Publisher Correction: Temporal control of gene expression by the pioneer factor Zelda through transient interactions in hubs.

The original version of this Article contained an error in Fig. 4a, in which the "=" sign of the equation was inadvertently replaced with a "-" sign. This has been corrected in the PDF and HTML versions of the Article.

Temporal control of gene expression by the pioneer factor Zelda through transient interactions in hubs.

Pioneer transcription factors can engage nucleosomal DNA, which leads to local chromatin remodeling and to the establishment of transcriptional competence. However, the impact of enhancer priming by pioneer factors on the temporal control of gene expression and on mitotic memory remains unclear. Here we employ quantitative live imaging methods and mathematical modeling to test the effect of the pioneer factor Zelda on transcriptional dynamics and memory in Drosophila embryos. We demonstrate that increasing the number of Zelda binding sites accelerates the kinetics of nuclei transcriptional activation regardless of their transcriptional past. Despite its known pioneering activities, we show that Zelda does not remain detectably associated with mitotic chromosomes and is neither necessary nor sufficient to foster memory. We further reveal that Zelda forms sub-nuclear dynamic hubs where Zelda binding events are transient. We propose that Zelda facilitates transcriptional activation by accumulating in microenvironments where it could accelerate the duration of multiple pre-initiation steps.

Natural Computing Applied to the Underground System: A Synergistic Approach for Smart Cities.

The management and proper use of the Urban Public Transport Systems (UPTS) constitutes a critical field that has not been investigated in accordance to its relevance and urgent idiosyncrasy within the Smart Cities realm. Swarm Intelligence is a very promising paradigm to deal with such complex and dynamic systems. It presents robust, scalable, and self-organized behavior to deal with dynamic and fast changing systems. The intelligence of cities can be modelled as a swarm of digital telecommunication networks (the nerves), ubiquitously embedded intelligence, sensors and tags, and software. In this paper, a new approach based on the use of the Natural Computing paradigm and Collective Computation is shown, more concretely taking advantage of an Ant Colony Optimization algorithm variation and Fireworks algorithms to build a system that makes the complete control of the UPTS a tangible reality.

Standards not that standard.

There is a general assent on the key role of standards in Synthetic Biology. In two consecutive letters to this journal, suggestions on the assembly methods for the Registry of standard biological parts have been described. We fully agree with those authors on the need of a more flexible building strategy and we highlight in the present work two major functional challenges standardization efforts have to deal with: the need of both universal and orthogonal behaviors. We provide experimental data that clearly indicate that such engineering requirements should not be taken for granted in Synthetic Biology.

A web application for the unspecific detection of differentially expressed DNA regions in strand-specific expression data.

UNLABELLED: Genomic technologies allow laboratories to produce large-scale data sets, either through the use of next-generation sequencing or microarray platforms. To explore these data sets and obtain maximum value from the data, researchers view their results alongside all the known features of a given reference genome. To study transcriptional changes that occur under a given condition, researchers search for regions of the genome that are differentially expressed between different experimental conditions. In order to identify these regions several algorithms have been developed over the years, along with some bioinformatic platforms that enable their use. However, currently available applications for comparative microarray analysis exclusively focus on changes in gene expression within known transcribed regions of predicted protein-coding genes, the changes that occur in non-predictable genetic elements, such as non-coding RNAs. Here, we present a web application for the visualization of strand-specific tiling microarray or next-generation sequencing data that allows customized detection of differentially expressed regions all along the genome in an unspecific manner, that allows identification of all RNA sequences, predictable or not. AVAILABILITY AND IMPLEMENTATION: The web application is freely accessible at http://tilingscan.uv.es/. TilingScan is implemented in PHP and JavaScript. CONTACT: vicente.arnau@uv.es SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Engineering bacteria to form a biofilm and induce clumping in Caenorhabditis elegans.

Bacteria are needed for a vast range of biotechnological processes, which they carry out either as pure cultures or in association with other bacteria and/or fungi. The potential of bacteria as biofactories is hampered, though, by their limited mobility in solid or semisolid media such as agricultural or domestic waste. This work represents an attempt toward overcoming this limitation by associating bacterial biotechnological properties with the transport ability of the nematode Caenorhabditis elegans. We report here biofilm formation on C. elegans by engineered Escherichia coli expressing a Xhenorhabdus nematophila adhesion operon and induction of nematode social feeding behavior (clumping) through an E. coli-mediated iRNA blocking on the expression of FLP-21, a neuropeptide involved in worm solitary behavior.

Area Cinco Saltos Cuenca del Río Neuquén: Diagnóstico y acciones correctivas en el manejo integral del recurso agua

Se realiza una investigación acerca del uso del recurso agua en el ámbito del ejido municipal de Cinco Saltos tanto en el ámbito urbano como rural. El ámbito de estudio y desarrollo de la experiencia, se localiza en la cuenca baja del Río Neuquén, entre los límites NO y SE de la localidad antes mencionada, abarcando una franja que a modo de transecta toma un área desde la planicie o meseta y sus cauces aluvionales, la bajada aluvio-coluvial, y el piso del valle con sus distintos escalones o terrazas - antiguas y recientes - y la planicie de inundación del Río Neuquén. Se estudia el comportamiento del hombre en relación con el recurso natural agua, los usos que de ella hace, consumo, riego, recreación y, como a partir de esos usos se generan desechos o efluentes tanto industriales como cloacales, como de drenaje y desag³e de las tierras irrigadas

Area Cinco Saltos Cuenca del Río Neuquén: Diagnóstico y acciones correctivas en el manejo integral del recurso agua

Se realiza una investigación acerca del uso del recurso agua en el ámbito del ejido municipal de Cinco Saltos tanto en el ámbito urbano como rural. El ámbito de estudio y desarrollo de la experiencia, se localiza en la cuenca baja del Río Neuquén, entre los límites NO y SE de la localidad antes mencionada, abarcando una franja que a modo de transecta toma un área desde la planicie o meseta y sus cauces aluvionales, la bajada aluvio-coluvial, y el piso del valle con sus distintos escalones o terrazas - antiguas y recientes - y la planicie de inundación del Río Neuquén. Se estudia el comportamiento del hombre en relación con el recurso natural agua, los usos que de ella hace, consumo, riego, recreación y, como a partir de esos usos se generan desechos o efluentes tanto industriales como cloacales, como de drenaje y desag³e de las tierras irrigadas