Genomic Organization of Duplicated Major Histocompatibility Complex Class I Regions in Atlantic Salmon (Salmo Salar)

Background: We have previously identified associations between major histocompatibility complex(MHC) class I and resistance towards bacterial and viral pathogens in Atlantic salmon. To evaluate if onlyMHC or also closely linked genes contributed to the observed resistance we ventured into sequencing ofthe duplicated MHC class I regions of Atlantic salmon.Results: Nine BACs covering more than 500 kb of the two duplicated MHC class I regions of Atlanticsalmon were sequenced and the gene organizations characterized. Both regions contained the proteasomecomponents PSMB8, PSMB9, PSMB9-like and PSMB10 in addition to the transporter for antigen processingTAP2, as well as genes for KIFC1, ZBTB22, DAXX, TAPBP, BRD2, COL11A2, RXRB and SLC39A7. TheIA region contained the recently reported MHC class I Sasa-ULA locus residing approximately 50 kbupstream of the major Sasa-UBA locus. The duplicated class IB region contained an MHC class I locusresembling the rainbow trout UCA locus, but although transcribed it was a pseudogene. No other MHCclass I-like genes were detected in the two duplicated regions. Two allelic BACs spanning the UBA locushad 99.2% identity over 125 kb, while the IA region showed 82.5% identity over 136 kb to the IB region.The Atlantic salmon IB region had an insert of 220 kb in comparison to the IA region containing threechitin synthase genes.Conclusion: We have characterized the gene organization of more than 500 kb of the two duplicatedMHC class I regions in Atlantic salmon. Although Atlantic salmon and rainbow trout are closely related,the gene organization of their IB region has undergone extensive gene rearrangements. The Atlanticsalmon has only one class I UCA pseudogene in the IB region while trout contains the four MHC UCA, UDA,UEA and UFA class I loci. The large differences in gene content and most likely function of the salmon andtrout class IB region clearly argues that sequencing of salmon will not necessarily provide informationrelevant for trout and vice versa

Dual-barrel conductance micropipet as a new approach to the study of ionic crystal dissolution kinetics

A new approach to the study of ionic crystal dissolution kinetics is described, based on the use of a dual-barrel theta conductance micropipet. The solution in the pipet is undersaturated with respect to the crystal of interest, and when the meniscus at the end of the micropipet makes contact with a selected region of the crystal surface, dissolution occurs causing the solution composition to change. This is observed, with better than 1 ms time resolution, as a change in the ion conductance current, measured across a potential bias between an electrode in each barrel of the pipet. Key attributes of this new technique are: (i) dissolution can be targeted at a single crystal surface; (ii) multiple measurements can be made quickly and easily by moving the pipet to a new location on the surface; (iii) materials with a wide range of kinetics and solubilities are open to study because the duration of dissolution is controlled by the meniscus contact time; (iv) fast kinetics are readily amenable to study because of the intrinsically high mass transport rates within tapered micropipets; (v) the experimental geometry is well-defined, permitting finite element method modeling to allow quantitative analysis of experimental data. Herein, we study the dissolution of NaCl as an example system, with dissolution induced for just a few milliseconds, and estimate a first-order heterogeneous rate constant of 7.5 (±2.5) × 10–5 cm s–1 (equivalent surface dissolution flux ca. 0.5 μmol cm–2 s–1 into a completely undersaturated solution). Ionic crystals form a huge class of materials whose dissolution properties are of considerable interest, and we thus anticipate that this new localized microscale surface approach will have considerable applicability in the future

All-sky LIGO Search for Periodic Gravitational Waves in the Early S5 Data

We report on an all-sky search with the LIGO detectors for periodic gravitational waves in the frequency range 50--1100 Hz and with the frequency's time derivative in the range -5.0E-9 Hz/s to zero. Data from the first eight months of the fifth LIGO science run (S5) have been used in this search, which is based on a semi-coherent method (PowerFlux) of summing strain power. Observing no evidence of periodic gravitational radiation, we report 95% confidence-level upper limits on radiation emitted by any unknown isolated rotating neutron stars within the search range. Strain limits below 1.E-24 are obtained over a 200-Hz band, and the sensitivity improvement over previous searches increases the spatial volume sampled by an average factor of about 100 over the entire search band. For a neutron star with nominal equatorial ellipticity of 1.0E-6, the search is sensitive to distances as great as 500 pc--a range that could encompass many undiscovered neutron stars, albeit only a tiny fraction of which would likely be rotating fast enough to be accessible to LIGO. This ellipticity is at the upper range thought to be sustainable by conventional neutron stars and well below the maximum sustainable by a strange quark star.Comment: 6 pages, 1 figur

First LIGO search for gravitational wave bursts from cosmic (super)strings

We report on a matched-filter search for gravitational wave bursts from cosmic string cusps using LIGO data from the fourth science run (S4) which took place in February and March 2005. No gravitational waves were detected in 14.9 days of data from times when all three LIGO detectors were operating. We interpret the result in terms of a frequentist upper limit on the rate of gravitational wave bursts and use the limits on the rate to constrain the parameter space (string tension, reconnection probability, and loop sizes) of cosmic string models.Comment: 11 pages, 3 figures. Replaced with version submitted to PR

All-sky search for periodic gravitational waves in LIGO S4 data

We report on an all-sky search with the LIGO detectors for periodic gravitational waves in the frequency range 50-1000 Hz and with the frequency's time derivative in the range -1.0E-8 Hz/s to zero. Data from the fourth LIGO science run (S4) have been used in this search. Three different semi-coherent methods of transforming and summing strain power from Short Fourier Transforms (SFTs) of the calibrated data have been used. The first, known as "StackSlide", averages normalized power from each SFT. A "weighted Hough" scheme is also developed and used, and which also allows for a multi-interferometer search. The third method, known as "PowerFlux", is a variant of the StackSlide method in which the power is weighted before summing. In both the weighted Hough and PowerFlux methods, the weights are chosen according to the noise and detector antenna-pattern to maximize the signal-to-noise ratio. The respective advantages and disadvantages of these methods are discussed. Observing no evidence of periodic gravitational radiation, we report upper limits; we interpret these as limits on this radiation from isolated rotating neutron stars. The best population-based upper limit with 95% confidence on the gravitational-wave strain amplitude, found for simulated sources distributed isotropically across the sky and with isotropically distributed spin-axes, is 4.28E-24 (near 140 Hz). Strict upper limits are also obtained for small patches on the sky for best-case and worst-case inclinations of the spin axes.Comment: 39 pages, 41 figures An error was found in the computation of the C parameter defined in equation 44 which led to its overestimate by 2^(1/4). The correct values for the multi-interferometer, H1 and L1 analyses are 9.2, 9.7, and 9.3, respectively. Figure 32 has been updated accordingly. None of the upper limits presented in the paper were affecte

Search for Gravitational Wave Bursts from Soft Gamma Repeaters

We present the results of a LIGO search for short-duration gravitational waves (GWs) associated with Soft Gamma Repeater (SGR) bursts. This is the first search sensitive to neutron star f-modes, usually considered the most efficient GW emitting modes. We find no evidence of GWs associated with any SGR burst in a sample consisting of the 27 Dec. 2004 giant flare from SGR 1806-20 and 190 lesser events from SGR 1806-20 and SGR 1900+14 which occurred during the first year of LIGO's fifth science run. GW strain upper limits and model-dependent GW emission energy upper limits are estimated for individual bursts using a variety of simulated waveforms. The unprecedented sensitivity of the detectors allows us to set the most stringent limits on transient GW amplitudes published to date. We find upper limit estimates on the model-dependent isotropic GW emission energies (at a nominal distance of 10 kpc) between 3x10^45 and 9x10^52 erg depending on waveform type, detector antenna factors and noise characteristics at the time of the burst. These upper limits are within the theoretically predicted range of some SGR models.Comment: 6 pages, 1 Postscript figur

Search for gravitational-wave bursts in LIGO data from the fourth science run

The fourth science run of the LIGO and GEO 600 gravitational-wave detectors, carried out in early 2005, collected data with significantly lower noise than previous science runs. We report on a search for short-duration gravitational-wave bursts with arbitrary waveform in the 64-1600 Hz frequency range appearing in all three LIGO interferometers. Signal consistency tests, data quality cuts, and auxiliary-channel vetoes are applied to reduce the rate of spurious triggers. No gravitational-wave signals are detected in 15.5 days of live observation time; we set a frequentist upper limit of 0.15 per day (at 90% confidence level) on the rate of bursts with large enough amplitudes to be detected reliably. The amplitude sensitivity of the search, characterized using Monte Carlo simulations, is several times better than that of previous searches. We also provide rough estimates of the distances at which representative supernova and binary black hole merger signals could be detected with 50% efficiency by this analysis.Comment: Corrected amplitude sensitivities (7% change on average); 30 pages, submitted to Classical and Quantum Gravit