Diversity and evolution of MicroRNA gene clusters

microRNA (miRNA) gene clusters are a group of miRNA genes clustered within a proximal distance on a chromosome. Although a large number of miRNA clusters have been uncovered in animal and plant genomes, the functional consequences of this arrangement are

Mixed source model and its adapted vocal tract filter estimate for voice transformation and synthesis

In current methods for voice transformation and speech synthesis, the vocal tract filter is usually assumed to be excited by a flat amplitude spectrum. In this article, we present a method using a mixed source model defined as a mixture of the Liljencrants-Fant (LF) model and Gaussian noise. Using the LF model, the base approach used in this presented work is therefore close to a vocoder using exogenous input like ARX-based methods or the Glottal Spectral Separation (GSS) method. Such approaches are therefore dedicated to voice processing promising an improved naturalness compared to generic signal models. To estimate the Vocal Tract Filter (VTF), using spectral division like in GSS, we show that a glottal source model can be used with any envelope estimation method conversely to ARX approach where a least square AR solution is used. We therefore derive a VTF estimate which takes into account the amplitude spectra of both deterministic and random components of the glottal source. The proposed mixed source model is controlled by a small set of intuitive and independent parameters. The relevance of this voice production model is evaluated, through listening tests, in the context of resynthesis, HMM-based speech synthesis, breathiness modification and pitch transposition. © 2012 Elsevier B.V. All rights reserved.

Numerical analysis of AC loss reduction in HTS superconducting coils using magnetic materials to divert flux

In this paper, the use of magnetic materials to divert flux in high-temperature superconductor superconducting coils and reduce transport ac loss is investigated. This particular technique is preferred over other techniques, such as striation, Roebel transposition, and twisted wires because it does not require modification to the conductor itself, which can be detrimental to the properties of the superconductor. The technique can also be implemented for existing coils. The analysis is carried out using a coil model based on the H formulation and implemented in comsol multiphysics. Both weakly and strongly magnetic materials are investigated, and it is shown that the use of such materials can divert flux and achieve a reduction in transport ac loss, which, in some cases, is quite significant. This analysis acts to provide a foundation for further optimization and experimental work in the future. © 2011 IEEE.

A miniature insertion element transposable in Microcystis sp FACHB 854

A 186-bp sequence with imperfect terminal inverted repeats and target direct repeats but without any transposase-encoding capacity was found to be transposable in an isolate derived from Microcystis sp. FACHB 854. This miniature insertion element, designated as ISM854-1, and with its homologues present at least 10 copies in the genome of Microcystis FACHB 854, is inserted into the 8-bp long and AT-rich target sequences, but none or few in other Microcystis strains. A variant of ISM854-1, denoted ISM854-1A, has perfect inverted repeat sequences and may transpose in pairs in a structure like a composite transposon. This is the first report of non-autonomous transposition of a mini-IS in a cyanobacterium.

Excision of Sleeping Beauty transposons: parameters and applications to gene therapy

A major problem in gene therapy is the determination of the rates at which gene transfer has occurred. Our work has focused on applications of the Sleeping Beauty (SB) transposon system as a non-viral vector for gene therapy. Excision of a transposon from a donor molecule and its integration into a cellular chromosome are catalyzed by SB transposase. In this study, we used a plasmid-based excision assay to study the excision step of transposition. We used the excision assay to evaluate the importance of various sequences that border the sites of excision inside and outside the transposon in order to determine the most active sequences for transposition from a donor plasmid. These findings together with our previous results in transposase binding to the terminal repeats suggest that the sequences in the transposon-junction of SB are involved in steps subsequent to DNA binding but before excision, and that they may have a role in transposase-transposon interaction. We found that SB transposons leave characteristically different footprints at excision sites in different cell types, suggesting that alternative repair machineries operate in concert with transposition. Most importantly, we found that the rates of excision correlate with the rates of transposition. We used this finding to assess transposition in livers of mice that were injected with the SB transposon and transposase. The excision assay appears to be a relatively quick and easy method to optimize protocols for delivery of genes in SB transposons to mammalian chromosomes in living animals. Copyright (C) 2004 John Wiley Sons, Ltd.

Gene transfer into genomes of human cells by the sleeping beauty transposon system

The Sleeping Beauty (SB) transposon system, derived from teleost fish sequences, is extremely effective at delivering DNA to vertebrate genomes, including those of humans. We have examined several parameters of the SB system to improve it as a potential, nonviral vector for gene therapy. Our investigation centered on three features: the carrying capacity of the transposon for efficient integration into chromosomes of HeLa cells, the effects of overexpression of the SB transposase gene on transposition rates, and improvements in the activity of SB transposase to increase insertion rates of transgenes into cellular chromosomes. We found that SB transposons of about 6 kb retained 50% of the maximal efficiency of transposition, which is sufficient to deliver 70-80% of identified human cDNAs with appropriate transcriptional regulatory sequences. Overexpression inhibition studies revealed that there are optimal ratios of SB transposase to transposon for maximal rates of transposition, suggesting that conditions of delivery of the two-part transposon system are important for the best gene-transfer efficiencies. We further refined the SB transposase to incorporate several amino acid substitutions, the result of which led to an improved transposase called SB11. With SB11 we are able to achieve transposition rates that are about 100-fold above those achieved with plasmids that insert into chromosomes by random recombination. With the recently described improvements to the transposon itself, the SB system appears to be a potential gene-transfer tool for human gene therapy.

Structure-function analysis of the inverted terminal repeats of the Sleeping Beauty transposon

Translocation of Sleeping Beauty (SB) transposon requires specific binding of SB transposase to inverted terminal repeats (ITRs) of about 230 bp at each end of the transposon, which is followed by a cut-and-paste transfer of the transposon into a target DNA sequence. The ITRs contain two imperfect direct repeats (DRs) of about 32 bp. The outer DRs are at the extreme ends of the transposon whereas the inner DRs are located inside the transposon, 165-166 bp from the outer DRs. Here we investigated the roles of the DR elements in transposition. Although there is a core transposase-binding sequence common to all of the DRs, additional adjacent sequences are required for transposition and these sequences vary in the different DRs. As a result, SB transposase binds less tightly to the outer DRs than to the inner DRs. Two DRs are required in each ITR for transposition but they are not interchangeable for efficient transposition. Each DR appears to have a distinctive role in transposition. The spacing and sequence between the DR elements in an ITR affect transposition rates, suggesting a constrained geometry is involved in the interactions of SB transposase molecules in order to achieve precise mobilization. Transposons are flanked by TA dinucleotide base-pairs that are important for excision; elimination of the TA motif on one side of the transposon significantly reduces transposition while loss of TAs on both flanks of the transposon abolishes transposition. These findings have led to the construction of a more advanced transposon that should be useful in gene transfer and insertional mutagenesis in vertebrates. (C) 2002 Elsevier Science Ltd. All rights reserved.

Noiseless method for checking the Peres separability criterion by local operations and classical communication

We present a method for checking the Peres separability criterion in an arbitrary bipartite quantum state rho(AB) within local operations and classical communication scenario. The method does not require noise operation which is needed in making the partial transposition map physically implementable. The main task for the two observers, Alice and Bob, is to measure some specific functions of the partial transposed matrix. With these functions, they can determine the eigenvalues of rho(T)(AB)(B), among which the minimum serves as an entanglement witness.

Detecting a set of entanglement measures in an unknown tripartite quantum state by local operations and classical communication

We propose a more general method for detecting a set of entanglement measures, i.e., negativities, in an arbitrary tripartite quantum state by local operations and classical communication. To accomplish the detection task using this method, three observers do not need to perform partial transposition maps by the structural physical approximation; instead, they only need to collectively measure some functions via three local networks supplemented by a classical communication. With these functions, they are able to determine the set of negativities related to the tripartite quantum state.

Entanglement conditions for mixed SU(2) and SU(1,1) systems

We derive a class of inequalities for detecting entanglement in the mixed SU(2) and SU(1, 1) systems based on the Schrodinger-Robertson indeterminacy relations in conjugation with the partial transposition. These inequalities are in general stronger than those based on the usual Heisenberg uncertainty relations for detecting entanglement. Furthermore, based on the complete reduction from SU(2) and SU(1,1) systems to bosonic systems, we derive some entanglement conditions for two-mode systems. We also use the partial reduction to obtain some inequalities in the mixed SU(2) (or SU(1, 1)) and bosonic systems.

Caratterizzazione geo-petrografica, petrologica e geochimica di rocce anatettiche del nord Sardegna

The High Grade Metamorphic Complex (HGMC) of Variscan basement of north Sardinia is characterized by the widespread of migmatites. This study is focused on two localities of NE Sardinia (Porto Ottiolu and Punta Sirenella) where ortho- and para-derivates migmatites outcrop. A geological and structural survey was carried out, leading to the realization of a geological schematic map of Punta Sirenella area. Several samples of different rocks were collected for petrographic, micro-structural minero-chemical and geochemical analyses. In the Porto Ottiolu area three main deformation phases have been identified; D1, characterized by tight folds with sub-horizontal axes, rarely preserved in paragneisses; D2, that produce a pervasive foliation oriented N100° 45°SW marked by biotite and sillimanite blastesis and locally transposed by shear zone oriented N170°; D3, late deformation phase caused symmetric folds with sub-horizontal axes with no axial plane schistosity. Leucosomes form pods and layers along S2 schistosity but also leucosomes along shear zones have been observed. In the Punta Sirenella area, three main deformation phases have been identified; D1, is manifested by the transposition of centimeter-sized leucosomes and is rarely observed in paragneisses were produce open folds with sub-vertical axes; D2, NW-SE oriented on whose XY plane three mineralogical lineation (quartz+plagioclase, fibrolite+quarz and muscovite) lie; D3, a ductile-brittle deformation phase that produce a mylonitc S3 foliation that locally become the most evident schistosity in the field oriented N140° steeply dipping toward NE. In both areas, leucosomes of sedimentary-derived migmatites are generally trondhjemitic pointing out for a H2O fluxed melting reaction, but also granitic leucosomes have been found, produced by muscovite dehydration melting. Leucosomes of migmatitic orthogneiss instead, have granitic compositions. Migmatization started early, during the compressional and crustal thickening (sin-D1, pre-D2) and was still active during exhumation stage. For each studied outcrop of migmatite pseudosections for the average mesosome composition have been calculated; these pseudosections have been used to model the P-T conditions of anatexis on the basis of the melt volume (%) of melt, Si/Al and Na/K molar ratios, modal content of garnet and Si content in metamorphic white mica. Further pseudosections have been calculated for the average composition of leucosomes in order to define the P-T conditions of the end of the crystallization through intersection of solidus curve and isopleths of Si content in white mica and/or XMg ratio in biotite. Thermodynamic modeling on ortho- and sedimentary-derived migmatites of Punta Sirenella yield P-T conditions of 1.1-1.3 GPa - 670-740°C for migmatitic event and 0.75-0.90 GPa - 660-730°C for the end of crystallization. These conditions are fit well with previous studies on adjacent rocks. Modeling of Porto Ottiolu ortho- and sedimentary-derived migmatites yield P-T conditions of 0.85-1.05 GPa - 690-730°C for migmatitic event and 0.35-0.55 GPa - 630-690°C strongly affected by re-equilibration during exhumation, expecially for crystallization conditions. Geochemical analyses of samples belonging to Porto Ottiolu and Punta Sirenella orthogneisses show a strong link with those of other orthogneisses outcropping in NE Sardinia (for instance, Lode-Mamone and Golfo Aranci) that are considered the intrusive counterparts of middle-Ordovician metavolcanics rocks outcropping in the Nappe Zone. Thus, the studied ortogneiss bodies, even lacking radiometric data, can be considered as belonging to the same magmatic cycle.

Naturalising the Highlands: geographies of mountain fieldwork in late-Victorian Scotland

Through a detailed examination of two late-Victorian field clubs dedicated to the exploration of alpine botany in the Scottish Highlands, this paper contributes to work on the historical geographies of civic science. By focusing on the scientific and social character of mountain fieldwork it analyses the reciprocal relations between the spaces, practices and science of Highland botanising and wider concerns with sociability, character and civic virtue. In so doing it investigates the transposition of a variety of discursive resources from evolutionism to tourism into the language and practices of botanical science. This focus enables the paper to complicate more general accounts of natural history in the Victorian period and to consider a number of methodological issues relevant to reconstructing the historical geographies of science.

The Y-procedure: How to extract the chemical transformation rate from reaction-diffusion data with no assumption on the kinetic model

The paper presents a new method to extract the chemical transformation rate from reaction–diffusion data with no assumption on the kinetic model (“kinetic model-free procedure”). It is a new non-steady-state kinetic characterization procedure for heterogeneous catalysts. The mathematical foundation of the Y-procedure is a Laplace-domain analysis of the two inert zones in a TZTR followed by transposition to the Fourier domain. When combined with time discretization and filtering the Y-procedure leads to an efficient practical method for reconstructing the concentration and reaction rate in the active zone. Using the Y-procedure the concentration and reaction rate of a non-steady state catalytic process can be determined without any pre-assumption regarding the type of kinetic dependence. The Y-procedure is the basis for advanced software for non-steady state kinetic data interpretation. The Y-procedure can be used to relate changes in the catalytic reaction rate and kinetic parameters to changes in the surface composition (storage) of a catalyst.

The discursive capacity of graphic design

The relationship between rhetoric and graphic design is presented in this article. The comparison between a classical orator and a graphic designer, between a discourse and a piece of design comes from the connections between with the communication and creativity. We will see how an application of the fundamentals of rhetoric can open new doors to the professional practice, the education of graphic design and the same theory of the rhetoric of the image.By the analysis of a design is exemplified the points of union that show how the arguments, operations, figures of discourse and rhetorical phases are present in the creative process of graphic design and how designers, perhaps unconsciously, use techniques that were traditional. In other words, graphic design is a rhetorical construction.There is then a transposition of a discourse model created by linguistic signs to a discourse model consists of visual and typographic signs, causing design is seen as a discursivediscipline that goes beyond the aesthetic component.

Comparative genomic analysis reveals species-dependent complexities that explain difficulties with microsatellite marker development in molluscs

Reliable population DNA molecular markers are difficult to develop for molluscs, the reasons for which are largely unknown. Identical protocols for microsatellite marker development were implemented in three gastropods. Success rates were lower for Gibbula cineraria compared to Littorina littorea and L. saxatilis. Comparative genomic analysis of 47.2?kb of microsatellite containing sequences (MCS) revealed a high incidence of cryptic repetitive DNA in their flanking regions. The majority of these were novel, and could be grouped into DNA families based upon sequence similarities. Significant inter-specific variation in abundance of cryptic repetitive DNA and DNA families was observed. Repbase scans show that a large proportion of cryptic repetitive DNA was identified as transposable elements (TEs). We argue that a large number of TEs and their transpositional activity may be linked to differential rates of DNA multiplication and recombination. This is likely to be an important factor explaining inter-specific variation in genome stability and hence microsatellite marker development success rates. Gastropods also differed significantly in the type of TEs classes (autonomous vs non-autonomous) observed. We propose that dissimilar transpositional mechanisms differentiate the TE classes in terms of their propensity for transposition, fixation and/or silencing. Consequently, the phylogenetic conservation of non-autonomous TEs, such as CvA, suggests that dispersal of these elements may have behaved as microsatellite-inducing elements. Results seem to indicate that, compared to autonomous, non-autonomous TEs maybe have a more active role in genome rearrangement processes. The implications of the findings for genomic rearrangement, stability and marker development are discussed.