Aaron Golden

CONFIRMATION OF THE ELECTRON CYCLOTRON MASER INSTABILITY AS THE DOMINANT SOURCE OF RADIO EMISSION FROM VERY LOW MASS STARS AND BROWN DWARFS

We report on radio observations of the M8.5 dwarf LSR J1835+3259 and the L3.5 dwarf 2MASS J00361617+1821104, which provide the strongest evidence to date that the electron cyclotron maser instability is the dominant mechanism producing radio emission in the magnetospheres of ultracool dwarfs. As has previously been reported for the M9 dwarf TVLM 513–46546, periodic pulses of 100% circularly polarized, coherent radio emission are detected from both dwarfs with periods of 2.84 ± 0.01 and 3.08 ± 0.05 hr, respectively, for LSR J1835+3259 and 2MASS J00361617+1821104. Importantly, periodic unpolarized radio emission is also detected from 2MASS J00361617+1821104, and brightness temperature limitations rule out gyrosynchrotron radiation as a source of this radio emission. The unpolarized emission from this and other ultracool dwarfs is also attributed to electron cyclotron maser emission, which has become depolarized on traversing the ultracool dwarf magnetosphere, possibly due to propagations effects such as scattering. Based on available v sin i data in the literature and rotation periods derived from the periodic radio data for the three confirmed sources of electron cyclotron maser emission, TVLM 513–46546, LSR J1835+3259, and 2MASS J00361617+1821104, we determine that the rotation axes of all three dwarfs are close to perpendicular to our line of sight. This suggests a possible geometrical selection effect due to the inherent directivity of electron cyclotron maser emission, that may account for the previously reported relationship between radio activity and v sin i observed for ultracool dwarfs. We also determine the radius of the dwarf LSR J1835+3259 to be ≥0.117 ± 0.012 R_☉. The implied size of the radius, together with the bolometric luminosity of the dwarf, suggests that either LSR J1835 is a young- or intermediate-age brown dwarf, or that current theoretical models underestimate the radii of ultracool dwarfs.

PERIODIC BURSTS OF COHERENT RADIO EMISSION FROM AN ULTRACOOL DWARF

We report the detection of periodic (p = 1.96 hr) bursts of extremely bright, 100% circularly polarized, coherent radio emission from the M9 dwarf TVLM 513-46546. Simultaneous photometric monitoring observations have established this periodicity to be the rotation period of the dwarf. These bursts, which were not present in previous observations of this target, confirm that ultracool dwarfs can generate persistent levels of broadband, coherent radio emission, associated with the presence of kG magnetic fields in a large-scale, stable configuration. Compact sources located at the magnetic polar regions produce highly beamed emission generated by the electron cyclotron maser instability, the same mechanism known to generate planetary coherent radio emission in our solar system. The narrow beams of radiation pass our line of sight as the dwarf rotates, producing the associated periodic bursts. The resulting radio light curves are analogous to the periodic light curves associated with pulsar radio emission highlighting TVLM 513-46546 as the prototype of a new class of transient radio source.

Rotational Modulation of the Radio Emission from the M9 Dwarf TVLM 513?46546: Broadband Coherent Emission at the Substellar Boundary?

The Very Large Array was used to observe the ultracool rapidly rotating M9 dwarf TVLM 513-46546 simultaneously at 4.88 and 8.44 GHz. The radio emission was determined to be persistent, variable, and periodic at both frequencies with a period of ~2 hr. This periodicity is in excellent agreement with the estimated period of rotation of the dwarf based on its v sin i of ~60 km s^(-1). This rotational modulation places strong constraints on the source size of the radio-emitting region and hence the brightness temperature of the associated emission. We find the resulting high brightness temperature, together with the inherent directivity of the rotationally modulated component of the emission, difficult to reconcile with incoherent gyrosynchrotron radiation. We conclude that a more likely source is coherent, electron cyclotron maser emission from the low-density regions above the magnetic poles. This model requires the magnetic field of TVLM 513-46546 to take the form of a large-scale, stable dipole or multipole with surface field strengths up to at least 3 kG. We discuss a mechanism by which broadband, persistent electron cyclotron maser emission can be sustained in the low-density regions of the magnetospheres of ultracool dwarfs. A second nonvarying, unpolarized component of the emission may be due to depolarization of the coherent electron cyclotron maser emission or, alternatively, incoherent gyrosynchrotron or synchrotron radiation from a population of electrons trapped in the large-scale magnetic field.

CG dinucleotide clustering is a species-specific property of the genome

Cytosines at cytosine-guanine (CG) dinucleotides are the near-exclusive target of DNA methyltransferases in mammalian genomes. Spontaneous deamination of methylcytosine to thymine makes methylated cytosines unusually susceptible to mutation and consequent depletion. The loci where CG dinucleotides remain relatively enriched, presumably due to their unmethylated status during the germ cell cycle, have been referred to as CpG islands. Currently, CpG islands are solely defined by base compositional criteria, allowing annotation of any sequenced genome. Using a novel bioinformatic approach, we show that CG clusters can be identified as an inherent property of genomic sequence without imposing a base compositional a priori assumption. We also show that the CG clusters co-localize in the human genome with hypomethylated loci and annotated transcription start sites to a greater extent than annotations produced by prior CpG island definitions. Moreover, this new approach allows CG clusters to be identified in a species-specific manner, revealing a degree of orthologous conservation that is not revealed by current base compositional approaches. Finally, our approach is able to identify methylating genomes (such as Takifugu rubripes) that lack CG clustering entirely, in which it is inappropriate to annotate CpG islands or CG clusters.

Enhanced optical emission during Crab giant radio pulses

We detected a correlation between optical and giant radio pulse emission from the Crab pulsar. Optical pulses coincident with the giant radio pulses were on average 3% brighter than those coincident with normal radio pulses. Combined with the lack of any other pulse profile changes, this result indicates that both the giant radio pulses and the increased optical emission are linked to an increase in the electron-positron plasma density.

Transcription factor binding site identification using the self-organizing map

MOTIVATION The automatic identification of over-represented motifs present in a collection of sequences continues to be a challenging problem in computational biology. In this paper, we propose a self-organizing map of position weight matrices as an alternative method for motif discovery. The advantage of this approach is that it can be used to simultaneously characterize every feature present in the dataset, thus lessening the chance that weaker signals will be missed. Features identified are ranked in terms of over-representation relative to a background model. RESULTS We present an implementation of this approach, named SOMBRERO (self-organizing map for biological regulatory element recognition and ordering), which is capable of discovering multiple distinct motifs present in a single dataset. Demonstrated here are the advantages of our approach on various datasets and SOMBREROs improved performance over two popular motif-finding programs, MEME and AlignACE. AVAILABILITY SOMBRERO is available free of charge from http://bioinf.nuigalway.ie/sombrero SUPPLEMENTARY INFORMATION http://bioinf.nuigalway.ie/sombrero/additional.

An integrated genome screen identifies the Wnt signaling pathway as a major target of WT1

WT1, a critical regulator of kidney development, is a tumor suppressor for nephroblastoma but in some contexts functions as an oncogene. A limited number of direct transcriptional targets of WT1 have been identified to explain its complex roles in tumorigenesis and organogenesis. In this study we performed genome-wide screening for direct WT1 targets, using a combination of ChIP–ChIP and expression arrays. Promoter regions bound by WT1 were highly G-rich and resembled the sites for a number of other widely expressed transcription factors such as SP1, MAZ, and ZNF219. Genes directly regulated by WT1 were implicated in MAPK signaling, axon guidance, and Wnt pathways. Among directly bound and regulated genes by WT1, nine were identified in the Wnt signaling pathway, suggesting that WT1 modulates a subset of Wnt components and responsive genes by direct binding. To prove the biological importance of the interplay between WT1 and Wnt signaling, we showed that WT1 blocked the ability of Wnt8 to induce a secondary body axis during Xenopus embryonic development. WT1 inhibited TCF-mediated transcription activated by Wnt ligand, wild type and mutant, stabilized β-catenin by preventing TCF4 loading onto a promoter. This was neither due to direct binding of WT1 to the TCF binding site nor to interaction between WT1 and TCF4, but by competition of WT1 and TCF4 for CBP. WT1 interference with Wnt signaling represents an important mode of its action relevant to the suppression of tumor growth and guidance of development.

The Distance and Radius of the Neutron Star PSR B0656+14

We present the result of astrometric observations of the radio pulsar PSR B0656+14, made using the Very Long Baseline Array. The parallax of the pulsar is π = 3.47 ± 0.36 milliarcsec, yielding a distance 288 pc. This independent distance estimate has been used to constrain existing models of thermal X-ray emission from the neutron stars photosphere. Simple blackbody fits to the X-ray data formally yield a neutron star radius R∞ ~ 7-8.5 km. With more realistic fits to a magnetized hydrogen atmosphere, any radius between ~13 and ~20 km is allowed.

Magnetospherically driven optical and radio aurorae at the end of the stellar main sequence

Aurorae are detected from all the magnetized planets in our Solar System, including Earth. They are powered by magnetospheric current systems that lead to the precipitation of energetic electrons into the high-latitude regions of the upper atmosphere. In the case of the gas-giant planets, these aurorae include highly polarized radio emission at kilohertz and megahertz frequencies produced by the precipitating electrons, as well as continuum and line emission in the infrared, optical, ultraviolet and X-ray parts of the spectrum, associated with the collisional excitation and heating of the hydrogen-dominated atmosphere. Here we report simultaneous radio and optical spectroscopic observations of an object at the end of the stellar main sequence, located right at the boundary between stars and brown dwarfs, from which we have detected radio and optical auroral emissions both powered by magnetospheric currents. Whereas the magnetic activity of stars like our Sun is powered by processes that occur in their lower atmospheres, these aurorae are powered by processes originating much further out in the magnetosphere of the dwarf star that couple energy into the lower atmosphere. The dissipated power is at least four orders of magnitude larger than what is produced in the Jovian magnetosphere, revealing aurorae to be a potentially ubiquitous signature of large-scale magnetospheres that can scale to luminosities far greater than those observed in our Solar System. These magnetospheric current systems may also play a part in powering some of the weather phenomena reported on brown dwarfs.

Gene-set analysis is severely biased when applied to genome-wide methylation data

MOTIVATION DNA methylation is an epigenetic mark that can stably repress gene expression. Because of its biological and clinical significance, several methods have been developed to compare genome-wide patterns of methylation between groups of samples. The application of gene set analysis to identify relevant groups of genes that are enriched for differentially methylated genes is often a major component of the analysis of these data. This can be used, for example, to identify processes or pathways that are perturbed in disease development. We show that gene-set analysis, as it is typically applied to genome-wide methylation assays, is severely biased as a result of differences in the numbers of CpG sites associated with different classes of genes and gene promoters. RESULTS We demonstrate this bias using published data from a study of differential CpG island methylation in lung cancer and a dataset we generated to study methylation changes in patients with long-standing ulcerative colitis. We show that several of the gene sets that seem enriched would also be identified with randomized data. We suggest two existing approaches that can be adapted to correct the bias. Accounting for the bias in the lung cancer and ulcerative colitis datasets provides novel biological insights into the role of methylation in cancer development and chronic inflammation, respectively. Our results have significant implications for many previous genome-wide methylation studies that have drawn conclusions on the basis of such strongly biased analysis. CONTACT cathal.seoighe@nuigalway.ie SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.