Hog1 bypasses stress-mediated down-regulation of transcription by RNA polymerase II redistribution and chromatin remodeling

Cells are subjected to dramatic changes of gene expression upon environmental changes. Stresscauses a general down-regulation of gene expression together with the induction of a set of stress-responsivegenes. The p38-related stress-activated protein kinase Hog1 is an important regulator of transcription uponosmostress in yeast. Genome-wide localization studies of RNA polymerase II (RNA Pol II) and Hog1 showed that stress induced major changes in RNA Pol II localization, with a shift toward stress-responsive genes relative to housekeeping genes. RNA Pol II relocalization required Hog1, which was also localized to stress-responsive loci. In addition to RNA Pol II-bound genes, Hog1 also localized to RNA polymerase III-bound genes, pointing to a wider role for Hog1 in transcriptional control than initially expected. Interestingly, an increasing association of Hog1 with stressresponsive genes was strongly correlated with chromatin remodeling and increased gene expression. Remarkably, MNase-Seq analysis showed that although chromatin structure was not significantly altered at a genome-wide level in response to stress, there was pronounced chromatin remodeling for those genes that displayed Hog1 association. Hog1 serves to bypass the general down-regulation of gene expression that occurs in response to osmostress, and does so both by targeting RNA Pol II machinery and by inducing chromatin remodeling at stressresponsive loci.

dKDM5/LID regulates H3K4me3 dynamics at the transcription-start site (TSS) of actively transcribed developmental genes

H3K4me3 is a histone modification that accumulates at the transcription-start site (TSS) of active genes and is known to be important for transcription activation. The way in which H3K4me3 is regulated at TSS and the actual molecular basis of its contribution to transcription remain largely unanswered. To address these questions, we have analyzed the contribution of dKDM5/LID, the main H3K4me3 demethylase in Drosophila, to the regulation of the pattern of H3K4me3. ChIP-seq results show that, at developmental genes, dKDM5/LID localizes at TSS and regulates H3K4me3. dKDM5/LID target genes are highly transcribed and enriched in active RNApol II and H3K36me3, suggesting a positive contribution to transcription. Expression-profiling show that, though weakly, dKDM5/LID target genes are significantly downregulated upon dKDM5/LID depletion. Furthermore, dKDM5/LID depletion results in decreased RNApol II occupancy, particularly by the promoter-proximal Pol lloser5 form. Our results also show that ASH2, an evolutionarily conserved factor that locates at TSS and is required for H3K4me3, binds and positively regulates dKDM5/LID target genes. However, dKDM5/LID and ASH2 do not bind simultaneously and recognize different chromatin states, enriched in H3K4me3 and not, respectively. These results indicate that, at developmental genes, dKDM5/LID and ASH2 coordinately regulate H3K4me3 at TSS and that this dynamic regulation contributes to transcription.

The genome and development-dependent transcriptomes of Pyronema confluens: a window into fungal evolution

Fungi are a large group of eukaryotes found in nearly all ecosystems. More than 250 fungal genomes have already been sequenced, greatly improving our understanding of fungal evolution, physiology, and development. However, for the Pezizomycetes, an early-diverging lineage of filamentous ascomycetes, there is so far only one genome available, namely that of the black truffle, Tuber melanosporum, a mycorrhizal species with unusual subterranean fruiting bodies. To help close the sequence gap among basal filamentous ascomycetes, and to allow conclusions about the evolution of fungal development, we sequenced the genome and assayed transcriptomes during development of Pyronema confluens, a saprobic Pezizomycete with a typical apothecium as fruiting body. With a size of 50 Mb and ~13,400 protein-coding genes, the genome is more characteristic of higher filamentous ascomycetes than the large, repeat-rich truffle genome; however, some typical features are different in the P. confluens lineage, e.g. the genomic environment of the mating type genes that is conserved in higher filamentous ascomycetes, but only partly conserved in P. confluens. On the other hand, P. confluens has a full complement of fungal photoreceptors, and expression studies indicate that light perception might be similar to distantly related ascomycetes and, thus, represent a basic feature of filamentous ascomycetes. Analysis of spliced RNA-seq sequence reads allowed the detection of natural antisense transcripts for 281 genes. The P. confluens genome contains an unusually high number of predicted orphan genes, many of which are upregulated during sexual development, consistent with the idea of rapid evolution of sex-associated genes. Comparative transcriptomics identified the transcription factor gene pro44 that is upregulated during development in P. confluens and the Sordariomycete Sordaria macrospora. The P. confluens pro44 gene (PCON_06721) was used to complement the S. macrospora pro44 deletion mutant, showing functional conservation of this developmental regulator.

Comparative transcriptomics of early dipteran development

BACKGROUND: Modern sequencing technologies have massively increased the amount of data available for comparative genomics. Whole-transcriptome shotgun sequencing (RNA-seq) provides a powerful basis for comparative studies. In particular, this approach holds great promise for emerging model species in fields such as evolutionary developmental biology (evo-devo). RESULTS: We have sequenced early embryonic transcriptomes of two non-drosophilid dipteran species: the moth midge Clogmia albipunctata, and the scuttle fly Megaselia abdita. Our analysis includes a third, published, transcriptome for the hoverfly Episyrphus balteatus. These emerging models for comparative developmental studies close an important phylogenetic gap between Drosophila melanogaster and other insect model systems. In this paper, we provide a comparative analysis of early embryonic transcriptomes across species, and use our data for a phylogenomic re-evaluation of dipteran phylogenetic relationships. CONCLUSIONS: We show how comparative transcriptomics can be used to create useful resources for evo-devo, and to investigate phylogenetic relationships. Our results demonstrate that de novo assembly of short (Illumina) reads yields high-quality, high-coverage transcriptomic data sets. We use these data to investigate deep dipteran phylogenetic relationships. Our results, based on a concatenation of 160 orthologous genes, provide support for the traditional view of Clogmia being the sister group of Brachycera (Megaselia, Episyrphus, Drosophila), rather than that of Culicomorpha (which includes mosquitoes and blackflies).

Job accessibility, employment and job-education mismatch in the metropolitan area of Barcelona

This paper analyses the effect of job accessibility by public and private transport on labour market outcomes in the metropolitan area of Barcelona. Beyond employment, we consider the effect of job accessibility on job-education mismatch, which represents a relevant aspect of job quality. We adopt a recursive system of equations that models car availability, employment and mismatch. Public transport accessibility appears as an exogenous variable in the three equations. Even though it may reflect endogenous residential sorting, falsification proofs suggest that the estimated effect of public transport accessibility is not entirely driven by the endogenous nature of residential decisions.

La movilidad laboral diaria: contrastes territoriales en el Eje Atlántico Gallego

Los procesos de aglomeración de la población y de las actividades en los nodos urbanos generan una serie de fuerzas centrífugas y centrípetas que, cada vez con más fuerza, ayudan a explicar gran parte de las actuales configuraciones territoriales. En las ciudades y sus inmediatas áreas de influencia surgen puestos de trabajo que atraen importantes movimientos de trabajadores desde unos focos a otros, dibujando estructuras territoriales de carácter axial por donde fluye un importante número de desplazamientos. Se presenta el caso de las dos provincias atlánticas gallegas, por ser un territorio que, a otras escalas de conjunto, muestra un mayor dinamismo.

Relaciones de complacencia y deberes para con los invitados

En la STS, 1a, 17.7.2007 (RJ 2007\4895, MP: Francisco Marín Castán), el Tribunal Supremo sostiene que los daños que sufre una amiga de los demandados en el inmueble de éstos al tropezar con un juguete abandonado en el suelo del pasillo, insuficientemente iluminado, no son indemnizables, porque dada la especial relación de confianza entre las partes, ese nivel extremo de diligencia no es exigible. El Tribunal parece aplicar al caso un patrón de diligencia quam in suis, la que despliega uno en sus propios asuntos, que permitiría limitar la responsabilidad a los casos de dolo o culpa grave. El trabajo comenta la sentencia y presenta, además, la clasificación entre invitee, licensee y trespasser que el Common Law norteamericano ha utilizado tradicionalmente para delimitar los niveles de cuidado de propietarios (o poseedores) de inmuebles y que el borrador No. 6 del Restatement (Third) of Torts, de 12.9.2007, ha simplificado, añadiendo a la regla tradicional de No Duty to Trespasser la de una negligencia simple para los Innocent Trespasser.

Dos raros incunables en lengua catalana

En este trabajo se ofrece una panorámica de los estimables fondos incunables de La Casa del Libro (San Juan, Puerto Rico) y se analizan los contenidos de dos impresos barceloneses en lengua catalana de temática religiosa: Vida e transit de Sanct Jheronim (1493) y Gamaliel (c. 1493). El examen de ambos ejemplares confirma su importancia, en especial del segimdo, pues se trata de un ejemplar único en el mundo. También se apuntan diversos aspectos de su dilatada trayectoria y se ofrece una hipótesis sobre su origen.

Finding and characterizing Partially Methylated Domains in human haematopoietic cells

DNA cytosine methylation has been demonstrated to be a central epigenetic modification that has essential roles in a myriad of cellular processes. Some examples of these include gene regulation, DNA-protein interactions, cellular differentiation, X-inactivation, maintenance of genome integrity by suppressing transposable elements and viruses, embryogenesis, genomic imprinting and tumourigenesis. This list is increasingly growing thanks to recent advances in genome-wide technologies, like Whole Genome Bisulfite Sequencing (WGBS-Seq). The development of this technology in research has allowed the identification of new features of the DNA methylation landscape that was not possible using previous technologies, like Partially Methylated Domains (PMDs). PMDs have been found in several cell lines, as well as in both healthy and cancer primary samples. They have been described as regions with high variability in methylation levels across individual CpG sites and intermediate methylation levels on average with respect to the genome. Here, we performed an extensive search of PMDs in a big dataset of different haematopoietic primary cells from both myeloid and lymphoid lineages. We found and characterized significant PMDs in plasma B cells, confirming that PMDs are a phenomenon that is restricted to certain differentiated cells. Additionally, we found loci aberrantly hypomethylated in a myeloma sample which overlapped with plasma B cell PMDs. Genome-wide comparison of the myeloma and plasma B cell sample revealed that this is probably also the case for other loci.

Factors explaining urban transport systems in large European cities: A cross-sectional approach

The paper analyses the link between human capital and regional economic growth in the European Union. Using different indicat The importance of effective and efficient mobility in large cities is becoming essential for planners and citizens due to its impact in terms of social, economic and geographic development. The aim of this research is to determine factors explaining urban transport systems by estimating aggregate supply and demand equations for 45 large European cities. Supply and Demand equations are separately and jointly determined using OLS and SUR estimation models. On one hand, our findings suggest the importance of economic variables on the supply of public transport. On the other, we highlight the role of those factors influencing the generalized cost of transport as main drivers of demand for public transit. Additionally, regional variables are introduced to capture institutional heterogeneity in this service, and we find that regional patterns are powerful explanatory determinants of urban transportation systems in Europe.

Effect of magnesium sulphate and L-tryptophan and genotype on the feed intake, behaviour and meat quality of pigs

Sixty-nine entire male pigs with different halothane genotype (homozygous halothanepositive – nn-, n=36; and homozygous halothane negative – NN-, n=33) were fed with a supplementation of magnesium sulphate (Mg) and/or L-tryptophan (Trp) in the diet for 5days before slaughter. Animals were housed individually and were submitted to stressful ante mortem conditions (mixed in the lorry according to treatments and transported 1h on rough roads). Individual feed intake was recorded during the 5-day treatment. At the abattoir, pig behaviour was assessed in the raceway to the stunning system and during the stunning period by exposure to CO2. Muscle pH, colour, water holding capacity, texture and cathepsin activities were determined to assess meat quality. The number of pigs with an individual feed intake lower than 2kg/day was significantly different among diets (P<0.05; Control: 8.7%; Mg&Trp: 43.5%; Trp:17.4%) and they were considered to have inadequate supplement intake. During the antemortem period, 15.2% of pigs included in the experiment died, and this percentagedecreased to 8.7% in those pigs with a feed intake > 2kg/day, all of them from thestress-sensitive pigs (nn). In general, no differences were observed in the behaviour ofpigs along the corridor leading to the stunning system and inside the CO2 stunningsystem. During the stunning procedure, Trp diet showed shorter periods of muscularexcitation than control and Mg&Trp diets. The combination of a stressful ante mortemtreatment and Mg&Trp supplementation led to carcasses with high incidence of severeskin lesions. Different meat quality results were found when considering all pigs orconsidering only those with adequate supplement intake. In this later case, Trp increased pH45 (6.15) vs Control diet (5.96) in the Longissimus thoracis (LT) muscle (P<0.05) and pH at 24h (Trp: 5.59 vs C: 5.47) led to a higher incidence of dark, firm and dry (DFD) traits in SM muscle (P<0.05). Genotype affected negatively all the meat quality traits. Seventy-five percent of LT and 60.0% of the SM muscles from nn pigs wereclassified as pale, soft and exudative (PSE), while none of the NN pigs showed these traits (P<0.0001). No significant differences were found between genotypes on the incidence of DFD meat. Due to the negative effects observed in the Mg&Trp group in feed intake and carcass quality, the utilization of a mixture of magnesium sulphate and tryptophan is not recommended

Is Self-employment a Way to Escape from Skill Mismatches?

During the last two decades, skill mismatches have become one of the most important issues of policy concern in the EU (European Commission, 2008). Hence, the literature has stressed the necessity to reduce skill mismatches. We contribute to this literature by analyzing the impact of the transition from salaried employment to self-employment on self-reported skill mismatches. To do so, we resort to the European Community Household Panel (ECHP) covering the period 1994–2001. Using panel data, we track individuals over time and measure their self-reported skill mismatch before and after the transition. Our empirical findings indicate not only that the average self-employee is less likely to declare being skill-mismatched but also that those individuals who transit from salaried employment to self-employment reduce their probability of skill mismatches after the transition. Keywords: Self-employment, skill mismatches, salaried employment. JEL Classification: L26, J24, B23 __________________________