Algorithms for Visualizing Phylogenetic Networks

We study the problem of visualizing phylogenetic networks, which are extensions of the Tree of Life in biology. We use a space filling visualization method, called DAGmaps, in order to obtain clear visualizations using limited space. In this paper, we restrict our attention to galled trees and galled networks and present linear time algorithms for visualizing them as DAGmaps.Comment: Appears in the Proceedings of the 24th International Symposium on Graph Drawing and Network Visualization (GD 2016

Extensive horizontal gene transfer during Staphylococcus aureus co-colonization in vivo.

Staphylococcus aureus is a commensal and major pathogen of humans and animals. Comparative genomics of S. aureus populations suggests that colonization of different host species is associated with carriage of mobile genetic elements (MGE), particularly bacteriophages and plasmids capable of encoding virulence, resistance, and immune evasion pathways. Antimicrobial-resistant S. aureus of livestock are a potential zoonotic threat to human health if they adapt to colonize humans efficiently. We utilized the technique of experimental evolution and co-colonized gnotobiotic piglets with both human- and pig-associated variants of the lineage clonal complex 398, and investigated growth and genetic changes over 16 days using whole genome sequencing. The human isolate survived co-colonization on piglets more efficiently than in vitro. During co-colonization, transfer of MGE from the pig to the human isolate was detected within 4 h. Extensive and repeated transfer of two bacteriophages and three plasmids resulted in colonization with isolates carrying a wide variety of mobilomes. Whole genome sequencing of progeny bacteria revealed no acquisition of core genome polymorphisms, highlighting the importance of MGE. Staphylococcus aureus bacteriophage recombination and integration into novel sites was detected experimentally for the first time. During colonization, clones coexisted and diversified rather than a single variant dominating. Unexpectedly, each piglet carried unique populations of bacterial variants, suggesting limited transmission of bacteria between piglets once colonized. Our data show that horizontal gene transfer occurs at very high frequency in vivo and significantly higher than that detectable in vitro

BVRI Surface Photometry of Isolated Spiral Galaxies

A release of multicolor broad band (BVRI) photometry for a subsample of 44 isolated spirals drawn from the Catalogue of Isolated Galaxies (CIG) is presented. Total magnitudes and colors at various circular apertures, as well as some global structural/morphological parameters are estimated. Morphology is reevaluated through optical and sharp/filtered R band images, (B-I) color index maps, and archive near-IR JHK images from the Two-Micron Survey. The CAS structural parameters (Concentration, Asymmetry, and Clumpiness) were calculated from the images in each one of the bands. The fraction of galaxies with well identified optical/near-IR bars (SB) is 63%, while a 17% more shows evidence of weak or suspected bars (SAB). The sample average value of the maximum bar ellipticity is 0.4. Half of the galaxies in the sample shows rings. We identify two candidates for isolated galaxies with disturbed morphology. The structural CAS parameters change with the observed band, and the tendencies they follow with the morphological type and global color are more evident in the redder bands. In any band, the major difference between our isolated spirals and a sample of interacting spirals is revealed in the A-S plane. A deep and uniformly observed sample of isolated galaxies is intended for various purposes including (i) comparative studies of environmental effects, (ii) confronting model predictions of galaxy evolution and (iii) evaluating the change of galaxy properties with redshift.Comment: 44 pages, 9 figures and 7 tables included. To appear in The Astronomical Journal. For the 43 appendix figures 4.1-4.43 see http://www.astroscu.unam.mx/~avila/Figs4.1_4.43.tar.gz (7.2 Mb tar.gz file

Regenerating Rat Liver: Correlations Between Estrogen Receptor Localization and Deoxyribonucleic Acid Synthesis

Estrogen receptor activity was quantitated in the cytosol and nucleus of normal rat liver and in regenerating rat liver at several time intervals after 75% hepatectomy. Cytosolic estradiol binding in regenerating liver decreases at 12, 24, and 48 h after hepatectomy and at 48 h is 30% of that in normal rat liver. Nuclear estrogen binding 48 h after surgery is elevated fivefold over normal values. No alterations in affinity of the receptor for estrogen have been observed. Specificity studies indicate that the estrogen receptors from both normal and regenerating liver were similar and are highly specific for estrogens. These changes in cellular distribution of receptors parallel increases in nuclear deoxyribonucleic acid synthesis and mitotic indices in the liver. © 1984, American Gastroenterological Association. All rights reserved

Further steps of hepatic stimulatory substance purification

The hepatic stimulatory substance (HSS) extracted from weanling rat livers was purified 381,000-fold using chromatographic techniques including nondissociating polyacrylamide gel electrophoresis (nondenaturing PAGE). The activity of this highly purified HSS, named Acr-F4, was assessed in two in vivo models. In 40% hepatectomized rats, it produced a fivefold increase in the proliferative rate normally seen following this partial hepatectomy. In Eck fistula dogs, the level of base increase in hepatocyte renewal was amplified threefold by an infusion of Acr-F4 (50 ng/kg/day). Acr-F4 had no influence on the regenerative response of the kidney following a unilateral nephrectomy or of the bowel following a 40% resection of the small bowel. On the basis of these findings, it can be concluded that HSS (Acr-F4) has a high biological activity and is organ specific. © 1991 Plenum Publishing Corporation