The chloroplast RNA helicase ISE2 is required for multiple chloroplast RNA processing steps in Arabidopsis thaliana

INCREASED SIZE EXCLUSION LIMIT2 (ISE2) is a chloroplast-localized RNA helicase that is indispensable for proper plant development. Chloroplasts in leaves with reduced ISE2expression have previously been shown to exhibit reduced thylakoid contents and increased stromal volume, indicative of defective development. It has recently been reported that ISE2 is required for the splicing of group II introns from chloroplast transcripts. The current study extends these findings, and presents evidence for ISE2’s role in multiple aspects of chloroplast RNA processing beyond group II intron splicing. Loss of ISE2 from Arabidopsis thaliana leaves resulted in defects in C-to-U RNA editing, altered accumulation of chloroplast transcripts and chloroplast-encoded proteins, and defective processing of chloroplast ribosomal RNAs. Potential ISE2 substrates were identified by RNA immunoprecipitation followed by next-generation sequencing (RIP-seq), and the diversity of RNA species identified supports ISE2’s involvement in multiple aspects of chloroplast RNA metabolism. Comprehensive phylogenetic analyses revealed that ISE2 is a non-canonical Ski2-like RNA helicase that represents a separate sub-clade unique to green photosynthetic organisms, consistent with its function as an essential protein. Thus ISE2’s evolutionary conservation may be explained by its numerous roles in regulating chloroplast gene expression

Real-time Analysis and Selection Biases in the Supernova Legacy Survey

The Supernova Legacy Survey (SNLS) has produced a high-quality, homogeneous sample of Type Ia supernovae (SNe Ia) out to redshifts greater than z=1. In its first four years of full operation (to June 2007), the SNLS discovered more than 3000 transient candidates, 373 of which have been confirmed spectroscopically as SNe Ia. Use of these SNe Ia in precision cosmology critically depends on an analysis of the observational biases incurred in the SNLS survey due to the incomplete sampling of the underlying SN Ia population. This paper describes our real-time supernova detection and analysis procedures, and uses detailed Monte Carlo simulations to examine the effects of Malmquist bias and spectroscopic sampling. Such sampling effects are found to become apparent at z~0.6, with a significant shift in the average magnitude of the spectroscopically confirmed SN Ia sample towards brighter values for z>0.75. We describe our approach to correct for these selection biases in our three-year SNLS cosmological analysis (SNLS3), and present a breakdown of the systematic uncertainties involved.Comment: Accepted for publication in A

Light echoes reveal an unexpectedly cool Eta Carinae during its 19th-century Great Eruption

Eta Carinae (Eta Car) is one of the most massive binary stars in the Milky Way. It became the second-brightest star in the sky during its mid-19th century "Great Eruption," but then faded from view (with only naked-eye estimates of brightness). Its eruption is unique among known astronomical transients in that it exceeded the Eddington luminosity limit for 10 years. Because it is only 2.3 kpc away, spatially resolved studies of the nebula have constrained the ejected mass and velocity, indicating that in its 19th century eruption, Eta Car ejected more than 10 M_solar in an event that had 10% of the energy of a typical core-collapse supernova without destroying the star. Here we report the discovery of light echoes of Eta Carinae which appear to be from the 1838-1858 Great Eruption. Spectra of these light echoes show only absorption lines, which are blueshifted by -210 km/s, in good agreement with predicted expansion speeds. The light-echo spectra correlate best with those of G2-G5 supergiant spectra, which have effective temperatures of ~5000 K. In contrast to the class of extragalactic outbursts assumed to be analogs of Eta Car's Great Eruption, the effective temperature of its outburst is significantly cooler than allowed by standard opaque wind models. This indicates that other physical mechanisms like an energetic blast wave may have triggered and influenced the eruption.Comment: Accepted for publication by Nature; 4 pages, 4 figures, SI: 6 pages, 3 figures, 5 table

Using Connected Vehicle Data to Reassess Dilemma Zone Performance of Heavy Vehicles

The rate of fatalities at signalized intersections involving heavy vehicles is nearly five times higher than for passenger vehicles in the US. Previous studies in the US have found that heavy vehicles are twice as likely to violate a red light compared with passenger vehicles. Current technologies leverage setback detection to extend green time for a particular phase and are based upon typical deceleration rates for passenger cars. Furthermore, dilemma zone detectors are not effective when the max out time expires and forces the onset of yellow. This study proposes the use of connected vehicle (CV) technology to trigger force gap out (FGO) before a vehicle is expected to arrive within the dilemma zone limit at max out time. The method leverages position data from basic safety messages (BSMs) to map-match virtual waypoints located up to 1,050 ft in advance of the stop bar. For a 55 mph approach, field tests determined that using a 6 ft waypoint radius at 50 ft spacings would be sufficient to match 95% of BSM data within a 5% lag threshold of 0.59 s. The study estimates that FGOs reduce dilemma zone incursions by 34% for one approach and had no impact for the other. For both approaches, the total dilemma zone incursions decreased from 310 to 225. Although virtual waypoints were used for evaluating FGO, the study concludes by recommending that trajectory-based processing logic be incorporated into controllers for more robust support of dilemma zone and other emerging CV applications

Tumour markers in breast cancer.

The clinical usefulness of 8 potential tumour markers has been evaluated in 69 patients with Stage I and II breast cancer and 57 patients with Stage III and IV. Serum CEA concentrations were raised in 13% of patients with local and 65% of those with advanced breast cancer. In patients with clinical evidence of progression or regression of tumour, serum CEA levels changed appropriately in 83% of cases. Taking 4 of the markers (carcinoembryonic antigen (CEA), lactalbumin, alpha subunit and haptoglobin) serum concentrations of one or more were raised in 33% of patients with local disease and 81% of those with advanced breast cancer. However, marker concentrations were often only marginally raised, and are unlikely to provide sensitive guide to tumour burden. CEA, lactalbumin and alpha subunit were detectable in 68%, 43% and 40% respectively of extracts of primary breast cancers

Connected Vehicle Corridor Deployment and Performance Measures for Assessment

In November 2016, the American Association of State Highway and Transportation Officials (AASHTO) announced the Signal Phase and Timing (SPaT) challenge to state and local agencies to kick start infrastructure deployments for V2I communications. The challenge involved the deployment of Dedicated Short Range Communication (DSRC) infrastructure with SPaT broadcasts (current intersection signal light phase) on at least 20 signalized intersections in all of the 50 states by 2020. Although the roadmap for agencies to partner with the automotive industry is still evolving, it is important for Indiana to not only support the SPaT challenge, but also identify mutually beneficial opportunities for INDOT to partner with the automotive industry as Indiana has the second largest automotive related Gross Domestic Product (GDP) in the country. During this study, connected traffic signal infrastructure was deployed at several locations around the state. The West Lafayette corridor SPaT message deployment was done using both traditional Dedicated Short Range Communication (DSRC) as well cellular communication. This report details the deployment locations, the various public and private sector stakeholders that were engaged during the field testing, and several vehicle-infrastructure communication experiments that were used to evaluate connected vehicle use cases. The findings of this research were as follows: The team successfully demonstrated use cases for placing virtual vehicle detection calls to a traffic signal controller using SPaT messages and evaluated latency. The team developed a scalable methodology for characterizing the probability of a traffic signal phase changing by time of day. This methodology of using agency traffic signal data for green light prediction and engine shut down at red lights is particularly useful to the automotive industry. The team successfully demonstrated that split failures, reduced roadway friction and hard braking events can be identified on the vehicle and transmitted to an agency. This enhanced probe data information is particularly valuable to agencies for identifying traffic signal timing problems, segments impacted by winter weather and location where drivers are encountering roadway conditions required hard braking. DSRC provides the lowest latency communication, but in general commercial cellular interface between vehicles and infrastructure provided acceptable latency for most use cases. For most applications, the team believes a commercial cellular interface between vehicles and infrastructure is the most scalable and feasible for an agency to maintain

The progenitor and early evolution of the Type IIb SN 2016gkg

We report initial observations and analysis on the Type IIb SN~2016gkg in the nearby galaxy NGC~613. SN~2016gkg exhibited a clear double-peaked light curve during its early evolution, as evidenced by our intensive photometric follow-up campaign. SN~2016gkg shows strong similarities with other Type IIb SNe, in particular with respect to the \he~emission features observed in both the optical and near infrared. SN~2016gkg evolved faster than the prototypical Type~IIb SN~1993J, with a decline similar to that of SN~2011dh after the first peak. The analysis of archival {\it Hubble Space Telescope} images indicate a pre-explosion source at SN~2016gkg's position, suggesting a progenitor star with a $\sim$mid F spectral type and initial mass $15-20$\msun, depending on the distance modulus adopted for NGC~613. Modeling the temperature evolution within $5\,\rm{days}$ of explosion, we obtain a progenitor radius of $\sim\,48-124$\rsun, smaller than that obtained from the analysis of the pre-explosion images ($240-320$\rsun).Comment: 7 pages, 5 figures. Submitted to ApJ Letter

Biologically active Phytophthora mating hormone prepared by catalytic asymmetric total synthesis

A Phytophthora mating hormone with an array of 1,5-stereogenic centers has been synthesized by using our recently developed methodology of catalytic enantioselective conjugate addition of Grignard reagents. We applied this methodology in a diastereo- and enantioselective iterative route and obtained two of the 16 possible stereoisomers of Phytophthora hormone α1. These synthetic stereoisomers induced the formation of sexual spores (oospores) in A2 mating type strains of three heterothallic Phytophthora species, P. infestans, P. capsici, and P. nicotianae but not in A1 mating type strains. The response was concentration-dependent, and the oospores were viable. These results demonstrate that the biological activity of the synthetic hormone resembles that of the natural hormone α1. Mating hormones are essential components in the sexual life cycle of a variety of organisms. For plant pathogens like Phytophthora, sexual reproduction is important as a source of genetic variation. Moreover, the thick-walled oospores are the most durable propagules that can survive harsh environmental conditions. Sexual reproduction can thus greatly affect disease epidemics. The availability of synthetic compounds mimicking the activity of Phytophthora mating hormone will be instrumental for further unravelling sexual reproduction in this important group of plant pathogens.