What is the Total Deuterium Abundance in the Local Galactic Disk?

Analyses of spectra obtained with the Far Ultraviolet Spectroscopic Explorer (FUSE) satellite, together with spectra from the Copernicus and IMAPS instruments, reveal an unexplained very wide range in the observed deuterium/hydrogen (D/H) ratios for interstellar gas in the Galactic disk beyond the Local Bubble. We argue that spatial variations in the depletion of deuterium onto dust grains can explain these local variations in the observed gas-phase D/H ratios. We present a variable deuterium depletion model that naturally explains the constant measured values of D/H inside the Local Bubble, the wide range of gas-phase D/H ratios observed in the intermediate regime (log N(H I} = 19.2-20.7), and the low gas-phase D/H ratios observed at larger hydrogen column densities. We consider empirical tests of the deuterium depletion hypothesis: (i) correlations of gas-phase D/H ratios with depletions of the refractory metals iron and silicon, and (ii) correlation with the molecular hydrogen rotational temperature. Both of these tests are consistent with deuterium depletion from the gas phase in cold, not recently shocked, regions of the ISM, and high gas-phase D/H ratios in gas that has been shocked or otherwise heated recently. We argue that the most representative value for the total (gas plus dust) D/H ratio within 1 kpc of the Sun is >=23.1 +/- 2.4 (1 sigma) parts per million (ppm). This ratio constrains Galactic chemical evolution models to have a very small deuterium astration factor, the ratio of primordial to total (D/H) ratio in the local region of the Galactic disk, which we estimate to be f_d <= 1.19 +/-0.16 (1 sigma) or <= 1.12 +/- 0.14 (1 sigma) depending on the adopted light element nuclear reaction rates.Comment: 19 pages, 9 figure

PhyloMarker—A Tool for Mining Phylogenetic Markers Through Genome Comparison: Application of the Mouse Lemur (Genus Microcebus) Phylogeny

Molecular phylogeny is a fundamental tool to understanding the evolution of all life forms. One common issue faced by molecular phylogeny is the lack of sufficient molecular markers. Here, we present PhyloMarker, a phylogenomic tool designed to find nuclear gene markers for the inference of phylogeny through multiple genome comparison. Around 800 candidate markers were identified by PhyloMarker through comparison of partial genomes of Microcebus and Otolemur. In experimental tests of 20 randomly selected markers, nine markers were successfully amplified by PCR and directly sequenced in all 17 nominal Microcebus species. Phylogenetic analyses of the sequence data obtained for 17 taxa and nine markers confirmed the distinct lineage inferred from previous mtDNA data. PhyloMarker has also been used by other projects including the herons (Ardeidae, Aves) phylogeny and the Wood mice (Muridae, Mammalia) phylogeny. All source code and sample data are made available at http://bioinfo-srv1.awh.unomaha.edu/phylomarker/

Targeted genome editing across species using ZFNs and TALENs

Evolutionary studies necessary to dissect diverse biological processes have been limited by the lack of reverse genetic approaches in most organisms with sequenced genomes. We established a broadly applicable strategy using zinc finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs) for targeted disruption of endogenous genes and cis-acting regulatory elements in diverged nematode species

The Case for Dynamic Models of Learners' Ontologies in Physics

In a series of well-known papers, Chi and Slotta (Chi, 1992; Chi & Slotta, 1993; Chi, Slotta & de Leeuw, 1994; Slotta, Chi & Joram, 1995; Chi, 2005; Slotta & Chi, 2006) have contended that a reason for students' difficulties in learning physics is that they think about concepts as things rather than as processes, and that there is a significant barrier between these two ontological categories. We contest this view, arguing that expert and novice reasoning often and productively traverses ontological categories. We cite examples from everyday, classroom, and professional contexts to illustrate this. We agree with Chi and Slotta that instruction should attend to learners' ontologies; but we find these ontologies are better understood as dynamic and context-dependent, rather than as static constraints. To promote one ontological description in physics instruction, as suggested by Slotta and Chi, could undermine novices' access to productive cognitive resources they bring to their studies and inhibit their transition to the dynamic ontological flexibility required of experts.Comment: The Journal of the Learning Sciences (In Press

Superhumps in Cataclysmic Binaries. XXIII. V442 Ophiuchi and RX J1643.7+3402

We report the results of long observing campaigns on two novalike variables: V442 Ophiuchi and RX J1643.7+3402. These stars have high-excitation spectra, complex line profiles signifying mass loss at particular orbital phases, and similar orbital periods (respectively 0.12433 and 0.12056 d). They are well-credentialed members of the SW Sex class of cataclysmic variables. Their light curves are also quite complex. V442 Oph shows periodic signals with periods of 0.12090(8) and 4.37(15) days, and RX J1643.7+3402 shows similar signals at 0.11696(8) d and 4.05(12) d. We interpret these short and long periods respectively as a "negative superhump" and the wobble period of the accretion disk. The superhump could then possibly arise from the heating of the secondary (and structures fixed in the orbital frame) by inner-disk radiation, which reaches the secondary relatively unimpeded since the disk is not coplanar. At higher frequencies, both stars show another type of variability: quasi-periodic oscillations (QPOs) with a period near 1000 seconds. Underlying these strong signals of low stability may be weak signals of higher stability. Similar QPOs, and negative superhumps, are quite common features in SW Sex stars. Both can in principle be explained by ascribing strong magnetism to the white dwarf member of the binary; and we suggest that SW Sex stars are borderline AM Herculis binaries, usually drowned by a high accretion rate. This would provide an ancestor channel for AM Hers, whose origin is still mysterious.Comment: PDF, 41 pages, 4 tables, 16 figures; accepted, in press, to appear December 2002, PASP; more info at http://cba.phys.columbia.edu

Varicella-Zoster viruses associated with post-herpetic neuralgia induce sodium current density increases in the ND7-23 Nav-1.8 neuroblastoma cell line

Post-herpetic neuralgia (PHN) is the most significant complication of herpes zoster caused by reactivation of latent Varicella-Zoster virus (VZV). We undertook a heterologous infection in vitro study to determine whether PHN-associated VZV isolates induce changes in sodium ion channel currents known to be associated with neuropathic pain. Twenty VZV isolates were studied blind from 11 PHN and 9 non-PHN subjects. Viruses were propagated in the MeWo cell line from which cell-free virus was harvested and applied to the ND7/23-Nav1.8 rat DRG x mouse neuroblastoma hybrid cell line which showed constitutive expression of the exogenous Nav 1.8, and endogenous expression of Nav 1.6 and Nav 1.7 genes all encoding sodium ion channels the dysregulation of which is associated with a range of neuropathic pain syndromes. After 72 hrs all three classes of VZV gene transcripts were detected in the absence of infectious virus. Single cell sodium ion channel recording was performed after 72 hr by voltage-clamping. PHN-associated VZV significantly increased sodium current amplitude in the cell line when compared with non-PHN VZV, wild-type (Dumas) or vaccine VZV strains ((POka, Merck and GSK). These sodium current increases were unaffected by acyclovir pre-treatment but were abolished by exposure to Tetrodotoxin (TTX) which blocks the TTX-sensitive fast Nav 1.6 and Nav 1.7 channels but not the TTX-resistant slow Nav 1.8 channel. PHN-associated VZV sodium current increases were therefore mediated in part by the Nav 1.6 and Nav 1.7 sodium ion channels. An additional observation was a modest increase in message levels of both Nav1.6 and Nav1.7 mRNA but not Nav 1.8 in PHN virally infected cells

Correlations of Behavioral Deficits with Brain Pathology Assessed through Longitudinal MRI and Histopathology in the R6/2 Mouse Model of HD

Huntington's disease (HD) is caused by the expansion of a CAG repeat in the huntingtin (HTT) gene. The R6/2 mouse model of HD expresses a mutant version of exon 1 HTT and develops motor and cognitive impairments, a widespread huntingtin (HTT) aggregate pathology and brain atrophy. Despite the vast number of studies that have been performed on this model, the association between the molecular and cellular neuropathology with brain atrophy, and with the development of behavioral phenotypes remains poorly understood. In an attempt to link these factors, we have performed longitudinal assessments of behavior (rotarod, open field, passive avoidance) and of regional brain abnormalities determined through magnetic resonance imaging (MRI) (whole brain, striatum, cortex, hippocampus, corpus callosum), as well as an end-stage histological assessment. Detailed correlative analyses of these three measures were then performed. We found a gender-dependent emergence of motor impairments that was associated with an age-related loss of regional brain volumes. MRI measurements further indicated that there was no striatal atrophy, but rather a lack of striatal growth beyond 8 weeks of age. T2 relaxivity further indicated tissue-level changes within brain regions. Despite these dramatic motor and neuroanatomical abnormalities, R6/2 mice did not exhibit neuronal loss in the striatum or motor cortex, although there was a significant increase in neuronal density due to tissue atrophy. The deposition of the mutant HTT (mHTT) protein, the hallmark of HD molecular pathology, was widely distributed throughout the brain. End-stage histopathological assessments were not found to be as robustly correlated with the longitudinal measures of brain atrophy or motor impairments. In conclusion, modeling pre-manifest and early progression of the disease in more slowly progressing animal models will be key to establishing which changes are causally related. © 2013 Rattray et al

Astrometric and Light-travel Time Orbits to Detect Low-mass Companions: A Case Study of the Eclipsing System R Canis Majoris

We discuss a method to determine orbital properties and masses of low-mass bodies orbiting eclipsing binaries. The analysis combines long-term eclipse timing modulations (light-travel time or LTT effect) with short-term, high-accuracy astrometry. As an illustration of the method, the results of a comprehensive study of Hipparcos astrometry and over a hundred years of eclipse timings of the Algol-type eclipsing binary R Canis Majoris are presented. A simultaneous solution of the astrometry and the LTTs yields an orbital period of P_12=92.8+/-1.3 yr, an LTT semiamplitude of 2574+/-57 s, an angular semi-major axis of a_12=117+/-5 mas, and values of the orbital eccentricity and inclination of e_12=0.49+/-0.05, and i_12=91.7+/-4.7 deg, respectively. Adopting the total mass of R CMa of M_12=1.24+/-0.05 Mo, the mass of the third body is M_3=0.34+/-0.02 Mo and the semi-major axis of its orbit is a_3=18.7+/-1.7 AU. From its mass, the third body is either a dM3-4 star or, more unlikely, a white dwarf. With the upcoming microarcsecond-level astrometric missions, the technique that we discuss can be successfully applied to detect and characterize long-period planetary-size objects and brown dwarfs around eclipsing binaries. Possibilities for extending the method to pulsating variables or stars with transiting planets are briefly addressed.Comment: 9 pages, 3 figures, accepted for publication in AJ (April 2002 issue