Deciphering the epitranscriptome: a green perspective

The advent of high-throughput sequencing technologies coupled with new detection methods of RNA modifications has enabled investigation of a new layer of gene regulation - the epitranscriptome. With over 100 known RNA modifications, understanding the repertoire of RNA modifications is a huge undertaking. This review summarizes what is known about RNA modifications with an emphasis on discoveries in plants. RNA ribose modifications, base methylations and pseudouridylation are required for normal development in Arabidopsis, as mutations in the enzymes modifying them have diverse effects on plant development and stress responses. These modifications can regulate RNA structure, turnover and translation. Transfer RNA and ribosomal RNA modifications have been mapped extensively and their functions investigated in many organisms, including plants. Recent work exploring the locations, functions and targeting of N6 -methyladenosine (m6 A), 5-methylcytosine (m5 C), pseudouridine (Ψ), and additional modifications in mRNAs and ncRNAs are highlighted, as well as those previously known on tRNAs and rRNAs. Many questions remain as to the exact mechanisms of targeting and functions of specific modified sites and whether these modifications have distinct functions in the different classes of RNAs.Alice Burgess, Rakesh David, Iain Robert Searl

Very Luminous Carbon Stars in the Outer Disk of the Triangulum Spiral Galaxy

Stars with masses in the range from about 1.3 to 3.5 Mo pass through an evolutionary stage where they become carbon stars. In this stage, which lasts a few Myr, these stars are extremely luminous pulsating giants. They are so luminous in the near-infrared that just a few of them can double the integrated luminosity of intermediate-age (0.6 to 2 Gyr) Magellanic Cloud clusters at 2.2 microns. Astronomers routinely use such near-infrared observations to minimize the effects of dust extinction, but it is precisely in this band that carbon stars can contribute hugely. The actual contribution of carbon stars to the outer disk light of evolving spiral galaxies has not previously been morphologically investigated. Here we report new and very deep near-IR images of the Triangulum spiral galaxy M33=NGC 598, delineating spectacular arcs of carbon stars in its outer regions. It is these arcs which dominate the near-infrared m=2 Fourier spectra of M33. We present near-infrared photometry with the Hale 5-m reflector, and propose that the arcs are the signature of accretion of low metallicity gas in the outer disk of M33.Comment: 4 pages, 4 figures. Revised version submitted to A&A Letter

Targeted search for continuous gravitational waves: Bayesian versus maximum-likelihood statistics

We investigate the Bayesian framework for detection of continuous gravitational waves (GWs) in the context of targeted searches, where the phase evolution of the GW signal is assumed to be known, while the four amplitude parameters are unknown. We show that the orthodox maximum-likelihood statistic (known as F-statistic) can be rediscovered as a Bayes factor with an unphysical prior in amplitude parameter space. We introduce an alternative detection statistic ("B-statistic") using the Bayes factor with a more natural amplitude prior, namely an isotropic probability distribution for the orientation of GW sources. Monte-Carlo simulations of targeted searches show that the resulting Bayesian B-statistic is more powerful in the Neyman-Pearson sense (i.e. has a higher expected detection probability at equal false-alarm probability) than the frequentist F-statistic.Comment: 12 pages, presented at GWDAW13, to appear in CQ

Colonization, mouse-style

Several recent papers, including one in BMC Evolutionary Biology, examine the colonization history of house mice. As well as background for the analysis of mouse adaptation, such studies offer a perspective on the history of movements of the humans that accidentally transported the mice

Bayesian detection of unmodeled bursts of gravitational waves

The data analysis problem of coherently searching for unmodeled gravitational-wave bursts in the data generated by a global network of gravitational-wave observatories has been at the center of research for almost two decades. As data from these detectors is starting to be analyzed, a renewed interest in this problem has been sparked. A Bayesian approach to the problem of coherently searching for gravitational wave bursts with a network of ground-based interferometers is here presented. We demonstrate how to systematically incorporate prior information on the burst signal and its source into the analysis. This information may range from the very minimal, such as best-guess durations, bandwidths, or polarization content, to complete prior knowledge of the signal waveforms and the distribution of sources through spacetime. We show that this comprehensive Bayesian formulation contains several previously proposed detection statistics as special limiting cases, and demonstrate that it outperforms them.Comment: 18 pages, 3 figures, revisions based on referee comment

Star counts in NGC 6397

I-band CCD images of a large area of the nearby globular cluster NGC~6397 have been used to construct a surface density profile and two luminosity and mass functions. The surface density profile extends out to 14\arcm from the cluster center and shows no sign of a tidal cutoff. The inner profile is a power-law with slope -0.8 steepening to -1.7 outside of 1\arcm. The mass functions are for fields at 4\arcm\ and 11\arcm from the cluster center and confirm the upturn in the mass function for stars less massive than about 0.4 M\solar. There appears to be an excess of low-mass stars over higher-mass stars in the outer field with respect to the inner, in qualitative agreement with expectations for mass segregation.Comment: 16 pages + 7 pages of tables, LaTeX using AASTeX macros, 11 figures available by request, IoA preprin

Rural Teachers\u27 Cultural and Epistemic Shifts in STEM Teaching and Learning

This article focuses on the ways in which integrated curriculum can improve STEM teaching and learning within rural spaces. Using a design-based research approach, this study focuses on rural teachers\u27 experiences of professional learning and development training as they learn to engage computing and maker technologies in their elementary classrooms as tools for teaching students about difficult histories of immigration, migration, and forced relocation across the United States

Understanding spatio-temporal variability in the reproduction ratio of the bluetongue (BTV-1) epidemic in southern Spain (Andalusia) in 2007 using epidemic trees

Andalusia (Southern Spain) is considered one of the main routes of introduction of bluetongue virus (BTV) into Europe, evidenced by a devastating epidemic caused by BTV-1 in 2007. Understanding the pattern and the drivers of BTV-1 spread in Andalusia is critical for effective detection and control of future epidemics. A long-standing metric for quantifying the behaviour of infectious diseases is the case-reproduction ratio (Rt), defined as the average number of secondary cases arising from a single infected case at time t (for t>0). Here we apply a method using epidemic trees to estimate the between-herd case reproduction ratio directly from epidemic data allowing the spatial and temporal variability in transmission to be described. We then relate this variability to predictors describing the hosts, vectors and the environment to better understand why the epidemic spread more quickly in some regions or periods. The Rt value for the BTV-1 epidemic in Andalusia peaked in July at 4.6, at the start of the epidemic, then decreased to 2.2 by August, dropped below 1 by September (0.8), and by October it had decreased to 0.02. BTV spread was the consequence of both local transmission within established disease foci and BTV expansion to distant new areas (i.e. new foci), which resulted in a high variability in BTV transmission, not only among different areas, but particularly through time, which suggests that general control measures applied at broad spatial scales are unlikely to be effective. This high variability through time was probably due to the impact of temperature on BTV transmission, as evidenced by a reduction in the value of Rt by 0.0041 for every unit increase (day) in the extrinsic incubation period (EIP), which is itself directly dependent on temperature. Moreover, within the range of values at which BTV-1 transmission occurred in Andalusia (20.6°C to 29.5°C) there was a positive correlation between temperature and Rt values, although the relationship was not linear, probably as a result of the complex relationship between temperature and the different parameters affecting BTV transmission. Rt values for BTV-1 in Andalusia fell below the threshold of 1 when temperatures dropped below 21°C, a much higher threshold than that reported in other BTV outbreaks, such as the BTV-8 epidemic in Northern Europe. This divergence may be explained by differences in the adaptation to temperature of the main vectors of the BTV-1 epidemic in Andalusia (Culicoides imicola) compared those of the BTV-8 epidemic in Northern Europe (Culicoides obsoletus). Importantly, we found that BTV transmission (Rt value) increased significantly in areas with higher densities of sheep. Our analysis also established that control of BTV-1 in Andalusia was complicated by the simultaneous establishment of several distant foci at the start of the epidemic, which may have been caused by several independent introductions of infected vectors from the North of Africa. We discuss the implications of these findings for BTV surveillance and control in this region of Europe