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Obscured High Mass X-Ray Binaries and Supergiant Fast X-ray Transients: Infrared Observations of INTEGRAL Sources (2008)

Chaty, Sylvain

A new type of high-energy binary system has been revealed by the INTEGRAL satellite. These sources are being unveiled by means of multi-wavelength optical, near- and mid-infrared observations. Among...

India is a secular state : a study of how teachers at Jiva Public School integrate religious education in their subjects (2008)

Edberg, Mikaela

This report is based on a field study that was carried out in India. The aim of this field study is to find out how the religious education is carried out at Jiva Public School in Faridabad. The...

Obscured High Mass X-Ray Binaries and Supergiant Fast X-ray Transients: Infrared Observations of INTEGRAL Sources (2008)

Chaty, Sylvain

A new type of high-energy binary system has been revealed by the INTEGRAL satellite. These sources are being unveiled by means of multi-wavelength optical, near- and mid-infrared observations. Among...

Acute effects of static stretching on vertical jump performance in children (2008)

Ertuğrul Gelen, Özcan Saygın, Kürşat Karacabey, Fatih Kılınç

This research has been made to define the acute effects of static streching on vertical jump performance in children. The research has been applied on 49 healthy male volunteer athletes who have been...

Advanced Modulation Formats for High-Bit-Rate Optical Networks (2008)

Haris, Muhammad

The objective of the proposed research is to investigate the performance of advanced modulation formats, specifically modified duobinary return-to zero (MD-RZ) modulation scheme and its long-haul...

Polynomial time algorithms for constant capacitated lot sizing problems with equal length step-wise linear costs (2008)

Akbalik, Ayse, Rapine, Christophe

This paper presents polynomial time algorithms for three extensions of the classical capacitated lot sizing problem (CLSP). We consider a constant batch size production with a fixed cost associated...

Graph decomposition into paths under length constraints (2008)

Teypaz, Nicolas, Rapine, Christophe

Given 2 integers a and b, we define an (a,b)-decomposition of a graph G =(V,E) as a partition of E into paths where the length of each path lies between a and b. In this definition paths are...

Stein's method on Wiener chaos (2008)

Nourdin, Ivan, Peccati, Giovanni

We combine Malliavin calculus with Stein's method, in order to derive explicit bounds in the Gaussian and Gamma approximations of random variables in a fixed Wiener chaos of a general Gaussian...

Polynomial time algorithms for constant capacitated lot sizing problems with equal length step-wise linear costs (2008)

Akbalik, Ayse, Rapine, Christophe

This paper presents polynomial time algorithms for three extensions of the classical capacitated lot sizing problem (CLSP). We consider a constant batch size production with a fixed cost associated...

Graph decomposition into paths under length constraints (2008)

Teypaz, Nicolas, Rapine, Christophe

Given 2 integers a and b, we define an (a,b)-decomposition of a graph G =(V,E) as a partition of E into paths where the length of each path lies between a and b. In this definition paths are...

Stein's method on Wiener chaos (2008)

Nourdin, Ivan, Peccati, Giovanni

We combine Malliavin calculus with Stein's method, in order to derive explicit bounds in the Gaussian and Gamma approximations of random variables in a fixed Wiener chaos of a general Gaussian...

A new small supernumerary marker chromosome, generating mosaic pure trisomy 16q11.1–q12.1 in a healthy man

Rodríguez, Laura, Liehr, Tomas, Martínez-Fernández, María Luisa, Lara, Ana, Torres, Antonio, Martínez-Frías, María Luisa

Here we report on a healthy and fertile 30 years old man, who was carrier of a small supernumerary marker chromosome (sSMC). The application of molecular techniques such as fluorescence in situ...

A case study of the reproducibility of transcriptional reporter cell-based RNAi screens in Drosophila

DasGupta, Ramanuj, Nybakken, Kent, Booker, Matthew, Mathey-Prevot, Bernard, Gonsalves, Foster, Changkakoty, Binita, ...

A second generation dsRNA library was used to re-assess factors that influence the outcome of transcriptional reporter-based whole-genome RNAi screens for the Wnt/Wingless (wg) and Hedgehog...

Regional differences in dosage compensation on the chicken Z chromosome

Melamed, Esther, Arnold, Arthur P

Microarray data analysis revealed a cluster of well compensated genes in the MHM (male-hypermethylated) region on chicken chromosome Zp, whereas Zq is enriched in non-compensated genes. The...

Atherosclerosis and liver inflammation induced by increased dietary cholesterol intake: a combined transcriptomics and metabolomics analysis

Kleemann, Robert, Verschuren, Lars, Van Erk, Marjan J, Nikolsky, Yuri, Cnubben, Nicole HP, Verheij, Elwin R, ...

With increasing dietary cholesterol intake the liver switches from a mainly resilient to a predominantly inflammatory state, which is associated with early lesion formation.

Rooting the eutherian tree: the power and pitfalls of phylogenomics

Nishihara, Hidenori, Okada, Norihiro, Hasegawa, Masami

In an attempt to root the eutherian tree using genome-scale data with the maximum likelihood method, a concatenate analysis supports a putatively wrong tree, whereas separate analyses of different...

Evolutionary dynamics of eukaryotic selenoproteomes: large selenoproteomes may associate with aquatic life and small with terrestrial life

Lobanov, Alexey V, Fomenko, Dmitri E, Zhang, Yan, Sengupta, Aniruddha, Hatfield, Dolph L, Gladyshev, Vadim N

In silico and metabolic labeling studies of the selenoproteomes of several eukaryotes revealed distinct selenoprotein patterns as well as an ancient origin of selenoproteins and massive, independent...

Drawing the tree of eukaryotic life based on the analysis of 2,269 manually annotated myosins from 328 species

Odronitz, Florian, Kollmar, Martin

The tree of eukaryotic life was reconstructed based on the analysis of 2,269 myosin motor domains from 328 organisms, confirming some accepted relationships of major taxa and resolving disputed and...

Identification of novel regulatory factor X (RFX) target genes by comparative genomics in Drosophila species

Laurençon, Anne, Dubruille, Raphaëlle, Efimenko, Evgeni, Grenier, Guillaume, Bissett, Ryan, Cortier, Elisabeth, ...

An RFX-binding site is shown to be conserved in the promoters of a subset of ciliary genes and a subsequent screen for this site in two Drosophila species identified novel RFX target genes that are...

Genome-wide investigation reveals pathogen-specific and shared signatures in the response of Caenorhabditis elegans to infection

Wong, Daniel, Bazopoulou, Daphne, Pujol, Nathalie, Tavernarakis, Nektarios, Ewbank, Jonathan J

Microarray analysis of the transcriptional response of C. elegans to four bacterial pathogens revealed that different infections trigger responses, some of which are common to all four pathogens,...

Identification of novel stem cell markers using gap analysis of gene expression data

Krzyzanowski, Paul M, Andrade-Navarro, Miguel A

A method for the detection of marker genes in large heterogeneous collections of gene expression data is described and applied to DNA microarray data generated from 83 mouse stem cell-related samples.

Characterization of heterotypic interaction effects in vitro to deconvolute global gene expression profiles in cancer

Buess, Martin, Nuyten, Dimitry SA, Hastie, Trevor, Nielsen, Torsten, Pesich, Robert, Brown, Patrick O

In an effort to deconvolute global gene-expression profiles, an interaction between some breast cancer cells and stromal fibroblasts was found to induce an interferon response, which may be...

Social regulation of gene expression in human leukocytes

Cole, Steve W, Hawkley, Louise C, Arevalo, Jesusa M, Sung, Caroline Y, Rose, Robert M, Cacioppo, John T

Analysis of differentially expressed in circulating leukocytes from people who chronically experienced high versus low levels of subjective social isolation (loneliness) revealed over-expression of...

The embryonic muscle transcriptome of Caenorhabditis elegans

Fox, Rebecca M, Watson, Joseph D, Von Stetina, Stephen E, McDermott, Joan, Brodigan, Thomas M, Fukushige, Tetsunari, ...

Fluorescence activated cell sorting and microarray profiling were used to identify 1,312 expressed genes that are enriched in myo-3::GFP-positive muscle cells of Caenorhabditis elegans.

Cross-species cluster co-conservation: a new method for generating protein interaction networks

Karimpour-Fard, Anis, Detweiler, Corrella S, Erickson, Kimberly D, Hunter, Lawrence, Gill, Ryan T

Cluster Co-Conservation (CCC) has been extended to a method for developing protein interaction networks based on co-conservation between protein pairs across multiple species, Cross-Species Cluster...

Metabolic peculiarities of Aspergillus niger disclosed by comparative metabolic genomics

Sun, Jibin, Lu, Xin, Rinas, Ursula, Zeng, An Ping

A genome-scale metabolic network and an in-depth genomic comparison of Aspergillus niger with seven other fungi is presented, revealing more than 1,100 enzyme-coding genes that are unique to A. niger.

Functional constraint and small insertions and deletions in the ENCODE regions of the human genome

Clark, Taane G, Andrew, Toby, Cooper, Gregory M, Margulies, Elliott H, Mullikin, James C, Balding, David J

Indel rates were observed to be reduced approximately twenty-fold in exonic ENCODE regions, five-fold in sequence that exhibits high evolutionary constraint in mammals and up to two-fold in some...

Genomic analysis reveals the major driving forces of bacterial life in the rhizosphere

Matilla, Miguel A, Espinosa-Urgel, Manuel, Rodríguez-Herva, José J, Ramos, Juan L, Ramos-González, María Isabel

A global analysis of Pseudomonas putida gene expression performed during the interaction with maize roots revealed how a bacterial population adjusts its genetic program to the specific conditions of...

Complexity and integration in the control of inner-ear development

Swiderski, Donald L, Gong, Tzy-Wen, Mustapha, Mirna

A report on the Sixth Molecular Biology of Hearing and Deafness Conference, Hinxton, UK, 11-14 July 2007.

Global 'worming'

Chalasani, Sreekanth H, Feinberg, Evan H, Hilliard, Massimo A

A report on the 16th International Caenorhabditis elegans Meeting, Los Angeles, USA, 27 June-1 July 2007.

The protamine family of sperm nuclear proteins

Balhorn, Rod

An overview of the vertebrate members of a diverse family of basic DNA-binding proteins that are synthesized in the late-stage spermatids of many animals and plants and condense the spermatid genome...

The monkey's perspective

Disotell, Todd R, Tosi, Anthony J

The sequencing of the genome of a female rhesus macaque (Macaca mulatta) of Indian origin will provide us with biomedical and evolutionary insights into both humans and Old World monkeys.

Hidden weapons of microbial destruction in plant genomes

Manners, John M

Recent bioinformatic analyses of sequenced plant genomes reveal a previously unrecognized abundance of genes encoding antimicrobial cysteine-rich peptides, representing a formidable and dynamic...

Strange days

Petsko, Gregory A

It's too bad that Al Gore who might be one of the few Democrats to be a good friend to science, who believes that reason, not faith or ideology, should decide issues, and who actually knows something...

Comparative genomic analysis of the Tribolium immune system

Zou, Zhen, Evans, Jay D, Lu, Zhiqiang, Zhao, Picheng, Williams, Michael, Sumathipala, Niranji, ...

The annotation, and comparison with homologous genes in other species, of immunity-related genes in the Tribolium castaneum genome allowed the identification of around 300 candidate defense proteins,...

Distribution patterns of small-molecule ligands in the protein universe and implications for origin of life and drug discovery

Ji, Hong-Fang, Kong, De-Xin, Shen, Liang, Chen, Ling-Ling, Ma, Bin-Guang, Zhang, Hong-Yu

Ligand-protein mapping was found to follow a power law and the preferential attachment principle, leading to the identification of the molecules, mostly nucleotide-containing compounds, that are...

Disruption and pseudoautosomal localization of the major histocompatibility complex in monotremes

Dohm, Juliane C, Tsend-Ayush, Enkhjargal, Reinhardt, Richard, Grützner, Frank, Himmelbauer, Heinz

The characterization and chromosomal mapping of major histocompatibility complex (MHC)-containing BAC clones from platypus and the short-beaked echidna reveals new insights into the evolution of both...

The temporal program of peripheral blood gene expression in the response of nonhuman primates to Ebola hemorrhagic fever

Rubins, Kathleen H, Hensley, Lisa E, Wahl-Jensen, Victoria, Daddario DiCaprio, Kathleen M, Young, Howard A, Reed, Douglas S, ...

Primate blood cells were analysed for changes in global gene expression patterns at several time points following infection with Ebola virus, providing insights into potential mechanisms of viral...

MicroRNAs show a wide diversity of expression profiles in the developing and mature central nervous system

Kapsimali, Marika, Kloosterman, Wigard P, De Bruijn, Ewart, Rosa, Frederic, Plasterk, Ronald HA, Wilson, Stephen W

A comprehensive analysis of the neuroanatomical expression profiles of 38 abundant conserved miRNAs in developing and adult zebrafish brain was performed.

Quantitative genomics of locomotor behavior in Drosophila melanogaster

Jordan, Katherine W, Carbone, Mary Anna, Yamamoto, Akihiko, Morgan, Theodore J, Mackay, Trudy FC

The locomotor behavior of Drosophila melanogaster was quantified in a large population of inbred lines derived from a single natural population, showing that many pleiotropic genes show correlated...

PyCogent: a toolkit for making sense from sequence

Knight, Rob, Maxwell, Peter, Birmingham, Amanda, Carnes, Jason, Caporaso, J Gregory, Easton, Brett C, ...

The COmparative GENomic Toolkit, a framework for probabilistic analyses of biological sequences, devising workflows and generating publication quality graphics, has been implemented in Python.

Species-specific shifts in centromere sequence composition are coincident with breakpoint reuse in karyotypically divergent lineages

Bulazel, Kira V, Ferreri, Gianni C, Eldridge, Mark DB, O'Neill, Rachel J

The evolution of three classes of centromere sequences across nine species of macropodine marsupials were compared with that of other genes, showing that each species has experienced differential...

The impact of chromatin modifiers on the timing of locus replication in mouse embryonic stem cells

Jørgensen, Helle F, Azuara, Véronique, Amoils, Shannon, Spivakov, Mikhail, Terry, Anna, Nesterova, Tatyana, ...

A panel of mutant embryonic stem (ES) cell lines lacking important chromatin modifiers was used to dissect the relationship between chromatin structure and replication timing, revealing the...

Genomic mapping of Suppressor of Hairy-wing binding sites in Drosophila

Adryan, Boris, Woerfel, Gertrud, Birch-Machin, Ian, Gao, Shan, Quick, Marie, Meadows, Lisa, ...

An analysis of Drosophila Su(Hw) binding allowed the identification of new, isolated, binding sites, and the construction of a new binding site consensus. Together with gene expression data, this...

A physical map of the bovine genome

Snelling, Warren M, Chiu, Readman, Schein, Jacqueline E, Hobbs, Matthew, Abbey, Colette A, Adelson, David L, ...

A new physical map of the bovine genome has been constructed by integrating data from genetic and radiation hybrid maps, and a new bovine BAC map, with the bovine genome draft assembly.

Comparative transcriptome analysis of embryonic and adult stem cells with extended and limited differentiation capacity

Ulloa-Montoya, Fernando, Kidder, Benjamin L, Pauwelyn, Karen A, Chase, Lucas G, Luttun, Aernout, Crabbe, Annelies, ...

Comparison of the transcriptomes of pluripotent embryonic stem cells, multipotent adult progenitor cells and lineage restricted mesenchymal stem cells identified a unique gene expression profile of...

Microarray-based gene expression profiles in multiple tissues of the domesticated silkworm, Bombyx mori

Xia, Qingyou, Cheng, Daojun, Duan, Jun, Wang, Genhong, Cheng, Tingcai, Zha, Xingfu, ...

Using a genome-wide oligonucleotide microarray, gene expression was surveyed in multiple silkworm tissues on day 3 of the fifth instar, providing a new resource for annotating the silkworm genome.

The global role of ppGpp synthesis in morphological differentiation and antibiotic production in Streptomyces coelicolor A3(2)

Hesketh, Andrew, Chen, Wenqiong Joan, Ryding, Jamie, Chang, Sherman, Bibb, Mervyn

The induction of ppGpp synthesis in Streptomyces coelicolor influenced the expression of several genomic elements characteristic of streptomycete biology, including antibiotic gene clusters,...

Network motif analysis of a multi-mode genetic-interaction network

Taylor, R James, Siegel, Andrew F, Galitski, Timothy

Statistical and computational methods for the extraction of biological information from dense multi-mode genetic-interaction networks were developed and implemented in open-source software.

Complexity, connectivity, and duplicability as barriers to lateral gene transfer

Wellner, Alon, Lurie, Mor N, Gophna, Uri

Laterally transferred genes are shown to be less involved in protein-protein interactions, and essential genes that exhibit low duplicability and high connectivity do exhibit mostly vertical descent.