Collective Almost Synchronization in Complex Networks

This work introduces the phenomenon of Collective Almost Synchronization (CAS), which describes a universal way of how patterns can appear in complex networks even for small coupling strengths. The CAS phenomenon appears due to the existence of an approximately constant local mean field and is characterized by having nodes with trajectories evolving around periodic stable orbits. Common notion based on statistical knowledge would lead one to interpret the appearance of a local constant mean field as a consequence of the fact that the behavior of each node is not correlated to the behaviors of the others. Contrary to this common notion, we show that various well known weaker forms of synchronization (almost, time-lag, phase synchronization, and generalized synchronization) appear as a result of the onset of an almost constant local mean field. If the memory is formed in a brain by minimising the coupling strength among neurons and maximising the number of possible patterns, then the CAS phenomenon is a plausible explanation for it.Comment: 3 figure

The evolutionary dynamics of the Helena retrotransposon revealed by sequenced Drosophila genomes

<p>Abstract</p> <p>Background</p> <p>Several studies have shown that genomes contain a mixture of transposable elements, some of which are still active and others ancient relics that have degenerated. This is true for the non-LTR retrotransposon <it>Helena</it>, of which only degenerate sequences have been shown to be present in some species (<it>Drosophila melanogaster</it>), whereas putatively active sequences are present in others (<it>D. simulans</it>). Combining experimental and population analyses with the sequence analysis of the 12 <it>Drosophila </it>genomes, we have investigated the evolution of <it>Helena</it>, and propose a possible scenario for the evolution of this element.</p> <p>Results</p> <p>We show that six species of <it>Drosophila </it>have the <it>Helena </it>transposable element at different stages of its evolution. The copy number is highly variable among these species, but most of them are truncated at the 5' ends and also harbor several internal deletions and insertions suggesting that they are inactive in all species, except in <it>D. mojavensis </it>in which quantitative RT-PCR experiments have identified a putative active copy.</p> <p>Conclusion</p> <p>Our data suggest that <it>Helena </it>was present in the common ancestor of the <it>Drosophila </it>genus, which has been vertically transmitted to the derived lineages, but that it has been lost in some of them. The wide variation in copy number and sequence degeneration in the different species suggest that the evolutionary dynamics of <it>Helena </it>depends on the genomic environment of the host species.</p

The protist Trichomonas vaginalis harbors multiple lineages of transcriptionally active Mutator-like elements

<p>Abstract</p> <p>Background</p> <p>For three decades the <it>Mutator </it>system was thought to be exclusive of plants, until the first homolog representatives were characterized in fungi and in early-diverging amoebas earlier in this decade.</p> <p>Results</p> <p>Here, we describe and characterize four families of <it>Mutator</it>-like elements in a new eukaryotic group, the Parabasalids. These <b><it>T</it></b><it>richomonas </it><b><it>v</it></b><it>aginalis </it><it><b>Mu</b>tator- <b>l</b>ike </it><it><b>e</b>lements</it>, or <it>TvMULEs</it>, are active in <it>T. vaginalis </it>and patchily distributed among 12 trichomonad species and isolates. Despite their relatively distinctive amino acid composition, the inclusion of the repeats <it>TvMULE1</it>, <it>TvMULE2</it>, <it>TvMULE3 </it>and <it>TvMULE4 </it>into the <it>Mutator </it>superfamily is justified by sequence, structural and phylogenetic analyses. In addition, we identified three new <it>TvMULE</it>-related sequences in the genome sequence of <it>Candida albicans</it>. While <it>TvMULE1 </it>is a member of the <it>MuDR </it>clade, predominantly from plants, the other three <it>TvMULEs</it>, together with the <it>C. albicans </it>elements, represent a new and quite distinct <it>Mutator </it>lineage, which we named <it>TvCaMULEs</it>. The finding of <it>TvMULE1 </it>sequence inserted into other putative repeat suggests the occurrence a novel TE family not yet described.</p> <p>Conclusion</p> <p>These findings expand the taxonomic distribution and the range of functional motif of <it>MULEs </it>among eukaryotes. The characterization of the dynamics of <it>TvMULEs </it>and other transposons in this organism is of particular interest because it is atypical for an asexual species to have such an extreme level of TE activity; this genetic landscape makes an interesting case study for causes and consequences of such activity. Finally, the extreme repetitiveness of the <it>T. vaginalis </it>genome and the remarkable degree of sequence identity within its repeat families highlights this species as an ideal system to characterize new transposable elements.</p

Distribuição de elementos transponíveis em cromossomos de coffea arabica

Nos últimos anos o Brasil vem se destacando na pesquisa genética de cafeeiros, principalmente na área de melhoramento. Recentemente, a pesquisa em biotecnologia de cafeeiros vem ganhando espaço devido aos trabalhos em genômica, estes trabalhos juntamente com estudos citogenéticos têm contribuído muito para o entendimento da organização genômica em algumas espécies de Coffea. Neste gênero com mais de 100 espécies, as mais importantes economicamente são Coffea arabica e C. Canephora. A primeira espécie é a única e tetraplóide (2n = 44) do gênero, enquanto as demais são auto-incompatíveis e diplóides. Apesar das análises citogenéticas e moleculares indicarem que C. arabica é um anfidiplóide, ainda existe dificuldade para se confirmar os seus parentais. Isto se deve possivelmente a alta similaridade do genoma entre estas espécies de Coffea, uma possível consequência da presença de famílias repetitivas de DNA comuns a essas espécies. Porém, ainda são escassos os estudos sobre a distribuição e caracterização de famílias de DNA repetitivos em Coffea. Estes estudos limitam-se a identificar regiões heterocromáticas e localização de sítios de DNA ribossômico (DNAr) 45S e 5S. Com relação aos elementos transponíveis (TEs), foi encontrado um predomínio de retrotransposons Copia e Gypsy. Uma vez que a identificação e localização destes elementos transponíveis pode auxiliar a compreensão da organização genômica das espécies de Coffea, o objetivo deste estudo foi identificar a distribuição cromossômica em C. arabica de três elementos transponíveis. Para isso sondas de três clones contendo as sequências de elementos transponíveis, dois transposons MuDR e Tip100 (Ca_TE-009, Ca_TE-050) e um retrotransposon LTR deal (Ca_TE-079), foram hibridadas em Coffea arabica. Os resultados indicam uma distribuição co-localizada entre os transposons analisados e regiões terminais heterocromáticas, contudo o retroelemento possui uma distribuição mais dispersa. Estudos futuros serão feitos para identificar a distribuição destes elementos transponíveis nas espécies consideradas progenitoras de C. arabica

Avaliação da associação de propofol e de cloridrato de alfentanil na manutenção anestésica por infusão intravenosa contínua em cães após medicação pré-anestésica com acepromazina

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Avaliação da associação de propofol e de citrato de sufentanil na manutenção anestésica por infusão intravenosa contínua em cães após medicação pré-anestésica com acepromazina

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Diversidade de bactérias de solo sob vegetação natural e cultivo de hortaliças.

Os microrganismos do solo são componentes essenciais na manutenção do equilíbrio físico-químico e biológico do mesmo e exercem importante função que inclui a degradação de resíduos de plantas e animais e a liberação de nutrientes na cadeia alimentar. Este trabalho teve como objetivo comparar a microbiota de um solo com cobertura de mata (SMS) e outro cultivado com hortaliças (SHC), supressivos ou não a Rhizoctonia solani. Foram feitas extrações do DNA total dos solos e a partir dos mesmos, amplificação por PCR dos genes 16S rDNA, clonagem dos fragmentos e seqüenciamento dos genes do RNA ribossomal. A análise dos resultados demonstrou que essa metodologia foi eficiente para avaliação de bactérias. No solo supressivo de mata os filos mais encontrados pertencem aos das Acidobactérias, Verrucomicrobia e Actinobactérias e no solo conducente cultivado com hortaliças a maioria pertence aos filos das Proteobactérias, Firmicutes e Bacteroidetes

Usefulness of chlorezidine gluconate in 2% aqueous solution for treating bacterial pododermatitis in dogs

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Transcriptional activity, chromosomal distribution and expression effects of transposable elements in Coffea genomes

Plant genomes are massively invaded by transposable elements (TEs), many of which are located near host genes and can thus impact gene expression. In flowering plants, TE expression can be activated (de-repressed) under certain stressful conditions, both biotic and abiotic, as well as by genome stress caused by hybridization. In this study, we examined the effects of these stress agents on TE expression in two diploid species of coffee, Coffea canephora and C. eugenioides, and their allotetraploid hybrid C. arabica. We also explored the relationship of TE repression mechanisms to host gene regulation via the effects of exonized TE sequences. Similar to what has been seen for other plants, overall TE expression levels are low in Coffea plant cultivars, consistent with the existence of effective TE repression mechanisms. TE expression patterns are highly dynamic across the species and conditions assayed here are unrelated to their classification at the level of TE class or family. In contrast to previous results, cell culture conditions per se do not lead to the de-repression of TE expression in C. arabica. Results obtained here indicate that differing plant drought stress levels relate strongly to TE repression mechanisms. TEs tend to be expressed at significantly higher levels in non-irrigated samples for the drought tolerant cultivars but in drought sensitive cultivars the opposite pattern was shown with irrigated samples showing significantly higher TE expression. Thus, TE genome repression mechanisms may be finely tuned to the ideal growth and/or regulatory conditions of the specific plant cultivars in which they are active. Analysis of TE expression levels in cell culture conditions underscored the importance of nonsense-mediated mRNA decay (NMD) pathways in the repression of Coffea TEs. These same NMD mechanisms can also regulate plant host gene expression via the repression of genes that bear exonized TE sequences. (Résumé d'auteur