Recovery of Small DNA Fragments from Serum Using Compaction Precipitation

Background: While most nucleic acids are intracellular, trace amounts of deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), including micro RNAs, can also be found in peripheral blood. Many studies have suggested the potential utility of these circulating nucleic acids in prenatal diagnosis, early cancer detection, and the diagnosis of infectious diseases. However, DNA circulating in blood is usually present at very low concentrations (ng/ml), and is in the form of relatively small fragments (,1,000 bp), making its isolation challenging. Methods: Here we report an improved method for the isolation of small DNA fragments from serum using selective precipitation by quaternary ammonium compaction agents. A 151 bp fragment of double-stranded DNA from the Escherichia coli bacteriophage lambda served as the model DNA in our experiments. DNA was serially diluted in serum until undetectable by conventional polymerase chain reaction (PCR), before being enriched by compaction precipitation. Results: Starting with concentrations two to three orders of magnitude lower than the PCR-detectable level (0.01 ng/ml), we were able to enrich the DNA to a detectable level using a novel compaction precipitation protocol. The isolated DNA product after compaction precipitation was largely free of serum contaminants and was suitable for downstream applications. Conclusions: Using compaction precipitation, we were able to isolate and concentrate small DNA from serum, and increase the sensitivity of detection by more than four orders of magnitude. We were able to recover and detect very low levels (0.01 ng/ml) of a small DNA fragment in serum. In addition to being very sensitive, the method is fast, simple, inexpensive, and avoids the use of toxic chemicals

A Note on Encodings of Phylogenetic Networks of Bounded Level

Driven by the need for better models that allow one to shed light into the question how life's diversity has evolved, phylogenetic networks have now joined phylogenetic trees in the center of phylogenetics research. Like phylogenetic trees, such networks canonically induce collections of phylogenetic trees, clusters, and triplets, respectively. Thus it is not surprising that many network approaches aim to reconstruct a phylogenetic network from such collections. Related to the well-studied perfect phylogeny problem, the following question is of fundamental importance in this context: When does one of the above collections encode (i.e. uniquely describe) the network that induces it? In this note, we present a complete answer to this question for the special case of a level-1 (phylogenetic) network by characterizing those level-1 networks for which an encoding in terms of one (or equivalently all) of the above collections exists. Given that this type of network forms the first layer of the rich hierarchy of level-k networks, k a non-negative integer, it is natural to wonder whether our arguments could be extended to members of that hierarchy for higher values for k. By giving examples, we show that this is not the case

Perinatal outcomes by mode of assisted conception and sub-fertility in an Australian data linkage cohort

BACKGROUND: Fertility treatment is associated with increased risk of major birth defects, which varies between in vitro fertilisation (IVF) and intracytoplasmic sperm injection (ICSI), and is significantly reduced by embryo freezing. We therefore examined a range of additional perinatal outcomes for these exposures. METHODS: All patients in South Australia receiving assisted conception between Jan 1986-Dec 2002 were linked to the state-wide perinatal collection (all births/stillbirths ≥20 weeks gestation or 400 g birth weight, n = 306 995). We examined stillbirth, mean birth weight, low birth weight (90th percentile), preterm birth (32-<37 weeks, <32 weeks gestation), postterm birth (≥41 weeks gestation), Apgar <7 at 5 minutes and neonatal death. RESULTS: Relative to spontaneous conceptions, singletons from assisted conception were more likely to be stillborn (OR = 1.82, 95% Confidence Interval (CI) 1.34-2.48), while survivors as a group were comprehensively disadvantaged at birth, including lower birth weight (-109 g, CI -129--89), very low birth weight (OR = 2.74, CI 2.19-3.43), very preterm birth (OR = 2.30, CI 1.82-2.90) and neonatal death (OR = 2.04, CI 1.27-3.26). Outcomes varied by type of assisted conception. Very low and low birth weight, very preterm and preterm birth, and neonatal death were markedly more common in singleton births from IVF and to a lesser degree, in births from ICSI. Using frozen-embryos eliminated all significant adverse outcomes associated with ICSI but not with IVF. However, frozen-embryo cycles were also associated with increased risk of macrosomia for IVF and ICSI singletons (OR = 1.36, CI 1.02-1.82; OR = 1.55, CI 1.05-2.28). Infertility status without treatment was also associated with adverse outcomes. CONCLUSIONS: Births after assisted conception show an extensive range of compromised outcomes that vary by treatment modality, that are substantially reduced after embryo freezing, but which co-occur with an increased risk of macrosomia.Jennifer L. Marino, Vivienne M. Moore, Kristyn J. Willson, Alice Rumbold, Melissa J. Whitrow, Lynne C. Giles, Michael J. Davie

Illumination in symbiotic binary stars: Non-LTE photoionization models. II. Wind case

We describe a non-LTE photoionization code to calculate the wind structure and emergent spectrum of a red giant wind illuminated by the hot component of a symbiotic binary system. We consider spherically symmetric winds with several different velocity and temperature laws and derive predicted line fluxes as a function of the red giant mass loss rate, \mdot. Our models generally match observations of the symbiotic stars EG And and AG Peg for \mdot about 10^{-8} \msunyr to 10^{-7} \msunyr. The optically thick cross- section of the red giant wind as viewed from the hot component is a crucial parameter in these models. Winds with cross-sections of 2--3 red giant radii reproduce the observed fluxes, because the wind density is then high, about 10^9 cm^{-3}. Our models favor winds with acceleration regions that either lie far from the red giant photosphere or extend for 2--3 red giant radii.Comment: 51 pages, LaTeX including three tables, requires 15 Encapsulated Postscript figures, to appear in Ap

Noise storm continua: power estimates for electron acceleration

We use a generic stochastic acceleration formalism to examine the power $L_{\rm in}$ (${\rm erg s^{-1}}$) input to nonthermal electrons that cause noise storm continuum emission. The analytical approach includes the derivation of the Green's function for a general second-order Fermi process, and its application to obtain the particular solution for the nonthermal electron distribution resulting from the acceleration of a Maxwellian source in the corona. We compare $L_{\rm in}$ with the power $L_{\rm out}$ observed in noise storm radiation. Using typical values for the various parameters, we find that $L_{\rm in} \sim 10^{23-26}$ ${\rm erg s^{-1}}$, yielding an efficiency estimate $\eta \equiv L_{\rm out}/L_{\rm in}$ in the range 10^{-10} \lsim \eta \lsim 10^{-6} for this nonthermal acceleration/radiation process. These results reflect the efficiency of the overall process, starting from electron acceleration and culminating in the observed noise storm emission.Comment: Accepted for publication in Solar Physic

A Study of an Outburst in the Classical Symbiotic Star Z And in a Colliding-Wind Model

Two-dimensional gas-dynamical modeling of the mass-flow structure is used to study the outburst development in the classical symbiotic star Z And. The stage-by-stage rise of the light during the outburst can be explained in the framework of the colliding winds model. We suggest a scenario for the development of the outburst and study the possible influence of the changes of the flow structure on the light of the system. The model variations of the luminosity due to the formation of a system of shocks are in good agreement with the observed light variations

Flotation Immunoassay: Masking the Signal from Free Reporters in Sandwich Immunoassays

In this work, we demonstrate that signal-masking reagents together with appropriate capture antibody carriers can eliminate the washing steps in sandwich immunoassays. A flotation immunoassay (FI) platform was developed with horseradish peroxidase chemiluminescence as the reporter system, the dye Brilliant Blue FCF as the signal-masking reagent, and buoyant silica micro-bubbles as the capture antibody carriers. Only reporters captured on micro-bubbles float above the dye and become visible in an analyte-dependent manner. These FIs are capable of detecting proteins down to attomole levels and as few as 106 virus particles. This signal-masking strategy represents a novel approach to simple, sensitive and quantitative immunoassays in both laboratory and point-of-care settings

Cosmic Ray Electrons in Groups and Clusters of Galaxies: Primary and Secondary Populations from a Numerical Cosmological Simulation

We study the generation and distribution of high energy electrons in cosmic environment and their observational consequences by carrying out the first cosmological simulation that includes directly cosmic ray (CR) particles. Starting from cosmological initial conditions we follow the evolution of primary and secondary electrons (CRE), CR ions (CRI) and a passive magnetic field. CRIs and primary CREs are injected and accelerated at large scale structure shocks. Secondary CREs are continuously generated through inelastic p-p collisions. We include spatial transport, adiabatic expansion/compression, Coulomb collisions, bremsstrahlung, synchrotron (SE)and inverse Compton (IC) emission. We find that, from the perspective of cosmic shock energy and acceleration efficiency, the few detections of hard X-ray radiation excess could be explained in the framework of IC emission of primary CREs in clusters undergoing high accretion/merger phase. Instead, IC emission from both primary and secondary CREs accounts at most for a small fraction of the radiation excesses detected in the extreme-UV (except for the Coma cluster as reported by Bowyer et al.1999). Next, we calculate the SE after normalizing the magnetic field so that for a Coma-like cluster ^1/2~3 \muG. Our results indicate that the SE from secondary CREs reproduces several general properties of radio halos, including the recently found P_1.4GHz vs T relation, the morphology and polarization of the emitting region and, to some extent, the spectral index. Moreover, SE from primary CREs turns out sufficient to power extended regions resembling radio relics observed at the outskirts of clusters. Again we find striking resemblance between morphology, polarization and spectral index of our synthetic maps and those reported in the literature.Comment: emulateapj, 27 pages, 10 figures, 5 tables; ApJ in pres

Azimuthal anisotropy and correlations in the hard scattering regime at RHIC

Azimuthal anisotropy ($v_2$) and two-particle angular correlations of high $p_T$ charged hadrons have been measured in Au+Au collisions at $\sqrt{s_{NN}}$=130 GeV for transverse momenta up to 6 GeV/c, where hard processes are expected to contribute significantly. The two-particle angular correlations exhibit elliptic flow and a structure suggestive of fragmentation of high $p_T$ partons. The monotonic rise of $v_2(p_T)$ for $p_T<2$ GeV/c is consistent with collective hydrodynamical flow calculations. At \pT>3 GeV/c a saturation of $v_2$ is observed which persists up to $p_T=6$ GeV/c.Comment: As publishe

Azimuthal anisotropy of K0S and Lambda + Lambda -bar production at midrapidity from Au+Au collisions at sqrt[sNN]=130 GeV

We report STAR results on the azimuthal anisotropy parameter v2 for strange particles K0S, Lambda , and Lambda -bar at midrapidity in Au+Au collisions at sqrt[sNN]=130 GeV at the Relativistic Heavy Ion Collider. The value of v2 as a function of transverse momentum, pt, of the produced particle and collision centrality is presented for both particles up to pt~3.0 GeV/c. A strong pt dependence in v2 is observed up to 2.0 GeV/c. The v2 measurement is compared with hydrodynamic model calculations. The physics implications of the pt integrated v2 magnitude as a function of particle mass are also discussed.Alle Autoren: C. Adler, Z. Ahammed, C. Allgower, J. Amonett, B. D. Anderson, M. Anderson, G. S. Averichev, J. Balewski, O. Barannikova, L. S. Barnby, J. Baudot, S. Bekele, V. V. Belaga, R. Bellwied, J. Berger, H. Bichsel, A. Billmeier, L. C. Bland, C. O. Blyth, B. E. Bonner, A. Boucham, A. Brandin, A. Bravar, R. V. Cadman, H. Caines, M. Calderón de la Barca Sánchez, A. Cardenas, J. Carroll, J. Castillo, M. Castro, D. Cebra, P. Chaloupka, S. Chattopadhyay, Y. Chen, S. P. Chernenko, M. Cherney, A. Chikanian, B. Choi, W. Christie, J. P. Coffin, T. M. Cormier, J. G. Cramer, H. J. Crawford, W. S. Deng, A. A. Derevschikov, L. Didenko, T. Dietel, J. E. Draper, V. B. Dunin, J. C. Dunlop, V. Eckardt, L. G. Efimov, V. Emelianov, J. Engelage, G. Eppley, B. Erazmus, P. Fachini, V. Faine, K. Filimonov, E. Finch, Y. Fisyak, D. Flierl, K. J. Foley, J. Fu, C. A. Gagliardi, N. Gagunashvili, J. Gans, L. Gaudichet, M. Germain, F. Geurts, V. Ghazikhanian, O. Grachov, V. Grigoriev, M. Guedon, E. Gushin, T. J. Hallman, D. Hardtke, J. W. Harris, T. W. Henry, S. Heppelmann, T. Herston, B. Hippolyte, A. Hirsch, E. Hjort, G. W. Hoffmann, M. Horsley, H. Z. Huang, T. J. Humanic, G. Igo, A. Ishihara, Yu. I. Ivanshin, P. Jacobs, W. W. Jacobs, M. Janik, I. Johnson, P. G. Jones, E. G. Judd, M. Kaneta, M. Kaplan, D. Keane, J. Kiryluk, A. Kisiel, J. Klay, S. R. Klein, A. Klyachko, A. S. Konstantinov, M. Kopytine, L. Kotchenda, A. D. Kovalenko, M. Kramer, P. Kravtsov, K. Krueger, C. Kuhn, A. I. Kulikov, G. J. Kunde, C. L. Kunz, R. Kh. Kutuev, A. A. Kuznetsov, L. Lakehal-Ayat, M. A. C. Lamont, J. M. Landgraf, S. Lange, C. P. Lansdell, B. Lasiuk, F. Laue, A. Lebedev, R. Lednický, V. M. Leontiev, M. J. LeVine, Q. Li, S. J. Lindenbaum, M. A. Lisa, F. Liu, L. Liu, Z. Liu, Q. J. Liu, T. Ljubicic, W. J. Llope, G. LoCurto, H. Long, R. S. Longacre, M. Lopez-Noriega, W. A. Love, T. Ludlam, D. Lynn, J. Ma, R. Majka, S. Margetis, C. Markert, L. Martin, J. Marx, H. S. Matis, Yu. A. Matulenko, T. S. McShane, F. Meissner, Yu. Melnick, A. Meschanin, M. Messer, M. L. Miller, Z. Milosevich, N. G. Minaev, J. Mitchell, V. A. Moiseenko, C. F. Moore, V. Morozov, M. M. de Moura, M. G. Munhoz, J. M. Nelson, P. Nevski, V. A. Nikitin, L. V. Nogach, B. Norman, S. B. Nurushev, G. Odyniec, A. Ogawa, V. Okorokov, M. Oldenburg, D. Olson, G. Paic, S. U. Pandey, Y. Panebratsev, S. Y. Panitkin, A. I. Pavlinov, T. Pawlak, V. Perevoztchikov, W. Peryt, V. A Petrov, M. Planinic, J. Pluta, N. Porile, J. Porter, A. M. Poskanzer, E. Potrebenikova, D. Prindle, C. Pruneau, J. Putschke, G. Rai, G. Rakness, O. Ravel, R. L. Ray, S. V. Razin, D. Reichhold, J. G. Reid, F. Retiere, A. Ridiger, H. G. Ritter, J. B. Roberts, O. V. Rogachevski, J. L. Romero, A. Rose, C. Roy, V. Rykov, I. Sakrejda, S. Salur, J. Sandweiss, A. C. Saulys, I. Savin, J. Schambach, R. P. Scharenberg, N. Schmitz, L. S. Schroeder, A. Schüttauf, K. Schweda, J. Seger, D. Seliverstov, P. Seyboth, E. Shahaliev, K. E. Shestermanov, S. S. Shimanskii, V. S. Shvetcov, G. Skoro, N. Smirnov, R. Snellings, P. Sorensen, J. Sowinski, H. M. Spinka, B. Srivastava, E. J. Stephenson, R. Stock, A. Stolpovsky, M. Strikhanov, B. Stringfellow, C. Struck, A. A. P. Suaide, E. Sugarbaker, C. Suire, M. Šumbera, B. Surrow, T. J. M. Symons, A. Szanto de Toledo, P. Szarwas, A. Tai, J. Takahashi, A. H. Tang, J. H. Thomas, M. Thompson, V. Tikhomirov, M. Tokarev, M. B. Tonjes, T. A. Trainor, S. Trentalange, R. E. Tribble, V. Trofimov, O. Tsai, T. Ullrich, D. G. Underwood, G. Van Buren, A. M. VanderMolen, I. M. Vasilevski, A. N. Vasiliev, S. E. Vigdor, S. A. Voloshin, F. Wang, H. Ward, J. W. Watson, R. Wells, G. D. Westfall, C. Whitten, Jr., H. Wieman, R. Willson, S. W. Wissink, R. Witt, J. Wood, N. Xu, Z. Xu, A. E. Yakutin, E. Yamamoto, J. Yang, P. Yepes, V. I. Yurevich, Y. V. Zanevski, I. Zborovský, H. Zhang, W. M. Zhang, R. Zoulkarneev, and A. N. Zubarev (STAR Collaboration