14,641 research outputs found
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 gâ1 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 todayâs 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 CoSi/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/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 -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
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