Molecular architecture of human polycomb repressive complex 2.

Polycomb Repressive Complex 2 (PRC2) is essential for gene silencing, establishing transcriptional repression of specific genes by tri-methylating Lysine 27 of histone H3, a process mediated by cofactors such as AEBP2. In spite of its biological importance, little is known about PRC2 architecture and subunit organization. Here, we present the first three-dimensional electron microscopy structure of the human PRC2 complex bound to its cofactor AEBP2. Using a novel internal protein tagging-method, in combination with isotopic chemical cross-linking and mass spectrometry, we have localized all the PRC2 subunits and their functional domains and generated a detailed map of interactions. The position and stabilization effect of AEBP2 suggests an allosteric role of this cofactor in regulating gene silencing. Regions in PRC2 that interact with modified histone tails are localized near the methyltransferase site, suggesting a molecular mechanism for the chromatin-based regulation of PRC2 activity.DOI:http://dx.doi.org/10.7554/eLife.00005.001

Computational Interrogation of Transcriptional and Post-Transcriptional Mechanisms Regulating Dendritic Development

The specification and modulation of cell-type specific dendritic morphologies plays a pivotal role in nervous system development, connectivity, structural plasticity, and function. Regulation of gene expression is controlled by a wide variety of cellular and molecular mechanisms, of which two major types are transcription factors (TFs) and microRNAs (miRNAs). In Drosophila, dendritic complexity of dendritic arborization (da) sensory neurons of the peripheral nervous system are known to be regulated by two transcription factors Cut and Knot, although much remains unknown about the molecular mechanisms and regulatory networks via which they regulate the final arbor shape through spatio-temporal modulation of dendritic development and dynamics. Here we use bioinformatics analysis of transcriptomic data to identify putative genomic targets of these TFs with a particular emphasis on those that effect neuronal cytoskeletal architecture. We use transcriptomic, as well as data from various genomic and protein interaction databases, to build a weighted functional gene regulatory network for Knot, to identify the biological pathways and downstream genes that this TF regulates. To corroborate bioinformatics network predictions, knot putative targets, which classify into neuronal and cytoskeletal functional groups, have been experimentally validated by in vivo genetic perturbations to elucidate their role in Knot-mediated Class IV (CIV) dendritogenesis. MicroRNAs (miRNAs) have emerged as key post-transcriptional regulators of gene expression, however identification of biologically-relevant target genes for this epigenetic regulatory mechanism remains a significant challenge. To address this knowledge gap, we have developed a novel R based tool, IntramiR-ExploreR, that facilitates integrated discovery of miRNA targets by incorporating target databases and novel target prediction algorithm to arrive at high confidence intragenic miRNA target predictions. We have explored the efficacy of this tool using D.melanogaster as a model organism for bioinformatics analyses and functional validation, and identified targets for 83 intragenic miRNAs. Predicted targets were validated, using in vivo genetic perturbation. Moreover, we are constructing interaction maps of intragenic miRNAs focusing on neural tissues to uncover regulatory codes via which these molecules regulate gene expression to direct cellular development

A Role for Protein Phosphatase 2A in the Proliferation-Quiescence Decision

Metazoans precisely control the number of cell divisions during organ or tissue development throughout their lifetime. In adult metazoans, most differentiated cells no longer proliferate and lie in a quiescent state, also termed cell cycle exit. The decision to proliferate or to lie in quiescence is essential for development and its dysregulation may lead to defects in organogenesis, wound healing and regeneration as well as tumor formation. However, at what stage of the cell cycle the proliferation-quiescence decision occurs and what molecular mechanisms control this decision remain controversial. Here my thesis work revealed a novel role for PP2A in promoting the transition to quiescence upon terminal differentiation during tissue development. Using Drosophila eyes and wings as a model, I found that compromising PP2A activity during the final cell cycle prior to a developmentally controlled cell cycle exit leads to extra cell divisions and delayed normal exit. By systematically testing the regulatory subunits of Drosophila PP2A, I discovered that the B56 family member widerborst (wdb) is required for the role of PP2A in promoting the transition to quiescence. In particular, the PP2A/B56 complex targets cyclin-dependent kinase 2 several hours after mitosis to promote entry into quiescence, indicating when the decision occurs and how PP2A impacts the decision. I also investigated the dynamic features of the proliferation-quiescence transition using time-lapse, live imaging in mammalian cell culture. By monitoring the proliferation-quiescence transition without cell synchronization, I discovered that the quiescent state is heterogeneous. Mammalian cells can enter into either a transient or a prolonged quiescent state after mitosis, prior to the next round of cell cycle even under conditions of abundant nutrients. Notably, I showed that two sister cells born of the same mitosis can make different cell cycle decisions, with one cell entering long-term quiescence while the other re-entering the cell cycle. Consistent with my work in the Drosophila model, PP2A in mammals also plays a conserved role in promoting the entry into quiescence. The novel role of PP2A in modulation of the proliferation-quiescence decision may contribute to its tumor suppressor role and impact the emerging problem of tumor dormancy.PhDMolecular, Cellular and Developmental BiologyUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/133389/1/sunda_1.pd

No Apparent Costs for Facultative Antibiotic Production by the Soil Bacterium Pseudomonas fluorescens Pf0-1

Background: Many soil-inhabiting bacteria are known to produce secondary metabolites that can suppress microorganisms competing for the same resources. The production of antimicrobial compounds is expected to incur fitness costs for the producing bacteria. Such costs form the basis for models on the co-existence of antibiotic-producing and non-antibiotic producing strains. However, so far studies quantifying the costs of antibiotic production by bacteria are scarce. The current study reports on possible costs, for antibiotic production by Pseudomonas fluorescens Pf0-1, a soil bacterium that is induced to produce a broad-spectrum antibiotic when it is confronted with non-related bacterial competitors or supernatants of their cultures. Methodology and Principal Findings: We measured the possible cost of antibiotic production for Pseudomonas fluorescens Pf0-1 by monitoring changes in growth rate with and without induction of antibiotic production by supernatant of a bacterial competitor, namely Pedobacter sp.. Experiments were performed in liquid as well as on semi-solid media under nutrient-limited conditions that are expected to most clearly reveal fitness costs. Our results did not reveal any significant costs for production of antibiotics by Pseudomonas fluorescens Pf0-1. Comparison of growth rates of the antibioticproducing wild-type cells with those of non-antibiotic producing mutants did not reveal costs of antibiotic production either. Significance: Based on our findings we propose that the facultative production of antibiotics might not be selected to mitigate metabolic costs, but instead might be advantageous because it limits the risk of competitors evolving resistance, or even the risk of competitors feeding on the compounds produced.

Application of Integrated Interface Schema (LIS) Over Multiple WDBS To Enhance Data Unit Annotation

An annotation wrapper for the search site is automatically build and can be used to interpret new result pages from the same web database.  A growing number of databases have become web accessible through HTML form based search interfaces. The data units revisit from the underlying database are regularly encoded into the result pages dynamically for human browsing. In this paper we present an automatic annotation approach that first line up the data units on a result page into different groups such that the data in the same group have the same semantic. Then for each group we annotate it from dissimilar aspects and cumulative the different annotations to expect a final annotation label for it. Our experiments specify that the proposed approach is superior and effectual

Enhance the data alignment results using multiple annotators

The Internet presents a huge amount of useful information which is usually formatted for its users.The information which is extracted from different databases it is also called as Web database.In online shopping our required information is not present in a single position.we need deep web data collection.In this project, we present an automatic annotation approach that all records  align into a table.And similar concepts of information form as a group it is called as aggregation.For each  and every group of similar contents we assign the labels from multiple number of structures then we create final annotation.After extract the records directly we align into a annotation.No need to perform first two steps.All the user can easily understand the meaningful results

Massive open star clusters using the VVV survey, I: presentation of the data and description of the approach

Context. The ESO Public Survey “VISTA Variables in the Vía Láctea” (VVV) provides deep multi-epoch infrared observations for unprecedented 562 sq. degrees of the Galactic bulge, and adjacent regions of the disk. Aims. The VVV observations will foster the construction of a sample of Galactic star clusters with reliable and homogeneously derived physical parameters (e.g., age, distance, and mass, etc.). In this first paper in a series, the methodology employed to establish cluster parameters for the envisioned database are elaborated upon by analysing four known young open clusters: Danks 1, Danks 2, RCW 79, and DBS 132. The analysis offers a first glimpse of the information that can be gleaned from the VVV observations for clusters in the final database. Methods. Wide-field, deep JHKs VVV observations, combined with new infrared spectroscopy, are employed to constrain fundamental parameters for a subset of clusters. Results. Results are inferred from VVV near-infrared photometry and numerous low resolution spectra (typically more than 10 per cluster). The high quality of the spectra and the deep wide–field VVV photometry enables us to precisely and independently determine the characteristics of the clusters studied, which we compare to previous determinations. An anomalous reddening law in the direction of the Danks clusters is found, specifically E(J − H)/E(H − Ks) = 2.20 ± 0.06, which exceeds published values for the inner Galaxy. The G305 star forming complex, which includes the Danks clusters, lies beyond the Sagittarius-Carina spiral arm and occupies the Centaurus arm. Finally, the first deep infrared colour-magnitude diagram of RCW 79 is presented, which reveals a sizeable pre-main sequence population. A list of candidate variable stars in G305 region is reported. Conclusions. This study demonstrates the strength of the dataset and methodology employed, and constitutes the first step of a broader study which shall include reliable parameters for a sizeable number of poorly characterised and/or newly discovered clusters.Fil: Chené, A.-N.. Universidad de Valparaíso; ChileFil: Borissova, J.. Universidad de Valparaíso; ChileFil: Clarke, J. R. A.. Universidad de Valparaíso; ChileFil: Bonatto, C.. Universidade Federal do Rio Grande do Sul; BrasilFil: Majaess, D. J.. Saint Marys University; CanadáFil: Moni Bidin, C.. Universidad de Concepción; ChileFil: Sale, S. E.. Universidad de Valparaíso; ChileFil: Mauro, F.. Universidad de Concepción; ChileFil: Kurtev, R.. Universidad de Valparaíso; ChileFil: Baume, Gustavo Luis. Universidad Nacional de La Plata. Facultad de Ciencias Astronómicas y Geofísicas; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Astrofísica La Plata. Universidad Nacional de La Plata. Facultad de Ciencias Astronómicas y Geofísicas. Instituto de Astrofísica La Plata; ArgentinaFil: Feinstein Baigorri, Carlos. Universidad Nacional de La Plata. Facultad de Ciencias Astronómicas y Geofísicas; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Astrofísica La Plata. Universidad Nacional de La Plata. Facultad de Ciencias Astronómicas y Geofísicas. Instituto de Astrofísica La Plata; ArgentinaFil: Ivanov, V. D.. European Southern Observatory; ChileFil: Geisler, Doug. Universidad de Concepción; ChileFil: Catelan, M.. The Milky Way Millennium Nucleus; ChileFil: Minniti, Dante. The Milky Way Millennium Nucleus; ChileFil: Lucas, P.. University Of Hertfordshire; Reino UnidoFil: de Grijs, R.. Peking University; ChinaFil: Kumar, M. S. N.. Centro de Astrofisica da Universidade do Porto; Portuga

The Ecology and Genetics of Cirsium dissectum (L.) Hill in the British Isles and Implications for its Conservation

The aim of this study was to research the ecology and genetics of Cirsium dissectum and to discuss the implications of the results for its conservation. The ecology of C. dissectum was described through a review of the literature. Site characteristics, plant communities and reproductive biology were investigated by examining 22 populations throughout the British Isles. Microsatellite genetic markers were used to investigate levels of genetic diversity within and between these populations. Within populations, relationships between genetic diversity, population size, fitness and habitat quality (concentrating on soil nutrients and vegetation structure) were explored using multiple regression and structural equation modelling. Differentiation between populations was examined by comparing rnicrosatellite markers with morphological traits and this was supplemented by a crossing experiment that investigated the effects of inbreeding and outbreeding. This study showed that C. dissectum was a clonal species with a mixed mating system. Previous research had suggested that clonal propagation was the dominant form of reproduction but this study showed that sexual reproduction was important in this species, as levels of genotypic diversity were high. There were interactions between population size, genetic diversity, plant fitness and habitat quality. Smaller populations of C. dissectum had lower genetic diversity and this subsequently reduced plant fitness. Higher levels of bare soil and phosphorus were related to higher levels of genetic diversity; bare soil may provide establishment gaps for seedlings and clonal offspring, while phosphorus may encourage flowering and/or seedling survival. Populations of C. dissectum showed high levels of genetic differentiation and strong isolation by distance using microsatellite genetic markers. Both microsatellite genetic markers and morphological traits revealed geographical structuring between populations, but this was less pronounced using the morphological traits. Plants in Ireland showed higher levels of morphological differentiation compared to Britain. C. dissectum showed strong, early acting inbreeding depression when plants were selfed and a trend towards outbreeding depression when genetically distant populations were crossed. Populations of C. dissectum should be conserved throughout the geographical range of the species in the British Isles. Sites should be managed so that habitat heterogeneity is maintained, enabling C. dissectum rosettes to flower and to maintain bare soil for seedling establishment. Habitat restoration should use seed collected from a number of local populations of the same habitat