A two-step method for identifying photopigment opsin and rhodopsin gene sequences underlying human color vision phenotypes.

PurposeTo present a detailed, reliable long range-PCR and sequencing (LR-PCR-Seq) procedure to identify human opsin gene sequences for variations in the long wavelength-sensitive (OPN1LW), medium wavelength-sensitive (OPN1MW), short wavelength-sensitive (OPN1SW), and rhodopsin (RHO) genes.MethodsColor vision was assessed for nine subjects using the Farnsworth-Munsell 100 hue test, Ishihara pseudoisochromatic plates, and the Rabin cone-contrast threshold procedure (ColorDX, Konan Medical). The color vision phenotypes were normal trichromacy (n = 3), potential tetrachromacy (n = 3), dichromacy (n = 2), and unexplained low color vision (n = 1). DNA was isolated from blood or saliva and LR-PCR amplified into individual products: OPN1LW (4,045 bp), OPN1MW (4,045 bp), OPN1SW (3,326 bp), and RHO (6,715 bp). Each product was sequenced using specific internal primer sets. Analysis was performed with Mutation Surveyor software.ResultsThe LR-PCR-Seq technique identified known single nucleotide polymorphisms (SNPs) in OPN1LW and OPN1MW gene codons (180, 230, 233, 277, and 285), as well as those for lesser studied codons (174, 178, 236, 274, 279, 298 and 309) in the OPN1LW and OPN1MW genes. Additionally, six SNP variants in the OPN1MW and OPN1LW genes not previously reported in the NCBI dbSNP database were identified. An unreported poly-T region within intron 5(c.36+126) of the rhodopsin gene was also found, and analysis showed it to be highly conserved in mammalian species.ConclusionsThis LR-PCR-Seq procedure (single PCR reaction per gene followed by sequencing) can identify exonic and intronic SNP variants in OPN1LW, OPN1MW, OPN1SW, and rhodopsin genes. There is no need for restriction enzyme digestion or multiple PCR steps that can introduce errors. Future studies will combine the LR-PCR-Seq with perceptual behavior measures, allowing for accurate correlations between opsin genotypes, retinal photopigment phenotypes, and color perception behaviors

Search for cold and hot gas in the ram pressure stripped Virgo dwarf galaxy IC3418

We present IRAM 30m sensitive upper limits on CO emission in the ram pressure stripped dwarf Virgo galaxy IC3418 and in a few positions covering HII regions in its prominent 17 kpc UV/Ha gas-stripped tail. In the central few arcseconds of the galaxy, we report a possible marginal detection of about 1x10^6 M_sun of molecular gas (assuming a Galactic CO-to-H_2 conversion factor) that could correspond to a surviving nuclear gas reservoir. We estimate that there is less molecular gas in the main body of IC3418, by at least a factor of 20, than would be expected from the pre-quenching UV-based star formation rate assuming the typical gas depletion timescale of 2 Gyr. Given the lack of star formation in the main body, we think the H_2-deficiency is real, although some of it may also arise from a higher CO-to-H_2 factor typical in low-metallicity, low-mass galaxies. The presence of HII regions in the tail of IC3418 suggests that there must be some dense gas; however, only upper limits of < 1x10^6 M_sun were found in the three observed points in the outer tail. This yields an upper limit on the molecular gas content of the whole tail < 1x10^7 M_sun, which is an amount similar to the estimates from the observed star formation rate over the tail. We also present strong upper limits on the X-ray emission of the stripped gas in IC3418 from a new Chandra observation. The measured X-ray luminosity of the IC3418 tail is about 280 times lower than that of ESO 137-001, a spiral galaxy in a more distant cluster with a prominent ram pressure stripped tail. Non-detection of any diffuse X-ray emission in the IC3418 tail may be due to a low gas content in the tail associated with its advanced evolutionary state and/or due to a rather low thermal pressure of the surrounding intra-cluster medium.Comment: 15 pages, 11 figures, A&A accepte

Scattering a pulse from a chaotic cavity: Transitioning from algebraic to exponential decay

The ensemble averaged power scattered in and out of lossless chaotic cavities decays as a power law in time for large times. In the case of a pulse with a finite duration, the power scattered from a single realization of a cavity closely tracks the power law ensemble decay initially, but eventually transitions to an exponential decay. In this paper, we explore the nature of this transition in the case of coupling to a single port. We find that for a given pulse shape, the properties of the transition are universal if time is properly normalized. We define the crossover time to be the time at which the deviations from the mean of the reflected power in individual realizations become comparable to the mean reflected power. We demonstrate numerically that, for randomly chosen cavity realizations and given pulse shapes, the probability distribution function of reflected power depends only on time, normalized to this crossover time.Comment: 23 pages, 5 figure

Magnetic field configuration associated with solar gamma ray flares in June, 1991

The vector magnetic field configuration of the solar active region AR 6659 that produced very high levels of flare activity in Jun. 1991 is described. The morphology and evolution of the photospheric fields are described for the period 7-10 Jun., and the flares taking place around these dates and their locations relative to the photospheric fields are indicated. By comparing the observed vector field with the potential field calculated from the observed line-of-sight flux, we identify the nonpotential characteristics of the fields along the magnetic neutral lines where the flares were observed. These results are compared with those from the earlier study of gamma-ray flares

Large-scale radio continuum properties of 19 Virgo cluster galaxies The influence of tidal interactions, ram pressure stripping, and accreting gas envelopes

Deep scaled array VLA 20 and 6cm observations including polarization of 19 Virgo spirals are presented. This sample contains 6 galaxies with a global minimum of 20cm polarized emission at the receding side of the galactic disk and quadrupolar type large-scale magnetic fields. In the new sample no additional case of a ram-pressure stripped spiral galaxy with an asymmetric ridge of polarized radio continuum emission was found. In the absence of a close companion, a truncated HI disk, together with a ridge of polarized radio continuum emission at the outer edge of the HI disk, is a signpost of ram pressure stripping. 6 out of the 19 observed galaxies display asymmetric 6cm polarized emission distributions. Three galaxies belong to tidally interacting pairs, two galaxies host huge accreting HI envelopes, and one galaxy had a recent minor merger. Tidal interactions and accreting gas envelopes can lead to compression and shear motions which enhance the polarized radio continuum emission. In addition, galaxies with low average star formation rate per unit area have a low average degree of polarization. Shear or compression motions can enhance the degree of polarization. The average degree of polarization of tidally interacting galaxies is generally lower than expected for a given rotation velocity and star formation activity. This low average degree of polarization is at least partly due to the absence of polarized emission from the thin disk. Ram pressure stripping can decrease whereas tidal interactions most frequently decreases the average degree of polarization of Virgo spiral galaxies. We found that moderate active ram pressure stripping has no influence on the spectral index, but enhances the global radio continuum emission with respect to the FIR emission, while an accreting gas envelope can but not necessarily enhances the radio continuum emission with respect to the FIR emission.Comment: 37 pages, 26 figures, accepted for publication in A&

Ram pressure stripping of the multiphase ISM in the Virgo cluster spiral galaxy NGC 4438

Ram pressure stripping of the multiphase ISM is studied in the perturbed Virgo cluster spiral galaxy NGC 4438. This galaxy underwent a tidal interaction ~100 Myr ago and is now strongly affected by ram pressure stripping. Deep VLA radio continuum observations at 6 and 20 cm are presented. We detect prominent extraplanar emission to the west of the galactic center, which extends twice as far as the other tracers of extraplanar material. The spectral index of the extraplanar emission does not steepen with increasing distance from the galaxy. This implies in situ re-acceleration of relativistic electrons. The comparison with multiwavelength observations shows that the magnetic field and the warm ionized interstellar medium traced by Halpha emission are closely linked. The kinematics of the northern extraplanar Halpha emission, which is ascribed to star formation, follow those of the extraplanar CO emission. In the western and southern extraplanar regions, the Halpha measured velocities are greater than those of the CO lines. We suggest that the ionized gas of this region is excited by ram pressure. The spatial and velocity offsets are consistent with a scenario where the diffuse ionized gas is more efficiently pushed by ram pressure stripping than the neutral gas. We suggest that the recently found radio-deficient regions compared to 24 mum emission are due to this difference in stripping efficiency.Comment: 8 pages, 6 figures, A&A, accepted for publicatio

Static Pressure of Hot Gas: Its Effect on the Gas Disks of Galaxies

The static pressure of the hot gas that fills clusters and groups of galaxies can affect significantly the volume density and thickness of the gas disks in galaxies. In combination with the dynamic pressure, the static pressure allows several observed peculiarities of spiral galaxies surrounded by a hot medium to be explained.Comment: 9 pages, 2 figures. This is a slightly modified version of the paper published in Astronomy Letters 2008, Vol. 34, No 11, p. 73

Observations of Stripped Edge-on Virgo Cluster Galaxies

We present observations of highly inclined, HI deficient, Virgo cluster spiral galaxies. Our high-resolution VLA HI observations of edge-on galaxies allow us to distinguish extraplanar gas from disk gas. All of our galaxies have truncated H-alpha disks, with little or no disk gas beyond a truncation radius. While all the gas disks are truncated, the observations show evidence for a continuum of stripping states: symmetric, undisturbed truncated gas disks indicate galaxies that were stripped long ago, while more asymmetric disks suggest ongoing or more recent stripping. We compare these timescale estimates with results obtained from two-dimensional stellar spectroscopy of the outer disks of galaxies in our sample. One of the galaxies in our sample, NGC 4522 is a clear example of active ram-pressure stripping, with 40% of its detected HI being extraplanar. As expected, the outer disk stellar populations of this galaxy show clear signs of recent (and, in fact, ongoing) stripping. Somewhat less expected, however, is the fact that the spectrum of the outer disk of this galaxy, with very strong Balmer absorption and no observable emission, would be classified as ``k+a'' if observed at higher redshift. Our observations of NGC 4522 and other galaxies at a range of cluster radii allow us to better understand the role that clusters play in the structure and evolution of disk galaxies.Comment: 4 pages, 2 figures, to appear in the proceedings of the Island Universes conference held in Terschelling, Netherlands, July 2005, ed. R. de Jong, version with high resolution figures can be downloaded from ftp://ftp.astro.yale.edu/pub/hugh/papers/iu_crowl_h.ps.g

Invest to Save: Report and Recommendations of the NSF-DELOS Working Group on Digital Archiving and Preservation

Digital archiving and preservation are important areas for research and development, but there is no agreed upon set of priorities or coherent plan for research in this area. Research projects in this area tend to be small and driven by particular institutional problems or concerns. As a consequence, proposed solutions from experimental projects and prototypes tend not to scale to millions of digital objects, nor do the results from disparate projects readily build on each other. It is also unclear whether it is worthwhile to seek general solutions or whether different strategies are needed for different types of digital objects and collections. The lack of coordination in both research and development means that there are some areas where researchers are reinventing the wheel while other areas are neglected. Digital archiving and preservation is an area that will benefit from an exercise in analysis, priority setting, and planning for future research. The WG aims to survey current research activities, identify gaps, and develop a white paper proposing future research directions in the area of digital preservation. Some of the potential areas for research include repository architectures and inter-operability among digital archives; automated tools for capture, ingest, and normalization of digital objects; and harmonization of preservation formats and metadata. There can also be opportunities for development of commercial products in the areas of mass storage systems, repositories and repository management systems, and data management software and tools.