ALBERT

Description: We present optical and near-infrared photometry and spectroscopy of SN 2009ib, a Type II-P supernova in NGC 1559. This object has moderate brightness, similar to those of the intermediate-luminosity SNe 2008in and 2009N. Its plateau phase is unusually long, lasting for about 130 d after explosion. The spectra are similar to those of the subluminous SN 2002gd, with moderate expansion velocities. We estimate the 56 Ni mass produced as 0.046 ± 0.015 M . We determine the distance to SN 2009ib using both the expanding photosphere method (EPM) and the standard candle method. We also apply EPM to SN 1986L, a Type II-P SN that exploded in the same galaxy. Combining the results of different methods, we conclude the distance to NGC 1559 as D  = 19.8 ± 3.0 Mpc. We examine archival, pre-explosion images of the field taken with the Hubble Space Telescope , and find a faint source at the position of the SN, which has a yellow colour [( V  –  I ) 0  = 0.85 mag]. Assuming it is a single star, we estimate its initial mass as M ZAMS  = 20 M . We also examine the possibility, that instead of the yellow source the progenitor of SN 2009ib is a red supergiant star too faint to be detected. In this case, we estimate the upper limit for the initial zero-age main sequence (ZAMS) mass of the progenitor to be ~14–17 M . In addition, we infer the physical properties of the progenitor at the explosion via hydrodynamical modelling of the observables, and estimate the total energy as ~0.55 10 51  erg, the pre-explosion radius as ~400 R , and the ejected envelope mass as ~15 M , which implies that the mass of the progenitor before explosion was ~16.5–17 M .

Description: We present optical and near-infrared observations of the type IIb supernova (SN) 2011fu from a few days to ~300 d after explosion. The SN presents a double-peaked light curve (LC) similar to that of SN 1993J, although more luminous and with a longer cooling phase after the primary peak. The spectral evolution is also similar to SN 1993J's, with hydrogen dominating the spectra to ~40 d, then helium gaining strength, and nebular emission lines appearing from ~60 d post-explosion. The velocities derived from the P-Cygni absorptions are overall similar to those of other type IIb SNe. We have found a strong similarity between the oxygen and magnesium line profiles at late times, which suggests that these lines are forming at the same location within the ejecta. The hydrodynamical modelling of the pseudo-bolometric LC and the observed photospheric velocities suggest that SN 2011fu was the explosion of an extended star ( R ~ 450 R ), in which 1.3  x  10 51  erg of kinetic energy were released and 0.15 M of 56 Ni were synthesized. In addition, a better reproduction of the observed early pseudo-bolometric LC is achieved if a more massive H-rich envelope than for other type IIb SNe is considered (0.3 M ). The hydrodynamical modelling of the LC and the comparison of our late-time spectra with nebular spectral models for type IIb SNe, point to a progenitor for SN 2011fu with a Zero Age Main Sequence (ZAMS) mass of 13–18 M .

Description: It has been argued that a substantial fraction of massive stars may end their lives without an optically bright supernova (SN), but rather collapse to form a black hole. Such an event would not be detected by current SN surveys, which are focused on finding bright transients. Kochanek et al. proposed a novel survey for such events, using repeated observations of nearby galaxies to search for the disappearance of a massive star. We present such a survey, using the first systematic analysis of archival Hubble Space Telescope images of nearby galaxies with the aim of identifying evolved massive stars which have disappeared, without an accompanying optically bright SN. We consider a sample of 15 galaxies, with at least three epochs of Hubble Space Telescope imaging taken between 1994 and 2013. Within this data, we find one candidate which is consistent with a 25–30 M yellow supergiant which has undergone an optically dark core-collapse.

Description: It has been argued that a substantial fraction of massive stars may end their lives without an optically bright supernova (SN), but rather collapse to form a black hole. Such an event would not be detected by current SN surveys, which are focused on finding bright transients. Kochanek et al. proposed a novel survey for such events, using repeated observations of nearby galaxies to search for the disappearance of a massive star. We present such a survey, using the first systematic analysis of archival Hubble Space Telescope images of nearby galaxies with the aim of identifying evolved massive stars which have disappeared, without an accompanying optically bright SN. We consider a sample of 15 galaxies, with at least three epochs of Hubble Space Telescope imaging taken between 1994 and 2013. Within this data, we find one candidate which is consistent with a 25–30 M yellow supergiant which has undergone an optically dark core-collapse.

Description: Article Fungi of the order Mucorales can cause life-threatening infections. Here, Chibucos et al . present genomic and transcriptomic analyses of a diverse set of Mucorales fungi, shedding light on their evolution and identifying potential therapeutic targets in the pathogens and the host. Nature Communications doi: 10.1038/ncomms12218 Authors: Marcus C. Chibucos, Sameh Soliman, Teclegiorgis Gebremariam, Hongkyu Lee, Sean Daugherty, Joshua Orvis, Amol C. Shetty, Jonathan Crabtree, Tracy H. Hazen, Kizee A. Etienne, Priti Kumari, Timothy D. O’Connor, David A. Rasko, Scott G. Filler, Claire M. Fraser, Shawn R. Lockhart, Christopher D. Skory, Ashraf S. Ibrahim, Vincent M. Bruno

Description: Sedimentary strata are the paramount source of geohistorical information. The ‘frozen accidents’ of individual deposits preserve evidence of past physical, chemical and biological processes at the Earth's surface, while the spatial relationships between strata (especially superposition) yield successions of events through time. There is, however, no one-to-one relationship between strata and time, and the interpretation of the stratigraphic record depends on an understanding of its limitations. Stratigraphic continuity and completeness are unattainable ideals, and it is the departures from those ideals – the often cryptic gaps in the record – that provide both its characteristic texture and the principal challenge to its analysis. The existence of gaps is clearly demonstrated by consideration of accumulation rates, but identifying and quantifying them in the field is far more difficult, as is assessing their impact on the degree to which the stratigraphic record represents the environments and processes of the past. These issues can be tackled in a variety of ways, from empirical considerations based on classical field observations, to new ways of analysing data, to the generation and analysis of very large numbers of synthetic datasets. The range of approaches to the fundamental questions of the relationship between strata and time continues to expand and to challenge long-established practices and conventions. Superposed sedimentary strata are the most accessible routes into deep time, and acceptance of their historical significance was a major scientific breakthrough. Given that the study of strata has been undertaken in something like its modern form for over two centuries, stratigraphy as a scientific discipline might be expected to have stabilized, as perhaps is indicated by stratigraphy textbooks suggesting that the subject is widely regarded as boring. Yet if there is a problem with stratigraphy, it is the converse: its development is increasingly punctuated by paradigm shifts triggered by new theories (evolution; global tectonics; eustasy; orbital forcing of climate change) and technological breakthroughs (digital computing; continuous seismic profiling; isotopic methods in chronology and palaeoclimatology). With this accelerating progress, it has become increasingly clear that the stratigraphic record yields only snapshots of Earth's past surface processes – the ‘frozen accidents’ that give the record its character and its enduring fascination. ‘Time is missing from sedimentary sequences on all scales ... This discontinuity gives recorded planetary (geological) time a different architecture to human time’ (Paola, C. 2003. Floods of record. Nature , 425 , 459). Strata and Time: Probing the Gaps in our Understanding was the title of the Geological Society's William Smith Meeting for 2012. Its aim was to explore the relationship between the preserved sedimentary rock record and the passage of geological time, identifying, evaluating and updating the models that lie behind current stratigraphic methods. This volume includes contributions by some of those who presented papers at the conference, together with two additional, related papers. The range of topics in these 15 papers is broad; from field-based studies to numerical modelling exercises, from theoretical considerations of the nature of the record to a study of hydrocarbon reservoir distribution. Critical to all of these studies is the relationship between sedimentary rock strata and geological time.

Description: Chromatin has a complex spatial organization in the cell nucleus that serves vital functional purposes. A variety of chromatin folding conformations has been detected by single-cell imaging and chromosome conformation capture-based approaches. However, a unified quantitative framework describing spatial chromatin organization is still lacking. Here, we explore the “strings and...

Description: In addition to coding for proteins, exons can also impact transcription by encoding regulatory elements such as enhancers. It has been debated whether such features confer heightened selective constraint, or evolve neutrally. We have addressed this question by developing a new approach to disentangle the sources of selection acting on exonic enhancers, in which we model the evolutionary rates of every possible substitution as a function of their effects on both protein sequence and enhancer activity. In three exonic enhancers, we found no significant association between evolutionary rates and effects on enhancer activity. This suggests that despite having biochemical activity, these exonic enhancers have no detectable selective constraint, and thus are unlikely to play a major role in protein evolution.

Description: Genomics of DNA cytosine methylation in Escherichia coli reveals its role in stationary phase transcription Nature Communications 3, 886 (2012). doi:10.1038/ncomms1878 Authors: Christina Kahramanoglou, Ana I. Prieto, Supriya Khedkar, Bettina Haase, Ankur Gupta, Vladimir Benes, Gillian M. Fraser, Nicholas M. Luscombe & Aswin S.N. Seshasayee