Predicting structural models for silicon clusters

This article introduces an efficient method to generate structural models for medium-sized silicon clusters. Geometrical information obtained from previous investigations of small clusters is initially sorted and then introduced into our predictor algorithm in order to generate structural models for large clusters. The method predicts geometries whose binding energies are close (95%) to the corresponding value for the ground-state with very low computational cost. These predictions can be used as a very good initial guess for any global optimization algorithm. As a test case, information from clusters up to 14 atoms was used to predict good models for silicon clusters up to 20 atoms. We believe that the new algorithm may enhance the performance of most optimization methods whenever some previous information is available. (C) 2003 Wiley Periodicals, Inc.

Structural and functional evidence that a B chromosome in the characid fish Astyanax scabripinnis is an isochromosome

Astyanax scabripinnis possesses a widespread polymorphism for metacentric B chromosomes as large as the largest chromosome pair in the A complement. on the basis of C-banding pattern, it was hypothesized that these B chromosomes are isochromosomes that have arisen by means of centromere misdivision and chromatid nondisjunction. In the present paper we test this hypothesis by analysing (i) the localization of a repetitive DNA sequence on both B chromosome arms, and (ii) synaptonemal complex formation, in order to test the functional homology of both arms. Genomic DNA digested with KpnI and analysed by gel electrophoresis showed fragments in a ladder-like pattern typical of tandemly repetitive DNA. These fragments were cloned and their tandem organization in the genome was confirmed. A 51-bp long consensus sequence, which was AT-rich (59%) and contained a variable region and two imperfect reverse sequences, was obtained. Fluorescence in situ hybridization (FISH) localized this repetitive DNA into noncentromeric constitutive heterochromatin which encompasses the terminal region of some acrocentric chromosomes, the NOR region, and interstitial polymorphic heterochromatin in chromosome 24. Most remarkably, tandem repeats were almost symmetrically placed in the two arms of the B chromosome, with the exception of two additional small clusters proximally located on the slightly longer arm. Synaptonemal complex (SC) analysis showed 26 completely paired SCs in males with 1B. The ring configuration of the B univalent persisting until metaphase I suggests that the two arms formed chiasmata. All these data provided strong support for the hypothesis that the B chromosome is an isochromosome.

Chromosome Mapping of Retrotransposable Elements Rex1 and Rex3 in Three Fish Species in the Subfamily Hypoptopomatinae (Teleostei, Siluriformes, Loricariidae)

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Thermostimulated sol-gel transition in suspensions of sulfate zirconium oxychloride

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Effect of presence of an acid catalyst on structure and properties of iron-doped siloxane-polyoxyethylene nanocomposites prepared by sol-gel

In this work we investigate the effect of hydrochloric acid (HC) addition on the structure and thermal and magnetic properties of iron-doped siloxane-polyoxyethylene (POE) hybrids prepared by the sol-gel route. X-ray powder diffraction (XRD) and X-ray absorption near edge structure (XANES) results reveal the dominance of ferrihydrite nanoparticles and a mixture of this phase with FeCl4- species in the hybrid prepared without and with HCl, respectively. Thermal analysis reveals the existence of two crystalline polymeric phases in the hybrid prepared with HCl whereas hybrids prepared without HCl are amorphous. The 105 and 60 Angstrom sized ferrihydrite nanoparticles were detected by SAXS analysis of the composite prepared without and with HCl, respectively. The magnetic results suggest that in both samples antiferromagnetic nanoparticles coexist with small clusters/isolated ions. In the sample without HCl addition, larger particles dominate the magnetic behavior, while the opposite occurs for the sample prepared using HCl catalyst. (C) 2004 Elsevier B.V. All rights reserved.

A LINE2 repetitive DNA sequence from the cichlid fish, Oreochromis niloticus: sequence analysis and chromosomal distribution

We report the cloning and characterization of a long interspersed nucleotide element (LINE) fi-om a cichlid fish, Oreochromis niloticus, and show the distribution of this element, called CiLINE2 for cichlid LINE2, in the chromosomes of this species. The identification of an open reading frame in CiLINE2 with amino acid sequence similarity to reverse transcriptases encoded by LINE-like elements in Caenorhabditis elegans, Platemys spixii, Schistosoma mansoni, Gallus gallus (CRI), Drosophila melanogaster (I factor), and Homo sapiens (LINE2), as well as the structure of the element, suggest it is a member of this family of non-long terminal repeat-containing retrotransposons. Search of a DNA sequence database identified sequences similar to CiLINE2 in four other fish species (Haplotaxodon microlepis, Oreochromis mossambicus, Pseudotropheus zebra, and Fugu rubripes). Southern blot hybridization experiments revealed the presence of sequences similar to CiLINE2 in all Tilapiini species analyzed from the genera Oreochromis, Tilapia, and Sarotherodon, and gave an estimated copy number of about 5500 for the haploid genome of O. niloticus. Fluorescent in situ hybridization showed that CiLINE2 sequences were organized in small clusters dispersed over all chromosomes of O. niloticus, with a higher concentration near chromosome ends. Furthermore the long arm of chromosome 1 was strikingly enriched with this sequence. The distribution of LINE2-related elements might underlie the difference in chromosome banding patterns observed between cold-blooded vertebrates and mammals.

Short interspersed repetitive elements (SINEs) from the cichlid fish, Oreochromis niloticus, and their chromosomal localization by fluorescent in situ hybridization

In the present study, we describe the cloning and characterization of a new SINE-like element from O. niloticus (ROn-2) and show the distribution of this SINE and a previously isolated SINE, ROn-1, in the chromosomes of O. niloticus. The ROn-2 element is 359 base pairs (bp) in length, contains short direct terminal repeats, a tRNA-related region similar to tRNA Val and tRNA Arg, a tRNA-unrelated region, and a poly-A tail. Analysis of the chromosomal distribution of ROn-1 and ROn-2 by fluorescent in situ hybridization showed that both SINE sequences are present in all chromosomes of tilapia, and organized in small clusters. The only exception was a large cluster of ROn-1 repeats found in the middle of the long arm of chromosome 1. In view of our data we discuss the hypothesis that the absence of large clusters of SINE sequences and the structural composition of these sequences may explain the absence of base-specific fluorochrome bands in the chromosomes of tilapia.

QK-Means: A clustering technique based on community detection and K-Means for deployment of cluster head nodes

Wireless Sensor Networks (WSN) are a special kind of ad-hoc networks that is usually deployed in a monitoring field in order to detect some physical phenomenon. Due to the low dependability of individual nodes, small radio coverage and large areas to be monitored, the organization of nodes in small clusters is generally used. Moreover, a large number of WSN nodes is usually deployed in the monitoring area to increase WSN dependability. Therefore, the best cluster head positioning is a desirable characteristic in a WSN. In this paper, we propose a hybrid clustering algorithm based on community detection in complex networks and traditional K-means clustering technique: the QK-Means algorithm. Simulation results show that QK-Means detect communities and sub-communities thus lost message rate is decreased and WSN coverage is increased. © 2012 IEEE.

Chromosome mapping of repetitive sequences in Anostomidae species: Implications for genomic and sex chromosome evolution

Background: Members of the Anostomidae family provide an interesting model system for the study of the influence of repetitive elements on genome composition, mainly because they possess numerous heterochromatic segments and a peculiar system of female heterogamety that is restricted to a few species of the Leporinus genus. The aim of this study was to isolate and identify important new repetitive DNA elements in Anostomidae through restriction enzyme digestion, followed by cloning, characterisation and chromosome mapping of this fragment. To identify repetitive elements in other Leporinus species and expand on studies of repetitive elements in Anostomidae, hybridisation experiments were also performed using previously described probes of LeSpeI repetitive elements. Results: The 628-base pair (bp) LeSpeII fragment was hybridised to metaphase cells of L. elongatus individuals as well as those of L. macrocephalus, L. obtusidens, L. striatus, L. lacustris, L. friderici, Schizodon borellii and S. isognathus. In L. elongatus, both male and female cells contained small clusters of LeSpeII repetitive elements dispersed on all of the chromosomes, with enrichment near most of the terminal portions of the chromosomes. In the female sex chromosomes of L. elongatus (Z2,Z2/W1W 2), however, this repeated element was absent. In the remaining species, a dispersed pattern of hybridisation was observed on all chromosomes irrespective of whether or not they were sex chromosomes. The repetitive element LeSpeI produced positive hybridisations signals only in L. elongatus, L. macrocephalus and L. obtusidens, i.e., species with differentiated sex chromosomes. In the remaining species, the LeSpeI element did not produce hybridisation signals. Conclusions: Results are discussed in terms of the effects of repetitive sequences on the differentiation of the Anostomidae genome, especially with respect to sex chromosome evolution. LeSpeII showed hybridisation patterns typical of Long Interspersed Elements (LINEs). The differential distribution of this element may be linked to sex chromosome differentiation in L. elongatus species. The relationship between sex chromosome specificity and the LeSpeI element is confirmed in the species L. elongatus, L. macrocephalus and L. obtusidens. © 2012 da Silva et al.; licensee BioMed Central Ltd.

Use of conventional electrochemical techniques to produce crystalline FeRh alloys induced by Ag seed layer

By combining galvanic displacement and electrodeposition techniques, an ordered Fe20Rh80 structure deposited onto brass was investigated by X-ray diffractometry, Mössbauer spectroscopy and magnetization measurements. Mössbauer and X-ray diffraction analyses suggest that the Fe-Rh alloy directly electrodeposited onto brass displays a nanocrystalline state while a similar alloy deposited onto Ag/brass shows a faced centered cubic-like structure, with dendrites-like features. These results directly indicate that the presence of Ag seed layer is responsible for the Fe-Rh alloy crystallization process. In addition, room temperature Mössbauer data indicate firstly paramagnetic states for two Fe-species. In the dominant Fe-species (major fraction of the Mössbauer spectra), Fe atoms are situated at a cubic environment and it can be attributed to the γ-Fe20Rh80 alloy based on their hyperfine parameters. In the second species, Fe atoms are placed in a non-local symmetry, which can be related to Fe atoms at the grain boundaries or/and Fe small clusters. These Fe-clusters are in superparamagnetic state at room temperature, but they may be ordered below 45 K, as suggested by magnetization data. © 2013 Elsevier B.V. All rights reserved.

Scattered organization of the histone multigene family and transposable elements in Synbranchus

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

High genetic diversity among Pseudomonas aeruginosa and Acinetobacter spp. isolated in a public hospital in Brazil

In Brazil and other regions of the world, Pseudomonas aeruginosa and Acinetobacter spp. have emerged as important agents of nosocomial infection and are commonly involved in outbreaks. The main objective of the present study was to evaluate the genetic relationship among P. aeruginosa and Acinetobacter spp. isolated from patients in a public university hospital in northwestern Parana, Brazil, and report their antimicrobial resistance profile. A total of 75 P. aeruginosa and 94 Acinetobacter spp. isolates were phenotypically identified and tested for antibiotic susceptibility using automated methodology. Polymyxin B was tested by disk diffusion for P. aeruginosa. Metallo-beta-lactamase (MBL) was detected using a disk approximation test. Genotyping was performed using enterobacterial repetitive intergenic consensus polymerase chain reaction (ERIC-PCR). Approximately 55% of the P. aeruginosa isolates and 92% of the Acinetobacter spp. isolates were multiresistant, but none were MBL-producers. ERIC-PCR revealed the presence of small clusters of carbapenem-resistant Acinetobacter spp., most likely OXA-type carbapenemase producers. Furthermore, high genetic diversity in P. aeruginosa and Acinetobacter spp. clinical isolates was observed, suggesting that cross-transmission is not very frequent in the studied hospital.

Chromosomal location of retrotransposable REX 1 in the genomes in five Prochilodus (Teleostei: Characiformes)

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Barriers to environmental management in clusters of small businesses in Brazil and Japan: from a lack of knowledge to a decline in traditional knowledge

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Small-angle X-ray scattering from wet gels prepared from co-hydrolysis of tetraethoxysilane and vinyltriethoxysilane

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)