Increasing biological complexity is positively correlated with the relative genome-wide expansion of non-protein-coding DNA sequences

Background: Prior to the current genomic era it was suggested that the number of protein-coding genes that an organism made use of was a valid measure of its complexity. It is now clear, however, that major incongruities exist and that there is only a weak relationship between biological complexity and the number of protein coding genes. For example, using the protein-coding gene number as a basis for evaluating biological complexity would make urochordates and insects less complex than nematodes, and humans less complex than rice. Results: We analyzed the ratio of noncoding to total genomic DNA (ncDNA/tgDNA) for 85 sequenced species and found that this ratio correlates well with increasing biological complexity. The ncDNA/tgDNA ratio is generally contained within the bandwidth of 0.05-0.24 for prokaryotes, but rises to 0.26-0.52 in unicellular eukaryotes, and to 0.62-0.985 for developmentally complex multicellular organisms. Significantly, prokaryotic species display a non-uniform species distribution approaching the mean of 0.1177 ncDNA/tgDNA (p=1.58 x 10^-13), and a nonlinear ncDNA/tgDNA relationship to genome size (r=0.15). Importantly, the ncDNA/tgDNA ratio corrects for ploidy, and is not substantially affected by variable loads of repetitive sequences. Conclusions: We suggest that the observed noncoding DNA increases and compositional patterns are primarily a function of increased information content. It is therefore possible that introns, intergenic sequences, repeat elements, and genomic DNA previously regarded as genetically inert may be far more important to the evolution and functional repertoire of complex organisms than has been previously appreciated.Comment: 25 pages, 2 figures, 1 tabl

Structure of the Draco Dwarf Spheroidal Galaxy

This article studies the structure of the Draco dwarf spheroidal galaxy with an emphasis on the question of whether the spatial distribution of its stars has been affected by the tidal interaction with the Milky Way, using R- and V-band CCD photometry for eleven fields. The article reports coordinates for the center, a position angle of the major axis, and the ellipticity. It also reports the results of searches for asymmetries in the structure of Draco. These results, and searches for a ``break'' in the radial profile and for the presence of principal sequences of Draco in a color-magnitude diagram for regions more than 50 arcmin from the center, yield no evidence that tidal forces from the Milky Way have affected the structure of Draco.Comment: 25 pages, 11 figures, 3 tables. Accepted for publication in A

Ethical complexities of screening for depression and intimate partner violence (IPV) in intervention studies

<p>Abstract</p> <p>Background</p> <p>Intervention studies for depression and intimate partner violence (IPV) commonly incorporate screening to identify eligible participants. The challenge is that current ethical evaluation is largely informed by the four principle approach applying principles of beneficence, non-maleficence, and respect for justice and autonomy. We examine three intervention studies for IPV, postnatal depression (PND) and depression that used screening from the perspective of principlism, followed by the perspective of a narrative and relational approach. We suggest that a narrative and relational approach to ethics brings to light concerns that principlism can overlook.</p> <p>Discussion</p> <p>The justification most commonly used to incorporate screening is that the potential benefits of identifying intervention efficacy balance the risk of individual harm. However, considerable risks do exist. The discovery of new information may result in further depression or worries, people might feel burdened, open to further risk, unsure of whether to disclose information to family members and disappointed if they are allocated to a control group. This raises questions about study design and whether the principle of equipoise remains an adequate justification in studies with vulnerable groups. In addition, autonomy is said to be respected because participants give informed consent to participate. However, the context of where recruitment is undertaken has been shown to influence how people make decisions.</p> <p>Summary</p> <p>The four principles have been subjected to criticisms in recent years but they remain prominent in public health and medical research. We provide a set of simple, interrogative questions that are narrative and relationally driven which may assist to further evaluate the potential impacts of using screening to identify eligible research participants in intervention studies. A narrative and relational based approach requires seeing people as situated within their social and cultural contexts, and as existing within relationships that are likely to be affected by the results of screening information.</p

The Age of the Inner Halo Globular Cluster NGC 6652

HST (V,I) photometry has been obtained for the inner halo globular cluster NGC 6652. The photometry reaches approximately 4 mag below the turn-off and includes a well populated horizontal branch. This cluster is located close to the Galactic center at a galactocentric distance of approximately 2.0 kpc with a reddening of E(V-I) = 0.15 +/- 0.02 and has a metallicity of [Fe/H] approximately -0.85. Based upon Delta(V) between the point on the sub-giant branch which is 0.05 mag redder than the turn-off and the horizontal branch, NGC 6652 is 11.7 +/- 1.6 Gyr old. Using this same Delta(V), precise differential ages for 47 Tuc (a thick disk globular), M107 and NGC 1851 (both halo clusters) were obtained. NGC 6652 appears to be the same age as 47 Tuc and NGC 1851 (within +/- 1.2 Gyr), while there is a slight suggestion that M107 is older than NGC 6652 by 2.3 +/- 1.5 Gyr. As this is a less than 2-sigma result, this issue needs to be investigated further before a definitive statement regarding the relative age of M107 and NGC 6652 may be made.Comment: accepted for publication in the Astronomical Journal, December 2000 issu

Transcriptome-wide identification of A > I RNA editing sites by inosine specific cleavage

Adenosine to inosine (A > I) RNA editing, which is catalyzed by the ADAR family of proteins, is one of the fundamental mechanisms by which transcriptomic diversity is generated. Indeed, a number of genome-wide analyses have shown that A > I editing is not limited to a few mRNAs, as originally thought, but occurs widely across the transcriptome, especially in the brain. Importantly, there is increasing evidence that A > I editing is essential for animal development and nervous system function. To more efficiently characterize the complete catalog of ADAR events in the mammalian transcriptome we developed a high-throughput protocol to identify A > I editing sites, which exploits the capacity of glyoxal to protect guanosine, but not inosine, from RNAse T1 treatment, thus facilitating extraction of RNA fragments with inosine bases at their termini for high-throughput sequencing. Using this method we identified 665 editing sites in mouse brain RNA, including most known sites and suite of novel sites that include nonsynonymous changes to protein-coding genes, hyperediting of genes known to regulate p53, and alterations to non-protein-coding RNAs. This method is applicable to any biological system for the de novo discovery of A > I editing sites, and avoids the complicated informatic and practical issues associated with editing site identification using traditional RNA sequencing data. This approach has the potential to substantially increase our understanding of the extent and function of RNA editing, and thereby to shed light on the role of transcriptional plasticity in evolution, development, and cognition

Classification of All Poisson-Lie Structures on an Infinite-Dimensional Jet Group

A local classification of all Poisson-Lie structures on an infinite-dimensional group $G_{\infty}$ of formal power series is given. All Lie bialgebra structures on the Lie algebra {\Cal G}_{\infty} of $G_{\infty}$ are also classified.Comment: 11 pages, AmSTeX fil

The relationship between transcription initiation RNAs and CCCTC-binding factor (CTCF) localization

Background: Transcription initiation RNAs (tiRNAs) are nuclear localized 18 nucleotide RNAs derived from sequences immediately downstream of RNA polymerase II (RNAPII) transcription start sites. Previous reports have shown that tiRNAs are intimately correlated with gene expression, RNA polymerase II binding and behaviors, and epigenetic marks associated with transcription initiation, but not elongation. Results: In the present work, we show that tiRNAs are commonly found at genomic CCCTC-binding factor (CTCF) binding sites in human and mouse, and that CTCF sites that colocalize with RNAPII are highly enriched for tiRNAs. To directly investigate the relationship between tiRNAs and CTCF we examined tiRNAs originating near the intronic CTCF binding site in the human tumor suppressor gene, p21 (cyclin-dependent kinase inhibitor 1A gene, also known as CDKN1A). Inhibition of CTCF-proximal tiRNAs resulted in increased CTCF localization and increased p21 expression, while overexpression of CTCF-proximal tiRNA mimics decreased CTCF localization and p21 expression. We also found that tiRNA-regulated CTCF binding influences the levels of trimethylated H3K27 at the alternate upstream p21 promoter, and affects the levels of alternate p21 (p21) transcripts. Extending these studies to another randomly selected locus with conserved CTCF binding we found that depletion of tiRNA alters nucleosome density proximal to sites of tiRNA biogenesis. Conclusions: Taken together, these data suggest that tiRNAs modulate local epigenetic structure, which in turn regulates CTCF localization

The Dwarf Spheroidal Companions to M31: Variable Stars in Andromeda VI

We have surveyed Andromeda VI, a dwarf spheroidal galaxy companion to M31, for variable stars using F450W and F555W observations obtained with the Hubble Space Telescope. A total of 118 variables were found, with 111 being RR Lyrae, 6 anomalous Cepheids, and 1 variable we were unable to classify. We find that the Andromeda VI anomalous Cepheids have properties consistent with those of anomalous Cepheids in other dwarf spheroidal galaxies. We revise the existing period-luminosity relations for these variables. Further, using these and other available data, we show that there is no clear difference between fundamental and first-overtone anomalous Cepheids in a period-amplitude diagram at shorter periods, unlike the RR Lyrae. For the Andromeda VI RR Lyrae, we find that they lie close to the Oosterhoff type I Galactic globular clusters in the period-amplitude diagram, although the mean period of the RRab stars, = 0.588 d, is slightly longer than the typical Oosterhoff type I cluster. The mean V magnitude of the RR Lyrae in Andromeda VI is 25.29+/-0.03, resulting in a distance 815+/-25 kpc on the Lee, Demarque, & Zinn distance scale. This is consistent with the distance derived from the I magnitude of the tip of the red giant branch. Similarly, the properties of the RR Lyrae indicate a mean abundance for Andromeda VI which is consistent with that derived from the mean red giant branch color.Comment: 23 pages, including 13 figures and 6 tables, emulateapj5/apjfonts style. Accepted by the Astronomical Journal. We recommend the interested reader to download the preprint with full-resolution figures, which can be found at http://www.noao.edu/noao/staff/pritzl/M31dwarfs.htm

A Survey for Low-Surface-Brightness Galaxies Around M31. I. The Newly Discovered Dwarf Andromeda V

We present images and a color-magnitude diagram for And V, a new dwarf spheroidal companion to M31 that was found using a digital filtering technique applied to 1550 square degrees of the second Palomar Sky Survey. And V resolves into stars easily in follow-up 4-m V- and I-band images, from which we deduce a distance of 810 +/- 45 kpc using the tip of the red giant branch method. Within the uncertainties, this distance is identical to the Population II distances for M31 and, combined with a projected separation of 112 kpc, provides strong support for a physical association between the two galaxies. There is no emission from And V detected in H alpha, 1.4 GHz radio continuum, or IRAS bandpasses, and there is no young population seen in the color-magnitude diagram that might suggest that And V is an irregular. Thus, the classification as a new dwarf spheroidal member of the Local Group seems secure. With an extinction-corrected central surface brightness of 25.2 V mag per square arcsec, a mean metal abundance of [Fe/H] approximately -1.5, and no evidence for upper AGB stars, And V resembles And I & III.Comment: Accepted for publication in The Astronomical Journal, November 1998 issue; 4 embedded PostScript figures, 4 JPEG figures; see http://aloe.tuc.noao.edu/jacoby/dwarfs.html for a complete full-resolution PostScript versio

Controlling Silver Nanoparticle Size and Morphology with Photostimulated Synthesis

Photo-induced synthesis and control over the size and shape of colloidal silver nanoparticles is investigated in contrast to photo-stimulated aggregation of small nanoparticles into large fractal-type structures. The feasibility of light-driven nanoengineering which enables manipulation of the sizes and shapes of the isolated nanoparticles is studied by varying the amount and type of the stabilizing agent and the type of optical irradiation.Comment: 10 pages, 7 figures, 11 image