The cell cycle–regulated genes of schizosaccharomyces pombe

Many genes are regulated as an innate part of the eukaryotic cell cycle, and a complex transcriptional network helps enable the cyclic behavior of dividing cells. This transcriptional network has been studied in Saccharomyces cerevisiae (budding yeast) and elsewhere. To provide more perspective on these regulatory mechanisms, we have used microarrays to measure gene expression through the cell cycle of Schizosaccharomyces pombe (fission yeast). The 750 genes with the most significant oscillations were identified and analyzed. There were two broad waves of cell cycle transcription, one in early/mid G2 phase, and the other near the G2/M transition. The early/mid G2 wave included many genes involved in ribosome biogenesis, possibly explaining the cell cycle oscillation in protein synthesis in S.pombe. The G2/M wave included at least three distinctly regulated clusters of genes: one large cluster including mitosis, mitotic exit, and cell separation functions, one small cluster dedicated to DNA replication, and another small cluster dedicated to cytokinesis and division. S. pombe cell cycle genes have relatively long, complex promoters containing groups of multiple DNA sequence motifs, often of two, three, or more different kinds. Many of the genes, transcription factors, and regulatory mechanisms are conserved between S. pombe and S. cerevisiae. Finally, we found preliminary evidence for a nearly genome-wide oscillation in gene expression: 2,000 or more genes undergo slight oscillations in expression as a function of the cell cycle, although whether this is adaptive, or incidental to other events in the cell, such as chromatin condensation, we do not know.

Natural or naturalized? phylogeography suggests that the abundant sea urchin arbacia lixula Is a recent Colonizer of the Mediterranean

We present the global phylogeography of the black sea urchin Arbacia lixula, an amphi-Atlantic echinoid with potential to strongly impact shallow rocky ecosystems. Sequences of the mitochondrial cytochrome c oxidase gene of 604 specimens from 24 localities were obtained, covering most of the distribution area of the species, including the Mediterranean and both shores of the Atlantic. Genetic diversity measures, phylogeographic patterns, demographic parameters and population differentiation were analysed. We found high haplotype diversity but relatively low nucleotide diversity, with 176 haplotypes grouped within three haplogroups: one is shared between Eastern Atlantic (including Mediterranean) and Brazilian populations, the second is found in Eastern Atlantic and the Mediterranean and the third is exclusively from Brazil. Significant genetic differentiation was found between Brazilian, Eastern Atlantic and Mediterranean regions, but no differentiation was found among Mediterranean sub-basins or among Eastern Atlantic sub-regions. The star-shaped topology of the haplotype network and the unimodal mismatch distributions of Mediterranean and Eastern Atlantic samples suggest that these populations have suffered very recent demographic expansions. These expansions could be dated 94-205 kya in the Mediterranean, and 31-67 kya in the Eastern Atlantic. In contrast, Brazilian populations did not show any signature of population expansion. Our results indicate that all populations of A. lixula constitute a single species. The Brazilian populations probably diverged from an Eastern Atlantic stock. The present-day genetic structure of the species in Eastern Atlantic and the Mediterranean is shaped by very recent demographic processes. Our results support the view (backed by the lack of fossil record) that A. lixula is a recent thermophilous colonizer which spread throughout the Mediterranean during a warm period of the Pleistocene, probably during the last interglacial. Implications for the possible future impact of A. lixula on shallow Mediterranean ecosystems in the context of global warming trends must be considered.

Common Variants of TLR1 Associate with Organ Dysfunction and Sustained Pro- Inflammatory Responses during Sepsis

Background: Toll-like receptors (TLRs) are critical components for host pathogen recognition and variants in genes participating in this response influence susceptibility to infections. Recently, TLR1 gene polymorphisms have been found correlated with whole blood hyper-inflammatory responses to pathogen-associated molecules and associated with sepsis-associated multiorgan dysfunction and acute lung injury (ALI). We examined the association of common variants of TLR1 gene with sepsis-derived complications in an independent study and with serum levels for four inflammatory biomarker among septic patients. Methodology/Principal Findings: Seven tagging single nucleotide polymorphisms of the TLR1 gene were genotyped in samples from a prospective multicenter case-only study of patients with severe sepsis admitted into a network of intensive care units followed for disease severity. Interleukin (IL)-1 b, IL-6, IL-10, and C-reactive protein (CRP) serum levels were measured at study entry, at 48 h and at 7th day. Alleles -7202G and 248Ser, and the 248Ser-602Ile haplotype were associated with circulatory dysfunction among severe septic patients (0.001<=p <= 0.022), and with reduced IL-10 (0.012<= p <=0.047) and elevated CRP (0.011<= p <=0.036) serum levels during the first week of sepsis development. Additionally, the -7202GG genotype was found to be associated with hospital mortality (p =0.017) and ALI (p =0.050) in a combined analysis with European Americans, suggesting common risk effects among studies Conclusions/Significance: These results partially replicate and extend previous findings, supporting that variants of TLR1 gene are determinants of severe complications during sepsis.

Diet-related buccal dental microwear patterns in central african pygmy foragers and bantu-speaking farmer and pastoralist populations.

Pygmy hunter-gatherers from Central Africa have shared a network of socioeconomic interactions with non-Pygmy Bantu speakers since agropastoral lifestyle spread across sub-Saharan Africa. Ethnographic studies have reported that their diets differ in consumption of both animal proteins and starch grains. Hunted meat and gathered plant foods, especially underground storage organs (USOs), are dietary staples for pygmies. However, scarce information exists about forager-farmer interaction and the agricultural products used by pygmies. Since the effects of dietary preferences on teeth in modern and past pygmies remain unknown, we explored dietary history through quantitative analysis of buccal microwear on cheek teeth in well-documented Baka pygmies. We then determined if microwear patterns differ among other Pygmy groups (Aka, Mbuti, and Babongo) and between Bantu-speaking farmer and pastoralist populations from past centuries. The buccal dental microwear patterns of Pygmy hunter-gatherers and non-Pygmy Bantu pastoralists show lower scratch densities, indicative of diets more intensively based on nonabrasive foodstuffs, compared with Bantu farmers, who consume larger amounts of grit from stoneground foods. The Baka pygmies showed microwear patterns similar to those of ancient Aka and Mbuti, suggesting that the mechanical properties of their preferred diets have not significantly changed through time. In contrast, Babongo pygmies showed scratch densities and lengths similar to those of the farmers, consistent with sociocultural contacts and genetic factors. Our findings support that buccal microwear patterns predict dietary habits independent of ecological conditions and reflect the abrasive properties of preferred or fallback foods such as USOs, which may have contributed to the dietary specializations of ancient human populations.

Asymmetric stochastic switching driven by intrinsic molecular noise

Low-copy-number molecules are involved in many functions in cells. The intrinsic fluctuations of these numbers can enable stochastic switching between multiple steady states, inducing phenotypic variability. Herein we present a theoretical and computational study based on Master Equations and Fokker-Planck and Langevin descriptions of stochastic switching for a genetic circuit of autoactivation. We show that in this circuit the intrinsic fluctuations arising from low-copy numbers, which are inherently state-dependent, drive asymmetric switching. These theoretical results are consistent with experimental data that have been reported for the bistable system of the gallactose signaling network in yeast. Our study unravels that intrinsic fluctuations, while not required to describe bistability, are fundamental to understand stochastic switching and the dynamical relative stability of multiple states.

A systems biology approach identifies molecular networks defining skeletal muscle abnormalities in chronic obstructive pulmonary disease.

Chronic Obstructive Pulmonary Disease (COPD) is an inflammatory process of the lung inducing persistent airflow limitation. Extensive systemic effects, such as skeletal muscle dysfunction, often characterize these patients and severely limit life expectancy. Despite considerable research efforts, the molecular basis of muscle degeneration in COPD is still a matter of intense debate. In this study, we have applied a network biology approach to model the relationship between muscle molecular and physiological response to training and systemic inflammatory mediators. Our model shows that failure to co- ordinately activate expression of several tissue remodelling and bioenergetics pathways is a specific landmark of COPD diseased muscles. Our findings also suggest that this phenomenon may be linked to an abnormal expression of a number of histone modifiers, which we discovered correlate with oxygen utilization. These observations raised the interesting possibility that cell hypoxia may be a key factor driving skeletal muscle degeneration in COPD patients.

Emergence of assortative mixing between clusters of cultured neurons

The analysis of the activity of neuronal cultures is considered to be a good proxy of the functional connectivity of in vivo neuronal tissues. Thus, the functional complex network inferred from activity patterns is a promising way to unravel the interplay between structure and functionality of neuronal systems. Here, we monitor the spontaneous self-sustained dynamics in neuronal cultures formed by interconnected aggregates of neurons (clusters). Dynamics is characterized by the fast activation of groups of clusters in sequences termed bursts. The analysis of the time delays between clusters' activations within the bursts allows the reconstruction of the directed functional connectivity of the network. We propose a method to statistically infer this connectivity and analyze the resulting properties of the associated complex networks. Surprisingly enough, in contrast to what has been reported for many biological networks, the clustered neuronal cultures present assortative mixing connectivity values, meaning that there is a preference for clusters to link to other clusters that share similar functional connectivity, as well as a rich-club core, which shapes a"connectivity backbone" in the network. These results point out that the grouping of neurons and the assortative connectivity between clusters are intrinsic survival mechanisms of the culture.

The whereabouts of an ancient wonderer: Global phylogeography of the solitary ascidian Styela plicata

Genetic tools have greatly aided in tracing the sources and colonization history of introduced species. However, recurrent introductions and repeated shuffling of populations may have blurred some of the genetic signals left by ancient introductions. Styela plicata is a solitary ascidian distributed worldwide. Although its origin remains unclear, this species is believed to have spread worldwide by travelling on ship's hulls. The goals of this study were to infer the genetic structure and global phylogeography of S. plicata and to look for present-day and historical genetic patterns. Two genetic markers were used: a fragment of the mitochondrial gene Cytochrome Oxidase subunit I (COI) and a fragment of the nuclear gene Adenine Nucleotide Transporter/ADP-ATP Translocase (ANT). A total of 368 individuals for COI and 315 for ANT were sequenced from 17 locations worldwide. The levels of gene diversity were moderate for COI to high for ANT. The Mediterranean populations showed the least diversity and allelic richness for both markers, while the Indian, Atlantic and Pacific Oceans had the highest gene and nucleotide diversities. Network and phylogenetic analyses with COI and ANT revealed two groups of alleles separated by 15 and 4 mutational steps, respectively. The existence of different lineages suggested an ancient population split. However, the geographic distributions of these groups did not show any consistent pattern, indicating different phylogeographic histories for each gene. Genetic divergence was significant for many population-pairs irrespective of the geographic distance among them. Stochastic introduction events are reflected in the uneven distribution of COI and ANT allele frequencies and groups among many populations. Our results confirmed that S. plicata has been present in all studied oceans for a long time, and that recurrent colonization events and occasional shuffling among populations have determined the actual genetic structure of this species.

La tria de codi en els treballadors d'una biblioteca pública de la ciutat de Barcelona : Anàlisi de discursos

Aquest treball analitza els discursos d'unes treballadores d'una biblioteca pública a la ciutat de Barcelona. El focus d'estudi principal se centra en establir la relació entre: 1) les ideologies lingüístiques; 2) la identitat, especialment la identitat catalana, castellana i espanyola; i 3) els usos que fan de la llengua catalana i castellana les treballadores.

Diseño e implementación de una base de datos relacional para la gestión de la red de bibliotecas

Implementar una base de datos para que pueda ser integrada en un aplicativo de gestión de una red de bibliotecas y que permita obtener de forma eficiente aquellos elementos valiosos para la toma de decisiones.

Multifunctionality and Diversity in Bacterial Biofilms

Bacteria are highly diverse and drive a bulk of ecosystem processes. Analysis of relationships between diversity and single specific ecosystem processes neglects the possibility that different species perform multiple functions at the same time. The degradation of dissolved organic carbon (DOC) followed by respiration is a key bacterial function that is modulated by the availability of DOC and the capability to produce extracellular enzymes. In freshwater ecosystems, biofilms are metabolic hotspots and major sites of DOC degradation. We manipulated the diversity of biofilm forming communities which were fed with DOC differing in availability. We characterized community composition using molecular fingerprinting (T-RFLP) and measured functioning as oxygen consumption rates, the conversion of DOC in the medium, bacterial abundance and the activities of five specific enzymes. Based on assays of the extracellular enzyme activity, we calculated how the likelihood of sustaining multiple functions was affected by reduced diversity. Carbon source and biofilm age were strong drivers of community functioning, and we demonstrate how the likelihood of sustaining multifunctionality decreases with decreasing diversity

lmplementació i avaluació d'un programa dirigit a I'alfabetització de les mares amb infants estrangers en la seva llengua i en català

Teixint Cultures és un projecte de recerca-acció comunitari que intenta promoure des de I'educació d'adults, I'aprenentatge de la llengua catalana a partir dels recursos Iingüístics que les mares d'origen africà tenen en la seva llengua familiar. El programa atén a mares d'origen immigrat amb fills menors de tres anys no escolaritzats al seu càrrec (la majoria de les quals té altres fills en edat escolar que assisteixen a la tarda a la biblioteca per fer els deures escolars). Tot el projecte esta vehiculat a partir dels contes infantils. De fet, intenta recuperar els contes de tradició oral provinents del continent africà per posteriorment elaborar materials educatius bilingües (en català i en les seves llengües) que es puguin utilitzar com a llibres educatius de consulta, tant per les biblioteques públiques com pels centres educatius. El programa es realitza de forma setmanal, al llarg de dues hores, a la biblioteca pública infantil d'en Massagran de Salt. Les mares expliquen contes i llegendes rellevants de la seva infància en la seva llengua i, a partir de diferents activitats de narració, traducció i dramatització de les històries basades en una metodologia de a dual-language D, elaboren textos escrits i narracions orals en català i en la seva llengua. Posteriorment són les mateixes participants les que editen els contes a I'ordinador i elaboren digitalment un llibre de contes bilingüe. Les sessions s'han registrat en àudio i vídeo i hem estudiat el procés d'implementació del programa i les estratègies multilingües utilitzades per les participants, els educadors i voluntaris. Els resultats evidencien el progrés de les dones en I'aprenentatge del català, la modificació de les seves actituds lingüístiques i de la seva autoimatge, així com I ‘impacte positiu del programa a la comunitat pel que fa al reconeixement dels recursos lingüístics i culturals de les minories ètniques.

Implementació i avaluació d'un programa dirigit a l'alfabetització de les mares amb infants estragers en la seva llengua i en català

El projecte « Teixint Cultures » és un projecte de recerca-acció comunitari que intenta promoure des de l’àmbit de l’educació d’adults, l’aprenentatge de la llengua catalana a partir dels recursos lingüístics que les mares d’origen africà tenen en la seva llengua familiar. El programa es porta a terme des d’una biblioteca pública infantil, i atén a mares d’origen immigrat amb fills menors de tres anys no escolaritzats al seu càrrec. Tot el projecte està vehiculat a partir dels contes infantils. De fet, intenta recuperar els contes de tradició oral provinents del continent africà per posteriorment elaborar materials educatius bilingües (en català i en les seves llengües) que es puguin utilitzar com a llibres educatius de consulta, tant per les biblioteques públiques com pels centres educatius. Els resultats s'agrupen entres àmbits a) descripció de les característiques metodològiques i organitzatives que han fet possible el projecte; b) impacte del projecte en les participants (aprenentatge del català, actituds, satisfacció i autoestima, pràctiques al voltant de la narració i la lectura de contes a la llar); i c) impacte del projecte a la biblioteca i al context local de la població de Salt. El futur del projecte es relaciona amb el Pla d'Entorn lligat amb l'establiment de relacions de continuïtat família-escola, implicació de les entitats i associacions de persones estrangeres i el tractament educatiu de la llengua familiar de l'alumnat.

Nucleotide, cytogenetic and expression impact of the human chromosome 8p23.1 inversion polymorphism

Background: The human chromosome 8p23.1 region contains a 3.8–4.5 Mb segment which can be found in different orientations (defined as genomic inversion) among individuals. The identification of single nucleotide polymorphisms (SNPs) tightly linked to the genomic orientation of a given region should be useful to indirectly evaluate the genotypes of large genomic orientations in the individuals. Results: We have identified 16 SNPs, which are in linkage disequilibrium (LD) with the 8p23.1 inversion as detected by fluorescent in situ hybridization (FISH). The variability of the 8p23.1 orientation in 150 HapMap samples was predicted using this set of SNPs and was verified by FISH in a subset of samples. Four genes (NEIL2, MSRA, CTSB and BLK) were found differentially expressed (p<0.0005) according to the orientation of the 8p23.1 region. Finally, we have found variable levels of mosaicism for the orientation of the 8p23.1 as determined by FISH. Conclusion: By means of dense SNP genotyping of the region, haplotype-based computational analyses and FISH experiments we could infer and verify the orientation status of alleles in the 8p23.1 region by detecting two short haplotype stretches at both ends of the inverted region, which are likely the relic of the chromosome in which the original inversion occurred. Moreover, an impact of 8p23.1 inversion on gene expression levels cannot be ruled out, since four genes from this region have statistically significant different expression levels depending on the inversion status. FISH results in lymphoblastoid cell lines suggest the presence of mosaicism regarding the 8p23.1 inversion.

A general definition and nomenclature for alternative splicing events

Understanding the molecular mechanisms responsible for the regulation of the transcriptome present in eukaryotic cells isone of the most challenging tasks in the postgenomic era. In this regard, alternative splicing (AS) is a key phenomenoncontributing to the production of different mature transcripts from the same primary RNA sequence. As a plethora ofdifferent transcript forms is available in databases, a first step to uncover the biology that drives AS is to identify thedifferent types of reflected splicing variation. In this work, we present a general definition of the AS event along with anotation system that involves the relative positions of the splice sites. This nomenclature univocally and dynamically assignsa specific ‘‘AS code’’ to every possible pattern of splicing variation. On the basis of this definition and the correspondingcodes, we have developed a computational tool (AStalavista) that automatically characterizes the complete landscape of ASevents in a given transcript annotation of a genome, thus providing a platform to investigate the transcriptome diversityacross genes, chromosomes, and species. Our analysis reveals that a substantial part—in human more than a quarter—ofthe observed splicing variations are ignored in common classification pipelines. We have used AStalavista to investigate andto compare the AS landscape of different reference annotation sets in human and in other metazoan species and found thatproportions of AS events change substantially depending on the annotation protocol, species-specific attributes, andcoding constraints acting on the transcripts. The AStalavista system therefore provides a general framework to conductspecific studies investigating the occurrence, impact, and regulation of AS.