Complete RNA inverse folding: computational design of functional hammerhead ribozymes

Nanotechnology and synthetic biology currently constitute one of the most innovative, interdisciplinary fields of research, poised to radically transform society in the 21st century. This paper concerns the synthetic design of ribonucleic acid molecules, using our recent algorithm, RNAiFold, which can determine all RNA sequences whose minimum free energy secondary structure is a user-specified target structure. Using RNAiFold, we design ten cis-cleaving hammerhead ribozymes, all of which are shown to be functional by a cleavage assay. We additionally use RNAiFold to design a functional cis-cleaving hammerhead as a modular unit of a synthetic larger RNA. Analysis of kinetics on this small set of hammerheads suggests that cleavage rate of computationally designed ribozymes may be correlated with positional entropy, ensemble defect, structural flexibility/rigidity and related measures. Artificial ribozymes have been designed in the past either manually or by SELEX (Systematic Evolution of Ligands by Exponential Enrichment); however, this appears to be the first purely computational design and experimental validation of novel functional ribozymes. RNAiFold is available at http://bioinformatics.bc.edu/clotelab/RNAiFold/.Comment: 17 pages, 2 tables, 7 figures, final version to appear in Nucleic Acids Researc

Species sensitivity of zeolite minerals for uptake of mercury solutes

The uptake of inorganic Hg2+ and organometallic CH3Hg+ from aqueous solutions by 11 different natural zeolites has been investigated using a batch distribution coefficient (Kd) method and supported by a preliminary voltammetric study. The effect of mercury concentration on theKd response is shown over an environmentally appropriate concentration range of 0.1-5 ppm inorganic and organometallic Hg using a batch factor of 100 ml g−1 and 20 h equilibration. Analcime and a Na-chabazite displayed the greatest methylmercury uptakes (Kd values at 1.5 ppm of 4023 and 3456, respectively), with mordenite as the smallest at 578. All uptake responses were greater for methylmercury than for the inorganic mercuric nitrate solutions, suggesting a distinctive sensitivity of zeolites to reaction with different types of solute species. It is likely that this sensitivity is attributable to the precise nature of the resultant Hg-zeolite bonds. Additionally, both the Si-Al ratio and the Na content of the initial natural zeolite samples are shown to influence the Kd responses, with positive correlations between Kd and Na content for all zeolites excluding mordenite

A Microservice Infrastructure for Distributed Communities of Practice

Non-formal learning in Communities of Practice (CoPs) makes up a significant portion of today’s knowledge gain. However, only little technological support is tailored specifically towards CoPs and their particular strengths and challenges. Even worse, CoPs often do not possess the resources to host or even develop a software ecosystem to support their activities. In this paper, we describe a distributed, microservice-based Web infrastructure for non-formal learning in CoPs. It mitigates the need for central infrastructures, coordination or facilitation and takes into account the constant change of these communities. As a real use case, we implement an inquiry-based learning application on-top of our infrastructure. Our evaluation results indicate the usefulness of this learning application, which shows promise for future work in the domain of community-hosted, microservice-based Web infrastructures for learning outside of formal settings

Ballistic Electron Emission Microscopy on CoSi2{}_2/Si(111) interfaces: band structure induced atomic-scale resolution and role of localized surface states

Applying a Keldysh Green`s function method it is shown that hot electrons injected from a STM-tip into a CoSi${}_2$/Si(111) system form a highly focused beam due to the silicide band structure. This explains the atomic resolution obtained in recent Ballistic Electron Emission Microscopy (BEEM) experiments. Localized surface states in the $(2 \times 1)$-reconstruction are found to be responsible for the also reported anticorrugation of the BEEM current. These results clearly demonstrate the importance of bulk and surface band structure effects for a detailed understanding of BEEM data.Comment: 5 pages, RevTex, 4 postscript figures, http://www.icmm.csic.es/Pandres/pedro.ht

Best Unbiased Estimates for the Microwave Background Anisotropies

It is likely that the observed distribution of the microwave background temperature over the sky is only one realization of the underlying random process associated with cosmological perturbations of quantum-mechanical origin. If so, one needs to derive the parameters of the random process, as accurately as possible, from the data of a single map. These parameters are of the utmost importance, since our knowledge of them would help us to reconstruct the dynamical evolution of the very early Universe. It appears that the lack of ergodicity of a random process on a 2-sphere does not allow us to do this with arbitrarily high accuracy. We are left with the problem of finding the best unbiased estimators of the participating parameters. A detailed solution to this problem is presented in this article. The theoretical error bars for the best unbiased estimates are derived and discussed.Comment: 26 pages, revtex; minor modifications, 8 new references, to be published in Phys. Rev.

Order and Frustration in Chiral Liquid Crystals

This paper reviews the complex ordered structures induced by chirality in liquid crystals. In general, chirality favors a twist in the orientation of liquid-crystal molecules. In some cases, as in the cholesteric phase, this favored twist can be achieved without any defects. More often, the favored twist competes with applied electric or magnetic fields or with geometric constraints, leading to frustration. In response to this frustration, the system develops ordered structures with periodic arrays of defects. The simplest example of such a structure is the lattice of domains and domain walls in a cholesteric phase under a magnetic field. More complex examples include defect structures formed in two-dimensional films of chiral liquid crystals. The same considerations of chirality and defects apply to three-dimensional structures, such as the twist-grain-boundary and moire phases.Comment: 39 pages, RevTeX, 14 included eps figure

Supernova 1987A: Rotation and a Binary Companion

In this paper we provide a possible link between the structure of the bipolar nebula surrounding SN1987A and the properties of its progenitor star. A Wind Blwon Bubble (WBB) scenario is emplyed, in which a fast, tenuous wind from a Blue Supergiant expands into a slow, dense wind, expelled during an earlier Red Supergiant phase. The bipolar shapre develops due to a pole-to-equator density contrast in the slow wind (ie, the slow wind forms a slow torus). We use the Wind Compressed Disk (WCD) model of Bjorkman & Cassinelli (1992) to determine the shape of the slow torus. In the WCD scenario, the shape of the torus is determined by the rotation of the progenitor star. We then use a self-similar semi-analytical method for wind blown bubble evolution to determine the shape of the resulting bipolar nebula. We find that the union of the wind-compressed-disk and bipolar-wind-blown- bubble models allows us to recover the salient properties of SN1987A's circumstellar nebula. In particular, the size, speed and density of SN1987A's inner ring are easily reproduced in our calculations. An exploration of parameter space shows the the red supergiant progenitor must be been rotating at > 0.3 of its breakup speed. We conclude that the progenitor was most likely spun up by a merger with a binary companion. Using a simple model for the binary merger we find that the companion is likely to have had a mass > 0.5 M_sun.Comment: 30 pages, 4 figure

A New View of the Circumstellar Environment of SN 1987A

We summarize the analysis of a uniform set of both previously-known and newly-discovered scattered-light echoes, detected within 30" of SN 1987A in ten years of optical imaging, and with which we have constructed the most complete three-dimensional model of the progenitor's circumstellar environment. Surrounding the SN is a richly-structured bipolar nebula. An outer, double-lobed ``peanut,'' which we believe is the contact discontinuity between the red supergiant and main sequence winds, is a prolate shell extending 28 ly along the poles and 11 ly near the equator. Napoleon's Hat, previously believed to be an independent structure, is the waist of this peanut, which is pinched to a radius of 6 ly. Interior, the innermost circumstellar material lies along a cylindrical hourglass, 1 ly in radius and 4 ly long, which connects to the peanut by a thick equatorial disk. The nebulae are inclined 41o south and 8o east of the line of sight, slightly elliptical in cross section, and marginally offset west of the SN. The 3-D geometry of the three circumstellar rings is studied, suggesting the equatorial ring is elliptical (b/a<0.98), and spatially offset in the same direction as the hourglass. Dust-scattering models suggest that between the hourglass and bipolar lobes: the gas density drops from 1--3 cm^{-3} to >0.03 cm^{-3}; the maximum dust-grain size increases from ~0.2 micron to 2 micron; and the Si:C dust ratio decreases. The nebulae have a total mass of ~1.7 Msun, yielding a red-supergiant mass loss around 5*10^{-6} Msun yr^{-1}.Comment: Accepted for publication in ApJ 2/14/05. 16 pages in emualteapj forma

Chemical abundance gradients from open clusters in the Milky Way disk: results from the APOGEE survey

Metallicity gradients provide strong constraints for understanding the chemical evolution of the Galaxy. We report on radial abundance gradients of Fe, Ni, Ca, Si, and Mg obtained from a sample of 304 red-giant members of 29 disk open clusters, mostly concentrated at galactocentric distances between ~8 - 15 kpc, but including two open clusters in the outer disk. The observations are from the APOGEE survey. The chemical abundances were derived automatically by the ASPCAP pipeline and these are part of the SDSS III Data Release 12. The gradients, obtained from least squares fits to the data, are relatively flat, with slopes ranging from -0.026 to -0.033 dex/kpc for the alpha-elements [O/H], [Ca/H], [Si/H] and [Mg/H] and -0.035 dex/kpc and -0.040 dex/kpc for [Fe/H] and [Ni/H], respectively. Our results are not at odds with the possibility that metallicity ([Fe/H]) gradients are steeper in the inner disk (R_GC ~7 - 12 kpc) and flatter towards the outer disk. The open cluster sample studied spans a significant range in age. When breaking the sample into age bins, there is some indication that the younger open cluster population in our sample (log age < 8.7) has a flatter metallicity gradient when compared with the gradients obtained from older open clusters.Comment: 4 pages, 3 figures, To appear in Astronomische Nachrichten, special issue "Reconstruction the Milky Way's History: Spectroscopic surveys, Asteroseismology and Chemo-dynamical models", Guest Editors C. Chiappini, J. Montalb\'an, and M. Steffen, AN 2016 (in press)

Characterization of BRD4 during mammalian post-meiotic sperm development

During spermiogenesis, the post-meiotic phase of mammalian spermatogenesis, transcription is progressively repressed as nuclei of haploid spermatids are compacted through a dramatic chromatin reorganization involving hyper-acetylation and replacement of most histones with protamines. Although BRDT functions in transcription and histone removal in spermatids, it is unknown whether other BET family proteins play a role. Immunofluorescence of spermatogenic cells revealed BRD4 in a ring around the nuclei of spermatids containing hyper-acetylated histones. The ring lies directly adjacent to the acroplaxome, the cytoskeletal base of the acrosome, previously linked to chromatin reorganization. The BRD4 ring does not form in acrosomal mutant mice. ChIP sequencing in spermatids revealed enrichment of BRD4 and acetylated histones at the promoters of active genes. BRD4 and BRDT show distinct and synergistic binding patterns, with a pronounced enrichment of BRD4 at spermatogenesis-specific genes. Direct association of BRD4 with acetylated H4 decreases in late spermatids as acetylated histones are removed from the condensing nucleus in a wave following the progressing acrosome. These data provide evidence for a prominent transcriptional role of BRD4 and suggest a possible removal mechanism for chromatin components from the genome via the progressing acrosome as transcription is repressed in response to chromatin condensation during spermiogenesis