ALBERT

Description: Motivation: The discovery of genomic structural variants (SVs) at high sensitivity and specificity is an essential requirement for characterizing naturally occurring variation and for understanding pathological somatic rearrangements in personal genome sequencing data. Of particular interest are integrated methods that accurately identify simple and complex rearrangements in heterogeneous sequencing datasets at single-nucleotide resolution, as an optimal basis for investigating the formation mechanisms and functional consequences of SVs. Results: We have developed an SV discovery method, called DELLY, that integrates short insert paired-ends, long-range mate-pairs and split-read alignments to accurately delineate genomic rearrangements at single-nucleotide resolution. DELLY is suitable for detecting copy-number variable deletion and tandem duplication events as well as balanced rearrangements such as inversions or reciprocal translocations. DELLY, thus, enables to ascertain the full spectrum of genomic rearrangements, including complex events. On simulated data, DELLY compares favorably to other SV prediction methods across a wide range of sequencing parameters. On real data, DELLY reliably uncovers SVs from the 1000 Genomes Project and cancer genomes, and validation experiments of randomly selected deletion loci show a high specificity. Availability: DELLY is available at www.korbel.embl.de/software.html Contact: tobias.rausch@embl.de

Description: City lights and urban air Nature Geoscience 4, 730 (2011). doi:10.1038/ngeo1300 Authors: H. Stark, S. S. Brown, K. W. Wong, J. Stutz, C. D. Elvidge, I. B. Pollack, T. B. Ryerson, W. P. Dube, N. L. Wagner & D. D. Parrish

Description: Recent observational and theoretical investigations have emphasized the importance of filamentary networks within molecular clouds as sites of star formation. Since such environments are more complex than those of isolated cores, it is essential to understand how the observed line profiles from collapsing cores with non-spherical geometry are affected by filaments. In this study, we investigate line profile asymmetries by performing radiative transfer calculations on hydrodynamic models of three collapsing cores that are embedded in filaments. We compare the results to those that are expected for isolated cores. We model the five lowest rotational transition line ( J = 1–0, 2–1, 3–2, 4–3 and 5–4) of both optically thick (HCN, HCO + ) as well as optically thin (N 2 H + , H 13 CO + ) molecules using constant abundance laws. We find that less than 50 per cent of simulated (1–0) transition lines show blue infall asymmetries due to obscuration by the surrounding filament. However, the fraction of collapsing cores that have a blue asymmetric emission line profile rises to 90 per cent when observed in the (4–3) transition. Since the densest gas towards the collapsing core can excite higher rotational states, upper level transitions are more likely to produce blue asymmetric emission profiles. We conclude that even in irregular, embedded cores one can trace infalling gas motions with blue asymmetric line profiles of optically thick lines by observing higher transitions. The best tracer of collapse motions of our sample is the (4–3) transition of HCN, but the (3–2) and (5–4) transitions of both HCN and HCO + are also good tracers.

Description: Most genomes, including yeast Saccharomyces cerevisiae , are pervasively transcribed producing numerous non-coding RNAs, many of which are unstable and eliminated by nuclear or cytoplasmic surveillance pathways. We previously showed that accumulation of PHO84 antisense RNA (asRNA), in cells lacking the nuclear exosome component Rrp6, is paralleled by repression of sense transcription in a process dependent on the Hda1 histone deacetylase (HDAC) and the H3K4 histone methyl transferase Set1. Here we investigate this process genome-wide and measure the whole transcriptome of various histone modification mutants in a rrp6 strain using tiling arrays. We confirm widespread occurrence of potentially antisense-dependent gene regulation and identify three functionally distinct classes of genes that accumulate asRNAs in the absence of Rrp6. These classes differ in whether the genes are silenced by the asRNA and whether the silencing is HDACs and histone methyl transferase-dependent. Among the distinguishing features of asRNAs with regulatory potential, we identify weak early termination by Nrd1/Nab3/Sen1, extension of the asRNA into the open reading frame promoter and dependence of the silencing capacity on Set1 and the HDACs Hda1 and Rpd3 particularly at promoters undergoing extensive chromatin remodelling. Finally, depending on the efficiency of Nrd1/Nab3/Sen1 early termination, asRNA levels are modulated and their capability of silencing is changed.

Description: Our understanding of population genetics comes primarily from studies of organisms with canonical life cycles and nuclear organization, either haploid or diploid, sexual, or asexual. Although this template yields satisfactory results for the study of animals and plants, the wide variety of genomic organizations and life cycles of unicellular eukaryotes can make these organisms behave differently in response to mutation, selection, and drift than predicted by traditional population genetic models. In this study, we show how each of these unique features of ciliates affects their evolutionary parameters in mutation–selection, selection–drift, and mutation–selection–drift situations. In general, ciliates are less efficient in eliminating deleterious mutations—these mutations linger longer and at higher frequencies in ciliate populations than in sexual populations—and more efficient in selecting beneficial mutations. Approaching this problem via analytical techniques and simulation allows us to make specific predictions about the nature of ciliate evolution, and we discuss the implications of these results with respect to the high levels of polymorphism and high rate of protein evolution reported for ciliates.

Description: Episodes of elevated bromine oxide (BrO) concentration are known to occur at high latitudes in the Arctic boundary layer and to lead to catalytic destruction of ozone at those latitudes; these events have not been observed at lower latitudes. With the use of differential optical absorption spectroscopy (DOAS), locally high BrO concentrations were observed at mid-latitudes at the Dead Sea, Israel, during spring 1997. Mixing ratios peaked daily at around 80 parts per trillion around noon and were correlated with low boundary-layer ozone mixing ratios.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hebestreit -- Stutz -- Rosen -- Matveiv V -- Peleg -- Luria -- Platt -- New York, N.Y. -- Science. 1999 Jan 1;283(5398):55-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉K. Hebestreit, J. Stutz, U. Platt, Institut fur Umweltphysik, Ruprecht-Karls-Universitat Heidelberg, Im Neuenheimer Feld 366, D-69120 Heidelberg, Germany. D. Rosen, V. Matveiv, M. Peleg, M. Luria, Environmental Science, School of Applie.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9872738" target="_blank"〉PubMed〈/a〉

Description: Using data collected at the Pierre Auger Observatory during the past 3.7 years, we demonstrated a correlation between the arrival directions of cosmic rays with energy above 6 x 10(19) electron volts and the positions of active galactic nuclei (AGN) lying within approximately 75 megaparsecs. We rejected the hypothesis of an isotropic distribution of these cosmic rays with at least a 99% confidence level from a prescribed a priori test. The correlation we observed is compatible with the hypothesis that the highest-energy particles originate from nearby extragalactic sources whose flux has not been substantially reduced by interaction with the cosmic background radiation. AGN or objects having a similar spatial distribution are possible sources.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pierre Auger Collaboration -- Abraham, J -- Abreu, P -- Aglietta, M -- Aguirre, C -- Allard, D -- Allekotte, I -- Allen, J -- Allison, P -- Alvarez, C -- Alvarez-Muniz, J -- Ambrosio, M -- Anchordoqui, L -- Andringa, S -- Anzalone, A -- Aramo, C -- Argiro, S -- Arisaka, K -- Armengaud, E -- Arneodo, F -- Arqueros, F -- Asch, T -- Asorey, H -- Assis, P -- Atulugama, B S -- Aublin, J -- Ave, M -- Avila, G -- Backer, T -- Badagnani, D -- Barbosa, A F -- Barnhill, D -- Barroso, S L C -- Bauleo, P -- Beatty, J -- Beau, T -- Becker, B R -- Becker, K H -- Bellido, J A -- Benzvi, S -- Berat, C -- Bergmann, T -- Bernardini, P -- Bertou, X -- Biermann, P L -- Billoir, P -- Blanch-Bigas, O -- Blanco, F -- Blasi, P -- Bleve, C -- Blumer, H -- Bohacova, M -- Bonifazi, C -- Bonino, R -- Boratav, M -- Brack, J -- Brogueira, P -- Brown, W C -- Buchholz, P -- Bueno, A -- Busca, N G -- Caballero-Mora, K S -- Cai, B -- Camin, D V -- Caruso, R -- Carvalho, W -- Castellina, A -- Catalano, O -- Cataldi, G -- Cazon-Boado, L -- Cester, R -- Chauvin, J -- Chiavassa, A -- Chinellato, J A -- Chou, A -- Chye, J -- Clark, P D J -- Clay, R W -- Colombo, E -- Conceicao, R -- Connolly, B -- Contreras, F -- Coppens, J -- Cordier, A -- Cotti, U -- Coutu, S -- Covault, C E -- Creusot, A -- Cronin, J -- Dagoret-Campagne, S -- Daumiller, K -- Dawson, B R -- de Almeida, R M -- De Donato, C -- de Jong, S J -- De La Vega, G -- de Mello Junior, W J M -- de Mello Neto, J R T -- De Mitri, I -- de Souza, V -- Del Peral, L -- Deligny, O -- Selva, A Della -- Fratte, C Delle -- Dembinski, H -- Di Giulio, C -- Diaz, J C -- Dobrigkeit, C -- D'Olivo, J C -- Dornic, D -- Dorofeev, A -- Dos Anjos, J C -- Dova, M T -- D'Urso, D -- Duvernois, M A -- Engel, R -- Epele, L -- Erdmann, M -- Escobar, C O -- Etchegoyen, A -- Facal San Luis, P -- Falcke, H -- Farrar, G -- Fauth, A C -- Fazzini, N -- Fernandez, A -- Ferrer, F -- Ferry, S -- Fick, B -- Filevich, A -- Filipcic, A -- Fleck, I -- Fonte, R -- Fracchiolla, C E -- Fulgione, W -- Garcia, B -- Garcia Gamez, D -- Garcia-Pinto, D -- Garrido, X -- Geenen, H -- Gelmini, G -- Gemmeke, H -- Ghia, P L -- Giller, M -- Glass, H -- Gold, M S -- Golup, G -- Albarracin, F Gomez -- Berisso, M Gomez -- Herrero, R Gomez -- Goncalves, P -- Goncalves do Amaral, M -- Gonzalez, D -- Gonzalez, J G -- Gonzalez, M -- Gora, D -- Gorgi, A -- Gouffon, P -- Grassi, V -- Grillo, A -- Grunfeld, C -- Guardincerri, Y -- Guarino, F -- Guedes, G P -- Gutierrez, J -- Hague, J D -- Hamilton, J C -- Hansen, P -- Harari, D -- Harmsma, S -- Harton, J L -- Haungs, A -- Hauschildt, T -- Healy, M D -- Hebbeker, T -- Heck, D -- Hojvat, C -- Holmes, V C -- Homola, P -- Horandel, J -- Horneffer, A -- Horvat, M -- Hrabovsky, M -- Huege, T -- Iarlori, M -- Insolia, A -- Ionita, F -- Italiano, A -- Kaducak, M -- Kampert, K H -- Keilhauer, B -- Kemp, E -- Kieckhafer, R M -- Klages, H O -- Kleifges, M -- Kleinfeller, J -- Knapik, R -- Knapp, J -- Koang, D-H -- Kopmann, A -- Krieger, A -- Kromer, O -- Kumpel, D -- Kunka, N -- Kusenko, A -- La Rosa, G -- Lachaud, C -- Lago, B L -- Lebrun, D -- Lebrun, P -- Lee, J -- Leigui de Oliveira, M A -- Letessier-Selvon, A -- Leuthold, M -- Lhenry-Yvon, I -- Lopez, R -- Lopez Aguera, A -- Lozano Bahilo, J -- Maccarone, M C -- Macolino, C -- Maldera, S -- Malek, M -- Mancarella, G -- Mancenido, M E -- Mandat, D -- Mantsch, P -- Mariazzi, A G -- Maris, I C -- Martello, D -- Martinez, J -- Martinez Bravo, O -- Mathes, H J -- Matthews, J -- Matthews, J A J -- Matthiae, G -- Maurizio, D -- Mazur, P O -- McCauley, T -- McEwen, M -- McNeil, R R -- Medina, M C -- Medina-Tanco, G -- Meli, A -- Melo, D -- Menichetti, E -- Menschikov, A -- Meurer, Chr -- Meyhandan, R -- Micheletti, M I -- Miele, G -- Miller, W -- Mollerach, S -- Monasor, M -- Monnier Ragaigne, D -- Montanet, F -- Morales, B -- Morello, C -- Moreno, E -- Moreno, J C -- Morris, C -- Mostafa, M -- Muller, M A -- Mussa, R -- Navarra, G -- Navarro, J L -- Navas, S -- Nellen, L -- Newman-Holmes, C -- Newton, D -- Thi, T Nguyen -- Nierstenhofer, N -- Nitz, D -- Nosek, D -- Nozka, L -- Oehlschlager, J -- Ohnuki, T -- Olinto, A -- Olmos-Gilbaja, V M -- Ortiz, M -- Ostapchenko, S -- Otero, L -- Pakk Selmi-Dei, D -- Palatka, M -- Pallotta, J -- Parente, G -- Parizot, E -- Parlati, S -- Pastor, S -- Patel, M -- Paul, T -- Pavlidou, V -- Payet, K -- Pech, M -- Pekala, J -- Pelayo, R -- Pepe, I M -- Perrone, L -- Petrera, S -- Petrinca, P -- Petrov, Y -- Ngoc, Dieppham -- Ngoc, Dongpham -- Pham Thi, T N -- Pichel, A -- Piegaia, R -- Pierog, T -- Pimenta, M -- Pinto, T -- Pirronello, V -- Pisanti, O -- Platino, M -- Pochon, J -- Porter, T A -- Privitera, P -- Prouza, M -- Quel, E J -- Rautenberg, J -- Reucroft, S -- Revenu, B -- Rezende, F A S -- Ridky, J -- Riggi, S -- Risse, M -- Riviere, C -- Rizi, V -- Roberts, M -- Robledo, C -- Rodriguez, G -- Rodriguez Frias, D -- Rodriguez Martino, J -- Rodriguez Rojo, J -- Rodriguez-Cabo, I -- Ros, G -- Rosado, J -- Roth, M -- Rouille-d'Orfeuil, B -- Roulet, E -- Rovero, A C -- Salamida, F -- Salazar, H -- Salina, G -- Sanchez, F -- Santander, M -- Santo, C E -- Santos, E M -- Sarazin, F -- Sarkar, S -- Sato, R -- Scherini, V -- Schieler, H -- Schmidt, F -- Schmidt, T -- Scholten, O -- Schovanek, P -- Schussler, F -- Sciutto, S J -- Scuderi, M -- Segreto, A -- Semikoz, D -- Settimo, M -- Shellard, R C -- Sidelnik, I -- Siffert, B B -- Sigl, G -- De Grande, N Smetniansky -- Smialkowski, A -- Smida, R -- Smith, A G K -- Smith, B E -- Snow, G R -- Sokolsky, P -- Sommers, P -- Sorokin, J -- Spinka, H -- Squartini, R -- Strazzeri, E -- Stutz, A -- Suarez, F -- Suomijarvi, T -- Supanitsky, A D -- Sutherland, M S -- Swain, J -- Szadkowski, Z -- Takahashi, J -- Tamashiro, A -- Tamburro, A -- Tascau, O -- Tcaciuc, R -- Thomas, D -- Ticona, R -- Tiffenberg, J -- Timmermans, C -- Tkaczyk, W -- Todero Peixoto, C J -- Tome, B -- Tonachini, A -- Torresi, D -- Travnicek, P -- Tripathi, A -- Tristram, G -- Tscherniakhovski, D -- Tueros, M -- Tunnicliffe, V -- Ulrich, R -- Unger, M -- Urban, M -- Valdes Galicia, J F -- Valino, I -- Valore, L -- van den Berg, A M -- van Elewyck, V -- Vazquez, R A -- Veberic, D -- Veiga, A -- Velarde, A -- Venters, T -- Verzi, V -- Videla, M -- Villasenor, L -- Vorobiov, S -- Voyvodic, L -- Wahlberg, H -- Wainberg, O -- Waldenmaier, T -- Walker, P -- Warner, D -- Watson, A A -- Westerhoff, S -- Wieczorek, G -- Wiencke, L -- Wilczynska, B -- Wilczynski, H -- Wileman, C -- Winnick, M G -- Wu, H -- Wundheiler, B -- Xu, J -- Yamamoto, T -- Younk, P -- Zas, E -- Zavrtanik, D -- Zavrtanik, M -- Zech, A -- Zepeda, A -- Ziolkowski, M -- Kegl, B -- New York, N.Y. -- Science. 2007 Nov 9;318(5852):938-43.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17991855" target="_blank"〉PubMed〈/a〉