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PLOS Genetics: New Articles PLOS http://www.plosgenetics.org/ email@example.com Publishing science info:doi/10.1371/feed.pgen This work is licensed under a Creative Commons Attribution-Share Alike 3.0 License http://www.plosgenetics.org/${webserver-url}images/favicon.ico http://www.plosgenetics.org/${webserver-url}images/favicon.ico 2015-03-30T10:47:35Z Subscribe with My Yahoo!Subscribe with NewsGatorSubscribe with My AOLSubscribe with BloglinesSubscribe with NetvibesSubscribe with GoogleSubscribe with Pageflakes The GATA Factor elt-1 Regulates C. elegans Developmental Timing by Promoting Expression of the let-7 Family MicroRNAs Max L. Cohen et al. info:doi/10.1371/journal.pgen.1005099 2015-03-27T21:00:00Z 2015-03-27T21:00:00Z
by Max L. Cohen, Sunhong Kim, Kiyokazu Morita, Seong Heon Kim, Min Han
 Postembryonic development in Caenorhabditis elegans is a powerful model for the study of the temporal regulation of development and for the roles of microRNAs in controlling gene expression. Stable switch-like changes in gene expression occur during development as stage-specific microRNAs are expressed and subsequently down-regulate other stage-specific factors, driving developmental progression. Key genes in this regulatory network are phylogenetically conserved and include the post-transcriptional microRNA repressor LIN-28; the nuclear hormone receptor DAF-12; and the microRNAs LIN-4, LET-7, and the three LET-7 family miRNAs (miR-48, miR-84, and miR-241). DAF-12 is known to regulate transcription of miR-48, miR-84 and miR-241, but its contribution is insufficient to account for all of the transcriptional regulation implied by the mutant phenotypes. In this work, the GATA-family transcription factor ELT-1 is identified from a genetic enhancer screen as a regulator of developmental timing in parallel to DAF-12, and is shown to do so by promoting the expression of the LET-7, miR-48, miR-84, and miR-241 microRNAs. The role of ELT-1 in developmental timing is shown to be separate from its role in cell-fate maintenance during post-embryonic development. In addition, analysis of Chromatin Immnoprecipitation (ChIP) data from the modENCODE project and this work suggest that the contribution of ELT-1 to the control of let-7 family microRNA expression is likely through direct transcription regulation. http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1005099 Mitochondrial Dysfunction Reveals the Role of mRNA Poly(A) Tail Regulation in Oculopharyngeal Muscular Dystrophy Pathogenesis Aymeric Chartier et al. info:doi/10.1371/journal.pgen.1005092 2015-03-27T21:00:00Z 2015-03-27T21:00:00Z
by Aymeric Chartier, Pierre Klein, Stéphanie Pierson, Nicolas Barbezier, Teresa Gidaro, François Casas, Steven Carberry, Paul Dowling, Laurie Maynadier, Maëlle Bellec, Martine Oloko, Claude Jardel, Bodo Moritz, George Dickson, Vincent Mouly, Kay Ohlendieck, Gillian Butler-Browne, Capucine Trollet, Martine Simonelig
 Oculopharyngeal muscular dystrophy (OPMD), a late-onset disorder characterized by progressive degeneration of specific muscles, results from the extension of a polyalanine tract in poly(A) binding protein nuclear 1 (PABPN1). While the roles of PABPN1 in nuclear polyadenylation and regulation of alternative poly(A) site choice are established, the molecular mechanisms behind OPMD remain undetermined. Here, we show, using Drosophila and mouse models, that OPMD pathogenesis depends on affected poly(A) tail lengths of specific mRNAs. We identify a set of mRNAs encoding mitochondrial proteins that are down-regulated starting at the earliest stages of OPMD progression. The down-regulation of these mRNAs correlates with their shortened poly(A) tails and partial rescue of their levels when deadenylation is genetically reduced improves muscle function. Genetic analysis of candidate genes encoding RNA binding proteins using the Drosophila OPMD model uncovers a potential role of a number of them. We focus on the deadenylation regulator Smaug and show that it is expressed in adult muscles and specifically binds to the down-regulated mRNAs. In addition, the first step of the cleavage and polyadenylation reaction, mRNA cleavage, is affected in muscles expressing alanine-expanded PABPN1. We propose that impaired cleavage during nuclear cleavage/polyadenylation is an early defect in OPMD. This defect followed by active deadenylation of specific mRNAs, involving Smaug and the CCR4-NOT deadenylation complex, leads to their destabilization and mitochondrial dysfunction. These results broaden our understanding of the role of mRNA regulation in pathologies and might help to understand the molecular mechanisms underlying neurodegenerative disorders that involve mitochondrial dysfunction. http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1005092 Mutation in MRPS34 Compromises Protein Synthesis and Causes Mitochondrial Dysfunction Tara R. Richman et al. info:doi/10.1371/journal.pgen.1005089 2015-03-27T21:00:00Z 2015-03-27T21:00:00Z
by Tara R. Richman, Judith A. Ermer, Stefan M. K. Davies, Kara L. Perks, Helena M. Viola, Anne-Marie J. Shearwood, Livia C. Hool, Oliver Rackham, Aleksandra Filipovska
 The evolutionary divergence of mitochondrial ribosomes from their bacterial and cytoplasmic ancestors has resulted in reduced RNA content and the acquisition of mitochondria-specific proteins. The mitochondrial ribosomal protein of the small subunit 34 (MRPS34) is a mitochondria-specific ribosomal protein found only in chordates, whose function we investigated in mice carrying a homozygous mutation in the nuclear gene encoding this protein. The Mrps34 mutation causes a significant decrease of this protein, which we show is required for the stability of the 12S rRNA, the small ribosomal subunit and actively translating ribosomes. The synthesis of all 13 mitochondrially-encoded polypeptides is compromised in the mutant mice, resulting in reduced levels of mitochondrial proteins and complexes, which leads to decreased oxygen consumption and respiratory complex activity. The Mrps34 mutation causes tissue-specific molecular changes that result in heterogeneous pathology involving alterations in fractional shortening of the heart and pronounced liver dysfunction that is exacerbated with age. The defects in mitochondrial protein synthesis in the mutant mice are caused by destabilization of the small ribosomal subunit that affects the stability of the mitochondrial ribosome with age. http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1005089 Transcriptomic Profiling of Yersinia pseudotuberculosis Reveals Reprogramming of the Crp Regulon by Temperature and Uncovers Crp as a Master Regulator of Small RNAs Aaron M. Nuss et al. info:doi/10.1371/journal.pgen.1005087 2015-03-27T21:00:00Z 2015-03-27T21:00:00Z
by Aaron M. Nuss, Ann Kathrin Heroven, Barbara Waldmann, Jan Reinkensmeier, Michael Jarek, Michael Beckstette, Petra Dersch
 One hallmark of pathogenic yersiniae is their ability to rapidly adjust their life-style and pathogenesis upon host entry. In order to capture the range, magnitude and complexity of the underlying gene control mechanisms we used comparative RNA-seq-based transcriptomic profiling of the enteric pathogen Y. pseudotuberculosis under environmental and infection-relevant conditions. We identified 1151 individual transcription start sites, multiple riboswitch-like RNA elements, and a global set of antisense RNAs and previously unrecognized trans-acting RNAs. Taking advantage of these data, we revealed a temperature-induced and growth phase-dependent reprogramming of a large set of catabolic/energy production genes and uncovered the existence of a thermo-regulated 'acetate switch', which appear to prime the bacteria for growth in the digestive tract. To elucidate the regulatory architecture linking nutritional status to virulence we also refined the CRP regulon. We identified a massive remodelling of the CRP-controlled network in response to temperature and discovered CRP as a transcriptional master regulator of numerous conserved and newly identified non-coding RNAs which participate in this process. This finding highlights a novel level of complexity of the regulatory network in which the concerted action of transcriptional regulators and multiple non-coding RNAs under control of CRP adjusts the control of Yersinia fitness and virulence to the requirements of their environmental and virulent life-styles. http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1005087 Systems Biology of Tissue-Specific Response to Anaplasma phagocytophilum Reveals Differentiated Apoptosis in the Tick Vector Ixodes scapularis Nieves Ayllón et al. info:doi/10.1371/journal.pgen.1005120 2015-03-27T21:00:00Z 2015-03-27T21:00:00Z
by Nieves Ayllón, Margarita Villar, Ruth C. Galindo, Katherine M. Kocan, Radek Šíma, Juan A. López, Jesús Vázquez, Pilar Alberdi, Alejandro Cabezas-Cruz, Petr Kopáček, José de la Fuente
 Anaplasma phagocytophilum is an emerging pathogen that causes human granulocytic anaplasmosis. Infection with this zoonotic pathogen affects cell function in both vertebrate host and the tick vector, Ixodes scapularis. Global tissue-specific response and apoptosis signaling pathways were characterized in I. scapularis nymphs and adult female midguts and salivary glands infected with A. phagocytophilum using a systems biology approach combining transcriptomics and proteomics. Apoptosis was selected for pathway-focused analysis due to its role in bacterial infection of tick cells. The results showed tissue-specific differences in tick response to infection and revealed differentiated regulation of apoptosis pathways. The impact of bacterial infection was more pronounced in tick nymphs and midguts than in salivary glands, probably reflecting bacterial developmental cycle. All apoptosis pathways described in other organisms were identified in I. scapularis, except for the absence of the Perforin ortholog. Functional characterization using RNA interference showed that Porin knockdown significantly increases tick colonization by A. phagocytophilum. Infection with A. phagocytophilum produced complex tissue-specific alterations in transcript and protein levels. In tick nymphs, the results suggested a possible effect of bacterial infection on the inhibition of tick immune response. In tick midguts, the results suggested that A. phagocytophilum infection inhibited cell apoptosis to facilitate and establish infection through up-regulation of the JAK/STAT pathway. Bacterial infection inhibited the intrinsic apoptosis pathway in tick salivary glands by down-regulating Porin expression that resulted in the inhibition of Cytochrome c release as the anti-apoptotic mechanism to facilitate bacterial infection. However, tick salivary glands may promote apoptosis to limit bacterial infection through induction of the extrinsic apoptosis pathway. These dynamic changes in response to A. phagocytophilum in I. scapularis tissue-specific transcriptome and proteome demonstrated the complexity of the tick response to infection and will contribute to characterize gene regulation in ticks. http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1005120 HOMER2, a Stereociliary Scaffolding Protein, Is Essential for Normal Hearing in Humans and Mice Hela Azaiez et al. info:doi/10.1371/journal.pgen.1005137 2015-03-27T21:00:00Z 2015-03-27T21:00:00Z
by Hela Azaiez, Amanda R. Decker, Kevin T. Booth, Allen C. Simpson, A. Eliot Shearer, Patrick L. M. Huygen, Fengxiao Bu, Michael S. Hildebrand, Paul T. Ranum, Seiji B. Shibata, Ann Turner, Yuzhou Zhang, William J. Kimberling, Robert A. Cornell, Richard J. H. Smith
 Hereditary hearing loss is a clinically and genetically heterogeneous disorder. More than 80 genes have been implicated to date, and with the advent of targeted genomic enrichment and massively parallel sequencing (TGE+MPS) the rate of novel deafness-gene identification has accelerated. Here we report a family segregating post-lingual progressive autosomal dominant non-syndromic hearing loss (ADNSHL). After first excluding plausible variants in known deafness-causing genes using TGE+MPS, we completed whole exome sequencing in three hearing-impaired family members. Only a single variant, p.Arg185Pro in HOMER2, segregated with the hearing-loss phenotype in the extended family. This amino acid change alters a highly conserved residue in the coiled-coil domain of HOMER2 that is essential for protein multimerization and the HOMER2-CDC42 interaction. As a scaffolding protein, HOMER2 is involved in intracellular calcium homeostasis and cytoskeletal organization. Consistent with this function, we found robust expression in stereocilia of hair cells in the murine inner ear and observed that over-expression of mutant p.Pro185 HOMER2 mRNA causes anatomical changes of the inner ear and neuromasts in zebrafish embryos. Furthermore, mouse mutants homozygous for the targeted deletion of Homer2 present with early-onset rapidly progressive hearing loss. These data provide compelling evidence that HOMER2 is required for normal hearing and that its sequence alteration in humans leads to ADNSHL through a dominant-negative mode of action. http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1005137 Synergistic Interactions between Drosophila Orthologues of Genes Spanned by De Novo Human CNVs Support Multiple-Hit Models of Autism Stuart J. Grice et al. info:doi/10.1371/journal.pgen.1004998 2015-03-27T21:00:00Z 2015-03-27T21:00:00Z
by Stuart J. Grice, Ji-Long Liu, Caleb Webber
 Autism spectrum disorders (ASDs) are highly heritable and characterised by deficits in social interaction and communication, as well as restricted and repetitive behaviours. Although a number of highly penetrant ASD gene variants have been identified, there is growing evidence to support a causal role for combinatorial effects arising from the contributions of multiple loci. By examining synaptic and circadian neurological phenotypes resulting from the dosage variants of unique human:fly orthologues in Drosophila, we observe numerous synergistic interactions between pairs of informatically-identified candidate genes whose orthologues are jointly affected by large de novo copy number variants (CNVs). These CNVs were found in the genomes of individuals with autism, including a patient carrying a 22q11.2 deletion. We first demonstrate that dosage alterations of the unique Drosophila orthologues of candidate genes from de novo CNVs that harbour only a single candidate gene display neurological defects similar to those previously reported in Drosophila models of ASD-associated variants. We then considered pairwise dosage changes within the set of orthologues of candidate genes that were affected by the same single human de novo CNV. For three of four CNVs with complete orthologous relationships, we observed significant synergistic effects following the simultaneous dosage change of gene pairs drawn from a single CNV. The phenotypic variation observed at the Drosophila synapse that results from these interacting genetic variants supports a concordant phenotypic outcome across all interacting gene pairs following the direction of human gene copy number change. We observe both specificity and transitivity between interactors, both within and between CNV candidate gene sets, supporting shared and distinct genetic aetiologies. We then show that different interactions affect divergent synaptic processes, demonstrating distinct molecular aetiologies. Our study illustrates mechanisms through which synergistic effects resulting from large structural variation can contribute to human disease. http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1004998 GAGA Factor Maintains Nucleosome-Free Regions and Has a Role in RNA Polymerase II Recruitment to Promoters Nicholas J. Fuda et al. info:doi/10.1371/journal.pgen.1005108 2015-03-27T21:00:00Z 2015-03-27T21:00:00Z
by Nicholas J. Fuda, Michael J. Guertin, Sumeet Sharma, Charles G. Danko, André L. Martins, Adam Siepel, John T. Lis
 Previous studies have shown that GAGA Factor (GAF) is enriched on promoters with paused RNA Polymerase II (Pol II), but its genome-wide function and mechanism of action remain largely uncharacterized. We assayed the levels of transcriptionally-engaged polymerase using global run-on sequencing (GRO-seq) in control and GAF-RNAi Drosophila S2 cells and found promoter-proximal polymerase was significantly reduced on a large subset of paused promoters where GAF occupancy was reduced by knock down. These promoters show a dramatic increase in nucleosome occupancy upon GAF depletion. These results, in conjunction with previous studies showing that GAF directly interacts with nucleosome remodelers, strongly support a model where GAF directs nucleosome displacement at the promoter and thereby allows the entry Pol II to the promoter and pause sites. This action of GAF on nucleosomes is at least partially independent of paused Pol II because intergenic GAF binding sites with little or no Pol II also show GAF-dependent nucleosome displacement. In addition, the insulator factor BEAF, the BEAF-interacting protein Chriz, and the transcription factor M1BP are strikingly enriched on those GAF-associated genes where pausing is unaffected by knock down, suggesting insulators or the alternative promoter-associated factor M1BP protect a subset of GAF-bound paused genes from GAF knock-down effects. Thus, GAF binding at promoters can lead to the local displacement of nucleosomes, but this activity can be restricted or compensated for when insulator protein or M1BP complexes also reside at GAF bound promoters. http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1005108 Ccr4-Not Regulates RNA Polymerase I Transcription and Couples Nutrient Signaling to the Control of Ribosomal RNA Biogenesis R. Nicholas Laribee et al. info:doi/10.1371/journal.pgen.1005113 2015-03-27T21:00:00Z 2015-03-27T21:00:00Z
by R. Nicholas Laribee, Amira Hosni-Ahmed, Jason J. Workman, Hongfeng Chen
 Ribosomal RNA synthesis is controlled by nutrient signaling through the mechanistic target of rapamycin complex 1 (mTORC1) pathway. mTORC1 regulates ribosomal RNA expression by affecting RNA Polymerase I (Pol I)-dependent transcription of the ribosomal DNA (rDNA) but the mechanisms involved remain obscure. This study provides evidence that the Ccr4-Not complex, which regulates RNA Polymerase II (Pol II) transcription, also functions downstream of mTORC1 to control Pol I activity. Ccr4-Not localizes to the rDNA and physically associates with the Pol I holoenzyme while Ccr4-Not disruption perturbs rDNA binding of multiple Pol I transcriptional regulators including core factor, the high mobility group protein Hmo1, and the SSU processome. Under nutrient rich conditions, Ccr4-Not suppresses Pol I initiation by regulating interactions with the essential transcription factor Rrn3. Additionally, Ccr4-Not disruption prevents reduced Pol I transcription when mTORC1 is inhibited suggesting Ccr4-Not bridges mTORC1 signaling with Pol I regulation. Analysis of the non-essential Pol I subunits demonstrated that the A34.5 subunit promotes, while the A12.2 and A14 subunits repress, Ccr4-Not interactions with Pol I. Furthermore, ccr4Δ is synthetically sick when paired with rpa12Δ and the double mutant has enhanced sensitivity to transcription elongation inhibition suggesting that Ccr4-Not functions to promote Pol I elongation. Intriguingly, while low concentrations of mTORC1 inhibitors completely inhibit growth of ccr4Δ, a ccr4Δ rpa12Δ rescues this growth defect suggesting that the sensitivity of Ccr4-Not mutants to mTORC1 inhibition is at least partially due to Pol I deregulation. Collectively, these data demonstrate a novel role for Ccr4-Not in Pol I transcriptional regulation that is required for bridging mTORC1 signaling to ribosomal RNA synthesis. http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1005113 Tertiary siRNAs Mediate Paramutation in C. elegans Alexandra Sapetschnig et al. info:doi/10.1371/journal.pgen.1005078 2015-03-26T21:00:00Z 2015-03-26T21:00:00Z
by Alexandra Sapetschnig, Peter Sarkies, Nicolas J. Lehrbach, Eric A. Miska
 In the nematode Caenorhabditis elegans, different small RNA-dependent gene silencing mechanisms act in the germline to initiate transgenerational gene silencing. Piwi-interacting RNAs (piRNAs) can initiate transposon and gene silencing by acting upstream of endogenous short interfering RNAs (siRNAs), which engage a nuclear RNA interference (RNAi) pathway to trigger transcriptional gene silencing. Once gene silencing has been established, it can be stably maintained over multiple generations without the requirement of the initial trigger and is also referred to as RNAe or paramutation. This heritable silencing depends on the integrity of the nuclear RNAi pathway. However, the exact mechanism by which silencing is maintained across generations is not understood. Here we demonstrate that silencing of piRNA targets involves the production of two distinct classes of small RNAs with different genetic requirements. The first class, secondary siRNAs, are localized close to the direct target site for piRNAs. Nuclear import of the secondary siRNAs by the Argonaute HRDE-1 leads to the production of a distinct class of small RNAs that map throughout the transcript, which we term tertiary siRNAs. Both classes of small RNAs are necessary for full repression of the target gene and can be maintained independently of the initial piRNA trigger. Consistently, we observed a form of paramutation associated with tertiary siRNAs. Once paramutated, a tertiary siRNA generating allele confers dominant silencing in the progeny regardless of its own transmission, suggesting germline-transmitted siRNAs are sufficient for multigenerational silencing. This work uncovers a multi-step siRNA amplification pathway that promotes germline integrity via epigenetic silencing of endogenous and invading genetic elements. In addition, the same pathway can be engaged in environmentally induced heritable gene silencing and could therefore promote the inheritance of acquired traits. http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1005078 A Genomic Portrait of Haplotype Diversity and Signatures of Selection in Indigenous Southern African Populations Emile R. Chimusa et al. info:doi/10.1371/journal.pgen.1005052 2015-03-26T21:00:00Z 2015-03-26T21:00:00Z
by Emile R. Chimusa, Ayton Meintjies, Milaine Tchanga, Nicola Mulder, Cathal Seioghe, Himla Soodyall, Rajkumar Ramesar
 We report a study of genome-wide, dense SNP (∼900K) and copy number polymorphism data of indigenous southern Africans. We demonstrate the genetic contribution to southern and eastern African populations, which involved admixture between indigenous San, Niger-Congo-speaking and populations of Eurasian ancestry. This finding illustrates the need to account for stratification in genome-wide association studies, and that admixture mapping would likely be a successful approach in these populations. We developed a strategy to detect the signature of selection prior to and following putative admixture events. Several genomic regions show an unusual excess of Niger-Kordofanian, and unusual deficiency of both San and Eurasian ancestry, which were considered the footprints of selection after population admixture. Several SNPs with strong allele frequency differences were observed predominantly between the admixed indigenous southern African populations, and their ancestral Eurasian populations. Interestingly, many candidate genes, which were identified within the genomic regions showing signals for selection, were associated with southern African-specific high-risk, mostly communicable diseases, such as malaria, influenza, tuberculosis, and human immunodeficiency virus/AIDs. This observation suggests a potentially important role that these genes might have played in adapting to the environment. Additionally, our analyses of haplotype structure, linkage disequilibrium, recombination, copy number variation and genome-wide admixture highlight, and support the unique position of San relative to both African and non-African populations. This study contributes to a better understanding of population ancestry and selection in south-eastern African populations; and the data and results obtained will support research into the genetic contributions to infectious as well as non-communicable diseases in the region. http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1005052 NLRC5 Exclusively Transactivates MHC Class I and Related Genes through a Distinctive SXY Module Kristina Ludigs et al. info:doi/10.1371/journal.pgen.1005088 2015-03-26T21:00:00Z 2015-03-26T21:00:00Z
by Kristina Ludigs, Queralt Seguín-Estévez, Sylvain Lemeille, Isabel Ferrero, Giorgia Rota, Sonia Chelbi, Chantal Mattmann, H. Robson MacDonald, Walter Reith, Greta Guarda
 MHC class II (MHCII) genes are transactivated by the NOD-like receptor (NLR) family member CIITA, which is recruited to SXY enhancers of MHCII promoters via a DNA-binding "enhanceosome" complex. NLRC5, another NLR protein, was recently found to control transcription of MHC class I (MHCI) genes. However, detailed understanding of NLRC5's target gene specificity and mechanism of action remained lacking. We performed ChIP-sequencing experiments to gain comprehensive information on NLRC5-regulated genes. In addition to classical MHCI genes, we exclusively identified novel targets encoding non-classical MHCI molecules having important functions in immunity and tolerance. ChIP-sequencing performed with Rfx5−/− cells, which lack the pivotal enhanceosome factor RFX5, demonstrated its strict requirement for NLRC5 recruitment. Accordingly, Rfx5-knockout mice phenocopy Nlrc5 deficiency with respect to defective MHCI expression. Analysis of B cell lines lacking RFX5, RFXAP, or RFXANK further corroborated the importance of the enhanceosome for MHCI expression. Although recruited by common DNA-binding factors, CIITA and NLRC5 exhibit non-redundant functions, shown here using double-deficient Nlrc5−/−CIIta−/− mice. These paradoxical findings were resolved by using a "de novo" motif-discovery approach showing that the SXY consensus sequence occupied by NLRC5 in vivo diverges significantly from that occupied by CIITA. These sequence differences were sufficient to determine preferential occupation and transactivation by NLRC5 or CIITA, respectively, and the S box was found to be the essential feature conferring NLRC5 specificity. These results broaden our knowledge on the transcriptional activities of NLRC5 and CIITA, revealing their dependence on shared enhanceosome factors but their recruitment to distinct enhancer motifs in vivo. Furthermore, we demonstrated selectivity of NLRC5 for genes encoding MHCI or related proteins, rendering it an attractive target for therapeutic intervention. NLRC5 and CIITA thus emerge as paradigms for a novel class of transcriptional regulators dedicated for transactivating extremely few, phylogenetically related genes. http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1005088 Osteopetrorickets due to Snx10 Deficiency in Mice Results from Both Failed Osteoclast Activity and Loss of Gastric Acid-Dependent Calcium Absorption Liang Ye et al. info:doi/10.1371/journal.pgen.1005057 2015-03-26T21:00:00Z 2015-03-26T21:00:00Z
by Liang Ye, Leslie R. Morse, Li Zhang, Hajime Sasaki, Jason C. Mills, Paul R. Odgren, Greg Sibbel, James R. L. Stanley, Gee Wong, Ariane Zamarioli, Ricardo A. Battaglino
 Mutations in sorting nexin 10 (Snx10) have recently been found to account for roughly 4% of all human malignant osteopetrosis, some of them fatal. To study the disease pathogenesis, we investigated the expression of Snx10 and created mouse models in which Snx10 was knocked down globally or knocked out in osteoclasts. Endocytosis is severely defective in Snx10-deficent osteoclasts, as is extracellular acidification, ruffled border formation, and bone resorption. We also discovered that Snx10 is highly expressed in stomach epithelium, with mutations leading to high stomach pH and low calcium solubilization. Global Snx10-deficiency in mice results in a combined phenotype: osteopetrosis (due to osteoclast defect) and rickets (due to high stomach pH and low calcium availability, resulting in impaired bone mineralization). Osteopetrorickets, the paradoxical association of insufficient mineralization in the context of a positive total body calcium balance, is thought to occur due to the inability of the osteoclasts to maintain normal calcium–phosphorus homeostasis. However, osteoclast-specific Snx10 knockout had no effect on calcium balance, and therefore led to severe osteopetrosis without rickets. Moreover, supplementation with calcium gluconate rescued mice from the rachitic phenotype and dramatically extended life span in global Snx10-deficient mice, suggesting that this may be a life-saving component of the clinical approach to Snx10-dependent human osteopetrosis that has previously gone unrecognized. We conclude that tissue-specific effects of Snx10 mutation need to be considered in clinical approaches to this disease entity. Reliance solely on hematopoietic stem cell transplantation can leave hypocalcemia uncorrected with sometimes fatal consequences. These studies established an essential role for Snx10 in bone homeostasis and underscore the importance of gastric acidification in calcium uptake. http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1005057 A RecA Protein Surface Required for Activation of DNA Polymerase V Angela J. Gruber et al. info:doi/10.1371/journal.pgen.1005066 2015-03-26T21:00:00Z 2015-03-26T21:00:00Z
by Angela J. Gruber, Aysen L. Erdem, Grzegorz Sabat, Kiyonobu Karata, Malgorzata M. Jaszczur, Dan D. Vo, Tayla M. Olsen, Roger Woodgate, Myron F. Goodman, Michael M. Cox
 DNA polymerase V (pol V) of Escherichia coli is a translesion DNA polymerase responsible for most of the mutagenesis observed during the SOS response. Pol V is activated by transfer of a RecA subunit from the 3'-proximal end of a RecA nucleoprotein filament to form a functional complex called DNA polymerase V Mutasome (pol V Mut). We identify a RecA surface, defined by residues 112-117, that either directly interacts with or is in very close proximity to amino acid residues on two distinct surfaces of the UmuC subunit of pol V. One of these surfaces is uniquely prominent in the active pol V Mut. Several conformational states are populated in the inactive and active complexes of RecA with pol V. The RecA D112R and RecA D112R N113R double mutant proteins exhibit successively reduced capacity for pol V activation. The double mutant RecA is specifically defective in the ATP binding step of the activation pathway. Unlike the classic non-mutable RecA S117F (recA1730), the RecA D112R N113R variant exhibits no defect in filament formation on DNA and promotes all other RecA activities efficiently. An important pol V activation surface of RecA protein is thus centered in a region encompassing amino acid residues 112, 113, and 117, a surface exposed at the 3'-proximal end of a RecA filament. The same RecA surface is not utilized in the RecA activation of the homologous and highly mutagenic RumA'2B polymerase encoded by the integrating-conjugative element (ICE) R391, indicating a lack of structural conservation between the two systems. The RecA D112R N113R protein represents a new separation of function mutant, proficient in all RecA functions except SOS mutagenesis. http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1005066 Mutations of Human NARS2, Encoding the Mitochondrial Asparaginyl-tRNA Synthetase, Cause Nonsyndromic Deafness and Leigh Syndrome Mariella Simon et al. info:doi/10.1371/journal.pgen.1005097 2015-03-25T21:00:00Z 2015-03-25T21:00:00Z
by Mariella Simon, Elodie M. Richard, Xinjian Wang, Mohsin Shahzad, Vincent H. Huang, Tanveer A. Qaiser, Prasanth Potluri, Sarah E. Mahl, Antonio Davila, Sabiha Nazli, Saege Hancock, Margret Yu, Jay Gargus, Richard Chang, Nada Al-sheqaih, William G. Newman, Jose Abdenur, Arnold Starr, Rashmi Hegde, Thomas Dorn, Anke Busch, Eddie Park, Jie Wu, Hagen Schwenzer, Adrian Flierl, Catherine Florentz, Marie Sissler, Shaheen N. Khan, Ronghua Li, Min-Xin Guan, Thomas B. Friedman, Doris K. Wu, Vincent Procaccio, Sheikh Riazuddin, Douglas C. Wallace, Zubair M. Ahmed, Taosheng Huang, Saima Riazuddin
 Here we demonstrate association of variants in the mitochondrial asparaginyl-tRNA synthetase NARS2 with human hearing loss and Leigh syndrome. A homozygous missense mutation ([c.637G>T; p.Val213Phe]) is the underlying cause of nonsyndromic hearing loss (DFNB94) and compound heterozygous mutations ([c.969T>A; p.Tyr323*] + [c.1142A>G; p.Asn381Ser]) result in mitochondrial respiratory chain deficiency and Leigh syndrome, which is a neurodegenerative disease characterized by symmetric, bilateral lesions in the basal ganglia, thalamus, and brain stem. The severity of the genetic lesions and their effects on NARS2 protein structure cosegregate with the phenotype. A hypothetical truncated NARS2 protein, secondary to the Leigh syndrome mutation p.Tyr323* is not detectable and p.Asn381Ser further decreases NARS2 protein levels in patient fibroblasts. p.Asn381Ser also disrupts dimerization of NARS2, while the hearing loss p.Val213Phe variant has no effect on NARS2 oligomerization. Additionally we demonstrate decreased steady-state levels of mt-tRNAAsn in fibroblasts from the Leigh syndrome patients. In these cells we show that a decrease in oxygen consumption rates (OCR) and electron transport chain (ETC) activity can be rescued by overexpression of wild type NARS2. However, overexpression of the hearing loss associated p.Val213Phe mutant protein in these fibroblasts cannot complement the OCR and ETC defects. Our findings establish lesions in NARS2 as a new cause for nonsyndromic hearing loss and Leigh syndrome. http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1005097 Correction: Highly Dynamic and Sex-Specific Expression of microRNAs During Early ES Cell Differentiation The PLOS Genetics Staff info:doi/10.1371/journal.pgen.1005077 2015-03-25T21:00:00Z 2015-03-25T21:00:00Z
by The PLOS Genetics Staff
 http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1005077 Glycosyl Phosphatidylinositol Anchor Biosynthesis Is Essential for Maintaining Epithelial Integrity during Caenorhabditis elegans Embryogenesis Yemima Budirahardja et al. info:doi/10.1371/journal.pgen.1005082 2015-03-25T21:00:00Z 2015-03-25T21:00:00Z
by Yemima Budirahardja, Thang Dinh Doan, Ronen Zaidel-Bar
 Glycosylphosphatidylinositol (GPI) is a post-translational modification resulting in the attachment of modified proteins to the outer leaflet of the plasma membrane. Tissue culture experiments have shown GPI-anchored proteins (GPI-APs) to be targeted to the apical membrane of epithelial cells. However, the in vivo importance of this targeting has not been investigated since null mutations in GPI biosynthesis enzymes in mice result in very early embryonic lethality. Missense mutations in the human GPI biosynthesis enzyme pigv are associated with a multiple congenital malformation syndrome with a high frequency of Hirschsprung disease and renal anomalies. However, it is currently unknown how these phenotypes are linked to PIGV function. Here, we identify a temperature-sensitive hypomorphic allele of PIGV in Caenorhabditis elegans, pigv-1(qm34), enabling us to study the role of GPI-APs in development. At the restrictive temperature we found a 75% reduction in GPI-APs at the surface of embryonic cells. Consequently, ~80% of pigv-1(qm34) embryos arrested development during the elongation phase of morphogenesis, exhibiting internal cysts and/or surface ruptures. Closer examination of the defects revealed them all to be the result of breaches in epithelial tissues: cysts formed in the intestine and excretory canal, and ruptures occurred through epidermal cells, suggesting weakening of the epithelial membrane or membrane-cortex connection. Knockdown of piga-1, another GPI biosynthesis enzymes resulted in similar phenotypes. Importantly, fortifying the link between the apical membrane and actin cortex by overexpression of the ezrin/radixin/moesin ortholog ERM-1, significantly rescued cyst formation and ruptures in the pigv-1(qm34) mutant. In conclusion, we discovered GPI-APs play a critical role in maintaining the integrity of the epithelial tissues, allowing them to withstand the pressure and stresses of morphogenesis. Our findings may help to explain some of the phenotypes observed in human syndromes associated with pigv mutations. http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1005082 A Cascade of Iron-Containing Proteins Governs the Genetic Iron Starvation Response to Promote Iron Uptake and Inhibit Iron Storage in Fission Yeast Javier Encinar del Dedo et al. info:doi/10.1371/journal.pgen.1005106 2015-03-25T21:00:00Z 2015-03-25T21:00:00Z
by Javier Encinar del Dedo, Natalia Gabrielli, Mercè Carmona, José Ayté, Elena Hidalgo
 Iron is an essential cofactor, but it is also toxic at high levels. In Schizosaccharomyces pombe, the sensor glutaredoxin Grx4 guides the activity of the repressors Php4 and Fep1 to mediate a complex transcriptional response to iron deprivation: activation of Php4 and inactivation of Fep1 leads to inhibition of iron usage/storage, and to promotion of iron import, respectively. However, the molecular events ruling the activity of this double-branched pathway remained elusive. We show here that Grx4 incorporates a glutathione-containing iron-sulfur cluster, alone or forming a heterodimer with the BolA-like protein Fra2. Our genetic study demonstrates that Grx4-Fra2, but not Fep1 nor Php4, participates not only in iron starvation signaling but also in iron-related aerobic metabolism. Iron-containing Grx4 binds and inactivates the Php4 repressor; upon iron deprivation, the cluster in Grx4 is probably disassembled, the proteins dissociate, and Php4 accumulates at the nucleus and represses iron consumption genes. Fep1 is also an iron-containing protein, and the tightly bound iron is required for transcriptional repression. Our data suggest that the cluster-containing Grx4-Fra2 heterodimer constitutively binds to Fep1, and upon iron deprivation the disassembly of the iron cluster between Grx4 and Fra2 promotes reverse metal transfer from Fep1 to Grx4-Fra2, and de-repression of iron-import genes. Our genetic and biochemical study demonstrates that the glutaredoxin Grx4 independently governs the Php4 and Fep1 repressors through metal transfer. Whereas iron loss from Grx4 seems to be sufficient to release Php4 and allow its nuclear accumulation, total or partial disassembly of the Grx4-Fra2 cluster actively participates in iron-containing Fep1 activation by sequestering its iron and decreasing its interaction with promoters. http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1005106 Accumulation of Glucosylceramide in the Absence of the Beta-Glucosidase GBA2 Alters Cytoskeletal Dynamics Diana Raju et al. info:doi/10.1371/journal.pgen.1005063 2015-03-24T21:00:00Z 2015-03-24T21:00:00Z
by Diana Raju, Sophie Schonauer, Hussein Hamzeh, Kevin C. Flynn, Frank Bradke, Katharina vom Dorp, Peter Dörmann, Yildiz Yildiz, Christian Trötschel, Ansgar Poetsch, Bernadette Breiden, Konrad Sandhoff, Heinz G. Körschen, Dagmar Wachten
 Glycosphingolipids are key elements of cellular membranes, thereby, controlling a variety of cellular functions. Accumulation of the simple glycosphingolipid glucosylceramide results in life-threatening lipid storage-diseases or in male infertility. How glucosylceramide regulates cellular processes is ill defined. Here, we reveal that glucosylceramide accumulation in GBA2 knockout-mice alters cytoskeletal dynamics due to a more ordered lipid organization in the plasma membrane. In dermal fibroblasts, accumulation of glucosylceramide augments actin polymerization and promotes microtubules persistence, resulting in a higher number of filopodia and lamellipodia and longer microtubules. Similar cytoskeletal defects were observed in male germ and Sertoli cells from GBA2 knockout-mice. In particular, the organization of F-actin structures in the ectoplasmic specialization and microtubules in the sperm manchette is affected. Thus, glucosylceramide regulates cytoskeletal dynamics, providing mechanistic insights into how glucosylceramide controls signaling pathways not only during sperm development, but also in other cell types. http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1005063 Opposite Phenotypes of Muscle Strength and Locomotor Function in Mouse Models of Partial Trisomy and Monosomy 21 for the Proximal Hspa13-App Region Véronique Brault et al. info:doi/10.1371/journal.pgen.1005062 2015-03-24T21:00:00Z 2015-03-24T21:00:00Z
by Véronique Brault, Arnaud Duchon, Caroline Romestaing, Ignasi Sahun, Stéphanie Pothion, Mona Karout, Christelle Borel, Doulaye Dembele, Jean-Charles Bizot, Nadia Messaddeq, Andrew J. Sharp, Damien Roussel, Stylianos E Antonarakis, Mara Dierssen, Yann Hérault
 The trisomy of human chromosome 21 (Hsa21), which causes Down syndrome (DS), is the most common viable human aneuploidy. In contrast to trisomy, the complete monosomy (M21) of Hsa21 is lethal, and only partial monosomy or mosaic monosomy of Hsa21 is seen. Both conditions lead to variable physiological abnormalities with constant intellectual disability, locomotor deficits, and altered muscle tone. To search for dosage-sensitive genes involved in DS and M21 phenotypes, we created two new mouse models: the Ts3Yah carrying a tandem duplication and the Ms3Yah carrying a deletion of the Hspa13-App interval syntenic with 21q11.2-q21.3. Here we report that the trisomy and the monosomy of this region alter locomotion, muscle strength, mass, and energetic balance. The expression profiling of skeletal muscles revealed global changes in the regulation of genes implicated in energetic metabolism, mitochondrial activity, and biogenesis. These genes are downregulated in Ts3Yah mice and upregulated in Ms3Yah mice. The shift in skeletal muscle metabolism correlates with a change in mitochondrial proliferation without an alteration in the respiratory function. However, the reactive oxygen species (ROS) production from mitochondrial complex I decreased in Ms3Yah mice, while the membrane permeability of Ts3Yah mitochondria slightly increased. Thus, we demonstrated how the Hspa13-App interval controls metabolic and mitochondrial phenotypes in muscles certainly as a consequence of change in dose of Gabpa, Nrip1, and Atp5j. Our results indicate that the copy number variation in the Hspa13-App region has a peripheral impact on locomotor activity by altering muscle function. http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1005062 Genome-Wide Association Studies in Dogs and Humans Identify ADAMTS20 as a Risk Variant for Cleft Lip and Palate Zena T. Wolf et al. info:doi/10.1371/journal.pgen.1005059 2015-03-23T21:00:00Z 2015-03-23T21:00:00Z
by Zena T. Wolf, Harrison A. Brand, John R. Shaffer, Elizabeth J. Leslie, Boaz Arzi, Cali E. Willet, Timothy C. Cox, Toby McHenry, Nicole Narayan, Eleanor Feingold, Xioajing Wang, Saundra Sliskovic, Nili Karmi, Noa Safra, Carla Sanchez, Frederic W. B. Deleyiannis, Jeffrey C. Murray, Claire M. Wade, Mary L. Marazita, Danika L. Bannasch
 Cleft lip with or without cleft palate (CL/P) is the most commonly occurring craniofacial birth defect. We provide insight into the genetic etiology of this birth defect by performing genome-wide association studies in two species: dogs and humans. In the dog, a genome-wide association study of 7 CL/P cases and 112 controls from the Nova Scotia Duck Tolling Retriever (NSDTR) breed identified a significantly associated region on canine chromosome 27 (unadjusted p=1.1 x 10-13; adjusted p= 2.2 x 10-3). Further analysis in NSDTR families and additional full sibling cases identified a 1.44 Mb homozygous haplotype (chromosome 27: 9.29 – 10.73 Mb) segregating with a more complex phenotype of cleft lip, cleft palate, and syndactyly (CLPS) in 13 cases. Whole-genome sequencing of 3 CLPS cases and 4 controls at 15X coverage led to the discovery of a frameshift mutation within ADAMTS20 (c.1360_1361delAA (p.Lys453Ilefs*3)), which segregated concordant with the phenotype. In a parallel study in humans, a family-based association analysis (DFAM) of 125 CL/P cases, 420 unaffected relatives, and 392 controls from a Guatemalan cohort, identified a suggestive association (rs10785430; p =2.67 x 10-6) with the same gene, ADAMTS20. Sequencing of cases from the Guatemalan cohort was unable to identify a causative mutation within the coding region of ADAMTS20, but four coding variants were found in additional cases of CL/P. In summary, this study provides genetic evidence for a role of ADAMTS20 in CL/P development in dogs and as a candidate gene for CL/P development in humans. http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1005059 The Fun30 Chromatin Remodeler Fft3 Controls Nuclear Organization and Chromatin Structure of Insulators and Subtelomeres in Fission Yeast Babett Steglich et al. info:doi/10.1371/journal.pgen.1005101 2015-03-23T21:00:00Z 2015-03-23T21:00:00Z
by Babett Steglich, Annelie Strålfors, Olga Khorosjutina, Jenna Persson, Agata Smialowska, Jean-Paul Javerzat, Karl Ekwall
 In eukaryotic cells, local chromatin structure and chromatin organization in the nucleus both influence transcriptional regulation. At the local level, the Fun30 chromatin remodeler Fft3 is essential for maintaining proper chromatin structure at centromeres and subtelomeres in fission yeast. Using genome-wide mapping and live cell imaging, we show that this role is linked to controlling nuclear organization of its targets. In fft3∆ cells, subtelomeres lose their association with the LEM domain protein Man1 at the nuclear periphery and move to the interior of the nucleus. Furthermore, genes in these domains are upregulated and active chromatin marks increase. Fft3 is also enriched at retrotransposon-derived long terminal repeat (LTR) elements and at tRNA genes. In cells lacking Fft3, these sites lose their peripheral positioning and show reduced nucleosome occupancy. We propose that Fft3 has a global role in mediating association between specific chromatin domains and the nuclear envelope. http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1005101 Bacterial Infection Drives the Expression Dynamics of microRNAs and Their isomiRs Katherine J. Siddle et al. info:doi/10.1371/journal.pgen.1005064 2015-03-20T21:00:00Z 2015-03-20T21:00:00Z
by Katherine J. Siddle, Ludovic Tailleux, Matthieu Deschamps, Yong-Hwee Eddie Loh, Cécile Deluen, Brigitte Gicquel, Christophe Antoniewski, Luis B. Barreiro, Laurent Farinelli, Lluís Quintana-Murci
 The optimal coordination of the transcriptional response of host cells to infection is essential for establishing appropriate immunological outcomes. In this context, the role of microRNAs (miRNAs) – important epigenetic regulators of gene expression – in regulating mammalian immune systems is increasingly well recognised. However, the expression dynamics of miRNAs, and that of their isoforms, in response to infection remains largely unexplored. Here, we characterized the genome-wide miRNA transcriptional responses of human dendritic cells, over time, to various mycobacteria differing in their virulence as well as to other bacteria outside the genus Mycobacterium, using small RNA-sequencing. We detected the presence of a core temporal response to infection, shared across bacteria, comprising 49 miRNAs, highlighting a set of miRNAs that may play an essential role in the regulation of basic cellular responses to stress. Despite such broadly shared expression dynamics, we identified specific elements of variation in the miRNA response to infection across bacteria, including a virulence-dependent induction of the miR-132/212 family in response to mycobacterial infections. We also found that infection has a strong impact on both the relative abundance of the miRNA hairpin arms and the expression dynamics of miRNA isoforms. That we observed broadly consistent changes in relative arm expression and isomiR distribution across bacteria suggests that this additional, internal layer of variability in miRNA responses represents an additional source of subtle miRNA-mediated regulation upon infection. Collectively, this study increases our understanding of the dynamism and role of miRNAs in response to bacterial infection, revealing novel features of their internal variability and identifying candidate miRNAs that may contribute to differences in the pathogenicity of mycobacterial infections. http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1005064 Neurospora Importin α Is Required for Normal Heterochromatic Formation and DNA Methylation Andrew D. Klocko et al. info:doi/10.1371/journal.pgen.1005083 2015-03-20T21:00:00Z 2015-03-20T21:00:00Z
by Andrew D. Klocko, Michael R. Rountree, Paula L. Grisafi, Shan M. Hays, Keyur K. Adhvaryu, Eric U. Selker
 Heterochromatin and associated gene silencing processes play roles in development, genome defense, and chromosome function. In many species, constitutive heterochromatin is decorated with histone H3 tri-methylated at lysine 9 (H3K9me3) and cytosine methylation. In Neurospora crassa, a five-protein complex, DCDC, catalyzes H3K9 methylation, which then directs DNA methylation. Here, we identify and characterize a gene important for DCDC function, dim-3 (defective in methylation-3), which encodes the nuclear import chaperone NUP-6 (Importin α). The critical mutation in dim-3 results in a substitution in an ARM repeat of NUP-6 and causes a substantial loss of H3K9me3 and DNA methylation. Surprisingly, nuclear transport of all known proteins involved in histone and DNA methylation, as well as a canonical transport substrate, appear normal in dim-3 strains. Interactions between DCDC members also appear normal, but the nup-6dim-3 allele causes the DCDC members DIM-5 and DIM-7 to mislocalize from heterochromatin and NUP-6dim-3 itself is mislocalized from the nuclear envelope, at least in conidia. GCN-5, a member of the SAGA histone acetyltransferase complex, also shows altered localization in dim-3, raising the possibility that NUP-6 is necessary to localize multiple chromatin complexes following nucleocytoplasmic transport. http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1005083 Zinc Finger Independent Genome-Wide Binding of Sp2 Potentiates Recruitment of Histone-Fold Protein Nf-y Distinguishing It from Sp1 and Sp3 Sara Völkel et al. info:doi/10.1371/journal.pgen.1005102 2015-03-20T21:00:00Z 2015-03-20T21:00:00Z
by Sara Völkel, Bastian Stielow, Florian Finkernagel, Thorsten Stiewe, Andrea Nist, Guntram Suske
 Transcription factors are grouped into families based on sequence similarity within functional domains, particularly DNA-binding domains. The Specificity proteins Sp1, Sp2 and Sp3 are paradigmatic of closely related transcription factors. They share amino-terminal glutamine-rich regions and a conserved carboxy-terminal zinc finger domain that can bind to GC rich motifs in vitro. All three Sp proteins are ubiquitously expressed; yet they carry out unique functions in vivo raising the question of how specificity is achieved. Crucially, it is unknown whether they bind to distinct genomic sites and, if so, how binding site selection is accomplished. In this study, we have examined the genomic binding patterns of Sp1, Sp2 and Sp3 in mouse embryonic fibroblasts by ChIP-seq. Sp1 and Sp3 essentially occupy the same promoters and localize to GC boxes. The genomic binding pattern of Sp2 is different; Sp2 primarily localizes at CCAAT motifs. Consistently, re-expression of Sp2 and Sp3 mutants in corresponding knockout MEFs revealed strikingly different modes of genomic binding site selection. Most significantly, while the zinc fingers dictate genomic binding of Sp3, they are completely dispensable for binding of Sp2. Instead, the glutamine-rich amino-terminal region is sufficient for recruitment of Sp2 to its target promoters in vivo. We have identified the trimeric histone-fold CCAAT box binding transcription factor Nf-y as the major partner for Sp2-chromatin interaction. Nf-y is critical for recruitment of Sp2 to co-occupied regulatory elements. Equally, Sp2 potentiates binding of Nf-y to shared sites indicating the existence of an extensive Sp2-Nf-y interaction network. Our results unveil strikingly different recruitment mechanisms of Sp1/Sp2/Sp3 transcription factor members uncovering an unexpected layer of complexity in their binding to chromatin in vivo. http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1005102 Phenotype Specific Analyses Reveal Distinct Regulatory Mechanism for Chronically Activated p53 Kristina Kirschner et al. info:doi/10.1371/journal.pgen.1005053 2015-03-19T21:00:00Z 2015-03-19T21:00:00Z
by Kristina Kirschner, Shamith A. Samarajiwa, Jonathan M. Cairns, Suraj Menon, Pedro A. Pérez-Mancera, Kosuke Tomimatsu, Camino Bermejo-Rodriguez, Yoko Ito, Tamir Chandra, Masako Narita, Scott K. Lyons, Andy G. Lynch, Hiroshi Kimura, Tetsuya Ohbayashi, Simon Tavaré, Masashi Narita
 The downstream functions of the DNA binding tumor suppressor p53 vary depending on the cellular context, and persistent p53 activation has recently been implicated in tumor suppression and senescence. However, genome-wide information about p53-target gene regulation has been derived mostly from acute genotoxic conditions. Using ChIP-seq and expression data, we have found distinct p53 binding profiles between acutely activated (through DNA damage) and chronically activated (in senescent or pro-apoptotic conditions) p53. Compared to the classical 'acute' p53 binding profile, 'chronic' p53 peaks were closely associated with CpG-islands. Furthermore, the chronic CpG-island binding of p53 conferred distinct expression patterns between senescent and pro-apoptotic conditions. Using the p53 targets seen in the chronic conditions together with external high-throughput datasets, we have built p53 networks that revealed extensive self-regulatory 'p53 hubs' where p53 and many p53 targets can physically interact with each other. Integrating these results with public clinical datasets identified the cancer-associated lipogenic enzyme, SCD, which we found to be directly repressed by p53 through the CpG-island promoter, providing a mechanistic link between p53 and the 'lipogenic phenotype', a hallmark of cancer. Our data reveal distinct phenotype associations of chronic p53 targets that underlie specific gene regulatory mechanisms. http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1005053 Small Regulatory RNA-Induced Growth Rate Heterogeneity of Bacillus subtilis Ruben A. T. Mars et al. info:doi/10.1371/journal.pgen.1005046 2015-03-19T21:00:00Z 2015-03-19T21:00:00Z
by Ruben A. T. Mars, Pierre Nicolas, Mariano Ciccolini, Ewoud Reilman, Alexander Reder, Marc Schaffer, Ulrike Mäder, Uwe Völker, Jan Maarten van Dijl, Emma L. Denham
 Isogenic bacterial populations can consist of cells displaying heterogeneous physiological traits. Small regulatory RNAs (sRNAs) could affect this heterogeneity since they act by fine-tuning mRNA or protein levels to coordinate the appropriate cellular behavior. Here we show that the sRNA RnaC/S1022 from the Gram-positive bacterium Bacillus subtilis can suppress exponential growth by modulation of the transcriptional regulator AbrB. Specifically, the post-transcriptional abrB-RnaC/S1022 interaction allows B. subtilis to increase the cell-to-cell variation in AbrB protein levels, despite strong negative autoregulation of the abrB promoter. This behavior is consistent with existing mathematical models of sRNA action, thus suggesting that induction of protein expression noise could be a new general aspect of sRNA regulation. Importantly, we show that the sRNA-induced diversity in AbrB levels generates heterogeneity in growth rates during the exponential growth phase. Based on these findings, we hypothesize that the resulting subpopulations of fast- and slow-growing B. subtilis cells reflect a bet-hedging strategy for enhanced survival of unfavorable conditions. http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1005046 Morphological Mutations: Lessons from the Cockscomb Denis Headon info:doi/10.1371/journal.pgen.1004979 2015-03-19T21:00:00Z 2015-03-19T21:00:00Z
by Denis Headon
 http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1004979 A Genomic Duplication is Associated with Ectopic Eomesodermin Expression in the Embryonic Chicken Comb and Two Duplex-comb Phenotypes Ben Dorshorst et al. info:doi/10.1371/journal.pgen.1004947 2015-03-19T21:00:00Z 2015-03-19T21:00:00Z
by Ben Dorshorst, Mohammad Harun-Or-Rashid, Alireza Jian Bagherpoor, Carl-Johan Rubin, Chris Ashwell, David Gourichon, Michèle Tixier-Boichard, Finn Hallböök, Leif Andersson
 Duplex-comb (D) is one of three major loci affecting comb morphology in the domestic chicken. Here we show that the two Duplex-comb alleles, V-shaped (D*V) and Buttercup (D*C), are both associated with a 20 Kb tandem duplication containing several conserved putative regulatory elements located 200 Kb upstream of the eomesodermin gene (EOMES). EOMES is a T-box transcription factor that is involved in mesoderm specification during gastrulation. In D*V and D*C chicken embryos we find that EOMES is ectopically expressed in the ectoderm of the comb-developing region as compared to wild-type embryos. The confinement of the ectopic expression of EOMES to the ectoderm is in stark contrast to the causal mechanisms underlying the two other major comb loci in the chicken (Rose-comb and Pea-comb) in which the transcription factors MNR2 and SOX5 are ectopically expressed strictly in the mesenchyme. Interestingly, the causal mutations of all three major comb loci in the chicken are now known to be composed of large-scale structural genomic variants that each result in ectopic expression of transcription factors. The Duplex-comb locus also illustrates the evolution of alleles in domestic animals, which means that alleles evolve by the accumulation of two or more consecutive mutations affecting the phenotype. We do not yet know whether the V-shaped or Buttercup allele correspond to the second mutation that occurred on the haplotype of the original duplication event. http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1004947 Escape from X Inactivation Varies in Mouse Tissues Joel B. Berletch et al. info:doi/10.1371/journal.pgen.1005079 2015-03-18T21:00:00Z 2015-03-18T21:00:00Z
by Joel B. Berletch, Wenxiu Ma, Fan Yang, Jay Shendure, William S. Noble, Christine M. Disteche, Xinxian Deng
 X chromosome inactivation (XCI) silences most genes on one X chromosome in female mammals, but some genes escape XCI. To identify escape genes in vivo and to explore molecular mechanisms that regulate this process we analyzed the allele-specific expression and chromatin structure of X-linked genes in mouse tissues and cells with skewed XCI and distinguishable alleles based on single nucleotide polymorphisms. Using a binomial model to assess allelic expression, we demonstrate a continuum between complete silencing and expression from the inactive X (Xi). The validity of the RNA-seq approach was verified using RT-PCR with species-specific primers or Sanger sequencing. Both common escape genes and genes with significant differences in XCI status between tissues were identified. Such genes may be candidates for tissue-specific sex differences. Overall, few genes (3–7%) escape XCI in any of the mouse tissues examined, suggesting stringent silencing and escape controls. In contrast, an in vitro system represented by the embryonic-kidney-derived Patski cell line showed a higher density of escape genes (21%), representing both kidney-specific escape genes and cell-line specific escape genes. Allele-specific RNA polymerase II occupancy and DNase I hypersensitivity at the promoter of genes on the Xi correlated well with levels of escape, consistent with an open chromatin structure at escape genes. Allele-specific CTCF binding on the Xi clustered at escape genes and was denser in brain compared to the Patski cell line, possibly contributing to a more compartmentalized structure of the Xi and fewer escape genes in brain compared to the cell line where larger domains of escape were observed. http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1005079


text:
the lonely mouse
Credits & Info
- Date
- 03/19/2009
- File Info
- Song
- 1 min 16 sec
- Score
- 4.23 / 5.00
Licensing Terms
- Attribution:
- You must give credit to the artist.
- Noncommercial:
- You may not use this work for commercial purposes unless you make specific arrangements with the artist.
- Share Alike:
- If you alter, transform, or build upon this image, you may distribute the resulting creation only under a license identical to this one.
- Score:
- Rated 4.23 / 5 stars
- Plays & Downloads:
- 1,075 Plays | 74 Downloads
- Share Links:
- Genres:
- Other - Miscellaneous
- None
Author Comments
Rated 4.5 / 5 stars
I feel at home
when I listen to this ;)
Rated 5 / 5 stars
I agree with breew.
That was the same thing I thought when I listened to it. Stirs up that emotional gut feeling you get when a song is really good.
Rated 5 / 5 stars
I have to say the title is misleading or thought provoking? but the song was very well put togther, simple and easy. light hearted and happy. you can imagine a mouse being happy what ever that may be, resting with content.
Rated 5 / 5 stars
Travels good.
The mouse is in the future, I will never meet him. I am sad. Nice song.
Rated 4.5 / 5 stars
A dream of a Mouse...
It was sad but can see a dream of where the mouse is happy .. dancing playing .. then the camra pulls back and there is a smile on the mouses face..as it dreams...
my mouse has nightmares. he eats to much cheese you see =D lol.
thank you! THANK YOU really for these reviews. =D

subset: commoncrawl


text:
Home Concert Tickets Schlager/ Volksmusik Senta Berger
Senta Berger Tickets
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text:
Love Black
I was thinking Totem, when I started collecting Black dishes from the Thrift store. I started last year when they were cheap. I think the thrift stores have been reading here and started raising the prices. I use to get the cups for 25 cents and tea pots for 1.00. Now they have gone up to 1.00 for glasses and 5.00 for tea pots. Anyhow...lol I got off track.
I saw this here years ago when people were doing bowling balls...
I am going to use a glass globe and use some of my black dishes as the totem for the bottom. Do you see that car..It is a avon bottle. Thrift store charged me 5.00 for that car. lol It is so cute I have to figure out how to incorporate it in one of the totems.
Is all that actually black glass? I have lots of black dishes - but they are black ceramic. I've rarely seen black glass.
The teapot decorated with the wired beads is very nice!! I've seen black & white totems on here & they looked lovely so you should be able to come up with something nice especially with that cute car- maybe a birdbath with that in the center! Jan
Wow! That will be an interesting totem! Love that bowling ball pic...quite unique! I have some of those black plates (w/France on the back) that I got at GWill ...but I use them (as plates) LOL!
I like your idea...will be fun to see what you come up with! TFS! Jeanne S.
I remember when that BB was first posted on MSN
garden junk-I loved it then and still do.
My DD chose the black dishes when she got married
20 years ago. The one she has, has sharper corners
than the ones pictured, and the mugs/cups were a
little different. We did buy some serving pieces
later when these came out.
Because I like black too, I have been picking up
pieces like yours to use--she won't let me have
nonacook, I have loved this bowling ball so long I saved it in my favorite crafts to do one day when I retired. Well that day has come I finally have time. I have so many projects in that file it should carry me into the grave. I even remember her explaination of how to cut the marbles to look like grapes. I am going to try this for sure. It is just so classy looking to me.
You think if you send your daughter on vacation you could slip in and trade out the dishes. Tell her you are updating her china. lol Have you had trouble finding black? It seems every time I step in the Thrift store I see a new piece of black. It may be time that all are getting rid of the black look.


text:
The verdict is in on round two of Apple and Samsung's epic patent battle in San Jose federal court, and Mercury News reporter Howard Mintz is there to cover all the action.
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text:
Just downriver from the French Quarter—New Orleans' oldest and most famous district—the wrought iron balconies and handsome Creole townhouses give way to a scruffier set of neighborhoods that are getting lots of attention lately thanks to new development plans.
The Faubourg Marigny and Bywater districts in recent years have become the city's new havens of bohemia—places where artists, musicians and eccentrics thrived after the French Quarter became overrun with tourists (many of them in search of 3-for-1 beer specials) and wealthy folks.
Now, locals—and good music—are more likely to be found at one of the bars in the Marigny than along bead-laden Bourbon Street.
Hurricane Katrina—the 2005 storm that went down as one of the deadliest in U.S. history—only strengthened the two neighborhoods' appeal. Like the French Quater, they escaped serious flooding due to their strategic location along the Mississippi River, on some of the city's highest ground. Today, these traditionally working-class neighborhoods are also the site for an ambitious project set to break ground in the fall that will transform much of the riverfront into a park. Not surprisingly, housing values have skyrocketed and investors are busy buying up the peeling shotgun structures that can still be had at bargain prices.
Running just north of these two neighborhoods is St. Claude Avenue—a stark dividing line between areas of increasing vibrancy and those where the poverty is more heavily entrenched and the flood damage, even four years after Katrina, pronounced. St. Claude today is a patchwork of grand and ramshackle buildings, many of them boarded up and abandoned or donning signs advertising payday loan outlets and fast-food joints. Followed for a few miles, St. Claude leads into the city's infamous Lower Ninth Ward.
But the avenue is staging a comeback. It is already home to a burgeoning arts community, with galleries and music venues cropping up with regularity alongside funky standards with names like Sweet Lorraine's and Saturn Bar.
This spring, a group of MIT urban planning students adopted the avenue, tasked with developing a plan for revitalization. In May, they presented their findings at a former St. Claude public school that has been converted into artists' studios and a performance space.
There is also talk of bringing the city's iconic streetcar back to the avenue, which was once home to one of 26 streetcar lines that crisscrossed the city at the peak of service in the mid-1920s. Plans to extend the streetcar to St. Claude Ave. have been in the works since the late 1990s, but floundered after funding for the project proved elusive. Transit officials and streetcar advocates are now optimistic that the plan can be realized with the help of public transit funding included in the federal stimulus package. The proposed extension is dubbed Desire, after the streetcar line that once ran parallel to St. Claude and lent its name to Tennessee Williams' play, A Streetcar Named Desire.
Among the other players agitating for the St. Claude transformation is developer Pres Kabacoff, who intends to soon begin construction on a multi-million dollar "Healing Center" to be housed in a former furniture store along the avenue. The multi-purpose center will include such signature urban amenities as a yoga studio, food co-op, organic café, and meditation space. An athletic 60-something who sports a silver goatee, Kabacoff, through his firm, was responsible in the early 1980s for the redevelopment of the city's Warehouse District, then a mishmash of discarded one-time manufacturing facilities, into the high-end condos and apartments of today.
Kabacoff's current venture, undertaken with his voodoo priestess girlfriend, has garnered widespread praise. Still, there are those who wonder how they figure in to the grand plans being hatched in their midst. The concerns are perhaps most pronounced among the residents of the mostly poor, African-American neighborhoods on the northern side of St. Claude.
As Reggie Lawson, an African-American resident of a nearby neighborhood told me: "You can't force evolution. They want coffee shops and antique boutiques and on and on and on. That's not the history of the neighborhood."
His concerns might be exaggerated, but they speak to an ongoing challenge among myriad ones confronting New Orleans as it continues to rebound from Katrina: balancing the new opportunities that stand to benefit the city as a whole with the interests of those that help make it so special in the first place.
Emilie Bahr is a guest blogger to AmericasQuarterly.org. She is a staff writer at New Orleans CityBusiness.
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Sabrina Karim
Bogotá, Colombia
Jenny Manrique
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Paula Ramón
Guatemala City, Guatemala
Louisa Reynolds
Nic Wirtz
Monterrey, Mexico
Arjan Shahani
Montreal, Canada
John Parisella
Ottawa, Canada
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Flora Charner
Stephen Kurczy
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Healthcare specialist consultancy joins MCA
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GE Healthcare Finnamore becomes newest MCA member
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MCA renews partnership with Raconteur to produce series of special reports in The Times in 2015
Local Government needs a radical rethink says MCA
—23 February 2015
The future of local government needs a radical rethink early in the new Parliament
30 separate consulting firms make MCA Awards 2015 shortlist
—26 January 2015
The main event in the UK's consulting calendar continues to attract a rich diversity of management consulting firms and consultants.
Seeking Professional Recognition through 'Chartered Management Consultant'
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The designation will be a badge of recognition for the skills, knowledge and professionalism of management consultants
UK consulting firms buoyant about growth
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Rate of growth to double in just two years as UK consulting continues to be a premium brand overseas.
MCA hits back on NHS use of management consulting
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Mindbench and Equiteq become Associate Members of the MCA
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2nd Annual Community Health Fair Coming to Missoula
The 2nd Annual Community Health Fair is coming to the Southgate Mall on Sunday, October 20th from Noon-4pm courtesy of students from the University of Montana Skaggs School of Pharmacy and local pharmacists.
It's an absolutely free event to spotlight American Pharmacists Months courtesy of healthcare screening, health tips and helpful advice.
A Real Grizzly Inside Washington-Grizzly Stadium? Sure, It Makes Sense [VIDEO]
I remember seeing the teaser photos of this real grizzly bear inside our University of Montana football field all over my Facebook timeline when they were taping this. It caused for many excited reactions ranging from "WHAT?" to "Go Griz!" to "Seriously...WHAT THE HECK?!!?" Still, even though the some photos surfaced, the reason remained a mystery. That is until now...
Man Killed Following St. Regis Standoff
An adult male is dead after a very tense standoff on a side road near Hwy 135 close to St. Regis. With guns drawn and bullet proof vests strapped on, Mineral County authorities, in cooperation with the Montana Highway Patrol held down the area near an intersection close to the OK Cafe, about one mile north of the St. Regis I-90 exit.
What is Ricin? [DEFINITION]
Ricin is in the news this week because the Secret Service says that a letter containing the substance and addressed to President Obama was received on Tuesday at a White House mail facility. Two more letters sent to Sen. Wicker and Senator Joe Manchin (D.-W.V.), has been found to contain ricin.
[UPDATE] Missoula Marathon Runners Presumed to Be Unharmed After Explosions at the Boston Marathon
Update: 3:45 p.m., April 15 – "As far as we know, none of the Missoula runners have been hurt," said Tim Brooker, co-owner of Missoula's The Runners Edge after speaking with Missoula runners who were at the Boston Marathon during today's explosions.
March Mascot Madness – Monte Advances to the Final Four [VOTE NOW]
Really, GuySpeed? You are making this too easy. Pitting our lovable mascot up against some of the (dare we say...) unattractive school mascots is just simply too unfair for our rivals. First, it was Otto the Orange which lost by a whopping 84% of the votes, and now this week, everyone's obvious favorite furry grizzly bear is up against yet another slightly odd looking team spirit costumed character.
Which Vehicles Are Being Recalled From Nissan, Honda and Toyota?
Toyota, Honda, and Nissan are issuing a recall of nearly 2 million cars all around the world for issues with air bags. Is your car safe?
Famous People Born in Montana [VIDEO/PICS]
Sure, you may live in Montana, but don't let the small population of our state allow you to think that your talents will never get noticed! According to the Biography Channel, our fantastic state is home to some of the greatest minds of our generation.
Mayor John Engen is a Master of Tweeting…with His MIND #SoMeT13US
To encourage Missoulians to vote for their town in the final round of the Social Media Tourism Symposium, Mayor John Engen reveals that he has an uncanny ability to tweet..with his mind! Impressive! You can too, and in this video he shows you how.
Vote for Missoula in #SoMeT13US, Receive Half Price Coffee at Liquid Planet Downtown
Missoula has made it to the final round of the Social Media Tourism Symposium online challenge! And here is all the more reason to vote for our town one final time as our friends at the Liquid Planet coffee shop are offering a special deal


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X post: tiny bathrooms in 1790s house
I posted this in bathrooms, but I thought Old House readers might "get it"--I am not sure what I would do if a were the buyer of a house like this, but to do a 2000s kitchen or bath in this house would be almost impossible:
I walked through a house from the 1790s today. The bathrooms were built adjacent to the chimneys and semi winder staircases in what was probably cabinet space.
They were 4 feet x 5 feet with the sink tucked in a niche.
The "bathtubs" were foot deep shower receptors with a corner seat circa 1963 or so and there was room to stand in front of the toilet and close the door.
It has been on the market quite a while because I think people are afraid of the bathrooms. (And kitchen which still has its third cooking fireplace. The two earlier ones are still in the basement.) Unfortunately, there is no way to do anything else with the bathrooms without destroying historic fabric.
I hope someone who understands this house, and understands that they may be more of a custodian to this house than an outright owner, buys it. If I had $800,000 I would :)
I "get it". My 1915-ish bathroom ceiling is 6ft tall and the entire room is tiny. Its adjacent to the chimney like you said it would be. It even has a tiny little window! My husband has to hunch over to use this little bathroom. Therefore, he avoids the room...its my little "cave"...a sanctuary where everyone clucks and wonders "how we live with it" and I secretly smile and internally shout "I love this tiny little room!"
there is no way to do anything else with the bathrooms without destroying historic fabric.
Any history you'd be sacrificing would be at least a century later, when those rooms were carved from existing space with a miser's eye. At most an 18th Century North American home would have a "close-stool"--a fancy name for cabinetry enclosing the chamber pot.
I lived for seven years with a tiny bath like that tucked in the corner of a hallway. A neighbour with the same style home gave it up and simply converted one of the bedrooms to a bath.
What if you have an outdoor privy? Do you preserve that too as part of history?
Agreed. My home had an outhouse until probably the 1950s. One of the parlours is now partitioned off into a bedroom and a decent sized bath.
I've lived in homes a heck of a lot older than this one in Europe, and nobody thinks twice about installing a decent bathroom in them, nor any other real necessity.
If I had an older home with an original bathroom, I'd want to preserve it, even if I had to install an additional one in an unused room. But, Your inglenook loo is an addition and not historically correct anyway.
I have a large kitchen hearth, and my kitchen is very rustic in tone, but on one side of it I have a computer station and on the other a built-in oven. Neither commodity I care to live without unless I have to. ;-)
The existing bathrooms are 150 years younger than the house, of course. That said, there are three 3/4 baths (I wouldnt consider those tubs real tubs) that are competely functional,(that could stand to have new finishes) and a pretty kitchen that is completely functional in the existing house. What there *isn't, is a millenium styled master suite or 'pro' kitchen. In 1963, someone figured out how to do it without stepping on the the rest of the house too much. I am not talking about preserving these bathrooms for the bathrooms' sake in any way. I was hoping that someone wouldnt go in and blow out two of the larger intact rooms to put in elaborate large baths and kitchen. I have seen bizarre disruptive renovations too often. If plenty of houses in this state existed thats one thing, but they are few and far between.
Yeah, our bathrooms were the back porch originally. At some point maybe in the 30s or 40 they were enclosed to make 2 bathrooms (pretty impressive to have two). Nothing near original to the house, but common in our neighborhood - the bathrooms are all in odd places.
We kept ours as is - fixing, but not expanding, as they're ok, but many of our neighbors have renovated or moved their bathrooms to more suitable locations. Not a big problem. With foresight and care, it's quite possible to maintain the historic fabric of the house while uprgrading a bathroom
That said, the "millenium master suite" or "pro kitchen" would likely be, well, lousy. I don't like them in modern houses anyway, so I wouldn't put one in an historic house. I'm all for upgrading with modern ammenities, but really, is a bathroom the size of a living room *really* necessary?
OK, I get it now. In an 800K house, I would want at least one normal sized bathroom large enough to accommodate a bath tub. I wouldn't mind a tiny additional bath like the one you described tucked away in a convenient place. But, honestly with the set-up there is now......it would be like living in an RV when it came time to clean up. That's why we sacrificed the second parlor in our home and converted the rest of it into a bedroom on the first floor for my mother, who had to move into our home when she became unable to live by herself anymore. This is the only bath in the house, however and I'm sure that by the "millenium master suite" mentality so prevalent today it would be a deal breaker for many people not only NOT to have a bath off our bedroom, but not to even have one on the second floor. It's amazing that we have survived. LOL I'm just thankful I don't have to make a run to the outhouse....because I have lived in homes with no modern facilities in them.
I wonder how many people who have those 'pro' kitchens even cook? Laughing again.


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3Shape A/S is a uniquely dynamic company whose aim it is to develop top-of-class solutions and maintain a leadership position by an open and tight cooperation with its distribution partners.
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LMTmag.com is an online network from LMT dedicated exclusively for members of the Dental Laboratory community. Join free to connect with 3Shape, Inc..
- 2Upvotes
What are your CAD/CAM suggestions for small labs?
Hi there - we're a 6 person lab in Missouri - bought a 3shape last november. The best thing we ever did! We looked at alot of other systems, but kept coming back to 3shape. . We also had asked around and wanted to know who provided the best training (we bought ours through Dentsply).... — tagged 3 products3Shape Dental System™
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CAD/CAMSeptember 3 at 1:24 pm
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What are your CAD/CAM suggestions for small labs?
3 shape hands down. i have HAD both. i no longer have dental wings — tagged 3Shape Dental System™ and 3Shape, Inc.April 17, 2014
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Which digital impression scans do you prefer working with? Are you referring you dentists to a certain company if they are interested in purchasing a scanner?
3Shape. Love working with 3Shape Trios — tagged 6 usersexocad America
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Dental WingsOctober 27 at 12:18 pm
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Can a 3Shape scanner "talk" to a Kavo Everest CAD/CAM system, or do I need to spend money on more software?
Yes, our Dental System software has an export function for the Kavo.
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What are your CAD/CAM suggestions for small labs?
The 3Shape is ideal for entry into the digital world. 3Shape does normally have an annual fee, but they do have a promo right now that waives that fee for 3 years. Let me know if you would like some additional information if you have't received it already. — tagged 3 products3Shape Dental System™
3Shape, Inc.
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What are your CAD/CAM suggestions for small labs?
You would love the Identica Blue Scanner powered by exocad!
It's a completely open CAD system and doesn't have annual fees! It has a user friendly interface and is the easiest system to learn when just getting into CAD/CAM!
I've worked with many different CAD systems over the last 13 years while working... — tagged 5 usersexocad America
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Medit Identica Blue 3D Scanner
Medit Identica Blue Scanner & Apex CAD Software


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Sleep Inn Airport
2300 International Ave SE
Albuquerque, NM 87106
Phone: (505) 244-3325
Fax: (505) 244-3312
Stone Mountain Bead Gallery
3100 Central Avenue Southeast
Albuquerque, NM 87106
+1 505 260 1121
Mo to Sa from 11:00 AM to 06:00 PM,Su from 12:00 PM to 04:00 PMStone Mountain Bead Gallery is a treasure chest full of beads, bangles and bows. Unique jewelry is displayed and various handicrafts from around the world are available. Here is your chance to design your own jewelry, with a huge inventory of everything you need to make good looking and stylish embellishments. Crystals, lapis, stones and gems, plus sterling silver are among the line of goods sold. Unusual sculptures and various pieces of art are for sale in addition to a wide array of tools.
Earn valuable points toward free nights.


text:
Michael Graham Richard
Michael has been with TreeHugger since 2005. He started out as a part-time writer, but after about a year (circa February 2006) he made the transition to full-time editor-in-chief. He held that role until January 2008 (the highlight of this period was of course the acquisition of TreeHugger.com by the Discovery Channel), and he's now editor of the Science & Technology and the Cars & Transportation categories (his two main loves).
It was reading The Ecology of Commerce by Paul Hawken and Good News For A Change by David Suzuki and Holly Dressel that changed his life. Before that, he knew about the problems, but didn't think too much about them. After, he knew there were solutions, and he couldn't think about anything else.
Michael's personal blog can be found at MichaelGR.com. You can also follow him on Google+.
Latest Stories from Michael Graham Richard - Page 17
8 U.S. states create an alliance to put 3.3 million zero-emission vehicles on the road
This is still just a tiny incentive compared to what the oil industry has received, but it's better than nothing.
Park rangers and poachers are gunning each other down over the Indian rhino
Poachers are literally waging a war against park rangers to killed rhinos.
For the first time, the U.S. residential sector beat the commercial sector in new solar PV
One more step forward for the clean energy future of the United States!
Consumer Reports gets 40 MPG in Honda Accord Hybrid review
If you're looking for a big sedan that burns less fuel than most sub-compacts, this might be a good option.
What's greener: Streaming video or watching a DVD?
This is the kind of things we like to know...
No danger from magnetic fields in electric cars, says European study
Not only are they safe, but they don't even produce much stronger magnetic fields than gasoline vehicles.
Pay $1 and get $400 off solar power from SolarCity (free installation too!)
Various solar installers have made getting solar power more affordable than ever. Here's one that sweetens the deal a bit!
Electric cars are selling much better than hybrids did
It's important to keep things in perspective and think long-term.
Energy Star now rates clothes dryers. This could reduce U.S. CO2 emissions by 22bn lbs per year!
Drying clothes uses an incredible amount of energy, it's clearly a low-hanging fruit for conservation and energy efficiency efforts.
Augmented reality app makes NYC subway maps come alive!
Giving you a mix of useful and just interesting information while you are waiting for your train...
One of the best supercell timelapses ever, shot in Climax, Kansas (video)
Sometimes nature puts on a show that is so awe-inspiring that the best thing to do is sit back and enjoy!
Tesla sees itself as an "energy innovation company as much as a car company"
Energy storage is crucial if we want to put a lot more renewables on the power grid.
Group of divers has a close encounter with a majestic whale shark (video)
Whale sharks are awesome!
"The ocean is so acidic that it is dissolving the shells of our baby oysters"
It's a great idea to break up the rather abstract concept of 'climate change' into more concrete pieces that show how it's affecting people and ecosystems more directly.
Antarctica loses about 160,000,000,000 tonnes of ice... every year
A gigatonne of ice here, a gigatonne of ice there... Soon enough we're talking about a meaningful quantity!
Range-extended version of BMW's i3 gets EPA rating: 117 MPGe, 39 mpg with 72-mile EV range
Deliveries of i3 REx are beginning this week in the United States.
Modi wants to use solar to bring power to the 400 million Indians without electricity
If solar power doesn't make sense in India, it doesn't make sense anywhere!
China wants 70,000 megawatts of solar by 2017, triple what they currently have
A step in the nice direction for a country that has huge problems with pollution.


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OSI-Approved Open Source (5,816)
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Networking Software
Showing page 1 of 257.
GroundWork Monitor
GET FREE SUPPORT: http://www.gwos.com/register-core517 weekly downloads
Nagios is a powerful, enterprise-class host, service, application, and network monitoring program. Designed to be fast, flexible, and rock-solid stable. Nagios runs on *NIX hosts and can monitor Windows, Linux/Unix/BSD, Netware, and network devices.12,240 weekly downloads
A next-generation framework for monitoring information systems and datacenters. Written in Perl and designed for extensibility and interoperability.0 weekly downloads
GINITS - PAX Projects
Intermodal Mass Public Transit Globally Integrated, Networked, Interoperable, Transport Systems-PAX Global Integrated Mass Public Transit Telecommunication Logistics DAta NETwork GIMP-TransTelLogD-Net- use for travel and as a civil notification system.0 weekly downloads
Map Network Drives WScript Generator
This is a little program that makes WScipt (windows script) that maps network drives on a windows computer. In Active Directory you can set this as a login script so that all your clients have the mapped network drive(s) that you have made.17 weekly downloads
nat64 Linux kernel module
It is an implementation of nat64 in kernel space1 weekly downloads
!EOF is not EOF. EOF is an acronym for Easy Open Framework. The framework offers a flexible but simple client/server fundament for variable network applications. Goal ist creating a really easy to use but hopefully even potent framework like others.0 weekly downloads
"Connect Four"
A client/server architecture to allow the creation and playing of a configurable "Connect Four" like game.2 weekly downloads
( IP range generator )
A simple, bash shell ip range generator. Also, let's see a good script, PROPING.3 weekly downloads
( pro ping )pinger network alert monitor
Pinger alert, STATICTICAL TABLES, send EMAILs or SMS by SMS GATEWAY12 weekly downloads
IM-Filter is a daemon which runs on a Linux firewall and filters ICQ traffic. The daemon can identify filetransfers, handle UIN and word blacklists, manage a list with currently logged in users and log messages sent via the ICQ protocol.1 weekly downloads
..::LvL Open Source
..::LvL Open Source includes a number of FreeBSD System Management tools. sysupdate.sh is designed for updating your FreeBSD system.1 weekly downloads
.NET Internet toolkit
.NetCyberKit aims to create a programmers internet toolkit for the Microsoft.Net framework. The library will include functionalilty for advanced DNS, finger and whois lookups. This library will be primarily written in VB.NET1 weekly downloads
.NET SerialPort library
SerialPortNet is an open source serial port communication library for Microsoft .NET. It's written in c#, implements complete .NET 2.0 specifications, and is designed to allow for multiple OSes and add-on 3rd party Serial to Network adapters.42 weekly downloads
.NET VNC Viewer
.NET VNC Viewer is a VNC viewer written entirely in C#. It is binary compatible with Smartphones, Pocket PCs and Windows desktops (.NET CF or .NET Framework). I write this because other VNC viewers on Pocket PC do not do full screen and screen rotation.54 weekly downloads
No description0 weekly downloads
Decoding Superimposed BPSK Modulated Wireless Transmissions1 weekly downloads
Cooperative Retransmissions Through Collisions1 weekly downloads
14all - a mrtg CGI frontend
14all is a frontend for mrtg (http://www.mrtg.org/). It takes over the generation of web pages and statistics graphs from mrtg. It adds flexibility in the display of the statistics and reduces the load of the mrtg daemon, allowing to log more sources.2 weekly downloads
1wire-Home-Automatisation Project in C++
C++ Server for a dynamic home-automatisation-network based on the 1wire protocol. Later it will have a php-based frontend.0 weekly downloads
360-FAAR Firewall Analysis Audit Repair
360-FAAR Analyze FW1 Cisco Netscreen Policy Offline Using Config/Logs41 weekly downloads
3D Network Visualiser
3D Network Visualiser - 3DNV is a java & java3d based project that interfaces with nmap and other tools to present a 3D representation of a computer network.0 weekly downloads
3d network monitor
A multi-platform graphical network analysis tool1 weekly downloads
3ff hardened gateway
3ff aims to provide a full features gateway for home or small office use. This distro is totaly modular and try to be secure as possible.0 weekly downloads
3proxy tiny free proxy server
Universal freeware proxy server with HTTP, HTTPS, SOCKS v4, SOCKS v4a, SOCKS v5, FTP, POP3, UDP and TCP portmapping, access control, bandwith control, traffic limitation and accounting based on username, client IP, target IP, day time, day of week, etc.43 weekly downloads


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Looking to get out and travel more this summer and have been doing pretty well with that! Instead of staying in hotels all the time, i've started to try and find campgrounds, bed and breakfasts, and other ways of exploring areas (and feeling private at the same time -- not huge on Hostels)!
I have no pets, allergies, or smoking habits and am quiet and respectful.
Food is my passion - as are animals (though I have none of mine own :( ) I also love to meet and talk to people and see new places. And family is huge to me.
That's my dad - my rockstar! - playing a show in vegas in my picture!
Trying to learn to knit and read more for fun!


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Summer Reading
Expand Messages
- I'm just curious what everyone is reading this summer. In summer I
usually read fiction while on holidays, but this hasn't been a typical
summer. I'm just finishing up The Teapot Dome Scandal by Layton
McCartney (about the scandal which rocked the Harding administration
in which Harding appointed a big oil nominee, Albert Fall, as
Secretary of the Interior, who in turn leased lucrative naval oil
reserve land to big oil companies in return for kickbacks.) It might
sound dry, but I've found it fascinating reading. (Amazon link below)
Before that I read some fiction by one of my favourite writers,
ex-criminal lawyer William Deverell. His latest is called Kill All the
Judges, about an environmentalist poet charged with the murder of a
judge. Quirky characters and great realistic courtroom banter. (Amazon
link below)
Before that, I finally got around to reading The Audacity of Hope by
Barack Obama. It's a very good discussion on a number of complex
issues including race, religion and broken government.
I think my next read will be either a bio of James Monroe or Thomas
Dewey. So many books, so little time.
So what are the rest of you reading?
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