Comparative Transcriptomics of Rice Genotypes with Contrasting Responses to Nitrogen Stress Reveals Genes Influencing Nitrogen Uptake through the Regulation of Root Architecture

The indiscriminate use of nitrogenous fertilizers continues unabated for commercial crop production, resulting in air and water pollution. The development of rice varieties with enhanced nitrogen use efficiency (NUE) will require a thorough understanding of the molecular basis of a plant\u27s response to low nitrogen (N) availability. The global expression profiles of root tissues collected from low and high N treatments at different time points in two rice genotypes, Pokkali and Bengal, with contrasting responses to N stress and contrasting root architectures were examined. Overall, the number of differentially expressed genes (DEGs) in Pokkali (indica) was higher than in Bengal (japonica) during low N and early N recovery treatments. Most low N DEGs in both genotypes were downregulated whereas early N recovery DEGs were upregulated. Of these, 148 Pokkali-specific DEGs might contribute to Pokkali\u27s advantage under N stress. These DEGs included transcription factors and transporters and were involved in stress responses, growth and development, regulation, and metabolism. Many DEGs are co-localized with quantitative trait loci (QTL) related to root growth and development, chlorate-resistance, and NUE. Our findings suggest that the superior growth performance of Pokkali under low N conditions could be due to the genetic differences in a diverse set of genes influencing N uptake through the regulation of root architecture

Whole-Genome Sequencing and RNA-Seq Reveal Differences in Genetic Mechanism for Flowering Response between Weedy Rice and Cultivated Rice

Flowering is a key agronomic trait that influences adaptation and productivity. Previous studies have indicated the genetic complexity associated with the flowering response in a photoinsensitive weedy rice accession PSRR-1 despite the presence of a photosensitive allele of a key flowering gene Hd1. In this study, we used whole-genome and RNA sequencing data from both cultivated and weedy rice to add further insights. The de novo assembly of unaligned sequences predicted 225 genes, in which 45 were specific to PSRR-1, including two genes associated with flowering. Comparison of the variants in PSRR-1 with the 3K rice genome (RG) dataset identified unique variants within the heading date QTLs. Analyses of the RNA-Seq result under both short-day (SD) and long-day (LD) conditions revealed that many differentially expressed genes (DEGs) colocalized with the flowering QTLs, and some DEGs such as Hd1, OsMADS56, Hd3a, and RFT1 had unique variants in PSRR-1. Ehd1, Hd1, OsMADS15, and OsMADS56 showed different alternate splicing (AS) events between genotypes and day length conditions. OsMADS56 was expressed in PSRR-1 but not in Cypress under both LD and SD conditions. Based on variations in both sequence and expression, the unique flowering response in PSRR-1 may be due to the high-impact variants of flowering genes, and OsMADS56 is proposed as a key regulator for its day-neutral flowering response

An X-ray Atlas of Groups of Galaxies

A search was conducted for a hot intragroup medium in 109 low-redshift galaxy groups observed with the ROSAT PSPC. Evidence for diffuse, extended X-ray emission is found in at least 61 groups. Approximately one-third of these detections have not been previously reported in the literature. Most of the groups are detected out to less than half of the virial radius with ROSAT. Although some spiral-rich groups do contain an intragroup medium, diffuse emission is restricted to groups that contain at least one early-type galaxy.Comment: 39 pages, 12 figures, to appear in The Astrophysical Journal Sup

Lyman-alpha and CIII] Emission in z=7-9 Galaxies: Accelerated Reionization Around Luminous Star Forming Systems?

We discuss new Keck/MOSFIRE spectroscopic observations of four luminous galaxies at z~7-9 selected to have intense optical line emission by Roberts-Borsani et al. (2016). Previous follow-up has revealed Lyman-alpha in two of the four galaxies. Our new MOSFIRE observations confirm that Lyman-alpha is present in the entire sample. We detect Lyman-alpha emission in COS-zs7-1, confirming its redshift as z=7.154, and we detect Lyman-alpha in EGS-zs8-2 at z=7.477, verifying a tentative detection presented in an earlier study. The ubiquity of Lyman-alpha in this sample is puzzling given that the IGM is likely significantly neutral over 7<z<9. To investigate this result in more detail, we have initiated a campaign to target UV metal emission in the four Lyman-alpha emitters as a probe of both the radiation field and the velocity offset of Lyman-alpha. Here we present the detection of intense CIII] emission in EGS-zs8-1, a galaxy from this sample previously shown to have Lyman-alpha at z=7.73. Photoionization models indicate that an intense radiation field and low metallicity are required to reproduce the intense CIII] and optical line emission. We argue that this extreme radiation field is likely to affect the local environment, increasing the transmission of Lyman-alpha through the galaxy. Moreover, the centroid of CIII] indicates that Lyman-alpha is redshifted from the systemic value by 340 km/s. This velocity offset is larger than that seen in less luminous systems, providing an additional explanation for the transmission of Lyman-alpha emission through the IGM. Since the transmission is further enhanced by the likelihood that such systems are also situated in the densest regions with the largest ionized bubbles, the visibility of Lyman-alpha at z>7 is expected to be strongly luminosity-dependent, with the most effective transmission occurring in systems with intense star formation.Comment: Submitted to MNRAS, 13 pages, 8 figure

A Novel Mutation of the NARROW LEAF 1 Gene Adversely Affects Plant Architecture in Rice (Oryza sativa L.)

Plant architecture is critical for enhancing the adaptability and productivity of crop plants. Mutants with an altered plant architecture allow researchers to elucidate the genetic network and the underlying mechanisms. In this study, we characterized a novel nal1 rice mutant with short height, small panicle, and narrow and thick deep green leaves that was identified from a cross between a rice cultivar and a weedy rice accession. Bulked segregant analysis coupled with genome re-sequencing and cosegregation analysis revealed that the overall mutant phenotype was caused by a 1395-bp deletion spanning over the last two exons including the transcriptional end site of the nal1 gene. This deletion resulted in chimeric transcripts involving nal1 and the adjacent gene, which were validated by a reference-guided assembly of transcripts followed by PCR amplification. A comparative transcriptome analysis of the mutant and the wild-type rice revealed 263 differentially expressed genes involved in cell division, cell expansion, photosynthesis, reproduction, and gibberellin (GA) and brassinosteroids (BR) signaling pathways, suggesting the important regulatory role of nal1. Our study indicated that nal1 controls plant architecture through the regulation of genes involved in the photosynthetic apparatus, cell cycle, and GA and BR signaling pathways

Radial Dependence of the Pattern Speed of M51

The grand-design spiral galaxy M51 has long been a crucial target for theories of spiral structure. Studies of this iconic spiral can address the question of whether strong spiral structure is transient (e.g. interaction-driven) or long-lasting. As a clue to the origin of the structure in M51, we investigate evidence for radial variation in the spiral pattern speed using the radial Tremaine-Weinberg (TWR) method. We implement the method on CO observations tracing the ISM-dominant molecular component. Results from the method's numerical implementation--combined with regularization, which smooths intrinsically noisy solutions--indicate two distinct patterns speeds inside 4 kpc at our derived major axis PA=170 deg., both ending at corotation and both significantly higher than the conventionally adopted global value. Inspection of the rotation curve suggests that the pattern speed interior to 2 kpc lacks an ILR, consistent with the leading structure seen in HST near-IR observations. We also find tentative evidence for a lower pattern speed between 4 and 5.3 kpc measured by extending the regularized zone. As with the original TW method, uncertainty in major axis position angle (PA) is the largest source of error in the calculation; in this study, where \delta PA=+/-5 deg. a ~20% error is introduced to the parameters of the speeds at PA=170 deg. Accessory to this standard uncertainty, solutions with PA=175 deg. (also admitted by the data) exhibit only one pattern speed inside 4 kpc, and we consider this circumstance under the semblance of a radially varying PA.Comment: 14 pages in emulateapj format, 12 figures, accepted for publication in Ap

Palbociclib has no clinically relevant effect on the QTc interval in patients with advanced breast cancer.

The aim of this study was to assess the potential effects of palbociclib in combination with letrozole on QTc. PALOMA-2, a phase 3, randomized, double-blind, placebo-controlled trial, compared palbociclib plus letrozole with placebo plus letrozole in postmenopausal women with estrogen receptor-positive, human epidermal growth factor receptor 2-negative advanced breast cancer. The study included a QTc evaluation substudy carried out as a definitive QT interval prolongation assessment for palbociclib. Time-matched triplicate ECGs were performed at 0, 2, 4, 6, and 8 h at baseline (Day 0) and on Cycle 1 Day 14. Additional ECGs were collected from all patients for safety monitoring. The QT interval was corrected for heart rate using Fridericia's correction (QTcF), Bazett's correction (QTcB), and a study-specific correction factor (QTcS). In total, 666 patients were randomized 2 : 1 to palbociclib plus letrozole or placebo plus letrozole. Of these, 125 patients were enrolled in the QTc evaluation substudy. No patients in the palbociclib plus letrozole arm of the substudy (N=77) had a maximum postbaseline QTcS or QTcF value of ≥ 480 ms, or a maximum increase from clock time-matched baseline for QTcS or QTcF values of ≥ 60 ms. The upper bounds of the one-sided 95% confidence interval for the mean change from time-matched baseline for QTcS, QTcF, and QTcB at all time points and at steady-state Cmax following repeated administration of 125 mg palbociclib were less than 10 ms. Palbociclib, when administered with letrozole at the recommended therapeutic dosing regimen, did not prolong the QT interval to a clinically relevant extent