First Measurements of the Complete Heavy-ion Charge State Distributions of C, O, and Fe Associated with Interplanetary Coronal Mass Ejections

We present the first analysis of the complete charge state distributions of heavy ions in interplanetary coronal mass ejections (CMEs), from singly charged to fully ionized. We develop a novel analysis technique that requires the combination and cross-calibration of two different data sets from the Solar Wind Ion Composition Spectrometer on the Advanced Composition Explorer . The first contains ions of higher charge states, and includes an identification of their mass, mass-per-charge, and energy-per-charge. The second data set contains singly and low-charge ions, and identifies only their mass-per-charge and energy-per-charge. Focusing on C, O, and Fe, we find ionic charge states representative of temperatures from ≤60,000 K to over 5,000,000 K contained within interplanetary CMEs observed near 1 AU. We interpret these data in the context of near-Sun observations of filament material associated with CMEs. We find that singly charged ions are embedded within selected interplanetary CMEs, and we examine their densities and durations. These data thus provide the most unambiguous in situ diagnostic of solar prominence plasma in the heliosphere.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/98556/1/0004-637X_751_1_20.pd

Heterochromatin: A Rapidly Evolving Species Barrier

Recent work has shown that changes in the sequence composition of heterochromatin, or in the factors that maintain that heterochromatin, may play an important role in speciation

Structure and Dynamics of the Sun's Open Magnetic Field

The solar magnetic field is the primary agent that drives solar activity and couples the Sun to the Heliosphere. Although the details of this coupling depend on the quantitative properties of the field, many important aspects of the corona - solar wind connection can be understood by considering only the general topological properties of those regions on the Sun where the field extends from the photosphere out to interplanetary space, the so-called open field regions that are usually observed as coronal holes. From the simple assumptions that underlie the standard quasi-steady corona-wind theoretical models, and that are likely to hold for the Sun, as well, we derive two conjectures on the possible structure and dynamics of coronal holes: (1) Coronal holes are unique in that every unipolar region on the photosphere can contain at most one coronal hole. (2) Coronal holes of nested polarity regions must themselves be nested. Magnetic reconnection plays the central role in enforcing these constraints on the field topology. From these conjectures we derive additional properties for the topology of open field regions, and propose several observational predictions for both the slowly varying and transient corona/solar wind.Comment: 26 pages, 6 figure

Recurrence quantification analysis as a tool for the characterization of molecular dynamics simulations

A molecular dynamics simulation of a Lennard-Jones fluid, and a trajectory of the B1 immunoglobulin G-binding domain of streptococcal protein G (B1-IgG) simulated in water are analyzed by recurrence quantification, which is noteworthy for its independence from stationarity constraints, as well as its ability to detect transients, and both linear and nonlinear state changes. The results demonstrate the sensitivity of the technique for the discrimination of phase sensitive dynamics. Physical interpretation of the recurrence measures is also discussed.Comment: 7 pages, 8 figures, revtex; revised for review for Phys. Rev. E (clarifications and expansion of discussion)-- addition of the 8 postscript figures previously omitted, but unchanged from version

Comprehensive analysis of the chromatin landscape in Drosophila melanogaster.

Chromatin is composed of DNA and a variety of modified histones and non-histone proteins, which have an impact on cell differentiation, gene regulation and other key cellular processes. Here we present a genome-wide chromatin landscape for Drosophila melanogaster based on eighteen histone modifications, summarized by nine prevalent combinatorial patterns. Integrative analysis with other data (non-histone chromatin proteins, DNase I hypersensitivity, GRO-Seq reads produced by engaged polymerase, short/long RNA products) reveals discrete characteristics of chromosomes, genes, regulatory elements and other functional domains. We find that active genes display distinct chromatin signatures that are correlated with disparate gene lengths, exon patterns, regulatory functions and genomic contexts. We also demonstrate a diversity of signatures among Polycomb targets that include a subset with paused polymerase. This systematic profiling and integrative analysis of chromatin signatures provides insights into how genomic elements are regulated, and will serve as a resource for future experimental investigations of genome structure and function

Esperanto for histones : CENP-A, not CenH3, is the centromeric histone H3 variant

The first centromeric protein identified in any species was CENP-A, a divergent member of the histone H3 family that was recognised by autoantibodies from patients with scleroderma-spectrum disease. It has recently been suggested to rename this protein CenH3. Here, we argue that the original name should be maintained both because it is the basis of a long established nomenclature for centromere proteins and because it avoids confusion due to the presence of canonical histone H3 at centromeres

On Solving the Coronal Heating Problem

This article assesses the current state of understanding of coronal heating, outlines the key elements of a comprehensive strategy for solving the problem, and warns of obstacles that must be overcome along the way.Comment: Accepted by Solar Physics; Published by Solar Physic

Physics of Solar Prominences: II - Magnetic Structure and Dynamics

Observations and models of solar prominences are reviewed. We focus on non-eruptive prominences, and describe recent progress in four areas of prominence research: (1) magnetic structure deduced from observations and models, (2) the dynamics of prominence plasmas (formation and flows), (3) Magneto-hydrodynamic (MHD) waves in prominences and (4) the formation and large-scale patterns of the filament channels in which prominences are located. Finally, several outstanding issues in prominence research are discussed, along with observations and models required to resolve them.Comment: 75 pages, 31 pictures, review pape

Homologous Flares and Magnetic Field Topology in Active Region NOAA 10501 on 20 November 2003

We present and interpret observations of two morphologically homologous flares that occurred in active region (AR) NOAA 10501 on 20 November 2003. Both flares displayed four homologous H-alpha ribbons and were both accompanied by coronal mass ejections (CMEs). The central flare ribbons were located at the site of an emerging bipole in the center of the active region. The negative polarity of this bipole fragmented in two main pieces, one rotating around the positive polarity by ~ 110 deg within 32 hours. We model the coronal magnetic field and compute its topology, using as boundary condition the magnetogram closest in time to each flare. In particular, we calculate the location of quasiseparatrix layers (QSLs) in order to understand the connectivity between the flare ribbons. Though several polarities were present in AR 10501, the global magnetic field topology corresponds to a quadrupolar magnetic field distribution without magnetic null points. For both flares, the photospheric traces of QSLs are similar and match well the locations of the four H-alpha ribbons. This globally unchanged topology and the continuous shearing by the rotating bipole are two key factors responsible for the flare homology. However, our analyses also indicate that different magnetic connectivity domains of the quadrupolar configuration become unstable during each flare, so that magnetic reconnection proceeds differently in both events.Comment: 24 pages, 10 figures, Solar Physics (accepted

Heterochromatic sequences in a Drosophila whole-genome shotgun assembly

BACKGROUND: Most eukaryotic genomes include a substantial repeat-rich fraction termed heterochromatin, which is concentrated in centric and telomeric regions. The repetitive nature of heterochromatic sequence makes it difficult to assemble and analyze. To better understand the heterochromatic component of the Drosophila melanogaster genome, we characterized and annotated portions of a whole-genome shotgun sequence assembly. RESULTS: WGS3, an improved whole-genome shotgun assembly, includes 20.7 Mb of draft-quality sequence not represented in the Release 3 sequence spanning the euchromatin. We annotated this sequence using the methods employed in the re-annotation of the Release 3 euchromatic sequence. This analysis predicted 297 protein-coding genes and six non-protein-coding genes, including known heterochromatic genes, and regions of similarity to known transposable elements. Bacterial artificial chromosome (BAC)-based fluorescence in situ hybridization analysis was used to correlate the genomic sequence with the cytogenetic map in order to refine the genomic definition of the centric heterochromatin; on the basis of our cytological definition, the annotated Release 3 euchromatic sequence extends into the centric heterochromatin on each chromosome arm. CONCLUSIONS: Whole-genome shotgun assembly produced a reliable draft-quality sequence of a significant part of the Drosophila heterochromatin. Annotation of this sequence defined the intron-exon structures of 30 known protein-coding genes and 267 protein-coding gene models. The cytogenetic mapping suggests that an additional 150 predicted genes are located in heterochromatin at the base of the Release 3 euchromatic sequence. Our analysis suggests strategies for improving the sequence and annotation of the heterochromatic portions of the Drosophila and other complex genomes