Genomic survey, characterization and expression profile analysis of the peptide transporter family in rice (Oryza sativa L.)

<p>Abstract</p> <p>Background</p> <p>Peptide transporter (PTR) family whose member can transport di-/tripeptides and nitrate is important for plant growth and development. Although the rice (<it>Oryza sativa </it>L.) genome has been sequenced for a few years, a genomic survey, characterization and expression profile analysis of the PTR family in this species has not been reported.</p> <p>Results</p> <p>In this study, we report a comprehensive identification, characterization, phylogenetic and evolutionary analysis of 84 PTR family members in rice (OsPTR) as well as their whole-life expression patterns. Chromosomal distribution and sequence analysis indicate that nearly 70% of OsPTR members are involved in the tandem and segmental duplication events. It suggests that genome duplication might be a major mechanism for expansion of this family. Highly conserved motifs were identified in most of the OsPTR members. Meanwhile, expression profile of <it>OsPTR </it>genes has been analyzed by using Affymetrix rice microarray and real-time PCR in two elite hybrid rice parents, Minghui 63 and Zhenshan 97. Seven genes are found to exhibit either preferential or tissue-specific expression during different development stages of rice. Under phytohormone (NAA, GA3 and KT) and light/dark treatments, 14 and 17 <it>OsPTR </it>genes are differentially expressed respectively. <it>Ka/Ks </it>analysis of the paralogous <it>OsPTR </it>genes indicates that purifying selection plays an important role in function maintenance of this family.</p> <p>Conclusion</p> <p>These investigations add to our understanding of the importance of OsPTR family members and provide useful reference for selecting candidate genes for functional validation studies of this family in rice.</p

A multi band study of the optically dark GRB 051028

Observations were made of the optical afterglow of GRB 051028 with the Lulin observatory's 1.0 m telescope and the WIDGET robotic telescope system. R band photometric data points were obtained on 2005 October 28 (UT), or 0.095-0.180 days after the burst. There is a possible plateau in the optical light curve around 0.1 days after the burst; the light curve resembles optically bright afterglows (e.g. GRB 041006, GRB 050319, GRB060605) in shape of the light curve but not in brightness. The brightness of the GRB 051028 afterglow is 3 magnitudes fainter than that of one of the dark events, GRB 020124. Optically dark GRBs have been attributed to dust extinction within the host galaxy or high redshift. However, the spectrum analysis of the X-rays implies that there is no significant absorption by the host galaxy. Furthermore, according to the model theoretical calculation of the Ly$\alpha$ absorption to find the limit of GRB 051028's redshift, the expected $R$ band absorption is not high enough to explain the darkness of the afterglow. While the present results disfavor either the high-redshift hypothesis or the high extinction scenario for optically dark bursts, they are consistent with the possibility that the brightness of the optical afterglow, intrinsically dark.Comment: 5page, 5 figures, 1 table, accepted for publication in PASJ Letter. PASJ styl

Testing the External Shock Model of Gamma-Ray Bursts using the Late-Time Simultaneous Optical and X-ray Afterglows

We study the ``normal'' decay phase of the X-ray afterglows of gamma-ray bursts (GRBs), which follows the shallow decay phase, using the events simultaneously observed in the R-band. The classical external shock model -- in which neither the delayed energy injection nor time-dependency of shock micro-physics is considered -- shows that the decay indices of the X-ray and R-band light curves, $\alpha_{\rm X}$ and $\alpha_{\rm O}$, obey a certain relation, and that in particular, $\alpha_{\rm O}-\alpha_{\rm X}$ should be larger than -1/4 unless the ambient density increases with the distance from the central engine. For our selected 14 samples, we have found that 4 events violate the limit at more than the 3$\sigma$ level, so that a fraction of events are outliers of the classical external shock model at the ``normal'' decay phase.Comment: Accepted for publication in ApJL. 12 page, 2 figures, 2 table

Prompt-to-afterglow transition of optical emission in a long gamma-ray burst consistent with a fireball

Long gamma-ray bursts (GRBs), which signify the end-life collapsing of very massive stars, are produced by extremely relativistic jets colliding into circumstellar medium. Huge energy is released both in the first few seconds, namely the internal dissipation phase that powers prompt emissions, and in the subsequent self-similar jet-deceleration phase that produces afterglows observed in broad-band electromagnetic spectrum. However, prompt optical emissions of GRBs have been rarely detected, seriously limiting our understanding of the transition between the two phases. Here we report detection of prompt optical emissions from a gamma-ray burst (i.e. GRB 201223A) using a dedicated telescope array with a high temporal resolution and a wide time coverage. The early phase coincident with prompt {\gamma}-ray emissions show a luminosity in great excess with respect to the extrapolation of {\gamma}-rays, while the later luminosity bump is consistent with onset of the afterglow. The clearly detected transition allows us to differentiate physical processes contributing to early optical emissions and to diagnose the composition of the jetComment: Authors' version of article published in Nature Astronomy, see their website for official versio

Evidence of gene-environment interaction for two genes on chromosome 4 and environmental tobacco smoke in controlling the risk of nonsyndromic cleft palate

Nonsyndromic cleft palate (CP) is one of the most common human birth defects and both genetic and environmental risk factors contribute to its etiology. We conducted a genome-wide association study (GWAS) using 550 CP case-parent trios ascertained in an international consortium. Stratified analysis among trios with different ancestries was performed to test for GxE interactions with common maternal exposures using conditional logistic regression models. While no single nucleotide polymorphism (SNP) achieved genome-wide significance when considered alone, markers in SLC2A9 and the neighboring WDR1 on chromosome 4p16.1 gave suggestive evidence of gene-environment interaction with environmental tobacco smoke (ETS) among 259 Asian trios when the models included a term for GxE interaction. Multiple SNPs in these two genes were associated with increased risk of nonsyndromic CP if the mother was exposed to ETS during the peri-conceptual period (3 months prior to conception through the first trimester). When maternal ETS was considered, fifteen of 135 SNPs mapping to SLC2A9 and 9 of 59 SNPs in WDR1 gave P values approaching genome-wide significance (10-6<P<10-4) in a test for GxETS interaction. SNPs rs3733585 and rs12508991 in SLC2A9 yielded P = 2.26×10-7 in a test for GxETS interaction. SNPs rs6820756 and rs7699512 in WDR1 also yielded P = 1.79×10-7 and P = 1.98×10-7 in a 1 df test for GxE interaction. Although further replication studies are critical to confirming these findings, these results illustrate how genetic associations for nonsyndromic CP can be missed if potential GxE interaction is not taken into account, and this study suggest SLC2A9 and WDR1 should be considered as candidate genes for CP. © 2014 Wu et al