Primary analysis of repeat elements of the Asian seabass (Lates calcarifer) transcriptome and genome

As part of our Asian seabass genome project, we are generating an inventory of repeat elements in the genome and transcriptome. The karyotype showed a diploid number of 2n = 24 chromosomes with a variable number of B-chromosomes. The transcriptome and genome of Asian seabass were searched for repetitive elements with experimental and bioinformatics tools. Six different types of repeats constituting 8–14% of the genome were characterized. Repetitive elements were clustered in the pericentromeric heterochromatin of all chromosomes, but some of them were preferentially accumulated in pretelomeric and pericentromeric regions of several chromosomes pairs and have chromosomes specific arrangement. From the dispersed class of fish-specific non-LTR retrotransposon elements Rex1 and MAUI-like repeats were analyzed. They were wide-spread both in the genome and transcriptome, accumulated on the pericentromeric and peritelomeric areas of all chromosomes. Every analyzed repeat was represented in the Asian seabass transcriptome, some showed differential expression between the gonads. The other group of repeats analyzed belongs to the rRNA multigene family. FISH signal for 5S rDNA was located on a single pair of chromosomes, whereas that for 18S rDNA was found on two pairs. A BAC-derived contig containing rDNA was sequenced and assembled into a scaffold containing incomplete fragments of 18S rDNA. Their assembly and chromosomal position revealed that this part of Asian seabass genome is extremely rich in repeats containing evolutionarily conserved and novel sequences. In summary, transcriptome assemblies and cDNA data are suitable for the identification of repetitive DNA from unknown genomes and for comparative investigation of conserved elements between teleosts and other vertebrates

Suppression of power-broadening in strong-coupling photoassociation in the presence of a Feshbach resonance

Photoassociation (PA) spectrum in the presence of a magnetic Feshbach resonance is analyzed. Nonperturbative solution of the problem yields analytical expressions for PA linewidth and shift which are applicable for arbitrary PA laser intensity and magnetic field tuning of Feshbach Resonance. We show that by tuning magnetic field close to Fano minimum, it is possible to suppress power broadening at increased laser intensities. This occurs due to quantum interference of PA transitions from unperturbed and perturbed continuum. Line narrowing at high laser intensities is accompanied by large spectral shifts. We briefly discuss important consequences of line narrowing in cold collisions.Comment: 12 pages, 5 figure

Stable mode-locked pulses from mid-infrared semiconductor lasers

We report the unequivocal demonstration of mid-infrared mode-locked pulses from a semiconductor laser. The train of short pulses was generated by actively modulating the current and hence the optical gain in a small section of an edge-emitting quantum cascade laser (QCL). Pulses with pulse duration at full-width-at-half-maximum of about 3 ps and energy of 0.5 pJ were characterized using a second-order interferometric autocorrelation technique based on a nonlinear quantum well infrared photodetector. The mode-locking dynamics in the QCLs was modelled and simulated based on Maxwell-Bloch equations in an open two-level system. We anticipate our results to be a significant step toward a compact, electrically-pumped source generating ultrashort light pulses in the mid-infrared and terahertz spectral ranges.Comment: 26 pages, 4 figure

The optimal form of the scanning near-field optical microscopy probe

A theoretical approach to determine the optimal form of the near-field optical microscope probe is proposed. An analytical expression of the optimal probe form with subwavelength aperture has been obtained. The advantages of the probe with the optimal form are illustrated using numerical calculations. The conducted calculations show 10 times greater light throughput and the reception possibility of the more compactly localized light at the output probe aperture which could indicate better spatial resolution of the optical images in near-field optical technique using optimal probe.Comment: 12 pages, 6 figure

Dimensional Crossover of Dilute Neon inside Infinitely Long Single-Walled Carbon Nanotubes Viewed from Specific Heats

A simple formula for coordinates of carbon atoms in a unit cell of a single-walled nanotube (SWNT) is presented and the potential of neon (Ne) inside an infinitely long SWNT is analytically derived under the assumption of pair-wise Lennard-Jones potential between Ne and carbon atoms. Specific heats of dilute Ne inside infinitely long (5, 5), (10, 10), (15, 15) and (20, 20) SWNT's are calculated at different temperatures. It is found that Ne inside four kinds of nanotubes exhibits 3-dimensional (3D) gas behavior at high temperature but different behaviors at low temperature: Ne inside (5, 5) nanotube behaves as 1D gas but inside (10, 10), (15, 15), and (20, 20) nanotubes behaves as 2D gas. Furthermore, at ultra low temperature, Ne inside (5, 5) nanotube still displays 1D behavior but inside (10, 10), (15, 15), and (20, 20) nanotubes behaves as lattice gas.Comment: 10 pages, 5 figure

The correlation between C/O ratio, metallicity and the initial WD mass for SNe Ia

In this paper, we want to check whether or not the carbon abundance can be affected by initial metallicity. We calculated a series of stellar evolution. We found that when $Z\leq0.02$, the carbon abundance is almost independent of metallicity if it is plotted against the initial WD mass. However, when $Z>0.02$, the carbon abundance is not only a function of the initial WD mass, but also metallicity, i.e. for a given initial WD mass, the higher the metallicity, the lower the carbon abundance. Based on some previous studies, i.e. both a high metallicity and a low carbon abundance lead to a lower production of $^{\rm 56}$Ni formed during SN Ia explosion, the effects of the carbon abundance and the metallicity on the amount of $^{\rm 56}$Ni are enhanced by each other, which may account for the variation of maximum luminosity of SNe Ia, at least qualitatively. Considering that the central density of WD before supernova explosion may also play a role on the production of $^{\rm 56}$Ni and the carbon abundance, the metallicity and the central density are all determined by the initial parameters of progenitor system, i.e. the initial WD mass, metallicity, orbital period and secondary mass, the amount of $^{\rm 56}$Ni might be a function of the initial parameters. Then, our results might construct a bridge linking the progenitor model and the explosion model of SNe Ia.Comment: 7pages, 4 figures, accepted for publication in A&

Specific heats of dilute neon inside long single-walled carbon nanotube and related problems

An elegant formula for coordinates of carbon atoms in a unit cell of a single-walled nanotube (SWNT) is presented and the potential of neon (Ne) inside an infinitely long SWNT is analytically derived out under the condition of the Lennard-Jones potential between Ne and carbon atoms. Specific heats of dilute Ne inside long (20, 20) SWNT are calculated at different temperatures. It is found that Ne exhibits 3-dimensional (3D) gas behavior at high temperature but behaves as 2D gas at low temperature. Especially, at ultra low temperature, Ne inside (20, 20) nanotubes behaves as lattice gas. A coarse method to determine the characteristic temperature $\mathcal{T}_c$ for low density gas in a potential is put forward. If $\mathcal{T}\gg \mathcal{T}_c$, we just need to use the classical statistical mechanics without solving the Shr\"{o}dinger equation to consider the thermal behavior of gas in the potential. But if $\mathcal{T}\sim \mathcal{T}_c$, we must solve the Shr\"{o}dinger equation. For Ne in (20,20) nanotube, we obtain $\mathcal{T}_c\approx 60$ K.Comment: 14 pages, 7 figure

CEDAR Electrodynamics Thermosphere Ionosphere (ETI) Challenge for systematic assessment of ionosphere/thermosphere models: Electron density, neutral density, NmF2, and hmF2 using space based observations

In an effort to quantitatively assess the current capabilities of Ionosphere/Thermosphere (IT) models, an IT model validation study using metrics was performed. This study is a main part of the CEDAR Electrodynamics Thermosphere Ionosphere (ETI) Challenge, which was initiated at the CEDAR workshop in 2009 to better comprehend strengths and weaknesses of models in predicting the IT system, and to trace improvements in ionospheric/thermospheric specification and forecast. For the challenge, two strong geomagnetic storms, four moderate storms, and three quiet time intervals were selected. For the selected events, we obtained four scores (i.e., RMS error, prediction efficiency, ratio of the maximum change in amplitudes, and ratio of the maximum amplitudes) to compare the performance of models in reproducing the selected physical parameters such as vertical drifts, electron and neutral densities, NmF2, and hmF2. In this paper, we present the results from comparing modeled values against space-based measurements including NmF2 and hmF2 from the CHAMP and COSMIC satellites, and electron and neutral densities at the CHAMP satellite locations. It is found that the accuracy of models varies with the metrics used, latitude and geomagnetic activity level

\u3cem\u3eRPGRIP1\u3c/em\u3e and Cone-Rod Dystrophy in Dogs

Cone–rod dystrophies (crd) represent a group of progressive inherited blinding diseases characterized by primary dysfunction and loss of cone photoreceptors accompanying or preceding rod death. Recessive crd type 1 was described in dogs associated with an RPGRIP1 exon 2 mutation, but with lack of complete concordance between genotype and phenotype. This review highlights role of the RPGRIP1, a component of complex protein networks, and its function in the primary cilium, and discusses the potential mechanisms of genotype–phenotype discordance observed in dogs with the RPGRIP1 mutation