25 research outputs found
Mu Transposon Insertion Sites and Meiotic Recombination Events Co-Localize with Epigenetic Marks for Open Chromatin across the Maize Genome
The Mu transposon system of maize is highly active, with each of the ∼50–100 copies transposing on average once each generation. The approximately one dozen distinct Mu transposons contain highly similar ∼215 bp terminal inverted repeats (TIRs) and generate 9-bp target site duplications (TSDs) upon insertion. Using a novel genome walking strategy that uses these conserved TIRs as primer binding sites, Mu insertion sites were amplified from Mu stocks and sequenced via 454 technology. 94% of ∼965,000 reads carried Mu TIRs, demonstrating the specificity of this strategy. Among these TIRs, 21 novel Mu TIRs were discovered, revealing additional complexity of the Mu transposon system. The distribution of >40,000 non-redundant Mu insertion sites was strikingly non-uniform, such that rates increased in proportion to distance from the centromere. An identified putative Mu transposase binding consensus site does not explain this non-uniformity. An integrated genetic map containing more than 10,000 genetic markers was constructed and aligned to the sequence of the maize reference genome. Recombination rates (cM/Mb) are also strikingly non-uniform, with rates increasing in proportion to distance from the centromere. Mu insertion site frequencies are strongly correlated with recombination rates. Gene density does not fully explain the chromosomal distribution of Mu insertion and recombination sites, because pronounced preferences for the distal portion of chromosome are still observed even after accounting for gene density. The similarity of the distributions of Mu insertions and meiotic recombination sites suggests that common features, such as chromatin structure, are involved in site selection for both Mu insertion and meiotic recombination. The finding that Mu insertions and meiotic recombination sites both concentrate in genomic regions marked with epigenetic marks of open chromatin provides support for the hypothesis that open chromatin enhances rates of both Mu insertion and meiotic recombination
Synchronous chaos and broad band gamma rhythm in a minimal multi-layer model of primary visual cortex
Visually induced neuronal activity in V1 displays a marked gamma-band
component which is modulated by stimulus properties. It has been argued that
synchronized oscillations contribute to these gamma-band activity [...
however,] even when oscillations are observed, they undergo temporal
decorrelation over very few cycles. This is not easily accounted for in
previous network modeling of gamma oscillations. We argue here that
interactions between cortical layers can be responsible for this fast
decorrelation. We study a model of a V1 hypercolumn, embedding a simplified
description of the multi-layered structure of the cortex. When the stimulus
contrast is low, the induced activity is only weakly synchronous and the
network resonates transiently without developing collective oscillations. When
the contrast is high, on the other hand, the induced activity undergoes
synchronous oscillations with an irregular spatiotemporal structure expressing
a synchronous chaotic state. As a consequence the population activity undergoes
fast temporal decorrelation, with concomitant rapid damping of the oscillations
in LFPs autocorrelograms and peak broadening in LFPs power spectra. [...]
Finally, we argue that the mechanism underlying the emergence of synchronous
chaos in our model is in fact very general. It stems from the fact that gamma
oscillations induced by local delayed inhibition tend to develop chaos when
coupled by sufficiently strong excitation.Comment: 49 pages, 11 figures, 7 table
Draft genome sequence of Burkholderia gladioli strain UCD-UG_CHAPALOTE (phylum Proteobacteria)
© 2015 Ettinger et al. Here, we present the draft genome of Burkholderia gladioli strain UCD-UG_CHAPALOTE. This strain is an endophyte isolated from surface sterilized seeds of an ancient Mexican landrace of corn, Chapalote. The genome contains 8,527,129 bp in 109 scaffolds