Interspecies hybridization on DNA resequencing microarrays: efficiency of sequence recovery and accuracy of SNP detection in human, ape, and codfish mitochondrial DNA genomes sequenced on a human-specific MitoChip

Background: Iterative DNA "resequencing" on oligonucleotide microarrays offers a high-throughput method to measure intraspecific biodiversity, one that is especially suited to SNP-dense gene regions such as vertebrate mitochondrial (mtDNA) genomes. However, costs of single-species design and microarray fabrication are prohibitive. A cost-effective, multi-species strategy is to hybridize experimental DNAs from diverse species to a common microarray that is tiled with oligonucleotide sets from multiple, homologous reference genomes. Such a strategy requires that cross-hybridization between the experimental DNAs and reference oligos from the different species not interfere with the accurate recovery of species-specific data. To determine the pattern and limits of such interspecific hybridization, we compared the efficiency of sequence recovery and accuracy of SNP identification by a 15,452-base human-specific microarray challenged with human, chimpanzee, gorilla, and codfish mtDNA genomes. Results: In the human genome, 99.67% of the sequence was recovered with 100.0% accuracy. Accuracy of SNP identification declines log-linearly with sequence divergence from the reference, from 0.067 to 0.247 errors per SNP in the chimpanzee and gorilla genomes, respectively. Efficiency of sequence recovery declines with the increase of the number of interspecific SNPs in the 25b interval tiled by the reference oligonucleotides. In the gorilla genome, which differs from the human reference by 10%, and in which 46% of these 25b regions contain 3 or more SNP differences from the reference, only 88% of the sequence is recoverable. In the codfish genome, which differs from the reference by > 30%, less than 4% of the sequence is recoverable, in short islands ≥ 12b that are conserved between primates and fish. Conclusion: Experimental DNAs bind inefficiently to homologous reference oligonucleotide sets on a resequencing microarray when their sequences differ by more than a few percent. The data suggest that interspecific cross-hybridization will not interfere with the accurate recovery of species-specific data from multispecies microarrays, provided that the species' DNA sequences differ by > 20% (mean of 5b differences per 25b oligo). Recovery of DNA sequence data from multiple, distantly-related species on a single multiplex gene chip should be a practical, highly-parallel method for investigating genomic biodiversity

A Floristic Survey of Selected Sites in the Loup River Valley, Nance County, Nebraska

The Loup River Valley of Nebraska contains natural, undisturbed wet meadows with significant plant diversity. Even though these sites are infrequent and are often intermixed with heavily grazed pastures or cultivated fields, they support numerous plant and animal species that do not occur elsewhere. We surveyed three study sites (an ungrazed wet meadow; a grazed wet meadow; and a riparian area) that totaled approximately 68.8 ha during the 2010 and 2011 growing seasons. We compiled an annotated vascular plants checklist for the study area that included 244 plant species of which about 49% (119) were new county records. The mean coefficient of conservatism (Cm) values for the ungrazed meadow, the grazed meadow, and the riparian site were 3.54, 3.07, and 3.35 respectively. The floristic quality indices (FQI) were 37.96 for the hay meadow, 28.14 for the grazed meadow, and 31.07 for the riparian site. Jaccard’s Index of Similarity (31.4%) indicated that the grazed and ungrazed meadows had a high degree of community similarity with each containing ~ 80% native species. Our study substantiates the significance of Nance County to the species richness and flora of Nebraska and the Great Plains. Future research and reconnaissance should include the identification and study of additional natural meadows in the lower Loup River Valley

Ariel - Volume 2 Number 2

Editors Delvyn C. Case, Jr. Paul M. Fernhoff News Editors Richard Bonanno Daniel B. Gould Ronald A. Hoffman Lay-Out Editor Carol Dolinskas Sports Editor James J. Nocon Contributing Editors MichaeI J. Blecker Lin Sey Edwards Jack Guralnik W. Cherry Light Features Editor Donald A. Bergman Stephen P. Flynn Business Manager Nick Grego Public Relations Robin A. Edward

How to Block Cartel Formation and Price-Fixing

Abstract written by the AEI-Brookings Joint Center: Allowing foreign buyers of goods produced by international cartels to pursue civil antitrust damages in U.S. courts would better deter cartel formation and price-fixing than do sanctions currently imposed by global criminal and civil justice systems.Technology and Industry, Regulatory Reform, Other Topics

B meson form factors from HQET simulations

We use simulations of heavy quark effective field theory to calculate the Isgur-Wise function, and we demonstrate the feasibility of calculating the matrix element for the B \to \pi + \leptons decay in the lattice heavy quark effective theory (HQET).Comment: 3 pages, 2 figures, talk presented at the lattice 97 conferenc

Toward a comprehensive system for constructing compartmental epidemic models

Compartmental models are valuable tools for investigating infectious diseases. Researchers building such models typically begin with a simple structure where compartments correspond to individuals with different epidemiological statuses, e.g., the classic SIR model which splits the population into susceptible, infected, and recovered compartments. However, as more information about a specific pathogen is discovered, or as a means to investigate the effects of heterogeneities, it becomes useful to stratify models further -- for example by age, geographic location, or pathogen strain. The operation of constructing stratified compartmental models from a pair of simpler models resembles the Cartesian product used in graph theory, but several key differences complicate matters. In this article we give explicit mathematical definitions for several so-called ``model products'' and provide examples where each is suitable. We also provide examples of model stratification where no existing model product will generate the desired result

Heavy-light decay constants---MILC results with the Wilson action

We present the current status of our ongoing calculations of pseudoscalar meson decay constants for mesons that contain one light and one heavy quark (f_B, f_{B_s}, f_D, f_{D_s}). We are currently generating new gauge configurations that include dynamical quarks and calculating the decay constants. In addition, we have several new results for the static approximation. Those results, as well as several refinements to the analysis, are new since Lattice '96. Our current (still preliminary) value for f_B is 156 +- 11 +- 30 +- 14 MeV, where the first error is from statistical and fitting errors, the second error is an estimate of other systematic errors within the quenched approximation and the third error is an estimate of the quenching error. For the ratio f_{B_s}/f_B, we get 1.11 +- 0.02 +- 0.03 +- 0.07.Comment: 8 pages, 9 figures, LaTeX, uses espcrs2, epsf, Invited talk presented by S. Gottlieb at Lattice QCD on Parallel Computers, University of Tsukuba, March, 1997, to appear in the proceeding

Extrasolar Planet Transits Observed at Kitt Peak National Observatory

We obtained J-, H- and JH-band photometry of known extrasolar planet transiting systems at the 2.1-m Kitt Peak National Observatory Telescope using the FLAMINGOS infrared camera between October 2008 and October 2011. From the derived lightcurves we have extracted the mid-transit times, transit depths and transit durations for these events. The precise mid-transit times obtained help improve the orbital periods and also constrain transit-time variations of the systems. For most cases the published system parameters successfully accounted for our observed lightcurves, but in some instances we derive improved planetary radii and orbital periods. We complemented our 2.1-m infrared observations using CCD z'-band and B-band photometry (plus two Hydrogen Alpha filter observations) obtained with the Kitt Peak Visitor's Center telescope, and with four H-band transits observed in October 2007 with the NSO's 1.6-m McMath-Pierce Solar Telescope. The principal highlights of our results are: 1) our ensemble of J-band planetary radii agree with optical radii, with the best-fit relation being: (Rp/R*)J = 0.0017 + 0.979 (Rp/R*)optical, 2) We observe star spot crossings during the transit of WASP-11/HAT-P-10, 3) we detect star spot crossings by HAT-P-11b (Kepler-3b), thus confirming that the magnetic evolution of the stellar active regions can be monitored even after the Kepler mission has ended, and 4) we confirm a grazing transit for HAT-P-27/WASP-40. In total we present 57 individual transits of 32 known exoplanet systems.Comment: 33 pages, 6 figures, accepted in Publications of the Astronomical Society of the Pacifi

A Fluorescent Aerogel for Capture and Identification of Interplanetary and Interstellar Dust

Contemporary interstellar dust has never been analyzed in the laboratory, despite its obvious astronomical importance and its potential as a probe of stellar nucleosynthesis and galactic chemical evolution. Here we report the discovery of a novel fluorescent aerogel which is capable of capturing hypervelocity dust grains and passively recording their kinetic energies. An array of these "calorimetric" aerogel collectors in low earth orbit would lead to the capture and identification of large numbers of interstellar dust grains.Comment: 13 pages, 4 figures, to appear in The Astrophysical Journa