Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and m6A modification

Understanding genome organization and gene regulation requires insight into RNA transcription, processing and modification. We adapted nanopore direct RNA sequencing to examine RNA from a wild-type accession of the model plant Arabidopsis thaliana and a mutant defective in mRNA methylation (m6A). Here we show that m6A can be mapped in full-length mRNAs transcriptome-wide and reveal the combinatorial diversity of cap-associated transcription start sites, splicing events, poly(A) site choice and poly(A) tail length. Loss of m6A from 3’ untranslated regions is associated with decreased relative transcript abundance and defective RNA 30 end formation. A functional consequence of disrupted m6A is a lengthening of the circadian period. We conclude that nanopore direct RNA sequencing can reveal the complexity of mRNA processing and modification in full-length single molecule reads. These findings can refine Arabidopsis genome annotation. Further, applying this approach to less well-studied species could transform our understanding of what their genomes encode

Multiwavelength Properties of the X-ray Sources in the Groth-Westphal Strip Field

We summarize the multiwavelength properties of X-ray sources detected in the 80 ks XMM-Newton observation of the Groth-Westphal Strip. We find 23 XMM-Newton sources within the WFPC2 fields. Ten spectroscopic redshifts are available from the DEEP and CFRS projects and 4 of these show broad Mg II emission (type 1 AGNs). Two of those without any broad lines, nevertheless, have [NeV] emission which is an unambiguous signature of AGN activity, one of which is a narrow-line Seyfert 1 and the other a type 2 AGN. We have made near-infrared (NIR) spectroscopic observations using the Subaru OHS/CISCO spectrometer for five of the X-ray sources for which we found no indication of an AGN activity in the optical spectrum. We have detected H-alpha+[NII] emission in four of them. A broad H-alpha component and/or a large [NII]/H-alpha ratio is seen, suggestive of AGN activity. Nineteen sources have been detected in the Ks band and four of these are extremely red objects (I814-Ks>4). The optical counterparts for the majority of the X-ray sources are bulge-dominated with colors consistent with evolving elliptical galaxies, with starburst/AGN contamination. Assuming that the known local relations among the bulge luminosity,central velocity dispersion, and the mass of the central blackhole hold at about z=1, the AGN bolometric luminosity to Eddington luminosity ratio ranges from 0.3% to 10%. (abridged)Comment: 18 pages, 6 figures, accepted for publication in Astronomical Journa

Confirmation of six Be X-ray binaries in the Small Magellanic Cloud

The X-ray binary population of the Small Magellanic Cloud (SMC) contains a large number of massive X-ray binaries, and the recent survey of the SMC by XMM–Newton has resulted in almost 50 more tentative high-mass X-ray binary (HMXB) candidates. Using probability parameters from Haberl and Sturm together with the optical spectra and timing in this work, we confirm six new massive X-ray binaries in the SMC. We also report two very probable binary periods of 36.4 d in XMM 1859 and of 72.2 d in XMM 2300. These Be X-ray binaries are likely part of the general SMC population, which rarely undergoes an X-ray outburst.This paper is based on ESO data from 079.D−0371 and 088.D−0352. The AAT observations have been supported by the OPTICON project (observing proposals 2011A/014 and 2012/A015), which is funded by the European Commission under the Seventh Framework Programme (FP7). VAM acknowledges financial support from the National Research Foundation of South Africa (Grant 93405) and the World Universities Network. RD, AM and IN from the University of Alicante acknowledge support from the Spanish Government Ministerio de Economía y Competitividad under grant AYA2015-68012-C2-2-P (MINECO/FEDER). ESB acknowledges support from a Claude Leon Foundation fellowship and from the Marie Curie Actions of the European Commission (FP7-COFUND). The OGLE project has received funding from the National Science Centre, Poland, grant MAESTRO 2014/14/A/ST9/00121 to AU

High speed photometry of faint Cataclysmic Variables - VII. Targets selected from the Sloan Digital Sky Survey and the Catalina Real-time Transient Survey

We present high speed photometric observations of 20 faint cataclysmic variables, selected from the Sloan Digital Sky Survey and Catalina catalogues. Measurements are given of 15 new directly measured orbital periods, including four eclipsing dwarf novae (SDSS0904+03, CSS0826-00, CSS1404-10 and CSS1626-12), two new polars (CSS0810+00 and CSS1503-22) and two dwarf novae with superhumps in quiescence (CSS0322+02 and CSS0826-00). Whilst most of the dwarf novae presented here have periods below 2 h, SDSS0805+07 and SSS0617-36 have relatively long orbital periods of 5.489 and 3.440 h, respectively. The double humped orbital modulations observed in SSS0221-26, CSS0345-01, CSS1300+11 and CSS1443-17 are typical of low mass transfer rate dwarf novae. The white dwarf primary of SDSS0919+08 is confirmed to have non-radial oscillations and quasi-periodic oscillations were observed in the short-period dwarf nova CSS1028-08 during outburst. We further report the detection of a new nova-like variable (SDSS1519+06). The frequency distribution of orbital periods of CVs in the Catalina survey has a high peak near ~80 min orbital period, independently confirming that found by Gaensicke et al (2009) from SDSS sources. We also observe a marked correlation between the median in the orbital period distribution and the outburst class, in the sense that dwarf novae with a single observed outburst (over the 5-year baseline of the CRTS coverage) occur predominantly at shortest orbital period.Comment: 17 pages, 38 figures, accepted for publication in MNRA

Post-transcriptional control of nuclear-encoded cytochrome oxidase subunits in Trypanosoma brucei: evidence for genome-wide conservation of life-cycle stage-specific regulatory elements

Trypanosomes represent an excellent model for the post-transcriptional regulation of gene expression because their genome is organized into polycistronic transcription units. However, few signals governing developmental stage-specific expression have been identified, with there being no compelling evidence for widespread conservation of regulatory motifs. As a tool to search for common regulatory sequences we have used the nuclear-encoded components of the cytochrome oxidase (COX) complex of the trypanosome respiratory chain. Components of this complex represent a form of post-transcriptional operon because trypanosome mitochondrial activity is unusual in being developmentally programmed. By genome analysis we identified the genes for seven components of the COX complex. Each mRNA exhibits bloodstream stage-specific instability, which is not mediated by the RNA silencing pathway but which is alleviated by cycloheximide. Reporter assays have identified regulatory regions within the 3′-untranslated regions of three COX mRNAs operating principally at the translational level, but also via mRNA stability. Interrogation of the mapped regions via oligonucleotide frequency scoring provides evidence for genome-wide conservation of regulatory sequences among a large cohort of procyclic-enriched transcripts. Analysis of the co-regulated subunits of a stage-specific enzyme is therefore a novel approach to uncover cryptic regulatory sequences controlling gene expression at the post-transcriptional level

Optical and X-ray studies of Be/X-ray binaries in the Small Magellanic Cloud

High-mass X-ray binaries (HMXBs) have proved to be some of the most interesting X-ray sources in the sky. The growing opulation of Small Magellanic Cloud (SMC) Be/X-ray binaries is monitored weekly with two 15ks RXTE observations. My thesis focuses on presenting the analysis of the X-ray data and the optical follow-up that enhances it. I present detailed studies of the H emission features in several prominent Be/X-ray binaries in the SMC and examine their outbursting nature by combining the OGLE optical light curves with the RXTE light curves. This has culminated in an orbital solution for SXP18.3 as well as measured orbital periods for SXP2.37, SXP172 and SXP202B. Through detections of quasi-periodic variations in the optical light curves, the details of interactions taking place between the Be star’s circumstellar disk and the neutron star are being revealed. These data are providing the building blocks that may help explain the physical processes that produce the circumstellar disk. In addition, the optical counterpart to SXP15.3 is discussed in the light of recent XMM-Newton results, raising doubt over the true optical counterpart

Delineating Functional Corridors Linking Leopard Habitat in the Eastern and Western Cape, South Africa

Natural landscapes are increasingly fragmented due to human activity. This contributes to isolation and inadequate gene flow among wildlife populations. These threats intensify where populations are already low, and gene flow is compromised. Ensuring habitat connectivity despite transformed landscapes can mitigate these risks. Leopards are associated with high levels of biodiversity and are the last widely occurring, free-roaming apex predator in South Africa. Although highly adaptable, leopard survival is reduced by human-caused mortality and habitat destruction. We aimed to assess the connectivity of leopard habitat in the Eastern Cape and Western Cape, South Africa. We predicted leopard habitat by correlating GPS data from 31 leopards to environmental features that included human-associated and natural landscapes. We used circuit theory to delineate corridors linking known leopard populations. Finally, using camera traps, we tested whether five predicted corridors were used by leopards. Leopard habitat was strongly correlated to moderate slopes and areas of natural land-cover and plantations, highlighting mountainous areas as important habitat with high connectivity probability. While most habitat patches showed some level of connectivity, leopards avoided highly transformed landscapes, potentially isolating some populations. Where corridors are not functional, active conservation measures for species connectivity becomes important

Nanopore Direct RNA Sequencing Maps the Arabidopsis m6A Epitranscriptome

Understanding genome organization and gene regulation requires insight into RNA transcription, processing and modification. We adapted Oxford Nanopore Direct RNA Sequencing to examine RNA from a wild-type accession of the model plant Arabidopsis thaliana and a mutant defective in mRNA methylation (m6A). Here we show that m6A can be mapped in full-length mRNAs transcriptome-wide and reveal the combinatorial diversity of cap-associated transcription start sites, splicing events, poly(A) site choice and poly(A) tail length. Loss of m6A from terminal exons is associated with decreased relative transcript abundance and defective RNA 3’ end formation. A functional consequence of disrupted m6A is a lengthening of the circadian period. We conclude that nanopore direct RNA sequencing can reveal the complexity of mRNA processing and modification in full-length single molecule reads. These findings refine Arabidopsis genome annotation and, if applied to less well-studied species, this approach has the potential to transform our understanding of what their genomes encode

Nanopore Direct RNA Sequencing Maps the Arabidopsis m6A Epitranscriptome

Understanding genome organization and gene regulation requires insight into RNA transcription, processing and modification. We adapted Oxford Nanopore Direct RNA Sequencing to examine RNA from a wild-type accession of the model plant Arabidopsis thaliana and a mutant defective in mRNA methylation (m6A). Here we show that m6A can be mapped in full-length mRNAs transcriptome-wide and reveal the combinatorial diversity of cap-associated transcription start sites, splicing events, poly(A) site choice and poly(A) tail length. Loss of m6A from terminal exons is associated with decreased relative transcript abundance and defective RNA 3’ end formation. A functional consequence of disrupted m6A is a lengthening of the circadian period. We conclude that nanopore direct RNA sequencing can reveal the complexity of mRNA processing and modification in full-length single molecule reads. These findings refine Arabidopsis genome annotation and, if applied to less well-studied species, this approach has the potential to transform our understanding of what their genomes encode