Functionalized paramagnetic nanoparticles for waste water treatment

An approach to the design, development and implementation of a new separation technology for use in the decontamination of radioactive waste streams is reported here. Calixarene-crown-6 derivatives with terminal carboxyl groups were synthesised and attached to nano-sized magnetoferritin molecules and their ability to sequester radioactive caesium(i) ions from aqueous solution was demonstrated. © 2010 The Royal Society of Chemistry

TRPV4: Molecular Conductor of a Diverse Orchestra

Transient receptor potential vanilloid type 4 (TRPV4) is a calcium-permeable nonselective cation channel, originally described in 2000 by research teams led by Schultz ( Nat Cell Biol 2: 695 –702, 2000) and Liedtke ( Cell 103: 525–535, 2000). TRPV4 is now recognized as being a polymodal ionotropic receptor that is activated by a disparate array of stimuli, ranging from hypotonicity to heat and acidic pH. Importantly, this ion channel is constitutively expressed and capable of spontaneous activity in the absence of agonist stimulation, which suggests that it serves important physiological functions, as does its widespread dissemination throughout the body and its capacity to interact with other proteins. Not surprisingly, therefore, it has emerged more recently that TRPV4 fulfills a great number of important physiological roles and that various disease states are attributable to the absence, or abnormal functioning, of this ion channel. Here, we review the known characteristics of this ion channel's structure, localization and function, including its activators, and examine its functional importance in health and disease.</jats:p

Transcriptomic characterisation and genomic glimpse into the toxigenic dinoflagellate Azadinium spinosum, with emphasis on polykeitde synthase genes

Background: Unicellular dinoflagellates are an important group of primary producers within the marine plankton community. Many of these species are capable of forming harmful algae blooms (HABs) and of producing potent phycotoxins, thereby causing deleterious impacts on their environment and posing a threat to human health. The recently discovered toxigenic dinoflagellate Azadinium spinosum is known to produce azaspiracid toxins. These toxins are most likely produced by polyketide synthases (PKS). Recently, PKS I-like transcripts have been identified in a number of dinoflagellate species. Despite the global distribution of A. spinosum, little is known about molecular features. In this study, we investigate the genomic and transcriptomic features of A. spinosum with a focus on polyketide synthesis and PKS evolution. Results: We identify orphan and homologous genes by comparing the transcriptome data of A. spinosum with a diverse set of 18 other dinoflagellates, five further species out of the Rhizaria Alveolate Stramelopile (RAS)-group, and one representative from the Plantae. The number of orphan genes in the analysed dinoflagellate species averaged 27%. In contrast, within the A. spinosum transcriptome, we discovered 12,661 orphan transcripts (18%). The dinoflagellates toxins known as azaspiracids (AZAs) are structurally polyethers; we therefore analyse the transcriptome of A. spinosum with respect to polyketide synthases (PKSs), the primary biosynthetic enzymes in polyketide synthesis.We find all the genes thought to be potentially essential for polyketide toxin synthesis to be expressed in A. spinosum,whose PKS transcripts fall into the dinoflagellate sub-clade in PKS evolution. Conclusions: Overall, we demonstrate that the number of orphan genes in the A. spinosum genome is relatively small compared to other dinoflagellate species. In addition, all PKS domains needed to produce the azaspiracid carbon backbone are present in A. spinosum. Our study underscores the extraordinary evolution of such gene clusters and, in particular, supports the proposed structural and functional paradigm for PKS Type I genes in dinoflagellates

Matching concepts across HOL libraries

Many proof assistant libraries contain formalizations of the same mathematical concepts. The concepts are often introduced (defined) in different ways, but the properties that they have, and are in turn formalized, are the same. For the basic concepts, like natural numbers, matching them between libraries is often straightforward, because of mathematical naming conventions. However, for more advanced concepts, finding similar formalizations in different libraries is a non-trivial task even for an expert. In this paper we investigate automatic discovery of similar concepts across libraries of proof assistants. We propose an approach for normalizing properties of concepts in formal libraries and a number of similarity measures. We evaluate the approach on HOL based proof assistants HOL4, HOL Light and Isabelle/HOL, discovering 398 pairs of isomorphic constants and types

Transcriptomic characterisation and genomic glimps into the toxigenic dinoflagellate Azadinium spinosum, with emphasis on polykeitde synthase genes

BACKGROUND: Unicellular dinoflagellates are an important group of primary producers within the marine plankton community. Many of these species are capable of forming harmful algae blooms (HABs) and of producing potent phycotoxins, thereby causing deleterious impacts on their environment and posing a threat to human health. The recently discovered toxigenic dinoflagellate Azadinium spinosum is known to produce azaspiracid toxins. These toxins are most likely produced by polyketide synthases (PKS). Recently, PKS I-like transcripts have been identified in a number of dinoflagellate species. Despite the global distribution of A. spinosum, little is known about molecular features. In this study, we investigate the genomic and transcriptomic features of A. spinosum with a focus on polyketide synthesis and PKS evolution. RESULTS: We identify orphan and homologous genes by comparing the transcriptome data of A. spinosum with a diverse set of 18 other dinoflagellates, five further species out of the Rhizaria Alveolate Stramelopile (RAS)-group, and one representative from the Plantae. The number of orphan genes in the analysed dinoflagellate species averaged 27%. In contrast, within the A. spinosum transcriptome, we discovered 12,661 orphan transcripts (18%). The dinoflagellates toxins known as azaspiracids (AZAs) are structurally polyethers; we therefore analyse the transcriptome of A. spinosum with respect to polyketide synthases (PKSs), the primary biosynthetic enzymes in polyketide synthesis. We find all the genes thought to be potentially essential for polyketide toxin synthesis to be expressed in A. spinosum, whose PKS transcripts fall into the dinoflagellate sub-clade in PKS evolution. CONCLUSIONS: Overall, we demonstrate that the number of orphan genes in the A. spinosum genome is relatively small compared to other dinoflagellate species. In addition, all PKS domains needed to produce the azaspiracid carbon backbone are present in A. spinosum. Our study underscores the extraordinary evolution of such gene clusters and, in particular, supports the proposed structural and functional paradigm for PKS Type I genes in dinoflagellates

OmniMapFree: A unified tool to visualise and explore sequenced genomes

<p>Abstract</p> <p>• Background</p> <p>Acquiring and exploring whole genome sequence information for a species under investigation is now a routine experimental approach. On most genome browsers, typically, only the DNA sequence, EST support, motif search results, and GO annotations are displayed. However, for many species, a growing volume of additional experimental information is available but this is rarely searchable within the landscape of the entire genome.</p> <p>• Results</p> <p>We have developed a generic software which permits users to view a single genome in entirety either within its chromosome or supercontig context within a single window. This software permits the genome to be displayed at any scales and with any features. Different data types and data sets are displayed onto the genome, which have been acquired from other types of studies including classical genetics, forward and reverse genetics, transcriptomics, proteomics and improved annotation from alternative sources. In each display, different types of information can be overlapped, then retrieved in the desired combinations and scales and used in follow up analyses. The displays generated are of publication quality.</p> <p>• Conclusions</p> <p>OmniMapFree provides a unified, versatile and easy-to-use software tool for studying a single genome in association with all the other datasets and data types available for the organism.</p

An International Ultraviolet Explorer Archival Study of Dwarf Novae in Outburst

We present a synthetic spectral analysis of nearly the entire far ultraviolet International Ultraviolet Explorer (IUE) archive of spectra of dwarf novae in or near outburst. The study includes 46 systems of all dwarf nova subtypes both above and below the period gap. The spectra were uniformly analyzed using synthetic spectral codes for optically thick accretion disks and stellar photospheres along with the best-available distance measurements or estimates. We present newly estimated accretion rates and discuss the implications of our study for disk accretion physics and CV evolution.Comment: Accepted for publication in the ApJ, Part

The First Two Years of Electromagnetic Follow-Up with Advanced LIGO and Virgo

We anticipate the first direct detections of gravitational waves (GWs) with Advanced LIGO and Virgo later this decade. Though this groundbreaking technical achievement will be its own reward, a still greater prize could be observations of compact binary mergers in both gravitational and electromagnetic channels simultaneously. During Advanced LIGO and Virgo's first two years of operation, 2015 through 2016, we expect the global GW detector array to improve in sensitivity and livetime and expand from two to three detectors. We model the detection rate and the sky localization accuracy for binary neutron star (BNS) mergers across this transition. We have analyzed a large, astrophysically motivated source population using real-time detection and sky localization codes and higher-latency parameter estimation codes that have been expressly built for operation in the Advanced LIGO/Virgo era. We show that for most BNS events the rapid sky localization, available about a minute after a detection, is as accurate as the full parameter estimation. We demonstrate that Advanced Virgo will play an important role in sky localization, even though it is anticipated to come online with only one-third as much sensitivity as the Advanced LIGO detectors. We find that the median 90% confidence region shrinks from ~500 square degrees in 2015 to ~200 square degrees in 2016. A few distinct scenarios for the first LIGO/Virgo detections emerge from our simulations.Comment: 17 pages, 11 figures, 5 tables. For accompanying data, see http://www.ligo.org/scientists/first2year

MinION Analysis and Reference Consortium: Phase 1 data release and analysis

The advent of a miniaturized DNA sequencing device with a high-throughput contextual sequencing capability embodies the next generation of large scale sequencing tools. The MinION™ Access Programme (MAP) was initiated by Oxford Nanopore Technologies™ in April 2014, giving public access to their USB-attached miniature sequencing device. The MinION Analysis and Reference Consortium (MARC) was formed by a subset of MAP participants, with the aim of evaluating and providing standard protocols and reference data to the community. Envisaged as a multi-phased project, this study provides the global community with the Phase 1 data from MARC, where the reproducibility of the performance of the MinION was evaluated at multiple sites. Five laboratories on two continents generated data using a control strain of Escherichia coli K-12, preparing and sequencing samples according to a revised ONT protocol. Here, we provide the details of the protocol used, along with a preliminary analysis of the characteristics of typical runs including the consistency, rate, volume and quality of data produced. Further analysis of the Phase 1 data presented here, and additional experiments in Phase 2 of E. coli from MARC are already underway to identify ways to improve and enhance MinION performance

Parameter estimation on gravitational waves from neutron-star binaries with spinning components

Inspiraling binary neutron stars are expected to be one of the most significant sources of gravitational-wave signals for the new generation of advanced ground-based detectors. We investigate how well we could hope to measure properties of these binaries using the Advanced LIGO detectors, which began operation in September 2015. We study an astrophysically motivated population of sources (binary components with masses $1.2~\mathrm{M}_\odot$--$1.6~\mathrm{M}_\odot$ and spins of less than $0.05$) using the full LIGO analysis pipeline. While this simulated population covers the observed range of potential binary neutron-star sources, we do not exclude the possibility of sources with parameters outside these ranges; given the existing uncertainty in distributions of mass and spin, it is critical that analyses account for the full range of possible mass and spin configurations. We find that conservative prior assumptions on neutron-star mass and spin lead to average fractional uncertainties in component masses of $\sim 16\%$, with little constraint on spins (the median $90\%$ upper limit on the spin of the more massive component is $\sim 0.7$). Stronger prior constraints on neutron-star spins can further constrain mass estimates, but only marginally. However, we find that the sky position and luminosity distance for these sources are not influenced by the inclusion of spin; therefore, if LIGO detects a low-spin population of BNS sources, less computationally expensive results calculated neglecting spin will be sufficient for guiding electromagnetic follow-up.Comment: 10 pages, 9 figure