ 0. The image of the cloud in each velocity channel includes simeq3 × 106 Nyquist-sampled pixels on a 20'' grid. The high sensitivity and large spatial dynamic range of the maps reveal a very complex, highly structured cloud morphology, including filaments, cavities, and rings. The axes of the striations seen in the 12CO emission from relatively diffuse gas are aligned with the direction of the magnetic field. We have developed a statistical method for analyzing the pixels in which 12CO but not 13CO is detected, which allows us to determine the CO column in the diffuse portion of the cloud, as well as in the denser regions in which we detect both isotopologues. Using a column-density-dependent model for the CO fractional abundance, we derive the mass of the region mapped to be 2.4 × 104 M⊙, more than twice as large as would be obtained using a canonical fixed fractional abundance of 13CO, and a factor of 3 greater than would be obtained considering only the high column density regions. We determine that half the mass of the cloud is in regions having column density below 2.1 × 1021 cm-2. The distribution of young stars in the region covered is highly nonuniform, with the probability of finding a star in a pixel with a specified column density rising sharply for N(H2) = 6 × 1021 cm-2. We determine a relatively low star formation efficiency (mass of young stars/mass of molecular gas), between 0.3% and 1.2%, and an average star formation rate during the past 3 Myr of 8 × 10-5 stars yr-1.

  3. Cortical Hubs Revealed by Intrinsic Functional Connectivity: Mapping, Assessment of Stability, and Relation to Alzheimer’s Disease

    PubMed Central

    Buckner, Randy L.; Sepulcre, Jorge; Talukdar, Tanveer; Krienen, Fenna; Liu, Hesheng; Hedden, Trey; Andrews-Hanna, Jessica R.; Sperling, Reisa A.; Johnson, Keith A.

    2009-01-01

    Recent evidence suggests that some brain areas act as hubs interconnecting distinct, functionally-specialized systems. These nexuses are intriguing because of their potential role in integration and also because they may augment metabolic cascades relevant to brain disease. To identify regions of high connectivity in the human cerebral cortex, we applied a computationally-efficient approach to map the degree of intrinsic functional connectivity across the brain. Analysis of two separate fMRI datasets (each n=24) demonstrated hubs throughout heteromodal areas of association cortex. Prominent hubs were located within posterior cingulate, lateral temporal, lateral parietal, and medial/lateral prefrontal cortices. Network analysis revealed that many, but not all, hubs were located within regions previously implicated as components of the default network. A third dataset (n=12) demonstrated that the locations of hubs were present across passive and active task states suggesting that they reflect a stable property of cortical network architecture. To obtain an accurate reference map, data were combined across 127 participants to yield a consensus estimate of cortical hubs. Using this consensus estimate, we explored whether the topography of hubs could explain the pattern of vulnerability in Alzheimer’s disease (AD) as some models suggest that regions of high activity and metabolism accelerate pathology. PET amyloid imaging in AD (n=10) as compared to older controls (n=29) showed high Aβ deposition in the locations of cortical hubs consistent with the possibility that hubs, while acting as critical waystations for information processing, may also augment the underlying pathological cascade in AD. PMID:19211893

  4. 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...

  5. 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...

  6. 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

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

    DOE PAGES

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

    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

  8. Association mapping reveals the genetic architecture of tomato response to water deficit: focus on major fruit quality traits.

    PubMed

    Albert, Elise; Segura, Vincent; Gricourt, Justine; Bonnefoi, Julien; Derivot, Laurent; Causse, Mathilde

    2016-12-01

    Water scarcity constitutes a crucial constraint for agriculture productivity. High-throughput approaches in model plant species identified hundreds of genes potentially involved in survival under drought, but few having beneficial effects on quality and yield. Nonetheless, controlled water deficit may improve fruit quality through higher concentration of flavor compounds. The underlying genetic determinants are still poorly known. In this study, we phenotyped 141 highly diverse small fruit tomato accessions for 27 traits under two contrasting watering conditions. A subset of 55 accessions exhibited increased metabolite contents and maintained yield under water deficit. Using 6100 single nucleotide polymorphisms (SNPs), association mapping revealed 31, 41, and 44 quantitative trait loci (QTLs) under drought, control, and both conditions, respectively. Twenty-five additional QTLs were interactive between conditions, emphasizing the interest in accounting for QTLs by watering regime interactions in fruit quality improvement. Combining our results with the loci previously identified in a biparental progeny resulted in 11 common QTLs and contributed to a first detailed characterization of the genetic determinants of response to water deficit in tomato. Major QTLs for fruit quality traits were dissected and candidate genes were proposed using expression and polymorphism data. The outcomes provide a basis for fruit quality improvement under deficit irrigation while limiting yield losses.

  9. 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

  10. Expression quantitative trait locus mapping across water availability environments reveals contrasting associations with genomic features in Arabidopsis.

    PubMed

    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

    2013-09-01

    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.

  11. Association mapping reveals the genetic architecture of tomato response to water deficit: focus on major fruit quality traits

    PubMed Central

    Albert, Elise; Segura, Vincent; Gricourt, Justine; Bonnefoi, Julien; Derivot, Laurent; Causse, Mathilde

    2016-01-01

    Water scarcity constitutes a crucial constraint for agriculture productivity. High-throughput approaches in model plant species identified hundreds of genes potentially involved in survival under drought, but few having beneficial effects on quality and yield. Nonetheless, controlled water deficit may improve fruit quality through higher concentration of flavor compounds. The underlying genetic determinants are still poorly known. In this study, we phenotyped 141 highly diverse small fruit tomato accessions for 27 traits under two contrasting watering conditions. A subset of 55 accessions exhibited increased metabolite contents and maintained yield under water deficit. Using 6100 single nucleotide polymorphisms (SNPs), association mapping revealed 31, 41, and 44 quantitative trait loci (QTLs) under drought, control, and both conditions, respectively. Twenty-five additional QTLs were interactive between conditions, emphasizing the interest in accounting for QTLs by watering regime interactions in fruit quality improvement. Combining our results with the loci previously identified in a biparental progeny resulted in 11 common QTLs and contributed to a first detailed characterization of the genetic determinants of response to water deficit in tomato. Major QTLs for fruit quality traits were dissected and candidate genes were proposed using expression and polymorphism data. The outcomes provide a basis for fruit quality improvement under deficit irrigation while limiting yield losses. PMID:27856709

  12. 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.

  13. 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.

  14. 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

  15. 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

    PubMed Central

    Shirasawa, Kenta; Bertioli, David J.; Varshney, Rajeev K.; Moretzsohn, Marcio C.; Leal-Bertioli, Soraya C. M.; Thudi, Mahendar; Pandey, Manish K.; Rami, Jean-Francois; Foncéka, Daniel; Gowda, Makanahally V. C.; Qin, Hongde; Guo, Baozhu; Hong, Yanbin; Liang, Xuanqiang; Hirakawa, Hideki; Tabata, Satoshi; Isobe, Sachiko

    2013-01-01

    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 populations derived from crosses between the A genome diploid species, Arachis duranensis and Arachis stenosperma; the B genome diploid species, Arachis ipaënsis and Arachis magna; and between the AB genome tetraploids, A. hypogaea and an artificial amphidiploid (A. ipaënsis × A. duranensis)4×, were used to construct genetic linkage maps: 10 linkage groups (LGs) of 544 cM with 597 loci for the A genome; 10 LGs of 461 cM with 798 loci for the B genome; and 20 LGs of 1442 cM with 1469 loci for the AB genome. The resultant maps plus 13 published maps were integrated into a consensus map covering 2651 cM with 3693 marker loci which was anchored to 20 consensus LGs corresponding to the A and B genomes. The comparative genomics with genome sequences of Cajanus cajan, Glycine max, Lotus japonicus, and Medicago truncatula revealed that the Arachis genome has segmented synteny relationship to the other legumes. The comparative maps in legumes, integrated tetraploid consensus maps, and genome-specific diploid maps will increase the genetic and genomic understanding of Arachis and should facilitate molecular breeding. PMID:23315685

  16. 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.

    PubMed

    Shirasawa, Kenta; Bertioli, David J; Varshney, Rajeev K; Moretzsohn, Marcio C; Leal-Bertioli, Soraya C M; Thudi, Mahendar; Pandey, Manish K; Rami, Jean-Francois; Foncéka, Daniel; Gowda, Makanahally V C; Qin, Hongde; Guo, Baozhu; Hong, Yanbin; Liang, Xuanqiang; Hirakawa, Hideki; Tabata, Satoshi; Isobe, Sachiko

    2013-04-01

    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 populations derived from crosses between the A genome diploid species, Arachis duranensis and Arachis stenosperma; the B genome diploid species, Arachis ipaënsis and Arachis magna; and between the AB genome tetraploids, A. hypogaea and an artificial amphidiploid (A. ipaënsis × A. duranensis)(4×), were used to construct genetic linkage maps: 10 linkage groups (LGs) of 544 cM with 597 loci for the A genome; 10 LGs of 461 cM with 798 loci for the B genome; and 20 LGs of 1442 cM with 1469 loci for the AB genome. The resultant maps plus 13 published maps were integrated into a consensus map covering 2651 cM with 3693 marker loci which was anchored to 20 consensus LGs corresponding to the A and B genomes. The comparative genomics with genome sequences of Cajanus cajan, Glycine max, Lotus japonicus, and Medicago truncatula revealed that the Arachis genome has segmented synteny relationship to the other legumes. The comparative maps in legumes, integrated tetraploid consensus maps, and genome-specific diploid maps will increase the genetic and genomic understanding of Arachis and should facilitate molecular breeding.

  17. 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

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

    PubMed

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

    2015-08-06

    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 makers. 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.

  19. 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.

  20. 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

  1. 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.

  2. A Global Orientation Map in the Primary Visual Cortex (V1): Could a Self Organizing Model Reveal Its Hidden Bias?

    PubMed Central

    Philips, Ryan T.; Chakravarthy, V. Srinivasa

    2017-01-01

    A remarkable accomplishment of self organizing models is their ability to simulate the development of feature maps in the cortex. Additionally, these models have been trained to tease out the differential causes of multiple feature maps, mapped on to the same output space. Recently, a Laterally Interconnected Synergetically Self Organizing Map (LISSOM) model has been used to simulate the mapping of eccentricity and meridional angle onto orthogonal axes in the primary visual cortex (V1). This model is further probed to simulate the development of the radial bias in V1, using a training set that consists of both radial (rectangular bars of random size and orientation) as well as non-radial stimuli. The radial bias describes the preference of the visual system toward orientations that match the angular position (meridional angle) of that orientation with respect to the point of fixation. Recent fMRI results have shown that there exists a coarse scale orientation map in V1, which resembles the meridional angle map, thereby providing a plausible neural basis for the radial bias. The LISSOM model, trained for the development of the retinotopic map, on probing for orientation preference, exhibits a coarse scale orientation map, consistent with these experimental results, quantified using the circular cross correlation (rc). The rc between the orientation map developed on probing with a thin annular ring containing sinusoidal gratings with a spatial frequency of 0.5 cycles per degree (cpd) and the corresponding meridional map for the same annular ring, has a value of 0.8894. The results also suggest that the radial bias goes beyond the current understanding of a node to node correlation between the two maps. PMID:28111542

  3. A Global Orientation Map in the Primary Visual Cortex (V1): Could a Self Organizing Model Reveal Its Hidden Bias?

    PubMed

    Philips, Ryan T; Chakravarthy, V Srinivasa

    2016-01-01

    A remarkable accomplishment of self organizing models is their ability to simulate the development of feature maps in the cortex. Additionally, these models have been trained to tease out the differential causes of multiple feature maps, mapped on to the same output space. Recently, a Laterally Interconnected Synergetically Self Organizing Map (LISSOM) model has been used to simulate the mapping of eccentricity and meridional angle onto orthogonal axes in the primary visual cortex (V1). This model is further probed to simulate the development of the radial bias in V1, using a training set that consists of both radial (rectangular bars of random size and orientation) as well as non-radial stimuli. The radial bias describes the preference of the visual system toward orientations that match the angular position (meridional angle) of that orientation with respect to the point of fixation. Recent fMRI results have shown that there exists a coarse scale orientation map in V1, which resembles the meridional angle map, thereby providing a plausible neural basis for the radial bias. The LISSOM model, trained for the development of the retinotopic map, on probing for orientation preference, exhibits a coarse scale orientation map, consistent with these experimental results, quantified using the circular cross correlation (rc ). The rc between the orientation map developed on probing with a thin annular ring containing sinusoidal gratings with a spatial frequency of 0.5 cycles per degree (cpd) and the corresponding meridional map for the same annular ring, has a value of 0.8894. The results also suggest that the radial bias goes beyond the current understanding of a node to node correlation between the two maps.

  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. Exceptional conservation of horse-human gene order on X chromosome revealed by high-resolution radiation hybrid mapping.

    PubMed

    Raudsepp, Terje; Lee, Eun-Joon; Kata, Srinivas R; Brinkmeyer, Candice; Mickelson, James R; Skow, Loren C; Womack, James E; Chowdhary, Bhanu P

    2004-02-24

    Development of a dense map of the horse genome is key to efforts aimed at identifying genes controlling health, reproduction, and performance. We herein report a high-resolution gene map of the horse (Equus caballus) X chromosome (ECAX) generated by developing and typing 116 gene-specific and 12 short tandem repeat markers on the 5,000-rad horse x hamster whole-genome radiation hybrid panel and mapping 29 gene loci by fluorescence in situ hybridization. The human X chromosome sequence was used as a template to select genes at 1-Mb intervals to develop equine orthologs. Coupled with our previous data, the new map comprises a total of 175 markers (139 genes and 36 short tandem repeats, of which 53 are fluorescence in situ hybridization mapped) distributed on average at approximately 880-kb intervals along the chromosome. This is the densest and most uniformly distributed chromosomal map presently available in any mammalian species other than humans and rodents. Comparison of the horse and human X chromosome maps shows remarkable conservation of gene order along the entire span of the chromosomes, including the location of the centromere. An overview of the status of the horse map in relation to mouse, livestock, and companion animal species is also provided. The map will be instrumental for analysis of X linked health and fertility traits in horses by facilitating identification of targeted chromosomal regions for isolation of polymorphic markers, building bacterial artificial chromosome contigs, or sequencing.

  6. Maps & minds : mapping through the ages

    USGS Publications Warehouse

    ,

    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.

  7. A Dense Brown Trout (Salmo trutta) Linkage Map Reveals Recent Chromosomal Rearrangements in the Salmo Genus and the Impact of Selection on Linked Neutral Diversity

    PubMed Central

    Leitwein, Maeva; Guinand, Bruno; Pouzadoux, Juliette; Desmarais, Erick; Berrebi, Patrick; Gagnaire, Pierre-Alexandre

    2017-01-01

    High-density linkage maps are valuable tools for conservation and eco-evolutionary issues. In salmonids, a complex rediploidization process consecutive to an ancient whole genome duplication event makes linkage maps of prime importance for investigating the evolutionary history of chromosome rearrangements. Here, we developed a high-density consensus linkage map for the brown trout (Salmo trutta), a socioeconomically important species heavily impacted by human activities. A total of 3977 ddRAD markers were mapped and ordered in 40 linkage groups using sex- and lineage-averaged recombination distances obtained from two family crosses. Performing map comparison between S. trutta and its sister species, S. salar, revealed extensive chromosomal rearrangements. Strikingly, all of the fusion and fission events that occurred after the S. salar/S. trutta speciation happened in the Atlantic salmon branch, whereas the brown trout remained closer to the ancestral chromosome structure. Using the strongly conserved synteny within chromosome arms, we aligned the brown trout linkage map to the Atlantic salmon genome sequence to estimate the local recombination rate in S. trutta at 3721 loci. A significant positive correlation between recombination rate and within-population nucleotide diversity (π) was found, indicating that selection constrains variation at linked neutral sites in brown trout. This new high-density linkage map provides a useful genomic resource for future aquaculture, conservation, and eco-evolutionary studies in brown trout. PMID:28235829

  8. 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

  9. 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

  10. 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.

  11. Global Anisotropies in TeV Cosmic Rays Related to the Sun's Local Galactic Environment from IBEX (Invited)

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

    The Interstellar Boundary Explorer (IBEX) observes enhanced Energetic Neutral Atoms (ENAs) emission from a narrow 'ribbon' likely centered on the local interstellar (LIS) magnetic field direction. Further, IBEX has revised the local interstellar velocity based on interstellar atom measurements. These new determinations are shown to be consistent with the interstellar modulation of TeV cosmic rays revealed in global anisotropy maps of Milagro, Asγ and IceCube.

  12. 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.

  13. 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.

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

    NASA Astrophysics Data System (ADS)

    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.

    2014-02-01

    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, 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.

  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 high-resolution whole-genome cattle-human comparative map reveals details of mammalian chromosome evolution.

    PubMed

    Everts-van der Wind, Annelie; Larkin, Denis M; Green, Cheryl A; Elliott, Janice S; Olmstead, Colleen A; Chiu, Readman; Schein, Jacqueline E; Marra, Marco A; Womack, James E; Lewin, Harris A

    2005-12-20

    Approximately 3,000 cattle bacterial artificial chromosome (BAC)-end sequences were added to the Illinois-Texas 5,000-rad RH (RH, radiation hybrid) map. The BAC-end sequences selected for mapping are approximately 1 Mbp apart on the human chromosomes as determined by blastn analysis. The map has 3,484 ordered markers, of which 3,204 are anchored in the human genome. Two hundred-and-one homologous synteny blocks (HSBs) were identified, of which 27 are previously undiscovered, 79 are extended, 26 were formed by previously unrecognized breakpoints in 18 previously defined HSBs, and 23 are the result of fusions. The comparative coverage relative to the human genome is approximately 91%, or 97% of the theoretical maximum. The positions of 64% of all cattle centromeres and telomeres were reassigned relative to their positions on the previous map, thus facilitating a more detailed comparative analysis of centromere and telomere evolution. As an example of the utility of the high-resolution map, 22 cattle BAC fingerprint contigs were directly anchored to cattle chromosome 19 [Bos taurus, (BTA) 19]. The order of markers on the cattle RH and fingerprint maps of BTA19 and the sequence-based map of human chromosome 17 [Homo sapiens, (HSA) 17] were found to be highly consistent, with only two minor ordering discrepancies between the RH map and fingerprint contigs. The high-resolution Illinois-Texas 5,000-rad RH and comparative maps will facilitate identification of candidate genes for economically important traits, the phylogenomic analysis of mammalian chromosomes, proofing of the BAC fingerprint map and, ultimately, aid the assembly of cattle whole-genome sequence.

  17. Cosmic electrons. [literature review

    NASA Technical Reports Server (NTRS)

    Ramaty, R.

    1974-01-01

    The published literature on cosmic electrons is summarized. The primary and secondary sources of cosmic electrons are discussed, and the propagation of the electrons in the interstellar medium is studied with respect to energy loss mechanisms, age distributions, and spectral modifications during flight. Various portions of the electron and positron spectra are then considered in relation to problems of astrophysics. New information is presented on such topics as the origin of low-energy positrons, the decay kinematics of the pi-mu-e process, the application of age distributions for nuclear cosmic rays to cosmic electrons, and the possibility of nonidentical sources for cosmic electrons and protons.

  18. 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.

  19. 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.

  20. 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

  1. 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

  2. SNP Discovery and Chromosome Anchoring Provide the First Physically-Anchored Hexaploid Oat Map and Reveal Synteny with Model Species

    PubMed Central

    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

    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

  3. Cosmic Inflation

    ScienceCinema

    Lincoln, Don

    2016-07-12

    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.

  4. 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.

  5. 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.

  6. Particle Astrophysics with Cosmic Neutrinos

    NASA Astrophysics Data System (ADS)

    Kheirandish, Ali

    IceCube's discovery of cosmic neutrinos offers a unique view of our universe and provides powerful insights into some of the most energetic and enigmatic objects in the cosmos. Cosmic neutrinos reveal an unobstructed view at wavelengths where the universe is opaque to photons. The existence of the cosmic-neutrino flux has challenged our understanding of the universe. It is somewhat counterintuitive that the most surprising property of the observed flux is its magnitude. An immediate inference from the large neutrino flux observed by IceCube, which is predominantly extragalactic in origin, is that the total energy density of neutrinos in the high-energy universe is similar to that of photons. The matching energy densities of the extragalactic gamma-ray flux detected by Fermi and the high-energy neutrino flux measured by IceCube suggest the possibility of a common origin. Therefore, rather than detecting some exotic sources, it looks more likely that IceCube observes the same universe as astronomers do. The finding implies that a large fraction of the energy in the non-thermal universe originates in hadronic processes, indicating a larger level than previously thought. The focus of this dissertation is on identifying the sources of high-energy cosmic neutrinos observed in IceCube. Moreover, with the lack of confirmation to date of any source (type of sources) as the dominant contributor to the observed neutrino flux, we have studied prospects for observing different sources in IceCube by considering both transient and steady sources in the sky. Finally, we introduce new techniques to study the strength of neutrino dark matter interactions with the properties of high-energy cosmic neutrinos.

  7. 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

  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

    2016-05-03

    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.

  9. Integration of high-resolution physical and genetic map reveals differential recombination frequency between chromosomes and the genome assembling quality in cucumber.

    PubMed

    Lou, Qunfeng; He, Yuhua; 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.

  10. Automated classification of interplanetary dust particles: Johnson Space Center Cosmic Dust Catalog Volume 15

    NASA Astrophysics Data System (ADS)

    Lasue, Jeremie; Stepinski, Tomasz; Bell, Samuel W.

    2010-05-01

    The ``Cosmic Dust Catalog,'' published by the NASA Johnson Space Center (JSC), describes thousands of interplanetary dust particles subjected to preliminary analysis and with labels indicating their origin. However, only about 80% of the particles are assigned unambiguous labels, the labels of the remaining 20% being uncertain. In addition, the Stardust mission results opened up the possibility that some particles classified as terrestrial contaminants are instead of cosmic (cometary) origin. In this article, we present a methodology for automatic classification of particles on the basis of similarity of their X-ray energy dispersive spectrometry spectra. The method is applied to the 467 particles constituting Volume 15 of the catalog. A first part of the analysis is to digitize the spectra from their scanned images. The digitized spectra are subjected to agglomerative clustering, which reveals 16 distinct clusters or compositional types of particles. The Sammon's map is used to visualize the relationship between different clusters; 6 clusters corresponding to cosmic particles and 10 clusters corresponding to terrestrial contaminants are clearly separated on the map indicating overall differences between diverse spectra of cosmic and terrestrial particles. By reconciling labels with the clustering structures, we propose the relabeling of 155 particles including the relabeling of 31 terrestrial contaminants into cosmic particles. The proposed relabeling needs to be confirmed by in-depth study of these particles. The paucity of particles with firmly determined cometary or asteroidal origin makes it difficult to establish whether the spectra based autoclassification can be utilized to discriminate between cometary and asteroidal particles. The methodology presented here can be used to classify all particles published in the catalog, as well as different samples for which comparable spectra are available.

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

    PubMed

    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

    2010-07-01

    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 approximately 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.

  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. Extended gene map reveals tripartite motif, C-type lectin, and Ig superfamily type genes within a subregion of the chicken MHC-B affecting infectious disease.

    PubMed

    Shiina, Takashi; Briles, W Elwood; Goto, Ronald M; Hosomichi, Kazuyoshi; Yanagiya, Kazuyo; Shimizu, Sayoko; Inoko, Hidetoshi; Miller, Marcia M

    2007-06-01

    MHC haplotypes have a remarkable influence on whether tumors form following infection of chickens with oncogenic Marek's disease herpesvirus. Although resistance to tumor formation has been mapped to a subregion of the chicken MHC-B region, the gene or genes responsible have not been identified. A full gene map of the subregion has been lacking. We have expanded the MHC-B region gene map beyond the 92-kb core previously reported for another haplotype revealing the presence of 46 genes within 242 kb in the Red Jungle Fowl haplotype. Even though MHC-B is structured differently, many of the newly revealed genes are related to loci typical of the MHC in other species. Other MHC-B loci are homologs of genes found within MHC paralogous regions (regions thought to be derived from ancient duplications of a primordial immune defense complex where genes have undergone differential silencing over evolutionary time) on other chromosomes. Still others are similar to genes that define the NK complex in mammals. Many of the newly mapped genes display allelic variability and fall within the MHC-B subregion previously shown to affect the formation of Marek's disease tumors and hence are candidates for genes conferring resistance.

  14. Anatomically-standardized maps reveal distinct patterns of cartilage thickness with increasing severity of medial compartment knee osteoarthritis.

    PubMed

    Favre, Julien; Erhart-Hledik, Jennifer C; Blazek, Katerina; Fasel, Benedikt; Gold, Garry E; Andriacchi, Thomas P

    2017-02-24

    While cartilage thickness alterations are a central element of knee osteoarthritis (OA), differences among disease stages are still incompletely understood. This study aimed to quantify the spatial-variations in cartilage thickness using anatomically-standardized thickness maps and test if there are characteristic patterns in patients with different stages of medial compartment knee OA. Magnetic resonance images were acquired for 75 non-OA and 100 OA knees of varying severities (Kellgren and Lawrence (KL) scores 1-4). Three-dimensional cartilage models were reconstructed and a shape matching technique was applied to convert the models into two-dimensional anatomically-standardized thickness maps. Difference thickness maps and statistical parametric mapping were used to compare the four OA and the non-OA subgroups. This analysis showed distinct thickness patterns for each clinical stage that formed a coherent succession from the non-OA to the KL 4 subgroups. Interestingly, the only significant difference for early stage (KL 1) was thicker femoral cartilage. With increase in disease severity, typical patterns developed, including thinner cartilage in the anterior area of the medial condyle (significant for KL 3 and 4) and thicker cartilage in the posterior area of the medial and lateral condyles (significant for all OA subgroups). The tibial patterns mainly consisted of thinner cartilage for both medial and lateral compartments (significant for KL 2-4). Comparing anatomically-standardized maps allowed identifying patterns of thickening and thinning over the entire cartilage surface, consequently improving the characterization of thickness differences associated with OA. The results also highlighted the value of anatomically-standardized maps to analyze spatial variations in cartilage thickness. This article is protected by copyright. All rights reserved.

  15. 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.

  16. Syntenic relationships between cucumber (Cucumis sativus L.) and melon (C. melo L.) chromosomes as revealed by comparative genetic mapping

    PubMed Central

    2011-01-01

    Background Cucumber, Cucumis sativus L. (2n = 2 × = 14) and melon, C. melo L. (2n = 2 × = 24) are two important vegetable species in the genus Cucumis (family Cucurbitaceae). Both species have an Asian origin that diverged approximately nine million years ago. Cucumber is believed to have evolved from melon through chromosome fusion, but the details of this process are largely unknown. In this study, comparative genetic mapping between cucumber and melon was conducted to examine syntenic relationships of their chromosomes. Results Using two melon mapping populations, 154 and 127 cucumber SSR markers were added onto previously reported F2- and RIL-based genetic maps, respectively. A consensus melon linkage map was developed through map integration, which contained 401 co-dominant markers in 12 linkage groups including 199 markers derived from the cucumber genome. Syntenic relationships between melon and cucumber chromosomes were inferred based on associations between markers on the consensus melon map and cucumber draft genome scaffolds. It was determined that cucumber Chromosome 7 was syntenic to melon Chromosome I. Cucumber Chromosomes 2 and 6 each contained genomic regions that were syntenic with melon chromosomes III+V+XI and III+VIII+XI, respectively. Likewise, cucumber Chromosomes 1, 3, 4, and 5 each was syntenic with genomic regions of two melon chromosomes previously designated as II+XII, IV+VI, VII+VIII, and IX+X, respectively. However, the marker orders in several syntenic blocks on these consensus linkage maps were not co-linear suggesting that more complicated structural changes beyond simple chromosome fusion events have occurred during the evolution of cucumber. Conclusions Comparative mapping conducted herein supported the hypothesis that cucumber chromosomes may be the result of chromosome fusion from a 24-chromosome progenitor species. Except for a possible inversion, cucumber Chromosome 7 has largely remained intact in the past nine million years

  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

    Chapman, Carol; Henry, Matthew; Bishop-Lilly, Kimberly A; 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.

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

    DOE PAGES

    Chapman, Carol; Henry, Matthew; Bishop-Lilly, Kimberly A.; ...

    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

  19. 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)

  20. 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.

  1. 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.

  2. 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.

  3. Quantitative trait locus mapping reveals complex genetic architecture of quantitative virulence in the wheat pathogen Zymoseptoria tritici.

    PubMed

    Stewart, Ethan L; Croll, Daniel; Lendenmann, Mark H; Sanchez-Vallet, Andrea; Hartmann, Fanny E; Palma-Guerrero, Javier; Ma, Xin; McDonald, Bruce A

    2016-11-21

    We conducted a comprehensive analysis of virulence in the fungal wheat pathogen Zymoseptoria tritici using quantitative trait locus (QTL) mapping. High-throughput phenotyping based on automated image analysis allowed the measurement of pathogen virulence on a scale and with a precision that was not previously possible. Across two mapping populations encompassing more than 520 progeny, 540 710 pycnidia were counted and their sizes and grey values were measured. A significant correlation was found between pycnidia size and both spore size and number. Precise measurements of percentage leaf area covered by lesions provided a quantitative measure of host damage. Combining these large and accurate phenotypic datasets with a dense panel of restriction site-associated DNA sequencing (RADseq) genetic markers enabled us to genetically dissect pathogen virulence into components related to host damage and those related to pathogen reproduction. We showed that different components of virulence can be under separate genetic control. Large- and small-effect QTLs were identified for all traits, with some QTLs specific to mapping populations, cultivars and traits and other QTLs shared among traits within the same mapping population. We associated the presence of four accessory chromosomes with small, but significant, increases in several virulence traits, providing the first evidence for a meaningful function associated with accessory chromosomes in this organism. A large-effect QTL involved in host specialization was identified on chromosome 7, leading to the identification of candidate genes having a large effect on virulence.

  4. 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…

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

    NASA Astrophysics Data System (ADS)

    Schwadron, Nathan; McComas, David; Funsten, Herbert; Zank, Gary; Christian, Eric; Frisch, Priscilla; Desiati, Paolo; Jokipii, Jack; Möbius, Eberhard; Adams, Fred

    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 (TeV) cosmic rays and diffusive propagation from supernova sources revealed in global anisotropy maps of ground-based high-energy cosmic-ray observatories (Milagro, Asgamma and IceCube). Further, we discuss recent observations by IBEX of the heliotail and its relationship with structures observed in TeV cosmic ray anisotropy maps. 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 local interstellar medium, particularly important at the time when the Voyager spacecraft are leaving our heliosphere.

  6. 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.

  7. Genomewide mapping reveals a combination of different genetic effects causing the genetic basis of heterosis in two elite rice hybrids.

    PubMed

    Li, Lanzhi; He, Xiaohong; Zhang, Hongyan; Wang, Zhiming; Sun, Congwei; Mou, Tongmin; Li, Xinqi; Zhang, Yuanming; Hu, Zhongli

    2015-06-01

    North Carolina design III (NCIII) is one of the most powerful and widely used mating designs for understanding the genetic basis of heterosis. However, the quantitative trait mapping (QTL) conducted in previous studies with this design was mainly based on analysis of variance (ANOVA), composite interval or multiple interval mapping methods. These methodologies could not investigate all kinds of genetic effects, especially epistatic effects, simultaneously on the whole genome. In this study, with a statistical method for mapping epistatic QTL associated with heterosis using the recombinant inbred line (RIL)-based NCIII design, we conducted QTL mapping for nine agronomic traits of two elite hybrids to characterize the mode of gene action contributing to heterosis on a whole genomewide scale. In total, 23 main-effect QTL (M-QTL) and 23 digenic interactions in IJ (indica x japonica) hybrids, 11 M-QTL and 82 digenic interactions in II (indica x indica) hybrid QTLs were identified in the present study. The variation explained by individual M-QTL or interactions ranged from 2.3 to 11.0%. The number of digenic interactions and the total variation explained by interactions of each trait were larger than those of M-QTL. The augmented genetic effect ratio of most M-QTL and digenic interactions in (L1 - L2) data of two backcross populations (L1 and L2) showed complete dominance or overdominance, and in (L1 + L2) data showed an additive effect. Our results indicated that the dominance, overdominance and epistatic effect were important in conditioning the genetic basis of heterosis of the two elite hybrids. The relative contributions of the genetic components varied with traits and the genetic basis of the two hybrids was different.

  8. 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

  9. 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.

  10. 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.

  11. 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…

  12. 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

  13. 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.

  14. Physical and genetic map of the Lactococcus lactis subsp. cremoris MG1363 chromosome: comparison with that of Lactococcus lactis subsp. lactis IL 1403 reveals a large genome inversion.

    PubMed Central

    Le Bourgeois, P; Lautier, M; van den Berghe, L; Gasson, M J; Ritzenthaler, P

    1995-01-01

    A physical and genetic map of the chromosome of the Lactococcus lactis subsp. cremoris reference strain MG1363 was established. The physical map was constructed for NotI, ApaI, and SmaI enzymes by using a strategy that combines creation of new rare restriction sites by the random-integration vector pRL1 and ordering of restriction fragments by indirect end-labeling experiments. The MG1363 chromosome appeared to be circular and 2,560 kb long. Seventy-seven chromosomal markers were located on the physical map by hybridization experiments. Integration via homologous recombination of pRC1-derived plasmids allowed a more precise location of some lactococcal genes and determination of their orientation on the chromosome. The MG1363 chromosome contains six rRNA operons; five are clustered within 15% of the chromosome and transcribed in the same direction. Comparison of the L. lactis subsp. cremoris MG1363 physical map with those of the two L. lactis subsp. lactis strains IL1403 and DL11 revealed a high degree of restriction polymorphism. At the genetic organization level, despite an overall conservation of gene organization, strain MG1363 presents a large inversion of half of the genome in the region containing the rRNA operons. PMID:7751295

  15. 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

  16. 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.

  17. 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).

  18. 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).

  19. Improved Culture Medium (TiKa) for Mycobacterium avium Subspecies Paratuberculosis (MAP) Matches qPCR Sensitivity and Reveals Significant Proportions of Non-viable MAP in Lymphoid Tissue of Vaccinated MAP Challenged Animals

    PubMed Central

    Bull, Tim J.; Munshi, Tulika; Mikkelsen, Heidi; Hartmann, Sofie B.; Sørensen, Maria R.; Garcia, Joanna S.; Lopez-Perez, Paula M.; Hofmann, Sven; Hilpert, Kai; Jungersen, Gregers

    2017-01-01

    The quantitative detection of viable pathogen load is an important tool in determining the degree of infection in animals and contamination of foodstuffs. Current conventional culture methods are limited in their ability to determine these levels in Mycobacterium avium subspecies paratuberculosis (MAP) due to slow growth, clumping and low recoverability issues. The principle goal of this study was to evaluate a novel culturing process (TiKa) with unique ability to stimulate MAP growth from low sample loads and dilutions. We demonstrate it was able to stimulate a mean 29-fold increase in recoverability and an improved sensitivity of up to three logs when compared with conventional culture. Using TiKa culture, MAP clumping was minimal and produced visible colonies in half the time required by standard culture methods. Parallel quantitative evaluation of the TiKa culture approach and qPCR on MAP loads in tissue and gut mucosal samples from a MAP vaccine-challenge study, showed good correlations between colony counts (cfu) and qPCR derived genome equivalents (Geq) over a large range of loads with a 30% greater sensitivity for TiKa culture approach at low loads (two logs). Furthermore, the relative fold changes in Geq and cfu from the TiKa culture approach suggests that non-mucosal tissue loads from MAP infected animals contained a reduced proportion of non-viable MAP (mean 19-fold) which was reduced significantly further (mean 190-fold) in vaccinated “reactor” calves. This study shows TiKa culture equates well with qPCR and provides important evidence that accuracy in estimating viable MAP load using DNA tests alone may vary significantly between samples of mucosal and lymphatic origin. PMID:28101082

  20. Improved Culture Medium (TiKa) for Mycobacterium avium Subspecies Paratuberculosis (MAP) Matches qPCR Sensitivity and Reveals Significant Proportions of Non-viable MAP in Lymphoid Tissue of Vaccinated MAP Challenged Animals.

    PubMed

    Bull, Tim J; Munshi, Tulika; Mikkelsen, Heidi; Hartmann, Sofie B; Sørensen, Maria R; Garcia, Joanna S; Lopez-Perez, Paula M; Hofmann, Sven; Hilpert, Kai; Jungersen, Gregers

    2016-01-01

    The quantitative detection of viable pathogen load is an important tool in determining the degree of infection in animals and contamination of foodstuffs. Current conventional culture methods are limited in their ability to determine these levels in Mycobacterium avium subspecies paratuberculosis (MAP) due to slow growth, clumping and low recoverability issues. The principle goal of this study was to evaluate a novel culturing process (TiKa) with unique ability to stimulate MAP growth from low sample loads and dilutions. We demonstrate it was able to stimulate a mean 29-fold increase in recoverability and an improved sensitivity of up to three logs when compared with conventional culture. Using TiKa culture, MAP clumping was minimal and produced visible colonies in half the time required by standard culture methods. Parallel quantitative evaluation of the TiKa culture approach and qPCR on MAP loads in tissue and gut mucosal samples from a MAP vaccine-challenge study, showed good correlations between colony counts (cfu) and qPCR derived genome equivalents (Geq) over a large range of loads with a 30% greater sensitivity for TiKa culture approach at low loads (two logs). Furthermore, the relative fold changes in Geq and cfu from the TiKa culture approach suggests that non-mucosal tissue loads from MAP infected animals contained a reduced proportion of non-viable MAP (mean 19-fold) which was reduced significantly further (mean 190-fold) in vaccinated "reactor" calves. This study shows TiKa culture equates well with qPCR and provides important evidence that accuracy in estimating viable MAP load using DNA tests alone may vary significantly between samples of mucosal and lymphatic origin.

  1. Mapping of barley alpha-amylases and outer subsite mutants reveals dynamic high-affinity subsites and barriers in the long substrate binding cleft.

    PubMed

    Kandra, Lili; Hachem, Maher Abou; Gyémánt, Gyöngyi; Kramhøft, Birte; Svensson, Birte

    2006-09-18

    Subsite affinity maps of long substrate binding clefts in barley alpha-amylases, obtained using a series of maltooligosaccharides of degree of polymerization of 3-12, revealed unfavorable binding energies at the internal subsites -3 and -5 and at subsites -8 and +3/+4 defining these subsites as binding barriers. Barley alpha-amylase 1 mutants Y105A and T212Y at subsite -6 and +4 resulted in release or anchoring of bound substrate, thus modifying the affinities of other high-affinity subsites (-2 and +2) and barriers. The double mutant Y105A-T212Y displayed a hybrid subsite affinity profile, converting barriers to binding areas. These findings highlight the dynamic binding energy distribution and the versatility of long maltooligosaccharide derivatives in mapping extended binding clefts in alpha-amylases.

  2. 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

  3. Genetic Architecture of Resistance to Alternaria brassicae in Arabidopsis thaliana: QTL Mapping Reveals Two Major Resistance-Conferring Loci

    PubMed Central

    Rajarammohan, Sivasubramanian; Kumar, Amarendra; Gupta, Vibha; Pental, Deepak; Pradhan, Akshay K.; Kaur, Jagreet

    2017-01-01

    Alternaria brassicae, a necrotrophic fungal pathogen, causes Alternaria blight, one of the most important diseases of oleiferous Brassica crops. The current study utilized Arabidopsis as a model to decipher the genetic architecture of defense against A. brassicae. Significant phenotypic variation that was largely genetically determined was observed among Arabidopsis accessions in response to pathogen challenge. Three biparental mapping populations were developed from three resistant accessions viz. CIBC-5, Ei-2, and Cvi-0 and two susceptible accessions – Gre-0 and Zdr-1 (commonly crossed to CIBC-5 and Ei-2). A total of six quantitative trait locus (QTLs) governing resistance to A. brassicae were identified, five of which were population-specific while one QTL was common between all the three mapping populations. Interestingly, the common QTL had varying phenotypic contributions in different populations, which can be attributed to the genetic background of the parental accessions. The presence of both common and population-specific QTLs indicate that resistance to A. brassicae is quantitative, and that different genes may mediate resistance to the pathogen in different accessions. Two of the QTLs had moderate-to-large effects, one of which explained nearly 50% of the variation. The large effect QTLs may therefore contain genes that could play a significant role in conferring resistance even in heterologous hosts. PMID:28286515

  4. 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.

  5. 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

  6. High-resolution sex-specific linkage maps of the mouse reveal polarized distribution of crossovers in male germline.

    PubMed

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

    2014-05-01

    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.

  7. 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

  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. The Cosmic Ray Leptons Puzzle

    NASA Astrophysics Data System (ADS)

    Brun, P.; Bertone, G.; Cirelli, M.; Moulin, E.

    2009-11-01

    Recent measurements of cosmic ray electrons and positrons by PAMELA, ATIC, Fermi and HESS have revealed interesting excesses and features in the GeV-TeV range. Many possible explanations have been suggested, invoking one or more nearby primary sources such as pulsars and supernova remnants, or dark matter. Based on the output of the TANGO in PARIS --Testing Astroparticle with the New GeV/TeV Observations in Positrons And electRons : Identifying the Sources-- workshop held in Paris in May 2009, we review here the latest experimental results and we discuss some virtues and drawbacks of the many theoretical interpretations proposed so far.

  10. 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.

  11. Cosmic-ray astrochemistry.

    PubMed

    Indriolo, Nick; McCall, Benjamin J

    2013-10-07

    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.

  12. Mapping of Saccharomyces cerevisiae metabolites in fermenting wheat straight-dough reveals succinic acid as pH-determining factor.

    PubMed

    Jayaram, Vinay B; Cuyvers, Sven; Lagrain, Bert; Verstrepen, Kevin J; Delcour, Jan A; Courtin, Christophe M

    2013-01-15

    Fermenting yeast does not merely cause dough leavening, but also contributes to the bread aroma and might alter dough rheology. Here, the yeast carbon metabolism was mapped during bread straight-dough fermentation. The concentration of most metabolites changed quasi linearly as a function of fermentation time. Ethanol and carbon dioxide concentrations reached up to 60 mmol/100g flour. Interestingly, high levels of glycerol (up to 10 mmol/100g flour) and succinic acid (up to 1.6 mmol/100g flour) were produced during dough fermentation. Further tests showed that, contrary to current belief, the pH decrease in fermenting dough is primarily caused by the production of succinic acid by the yeast instead of carbon dioxide dissolution or bacterial organic acids. Together, our results provide a comprehensive overview of metabolite production during dough fermentation and yield insight into the importance of some of these metabolites for dough properties.

  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.

  14. Cultivar-Based Introgression Mapping Reveals Wild Species-Derived Pm-0, the Major Powdery Mildew Resistance Locus in Squash

    PubMed Central

    Holdsworth, William L.; LaPlant, Kyle E.; Bell, Duane C.; Jahn, Molly M.; Mazourek, Michael

    2016-01-01

    Powdery mildew is a major fungal disease on squash and pumpkin (Cucurbita spp.) in the US and throughout the world. Genetic resistance to the disease is not known to occur naturally within Cucurbita pepo and only infrequently in Cucurbita moschata, but has been achieved in both species through the introgression of a major resistance gene from the wild species Cucurbita okeechobeensis subsp. martinezii. At present, this gene, Pm-0, is used extensively in breeding, and is found in nearly all powdery mildew-resistant C. pepo and C. moschata commercial cultivars. In this study, we mapped C. okeechobeensis subsp. martinezii-derived single nucleotide polymorphism (SNP) alleles in a set of taxonomically and morphologically diverse and resistant C. pepo and C. moschata cultivars bred at Cornell University that, by common possession of Pm-0, form a shared-trait introgression panel. High marker density was achieved using genotyping-by-sequencing, which yielded over 50,000 de novo SNP markers in each of the three Cucurbita species genotyped. A single 516.4 kb wild-derived introgression was present in all of the resistant cultivars and absent in a diverse set of heirlooms that predated the Pm-0 introgression. The contribution of this interval to powdery mildew resistance was confirmed by association mapping in a C. pepo cultivar panel that included the Cornell lines, heirlooms, and 68 additional C. pepo cultivars and with an independent F2 population derived from C. okeechobeensis subsp. martinezii x C. moschata. The interval was refined to a final candidate interval of 76.4 kb and CAPS markers were developed inside this interval to facilitate marker-assisted selection. PMID:27936008

  15. A complex recombination pattern in the genome of allotetraploid Brassica napus as revealed by a high-density genetic map.

    PubMed

    Cai, Guangqin; Yang, Qingyong; 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.

  16. Cultivar-Based Introgression Mapping Reveals Wild Species-Derived Pm-0, the Major Powdery Mildew Resistance Locus in Squash.

    PubMed

    Holdsworth, William L; LaPlant, Kyle E; Bell, Duane C; Jahn, Molly M; Mazourek, Michael

    2016-01-01

    Powdery mildew is a major fungal disease on squash and pumpkin (Cucurbita spp.) in the US and throughout the world. Genetic resistance to the disease is not known to occur naturally within Cucurbita pepo and only infrequently in Cucurbita moschata, but has been achieved in both species through the introgression of a major resistance gene from the wild species Cucurbita okeechobeensis subsp. martinezii. At present, this gene, Pm-0, is used extensively in breeding, and is found in nearly all powdery mildew-resistant C. pepo and C. moschata commercial cultivars. In this study, we mapped C. okeechobeensis subsp. martinezii-derived single nucleotide polymorphism (SNP) alleles in a set of taxonomically and morphologically diverse and resistant C. pepo and C. moschata cultivars bred at Cornell University that, by common possession of Pm-0, form a shared-trait introgression panel. High marker density was achieved using genotyping-by-sequencing, which yielded over 50,000 de novo SNP markers in each of the three Cucurbita species genotyped. A single 516.4 kb wild-derived introgression was present in all of the resistant cultivars and absent in a diverse set of heirlooms that predated the Pm-0 introgression. The contribution of this interval to powdery mildew resistance was confirmed by association mapping in a C. pepo cultivar panel that included the Cornell lines, heirlooms, and 68 additional C. pepo cultivars and with an independent F2 population derived from C. okeechobeensis subsp. martinezii x C. moschata. The interval was refined to a final candidate interval of 76.4 kb and CAPS markers were developed inside this interval to facilitate marker-assisted selection.

  17. Anisotropies in TeV Cosmic Rays Related to the IBEX Ribbon

    NASA Astrophysics Data System (ADS)

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

    2014-08-01

    The Interstellar Boundary Explorer (IBEX) observes enhanced Energetic Neutral Atoms (ENAs) emission in the keV energy range from a narrow (~20° wide) "ribbon" in the sky that appears to be centered on the direction of the local interstellar (LIS) magnetic field. The Milagro collaboration, the Asγ collaboration and the IceCube observatory have recently made global maps of cosmic ray fluxes in the TeV energy range, revealing anisotropic structures ordered in part by the local interstellar magnetic field and the interstellar flow. This paper following from a recent publication in Science makes the link between these disparate observations by developing a simple model of the magnetic structure surrounding the heliosphere in the Local Interstellar Medium (LISM) that is consistent with both IBEX ENA fluxes and TeV cosmic ray anisotropies. The model also employs the revised velocity direction of the LIC derived from neutral He observations by IBEX. By modeling the propagation of cosmic rays through this magnetic field structure, we specifically show that (1) the large-scale TeV anisotropy provides a roughly consistent orientation for the local interstellar magnetic field at the center of the IBEX Ribbon and corroborates the ~ 3 μG magnitude of the local interstellar magnetic field derived from IBEX observations of the global heliosphere; (2) and small-scale structures in cosmic rays (over < 30° angular scales) are influenced by the interstellar field interaction with the heliosphere at energies < 10 TeV. Thus, we provide a link between IBEX ENA observations, IBEX neutral observations of interstellar He, and TeV cosmic ray anisotropies, which are strongly influenced by the interactions between the local interstellar magnetic field, the flow of the local interstellar plasma, and the global heliosphere.

  18. High-density nucleosome occupancy map of human chromosome 9p21-22 reveals chromatin organization of the type I interferon gene cluster.

    PubMed

    Freaney, Jonathan E; Zhang, Quanwei; Yigit, Erbay; Kim, Rebecca; Widom, Jonathan; Wang, Ji-Ping; Horvath, Curt M

    2014-09-01

    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.

  19. Comparative genetic mapping between octoploid and diploid Fragaria species reveals a high level of colinearity between their genomes and the essentially disomic behavior of the cultivated octoploid strawberry.

    PubMed

    Rousseau-Gueutin, Mathieu; Lerceteau-Köhler, Estelle; Barrot, Laure; Sargent, Daniel James; Monfort, Amparo; Simpson, David; Arús, Pere; Guérin, Guy; Denoyes-Rothan, Béatrice

    2008-08-01

    Macrosynteny and colinearity between Fragaria (strawberry) species showing extreme levels of ploidy have been studied through comparative genetic mapping between the octoploid cultivated strawberry (F. xananassa) and its diploid relatives. A comprehensive map of the octoploid strawberry, in which almost all linkage groups are ranged into the seven expected homoeologous groups was obtained, thus providing the first reference map for the octoploid Fragaria. High levels of conserved macrosynteny and colinearity were observed between homo(eo)logous linkage groups and between the octoploid homoeologous groups and their corresponding diploid linkage groups. These results reveal that the polyploidization events that took place along the evolution of the Fragaria genus and the more recent juxtaposition of two octoploid strawberry genomes in the cultivated strawberry did not trigger any major chromosomal rearrangements in genomes involved in F. xananassa. They further suggest the existence of a close relationship between the diploid Fragaria genomes. In addition, despite the possible existence of residual levels of polysomic segregation suggested by the observation of large linkage groups in coupling phase only, the prevalence of linkage groups in coupling/repulsion phase clearly demonstrates that the meiotic behavior is mainly disomic in the cultivated strawberry.

  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. Astrophysics: Cosmic jet engines

    NASA Astrophysics Data System (ADS)

    Young, Andy

    2010-02-01

    In some galaxies, matter falling onto a supermassive black hole is ejected in narrow jets moving at close to the speed of light. New observations provide insight into the workings of these cosmic accelerators.

  3. Cosmic Ray Astronomy

    NASA Technical Reports Server (NTRS)

    Wu, S. T.

    2000-01-01

    The cosmic ray division participation in the cooperative agreement was activated in the second year. The scientific goals will be analysis of cosmic ray data from the Japanese-American Cooperative Emulsion Experiments (JACEE). Measurements of primary cosmic rays in the JACEE emulsion chambers will be made to derive for each detected particle the deposited energy in the chamber and the primary charge (atomic number). The data will be corrected to the primary flux above the atmosphere, and the composition and energy spectra will be derived. The spectra of the individual elements will be interpreted in context with the supernova shock and other models of cosmic ray acceleration. Additional information is contained in the original extended abstract.

  4. Genetic and Targeted eQTL Mapping Reveals Strong Candidate Genes Modulating the Stress Response During Chicken Domestication

    PubMed Central

    Fallahsharoudi, Amir; de Kock, Neil; Johnsson, Martin; Bektic, Lejla; Ubhayasekera, S. J. Kumari A.; Bergquist, Jonas; Wright, Dominic; Jensen, Per

    2016-01-01

    The stress response has been largely modified in all domesticated animals, offering a strong tool for genetic mapping. In chickens, ancestral Red Junglefowl react stronger both in terms of physiology and behavior to a brief restraint stress than domesticated White Leghorn, demonstrating modified functions of the hypothalamic–pituitary–adrenal (HPA) axis. We mapped quantitative trait loci (QTL) underlying variations in stress-induced hormone levels using 232 birds from the 12th generation of an advanced intercross between White Leghorn and Red Junglefowl, genotyped for 739 genetic markers. Plasma levels of corticosterone, dehydroepiandrosterone (DHEA), and pregnenolone (PREG) were measured using LC-MS/MS in all genotyped birds. Transcription levels of the candidate genes were measured in the adrenal glands or hypothalamus of 88 out of the 232 birds used for hormone assessment. Genes were targeted for expression analysis when they were located in a hormone QTL region and were differentially expressed in the pure breed birds. One genome-wide significant QTL on chromosome 5 and two suggestive QTL together explained 20% of the variance in corticosterone response. Two significant QTL for aldosterone on chromosome 2 and 5 (explaining 19% of the variance), and one QTL for DHEA on chromosome 4 (explaining 5% of the variance), were detected. Orthologous DNA regions to the significant corticosterone QTL have been previously associated with the physiological stress response in other species but, to our knowledge, the underlying gene(s) have not been identified. SERPINA10 had an expression QTL (eQTL) colocalized with the corticosterone QTL on chromosome 5 and PDE1C had an eQTL colocalized with the aldosterone QTL on chromosome 2. Furthermore, in both cases, the expression levels of the genes were correlated with the plasma levels of the hormones. Hence, both these genes are strong putative candidates for the domestication-induced modifications of the stress response in

  5. 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

  6. Magnetic Resonance Q Mapping Reveals a Decrease in Microvessel Density in the arcAβ Mouse Model of Cerebral Amyloidosis.

    PubMed

    Ielacqua, Giovanna D; Schlegel, Felix; Füchtemeier, Martina; Xandry, Jael; Rudin, Markus; Klohs, Jan

    2015-01-01

    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 [Formula: see text] obtained from pre- and post-contrast gradient echo data was used for the alternative determination of rCBV [rCBV([Formula: see text])]. Linear mixed effects modeling found no significant association between rCBV(DSC), rCBV([Formula: see text]), 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([Formula: see text]) 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

  7. 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

  8. 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

  9. Spider casts its web on the cosmic microwave background

    NASA Astrophysics Data System (ADS)

    Banks, Michael

    2015-02-01

    An experiment successfully touched down in Antarctica last month after gathering data on the cosmic microwave background (CMB) that could reveal the faint remnants of gravitational waves created during that rapid expansion of the very early universe known as inflation.

  10. 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.

  11. 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.

  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

    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

  14. 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

    2016-02-09

    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.

  15. 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.

  16. Quantitative mapping of zinc fluxes in the mammalian egg reveals the origin of fertilization-induced zinc sparks

    DOE PAGES

    Que, Emily L.; Bleher, Reiner; Duncan, Francesca E.; ...

    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

  17. Genetic Interaction Mapping Reveals a Role for the SWI/SNF Nucleosome Remodeler in Spliceosome Activation in Fission Yeast

    PubMed Central

    Patrick, Kristin L.; Ryan, Colm J.; Xu, Jiewei; Lipp, Jesse J.; Nissen, Kelly E.; Roguev, Assen; Shales, Michael; Krogan, Nevan J.; Guthrie, Christine

    2015-01-01

    Although numerous regulatory connections between pre-mRNA splicing and chromatin have been demonstrated, the precise mechanisms by which chromatin factors influence spliceosome assembly and/or catalysis remain unclear. To probe the genetic network of pre-mRNA splicing in the fission yeast Schizosaccharomyces pombe, we constructed an epistatic mini-array profile (E-MAP) and discovered many new connections between chromatin and splicing. Notably, the nucleosome remodeler SWI/SNF had strong genetic interactions with components of the U2 snRNP SF3 complex. Overexpression of SF3 components in ΔSWI/SNF cells led to inefficient splicing of many fission yeast introns, predominantly those with non-consensus splice sites. Deletion of SWI/SNF decreased recruitment of the splicing ATPase Prp2, suggesting that SWI/SNF promotes co-transcriptional spliceosome assembly prior to first step catalysis. Importantly, defects in SWI/SNF as well as SF3 overexpression each altered nucleosome occupancy along intron-containing genes, illustrating that the chromatin landscape both affects—and is affected by—co-transcriptional splicing. PMID:25825871

  18. A high performance biometric signal and image processing method to reveal blood perfusion towards 3D oxygen saturation mapping

    NASA Astrophysics Data System (ADS)

    Imms, Ryan; Hu, Sijung; Azorin-Peris, Vicente; Trico, Michaël.; Summers, Ron

    2014-03-01

    Non-contact imaging photoplethysmography (PPG) is a recent development in the field of physiological data acquisition, currently undergoing a large amount of research to characterize and define the range of its capabilities. Contact-based PPG techniques have been broadly used in clinical scenarios for a number of years to obtain direct information about the degree of oxygen saturation for patients. With the advent of imaging techniques, there is strong potential to enable access to additional information such as multi-dimensional blood perfusion and saturation mapping. The further development of effective opto-physiological monitoring techniques is dependent upon novel modelling techniques coupled with improved sensor design and effective signal processing methodologies. The biometric signal and imaging processing platform (bSIPP) provides a comprehensive set of features for extraction and analysis of recorded iPPG data, enabling direct comparison with other biomedical diagnostic tools such as ECG and EEG. Additionally, utilizing information about the nature of tissue structure has enabled the generation of an engineering model describing the behaviour of light during its travel through the biological tissue. This enables the estimation of the relative oxygen saturation and blood perfusion in different layers of the tissue to be calculated, which has the potential to be a useful diagnostic tool.

  19. 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.

  20. Mapping of ionomic traits in Mimulus guttatus reveals Mo and Cd QTLs that colocalize with MOT1 homologues.

    PubMed

    Lowry, David B; Sheng, Calvin C; Zhu, Zhirui; Juenger, Thomas E; Lahner, Brett; Salt, David E; Willis, John H

    2012-01-01

    Natural variation in the regulation of the accumulation of mineral nutrients and trace elements in plant tissues is crucial to plant metabolism, development, and survival across different habitats. Studies of the genetic basis of natural variation in nutrient metabolism have been facilitated by the development of ionomics. Ionomics is a functional genomic approach for the identification of the genes and gene networks that regulate the elemental composition, or ionome, of an organism. In this study, we evaluated the genetic basis of divergence in elemental composition between an inland annual and a coastal perennial accession of Mimulus guttatus using a recombinant inbred line (RIL) mapping population. Out of 20 elements evaluated, Mo and Cd were the most divergent in accumulation between the two accessions and were highly genetically correlated in the RILs across two replicated experiments. We discovered two major quantitative trait loci (QTL) for Mo accumulation, the largest of which consistently colocalized with a QTL for Cd accumulation. Interestingly, both Mo QTLs also colocalized with the two M. guttatus homologues of MOT1, the only known plant transporter to be involved in natural variation in molybdate uptake.

  1. Quantitative network mapping of the human kinome interactome reveals new clues for rational kinase inhibitor discovery and individualized cancer therapy

    PubMed Central

    Cheng, Feixiong; Jia, Peilin; Wang, Quan; Zhao, Zhongming

    2014-01-01

    The human kinome is gaining importance through its promising cancer therapeutic targets, yet no general model to address the kinase inhibitor resistance has emerged. Here, we constructed a systems biology-based framework to catalogue the human kinome, including 538 kinase genes, in the broader context of the human interactome. Specifically, we constructed three networks: a kinase-substrate interaction network containing 7,346 pairs connecting 379 kinases to 36,576 phosphorylation sites in 1,961 substrates, a protein-protein interaction network (PPIN) containing 92,699 pairs, and an atomic resolution PPIN containing 4,278 pairs. We identified the conserved regulatory phosphorylation motifs (e.g., Ser/Thr-Pro) using a sequence logo analysis. We found the typical anticancer target selection strategy that uses network hubs as drug targets, might lead to a high adverse drug reaction risk. Furthermore, we found the distinct network centrality of kinases creates a high anticancer drug resistance risk by feedback or crosstalk mechanisms within cellular networks. This notion is supported by the systematic network and pathway analyses that anticancer drug resistance genes are significantly enriched as hubs and heavily participate in multiple signaling pathways. Collectively, this comprehensive human kinome interactome map sheds light on anticancer drug resistance mechanisms and provides an innovative resource for rational kinase inhibitor design. PMID:25003367

  2. High-resolution physical mapping in Pennisetum squamulatum reveals extensive chromosomal heteromorphism of the genomic region associated with apomixis.

    PubMed

    Akiyama, Yukio; Conner, Joann A; Goel, Shailendra; Morishige, Daryl T; Mullet, John E; Hanna, Wayne W; Ozias-Akins, Peggy

    2004-04-01

    Gametophytic apomixis is asexual reproduction as a consequence of parthenogenetic development of a chromosomally unreduced egg. The trait leads to the production of embryos with a maternal genotype, i.e. progeny are clones of the maternal plant. The application of the trait in agriculture could be a tremendous tool for crop improvement through conventional and nonconventional breeding methods. Unfortunately, there are no major crops that reproduce by apomixis, and interspecific hybridization with wild relatives has not yet resulted in commercially viable germplasm. Pennisetum squamulatum is an aposporous apomict from which the gene(s) for apomixis has been transferred to sexual pearl millet by backcrossing. Twelve molecular markers that are linked with apomixis coexist in a tight linkage block called the apospory-specific genomic region (ASGR), and several of these markers have been shown to be hemizygous in the polyploid genome of P. squamulatum. High resolution genetic mapping of these markers has not been possible because of low recombination in this region of the genome. We now show the physical arrangement of bacterial artificial chromosomes containing apomixis-linked molecular markers by high resolution fluorescence in situ hybridization on pachytene chromosomes. The size of the ASGR, currently defined as the entire hemizygous region that hybridizes with apomixis-linked bacterial artificial chromosomes, was estimated on pachytene and mitotic chromosomes to be approximately 50 Mbp (a quarter of the chromosome). The ASGR includes highly repetitive sequences from an Opie-2-like retrotransposon family that are particularly abundant in this region of the genome.

  3. 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

    2012-09-07

    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.

  4. Family-based linkage and association mapping reveals novel genes affecting Plum pox virus infection in Arabidopsis thaliana.

    PubMed

    Pagny, Gaëlle; Paulstephenraj, Pauline S; Poque, Sylvain; Sicard, Ophélie; Cosson, Patrick; Eyquard, Jean-Philippe; Caballero, Mélodie; Chague, Aurélie; Gourdon, Germain; Negrel, Lise; Candresse, Thierry; Mariette, Stéphanie; Decroocq, Véronique

    2012-11-01

    Sharka is a devastating viral disease caused by the Plum pox virus (PPV) in stone fruit trees and few sources of resistance are known in its natural hosts. Since any knowledge gained from Arabidopsis on plant virus susceptibility factors is likely to be transferable to crop species, Arabidopsis's natural variation was searched for host factors essential for PPV infection. To locate regions of the genome associated with susceptibility to PPV, linkage analysis was performed on six biparental populations as well as on multiparental lines. To refine quantitative trait locus (QTL) mapping, a genome-wide association analysis was carried out using 147 Arabidopsis accessions. Evidence was found for linkage on chromosomes 1, 3 and 5 with restriction of PPV long-distance movement. The most relevant signals occurred within a region at the bottom of chromosome 3, which comprises seven RTM3-like TRAF domain-containing genes. Since the resistance mechanism analyzed here is recessive and the rtm3 knockout mutant is susceptible to PPV infection, it suggests that other gene(s) present in the small identified region encompassing RTM3 are necessary for PPV long-distance movement. In consequence, we report here the occurrence of host factor(s) that are indispensable for virus long-distance movement.

  5. Single-nucleotide resolution mapping of the Gossypium raimondii transcriptome reveals a new mechanism for alternative splicing of introns.

    PubMed

    Li, Qin; Xiao, Guanghui; Zhu, Yu-Xian

    2014-05-01

    Alternative splicing (AS) is a vital genetic mechanism that enhances the diversity of eukaryotic transcriptomes. Here, we generated 8.3 Gb high-quality RNA-sequencing data from cotton (Gossypium raimondii) and performed a systematic, comparative analysis of AS events. We mapped 85% of the RNA-sequencing data onto the reference genome and identified 154368 splice junctions with 16437 as events in 10197 genes. Intron retention constituted the majority (40%) of all AS events in G. raimondii. Comparison across 11 eukaryote species showed that intron retention is the most common AS type in higher plants. Although transposable elements (TEs) were found in only 2.9% of all G. raimondii introns, they are present in 43% of the retained introns, suggesting that TE-insertion may be an important mechanism for intron retention during AS. The majority of the TE insertions are concentrated 0-40 nt upstream of the 3'-splice site, substantially altering the distribution of branch points from preferred positions and reducing the efficiency of intron splicing by decreasing RNA secondary structure flexibility. Our data suggest that TE-insertion-induced changes in branch point-site distribution are important for intron retention-type AS. Our findings may help explain the vast differences in intron-retention frequencies between vertebrates and higher plants.

  6. Genetic interaction mapping reveals a role for the SWI/SNF nucleosome remodeler in spliceosome activation in fission yeast.

    PubMed

    Patrick, Kristin L; Ryan, Colm J; Xu, Jiewei; Lipp, Jesse J; Nissen, Kelly E; Roguev, Assen; Shales, Michael; Krogan, Nevan J; Guthrie, Christine

    2015-03-01

    Although numerous regulatory connections between pre-mRNA splicing and chromatin have been demonstrated, the precise mechanisms by which chromatin factors influence spliceosome assembly and/or catalysis remain unclear. To probe the genetic network of pre-mRNA splicing in the fission yeast Schizosaccharomyces pombe, we constructed an epistatic mini-array profile (E-MAP) and discovered many new connections between chromatin and splicing. Notably, the nucleosome remodeler SWI/SNF had strong genetic interactions with components of the U2 snRNP SF3 complex. Overexpression of SF3 components in ΔSWI/SNF cells led to inefficient splicing of many fission yeast introns, predominantly those with non-consensus splice sites. Deletion of SWI/SNF decreased recruitment of the splicing ATPase Prp2, suggesting that SWI/SNF promotes co-transcriptional spliceosome assembly prior to first step catalysis. Importantly, defects in SWI/SNF as well as SF3 overexpression each altered nucleosome occupancy along intron-containing genes, illustrating that the chromatin landscape both affects--and is affected by--co-transcriptional splicing.

  7. Intracortical Microstimulation Maps of Motor, Somatosensory, and Posterior Parietal Cortex in Tree Shrews (Tupaia belangeri) Reveal Complex Movement Representations.

    PubMed

    Baldwin, Mary K L; Cooke, Dylan F; Krubitzer, Leah

    2017-02-01

    Long-train intracortical microstimulation (LT-ICMS) is a popular method for studying the organization of motor and posterior parietal cortex (PPC) in mammals. In primates, LT-ICMS evokes both multijoint and multiple-body-part movements in primary motor, premotor, and PPC. In rodents, LT-ICMS evokes complex movements of a single limb in motor cortex. Unfortunately, very little is known about motor/PPC organization in other mammals. Tree shrews are closely related to both primates and rodents and could provide insights into the evolution of complex movement domains in primates. The present study investigated the extent of cortex in which movements could be evoked with ICMS and the characteristics of movements elicited using both short train (ST) and LT-ICMS in tree shrews. We demonstrate that LT-ICMS and ST-ICMS maps are similar, with the movements elicited with ST-ICMS being truncated versions of those elicited with LT-ICMS. In addition, LT-ICMS-evoked complex movements within motor cortex similar to those in rodents. More complex movements involving multiple body parts such as the hand and mouth were also elicited in motor cortex and PPC, as in primates. Our results suggest that complex movement networks present in PPC and motor cortex were present in mammals prior to the emergence of primates.

  8. The cosmic web in our own backyard.

    PubMed

    Ibata, Rodrigo A; Lewis, Geraint F

    2008-01-04

    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.

  9. Mapping of PARK2 and PACRG overlapping regulatory region reveals LD structure and functional variants in association with leprosy in unrelated indian population groups.

    PubMed

    Chopra, Rupali; Ali, Shafat; Srivastava, Amit K; Aggarwal, Shweta; Kumar, Bhupender; Manvati, Siddharth; Kalaiarasan, Ponnusamy; Jena, Mamta; Garg, Vijay K; Bhattacharya, Sambit N; Bamezai, Rameshwar N K

    2013-01-01

    Leprosy is a chronic infectious disease caused by Mycobacterium Leprae, where the host genetic background plays an important role toward the disease pathogenesis. Various studies have identified a number of human genes in association with leprosy or its clinical forms. However, non-replication of results has hinted at the heterogeneity among associations between different population groups, which could be due to differently evolved LD structures and differential frequencies of SNPs within the studied regions of the genome. A need for systematic and saturated mapping of the associated regions with the disease is warranted to unravel the observed heterogeneity in different populations. Mapping of the PARK2 and PACRG gene regulatory region with 96 SNPs, with a resolution of 1 SNP per 1 Kb for PARK2 gene regulatory region in a North Indian population, showed an involvement of 11 SNPs in determining the susceptibility towards leprosy. The association was replicated in a geographically distinct and unrelated population from Orissa in eastern India. In vitro reporter assays revealed that the two significantly associated SNPs, located 63.8 kb upstream of PARK2 gene and represented in a single BIN of 8 SNPs, influenced the gene expression. A comparison of BINs between Indian and Vietnamese populations revealed differences in the BIN structures, explaining the heterogeneity and also the reason for non-replication of the associated genomic region in different populations.

  10. Mapping of PARK2 and PACRG Overlapping Regulatory Region Reveals LD Structure and Functional Variants in Association with Leprosy in Unrelated Indian Population Groups

    PubMed Central

    Chopra, Rupali; Aggarwal, Shweta; Kumar, Bhupender; Manvati, Siddharth; Kalaiarasan, Ponnusamy; Jena, Mamta; Garg, Vijay K.; Bhattacharya, Sambit N.; Bamezai, Rameshwar N. K.

    2013-01-01

    Leprosy is a chronic infectious disease caused by Mycobacterium Leprae, where the host genetic background plays an important role toward the disease pathogenesis. Various studies have identified a number of human genes in association with leprosy or its clinical forms. However, non-replication of results has hinted at the heterogeneity among associations between different population groups, which could be due to differently evolved LD structures and differential frequencies of SNPs within the studied regions of the genome. A need for systematic and saturated mapping of the associated regions with the disease is warranted to unravel the observed heterogeneity in different populations. Mapping of the PARK2 and PACRG gene regulatory region with 96 SNPs, with a resolution of 1 SNP per 1 Kb for PARK2 gene regulatory region in a North Indian population, showed an involvement of 11 SNPs in determining the susceptibility towards leprosy. The association was replicated in a geographically distinct and unrelated population from Orissa in eastern India. In vitro reporter assays revealed that the two significantly associated SNPs, located 63.8 kb upstream of PARK2 gene and represented in a single BIN of 8 SNPs, influenced the gene expression. A comparison of BINs between Indian and Vietnamese populations revealed differences in the BIN structures, explaining the heterogeneity and also the reason for non-replication of the associated genomic region in different populations. PMID:23861666

  11. Microsatellite organization in the grasshopper Abracris flavolineata (Orthoptera: Acrididae) revealed by FISH mapping: remarkable spreading in the A and B chromosomes.

    PubMed

    Milani, Diogo; Cabral-de-Mello, Diogo Cavalcanti

    2014-01-01

    With the aim of acquiring deeper knowledge about repetitive DNAs chromosomal organization in grasshoppers, we used fluorescent in situ hybridization (FISH) to map the distribution of 16 microsatellite repeats, including mono-, di-, tri- and tetra-nucleotides, in the chromosomes of the species Abracris flavolineata (Acrididae), which harbors B chromosome. FISH revealed two main patterns: (i) exclusively scattered signals, and (ii) scattered and specific signals, forming evident blocks. The enrichment was observed in both euchromatic and heterochromatic areas and only the motif (C)30 was absent in heterochromatin. The A and B chromosomes were enriched with all the elements that were mapped, being observed in the B chromosome more distinctive blocks for (GA)15 and (GAG)10. For A complement distinctive blocks were noticed for (A)30, (CA)15, (CG)15, (GA)15, (CAC)10, (CAA)10, (CGG)10, (GAA)10, (GAC)10 and (GATA)8. These results revealed an intense spreading of microsatellites in the A. flavolineata genome that was independent of the A+T or G+C enrichment in the repeats. The data indicate that the microsatellites compose the B chromosome and could be involved in the evolution of this element in this species, although no specific relationship with any A chromosome was observed to discuss about its origin. The systematic analysis presented here contributes to the knowledge of repetitive DNA chromosomal organization among grasshoppers including the B chromosomes.

  12. Fine mapping analysis of HLA-DP/DQ gene clusters on chromosome 6 reveals multiple susceptibility loci for HBV infection.

    PubMed

    Tao, Jingjing; Su, Kunkai; Yu, Chengbo; Liu, Xiaoli; Wu, Wei; Xu, Wei; Jiang, Bingxun; Luo, Rui; Yao, Jian; Zhou, Jiawei; Zhan, Yan; Ye, Chao; Yuan, Wenji; Jiang, Xianzhong; Cui, Wenyan; Li, Ming D; Li, Lianjuan

    2015-12-01

    Recent genome-wide association studies have revealed the HLA region on chromosome 6p21 as a susceptibility locus for hepatitis B virus (HBV) infection, a finding subsequently replicated in independent samples. However, only limited single nucleotide polymorphisms (SNPs) were analyzed in most of these studies, and it remains to be determined which SNPs contribute to the detected association. After genotyping 140 SNPs within this genomic region in a total of 1657 HBV-positive patients and 1456 HBV-negative controls, we conducted a series of genetic epidemiological and bioinformatics analysis, including individual SNP-based association analysis, haplotype-based association analysis, and conditional analysis. We identified 76 SNPs and 5 LD blocks in HLA-DP/DQ clusters that are significantly associated with HBV infection, with the smallest P value being 3.88 × 10(-18) for rs9277535 in HLA-DPB1. With conditional analysis, we further revealed that the genes contributing to the effects of variants in HLA-DP/DQ on infection are independent of each other, and the LD block 5 in the 3'-UTR region of HLA-DPB1 had a predominant effect in the association of HLA-DP with HBV infection. We also found that the SNPs in the 3'-UTR region of HLA-DPB1 were significant between the subgroups of inactive HBV carrier, chronic hepatitis B, or hepatic cirrhosis from the case group and the spontaneous HBV-clearance subgroup from the control group. Finally, we did further association analysis of SNPs in this region with different subgroups from the case group, which revealed no association of these SNPs with the progression of HBV-related diseases. In sum, we showed, for the first time, that the HLA-DP/DQ clusters contribute independently to HBV infection, and the 3'-UTR region of HLA-DPB1 represents an important functional region involved in HBV infection.

  13. Strong Cosmic Censorship

    NASA Astrophysics Data System (ADS)

    Isenberg, James

    2017-01-01

    The Hawking-Penrose theorems tell us that solutions of Einstein's equations are generally singular, in the sense of the incompleteness of causal geodesics (the paths of physical observers). These singularities might be marked by the blowup of curvature and therefore crushing tidal forces, or by the breakdown of physical determinism. Penrose has conjectured (in his `Strong Cosmic Censorship Conjecture`) that it is generically unbounded curvature that causes singularities, rather than causal breakdown. The verification that ``AVTD behavior'' (marked by the domination of time derivatives over space derivatives) is generically present in a family of solutions has proven to be a useful tool for studying model versions of Strong Cosmic Censorship in that family. I discuss some of the history of Strong Cosmic Censorship, and then discuss what is known about AVTD behavior and Strong Cosmic Censorship in families of solutions defined by varying degrees of isometry, and discuss recent results which we believe will extend this knowledge and provide new support for Strong Cosmic Censorship. I also comment on some of the recent work on ``Weak Null Singularities'', and how this relates to Strong Cosmic Censorship.

  14. A Sequence-Anchored Linkage Map of the Plant–Parasitic Nematode Meloidogyne hapla Reveals Exceptionally High Genome-Wide Recombination

    PubMed Central

    Thomas, Varghese P.; Fudali, Sylwia L.; Schaff, Jennifer E.; Liu, Qingli; Scholl, Elizabeth H.; Opperman, Charles H.; Bird, David McK; Williamson, Valerie M.

    2012-01-01

    Root-knot nematodes (Meloidogyne spp.) cause major yield losses to many of the world’s crops, but efforts to understand how these pests recognize and interact with their hosts have been hampered by a lack of genetic resources. Starting with progeny of a cross between inbred strains (VW8 and VW9) of Meloidogyne hapla that differed in host range and behavioral traits, we exploited the novel, facultative meiotic parthenogenic reproductive mode of this species to produce a genetic linkage map. Molecular markers were derived from SNPs identified between the sequenced and annotated VW9 genome and de novo sequence of VW8. Genotypes were assessed in 183 F2 lines. The colinearity of the genetic and physical maps supported the veracity of both. Analysis of local crossover intervals revealed that the average recombination rate is exceptionally high compared with that in other metazoans. In addition, F2 lines are largely homozygous for markers flanking crossover points, and thus resemble recombinant inbred lines. We suggest that the unusually high recombination rate may be an adaptation to generate within-population genetic diversity in this organism. This work presents the most comprehensive linkage map of a parasitic nematode to date and, together with genomic and transcript sequence resources, empowers M. hapla as a tractable model. Alongside the molecular map, these progeny lines can be used for analyses of genome organization and the inheritance of phenotypic traits that have key functions in modulating parasitism, behavior, and survival and for the eventual identification of the responsible genes. PMID:22870404

  15. Nucleosome maps of the human cytomegalovirus genome reveal a temporal switch in chromatin organization linked to a major IE protein.

    PubMed

    Zalckvar, Einat; Paulus, Christina; Tillo, Desiree; Asbach-Nitzsche, Alexandra; Lubling, Yaniv; Winterling, Carla; Strieder, Nicholas; Mücke, Katrin; Goodrum, Felicia; Segal, Eran; Nevels, Michael

    2013-08-06

    Human CMV (hCMV) establishes lifelong infections in most of us, causing developmental defects in human embryos and life-threatening disease in immunocompromised individuals. During productive infection, the viral >230,000-bp dsDNA genome is expressed widely and in a temporal cascade. The hCMV genome does not carry histones when encapsidated but has been proposed to form nucleosomes after release into the host cell nucleus. Here, we present hCMV genome-wide nucleosome occupancy and nascent transcript maps during infection of permissive human primary cells. We show that nucleosomes occupy nuclear viral DNA in a nonrandom and highly predictable fashion. At early times of infection, nucleosomes associate with the hCMV genome largely according to their intrinsic DNA sequence preferences, indicating that initial nucleosome formation is genetically encoded in the virus. However, as infection proceeds to the late phase, nucleosomes redistribute extensively to establish patterns mostly determined by nongenetic factors. We propose that these factors include key regulators of viral gene expression encoded at the hCMV major immediate-early (IE) locus. Indeed, mutant virus genomes deficient for IE1 expression exhibit globally increased nucleosome loads and reduced nucleosome dynamics compared with WT genomes. The temporal nucleosome occupancy differences between IE1-deficient and WT viruses correlate inversely with changes in the pattern of viral nascent and total transcript accumulation. These results provide a framework of spatial and temporal nucleosome organization across the genome of a major human pathogen and suggest that an hCMV major IE protein governs overall viral chromatin structure and function.

  16. Fine-mapping butyrophilin family genes revealed several polymorphisms influencing viral genotype selection in hepatitis C infection.

    PubMed

    Ampuero, J; del Campo, J A; Rojas, L; García-Lozano, R J; Buti, M; Solá, R; Forns, X; Moreno-Otero, R; Andrade, R; Diago, M; Salmerón, J; Rodrigo, L; Pons, J A; Navarro, J M; Calleja, J L; García-Samaniego, J; García-Valdecasas, M; Rojas, Á; Millán, R; González-Escribano, M F; Romero-Gómez, M

    2015-01-01

    Host-viral genetic interaction has a key role in hepatitis C infection (HCV) and maybe in the viral selection. In a preliminary GWAS analysis, we identified BTN3A2 rs9104 to be associated with HCV genotype 1. Therefore, our aim was to determine the influence of BTN family on the selection of HCV genotype. We performed a fine-mapping analysis of BTN gene region in a cohort of chronic HCV infection (N=841), validating significant results in another independent chronic HCV infection cohort (N=637), according to selection of viral genotype. BTN3A2 rs9104, BTN3A2 rs733528, BTN2A1 rs6929846, BTN2A1 rs7763910 and BTN3A3 rs13220495 were associated with viral genotype selection. Interestingly, BTN3A2 rs9104 GG genotype was closely related to genotype 1 infection (80.7% (394/488) compared with genotype 3 infection (53.5% (23/43); P=0.0001) in patients harboring IL28B-CT/TT genotype, although this effect was not observed in IL28B-CC genotype. Similarly, BTN3A3 rs13220495 CC genotype was linked to genotype 3 infection (100% (32/32)) compared to genotype 1 (87.3% (137/157); P=0.028) in patients harboring IL28B-CC genotype, but did not in IL28B-CT/TT genotype. Genetic variants in the butyrophilin family genes may alter susceptibility to infection, selecting HCV genotype and influencing disease progression. BTN3A2 rs9104 was strongly associated with genotype 1 infection and the haplotype BTN3A3 rs13220495 CC+IL28B genotype CC was universal in patients with hepatitis C genotype 3a.

  17. 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

  18. 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

  19. Comprehensive Binary Interaction Mapping of SH2 Domains via Fluorescence Polarization Reveals Novel Functional Diversification of ErbB Receptors

    PubMed Central

    Ciaccio, Mark F.; Chuu, Chih-pin; Jones, Richard B.

    2012-01-01

    First-generation interaction maps of Src homology 2 (SH2) domains with receptor tyrosine kinase (RTK) phosphosites have previously been generated using protein microarray (PM) technologies. Here, we developed a large-scale fluorescence polarization (FP) methodology that was able to characterize interactions between SH2 domains and ErbB receptor phosphosites with higher fidelity and sensitivity than was previously achieved with PMs. We used the FP assay to query the interaction of synthetic phosphopeptides corresponding to 89 ErbB receptor intracellular tyrosine sites against 93 human SH2 domains and 2 phosphotyrosine binding (PTB) domains. From 358,944 polarization measurements, the affinities for 1,405 unique biological interactions were determined, 83% of which are novel. In contrast to data from previous reports, our analyses suggested that ErbB2 was not more promiscuous than the other ErbB receptors. Our results showed that each receptor displays unique preferences in the affinity and location of recruited SH2 domains that may contribute to differences in downstream signaling potential. ErbB1 was enriched versus the other receptors for recruitment of domains from RAS GEFs whereas ErbB2 was enriched for recruitment of domains from tyrosine and phosphatidyl inositol phosphatases. ErbB3, the kinase inactive ErbB receptor family member, was predictably enriched for recruitment of domains from phosphatidyl inositol kinases and surprisingly, was enriched for recruitment of domains from tyrosine kinases, cytoskeletal regulatory proteins, and RHO GEFs but depleted for recruitment of domains from phosphatidyl inositol phosphatases. Many novel interactions were also observed with phosphopeptides corresponding to ErbB receptor tyrosines not previously reported to be phosphorylated by mass spectrometry, suggesting the existence of many biologically relevant RTK sites that may be phosphorylated but below the detection threshold of standard mass spectrometry procedures. This

  20. Naturalistic FMRI mapping reveals superior temporal sulcus as the hub for the distributed brain network for social perception.

    PubMed

    Lahnakoski, Juha M; Glerean, Enrico; Salmi, Juha; Jääskeläinen, Iiro P; Sams, Mikko; Hari, Riitta; Nummenmaa, Lauri

    2012-01-01

    Despite the abundant data on brain networks processing static social signals, such as pictures of faces, the neural systems supporting social perception in naturalistic conditions are still poorly understood. Here we delineated brain networks subserving social perception under naturalistic conditions in 19 healthy humans who watched, during 3-T functional magnetic resonance imaging (fMRI), a set of 137 short (approximately 16 s each, total 27 min) audiovisual movie clips depicting pre-selected social signals. Two independent raters estimated how well each clip represented eight social features (faces, human bodies, biological motion, goal-oriented actions, emotion, social interaction, pain, and speech) and six filler features (places, objects, rigid motion, people not in social interaction, non-goal-oriented action, and non-human sounds) lacking social content. These ratings were used as predictors in the fMRI analysis. The posterior superior temporal sulcus (STS) responded to all social features but not to any non-social features, and the anterior STS responded to all social features except bodies and biological motion. We also found four partially segregated, extended networks for processing of specific social signals: (1) a fronto-temporal network responding to multiple social categories, (2) a fronto-parietal network preferentially activated to bodies, motion, and pain, (3) a temporo-amygdalar network responding to faces, social interaction, and speech, and (4) a fronto-insular network responding to pain, emotions, social interactions, and speech. Our results highlight the role of the pSTS in processing multiple aspects of social information, as well as the feasibility and efficiency of fMRI mapping under conditions that resemble the complexity of real life.

  1. 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.

  2. The Astrobiological Case for Our Cosmic Ancestry

    NASA Astrophysics Data System (ADS)

    Wickramasinghe, Chandra

    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 most 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.

  3. 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.

  4. 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

  5. Multiple Sex-Associated Regions and a Putative Sex Chromosome in Zebrafish Revealed by RAD Mapping and Population Genomics

    PubMed Central

    Anderson, Jennifer L.; Rodríguez Marí, Adriana; Braasch, Ingo; Amores, Angel; Hohenlohe, Paul; Batzel, Peter; Postlethwait, John H.

    2012-01-01

    Within vertebrates, major sex determining genes can differ among taxa and even within species. In zebrafish (Danio rerio), neither heteromorphic sex chromosomes nor single sex determination genes of large effect, like Sry in mammals, have yet been identified. Furthermore, environmental factors can influence zebrafish sex determination. Although progress has been made in understanding zebrafish gonad differentiation (e.g. the influence of germ cells on gonad fate), the primary genetic basis of zebrafish sex determination remains poorly understood. To identify genetic loci associated with sex, we analyzed F2 offspring of reciprocal crosses between Oregon *AB and Nadia (NA) wild-type zebrafish stocks. Genome-wide linkage analysis, using more than 5,000 sequence-based polymorphic restriction site associated (RAD-tag) markers and population genomic analysis of more than 30,000 single nucleotide polymorphisms in our *ABxNA crosses revealed a sex-associated locus on the end of the long arm of chr-4 for both cross families, and an additional locus in the middle of chr-3 in one cross family. Additional sequencing showed that two SNPs in dmrt1 previously suggested to be functional candidates for sex determination in a cross of ABxIndia wild-type zebrafish, are not associated with sex in our AB fish. Our data show that sex determination in zebrafish is polygenic and that different genes may influence sex determination in different strains or that different genes become more important under different environmental conditions. The association of the end of chr-4 with sex is remarkable because, unique in the karyotype, this chromosome arm shares features with known sex chromosomes: it is highly heterochromatic, repetitive, late replicating, and has reduced recombination. Our results reveal that chr-4 has functional and structural properties expected of a sex chromosome. PMID:22792396

  6. Inflation, string theory and cosmic strings

    NASA Astrophysics Data System (ADS)

    Chernoff, David F.; Tye, S.-H. Henry

    2015-02-01

    At its very beginning, the universe is believed to have grown exponentially in size via the mechanism of inflation. The almost scale-invariant density perturbation spectrum predicted by inflation is strongly supported by cosmological observations, in particular the cosmic microwave background (MB) radiation. However, the universe's precise inflationary scenario remains a profound problem for cosmology and for fundamental physics. String theory, the most-studied theory as the final physical theory of nature, should provide an answer to this question. Some of the proposals on how inflation is realized in string theory are reviewed. Since everything is made of strings, some string loops of cosmological sizes are likely to survive in the hot big bang that followed inflation. They appear as cosmic strings, which can have intricate properties. Because of the warped geometry in flux compactification of the extra spatial dimensions in string theory, some of the cosmic strings may have tensions substantially below the Planck or string scale. Such strings cluster in a manner similar to dark matter leading to hugely enhanced densities. As a result, numerous fossil remnants of the low tension cosmic strings may exist within the galaxy. They can be revealed through the optical lensing of background stars in the near future and studied in detail through gravitational wave emission. We anticipate that these cosmic strings will permit us to address central questions about the properties of string theory as well as the birth of our universe.

  7. The Multi-phase Cold Fountain in M82 Revealed by a Wide, Sensitive Map of the Molecular Interstellar Medium

    NASA Astrophysics Data System (ADS)

    Leroy, Adam K.; Walter, Fabian; Martini, Paul; Roussel, Hélène; Sandstrom, Karin; Ott, Jürgen; Weiss, Axel; Bolatto, Alberto D.; Schuster, Karl; Dessauges-Zavadsky, Miroslava

    2015-12-01

    We present a wide area (≈8 × 8 kpc), sensitive map of CO (2-1) emission around the nearby starburst galaxy M82. Molecular gas extends far beyond the stellar disk, including emission associated with the well-known outflow as far as 3 kpc from M82's midplane. Kinematic signatures of the outflow are visible in both the CO and H i emission: both tracers show a minor axis velocity gradient and together they show double peaked profiles, consistent with a hot outflow bounded by a cone made of a mix of atomic and molecular gas. Combining our CO and H i data with observations of the dust continuum, we study the changing properties of the cold outflow as it leaves the disk. While H2 dominates the ISM near the disk, the dominant phase of the cool medium changes as it leaves the galaxy and becomes mostly atomic after about a kpc. Several arguments suggest that regardless of phase, the mass in the cold outflow does not make it far from the disk; the mass flux through surfaces above the disk appears to decline with a projected scale length of ≈1-2 kpc. The cool material must also end up distributed over a much wider angle than the hot outflow based on the nearly circular isophotes of dust and CO at low intensity and the declining rotation velocities as a function of height from the plane. The minor axis of M82 appears so striking at many wavelengths because the interface between the hot wind cavity and the cool gas produces Hα, hot dust, polycyclic aromatic hydrocarbon emission, and scattered UV light. We also show the level at which a face-on version of M82 would be detectable as an outflow based on unresolved spectroscopy. Finally, we consider multiple constraints on the CO-to-H2 conversion factor, which must change across the galaxy but appears to be only a factor of ≈2 lower than the Galactic value in the outflow.

  8. THE MULTI-PHASE COLD FOUNTAIN IN M82 REVEALED BY A WIDE, SENSITIVE MAP OF THE MOLECULAR INTERSTELLAR MEDIUM

    SciTech Connect

    Leroy, Adam K.; Martini, Paul; Walter, Fabian; Roussel, Hélène; Sandstrom, Karin; Ott, Jürgen; Weiss, Axel; Bolatto, Alberto D.; Schuster, Karl; Dessauges-Zavadsky, Miroslava

    2015-12-01

    We present a wide area (≈8 × 8 kpc), sensitive map of CO (2–1) emission around the nearby starburst galaxy M82. Molecular gas extends far beyond the stellar disk, including emission associated with the well-known outflow as far as 3 kpc from M82's midplane. Kinematic signatures of the outflow are visible in both the CO and H i emission: both tracers show a minor axis velocity gradient and together they show double peaked profiles, consistent with a hot outflow bounded by a cone made of a mix of atomic and molecular gas. Combining our CO and H i data with observations of the dust continuum, we study the changing properties of the cold outflow as it leaves the disk. While H{sub 2} dominates the ISM near the disk, the dominant phase of the cool medium changes as it leaves the galaxy and becomes mostly atomic after about a kpc. Several arguments suggest that regardless of phase, the mass in the cold outflow does not make it far from the disk; the mass flux through surfaces above the disk appears to decline with a projected scale length of ≈1–2 kpc. The cool material must also end up distributed over a much wider angle than the hot outflow based on the nearly circular isophotes of dust and CO at low intensity and the declining rotation velocities as a function of height from the plane. The minor axis of M82 appears so striking at many wavelengths because the interface between the hot wind cavity and the cool gas produces Hα, hot dust, polycyclic aromatic hydrocarbon emission, and scattered UV light. We also show the level at which a face-on version of M82 would be detectable as an outflow based on unresolved spectroscopy. Finally, we consider multiple constraints on the CO-to-H{sub 2} conversion factor, which must change across the galaxy but appears to be only a factor of ≈2 lower than the Galactic value in the outflow.

  9. Atypical category processing and hemispheric asymmetries in high-functioning children with autism: revealed through high-density EEG mapping.

    PubMed

    Fiebelkorn, Ian C; Foxe, John J; McCourt, Mark E; Dumas, Kristina N; Molholm, Sophie

    2013-05-01

    Behavioral evidence for an impaired ability to group objects based on similar physical or semantic properties in autism spectrum disorders (ASD) has been mixed. Here, we recorded brain activity from high-functioning children with ASD as they completed a visual-target detection task. We then assessed the extent to which object-based selective attention automatically generalized from targets to non-target exemplars from the same well-known object class (e.g., dogs). Our results provide clear electrophysiological evidence that children with ASD (N=17, aged 8-13 years) process the similarity between targets (e.g., a specific dog) and same-category non-targets (SCNT) (e.g., another dog) to a lesser extent than do their typically developing (TD) peers (N=21). A closer examination of the data revealed striking hemispheric asymmetries that were specific to the ASD group. These findings align with mounting evidence in the autism literature of anatomic underconnectivity between the cerebral hemispheres. Years of research in individuals with TD have demonstrated that the left hemisphere (LH) is specialized toward processing local (or featural) stimulus properties and the right hemisphere (RH) toward processing global (or configural) stimulus properties. We therefore propose a model where a lack of communication between the hemispheres in ASD, combined with typical hemispheric specialization, is a root cause for impaired categorization and the oft-observed bias to process local over global stimulus properties.

  10. 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

  11. Fluorescence mapping of mitochondrial TIM23 complex reveals a water-facing, substrate-interacting helix surface.

    PubMed

    Alder, Nathan N; Jensen, Robert E; Johnson, Arthur E

    2008-08-08

    Protein translocation across the mitochondrial inner membrane is mediated by the TIM23 complex. While its central component, Tim23, is believed to form a protein-conducting channel, the regions of this subunit that face the imported protein are unknown. To examine Tim23 structure and environment in intact membranes at high resolution, various derivatives, each with a single, environment-sensitive fluorescent probe positioned at a specific site, were assembled into functional TIM23 complexes in active mitochondria and analyzed by multiple spectral techniques. Probes placed sequentially throughout a transmembrane region that was identified by crosslinking as part of the protein-conducting channel revealed an alpha helix in an amphipathic environment. Probes on the aqueous-facing helical surface specifically underwent spectral changes during protein import, and their accessibility to hydrophilic quenching agents is considered in terms of channel gating. This approach has therefore provided an unprecedented view of a translocon channel structure in an intact, fully operational, membrane-embedded complex.

  12. Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes.

    PubMed

    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

    2011-05-01

    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.

  13. 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

  14. Mapping physiological G protein-coupled receptor signaling pathways reveals a role for receptor phosphorylation in airway contraction.

    PubMed

    Bradley, Sophie J; Wiegman, Coen H; 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

    2016-04-19

    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.

  15. Homozygosity mapping and whole exome sequencing reveal a novel homozygous COL18A1 mutation causing Knobloch syndrome.

    PubMed

    Haghighi, Alireza; Tiwari, Amit; 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.

  16. 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

  17. 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.

  18. The Reionization of Cosmic Hydrogen by the First Galaxies

    NASA Astrophysics Data System (ADS)

    Loeb, Abraham

    Cosmology is by now a mature experimental science. We are privileged to live at a time when the story of genesis (how the Universe started and developed) can be critically explored by direct observations. Looking deep into the Universe through powerful telescopes, we can see images of the Universe when it was younger because of the finite time it takes for light to travel to us from distant sources. Existing data sets include an image of the Universe when it was 0.4 million years old (in the form of the cosmic microwave background), as well as images of individual galaxies when the Universe was older than a billion years. But there is a serious challenge: in between these two epochs was a period when the Universe was dark, stars had not yet formed, and the cosmic microwave background no longer traced the distribution of matter. And this is precisely the most interesting period, when the primordial soup evolved into the rich zoo of objects we now see. The observers are moving ahead along several fronts. The first involves the construction of large infrared telescopes on the ground and in space, that will provide us with new photos of the first galaxies. Current plans include ground-based telescopes which are 24-42 m in diameter, and NASA's successor to the Hubble Space Telescope, called the James Webb Space Telescope. In addition, several observational groups around the globe are constructing radio arrays that will be capable of mapping the three-dimensional distribution of cosmic hydrogen in the infant Universe. These arrays are aiming to detect the long-wavelength (redshifted 21 cm) radio emission from hydrogen atoms. The images from these antenna arrays will reveal how the non-uniform distribution of neutral hydrogen evolved with cosmic time and eventually was extinguished by the ultraviolet radiation from the first galaxies. Theoretical research has focused in recent years on predicting the expected signals for the above instruments and motivating these

  19. 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

  20. Next-generation sequencing, FISH mapping and synteny-based modeling reveal mechanisms of decreasing dysploidy in Cucumis.

    PubMed

    Yang, Luming; Koo, Dal-Hoe; Li, Dawei; Zhang, Tao; Jiang, Jiming; Luan, Feishi; Renner, Susanne S; Hénaff, Elizabeth; Sanseverino, Walter; Garcia-Mas, Jordi; Casacuberta, Josep; Senalik, Douglas A; Simon, Philipp W; Chen, Jinfeng; Weng, Yiqun

    2014-01-01

    In the large Cucurbitaceae genus Cucumis, cucumber (C. sativus) is the only species with 2n = 2x = 14 chromosomes. The majority of the remaining species, including melon (C. melo) and the sister species of cucumber, C. hystrix, have 2n = 2x = 24 chromosomes, implying a reduction from n = 12 to n = 7. To understand the underlying mechanisms, we investigated chromosome synteny among cucumber, C. hystrix and melon using integrated and complementary approaches. We identified 14 inversions and a C. hystrix lineage-specific reciprocal inversion between C. hystrix and melon. The results reveal the location and orientation of 53 C. hystrix syntenic blocks on the seven cucumber chromosomes, and allow us to infer at least 59 chromosome rearrangement events that led to the seven cucumber chromosomes, including five fusions, four translocations, and 50 inversions. The 12 inferred chromosomes (AK1-AK12) of an ancestor similar to melon and C. hystrix had strikingly different evolutionary fates, with cucumber chromosome C1 apparently resulting from insertion of chromosome AK12 into the centromeric region of translocated AK2/AK8, cucumber chromosome C3 originating from a Robertsonian-like translocation between AK4 and AK6, and cucumber chromosome C5 originating from fusion of AK9 and AK10. Chromosomes C2, C4 and C6 were the result of complex reshuffling of syntenic blocks from three (AK3, AK5 and AK11), three (AK5, AK7 and AK8) and five (AK2, AK3, AK5, AK8 and AK11) ancestral chromosomes, respectively, through 33 fusion, translocation and inversion events. Previous results (Huang, S., Li, R., Zhang, Z. et al., , Nat. Genet. 41, 1275-1281; Li, D., Cuevas, H.E., Yang, L., Li, Y., Garcia-Mas, J., Zalapa, J., Staub, J.E., Luan, F., Reddy, U., He, X., Gong, Z., Weng, Y. 2011a, BMC Genomics, 12, 396) showing that cucumber C7 stayed largely intact during the entire evolution of Cucumis are supported. Results from this study allow a fine-scale understanding of the

  1. Genome-Wide Association Study and QTL Mapping Reveal Genomic Loci Associated with Fusarium Ear Rot Resistance in Tropical Maize Germplasm

    PubMed Central

    Chen, Jiafa; Shrestha, Rosemary; Ding, Junqiang; Zheng, Hongjian; Mu, Chunhua; Wu, Jianyu; Mahuku, George

    2016-01-01

    Fusarium ear rot (FER) incited by Fusarium verticillioides is a major disease of maize that reduces grain quality globally. Host resistance is the most suitable strategy for managing the disease. We report the results of genome-wide association study (GWAS) to detect alleles associated with increased resistance to FER in a set of 818 tropical maize inbred lines evaluated in three environments. Association tests performed using 43,424 single-nucleotide polymorphic (SNPs) markers identified 45 SNPs and 15 haplotypes that were significantly associated with FER resistance. Each associated SNP locus had relatively small additive effects on disease resistance and accounted for 1–4% of trait variation. These SNPs and haplotypes were located within or adjacent to 38 candidate genes, 21 of which were candidate genes associated with plant tolerance to stresses, including disease resistance. Linkage mapping in four biparental populations to validate GWAS results identified 15 quantitative trait loci (QTL) associated with F. verticillioides resistance. Integration of GWAS and QTL to the maize physical map showed eight colocated loci on chromosomes 2, 3, 4, 5, 9, and 10. QTL on chromosomes 2 and 9 are new. These results reveal that FER resistance is a complex trait that is conditioned by multiple genes with minor effects. The value of selection on identified markers for improving FER resistance is limited; rather, selection to combine small effect resistance alleles combined with genomic selection for polygenic background for both the target and general adaptation traits might be fruitful for increasing FER resistance in maize. PMID:27742723

  2. 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

  3. 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.

  4. 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.

  5. The bispectrum of cosmic string temperature fluctuations including recombination effects

    SciTech Connect

    Regan, Donough; Hindmarsh, Mark E-mail: m.b.hindmarsh@sussex.ac.uk

    2015-10-01

    We calculate the cosmic microwave background temperature bispectrum from cosmic strings, including the contributions from the last scattering surface, using a well-established Gaussian model for the string energy-momentum correlation functions, and a simplified model for the cosmic fluid. We check our approximation for the integrated Sachs-Wolfe (ISW) contribution against the bispectrum obtained from the full sky map of the cosmic string ISW signal used by the Planck team, obtaining good agreement. We validate our model for the last scattering surface contribution by comparing the predicted temperature power spectrum with that obtained from a full Boltzmann code treatment applied to the Unconnected Segment Model of a string network. We find that including the last scattering contribution has only a small impact on the upper limit on the string tension resulting from the bispectrum at Planck resolutions, and argue that the bispectrum is unlikely to be competitive with the power spectrum at any resolution.

  6. Cosmic Needles versus Cosmic Microwave Background Radiation

    NASA Astrophysics Data System (ADS)

    Li, Aigen

    2003-02-01

    It has been suggested by a number of authors that the 2.7 K cosmic microwave background (CMB) radiation might have arisen from the radiation of ``Population III'' objects thermalized by conducting cosmic graphite/iron needle-shaped dust. Due to a lack of an accurate solution to the absorption properties of exceedingly elongated grains, in existing literature which studies the CMB thermalizing process they are generally modeled as (1) needle-like spheroids in terms of the Rayleigh approximation, (2) infinite cylinders, and (3) antennae. We show here that the Rayleigh approximation is not valid since the Rayleigh criterion is not satisfied for highly conducting needles. We also show that the available intergalactic iron dust, if modeled as infinite cylinders, is not sufficient to supply the required opacity at long wavelengths to obtain the observed isotropy and Planckian nature of the CMB. If appealing to the antenna theory, conducting iron needles with exceedingly large elongations ( >104) appear able to provide sufficient opacity to thermalize the CMB within the iron density limit. But the applicability of the antenna theory to exceedingly thin needles of nanometer/micrometer thickness has not yet been verified.

  7. 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.

  8. Systematic mapping of Fragile X granules in the developing mouse brain reveals a potential role for presynaptic FMRP in sensorimotor functions

    PubMed Central

    Akins, Michael R.; LeBlanc, Hannah F.; Stackpole, Emily E.; Chyung, Eunice; Fallon, Justin R.

    2014-01-01

    Loss of Fragile X mental retardation protein (FMRP) leads to Fragile X syndrome (FXS), the most common form of inherited intellectual disability and autism. Although the functions of FMRP and its homologues FXR1P and FXR2P are well studied in the somatodendritic domain, recent evidence suggests that this family of RNA binding proteins also plays a role in the axonal and presynaptic compartments. Fragile X granules (FXGs) are morphologically- and genetically-defined structures containing Fragile X proteins that are expressed axonally and presynaptically in a subset of circuits. To further understand the role of presynaptic Fragile X proteins in the brain we have systematically mapped the FXG distribution in the mouse central nervous system. This analysis revealed both the circuits and the neuronal types that express FXGs. FXGs are enriched in circuits that mediate sensory processing and motor planning - functions that are particularly perturbed in FXS patients. Analysis of FXG expression in the hippocampus suggests that CA3 pyramidal neurons utilize presynaptic Fragile X proteins to modulate recurrent but not feedforward processing. Neuron-specific FMRP mutants revealed a requirement for neuronal FMRP in the regulation of FXGs. Finally, conditional FMRP ablation demonstrated that FXGs are expressed in axons of thalamic relay nuclei that innervate cortex, but not in axons of thalamic reticular nuclei, striatal nuclei, or cortical neurons that innervate thalamus. Together, these findings support the proposal that dysregulation of axonal and presynaptic Fragile X proteins contribute to the neurological symptoms of FXS. PMID:22522693

  9. Karyotypic analysis and FISH mapping of microsatellite motifs reveal highly differentiated XX/XY sex chromosomes in the pink-tailed worm-lizard (Aprasia parapulchella, Pygopodidae, Squamata)

    PubMed Central

    2013-01-01

    Background The infraorder Gekkota is intriguing because it contains multiple chromosomal and environmental sex determination systems that vary even among closely related taxa. Here, we compare male and females karyotypes of the pink-tailed worm-lizard (Aprasia parapulchella), a small legless lizard belonging to the endemic Australian family Pygopodidae. Results We applied comparative genomic hybridization to reveal an XX/XY sex chromosome system in which the Y chromosome is highly differentiated from the X in both gross morphology and DNA sequence. In addition, FISH mapping has revealed that two microsatellite repeat motifs, (AGAT)n and (AC)n, have been amplified multiple times on the Y chromosome. Conclusion XY karyotypes are found in other pygopodids (Delma inornata and Lialis burtonis), suggesting that the common ancestor of Pygopodidae also had XY sex chromosomes. However, the morphology and size of the Y chromosomes are different among the three species, suggesting that the processes underlying the evolution of sex chromosomes in the Pygopodidae involved chromosome rearrangements and accumulation and amplification of repeats. PMID:24344753

  10. High-throughput mapping of the promoters of the mouse olfactory receptor genes reveals a new type of mammalian promoter and provides insight into olfactory receptor gene regulation

    PubMed Central

    Clowney, E. Josephine; Magklara, Angeliki; Colquitt, Bradley M.; Pathak, Nidhi; Lane, Robert P.; Lomvardas, Stavros

    2011-01-01

    The olfactory receptor (OR) genes are the largest mammalian gene family and are expressed in a monogenic and monoallelic fashion in olfactory neurons. Using a high-throughput approach, we mapped the transcription start sites of 1085 of the 1400 murine OR genes and performed computational analysis that revealed potential transcription factor binding sites shared by the majority of these promoters. Our analysis produced a hierarchical model for OR promoter recognition in which unusually high AT content, a unique epigenetic signature, and a stereotypically positioned O/E site distinguish OR promoters from the rest of the murine promoters. Our computations revealed an intriguing correlation between promoter AT content and evolutionary plasticity, as the most AT-rich promoters regulate rapidly evolving gene families. Within the AT-rich promoter category the position of the TATA-box does not correlate with the transcription start site. Instead, a spike in GC composition might define the exact location of the TSS, introducing the concept of “genomic contrast” in transcriptional regulation. Finally, our experiments show that genomic neighborhood rather than promoter sequence correlates with the probability of different OR genes to be expressed in the same olfactory cell. PMID:21705439

  11. 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…

  12. 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

  13. 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

  14. 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

  15. 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.

  16. 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)

  17. Concept Mapping

    ERIC Educational Resources Information Center

    Technology & Learning, 2005

    2005-01-01

    Concept maps are graphical ways of working with ideas and presenting information. They reveal patterns and relationships and help students to clarify their thinking, and to process, organize and prioritize. Displaying information visually--in concept maps, word webs, or diagrams--stimulates creativity. Being able to think logically teaches…

  18. The genome and linkage map of the northern pike (Esox lucius): conserved synteny revealed between the salmonid sister group and the Neoteleostei.

    PubMed

    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 of the

  19. Nuclear Magnetic Resonance Structural Mapping Reveals Promiscuous Interactions between Clathrin-Box Motif Sequences and the N-Terminal Domain of the Clathrin Heavy Chain

    PubMed Central

    2016-01-01

    The recruitment and organization of clathrin at endocytic sites first to form coated pits and then clathrin-coated vesicles depend on interactions between the clathrin N-terminal domain (TD) and multiple clathrin binding sequences on the cargo adaptor and accessory proteins that are concentrated at such sites. Up to four distinct protein binding sites have been proposed to be present on the clathrin TD, with each site proposed to interact with a distinct clathrin binding motif. However, an understanding of how such interactions contribute to clathrin coat assembly must take into account observations that any three of these four sites on clathrin TD can be mutationally ablated without causing loss of clathrin-mediated endocytosis. To take an unbiased approach to mapping binding sites for clathrin-box motifs on clathrin TD, we used isothermal titration calorimetry (ITC) and nuclear magnetic resonance spectroscopy. Our ITC experiments revealed that a canonical clathrin-box motif peptide from the AP-2 adaptor binds to clathrin TD with a stoichiometry of 3:1. Assignment of 90% of the total visible amide resonances in the TROSY-HSQC spectrum of 13C-, 2H-, and 15N-labeled TD40 allowed us to map these three binding sites by analyzing the chemical shift changes as clathrin-box motif peptides were titrated into clathrin TD. We found that three different clathrin-box motif peptides can each simultaneously bind not only to the previously characterized clathrin-box site but also to the W-box site and the β-arrestin splice loop site on a single TD. The promiscuity of these binding sites can help explain why their mutation does not lead to larger effects on clathrin function and suggests a mechanism by which clathrin may be transferred between different proteins during the course of an endocytic event. PMID:25844500

  20. Rock-avalanche dynamics revealed by large-scale field mapping and seismic signals at a highly mobile avalanche in the West Salt Creek valley, western Colorado

    USGS Publications Warehouse

    Coe, Jeffrey A.; Baum, Rex L.; Allstadt, Kate; Kochevar, Bernard; Schmitt, Robert G.; Morgan, Matthew L.; White, Jonathan L.; Stratton, Benjamin T.; Hayashi, Timothy A.; Kean, Jason W.

    2016-01-01

    On 25 May 2014, a rain-on-snow–induced rock avalanche occurred in the West Salt Creek valley on the northern flank of Grand Mesa in western Colorado (United States). The avalanche mobilized from a preexisting rock slide in the Green River Formation and traveled 4.6 km down the confined valley, killing three people. The avalanche was rare for the contiguous United States because of its large size (54.5 Mm3) and high mobility (height/length = 0.14). To understand the avalanche failure sequence, mechanisms, and mobility, we conducted a forensic analysis using large-scale (1:1000) structural mapping and seismic data. We used high-resolution, unmanned aircraft system imagery as a base for field mapping, and analyzed seismic data from 22 broadband stations (distances < 656 km from the rock-slide source area) and one short-period network. We inverted broadband data to derive a time series of forces that the avalanche exerted on the earth and tracked these forces using curves in the avalanche path. Our results revealed that the rock avalanche was a cascade of landslide events, rather than a single massive failure. The sequence began with an early morning landslide/debris flow that started ∼10 h before the main avalanche. The main avalanche lasted ∼3.5 min and traveled at average velocities ranging from 15 to 36 m/s. For at least two hours after the avalanche ceased movement, a central, hummock-rich core continued to move slowly. Since 25 May 2014, numerous shallow landslides, rock slides, and rock falls have created new structures and modified avalanche topography. Mobility of the main avalanche and central core was likely enhanced by valley floor material that liquefied from undrained loading by the overriding avalanche. Although the base was likely at least partially liquefied, our mapping indicates that the overriding avalanche internally deformed predominantly by sliding along discrete shear surfaces in material that was nearly dry and had substantial frictional

  1. Data analysis of cosmic microwave background experiments

    NASA Astrophysics Data System (ADS)

    Abroe, Matthew Edmund

    2004-12-01

    The cosmic microwave background (CMB) is a powerful tool for determining and constraining the fundamental properties of our universe. In this thesis we present various computational and statistical techniques used to analyze datasets from CMB experiments, and apply them to both simulated and actual datasets. The algorithms presented in this thesis perform a variety of tasks in relation to the goal of extracting scientific information from CMB data sets. The CMB anisotropy power spectrum is sensitive to numerous parameters that determine the evolutionary and large scale properties of our universe. Now that numerous experiments have mapped the CMB intensity fluctuations on overlapping regions of the sky it is important to ensure that the various experiments are indeed observing the same signal. We cross-correlate the cosmic microwave background temperature anisotropy maps from the WMAP, MAXIMA-I, and MAXIMA-II experiments. The results conclusively show that the three experiments not only display the same statistical properties of the CMB anisotropy, but also detect the same features wherever the observed sky areas overlap. We conclude that the contribution of systematic errors to these maps is negligible and that MAXIMA and WMAP have accurately mapped the cosmic microwave background anisotropy. Due to a quadrapole anisotropy at last scattering it is predicted that the CMB photons should be linearly polarized, and that the polarization intensity will be roughly an order of magnitude lower than the intensity fluctuations. Two computationally intensive methods for simulating the CMB polarization signal on the sky are presented. Now that CMB polarization experiments are currently producing data sets new algorithms for analyzing polarization time stream data must be developed and tested. We demonstrate how to generate simulations of a polarization experiment in the temporal domain and apply these simulations to the MAXIPOL case. We develop a maximum likelihood map making

  2. Cosmic Magnetic Fields: Observations and Prospects

    NASA Astrophysics Data System (ADS)

    Beck, Rainer

    2011-09-01

    Synchrotron emission, its polarization and its Faraday rotation at radio frequencies of 0.2-10 GHz are powerful tools to study the strength and structure of cosmic magnetic fields. Unpolarized emission traces turbulent fields which are strongest in galactic spiral arms and bars (20-30 μG) and in central starburst regions (50-100 μG). Such fields are dynamically important, e.g. they can drive gas inflows in central regions. Polarized emission traces ordered fields which can be regular (uni-directional) or anisotropic random (generated from isotropic random fields by compression or shear). Ordered fields with spiral patterns exist in grand-design, barred and flocculent galaxies, and in central regions of starburst galaxies. The strongest ordered (mostly regular) fields of 10-15 μG strength are generally found in galactic interarm regions and follow the orientation of adjacent gas spiral arms. Faraday rotation measures (RM) of the diffuse polarized radio emission from the disks of several spiral galaxies reveal large-scale patterns, which are signatures of regular fields probably generated by a mean-field dynamo. Ordered fields in interacting galaxies have asymmetric distributions and are an excellent tracer of past interactions between galaxies or with the intergalactic medium. Ordered magnetic fields are also observed in radio halos around edge-on galaxies, out to large distances from the plane, with X-shaped patterns.--The strength of the total magnetic field in our Milky Way is about 6 μG near the solar radius, but several mG in dense clouds, pulsar wind nebulae, and filaments near the Galactic Center. Diffuse polarized radio emission and Faraday rotation data from pulsars and background sources show spiral fields with large-scale reversals, but the overall field structure in our Galaxy is still under debate.--Diffuse radio emission from the halos of galaxy clusters is mostly unpolarized because intracluster magnetic fields are turbulent, while cluster

  3. Anisotropies in TeV Cosmic Rays Related to Entry into the Heliosphere and the IBEX Ribbon

    NASA Astrophysics Data System (ADS)

    Schwadron, N. A.; Adams, F.; Funsten, H. O.; Desiati, P.; Frisch, P. C.; McComas, D. J.

    2012-12-01

    The Interstellar Boundary Explorer (IBEX) observes enhanced Energetic Neutral Atoms (ENAs) emission in the keV energy range from a narrow (~20 wide°) "ribbon'" in the sky that appears to be centered on the direction of the local interstellar (LIS) magnetic field. The Milagro collaboration, the Asγ collaboration and the IceCube observatory have recently made global maps of cosmic ray fluxes in the TeV energy range, revealing anisotropic structures ordered in part by the local interstellar magnetic field and the interstellar flow. In this talk, we make the link between these disparate observations by developing a simple model of the magnetic structure surrounding the heliosphere in the Local Interstellar Medium (LISM) that is consistent with both IBEX ENA fluxes and TeV cosmic ray anisotropies. By modeling the propagation of cosmic rays through this magnetic field structure, we specifically show that (1) the source of large-scale TeV anisotropies is likely due to the interaction between the Local Interstellar Cloud and the Blue Cloud; (2) the large-scale TeV anisotropy provides a consistent orientation for the local interstellar magnetic field at the center of the IBEX Ribbon and corroborates the ~3 μG magnitude of the local interstellar magnetic field derived from IBEX observations of the global heliosphere; (3) small-scale structures in cosmic rays (over <30° angular scales) are influenced by the interstellar field interaction with the heliosphere at energies <10 TeV; and (4) interstellar flow and heliotail signatures appear in model results at lower energies (e.g., <5 TeV). Thus, we provide a critical link between IBEX ENA observations and TeV cosmic ray anisotropies, which are strongly influenced by the interactions between the local interstellar magnetic field, the flow of the local interstellar plasma, and the global heliosphere.

  4. Anisotropies in TeV Cosmic Rays Related to the Local Interstellar Magnetic Field from the IBEX Ribbon

    NASA Astrophysics Data System (ADS)

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

    2015-01-01

    The Interstellar Boundary Explorer (IBEX) observes enhanced Energetic Neutral Atoms (ENAs) emission in the keV energy range from a narrow (~20° wide) "ribbon" in the sky that appears to be centered on the direction of the local interstellar (LIS) magnetic field. The Milagro collaboration, the Asγ collaboration and the IceCube observatory have recently made global maps of cosmic ray fluxes in the TeV energy range, revealing anisotropic structures ordered in part by the local interstellar magnetic field and the interstellar flow. This paper following from a recent publication in Science makes the link between these disparate observations by developing a simple model of the magnetic structure surrounding the heliosphere in the Local Interstellar Medium (LISM) that is consistent with both IBEX ENA fluxes and TeV cosmic ray anisotropies. The model also employs the revised velocity direction of the LIC derived from neutral He observations by IBEX. By modeling the propagation of cosmic rays through this magnetic field structure, we specifically show that (1) the large-scale TeV anisotropy provides a roughly consistent orientation for the local interstellar magnetic field at the center of the IBEX Ribbon and corroborates the ~ 3 μG magnitude of the local interstellar magnetic field derived from IBEX observations of the global heliosphere; (2) and small-scale structures in cosmic rays (over < 30° angular scales) are influenced by the interstellar field interaction with the heliosphere at energies < 10 TeV. Thus, we provide a link between IBEX ENA observations, IBEX neutral observations of interstellar He, and TeV cosmic ray anisotropies, which are strongly influenced by the interactions between the local interstellar magnetic field, the flow of the local interstellar plasma, and the global heliosphere.

  5. Proteoform Profile Mapping of the Human Serum Complement Component C9 Revealing Unexpected New Features of N-, O-, and C-Glycosylation

    PubMed Central

    2017-01-01

    The human complement C9 protein (∼65 kDa) is a member of the complement pathway. It plays an essential role in the membrane attack complex (MAC), which forms a lethal pore on the cellular surface of pathogenic bacteria. Here, we charted in detail the structural microheterogeneity of C9 purified from human blood serum, using an integrative workflow combining high-resolution native mass spectrometry and (glyco)peptide-centric proteomics. The proteoform profile of C9 was acquired by high-resolution native mass spectrometry, which revealed the co-occurrence of ∼50 distinct mass spectrometry (MS) signals. Subsequent peptide-centric analysis, through proteolytic digestion of C9 and liquid chromatography (LC)-tandem mass spectrometry (MS/MS) measurements of the resulting peptide mixtures, provided site-specific quantitative profiles of three different types of C9 glycosylation and validation of the native MS data. Our study provides a detailed specification, validation, and quantification of 15 co-occurring C9 proteoforms and the first direct experimental evidence of O-linked glycans in the N-terminal region. Additionally, next to the two known glycosylation sites, a third novel, albeit low abundant, N-glycosylation site on C9 is identified, which surprisingly does not possess the canonical N-glycosylation sequence N-X-S/T. Our data also reveal a binding of up to two Ca2+ ions to C9. Mapping all detected and validated sites of modifications on a structural model of C9, as present in the MAC, hints at their putative roles in pore formation or receptor interactions. The applied methods herein represent a powerful tool for the unbiased in-depth analysis of plasma proteins and may advance biomarker discovery, as aberrant glycosylation profiles may be indicative of the pathophysiological state of the patients. PMID:28221766

  6. 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

  7. 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

  8. Mapping the Heavens: Probing Cosmology with Large Surveys

    ScienceCinema

    Frieman, Joshua [Fermilab

    2016-07-12

    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.

  9. Cosmic structure formation

    NASA Technical Reports Server (NTRS)

    Bertschinger, Edumund

    1994-01-01

    This article reviews the prevailing paradigm for how galaxies and larger structures formed in the universe: gravitational instability. Basic observational facts are summarized to motivate the standard cosmological framework underlying most detailed investigations of structure formation. The observed univers approaches spatial uniformity on scales larger than about 10(exp 26) cm. On these scales gravitational dynamics is almost linear and therefore relatively easy to relate to observations of large-scale structure. On smaller scales cosmic structure is complicated not only by nonlinear gravitational clustering but also by nonlinear nongravitational gas dynamical processes. The complexity of these phenomena makes galaxy formation one of the grand challenge problems of the physical sciences. No fully satisfactory theory can presently account in detail for the observed cosmic structure. However, as this article summarizes, significant progress has been made during the last few years.

  10. 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.

  11. Cosmic Origin of Quantization

    NASA Astrophysics Data System (ADS)

    Calogero, Francesco

    An estimate is presented of the angular momentum associated with the stochastic cosmic tremor, which has been hypothesized to be caused by universal gravitation and by the granularity of matter, and to be itself the cause of quantization ("cosmic origin of quantization"). If that universal tremor has the spatial coherence which is instrumental in order that the estimated action associated with it have the order of magnitude of Planck's constant h, then the estimated order of magnitude of the angular momentum associated with it also has the same value. We moreover indicate how these findings (originally based on a simplified model of the Universe, as being made up only of particles having the nucleon mass) are affected (in fact, essentially unaffected) by the possible presence in the mass of the Universe of a large component made up of particles much lighter than nucleons ("dark", or "missing", mass).

  12. Note on cosmic censorship

    NASA Astrophysics Data System (ADS)

    Tipler, F. J.

    1985-05-01

    A number of recent theorems by Krolak (1983) and Newman (1983) purport to prove cosmic censorship by showing that strong-curvature singularities must be hidden behind horizons. It is shown that the 'null strong-curvature' condition which Newman imposes on certain classes of null geodesics to restrict curvature growth in the space-time does not hold in many physically realistic space-times: it is not satisfied by any null geodesic in the relevant class in any open Friedmann cosmological model, nor does it hold for any null geodesic in the relevant class in maximal Schwarzschild space. More generally it is argued that the singularity predicted by the Penrose singularity theorem is unlikely to be of the type eliminated by Newman. Thus the Newman theorems are probably without physical significance. The Krolak theorems, although based on a physically significant definition of strong curvature singularity, are mathematically invalid, and this approach cannot be used to obtain a cosmic-censorship theorem.

  13. Comparative genome mapping of the deer mouse (Peromyscus maniculatus) reveals greater similarity to rat (Rattus norvegicus) than to the lab mouse (Mus musculus)

    PubMed Central

    2008-01-01

    Background Deer mice (Peromyscus maniculatus) and congeneric species are the most common North American mammals. They represent an emerging system for the genetic analyses of the physiological and behavioral bases of habitat adaptation. Phylogenetic evidence suggests a much more ancient divergence of Peromyscus from laboratory mice (Mus) and rats (Rattus) than that separating latter two. Nevertheless, early karyotypic analyses of the three groups suggest Peromyscus to be exhibit greater similarities with Rattus than with Mus. Results Comparative linkage mapping of an estimated 35% of the deer mouse genome was done with respect to the Rattus and Mus genomes. We particularly focused on regions that span synteny breakpoint regions between the rat and mouse genomes. The linkage analysis revealed the Peromyscus genome to have a higher degree of synteny and gene order conservation with the Rattus genome. Conclusion These data suggest that: 1. the Rattus and Peromyscus genomes more closely represent ancestral Muroid and rodent genomes than that of Mus. 2. the high level of genome rearrangement observed in Muroid rodents is especially pronounced in Mus. 3. evolution of genome organization can operate independently of more commonly assayed measures of genetic change (e.g. SNP frequency). PMID:18302785

  14. Transcriptional mapping and nucleotide sequence of the Listeria monocytogenes hlyA region reveal structural features that may be involved in regulation.

    PubMed Central

    Mengaud, J; Vicente, M F; Cossart, P

    1989-01-01

    DNA sequence analysis of the regions adjacent to the hlyA gene, which encodes listeriolysin O, an essential virulence factor of Listeria monocytogenes, revealed the presence of two open reading frames (ORFs): ORF D located 304 base pairs downstream from hlyA, and ORF U located 224 base pairs upstream from and in opposite direction to hlyA. Promoter mapping performed with RNAs extracted from cells growing exponentially in rich medium showed that the three ORFs are independently transcribed. hlyA is transcribed from two promoters separated by 10 base pairs (P1 hlyA and P2 hlyA). ORF U is transcribed in the opposite direction from an adjacent promoter. These two promoter regions are separated by a palindromic sequence T-T-A-A-C-A-A/T-T-G-T-T-A-A. This palindrome was also found upstream from the ORF D promoter, suggesting that all three genes are similarly regulated. Images PMID:2509367

  15. Extensive chromosome homoeology among Brassiceae species were revealed by comparative genetic mapping with high-density EST-based SNP markers in radish (Raphanus sativus L.).

    PubMed

    Li, Feng; Hasegawa, Yoichi; Saito, Masako; Shirasawa, Sachiko; Fukushima, Aki; Ito, Toyoaki; Fujii, Hiroshi; Kishitani, Sachie; Kitashiba, Hiroyasu; Nishio, Takeshi

    2011-10-01

    A linkage map of expressed sequence tag (EST)-based markers in radish (Raphanus sativus L.) was constructed using a low-cost and high-efficiency single-nucleotide polymorphism (SNP) genotyping method named multiplex polymerase chain reaction-mixed probe dot-blot analysis developed in this study. Seven hundred and forty-six SNP markers derived from EST sequences of R. sativus were assigned to nine linkage groups with a total length of 806.7 cM. By BLASTN, 726 markers were found to have homologous genes in Arabidopsis thaliana, and 72 syntenic regions, which have great potential for utilizing genomic information of the model species A. thaliana in basic and applied genetics of R. sativus, were identified. By construction and analysis of the genome structures of R. sativus based on the 24 genomic blocks within the Brassicaceae ancestral karyotype, 23 of the 24 genomic blocks were detected in the genome of R. sativus, and half of them were found to be triplicated. Comparison of the genome structure of R. sativus with those of the A, B, and C genomes of Brassica species and that of Sinapis alba L. revealed extensive chromosome homoeology among Brassiceae species, which would facilitate transfer of the genomic information from one Brassiceae species to another.

  16. Extensive Chromosome Homoeology among Brassiceae Species Were Revealed by Comparative Genetic Mapping with High-Density EST-Based SNP Markers in Radish (Raphanus sativus L.)‡

    PubMed Central

    Li, Feng; Hasegawa, Yoichi; Saito, Masako; Shirasawa, Sachiko; Fukushima, Aki; Ito, Toyoaki; Fujii, Hiroshi; Kishitani, Sachie; Kitashiba, Hiroyasu; Nishio, Takeshi

    2011-01-01

    A linkage map of expressed sequence tag (EST)-based markers in radish (Raphanus sativus L.) was constructed using a low-cost and high-efficiency single-nucleotide polymorphism (SNP) genotyping method named multiplex polymerase chain reaction–mixed probe dot-blot analysis developed in this study. Seven hundred and forty-six SNP markers derived from EST sequences of R. sativus were assigned to nine linkage groups with a total length of 806.7 cM. By BLASTN, 726 markers were found to have homologous genes in Arabidopsis thaliana, and 72 syntenic regions, which have great potential for utilizing genomic information of the model species A. thaliana in basic and applied genetics of R. sativus, were identified. By construction and analysis of the genome structures of R. sativus based on the 24 genomic blocks within the Brassicaceae ancestral karyotype, 23 of the 24 genomic blocks were detected in the genome of R. sativus, and half of them were found to be triplicated. Comparison of the genome structure of R. sativus with those of the A, B, and C genomes of Brassica species and that of Sinapis alba L. revealed extensive chromosome homoeology among Brassiceae species, which would facilitate transfer of the genomic information from one Brassiceae species to another. PMID:21816873

  17. 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

  18. 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.

  19. Analysis of North Sky Cosmic Ray Anisotropy with Atmospheric Neutrinos

    NASA Astrophysics Data System (ADS)

    Wills, Elizabeth; IceCube Collaboration

    2017-01-01

    Since the discovery of Cosmic Ray anisotropy, no experiment has definitively discovered the source of this unexpected phenomenon. Studying the cosmic rays' neutral daughter particles with pointing capabilities, like neutrinos, could shed new light. This can be done at two levels; a source which produces cosmic rays must also produce high energy astrophysical neutrinos, and low energy atmospheric neutrinos are made when the cosmic rays interact with the atmosphere. This analysis focuses on atmospheric neutrinos detected by IceCube, a Cherenkov detector instrumenting a kilometer cubed of glacial ice at the South Pole. The anisotropy and its energy dependence have been studied in the Southern sky using atmospheric muons by IceCube. In the North, gamma ray detectors, such as HAWC, and Argo-YBJ, have observed this anisotropy in cosmic ray showers. Thus far, no single- detector full-sky map exists of the anisotropy. Using IceCube's neutrino data, we can complement these studies with an exploration of the northern sky anisotropy at higher energies of cosmic rays. This could bring us much closer to understanding the complete picture of this anisotropy across energy levels and the whole sky.

  20. 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.

  1. Web life: Cosmic Diary

    NASA Astrophysics Data System (ADS)

    2009-03-01

    What is it? Cosmic Diary brings together a smorgasbord of blogging astronomers from around the world, with more than 50 contributors commenting on new discoveries and long-standing questions in astronomy - as well as offering insights into their ordinary working lives and outside interests. The site is sponsored by the International Astronomical Union and UNESCO, and it is one of 11 "cornerstone projects" of the International Year of Astronomy 2009 (IYA2009).

  2. 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.

  3. 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)

  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. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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

  10. Cosmic strings and galaxy formation

    NASA Technical Reports Server (NTRS)

    Bertschinger, Edmund

    1989-01-01

    The cosmogonical model proposed by Zel'dovich and Vilenkin (1981), in which superconducting cosmic strings act as seeds for the origin of structure in the universe, is discussed, summarizing the results of recent theoretical investigations. Consideration is given to the formation of cosmic strings, the microscopic structure of strings, gravitational effects, cosmic string evolution, and the formation of galaxies and large-scale structure. Simulation results are presented in graphs, and several outstanding issues are listed and briefly characterized.

  11. 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

  12. The Cosmic Background Explorer /COBE/

    NASA Technical Reports Server (NTRS)

    Mather, J. C.

    1982-01-01

    The Cosmic Background Explorer (COBE) satellite, under study by NASA since 1976, will map the spectrum and the angular distribution of diffuse radiation from the universe over the entire wavelength range from 1 micron to 1.3 cm. It carries three instruments: a set of differential microwave radiometers (DMR) at 23.5, 31.4, 53, and 90GHz, a far infrared absolute spectrophotometer (FIRAS) covering 1 to 100 per cm, and a diffuse infrared background experiment (DIRBE) covering 1 to 300 microns. They will use the ideal space environment, a one year lifetime, and standard instrument techniques to achieve orders of magnitude improvements in sensitivity and accuracy, providing a fundamental data base for cosmology. The instruments are united by common purpose as well as similar environmental and orbital requirements. The data from all three experiments will be analyzed together, to distinguish nearby sources of radiation from the cosmologically interesting diffuse background radiations. Construction is planned to begin in 1982 for a launch in 1988.

  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. Angular correlation of cosmic neutrinos with ultrahigh-energy cosmic rays and implications for their sources

    SciTech Connect

    Moharana, Reetanjali; Razzaque, Soebur E-mail: srazzaque@uj.ac.za

    2015-08-01

    Cosmic neutrino events detected by the IceCube Neutrino Observatory with energy 0∼> 3 TeV have poor angular resolutions to reveal their origin. Ultrahigh-energy cosmic rays (UHECRs), with better angular resolutions at 0>6 EeV energies, can be used to check if the same astrophysical sources are responsible for producing both neutrinos and UHECRs. We test this hypothesis, with statistical methods which emphasize invariant quantities, by using data from the Pierre Auger Observatory, Telescope Array and past cosmic-ray experiments. We find that the arrival directions of the cosmic neutrinos are correlated with 0≥ 10 EeV UHECR arrival directions at confidence level ≈ 90%. The strength of the correlation decreases with decreasing UHECR energy and no correlation exists at energy 0∼ 6 EeV . A search in astrophysical databases within 3{sup o} of the arrival directions of UHECRs with energy 0≥ 10 EeV, that are correlated with the IceCube cosmic neutrinos, resulted in 18 sources from the Swift-BAT X-ray catalog with redshift z≤ 0.06. We also found 3 objects in the Kühr catalog of radio sources using the same criteria. The sources are dominantly Seyfert galaxies with Cygnus A being the most prominent member. We calculate the required neutrino and UHECR fluxes to produce the observed correlated events, and estimate the corresponding neutrino luminosity (25 TeV–2.2 PeV) and cosmic-ray luminosity (500 TeV–180 EeV), assuming the sources are the ones we found in the Swift-BAT and Kühr catalogs. We compare these luminosities with the X-ray luminosity of the corresponding sources and discuss possibilities of accelerating protons to 0∼> 10 EeV and produce neutrinos in these sources.

  15. The Origin of Cosmic Rays

    ScienceCinema

    Blasi, Pasquale [INAF/Arcetri-Italy and Fermilab, Italy

    2016-07-12

    Cosmic Rays reach the Earth from space with energies of up to more than 1020 eV, carrying information on the most powerful particle accelerators that Nature has been able to assemble. Understanding where and how cosmic rays originate has required almost one century of investigations, and, although the last word is not written yet, recent observations and theory seem now to fit together to provide us with a global picture of the origin of cosmic rays of unprecedented clarity. Here we will describe what we learned from recent observations of astrophysical sources (such as supernova remnants and active galaxies) and we will illustrate what these observations tell us about the physics of particle acceleration and transport. We will also discuss the “end” of the Galactic cosmic ray spectrum, which bridges out attention towards the so called ultra high energy cosmic rays (UHECRs). At ~1020 eV the gyration scale of cosmic rays in cosmic magnetic fields becomes large enough to allow us to point back to their sources, thereby allowing us to perform “cosmic ray astronomy”, as confirmed by the recent results obtained with the Pierre Auger Observatory. We will discuss the implications of these observations for the understanding of UHECRs, as well as some questions which will likely remain unanswered and will be the target of the next generation of cosmic ray experiments.

  16. 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.

  17. Cosmic ray hazards in the solar system.

    NASA Technical Reports Server (NTRS)

    Milford, S. N.

    1965-01-01

    Cosmic ray hazards in solar system considered from measurements of cosmic ray energy and charge spectra near Earth and in interplanetary space near Earth, together with interaction of cosmic rays with Moon surface

  18. Control over the strength of connections between modules: a double dissociation between stimulus format and task revealed by Granger causality mapping in fMRI.

    PubMed

    Anderson, Britt; Soliman, Sherif; O'Malley, Shannon; Danckert, James; Besner, Derek

    2015-01-01

    Drawing on theoretical and computational work with the localist dual route reading model and results from behavioral studies, Besner et al. (2011) proposed that the ability to perform tasks that require overriding stimulus-specific defaults (e.g., semantics when naming Arabic numerals, and phonology when evaluating the parity of number words) necessitate the ability to modulate the strength of connections between cognitive modules for lexical representation, semantics, and phonology on a task- and stimulus-specific basis. We used functional magnetic resonance imaging to evaluate this account by assessing changes in functional connectivity while participants performed tasks that did and did not require such stimulus-task default overrides. The occipital region showing the greatest modulation of BOLD signal strength for the two stimulus types was used as the seed region for Granger causality mapping (GCM). Our GCM analysis revealed a region of rostromedial frontal cortex with a crossover interaction. When participants performed tasks that required overriding stimulus type defaults (i.e., parity judgments of number words and naming Arabic numerals) functional connectivity between the occipital region and rostromedial frontal cortex was present. Statistically significant functional connectivity was absent when the tasks were the default for the stimulus type (i.e., parity judgments of Arabic numerals and reading number words). This frontal region (BA 10) has previously been shown to be involved in goal-directed behavior and maintenance of a specific task set. We conclude that overriding stimulus-task defaults requires a modulation of connection strengths between cognitive modules and that the override mechanism predicted from cognitive theory is instantiated by frontal modulation of neural activity of brain regions specialized for sensory processing.

  19. 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

  20. 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.

  1. 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

  2. The Emergence of Cosmic Education. Spotlight: Cosmic Education.

    ERIC Educational Resources Information Center

    Trudeau, Sr. Christina Marie

    2002-01-01

    Discusses the influence of Hindu, Moslem, and Buddhist metaphysics on Maria Montessori's own pedagogical philosophy of Cosmic Education, which she regarded as the core of all learning experiences, after her visit to India. Considers the relationship between Montessori's ideas of child development and Cosmic Education, and the effect of Indian…

  3. On Becoming a Cosmic Educator. Spotlight: Cosmic Education.

    ERIC Educational Resources Information Center

    Maier, Biff

    2002-01-01

    Discusses Maria Montessori's five pedagogical guidelines for her Cosmic Education concept: starting with the larger context; treating planet Earth as a cosmic organism; stressing similarities among seemingly different groups of people, organisms, or objects; showing chains of interdependence among all things; and examining behavior from a cosmic…

  4. 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.

  5. 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...

  6. CosmicSIG science and plans

    NASA Astrophysics Data System (ADS)

    Olinto, Angela V.

    2014-03-01

    Recent activities of the Cosmic Ray Science Interest Group (CosmicSIG) of the Physics of the Cosmos PAG will be reviewed. CosmicSIG was formed to provide an assessment to NASA HQ and the PCOS program office of the status of current and future missions in the area of cosmic-ray astrophysics. CosmicSIG also strives to act as a focal point and forum for the cosmic ray community.

  7. Cosmic Background Radiation

    NASA Astrophysics Data System (ADS)

    Sidharth, B. G.; Valluri, S. R.

    2015-08-01

    It is shown that a collection of photons with nearly the same frequency exhibits a "condensation" type of phenomenon corresponding to a peak intensity. The observed cosmic background radiation can be explained from this standpoint. We have obtained analogous results by extremization of the occupation number for photons with the use of the Lambert W function. Some of the interesting applications of this function are briefly discussed in the context of graphene which exhibits an interesting two dimensional structure with several characteristic properties and diverse practical applications.

  8. Antiprotons in cosmic rays

    NASA Technical Reports Server (NTRS)

    Balasubrahmanyan, V. K.; Ormes, J. F.; Streitmatter, R. E.

    1987-01-01

    Recent experimental observations and results are discussed. It was found that the approximately 50 antiprotons collected in balloon experiments to date have generated considerable theoretical interest. Clearly, confirmatory experiments and measurements over an extended energy range are required before definite conclusions are drawn. Antiproton measurements have a bearing on astrophysical problems ranging from cosmic ray propagation to issues of cosmological import. The next generation of balloon experiments and the Particle Astrophysics Magnet Facility being discussed for operation on NASA's space station should provide data and insights of highest interest.

  9. Wormhole cosmic censorship

    NASA Astrophysics Data System (ADS)

    Matos, Tonatiuh; Ureña-López, L. Arturo; Miranda, Galaxia

    2016-05-01

    We analyze the properties of a Kerr-like wormhole supported by phantom matter, which is an exact solution of the Einstein-phantom field equations. It is shown that the solution has a naked ring singularity which is unreachable to null geodesics falling freely from the outside. Similarly to Roger Penrose's cosmic censorship, that states that all naked singularities in the Universe must be protected by event horizons, here we conjecture from our results that a naked singularity can also be fully protected by the intrinsic properties of a wormhole's throat.

  10. Cosmological cosmic strings

    NASA Technical Reports Server (NTRS)

    Gregory, Ruth

    1988-01-01

    The effect of an infinite cosmic string on a cosmological background is investigated. It is found that the metric is approximately a scaled version of the empty space string metric, i.e., conical in nature. Results are used to place bounds on the amount of cylindrical gravitational radiation currently emitted by such a string. The gravitational radiation equations are then analyzed explicitly and it is shown that even initially large disturbances are rapidly damped as the expansion proceeds. The implications of the gravitational radiation background and the limitations of the quadrupole formula are discussed.

  11. The Cosmic Background Explorer

    NASA Technical Reports Server (NTRS)

    Gulkis, Samuel; Lubin, Philip M.; Meyer, Stephan S.; Silverberg, Robert F.

    1990-01-01

    The Cosmic Background Explorer (CBE), NASA's cosmological satellite which will observe a radiative relic of the big bang, is discussed. The major questions connected to the big bang theory which may be clarified using the CBE are reviewed. The satellite instruments and experiments are described, including the Differential Microwave Radiometer, which measures the difference between microwave radiation emitted from two points on the sky, the Far-Infrared Absolute Spectrophotometer, which compares the spectrum of radiation from the sky at wavelengths from 100 microns to one cm with that from an internal blackbody, and the Diffuse Infrared Background Experiment, which searches for the radiation from the earliest generation of stars.

  12. Is the Cosmic Microwave Background a Shell Around Us? or are the Microwaves Everywhere in the Universe?

    NASA Technical Reports Server (NTRS)

    Mather, John

    2015-01-01

    A: The cosmic microwave background (CMB) radiation fills the universe and travels in all directions. As we see it from here in satellite maps, it is about equally bright in all directions, and thats one of the main reasons we know its cosmic.

  13. Growth of Cosmic Structure: Probing Dark Energy Beyond Expansion

    DOE PAGES

    Huterer, Dragan; Kirkby, David; Bean, Rachel; ...

    2014-03-15

    The quantity and quality of cosmic structure observations have greatly accelerated in recent years, and further leaps forward will be facilitated by imminent projects. These will enable us to map the evolution of dark and baryonic matter density fluctuations over cosmic history. The way that these fluctuations vary over space and time is sensitive to several pieces of fundamental physics: the primordial perturbations generated by GUT-scale physics; neutrino masses and interactions; the nature of dark matter and dark energy. We focus on the last of these here: the ways that combining probes of growth with those of the cosmic expansionmore » such as distance-redshift relations will pin down the mechanism driving the acceleration of the Universe.« less

  14. Growth of cosmic structure: Probing dark energy beyond expansion

    SciTech Connect

    Huterer, Dragan; Kirkby, David; Bean, Rachel; Connolly, Andrew; Dawson, Kyle; Dodelson, Scott; Evrard, August; Jain, Bhuvnesh; Jarvis, Michael; Linder, Eric; Mandelbaum, Rachel; May, Morgan; Raccanelli, Alvise; Reid, Beth; Rozo, Eduardo; Schmidt, Fabian; Sehgal, Neelima; Slosar, Anže; van Engelen, Alex; Wu, Hao-Yi; Zhao, Gongbo

    2015-03-01

    The quantity and quality of cosmic structure observations have greatly accelerated in recent years, and further leaps forward will be facilitated by imminent projects. These will enable us to map the evolution of dark and baryonic matter density fluctuations over cosmic history. The way that these fluctuations vary over space and time is sensitive to several pieces of fundamental physics: the primordial perturbations generated by GUT-scale physics; neutrino masses and interactions; the nature of dark matter and dark energy. We focus on the last of these here: the ways that combining probes of growth with those of the cosmic expansion such as distance-redshift relations will pin down the mechanism driving the acceleration of the Universe.

  15. Cosmic Rays and Experiment CZELTA

    SciTech Connect

    Smolek, Karel; Nyklicek, Michal

    2007-11-26

    This paper gives a review of the physics of cosmic rays with emphasis on the methods of detection and study. A summary is given of the Czech project CZELTA which is part of a multinational program to study cosmic rays with energies above 10{sup 14} eV.

  16. Superbubbles and Local Cosmic Rays

    NASA Technical Reports Server (NTRS)

    Streitmatter, Robert E.; Jones, Frank C.

    2005-01-01

    We consider the possibility that distinctive features of the local cosmic ray spectra and composition are influenced by the Solar system being embedded within the cavity of an ancient superbubble. Shifts in the measured cosmic ray composition between 10(exp 11) and 10(exp 20) eV as well as the "knee" and "second knee" may be understood in this picture.

  17. Testing Galactic Cosmic Ray Models

    NASA Technical Reports Server (NTRS)

    Adams, James H., Jr.

    2009-01-01

    Models of the Galactic Cosmic Ray Environment are used for designing and planning space missions. The existing models will be reviewed. Spectral representations from these models will be compared with measurements of galactic cosmic ray spectra made on balloon flights and satellite flights over a period of more than 50 years.

  18. Testing Galactic Cosmic Ray Models

    NASA Technical Reports Server (NTRS)

    Adams, James H., Jr.

    2010-01-01

    Models of the Galactic Cosmic Ray Environment are used for designing and planning space missions. The exising models will be reviewed. Spectral representations from these models will be compared with measurements of galactic cosmic ray spectra made on balloon flights and satellite flights over a period of more than 50 years.

  19. Cosmic Ray Neutron Flux Measurements

    NASA Astrophysics Data System (ADS)

    Dayananda, Mathes

    2009-11-01

    Cosmic rays are high-energetic particles originating from outer space that bombard the upper atmosphere of the Earth. Almost 90% of cosmic ray particles consist of protons, electrons and heavy ions. When these particles hit the Earth's atmosphere, cascade of secondary particles are formed. The most abundant particles reach to the surface of the Earth are muons, electrons and neutrons. In recent years many research groups are looking into potential applications of the effects of cosmic ray radiation at the surface of the Earth [1, 2]. At Georgia State University we are working on a long-term measurement of cosmic ray flux distribution. This study includes the simultaneous measurement of cosmic ray muons, neutrons and gamma particles at the Earth surface in downtown Atlanta. The initial effort is focusing on the correlation studies of the cosmic ray particle flux distribution and the atmospheric weather conditions. In this presentation, I will talk about the development of a cosmic ray detector using liquid scintillator and the preliminary results. [4pt] [1] K.Borozdin, G.Hogan, C.Morris, W.Priedhorsky, A.Saunders, L.Shultz, M.Teasdale, ``Radiographic imaging with cosmic-ray muons'', Nature, Vol.422, p.277, Mar.2003[0pt] [2] Svensmark Henrik, Physical Review 81, 3, (1998)

  20. Single-molecule analysis of the microtubule cross-linking protein MAP65-1 reveals a molecular mechanism for contact-angle-dependent microtubule bundling.

    PubMed

    Tulin, Amanda; McClerklin, Sheri; Huang, Yue; Dixit, Ram

    2012-02-22

    Bundling of microtubules (MTs) is critical for the formation of complex MT arrays. In land plants, the interphase cortical MTs form bundles specifically following shallow-angle encounters between them. To investigate how cells select particular MT contact angles for bundling, we used an in vitro reconstitution approach consisting of dynamic MTs and the MT-cross-linking protein MAP65-1. We found that MAP65-1 binds to MTs as monomers and inherently targets antiparallel MTs for bundling. Dwell-time analysis showed that the affinity of MAP65-1 for antiparallel overlapping MTs is about three times higher than its affinity for single MTs and parallel overlapping MTs. We also found that purified MAP65-1 exclusively selects shallow-angle MT encounters for bundling, indicating that this activity is an intrinsic property of MAP65-1. Reconstitution experiments with mutant MAP65-1 proteins with different numbers of spectrin repeats within the N-terminal rod domain showed that the length of the rod domain is a major determinant of the range of MT bundling angles. The length of the rod domain also determined the distance between MTs within a bundle. Together, our data show that the rod domain of MAP65-1 acts both as a spacer and as a structural element that specifies the MT encounter angles that are conducive for bundling.

  1. Genuine cosmic hair

    NASA Astrophysics Data System (ADS)

    Kastor, David; Ray, Sourya; Traschen, Jennie

    2017-02-01

    We show that asymptotically future de Sitter (AFdS) spacetimes carry ‘genuine’ cosmic hair; information that is analogous to the mass and angular momentum of asymptotically flat spacetimes and that characterizes how an AFdS spacetime approaches its asymptotic form. We define new ‘cosmological tension’ charges associated with future asymptotic spatial translation symmetries, which are analytic continuations of the ADM mass and tensions of asymptotically planar AdS spacetimes, and which measure the leading anisotropic corrections to the isotropic, exponential de Sitter expansion rate. A cosmological Smarr relation, holding for AFdS spacetimes having exact spatial translation symmetry, is derived. This formula relates cosmological tension, which is evaluated at future infinity, to properties of the cosmology at early times, together with a ‘cosmological volume’ contribution that is analogous to the thermodynamic volume of AdS black holes. Smarr relations for different spatial directions imply that the difference in expansion rates between two directions at late times is related in a simple way to their difference at early times. Hence information about the very early universe can be inferred from cosmic hair, which is potentially observable in a late time de Sitter phase. Cosmological tension charges and related quantities are evaluated for Kasner–de Sitter spacetimes, which serve as our primary examples.

  2. Cosmic Diffuse Analysis

    NASA Technical Reports Server (NTRS)

    Ryan, James M.

    1999-01-01

    The final analysis of the COMPTEL cosmic diffuse flux analysis is summarized in the accompanying figure. It shows the intensity of the cosmic diffuse flux spectrum measured jointly between the Virgo region and the South Galactic pole. This spectrum represents flux per unit solid angle over the range of 0.8 to 30 MeV. It contains the first positive measurement of the flux above 10 MeV. The spectrum merges smoothly with that measured with the EGRET instrument, starting at 30 MeV. It also merges smoothly with the latest results of the HEAO-1 measurements. However, the spectrum below is softer than the spectrum above the COMPTEL energy band. In the COMPTEL energy band there must exist a change in spectral shape as the source objects or processes change from the lower energy regime to the higher energy regime. The details of the analysis and the implications and meanings of the results are spelled out in the thesis of Dr. Cheenu Kappadath which is enclosed.

  3. 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 May 1994. Tables showing the current inventory of programs available from COSMIC are presented and program processing and evaluation activities are summarized. Nine articles were prepared for publication in the NASA Tech Brief Journal. These articles (included in this report) describe the following software items: (1) WFI - Windowing System for Test and Simulation; (2) HZETRN - A Free Space Radiation Transport and Shielding Program; (3) COMGEN-BEM - Composite Model Generation-Boundary Element Method; (4) IDDS - Interactive Data Display System; (5) CET93/PC - Chemical Equilibrium with Transport Properties, 1993; (6) SDVIC - Sub-pixel Digital Video Image Correlation; (7) TRASYS - Thermal Radiation Analyzer System (HP9000 Series 700/800 Version without NASADIG); (8) NASADIG - NASA Device Independent Graphics Library, Version 6.0 (VAX VMS Version); and (9) NASADIG - NASA Device Independent Graphics Library, Version 6.0 (UNIX Version). Activities in the areas of marketing, customer service, benefits identification, maintenance and support, and dissemination are also described along with a budget summary.

  4. COSMIC monthly progress report

    NASA Technical Reports Server (NTRS)

    1993-01-01

    Activities of the Computer Software Management and Information Center (COSMIC) are summarized for the month of August, 1993. Tables showing the current inventory of programs available from COSMIC are presented and program processing and evaluation activities are discussed. Ten articles were prepared for publication in the NASA Tech Brief Journal. These articles (included in this report) describe the following software items: (1) MOM3D - A Method of Moments Code for Electromagnetic Scattering (UNIX Version); (2) EM-Animate - Computer Program for Displaying and Animating the Steady-State Time-Harmonic Electromagnetic Near Field and Surface-Current Solutions; (3) MOM3D - A Method of Moments Code for Electromagnetic Scattering (IBM PC Version); (4) M414 - MIL-STD-414 Variable Sampling Procedures Computer Program; (5) MEDOF - Minimum Euclidean Distance Optimal Filter; (6) CLIPS 6.0 - C Language Integrated Production System, Version 6.0 (Macintosh Version); (7) CLIPS 6.0 - C Language Integrated Production System, Version 6.0 (IBM PC Version); (8) CLIPS 6.0 - C Language Integrated Production System, Version 6.0 (UNIX Version); (9) CLIPS 6.0 - C Language Integrated Production System, Version 6.0 (DEC VAX VMS Version); and (10) TFSSRA - Thick Frequency Selective Surface with Rectangular Apertures. Activities in the areas of marketing, customer service, benefits identification, maintenance and support, and dissemination are also described along with a budget summary.

  5. Testing Cosmic Inflation

    NASA Technical Reports Server (NTRS)

    Chuss, David

    2010-01-01

    The Cosmic Microwave Background (CMB) has provided a wealth of information about the history and physics of the early Universe. Much progress has been made on uncovering the emerging Standard Model of Cosmology by such experiments as COBE and WMAP, and ESA's Planck Surveyor will likely increase our knowledge even more. Despite the success of this model, mysteries remain. Currently understood physics does not offer a compelling explanation for the homogeneity, flatness, and the origin of structure in the Universe. Cosmic Inflation, a brief epoch of exponential expansion, has been posted to explain these observations. If inflation is a reality, it is expected to produce a background spectrum of gravitational waves that will leave a small polarized imprint on the CMB. Discovery of this signal would give the first direct evidence for inflation and provide a window into physics at scales beyond those accessible to terrestrial particle accelerators. I will briefly review aspects of the Standard Model of Cosmology and discuss our current efforts to design and deploy experiments to measure the polarization of the CMB with the precision required to test inflation.

  6. Cosmic Ray Physics at CERN

    NASA Astrophysics Data System (ADS)

    Fernandéz, A.; Gámez, E.; López, R.; Román, S.; Zepeda, A.

    2003-06-01

    In recent decades, cosmic ray air showers initiated by high-energy proton or nucleus collisions in the atmosphere have been studied with large area experiments on the surface of the Earth or with muon measurements deep underground. In principle, these cosmic ray experiments explore two completely different realms of physics, particle astrophysics and particle interaction physics, which are, however, intimately related by the interpretation of the data. In this paper we briefly review the cosmic ray physics activities developed at CERN in the last years. In particular we present some results from a small underground cosmic ray experiment and we discuss the capabilities of ALICE to detect high multiplicity muon events arising from cosmic ray air showers and some other astroparticle phenomena.

  7. 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.

  8. Global Mapping of Cell Type–Specific Open Chromatin by FAIRE-seq Reveals the Regulatory Role of the NFI Family in Adipocyte Differentiation

    PubMed Central

    Yu, Jing; Hirose-Yotsuya, Lisa; Take, Kazumi; Sun, Wei; Iwabu, Masato; Okada-Iwabu, Miki; Fujita, Takanori; Aoyama, Tomohisa; Tsutsumi, Shuichi; Ueki, Kohjiro; Kodama, Tatsuhiko; Sakai, Juro; Aburatani, Hiroyuki; Kadowaki, Takashi

    2011-01-01

    Identification of regulatory elements within the genome is crucial for understanding the mechanisms that govern cell type–specific gene expression. We generated genome-wide maps of open chromatin sites in 3T3-L1 adipocytes (on day 0 and day 8 of differentiation) and NIH-3T3 fibroblasts using formaldehyde-assisted isolation of regulatory elements coupled with high-throughput sequencing (FAIRE-seq). FAIRE peaks at the promoter were associated with active transcription and histone modifications of H3K4me3 and H3K27ac. Non-promoter FAIRE peaks were characterized by H3K4me1+/me3-, the signature of enhancers, and were largely located in distal regions. The non-promoter FAIRE peaks showed dynamic change during differentiation, while the promoter FAIRE peaks were relatively constant. Functionally, the adipocyte- and preadipocyte-specific non-promoter FAIRE peaks were, respectively, associated with genes up-regulated and down-regulated by differentiation. Genes highly up-regulated during differentiation were associated with multiple clustered adipocyte-specific FAIRE peaks. Among the adipocyte-specific FAIRE peaks, 45.3% and 11.7% overlapped binding sites for, respectively, PPARγ and C/EBPα, the master regulators of adipocyte differentiation. Computational motif analyses of the adipocyte-specific FAIRE peaks revealed enrichment of a binding motif for nuclear family I (NFI) transcription factors. Indeed, ChIP assay showed that NFI occupy the adipocyte-specific FAIRE peaks and/or the PPARγ binding sites near PPARγ, C/EBPα, and aP2 genes. Overexpression of NFIA in 3T3-L1 cells resulted in robust induction of these genes and lipid droplet formation without differentiation stimulus. Overexpression of dominant-negative NFIA or siRNA–mediated knockdown of NFIA or NFIB significantly suppressed both induction of genes and lipid accumulation during differentiation, suggesting a physiological function of these factors in the adipogenic program. Together, our study

  9. BOLD Imaging in Awake Wild-Type and Mu-Opioid Receptor Knock-Out Mice Reveals On-Target Activation Maps in Response to Oxycodone.

    PubMed

    Moore, Kelsey; Madularu, Dan; Iriah, Sade; Yee, Jason R; Kulkarni, Praveen; Darcq, Emmanuel; Kieffer, Brigitte L; Ferris, Craig F

    2016-01-01

    Blood oxygen level dependent (BOLD) imaging in awake mice was used to identify differences in brain activity between wild-type, and Mu (μ) opioid receptor knock-outs (MuKO) in response to oxycodone (OXY). Using a segmented, annotated MRI mouse atlas and computational analysis, patterns of integrated positive and negative BOLD activity were identified across 122 brain areas. The pattern of positive BOLD showed enhanced activation across the brain in WT mice within 15 min of intraperitoneal administration of 2.5 mg of OXY. BOLD activation was detected in 72 regions out of 122, and was most prominent in areas of high μ opioid receptor density (thalamus, ventral tegmental area, substantia nigra, caudate putamen, basal amygdala, and hypothalamus), and focus on pain circuits indicated strong activation in major pain processing centers (central amygdala, solitary tract, parabrachial area, insular cortex, gigantocellularis area, ventral thalamus primary sensory cortex, and prelimbic cortex). Importantly, the OXY-induced positive BOLD was eliminated in MuKO mice in most regions, with few exceptions (some cerebellar nuclei, CA3 of the hippocampus, medial amygdala, and preoptic areas). This result indicates that most effects of OXY on positive BOLD are mediated by the μ opioid receptor (on-target effects). OXY also caused an increase in negative BOLD in WT mice in few regions (16 out of 122) and, unlike the positive BOLD response the negative BOLD was only partially eliminated in the MuKO mice (cerebellum), and in some case intensified (hippocampus). Negative BOLD analysis therefore shows activation and deactivation events in the absence of the μ receptor for some areas where receptor expression is normally extremely low or absent (off-target effects). Together, our approach permits establishing opioid-induced BOLD activation maps in awake mice. In addition, comparison of WT and MuKO mutant mice reveals both on-target and off-target activation events, and set an OXY brain

  10. BOLD Imaging in Awake Wild-Type and Mu-Opioid Receptor Knock-Out Mice Reveals On-Target Activation Maps in Response to Oxycodone

    PubMed Central

    Moore, Kelsey; Madularu, Dan; Iriah, Sade; Yee, Jason R.; Kulkarni, Praveen; Darcq, Emmanuel; Kieffer, Brigitte L.; Ferris, Craig F.

    2016-01-01

    Blood oxygen level dependent (BOLD) imaging in awake mice was used to identify differences in brain activity between wild-type, and Mu (μ) opioid receptor knock-outs (MuKO) in response to oxycodone (OXY). Using a segmented, annotated MRI mouse atlas and computational analysis, patterns of integrated positive and negative BOLD activity were identified across 122 brain areas. The pattern of positive BOLD showed enhanced activation across the brain in WT mice within 15 min of intraperitoneal administration of 2.5 mg of OXY. BOLD activation was detected in 72 regions out of 122, and was most prominent in areas of high μ opioid receptor density (thalamus, ventral tegmental area, substantia nigra, caudate putamen, basal amygdala, and hypothalamus), and focus on pain circuits indicated strong activation in major pain processing centers (central amygdala, solitary tract, parabrachial area, insular cortex, gigantocellularis area, ventral thalamus primary sensory cortex, and prelimbic cortex). Importantly, the OXY-induced positive BOLD was eliminated in MuKO mice in most regions, with few exceptions (some cerebellar nuclei, CA3 of the hippocampus, medial amygdala, and preoptic areas). This result indicates that most effects of OXY on positive BOLD are mediated by the μ opioid receptor (on-target effects). OXY also caused an increase in negative BOLD in WT mice in few regions (16 out of 122) and, unlike the positive BOLD response the negative BOLD was only partially eliminated in the MuKO mice (cerebellum), and in some case intensified (hippocampus). Negative BOLD analysis therefore shows activation and deactivation events in the absence of the μ receptor for some areas where receptor expression is normally extremely low or absent (off-target effects). Together, our approach permits establishing opioid-induced BOLD activation maps in awake mice. In addition, comparison of WT and MuKO mutant mice reveals both on-target and off-target activation events, and set an OXY brain

  11. Genome-Wide Association Study Reveals Genetic Architecture of Eating Behavior in Pigs and Its Implications for Humans Obesity by Comparative Mapping

    PubMed Central

    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

  12. CMB maximum temperature asymmetry axis: Alignment with other cosmic asymmetries

    NASA Astrophysics Data System (ADS)

    Mariano, Antonio; Perivolaropoulos, Leandros

    2013-02-01

    We use a global pixel-based estimator to identify the axis of the residual Maximum Temperature Asymmetry (MTA) (after the dipole subtraction) of the WMAP seven-year Internal Linear Combination (ILC) cosmic microwave background temperature sky map. The estimator is based on considering the temperature differences between opposite pixels in the sky at various angular resolutions (4°-15°) and selecting the axis that maximizes this difference. We consider three large-scale HEALPix resolutions: Nside=16(3.7°), Nside=8(7.3°) and Nside=4(14.7°). We compare the direction and magnitude of this asymmetry with three other cosmic asymmetry axes (α dipole, dark energy dipole and dark flow) and find that the four asymmetry axes are abnormally close to each other. We compare the observed MTA axis with the corresponding MTA axes of 104 Gaussian isotropic simulated ILC maps (based on ΛCDM). The fraction of simulated ILC maps that reproduce the observed magnitude of the MTA asymmetry and alignment with the observed α dipole is in the range of 0.1%-0.5% (depending on the resolution chosen for the cosmic microwave background map). The corresponding magnitude+alignment probabilities with the other two asymmetry axes (dark energy dipole and dark flow) are at the level of about 1%. We propose Extended Topological Quintessence as a physical model qualitatively consistent with this coincidence of directions.

  13. Test of the cosmic evolution using Gaussian processes

    NASA Astrophysics Data System (ADS)

    Zhang, Ming-Jian; Xia, Jun-Qing

    2016-12-01

    Much focus was on the possible slowing down of cosmic acceleration under the dark energy parametrization. In the present paper, we investigate this subject using the Gaussian processes (GP), without resorting to a particular template of dark energy. The reconstruction is carried out by abundant data including luminosity distance from Union2, Union2.1 compilation and gamma-ray burst, and dynamical Hubble parameter. It suggests that slowing down of cosmic acceleration cannot be presented within 95% C.L., in considering the influence of spatial curvature and Hubble constant. In order to reveal the reason of tension between our reconstruction and previous parametrization constraint for Union2 data, we compare them and find that slowing down of acceleration in some parametrization is only a ``mirage". Although these parameterizations fits well with the observational data, their tension can be revealed by high order derivative of distance D. Instead, GP method is able to faithfully model the cosmic expansion history.

  14. Cosmic ray anisotropies to 5 PeV

    SciTech Connect

    Erlykin, A. D.; Wolfendale, A. W. E-mail: a.w.wolfendale@durham.ac.uk

    2013-04-01

    Several large cosmic ray (CR) detectors have recently provided data on the arrival directions of CR, which taken together with previous data recorded over many decades allow the amplitude and phase of the first harmonic to be derived with reasonable precision and up to higher energies. We find a high degree of consistency amongst the various measurements. The new data indicate that at an energy above ∼ 0.1 PeV a change of the CR anisotropy sets in. The amplitude of the first harmonic, which rises to 3 TeV, then diminishes and begins to rise again. The direction of the phase also changes to the opposite one. A measure of understanding follows from the use of two-dimensional maps of cosmic ray excesses over the mean background. When the energy of cosmic rays approaches the PeV region, the excess of cosmic rays moves from the Galactic Anti-Centre to the opposite direction of the Galactic Centre. The possible role of such potential cosmic ray sources as the supernovae Monogem Ring and Vela, which could help to explain some of the observed results, is discussed.

  15. Quantifying mesoscale soil moisture with the cosmic-ray rover

    NASA Astrophysics Data System (ADS)

    Chrisman, B.; Zreda, M.

    2013-06-01

    Soil moisture governs the surface fluxes of mass and energy and is a major influence on floods and drought. Existing techniques measure soil moisture either at a point or over a large area many kilometers across. To bridge these two scales we used the cosmic-ray rover, an instrument similar to the recently developed COSMOS probe, but bigger and mobile. This paper explores the challenges and opportunities for mapping soil moisture over large areas using the cosmic-ray rover. In 2012, soil moisture was mapped 22 times in a 25 km × 40 km survey area of the Tucson Basin at 1 km2 resolution, i.e., a survey area extent comparable to that of a pixel for the Soil Moisture and Ocean Salinity (SMOS) satellite mission. The soil moisture distribution is dominated by climatic variations, notably by the North American monsoon, that results in a systematic increase in the standard deviation, observed up to 0.022 m3 m-3, as a function of the mean, between 0.06 and 0.14 m3 m-3. Two techniques are explored to use the cosmic-ray rover data for hydrologic applications: (1) interpolation of the 22 surveys into a daily soil moisture product by defining an approach to utilize and quantify the observed temporal stability producing an average correlation coefficient of 0.82 for the soil moisture distributions that were surveyed and (2) estimation of soil moisture profiles by combining surface moisture from satellite microwave sensors with deeper measurements from the cosmic-ray rover. The interpolated soil moisture and soil moisture profile estimates allow for basin-wide mass balance calculation of evapotranspiration, totaling 241 mm for the year 2012. Generating soil moisture maps with cosmic-ray rover at this intermediate scale may help in the calibration and validation of satellite campaigns and may also aid in various large scale hydrologic studies.

  16. Cosmic Dawn Science Interest Group

    NASA Astrophysics Data System (ADS)

    Lazio, T. Joseph W.; Cosmic Origins Program Analysis Group

    2016-01-01

    Cosmic Dawn was identified as one of the three science objectives for this decade in the _New Worlds, New Horizons_ Decadal report, and it will likely continue to be a research focus well into the next decade. Cosmic Dawn refers to the interval during which the Universe transitioned from a nearly completely neutral state back to a nearly fully ionized state and includes the time during which the first stars formed and the first galaxies assembled.The Cosmic Dawn Science Interest Group (SIG) was formed recently under the auspices of the Cosmic Origins Program Analysis Group (COPAG). The Cosmic Dawn SIG focusses on the science cases, observations, and technology development needed to address the "great mystery" of Cosmic Origins. The reach of this SIG is broad, involving the nature of the first stars and the detectability of gamma-ray bursts at high redshifts, the extent to which the first galaxies and first supermassive black holes grew together, and the technology required to pursue these questions.For further information, consult the Cosmic Dawn SIG Web site http://cd-sig.jpl.nasa.gov/ and join the mailing list (by contacting the author).Part of this research was carried out at the Jet Propulsion Laboratory, California Institute of Technology, under a contract with the National Aeronautics and Space Administration.

  17. THE COSMIC ORIGINS SPECTROGRAPH

    SciTech Connect

    Green, James C.; Michael Shull, J.; Snow, Theodore P.; Stocke, John; Froning, Cynthia S.; Osterman, Steve; Beland, Stephane; Burgh, Eric B.; Danforth, Charles; France, Kevin; Ebbets, Dennis; Heap, Sara H.; Leitherer, Claus; Sembach, Kenneth; Linsky, Jeffrey L.; Savage, Blair D.; Siegmund, Oswald H. W.; Spencer, John; Alan Stern, S.; Welsh, Barry; and others

    2012-01-01

    The Cosmic Origins Spectrograph (COS) is a moderate-resolution spectrograph with unprecedented sensitivity that was installed into the Hubble Space Telescope (HST) in 2009 May, during HST Servicing Mission 4 (STS-125). We present the design philosophy and summarize the key characteristics of the instrument that will be of interest to potential observers. For faint targets, with flux F{sub {lambda}} Almost-Equal-To 1.0 Multiplication-Sign 10{sup -14} erg cm{sup -2} s{sup -1} A{sup -1}, COS can achieve comparable signal to noise (when compared to Space Telescope Imaging Spectrograph echelle modes) in 1%-2% of the observing time. This has led to a significant increase in the total data volume and data quality available to the community. For example, in the first 20 months of science operation (2009 September-2011 June) the cumulative redshift pathlength of extragalactic sight lines sampled by COS is nine times than sampled at moderate resolution in 19 previous years of Hubble observations. COS programs have observed 214 distinct lines of sight suitable for study of the intergalactic medium as of 2011 June. COS has measured, for the first time with high reliability, broad Ly{alpha} absorbers and Ne VIII in the intergalactic medium, and observed the He II reionization epoch along multiple sightlines. COS has detected the first CO emission and absorption in the UV spectra of low-mass circumstellar disks at the epoch of giant planet formation, and detected multiple ionization states of metals in extra-solar planetary atmospheres. In the coming years, COS will continue its census of intergalactic gas, probe galactic and cosmic structure, and explore physics in our solar system and Galaxy.

  18. Cosmic Dust Catalog

    NASA Astrophysics Data System (ADS)

    Warren, J.; Watts, L.; Thomas-Keprta, K.; Wentworth, S.; Dodson, A.; Zolensky, Michael E.

    1997-07-01

    Since May 1981, the National Aeronautics and Space Administration (NASA) has used aircraft to collect cosmic dust (CD) particles from Earth's stratosphere. Specially designed dust collectors are prepared for flight and processed after flight in an ultraclean (Class-100) laboratory constructed for this purpose at the Lyndon B. Johnson Space Center (JSC) in Houston, Texas. Particles are individually retrieved from the collectors, examined and cataloged, and then made available to the scientific community for research. Cosmic dust thereby joins lunar samples and meteorites as an additional source of extraterrestrial materials for scientific study. This catalog summarizes preliminary observations on 468 particles retrieved from collection surfaces L2021 and L2036. These surfaces were flat plate Large Area Collectors (with a 300 cm2 surface area each) which was coated with silicone oil (dimethyl siloxane) and then flown aboard a NASA ER-2 aircraft during a series of flights that were made during January and February of 1994 (L2021) and June 7 through July 5 of 1994 (L2036). Collector L2021 was flown across the entire southern margin of the US (California to Florida), and collector L2036 was flown from California to Wallops Island, VA and on to New England. These collectors were installed in a specially constructed wing pylon which ensured that the necessary level of cleanliness was maintained between periods of active sampling. During successive periods of high altitude (20 km) cruise, the collectors were exposed in the stratosphere by barometric controls and then retracted into sealed storage container-s prior to descent. In this manner, a total of 35.8 hours of stratospheric exposure was accumulated for collector L2021, and 26 hours for collector L2036.

  19. The Cosmic Origins Spectrograph

    NASA Technical Reports Server (NTRS)

    Green, James C.; Froning, Cynthia S.; Osterman, Steve; Ebbets, Dennis; Heap, Sara H.; Leitherer, Claus; Linsky, Jeffrey L.; Savage, Blair D.; Sembach, Kenneth; Shull, J. Michael; Siegmund, Oswald H. W.; Snow, Theodore P.; Spencer, John; Stern, S. Alan; Stocke, John; Welsh, Barry; Beland, Stephane; Burgh, Eric B.; Danforth, Charles; France, Kevin; Keeney, Brian; McPhate, Jason; Penton, Steven V; Andrews, John; Morse, Jon

    2010-01-01

    The Cosmic Origins Spectrograph (COS) is a moderate-resolution spectrograph with unprecedented sensitivity that was installed into the Hubble Space Telescope (HST) in May 2009, during HST Servicing Mission 4 (STS-125). We present the design philosophy and summarize the key characteristics of the instrument that will be of interest to potential observers. For faint targets, with flux F(sub lambda) approximates 1.0 X 10(exp -14) ergs/s/cm2/Angstrom, COS can achieve comparable signal to noise (when compared to STIS echelle modes) in 1-2% of the observing time. This has led to a significant increase in the total data volume and data quality available to the community. For example, in the first 20 months of science operation (September 2009 - June 2011) the cumulative redshift pathlength of extragalactic sight lines sampled by COS is 9 times that sampled at moderate resolution in 19 previous years of Hubble observations. COS programs have observed 214 distinct lines of sight suitable for study of the intergalactic medium as of June 2011. COS has measured, for the first time with high reliability, broad Lya absorbers and Ne VIII in the intergalactic medium, and observed the HeII reionization epoch along multiple sightlines. COS has detected the first CO emission and absorption in the UV spectra of low-mass circumstellar disks at the epoch of giant planet formation, and detected multiple ionization states of metals in extra-solar planetary atmospheres. In the coming years, COS will continue its census of intergalactic gas, probe galactic and cosmic structure, and explore physics in our solar system and Galaxy.

  20. The Cosmic Origins Spectrograph

    NASA Astrophysics Data System (ADS)

    Green, James C.; Froning, Cynthia S.; Osterman, Steve; Ebbets, Dennis; Heap, Sara H.; Leitherer, Claus; Linsky, Jeffrey L.; Savage, Blair D.; Sembach, Kenneth; Shull, J. Michael; Siegmund, Oswald H. W.; Snow, Theodore P.; Spencer, John; Stern, S. Alan; Stocke, John; Welsh, Barry; Béland, Stéphane; Burgh, Eric B.; Danforth, Charles; France, Kevin; Keeney, Brian; McPhate, Jason; Penton, Steven V.; Andrews, John; Brownsberger, Kenneth; Morse, Jon; Wilkinson, Erik

    2012-01-01

    The Cosmic Origins Spectrograph (COS) is a moderate-resolution spectrograph with unprecedented sensitivity that was installed into the Hubble Space Telescope (HST) in 2009 May, during HST Servicing Mission 4 (STS-125). We present the design philosophy and summarize the key characteristics of the instrument that will be of interest to potential observers. For faint targets, with flux F λ ≈ 1.0 × 10-14 erg cm-2 s-1 Å-1, COS can achieve comparable signal to noise (when compared to Space Telescope Imaging Spectrograph echelle modes) in 1%-2% of the observing time. This has led to a significant increase in the total data volume and data quality av