Building in vitro tools for livestock genomics:chromosomal variation within the PK15 cell line

BACKGROUND: Cultured porcine cell lines are powerful tools for functional genomics and in vitro phenotypic testing of candidate causal variants. However, to be utilised for genomic or variant interrogation assays, the genome sequence and structure of cultured cell lines must be realised. In this work, we called variants and used read coverage in combination with within-sample allele frequency to detect potential aneuploidy in two immortalised porcine kidney epithelial (PK15) cell lines and in a pig embryonic fibroblast line.RESULTS: We compared two PK15 cultured cells samples: a new American Type Culture Collection (ATCC) sample and one that has been utilised and passaged within the laboratory for an extended period (&gt; 10 years). Read coverage and within-sample allele frequencies showed that several chromosomes are fully or partially aneuploid in both PK15 lines, including potential trisomy of chromosome 4 and tetrasomy of chromosome 17. The older PK15 line showed evidence of additional structural variation and potentially clonal variation. By comparison, the pig embryonic fibroblast line was free from the gross aneuploidies seen in the PK15s.CONCLUSIONS: Our results show that the PK15 cell lines examined have aneuploidies and complex structural variants in their genomes. We propose that screening for aneuploidy should be considered for cell lines, and discuss implications for livestock genomics.</p

Exchange anisotropy pinning of a standing spin wave mode

Standing spin waves in a thin film are used as sensitive probes of interface pinning induced by an antiferromagnet through exchange anisotropy. Using coplanar waveguide ferromagnetic resonance, pinning of the lowest energy spin wave thickness mode in Ni(80)Fe(20)/Ir(25)Mn(75) exchange biased bilayers was studied for a range of IrMn thicknesses. We show that pinning of the standing mode can be used to amplify, relative to the fundamental resonance, frequency shifts associated with exchange bias. The shifts provide a unique `fingerprint' of the exchange bias and can be interpreted in terms of an effective ferromagnetic film thickness and ferromagnet/antiferromagnet interface anisotropy. Thermal effects are studied for ultra-thin antiferromagnetic Ir(25)Mn(75) thicknesses, and the onset of bias is correlated with changes in the pinning fields. The pinning strength magnitude is found to grow with cooling of the sample, while the effective ferromagnetic film thickness simultaneously decreases. These results suggest that exchange bias involves some deformation of magnetic order in the interface region.Comment: 7 pages, 7 figure

High speed video capture for mobile phone cameras

We consider an electromechanical model for the operation of a voice coil motor in a mobile phone camera, with the aim of optimizing how a lens can be moved to a desired focusing motion. Although a methodology is developed for optimizing lens shift, there is some concern about the experimentally-determined model parameters that are at our disposal. Central to the model is the value of the estimated magnetic force constant, Kf: its value determines how far it is actually possible to move lens, but it appears that, from the value given, it would not be possible to shift the lens through the displacements desired. Furthermore, earlier experiments have also estimated the value of the back EMF constant, Kg , to be roughly five times greater than Kf, even though we present two theoretical arguments that show that Kf = Kg: a conclusion supported by readily-available manufacturers’ data

Interaction of internal waves and mean flow observed near a coast

Vortex stretching has been proposed as a possible mechanism by which internal waves can extract energy from the mean flow. Relationships between the slowly varying (ω \u3c 0.25 cpd) and rapidly varying (0.13 cph \u3c ω \u3c 0.5 cph) components of the flow have been examined in a 4-month-long data set taken off the coast of British Columbia. The rapidly varying component of horizontal velocity generally rotates clockwise, and is in rough agreement with internal wave dynamics. It is horizontally incoherent within a distance of 10 km and is vertically coherent across the water column with a nearly 180° phase change. Scatter plots show that the wavefield is anisotropic, with the Reynolds stresses generally obeying uv \u3c 0, vw \u3c 0 and uw \u3e 0, where (u, v, w) are the fluctuating velocity components in the (onshore, alongshore, upward) directions. Instances have been found in which time variations of uv and the mean horizontal shear rate Vx are negatively correlated, with an implied horizontal viscosity of VH ∼ (3 ± 2) × 105 cm2/s. No correlation of vw and the mean vertical shear Vz is found. It is suggested that nonlocal behavior is important because propagation times in the vertical are smaller than the interaction times of the wave packets. With the observed shear rates and the wave energy levels, the vertical viscosity is unlikely to be beyond the range ± 20 cm2/s

Electronic structure, magnetism, and disorder in the Heusler compound Co2_2TiSn

Polycrystalline samples of the half-metallic ferromagnet Heusler compound Co$_2$TiSn have been prepared and studied using bulk techniques (X-ray diffraction and magnetization) as well as local probes ($^{119}$Sn M\"ossbauer spectroscopy and $^{59}$Co nuclear magnetic resonance spectroscopy) in order to determine how disorder affects half-metallic behavior and also, to establish the joint use of M\"ossbauer and NMR spectroscopies as a quantitative probe of local ion ordering in these compounds. Additionally, density functional electronic structure calculations on ordered and partially disordered Co$_2$TiSn compounds have been carried out at a number of different levels of theory in order to simultaneously understand how the particular choice of DFT scheme as well as disorder affect the computed magnetization. Our studies suggest that a sample which seems well-ordered by X-ray diffraction and magnetization measurements can possess up to 10% of antisite (Co/Ti) disordering. Computations similarly suggest that even 12.5% antisite Co/Ti disorder does not destroy the half-metallic character of this material. However, the use of an appropriate level of non-local DFT is crucial.Comment: 11 pages and 5 figure

Response of OH airglow emissions to mesospheric gravity waves and comparisons with full-wave model simulation at a low-latitude Indian station

Quasi-monochromatic gravity-wave-induced oscillations, monitored using the mesospheric OH airglow emission over Kolhapur (16.8° N, 74.2° E), India, during January to April 2010 and January to December 2011, have been characterized using the Krassovsky method. The nocturnal variability reveals prominent wave signatures with periods ranging from 5.2 to 10.8 h as the dominant nocturnal wave with embedded short-period waves having wave periods of 1.5–4.4 h. The results show that the magnitude of the Krassovsky parameter, viz. |η|, ranged from 2.1 to 10.2 h for principal or long nocturnal waves (5.2–10.8 h observed periods), and from 1.5 to 5.4 h for the short waves (1.5–4.4 h observed periods) during the years of 2010 and 2011, respectively. The phase (i.e., Φ) values of the Krassovsky parameters exhibited larger variability and varied from −8.1 to −167°. The deduced mean vertical wavelengths are found to be approximately −60.2 ± 20 and −42.8 ± 35 km for long- and short-period waves for the year 2010. Similarly, for 2011 the mean vertical wavelengths are found to be approximately −77.6 ± 30 and −59.2 ± 30 km for long and short wave periods, respectively, indicating that the observations over Kolhapur were dominated by upward-propagating waves. We use a full-wave model to simulate the response of OH emission to the wave motion and compare the results with observed values

Numerical and statistical evidence for long-range ducted gravity wave propagation over Halley, Antarctica

Abundant short‒period, small‒scale gravity waves have been identified in the mesosphere and lower thermosphere over Halley, Antarctica, via ground‒based airglow image data. Although many are observed as freely propagating at the heights of the airglow layers, new results under modeled conditions reveal that a significant fraction of these waves may be subject to reflections at altitudes above and below. The waves may at times be trapped within broad thermal ducts, spanning from the tropopause or stratopause to the base of the thermosphere (∼140 km), which may facilitate long‒range propagation (∼1000s of km) under favorable wind conditions