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  1. Meta-analysis of small RNA-sequencing errors reveals ubiquitous post-transcriptional RNA modifications.

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    Ebhardt, H Alexander; Tsang, Herbert H; Dai, Denny C; Liu, Yifeng; Bostan, Babak; Fahlman, Richard P

    2009-05-01

    Recent advances in DNA-sequencing technology have made it possible to obtain large datasets of small RNA sequences. Here we demonstrate that not all non-perfectly matched small RNA sequences are simple technological sequencing errors, but many hold valuable biological information. Analysis of three small RNA datasets originating from Oryza sativa and Arabidopsis thaliana small RNA-sequencing projects demonstrates that many single nucleotide substitution errors overlap when aligning homologous non-identical small RNA sequences. Investigating the sites and identities of substitution errors reveal that many potentially originate as a result of post-transcriptional modifications or RNA editing. Modifications include N1-methyl modified purine nucleotides in tRNA, potential deamination or base substitutions in micro RNAs, 3' micro RNA uridine extensions and 5' micro RNA deletions. Additionally, further analysis of large sequencing datasets reveal that the combined effects of 5' deletions and 3' uridine extensions can alter the specificity by which micro RNAs associate with different Argonaute proteins. Hence, we demonstrate that not all sequencing errors in small RNA datasets are technical artifacts, but that these actually often reveal valuable biological insights to the sites of post-transcriptional RNA modifications.

  2. Comparative phosphoproteomics reveals components of host cell invasion and post-transcriptional regulation during Francisella infection

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    Nakayasu, Ernesto S.; Tempel, Rebecca; Cambronne, Xiaolu A.; Petyuk, Vladislav A.; Jones, Marcus B.; Gritsenko, Marina A.; Monroe, Matthew E.; Yang, Feng; Smith, Richard D.; Adkins, Joshua N.; Heffron, Fred

    2013-09-22

    Francisella tularensis is a facultative intracellular bacterium that causes the deadly disease tularemia. Most evidence suggests that Francisella is not well recognized by the innate immune system that normally leads to cytokine expression and cell death. In previous work, we identified new bacterial factors that were hyper-cytotoxic to macrophages. Four of the identified hyper-cytotoxic strains (lpcC, manB, manC and kdtA) had an impaired lipopolysaccharide (LPS) synthesis and produced an exposed lipid A lacking the O-antigen. These mutants were not only hyper-cytotoxic but also were phagocytosed at much higher rates compared to the wild type parent strain. To elucidate the cellular signaling underlying this enhanced phagocytosis and cell death, we performed a large-scale comparative phosphoproteomic analysis of cells infected with wild-type and delta-lpcC F. novicida. Our data suggest that not only actin but also intermediate filaments and microtubules are important for F. novicida entry into the host cells. In addition, we observed differential phosphorylation of tristetraprolin (TTP), a key component of the mRNA-degrading machinery that controls the expression of a variety of genes including many cytokines. Infection with the delta-lpcC mutant induced the hyper-phosphorylation and inhibition of TTP, leading to the production of cytokines such as IL-1beta and TNF-alpha which may kill the host cells by triggering apoptosis. Together, our data provide new insights for Francisella invasion and a post-transcriptional mechanism that prevents the expression of host immune response factors that controls infection by this pathogen.

  3. Integrated Analysis of Thyroid Cancer Public Datasets Reveals Role of Post-Transcriptional Regulation on Tumor Progression by Targeting of Immune System Mediators.

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    Murilo V Geraldo

    Full Text Available Papillary thyroid carcinoma (PTC is a well-differentiated thyroid tumor that accounts for approximately 80% of thyroid cancer cases. On other hand, anaplastic thyroid carcinoma (ATC is a less frequent, but aggressive subtype, with poor prognosis. MicroRNAs (miRNAs, small non-coding RNAs, have emerged as potent post-transcriptional regulators of gene expression, which modulate the expression of cancer-related genes. Computational analyses estimate that a single miRNA may modulate hundreds of mRNA targets and, at the same time, cooperate with others to regulate one single mRNA transcript. Due to the large number of predicted targets and possible interactions, only a small number of miRNAs have characterized biological roles, and the panorama of miRNA-mediated regulation in thyroid cancer remains to be understood. Taking into consideration the large amount of gene expression data deposited in public databases we aligned miRNA target prediction and gene expression data from public PTC and ATC datasets to construct a network of post-transcriptional regulation in thyroid cancer. After a gene set enrichment analysis we identified signaling pathways and biological processes potentially modulated by the miRNAs deregulated in PTC and ATC. Our results show miRNA-mRNA interaction that could contribute with the de-regulation of key tumor-host mediators, such as extra-cellular matrix molecules, interleukins and interleukin receptors, which could drive a more aggressive behavior and tumor progression. Moreover, our analysis through The Cancer Genome Atlas (TCGA database revealed that aberrant expression of ECM and cytokines genes is frequent in PTC and is associated with aggressive behavior and decreased overall survival rate. In conclusion, we shed light on the post-transcriptional regulation of gene expression in differentiated and undifferentiated thyroid cancers, revealing a potential role of miRNAs in modulation of tumor-host interaction molecules

  4. The L1TD1 Protein Interactome Reveals the Importance of Post-transcriptional Regulation in Human Pluripotency

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    Maheswara Reddy Emani

    2015-03-01

    Full Text Available The RNA-binding protein L1TD1 is one of the most specific and abundant proteins in pluripotent stem cells and is essential for the maintenance of pluripotency in human cells. Here, we identify the protein interaction network of L1TD1 in human embryonic stem cells (hESCs and provide insights into the interactome network constructed in human pluripotent cells. Our data reveal that L1TD1 has an important role in RNA splicing, translation, protein traffic, and degradation. L1TD1 interacts with multiple stem-cell-specific proteins, many of which are still uncharacterized in the context of development. Further, we show that L1TD1 is a part of the pluripotency interactome network of OCT4, SOX2, and NANOG, bridging nuclear and cytoplasmic regulation and highlighting the importance of RNA biology in pluripotency.

  5. Comparative Analysis of mRNA Isoform Expression in Cardiac Hypertrophy and Development Reveals Multiple Post-Transcriptional Regulatory Modules

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    Park, Ji Yeon; Li, Wencheng; Zheng, Dinghai; Zhai, Peiyong; Zhao, Yun; Matsuda, Takahisa; Vatner, Stephen F.; Sadoshima, Junichi; Tian, Bin

    2011-01-01

    Cardiac hypertrophy is enlargement of the heart in response to physiological or pathological stimuli, chiefly involving growth of myocytes in size rather than in number. Previous studies have shown that the expression pattern of a group of genes in hypertrophied heart induced by pressure overload resembles that at the embryonic stage of heart development, a phenomenon known as activation of the “fetal gene program”. Here, using a genome-wide approach we systematically defined genes and pathways regulated in short- and long-term cardiac hypertrophy conditions using mice with transverse aortic constriction (TAC), and compared them with those regulated at different stages of embryonic and postnatal development. In addition, exon-level analysis revealed widespread mRNA isoform changes during cardiac hypertrophy resulting from alternative usage of terminal or internal exons, some of which are also developmentally regulated and may be attributable to decreased expression of Fox-1 protein in cardiac hypertrophy. Genes with functions in certain pathways, such as cell adhesion and cell morphology, are more likely to be regulated by alternative splicing. Moreover, we found 3′UTRs of mRNAs were generally shortened through alternative cleavage and polyadenylation in hypertrophy, and microRNA target genes were generally de-repressed, suggesting coordinated mechanisms to increase mRNA stability and protein production during hypertrophy. Taken together, our results comprehensively delineated gene and mRNA isoform regulation events in cardiac hypertrophy and revealed their relations to those in development, and suggested that modulation of mRNA isoform expression plays an importance role in heart remodeling under pressure overload. PMID:21799842

  6. The post-transcriptional operon

    DEFF Research Database (Denmark)

    2011-01-01

    A post-transcriptional operon is a set of monocistronic mRNAs encoding functionally related proteins that are co-regulated by a group of RNA-binding proteins and/or small non-coding RNAs so that protein expression is coordinated at the post-transcriptional level. The post-transcriptional operon...... model (PTO) is used to describe data from an assortment of methods (e.g. RIP-Chip, CLIP-Chip, miRNA profiling, ribosome profiling) that globally address the functionality of mRNA. Several examples of post-transcriptional operons have been documented in the literature and demonstrate the usefulness...

  7. Mycobacterial RNA isolation optimized for non-coding RNA: high fidelity isolation of 5S rRNA from Mycobacterium bovis BCG reveals novel post-transcriptional processing and a complete spectrum of modified ribonucleosides.

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    Hia, Fabian; Chionh, Yok Hian; Pang, Yan Ling Joy; DeMott, Michael S; McBee, Megan E; Dedon, Peter C

    2015-03-11

    A major challenge in the study of mycobacterial RNA biology is the lack of a comprehensive RNA isolation method that overcomes the unusual cell wall to faithfully yield the full spectrum of non-coding RNA (ncRNA) species. Here, we describe a simple and robust procedure optimized for the isolation of total ncRNA, including 5S, 16S and 23S ribosomal RNA (rRNA) and tRNA, from mycobacteria, using Mycobacterium bovis BCG to illustrate the method. Based on a combination of mechanical disruption and liquid and solid-phase technologies, the method produces all major species of ncRNA in high yield and with high integrity, enabling direct chemical and sequence analysis of the ncRNA species. The reproducibility of the method with BCG was evident in bioanalyzer electrophoretic analysis of isolated RNA, which revealed quantitatively significant differences in the ncRNA profiles of exponentially growing and non-replicating hypoxic bacilli. The method also overcame an historical inconsistency in 5S rRNA isolation, with direct sequencing revealing a novel post-transcriptional processing of 5S rRNA to its functional form and with chemical analysis revealing seven post-transcriptional ribonucleoside modifications in the 5S rRNA. This optimized RNA isolation procedure thus provides a means to more rigorously explore the biology of ncRNA species in mycobacteria. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  8. Integrated miRNA, mRNA and protein expression analysis reveals the role of post-transcriptional regulation in controlling CHO cell growth rate

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    Clarke Colin

    2012-11-01

    Full Text Available Abstract Background To study the role of microRNA (miRNA in the regulation of Chinese hamster ovary (CHO cell growth, qPCR, microarray and quantitative LC-MS/MS analysis were utilised for simultaneous expression profiling of miRNA, mRNA and protein. The sample set under investigation consisted of clones with variable cellular growth rates derived from the same population. In addition to providing a systems level perspective on cell growth, the integration of multiple profiling datasets can facilitate the identification of non-seed miRNA targets, complement computational prediction tools and reduce false positive and false negative rates. Results 51 miRNAs were associated with increased growth rate (35 miRNAs upregulated and 16 miRNAs downregulated. Gene ontology (GO analysis of genes (n=432 and proteins (n=285 found to be differentially expressed (DE identified biological processes driving proliferation including mRNA processing and translation. To investigate the influence of miRNA on these processes we combined the proteomic and transcriptomic data into two groups. The first set contained candidates where evidence of translational repression was observed (n=158. The second group was a mixture of proteins and mRNAs where evidence of translational repression was less clear (n=515. The TargetScan algorithm was utilised to predict potential targets within these two groups for anti-correlated DE miRNAs. Conclusions The evidence presented in this study indicates that biological processes such as mRNA processing and protein synthesis are correlated with growth rate in CHO cells. Through the integration of expression data from multiple levels of the biological system a number of proteins central to these processes including several hnRNPs and components of the ribosome were found to be post-transcriptionally regulated. We utilised the expression data in conjunction with in-silico tools to identify potential miRNA-mediated regulation of m

  9. Post-transcriptional regulation of ribosome biogenesis in yeast

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    Isabelle C. Kos-Braun

    2017-05-01

    Full Text Available Most microorganisms are exposed to the constantly and often rapidly changing environment. As such they evolved mechanisms to balance their metabolism and energy expenditure with the resources available to them. When resources become scarce or conditions turn out to be unfavourable for growth, cells reduce their metabolism and energy usage to survive. One of the major energy consuming processes in the cell is ribosome biogenesis. Unsurprisingly, cells encountering adverse conditions immediately shut down production of new ribosomes. It is well established that nutrient depletion leads to a rapid repression of transcription of the genes encoding ribosomal proteins, ribosome biogenesis factors as well as ribosomal RNA (rRNA. However, if pre-rRNA processing and ribosome assembly are regulated post-transcriptionally remains largely unclear. We have recently uncovered that the yeast Saccharomyces cerevisiae rapidly switches between two alternative pre-rRNA processing pathways depending on the environmental conditions. Our findings reveal a new level of complexity in the regulation of ribosome biogenesis.

  10. Post-transcriptional regulation of gene expression in Yersinia species

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    Chelsea A Schiano

    2012-11-01

    Full Text Available Proper regulation of gene expression is required by bacterial pathogens to respond to continually changing environmental conditions and the host response during the infectious process. While transcriptional regulation is perhaps the most well understood form of controlling gene expression, recent studies have demonstrated the importance of post-transcriptional mechanisms of gene regulation that allow for more refined management of the bacterial response to host conditions. Yersinia species of bacteria are known to use various forms of post-transcriptional regulation for control of many virulence-associated genes. These include regulation by cis- and trans-acting small non-coding RNAs, RNA-binding proteins, RNases, and thermoswitches. The effects of these and other regulatory mechanisms on Yersinia physiology can be profound and have been shown to influence type III secretion, motility, biofilm formation, host cell invasion, intracellular survival and replication, and more. In this review, we will discuss these and other post-transcriptional mechanisms and their influence on virulence gene regulation, with a particular emphasis on how these processes influence the virulence of Yersinia in the host.

  11. Post-transcriptional regulation of long noncoding RNAs in cancer.

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    Shi, Xuefei; Sun, Ming; Wu, Ying; Yao, Yanwen; Liu, Hongbing; Wu, Guannan; Yuan, Dongmei; Song, Yong

    2015-02-01

    It is a great surprise that the genomes of mammals and other eukaryotes harbor many thousands of long noncoding RNAs (lncRNAs). Although these long noncoding transcripts were once considered to be simply transcriptional noise or cloning artifacts, multiple studies have suggested that lncRNAs are emerging as new players in diverse human diseases, especially in cancer, and that the molecular mechanisms of lncRNAs need to be elucidated. More recently, evidence has begun to accumulate describing the complex post-transcriptional regulation in which lncRNAs are involved. It was reported that lncRNAs can be implicated in degradation, translation, pre-messenger RNA (mRNA) splicing, and protein activities and even as microRNAs (miRNAs) sponges in both a sequence-dependent and sequence-independent manner. In this review, we present an updated vision of lncRNAs and summarize the mechanism of post-transcriptional regulation by lncRNAs, providing new insight into the functional cellular roles that they may play in human diseases, with a particular focus on cancers.

  12. Hierarchical Post-transcriptional Regulation of Colicin E2 Expression in Escherichia coli.

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    Matthias Lechner

    2016-12-01

    Full Text Available Post-transcriptional regulation of gene expression plays a crucial role in many bacterial pathways. In particular, the translation of mRNA can be regulated by trans-acting, small, non-coding RNAs (sRNAs or mRNA-binding proteins, each of which has been successfully treated theoretically using two-component models. An important system that includes a combination of these modes of post-transcriptional regulation is the Colicin E2 system. DNA damage, by triggering the SOS response, leads to the heterogeneous expression of the Colicin E2 operon including the cea gene encoding the toxin colicin E2, and the cel gene that codes for the induction of cell lysis and release of colicin. Although previous studies have uncovered the system's basic regulatory interactions, its dynamical behavior is still unknown. Here, we develop a simple, yet comprehensive, mathematical model of the colicin E2 regulatory network, and study its dynamics. Its post-transcriptional regulation can be reduced to three hierarchically ordered components: the mRNA including the cel gene, the mRNA-binding protein CsrA, and an effective sRNA that regulates CsrA. We demonstrate that the stationary state of this system exhibits a pronounced threshold in the abundance of free mRNA. As post-transcriptional regulation is known to be noisy, we performed a detailed stochastic analysis, and found fluctuations to be largest at production rates close to the threshold. The magnitude of fluctuations can be tuned by the rate of production of the sRNA. To study the dynamics in response to an SOS signal, we incorporated the LexA-RecA SOS response network into our model. We found that CsrA regulation filtered out short-lived activation peaks and caused a delay in lysis gene expression for prolonged SOS signals, which is also seen in experiments. Moreover, we showed that a stochastic SOS signal creates a broad lysis time distribution. Our model thus theoretically describes Colicin E2 expression dynamics

  13. Post-transcriptional gene regulation by mRNA modifications

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    Zhao, Boxuan Simen; Roundtree, Ian A.; He, Chuan

    2016-01-01

    The recent discovery of reversible mRNA methylation has opened a new realm of post-transcriptional gene regulation in eukaryotes. The identification and functional characterization of proteins that specifically recognize RNA N6-methyladenosine (m6A) unveiled it as a modification that cells utilize to accelerate mRNA metabolism and translation. N6-adenosine methylation directs mRNAs to distinct fates by grouping them for differential processing, translation and decay in processes such as cell differentiation, embryonic development and stress responses. Other mRNA modifications, including N1-methyladenosine (m1A), 5-methylcytosine (m5C) and pseudouridine, together with m6A form the epitranscriptome and collectively code a new layer of information that controls protein synthesis. PMID:27808276

  14. [Epigenetic, post-transcriptional and metabolic mechanisms of macrophage reprogramming].

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    Malyshev, I Y

    2015-01-01

    A key role in the ability of immunity to adequately respond to pathogenic factors play macrophages. Depending on the type of infection and the microenvironment macrophages can rapidly change their phenotype towards the proinflammatory M1 or antiinflammatory M2 one. The process of changing the cell phenotype is termed "reprogramming". This process plays a central role in the immune response and therefore its disturbance triggers the development of disease. Reprogramming of macrophages is provided by intracellular signaling pathways. These paths can also control epigenetic, post-transcriptional and metabolic mechanisms of phenotypic activity of macrophages. Epigenetic mechanisms can be divided into the reprogramming mechanisms towards M1 and M2 phenotype. A key component of post-transcriptional regulation is micro-mRNA (miR). On M1- and M2-stimuli macrophages express different sets of miRs. MiRs may form a positive feedback mechanism for quick reprogramming of macrophages and negative feedback mechanisms, to limit excessive inflammation in the case of M1 phenotype and to restrict fall bactericidal activity in the case of M2 phenotype. Reprogramming of macrophages leads to a change in the metabolism of these cells. Formation of M1 phenotype accompanied by a shift of the arginine metabolism towards NO-synthase activation and increased production of NO, an increase in the contribution of glycolysis to ATP production, increased deposition of bacteriostatic iron. Formation of the M2 phenotype is accompanied by a shift of the arginine metabolism towards arginase 1 activation and increasing production of urea, increased ATP synthesis in mitochondria and increased capture of fatty acids, increased the capture of heme iron. Metabolic control of macrophage phenotype also involves the positive and negative feedback. In general, macrophage reprogramming involves very good coordinated and adapted to each other changes in the activity of signaling, epigenetic, post

  15. DMPD: Post-transcriptional regulation of proinflammatory proteins. [Dynamic Macrophage Pathway CSML Database

    Lifescience Database Archive (English)

    Full Text Available 15075353 Post-transcriptional regulation of proinflammatory proteins. Anderson P, P...l) (.csml) Show Post-transcriptional regulation of proinflammatory proteins. PubmedID 15075353 Title Post-tr...anscriptional regulation of proinflammatory proteins. Authors Anderson P, Phillip

  16. The post-transcriptional regulatory system CSR controls the balance of metabolic pools in upper glycolysis of Escherichia coli.

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    Morin, Manon; Ropers, Delphine; Letisse, Fabien; Laguerre, Sandrine; Portais, Jean-Charles; Cocaign-Bousquet, Muriel; Enjalbert, Brice

    2016-05-01

    Metabolic control in Escherichia coli is a complex process involving multilevel regulatory systems but the involvement of post-transcriptional regulation is uncertain. The post-transcriptional factor CsrA is stated as being the only regulator essential for the use of glycolytic substrates. A dozen enzymes in the central carbon metabolism (CCM) have been reported as potentially controlled by CsrA, but its impact on the CCM functioning has not been demonstrated. Here, a multiscale analysis was performed in a wild-type strain and its isogenic mutant attenuated for CsrA (including growth parameters, gene expression levels, metabolite pools, abundance of enzymes and fluxes). Data integration and regulation analysis showed a coordinated control of the expression of glycolytic enzymes. This also revealed the imbalance of metabolite pools in the csrA mutant upper glycolysis, before the phosphofructokinase PfkA step. This imbalance is associated with a glucose-phosphate stress. Restoring PfkA activity in the csrA mutant strain suppressed this stress and increased the mutant growth rate on glucose. Thus, the carbon storage regulator system is essential for the effective functioning of the upper glycolysis mainly through its control of PfkA. This work demonstrates the pivotal role of post-transcriptional regulation to shape the carbon metabolism. © 2016 John Wiley & Sons Ltd.

  17. Extensive exometabolome analysis reveals extended overflow metabolism in various microorganisms

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    Paczia Nicole

    2012-09-01

    Full Text Available Abstract Overflow metabolism is well known for yeast, bacteria and mammalian cells. It typically occurs under glucose excess conditions and is characterized by excretions of by-products such as ethanol, acetate or lactate. This phenomenon, also denoted the short-term Crabtree effect, has been extensively studied over the past few decades, however, its basic regulatory mechanism and functional role in metabolism is still unknown. Here we present a comprehensive quantitative and time-dependent analysis of the exometabolome of Escherichia coli, Corynebacterium glutamicum, Bacillus licheniformis, and Saccharomyces cerevisiae during well-controlled bioreactor cultivations. Most surprisingly, in all cases a great diversity of central metabolic intermediates and amino acids is found in the culture medium with extracellular concentrations varying in the micromolar range. Different hypotheses for these observations are formulated and experimentally tested. As a result, the intermediates in the culture medium during batch growth must originate from passive or active transportation due to a new phenomenon termed “extended” overflow metabolism. Moreover, we provide broad evidence that this could be a common feature of all microorganism species when cultivated under conditions of carbon excess and non-inhibited carbon uptake. In turn, this finding has consequences for metabolite balancing and, particularly, for intracellular metabolite quantification and 13C-metabolic flux analysis.

  18. RNA-binding proteins involved in post-transcriptional regulation in bacteria

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    Elke eVan Assche

    2015-03-01

    Full Text Available Post-transcriptional regulation is a very important mechanism to control gene expression in changing environments. In the past decade, a lot of interest has been directed towards the role of small RNAs in bacterial post-transcriptional regulation. However, small RNAs are not the only molecules controlling gene expression at this level, RNA-binding proteins play an important role as well. CsrA and Hfq are the two best studied bacterial proteins of this type, but recently, additional proteins involved in post-transcriptional control have been identified. This review focuses on the general working mechanisms of post-transcriptionally active RNA-binding proteins, which include (i adaptation of the susceptibility of mRNAs and sRNAs to RNases, (ii modulating the accessibility of the ribosome binding site of mRNAs, (iii recruiting and assisting in the interaction of mRNAs with other molecules and (iv regulating transcription terminator / antiterminator formation, and gives an overview of both the well-studied and the newly identified proteins that are involved in post-transcriptional regulatory processes. Additionally, the post-transcriptional mechanisms by which the expression or the activity of these proteins is regulated, are described. For many of the newly identified proteins, however, mechanistic questions remain. Most likely, more post-transcriptionally active proteins will be identified in the future.

  19. Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome

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    Peng, Zhiyu; Cheng, Yanbing; Tan, Bertrand Chin-Ming

    2012-01-01

    RNA editing is a post-transcriptional event that recodes hereditary information. Here we describe a comprehensive profile of the RNA editome of a male Han Chinese individual based on analysis of ∼767 million sequencing reads from poly(A)(+), poly(A)(-) and small RNA samples. We developed a comput......RNA editing is a post-transcriptional event that recodes hereditary information. Here we describe a comprehensive profile of the RNA editome of a male Han Chinese individual based on analysis of ∼767 million sequencing reads from poly(A)(+), poly(A)(-) and small RNA samples. We developed...

  20. Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome

    DEFF Research Database (Denmark)

    Peng, Zhiyu; Cheng, Yanbing; Tan, Bertrand Chin-Ming

    2012-01-01

    RNA editing is a post-transcriptional event that recodes hereditary information. Here we describe a comprehensive profile of the RNA editome of a male Han Chinese individual based on analysis of ∼767 million sequencing reads from poly(A)(+), poly(A)(-) and small RNA samples. We developed...

  1. Apparent ploidy effects on silencing are post-transcriptional at HML and telomeres in Saccharomyces cerevisiae.

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    Jenny M McLaughlan

    Full Text Available The repression of genes in regions of heterochromatin is known as transcriptional silencing. It occurs in a wide range of organisms and can have importance in adaptation to the environment, developmental changes and disease. The model organism Saccharomyces cerevisiae has been used for many years to study transcriptional silencing, but until recently no study has been made in relation to ploidy. The aim of this work was to compare transcriptional silencing in haploids and diploids at both telomeres and the hidden mating-type (HM loci. Transcriptional silencing was assayed, by growth on 5-fluoroorotic acid (5-FOA media or by flow cytometry, on strains where a telomere or HM locus was marked. RNA levels were measured by quantitative RT-PCR to confirm that effects were transcriptional. 5-FOA assays and flow cytometry were consistent with transcriptional silencing at telomeres and at HML being reduced as ploidy increases which agreed with conclusions in previous publications. However, QRT-PCR revealed that transcriptional silencing was unaffected by ploidy and thus protein levels were increasing independently of RNA levels. At telomere XI left (XI-L, changes in protein level were strongly influenced by mating-type, whereas at HML mating-type had much less influence. The post-transcriptional effects seen in this study, illustrate the often ignored need to measure RNA levels when assaying transcriptional silencing in Saccharomyces cerevisiae.

  2. Structural landscape of base pairs containing post-transcriptional modifications in RNA.

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    Seelam, Preethi P; Sharma, Purshotam; Mitra, Abhijit

    2017-06-01

    Base pairs involving post-transcriptionally modified nucleobases are believed to play important roles in a wide variety of functional RNAs. Here we present our attempts toward understanding the structural and functional role of naturally occurring modified base pairs using a combination of X-ray crystal structure database analysis, sequence analysis, and advanced quantum chemical methods. Our bioinformatics analysis reveals that despite their presence in all major secondary structural elements, modified base pairs are most prevalent in tRNA crystal structures and most commonly involve guanine or uridine modifications. Further, analysis of tRNA sequences reveals additional examples of modified base pairs at structurally conserved tRNA regions and highlights the conservation patterns of these base pairs in three domains of life. Comparison of structures and binding energies of modified base pairs with their unmodified counterparts, using quantum chemical methods, allowed us to classify the base modifications in terms of the nature of their electronic structure effects on base-pairing. Analysis of specific structural contexts of modified base pairs in RNA crystal structures revealed several interesting scenarios, including those at the tRNA:rRNA interface, antibiotic-binding sites on the ribosome, and the three-way junctions within tRNA. These scenarios, when analyzed in the context of available experimental data, allowed us to correlate the occurrence and strength of modified base pairs with their specific functional roles. Overall, our study highlights the structural importance of modified base pairs in RNA and points toward the need for greater appreciation of the role of modified bases and their interactions, in the context of many biological processes involving RNA. © 2017 Seelam et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  3. Post-transcriptional Control of Tumor Cell Autonomous Metastatic Potential by CCR4-NOT Deadenylase CNOT7.

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    Farhoud Faraji

    2016-01-01

    Full Text Available Accumulating evidence supports the role of an aberrant transcriptome as a driver of metastatic potential. Deadenylation is a general regulatory node for post-transcriptional control by microRNAs and other determinants of RNA stability. Previously, we demonstrated that the CCR4-NOT scaffold component Cnot2 is an inherited metastasis susceptibility gene. In this study, using orthotopic metastasis assays and genetically engineered mouse models, we show that one of the enzymatic subunits of the CCR4-NOT complex, Cnot7, is also a metastasis modifying gene. We demonstrate that higher expression of Cnot7 drives tumor cell autonomous metastatic potential, which requires its deadenylase activity. Furthermore, metastasis promotion by CNOT7 is dependent on interaction with CNOT1 and TOB1. CNOT7 ribonucleoprotein-immunoprecipitation (RIP and integrated transcriptome wide analyses reveal that CNOT7-regulated transcripts are enriched for a tripartite 3'UTR motif bound by RNA-binding proteins known to complex with CNOT7, TOB1, and CNOT1. Collectively, our data support a model of CNOT7, TOB1, CNOT1, and RNA-binding proteins collectively exerting post-transcriptional control on a metastasis suppressive transcriptional program to drive tumor cell metastasis.

  4. Systematic identification of factors involved in post-transcriptional processes in wheat grain.

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    Lopato, Sergiy; Borisjuk, Ljudmilla; Milligan, Andrew S; Shirley, Neil; Bazanova, Natalia; Parsley, Kate; Langridge, Peter

    2006-11-01

    Post-transcriptional processing of primary transcripts can significantly affect both the quantity and the structure of mature mRNAs and the corresponding protein products. It is an important mechanism of gene regulation in animals, yeast and plants. Here we have investigated the interactive networks of pre-mRNA processing factors in the developing grain of wheat (Triticum aestivum), one of the world's major food staples. As a first step we isolated a homologue of the plant specific AtRSZ33 splicing factor, which has been shown to be involved in the early stages of embryo development in Arabidopsis. Real-time PCR showed that the wheat gene, designated TaRSZ38, is expressed mainly in young, developing organs (flowers, root, stem), and expression peaks in immature grain. In situ hybridization and immunodetection revealed preferential abundance of TaRSZ38 in mitotically active tissues of the major storage organ of the grain, the endosperm. The protein encoded by TaRSZ38 was subsequently used as a starting bait in a two-hybrid screen to identify additional factors in grain that are involved in pre-mRNA processing. Most of the identified proteins showed high homology to known splicing factors and splicing related proteins, supporting a role for TaRSZ38 in spliceosome formation and 5' site selection. Several clones were selected as baits in further yeast two-hybrid screens. In total, cDNAs for 16 proteins were isolated. Among these proteins, TaRSZ22, TaSRp30, TaU1-70K, and the large and small subunits of TaU2AF, are wheat homologues of known plant splicing factors. Several, additional proteins are novel for plants and show homology to known pre-mRNA splicing, splicing related and mRNA export factors from yeast and mammals.

  5. Post-transcriptional exon shuffling events in humans can be evolutionarily conserved and abundant.

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    Al-Balool, Haya H; Weber, David; Liu, Yilei; Wade, Mark; Guleria, Kamlesh; Nam, Pitsien Lang Ping; Clayton, Jake; Rowe, William; Coxhead, Jonathan; Irving, Julie; Elliott, David J; Hall, Andrew G; Santibanez-Koref, Mauro; Jackson, Michael S

    2011-11-01

    In silico analyses have established that transcripts from some genes can be processed into RNAs with rearranged exon order relative to genomic structure (post-transcriptional exon shuffling, or PTES). Although known to contribute to transcriptome diversity in some species, to date the structure, distribution, abundance, and functional significance of human PTES transcripts remains largely unknown. Here, using high-throughput transcriptome sequencing, we identify 205 putative human PTES products from 176 genes. We validate 72 out of 112 products analyzed using RT-PCR, and identify additional PTES products structurally related to 61% of validated targets. Sequencing of these additional products reveals GT-AG dinucleotides at >95% of the splice junctions, confirming that they are processed by the spliceosome. We show that most PTES transcripts are expressed in a wide variety of human tissues, that they can be polyadenylated, and that some are conserved in mouse. We also show that they can extend into 5' and 3' UTRs, consistent with formation via trans-splicing of independent pre-mRNA molecules. Finally, we use real-time PCR to compare the abundance of PTES exon junctions relative to canonical exon junctions within the transcripts from seven genes. PTES exon junctions are present at 90% of the levels of canonical junctions, with transcripts from MAN1A2, PHC3, TLE4, and CDK13 exhibiting the highest levels. This is the first systematic experimental analysis of PTES in human, and it suggests both that the phenomenon is much more widespread than previously thought and that some PTES transcripts could be functional.

  6. Temperature exerts control of Bacillus cereus emetic toxin production on post-transcriptional levels

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    Markus Kranzler

    2016-10-01

    Full Text Available In recent years, the emetic toxin cereulide, produced by Bacillus cereus, has gained high relevance in food production and food safety. Cereulide is synthesized nonribosomal by the multi-enzyme complex Ces-NRPS, which is encoded on a megaplasmid that shares its backbone with the Bacillus anthracis pX01 toxin plasmid. Due to its resistance against heat, proteolysis and extreme pH conditions, the formation of this highly potent depsipeptide toxin is of serious concern in food processing procedures including slow cooling procedures and /or storage of intermediate products at ambient temperatures. So far, systematic data on the effect of extrinsic factors on cereulide synthesis has been lacking. Thus, we investigated the influence of temperature, a central extrinsic parameter in food processing, on the regulation of cereulide synthesis on transcriptional, translational and post-translational levels over the growth temperature range of emetic B. cereus. Bacteria were grown in 3°C interval steps from 12°C to 46°C and cereulide synthesis was followed from ces gene transcription to cereulide toxin production. This systematic study revealed that temperature is a cardinal parameter, which primarily impacts cereulide synthesis on post-transcriptional levels, thereby altering the composition of cereulide isoforms. Our work also highlights that the risk of cereulide production could not be predicted from growth parameters or sole cell numbers. Furthermore, for the first time we could show that the formation of the recently identified cereulide isoforms is highly temperature dependent, which may have great importance in terms of food safety and predictive microbiology. Notably the production of isocereulide A, which is about 10-fold more cytotoxic than cereulide, was specifically supported at low temperatures.

  7. The 5th Symposium on Post-Transcriptional Regulation of Plant Gene Expression (PTRoPGE)

    Energy Technology Data Exchange (ETDEWEB)

    Karen S. Browning; Marie Petrocek; Bonnie Bartel

    2006-06-01

    The 5th Symposium on Post-Transcriptional Regulation of Plant Gene Expression (PTRoPGE) will be held June 8-12, 2005 at the University of Texas at Austin. Exciting new and ongoing discoveries show significant regulation of gene expression occurs after transcription. These post-transcriptional control events in plants range from subtle regulation of transcribed genes and phosphorylation, to the processes of gene regulation through small RNAs. This meeting will focus on the regulatory role of RNA, from transcription, through translation and finally degradation. The cross-disciplinary design of this meeting is necessary to encourage interactions between researchers that have a common interest in post-transcriptional gene expression in plants. By bringing together a diverse group of plant molecular biologist and biochemists at all careers stages from across the world, this meeting will bring about more rapid progress in understanding how plant genomes work and how genes are finely regulated by post-transcriptional processes to ultimately regulate cells.

  8. miR-200b mediates post-transcriptional repression of ZFHX1B

    DEFF Research Database (Denmark)

    Christoffersen, Nanna Rønbjerg; Silahtaroglu, Asli; Ørom, Ulf Lupo Andersson

    2007-01-01

    MicroRNAs have important functions during animal development and homeostasis through post-transcriptional regulation of their cognate mRNA targets. ZFHX1B is a transcriptional repressor involved in the TGFbeta signaling pathway and in processes of epithelial to mesenchymal transition via regulation...

  9. Elongation factor P mediates a novel post-transcriptional regulatory pathway critical for bacterial virulence

    DEFF Research Database (Denmark)

    Zou, S Betty; Roy, Hervé; Ibba, Michael

    2012-01-01

    of the pathogen to respond to external cues are typically attenuating. Here we discuss our recent discovery of a novel post-transcriptional regulatory pathway critical for Salmonella virulence and stress resistance. The enzymes PoxA and YjeK coordinately attach a unique beta-amino acid onto a highly conserved...

  10. Tinkering evolution of post-transcriptional RNA regulons: puf3p in fungi as an example.

    Directory of Open Access Journals (Sweden)

    Huifeng Jiang

    2010-07-01

    Full Text Available Genome-wide studies of post-transcriptional mRNA regulation in model organisms indicate a "post-transcriptional RNA regulon" model, in which a set of functionally related genes is regulated by mRNA-binding RNAs or proteins. One well-studied post-transcriptional regulon by Puf3p functions in mitochondrial biogenesis in budding yeast. The evolution of the Puf3p regulon remains unclear because previous studies have shown functional divergence of Puf3p regulon targets among yeast, fruit fly, and humans. By analyzing evolutionary patterns of Puf3p and its targeted genes in forty-two sequenced fungi, we demonstrated that, although the Puf3p regulon is conserved among all of the studied fungi, the dedicated regulation of mitochondrial biogenesis by Puf3p emerged only in the Saccharomycotina clade. Moreover, the evolution of the Puf3p regulon was coupled with evolution of codon usage bias in down-regulating expression of genes that function in mitochondria in yeast species after genome duplication. Our results provide a scenario for how evolution like a tinker exploits pre-existing materials of a conserved post-transcriptional regulon to regulate gene expression for novel functional roles.

  11. Small RNAs and Argonaute proteins: key players in post-transcriptional gene silencing

    NARCIS (Netherlands)

    Steiner, F.A.

    2007-01-01

    Small RNAs are important transcriptional and post-transcriptional regulators of gene expression. Many classes of small RNAs have been discovered, each carrying out specialized functions. siRNAs and miRNAs are best studies. siRNAs function in the process of RNAi and are thought to defend the genome

  12. Nuclear-encoded factors involved in post-transcriptional processing and modification of mitochondrial tRNAs in human disease

    Directory of Open Access Journals (Sweden)

    Christopher A Powell

    2015-03-01

    Full Text Available The human mitochondrial genome (mtDNA encodes twenty-two tRNAs (mt-tRNAs that are necessary for the intraorganellar translation of the thirteen mtDNA-encoded subunits of the mitochondrial respiratory chain complexes. Maturation of mt-tRNAs involves 5’ and 3’ nucleolytic excision from precursor RNAs, as well as extensive post-transcriptional modifications. Recent data suggest that over 7 % of all mt-tRNA residues in mammals undergo post-transcriptional modification, with over 30 different modified mt-tRNA positions so far described. These processing and modification steps are necessary for proper mt-tRNA function, and are performed by dedicated, nuclear-encoded enzymes. Recent growing evidence suggests that mutations in these nuclear genes, leading to incorrect maturation of mt-tRNAs, are a cause of human mitochondrial disease. Furthermore, mtDNA mutations in mt-tRNA genes, which may also affect mt-tRNA function, processing and modification, are also frequently associated with human disease. In theory, all pathogenic mt-tRNA variants should be expected to affect only a single process, which is mitochondrial translation, albeit to various extents. However, the clinical manifestations of mitochondrial disorders linked to mutations in mt-tRNAs are extremely heterogeneous, ranging from defects of a single tissue to complex multisystem disorders. This review focuses on the current knowledge of nuclear genes coding for proteins involved in mt-tRNA maturation that have been linked to human mitochondrial pathologies. We further discuss the possibility that tissue specific regulation of mt-tRNA modifying enzymes could play an important role in the clinical heterogeneity observed for mitochondrial diseases caused by mutations in mt-tRNA genes.

  13. Meta-analysis of small RNA-sequencing errors reveals ubiquitous post-transcriptional RNA modifications

    OpenAIRE

    Ebhardt, H. Alexander; Tsang, Herbert H.; Dai, Denny C.; Liu, Yifeng; Bostan, Babak; Fahlman, Richard P.

    2009-01-01

    Recent advances in DNA-sequencing technology have made it possible to obtain large datasets of small RNA sequences. Here we demonstrate that not all non-perfectly matched small RNA sequences are simple technological sequencing errors, but many hold valuable biological information. Analysis of three small RNA datasets originating from Oryza sativa and Arabidopsis thaliana small RNA-sequencing projects demonstrates that many single nucleotide substitution errors overlap when aligning homologous...

  14. Deep sequencing analysis of small noncoding RNA and mRNA targets of the global post-transcriptional regulator, Hfq.

    Directory of Open Access Journals (Sweden)

    Alexandra Sittka

    2008-08-01

    Full Text Available Recent advances in high-throughput pyrosequencing (HTPS technology now allow a thorough analysis of RNA bound to cellular proteins, and, therefore, of post-transcriptional regulons. We used HTPS to discover the Salmonella RNAs that are targeted by the common bacterial Sm-like protein, Hfq. Initial transcriptomic analysis revealed that Hfq controls the expression of almost a fifth of all Salmonella genes, including several horizontally acquired pathogenicity islands (SPI-1, -2, -4, -5, two sigma factor regulons, and the flagellar gene cascade. Subsequent HTPS analysis of 350,000 cDNAs, derived from RNA co-immunoprecipitation (coIP with epitope-tagged Hfq or control coIP, identified 727 mRNAs that are Hfq-bound in vivo. The cDNA analysis discovered new, small noncoding RNAs (sRNAs and more than doubled the number of sRNAs known to be expressed in Salmonella to 64; about half of these are associated with Hfq. Our analysis explained aspects of the pleiotropic effects of Hfq loss-of-function. Specifically, we found that the mRNAs of hilD (master regulator of the SPI-1 invasion genes and flhDC (flagellar master regulator were bound by Hfq. We predicted that defective SPI-1 secretion and flagellar phenotypes of the hfq mutant would be rescued by overexpression of HilD and FlhDC, and we proved this to be correct. The combination of epitope-tagging and HTPS of immunoprecipitated RNA detected the expression of many intergenic chromosomal regions of Salmonella. Our approach overcomes the limited availability of high-density microarrays that have impeded expression-based sRNA discovery in microorganisms. We present a generic strategy that is ideal for the systems-level analysis of the post-transcriptional regulons of RNA-binding proteins and for sRNA discovery in a wide range of bacteria.

  15. High SINE RNA Expression Correlates with Post-Transcriptional Downregulation of BRCA1

    Directory of Open Access Journals (Sweden)

    Giovanni Bosco

    2013-04-01

    Full Text Available Short Interspersed Nuclear Elements (SINEs are non-autonomous retrotransposons that comprise a large fraction of the human genome. SINEs are demethylated in human disease, but whether SINEs become transcriptionally induced and how the resulting transcripts may affect the expression of protein coding genes is unknown. Here, we show that downregulation of the mRNA of the tumor suppressor gene BRCA1 is associated with increased transcription of SINEs and production of sense and antisense SINE small RNAs. We find that BRCA1 mRNA is post-transcriptionally down-regulated in a Dicer and Drosha dependent manner and that expression of a SINE inverted repeat with sequence identity to a BRCA1 intron is sufficient for downregulation of BRCA1 mRNA. These observations suggest that transcriptional activation of SINEs could contribute to a novel mechanism of RNA mediated post-transcriptional silencing of human genes.

  16. Intersections of post-transcriptional gene regulatory mechanisms with intermediary metabolism.

    Science.gov (United States)

    Arif, Waqar; Datar, Gandhar; Kalsotra, Auinash

    2017-03-01

    Intermediary metabolism studies have typically concentrated on four major regulatory mechanisms-substrate availability, allosteric enzyme regulation, post-translational enzyme modification, and regulated enzyme synthesis. Although transcriptional control has been a big focus, it is becoming increasingly evident that many post-transcriptional events are deeply embedded within the core regulatory circuits of enzyme synthesis/breakdown that maintain metabolic homeostasis. The prominent post-transcriptional mechanisms affecting intermediary metabolism include alternative pre-mRNA processing, mRNA stability and translation control, and the more recently discovered regulation by noncoding RNAs. In this review, we discuss the latest advances in our understanding of these diverse mechanisms at the cell-, tissue- and organismal-level. We also highlight the dynamics, complexity and non-linear nature of their regulatory roles in metabolic decision making, and deliberate some of the outstanding questions and challenges in this rapidly expanding field. Copyright © 2017 Elsevier B.V. All rights reserved.

  17. Post-transcriptional regulation of ITGB6 protein levels in damaged skeletal muscle

    OpenAIRE

    Ducceschi, Melissa; Clifton, Lisa G.; Stimpson, Stephen A; Billin, Andrew N.

    2014-01-01

    We have identified integrin beta 6 (Itgb6) as a transcript highly enriched in skeletal muscle. This finding is unexpected because Itgb6 is typically associated with epithelial expression domains in normal tissue. Further we find that ITGB6 protein expression in muscle is post-transcriptionally regulated. Uninjured muscle expresses Itgb6 RNA but no ITGB6 protein is detectable. Muscle injury induces ITGB6 protein accumulation rapidly post-injury in myofibers adjacent to the site of injury. As r...

  18. Post-transcriptional exon shuffling events in humans can be evolutionarily conserved and abundant

    OpenAIRE

    Al-Balool, Haya H.; Weber, David; Liu, Yilei; Wade, Mark; Guleria, Kamlesh; Nam, Pitsien Lang Ping; Clayton, Jake; Rowe, William; Coxhead, Jonathan; Irving, Julie; Elliott, David J.; Hall, Andrew G.; Santibanez-Koref, Mauro; Jackson, Michael S.

    2011-01-01

    In silico analyses have established that transcripts from some genes can be processed into RNAs with rearranged exon order relative to genomic structure (post-transcriptional exon shuffling, or PTES). Although known to contribute to transcriptome diversity in some species, to date the structure, distribution, abundance, and functional significance of human PTES transcripts remains largely unknown. Here, using high-throughput transcriptome sequencing, we identify 205 putative human PTES produc...

  19. Regulation of Adult CNS Axonal Regeneration by the Post-transcriptional Regulator Cpeb1

    Directory of Open Access Journals (Sweden)

    Wilson Pak-Kin Lou

    2018-01-01

    Full Text Available Adult mammalian central nervous system (CNS neurons are unable to regenerate following axonal injury, leading to permanent functional impairments. Yet, the reasons underlying this regeneration failure are not fully understood. Here, we studied the transcriptome and translatome shortly after spinal cord injury. Profiling of the total and ribosome-bound RNA in injured and naïve spinal cords identified a substantial post-transcriptional regulation of gene expression. In particular, transcripts associated with nervous system development were down-regulated in the total RNA fraction while remaining stably loaded onto ribosomes. Interestingly, motif association analysis of post-transcriptionally regulated transcripts identified the cytoplasmic polyadenylation element (CPE as enriched in a subset of these transcripts that was more resistant to injury-induced reduction at the transcriptome level. Modulation of these transcripts by overexpression of the CPE binding protein, Cpeb1, in mouse and Drosophila CNS neurons promoted axonal regeneration following injury. Our study uncovered a global evolutionarily conserved post-transcriptional mechanism enhancing regeneration of injured CNS axons.

  20. Establishment of a TGFβ-induced post-transcriptional EMT gene signature.

    Directory of Open Access Journals (Sweden)

    George S Hussey

    Full Text Available A major challenge in the clinical management of human cancers is to accurately stratify patients according to risk and likelihood of a favorable response. Stratification is confounded by significant phenotypic heterogeneity in some tumor types, often without obvious criteria for subdivision. Despite intensive transcriptional array analyses, the identity and validation of cancer specific 'signature genes' remains elusive, partially because the transcriptome does not mirror the proteome. The simplification associated with transcriptomic profiling does not take into consideration changes in the relative expression among transcripts that arise due to post-transcriptional regulatory events. We have previously shown that TGFβ post-transcriptionally regulates epithelial-mesenchymal transition (EMT by causing increased expression of two transcripts, Dab2 and ILEI, by modulating hnRNP E1 phosphorylation. Using a genome-wide combinatorial approach involving expression profiling and RIP-Chip analysis, we have identified a cohort of translationally regulated mRNAs that are induced during TGFβ-mediated EMT. Coordinated translational regulation by hnRNP E1 constitutes a post-transcriptional regulon inhibiting the expression of related EMT-facilitating genes, thus enabling the cell to rapidly and coordinately regulate multiple EMT-facilitating genes.

  1. Control of Candida albicans morphology and pathogenicity by post-transcriptional mechanisms

    Science.gov (United States)

    2017-01-01

    Candida albicans is a major human fungal pathogen responsible for both systemic and mucosal infections in a wide variety of immunocompromised individuals. Because the ability of C. albicans to undergo a reversible morphological transition from yeast to filaments is important for virulence, significant research efforts have focused on mechanisms that control this transition. While transcriptional and post-translational mechanisms have been well-studied, considerably less is known about the role of post-transcriptional mechanisms. However, in recent years several discoveries have begun to shed light on this important, but understudied, area. Here, I will review a variety of post-transcriptional mechanisms that have recently been shown to control C. albicans morphology, virulence and/or virulence-related processes, including those involving alternative transcript localization, mRNA stability and translation. I will also discuss the role that these mechanisms play in other pathogens as well as the potential they may hold to serve as targets for new antifungal strategies. Ultimately, gaining a better understanding of C. albicans post-transcriptional mechanisms will significantly improve our knowledge of how morphogenesis and virulence are controlled in fungal pathogens and open new avenues for the development of novel and more effective antifungals. PMID:27312239

  2. Organization and post-transcriptional processing of focal adhesion kinase gene

    Directory of Open Access Journals (Sweden)

    Enslen Hervé

    2006-08-01

    Full Text Available Abstract Background Focal adhesion kinase (FAK is a non-receptor tyrosine kinase critical for processes ranging from embryo development to cancer progression. Although isoforms with specific molecular and functional properties have been characterized in rodents and chicken, the organization of FAK gene throughout phylogeny and its potential to generate multiple isoforms are not well understood. Here, we study the phylogeny of FAK, the organization of its gene, and its post-transcriptional processing in rodents and human. Results A single orthologue of FAK and the related PYK2 was found in non-vertebrate species. Gene duplication probably occurred in deuterostomes after the echinoderma embranchment, leading to the evolution of PYK2 with distinct properties. The amino acid sequence of FAK and PYK2 is conserved in their functional domains but not in their linker regions, with the absence of autophosphorylation site in C. elegans. Comparison of mouse and human FAK genes revealed the existence of multiple combinations of conserved and non-conserved 5'-untranslated exons in FAK transcripts suggesting a complex regulation of their expression. Four alternatively spliced coding exons (13, 14, 16, and 31, previously described in rodents, are highly conserved in vertebrates. Cis-regulatory elements known to regulate alternative splicing were found in conserved alternative exons of FAK or in the flanking introns. In contrast, other reported human variant exons were restricted to Homo sapiens, and, in some cases, other primates. Several of these non-conserved exons may correspond to transposable elements. The inclusion of conserved alternative exons was examined by RT-PCR in mouse and human brain during development. Inclusion of exons 14 and 16 peaked at the end of embryonic life, whereas inclusion of exon 13 increased steadily until adulthood. Study of various tissues showed that inclusion of these exons also occurred, independently from each other, in a

  3. Post-transcriptional Mechanisms Contribute Little to Phenotypic Variation in Snake Venoms.

    Science.gov (United States)

    Rokyta, Darin R; Margres, Mark J; Calvin, Kate

    2015-09-09

    Protein expression is a major link in the genotype-phenotype relationship, and processes affecting protein abundances, such as rates of transcription and translation, could contribute to phenotypic evolution if they generate heritable variation. Recent work has suggested that mRNA abundances do not accurately predict final protein abundances, which would imply that post-transcriptional regulatory processes contribute significantly to phenotypes. Post-transcriptional processes also appear to buffer changes in transcriptional patterns as species diverge, suggesting that the transcriptional changes have little or no effect on the phenotypes undergoing study. We tested for concordance between mRNA and protein expression levels in snake venoms by means of mRNA-seq and quantitative mass spectrometry for 11 snakes representing 10 species, six genera, and three families. In contrast to most previous work, we found high correlations between venom gland transcriptomes and venom proteomes for 10 of our 11 comparisons. We tested for protein-level buffering of transcriptional changes during species divergence by comparing the difference between transcript abundance and protein abundance for three pairs of species and one intraspecific pair. We found no evidence for buffering during divergence of our three species pairs but did find evidence for protein-level buffering for our single intraspecific comparison, suggesting that buffering, if present, was a transient phenomenon in venom divergence. Our results demonstrated that post-transcriptional mechanisms did not contribute significantly to phenotypic evolution in venoms and suggest a more prominent and direct role for cis-regulatory evolution in phenotypic variation, particularly for snake venoms. Copyright © 2015 Rokyta et al.

  4. Post-transcriptional regulation of ribosomal protein genes during serum starvation in Entamoeba histolytica.

    Science.gov (United States)

    Ahamad, Jamaluddin; Ojha, Sandeep; Srivastava, Ankita; Bhattacharya, Alok; Bhattacharya, Sudha

    2015-06-01

    Ribosome synthesis involves all three RNA polymerases which are co-ordinately regulated to produce equimolar amounts of rRNAs and ribosomal proteins (RPs). Unlike model organisms where transcription of rRNA and RP genes slows down during stress, in E. histolytica rDNA transcription continues but pre-rRNA processing slows down and unprocessed pre-rRNA accumulates during serum starvation. To investigate the regulation of RP genes under stress we measured transcription of six selected RP genes from the small- and large-ribosomal subunits (RPS6, RPS3, RPS19, RPL5, RPL26, RPL30) representing the early-, mid-, and late-stages of ribosomal assembly. Transcripts of these genes persisted in growth-stressed cells. Expression of luciferase reporter under the control of two RP genes (RPS19 and RPL30) was studied during serum starvation and upon serum replenishment. Although luciferase transcript levels remained unchanged during starvation, luciferase activity steadily declined to 7.8% and 15% of control cells, respectively. After serum replenishment the activity increased to normal levels, suggesting post-transcriptional regulation of these genes. Mutations in the sequence -2 to -9 upstream of AUG in the RPL30 gene resulted in the phenotype expected of post-transcriptional regulation. Transcription of luciferase reporter was unaffected in this mutant, and luciferase activity did not decline during serum starvation, showing that this sequence is required to repress translation of RPL30 mRNA, and mutations in this region relieve repression. Our data show that during serum starvation E. histolytica blocks ribosome biogenesis post-transcriptionally by inhibiting pre-rRNA processing on the one hand, and the translation of RP mRNAs on the other. Copyright © 2015 Elsevier B.V. All rights reserved.

  5. Post-transcriptional Regulation of De Novo Lipogenesis by mTORC1-S6K1-SRPK2 Signaling.

    Science.gov (United States)

    Lee, Gina; Zheng, Yuxiang; Cho, Sungyun; Jang, Cholsoon; England, Christina; Dempsey, Jamie M; Yu, Yonghao; Liu, Xiaolei; He, Long; Cavaliere, Paola M; Chavez, Andre; Zhang, Erik; Isik, Meltem; Couvillon, Anthony; Dephoure, Noah E; Blackwell, T Keith; Yu, Jane J; Rabinowitz, Joshua D; Cantley, Lewis C; Blenis, John

    2017-12-14

    mTORC1 is a signal integrator and master regulator of cellular anabolic processes linked to cell growth and survival. Here, we demonstrate that mTORC1 promotes lipid biogenesis via SRPK2, a key regulator of RNA-binding SR proteins. mTORC1-activated S6K1 phosphorylates SRPK2 at Ser494, which primes Ser497 phosphorylation by CK1. These phosphorylation events promote SRPK2 nuclear translocation and phosphorylation of SR proteins. Genome-wide transcriptome analysis reveals that lipid biosynthetic enzymes are among the downstream targets of mTORC1-SRPK2 signaling. Mechanistically, SRPK2 promotes SR protein binding to U1-70K to induce splicing of lipogenic pre-mRNAs. Inhibition of this signaling pathway leads to intron retention of lipogenic genes, which triggers nonsense-mediated mRNA decay. Genetic or pharmacological inhibition of SRPK2 blunts de novo lipid synthesis, thereby suppressing cell growth. These results thus reveal a novel role of mTORC1-SRPK2 signaling in post-transcriptional regulation of lipid metabolism and demonstrate that SRPK2 is a potential therapeutic target for mTORC1-driven metabolic disorders. Copyright © 2017 Elsevier Inc. All rights reserved.

  6. RNAi mediates post-transcriptional repression of gene expression in fission yeast Schizosaccharomyces pombe

    Energy Technology Data Exchange (ETDEWEB)

    Smialowska, Agata, E-mail: smialowskaa@gmail.com [Center for Biosciences, Department of Biosciences and Nutrition, Karolinska Institute, Huddinge 141-83 (Sweden); School of Life Sciences, Södertörn Högskola, Huddinge 141-89 (Sweden); Djupedal, Ingela; Wang, Jingwen [Center for Biosciences, Department of Biosciences and Nutrition, Karolinska Institute, Huddinge 141-83 (Sweden); Kylsten, Per [School of Life Sciences, Södertörn Högskola, Huddinge 141-89 (Sweden); Swoboda, Peter [Center for Biosciences, Department of Biosciences and Nutrition, Karolinska Institute, Huddinge 141-83 (Sweden); Ekwall, Karl, E-mail: Karl.Ekwall@ki.se [Center for Biosciences, Department of Biosciences and Nutrition, Karolinska Institute, Huddinge 141-83 (Sweden); School of Life Sciences, Södertörn Högskola, Huddinge 141-89 (Sweden)

    2014-02-07

    Highlights: • Protein coding genes accumulate anti-sense sRNAs in fission yeast S. pombe. • RNAi represses protein-coding genes in S. pombe. • RNAi-mediated gene repression is post-transcriptional. - Abstract: RNA interference (RNAi) is a gene silencing mechanism conserved from fungi to mammals. Small interfering RNAs are products and mediators of the RNAi pathway and act as specificity factors in recruiting effector complexes. The Schizosaccharomyces pombe genome encodes one of each of the core RNAi proteins, Dicer, Argonaute and RNA-dependent RNA polymerase (dcr1, ago1, rdp1). Even though the function of RNAi in heterochromatin assembly in S. pombe is established, its role in controlling gene expression is elusive. Here, we report the identification of small RNAs mapped anti-sense to protein coding genes in fission yeast. We demonstrate that these genes are up-regulated at the protein level in RNAi mutants, while their mRNA levels are not significantly changed. We show that the repression by RNAi is not a result of heterochromatin formation. Thus, we conclude that RNAi is involved in post-transcriptional gene silencing in S. pombe.

  7. Tuning the engine: an introduction to resources on post-transcriptional regulation of gene expression.

    Science.gov (United States)

    Dassi, Erik; Quattrone, Alessandro

    2012-10-01

    In the last years post-transcriptional regulation (PTR) of gene expression has been increasingly recognized to be a powerful and general determinant of the quantitative changes in proteomes, and therefore a driving force for cell phenotypes. By means of networks of trans-factors on one hand, and cis-elements found primarily in untranslated regions (UTRs) of mRNA on the other hand, mRNA availability to translation and translation rates are tightly controlled and can be rapidly tuned according to the changing state of the cell. A number of dedicated resources and tools, including databases and predictive algorithms, have been proposed as bioinformatics aids for the study of this fundamental layer of gene expression regulation. Their use, however, is rendered difficult by heterogeneity and fragmentation.   This review aims to locate these resources in their proper space, classifying them according to their goals, limitations and integration capabilities and, in the end, to provide the user with an initial toolbox for the bioinformatic analysis of post-transcriptional regulation of gene expression. The accompanying website, available at www.ptrguide.org, lists all resources, provides summary and features for each one and will be regularly updated in the future.

  8. Genome wide analysis of human genes transcriptionally and post-transcriptionally regulated by the HTLV-I protein p30.

    Science.gov (United States)

    Taylor, John M; Ghorbel, Sofiane; Nicot, Christophe

    2009-07-14

    Human T-cell leukemia virus type 1 (HTLV-I) is a human retrovirus that is etiologically linked to adult T-cell leukemia (ATL), an aggressive and fatal lymphoproliferative disease. The viral transactivator, Tax, is thought to play an important role during the initial stages of CD4+ T-cell immortalization by HTLV-1. Tax has been shown to activate transcription through CREB/ATF and NF-KB, and to alter numerous signaling pathways. These pleiotropic effects of Tax modify the expression of a wide array of cellular genes. Another viral protein encoded by HTLV-I, p30, has been shown to affect virus replication at the transcriptional and posttranscriptional levels. Little is currently known regarding the effect of p30 on the expression and nuclear export of cellular host mRNA transcripts. Identification of these RNA may reveal new targets and increase our understanding of HTLV-I pathogenesis. In this study, using primary peripheral blood mononuclear cells, we report a genome wide analysis of human genes transcriptionally and post-transcriptionally regulated by the HTLV-I protein p30. Using microarray analysis, we analyzed total and cytoplasmic cellular mRNA transcript levels isolated from PBMCs to assess the effect of p30 on cellular RNA transcript expression and their nuclear export. We report p30-dependent transcription resulting in the 2.5 fold up-regulation of 15 genes and the down-regulation of 65 human genes. We further tested nuclear export of cellular mRNA and found that p30 expression also resulted in a 2.5 fold post-transcriptional down-regulation of 90 genes and the up-regulation of 33 genes. Overall, our study describes that expression of the HTLV-I protein p30 both positively and negatively alters the expression of cellular transcripts. Our study identifies for the first time the cellular genes for which nuclear export is affected by p30. These results suggest that p30 may possess a more global function with respect to mRNA transcription and the nuclear

  9. Genome wide analysis of human genes transcriptionally and post-transcriptionally regulated by the HTLV-I protein p30

    Directory of Open Access Journals (Sweden)

    Nicot Christophe

    2009-07-01

    Full Text Available Abstract Background Human T-cell leukemia virus type 1 (HTLV-I is a human retrovirus that is etiologically linked to adult T-cell leukemia (ATL, an aggressive and fatal lymphoproliferative disease. The viral transactivator, Tax, is thought to play an important role during the initial stages of CD4+ T-cell immortalization by HTLV-1. Tax has been shown to activate transcription through CREB/ATF and NF-KB, and to alter numerous signaling pathways. These pleiotropic effects of Tax modify the expression of a wide array of cellular genes. Another viral protein encoded by HTLV-I, p30, has been shown to affect virus replication at the transcriptional and posttranscriptional levels. Little is currently known regarding the effect of p30 on the expression and nuclear export of cellular host mRNA transcripts. Identification of these RNA may reveal new targets and increase our understanding of HTLV-I pathogenesis. In this study, using primary peripheral blood mononuclear cells, we report a genome wide analysis of human genes transcriptionally and post-transcriptionally regulated by the HTLV-I protein p30. Results Using microarray analysis, we analyzed total and cytoplasmic cellular mRNA transcript levels isolated from PBMCs to assess the effect of p30 on cellular RNA transcript expression and their nuclear export. We report p30-dependent transcription resulting in the 2.5 fold up-regulation of 15 genes and the down-regulation of 65 human genes. We further tested nuclear export of cellular mRNA and found that p30 expression also resulted in a 2.5 fold post-transcriptional down-regulation of 90 genes and the up-regulation of 33 genes. Conclusion Overall, our study describes that expression of the HTLV-I protein p30 both positively and negatively alters the expression of cellular transcripts. Our study identifies for the first time the cellular genes for which nuclear export is affected by p30. These results suggest that p30 may possess a more global function

  10. Post-transcriptional regulation of BRCA1 through its coding sequence by the miR-15/107 group of miRNAs

    Directory of Open Access Journals (Sweden)

    Kevin eQuann

    2015-07-01

    Full Text Available MicroRNAs (miRNAs are important post-transcriptional regulators of gene expression that act by degrading their RNA targets or by repressing the translation of messenger RNAs (mRNAs. Initially thought to primarily target the 3´ untranslated region (3´UTR of mRNAs, miRNAs have since been shown to also target the 5´UTR and coding sequence. In this work, we focus on the post-transcriptional regulation of the BRCA1 gene, a major tumor suppressor and regulator of double-stranded break DNA repair and show that its mRNA is targeted by many members of the miR-15/107 group at a site located within the coding sequence. Ectopic expression of these miRNAs across a panel of nine cell lines demonstrated widespread suppression of BRCA1 mRNA levels. Additionally, by cloning a putative target site from BRCA1’s amino acid coding sequence into a luciferase reporter plasmid we confirmed the direct interaction of these miRNAs with this BRCA1 target. We also examined the relationship between ectopic expression of these targeting miRNAs and BRCA1 protein levels in immortalized pancreatic epithelium (hTERT-HPNE, colorectal adenocarcinoma (HCT-116 and pancreatic adenocarcinoma (MIA PaCa-2 cell lines and found protein abundance to be variably regulated in a cell-type specific manner that was not necessarily concordant with mRNA transcript availability. Our findings reveal a previously unrecognized aspect of BRCA1’s miRNA-mediated post-transcriptional regulation, namely the targeting of its amino acid coding region by the miR-15/107 group of miRNAs. The resulting regulation is apparently complex and cell-specific, an observation that may have implications for BRCA1-mediated DNA repair across tissue types.

  11. [Extensive cutaneous candidiasis revealing cutaneous T-cell lymphoma: 2 cases].

    Science.gov (United States)

    Duong, T; Ingen-Housz-Oro, S; Gaulier, A; Petit, A; Dubertret, L; Sigal-Grinberg, M

    2006-01-01

    During the course of immunodeficiency diseases, severe candidiasis can occur with extensive cutaneous and mucous membrane lesions. However, blood dyscrasias are very rarely revealed by diffuse candidiasis. We report two case of cutaneous T-cell lymphoma revealed by extensive and atypical cutaneous candidiasis. Case No. 1:A 72-year-old woman presented a pruritic rash of circinate, serpiginous patches on glabrous skin and skinfolds with multiple intertrigo and rapidly worsening palmoplantar keratoderma. All mycological skin specimens tested positive for Candida albicans. Histological examination of a biopsy sample from a serpiginous patch revealed the presence of fungal elements while palmoplantar keratoderma biopsy showed an epidermotropic lymphocytic infiltrate in the superficial dermis evocative of mycosis fungoides. Blood tests showed a white cell count of 28 600/mm3 with 14% circulating Sezary cells and a T-cell clone. The T-cell lymphoma was treated with methotrexate, but the disease worsened a few months later, progressing to CD30- large T-cell pleomorphic lymphoma. The patient died of severe sepsis. Case No 2:A 60-year-old man presented a macular rash over the face, trunk and skinfolds as well as erythematous scaly annular plaques of the glabrous skin with lymphadenopathy. Cultures of skin scrapings were all positive for Candida albicans. Blood tests showed a white cell count of 15 000/mm3 with 30% circulating Sezary cells. A trunk patch biopsy revealed the histological appearance of mycosis fungoides. There was a T-cell clone in the peripheral blood and skin. In both cases, the patients presented with widespread annular and erythematous scaly lesions of the glabrous skin and skinfolds with evidence of Candida albicans on fungal tests of all skin scrapings. The discovery of circulating Sezary cells on a systematic smear for hyperleukocytosis led us to suspect underlying cutaneous T-cell lymphoma, which was confirmed by biopsy of the skin lesions accompanying

  12. Deep sequencing analysis of small noncoding RNA and mRNA targets of the global post-transcriptional regulator, Hfq

    DEFF Research Database (Denmark)

    Sittka, A; Lucchini, S; Papenfort, K

    2008-01-01

    -immunoprecipitation (coIP) with epitope-tagged Hfq or control coIP, identified 727 mRNAs that are Hfq-bound in vivo. The cDNA analysis discovered new, small noncoding RNAs (sRNAs) and more than doubled the number of sRNAs known to be expressed in Salmonella to 64; about half of these are associated with Hfq. Our analysis......Recent advances in high-throughput pyrosequencing (HTPS) technology now allow a thorough analysis of RNA bound to cellular proteins, and, therefore, of post-transcriptional regulons. We used HTPS to discover the Salmonella RNAs that are targeted by the common bacterial Sm-like protein, Hfq. Initial...... transcriptomic analysis revealed that Hfq controls the expression of almost a fifth of all Salmonella genes, including several horizontally acquired pathogenicity islands (SPI-1, -2, -4, -5), two sigma factor regulons, and the flagellar gene cascade. Subsequent HTPS analysis of 350,000 cDNAs, derived from RNA co...

  13. Regulation of host-pathogen interactions via the post-transcriptional Csr/Rsm system.

    Science.gov (United States)

    Kusmierek, Maria; Dersch, Petra

    2017-12-02

    A successful colonization of specific hosts requires a rapid and efficient adaptation of the virulence-relevant gene expression program by bacterial pathogens. An important element in this endeavor is the Csr/Rsm system. This multi-component, post-transcriptional control system forms a central hub within complex regulatory networks and coordinately adjusts virulence properties with metabolic and physiological attributes of the pathogen. A key function is elicited by the RNA-binding protein CsrA/RsmA. CsrA/RsmA interacts with numerous target mRNAs, many of which encode crucial virulence factors, and alters their translation, stability or elongation of transcription. Recent studies highlighted that important colonization factors, toxins, and bacterial secretion systems are under CsrA/RsmA control. CsrA/RsmA deficiency impairs host colonization and attenuates virulence, making this post-transcriptional regulator a suitable drug target. The CsrA/RsmA protein can be inactivated through sequestration by non-coding RNAs, or via binding to specific highly abundant mRNAs and interacting proteins. The wide range of interaction partners and RNA targets, as well as the overarching, interlinked genetic control circuits illustrate the complexity of this regulatory system in the different pathogens. Future work addressing spatio-temporal changes of Csr/Rsm-mediated control during the course of an infection will help us to understand how bacteria reprogram their expression profile to cope with continuous changes experienced in colonized niches. Copyright © 2017 Elsevier Ltd. All rights reserved.

  14. Coordinated Evolution of Transcriptional and Post-Transcriptional Regulation for Mitochondrial Functions in Yeast Strains.

    Directory of Open Access Journals (Sweden)

    Xuepeng Sun

    Full Text Available Evolution of gene regulation has been proposed to play an important role in environmental adaptation. Exploring mechanisms underlying coordinated evolutionary changes at various levels of gene regulation could shed new light on how organism adapt in nature. In this study, we focused on regulatory differences between a laboratory Saccharomyces cerevisiae strain BY4742 and a pathogenic S. cerevisiae strain, YJM789. The two strains diverge in many features, including growth rate, morphology, high temperature tolerance, and pathogenicity. Our RNA-Seq and ribosomal footprint profiling data showed that gene expression differences are pervasive, and genes functioning in mitochondria are mostly divergent between the two strains at both transcriptional and translational levels. Combining functional genomics data from other yeast strains, we further demonstrated that significant divergence of expression for genes functioning in the electron transport chain (ETC was likely caused by differential expression of a transcriptional factor, HAP4, and that post-transcriptional regulation mediated by an RNA-binding protein, PUF3, likely led to expression divergence for genes involved in mitochondrial translation. We also explored mito-nuclear interactions via mitochondrial DNA replacement between strains. Although the two mitochondrial genomes harbor substantial sequence divergence, neither growth nor gene expression were affected by mitochondrial DNA replacement in both fermentative and respiratory growth media, indicating compatible mitochondrial and nuclear genomes between these two strains in the tested conditions. Collectively, we used mitochondrial functions as an example to demonstrate for the first time that evolution at both transcriptional and post-transcriptional levels could lead to coordinated regulatory changes underlying strain specific functional variations.

  15. The Caenorhabditis globin gene family reveals extensive nematode-specific radiation and diversification

    Directory of Open Access Journals (Sweden)

    Vinogradov Serge N

    2008-10-01

    Full Text Available Abstract Background Globin isoforms with variant properties and functions have been found in the pseudocoel, body wall and cuticle of various nematode species and even in the eyespots of the insect-parasite Mermis nigrescens. In fact, much higher levels of complexity exist, as shown by recent whole genome analysis studies. In silico analysis of the genome of Caenorhabditis elegans revealed an unexpectedly high number of globin genes featuring a remarkable diversity in gene structure, amino acid sequence and expression profiles. Results In the present study we have analyzed whole genomic data from C. briggsae, C. remanei, Pristionchus pacificus and Brugia malayi and EST data from several other nematode species to study the evolutionary history of the nematode globin gene family. We find a high level of conservation of the C. elegans globin complement, with even distantly related nematodes harboring orthologs to many Caenorhabditis globins. Bayesian phylogenetic analysis resolves all nematode globins into two distinct globin classes. Analysis of the globin intron-exon structures suggests extensive loss of ancestral introns and gain of new positions in deep nematode ancestors, and mainly loss in the Caenorhabditis lineage. We also show that the Caenorhabditis globin genes are expressed in distinct, mostly non-overlapping, sets of cells and that they are all under strong purifying selection. Conclusion Our results enable reconstruction of the evolutionary history of the globin gene family in the nematode phylum. A duplication of an ancestral globin gene occurred before the divergence of the Platyhelminthes and the Nematoda and one of the duplicated genes radiated further in the nematode phylum before the split of the Spirurina and Rhabditina and was followed by further radiation in the lineage leading to Caenorhabditis. The resulting globin genes were subject to processes of subfunctionalization and diversification leading to cell

  16. Extensive hydrothermal activity in the NE Lau basin revealed by ROV dives

    Science.gov (United States)

    Embley, R. W.; Resing, J. A.; Tebo, B.; Baker, E. T.; Butterfield, D. A.; Chadwick, B.; Davis, R.; de Ronde, C. E. J.; Lilley, M. D.; Lupton, J. E.; Merle, S. G.; Rubin, K. H.; Shank, T. M.; Walker, S. L.; Arculus, R. J.; Bobbitt, A. M.; Buck, N. J.; Caratori Tontini, F.; Crowhurst, P. V.; Mitchell, E.; Olson, E. J.; Ratmeyer, V.; Richards, S.; Roe, K. K.; Kenner-Chavis, P.; Martinez-Lyons, A.; Sheehan, C.; Brian, R.

    2014-12-01

    Dives with the QUEST 4000 ROV (Remotely Operated Vehicle) in September 2012 discovered nine hydrothermal sites in the arc and rear-arc region of the NE Lau Basin in 1150 m to 2630 m depth. These sites, originally detected by water column and seafloor surveys conducted in 2008-2011, include: (1) a paired sulfur-rich/black smoker field on the summit of a tectonically deformed magmatic arc volcano (Niua), (2) fracture-controlled black smoker venting on several small en echelon seamounts (north Matas) that lie between the magmatic arc and the backarc spreading center and (3) a magmatic degassing site on the summit of a dacite cone within a large (~12 km diameter) caldera volcano (Niuatahi). Dives at West Mata Seamount, which was undergoing strombolian volcanic activity and effusive rift-zone eruptions from 2008 to 2010, revealed a dormant volcanic phase in September 2012, with continued low-temperature diffuse venting. The high-temperature venting is likely driven by magmatic heat indicative of underlying partial melt zones and/or melt pockets distributed through the region. The occurrence of the youngest known boninite eruptions on the Mata volcanoes is consistent with subduction fluid flux melting extending into the rear-arc zone. Extension related to the transition from subduction to strike-slip motion of the northern Tonga Arc over the active Subduction-Transform Edge Propagator (STEP) fault probably contributes to the enhanced volcanism/hydrothermal activity in the NE Lau Basin. Chemosynthetic ecosystems at these sites range from mostly motile, lower diversity ecosystems at the eruptive/magmatically-degassing sites to higher diversity ecosystems with less mobile faunal components at the black-smoker systems. The wide range of fluid chemistry, water depth and geologic settings of the hydrothermal systems in this area provides an intriguing template to study the interaction of hydrothermal fluid chemistry, chemosynthetic habitats and their geologic underpinning

  17. Comparative Genomics Analyses Reveal Extensive Chromosome Colinearity and Novel Quantitative Trait Loci in Eucalyptus.

    Directory of Open Access Journals (Sweden)

    Fagen Li

    Full Text Available Dense genetic maps, along with quantitative trait loci (QTLs detected on such maps, are powerful tools for genomics and molecular breeding studies. In the important woody genus Eucalyptus, the recent release of E. grandis genome sequence allows for sequence-based genomic comparison and searching for positional candidate genes within QTL regions. Here, dense genetic maps were constructed for E. urophylla and E. tereticornis using genomic simple sequence repeats (SSR, expressed sequence tag (EST derived SSR, EST-derived cleaved amplified polymorphic sequence (EST-CAPS, and diversity arrays technology (DArT markers. The E. urophylla and E. tereticornis maps comprised 700 and 585 markers across 11 linkage groups, totaling at 1,208.2 and 1,241.4 cM in length, respectively. Extensive synteny and colinearity were observed as compared to three earlier DArT-based eucalypt maps (two maps with E. grandis × E. urophylla and one map of E. globulus and with the E. grandis genome sequence. Fifty-three QTLs for growth (10-56 months of age and wood density (56 months were identified in 22 discrete regions on both maps, in which only one colocalizaiton was found between growth and wood density. Novel QTLs were revealed as compared with those previously detected on DArT-based maps for similar ages in Eucalyptus. Eleven to 585 positional candidate genes were obained for a 56-month-old QTL through aligning QTL confidence interval with the E. grandis genome. These results will assist in comparative genomics studies, targeted gene characterization, and marker-assisted selection in Eucalyptus and the related taxa.

  18. PSD-95 is post-transcriptionally repressed during early neural development by PTBP1 and PTBP2

    DEFF Research Database (Denmark)

    Zheng, Sika; Gray, Erin E; Chawla, Geetanjali

    2012-01-01

    Postsynaptic density protein 95 (PSD-95) is essential for synaptic maturation and plasticity. Although its synaptic regulation has been widely studied, the control of PSD-95 cellular expression is not understood. We found that Psd-95 was controlled post-transcriptionally during neural development...

  19. Harnessing CRISPR/Cas systems for programmable transcriptional and post-transcriptional regulation

    KAUST Repository

    Mahas, Ahmed

    2017-11-29

    Genome editing has enabled broad advances and novel approaches in studies of gene function and structure; now, emerging methods aim to precisely engineer post-transcriptional processes. Developing precise, efficient molecular tools to alter the transcriptome holds great promise for biotechnology and synthetic biology applications. Different approaches have been employed for targeted degradation of RNA species in eukaryotes, but they lack programmability and versatility, thereby limiting their utility for diverse applications. The CRISPR/Cas9 system has been harnessed for genome editing in many eukaryotic species and, using a catalytically inactive Cas9 variant, the CRISPR/dCas9 system has been repurposed for transcriptional regulation. Recent studies have used other CRISPR/Cas systems for targeted RNA degradation and RNA-based manipulations. For example, Cas13a, a Type VI-A endonuclease, has been identified as an RNA-guided RNA ribonuclease and used for manipulation of RNA. Here, we discuss different modalities for targeted RNA interference with an emphasis on the potential applications of CRISPR/Cas systems as programmable transcriptional regulators for broad uses, including functional biology, biotechnology, and synthetic biology applications.

  20. Transcriptional and post-transcriptional regulation of nucleotide excision repair genes in human cells

    Energy Technology Data Exchange (ETDEWEB)

    Lefkofsky, Hailey B. [Translational Oncology Program, University of Michigan Medical School, Ann Arbor, MI (United States); Veloso, Artur [Translational Oncology Program, University of Michigan Medical School, Ann Arbor, MI (United States); Department of Radiation Oncology, University of Michigan Medical School, Ann Arbor, MI (United States); Bioinformatics Program, Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI (United States); Ljungman, Mats, E-mail: ljungman@umich.edu [Translational Oncology Program, University of Michigan Medical School, Ann Arbor, MI (United States); Department of Radiation Oncology, University of Michigan Medical School, Ann Arbor, MI (United States); Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI (United States)

    2015-06-15

    Nucleotide excision repair (NER) removes DNA helix-distorting lesions induced by UV light and various chemotherapeutic agents such as cisplatin. These lesions efficiently block the elongation of transcription and need to be rapidly removed by transcription-coupled NER (TC-NER) to avoid the induction of apoptosis. Twenty-nine genes have been classified to code for proteins participating in nucleotide excision repair (NER) in human cells. Here we explored the transcriptional and post-transcriptional regulation of these NER genes across 13 human cell lines using Bru-seq and BruChase-seq, respectively. Many NER genes are relatively large in size and therefore will be easily inactivated by UV-induced transcription-blocking lesions. Furthermore, many of these genes produce transcripts that are rather unstable. Thus, these genes are expected to rapidly lose expression leading to a diminished function of NER. One such gene is ERCC6 that codes for the CSB protein critical for TC-NER. Due to its large gene size and high RNA turnover rate, the ERCC6 gene may act as dosimeter of DNA damage so that at high levels of damage, ERCC6 RNA levels would be diminished leading to the loss of CSB expression, inhibition of TC-NER and the promotion of cell death.

  1. SF2/ASF autoregulation involves multiple layers of post-transcriptional and translational control.

    Science.gov (United States)

    Sun, Shuying; Zhang, Zuo; Sinha, Rahul; Karni, Rotem; Krainer, Adrian R

    2010-03-01

    SF2/ASF is a prototypical serine- and arginine-rich protein, with important roles in splicing and other aspects of mRNA metabolism. Splicing factor, arginine/serine-rich 1 (SFRS1), the gene encoding SF2/ASF, is a potent proto-oncogene with abnormal expression in many tumors. We found that SF2/ASF negatively autoregulates its expression to maintain homeostatic levels. We characterized six alternatively spliced SF2/ASF mRNA isoforms: the major isoform encodes full-length protein, whereas the others are either retained in the nucleus or degraded by nonsense-mediated mRNA decay. Unproductive splicing accounts for only part of the autoregulation, which occurs primarily at the translational level. The effect is specific to SF2/ASF and requires RNA recognition motif 2 (RRM2). The ultraconserved 3' untranslated region (UTR) is necessary and sufficient for downregulation. SF2/ASF overexpression shifts the distribution of target mRNA toward monoribosomes, and translational repression is partly independent of Dicer and a 5' cap. Thus, multiple post-transcriptional and translational mechanisms are involved in fine-tuning the expression of SF2/ASF.

  2. RNAi mediates post-transcriptional repression of gene expression in fission yeast Schizosaccharomyces pombe.

    Science.gov (United States)

    Smialowska, Agata; Djupedal, Ingela; Wang, Jingwen; Kylsten, Per; Swoboda, Peter; Ekwall, Karl

    2014-02-07

    RNA interference (RNAi) is a gene silencing mechanism conserved from fungi to mammals. Small interfering RNAs are products and mediators of the RNAi pathway and act as specificity factors in recruiting effector complexes. The Schizosaccharomyces pombe genome encodes one of each of the core RNAi proteins, Dicer, Argonaute and RNA-dependent RNA polymerase (dcr1, ago1, rdp1). Even though the function of RNAi in heterochromatin assembly in S. pombe is established, its role in controlling gene expression is elusive. Here, we report the identification of small RNAs mapped anti-sense to protein coding genes in fission yeast. We demonstrate that these genes are up-regulated at the protein level in RNAi mutants, while their mRNA levels are not significantly changed. We show that the repression by RNAi is not a result of heterochromatin formation. Thus, we conclude that RNAi is involved in post-transcriptional gene silencing in S. pombe. Copyright © 2014 Elsevier Inc. All rights reserved.

  3. PTESFinder: a computational method to identify post-transcriptional exon shuffling (PTES) events.

    Science.gov (United States)

    Izuogu, Osagie G; Alhasan, Abd A; Alafghani, Hani M; Santibanez-Koref, Mauro; Elliott, David J; Elliot, David J; Jackson, Michael S

    2016-01-13

    Transcripts, which have been subject to Post-transcriptional exon shuffling (PTES), have an exon order inconsistent with the underlying genomic sequence. These have been identified in a wide variety of tissues and cell types from many eukaryotes, and are now known to be mostly circular, cytoplasmic, and non-coding. Although there is no uniformly ascribed function, several have been shown to be involved in gene regulation. Accurate identification of these transcripts can, however, be difficult due to artefacts from a wide variety of sources. Here, we present a computational method, PTESFinder, to identify these transcripts from high throughput RNAseq data. Uniquely, it systematically excludes potential artefacts emanating from pseudogenes, segmental duplications, and template switching, and outputs both PTES and canonical exon junction counts to facilitate comparative analyses. In comparison with four existing methods, PTESFinder achieves highest specificity and comparable sensitivity at a variety of read depths. PTESFinder also identifies between 13 % and 41.6 % more structures, compared to publicly available methods recently used to identify human circular RNAs. With high sensitivity and specificity, user-adjustable filters that target known sources of false positives, and tailored output to facilitate comparison of transcript levels, PTESFinder will facilitate the discovery and analysis of these poorly understood transcripts.

  4. Post-transcriptional regulation of expression of the Bronze2 gene of Zea mays L.

    Science.gov (United States)

    Pairoba, Claudio F; Walbot, Virginia

    2003-09-01

    The glutathione S-transferase encoded by Bronze2 performs the last genetically defined step in maize anthocyanin biosynthesis, being required for pigment sequestration into vacuoles. The Bz2 primary transcript contains a single intron; in maize leaves both spliced and unspliced Bz2 transcripts are usually present and are predicted to encode 26 and 14 kDa proteins, respectively. To increase understanding of the role and regulation of Bz2 transcript splicing, we examined Bz2 expression during development in transgenic maize plants expressing a 35S:Bz2 (35S:mycBz2i) gene and, by transient expression analysis, in Black Mexican Sweet maize protoplasts. We show here that the gene is expressed in diverse tissues that lack functional copies of one or both transcription factors regulating anthocyanin synthesis, that transcript levels are much higher when the R/B plus C1/Pl transcription factors are present, and that the splicing decision depends on local sequence context. The predicted 14 kDa protein was never detected indicating that unspliced transcripts are likely to be non-coding. The native 26 kDa BZ2 protein is loosely membrane-bound, but it was detectable only in tissues accumulating anthocyanin. Consequently, BZ2 accumulation appears to be limited by stringent post-transcriptional regulation.

  5. Nucleic acid-based techniques for post-transcriptional regulation of molecular targets.

    Science.gov (United States)

    Jarad, George; Simske, Jeffrey S; Sedor, John R; Schelling, Jeffrey R

    2003-07-01

    Messenger RNA, transfer RNA and ribosomal RNA were defined long ago as essential components for transmission of genetic code from DNA. However, there are many other, less commonly recognized RNAs, such as ribozymes and small interfering RNAs, which are distinguished by their ability to inhibit RNA function. This review describes the basic molecular concepts and potential therapeutic applications of RNA inhibition by a variety of molecules, including ribozymes, antisense oligonucleotides, aptamers and small interfering RNAs. A tremendous amount of data has recently emerged about double-stranded small interfering RNAs, which bind and degrade corresponding messenger RNAs by a process called RNA interference. Though native small interfering RNAs have been shown to be biologically relevant in animals and plants, synthetic types have rapidly become powerful tools for post-transcriptional inhibition of specific gene products to determine functional consequences in simple organisms and in-vitro model systems. More established means of RNA inhibition, such as with ribozyme and antisense strategies, continue to be viable options for in-vitro experiments, and form the basis for many ongoing clinical trials. Ribozymes, antisense oligonucleotides, aptamers and small interfering RNAs are potentially useful reagents for in-vitro investigation and for treatment of kidney and hypertension diseases.

  6. RNA Binding Protein-Mediated Post-Transcriptional Gene Regulation in Medulloblastoma

    Science.gov (United States)

    Bish, Rebecca; Vogel, Christine

    2014-01-01

    Medulloblastoma, the most common malignant brain tumor in children, is a disease whose mechanisms are now beginning to be uncovered by high-throughput studies of somatic mutations, mRNA expression patterns, and epigenetic profiles of patient tumors. One emerging theme from studies that sequenced the tumor genomes of large cohorts of medulloblastoma patients is frequent mutation of RNA binding proteins. Proteins which bind multiple RNA targets can act as master regulators of gene expression at the post-transcriptional level to co-ordinate cellular processes and alter the phenotype of the cell. Identification of the target genes of RNA binding proteins may highlight essential pathways of medulloblastomagenesis that cannot be detected by study of transcriptomics alone. Furthermore, a subset of RNA binding proteins are attractive drug targets. For example, compounds that are under development as anti-viral targets due to their ability to inhibit RNA helicases could also be tested in novel approaches to medulloblastoma therapy by targeting key RNA binding proteins. In this review, we discuss a number of RNA binding proteins, including Musashi1 (MSI1), DEAD (Asp-Glu-Ala-Asp) box helicase 3 X-linked (DDX3X), DDX31, and cell division cycle and apoptosis regulator 1 (CCAR1), which play potentially critical roles in the growth and/or maintenance of medulloblastoma. PMID:24608801

  7. Post-transcriptional regulation of thioredoxin by the stress inducible heterogenous ribonucleoprotein A18.

    Science.gov (United States)

    Yang, Ruiqing; Weber, David J; Carrier, France

    2006-01-01

    Thioredoxin (TRX) is a key protein of the cellular redox metabolism, which expression is increased in several tumors especially gastric tumors. Even though ultraviolet (UV) and hypoxia specifically induce TRX, the mechanisms that lead to increased TRX levels are still ill defined. Here, we show that the heterogenous ribonucleoprotein A18 (hnRNP A18) RNA Binding Domain (RBD) and the arginine, glycine (RGG) rich domain can bind TRX 3'-untranslated region (3'-UTR) independently but both domains are required for maximal binding. Immunoprecipitation (IP) of hnRNP A18-mRNAs complexes and co-localization of hnRNP A18 and TRX transcripts on ribosomal fractions confirm the interaction of hnRNP A18 with TRX transcripts in cells. Moreover, down regulation of hnRNP A18 correlates with a significant reduction of TRX protein levels. In addition, hnRNP A18 increases TRX translation and interacts with the eukaryotic Initiation Factor 4G (eIF4G), a component of the general translational machinery. Furthermore, hnRNP A18 phosphorylation by the hypoxia inducible GSK3beta increases hnRNP A18 RNA binding activity in vitro and in RKO cells in response to UV radiation. These data support a regulatory role for hnRNP A18 in TRX post-transcriptional expression possibly through a kissing loop model bridging TRX 3'- and 5'-UTRs through eIF4G.

  8. Transcriptional and post-transcriptional control of the plant circadian gene regulatory network.

    Science.gov (United States)

    Hernando, C Esteban; Romanowski, Andrés; Yanovsky, Marcelo J

    2017-01-01

    The circadian clock drives rhythms in multiple physiological processes allowing plants to anticipate and adjust to periodic changes in environmental conditions. These physiological rhythms are associated with robust oscillations in the expression of thousands of genes linked to the control of photosynthesis, cell elongation, biotic and abiotic stress responses, developmental processes such as flowering, and the clock itself. Given its pervasive effects on plant physiology, it is not surprising that circadian clock genes have played an important role in the domestication of crop plants and in the improvement of crop productivity. Therefore, identifying the principles governing the dynamics of the circadian gene regulatory network in plants could strongly contribute to further speed up crop improvement. Here we provide an historical as well as a current description of our knowledge of the molecular mechanisms underlying circadian rhythms in plants. This work focuses on the transcriptional and post-transcriptional regulatory layers that control the very core of the circadian clock, and some of its complex interactions with signaling pathways that help synchronize plant growth and development to daily and seasonal changes in the environment. This article is part of a Special Issue entitled: Plant Gene Regulatory Mechanisms and Networks, edited by Dr. Erich Grotewold and Dr. Nathan Springer. Copyright © 2016 Elsevier B.V. All rights reserved.

  9. Regulation of Rab5 isoforms by transcriptional and post-transcriptional mechanisms in yeast.

    Science.gov (United States)

    Schmidt, Oliver; Weyer, Yannick; Fink, Matthias J; Müller, Martin; Weys, Sabine; Bindreither, Marietta; Teis, David

    2017-09-01

    Rab5 GTPases are master regulators of early endosome biogenesis and transport. The genome of Saccharomyces cerevisiae encodes three Rab5 proteins: Vps21, the major isoform, Ypt52 and Ypt53. Here, we show that Vps21 is the most abundant Rab5 protein and Ypt53 is the least abundant. In stressed cells, Ypt53 levels increase but never exceed that of Vps21. Its induction requires the transcription factors Crz1 and Gis1. In growing cells, the expression of Ypt53 is suppressed by post-transcriptional mechanisms mediated by the untranslated regions of the YPT53 mRNA. Based on genetic experiments, these sequences appear to stimulate deadenylation, Pat1-activated decapping and Xrn1-mediated mRNA degradation. Once this regulation is bypassed, Ypt53 protein levels surpass Vps21, and Ypt53 is sufficient to maintain endosomal function and cell growth. © 2017 The Authors. FEBS Letters published by John Wiley & Sons Ltd on behalf of Federation of European Biochemical Societies.

  10. A Novel RNA-Binding Protein Involves ABA Signaling by Post-transcriptionally Repressing ABI2.

    Science.gov (United States)

    Xu, Jianwen; Chen, Yihan; Qian, Luofeng; Mu, Rong; Yuan, Xi; Fang, Huimin; Huang, Xi; Xu, Enshun; Zhang, Hongsheng; Huang, Ji

    2017-01-01

    The Stress Associated RNA-binding protein 1 (SRP1) repressed by ABA, salt and cold encodes a C2C2-type zinc finger protein in Arabidopsis. The knock-out mutation in srp1 reduced the sensitivity of seed to ABA and salt stress during germination and post-germinative growth stages. In contrast, SRP1-overexpressing seedlings were more sensitive to ABA and salt compared to wild type plants. In the presence of ABA, the transcript levels of ABA signaling and germination-related genes including ABI3. ABI5. EM1 and EM6 were less induced in srp1 compared to WT. Interestingly, expression of ABI2 encoding a protein phosphatase 2C protein were significantly up-regulated in srp1 mutants. By in vitro analysis, SRP1 was identified as a novel RNA-binding protein directly binding to 3'UTR of ABI2 mRNA. Moreover, transient expression assay proved the function of SRP1 in reducing the activity of luciferase whose coding sequence was fused with the ABI2 3'UTR. Together, it is suggested that SRP1 is involved in the ABA signaling by post-transcriptionally repressing ABI2 expression in Arabidopsis.

  11. Post-transcriptional control of the mammalian circadian clock: implications for health and disease.

    Science.gov (United States)

    Preußner, Marco; Heyd, Florian

    2016-06-01

    Many aspects of human physiology and behavior display rhythmicity with a period of approximately 24 h. Rhythmic changes are controlled by an endogenous time keeper, the circadian clock, and include sleep-wake cycles, physical and mental performance capability, blood pressure, and body temperature. Consequently, many diseases, such as metabolic, sleep, autoimmune and mental disorders and cancer, are connected to the circadian rhythm. The development of therapies that take circadian biology into account is thus a promising strategy to improve treatments of diverse disorders, ranging from allergic syndromes to cancer. Circadian alteration of body functions and behavior are, at the molecular level, controlled and mediated by widespread changes in gene expression that happen in anticipation of predictably changing requirements during the day. At the core of the molecular clockwork is a well-studied transcription-translation negative feedback loop. However, evidence is emerging that additional post-transcriptional, RNA-based mechanisms are required to maintain proper clock function. Here, we will discuss recent work implicating regulated mRNA stability, translation and alternative splicing in the control of the mammalian circadian clock, and its role in health and disease.

  12. Seventeen new complete mtDNA sequences reveal extensive mitochondrial genome evolution within the Demospongiae.

    Directory of Open Access Journals (Sweden)

    Xiujuan Wang

    Full Text Available Two major transitions in animal evolution--the origins of multicellularity and bilaterality--correlate with major changes in mitochondrial DNA (mtDNA organization. Demosponges, the largest class in the phylum Porifera, underwent only the first of these transitions and their mitochondrial genomes display a peculiar combination of ancestral and animal-specific features. To get an insight into the evolution of mitochondrial genomes within the Demospongiae, we determined 17 new mtDNA sequences from this group and analyzing them with five previously published sequences. Our analysis revealed that all demosponge mtDNAs are 16- to 25-kbp circular molecules, containing 13-15 protein genes, 2 rRNA genes, and 2-27 tRNA genes. All but four pairs of sampled genomes had unique gene orders, with the number of shared gene boundaries ranging from 1 to 41. Although most demosponge species displayed low rates of mitochondrial sequence evolution, a significant acceleration in evolutionary rates occurred in the G1 group (orders Dendroceratida, Dictyoceratida, and Verticillitida. Large variation in mtDNA organization was also observed within the G0 group (order Homosclerophorida including gene rearrangements, loss of tRNA genes, and the presence of two introns in Plakortis angulospiculatus. While introns are rare in modern-day demosponge mtDNA, we inferred that at least one intron was present in cox1 of the common ancestor of all demosponges. Our study uncovered an extensive mitochondrial genomic diversity within the Demospongiae. Although all sampled mitochondrial genomes retained some ancestral features, including a minimally modified genetic code, conserved structures of tRNA genes, and presence of multiple non-coding regions, they vary considerably in their size, gene content, gene order, and the rates of sequence evolution. Some of the changes in demosponge mtDNA, such as the loss of tRNA genes and the appearance of hairpin-containing repetitive elements

  13. High extensibility of stress fibers revealed by in vitro micromanipulation with fluorescence imaging

    Energy Technology Data Exchange (ETDEWEB)

    Matsui, Tsubasa S. [Department of Biomolecular Sciences, Tohoku University (Japan); Sato, Masaaki [Department of Biomedical Engineering, Tohoku University (Japan); Department of Bioengineering and Robotics, Tohoku University (Japan); Deguchi, Shinji, E-mail: deguchi@nitech.ac.jp [Department of Bioengineering and Robotics, Tohoku University (Japan)

    2013-05-10

    Highlights: •We isolate contractile stress fibers from vascular smooth muscle cells. •We measure the extensibility of individual stress fibers. •We present the first direct evidence that individual stress fibers are highly extensible. •We quantitatively determine the local strain along the length of stress fibers. •The high extensibility we found is beyond that explained by a conventional model. -- Abstract: Stress fibers (SFs), subcellular bundles of actin and myosin filaments, are physically connected at their ends to cell adhesions. The intracellular force transmitted via SFs plays an essential role in cell adhesion regulation and downstream signaling. However, biophysical properties intrinsic to individual SFs remain poorly understood partly because SFs are surrounded by other cytoplasmic components that restrict the deformation of the embedded materials. To characterize their inherent properties independent of other structural components, we isolated SFs from vascular smooth muscle cells and mechanically stretched them by in vitro manipulation while visualizing strain with fluorescent quantum dots attached along their length. SFs were elongated along their entire length, with the length being approximately 4-fold of the stress-free length. This surprisingly high extensibility was beyond that explained by the tandem connection of actin filaments and myosin II bipolar filaments present in SFs, thus suggesting the involvement of other structural components in their passive biophysical properties.

  14. Transcriptional and post-transcriptional mechanisms for oncogenic overexpression of ether a go-go K+ channel.

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    Huixian Lin

    Full Text Available The human ether-à-go-go-1 (h-eag1 K(+ channel is expressed in a variety of cell lines derived from human malignant tumors and in clinical samples of several different cancers, but is otherwise absent in normal tissues. It was found to be necessary for cell cycle progression and tumorigenesis. Specific inhibition of h-eag1 expression leads to inhibition of tumor cell proliferation. We report here that h-eag1 expression is controlled by the p53-miR-34-E2F1 pathway through a negative feed-forward mechanism. We first established E2F1 as a transactivator of h-eag1 gene through characterizing its promoter region. We then revealed that miR-34, a known transcriptional target of p53, is an important negative regulator of h-eag1 through dual mechanisms by directly repressing h-eag1 at the post-transcriptional level and indirectly silencing h-eag1 at the transcriptional level via repressing E2F1. There is a strong inverse relationship between the expression levels of miR-34 and h-eag1 protein. H-eag1antisense antagonized the growth-stimulating effects and the upregulation of h-eag1 expression in SHSY5Y cells, induced by knockdown of miR-34, E2F1 overexpression, or inhibition of p53 activity. Therefore, p53 negatively regulates h-eag1 expression by a negative feed-forward mechanism through the p53-miR-34-E2F1 pathway. Inactivation of p53 activity, as is the case in many cancers, can thus cause oncogenic overexpression of h-eag1 by relieving the negative feed-forward regulation. These findings not only help us understand the molecular mechanisms for oncogenic overexpression of h-eag1 in tumorigenesis but also uncover the cell-cycle regulation through the p53-miR-34-E2F1-h-eag1 pathway. Moreover, these findings place h-eag1 in the p53-miR-34-E2F1-h-eag1 pathway with h-eag as a terminal effecter component and with miR-34 (and E2F1 as a linker between p53 and h-eag1. Our study therefore fills the gap between p53 pathway and its cellular function mediated by h

  15. Extensive genetic diversity and substructuring among zebrafish strains revealed through copy number variant analysis

    Science.gov (United States)

    Brown, Kim H.; Dobrinski, Kimberly P.; Gokcumen, Omer; Mills, Ryan E.; Shi, Xinghua; Chong, Wilson W. S.; Chen, Jin Yun Helen; Yoo, Paulo; David, Sthuthi; Peterson, Samuel M.; Raj, Towfique; Choy, Kwong Wai; Stranger, Barbara E.; Williamson, Robin E.; Zon, Leonard I.; Freeman, Jennifer L.; Lee, Charles

    2012-01-01

    Copy number variants (CNVs) represent a substantial source of genomic variation in vertebrates and have been associated with numerous human diseases. Despite this, the extent of CNVs in the zebrafish, an important model for human disease, remains unknown. Using 80 zebrafish genomes, representing three commonly used laboratory strains and one native population, we constructed a genome-wide, high-resolution CNV map for the zebrafish comprising 6,080 CNV elements and encompassing 14.6% of the zebrafish reference genome. This amount of copy number variation is four times that previously observed in other vertebrates, including humans. Moreover, 69% of the CNV elements exhibited strain specificity, with the highest number observed for Tubingen. This variation likely arose, in part, from Tubingen's large founding size and composite population origin. Additional population genetic studies also provided important insight into the origins and substructure of these commonly used laboratory strains. This extensive variation among and within zebrafish strains may have functional effects that impact phenotype and, if not properly addressed, such extensive levels of germ-line variation and population substructure in this commonly used model organism can potentially confound studies intended for translation to human diseases. PMID:22203992

  16. Crystal structure of Venezuelan hemorrhagic fever virus fusion glycoprotein reveals a class 1 postfusion architecture with extensive glycosylation.

    Science.gov (United States)

    Parsy, Marie-Laure; Harlos, Karl; Huiskonen, Juha T; Bowden, Thomas A

    2013-12-01

    Guanarito virus (GTOV) is an emergent and deadly pathogen. We present the crystal structure of the glycosylated GTOV fusion glycoprotein to 4.1-Å resolution in the postfusion conformation. Our structure reveals a classical six-helix bundle and presents direct verification that New World arenaviruses exhibit class I viral membrane fusion machinery. The structure provides visualization of an N-linked glycocalyx coat, and consideration of glycan dynamics reveals extensive coverage of the underlying protein surface, following virus-host membrane fusion.

  17. In vivo quantification reveals extensive natural variation in mitochondrial form and function in Caenorhabditis briggsae.

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    Kiley A Hicks

    Full Text Available We have analyzed natural variation in mitochondrial form and function among a set of Caenorhabditis briggsae isolates known to harbor mitochondrial DNA structural variation in the form of a heteroplasmic nad5 gene deletion (nad5Δ that correlates negatively with organismal fitness. We performed in vivo quantification of 24 mitochondrial phenotypes including reactive oxygen species level, membrane potential, and aspects of organelle morphology, and observed significant among-isolate variation in 18 traits. Although several mitochondrial phenotypes were non-linearly associated with nad5Δ levels, most of the among-isolate phenotypic variation could be accounted for by phylogeographic clade membership. In particular, isolate-specific mitochondrial membrane potential was an excellent predictor of clade membership. We interpret this result in light of recent evidence for local adaptation to temperature in C. briggsae. Analysis of mitochondrial-nuclear hybrid strains provided support for both mtDNA and nuclear genetic variation as drivers of natural mitochondrial phenotype variation. This study demonstrates that multicellular eukaryotic species are capable of extensive natural variation in organellar phenotypes and highlights the potential of integrating evolutionary and cell biology perspectives.

  18. Multiple ITS copies reveal extensive hybridization within Rheum (Polygonaceae, a genus that has undergone rapid radiation.

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    Dongshi Wan

    Full Text Available BACKGROUND: During adaptive radiation events, characters can arise multiple times due to parallel evolution, but transfer of traits through hybridization provides an alternative explanation for the same character appearing in apparently non-sister lineages. The signature of hybridization can be detected in incongruence between phylogenies derived from different markers, or from the presence of two divergent versions of a nuclear marker such as ITS within one individual. METHODOLOGY/PRINCIPAL FINDINGS: In this study, we cloned and sequenced ITS regions for 30 species of the genus Rheum, and compared them with a cpDNA phylogeny. Seven species contained two divergent copies of ITS that resolved in different clades from one another in each case, indicating hybridization events too recent for concerted evolution to have homogenised the ITS sequences. Hybridization was also indicated in at least two further species via incongruence in their position between ITS and cpDNA phylogenies. None of the ITS sequences present in these nine species matched those detected in any other species, which provides tentative evidence against recent introgression as an explanation. Rheum globulosum, previously indicated by cpDNA to represent an independent origin of decumbent habit, is indicated by ITS to be part of clade of decumbent species, which acquired cpDNA of another clade via hybridization. However decumbent and glasshouse morphology are confirmed to have arisen three and two times, respectively. CONCLUSIONS: These findings suggested that hybridization among QTP species of Rheum has been extensive, and that a role of hybridization in diversification of Rheum requires investigation.

  19. Genomic profiling reveals extensive heterogeneity in somatic DNA copy number aberrations of canine hemangiosarcoma.

    Science.gov (United States)

    Thomas, Rachael; Borst, Luke; Rotroff, Daniel; Motsinger-Reif, Alison; Lindblad-Toh, Kerstin; Modiano, Jaime F; Breen, Matthew

    2014-09-01

    Canine hemangiosarcoma is a highly aggressive vascular neoplasm associated with extensive clinical and anatomical heterogeneity and a grave prognosis. Comprehensive molecular characterization of hemangiosarcoma may identify novel therapeutic targets and advanced clinical management strategies, but there are no published reports of tumor-associated genome instability and disrupted gene dosage in this cancer. We performed genome-wide microarray-based somatic DNA copy number profiling of 75 primary intra-abdominal hemangiosarcomas from five popular dog breeds that are highly predisposed to this disease. The cohort exhibited limited global genomic instability, compared to other canine sarcomas studied to date, and DNA copy number aberrations (CNAs) were predominantly of low amplitude. Recurrent imbalances of several key cancer-associated genes were evident; however, the global penetrance of any single CNA was low and no distinct hallmark aberrations were evident. Copy number gains of dog chromosomes 13, 24, and 31, and loss of chromosome 16, were the most recurrent CNAs involving large chromosome regions, but their relative distribution within and between cases suggests they most likely represent passenger aberrations. CNAs involving CDKN2A, VEGFA, and the SKI oncogene were identified as potential driver aberrations of hemangiosarcoma development, highlighting potential targets for therapeutic modulation. CNA profiles were broadly conserved between the five breeds, although subregional variation was evident, including a near twofold lower incidence of VEGFA gain in Golden Retrievers versus other breeds (22 versus 40 %). These observations support prior transcriptional studies suggesting that the clinical heterogeneity of this cancer may reflect the existence of multiple, molecularly distinct subtypes of canine hemangiosarcoma.

  20. RNA Expression and Post-Transcriptional Editing Analyses of Cucumber Plastids Reveals Genetic Differences Associated with Chilling Tolerance

    Science.gov (United States)

    Tolerance to chilling injury in cucumber (Cucumis sativus L.) is associated with three plastomic single nucleotide polymorphisms (ptSNPs) at bp positions 4,813, 56,561, and 126,349 that are co-inherited. An understanding of the genetic expression of these ptSNPs as a response to chilling is critical...

  1. Metagenomics reshapes the concepts of RNA virus evolution by revealing extensive horizontal virus transfer.

    Science.gov (United States)

    Dolja, Valerian V; Koonin, Eugene V

    2017-11-08

    Virus metagenomics is a young research filed but it has already transformed our understanding of virus diversity and evolution, and illuminated at a new level the connections between virus evolution and the evolution and ecology of the hosts. In this review article, we examine the new picture of the evolution of RNA viruses, the dominant component of the eukaryotic virome, that is emerging from metagenomic data analysis. The major expansion of many groups of RNA viruses through metagenomics allowed the construction of substantially improved phylogenetic trees for the conserved virus genes, primarily, the RNA-dependent RNA polymerases (RdRp). In particular, a new superfamily of widespread, small positive-strand RNA viruses was delineated that unites tombus-like and noda-like viruses. Comparison of the genome architectures of RNA viruses discovered by metagenomics and by traditional methods reveals an extent of gene module shuffling among diverse virus genomes that far exceeds the previous appreciation of this evolutionary phenomenon. Most dramatically, inclusion of the metagenomic data in phylogenetic analyses of the RdRp resulted in the identification of numerous, strongly supported groups that encompass RNA viruses from diverse hosts including different groups of protists, animals and plants. Notwithstanding potential caveats, in particular, incomplete and uneven sampling of eukaryotic taxa, these highly unexpected findings reveal horizontal virus transfer (HVT) between diverse hosts as the central aspect of RNA virus evolution. The vast and diverse virome of invertebrates, particularly nematodes and arthropods, appears to be the reservoir, from which the viromes of plants and vertebrates evolved via multiple HVT events. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

  2. 3-(3-amino-3-carboxypropyl)-5,6-Dihydrouridine is one of two novel post-transcriptional modifications in tRNALys(UUU) from Trypanosoma brucei

    DEFF Research Database (Denmark)

    Krog, Jesper Schak; Español, Yaiza; Giessing, Anders M B

    2011-01-01

    was MALDI-TOF MS of two independent digests of the tRNA, with RNase A and RNase T1, respectively. This revealed digestion products harbouring mass-changing modifications. Next, the modifications were mapped at the nucleotide level in the RNase products by tandem MS. Comparison with the sequence....... Furthermore, the tRNA has to be investigated with single-nucleotide resolution in order to ensure complete mapping of all modifications. In the present work, we characterized tRNA(Lys) (UUU) from Trypanosoma brucei, and provide a complete overview of its post-transcriptional modifications. The first step...

  3. In Vivo Microscopy Reveals Extensive Embedding of Capillaries within the Sarcolemma of Skeletal Muscle Fibers

    Science.gov (United States)

    Glancy, Brian; Hsu, Li-Yueh; Dao, Lam; Bakalar, Matthew; French, Stephanie; Chess, David J.; Taylor, Joni L.; Picard, Martin; Aponte, Angel; Daniels, Mathew P.; Esfahani, Shervin; Cushman, Samuel; Balaban, Robert S.

    2013-01-01

    Objective To provide insight into mitochondrial function in vivo, we evaluated the 3D spatial relationship between capillaries, mitochondria, and muscle fibers in live mice. Methods 3D volumes of in vivo murine Tibialis anterior muscles were imaged by multi-photon microscopy (MPM). Muscle fiber type, mitochondrial distribution, number of capillaries, and capillary-to-fiber contact were assessed. The role of myoglobin-facilitated diffusion was examined in myoglobin knockout mice. Distribution of GLUT4 was also evaluated in the context of the capillary and mitochondrial network. Results MPM revealed that 43.6 ± 3.3% of oxidative fiber capillaries had ≥ 50% of their circumference embedded in a groove in the sarcolemma, in vivo. Embedded capillaries were tightly associated with dense mitochondrial populations lateral to capillary grooves and nearly absent below the groove. Mitochondrial distribution, number of embedded capillaries, and capillary-to-fiber contact were proportional to fiber oxidative capacity and unaffected by myoglobin knockout. GLUT4 did not preferentially localize to embedded capillaries. Conclusions Embedding capillaries in the sarcolemma may provide a regulatory mechanism to optimize delivery of oxygen to heterogeneous groups of muscle fibers. We hypothesize that mitochondria locate to paravascular regions due to myofibril voids created by embedded capillaries, not to enhance the delivery of oxygen to the mitochondria. PMID:25279425

  4. The bladed Bangiales (Rhodophyta) of the South Eastern Pacific: Molecular species delimitation reveals extensive diversity.

    Science.gov (United States)

    Guillemin, Marie-Laure; Contreras-Porcia, Loretto; Ramírez, María Eliana; Macaya, Erasmo C; Contador, Cristian Bulboa; Woods, Helen; Wyatt, Christopher; Brodie, Juliet

    2016-01-01

    A molecular taxonomic study of the bladed Bangiales of the South Eastern Pacific (coast of Chile) was undertaken based on sequence data of the mitochondrial COI and chloroplast rbcL for 193 specimens collected from Arica (18°S) in the north to South Patagonia (53°S) in the south. The results revealed for the first time that four genera, Porphyra, Pyropia, Fuscifolium and Wildemania were present in the region. Species delimitation was determined based on a combination of a General Mixed Yule Coalescence model (GMYC) and Automatic Barcode Gap Discovery (ABGD) coupled with detection of monophyly in tree reconstruction. The overall incongruence between the species delimitation methods within each gene was 29%. The GMYC method led to over-splitting groups, whereas the ABGD method had a tendency to lump groups. Taking a conservative approach to the number of putative species, at least 18 were recognized and, with the exception of the recently described Pyropia orbicularis, all were new to the Chilean flora. Porphyra and Pyropia were the most diverse genera with eight 'species' each, whereas only a 'single' species each was found for Fuscifolium and Wildemania. There was also evidence of recently diverging groups: Wildemania sp. was distinct but very closely related to W. amplissima from the Northern Hemisphere and raises questions in relation to such disjunct distributions. Pyropia orbicularis was very closely related to two other species, making species delimitation very difficult but provides evidence of an incipient speciation. The difference between the 'species' discovered and those previously reported for the region is discussed in relation to the difficulty of distinguishing species based on morphological identification. Copyright © 2015 Elsevier Inc. All rights reserved.

  5. Comparative study of human mitochondrial proteome reveals extensive protein subcellular relocalization after gene duplications

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    Huang Yong

    2009-11-01

    Full Text Available Abstract Background Gene and genome duplication is the principle creative force in evolution. Recently, protein subcellular relocalization, or neolocalization was proposed as one of the mechanisms responsible for the retention of duplicated genes. This hypothesis received support from the analysis of yeast genomes, but has not been tested thoroughly on animal genomes. In order to evaluate the importance of subcellular relocalizations for retention of duplicated genes in animal genomes, we systematically analyzed nuclear encoded mitochondrial proteins in the human genome by reconstructing phylogenies of mitochondrial multigene families. Results The 456 human mitochondrial proteins selected for this study were clustered into 305 gene families including 92 multigene families. Among the multigene families, 59 (64% consisted of both mitochondrial and cytosolic (non-mitochondrial proteins (mt-cy families while the remaining 33 (36% were composed of mitochondrial proteins (mt-mt families. Phylogenetic analyses of mt-cy families revealed three different scenarios of their neolocalization following gene duplication: 1 relocalization from mitochondria to cytosol, 2 from cytosol to mitochondria and 3 multiple subcellular relocalizations. The neolocalizations were most commonly enabled by the gain or loss of N-terminal mitochondrial targeting signals. The majority of detected subcellular relocalization events occurred early in animal evolution, preceding the evolution of tetrapods. Mt-mt protein families showed a somewhat different pattern, where gene duplication occurred more evenly in time. However, for both types of protein families, most duplication events appear to roughly coincide with two rounds of genome duplications early in vertebrate evolution. Finally, we evaluated the effects of inaccurate and incomplete annotation of mitochondrial proteins and found that our conclusion of the importance of subcellular relocalization after gene duplication on

  6. Biocytin filling of adult gonadotropin-releasing hormone neurons in situ reveals extensive, spiny, dendritic processes.

    Science.gov (United States)

    Campbell, Rebecca E; Han, Seong-Kyu; Herbison, Allan E

    2005-03-01

    Ultrastructural studies suggest that GnRH neurons receive relatively few synaptic inputs. However, these techniques are biased toward the analysis of portions of the neuron containing GnRH peptide. Using acute brain slices prepared from transgenic GnRH-green fluorescent protein mice, individual fluorescing GnRH neurons were identified, patched, and filled with the small-molecular-weight dye biocytin. Cells were subsequently visualized with an avidin-conjugated fluorophore, and their morphological characteristics were analyzed by confocal microscopy. In total, 45 GnRH neurons from seven adult male and eight diestrus female mice were examined. Unexpectedly, we found that GnRH neurons possess remarkably long dendritic processes, in some cases extending over 1000 microm distal to the cell body. The somata and dendrites of all GnRH neurons were decorated with an assortment of spine-like protrusions, including filopodia, in an heterogeneous manner. Overall, GnRH neurons had a mean dendritic spine density of 0.4 spines/microm, with the highest densities found in the first 50 microm of the dendrite. GnRH neurons with dendrites running in a horizontal orientation had significantly (P < 0.05) more spines than dendrites with a vertical orientation. The comparison of male and female GnRH neurons revealed no sexually differentiated characteristics of somal or dendritic spine density. Using a technique in which the full extent of the GnRH neuron can be visualized, we demonstrate here a previously unrecognized GnRH neuron morphology of long dendrites covered in spines. These observations suggest that GnRH neurons are not poorly innervated and that they receive abundant excitatory synaptic inputs.

  7. Proteome remodelling by the stress sigma factor RpoS/σS in Salmonella: identification of small proteins and evidence for post-transcriptional regulation.

    Science.gov (United States)

    Lago, Magali; Monteil, Véronique; Douche, Thibaut; Guglielmini, Julien; Criscuolo, Alexis; Maufrais, Corinne; Matondo, Mariette; Norel, Françoise

    2017-05-18

    The RpoS/σS sigma subunit of RNA polymerase is the master regulator of the general stress response in many Gram-negative bacteria. Extensive studies have been conducted on σS-regulated gene expression at the transcriptional level. In contrast, very limited information regarding the impact of σS on global protein production is available. In this study, we used a mass spectrometry-based proteomics approach to explore the wide σS-dependent proteome of the human pathogen Salmonella enterica serovar Typhimurium. Our present goals were twofold: (1) to survey the protein changes associated with the ΔrpoS mutation and (2) to assess the coding capacity of σS-dependent small RNAs. Our proteomics data, and complementary assays, unravelled the large impact of σS on the Salmonella proteome, and validated expression and σS regulation of twenty uncharacterized small proteins of 27 to 96 amino acids. Furthermore, a large number of genes regulated at the protein level only were identified, suggesting that post-transcriptional regulation is an important component of the σS response. Novel aspects of σS in the control of important catabolic pathways such as myo-inositol, L-fucose, propanediol, and ethanolamine were illuminated by this work, providing new insights into the physiological remodelling involved in bacterial adaptation to a non-actively growing state.

  8. 1,25-Dihydroxyvitamin D3 inhibits cytokine production by human blood monocytes at the post-transcriptional level

    DEFF Research Database (Denmark)

    Müller, K; Haahr, P M; Diamant, M

    1992-01-01

    D3, and the synthetic analogue MC 903 ('Calcipotriol') were examined in parallel. 1,25-(OH)2D3 dose-dependently inhibited the production of IL-alpha, IL-6 and TNF-alpha by Escherichia coli lipopolysaccharide (LPS)-stimulated monocytes, without affecting superoxide production. MC 903 had comparable...... was not caused by impaired production of mRNA. Taken together, the study demonstrates a vitamin D-induced inhibitory effect of LPS-driven monokine production, which is most likely a vitamin D-receptor mediated phenomenon exerted at a post-transcriptional, presecretory level. Impaired monokine production may...

  9. Analysis of global gene expression in Brachypodium distachyon reveals extensive network plasticity in response to abiotic stress.

    Directory of Open Access Journals (Sweden)

    Henry D Priest

    Full Text Available Brachypodium distachyon is a close relative of many important cereal crops. Abiotic stress tolerance has a significant impact on productivity of agriculturally important food and feedstock crops. Analysis of the transcriptome of Brachypodium after chilling, high-salinity, drought, and heat stresses revealed diverse differential expression of many transcripts. Weighted Gene Co-Expression Network Analysis revealed 22 distinct gene modules with specific profiles of expression under each stress. Promoter analysis implicated short DNA sequences directly upstream of module members in the regulation of 21 of 22 modules. Functional analysis of module members revealed enrichment in functional terms for 10 of 22 network modules. Analysis of condition-specific correlations between differentially expressed gene pairs revealed extensive plasticity in the expression relationships of gene pairs. Photosynthesis, cell cycle, and cell wall expression modules were down-regulated by all abiotic stresses. Modules which were up-regulated by each abiotic stress fell into diverse and unique gene ontology GO categories. This study provides genomics resources and improves our understanding of abiotic stress responses of Brachypodium.

  10. Post-Transcriptional Control of Gene Expression in Mouse Early Embryo Development: A View from the Tip of the Iceberg

    Directory of Open Access Journals (Sweden)

    Claudio Sette

    2011-04-01

    Full Text Available Fertilization is a very complex biological process that requires the perfect cooperation between two highly specialized cells: the male and female gametes. The oocyte provides the physical space where this process takes place, most of the energetic need, and half of the genetic contribution. The spermatozoon mostly contributes the other half of the chromosomes and it is specialized to reach and to penetrate the oocyte. Notably, the mouse oocyte and early embryo are transcriptionally inactive. Hence, they fully depend on the maternal mRNAs and proteins stored during oocyte maturation to drive the onset of development. The new embryo develops autonomously around the four-cell stage, when maternal supplies are exhausted and the zygotic genome is activated in mice. This oocyte-to-embryo transition needs an efficient and tightly regulated translation of the maternally-inherited mRNAs, which likely contributes to embryonic genome activation. Full understanding of post-transcriptional regulation of gene expression in early embryos is crucial to understand the reprogramming of the embryonic genome, it might help driving reprogramming of stem cells in vitro and will likely improve in vitro culturing of mammalian embryos for assisted reproduction. Nevertheless, the knowledge of the mechanism(s underlying this fundamental step in embryogenesis is still scarce, especially if compared to other model organisms. We will review here the current knowledge on the post-transcriptional control of gene expression in mouse early embryos and discuss some of the unanswered questions concerning this fascinating field of biology.

  11. Discrete domains of MARCH1 mediate its localization, functional interactions, and post-transcriptional control of expression1

    Science.gov (United States)

    Jabbour, Maurice; Campbell, Erin M.; Fares, Hanna; Lybarger, Lonnie

    2009-01-01

    Within antigen presenting cells (APC), ubiquitination regulates the trafficking of immune modulators such as MHC class II and CD86 (B7.2) molecules. MARCH1 (membrane-associated RING-CH), a newly identified ubiquitin E3 ligase expressed in APC, ubiquitinates MHC class II thereby reducing its surface expression. Following LPS-induced maturation of dendritic cells (DC), MARCH1 mRNA is downregulated and MHC class II is redistributed to the cell surface from endosomal compartments. Here, we show that MARCH1 expression is also regulated at the post-transcriptional level. In primary DC and APC cell lines of murine origin, MARCH1 had a half-life of less than 30 min. MARCH1 degradation appears to occur partly in lysosomes, since inhibiting lysosomal activity stabilized MARCH1. Similar stabilization was observed when MARCH1-expressing cells were treated with cysteine protease inhibitors. Mutational analyses of MARCH1 defined discrete domains required for destabilization, proper localization, and functional interaction with substrates. Together, these data suggest that MARCH1 expression is regulated at a post-transcriptional level by trafficking within the endo-lysosomal pathway where MARCH1 is proteolysed. The short half-life of MARCH1 permits very rapid changes in the levels of the protein in response to changes in the mRNA, resulting in efficient induction of antigen presentation once APC receive maturational signals. PMID:19880452

  12. SSR markers in transcripts of genes linked to post-transcriptional and transcriptional regulatory functions during vegetative and reproductive development of Elaeis guineensis.

    Science.gov (United States)

    Tranbarger, Timothy John; Kluabmongkol, Wanwisa; Sangsrakru, Duangjai; Morcillo, Fabienne; Tregear, James W; Tragoonrung, Somvong; Billotte, Norbert

    2012-01-03

    The oil palm (Elaeis guineensis Jacq.) is a perennial monocotyledonous tropical crop species that is now the world's number one source of edible vegetable oil, and the richest dietary source of provitamin A. While new elite genotypes from traditional breeding programs provide steady yield increases, the long selection cycle (10-12 years) and the large areas required to cultivate oil palm make genetic improvement slow and labor intensive. Molecular breeding programs have the potential to make significant impacts on the rate of genetic improvement but the limited molecular resources, in particular the lack of molecular markers for agronomic traits of interest, restrict the application of molecular breeding schemes for oil palm. In the current study, 6,103 non-redundant ESTs derived from cDNA libraries of developing vegetative and reproductive tissues were annotated and searched for simple sequence repeats (SSRs). Primer pairs from sequences flanking 289 EST-SSRs were tested to detect polymorphisms in elite breeding parents and their crosses. 230 of these amplified PCR products, 88 of which were polymorphic within the breeding material tested. A detailed analysis and annotation of the EST-SSRs revealed the locations of the polymorphisms within the transcripts, and that the main functional category was related to transcription and post-transcriptional regulation. Indeed, SSR polymorphisms were found in sequences encoding AP2-like, bZIP, zinc finger, MADS-box, and NAC-like transcription factors in addition to other transcriptional regulatory proteins and several RNA interacting proteins. The identification of new EST-SSRs that detect polymorphisms in elite breeding material provides tools for molecular breeding strategies. The identification of SSRs within transcripts, in particular those that encode proteins involved in transcriptional and post-transcriptional regulation, will allow insight into the functional roles of these proteins by studying the phenotypic traits

  13. Post-transcriptional silencing of the SGE1 gene induced by a dsRNA hairpin in Fusarium oxysporum f. sp cubense, the causal agent of Panama disease.

    Science.gov (United States)

    Fernandes, J S; Angelo, P C S; Cruz, J C; Santos, J M M; Sousa, N R; Silva, G F

    2016-04-04

    Fusarium oxysporum f. sp cubense (Foc), the causal agent of Panama disease, is responsible for economic losses in banana crops worldwide. The identification of genes that effectively act on pathogenicity and/or virulence may contribute to the development of different strategies for disease control and the production of resistant plants. The objective of the current study was to analyze the importance of SGE1 gene expression in Foc virulence through post-transcriptional silencing using a double-stranded RNA hairpin. Thirteen transformants were selected based on different morphological characteristics, and sporulation in these transformants was significantly reduced by approximately 95% (P < 0.05) compared to that of the wild-type strain. The relative SGE1 expression levels in the transformant strains were reduced by 27 to 47% compared to those in the wild-type strain. A pathogenicity analysis revealed that the transformants were able to reach the rhizomes and pseudostems of the inoculated banana plants. However, the transformants induced initial disease symptoms in the banana plants approximately 10 days later than that by the wild-type Foc, and initial disease symptoms persisted even at 45 days after inoculation. These results indicate that the SGE1 gene is directly involved in the virulence of Foc. Therefore, SGE1 may be a potential candidate for host-induced gene silencing in banana plants.

  14. A hairpin within YAP mRNA 3′UTR functions in regulation at post-transcription level

    Energy Technology Data Exchange (ETDEWEB)

    Gao, Yuen; Wang, Yuan; Feng, Jinyan; Feng, Guoxing; Zheng, Minying; Yang, Zhe; Xiao, Zelin; Lu, Zhanping [State Key Laboratory of Medicinal Chemical Biology, Department of Cancer Research, College of Life Sciences, Nankai University, Tianjin 300071 (China); Ye, Lihong [State Key Laboratory of Medicinal Chemical Biology, Department of Biochemistry, College of Life Sciences, Nankai University, Tianjin 300071 (China); Zhang, Xiaodong, E-mail: zhangxd@nankai.edu.cn [State Key Laboratory of Medicinal Chemical Biology, Department of Cancer Research, College of Life Sciences, Nankai University, Tianjin 300071 (China)

    2015-04-03

    The central dogma of gene expression is that DNA is transcribed into messenger RNAs, which in turn serve as the template for protein synthesis. Recently, it has been reported that mRNAs display regulatory roles that rely on their ability to compete for microRNA binding, independent of their protein-coding function. However, the regulatory mechanism of mRNAs remains poorly understood. Here, we report that a hairpin within YAP mRNA 3′untranslated region (3′UTR) functions in regulation at post-transcription level through generating endogenous siRNAs (esiRNAs). Bioinformatics analysis for secondary structure showed that YAP mRNA displayed a hairpin structure (termed standard hairpin, S-hairpin) within its 3′UTR. Surprisingly, we observed that the overexpression of S-hairpin derived from YAP 3′UTR (YAP-sh) increased the luciferase reporter activities of transcriptional factor NF-κB and AP-1 in 293T cells. Moreover, we identified that a fragment from YAP-sh, an esiRNA, was able to target mRNA 3′UTR of NF2 (a member of Hippo-signaling pathway) and YAP mRNA 3′UTR itself in hepatoma cells. Thus, we conclude that the YAP-sh within YAP mRNA 3′UTR may serve as a novel regulatory element, which functions in regulation at post-transcription level. Our finding provides new insights into the mechanism of mRNAs in regulatory function. - Highlights: • An S-hairpin within YAP mRNA 3′UTR possesses regulatory function. • YAP-sh acts as a regulatory element for YAP at post-transcription level. • YAP-sh-3p20, an esiRNA derived from YAP-sh, targets mRNAs of YAP and NF2. • YAP-sh-3p20 depresses the proliferation of HepG2 cells in vitro.

  15. Post-transcriptional control by bacteriophage T4: mRNA decay and inhibition of translation initiation

    Directory of Open Access Journals (Sweden)

    Miller Eric S

    2010-12-01

    Full Text Available Abstract Over 50 years of biological research with bacteriophage T4 includes notable discoveries in post-transcriptional control, including the genetic code, mRNA, and tRNA; the very foundations of molecular biology. In this review we compile the past 10 - 15 year literature on RNA-protein interactions with T4 and some of its related phages, with particular focus on advances in mRNA decay and processing, and on translational repression. Binding of T4 proteins RegB, RegA, gp32 and gp43 to their cognate target RNAs has been characterized. For several of these, further study is needed for an atomic-level perspective, where resolved structures of RNA-protein complexes are awaiting investigation. Other features of post-transcriptional control are also summarized. These include: RNA structure at translation initiation regions that either inhibit or promote translation initiation; programmed translational bypassing, where T4 orchestrates ribosome bypass of a 50 nucleotide mRNA sequence; phage exclusion systems that involve T4-mediated activation of a latent endoribonuclease (PrrC and cofactor-assisted activation of EF-Tu proteolysis (Gol-Lit; and potentially important findings on ADP-ribosylation (by Alt and Mod enzymes of ribosome-associated proteins that might broadly impact protein synthesis in the infected cell. Many of these problems can continue to be addressed with T4, whereas the growing database of T4-related phage genome sequences provides new resources and potentially new phage-host systems to extend the work into a broader biological, evolutionary context.

  16. Blackcurrant anthocyanins stimulated cholesterol transport via post-transcriptional induction of LDL receptor in Caco-2 cells.

    Science.gov (United States)

    Kim, Bohkyung; Bae, Minkyung; Park, Young-Ki; Ma, Hang; Yuan, Tao; Seeram, Navindra P; Lee, Ji-Young

    2017-07-17

    We previously showed that polyphenol-rich blackcurrant extract (BCE) showed a hypocholesterolemic effect in mice fed a high fat diet. As direct cholesterol removal from the body via the intestine has been recently appreciated, we investigated the effect of BCE on the modulation of genes involved in intestinal cholesterol transport using Caco-2 cells as an in vitro model. Caco-2 cells were treated with BCE to determine its effects on mRNA and protein expression of genes important for intestinal cholesterol transport, low-density lipoprotein (LDL) uptake, cellular cholesterol content, and cholesterol transport from basolateral to apical membrane of Caco-2 cell monolayers. Cells were also treated with anthocyanin-rich or -poor fraction of BCE to determine the role of anthocyanin on BCE effects. BCE significantly increased protein levels of LDL receptor (LDLR) without altering its mRNA, which consequently increased LDL uptake into Caco-2 cells. This post-transcriptional induction of LDLR by BCE was markedly attenuated in the presence of rapamycin, an inhibitor of mechanistic target of rapamycin complex 1 (mTORC1). In addition, BCE altered genes involved in cholesterol transport in the enterocytes, including apical and basolateral cholesterol transporters, in such a way that could enhance cholesterol flux from the basolateral to apical side of the enterocytes. Indeed, BCE significantly increased the flux of LDL-derived cholesterol from the basolateral to the apical chamber of Caco-2 monolayer. LDLR protein levels were markedly increased by anthocyanin-rich fraction, but not by anthocyanin-free fraction. mTORC1-dependent post-transcriptional induction of LDLR by BCE anthocyanins drove the transport of LDL-derived cholesterol to the apical side of the enterocytes. This may represent a potential mechanism for the hypocholesterolemic effect of BCE.

  17. Hypermethylation and post-transcriptional regulation of DNA methyltransferases in the ovarian carcinomas of the laying hen.

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    Jin-Young Lee

    Full Text Available DNA methyltransferases (DNMTs are key regulators of DNA methylation and have crucial roles in carcinogenesis, embryogenesis and epigenetic modification. In general, DNMT1 has enzymatic activity affecting maintenance of DNA methylation, whereas DNMT3A and DNMT3B are involved in de novo methylation events. Although DNMT genes are well known in mammals including humans and mice, they are not well studied in avian species, especially the laying hen which is recognized as an excellent animal model for research on human ovarian carcinogenesis. Results of the present study demonstrated that expression of DNMT1, DNMT3A and DNMT3B genes was significantly increased, particularly in the glandular epithelia (GE of cancerous ovaries, but not normal ovaries. Consistent with this result, immunoreactive 5-methylcytosine protein was predominantly abundant in nuclei of stromal and GE cells of cancerous ovaries, but it was also found that, to a lesser extent, in nuclei of stromal cells of normal ovaries. Methylation-specific PCR analysis detected hypermethylation of the promoter regions of the tumor suppressor genes in the initiation and development of chicken ovarian cancer. Further, several microRNAs, specifically miR-1741, miR-16c, and miR-222, and miR-1632 were discovered to influence expression of DNMT3A and DNMT3B, respectively, via their 3'-UTR which suggests post-transcriptional regulation of their expression in laying hens. Collectively, results of the present study demonstrated increased expression of DNMT genes in cancerous ovaries of laying hens and post-transcriptional regulation of those genes by specific microRNAs, as well as control of hypermethylation of the promoters of tumor suppressor genes.

  18. Genome and phylogenetic analyses of Trypanosoma evansi reveal extensive similarity to T. brucei and multiple independent origins for dyskinetoplasty.

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    Jason Carnes

    2015-01-01

    Full Text Available Two key biological features distinguish Trypanosoma evansi from the T. brucei group: independence from the tsetse fly as obligatory vector, and independence from the need for functional mitochondrial DNA (kinetoplast or kDNA. In an effort to better understand the molecular causes and consequences of these differences, we sequenced the genome of an akinetoplastic T. evansi strain from China and compared it to the T. b. brucei reference strain. The annotated T. evansi genome shows extensive similarity to the reference, with 94.9% of the predicted T. b. brucei coding sequences (CDS having an ortholog in T. evansi, and 94.6% of the non-repetitive orthologs having a nucleotide identity of 95% or greater. Interestingly, several procyclin-associated genes (PAGs were disrupted or not found in this T. evansi strain, suggesting a selective loss of function in the absence of the insect life-cycle stage. Surprisingly, orthologous sequences were found in T. evansi for all 978 nuclear CDS predicted to represent the mitochondrial proteome in T. brucei, although a small number of these may have lost functionality. Consistent with previous results, the F1FO-ATP synthase γ subunit was found to have an A281 deletion, which is involved in generation of a mitochondrial membrane potential in the absence of kDNA. Candidates for CDS that are absent from the reference genome were identified in supplementary de novo assemblies of T. evansi reads. Phylogenetic analyses show that the sequenced strain belongs to a dominant group of clonal T. evansi strains with worldwide distribution that also includes isolates classified as T. equiperdum. At least three other types of T. evansi or T. equiperdum have emerged independently. Overall, the elucidation of the T. evansi genome sequence reveals extensive similarity of T. brucei and supports the contention that T. evansi should be classified as a subspecies of T. brucei.

  19. Genome and phylogenetic analyses of Trypanosoma evansi reveal extensive similarity to T. brucei and multiple independent origins for dyskinetoplasty.

    Science.gov (United States)

    Carnes, Jason; Anupama, Atashi; Balmer, Oliver; Jackson, Andrew; Lewis, Michael; Brown, Rob; Cestari, Igor; Desquesnes, Marc; Gendrin, Claire; Hertz-Fowler, Christiane; Imamura, Hideo; Ivens, Alasdair; Kořený, Luděk; Lai, De-Hua; MacLeod, Annette; McDermott, Suzanne M; Merritt, Chris; Monnerat, Severine; Moon, Wonjong; Myler, Peter; Phan, Isabelle; Ramasamy, Gowthaman; Sivam, Dhileep; Lun, Zhao-Rong; Lukeš, Julius; Stuart, Ken; Schnaufer, Achim

    2015-01-01

    Two key biological features distinguish Trypanosoma evansi from the T. brucei group: independence from the tsetse fly as obligatory vector, and independence from the need for functional mitochondrial DNA (kinetoplast or kDNA). In an effort to better understand the molecular causes and consequences of these differences, we sequenced the genome of an akinetoplastic T. evansi strain from China and compared it to the T. b. brucei reference strain. The annotated T. evansi genome shows extensive similarity to the reference, with 94.9% of the predicted T. b. brucei coding sequences (CDS) having an ortholog in T. evansi, and 94.6% of the non-repetitive orthologs having a nucleotide identity of 95% or greater. Interestingly, several procyclin-associated genes (PAGs) were disrupted or not found in this T. evansi strain, suggesting a selective loss of function in the absence of the insect life-cycle stage. Surprisingly, orthologous sequences were found in T. evansi for all 978 nuclear CDS predicted to represent the mitochondrial proteome in T. brucei, although a small number of these may have lost functionality. Consistent with previous results, the F1FO-ATP synthase γ subunit was found to have an A281 deletion, which is involved in generation of a mitochondrial membrane potential in the absence of kDNA. Candidates for CDS that are absent from the reference genome were identified in supplementary de novo assemblies of T. evansi reads. Phylogenetic analyses show that the sequenced strain belongs to a dominant group of clonal T. evansi strains with worldwide distribution that also includes isolates classified as T. equiperdum. At least three other types of T. evansi or T. equiperdum have emerged independently. Overall, the elucidation of the T. evansi genome sequence reveals extensive similarity of T. brucei and supports the contention that T. evansi should be classified as a subspecies of T. brucei.

  20. Post-transcriptional regulation on a global scale: form and function of Csr/Rsm systems.

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    Romeo, Tony; Vakulskas, Christopher A; Babitzke, Paul

    2013-02-01

    Originally described as a repressor of gene expression in the stationary phase of growth, CsrA (RsmA) regulates primary and secondary metabolic pathways, biofilm formation, motility, virulence circuitry of pathogens, quorum sensing and stress response systems by binding to conserved sequences in its target mRNAs and altering their translation and/or turnover. While the binding of CsrA to RNA is understood at an atomic level, new mechanisms of gene activation and repression by this protein are still emerging. In the γ-proteobacteria, small non-coding RNAs (sRNAs) use molecular mimicry to sequester multiple CsrA dimers away from mRNA. In contrast, the FliW protein of Bacillus subtilis inhibits CsrA activity by binding to this protein, thereby establishing a checkpoint in flagellum morphogenesis. Turnover of CsrB and CsrC sRNAs in Escherichia coli requires a specificity protein of the GGDEF-EAL domain superfamily, CsrD, in addition to the housekeeping nucleases RNase E and PNPase. The Csr system of E. coli contains extensive autoregulatory circuitry, which governs the expression and activity of CsrA. Interaction of the Csr system with transcriptional regulatory networks results in a variety of complex response patterns. This minireview will highlight basic principles and new insights into the workings of these complex eubacterial regulatory systems. © 2012 Society for Applied Microbiology and Blackwell Publishing Ltd.

  1. Post-transcriptional regulation of neurofibromin level in cultured human melanocytes in response to growth factors.

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    Griesser, J; Kaufmann, D; Maier, B; Mailhammer, R; Kuehl, P; Krone, W

    1997-03-01

    Among the symptoms that characterize neurofibromatosis type 1 (NF1) are pigmentation anomalies such as cafe au lait spots. It has been suggested that the reduction of the neurofibromin level in the epidermis of NF1 patients is responsible for the observed signs such as altered melanogenesis and altered density of melanocytes. Our studies show that in cultured normal human melanocytes, the neurofibromin level can be varied in vitro over a wide range by using different culture conditions. The influence of factors that control differentiation and proliferation of melanocytes on neurofibromin levels was studied. Immunoprecipitation followed by western blotting showed a 3- to 4-fold increase of neurofibromin after stimulation by PMA or bFGF, respectively, and a 1.5-fold increase in cells stimulated with steel factor. The increase of neurofibromin was not paralleled by a higher NF1 mRNA level as proved by northern blotting. Pulse-chase experiments with 35S-labeled melanocytes revealed an approximately 3-fold increase in the half-life of neurofibromin in bFGF- or PMA-stimulated cells compared to controls. These results indicate that the neurofibromin level of cultured melanocytes can be regulated by a mechanism independent of NF1 gene transcription and translation, which might influence the degradation rate of the protein.

  2. Estrogen Promotes Hepatic Synthesis of Long-Chain Polyunsaturated Fatty Acids by Regulating ELOVL5 at Post-Transcriptional Level in Laying Hens.

    Science.gov (United States)

    Zhang, Meng; Li, Cui-Cui; Li, Fang; Li, Hong; Liu, Xiao-Jun; Loor, Juan J; Kang, Xiang-Tao; Sun, Gui-Rong

    2017-06-30

    The very long chain fatty acid elongase (ELOVL) plays an important role in the synthesis of long-chain polyunsaturated fatty acids (LCPUFA). Previous studies suggest that chicken could be an alternate source of eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA). In this study, we detected that ELOVL5, which plays a key role in the biosynthesis of omega-3 (n-3) and omega-6 (n-6) polyunsaturated fatty acids (PUFA), was highly expressed in the liver of laying hens and increased rapidly after sexual maturity. Bioinformatic analysis revealed ELOVL fatty acid elongase 5 (ELOVL5) gene as a putative target of miR-218-5p, miR-19a-3p, miR-19b-3p, miR-30a-5p, miR-30b-5p, and miR-30e-5p. We demonstrated estrogen downregulated microRNA (miRNA), and that ELOVL5 is a direct target of miR-218-5p, which was located in intron 14 of the Slit guidance ligand 2 (SLIT2) gene and co-expressed with the host gene. Overall, estrogen enhanced hepatic synthesis of LCPUFA by functioning as a negative regulator of miRNA thereby augmenting the expression of these miRNA target genes, especially ELOVL5, which plays a key role in the biosynthesis of n-3 and n-6 LCPUFA. This study provides a novel model for the use of estrogen in the poultry industry as an inducer of ELOVL5 expression to enhance hepatic n-3 and n-6 LCPUFA synthesis at the post-transcriptional level.

  3. Predominantly post-transcriptional regulation of activation molecules in chronic lymphocytic leukemia: the case of transferrin receptors.

    Science.gov (United States)

    Chiotoglou, Ioanna; Smilevska, Tatjana; Samara, Maria; Likousi, Sophia; Belessi, Chrysoula; Athanasiadou, Ioanna; Stavroyianni, Niki; Samara, Stavroula; Laoutaris, Nikolaos; Vamvakopoulos, Nikolaos; Anagnostopoulos, Achilles; Fassas, Athanasios; Stamatopoulos, Kostas; Kollia, Panagoula

    2008-01-01

    Transcriptional and post-transcriptional control mechanisms have a differential impact on cellular physiology depending on activation status. Several lines of evidence suggest that chronic lymphocytic leukemia (CLL) malignant B cells resemble antigen-experienced and activated B cells. In the present study, we investigated the expression of transferrin receptor 1 (TfR1, CD71), one of the "classical" markers up-regulated upon B-cell activation, and TfR2, a novel receptor for transferrin, in peripheral blood CD19+ B cells from ten healthy individuals and 76 patients with CLL so as to gain insight into potential disease-related differences in underlying regulatory mechanisms. Marked differences in the production and expression of these receptors were detected in malignant but not in normal B cells. Specifically, TfR1 mRNA and protein levels were significantly higher in comparison to TfR2, both in normal and malignant B cells. Furthermore, discrepancies between TfR mRNA and protein expression were observed in CLL; in contrast, mRNA and protein expression levels were generally concordant in normal B cells. Exposure to actinomycin D decreased TfR1 and TfR2 mRNA levels in normal CD19+ B cells but had no effect on CLL malignant cells. The protein synthesis inhibitor cycloheximide had opposing effects in normal vs. CLL malignant B cells: thus, TfR1 and TfR2 mRNA levels were increased in normal B cells, whereas they were unaffected or even suppressed in CLL malignant B cells. These results allude to differential regulation of TfR1 and TfR2 expression in normal B cells vs. CLL. In normal B cells, transcriptional mechanisms exert a critical control over TfR1 and TfR2 expression, whereas in CLL post-transcriptional mechanisms seem to play a complementary and perhaps more important role. This type of control appears to be especially suited for modulation of genes implicated in proliferation of activated cells, like CLL malignant B cells.

  4. Columbia University: Computational Human High-grade Glioblastoma Multiforme Interactome - miRNA (Post-transcriptional) Layer | Office of Cancer Genomics

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    The Human High-Grade Glioma Interactome (HGi) contains a genome-wide complement of molecular interactions that are Glioblastoma Multiforme (GBM)-specific. HGi v3 contains the post-transcriptional layer of the HGi, which includes the miRNA-target (RNA-RNA) layer of the interactome. Read the Abstract

  5. Systematic inference of copy-number genotypes from personal genome sequencing data reveals extensive olfactory receptor gene content diversity.

    Science.gov (United States)

    Waszak, Sebastian M; Hasin, Yehudit; Zichner, Thomas; Olender, Tsviya; Keydar, Ifat; Khen, Miriam; Stütz, Adrian M; Schlattl, Andreas; Lancet, Doron; Korbel, Jan O

    2010-11-11

    Copy-number variations (CNVs) are widespread in the human genome, but comprehensive assignments of integer locus copy-numbers (i.e., copy-number genotypes) that, for example, enable discrimination of homozygous from heterozygous CNVs, have remained challenging. Here we present CopySeq, a novel computational approach with an underlying statistical framework that analyzes the depth-of-coverage of high-throughput DNA sequencing reads, and can incorporate paired-end and breakpoint junction analysis based CNV-analysis approaches, to infer locus copy-number genotypes. We benchmarked CopySeq by genotyping 500 chromosome 1 CNV regions in 150 personal genomes sequenced at low-coverage. The assessed copy-number genotypes were highly concordant with our performed qPCR experiments (Pearson correlation coefficient 0.94), and with the published results of two microarray platforms (95-99% concordance). We further demonstrated the utility of CopySeq for analyzing gene regions enriched for segmental duplications by comprehensively inferring copy-number genotypes in the CNV-enriched >800 olfactory receptor (OR) human gene and pseudogene loci. CopySeq revealed that OR loci display an extensive range of locus copy-numbers across individuals, with zero to two copies in some OR loci, and two to nine copies in others. Among genetic variants affecting OR loci we identified deleterious variants including CNVs and SNPs affecting ~15% and ~20% of the human OR gene repertoire, respectively, implying that genetic variants with a possible impact on smell perception are widespread. Finally, we found that for several OR loci the reference genome appears to represent a minor-frequency variant, implying a necessary revision of the OR repertoire for future functional studies. CopySeq can ascertain genomic structural variation in specific gene families as well as at a genome-wide scale, where it may enable the quantitative evaluation of CNVs in genome-wide association studies involving high

  6. Genome-Wide Transcriptome Analysis Reveals Extensive Alternative Splicing Events in the Protoscoleces of Echinococcus granulosus and Echinococcus multilocularis.

    Science.gov (United States)

    Liu, Shuai; Zhou, Xiaosu; Hao, Lili; Piao, Xianyu; Hou, Nan; Chen, Qijun

    2017-01-01

    Alternative splicing (AS), as one of the most important topics in the post-genomic era, has been extensively studied in numerous organisms. However, little is known about the prevalence and characteristics of AS in Echinococcus species, which can cause significant health problems to humans and domestic animals. Based on high-throughput RNA-sequencing data, we performed a genome-wide survey of AS in two major pathogens of echinococcosis-Echinococcus granulosus and Echinococcus multilocularis. Our study revealed that the prevalence and characteristics of AS in protoscoleces of the two parasites were generally consistent with each other. A total of 6,826 AS events from 3,774 E. granulosus genes and 6,644 AS events from 3,611 E. multilocularis genes were identified in protoscolex transcriptomes, indicating that 33-36% of genes were subject to AS in the two parasites. Strikingly, intron retention instead of exon skipping was the predominant type of AS in Echinococcus species. Moreover, analysis of the Kyoto Encyclopedia of Genes and Genomes pathway indicated that genes that underwent AS events were significantly enriched in multiple pathways mainly related to metabolism (e.g., purine, fatty acid, galactose, and glycerolipid metabolism), signal transduction (e.g., Jak-STAT, VEGF, Notch, and GnRH signaling pathways), and genetic information processing (e.g., RNA transport and mRNA surveillance pathways). The landscape of AS obtained in this study will not only facilitate future investigations on transcriptome complexity and AS regulation during the life cycle of Echinococcus species, but also provide an invaluable resource for future functional and evolutionary studies of AS in platyhelminth parasites.

  7. Whole exome sequencing in 342 congenital cardiac left sided lesion cases reveals extensive genetic heterogeneity and complex inheritance patterns

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    Alexander H. Li

    2017-10-01

    Full Text Available Abstract Background Left-sided lesions (LSLs account for an important fraction of severe congenital cardiovascular malformations (CVMs. The genetic contributions to LSLs are complex, and the mutations that cause these malformations span several diverse biological signaling pathways: TGFB, NOTCH, SHH, and more. Here, we use whole exome sequence data generated in 342 LSL cases to identify likely damaging variants in putative candidate CVM genes. Methods Using a series of bioinformatics filters, we focused on genes harboring population-rare, putative loss-of-function (LOF, and predicted damaging variants in 1760 CVM candidate genes constructed a priori from the literature and model organism databases. Gene variants that were not observed in a comparably sequenced control dataset of 5492 samples without severe CVM were then subjected to targeted validation in cases and parents. Whole exome sequencing data from 4593 individuals referred for clinical sequencing were used to bolster evidence for the role of candidate genes in CVMs and LSLs. Results Our analyses revealed 28 candidate variants in 27 genes, including 17 genes not previously associated with a human CVM disorder, and revealed diverse patterns of inheritance among LOF carriers, including 9 confirmed de novo variants in both novel and newly described human CVM candidate genes (ACVR1, JARID2, NR2F2, PLRG1, SMURF1 as well as established syndromic CVM genes (KMT2D, NF1, TBX20, ZEB2. We also identified two genes (DNAH5, OFD1 with evidence of recessive and hemizygous inheritance patterns, respectively. Within our clinical cohort, we also observed heterozygous LOF variants in JARID2 and SMAD1 in individuals with cardiac phenotypes, and collectively, carriers of LOF variants in our candidate genes had a four times higher odds of having CVM (odds ratio = 4.0, 95% confidence interval 2.5–6.5. Conclusions Our analytical strategy highlights the utility of bioinformatic resources, including human

  8. Whole exome sequencing in 342 congenital cardiac left sided lesion cases reveals extensive genetic heterogeneity and complex inheritance patterns.

    Science.gov (United States)

    Li, Alexander H; Hanchard, Neil A; Furthner, Dieter; Fernbach, Susan; Azamian, Mahshid; Nicosia, Annarita; Rosenfeld, Jill; Muzny, Donna; D'Alessandro, Lisa C A; Morris, Shaine; Jhangiani, Shalini; Parekh, Dhaval R; Franklin, Wayne J; Lewin, Mark; Towbin, Jeffrey A; Penny, Daniel J; Fraser, Charles D; Martin, James F; Eng, Christine; Lupski, James R; Gibbs, Richard A; Boerwinkle, Eric; Belmont, John W

    2017-10-31

    Left-sided lesions (LSLs) account for an important fraction of severe congenital cardiovascular malformations (CVMs). The genetic contributions to LSLs are complex, and the mutations that cause these malformations span several diverse biological signaling pathways: TGFB, NOTCH, SHH, and more. Here, we use whole exome sequence data generated in 342 LSL cases to identify likely damaging variants in putative candidate CVM genes. Using a series of bioinformatics filters, we focused on genes harboring population-rare, putative loss-of-function (LOF), and predicted damaging variants in 1760 CVM candidate genes constructed a priori from the literature and model organism databases. Gene variants that were not observed in a comparably sequenced control dataset of 5492 samples without severe CVM were then subjected to targeted validation in cases and parents. Whole exome sequencing data from 4593 individuals referred for clinical sequencing were used to bolster evidence for the role of candidate genes in CVMs and LSLs. Our analyses revealed 28 candidate variants in 27 genes, including 17 genes not previously associated with a human CVM disorder, and revealed diverse patterns of inheritance among LOF carriers, including 9 confirmed de novo variants in both novel and newly described human CVM candidate genes (ACVR1, JARID2, NR2F2, PLRG1, SMURF1) as well as established syndromic CVM genes (KMT2D, NF1, TBX20, ZEB2). We also identified two genes (DNAH5, OFD1) with evidence of recessive and hemizygous inheritance patterns, respectively. Within our clinical cohort, we also observed heterozygous LOF variants in JARID2 and SMAD1 in individuals with cardiac phenotypes, and collectively, carriers of LOF variants in our candidate genes had a four times higher odds of having CVM (odds ratio = 4.0, 95% confidence interval 2.5-6.5). Our analytical strategy highlights the utility of bioinformatic resources, including human disease records and model organism phenotyping, in novel gene

  9. Transcriptional and post-transcriptional regulation of SPAST, the gene most frequently mutated in hereditary spastic paraplegia.

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    Brian J Henson

    Full Text Available Hereditary spastic paraplegias (HSPs comprise a group of neurodegenerative disorders that are characterized by progressive spasticity of the lower extremities, due to axonal degeneration in the corticospinal motor tracts. HSPs are genetically heterogeneous and show autosomal dominant inheritance in ∼70-80% of cases, with additional cases being recessive or X-linked. The most common type of HSP is SPG4 with mutations in the SPAST gene, encoding spastin, which occurs in 40% of dominantly inherited cases and in ∼10% of sporadic cases. Both loss-of-function and dominant-negative mutation mechanisms have been described for SPG4, suggesting that precise or stoichiometric levels of spastin are necessary for biological function. Therefore, we hypothesized that regulatory mechanisms controlling expression of SPAST are important determinants of spastin biology, and if altered, could contribute to the development and progression of the disease. To examine the transcriptional and post-transcriptional regulation of SPAST, we used molecular phylogenetic methods to identify conserved sequences for putative transcription factor binding sites and miRNA targeting motifs in the SPAST promoter and 3'-UTR, respectively. By a variety of molecular methods, we demonstrate that SPAST transcription is positively regulated by NRF1 and SOX11. Furthermore, we show that miR-96 and miR-182 negatively regulate SPAST by effects on mRNA stability and protein level. These transcriptional and miRNA regulatory mechanisms provide new functional targets for mutation screening and therapeutic targeting in HSP.

  10. Transcriptional and Post-Transcriptional Regulation of SPAST, the Gene Most Frequently Mutated in Hereditary Spastic Paraplegia

    Science.gov (United States)

    Henson, Brian J.; Zhu, Wan; Hardaway, Kelsey; Wetzel, Jaime L.; Stefan, Mihaela; Albers, Kathryn M.; Nicholls, Robert D.

    2012-01-01

    Hereditary spastic paraplegias (HSPs) comprise a group of neurodegenerative disorders that are characterized by progressive spasticity of the lower extremities, due to axonal degeneration in the corticospinal motor tracts. HSPs are genetically heterogeneous and show autosomal dominant inheritance in ∼70–80% of cases, with additional cases being recessive or X-linked. The most common type of HSP is SPG4 with mutations in the SPAST gene, encoding spastin, which occurs in 40% of dominantly inherited cases and in ∼10% of sporadic cases. Both loss-of-function and dominant-negative mutation mechanisms have been described for SPG4, suggesting that precise or stoichiometric levels of spastin are necessary for biological function. Therefore, we hypothesized that regulatory mechanisms controlling expression of SPAST are important determinants of spastin biology, and if altered, could contribute to the development and progression of the disease. To examine the transcriptional and post-transcriptional regulation of SPAST, we used molecular phylogenetic methods to identify conserved sequences for putative transcription factor binding sites and miRNA targeting motifs in the SPAST promoter and 3′-UTR, respectively. By a variety of molecular methods, we demonstrate that SPAST transcription is positively regulated by NRF1 and SOX11. Furthermore, we show that miR-96 and miR-182 negatively regulate SPAST by effects on mRNA stability and protein level. These transcriptional and miRNA regulatory mechanisms provide new functional targets for mutation screening and therapeutic targeting in HSP. PMID:22574173

  11. Effect of BRAFV600E mutation on transcription and post-transcriptional regulation in a papillary thyroid carcinoma model

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    Guenther Simone M

    2007-03-01

    Full Text Available Abstract Background microRNAs (miRNAs are a group of non-coding single stranded RNAs measuring approximately 22 nucleotides in length that have been found to control cell growth, differentiation and apoptosis. They negatively regulate target genes and have recently been implicated in tumourigenesis. Furthermore, miRNA expression profiling correlates with various cancers, with these genes thought to act as both tumour suppressors and oncogenes. Recently, a point mutation in the BRAF gene leading to a V600E substitution has been identified as the most common genetic change in papillary thyroid carcinoma (PTC occurring in 29–69% of cases. This mutation leads to aberrant MAPK activation that is implicated in tumourigenesis. Aim The aim of this study was to identify the effect that BRAF oncogene has on post-transcriptional regulation in PTC by using microRNA analysis. Results A unique miRNA expression signature differentiated between PTC cell lines with BRAF mutations and a normal thyroid cell line. 15 miRNAs were found to be upregulated and 23 miRNAs were downregulated. Several of these up/down regulated miRNAs may be involved in PTC pathogenesis. miRNA profiling will assist in the elucidation of disease pathogenesis and identification biomarkers and targets.

  12. Post-transcriptional Regulation of Keratinocyte Progenitor Cell Expansion, Differentiation and Hair Follicle Regression by miR-22.

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    Shukai Yuan

    2015-05-01

    Full Text Available Hair follicles (HF undergo precisely regulated recurrent cycles of growth, cessation, and rest. The transitions from anagen (growth, to catagen (regression, to telogen (rest involve a physiological involution of the HF. This process is likely coordinated by a variety of mechanisms including apoptosis and loss of growth factor signaling. However, the precise molecular mechanisms underlying follicle involution after hair keratinocyte differentiation and hair shaft assembly remain poorly understood. Here we demonstrate that a highly conserved microRNA, miR-22 is markedly upregulated during catagen and peaks in telogen. Using gain- and loss-of-function approaches in vivo, we find that miR-22 overexpression leads to hair loss by promoting anagen-to-catagen transition of the HF, and that deletion of miR-22 delays entry to catagen and accelerates the transition from telogen to anagen. Ectopic activation of miR-22 results in hair loss due to the repression a hair keratinocyte differentiation program and keratinocyte progenitor expansion, as well as promotion of apoptosis. At the molecular level, we demonstrate that miR-22 directly represses numerous transcription factors upstream of phenotypic keratin genes, including Dlx3, Foxn1, and Hoxc13. We conclude that miR-22 is a critical post-transcriptional regulator of the hair cycle and may represent a novel target for therapeutic modulation of hair growth.

  13. Post-transcriptional silencing of flavonol synthase mRNA in tobacco leads to fruits with arrested seed set.

    Directory of Open Access Journals (Sweden)

    Monika Mahajan

    Full Text Available Flavonoids are synthesized by phenylpropanoid pathway. They are known to participate in large number of physiological and biochemical processes in plants. Parthenocarpy and male sterility has earlier been reported by silencing chalcone synthase (CHS encoding gene. Silencing of CHS has blocked the synthesis of most of useful flavonoids including flavan-3-ols and flavonols. Also, these studies could not identify whether parthenocarpy/male sterility were due to lack of flavan-3-ols or flavonols or both. Flavonol synthase (FLS is an important enzyme of flavonoid pathway that catalyzes the formation of flavonols. In this article, we propose a novel strategy towards the generation of seedless or less-seeded fruits by downregulation of flavonol biosynthesis in tobacco (Nicotiana tabacum cv Xanthi through post-transcriptional gene silencing (PTGS of FLS encoding mRNA. The FLS silenced lines were observed for 20-80% reduction in FLS encoding gene expression and 25-93% reduction in flavonol (quercetin content. Interestingly, these FLS silenced tobacco lines also showed reduction in their anthocyanidins content. While the content of flavan-3-ols (catechin, epi-catechin and epi-gallocatechin was found to be increased in FLS silenced lines. The delayed flowering in FLS silenced lines could be due to decrease in level of indole acetic acid (IAA at apical region of their shoots. Furthermore, the pollen germination was hampered and pollens were unable to produce functional pollen tube in FLS silenced tobacco lines. Pods of FLS silenced lines contained significantly less number of seeds. The in vitro and in vivo studies where 1 µM quercetin was supplied to germination media, documented the restoration of normal pollen germination and pollen tube growth. This finding identified the role of flavonols particularly quercetin in pollen germination as well as in the regulation of plant fertility. Results also suggest a novel approach towards generation of seedless

  14. Post-transcriptional generation of miRNA variants by multiple nucleotidyl transferases contributes to miRNA transcriptome complexity

    Science.gov (United States)

    Wyman, Stacia K.; Knouf, Emily C.; Parkin, Rachael K.; Fritz, Brian R.; Lin, Daniel W.; Dennis, Lucas M.; Krouse, Michael A.; Webster, Philippa J.; Tewari, Muneesh

    2011-01-01

    Modification of microRNA sequences by the 3′ addition of nucleotides to generate so-called “isomiRs” adds to the complexity of miRNA function, with recent reports showing that 3′ modifications can influence miRNA stability and efficiency of target repression. Here, we show that the 3′ modification of miRNAs is a physiological and common post-transcriptional event that shows selectivity for specific miRNAs and is observed across species ranging from C. elegans to human. The modifications result predominantly from adenylation and uridylation and are seen across tissue types, disease states, and developmental stages. To quantitatively profile 3′ nucleotide additions, we developed and validated a novel assay based on NanoString Technologies' nCounter platform. For certain miRNAs, the frequency of modification was altered by processes such as cell differentiation, indicating that 3′ modification is a biologically regulated process. To investigate the mechanism of 3′ nucleotide additions, we used RNA interference to screen a panel of eight candidate miRNA nucleotidyl transferases for 3′ miRNA modification activity in human cells. Multiple enzymes, including MTPAP, PAPD4, PAPD5, ZCCHC6, ZCCHC11, and TUT1, were found to govern 3′ nucleotide addition to miRNAs in a miRNA-specific manner. Three of these enzymes–MTPAP, ZCCHC6, and TUT1–have not previously been known to modify miRNAs. Collectively, our results indicate that 3′ modification observed in next-generation small RNA sequencing data is a biologically relevant process, and identify enzymatic mechanisms that may lead to new approaches for modulating miRNA activity in vivo. PMID:21813625

  15. Resveratrol post-transcriptionally regulates pro-inflammatory gene expression via regulation of KSRP RNA binding activity

    Science.gov (United States)

    Bollmann, Franziska; Art, Julia; Henke, Jenny; Schrick, Katharina; Besche, Verena; Bros, Matthias; Li, Huige; Siuda, Daniel; Handler, Norbert; Bauer, Florian; Erker, Thomas; Behnke, Felix; Mönch, Bettina; Härdle, Lorena; Hoffmann, Markus; Chen, Ching-Yi; Förstermann, Ulrich; Dirsch, Verena M.; Werz, Oliver; Kleinert, Hartmut; Pautz, Andrea

    2014-01-01

    Resveratrol shows beneficial effects in inflammation-based diseases like cancer, cardiovascular and chronic inflammatory diseases. Therefore, the molecular mechanisms of the anti-inflammatory resveratrol effects deserve more attention. In human epithelial DLD-1 and monocytic Mono Mac 6 cells resveratrol decreased the expression of iNOS, IL-8 and TNF-α by reducing mRNA stability without inhibition of the promoter activity. Shown by pharmacological and siRNA-mediated inhibition, the observed effects are SIRT1-independent. Target-fishing and drug responsive target stability experiments showed selective binding of resveratrol to the RNA-binding protein KSRP, a central post-transcriptional regulator of pro-inflammatory gene expression. Knockdown of KSRP expression prevented resveratrol-induced mRNA destabilization in human and murine cells. Resveratrol did not change KSRP expression, but immunoprecipitation experiments indicated that resveratrol reduces the p38 MAPK-related inhibitory KSRP threonine phosphorylation, without blocking p38 MAPK activation or activity. Mutation of the p38 MAPK target site in KSRP blocked the resveratrol effect on pro-inflammatory gene expression. In addition, resveratrol incubation enhanced KSRP-exosome interaction, which is important for mRNA degradation. Finally, resveratrol incubation enhanced its intra-cellular binding to the IL-8, iNOS and TNF-α mRNA. Therefore, modulation of KSRP mRNA binding activity and, thereby, enhancement of mRNA degradation seems to be the common denominator of many anti-inflammatory effects of resveratrol. PMID:25352548

  16. Neural expression and post-transcriptional dosage compensation of the steroid metabolic enzyme 17β-HSD type 4

    Directory of Open Access Journals (Sweden)

    Wise Petra M

    2010-04-01

    Full Text Available Abstract Background Steroids affect many tissues, including the brain. In the zebra finch, the estrogenic steroid estradiol (E2 is especially effective at promoting growth of the neural circuit specialized for song. In this species, only the males sing and they have a much larger and more interconnected song circuit than females. Thus, it was surprising that the gene for 17β-hydroxysteroid dehydrogenase type 4 (HSD17B4, an enzyme that converts E2 to a less potent estrogen, had been mapped to the Z sex chromosome. As a consequence, it was likely that HSD17B4 was differentially expressed in males (ZZ and females (ZW because dosage compensation of Z chromosome genes is incomplete in birds. If a higher abundance of HSD17B4 mRNA in males than females was translated into functional enzyme in the brain, then contrary to expectation, males could produce less E2 in their brains than females. Results Here, we used molecular and biochemical techniques to confirm the HSD17B4 Z chromosome location in the zebra finch and to determine that HSD17B4 mRNA and activity were detectable in the early developing and adult brain. As expected, HSD17B4 mRNA expression levels were higher in males compared to females. This provides further evidence of the incomplete Z chromosome inactivation mechanisms in birds. We detected HSD17B4 mRNA in regions that suggested a role for this enzyme in the early organization and adult function of song nuclei. We did not, however, detect significant sex differences in HSD17B4 activity levels in the adult brain. Conclusions Our results demonstrate that the HSD17B4 gene is expressed and active in the zebra finch brain as an E2 metabolizing enzyme, but that dosage compensation of this Z-linked gene may occur via post-transcriptional mechanisms.

  17. Caveolin-1-mediated post-transcriptional regulation of inducible nitric oxide synthase in human colon carcinoma cells

    Directory of Open Access Journals (Sweden)

    EMANUELA FELLEY-BOSCO

    2002-01-01

    Full Text Available Reactive oxygen species are now widely recognized as important players contributing both to cell homeostasis and the development of disease. In this respect nitric oxide (NO is no exception. The discussion here will center on regulation of the inducible form of nitric oxide synthase (iNOS for two reasons. First, only iNOS produces micromolar NO concentrations, amounts that are high by comparison with the picomolar to nanomolar concentrations resulting from Ca2+-controlled NO production by endothelial eNOS or neuronal nNOS. Second, iNOS is not constitutively expressed in cells and regulation of this isoenzyme, in contrast to endothelial eNOS or neuronal nNOS, is widely considered to occur at the transcriptional level only. In particular, we were interested in the possibility that caveolin-1, a protein that functions as a tumor suppressor in colon carcinoma cells (Bender et al., 2002; this issue, might regulate iNOS activity. Our results provide evidence for the existence of a post-transcriptional mechanism controlling iNOS protein levels that involves caveolin-1-dependent sequestration of iNOS within a detergent-insoluble compartment. Interestingly, despite the high degree of conservation of the caveolin-1 scaffolding domain binding motif within all NOS enzymes, the interaction detected between caveolin-1 and iNOS in vitro is crucially dependent on presence of a caveolin-1 sequence element immediately adjacent to the scaffolding domain. A model is presented summarizing the salient aspects of these results. These observations are important in the context of tumor biology, since down-regulation of caveolin-1 is predicted to promote uncontrolled iNOS activity, genotoxic damage and thereby facilitate tumor development in humans

  18. Autotaxin Expression Is Regulated at the Post-transcriptional Level by the RNA-binding Proteins HuR and AUF1*

    OpenAIRE

    Sun, Shuhong; Zhang, Xiaotian; Lyu, Lin; Li, Xixi; Yao, Siliang; Zhang, Junjie

    2016-01-01

    Autotaxin (ATX) is a key enzyme that converts lysophosphatidylcholine (LPC) into lysophosphatidic acid (LPA), a lysophospholipid mediator that regulates cellular activities through its specific G protein-coupled receptors. The ATX-LPA axis plays an important role in various physiological and pathological processes, especially in inflammation and cancer development. Although the transcriptional regulation of ATX has been widely studied, the post-transcriptional regulation of ATX is largely unk...

  19. Extensive Direct Subcortical Cerebellum-Basal Ganglia Connections in Human Brain as Revealed by Constrained Spherical Deconvolution Tractography.

    Science.gov (United States)

    Milardi, Demetrio; Arrigo, Alessandro; Anastasi, Giuseppe; Cacciola, Alberto; Marino, Silvia; Mormina, Enricomaria; Calamuneri, Alessandro; Bruschetta, Daniele; Cutroneo, Giuseppina; Trimarchi, Fabio; Quartarone, Angelo

    2016-01-01

    The connections between the cerebellum and basal ganglia were assumed to occur at the level of neocortex. However evidences from animal data have challenged this old perspective showing extensive subcortical pathways linking the cerebellum with the basal ganglia. Here we tested the hypothesis if these connections also exist between the cerebellum and basal ganglia in the human brain by using diffusion magnetic resonance imaging and tractography. Fifteen healthy subjects were analyzed by using constrained spherical deconvolution technique obtained with a 3T magnetic resonance imaging scanner. We found extensive connections running between the subthalamic nucleus and cerebellar cortex and, as novel result, we demonstrated a direct route linking the dentate nucleus to the internal globus pallidus as well as to the substantia nigra. These findings may open a new scenario on the interpretation of basal ganglia disorders.

  20. Parallel Comparison of N-Linked Glycopeptide Enrichment Techniques Reveals Extensive Glycoproteomic Analysis of Plasma Enabled by SAX-ERLIC.

    Science.gov (United States)

    Totten, Sarah M; Feasley, Christa L; Bermudez, Abel; Pitteri, Sharon J

    2017-03-03

    Protein glycosylation is of increasing interest due to its important roles in protein function and aberrant expression with disease. Characterizing protein glycosylation remains analytically challenging due to its low abundance, ion suppression issues, and microheterogeneity at glycosylation sites, especially in complex samples such as human plasma. In this study, the utility of three common N-linked glycopeptide enrichment techniques is compared using human plasma. By analysis on an LTQ-Orbitrap Elite mass spectrometer, electrostatic repulsion hydrophilic interaction liquid chromatography using strong anion exchange solid-phase extraction (SAX-ERLIC) provided the most extensive N-linked glycopeptide enrichment when compared with multilectin affinity chromatography (M-LAC) and Sepharose-HILIC enrichments. SAX-ERLIC enrichment yielded 191 unique glycoforms across 72 glycosylation sites from 48 glycoproteins, which is more than double that detected using other enrichment techniques. The greatest glycoform diversity was observed in SAX-ERLIC enrichment, with no apparent bias toward specific glycan types. SAX-ERLIC enrichments were additionally analyzed by an Orbitrap Fusion Lumos mass spectrometer to maximize glycopeptide identifications for a more comprehensive assessment of protein glycosylation. In these experiments, 829 unique glycoforms were identified across 208 glycosylation sites from 95 plasma glycoproteins, a significant improvement from the initial method comparison and one of the most extensive site-specific glycosylation analysis in immunodepleted human plasma to date. Data are available via ProteomeXchange with identifier PXD005655.

  1. The initiation and tectonic regimes of the Cenozoic extension in the Bohai Bay Basin, North China revealed by numerical modelling

    Science.gov (United States)

    Li, Lu; Qiu, Nansheng

    2017-06-01

    In this study the dynamic aspects of the Cenozoic extension in the Bohai Bay Basin are considered in the context of initial thickness of the crust and lithosphere, tectonic force, strain rate and thermal rheology, which are directly or indirectly estimated from a pure shear extensional model. It is accordingly reasonable to expect that, in the Bohai Bay Basin, the thickness variation could be present prior to the initiation of extension. The extensional deformation is localized by a thickness variation of the crust and lithosphere and the heterogeneity of the initial thickness plays an important role in rifting dynamics. The onset of rifting requires a critical tectonic force (initial tectonic force) to be applied, which then immediately begins to decay gradually. Rifting will only occur when the total effective buoyancy force of the subducting slab reaches a critical level, after a certain amount of subduction taking place. The magnitude of the tectonic force decreases with time in the early phase of rifting, which indicates the weakening due to the increase in geothermal gradient. In order to deform the continental lithosphere within the currently accepted maximum magnitude of the force derived from subducted slab roll-back, the following conditions should be satisfied: (1) the thickness of the continental lithosphere is significantly thin and less than 125 km and (2) the lithosphere has a wet and hot rheology, which provides implications for rheological layering in continental lithosphere. Our results are strongly supported by the ;crème brûlée; model, in which the lower crust and mantle are relatively ductile.

  2. Molecular species delimitation methods and population genetics data reveal extensive lineage diversity and cryptic species in Aglaopheniidae (Hydrozoa).

    Science.gov (United States)

    Postaire, Bautisse; Magalon, Hélène; Bourmaud, Chloé A-F; Bruggemann, J Henrich

    2016-12-01

    A comprehensive inventory of global biodiversity would be greatly improved by automating methods for species delimitation. The Automatic Barcode Gap Discovery method, the Poisson tree processes algorithm and the Generalized mixed Yule-coalescent model have been proposed as means of increasing the rate of biodiversity description using single locus data. We applied these methods to explore the diversity within the Aglaopheniidae, a hydrozoan family with many species widely distributed across tropical and temperate oceans. Our analyses revealed widespread cryptic diversity in this family, almost half of the morpho-species presenting several independent evolutionary lineages, as well as support for cases of synonymy. For two common species of this family, Lytocarpia brevirostris and Macrorhynchia phoenicea, we compared the outputs to clustering analyses based on microsatellite data and to nuclear gene phylogenies. For L. brevirostris, microsatellite data were congruent with results of the species delimitation methods, revealing the existence of two cryptic species with Indo-Pacific distribution. For M. phoenicea, all analyses confirmed the presence of two cryptic species within the South-Western Indian Ocean. Our study suggests that the diversity of Aglaopheniidae might be much higher than assumed, likely related to low dispersal capacities. Sequence-based species delimitation methods seem highly valuable to reveal cryptic diversity in hydrozoans; their application in an integrative framework will be very useful in describing the phyletic diversity of these organisms. Copyright © 2016 Elsevier Inc. All rights reserved.

  3. Integrated mRNA and microRNA analysis identifies genes and small miRNA molecules associated with transcriptional and post-transcriptional-level responses to both drought stress and re-watering treatment in tobacco.

    Science.gov (United States)

    Chen, Qiansi; Li, Meng; Zhang, Zhongchun; Tie, Weiwei; Chen, Xia; Jin, Lifeng; Zhai, Niu; Zheng, Qingxia; Zhang, Jianfeng; Wang, Ran; Xu, Guoyun; Zhang, Hui; Liu, Pingping; Zhou, Huina

    2017-01-10

    Drought stress is one of the most severe problem limited agricultural productivity worldwide. It has been reported that plants response to drought-stress by sophisticated mechanisms at both transcriptional and post-transcriptional levels. However, the precise molecular mechanisms governing the responses of tobacco leaves to drought stress and water status are not well understood. To identify genes and miRNAs involved in drought-stress responses in tobacco, we performed both mRNA and small RNA sequencing on tobacco leaf samples from the following three treatments: untreated-control (CL), drought stress (DL), and re-watering (WL). In total, we identified 798 differentially expressed genes (DEGs) between the DL and CL (DL vs. CL) treatments and identified 571 DEGs between the WL and DL (WL vs. DL) treatments. Further analysis revealed 443 overlapping DEGs between the DL vs. CL and WL vs. DL comparisons, and, strikingly, all of these genes exhibited opposing expression trends between these two comparisons, strongly suggesting that these overlapping DEGs are somehow involved in the responses of tobacco leaves to drought stress. Functional annotation analysis showed significant up-regulation of genes annotated to be involved in responses to stimulus and stress, (e.g., late embryogenesis abundant proteins and heat-shock proteins) antioxidant defense (e.g., peroxidases and glutathione S-transferases), down regulation of genes related to the cell cycle pathway, and photosynthesis processes. We also found 69 and 56 transcription factors (TFs) among the DEGs in, respectively, the DL vs. CL and the WL vs. DL comparisons. In addition, small RNA sequencing revealed 63 known microRNAs (miRNA) from 32 families and 368 novel miRNA candidates in tobacco. We also found that five known miRNA families (miR398, miR390, miR162, miR166, and miR168) showed differential regulation under drought conditions. Analysis to identify negative correlations between the differentially expressed mi

  4. Live cell linear dichroism imaging reveals extensive membrane ruffling within the docking structure of natural killer cell immune synapses

    DEFF Research Database (Denmark)

    Benninger, Richard K P; Vanherberghen, Bruno; Young, Stephen

    2009-01-01

    We have applied fluorescence imaging of two-photon linear dichroism to measure the subresolution organization of the cell membrane during formation of the activating (cytolytic) natural killer (NK) cell immune synapse (IS). This approach revealed that the NK cell plasma membrane is convoluted...... into ruffles at the periphery, but not in the center of a mature cytolytic NK cell IS. Time-lapse imaging showed that the membrane ruffles formed at the initial point of contact between NK cells and target cells and then spread radialy across the intercellular contact as the size of the IS increased, becoming...

  5. Spatially Extensive Standardized Surveys Reveal Widespread, Multi-Decadal Increase in East Antarctic Adélie Penguin Populations.

    Science.gov (United States)

    Southwell, Colin; Emmerson, Louise; McKinlay, John; Newbery, Kym; Takahashi, Akinori; Kato, Akiko; Barbraud, Christophe; DeLord, Karine; Weimerskirch, Henri

    2015-01-01

    Seabirds are considered to be useful and practical indicators of the state of marine ecosystems because they integrate across changes in the lower trophic levels and the physical environment. Signals from this key group of species can indicate broad scale impacts or response to environmental change. Recent studies of penguin populations, the most commonly abundant Antarctic seabirds in the west Antarctic Peninsula and western Ross Sea, have demonstrated that physical changes in Antarctic marine environments have profound effects on biota at high trophic levels. Large populations of the circumpolar-breeding Adélie penguin occur in East Antarctica, but direct, standardized population data across much of this vast coastline have been more limited than in other Antarctic regions. We combine extensive new population survey data, new population estimation methods, and re-interpreted historical survey data to assess decadal-scale change in East Antarctic Adélie penguin breeding populations. We show that, in contrast to the west Antarctic Peninsula and western Ross Sea where breeding populations have decreased or shown variable trends over the last 30 years, East Antarctic regional populations have almost doubled in abundance since the 1980's and have been increasing since the earliest counts in the 1960's. The population changes are associated with five-year lagged changes in the physical environment, suggesting that the changing environment impacts primarily on the pre-breeding age classes. East Antarctic marine ecosystems have been subject to a number of changes over the last 50 years which may have influenced Adélie penguin population growth, including decadal-scale climate variation, an inferred mid-20th century sea-ice contraction, and early-to-mid 20th century exploitation of fish and whale populations.

  6. Spatially Extensive Standardized Surveys Reveal Widespread, Multi-Decadal Increase in East Antarctic Adélie Penguin Populations.

    Directory of Open Access Journals (Sweden)

    Colin Southwell

    Full Text Available Seabirds are considered to be useful and practical indicators of the state of marine ecosystems because they integrate across changes in the lower trophic levels and the physical environment. Signals from this key group of species can indicate broad scale impacts or response to environmental change. Recent studies of penguin populations, the most commonly abundant Antarctic seabirds in the west Antarctic Peninsula and western Ross Sea, have demonstrated that physical changes in Antarctic marine environments have profound effects on biota at high trophic levels. Large populations of the circumpolar-breeding Adélie penguin occur in East Antarctica, but direct, standardized population data across much of this vast coastline have been more limited than in other Antarctic regions. We combine extensive new population survey data, new population estimation methods, and re-interpreted historical survey data to assess decadal-scale change in East Antarctic Adélie penguin breeding populations. We show that, in contrast to the west Antarctic Peninsula and western Ross Sea where breeding populations have decreased or shown variable trends over the last 30 years, East Antarctic regional populations have almost doubled in abundance since the 1980's and have been increasing since the earliest counts in the 1960's. The population changes are associated with five-year lagged changes in the physical environment, suggesting that the changing environment impacts primarily on the pre-breeding age classes. East Antarctic marine ecosystems have been subject to a number of changes over the last 50 years which may have influenced Adélie penguin population growth, including decadal-scale climate variation, an inferred mid-20th century sea-ice contraction, and early-to-mid 20th century exploitation of fish and whale populations.

  7. Autotaxin Expression Is Regulated at the Post-transcriptional Level by the RNA-binding Proteins HuR and AUF1*

    Science.gov (United States)

    Sun, Shuhong; Zhang, Xiaotian; Lyu, Lin; Li, Xixi; Yao, Siliang; Zhang, Junjie

    2016-01-01

    Autotaxin (ATX) is a key enzyme that converts lysophosphatidylcholine (LPC) into lysophosphatidic acid (LPA), a lysophospholipid mediator that regulates cellular activities through its specific G protein-coupled receptors. The ATX-LPA axis plays an important role in various physiological and pathological processes, especially in inflammation and cancer development. Although the transcriptional regulation of ATX has been widely studied, the post-transcriptional regulation of ATX is largely unknown. In this study, we identified conserved adenylate-uridylate (AU)-rich elements in the ATX mRNA 3′-untranslated region (3′UTR). The RNA-binding proteins HuR and AUF1 directly bound to the ATX mRNA 3′UTR and had antagonistic functions in ATX expression. HuR enhanced ATX expression by increasing ATX mRNA stability, whereas AUF1 suppressed ATX expression by promoting ATX mRNA decay. HuR and AUF1 were involved in ATX regulation in Colo320 human colon cancer cells and the LPS-stimulated human monocytic THP-1 cells. HuR knockdown suppressed ATX expression in B16 mouse melanoma cells, leading to inhibition of cell migration. This effect was reversed by AUF1 knockdown to recover ATX expression or by the addition of LPA. These results suggest that the post-transcriptional regulation of ATX expression by HuR and AUF1 modulates cancer cell migration. In summary, we identified HuR and AUF1 as novel post-transcriptional regulators of ATX expression, thereby elucidating a novel mechanism regulating the ATX-LPA axis. PMID:27784781

  8. Isoforms of elongation factor eEF1A may be differently regulated at post-transcriptional level in breast cancer progression

    Directory of Open Access Journals (Sweden)

    Vislovukh A. A.

    2013-01-01

    Full Text Available Eukaryotic translation elongation factor 1A exists as two 98 % homologous isoforms: eEF1A1 (A1 and eEF1A2 (A2 which are tissue and development specific. Despite high homology in an open reading frame (ORF region, mRNAs coding for eEF1A1 and eEF1A2 are different in their untranslated regions (UTR, suggesting a possibility of their dissimilar post-transcriptional regulation. Aim. To analyze the existence of cis-acting motifs in the UTRs of EEF1A1/A2 mRNAs, to confirm the possibility of post-transcriptional control of eEF1A1 and eEF1A2 expression. Methods. An ensemble of bioinformatic methods was applied to predict regulatory motifs in the UTRs of EEF1A1/A2 mRNAs. Dual-luciferase reporter assay was employed to detect post-transcriptional regulation of eEF1A1/A2 expression. Results. Numerous regulatory motifs in the UTR of EEF1A1/A2 mRNAs were found bioinformatically. The experimental evidence was obtained for the existence of negative regulation of EEF1A1 and positive regulation of EEF1A2 mRNA in the model of breast cancer development. Conclusions. EEF1A1 and EEF1A2 mRNAs contain distinct motifs in the UTRs and are differently regulated in cancer suggesting the possibility of their control by different cellular signals.

  9. The genome of th17 cell-inducing segmented filamentous bacteria reveals extensive auxotrophy and adaptations to the intestinal environment.

    Science.gov (United States)

    Sczesnak, Andrew; Segata, Nicola; Qin, Xiang; Gevers, Dirk; Petrosino, Joseph F; Huttenhower, Curtis; Littman, Dan R; Ivanov, Ivaylo I

    2011-09-15

    Perturbations of the composition of the symbiotic intestinal microbiota can have profound consequences for host metabolism and immunity. In mice, segmented filamentous bacteria (SFB) direct the accumulation of potentially proinflammatory Th17 cells in the intestinal lamina propria. We present the genome sequence of SFB isolated from monocolonized mice, which classifies SFB phylogenetically as a unique member of Clostridiales with a highly reduced genome. Annotation analysis demonstrates that SFB depend on their environment for amino acids and essential nutrients and may utilize host and dietary glycans for carbon, nitrogen, and energy. Comparative analyses reveal that SFB are functionally related to members of the genus Clostridium and several pathogenic or commensal "minimal" genera, including Finegoldia, Mycoplasma, Borrelia, and Phytoplasma. However, SFB are functionally distinct from all 1200 examined genomes, indicating a gene complement representing biology relatively unique to their role as a gut commensal closely tied to host metabolism and immunity. Copyright © 2011 Elsevier Inc. All rights reserved.

  10. A functional screen reveals an extensive layer of transcriptional and splicing control underlying RAS/MAPK signaling in Drosophila.

    Directory of Open Access Journals (Sweden)

    Dariel Ashton-Beaucage

    2014-03-01

    Full Text Available The small GTPase RAS is among the most prevalent oncogenes. The evolutionarily conserved RAF-MEK-MAPK module that lies downstream of RAS is one of the main conduits through which RAS transmits proliferative signals in normal and cancer cells. Genetic and biochemical studies conducted over the last two decades uncovered a small set of factors regulating RAS/MAPK signaling. Interestingly, most of these were found to control RAF activation, thus suggesting a central regulatory role for this event. Whether additional factors are required at this level or further downstream remains an open question. To obtain a comprehensive view of the elements functionally linked to the RAS/MAPK cascade, we used a quantitative assay in Drosophila S2 cells to conduct a genome-wide RNAi screen for factors impacting RAS-mediated MAPK activation. The screen led to the identification of 101 validated hits, including most of the previously known factors associated to this pathway. Epistasis experiments were then carried out on individual candidates to determine their position relative to core pathway components. While this revealed several new factors acting at different steps along the pathway--including a new protein complex modulating RAF activation--we found that most hits unexpectedly work downstream of MEK and specifically influence MAPK expression. These hits mainly consist of constitutive splicing factors and thereby suggest that splicing plays a specific role in establishing MAPK levels. We further characterized two representative members of this group and surprisingly found that they act by regulating mapk alternative splicing. This study provides an unprecedented assessment of the factors modulating RAS/MAPK signaling in Drosophila. In addition, it suggests that pathway output does not solely rely on classical signaling events, such as those controlling RAF activation, but also on the regulation of MAPK levels. Finally, it indicates that core splicing

  11. Transcriptional Profiling of Coxiella burnetii Reveals Extensive Cell Wall Remodeling in the Small Cell Variant Developmental Form

    Science.gov (United States)

    Sandoz, Kelsi M.; Popham, David L.; Beare, Paul A.; Sturdevant, Daniel E.; Hansen, Bryan; Nair, Vinod; Heinzen, Robert A.

    2016-01-01

    A hallmark of Coxiella burnetii, the bacterial cause of human Q fever, is a biphasic developmental cycle that generates biologically, ultrastructurally, and compositionally distinct large cell variant (LCV) and small cell variant (SCV) forms. LCVs are replicating, exponential phase forms while SCVs are non-replicating, stationary phase forms. The SCV has several properties, such as a condensed nucleoid and an unusual cell envelope, suspected of conferring enhanced environmental stability. To identify genetic determinants of the LCV to SCV transition, we profiled the C. burnetii transcriptome at 3 (early LCV), 5 (late LCV), 7 (intermediate forms), 14 (early SCV), and 21 days (late SCV) post-infection of Vero epithelial cells. Relative to early LCV, genes downregulated in the SCV were primarily involved in intermediary metabolism. Upregulated SCV genes included those involved in oxidative stress responses, arginine acquisition, and cell wall remodeling. A striking transcriptional signature of the SCV was induction (>7-fold) of five genes encoding predicted L,D transpeptidases that catalyze nonclassical 3–3 peptide cross-links in peptidoglycan (PG), a modification that can influence several biological traits in bacteria. Accordingly, of cross-links identified, muropeptide analysis showed PG of SCV with 46% 3–3 cross-links as opposed to 16% 3–3 cross-links for LCV. Moreover, electron microscopy revealed SCV with an unusually dense cell wall/outer membrane complex as compared to LCV with its clearly distinguishable periplasm and inner and outer membranes. Collectively, these results indicate the SCV produces a unique transcriptome with a major component directed towards remodeling a PG layer that likely contributes to Coxiella’s environmental resistance. PMID:26909555

  12. Extensive Pyrosequencing Reveals Frequent Intra-Genomic Variations of Internal Transcribed Spacer Regions of Nuclear Ribosomal DNA

    Science.gov (United States)

    Li, Dezhu; Sun, Yongzhen; Niu, Yunyun; Chen, Zhiduan; Luo, Hongmei; Pang, Xiaohui; Sun, Zhiying; Liu, Chang; Lv, Aiping; Deng, Youping; Larson-Rabin, Zachary; Wilkinson, Mike; Chen, Shilin

    2012-01-01

    Background Internal transcribed spacer of nuclear ribosomal DNA (nrDNA) is already one of the most popular phylogenetic and DNA barcoding markers. However, the existence of its multiple copies has complicated such usage and a detailed characterization of intra-genomic variations is critical to address such concerns. Methodology/Principal Findings In this study, we used sequence-tagged pyrosequencing and genome-wide analyses to characterize intra-genomic variations of internal transcribed spacer 2 (ITS2) regions from 178 plant species. We discovered that mutation of ITS2 is frequent, with a mean of 35 variants per species. And on average, three of the most abundant variants make up 91% of all ITS2 copies. Moreover, we found different congeneric species share identical variants in 13 genera. Interestingly, different species across different genera also share identical variants. In particular, one minor variant of ITS2 in Eleutherococcus giraldii was found identical to the ITS2 major variant of Panax ginseng, both from Araliaceae family. In addition, DNA barcoding gap analysis showed that the intra-genomic distances were markedly smaller than those of the intra-specific or inter-specific variants. When each of 5543 variants were examined for its species discrimination efficiency, a 97% success rate was obtained at the species level. Conclusions Identification of identical ITS2 variants across intra-generic or inter-generic species revealed complex species evolutionary history, possibly, horizontal gene transfer and ancestral hybridization. Although intra-genomic multiple variants are frequently found within each genome, the usage of the major variants alone is sufficient for phylogeny construction and species determination in most cases. Furthermore, the inclusion of minor variants further improves the resolution of species identification. PMID:22952830

  13. Extensive geographical and social structure in the paternal lineages of Saudi Arabia revealed by analysis of 27 Y-STRs.

    Science.gov (United States)

    Khubrani, Yahya M; Wetton, Jon H; Jobling, Mark A

    2018-03-01

    Saudi Arabia's indigenous population is organized into patrilineal descent groups, but to date, little has been done to characterize its population structure, in particular with respect to the male-specific region of the Y chromosome. We have used the 27-STR Yfiler ® Plus kit to generate haplotypes in 597 unrelated Saudi males, classified into five geographical regions (North, South, Central, East and West). Overall, Yfiler ® Plus provides a good discrimination capacity of 95.3%, but this is greatly reduced (74.7%) when considering the reduced Yfiler ® set of 17 Y-STRs, justifying the use of the expanded set of markers in this population. Comparison of the five geographical divisions reveals striking differences, with low diversity and similar haplotype spectra in the Central and Northern regions, and high diversity and similar haplotype spectra in the East and West. These patterns likely reflect the geographical isolation of the desert heartland of the peninsula, and the proximity to the sea of the Eastern and Western areas, and consequent historical immigration. We predicted haplogroups from Y-STR haplotypes, testing the performance of prediction by using a large independent set of Saudi Arabian Y-STR + Y-SNP data. Prediction indicated predominance (71%) of haplogroup J1, which was significantly more common in Central, Northern and Southern groups than in East and West, and formed a star-like expansion cluster in a median-joining network with an estimated age of ∼2800 years. Most of our 597 participants were sampled within Saudi Arabia itself, but ∼16% were sampled in the UK. Despite matching these two groups by home sub-region, we observed significant differences in haplotype and predicted haplogroup constitutions overall, and for most sub-regions individually. This suggests social structure influencing the probability of leaving Saudi Arabia, correlated with different Y-chromosome compositions. The UK-recruited sample is an inappropriate proxy for

  14. Post-transcriptional regulation of lipoprotein receptors by the E3-ubiquitin ligase inducible degrader of the low-density lipoprotein receptor.

    Science.gov (United States)

    Sorrentino, Vincenzo; Zelcer, Noam

    2012-06-01

    The hepatic low-density lipoprotein receptor (LDLR) pathway is essential for clearing circulating LDL and is an important therapeutic target for treating cardiovascular disease. Abundance of the LDLR is subject to both transcriptional and nontranscriptional control. Here, we highlight a new post-transcriptional mechanism for controlling LDLR function via ubiquitination of the receptor by the E3-ubiquitin ligase inducible degrader of the LDLR (IDOL). IDOL is a recently identified transcriptional target of the liver X receptors. Acting as an E3-ubiquitin ligase IDOL promotes ubiquitination of the LDLR, thereby marking it for lysosomal degradation. The determinants required for degradation of the LDLR by IDOL have been largely identified. IDOL also targets two related lipoprotein receptors, the very low-density lipoprotein receptor and apolipoprotein E receptor 2. Despite several similarities, the IDOL, and PCSK9 pathways for controlling LDLR abundance seem independent of each other. Genome-wide association studies have recently identified IDOL as a locus influencing variability in circulating levels of LDL, thereby highlighting the possible role of IDOL in human lipoprotein metabolism. Transcriptional induction of IDOL by liver X receptor defines a new post-transcriptional pathway for controlling LDLR abundance and LDL uptake independent of sterol regulatory element binding proteins. Targeting IDOL activity may offer a novel therapeutic approach complementary to statins for treating cardiovascular disease.

  15. What do fault patterns reveal about the latest phase of extension within the Northern Snake Range metamorphic core complex, Nevada, USA?

    Science.gov (United States)

    Ismat, Zeshan; Riley, Paul; Lerback, Jory

    2016-08-01

    The Northern Snake Range is a classic example of a metamorphic core complex, Basin-and-Range province, United States. It is composed of a plastically deformed footwall and a brittlely deformed hanging wall, separated by the Northern Snake Range low-angle detachment (NSRD). Brittle deformation, however, is not confined to the hanging wall. This paper focuses on exposures in Cove Canyon, located on the SE flank of the Northern Snake Range, where penetrative, homogeneous faults are well exposed throughout the hanging wall, footwall and NSRD, and overprint early plastic deformation. These late-stage fault sets assisted Eocene-Miocene extension. Detailed analysis of the faults reveals the following: (1) The shortening direction defined by faults is similar to the shortening direction defined by the stretching lineation in the footwall mylonites, indicating that the extensional kinematic history remained unchanged as the rocks were uplifted into the elastico-frictional regime. (2) After ∼17 Ma, extension may have continued entirely within elastic-frictional regime via cataclastic flow. (3) This latest deformation phase may have been accommodated by a single, continuous event. (3) Faults within NSRD boudins indicate that deformation within the detachment zone was non-coaxial during the latest phase of extension.

  16. The post-transcriptional regulator rsmA/csrA activates T3SS by stabilizing the 5' UTR of hrpG, the master regulator of hrp/hrc genes, in Xanthomonas.

    Directory of Open Access Journals (Sweden)

    Maxuel O Andrade

    2014-02-01

    Full Text Available The RsmA/CsrA family of the post-transcriptional regulators of bacteria is involved in the regulation of many cellular processes, including pathogenesis. In this study, we demonstrated that rsmA not only is required for the full virulence of the phytopathogenic bacterium Xanthomonas citri subsp. citri (XCC but also contributes to triggering the hypersensitive response (HR in non-host plants. Deletion of rsmA resulted in significantly reduced virulence in the host plant sweet orange and a delayed and weakened HR in the non-host plant Nicotiana benthamiana. Microarray, quantitative reverse-transcription PCR, western-blotting, and GUS assays indicated that RsmA regulates the expression of the type 3 secretion system (T3SS at both transcriptional and post-transcriptional levels. The regulation of T3SS by RsmA is a universal phenomenon in T3SS-containing bacteria, but the specific mechanism seems to depend on the interaction between a particular bacterium and its hosts. For Xanthomonads, the mechanism by which RsmA activates T3SS remains unknown. Here, we show that RsmA activates the expression of T3SS-encoding hrp/hrc genes by directly binding to the 5' untranslated region (UTR of hrpG, the master regulator of the hrp/hrc genes in XCC. RsmA stabilizes hrpG mRNA, leading to increased accumulation of HrpG proteins and subsequently, the activation of hrp/hrc genes. The activation of the hrp/hrc genes by RsmA via HrpG was further supported by the observation that ectopic overexpression of hrpG in an rsmA mutant restored its ability to cause disease in host plants and trigger HR in non-host plants. RsmA also stabilizes the transcripts of another T3SS-associated hrpD operon by directly binding to the 5' UTR region. Taken together, these data revealed that RsmA primarily activates T3SS by acting as a positive regulator of hrpG and that this regulation is critical to the pathogenicity of XCC.

  17. The Post-transcriptional Regulator rsmA/csrA Activates T3SS by Stabilizing the 5′ UTR of hrpG, the Master Regulator of hrp/hrc Genes, in Xanthomonas

    Science.gov (United States)

    Andrade, Maxuel O.; Farah, Chuck S.; Wang, Nian

    2014-01-01

    The RsmA/CsrA family of the post-transcriptional regulators of bacteria is involved in the regulation of many cellular processes, including pathogenesis. In this study, we demonstrated that rsmA not only is required for the full virulence of the phytopathogenic bacterium Xanthomonas citri subsp. citri (XCC) but also contributes to triggering the hypersensitive response (HR) in non-host plants. Deletion of rsmA resulted in significantly reduced virulence in the host plant sweet orange and a delayed and weakened HR in the non-host plant Nicotiana benthamiana. Microarray, quantitative reverse-transcription PCR, western-blotting, and GUS assays indicated that RsmA regulates the expression of the type 3 secretion system (T3SS) at both transcriptional and post-transcriptional levels. The regulation of T3SS by RsmA is a universal phenomenon in T3SS-containing bacteria, but the specific mechanism seems to depend on the interaction between a particular bacterium and its hosts. For Xanthomonads, the mechanism by which RsmA activates T3SS remains unknown. Here, we show that RsmA activates the expression of T3SS-encoding hrp/hrc genes by directly binding to the 5′ untranslated region (UTR) of hrpG, the master regulator of the hrp/hrc genes in XCC. RsmA stabilizes hrpG mRNA, leading to increased accumulation of HrpG proteins and subsequently, the activation of hrp/hrc genes. The activation of the hrp/hrc genes by RsmA via HrpG was further supported by the observation that ectopic overexpression of hrpG in an rsmA mutant restored its ability to cause disease in host plants and trigger HR in non-host plants. RsmA also stabilizes the transcripts of another T3SS-associated hrpD operon by directly binding to the 5′ UTR region. Taken together, these data revealed that RsmA primarily activates T3SS by acting as a positive regulator of hrpG and that this regulation is critical to the pathogenicity of XCC. PMID:24586158

  18. B cell differentiation in EBV-positive Burkitt Lymphoma is impaired at post-transcriptional level by miRNA altered expression

    DEFF Research Database (Denmark)

    Leucci, E; Onnis, A; Cocco, M

    2009-01-01

    levels of expression similar to normal controls, including microdissected GC cells.In addition, we found evidence that hsa-miR-127 is involved in B cell differentiation process through post transcriptional regulation of BLIMP1 and XBP1. The over-expression of this miRNA may thus represent a key event...... investigated the expression of specific miRNAs predicted to be involved in B cell differentiation and we found that hsa-miR-127 is differentially expressed between EBV-positive and EBV-negative BLs. In particular, it was strongly up-regulated only in EBV-positive BL samples, whereas EBV-negative cases showed...... in the lymphomagenesis of EBV positive BL, by blocking the B cell differentiation process. (c) 2009 UICC....

  19. Post-transcriptional and post-translational regulations of drought and heat response in plants: a spider’s web of mechanisms

    Science.gov (United States)

    Guerra, Davide; Crosatti, Cristina; Khoshro, Hamid H.; Mastrangelo, Anna M.; Mica, Erica; Mazzucotelli, Elisabetta

    2015-01-01

    Drought and heat tolerance are complex quantitative traits. Moreover, the adaptive significance of some stress-related traits is more related to plant survival than to agronomic performance. A web of regulatory mechanisms fine-tunes the expression of stress-related traits and integrates both environmental and developmental signals. Both post-transcriptional and post-translational modifications contribute substantially to this network with a pivotal regulatory function of the transcriptional changes related to cellular and plant stress response. Alternative splicing and RNA-mediated silencing control the amount of specific transcripts, while ubiquitin and SUMO modify activity, sub-cellular localization and half-life of proteins. Interactions across these modification mechanisms ensure temporally and spatially appropriate patterns of downstream-gene expression. For key molecular components of these regulatory mechanisms, natural genetic diversity exists among genotypes with different behavior in terms of stress tolerance, with effects upon the expression of adaptive morphological and/or physiological target traits. PMID:25717333

  20. MCPIP-1, alias Regnase-1 controls epithelial inflammation by post-transcriptional regulation of IL-8 production

    Science.gov (United States)

    Dobosz, E.; Wilamowski, M.; Lech, M.; Bugara, B.; Jura, J.; Potempa, J.; Koziel, J.

    2016-01-01

    Pattern recognition receptors are critical for the detection of invading microorganisms. They activate multiple pathways that lead to the induction of pro-inflammatory responses and pathogen clearance. The intensity and duration of this immune reaction must be tightly controlled spatially and temporally in every tissue by different negative regulators. We hypothesized that monocyte chemoattractant protein-1–induced protein-1 (MCPIP-1) might play a role in maintaining immune homeostasis in the epithelium both under physiological conditions and upon bacterial infection. To this end, we examined the distribution of MCPIP-1 transcript and protein in various tissues. The MCPIP-1 protein level was higher in epithelial cells than in myeloid cells. MCPIP-1 exerted RNase activity towards the IL-8 transcript and the life-span of IL-8 was determined by the presence of the stem-loops/hairpin (SL) structures at the 3′ UTR region of IL-8 mRNA. Moreover, using fully active, purified recombinant MCPIP-1 protein, we elucidated the mechanism by which MCPIP-1 controls the IL-8 mRNA level. In conclusion, we uncovered a novel IL-8–dependent mechanism via which MCPIP-1 maintains epithelial homeostasis. This study reveals for the first time that MCPIP-1 plays a crucial anti-inflammatory role not only in myeloid cells but also in epithelial cells. PMID:27513529

  1. Post-Transcriptional Up-Regulation of PDGF-C by HuR in Advanced and Stressed Breast Cancer

    Directory of Open Access Journals (Sweden)

    Nian-An Luo

    2014-11-01

    Full Text Available Breast cancer is a heterogeneous disease characterized by multiple genetic alterations leading to the activation of growth factor signaling pathways that promote cell proliferation. Platelet-derived growth factor-C (PDGF-C is overexpressed in various malignancies; however, the involvement of PDGF-C in breast cancers and the mechanisms underlying PDGF-C deregulation remain unclear. Here, we show that PDGF-C is overexpressed in clinical breast cancers and correlates with poor prognosis. PDGF-C up-regulation was mediated by the human embryonic lethal abnormal vision-like protein HuR, which stabilizes the PDGF-C transcript by binding to two predicted AU-rich elements (AREs in the 3'-untranslated region (3'-UTR. HuR is up-regulated in hydrogen peroxide-treated or ultraviolet-irradiated breast cancer cells. Clinically, HuR levels are correlated with PDGF-C expression and histological grade or pathological tumor-node-metastasis (pTNM stage. Our findings reveal a novel mechanism underlying HuR-mediated breast cancer progression, and suggest that HuR and PDGF-C are potential molecular candidates for targeted therapy of breast cancers.

  2. Translatome profiling in dormant and nondormant sunflower (Helianthus annuus) seeds highlights post-transcriptional regulation of germination.

    Science.gov (United States)

    Layat, Elodie; Leymarie, Juliette; El-Maarouf-Bouteau, Hayat; Caius, José; Langlade, Nicolas; Bailly, Christophe

    2014-12-01

    Seed dormancy, which blocks germination in apparently favourable conditions, is a key regulatory control point of plant population establishment. As germination requires de novo translation, its regulation by dormancy is likely to be related to the association of individual transcripts to polysomes. Here, the polysome-associated mRNAs, that is, the translatome, were fractionated and characterized with microarrays in dormant and nondormant sunflower (Helianthus annuus) embryos during their imbibition at 10°C, a temperature preventing germination of dormant embryos. Profiling of mRNAs in polysomal complexes revealed that the translatome differs between germinating and nongerminating embryos. Association of transcripts with polysomes reached a maximum after 15 h of imbibition; at this time-point 194 polysome-associated transcripts were specifically found in nondormant embryos and 47 in dormant embryos only. The proteins corresponding to the polysomal mRNAs in nondormant embryos appeared to be very pertinent for germination and were involved mainly in transport, regulation of transcription or cell wall modifications. This work demonstrates that seed germination results from a timely regulated and selective recruitment of mRNAs to polysomes, thus opening novel fields of investigation for the understanding of this developmental process. © 2014 The Authors. New Phytologist © 2014 New Phytologist Trust.

  3. Post-transcriptional regulation of human breast cancer cell proteome by unliganded estrogen receptor β via microRNAs.

    Science.gov (United States)

    Nassa, Giovanni; Tarallo, Roberta; Giurato, Giorgio; De Filippo, Maria Rosaria; Ravo, Maria; Rizzo, Francesca; Stellato, Claudia; Ambrosino, Concetta; Baumann, Marc; Lietzèn, Niina; Nyman, Tuula A; Weisz, Alessandro

    2014-04-01

    Estrogen receptor β (ERβ) is a member of the nuclear receptor family of homeostatic regulators that is frequently lost in breast cancer (BC), where its presence correlates with a better prognosis and a less aggressive clinical outcome of the disease. In contrast to ERα, its closest homolog, ERβ shows significant estrogen-independent activities, including the ability to inhibit cell cycle progression and regulate gene transcription in the absence of the ligand. Investigating the nature and extent of this constitutive activity of ERβ in BC MCF-7 and ZR-75.1 cells by means of microRNA (miRNA) sequencing, we identified 30 miRNAs differentially expressed in ERβ+ versus ERβ- cells in the absence of ligand, including up-regulated oncosuppressor miRs such miR-30a. In addition, a significant fraction of >1,600 unique proteins identified in MCF-7 cells by iTRAQ quantitative proteomics were either increased or decreased by ERβ, revealing regulation of multiple cell pathways by ligand-free receptors. Transcriptome analysis showed that for a large number of proteins regulated by ERβ, the corresponding mRNAs are unaffected, including a large number of putative targets of ERβ-regulated miRNAs, indicating a central role of miRNAs in mediating BC cell proteome regulation by ERβ. Expression of a mimic of miR-30a-5p, a direct target and downstream effector of ERβ in BC, led to the identification of several target transcripts of this miRNA, including 11 encoding proteins whose intracellular concentration was significantly affected by unliganded receptor. These results demonstrate a significant effect of ligand-free ERβ on BC cell functions via modulation of the cell proteome and suggest that miRNA regulation might represent a key event in the control of the biological and clinical phenotype of hormone-responsive BC by this nuclear receptor.

  4. Post-transcriptional Regulation of Human Breast Cancer Cell Proteome by Unliganded Estrogen Receptor β via microRNAs*

    Science.gov (United States)

    Nassa, Giovanni; Tarallo, Roberta; Giurato, Giorgio; De Filippo, Maria Rosaria; Ravo, Maria; Rizzo, Francesca; Stellato, Claudia; Ambrosino, Concetta; Baumann, Marc; Lietzèn, Niina; Nyman, Tuula A.; Weisz, Alessandro

    2014-01-01

    Estrogen receptor β (ERβ) is a member of the nuclear receptor family of homeostatic regulators that is frequently lost in breast cancer (BC), where its presence correlates with a better prognosis and a less aggressive clinical outcome of the disease. In contrast to ERα, its closest homolog, ERβ shows significant estrogen-independent activities, including the ability to inhibit cell cycle progression and regulate gene transcription in the absence of the ligand. Investigating the nature and extent of this constitutive activity of ERβ in BC MCF-7 and ZR-75.1 cells by means of microRNA (miRNA) sequencing, we identified 30 miRNAs differentially expressed in ERβ+ versus ERβ− cells in the absence of ligand, including up-regulated oncosuppressor miRs such miR-30a. In addition, a significant fraction of >1,600 unique proteins identified in MCF-7 cells by iTRAQ quantitative proteomics were either increased or decreased by ERβ, revealing regulation of multiple cell pathways by ligand-free receptors. Transcriptome analysis showed that for a large number of proteins regulated by ERβ, the corresponding mRNAs are unaffected, including a large number of putative targets of ERβ-regulated miRNAs, indicating a central role of miRNAs in mediating BC cell proteome regulation by ERβ. Expression of a mimic of miR-30a-5p, a direct target and downstream effector of ERβ in BC, led to the identification of several target transcripts of this miRNA, including 11 encoding proteins whose intracellular concentration was significantly affected by unliganded receptor. These results demonstrate a significant effect of ligand-free ERβ on BC cell functions via modulation of the cell proteome and suggest that miRNA regulation might represent a key event in the control of the biological and clinical phenotype of hormone-responsive BC by this nuclear receptor. PMID:24525454

  5. Extensive Chromosome Homoeology among Brassiceae Species Were Revealed by Comparative Genetic Mapping with High-Density EST-Based SNP Markers in Radish (Raphanus sativus L.)‡

    Science.gov (United States)

    Li, Feng; Hasegawa, Yoichi; Saito, Masako; Shirasawa, Sachiko; Fukushima, Aki; Ito, Toyoaki; Fujii, Hiroshi; Kishitani, Sachie; Kitashiba, Hiroyasu; Nishio, Takeshi

    2011-01-01

    A linkage map of expressed sequence tag (EST)-based markers in radish (Raphanus sativus L.) was constructed using a low-cost and high-efficiency single-nucleotide polymorphism (SNP) genotyping method named multiplex polymerase chain reaction–mixed probe dot-blot analysis developed in this study. Seven hundred and forty-six SNP markers derived from EST sequences of R. sativus were assigned to nine linkage groups with a total length of 806.7 cM. By BLASTN, 726 markers were found to have homologous genes in Arabidopsis thaliana, and 72 syntenic regions, which have great potential for utilizing genomic information of the model species A. thaliana in basic and applied genetics of R. sativus, were identified. By construction and analysis of the genome structures of R. sativus based on the 24 genomic blocks within the Brassicaceae ancestral karyotype, 23 of the 24 genomic blocks were detected in the genome of R. sativus, and half of them were found to be triplicated. Comparison of the genome structure of R. sativus with those of the A, B, and C genomes of Brassica species and that of Sinapis alba L. revealed extensive chromosome homoeology among Brassiceae species, which would facilitate transfer of the genomic information from one Brassiceae species to another. PMID:21816873

  6. Extensive chromosome homoeology among Brassiceae species were revealed by comparative genetic mapping with high-density EST-based SNP markers in radish (Raphanus sativus L.).

    Science.gov (United States)

    Li, Feng; Hasegawa, Yoichi; Saito, Masako; Shirasawa, Sachiko; Fukushima, Aki; Ito, Toyoaki; Fujii, Hiroshi; Kishitani, Sachie; Kitashiba, Hiroyasu; Nishio, Takeshi

    2011-10-01

    A linkage map of expressed sequence tag (EST)-based markers in radish (Raphanus sativus L.) was constructed using a low-cost and high-efficiency single-nucleotide polymorphism (SNP) genotyping method named multiplex polymerase chain reaction-mixed probe dot-blot analysis developed in this study. Seven hundred and forty-six SNP markers derived from EST sequences of R. sativus were assigned to nine linkage groups with a total length of 806.7 cM. By BLASTN, 726 markers were found to have homologous genes in Arabidopsis thaliana, and 72 syntenic regions, which have great potential for utilizing genomic information of the model species A. thaliana in basic and applied genetics of R. sativus, were identified. By construction and analysis of the genome structures of R. sativus based on the 24 genomic blocks within the Brassicaceae ancestral karyotype, 23 of the 24 genomic blocks were detected in the genome of R. sativus, and half of them were found to be triplicated. Comparison of the genome structure of R. sativus with those of the A, B, and C genomes of Brassica species and that of Sinapis alba L. revealed extensive chromosome homoeology among Brassiceae species, which would facilitate transfer of the genomic information from one Brassiceae species to another.

  7. Comparison of different cells of Haematococcus pluvialis reveals an extensive acclimation mechanism during its aging process: from a perspective of photosynthesis.

    Directory of Open Access Journals (Sweden)

    Wenhui Gu

    Full Text Available Both biomass dominated green vegetative cells (GV and astaxanthin-dominated orange resting cells (OR affect the final astaxanthin yield in industry. Examination of Haematococcus pluvialis revealed that the OR cells greatly varied from the GV cells at both cellular and subcellular levels. In particular, the thylakoid membranes in the OR were disassembled and fragmented. Furthermore, the OR conserved most of the photosynthetic pigments, with elevated concentrations of violaxanthin, antheraxanthin, and neoxanthin. Notably, moderate photosynthesis was detected in OR, even though most of the thylakoid membranes were disassembled, when compared with those in the GV. However, the energy distribution pattern between photosystem I and II (PSI and PSII in the OR favored PSI, which was also confirmed by 77-K fluorescence. As zeaxanthin was not detected in the OR, we attribute the acclimation role to astaxanthin, instead of xanthophyll cycle. Additionally, proteomic-scale comparison analysis of thylakoids of the OR and GV indicated no photosynthetically remarkable variations. However, an extensive acclimation mechanism of H. pluvialis was proposed, in which proteins in thylakoid of GV were noted to be involved in biomass accumulation and those in OR were involved in stress response. Conclusions of the comparative analysis might provide some physiological background of OR for astaxanthin production by using H. pluvialis.

  8. Comparison of Spinach Sex Chromosomes with Sugar Beet Autosomes Reveals Extensive Synteny and Low Recombination at the Male-Determining Locus.

    Science.gov (United States)

    Takahata, Satoshi; Yago, Takumi; Iwabuchi, Keisuke; Hirakawa, Hideki; Suzuki, Yutaka; Onodera, Yasuyuki

    2016-01-01

    Spinach (Spinacia oleracea, 2n = 12) and sugar beet (Beta vulgaris, 2n = 18) are important crop members of the family Chenopodiaceae ss Sugar beet has a basic chromosome number of 9 and a cosexual breeding system, as do most members of the Chenopodiaceae ss. family. By contrast, spinach has a basic chromosome number of 6 and, although certain cultivars and genotypes produce monoecious plants, is considered to be a dioecious species. The loci determining male and monoecious sexual expression were mapped to different loci on the spinach sex chromosomes. In this study, a linkage map with 46 mapped protein-coding sequences was constructed for the spinach sex chromosomes. Comparison of the linkage map with a reference genome sequence of sugar beet revealed that the spinach sex chromosomes exhibited extensive synteny with sugar beet chromosomes 4 and 9. Tightly linked protein-coding genes linked to the male-determining locus in spinach corresponded to genes located in or around the putative pericentromeric and centromeric regions of sugar beet chromosomes 4 and 9, supporting the observation that recombination rates were low in the vicinity of the male-determining locus. The locus for monoecism was confined to a chromosomal segment corresponding to a region of approximately 1.7Mb on sugar beet chromosome 9, which may facilitate future positional cloning of the locus. © The American Genetic Association 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  9. Comparison of different cells of Haematococcus pluvialis reveals an extensive acclimation mechanism during its aging process: from a perspective of photosynthesis.

    Science.gov (United States)

    Gu, Wenhui; Xie, Xiujun; Gao, Shan; Zhou, Wei; Pan, Guanghua; Wang, Guangce

    2013-01-01

    Both biomass dominated green vegetative cells (GV) and astaxanthin-dominated orange resting cells (OR) affect the final astaxanthin yield in industry. Examination of Haematococcus pluvialis revealed that the OR cells greatly varied from the GV cells at both cellular and subcellular levels. In particular, the thylakoid membranes in the OR were disassembled and fragmented. Furthermore, the OR conserved most of the photosynthetic pigments, with elevated concentrations of violaxanthin, antheraxanthin, and neoxanthin. Notably, moderate photosynthesis was detected in OR, even though most of the thylakoid membranes were disassembled, when compared with those in the GV. However, the energy distribution pattern between photosystem I and II (PSI and PSII) in the OR favored PSI, which was also confirmed by 77-K fluorescence. As zeaxanthin was not detected in the OR, we attribute the acclimation role to astaxanthin, instead of xanthophyll cycle. Additionally, proteomic-scale comparison analysis of thylakoids of the OR and GV indicated no photosynthetically remarkable variations. However, an extensive acclimation mechanism of H. pluvialis was proposed, in which proteins in thylakoid of GV were noted to be involved in biomass accumulation and those in OR were involved in stress response. Conclusions of the comparative analysis might provide some physiological background of OR for astaxanthin production by using H. pluvialis.

  10. The expression, induction and pharmacological activity of CYP1A2 are post-transcriptionally regulated by microRNA hsa-miR-132-5p.

    Science.gov (United States)

    Chen, Yinting; Zeng, Linjuan; Wang, Yong; Tolleson, William H; Knox, Bridgett; Chen, Si; Ren, Zhen; Guo, Lei; Mei, Nan; Qian, Feng; Huang, Kaihong; Liu, David; Tong, Weida; Yu, Dianke; Ning, Baitang

    2017-12-01

    Cytochrome P450 1A2 (CYP1A2) is one of the most abundant and important drug metabolizing enzymes in human liver. However, little is known about the post-transcriptional regulation of CYP1A2, especially the mechanisms involving microRNAs (miRNAs). This study applied a systematic approach to investigate the post-transcriptional regulation of CYP1A2 by miRNAs. Candidate miRNAs targeting the 3'-untranslated region (3'-UTR) of CYP1A2 were screened in silico, resulting in the selection of sixty-two potential miRNAs for further analysis. The levels of two miRNAs, hsa-miR-132-5p and hsa-miR-221-5p, were inversely correlated with the expression of CYP1A2 mRNA transcripts in normal human liver tissue samples represented in The Cancer Genome Atlas (TCGA) dataset. The interactions between these miRNAs and cognate CYP1A2 mRNA sequences were evaluated using luciferase reporter gene studies and electrophoretic mobility shift assays, by which a direct interaction was confirmed involving hsa-miR-132-5p and a cognate binding site present in the CYP1A2 3'-UTR. Experiments by which hsa-miR-132-5p or random miRNA controls were introduced into HepG2, Huh-7 and HepaRG hepatic cell lines showed that only hsa-miR-132-5p suppressed the endogenous and lansoprazole-induced expression of CYP1A2, at biological activity, protein production, and mRNA transcript levels. Furthermore, 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT), and lactate dehydrogenase (LDH) assays showed that hsa-miR-132-5p attenuates CYP1A2-mediated, lansoprazole-enhanced, flutamide-induced hepatic cell toxicity. Results from multilayer experiments demonstrate that hsa-miR-132-5p suppresses the expression of CYP1A2 and that this suppression is able to decrease the extent of an adverse drug-drug interaction involving lansoprazole and flutamide. Published by Elsevier Inc.

  11. Post-Transcriptional Regulation of Chemokine Receptor CXCR4 by Estrogen in HER2 Overexpressing, Estrogen Receptor-Positive Breast Cancer Cells

    Science.gov (United States)

    Sengupta, Surojeet; Schiff, Rachel; Katzenellenbogen, Benita S.

    2008-01-01

    Expression of the chemokine receptor CXCR4, a G protein-coupled receptor, and HER2, a receptor tyrosine kinase, strongly correlates with the aggressive and metastatic potential of breast cancer cells. We studied estrogen regulation of CXCR4 in estrogen receptor (ER)-positive MCF-7 breast cancer cells overexpressing HER2 (MCF7-HER2). Although estrogen evoked no change in CXCR4 mRNA levels, CXCR4 protein was significantly up-regulated after estrogen treatment of these cells, whereas estrogen had no effect on CXCR4 protein level in parental MCF7 cells that are low in HER2. Use of the CXCR4 specific inhibitor, AMD 3100, indicated that this increase in CXCR4 protein was partially responsible for the increase in estrogen-induced migration of these cells. The estrogen-induced increase in CXCR4 protein in MCF-7-HER2 cells was abrogated by the antiestrogen ICI 182780 and by gefitinib (Iressa; a phosphotyrosine kinase inhibitor), indicating an ER-mediated effect and confirming involvement of receptor tyrosine kinases, respectively. Using specific pathway inhibitors, we show that the estrogen-induced increase in CXCR4 involves PI3K/AKT, MAPK and mTOR pathways. PI3K/AKT and MAPK pathways are known to result in the phosphorylation and functional inactivation of tuberin (TSC2) of tuberous sclerosis complex thereby negating its inhibitory effects on mTOR, which in turn stimulates the translational machinery. Small interfering RNA (siRNA) mediated knockdown of tuberin elevated the level of CXCR4 protein in MCF7-HER2 cells and also nullified further estrogen up-regulation of CXCR4. This study suggests a pivotal role of PI3K, MAPK and mTOR pathways, via tuberin, in post-transcriptional control of CXCR4, initiated through estrogen-stimulated crosstalk between ER and HER2. Thus, post-transcriptional regulation of CXCR4 by estrogens acting through ER via kinase pathways may play a critical role in determining the metastatic potential of breast cancer cells. PMID:18807177

  12. Post-Transcriptional Regulation of KLF4 by High-Risk Human Papillomaviruses Is Necessary for the Differentiation-Dependent Viral Life Cycle.

    Directory of Open Access Journals (Sweden)

    Vignesh Kumar Gunasekharan

    2016-07-01

    Full Text Available Human papillomaviruses (HPVs are epithelial tropic viruses that link their productive life cycles to the differentiation of infected host keratinocytes. A subset of the over 200 HPV types, referred to as high-risk, are the causative agents of most anogenital malignancies. HPVs infect cells in the basal layer, but restrict viral genome amplification, late gene expression, and capsid assembly to highly differentiated cells that are active in the cell cycle. In this study, we demonstrate that HPV proteins regulate the expression and activities of a critical cellular transcription factor, KLF4, through post-transcriptional and post-translational mechanisms. Our studies show that KLF4 regulates differentiation as well as cell cycle progression, and binds to sequences in the upstream regulatory region (URR to regulate viral transcription in cooperation with Blimp1. KLF4 levels are increased in HPV-positive cells through a post-transcriptional mechanism involving E7-mediated suppression of cellular miR-145, as well as at the post-translational level by E6-directed inhibition of its sumoylation and phosphorylation. The alterations in KLF4 levels and functions results in activation and suppression of a subset of KLF4 target genes, including TCHHL1, VIM, ACTN1, and POT1, that is distinct from that seen in normal keratinocytes. Knockdown of KLF4 with shRNAs in cells that maintain HPV episomes blocked genome amplification and abolished late gene expression upon differentiation. While KLF4 is indispensable for the proliferation and differentiation of normal keratinocytes, it is necessary only for differentiation-associated functions of HPV-positive keratinocytes. Increases in KLF4 levels alone do not appear to be sufficient to explain the effects on proliferation and differentiation of HPV-positive cells indicating that additional modifications are important. KLF4 has also been shown to be a critical regulator of lytic Epstein Barr virus (EBV replication

  13. Post-transcriptional regulation of the Streptomyces coelicolor stress responsive sigma factor, SigH, involves translational control, proteolytic processing, and an anti-sigma factor homolog.

    Science.gov (United States)

    Viollier, Patrick H; Weihofen, Andreas; Folcher, Marc; Thompson, Charles J

    2003-01-24

    The sigH gene encodes a sigma factor whose transcription is controlled by stress regulatory systems and the developmental program in Streptomyces coelicolor. Here, we describe developmentally regulated post-transcriptional control systems for SigH. sigH is expressed as three primary translation products, SigH-sigma(37), SigH-sigma(51), and SigH-sigma(52). In vitro, SigH-sigma(52) was comparable to SigH-sigma(37) in its ability to associate with RNA polymerase core enzyme and specifically initiate transcription in vitro. While SigH-sigma(51/52) were the primary gene products observed throughout early phases of growth, their abundance decreased during later stages in liquid or solid phase cultures while levels of shorter, C-terminally encoded products increased. These included SigH-sigma(37), a product of the downstream translational initiation site, as well as two proteolytic derivatives of SigH-sigma(51/52) (34kDa and 38kDa). Accumulation of SigH-sigma(37) and processing of SigH-sigma(51/52) into these stable 34kDa and 38kDa derivatives correlated with morphological changes on solid medium and physiological maturation in liquid medium. SigH-sigma(51/52) processing did not occur on medium non-permissive for aerial mycelium formation or in one particular developmental mutant (brgA). The proteolytic activity could be detected in vitro using crude extracts of stationary phase cultures, but was absent from exponential phase cultures. prsH, the gene upstream of sigH having sequence similarity to known anti-sigma factors, was able to bind to, and thus presumably inactivate SigH-sigma(52), SigH-sigma(51), and SigH-sigma(37). We have shown elsewhere that prsH was conditionally required for colonial development. Thus, while at least one transcriptional regulator is known to bring about the accumulation of sigH mRNA at different times and different locations in colonies, the post-transcriptional processes described here regulate the activity of different SigH isoforms and

  14. Identification of novel microRNAs in post-transcriptional control of Nrf2 expression and redox homeostasis in neuronal, SH-SY5Y cells.

    Directory of Open Access Journals (Sweden)

    Madhusudhanan Narasimhan

    Full Text Available Nuclear factor-erythroid 2-related factor 2 (Nrf2/NFE2L2, a redox-sensitive transcription factor plays a critical role in adaptation to cellular stress and affords cellular defense by initiating transcription of antioxidative and detoxification genes. While a protein can be regulated at multiple levels, control of Nrf2 has been largely studied at post-translational regulation points by Keap1. Importantly, post-transcriptional/translational based regulation of Nrf2 is less understood and to date there are no reports on such mechanisms in neuronal systems. In this context, studies involving the role of microRNAs (miRs which are normally considered as fine tuning regulators of protein production through translation repression and/or post-transcriptional alterations, are in place. In the current study, based on in-silico analysis followed by immunoblotting and real time analysis, we have identified and validated for the first time that human NFE2L2 could be targeted by miR153/miR27a/miR142-5p/miR144 in neuronal, SH-SY5Y cells. Co-transfection studies with individual miR mimics along with either WT 3' UTR of human Nrf2 or mutated miRNA targeting seed sequence within Nrf2 3' UTR, demonstrated that Nrf2 is a direct regulatory target of these miRs. In addition, ectopic expression of miR153/miR27a/miR142-5p/miR144 affected Nrf2 mRNA abundance and nucleo-cytoplasmic concentration of Nrf2 in a Keap1 independent manner resulting in inefficient transactivating ability of Nrf2. Furthermore, forced expression of miRs diminished GCLC and GSR expression resulting in alteration of Nrf2 dependent redox homeostasis. Finally, bioinformatics based miRNA-disease network analysis (MDN along with extended computational network analysis of Nrf2 associated pathologic processes suggests that if in a particular cellular scenario where any of these miR153/miR27a/miR142-5p/miR144 either individually or as a group is altered, it could affect Nrf2 thus triggering and

  15. Tristetraprolin Down-Regulation Contributes to Persistent TNF-Alpha Expression Induced by Cigarette Smoke Extract through a Post-Transcriptional Mechanism

    Science.gov (United States)

    Cheng, Ming-Liang; Zhang, Quan; Mu, Mao; Li, Hong; Luo, Yuan; Liang, Yue-Dong; Luo, Xin-Hua; Gao, Chang-Qing; Jackson, Patricia L.; Wells, J. Michael; Zhou, Yong; Hu, Meng; Cai, Guoqiang; Thannickal, Victor J.; Steele, Chad; Blalock, J. Edwin; Han, Xiaosi; Chen, Ching-Yi; Ding, Qiang

    2016-01-01

    Rationale Tumor necrosis factor-alpha (TNF-α) is a potent pro-inflammatory mediator and its expression is up-regulated in chronic obstructive pulmonary disease (COPD). Tristetraprolin (TTP) is implicated in regulation of TNF-α expression; however, whether TTP is involved in cigarette smoke-induced TNF-α expression has not been determined. Methods TTP expression was examined by western blot analysis in murine alveolar macrophages and alveolar epithelial cells challenged without or with cigarette smoke extract (CSE). TNF-α mRNA stability, and the decay of TNF-α mRNA, were determined by real-time quantitative RT-PCR. TNF-α protein levels were examined at the same time in these cells. To identify the molecular mechanism involved, a construct expressing the human beta-globin reporter mRNA containing the TNF-α 3’-untranslated region was generated to characterize the TTP targeted site within TNF-α mRNA. Results CSE induced TTP down-regulation in alveolar macrophages and alveolar epithelial cells. Reduced TTP expression resulted in significantly increased TNF-α mRNA stability. Importantly, increased TNF-α mRNA stability due to impaired TTP function resulted in significantly increased TNF-α levels in these cells. Forced TTP expression abrogated the increased TNF-α mRNA stability and expression induced by CSE. By using the globin reporter construct containing TNF-α mRNA 3’-untranslated region, the data indicate that TTP directly targets the adenine- and uridine-rich region (ARE) of TNF-α mRNA and negatively regulates TNF-α expression at the post-transcriptional level. Conclusion The data demonstrate that cigarette smoke exposure reduces TTP expression and impairs TTP function, resulting in significantly increased TNF-α mRNA stability and excessive TNF-α expression in alveolar macrophages and epithelial cells. The data suggest that TTP is a novel post-transcriptional regulator and limits excessive TNF-α expression and inflammatory response induced by

  16. Opposing Post-transcriptional Control of InR by FMRP and LIN-28 Adjusts Stem Cell-Based Tissue Growth

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    Arthur Luhur

    2017-12-01

    Full Text Available Summary: Although the intrinsic mechanisms that control whether stem cells divide symmetrically or asymmetrically underlie tissue growth and homeostasis, they remain poorly defined. We report that the RNA-binding protein fragile X mental retardation protein (FMRP limits the symmetric division, and resulting expansion, of the stem cell population during adaptive intestinal growth in Drosophila. The elevated insulin sensitivity that FMRP-deficient progenitor cells display contributes to their accelerated expansion, which is suppressed by the depletion of insulin-signaling components. This FMRP activity is mediated solely via a second conserved RNA-binding protein, LIN-28, known to boost insulin signaling in stem cells. Via LIN-28, FMRP controls progenitor cell behavior by post-transcriptionally repressing the level of insulin receptor (InR. This study identifies the stem cell-based mechanism by which FMRP controls tissue adaptation, and it raises the possibility that defective adaptive growth underlies the accelerated growth, gastrointestinal, and other symptoms that affect fragile X syndrome patients. : Luhur et al. report that FMRP acts via LIN-28 in progenitor cells to dampen the adaptive expansion of intestinal tissue in the fruit fly, raising the possibility that defective LIN28-mediated adaptive growth underlies some of the symptoms that affect fragile X syndrome patients. Keywords: FMRP, fmr1, LIN-28, insulin receptor, IIS, adaptive growth, tissue resizing, intestinal stem cell, insulin sensitivity

  17. Post-transcriptional gene silencing of the p23 silencing suppressor of Citrus tristeza virus confers resistance to the virus in transgenic Mexican lime.

    Science.gov (United States)

    Fagoaga, Carmen; López, Carmelo; de Mendoza, Alfonso Hermoso; Moreno, Pedro; Navarro, Luis; Flores, Ricardo; Peña, Leandro

    2006-01-01

    Previously, we have shown that most Mexican limes (Citrus aurantifolia (Christ.) Swing.) expressing the p23 gene of Citrus tristeza virus (CTV) exhibit aberrations resembling viral leaf symptoms. Here we report that five independent transgenic lines having normal phenotype displayed characteristics typical of post-transcriptional gene silencing (PTGS): multiple copies of the transgene, low levels of the corresponding mRNA, methylation of the silenced transgene, and accumulation of p23-specific small interfering RNAs (siRNAs). When graft- or aphid-inoculated with CTV, some propagations of these silenced lines were immune: they neither expressed symptoms nor accumulated virions and viral RNA as estimated by DAS-ELISA and Northern blot hybridization, respectively. Other propagations were moderately resistant because they became infected later and showed attenuated symptoms compared to controls. The susceptible propagations, in addition to symptom expression and elevated virus titer, accumulated p23-specific siRNAs at levels significantly higher than immune or non-inoculated propagations, and showed transgene demethylation. This variable response among clonal transformants indicates that factors other than the genetic background of the transgenic plants play a key role in PTGS-mediated resistance.

  18. A structured RNA in hepatitis B virus post-transcriptional regulatory element represses alternative splicing in a sequence-independent and position-dependent manner.

    Science.gov (United States)

    Huang, Chen; Xie, Mao-Hua; Liu, Wei; Yang, Bo; Yang, Fan; Huang, Jingang; Huang, Jie; Wu, Qijia; Fu, Xiang-Dong; Zhang, Yi

    2011-05-01

    Hepatitis B virus (HBV) transcripts are subjected to multiple splicing decisions, but the mechanism of splicing regulation remains poorly understood. In this study, we used a well-investigated alternative splicing reporter to dissect splicing regulatory elements residing in the post-transcriptional regulatory element (PRE) of HBV. A strong intronic splicing silencer (ISS) with a minimal functional element of 105 nucleotides (referred to as PRE-ISS) was identified and, interestingly, both the sense and antisense strands of the element were found to strongly suppress alternative splicing in multiple human cell lines. PRE-ISS folds into a double-hairpin structure, in which substitution mutations disrupting the double-hairpin structure abolish the splicing silencer activity. Although it harbors two previously identified binding sites for polypyrimidine tract binding protein, PRE-ISS represses splicing independent of this protein. The silencing function of PRE-ISS exhibited a strong position dependence, decreasing with the distance from affected splice sites. PRE-ISS does not belong to the intronic region of any HBV splicing variants identified thus far, preventing the testing of this intronic silencer function in the regulation of HBV splicing. These findings, together with the identification of multiple sense-antisense ISSs in the HBV genome, support the hypothesis that a sequence-independent and structure-dependent regulatory mechanism may have evolved to repress cryptic splice sites in HBV transcripts, thereby preventing their aberrant splicing during viral replication in the host. © 2011 The Authors Journal compilation © 2011 FEBS.

  19. Efficient use of artificial micro-RNA to downregulate the expression of genes at the post-transcriptional level in Arabidopsis thaliana.

    Science.gov (United States)

    Ud-Din, A; Rauf, M; Ghafoor, S; Khattak, M N K; Hameed, M W; Shah, H; Jan, S; Muhammad, K; Rehman, A; Inamullah

    2016-04-07

    Micro-RNAs are cellular components regulating gene expression at the post-transcription level. In the present study, artificial micro-RNAs were used to decrease the transcript level of two genes, AtExpA8 (encoding an expansin) and AHL25 (encoding an AT-hook motif nuclear localized protein) in Arabidopsis thaliana. The backbone of the Arabidopsis endogenous MIR319a micro-RNA was used in a site-directed mutagenesis approach for the generation of artificial micro-RNAs targeting two genes. The recombinant cassettes were expressed under the control of the CaMV 35S promoter in individual A. thaliana plants. Transgenic lines of the third generation were tested by isolating total RNA and by subsequent cDNA synthesis using oligo-dT18 primers and mRNAs as templates. The expression of the two target genes was checked through quantitative real-time polymerase chain reaction to confirm reduced transcript levels for AtExpA8 and AHL25. Downregulation of AtExpA8 resulted in the formation of short hypocotyls compared with those of the wild-type control in response to low pH and high salt concentration. This technology could be used to prevent the expression of exogenous and invading genes posing a threat to the normal cellular physiology of the host plant.

  20. Transcriptional, post-transcriptional and chromatin-associated regulation of pri-miRNAs, pre-miRNAs and moRNAs

    DEFF Research Database (Denmark)

    Nepal, Chirag; Coolen, Marion; Hadzhiev, Yavor

    2015-01-01

    MicroRNAs (miRNAs) play a major role in the post-transcriptional regulation of target genes, especially in development and differentiation. Our understanding about the transcriptional regulation of miRNA genes is limited by inadequate annotation of primary miRNA (pri-miRNA) transcripts. Here, we......-translational histone modifications (H3K4me3, H2A.Z) and RNA polymerase II (RNAPII) occupancy. We validated seven miR-9 pri-miRNAs by in situ hybridization and showed similar expression patterns as mature miR-9. In addition, processing of an alternative intronic promoter of miR-9-5 was validated by 5' RACE PCR....... Furthermore, we demonstrated that CAGE-seq also detects 3'-end processing of pre-miRNAs on Drosha cleavage site that correlates with miRNA-offset RNAs (moRNAs) production and provides a new tool for detecting Drosha processing events and predicting pre-miRNA processing by a genome-wide assay....

  1. Post-transcriptional and post-translational regulations of drought and heat response in plants: a spider’s web of mechanisms

    Directory of Open Access Journals (Sweden)

    Davide eGuerra

    2015-02-01

    Full Text Available Drought and heat tolerance are complex quantitative traits. Moreover, the adaptive significance of some stress-related traits is more related to plant survival than to agronomic performance. A web of regulatory mechanisms fine-tunes the expression of stress-related traits and integrates both environmental and developmental signals. Both post-transcriptional and post-translational modifications contribute substantially to this network with a pivotal regulatory function of the transcriptional changes related to cellular and plant stress response. Alternative splicing and RNA-mediated silencing control the amount of specific transcripts, while ubiquitin and SUMO modify activity, sub-cellular localization and half-life of proteins. Interactions across these modification mechanisms ensure temporally and spatially appropriate patterns of downstream-gene expression. For key molecular components of these regulatory mechanisms, natural genetic diversity exists among genotypes with different behavior in terms of stress tolerance, with effects upon the expression of adaptive morphological and/or physiological target traits.

  2. Transcriptional and post-transcriptional down-regulation of cyclin D1 contributes to C6 glioma cell differentiation induced by forskolin.

    Science.gov (United States)

    He, Songmin; Zhu, Wenbo; Zhou, Yuxi; Huang, Yijun; Ou, Yanqiu; Li, Yan; Yan, Guangmei

    2011-09-01

    Malignant gliomas are the most common and lethal intracranial tumors, and differentiation therapy shows great potential to be a promising candidate for their treatment. Here, we have elaborated that a PKA activator, forskolin, represses cell growth via cell cycle arrest in the G0/G1 phase and induces cell differentiation characteristic with elongated processes and restoration of GFAP expression. In mechanisms, we verified that forskolin significantly diminishes the mRNA and protein level of a key cell cycle regulator cyclin D1, and maintenance of low cyclin D1 expression level was required for forskolin-induced proliferation inhibition and differentiation by gain and loss of function approaches. In addition, that forskolin down-regulated the cyclin D1 by proteolytic (post-transcriptional) mechanisms was dependent on GSK-3β activation at Ser9. The pro-differentiation activity of forskolin and related molecular mechanisms imply that forskolin can be developed into a candidate for the future in differentiation therapy of glioma, and cyclin D1 is a promising target for pro-differentiation strategy. Copyright © 2011 Wiley-Liss, Inc.

  3. Quantitative proteomics unravels that the post-transcriptional regulator Crc modulates the generation of vesicles and secreted virulence determinants of Pseudomonas aeruginosa

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    Jose Antonio Reales-Calderón

    2015-09-01

    Full Text Available Crc is a post-transcriptional regulator in Pseudomonas aeruginosa that modulates its metabolism, but also its susceptibility to antibiotics and virulence. Most of P. aeruginosa virulence factors are secreted or engulfed in vesicles. A Crc deficient mutant was created and the extracellular vesicles associated exoproteome and the vesicle-free secretome was quantified using iTRAQ. Fifty vesicles-associated proteins were more abundant and 14 less abundant in the Crc-defective strain, whereas 37 were more abundant and 17 less abundant in the vesicle-free secretome. Different virulence determinants, such as ToxA, protease IV, azurin, chitin-binding protein, PlcB and Hcp1, were less abundant in the Crc-defective mutant. We also observed that the crc mutant presented an impaired vesicle-associated secretion of quorum sensing signal molecules and less cytotoxicity than its wild-type strain, in agreement with the low secretion of proteins related to virulence. Our results offer new insights into the mechanisms by which Crc regulates P. aeruginosa virulence, through the modulation of vesicle formation and secretion of both virulence determinants and quorum sensing signals.

  4. Heterologous expression of plant virus genes that suppress post-transcriptional gene silencing results in suppression of RNA interference in Drosophila cells

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    Canto Tomas

    2004-08-01

    Full Text Available Abstract Background RNA interference (RNAi in animals and post-transcriptional gene silencing (PTGS in plants are related phenomena whose functions include the developmental regulation of gene expression and protection from transposable elements and viruses. Plant viruses respond by expressing suppressor proteins that interfere with the PTGS system. Results Here we demonstrate that both transient and constitutive expression of the Tobacco etch virus HC-Pro silencing suppressor protein, which inhibits the maintenance of PTGS in plants, prevents dsRNA-induced RNAi of a lacZ gene in cultured Drosophila cells. Northern blot analysis of the RNA present in Drosophila cells showed that HC-Pro prevented degradation of lacZ RNA during RNAi but that there was accumulation of the short (23nt RNA species associated with RNAi. A mutant HC-Pro that does not suppress PTGS in plants also does not affect RNAi in Drosophila. Similarly, the Cucumber mosaic virus 2b protein, which inhibits the systemic spread of PTGS in plants, does not suppress RNAi in Drosophila cells. In addition, we have used the Drosophila system to demonstrate that the 16K cysteine-rich protein of Tobacco rattle virus, which previously had no known function, is a silencing suppressor protein. Conclusion These results indicate that at least part of the process of RNAi in Drosophila and PTGS in plants is conserved, and that plant virus silencing suppressor proteins may be useful tools to investigate the mechanism of RNAi.

  5. Insight into post-transcriptional gene regulation: stress-responsive microRNAs and their role in the environmental stress survival of tolerant animals.

    Science.gov (United States)

    Biggar, Kyle K; Storey, Kenneth B

    2015-05-01

    Living animals are constantly faced with various environmental stresses that challenge normal life, including: oxygen limitation, very low or high temperature, as well as restriction of water and food. It has been well established that in response to these stresses, tolerant organisms regularly respond with a distinct suite of cellular modifications that involve transcriptional, translational and post-translational modification. In recent years, a new mechanism of rapid and reversible transcriptome regulation, via the action of non-coding RNA molecules, has emerged into post-transcriptional regulation and has since been shown to be part of the survival response. However, these RNA-based mechanisms by which tolerant organisms respond to stressed conditions are not well understood. Recent studies have begun to show that non-coding RNAs control gene expression and translation of mRNA to protein, and can also have regulatory influence over major cellular processes. For example, select microRNAs have been shown to have regulatory influence over the cell cycle, apoptosis, signal transduction, muscle atrophy and fatty acid metabolism during periods of environmental stress. As we are on the verge of dissecting the roles of non-coding RNA in environmental stress adaptation, this Commentary summarizes the hallmark alterations in microRNA expression that facilitate stress survival. © 2015. Published by The Company of Biologists Ltd.

  6. Post-transcriptional control of c-myc proto-oncogene expression by glucocorticoid hormones in human T lymphoblastic leukemia cells

    Energy Technology Data Exchange (ETDEWEB)

    Maroder, M.; Vacca, A.; Screpanti, I.; Petrangeli, E.; Frati, L. (Univ. La Sapienza, Roma (Italy)); Martinotti, S.; Gulino, A. (Univ. of L' Aquila (Italy))

    1990-03-11

    The authors have studied the regulation of the human c-myc proto-oncogene by glucocorticoid hormones in T lymphoblastic leukemic cells. A significant decrease (50%) of the steady state levels of c-myc mRNA was observed as early as 3 hours after dexamethasone treatment of CEM-1.3 human lymphoma cells, reaching less than 5% values, with respect to untreated cells, 24 hours after hormone administration. Nuclear run-on experiments showed no modifications of the transcriptional rate from the first exon. However, a slight decrease (15%) of the transcript elongation from the first exon/first intron boundary was observed in the dexamethasone-treated cells. Using actinomycin D to block gene transcription, they observed a significant increase in the rate of c-myc RNA specific decay after dexamethasone treatment. The data suggest that dexamethasone is able to inhibit human c-myc gene expression primarily at the post-transcriptional level, through the synthesis of hormone-transcriptional level, through the synthesis of hormone-induced regulatory protein(s) controlling c-myc transcript stability.

  7. Involvement of vacuolar processing enzyme SlVPE5 in post-transcriptional process of invertase in sucrose accumulation in tomato.

    Science.gov (United States)

    Wang, Ning; Duhita, Narendra; Ariizumi, Toru; Ezura, Hiroshi

    2016-11-01

    Enhancing the flavor of fruits plays a fundamental role in improving fruit quality, and volatile compositions as well as acid and sugar accumulation are significant factors that have an impact on the acceptability of sensory responses by human beings. Vacuoles in plants not only function as cell compartments that store amino acids, sugars and other metabolites but also act as lytic organelles where vacuolar proteins are post-translationally processed into mature forms or degraded by the action of vacuolar processing enzyme (VPE). We have previously characterized VPE genes (SlVPE1-5) during fruit development in tomato and discovered that the VPE enzyme activity negatively interfered with sugar accumulation in mature fruits. Comparative proteomic analysis demonstrated that acid invertase was one of the molecular targets of SlVPE5, which is involved in the hydrolysis of sucrose. This study also showed that decreased VPE enzyme activity due to suppression of SlVPE5 by RNAi strategy (RNAi-SlVPE5) accompanied with decreased enzyme activity of acid invertase. Further, we identified the enzyme activity of acid invertase was not well correlated with mRNA levels in the RNAi-SlVPE5 line. These results suggest that SlVPE5 regulates post-transcriptional processing through de novo synthesis of the acid invertase protein to suppress enzyme activity, thereby eventually ensuring sucrose hydrolysis. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

  8. Transcriptional and post-transcriptional regulation of ribulose 1,5-bisphosphate carboxylase gene expression in light- and dark-grown amaranth cotyledons.

    Science.gov (United States)

    Berry, J O; Nikolau, B J; Carr, J P; Klessig, D F

    1985-01-01

    The regulation of expression of the genes encoding the large subunit (LSU) and small subunit (SSU) of ribulose 1,5-bisphosphate carboxylase (RuBPCase) was examined in 1- through 8-day-old, dark-grown (etiolated) and light-grown amaranth cotyledons. RuBPCase specific activity in light-grown cotyledons increased during this 8-day period to a level 15-fold higher than in dark-grown cotyledons. Under both growth conditions, the accumulation of the LSU and SSU polypeptides was not coordinated. Initial detection of the SSU occurred 1 and 2 days after the appearance of the LSU in light- and dark-grown cotyledons, respectively. Furthermore, although the levels of the LSU were similar in both light- and dark-grown seedlings, the amount of the SSU followed clearly the changes in enzyme activity. Synthesis of these two polypeptides was dramatically different in etiolated versus light-grown cotyledons. In light the synthesis of both subunits was first observed on day 2 and continued throughout the growth of the cotyledons. In darkness the rate of synthesis of both subunits was much lower than in light and occurred only as a burst between days 2 and 5 after planting. However, mRNAs for both subunits were present in etiolated cotyledons at similar levels on days 4 through 7 (by Northern analysis) and were functional in vitro, despite their apparent inactivity in vivo after day 5. In addition, since both LSU and SSU mRNA levels were lower in dark- than in light-grown seedlings, our results indicate that both transcriptional and post-transcriptional controls modulate RuBPCase production in developing amaranth cotyledons. Images PMID:3837189

  9. MicroRNA-20a/b regulates cholesterol efflux through post-transcriptional repression of ATP-binding cassette transporter A1.

    Science.gov (United States)

    Liang, Bin; Wang, Xin; Song, Xiaosu; Bai, Rui; Yang, Huiyu; Yang, Zhiming; Xiao, Chuanshi; Bian, Yunfei

    2017-09-01

    ATP-binding cassette transporter A1 (ABCA1) plays a crucial role in reverse cholesterol transport and exhibits anti-atherosclerosis effects. Some microRNAs (miRs) regulate ABCA1 expression, and recent studies have shown that miR-20a/b might play a critical role in atherosclerotic diseases. Here, we attempted to clarify the potential contribution of miR-20a/b in post-transcriptional regulation of ABCA1, cholesterol efflux, and atherosclerosis. We performed bioinformatics analysis and found that miR-20a/b was highly conserved and directly bound to ABCA1 mRNA with low binding free energy. Luciferase-reporter assay also confirmed that miR-20a/b significantly reduced luciferase activity associated with the ABCA1 3' untranslated region reporter construct. Additionally, miR-20a/b decreased ABCA1 expression, which, in turn, decreased cholesterol efflux and increased cholesterol content in THP-1 and RAW 264.7 macrophage-derived foam cells. In contrast, miR-20a/b inhibitors increased ABCA1 expression and cholesterol efflux, decreased cholesterol content, and inhibited foam-cell formation. Consistent with our in vitro results, miR-20a/b-treated ApoE -/- mice showed decreased ABCA1expression in the liver and reductions of reverse cholesterol transport in vivo. Furthermore, miR-20a/b regulated the formation of nascent high-density lipoprotein and promoted atherosclerotic development, whereas miR-20a/b knockdown attenuated atherosclerotic formation. miR-20 is a new miRNA capable of targeting ABCA1 and regulating ABCA1 expression. Therefore, miR-20 inhibition constitutes a new strategy for ABCA1-based treatment of atherosclerosis. Copyright © 2017 Elsevier B.V. All rights reserved.

  10. Host-induced post-transcriptional hairpin RNA-mediated gene silencing of vital fungal genes confers efficient resistance against Fusarium wilt in banana.

    Science.gov (United States)

    Ghag, Siddhesh B; Shekhawat, Upendra K S; Ganapathi, Thumballi R

    2014-06-01

    Fusarium wilt, caused by Fusarium oxysporum f. sp. cubense (Foc), is among the most destructive diseases of banana (Musa spp.). Because no credible control measures are available, development of resistant cultivars through genetic engineering is the only option. We investigated whether intron hairpin RNA (ihpRNA)-mediated expression of small interfering RNAs (siRNAs) targeted against vital fungal genes (velvet and Fusarium transcription factor 1) in transgenic banana could achieve effective resistance against Foc. Partial sequences of these two genes were assembled as ihpRNAs in suitable binary vectors (ihpRNA-VEL and ihpRNA-FTF1) and transformed into embryogenic cell suspensions of banana cv. Rasthali by Agrobacterium-mediated genetic transformation. Eleven transformed lines derived from ihpRNA-VEL and twelve lines derived from ihpRNA-FTF1 were found to be free of external and internal symptoms of Foc after 6-week-long greenhouse bioassays. The five selected transgenic lines for each construct continued to resist Foc at 8 months postinoculation. Presence of specific siRNAs derived from the two ihpRNAs in transgenic banana plants was confirmed by Northern blotting and Illumina sequencing of small RNAs derived from the transgenic banana plants. The present study represents an important effort in proving that host-induced post-transcriptional ihpRNA-mediated gene silencing of vital fungal genes can confer efficient resistance against debilitating pathogens in crop plants. © 2014 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

  11. Role of a redox-based methylation switch in mRNA life cycle ( pre- & post- transcriptional maturation and protein turnover : Implications in neurological disorders

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    MALAV SUCHIN TRIVEDI

    2012-06-01

    Full Text Available Homeostatic synaptic scaling in response to neuronal stimulus or activation, as well as due to changes in cellular niche, is an important phenomenon for memory consolidation, retrieval, and other similar cognitive functions. Neurological disorders and cognitive disabilities in autism, Rett syndrome, schizophrenia, dementia etc., are strongly correlated to alterations in protein expression (both synaptic and cytoplasmic. This correlation suggests that efficient temporal regulation of synaptic protein expression is important for synaptic plasticity. In addition, equilibrium between mRNA processing, protein translation and protein turnover is a critical sensor/trigger for recording synaptic information, normal cognition and behavior. Thus a regulatory switch, controlling the lifespan, maturation and processing of mRNA, might influence cognition and adaptive behavior. Here, we propose a two part novel hypothesis that methylation might act as this suggested coordinating switch to critically regulate mRNA maturation at 1.The pre-transcription level, by regulating precursor-RNA (pre-RNA processing into mRNA, via other non-coding RNAs and their influence on splicing phenomenon, and 2. the post-transcription level by modulating the regulatory functions of ribonucleoproteins (RNP and RNA binding proteins (RNABP in mRNA translation, dendritic translocation as well as protein synthesis and synaptic turnover. DNA methylation changes are well recognized and highly correlated to gene expression levels as well as, learning and memory; however, RNA methylation changes are recently characterized and yet their functional implications are not established. This review article provides some insight on the intriguing consequences of changes in methylation levels on mRNA life-cycle. We also suggest that, since methylation is under the control of glutathione antioxidant levels, the redox status of neurons might be the central regulatory switch for methylation

  12. The Anopheles gambiae cE5, a tight- and fast-binding thrombin inhibitor with post-transcriptionally regulated salivary-restricted expression.

    Science.gov (United States)

    Ronca, Raffaele; Kotsyfakis, Michalis; Lombardo, Fabrizio; Rizzo, Cinzia; Currà, Chiara; Ponzi, Marta; Fiorentino, Gabriella; Ribeiro, Josè M C; Arcà, Bruno

    2012-09-01

    Mosquito saliva carries a large number of factors with anti-hemostatic, anti-inflammatory and immuno-modulatory activities. The cE5 protein was initially identified during an Anopheles gambiae salivary gland transcriptome study and later shown to share sequence similarity with anophelin, a thrombin inhibitor from the saliva of the New World mosquito Anopheles albimanus. The cE5 gene was found to encode different mRNA isoforms coexisting in several tissues of both male and female mosquitoes, a highly unusual profile for a gene potentially encoding an anti-thrombin and involved in blood feeding. Expression of the cE5 protein and assessment of its activity and inhibitory properties showed that it is a highly specific and tight-binding thrombin inhibitor, which differs from the A. albimanus orthologue for the fast-binding kinetics. Despite the widespread occurrence of cE5 transcripts in different mosquito tissues the corresponding protein was only found in female salivary glands, where it undergoes post-translational modification. Therefore, tissue-specific restriction of the A. gambiae cE5 is not achieved by transcriptional control, as common for mosquito salivary genes involved in hematophagy, but by post-trascriptional gene regulatory mechanisms. Our observations provide a paradigm of post-transcriptional regulation as key determinant of tissue specificity for a protein from an important disease vector and point out that transcriptomic data should be interpreted with caution in the absence of concomitant proteomic support. Copyright © 2012 Elsevier Ltd. All rights reserved.

  13. Transient Co-Expression of Post-Transcriptional Gene Silencing Suppressors for Increased in Planta Expression of a Recombinant Anthrax Receptor Fusion Protein

    Directory of Open Access Journals (Sweden)

    Kittipong Rattanaporn

    2011-08-01

    Full Text Available Potential epidemics of infectious diseases and the constant threat of bioterrorism demand rapid, scalable, and cost-efficient manufacturing of therapeutic proteins. Molecular farming of tobacco plants provides an alternative for the recombinant production of therapeutics. We have developed a transient production platform that uses Agrobacterium infiltration of Nicotiana benthamiana plants to express a novel anthrax receptor decoy protein (immunoadhesin, CMG2-Fc. This chimeric fusion protein, designed to protect against the deadly anthrax toxins, is composed of the von Willebrand factor A (VWA domain of human capillary morphogenesis 2 (CMG2, an effective anthrax toxin receptor, and the Fc region of human immunoglobulin G (IgG. We evaluated, in N. benthamiana intact plants and detached leaves, the expression of CMG2-Fc under the control of the constitutive CaMV 35S promoter, and the co-expression of CMG2-Fc with nine different viral suppressors of post-transcriptional gene silencing (PTGS: p1, p10, p19, p21, p24, p25, p38, 2b, and HCPro. Overall, transient CMG2-Fc expression was higher on intact plants than detached leaves. Maximum expression was observed with p1 co-expression at 3.5 days post-infiltration (DPI, with a level of 0.56 g CMG2-Fc per kg of leaf fresh weight and 1.5% of the total soluble protein, a ten-fold increase in expression when compared to absence of suppression. Co-expression with the p25 PTGS suppressor also significantly increased the CMG2-Fc expression level after just 3.5 DPI.

  14. Transient co-expression of post-transcriptional gene silencing suppressors for increased in planta expression of a recombinant anthrax receptor fusion protein.

    Science.gov (United States)

    Arzola, Lucas; Chen, Junxing; Rattanaporn, Kittipong; Maclean, James M; McDonald, Karen A

    2011-01-01

    Potential epidemics of infectious diseases and the constant threat of bioterrorism demand rapid, scalable, and cost-efficient manufacturing of therapeutic proteins. Molecular farming of tobacco plants provides an alternative for the recombinant production of therapeutics. We have developed a transient production platform that uses Agrobacterium infiltration of Nicotiana benthamiana plants to express a novel anthrax receptor decoy protein (immunoadhesin), CMG2-Fc. This chimeric fusion protein, designed to protect against the deadly anthrax toxins, is composed of the von Willebrand factor A (VWA) domain of human capillary morphogenesis 2 (CMG2), an effective anthrax toxin receptor, and the Fc region of human immunoglobulin G (IgG). We evaluated, in N. benthamiana intact plants and detached leaves, the expression of CMG2-Fc under the control of the constitutive CaMV 35S promoter, and the co-expression of CMG2-Fc with nine different viral suppressors of post-transcriptional gene silencing (PTGS): p1, p10, p19, p21, p24, p25, p38, 2b, and HCPro. Overall, transient CMG2-Fc expression was higher on intact plants than detached leaves. Maximum expression was observed with p1 co-expression at 3.5 days post-infiltration (DPI), with a level of 0.56 g CMG2-Fc per kg of leaf fresh weight and 1.5% of the total soluble protein, a ten-fold increase in expression when compared to absence of suppression. Co-expression with the p25 PTGS suppressor also significantly increased the CMG2-Fc expression level after just 3.5 DPI.

  15. Leaf carbohydrates influence transcriptional and post-transcriptional regulation of nocturnal carboxylation and starch degradation in the facultative CAM plant, Mesembryanthemum crystallinum.

    Science.gov (United States)

    Taybi, Tahar; Cushman, John C; Borland, Anne M

    2017-11-01

    Nocturnal degradation of transitory starch is a limiting factor for the optimal function of crassulacean acid metabolism and must be coordinated with phosphoenolypyruvate carboxylase (PEPC)-mediated CO2 uptake to optimise carbon gain over the diel cycle. The aim of this study was to test the hypothesis that nocturnal carboxylation is coordinated with starch degradation in CAM via a mechanism whereby the products of these pathways regulate diel transcript abundance and enzyme activities for both processes. To test this hypothesis, a starch and CAM-deficient mutant of Mesembryanthemum crystallinum was compared with wild type plants under well-watered and saline (CAM-inducing) conditions. Exposure to salinity increased the transcript abundance of genes required for nocturnal carboxylation, starch and sucrose degradation in both wild type and mutant, but the transcript abundance of several of these genes was not sustained over the dark period in the low-carbohydrate, CAM-deficient mutant. The diel pattern of transcript abundance for PEPC mirrored that of PEPC protein, as did the transcripts, protein, and activity of chloroplastic starch phosphorylase in both wild type and mutant, suggesting robust diel coordination of these metabolic processes. Activities of several amylase isoforms were low or lacking in the mutant, whilst the activity of a cytosolic isoform of starch phosphorylase was significantly elevated, indicating contrasting modes of metabolic regulation for the hydrolytic and phosphorylytic routes of starch degradation. Externally supplied sucrose resulted in an increase in nocturnal transcript abundance of genes required for nocturnal carboxylation and starch degradation. These results demonstrate that carbohydrates impact on transcriptional and post-transcriptional regulation of nocturnal carboxylation and starch degradation in CAM. Copyright © 2017 Elsevier GmbH. All rights reserved.

  16. Variations in fault-slip data and cooling history reveal corridor of heterogeneous backarc extension in the eastern Aegean Sea region

    Science.gov (United States)

    Ring, Uwe; Gessner, Klaus; Thomson, Stuart

    2017-03-01

    We report fault-slip data across the boundary between the highly extended and largely submerged crust underlying the Aegean Sea from Samos in the north to eastern Crete in the south, and the much less extended and emergent crust of western Anatolia. We identify three brittle deformation increments, a late Miocene (mainly Pliocene) to Recent crustal stretching increment, an intermittent early to late Miocene shortening increment concurrent with extension and magmatism, and a Miocene extensional event. The youngest increment documents late Miocene to Recent NNE extension over large areas, but can locally also be oriented SE (Amorgos and Astipalea Islands), and ESE (eastern Crete) suggesting overall oblate strain geometry. The intermittent Miocene ( 24-5 Ma) fault-slip records suggest overall prolate strain geometry, where NNE stretching is accompanied by E-W shortening. The older extension event is mainly NNE directed but on Samos Island extension is E-W, probably reflecting local extension in a sinistral wrench corridor in the early/mid Miocene. Overall it seems that since the early Miocene NNE-trending extension is the dominant regime in the eastern Aegean with an intermittent component of short-lived E-W shortening. The existence of a corridor of heterogeneous crustal deformation - which is spatially associated with uncharacteristically old fission track ages - and the apparent change in strain geometry in time challenge concepts that propose that the eastern Aegean Sea and western Anatolia have been deformed as a continuous tectonic domain since the Miocene. We propose that the regional variation in extensional strain geometry resulted from a sinistral wrench component that was superimposed on the regional 'background' NNE extension by translation across a diffuse plate boundary. We conclude that the eastern shoreline of the Aegean Sea is controlled by a Miocene to Recent sinistral wrench corridor that accommodated movement between different lithospheric domains.

  17. LC-MS Proteomics Analysis of the Insulin/IGF-1 Deficient Caenorhabditis elegans daf-2(e1370) Mutant Reveals Extensive Restructuring of Intermediary Metabolism

    Energy Technology Data Exchange (ETDEWEB)

    Depuydt, Geert G.; Xie, Fang; Petyuk, Vladislav A.; Smolders, Arne; Brewer, Heather M.; Camp, David G.; Smith, Richard D.; Braeckman, Bart P.

    2014-02-20

    The insulin/IGF-1 receptor is a major known determinant of dauer formation, stress resistance, longevity and metabolism in C. elegans. In the past, whole-genome transcript profiling was used extensively to study differential gene expression in response to reduced insulin/IGF-1 signaling, including expression levels of metabolism-associated genes. Taking advantage of the recent developments in quantitative liquid chromatography mass-spectrometry (LC-MS) based proteomics, we profiled the proteomic changes that occur in response to activation of the DAF-16 transcription factor in the germline-less glp-4(bn2); daf-2(e1370) receptor mutant. Strikingly, the daf-2 profile suggests extensive reorganization of intermediary metabolism, characterized by the up-regulation of many core intermediary metabolic pathways. These include, glycolysis/gluconeogenesis, glycogenesis, pentose phosphate cycle, citric acid cycle, glyoxylate shunt, fatty acid β-oxidation, one-carbon metabolism, propionate and tyrosine catabolism, and complex I, II, III and V of the electron transport chain. Interestingly, we found simultaneous activation of reciprocally regulated metabolic pathways, which is indicative for spatio-temporal coordination of energy metabolism and/or extensive post-translational regulation of these enzymes. This restructuring of daf-2 metabolism is reminiscent to that of hypometabolic dauers, allowing the efficient and economical utilization of internal nutrient reserves, possibly also shunting metabolites through alternative energy-generating pathways, in order to sustain longevity.

  18. LC–MS Proteomics Analysis of the Insulin/IGF-1-Deficient Caenorhabditis elegans daf-2(e1370) Mutant Reveals Extensive Restructuring of Intermediary Metabolism

    Energy Technology Data Exchange (ETDEWEB)

    Depuydt, Geert; Xie, Fang; Petyuk, Vladislav A.; Smolders, Arne; Brewer, Heather M.; Camp, David G.; Smith, Richard D.; Braeckman, Bart P.

    2014-04-04

    The insulin/IGF-1 receptor is a major known determinant of dauer formation, stress resistance, longevity, and metabolism in Caenorhabditis elegans. In the past, whole-genome transcript profiling was used extensively to study differential gene expression in response to reduced insulin/IGF-1 signaling, including the expression levels of metabolism-associated genes. Taking advantage of the recent developments in quantitative liquid chromatography mass spectrometry (LC–MS)-based proteomics, we profiled the proteomic changes that occur in response to activation of the DAF-16 transcription factor in the germline-less glp-4(bn2);daf-2(e1370) receptor mutant. Strikingly, the daf-2 profile suggests extensive reorganization of intermediary metabolism, characterized by the upregulation of many core intermediary metabolic pathways. These include glycolysis/gluconeogenesis, glycogenesis, pentose phosphate cycle, citric acid cycle, glyoxylate shunt, fatty acid β-oxidation, one-carbon metabolism, propionate and tyrosine catabolism, and complexes I, II, III, and V of the electron transport chain. Interestingly, we found simultaneous activation of reciprocally regulated metabolic pathways, which is indicative of spatiotemporal coordination of energy metabolism and/or extensive post-translational regulation of these enzymes. Finally, this restructuring of daf-2 metabolism is reminiscent to that of hypometabolic dauers, allowing the efficient and economical utilization of internal nutrient reserves and possibly also shunting metabolites through alternative energy-generating pathways to sustain longevity.

  19. Creep, flow, and phase slippage regimes: an extensive view of the sliding charge-density wave revealed by coherent X-ray diffraction.

    Science.gov (United States)

    Pinsolle, E; Kirova, N; Jacques, V L R; Sinchenko, A A; Le Bolloc'h, D

    2012-12-21

    Coherent x-ray diffraction experiments have been used to probe the dynamics of the charge density wave (CDW) in the quasi-1D system NbSe(3). The 2k(F) satellite reflection associated with the CDW has been measured with respect to external dc currents, below and above the depinning current. These measurements illustrate for the first time the extensive behavior of a moving electronic crystal: the creep regime, with nucleation of CDW dislocations, the flow regime, with motional ordering, along with phase slippage and the role of strong pinning due to an extrinsic defect.

  20. Collision of extensive exocrine and neuroendocrine neoplasms in multiple endocrine neoplasia type 1 revealed by cytogenetic analysis of loss of heterozygosity: a case report.

    Science.gov (United States)

    Moriyoshi, Koki; Minamiguchi, Sachiko; Miyagawa-Hayashino, Aya; Fujimoto, Masakazu; Kawaguchi, Michiya; Haga, Hironori

    2013-09-01

    The combination of exocrine and neuroendocrine neoplasms is rarely found in the pancreas. These combined lesions vary from a clonal tumor with mixed differentiation to the incidental co-existence of two or more independent tumors, but the differential diagnosis is sometimes difficult. Here we report a case of multiple endocrine neoplasia type 1 (MEN1) with extensive ductal and neuroendocrine neoplastic changes. These two types of tumors admixed markedly in some parts, which made it difficult to determine the pathological diagnosis based on histological findings. Cytogenetic analysis showed that loss of heterozygosity (LOH) of the MEN1 locus exists in neuroendocrine but not in exocrine neoplasms, indicating that independent mechanisms of tumorigenesis may occur in these two types of tumors. This case shows the usefulness of cytogenetic analysis for the diagnosis of combined tumors of the pancreas. Extensive exocrine neoplastic change, including pancreatic intraepithelial neoplasia (PanIN) in virtually all pancreatic ducts and a focus of intraductal papillary mucinous neoplasm (IPMN) with focal invasion, was a distinguishing feature of the present case. The possible association of ductal tumorigenesis and a MEN1 background is discussed. © 2013 The Authors. Pathology International © 2013 Japanese Society of Pathology and Wiley Publishing Asia Pty Ltd.

  1. Quantitative 1H NMR metabolomics reveals extensive metabolic reprogramming of primary and secondary metabolism in elicitor-treated opium poppy cell cultures

    Directory of Open Access Journals (Sweden)

    Vogel Hans J

    2008-01-01

    Full Text Available Abstract Background Opium poppy (Papaver somniferum produces a diverse array of bioactive benzylisoquinoline alkaloids and has emerged as a model system to study plant alkaloid metabolism. The plant is cultivated as the only commercial source of the narcotic analgesics morphine and codeine, but also produces many other alkaloids including the antimicrobial agent sanguinarine. Modulations in plant secondary metabolism as a result of environmental perturbations are often associated with the altered regulation of other metabolic pathways. As a key component of our functional genomics platform for opium poppy we have used proton nuclear magnetic resonance (1H NMR metabolomics to investigate the interplay between primary and secondary metabolism in cultured opium poppy cells treated with a fungal elicitor. Results Metabolite fingerprinting and compound-specific profiling showed the extensive reprogramming of primary metabolic pathways in association with the induction of alkaloid biosynthesis in response to elicitor treatment. Using Chenomx NMR Suite v. 4.6, a software package capable of identifying and quantifying individual compounds based on their respective signature spectra, the levels of 42 diverse metabolites were monitored over a 100-hour time course in control and elicitor-treated opium poppy cell cultures. Overall, detectable and dynamic changes in the metabolome of elicitor-treated cells, especially in cellular pools of carbohydrates, organic acids and non-protein amino acids were detected within 5 hours after elicitor treatment. The metabolome of control cultures also showed substantial modulations 80 hours after the start of the time course, particularly in the levels of amino acids and phospholipid pathway intermediates. Specific flux modulations were detected throughout primary metabolism, including glycolysis, the tricarboxylic acid cycle, nitrogen assimilation, phospholipid/fatty acid synthesis and the shikimate pathway, all of which

  2. A rapid, high-throughput viability assay for Blastocystis spp. reveals metronidazole resistance and extensive subtype-dependent variations in drug susceptibilities.

    Science.gov (United States)

    Mirza, Haris; Teo, Joshua D W; Upcroft, Jacqui; Tan, Kevin S W

    2011-02-01

    Blastocystis is an emerging protistan parasite of controversial pathogenesis. Although metronidazole (Mz) is standard therapy for Blastocystis infections, there have been accumulating reports of treatment failure, suggesting the existence of drug-resistant isolates. Furthermore, very little is known about Blastocystis susceptibility to standard antimicrobials. In the present study, we established resazurin and XTT viability microassays for Blastocystis spp. belonging to subtypes 4 and 7, both of which have been suggested to represent pathogenic zoonotic subtypes. The optimized resazurin assay was used to screen a total of 19 compounds against both subtypes. Interestingly, subtype 7 parasites were resistant to Mz, a 1-position-substituted 5-nitroimidazole (5-NI), while subtype 4 parasites were sensitive. Some cross-resistance was observed to tinidazole, another 1-position 5-NI. Conversely, subtype 4 parasites were resistant to emetine, while subtype 7 parasites were sensitive. Position 2 5-NIs were effective against both subtypes, as were ornidazole, nitazoxanide, furazolidone, mefloquine, quinicrine, quinine, cotrimoxazole (trimethoprim-sulfamethoxazole), and iodoacetamide. Both subtypes were resistant to chloroquine, doxycycline, paromomycin, ampicillin, and pyrimethamine. This is the first study to report extensive variations in drug sensitivities among two clinically important subtypes. Our study highlights the need to reevaluate established treatment regimens for Blastocystis infections and offers clear new treatment options for Mz treatment failures.

  3. Systematic examination of publicly-available information reveals the diverse and extensive corporate political activity of the food industry in Australia.

    Science.gov (United States)

    Mialon, Melissa; Swinburn, Boyd; Allender, Steven; Sacks, Gary

    2016-03-22

    The political influence of the food industry, referred to as corporate political activity (CPA), represents a potential barrier to the development and implementation of effective public health policies for non-communicable diseases prevention. This paper reports on the feasibility and limitations of using publicly-available information to identify and monitor the CPA of the food industry in Australia. A systematic search was conducted for information from food industry, government and other publicly-available data sources in Australia. Data was collected in relation to five key food industry actors: the Australian Food and Grocery Council; Coca Cola; McDonald's; Nestle; and Woolworths, for the period January 2012 to February 2015. Data analysis was guided by an existing framework for classifying CPA strategies of the food industry. The selected food industry actors used multiple CPA strategies, with 'information and messaging' and 'constituency building' strategies most prominent. The systematic analysis of publicly-available information over a limited period was able to identify diverse and extensive CPA strategies of the food industry in Australia. This approach can contribute to accountability mechanisms for NCD prevention.

  4. Systematic examination of publicly-available information reveals the diverse and extensive corporate political activity of the food industry in Australia

    Directory of Open Access Journals (Sweden)

    Melissa Mialon

    2016-03-01

    Full Text Available Abstract Background The political influence of the food industry, referred to as corporate political activity (CPA, represents a potential barrier to the development and implementation of effective public health policies for non-communicable diseases prevention. This paper reports on the feasibility and limitations of using publicly-available information to identify and monitor the CPA of the food industry in Australia. Methods A systematic search was conducted for information from food industry, government and other publicly-available data sources in Australia. Data was collected in relation to five key food industry actors: the Australian Food and Grocery Council; Coca Cola; McDonald’s; Nestle; and Woolworths, for the period January 2012 to February 2015. Data analysis was guided by an existing framework for classifying CPA strategies of the food industry. Results The selected food industry actors used multiple CPA strategies, with ‘information and messaging’ and ‘constituency building’ strategies most prominent. Conclusions The systematic analysis of publicly-available information over a limited period was able to identify diverse and extensive CPA strategies of the food industry in Australia. This approach can contribute to accountability mechanisms for NCD prevention.

  5. Characterization of genomic variations in SNPs of PE_PGRS genes reveals deletions and insertions in extensively drug resistant (XDR) M. tuberculosis strains from Pakistan

    KAUST Repository

    Kanji, Akbar

    2015-03-01

    Background: Mycobacterium tuberculosis (MTB) PE_PGRS genes belong to the PE multi-gene family. Although the function of the members of the PE_PGRS multi-gene family is not yet known, it is hypothesized that the PE_PGRS genes may be associated with genetic variability. Material and methods: Whole genome sequencing analysis was performed on (n= 37) extensively drug resistant (XDR) MTB strains from Pakistan which included Central Asian (n= 23), East African Indian (n= 2), X3 (n= 1), T group (n= 3) and Orphan (n= 8) MTB strains. Results: By analyzing 42 PE_PGRS genes, 111 SNPs were identified, of which 13 were non-synonymous SNPs (nsSNPs). The nsSNPs identified in the PE_PGRS genes were as follows: 6, 9, 10 and 55 present in each of the CAS, EAI, Orphan, T1 and X3 XDR MTB strains studied. Deletions in PE_PGRS genes: 19, 21 and 23 were observed in 7 (35.0%) CAS1 and 3 (37.5%) in Orphan XDR MTB strains, while deletions in the PE_PGRS genes: 49 and 50 were observed in 36 (95.0%) CAS1 and all CAS, CAS2 and Orphan XDR MTB strains. An insertion in PE_PGRS6 gene was observed in all CAS, EAI3 and Orphan, while insertions in the PE_PGRS genes 19 and 33 were observed in 19 (95%) CAS1 and all CAS, CAS2, EAI3 and Orphan XDR MTB strains. Conclusion: Genetic diversity in PE_PGRS genes contributes to antigenic variability and may result in increased immunogenicity of strains. This is the first study identifying variations in nsSNPs, Insertions and Deletions in the PE_PGRS genes of XDR-TB strains from Pakistan. It highlights common genetic variations which may contribute to persistence.

  6. Characterization of genomic variations in SNPs of PE_PGRS genes reveals deletions and insertions in extensively drug resistant (XDR) M. tuberculosis strains from Pakistan

    KAUST Repository

    Kanji, Akbar

    2015-01-21

    Background Mycobacterium tuberculosis (MTB) PE_PGRS genes belong to the PE multigene family. Although the function of PE_PGRS genes is unknown, it is hypothesized that the PE_PGRS genes may be associated with antigenic variability in MTB. Material and methods Whole genome sequencing analysis was performed on (n = 37) extensively drug-resistant (XDR) MTB strains from Pakistan, which included Lineage 1 (East African Indian, n = 2); Other lineage 1 (n = 3); Lineage 3 (Central Asian, n = 24); Other lineage 3 (n = 4); Lineage 4 (X3, n = 1) and T group (n = 3) MTB strains. Results There were 107 SNPs identified from the analysis of 42 PE_PGRS genes; of these, 13 were non-synonymous SNPs (nsSNPs). The nsSNPs identified in PE_PGRS genes – 6, 9 and 10 – were common in all EAI, CAS, Other lineages (1 and 3), T1 and X3. Deletions (DELs) in PE_PGRS genes – 3 and 19 – were observed in 17 (80.9%) CAS1 and 6 (85.7%) in Other lineages (1 and 3) XDR MTB strains, while DELs in the PE_PGRS49 were observed in all CAS1, CAS, CAS2 and Other lineages (1 and 3) XDR MTB strains. All CAS, EAI and Other lineages (1 and 3) strains showed insertions (INS) in PE_PGRS6 gene, while INS in the PE_PGRS genes 19 and 33 were observed in 20 (95.2%) CAS1, all CAS, CAS2, EAI and Other lineages (1 and 3) XDR MTB strains. Conclusion Genetic diversity in PE_PGRS genes contributes to antigenic variability and may result in increased immunogenicity of strains. This is the first study identifying variations in nsSNPs and INDELs in the PE_PGRS genes of XDR-TB strains from Pakistan. It highlights common genetic variations which may contribute to persistence.

  7. SRC Homology 2 Domain Binding Sites in Insulin, IGF-1 and FGF receptor mediated signaling networks reveal an extensive potential interactome

    Directory of Open Access Journals (Sweden)

    Liu Bernard A

    2012-09-01

    Full Text Available Abstract Specific peptide ligand recognition by modular interaction domains is essential for the fidelity of information flow through the signal transduction networks that control cell behavior in response to extrinsic and intrinsic stimuli. Src homology 2 (SH2 domains recognize distinct phosphotyrosine peptide motifs, but the specific sites that are phosphorylated and the complement of available SH2 domains varies considerably in individual cell types. Such differences are the basis for a wide range of available protein interaction microstates from which signaling can evolve in highly divergent ways. This underlying complexity suggests the need to broadly map the signaling potential of systems as a prerequisite for understanding signaling in specific cell types as well as various pathologies that involve signal transduction such as cancer, developmental defects and metabolic disorders. This report describes interactions between SH2 domains and potential binding partners that comprise initial signaling downstream of activated fibroblast growth factor (FGF, insulin (Ins, and insulin-like growth factor-1 (IGF-1 receptors. A panel of 50 SH2 domains screened against a set of 192 phosphotyrosine peptides defines an extensive potential interactome while demonstrating the selectivity of individual SH2 domains. The interactions described confirm virtually all previously reported associations while describing a large set of potential novel interactions that imply additional complexity in the signaling networks initiated from activated receptors. This study of pTyr ligand binding by SH2 domains provides valuable insight into the selectivity that underpins complex signaling networks that are assembled using modular protein interaction domains.

  8. Genome-wide expression profile of the response to spinal cord injury in Xenopus laevis reveals extensive differences between regenerative and non-regenerative stages

    Science.gov (United States)

    2014-01-01

    Background Xenopus laevis has regenerative and non-regenerative stages. As a tadpole, it is fully capable of functional recovery after a spinal cord injury, while its juvenile form (froglet) loses this capability during metamorphosis. We envision that comparative studies between regenerative and non-regenerative stages in Xenopus could aid in understanding why spinal cord regeneration fails in human beings. Results To identify the mechanisms that allow the tadpole to regenerate and inhibit regeneration in the froglet, we obtained a transcriptome-wide profile of the response to spinal cord injury in Xenopus regenerative and non-regenerative stages. We found extensive transcriptome changes in regenerative tadpoles at 1 day after injury, while this was only observed by 6 days after injury in non-regenerative froglets. In addition, when comparing both stages, we found that they deployed a very different repertoire of transcripts, with more than 80% of them regulated in only one stage, including previously unannotated transcripts. This was supported by gene ontology enrichment analysis and validated by RT-qPCR, which showed that transcripts involved in metabolism, response to stress, cell cycle, development, immune response and inflammation, neurogenesis, and axonal regeneration were regulated differentially between regenerative and non-regenerative stages. Conclusions We identified differences in the timing of the transcriptional response and in the inventory of regulated transcripts and biological processes activated in response to spinal cord injury when comparing regenerative and non-regenerative stages. These genes and biological processes provide an entry point to understand why regeneration fails in mammals. Furthermore, our results introduce Xenopus laevis as a genetic model organism to study spinal cord regeneration. PMID:24885550

  9. Evolution of extensively drug-resistant tuberculosis over four decades revealed by whole genome sequencing of Mycobacterium tuberculosis from KwaZulu-Natal, South Africa

    Directory of Open Access Journals (Sweden)

    Keira A Cohen

    2015-01-01

    Full Text Available The largest global outbreak of extensively drug-resistant (XDR tuberculosis (TB was identified in Tugela Ferry, KwaZulu-Natal (KZN, South Africa in 2005. The antecedents and timing of the emergence of drug resistance in this fatal epidemic XDR outbreak are unknown, and it is unclear whether drug resistance in this region continues to be driven by clonal spread or by the development of de novo resistance. A whole genome sequencing and drug susceptibility testing (DST was performed on 337 clinical isolates of Mycobacterium tuberculosis (M.tb collected in KZN from 2008 to 2013, in addition to three historical isolates, one of which was isolated during the Tugela Ferry outbreak. Using a variety of whole genome comparative approaches, 11 drug-resistant clones of M.tb circulating from 2008 to 2013 were identified, including a 50-member clone of XDR M.tb that was highly related to the Tugela Ferry XDR outbreak strain. It was calculated that the evolutionary trajectory from first-line drug resistance to XDR in this clone spanned more than four decades and began at the start of the antibiotic era. It was also observed that frequent de novo evolution of MDR and XDR was present, with 56 and 9 independent evolutions, respectively. Thus, ongoing amplification of drug-resistance in KwaZulu-Natal is driven by both clonal spread and de novo acquisition of resistance. In drug-resistant TB, isoniazid resistance was overwhelmingly the initial resistance mutation to be acquired, which would not be detected by current rapid molecular diagnostics that assess only rifampicin resistance.

  10. Genome-Wide Profiling of Liver X Receptor, Retinoid X Receptor, and Peroxisome Proliferator-Activated Receptor α in Mouse Liver Reveals Extensive Sharing of Binding Sites

    DEFF Research Database (Denmark)

    Boergesen, Michael; Pedersen, Thomas Åskov; Gross, Barbara

    2012-01-01

    The liver X receptors (LXRs) are nuclear receptors that form permissive heterodimers with retinoid X receptor (RXR) and are important regulators of lipid metabolism in the liver. We have recently shown that RXR agonist-induced hypertriglyceridemia and hepatic steatosis in mice are dependent on LXRs...... and correlate with an LXR-dependent hepatic induction of lipogenic genes. To further investigate the roles of RXR and LXR in the regulation of hepatic gene expression, we have mapped the ligand-regulated genome-wide binding of these factors in mouse liver. We find that the RXR agonist bexarotene primarily...... increases the genomic binding of RXR, whereas the LXR agonist T0901317 greatly increases both LXR and RXR binding. Functional annotation of putative direct LXR target genes revealed a significant association with classical LXR-regulated pathways as well as peroxisome proliferator-activated receptor (PPAR...

  11. Evolution of RLSB, a nuclear-encoded S1 domain RNA binding protein associated with post-transcriptional regulation of plastid-encoded rbcL mRNA in vascular plants.

    Science.gov (United States)

    Yerramsetty, Pradeep; Stata, Matt; Siford, Rebecca; Sage, Tammy L; Sage, Rowan F; Wong, Gane Ka-Shu; Albert, Victor A; Berry, James O

    2016-06-29

    RLSB, an S-1 domain RNA binding protein of Arabidopsis, selectively binds rbcL mRNA and co-localizes with Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) within chloroplasts of C3 and C4 plants. Previous studies using both Arabidopsis (C3) and maize (C4) suggest RLSB homologs are post-transcriptional regulators of plastid-encoded rbcL mRNA. While RLSB accumulates in all Arabidopsis leaf chlorenchyma cells, in C4 leaves RLSB-like proteins accumulate only within Rubisco-containing bundle sheath chloroplasts of Kranz-type species, and only within central compartment chloroplasts in the single cell C4 plant Bienertia. Our recent evidence implicates this mRNA binding protein as a primary determinant of rbcL expression, cellular localization/compartmentalization, and photosynthetic function in all multicellular green plants. This study addresses the hypothesis that RLSB is a highly conserved Rubisco regulatory factor that occurs in the chloroplasts all higher plants. Phylogenetic analysis has identified RLSB orthologs and paralogs in all major plant groups, from ancient liverworts to recent angiosperms. RLSB homologs were also identified in algae of the division Charophyta, a lineage closely related to land plants. RLSB-like sequences were not identified in any other algae, suggesting that it may be specific to the evolutionary line leading to land plants. The RLSB family occurs in single copy across most angiosperms, although a few species with two copies were identified, seemingly randomly distributed throughout the various taxa, although perhaps correlating in some cases with known ancient whole genome duplications. Monocots of the order Poales (Poaceae and Cyperaceae) were found to contain two copies, designated here as RLSB-a and RLSB-b, with only RLSB-a implicated in the regulation of rbcL across the maize developmental gradient. Analysis of microsynteny in angiosperms revealed high levels of conservation across eudicot species and for both paralogs in

  12. Deep-sequencing of Marburg virus genome during sequential mouse passaging and cell-culture adaptation reveals extensive changes over time.

    Science.gov (United States)

    Wei, Haiyan; Audet, Jonathan; Wong, Gary; He, Shihua; Huang, Xueyong; Cutts, Todd; Theriault, Steven; Xu, Bianli; Kobinger, Gary; Qiu, Xiangguo

    2017-06-13

    Marburg virus (MARV) has caused outbreaks of filoviral hemorrhagic fever since its discovery in 1967. The largest and deadliest outbreak occurred in Angola in 2005, with 252 cases and 227 deaths. In 2014, we developed a mouse-adapted MARV, Angola variant through serial passaging in mice. The mouse-adapted MARV exhibits many of the hallmarks of MARV disease in humans. By applying deep-sequencing to every passage of the virus, we are able to study virus evolution in this host with surprising precision. We show that two regions go through substantial changes: the intergenic region between NP and VP35, as well as the first 100 amino acids of the VP40 protein. Our results also reveal that there were profound changes during the production of the final virus stock in cell culture. Overall, our results show that a handful of regions carry most of the mutations acquired during the adaptation of the virus to a new host and that many mutations become fixed very early during the adaptation process.

  13. Evolutionary inferences based on ITS rDNA and actin sequences reveal extensive diversity of the common lichen alga Asterochloris (Trebouxiophyceae, Chlorophyta).

    Science.gov (United States)

    Skaloud, Pavel; Peksa, Ondrej

    2010-01-01

    The genus Asterochloris is one of the most common lichen photobionts. We present a molecular investigation of 41 cultured strains, for which nuclear-encoded ITS rDNA and partial actin I sequences were determined. The loci studied revealed considerable differences in their evolutionary dynamics as well as sequence variation. As compared to ITS data, the actin sequences show much greater variation, and the phylogenies yield strong resolution and support of many internal branches. The partitioning of ITS dataset into several regions yielded better node resolution. We recognized 16 well-supported monophyletic lineages, of which one represents the type species of the genus (Asterochloris phycobiontica), and six correspond to species previously classified to the genus Trebouxia (T. erici, T. excentrica, T. glomerata, T. irregularis, T. italiana and T. magna). Only 15% of isolated photobionts considered in our study could be assigned with certainty to previously described species, emphasizing amazing cryptic variability in Asterochloris. Concurrently with the formal delimitation of the genus Asterochloris, we propose new combinations for the former Trebouxia species; furthermore, T. pyriformis is reduced to a synonym of A. glomerata. The present knowledge of global diversity of Asterochloris algae is discussed.

  14. Extensive sampling of polar bears (Ursus maritimus) in the Northwest Passage (Canadian Arctic Archipelago) reveals population differentiation across multiple spatial and temporal scales

    Science.gov (United States)

    Campagna, Leonardo; Van Coeverden de Groot, Peter J; Saunders, Brenda L; Atkinson, Stephen N; Weber, Diana S; Dyck, Markus G; Boag, Peter T; Lougheed, Stephen C

    2013-01-01

    As global warming accelerates the melting of Arctic sea ice, polar bears (Ursus maritimus) must adapt to a rapidly changing landscape. This process will necessarily alter the species distribution together with population dynamics and structure. Detailed knowledge of these changes is crucial to delineating conservation priorities. Here, we sampled 361 polar bears from across the center of the Canadian Arctic Archipelago spanning the Gulf of Boothia (GB) and M'Clintock Channel (MC). We use DNA microsatellites and mitochondrial control region sequences to quantify genetic differentiation, estimate gene flow, and infer population history. Two populations, roughly coincident with GB and MC, are significantly differentiated at both nuclear (FST = 0.01) and mitochondrial (ΦST = 0.47; FST = 0.29) loci, allowing Bayesian clustering analyses to assign individuals to either group. Our data imply that the causes of the mitochondrial and nuclear genetic patterns differ. Analysis of mtDNA reveals the matrilineal structure dates at least to the Holocene, and is common to individuals throughout the species’ range. These mtDNA differences probably reflect both genetic drift and historical colonization dynamics. In contrast, the differentiation inferred from microsatellites is only on the scale of hundreds of years, possibly reflecting contemporary impediments to gene flow. Taken together, our data suggest that gene flow is insufficient to homogenize the GB and MC populations and support the designation of GB and MC as separate polar bear conservation units. Our study also provide a striking example of how nuclear DNA and mtDNA capture different aspects of a species demographic history. PMID:24102001

  15. Comparative genomics study of polyhydroxyalkanoates (PHA) and ectoine relevant genes from Halomonas sp. TD01 revealed extensive horizontal gene transfer events and co-evolutionary relationships.

    Science.gov (United States)

    Cai, Lei; Tan, Dan; Aibaidula, Gulsimay; Dong, Xin-Ran; Chen, Jin-Chun; Tian, Wei-Dong; Chen, Guo-Qiang

    2011-11-01

    Halophilic bacteria have shown their significance in industrial production of polyhydroxyalkanoates (PHA) and are gaining more attention for genetic engineering modification. Yet, little information on the genomics and PHA related genes from halophilic bacteria have been disclosed so far. The draft genome of moderately halophilic bacterium, Halomonas sp. TD01, a strain of great potential for industrial production of short-chain-length polyhydroxyalkanoates (PHA), was analyzed through computational methods to reveal the osmoregulation mechanism and the evolutionary relationship of the enzymes relevant to PHA and ectoine syntheses. Genes involved in the metabolism of PHA and osmolytes were annotated and studied in silico. Although PHA synthase, depolymerase, regulator/repressor and phasin were all involved in PHA metabolic pathways, they demonstrated different horizontal gene transfer (HGT) events between the genomes of different strains. In contrast, co-occurrence of ectoine genes in the same genome was more frequently observed, and ectoine genes were more likely under coincidental horizontal gene transfer than PHA related genes. In addition, the adjacent organization of the homologues of PHA synthase phaC1 and PHA granule binding protein phaP was conserved in the strain TD01, which was also observed in some halophiles and non-halophiles exclusively from γ-proteobacteria. In contrast to haloarchaea, the proteome of Halomonas sp. TD01 did not show obvious inclination towards acidity relative to non-halophilic Escherichia coli MG1655, which signified that Halomonas sp. TD01 preferred the accumulation of organic osmolytes to ions in order to balance the intracellular osmotic pressure with the environment. The accessibility of genome information would facilitate research on the genetic engineering of halophilic bacteria including Halomonas sp. TD01.

  16. Extensive sampling of polar bears (Ursus maritimus) in the Northwest Passage (Canadian Arctic Archipelago) reveals population differentiation across multiple spatial and temporal scales.

    Science.gov (United States)

    Campagna, Leonardo; Van Coeverden de Groot, Peter J; Saunders, Brenda L; Atkinson, Stephen N; Weber, Diana S; Dyck, Markus G; Boag, Peter T; Lougheed, Stephen C

    2013-09-01

    As global warming accelerates the melting of Arctic sea ice, polar bears (Ursus maritimus) must adapt to a rapidly changing landscape. This process will necessarily alter the species distribution together with population dynamics and structure. Detailed knowledge of these changes is crucial to delineating conservation priorities. Here, we sampled 361 polar bears from across the center of the Canadian Arctic Archipelago spanning the Gulf of Boothia (GB) and M'Clintock Channel (MC). We use DNA microsatellites and mitochondrial control region sequences to quantify genetic differentiation, estimate gene flow, and infer population history. Two populations, roughly coincident with GB and MC, are significantly differentiated at both nuclear (F ST = 0.01) and mitochondrial (ΦST = 0.47; F ST = 0.29) loci, allowing Bayesian clustering analyses to assign individuals to either group. Our data imply that the causes of the mitochondrial and nuclear genetic patterns differ. Analysis of mtDNA reveals the matrilineal structure dates at least to the Holocene, and is common to individuals throughout the species' range. These mtDNA differences probably reflect both genetic drift and historical colonization dynamics. In contrast, the differentiation inferred from microsatellites is only on the scale of hundreds of years, possibly reflecting contemporary impediments to gene flow. Taken together, our data suggest that gene flow is insufficient to homogenize the GB and MC populations and support the designation of GB and MC as separate polar bear conservation units. Our study also provide a striking example of how nuclear DNA and mtDNA capture different aspects of a species demographic history.

  17. Scanning the landscape of genome architecture of non-O1 and non-O139 Vibrio cholerae by whole genome mapping reveals extensive population genetic diversity.

    Science.gov (United States)

    Chapman, Carol; Henry, Matthew; Bishop-Lilly, Kimberly A; Awosika, Joy; Briska, Adam; Ptashkin, Ryan N; Wagner, Trevor; Rajanna, Chythanya; Tsang, Hsinyi; Johnson, Shannon L; Mokashi, Vishwesh P; Chain, Patrick S G; Sozhamannan, Shanmuga

    2015-01-01

    Historically, cholera outbreaks have been linked to V. cholerae O1 serogroup strains or its derivatives of the O37 and O139 serogroups. A genomic study on the 2010 Haiti cholera outbreak strains highlighted the putative role of non O1/non-O139 V. cholerae in causing cholera and the lack of genomic sequences of such strains from around the world. Here we address these gaps by scanning a global collection of V. cholerae strains as a first step towards understanding the population genetic diversity and epidemic potential of non O1/non-O139 strains. Whole Genome Mapping (Optical Mapping) based bar coding produces a high resolution, ordered restriction map, depicting a complete view of the unique chromosomal architecture of an organism. To assess the genomic diversity of non-O1/non-O139 V. cholerae, we applied a Whole Genome Mapping strategy on a well-defined and geographically and temporally diverse strain collection, the Sakazaki serogroup type strains. Whole Genome Map data on 91 of the 206 serogroup type strains support the hypothesis that V. cholerae has an unprecedented genetic and genomic structural diversity. Interestingly, we discovered chromosomal fusions in two unusual strains that possess a single chromosome instead of the two chromosomes usually found in V. cholerae. We also found pervasive chromosomal rearrangements such as duplications and indels in many strains. The majority of Vibrio genome sequences currently in public databases are unfinished draft sequences. The Whole Genome Mapping approach presented here enables rapid screening of large strain collections to capture genomic complexities that would not have been otherwise revealed by unfinished draft genome sequencing and thus aids in assembling and finishing draft sequences of complex genomes. Furthermore, Whole Genome Mapping allows for prediction of novel V. cholerae non-O1/non-O139 strains that may have the potential to cause future cholera outbreaks.

  18. Comparative genomics study of polyhydroxyalkanoates (PHA and ectoine relevant genes from Halomonas sp. TD01 revealed extensive horizontal gene transfer events and co-evolutionary relationships

    Directory of Open Access Journals (Sweden)

    Cai Lei

    2011-11-01

    Full Text Available Abstract Background Halophilic bacteria have shown their significance in industrial production of polyhydroxyalkanoates (PHA and are gaining more attention for genetic engineering modification. Yet, little information on the genomics and PHA related genes from halophilic bacteria have been disclosed so far. Results The draft genome of moderately halophilic bacterium, Halomonas sp. TD01, a strain of great potential for industrial production of short-chain-length polyhydroxyalkanoates (PHA, was analyzed through computational methods to reveal the osmoregulation mechanism and the evolutionary relationship of the enzymes relevant to PHA and ectoine syntheses. Genes involved in the metabolism of PHA and osmolytes were annotated and studied in silico. Although PHA synthase, depolymerase, regulator/repressor and phasin were all involved in PHA metabolic pathways, they demonstrated different horizontal gene transfer (HGT events between the genomes of different strains. In contrast, co-occurrence of ectoine genes in the same genome was more frequently observed, and ectoine genes were more likely under coincidental horizontal gene transfer than PHA related genes. In addition, the adjacent organization of the homologues of PHA synthase phaC1 and PHA granule binding protein phaP was conserved in the strain TD01, which was also observed in some halophiles and non-halophiles exclusively from γ-proteobacteria. In contrast to haloarchaea, the proteome of Halomonas sp. TD01 did not show obvious inclination towards acidity relative to non-halophilic Escherichia coli MG1655, which signified that Halomonas sp. TD01 preferred the accumulation of organic osmolytes to ions in order to balance the intracellular osmotic pressure with the environment. Conclusions The accessibility of genome information would facilitate research on the genetic engineering of halophilic bacteria including Halomonas sp. TD01.

  19. Global analysis of estrogen receptor beta binding to breast cancer cell genome reveals an extensive interplay with estrogen receptor alpha for target gene regulation.

    Science.gov (United States)

    Grober, Oli M V; Mutarelli, Margherita; Giurato, Giorgio; Ravo, Maria; Cicatiello, Luigi; De Filippo, Maria Rosaria; Ferraro, Lorenzo; Nassa, Giovanni; Papa, Maria Francesca; Paris, Ornella; Tarallo, Roberta; Luo, Shujun; Schroth, Gary P; Benes, Vladimir; Weisz, Alessandro

    2011-01-14

    Estrogen receptors alpha (ERα) and beta (ERβ) are transcription factors (TFs) that mediate estrogen signaling and define the hormone-responsive phenotype of breast cancer (BC). The two receptors can be found co-expressed and play specific, often opposite, roles, with ERβ being able to modulate the effects of ERα on gene transcription and cell proliferation. ERβ is frequently lost in BC, where its presence generally correlates with a better prognosis of the disease. The identification of the genomic targets of ERβ in hormone-responsive BC cells is thus a critical step to elucidate the roles of this receptor in estrogen signaling and tumor cell biology. Expression of full-length ERβ in hormone-responsive, ERα-positive MCF-7 cells resulted in a marked reduction in cell proliferation in response to estrogen and marked effects on the cell transcriptome. By ChIP-Seq we identified 9702 ERβ and 6024 ERα binding sites in estrogen-stimulated cells, comprising sites occupied by either ERβ, ERα or both ER subtypes. A search for TF binding matrices revealed that the majority of the binding sites identified comprise one or more Estrogen Response Element and the remaining show binding matrixes for other TFs known to mediate ER interaction with chromatin by tethering, including AP2, E2F and SP1. Of 921 genes differentially regulated by estrogen in ERβ+ vs ERβ- cells, 424 showed one or more ERβ site within 10 kb. These putative primary ERβ target genes control cell proliferation, death, differentiation, motility and adhesion, signal transduction and transcription, key cellular processes that might explain the biological and clinical phenotype of tumors expressing this ER subtype. ERβ binding in close proximity of several miRNA genes and in the mitochondrial genome, suggests the possible involvement of this receptor in small non-coding RNA biogenesis and mitochondrial genome functions. Results indicate that the vast majority of the genomic targets of ERβ can bind

  20. Global analysis of estrogen receptor beta binding to breast cancer cell genome reveals an extensive interplay with estrogen receptor alpha for target gene regulation

    Directory of Open Access Journals (Sweden)

    Papa Maria

    2011-01-01

    Full Text Available Abstract Background Estrogen receptors alpha (ERα and beta (ERβ are transcription factors (TFs that mediate estrogen signaling and define the hormone-responsive phenotype of breast cancer (BC. The two receptors can be found co-expressed and play specific, often opposite, roles, with ERβ being able to modulate the effects of ERα on gene transcription and cell proliferation. ERβ is frequently lost in BC, where its presence generally correlates with a better prognosis of the disease. The identification of the genomic targets of ERβ in hormone-responsive BC cells is thus a critical step to elucidate the roles of this receptor in estrogen signaling and tumor cell biology. Results Expression of full-length ERβ in hormone-responsive, ERα-positive MCF-7 cells resulted in a marked reduction in cell proliferation in response to estrogen and marked effects on the cell transcriptome. By ChIP-Seq we identified 9702 ERβ and 6024 ERα binding sites in estrogen-stimulated cells, comprising sites occupied by either ERβ, ERα or both ER subtypes. A search for TF binding matrices revealed that the majority of the binding sites identified comprise one or more Estrogen Response Element and the remaining show binding matrixes for other TFs known to mediate ER interaction with chromatin by tethering, including AP2, E2F and SP1. Of 921 genes differentially regulated by estrogen in ERβ+ vs ERβ- cells, 424 showed one or more ERβ site within 10 kb. These putative primary ERβ target genes control cell proliferation, death, differentiation, motility and adhesion, signal transduction and transcription, key cellular processes that might explain the biological and clinical phenotype of tumors expressing this ER subtype. ERβ binding in close proximity of several miRNA genes and in the mitochondrial genome, suggests the possible involvement of this receptor in small non-coding RNA biogenesis and mitochondrial genome functions. Conclusions Results indicate that the

  1. Post-transcriptional control of chloroplast gene expression. Accumulation of stable psaC mRNA is due to downstream RNA cleavages in the ndhD gene.

    Science.gov (United States)

    Del Campo, Eva M; Sabater, Bartolomé; Martín, Mercedes

    2002-09-27

    Intergenic cleavages, intron splicing, and editing of primary transcripts of the plastid ndhH-D operon produce multiple overlapping RNAs, of which the most abundant by far is the monocistronic 400-nucleotide mRNA of psaC (encoding the PsaC protein of photosystem I), in contrast with the low level of transcripts of the six ndh genes. Like other plastid operons containing genes for functionally unrelated proteins, the contrasting accumulation of ndh and psaC transcripts provides a model to investigate the mechanisms of the post-transcriptional control of gene expression, a feature of chloroplast genetic machinery, with a minimum of interference by transcriptional control. In leek (Allium porrum L), the ndhD transcript (which follows the psaC gene and ends the ndhH-D operon) requires C --> U editing to restore its start codon and may be used as a marker for the processing of psaC and ndhD transcripts. By determining the editing state and 5' end sequences of specific transcripts, we demonstrated that stable monocistronic psaC mRNA results from downstream cleavages in the ndhD sequence, which renders non-functional ndhD transcripts as by-products. Alternative psaC-ndhD intergenic cleavages produce complete mRNAs for both genes, but only take place in precursors containing editing-restored ndhD start codons. Hence, post-transcriptional control acts by promoting the ndhD cleavage alternative, which allows the accumulation of psaC mRNA at the expense of ndhD mRNA levels.

  2. Isolation and Identification of Post-Transcriptional Gene Silencing-Related Micro-RNAs by Functionalized Silicon Nanowire Field-effect Transistor

    Science.gov (United States)

    Chen, Kuan-I.; Pan, Chien-Yuan; Li, Keng-Hui; Huang, Ying-Chih; Lu, Chia-Wei; Tang, Chuan-Yi; Su, Ya-Wen; Tseng, Ling-Wei; Tseng, Kun-Chang; Lin, Chi-Yun; Chen, Chii-Dong; Lin, Shih-Shun; Chen, Yit-Tsong

    2015-11-01

    Many transcribed RNAs are non-coding RNAs, including microRNAs (miRNAs), which bind to complementary sequences on messenger RNAs to regulate the translation efficacy. Therefore, identifying the miRNAs expressed in cells/organisms aids in understanding genetic control in cells/organisms. In this report, we determined the binding of oligonucleotides to a receptor-modified silicon nanowire field-effect transistor (SiNW-FET) by monitoring the changes in conductance of the SiNW-FET. We first modified a SiNW-FET with a DNA probe to directly and selectively detect the complementary miRNA in cell lysates. This SiNW-FET device has 7-fold higher sensitivity than reverse transcription-quantitative polymerase chain reaction in detecting the corresponding miRNA. Next, we anchored viral p19 proteins, which bind the double-strand small RNAs (ds-sRNAs), on the SiNW-FET. By perfusing the device with synthesized ds-sRNAs of different pairing statuses, the dissociation constants revealed that the nucleotides at the 3‧-overhangs and pairings at the terminus are important for the interactions. After perfusing the total RNA mixture extracted from Nicotiana benthamiana across the device, this device could enrich the ds-sRNAs for sequence analysis. Finally, this bionanoelectronic SiNW-FET, which is able to isolate and identify the interacting protein-RNA, adds an additional tool in genomic technology for the future study of direct biomolecular interactions.

  3. Adenosine-to-inosine RNA editing controls cathepsin S expression in atherosclerosis by enabling HuR-mediated post-transcriptional regulation.

    Science.gov (United States)

    Stellos, Konstantinos; Gatsiou, Aikaterini; Stamatelopoulos, Kimon; Perisic Matic, Ljubica; John, David; Lunella, Federica Francesca; Jaé, Nicolas; Rossbach, Oliver; Amrhein, Carolin; Sigala, Frangiska; Boon, Reinier A; Fürtig, Boris; Manavski, Yosif; You, Xintian; Uchida, Shizuka; Keller, Till; Boeckel, Jes-Niels; Franco-Cereceda, Anders; Maegdefessel, Lars; Chen, Wei; Schwalbe, Harald; Bindereif, Albrecht; Eriksson, Per; Hedin, Ulf; Zeiher, Andreas M; Dimmeler, Stefanie

    2016-10-01

    Adenosine-to-inosine (A-to-I) RNA editing, which is catalyzed by a family of adenosine deaminase acting on RNA (ADAR) enzymes, is important in the epitranscriptomic regulation of RNA metabolism. However, the role of A-to-I RNA editing in vascular disease is unknown. Here we show that cathepsin S mRNA (CTSS), which encodes a cysteine protease associated with angiogenesis and atherosclerosis, is highly edited in human endothelial cells. The 3' untranslated region (3' UTR) of the CTSS transcript contains two inverted repeats, the AluJo and AluSx+ regions, which form a long stem-loop structure that is recognized by ADAR1 as a substrate for editing. RNA editing enables the recruitment of the stabilizing RNA-binding protein human antigen R (HuR; encoded by ELAVL1) to the 3' UTR of the CTSS transcript, thereby controlling CTSS mRNA stability and expression. In endothelial cells, ADAR1 overexpression or treatment of cells with hypoxia or with the inflammatory cytokines interferon-γ and tumor-necrosis-factor-α induces CTSS RNA editing and consequently increases cathepsin S expression. ADAR1 levels and the extent of CTSS RNA editing are associated with changes in cathepsin S levels in patients with atherosclerotic vascular diseases, including subclinical atherosclerosis, coronary artery disease, aortic aneurysms and advanced carotid atherosclerotic disease. These results reveal a previously unrecognized role of RNA editing in gene expression in human atherosclerotic vascular diseases.

  4. Structural and functional analysis of myostatin-2 promoter alleles from the marine fish Sparus aurata: evidence for strong muscle-specific promoter activity and post-transcriptional regulation.

    Science.gov (United States)

    Nadjar-Boger, Elisabeth; Hinits, Yaniv; Funkenstein, Bruria

    2012-09-25

    Myostatin (MSTN) is a negative regulator of skeletal muscle growth. In contrast to mammals, fish possess at least two paralogs of MSTN: MSTN-1 and MSTN-2. In this study, we analyzed the structural-functional features of the four variants of Sparus aurata MSTN-2 5'-flanking region: saMSTN-2a, saMSTN-2as, saMSTN-2b and saMSTN-2c. In silico analysis revealed numerous putative cis regulatory elements including several E-boxes known as binding sites to myogenic transcription factors. Transient transfection experiments using non-muscle and muscle cell lines showed surprisingly high transcriptional activity in muscle cells, suggesting the presence of regulatory elements unique to differentiated myotubes. These observations were confirmed by in situ intramuscular injections of promoter DNA followed by reporter gene assays. Moreover, high promoter activity was found in differentiated neural cell, in agreement with MSTN-2 expression in brain. Progressive 5'-deletion analysis, using reporter gene assays, showed that the core promoter is located within the first -127 bp upstream of the ATG, and suggested the presence of regulatory elements that either repress or induce transcriptional activity. Transient transgenic zebrafish provided evidence for saMSTN-2 promoter ability to direct GFP expression to myofibers. Finally, our data shows that although no mature saMSTN-2 mRNA is observed in muscle; unspliced forms accumulate, confirming high level of transcription. In conclusion, our study shows for the first time that MSTN-2 promoter is a very robust promoter, especially in muscle cells. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

  5. Computational Investigations of Post-Transcriptional Regulation

    DEFF Research Database (Denmark)

    Rasmussen, Simon Horskjær

    MicroRNAs (miRNAs) are small non-coding RNAs that mediate degradation and translational repression of target mRNAs. miRNAs rely on RNA-binding proteins (RBPs) in every step of their biogenesis, localization, targeting and execution of the regulatory effect. With the recent introduction...... and diversification of genomewide Next Generation Sequencing (NGS) technologies, it has become possible to study interaction of miRNAs and RBPs in greater detail. miRNA-binding to an mRNA can have different outcomes, which depends on the RBPs they interact with. In two papers in this thesis, the link between RBPs...... and miRNA regulation was studied by cross-linking immunoprecipitation (CLIP) and RBP double knockdown experiments. A comprehensive analysis of 107 CLIP datasets of 49 RBPs demonstrated that RBPs modulate miRNA regulation. Results suggest it is mediated by RBP-binding hotspots that likely...

  6. IGF-1 deficiency in a critical period early in life influences the vascular aging phenotype in mice by altering miRNA-mediated post-transcriptional gene regulation: implications for the developmental origins of health and disease hypothesis.

    Science.gov (United States)

    Tarantini, Stefano; Giles, Cory B; Wren, Jonathan D; Ashpole, Nicole M; Valcarcel-Ares, M Noa; Wei, Jeanne Y; Sonntag, William E; Ungvari, Zoltan; Csiszar, Anna

    2016-08-01

    Epidemiological findings support the concept of Developmental Origins of Health and Disease, suggesting that early-life hormonal influences during a sensitive period of development have a fundamental impact on vascular health later in life. The endocrine changes that occur during development are highly conserved across mammalian species and include dramatic increases in circulating IGF-1 levels during adolescence. The present study was designed to characterize the effect of developmental IGF-1 deficiency on the vascular aging phenotype. To achieve that goal, early-onset endocrine IGF-1 deficiency was induced in mice by knockdown of IGF-1 in the liver using Cre-lox technology (Igf1 f/f mice crossed with mice expressing albumin-driven Cre recombinase). This model exhibits low-circulating IGF-1 levels during the peripubertal phase of development, which is critical for the biology of aging. Due to the emergence of miRNAs as important regulators of the vascular aging phenotype, the effect of early-life IGF-1 deficiency on miRNA expression profile in the aorta was examined in animals at 27 months of age. We found that developmental IGF-1 deficiency elicits persisting late-life changes in miRNA expression in the vasculature, which significantly differed from those in mice with adult-onset IGF-1 deficiency (TBG-Cre-AAV8-mediated knockdown of IGF-1 at 5 month of age in Igf1 f/f mice). Using a novel computational approach, we identified miRNA target genes that are co-expressed with IGF-1 and associate with aging and vascular pathophysiology. We found that among the predicted targets, the expression of multiple extracellular matrix-related genes, including collagen-encoding genes, were downregulated in mice with developmental IGF-1 deficiency. Collectively, IGF-1 deficiency during a critical period during early in life results in persistent changes in post-transcriptional miRNA-mediated control of genes critical targets for vascular health, which likely contribute to the

  7. Journal of Agricultural Extension

    African Journals Online (AJOL)

    Mission Statement The mission of the "Journal of Agricultural Extension" is to publish conceptual papers and empirical research that tests, extends, or builds agricultural extension theory and contributes to the practice of extension worldwide. Scope of journal The Journal of Agricultural Extension" is devoted to the ...

  8. Polarization extension mechanism revealed through dynamic ferroelectric hysteresis and electric field driven structural distortions in lead free Na0.5Bi0.5TiO3 ceramic

    Science.gov (United States)

    Karthik, T.; Asthana, Saket

    2017-09-01

    The electric field amplitude (E o) dependent dynamic ferroelectric hysteresis and polarization current density curves measured at room temperature for Na0.5Bi0.5TiO3 (NBT), showed three different stages of polarization reversal mechanism. The scaling relationship confirmed the dominance of domain wall motion at Stage I (i.e. upto E o  <  35 kV cm-1), followed by domain switching at Stage II (35 kV cm-1  <  E o  <  60 kV cm-1). Interestingly, a unique behaviour with two sub stages was observed in Stage III (60 kV cm-1  <  E o  <  90 kV cm-1), with two distinct switching mechanisms viz., polarization rotation at Stage III-A and polarization extension at Stage III-B. X-ray diffraction analysis based on the Rietveld refined atomic positional co-ordinates, in electrically poled system strongly favors the polarization extension mechanism proposed at Stage III-B. The measured E o-dependent longitudinal piezoelectric response (d 33 and g33) values match closely with our proposed polarization reversal mechanism.

  9. Agricultural extension, research, and development for increased ...

    African Journals Online (AJOL)

    Analysis of the data collected revealed that the improvement of agricultural production, with the goal of sustainable food security, in South Africa, might not be achieved without an effective agricultural extension service that is strongly linked to research. It was also found that public sector extension work is a necessity for the ...

  10. Marketing Extension Needs for Sustainable Extension Practices ...

    African Journals Online (AJOL)

    The study investigated the marketing extension needs of cassava farmers in Surulere Local Government Area of Oyo State. Multistage sampling technique was used to select one hundred and five respondents from the list of contact farmers obtained from the state Agricultural Development Programme (ADP). Interview ...

  11. Less extensive surgery compared to extensive surgery

    DEFF Research Database (Denmark)

    Lauszus, Finn F; Petersen, Astrid C; Neumann, Gudrun

    2014-01-01

    OBJECTIVE: To describe the outcome of adult granulosa cell tumor (AGCT) with respect to initial clinical findings, methods of surgery, and perioperative treatment. STUDY DESIGN: Retrospective follow-up study. Setting: All hospitals in Jutland. Sample: 163 women diagnosed with AGCT. Methods: Follo...... with similar survival compared to extensive surgery, but with advancing age conservative surgery increased the risk of relapse and death....

  12. Hyper conserved elements in vertebrate mRNA 3'-UTRs reveal a translational network of RNA-binding proteins controlled by HuR.

    Science.gov (United States)

    Dassi, Erik; Zuccotti, Paola; Leo, Sara; Provenzani, Alessandro; Assfalg, Michael; D'Onofrio, Mariapina; Riva, Paola; Quattrone, Alessandro

    2013-03-01

    Little is known regarding the post-transcriptional networks that control gene expression in eukaryotes. Additionally, we still need to understand how these networks evolve, and the relative role played in them by their sequence-dependent regulatory factors, non-coding RNAs (ncRNAs) and RNA-binding proteins (RBPs). Here, we used an approach that relied on both phylogenetic sequence sharing and conservation in the whole mapped 3'-untranslated regions (3'-UTRs) of vertebrate species to gain knowledge on core post-transcriptional networks. The identified human hyper conserved elements (HCEs) were predicted to be preferred binding sites for RBPs and not for ncRNAs, namely microRNAs and long ncRNAs. We found that the HCE map identified a well-known network that post-transcriptionally regulates histone mRNAs. We were then able to discover and experimentally confirm a translational network composed of RNA Recognition Motif (RRM)-type RBP mRNAs that are positively controlled by HuR, another RRM-type RBP. HuR shows a preference for these RBP mRNAs bound in stem-loop motifs, confirming its role as a 'regulator of regulators'. Analysis of the transcriptome-wide HCE distribution revealed a profile of prevalently small clusters separated by unconserved intercluster RNA stretches, which predicts the formation of discrete small ribonucleoprotein complexes in the 3'-UTRs.

  13. Kentucky's Urban Extension Focus

    Science.gov (United States)

    Young, Jeffery; Vavrina, Charles

    2014-01-01

    Defining the success of Urban Extension units is sometimes challenging. For those Extension agents, specialists, administrators, and others who have worked to bring solid, research-based programming to urban communities, it is no surprise that working in these communities brings its own unique and sometimes difficult challenges. Kentucky's Urban…

  14. Priorities for Extension.

    Science.gov (United States)

    Hayward, J. A.

    Agricultural extension is one component in an array including research, training, education, marketing, international trade, etc. which develop together to bring about growth, and sustained growth determines the priorities for extension. These priorities depend inevitably on the stage of development of a country or region, and on the current…

  15. University Extension Before 1915

    Science.gov (United States)

    Eklund, Lowell R.

    1976-01-01

    The author traces university extension from its elite English roots to evolving forces toward democratization of educational opportunities and the simultaneous emergence of similar American programs such as library-related night schools, the Lyceum movement, Chataqua, the Philadelphia Society for Extension of University Teaching, and the…

  16. Algebraic extensions of fields

    CERN Document Server

    McCarthy, Paul J

    1991-01-01

    ""...clear, unsophisticated and direct..."" - MathThis textbook is intended to prepare graduate students for the further study of fields, especially algebraic number theory and class field theory. It presumes some familiarity with topology and a solid background in abstract algebra. Chapter 1 contains the basic results concerning algebraic extensions. In addition to separable and inseparable extensions and normal extensions, there are sections on finite fields, algebraically closed fields, primitive elements, and norms and traces. Chapter 2 is devoted to Galois theory. Besides the fundamenta

  17. Dettol: Managing Brand Extensions

    OpenAIRE

    Anand Kumar Jaiswal; Arpita Srivastav; Dhwani Kothari

    2009-01-01

    This case is about evolution of a parent brand and its subsequent extensions into different product categories. Dettol as a brand has immense trust and loyalty from the consumers. Since the 1930s when Dettol was introduced in India, it has occupied a distinct position in the mind of its consumers. To achieve fast growth and leverage the strong brand equity of Dettol, Reckitt Benckiser India Limited (RBIL) rolled out a number of brand extensions. Some of these extensions such as Dettol soap an...

  18. Ancient Ethiopian genome reveals extensive Eurasian admixture in Eastern Africa

    KAUST Repository

    Gallego Llorente, M.

    2015-10-09

    Characterizing genetic diversity in Africa is a crucial step for most analyses reconstructing the evolutionary history of anatomically modern humans. However, historic migrations from Eurasia into Africa have affected many contemporary populations, confounding inferences. Here, we present a 12.5×coverage ancient genome of an Ethiopian male ("Mota") who lived approximately 4500 years ago. We use this genome to demonstrate that the Eurasian backflow into Africa came from a population closely related to Early Neolithic farmers, who had colonized Europe 4000 years earlier. The extent of this backflow was much greater than previously reported, reaching all the way to Central, West, and Southern Africa, affecting even populations such as Yoruba and Mbuti, previously thought to be relatively unadmixed, who harbor 6 to 7% Eurasian ancestry.

  19. Type extension trees

    DEFF Research Database (Denmark)

    Jaeger, Manfred

    2006-01-01

    We introduce type extension trees as a formal representation language for complex combinatorial features of relational data. Based on a very simple syntax this language provides a unified framework for expressing features as diverse as embedded subgraphs on the one hand, and marginal counts of at...... of attribute values on the other. We show by various examples how many existing relational data mining techniques can be expressed as the problem of constructing a type extension tree and a discriminant function....

  20. Timed Extensions for SDL

    OpenAIRE

    Bozga, Marius; Graf, Susanne; Mounier, Laurent; Ober, Iulian; Roux, Jean-Luc; Vincent, Daniel

    2001-01-01

    International audience; In this paper we propose some extensions necessary to enable the specification and description language SDL to become an appropriate formalism for the design of real-time and embedded systems. The extensions we envisage concern both roles of SDL: First, in order to make SDL a real-time specification language, allowing to correctly simulate and verify real-time specifications, we propose a set of annotations to express in a flexible way assumptions and assertions on tim...

  1. Gamut extension for cinema

    OpenAIRE

    Zamir, Syed Waqas,; Vazquez-Corral, Javier; Bertalmío, Marcelo

    2017-01-01

    Emerging display technologies are able to produce images with a much wider color gamut than those of conventional distribution gamuts for cinema and TV, creating an opportunity for the development of gamut extension algorithms (GEAs) that exploit the full color potential of these new systems. In this paper, we present a novel GEA, implemented as a PDE-based optimization procedure related to visual perception models, that performs gamut extension (GE) by taking into account the analysis of dis...

  2. Constraints to agricultural extension work in Ethiopia: the insiders ...

    African Journals Online (AJOL)

    This paper examines principal obstacles to agricultural extension work in Ethiopia. The historical review reveals that extension programs and policies have been formulated without due consideration to the farmers' opinion, the various extension approaches have been biased against the livestock sub-sector, and research ...

  3. Android Access Control Extension

    Directory of Open Access Journals (Sweden)

    Anton Baláž

    2015-12-01

    Full Text Available The main objective of this work is to analyze and extend security model of mobile devices running on Android OS. Provided security extension is a Linux kernel security module that allows the system administrator to restrict program's capabilities with per-program profiles. Profiles can allow capabilities like network access, raw socket access, and the permission to read, write, or execute files on matching paths. Module supplements the traditional Android capability access control model by providing mandatory access control (MAC based on path. This extension increases security of access to system objects in a device and allows creating security sandboxes per application.

  4. Mobile Applications for Extension

    Science.gov (United States)

    Drill, Sabrina L.

    2012-01-01

    Mobile computing devices (smart phones, tablets, etc.) are rapidly becoming the dominant means of communication worldwide and are increasingly being used for scientific investigation. This technology can further our Extension mission by increasing our power for data collection, information dissemination, and informed decision-making. Mobile…

  5. Selecting Extensive Reading Materials

    Science.gov (United States)

    Jacobs, George M.

    2014-01-01

    This article offers guidance to teachers and students in selecting materials for extensive reading (ER). First, the article explains characteristics of ER and reviews some of the potential gains for students who do ER. Second, the article considers criteria for teachers to bear in mind when selecting ER materials. Third, the article then suggests…

  6. Gamut Extension for Cinema.

    Science.gov (United States)

    Zamir, Syed Waqas; Vazquez-Corral, Javier; Bertalmio, Marcelo

    2017-04-01

    Emerging display technologies are able to produce images with a much wider color gamut than those of conventional distribution gamuts for cinema and TV, creating an opportunity for the development of gamut extension algorithms (GEAs) that exploit the full color potential of these new systems. In this paper, we present a novel GEA, implemented as a PDE-based optimization procedure related to visual perception models, that performs gamut extension (GE) by taking into account the analysis of distortions in hue, chroma, and saturation. User studies performed using a digital cinema projector under cinematic (low ambient light, large screen) conditions show that the proposed algorithm outperforms the state of the art, producing gamut extended images that are perceptually more faithful to the wide-gamut ground truth, as well as free of color artifacts and hue shifts. We also show how currently available image quality metrics, when applied to the GE problem, provide results that do not correlate with users' choices.

  7. Need for Methamphetamine Programming in Extension Education

    Science.gov (United States)

    Beaudreault, Amy R.; Miller, Larry E.

    2011-01-01

    The study reported sought to identify the prevention education needs involving methamphetamine through survey methodology. The study focused on a random sample of U.S. states and the Extension Directors within each state, resulting in a 70% response rate (n = 134). Findings revealed that 11% reported they had received methamphetamine user…

  8. Newspapers' agricultural agenda setting and extension agents ...

    African Journals Online (AJOL)

    Newspapers content were analyzed from January to June 2002 for agricultural issues raised in them. Data were analyzed using frequencies, percentages, and Spearman rho correlation coefficient. The results revealed that extension agents ranked storage problems as most important (4.24) and investment in agriculture ...

  9. Rural Development And Agricultural Extension Administration In ...

    African Journals Online (AJOL)

    This paper reviewed the wide range of policies and approaches formulated and implemented to effect agricultural and rural development in Nigeria. The paper reveals that the common feature of all the strategies is the use of institutionalized agricultural extension service, devoted principally to augment smallholder ...

  10. attitude of extension personnel to training and visit extension system ...

    African Journals Online (AJOL)

    ISAAC E. ILEVBAOJE. ABSTRACT. This study was undertaken to find out the attitudes of extension workers to the training and visit (T&V) extension system as a complimentary step to specify if this extension approach is on course in Nigeria. Results obtained indicate that about 10. 8, 65.8 and 23.3% of the extension ...

  11. Selecting Extensive Reading Materials

    Directory of Open Access Journals (Sweden)

    George M Jacobs

    2014-05-01

    Full Text Available This article offers guidance to teachers and students in selecting materials for extensive reading (ER. First, the article explains characteristics of ER and reviews some of the potential gains for students who do ER. Second, the article considers criteria for teachers to bear in mind when selecting ER materials. Third, the article then suggests ways that teachers and students can find ER materials. Fourth, guidance is provided to students for when they select what to read from among the ER materials available to them. Finally, advice is given on integrating ER with course textbooks.

  12. Open Extension Topology

    Directory of Open Access Journals (Sweden)

    Вячеслав Бабич

    2015-10-01

    Full Text Available The paper contains the results which describe the properties of such general topological construction as open extension topology. In particular, we prove that this topology is not transitive. We find the base of the least cardinality for the topology and local one for the neighborhood system of every point. We calculate the interior, the closure, and the sets of isolated and limit points of any set. Also we prove that this space is path connected and is not metrizable, and investigate its cardinal invariants and separation axioms.

  13. Extensive air showers

    CERN Document Server

    Rao, M V S

    1997-01-01

    Ultrahigh energy cosmic rays carry information about their sources and the intervening medium apart from providing a beam of particles for studying certain features of high energy interactions currently inaccessible at man-made accelerators. They can at present be studied only via the extensive air showers (EAS's) they generate while passing through the Earth's atmosphere, since their fluxes are too low for the experiments of limited capability flown in balloons and satellites. The EAS is generated by a series of interactions of the primary cosmic ray and its progeny with the atmospheric nucle

  14. Logic regression and its extensions.

    Science.gov (United States)

    Schwender, Holger; Ruczinski, Ingo

    2010-01-01

    Logic regression is an adaptive classification and regression procedure, initially developed to reveal interacting single nucleotide polymorphisms (SNPs) in genetic association studies. In general, this approach can be used in any setting with binary predictors, when the interaction of these covariates is of primary interest. Logic regression searches for Boolean (logic) combinations of binary variables that best explain the variability in the outcome variable, and thus, reveals variables and interactions that are associated with the response and/or have predictive capabilities. The logic expressions are embedded in a generalized linear regression framework, and thus, logic regression can handle a variety of outcome types, such as binary responses in case-control studies, numeric responses, and time-to-event data. In this chapter, we provide an introduction to the logic regression methodology, list some applications in public health and medicine, and summarize some of the direct extensions and modifications of logic regression that have been proposed in the literature. Copyright © 2010 Elsevier Inc. All rights reserved.

  15. A combination of improved differential and global RNA-seq reveals pervasive transcription initiation and events in all stages of the life-cycle of functional RNAs in Propionibacterium acnes, a major contributor to wide-spread human disease.

    Science.gov (United States)

    Lin, Yu-fei; A, David Romero; Guan, Shuang; Mamanova, Lira; McDowall, Kenneth J

    2013-09-14

    Sequencing of the genome of Propionibacterium acnes produced a catalogue of genes many of which enable this organism to colonise skin and survive exposure to the elements. Despite this platform, there was little understanding of the gene regulation that gives rise to an organism that has a major impact on human health and wellbeing and causes infections beyond the skin. To address this situation, we have undertaken a genome-wide study of gene regulation using a combination of improved differential and global RNA-sequencing and an analytical approach that takes into account the inherent noise within the data. We have produced nucleotide-resolution transcriptome maps that identify and differentiate sites of transcription initiation from sites of stable RNA processing and mRNA cleavage. Moreover, analysis of these maps provides strong evidence for 'pervasive' transcription and shows that contrary to initial indications it is not biased towards the production of antisense RNAs. In addition, the maps reveal an extensive array of riboswitches, leaderless mRNAs and small non-protein-coding RNAs alongside vegetative promoters and post-transcriptional events, which includes unusual tRNA processing. The identification of such features will inform models of complex gene regulation, as illustrated here for ribonucleotide reductases and a potential quorum-sensing, two-component system. The approach described here, which is transferable to any bacterial species, has produced a step increase in whole-cell knowledge of gene regulation in P. acnes. Continued expansion of our maps to include transcription associated with different growth conditions and genetic backgrounds will provide a new platform from which to computationally model the gene expression that determines the physiology of P. acnes and its role in human disease.

  16. Attitude Of Extension Personnel To Training And Visit Extension ...

    African Journals Online (AJOL)

    In order to make the attitudes of extension workers more affirmative, the paper recommended, inter alia, staff motivation, minimizing political and administrative interference in staff work and a reasonable reduction in the work load of extension staff. Key words: attitude, extension personnel, training and visit. Journal of ...

  17. Community health nursing and cooperative extension: a natural partnership.

    Science.gov (United States)

    Bigbee, Jeri L; Hampton, Carol; Blanford, Diane; Ketner, Paulette

    2009-10-01

    Community health nursing and cooperative extension represent two influential and respected disciplines in rural and frontier communities. The history and philosophy of the two disciplines reveal commonalities related to community-based health promotion and dissemination of research. A review of the extension and health sciences literature revealed some evidence of collaboration between extension and health science professionals, however very little documentation specifically of nurses' involvement with extension professionals. An exemplar of a highly effective ongoing cooperation between rural public health nurses and extension educators in one Idaho county is provided. This local interdisciplinary effort has resulted in enhanced community health promotion services, positive interprofessional relationships, and maximization of scarce resources. Nursing-extension collaboration presents creative opportunities for interdisciplinary practice, research, and educational innovations to enhance the health of rural and frontier communities.

  18. Extensive xanthogranulomatous cystitis mimicking bladder cancer

    Directory of Open Access Journals (Sweden)

    Amir M Ali

    2014-01-01

    Full Text Available Xanthogranulomatous cystitis (XC is a rare benign disease of unknown etiology. A 39-year-old female presented with 2 month history of urgency, dysuria, lower abdominal mass. On physical examination a hard hypogastric mass was present fixed to the rectus muscle. Computerized tomography (CT abdomen showed heterogeneous enhancing mass arising from the anterior bladder wall with infiltration of the overlying parietal wall. Cystoscopy revealed extensive growth involving the entire wall of the bladder. A biopsy showed cystitis with focal areas suggestive of urothelial neoplasia of unknown malignant potential. Suspecting bladder cancer, we proceeded with radical cystectomy with ileal conduit. Histopathology revealed cystitis cystica with XC of the entire bladder. This is, to our knowledge, the first time that a case has been found to be so extensive with infiltration of the parietal wall and second time that radical cystectomy has been performed for XC.

  19. Challenges of extension workers in reaching rural women farmers in ...

    African Journals Online (AJOL)

    Questionnaire was used to collect data from a sample size of 52 extension workers. Data were analyzed using percentage, mean statistic, chart and factor analysis. Results revealed that training and visit method (100%) and farmer group (98.1%) were the major extension approach used in reaching rural women farmers in ...

  20. Perceived Factors Affecting Performance Of Extension Workers In ...

    African Journals Online (AJOL)

    Data for the study was collected from 83 Extension agents from the Imo State Agricultural Development Programme (ADP). Results of the study revealed that the organizational factors that affect performance are mobility/logistic factors, job design and Administration. It is therefore recommended that Agricultural extension ...

  1. Research-Based Implications from Extensive Early Reading Interventions

    Science.gov (United States)

    Wanzek, Jeanne; Vaughn, Sharon

    2007-01-01

    A synthesis of the extant research on extensive early reading interventions for students with reading difficulties and disabilities is provided. Findings from 18 studies published between 1995 and 2005 revealed positive outcomes for students participating in extensive interventions. Results indicated higher effects for studies providing…

  2. The Impact Of Information And Communication In Extension ...

    African Journals Online (AJOL)

    The article examines the impact of information and communication in extension services to rural farmers in Niger- Delta. Questionnaire, interview and personal observation methods were employed to elicit information on the impact information and communication in extension services to rural farmers. The study reveals the ...

  3. attitude of extension personnel to training and visit extension system ...

    African Journals Online (AJOL)

    the training and visit (T&V) extension system as a complimentary step to specify if this extension approach is ... at 5 percent level of probability, the mean score for the project headquarters staff (106.25) was highest while ... which offered them the opportunity to use their knowledge and skills. Asiabiaka (1991) studied women ...

  4. Robotic hand with modular extensions

    Energy Technology Data Exchange (ETDEWEB)

    Salisbury, Curt Michael; Quigley, Morgan

    2015-01-20

    A robotic device is described herein. The robotic device includes a frame that comprises a plurality of receiving regions that are configured to receive a respective plurality of modular robotic extensions. The modular robotic extensions are removably attachable to the frame at the respective receiving regions by way of respective mechanical fuses. Each mechanical fuse is configured to trip when a respective modular robotic extension experiences a predefined load condition, such that the respective modular robotic extension detaches from the frame when the load condition is met.

  5. Think - Baltic Extension / Kalle Kask

    Index Scriptorium Estoniae

    Kask, Kalle

    2002-01-01

    Tallinna TÜ Rehabilitatsiooni tehnoloogia keskus korraldas pressikonverentsi, kus tutvustati osalemist EL V raamprogrammis Think - Baltic Extension, mis on suunatud puuetega inimeste tööhõive tagamisele

  6. Microarray analysis of rice d1 (RGA1 mutant reveals the potential role of G-protein alpha subunit in regulating multiple abiotic stresses such as drought, salinity, heat and cold

    Directory of Open Access Journals (Sweden)

    Annie Prasanna Jangam

    2016-01-01

    , carbohydrates, receptors and lipids, morphogenesis, flower development and cell homeostasis. We also mined 63 miRNAs that bind to the stress responsive transcripts identified in this study, indicating their post-transcriptional regulation. Overall, these results indicate the potentially extensive role of RGA1 in the regulation of multiple abiotic stresses in rice for further validation.

  7. Molecular Mechanisms Regulating Hepcidin Revealed by Hepcidin Disorders

    Directory of Open Access Journals (Sweden)

    Clara Camaschella

    2011-01-01

    Full Text Available Iron is essential for human life, but toxic if present in excess. To avoid iron overload and maintain iron homeostasis, all cells are able to regulate their iron content through the post-transcriptional control of iron genes operated by the cytosolic iron regulatory proteins that interact with iron responsive elements on iron gene mRNA. At the systemic level, iron homeostasis is regulated by the liver peptide hepcidin. Disruption of these regulatory loops leads to genetic diseases characterized by iron deficiency (iron-refractory iron-deficiency anemia or iron overload (hemochromatosis. Alterations of the same systems are also found in acquired disorders, such as iron-loading anemias characterized by ineffective erythropoiesis and anemia of chronic diseases (ACD associated with common inflammatory conditions. In ACD, iron is present in the body, but maldistributed, being deficient for erythropoiesis, but sequestered in macrophages. Studies of the hepcidin regulation by iron and inflammatory cytokines are revealing new pathways that might become targets of new therapeutic intervention in iron disorders.

  8. Extensive intestinal spirochaetosis in pigs challenged with Brachyspira pilosicoli

    DEFF Research Database (Denmark)

    Jensen, Tim Kåre; Boye, Mette; Møller, Kristian

    2004-01-01

    of the study). Mild mucosal reddening and flecks of pus characterized the gross lesions, while diffuse, catarrhal colitis was revealed microscopically in all animals. Intestinal spirochaetosis with moderate to densely packed end-attached B. pilosicoli organisms was revealed extensively on the mucosal surface...

  9. Extensive Reading Coursebooks in China

    Science.gov (United States)

    Renandya, Willy A.; Hu, Guangwei; Xiang, Yu

    2015-01-01

    This article reports on a principle-based evaluation of eight dedicated extensive reading coursebooks published in mainland China and used in many universities across the country. The aim is to determine the extent to which these coursebooks reflect a core set of nine second language acquisition and extensive reading principles. Our analysis shows…

  10. Fuzzy extended preferences: fuzzified extension

    OpenAIRE

    Montero, Javier

    1988-01-01

    This paper deals with decision-making problems where a fuzzy preference relation with no unfuzzy nondominated alternatives has been defined. While in the first part randomized extension was considered in order to get a solution, in this second part an aggregative approach to fuzzified extension will be developed.

  11. Frames and extension problems I

    DEFF Research Database (Denmark)

    Christensen, Ole

    2014-01-01

    In this article we present a short survey of frame theory in Hilbert spaces. We discuss Gabor frames and wavelet frames and set the stage for a discussion of various extension principles; this will be presented in the article Frames and extension problems II (joint with H.O. Kim and R.Y. Kim)....

  12. Research-extension-farmer linkages

    African Journals Online (AJOL)

    charged with the role of articulating the most appropriate research and extension systems for Uganda. Following the recommendations of these working groups, national agricultural research and extension strategies and plans were adopted ..... meetings at institutes have been taking place regularly since 1994. These take ...

  13. Homomorphisms between C∗ -algebra extensions

    Indian Academy of Sciences (India)

    -algebra extensions. CHANGGUO WEI. School of Mathematical Sciences, Ocean University of China, Qingdao 266071, ... into the other in general, so we have to consider properties of extension homomorphisms before studying the ..... Theory (Dalhousie Univ., Halifax, N.S., 1973) Lecture Notes in Math. (Berlin: Springer).

  14. EXTENSION WORKERS' OPINIONS REGARDING THE ...

    African Journals Online (AJOL)

    The primary purpose of the study was to determine extension worker's opinions regarding the influence of the National Maize Competition (NAMCOM) on the farmers' agricultural practices and experiences in the Manzini region. A census population of front-line extension workers in charge of the participating areas in ...

  15. Repeat Customer Success in Extension

    Science.gov (United States)

    Bess, Melissa M.; Traub, Sarah M.

    2013-01-01

    Four multi-session research-based programs were offered by two Extension specialist in one rural Missouri county. Eleven participants who came to multiple Extension programs could be called "repeat customers." Based on the total number of participants for all four programs, 25% could be deemed as repeat customers. Repeat customers had…

  16. Journal of Agricultural Extension submitted to Agricultural Extension ...

    African Journals Online (AJOL)

    PROF. MADUKWE

    followed by lack of contact with extension agents (71.7%) and gender ... As women typically confront narrower range of labour markets than men, and lower wage ..... gap in accessibility to productive resources between male and female heads ...

  17. Extensions of the Poincare group

    CERN Document Server

    Antoniadis, Ignatios; Savvidy, George

    2011-01-01

    We construct an extension of the Poincare group which involves a mixture of internal and space-time supersymmetries. The resulting group is an extension of the superPoincare group with infinitely many generators which carry internal and space-time indices. It is a closed algebra since all Jacobi identities are satisfied and it has therefore explicit matrix representations. We investigate the massless case and construct the irreducible representations of the extended symmetry. They are divided into two sets, longitudinal and transversal representations. The transversal representations involve an infinite series of integer and half-integer helicities. Finally we suggest an extension of the conformal group along the same line.

  18. Programming Reactive Extensions and LINQ

    CERN Document Server

    Liberty, Jesse

    2011-01-01

    Pro Reactive Extensions and LINQ is a deep dive into the next important technology for .NET developers: Reactive Extensions. This in-depth tutorial goes beyond what is available anywhere else to teach how to write WPF, Silverlight, and Windows Phone applications using the Reactive Extensions (Rx) to handle events and asynchronous method calls. Reactive programming allows you to turn those aspects of your code that are currently imperative into something much more event-driven and flexible. For this reason, it's sometimes referred to as LINQ for Events. Reactive programming hinges on the concep

  19. Learning Joomla! 3 extension development

    CERN Document Server

    Plummer, Tim

    2013-01-01

    A practical guide with step-by-step examples that build on each other so you can learn by doing and get hands-on knowledge about creating your plugins, modules, and components in Joomla.""Learning Joomla! 3 Extension Development, Third Edition"" is for developers who want to create their own Joomla extensions. It is assumed you will have some basic PHP, HTML, and CSS knowledge, but you don't need any prior Joomla programming experience. This book will also be useful to people who just want to make minor customizations to existing Joomla extensions and build on the work of others in the open so

  20. Correlation between extension-block K-wire insertion angle and postoperative extension loss in mallet finger fracture.

    Science.gov (United States)

    Lee, S K; Kim, Y H; Moon, K H; Choy, W S

    2017-10-09

    Extension-block pinning represents a simple and reliable surgical technique. Although this procedure is commonly performed successfully, some patients develop postoperative extension loss. To date, the relationship between extension-block Kirschner wire (K-wire) insertion angle and postoperative extension loss in mallet finger fracture remains unclear. We aimed to clarify this relationship and further evaluate how various operative and non-operative factors affect postoperative extension loss after extension-block pinning for mallet finger fracture. A retrospective study was conducted to investigate a relationship between extension block K-wire insertion angle and postoperative extension loss. The inclusion criteria were: (1) a dorsal intra-articular fracture fragment involving 30% of the base of the distal phalanx with or without volar subluxation of the distal phalanx; and (2) angle and fixation angle of the distal interphalangeal (DIP) joint were assessed using lateral radiograph at immediate postoperative time. Postoperative extension loss was assessed by using lateral radiograph at latest follow-up. Extension-block K-wire insertion angle was defined as the acute angle between extension block K-wire and longitudinal axis of middle phalangeal head. DIP joint fixation angle was defined as the acute angle between the distal phalanx and middle phalanx longitudinal axes. Seventy-five patients were included. The correlation analysis revealed that extension-block K-wire insertion angle had a negative correlation with postoperative extension loss, whereas fracture size and time to operation had a positive correlation (correlation coefficient for extension block K-wire angle: -0.66, facture size: +0.67, time to operation: +0.60). When stratifying patients in terms of negative and positive fixation angle of the DIP joint, the independent t-test showed that mean postoperative extension loss is -3.67° and +4.54° (DIP joint fixation angles of angle (30°, 30°-40°, >40

  1. Horizontal Brand Extension and Customer perception

    OpenAIRE

    Khan, Khalid; Janthimapornkij, Rattanawilai

    2011-01-01

    Company use different method for extended their business to different market and to different segment. They use different method; brand extension is one of popular strategy for extension of business. Brand extension does not become successful for every brand, it is very risky. The purpose of this thesis is to study horizontal brand extension and customer perception. We will discuss horizontal brand extension and its two main types franchise brand extension and line extension. Brand extension ...

  2. Boiler-turbine life extension

    Energy Technology Data Exchange (ETDEWEB)

    Natzkov, S. [TOTEMA, Ltd., Sofia (Bulgaria); Nikolov, M. [CERB, Sofia (Bulgaria)

    1995-12-01

    The design life of the main power equipment-boilers and turbines is about 105 working hours. The possibilities for life extension are after normatively regulated control tests. The diagnostics and methodology for Boilers and Turbines Elements Remaining Life Assessment using up to date computer programs, destructive and nondestructive control of metal of key elements of units equipment, metal creep and low cycle fatigue calculations. As well as data for most common damages and some technical decisions for elements life extension are presented.

  3. Frames and extension problems II

    DEFF Research Database (Denmark)

    Christensen, Ole; Kim, Hong Oh; Kim, Rae Young

    2014-01-01

    This article is a follow-up on the article Frames and Extension Problems I. Here we will go into more recent progress on the topic and also present some open problems.......This article is a follow-up on the article Frames and Extension Problems I. Here we will go into more recent progress on the topic and also present some open problems....

  4. Agricultural extension and mass media.

    Science.gov (United States)

    Perraton, H

    1983-12-01

    To learn more about the use of the mass media for agricultural extension, the World Bank has considered the efforts of 2 units: INADES-formation in West Africa and the Extension Aids Branch of Malawi. The INADES-formation study focuses on Cameroon but also considers work in Rwanda and the Ivory Coast. Some general conclusions emerge from a comparison of the 2 organizations. Malawi operates an extension service which reaches farmers through extension agents, through farmer training centers, and through mass media. The Extension Aids Branch (EAB) has responsibility for its media work and broadcasts 4 1/2 hours of radio each week. Its 6 regular radio programs include a general program which interviews farmers, a music request program in which the music is interspersed with farming advice, a farming family serial, and a daily broadcast of agricultural news and information. The 17 cinema vans show some agricultural films, made by EAB, some entertainment films, and some government information films from departments other than the ministry of agriculture. EAB also has a well-developed program of research and evaluation of its own work. INADES-formation, the training section of INADES, works towards social and economic development of the population. It teaches peasant farmers and extension agents and does this through running face-to-face seminars, by publishing a magazine, "Agripromo," and through correspondence courses. In 1978-79 INADES-formation enrolled some 4500 farmers and extension agents as students. Both of these organizations work to teach farmers better agriculture techniques, and both were created in response to the fact that agricultural extension agents cannot meet all the farmers in their area. Despite the similarity of objective, there are differences in methods and philosophy. The EAB works in a single country and uses a variety of mass media, with print playing a minor role. INADES-formation is an international and nongovernmental organization and its

  5. Farmers' perception of agricultural extension service delivery in ...

    African Journals Online (AJOL)

    The study further revealed that extension activities had low impact on improving farm production yield and profitability (M=1.9, SD=±0.67) and enabling farmers to identify their own needs, problems and solve them (M=1.9, SD=±0.69). In conclusion it was found that extension is efficient, effective and visible in the study area.

  6. The Use of Extensive Reading in Teaching Reading

    OpenAIRE

    Ferdila, Raihani

    2014-01-01

    The study investigates benefits of using extensive reading in teaching reading and as well as students' attitudes toward it. A case study design as a part of qualitative research was employed in this study. The data were collected through classroom observation, questionnaire and interview. The participants of this study were a class of second graders in one of the public junior high schools in Bandung. The findings reveal that extensive reading was beneficial in teaching reading. There are fi...

  7. RURAL EXTENSION EPISTEMOLOGY AND THE TIME OF TOTAL EXTENSION

    Directory of Open Access Journals (Sweden)

    Silvio Calgaro Neto

    2016-09-01

    Full Text Available This article is dedicated to explore the field of knowledge related to rural extension. In general, a three complementary perspective is used as theoretical strategy to present this epistemological study. The first perspective, seeks to accomplish a brief archeology of rural extension, identifying the remarkable historical passages. At the second, we look to some theoretical models through the modern epistemological platform. Finally, the third perspective, aims to present a methodological proposal that contemplate this epistemic characteristics, relating with the contemporary transformations observed in the knowledge construction and technological transference for a rural development. Keywords: Total institutions. University.

  8. Extensive mass spectrometry-based analysis of the fission yeast proteome: the Schizosaccharomyces pombe PeptideAtlas.

    Science.gov (United States)

    Gunaratne, Jayantha; Schmidt, Alexander; Quandt, Andreas; Neo, Suat Peng; Saraç, Omer Sinan; Gracia, Tannia; Loguercio, Salvatore; Ahrné, Erik; Xia, Rachel Li Hai; Tan, Keng Hwa; Lössner, Christopher; Bähler, Jürg; Beyer, Andreas; Blackstock, Walter; Aebersold, Ruedi

    2013-06-01

    We report a high quality and system-wide proteome catalogue covering 71% (3,542 proteins) of the predicted genes of fission yeast, Schizosaccharomyces pombe, presenting the largest protein dataset to date for this important model organism. We obtained this high proteome and peptide (11.4 peptides/protein) coverage by a combination of extensive sample fractionation, high resolution Orbitrap mass spectrometry, and combined database searching using the iProphet software as part of the Trans-Proteomics Pipeline. All raw and processed data are made accessible in the S. pombe PeptideAtlas. The identified proteins showed no biases in functional properties and allowed global estimation of protein abundances. The high coverage of the PeptideAtlas allowed correlation with transcriptomic data in a system-wide manner indicating that post-transcriptional processes control the levels of at least half of all identified proteins. Interestingly, the correlation was not equally tight for all functional categories ranging from r(s) >0.80 for proteins involved in translation to r(s) pombe PeptideAtlas together with the generated proteotypic peptide spectral library will be a useful resource for future targeted, in-depth, and quantitative proteomic studies on this microorganism.

  9. African Journal of Livestock Extension

    African Journals Online (AJOL)

    African Journal of Livestock Extension aims to bring to the fore the role and significance of livestock in maintaining rural, peri-urban and urban households, vis-à-vis its impact on poverty alleviation, household nutritional status, economic coping strategy and provision of employment. The focus of the journal relates to all ...

  10. Longest common extensions in trees

    DEFF Research Database (Denmark)

    Bille, Philip; Gawrychowski, Pawel; Gørtz, Inge Li

    2016-01-01

    The longest common extension (LCE) of two indices in a string is the length of the longest identical substrings starting at these two indices. The LCE problem asks to preprocess a string into a compact data structure that supports fast LCE queries. In this paper we generalize the LCE problem to t...

  11. Dept. of Agricultural Economics & Extension

    African Journals Online (AJOL)

    duce poverty include education, credit, durable assets, living in the forest belt and in the south of the country. .... underscores the importance of education and extension services in the technology adoption/diffusion process. Poverty is a ...... Detwerminantes de la Pobreza de los hogares, México. Revista Mexicana de ...

  12. Extension Resources for International Trade

    Science.gov (United States)

    Seal, Susan D.

    2016-01-01

    With the opening of additional trade partnerships, the reduction of global transportation and communication costs, and the increase in demand for U.S. agricultural products and services, international trade is an area of great importance to more and more Extension clients and stakeholders. This article provides information about the primary…

  13. Symmetrical Extensions of Dirichlet Operators

    CERN Document Server

    Us, A G

    1997-01-01

    There is constructed and considered the extension of classical Diriclet operator corresponding to uniformly log-concave measure in the space of symmetric differential forms. Sufficient conditions for its essential self-adjointness in one-dimensional case as well as for the same of its "sypersymmetric" part in general situations are given.

  14. Extensiveness of Farmers' Buying Process

    NARCIS (Netherlands)

    Kool, M.; Meulenberg, M.T.G.; Broens, D.F.

    1997-01-01

    In this article we study farmers' buying processes, in particular the selection of a supplier for a given farm input. Extensiveness of farmers' buying processes is defined as the degree information acquisition and alternative evaluation effort carried out to prepare that selection. Hypotheses,

  15. Poincare Algebra Extension with Tensor Generator

    OpenAIRE

    Soroka, Dmitrij V.; Soroka, Vyacheslav A.

    2005-01-01

    A tensor extension of the Poincar\\'e algebra is proposed for the arbitrary dimensions. Casimir operators of the extension are constructed. A possible supersymmetric generalization of this extension is also found in the dimensions $D=2,3,4$.

  16. Tensor extension of the Poincare algebra

    Energy Technology Data Exchange (ETDEWEB)

    Soroka, Dmitrij V. [Kharkov Institute of Physics and Technology, 61108 Kharkov (Ukraine)]. E-mail: dsoroka@kipt.kharkov.ua; Soroka, Vyacheslav A. [Kharkov Institute of Physics and Technology, 61108 Kharkov (Ukraine)]. E-mail: vsoroka@kipt.kharkov.ua

    2005-02-10

    A tensor extension of the Poincare algebra is proposed for the arbitrary dimensions. Casimir operators of the extension are constructed. A possible supersymmetric generalization of this extension is also found in the dimensions D=2,3,4.

  17. Genome-wide transcriptome analyses of silicon metabolism in Phaeodactylum tricornutum reveal the multilevel regulation of silicic acid transporters.

    Directory of Open Access Journals (Sweden)

    Guillaume Sapriel

    2009-10-01

    Full Text Available Diatoms are largely responsible for production of biogenic silica in the global ocean. However, in surface seawater, Si(OH(4 can be a major limiting factor for diatom productivity. Analyzing at the global scale the genes networks involved in Si transport and metabolism is critical in order to elucidate Si biomineralization, and to understand diatoms contribution to biogeochemical cycles.Using whole genome expression analyses we evaluated the transcriptional response to Si availability for the model species Phaeodactylum tricornutum. Among the differentially regulated genes we found genes involved in glutamine-nitrogen pathways, encoding putative extracellular matrix components, or involved in iron regulation. Some of these compounds may be good candidates for intracellular intermediates involved in silicic acid storage and/or intracellular transport, which are very important processes that remain mysterious in diatoms. Expression analyses and localization studies gave the first picture of the spatial distribution of a silicic acid transporter in a diatom model species, and support the existence of transcriptional and post-transcriptional regulations.Our global analyses revealed that about one fourth of the differentially expressed genes are organized in clusters, underlying a possible evolution of P. tricornutum genome, and perhaps other pennate diatoms, toward a better optimization of its response to variable environmental stimuli. High fitness and adaptation of diatoms to various Si levels in marine environments might arise in part by global regulations from gene (expression level to genomic (organization in clusters, dosage compensation by gene duplication, and by post-transcriptional regulation and spatial distribution of SIT proteins.

  18. Linear programming foundations and extensions

    CERN Document Server

    Vanderbei, Robert J

    2001-01-01

    Linear Programming: Foundations and Extensions is an introduction to the field of optimization. The book emphasizes constrained optimization, beginning with a substantial treatment of linear programming, and proceeding to convex analysis, network flows, integer programming, quadratic programming, and convex optimization. The book is carefully written. Specific examples and concrete algorithms precede more abstract topics. Topics are clearly developed with a large number of numerical examples worked out in detail. Moreover, Linear Programming: Foundations and Extensions underscores the purpose of optimization: to solve practical problems on a computer. Accordingly, the book is coordinated with free efficient C programs that implement the major algorithms studied: -The two-phase simplex method; -The primal-dual simplex method; -The path-following interior-point method; -The homogeneous self-dual methods. In addition, there are online JAVA applets that illustrate various pivot rules and variants of the simplex m...

  19. Extension agents and conflict narratives

    DEFF Research Database (Denmark)

    Bond, Jennifer Lauren

    2016-01-01

    Purpose: This work investigated the narratives of development extensionists in relation to natural resource conflict, in order to understand the competing discourses surrounding the wicked problems of natural resource management in Laikipia County, Kenya. Methodology: Q methodology was used...... to elicit the conflict narratives present among extension professionals. A concourse of 221 statements were devised from interviews and group discussions with key informants and a final sample of 49 statements was used for the sorting. Thirteen Q-sorts were undertaken with among rural extension...... professionals from government, non-government, faith-based and private organizations. Findings: Four factors were elicited from the data, labelled—A: ‘Improved Leadership’; B: ‘Resource-centred conflict’; C: ‘Improved Governance’; and D: ‘Improved Management’. Practical Implications: Narratives of neo...

  20. Rosacea with extensive extrafacial lesions

    OpenAIRE

    Pereira, TM; Vieira, AP; Sousa-Basto, A

    2008-01-01

    Rosacea is a very common skin disorder in the clinical practice that primarily affects the convex areas of the face. Extrafacial rosacea lesions have occasionally been described, but extensive involvement is exceptional. In the absence of its typical clinical or histological features, the diagnosis of extrafacial rosacea may be problematic. We describe an unusual case of rosacea with very exuberant extrafacial lesions, when compared with the limited involvement of the face.

  1. An Extension for ESO Headquarters

    Science.gov (United States)

    Fischer, Robert; Walsh, Jeremy

    2009-03-01

    The ESO Headquarters was completed in 1980, but is now too small to house all the ESO staff and currently only about 50% reside in the original building. A decision was taken to seek an extension to the Headquarters building in close proximity to the current one and a competition was launched for architectural designs. Three designs were shortlisted and the process of selection for the final design is described. Construction will begin in 2010 and is due for completion in 2012.

  2. Building the capacity of agricultural extension personnel for effective ...

    African Journals Online (AJOL)

    Findings reveal a tremendous shortage in the number and quality of extension personnel across the country as major reason for the poor performance of the ADPs thereby leaving no hope for the “beautiful” transformation agenda. This paper strongly recommends immediate recruitment of new hands as well as full ...

  3. Determinants Of Job Satisfaction Of Field Extension Workers In ...

    African Journals Online (AJOL)

    Three major factors were identified as strong determinants of job satisfaction of the field extension workers namely interpersonal relationship, organizational policies, and conditions of service. The study revealed that attainment of certain policy issues depends largely on interpersonal relationship in the organization.

  4. Factors Influencing Perceptions of Service Quality in Cooperative Extension Workers

    Science.gov (United States)

    Anaza, Nwamaka A.; Rutherford, Brian N.; Widdows, Richard

    2012-01-01

    The authors examined the direct and indirect impact of empowerment on service quality as perceived by Extension staff. Using a sample 283 respondents, the results revealed that along with empowerment, constructs such as job satisfaction and organizational identification positively affected service quality. Undoubtedly, each of these variables…

  5. Sources And Use Of Extension Information Among Maize Farmers In ...

    African Journals Online (AJOL)

    Furthermore, findings revealed that the respondents utilized extension information, to a great extent on the following technologies/recommendations; improved maize, seed rate, seed dressing, plant spacing, fertilizer application, post-harvest processing, and storage. Recommendations on herbicides and pesticides were ...

  6. Identifying Invasive Species Educational Needs in Florida: Opportunities for Extension

    Science.gov (United States)

    Huang, Pei-wen; Lamm, Alexa J.

    2016-01-01

    Florida's ecology has been adversely affected by invasive species. In Florida, a study was conducted to explore opportunities for Extension educators to contribute to combating the issue of invasive species. Florida residents' responses were captured through the use of an online public opinion survey. The findings revealed a need for invasive…

  7. Extensive Growth of an Anaplastic Meningioma

    Directory of Open Access Journals (Sweden)

    Hajrullah Ahmeti

    2013-01-01

    Full Text Available We present the case of a 30-year-old male patient with an almost complete destruction of the calvarial bone through an anaplastic meningioma diagnosed in line with dizziness. Neuroimaging revealed an extensive growing, contrast enhancing lesion expanding at the supra- and infratentorial convexity, infiltrating and destroying large parts of the skull, and infiltrating the skin. Due to progressive ataxia and dysarthria with proven tumor growth in the posterior fossa in the continuing course, parts of the tumor were resected. A surgical procedure with the aim of complete tumor resection in a curative manner was not possible. Six months after the first operation, due to a new tumor progression, most extensive tumor resection was performed. Due to the aggressive and destructive growth with a high rate of recurrence and tendency of metastases, anaplastic meningiomas can be termed as malignant tumors. The extrinsic growth masks the tumor until they reach a size, which makes these tumors almost unresectable. In the best case scenarios, the five-year survival is about 50%. With the presented case, we would like to show the aggressive behavior of anaplastic meningiomas in a very illustrative way. Chemotherapy, radiotherapy, and surgery reach their limits in this tumor entity.

  8. Parallel Extension Tectonics (PET): Early Cretaceous tectonic extension of the Eastern Eurasian continent

    Science.gov (United States)

    Liu, Junlai; Ji, Mo; Ni, Jinlong; Guan, Huimei; Shen, Liang

    2017-04-01

    The present study reports progress of our recent studies on the extensional structures in eastern North China craton and contiguous areas. We focus on characterizing and timing the formation/exhumation of the extensional structures, the Liaonan metamorphic core complex (mcc) and the Dayingzi basin from the Liaodong peninsula, the Queshan mcc, the Wulian mcc and the Zhucheng basin from the Jiaodong peninsula, and the Dashan magmatic dome within the Sulu orogenic belt. Magmatic rocks (either volcanic or plutonic) are ubiquitous in association with the tectonic extension (both syn- and post-kinematic). Evidence for crustal-mantle magma mixing are popular in many syn-kinematic intrusions. Geochemical analysis reveals that basaltic, andesitic to rhyolitic magmas were generated during the tectonic extension. Sr-Nd isotopes of the syn-kinematic magmatic rocks suggest that they were dominantly originated from ancient or juvenile crust partly with mantle signatures. Post-kinematic mafic intrusions with ages from ca. 121 Ma to Cenozoic, however, are of characteristic oceanic island basalts (OIB)-like trace element distribution patterns and relatively depleted radiogenic Sr-Nd isotope compositions. Integrated studies on the extensional structures, geochemical signatures of syn-kinematic magmatic rocks (mostly of granitic) and the tectono-magmatic relationships suggest that extension of the crust and the mantle lithosphere triggered the magmatisms from both the crust and the mantle. The Early Cretaceous tectono-magmatic evolution of the eastern Eurasian continent is governed by the PET in which the tectonic processes is subdivided into two stages, i.e. an early stage of tectonic extension, and a late stage of collapse of the extended lithosphere and transformation of lithospheric mantle. During the early stage, tectonic extension of the lithosphere led to detachment faulting in both the crust and mantle, resulted in the loss of some of the subcontinental roots, gave rise to

  9. Mapping the mouse Allelome reveals tissue-specific regulation of allelic expression

    Science.gov (United States)

    Andergassen, Daniel; Dotter, Christoph P; Wenzel, Daniel; Sigl, Verena; Bammer, Philipp C; Muckenhuber, Markus; Mayer, Daniela; Kulinski, Tomasz M; Theussl, Hans-Christian; Penninger, Josef M; Bock, Christoph; Barlow, Denise P; Pauler, Florian M; Hudson, Quanah J

    2017-01-01

    To determine the dynamics of allelic-specific expression during mouse development, we analyzed RNA-seq data from 23 F1 tissues from different developmental stages, including 19 female tissues allowing X chromosome inactivation (XCI) escapers to also be detected. We demonstrate that allelic expression arising from genetic or epigenetic differences is highly tissue-specific. We find that tissue-specific strain-biased gene expression may be regulated by tissue-specific enhancers or by post-transcriptional differences in stability between the alleles. We also find that escape from X-inactivation is tissue-specific, with leg muscle showing an unexpectedly high rate of XCI escapers. By surveying a range of tissues during development, and performing extensive validation, we are able to provide a high confidence list of mouse imprinted genes including 18 novel genes. This shows that cluster size varies dynamically during development and can be substantially larger than previously thought, with the Igf2r cluster extending over 10 Mb in placenta. DOI: http://dx.doi.org/10.7554/eLife.25125.001 PMID:28806168

  10. Coal Combustion Products Extension Program

    Energy Technology Data Exchange (ETDEWEB)

    Tarunjit S. Butalia; William E. Wolfe

    2006-01-11

    This final project report presents the activities and accomplishments of the ''Coal Combustion Products Extension Program'' conducted at The Ohio State University from August 1, 2000 to June 30, 2005 to advance the beneficial uses of coal combustion products (CCPs) in highway and construction, mine reclamation, agricultural, and manufacturing sectors. The objective of this technology transfer/research program at The Ohio State University was to promote the increased use of Ohio CCPs (fly ash, FGD material, bottom ash, and boiler slag) in applications that are technically sound, environmentally benign, and commercially competitive. The project objective was accomplished by housing the CCP Extension Program within The Ohio State University College of Engineering with support from the university Extension Service and The Ohio State University Research Foundation. Dr. Tarunjit S. Butalia, an internationally reputed CCP expert and registered professional engineer, was the program coordinator. The program coordinator acted as liaison among CCP stakeholders in the state, produced information sheets, provided expertise in the field to those who desired it, sponsored and co-sponsored seminars, meetings, and speaking at these events, and generally worked to promote knowledge about the productive and proper application of CCPs as useful raw materials. The major accomplishments of the program were: (1) Increase in FGD material utilization rate from 8% in 1997 to more than 20% in 2005, and an increase in overall CCP utilization rate of 21% in 1997 to just under 30% in 2005 for the State of Ohio. (2) Recognition as a ''voice of trust'' among Ohio and national CCP stakeholders (particularly regulatory agencies). (3) Establishment of a national and international reputation, especially for the use of FGD materials and fly ash in construction applications. It is recommended that to increase Ohio's CCP utilization rate from 30% in 2005 to

  11. EXTENSION OPERATOR AND NEURON NETWORK

    OpenAIRE

    LUIZ CARLOS C PEDROZA

    1997-01-01

    Na tese se desenvolve a teoria do Operador de extensão (OPEX) e utiliza-se desta para compreender melhor algumas questões relativas a teoria de Redes Neurais(RN). A abordagem de Redes Neurais pela ótica do Operador de Extensão possibilita também um melhoramento no algoritmo de retropropagação de erro usado no treinamento supervisionado das Redes Neurais. In this thesis, theory of Extension Operator is developed and used to understand some questions related to ...

  12. Combined Dietotherapy after Extensive Hepatectomies

    Directory of Open Access Journals (Sweden)

    V. V. Kiselev

    2007-01-01

    Full Text Available Objective: to compare the time course of nutritional changes in relation to the components of nutritive support in the early postoperative period after extensive hepatectomies.Subjects and methods. Beginning with the 1st postoperative day, 12 patients had parenteral feeding comprising 20% glucose, fat emulsions, and specialized amino acid solutions (Group 1. Beginning with the same day, 14 patients were given the parenteral formula Oliclinomel (Group 2. Starting from the 2nd postoperative day, both groups additionally received a balanced feeding formula by sipping.Results. Postoperatively, first-to-second degree encephalopathy was recorded in both groups. Positive changes as consciousness recovery were found in both Group 1 in which the patients used branched-chain amino acid-enriched solutions and Group 2 (parenteral Oliclinomel feeding. The patients under examination were not given albumin solutions and fresh frozen plasma in the postoperative period. Moreover, by postoperative day 7, there were significant increases in the levels of albumin and total protein in Groups 1 and 2, in those of cholinesterase and the absolute count of lymphocytes, and a reduction in the concentration of C-reactive protein.Conclusion. Combined parenteral and enteral feedings are effective in patients after extensive hepatectomies. The parenteral feeding formula Oliclinomel may be used in this group of patients. 

  13. An Expressive Extension of TLC

    DEFF Research Database (Denmark)

    Henriksen, Jesper Gulmann

    2002-01-01

    A temporal logic of causality (TLC) was introduced by Alur, Penczek and Peled in [1]. It is basically a linear time temporal logic interpreted over Mazurkiewicz traces which allows quantification over causal chains. Through this device one can directly formulate causality properties of distributed...... systems. In this paper we consider an extension of TLC by strengthening the chain quantification operators. We show that our logic TLC* adds to the expressive power of TLC. We do so by defining an Ehrenfeucht-Fraïssé game to capture the expressive power of TLC. We then exhibit a property and by means...... of this game prove that the chosen property is not definable in TLC. We then show that the same property is definable in TLC*. We prove in fact the stronger result that TLC* is expressively stronger than TLC exactly when the dependency relation associated with the underlying trace alphabet is not transitive....

  14. Fluorescein-related extensive jaundice.

    Science.gov (United States)

    Kalkan, Asim; Turedi, Suleyman; Aydin, Ibrahim

    2015-03-01

    Fluorescein is a chemical dye frequently used in eye diseases to assess blood flow in the retina, choroid tissue, and iris. Although it has many known adverse effects, it has not previously been reported to lead to jaundice. The purpose of this case report was to emphasize that for patients presenting at the emergency department with jaundice symptoms, it should not be forgotten by emergency physicians that jaundice can develop after fluorescein angiography. Case: A 65-year-old woman presented at the emergency department with extensive jaundice that had developed on her entire body a few hours after fluorescein angiography applied because of vision impairment. The test results for all the diseases considered to cause jaundice were normal,and fluorescein-related jaundice was diagnosed. Conclusion: A detailed anamnesis should be taken when jaundice is seen in patients who have undergone fluorescein angiography, and it should not be forgotten that fluorescein dye is a rare cause of jaundice.

  15. Competency Modeling in Extension Education: Integrating an Academic Extension Education Model with an Extension Human Resource Management Model

    Science.gov (United States)

    Scheer, Scott D.; Cochran, Graham R.; Harder, Amy; Place, Nick T.

    2011-01-01

    The purpose of this study was to compare and contrast an academic extension education model with an Extension human resource management model. The academic model of 19 competencies was similar across the 22 competencies of the Extension human resource management model. There were seven unique competencies for the human resource management model.…

  16. Dissecting the fission yeast regulatory network reveals phase-specific control elements of its cell cycle

    Directory of Open Access Journals (Sweden)

    Liu Liwen

    2009-09-01

    Full Text Available Abstract Background Fission yeast Schizosaccharomyces pombe and budding yeast Saccharomyces cerevisiae are among the original model organisms in the study of the cell-division cycle. Unlike budding yeast, no large-scale regulatory network has been constructed for fission yeast. It has only been partially characterized. As a result, important regulatory cascades in budding yeast have no known or complete counterpart in fission yeast. Results By integrating genome-wide data from multiple time course cell cycle microarray experiments we reconstructed a gene regulatory network. Based on the network, we discovered in addition to previously known regulatory hubs in M phase, a new putative regulatory hub in the form of the HMG box transcription factor SPBC19G7.04. Further, we inferred periodic activities of several less known transcription factors over the course of the cell cycle, identified over 500 putative regulatory targets and detected many new phase-specific and conserved cis-regulatory motifs. In particular, we show that SPBC19G7.04 has highly significant periodic activity that peaks in early M phase, which is coordinated with the late G2 activity of the forkhead transcription factor fkh2. Finally, using an enhanced Bayesian algorithm to co-cluster the expression data, we obtained 31 clusters of co-regulated genes 1 which constitute regulatory modules from different phases of the cell cycle, 2 whose phase order is coherent across the 10 time course experiments, and 3 which lead to identification of phase-specific control elements at both the transcriptional and post-transcriptional levels in S. pombe. In particular, the ribosome biogenesis clusters expressed in G2 phase reveal new, highly conserved RNA motifs. Conclusion Using a systems-level analysis of the phase-specific nature of the S. pombe cell cycle gene regulation, we have provided new testable evidence for post-transcriptional regulation in the G2 phase of the fission yeast cell cycle

  17. Extension contact and professional competencies needed by ...

    African Journals Online (AJOL)

    Extension contact and professional competencies needed by extension agents in the Central Region of Ghana for effective transfer of fish-processing technologies to small-scale women in fish processing - Provisional Communication.

  18. 7 CFR 15b.27 - Extension education.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 1 2010-01-01 2010-01-01 false Extension education. 15b.27 Section 15b.27 Agriculture... Education § 15b.27 Extension education. (a) General. A recipient to which this subpart applies that provides extension education may not, on the basis of handicap, exclude qualified handicapped persons. A recipient...

  19. Improving the Extension Facilities in C+

    Energy Technology Data Exchange (ETDEWEB)

    Dubois, P F; Scott, B A

    1999-09-24

    CXX is a facility for extending Python using C++. Recently, the authors have substantially revised and improved the way in which you create extension objects and extension modules in C++. The method is now much more natural and has much less overhead, both in the code generated and in the effort needed to create the objects and extensions.

  20. Effectiveness Of Communication Outreach Strategies Of Extension ...

    African Journals Online (AJOL)

    Communication is a major component of agricultural extension and extension agents utilize various methods to deliver messages to their clienteles. The paper focused on the effectiveness of communication outreach strategies of extension agents in Imo State, Nigeria. Data for the study was collected with the aid of ...

  1. Agricultural Extension training needs of the Nongovernment ...

    African Journals Online (AJOL)

    Extension practitioners from the private sector are highly trained in the Natural Science. Some shortfalls in their Extension Science training have been identified. Perceived training needs in the Extension Science within this sector have been privatised. A number of possible training inputs and options are suggested. Options ...

  2. Extensive Reading and the Effect of Shadowing

    Science.gov (United States)

    Nakanishi, Takayuki; Ueda, Atsuko

    2011-01-01

    The aim of this study is to investigate the effects of extensive reading (ER) and shadowing on performance on reading comprehension tests. This study addressed the following research questions: (a) Can extensive reading improve students' reading comprehension? and (b) can shadowing enhance the effects of extensive reading? The participants in the…

  3. Rural Extension Services. Policy Research Working Paper.

    Science.gov (United States)

    Anderson, Jock R.; Feder, Gershon

    This paper analyzes the considerations that lead policy makers to undertake extension investments as a key public responsibility, as well as the complex set of factors and intra-agency incentives that explain variations in performance between different extension systems. The goals of extension include transferring knowledge from researchers to…

  4. Extensions of cutting problems: setups

    Directory of Open Access Journals (Sweden)

    Sebastian Henn

    2013-08-01

    Full Text Available Even though the body of literature in the area of cutting and packing is growing rapidly, research seems to focus on standard problems in the first place, while practical aspects are less frequently dealt with. This is particularly true for setup processes which arise in industrial cutting processes whenever a new cutting pattern is started (i.e. a pattern is different from its predecessor and the cutting equipment has to be prepared in order to meet the technological requirements of the new pattern. Setups involve the consumption of resources and the loss of production time capacity. Therefore, consequences of this kind must explicitly be taken into account for the planning and control of industrial cutting processes. This results in extensions to traditional models which will be reviewed here. We show how setups can be represented in such models, and we report on the algorithms which have been suggested for the determination of solutions of the respective models. We discuss the value of these approaches and finally point out potential directions of future research.

  5. [Extensively drug-resistant tuberculosis].

    Science.gov (United States)

    Lange, C; Grobusch, M P; Wagner, D

    2008-02-01

    Recently an increasing number of antibiotic-resistant MYCOBACTERIUM TUBERCULOSIS (MTB) strains have been described worldwide. The term XDR- (extensively drug-resistant) tuberculosis (TB) has been introduced by the World Health Organisation (WHO) to characterize multi-drug-resistant MTB strains that are in vitro resistant against fluorochinolones and one of the injectible substances amikacin, capreomycin or kanamycin in addition to isoniazid and rifampin. Strains of XDR-MTB are currently increasingly seen in HIV-seropositive individuals with tuberculosis in southern Africa, where these strains are passed by person-to person contact. XDR-TB has become a serious problem for the health administrations in this region. In contrast, cases of XDR-TB are only rarely seen in Germany so far, mainly among the population of pre-treated migrants from eastern Europe. The development of rapid diagnostic tests for resistance testing and new drugs for the treatment of tuberculosis has lacked support for several decades. The sudden emergence of XDR-MTB strains now warrants immediate action for the development of such tests and new classes of antibiotics to give all patients with TB a chance for a successful treatment.

  6. XPL the Extensible Presentation Language

    Directory of Open Access Journals (Sweden)

    A. Santangelo

    2009-01-01

    Full Text Available The last decade has witnessed a growing interest in the development of web interfaces enabling both multiple ways to access contents and, at the same time, fruition by multiple modalities of interaction (point-and-click, contents reading, voice commands, gestures, etc.. In this paper we describe a framework aimed at streamlining the design process of multi-channel, multimodal interfaces enabling full reuse of software components. This framework is called the eXtensible Presentation architecture and Language (XPL, a presentation language based on design pattern paradigm that keeps separated the presentation layer from the underlying programming logic. The language supplies a methodology to expedite multimodal interface development and to reduce the effort to implement interfaces for multiple access devices, by means of using the same code. This paper describes a methodology approach based on Visual Design Pattern (ViDP and Verbal Design Pattern (VeDP, offering examples of multimodal and multichannel interfaces created with the XPL Editor.

  7. Anaesthetic management of a case of schwannoma with intraoral extension

    Directory of Open Access Journals (Sweden)

    Mamta Bhardwaj

    2015-04-01

    Full Text Available Schwannoma is a benign nerve sheath tumour. This benign lesion frequently occurs in the soft tissues of head and neck region and has various complicated growth patterns. These patients can present a challenge to the anaesthesiologist due to intraoral extension, leading to difficult mask ventilation and intubation. We report a 16 year old male with mandibular nerve schwannoma with intraoral extension. Intraoral examination revealed a diffuse swelling in the left side of soft palate with deviation of uvula to right side. He was advised gargles with 4 ml of 2% xylocaine viscous and 2–3 puffs of 10% xylocaine spray done in oral cavity and oropharynx. Check laryngoscopy revealed Cormack and Lehane grade 1 view. Patient was intubated using standard induction technique and successfully managed

  8. Extensive Reading in the EFL Classroom: Benefits of a Face-to-Face Collaboration Activity

    Science.gov (United States)

    Kirchhoff, Cheryl

    2015-01-01

    Extensive reading is an approach to language education that has shown great promise for foreign language learners to acquire language; however, implementation reveals difficulty in maintaining student motivation to read over long periods of time. This study investigates students' experience of face-to-face talk about books in an extensive reading…

  9. Deep small RNA sequencing from the nematode Ascaris reveals conservation, functional diversification, and novel developmental profiles

    Science.gov (United States)

    Wang, Jianbin; Czech, Benjamin; Crunk, Amanda; Wallace, Adam; Mitreva, Makedonka; Hannon, Gregory J.; Davis, Richard E.

    2011-01-01

    Eukaryotic cells express several classes of small RNAs that regulate gene expression and ensure genome maintenance. Endogenous siRNAs (endo-siRNAs) and Piwi-interacting RNAs (piRNAs) mainly control gene and transposon expression in the germline, while microRNAs (miRNAs) generally function in post-transcriptional gene silencing in both somatic and germline cells. To provide an evolutionary and developmental perspective on small RNA pathways in nematodes, we identified and characterized known and novel small RNA classes through gametogenesis and embryo development in the parasitic nematode Ascaris suum and compared them with known small RNAs of Caenorhabditis elegans. piRNAs, Piwi-clade Argonautes, and other proteins associated with the piRNA pathway have been lost in Ascaris. miRNAs are synthesized immediately after fertilization in utero, before pronuclear fusion, and before the first cleavage of the zygote. This is the earliest expression of small RNAs ever described at a developmental stage long thought to be transcriptionally quiescent. A comparison of the two classes of Ascaris endo-siRNAs, 22G-RNAs and 26G-RNAs, to those in C. elegans, suggests great diversification and plasticity in the use of small RNA pathways during spermatogenesis in different nematodes. Our data reveal conserved characteristics of nematode small RNAs as well as features unique to Ascaris that illustrate significant flexibility in the use of small RNAs pathways, some of which are likely an adaptation to Ascaris' life cycle and parasitism. PMID:21685128

  10. Comprehensive RNA Polymerase II Interactomes Reveal Distinct and Varied Roles for Each Phospho-CTD Residue

    Directory of Open Access Journals (Sweden)

    Kevin M. Harlen

    2016-06-01

    Full Text Available Transcription controls splicing and other gene regulatory processes, yet mechanisms remain obscure due to our fragmented knowledge of the molecular connections between the dynamically phosphorylated RNA polymerase II (Pol II C-terminal domain (CTD and regulatory factors. By systematically isolating phosphorylation states of the CTD heptapeptide repeat (Y1S2P3T4S5P6S7, we identify hundreds of protein factors that are differentially enriched, revealing unappreciated connections between the Pol II CTD and co-transcriptional processes. These data uncover a role for threonine-4 in 3′ end processing through control of the transition between cleavage and termination. Furthermore, serine-5 phosphorylation seeds spliceosomal assembly immediately downstream of 3′ splice sites through a direct interaction with spliceosomal subcomplex U1. Strikingly, threonine-4 phosphorylation also impacts splicing by serving as a mark of co-transcriptional spliceosome release and ensuring efficient post-transcriptional splicing genome-wide. Thus, comprehensive Pol II interactomes identify the complex and functional connections between transcription machinery and other gene regulatory complexes.

  11. Deep sequencing reveals unique small RNA repertoire that is regulated during head regeneration in Hydra magnipapillata.

    Science.gov (United States)

    Krishna, Srikar; Nair, Aparna; Cheedipudi, Sirisha; Poduval, Deepak; Dhawan, Jyotsna; Palakodeti, Dasaradhi; Ghanekar, Yashoda

    2013-01-07

    Small non-coding RNAs such as miRNAs, piRNAs and endo-siRNAs fine-tune gene expression through post-transcriptional regulation, modulating important processes in development, differentiation, homeostasis and regeneration. Using deep sequencing, we have profiled small non-coding RNAs in Hydra magnipapillata and investigated changes in small RNA expression pattern during head regeneration. Our results reveal a unique repertoire of small RNAs in hydra. We have identified 126 miRNA loci; 123 of these miRNAs are unique to hydra. Less than 50% are conserved across two different strains of Hydra vulgaris tested in this study, indicating a highly diverse nature of hydra miRNAs in contrast to bilaterian miRNAs. We also identified siRNAs derived from precursors with perfect stem-loop structure and that arise from inverted repeats. piRNAs were the most abundant small RNAs in hydra, mapping to transposable elements, the annotated transcriptome and unique non-coding regions on the genome. piRNAs that map to transposable elements and the annotated transcriptome display a ping-pong signature. Further, we have identified several miRNAs and piRNAs whose expression is regulated during hydra head regeneration. Our study defines different classes of small RNAs in this cnidarian model system, which may play a role in orchestrating gene expression essential for hydra regeneration.

  12. Comprehensive Analysis of mRNA Methylation Reveals Enrichment in 3' UTRs and Near Stop Codons

    Science.gov (United States)

    Meyer, Kate D.; Saletore, Yogesh; Zumbo, Paul; Elemento, Olivier; Mason, Christopher E.; Jaffrey, Samie R.

    2012-01-01

    SUMMARY Methylation of the N6 position of adenosine (m6A) is a post-transcriptional modification of RNA whose prevalence and physiological relevance is poorly understood. The recent discovery that FTO, an obesity risk gene, encodes an m6A demethylase implicates m6A as an important regulator of physiological processes. Here we present a method for transcriptome-wide m6A localization, which combines m6A-specific methylated RNA immunoprecipitation with next-generation sequencing (MeRIP-Seq). We use this method to identify mRNAs of 7,676 mammalian genes that contain m6A, indicating that m6A is a common base modification of mRNA. The m6A modification exhibits tissue-specific regulation and is markedly increased throughout brain development. We find that m6A sites are enriched near stop codons and in 3' UTRs, and we uncover an association between m6A residues and microRNA binding sites within 3' UTRs. These findings provide a resource for identifying transcripts that are substrates for adenosine methylation and reveal insights into the epigenetic regulation of the mammalian transcriptome. PMID:22608085

  13. Two endogenous proteins that induce cell wall extension in plants

    Science.gov (United States)

    McQueen-Mason, S.; Durachko, D. M.; Cosgrove, D. J.

    1992-01-01

    Plant cell enlargement is regulated by wall relaxation and yielding, which is thought to be catalyzed by elusive "wall-loosening" enzymes. By employing a reconstitution approach, we found that a crude protein extract from the cell walls of growing cucumber seedlings possessed the ability to induce the extension of isolated cell walls. This activity was restricted to the growing region of the stem and could induce the extension of isolated cell walls from various dicot stems and the leaves of amaryllidaceous monocots, but was less effective on grass coleoptile walls. Endogenous and reconstituted wall extension activities showed similar sensitivities to pH, metal ions, thiol reducing agents, proteases, and boiling in methanol or water. Sequential HPLC fractionation of the active wall extract revealed two proteins with molecular masses of 29 and 30 kD associated with the activity. Each protein, by itself, could induce wall extension without detectable hydrolytic breakdown of the wall. These proteins appear to mediate "acid growth" responses of isolated walls and may catalyze plant cell wall extension by a novel biochemical mechanism.

  14. Inducible Interleukin 32 (IL-32) Exerts Extensive Antiviral Function via Selective Stimulation of Interferon λ1 (IFN-λ1)*

    Science.gov (United States)

    Li, Yongkui; Xie, Jiajia; Xu, Xiupeng; Liu, Li; Wan, Yushun; Liu, Yingle; Zhu, Chengliang; Zhu, Ying

    2013-01-01

    Interleukin (IL)-32 has been recognized as a proinflammatory cytokine that participates in responses to viral infection. However, little is known about how IL-32 is induced in response to viral infection and the mechanisms of IL-32-mediated antiviral activities. We discovered that IL-32 is elevated by hepatitis B virus (HBV) infection both in vitro and in vivo and that HBV induced IL-32 expression at the level of both transcription and post-transcription. Furthermore, microRNA-29b was found to be a key factor in HBV-regulated IL-32 expression by directly targeting the mRNA 3′-untranslated region of IL-32. Antiviral analysis showed that IL-32 was not sufficient to alter HBV replication in HepG2.2.15 cells. To mimic the viremic phase of viral infection, freshly isolated peripheral blood mononuclear cells were treated with IL-32γ, the secretory isoform, and the supernatants were used for antiviral assays. Surprisingly, these supernatants exhibited extensive antiviral activity against multiplex viruses besides HBV. Thus, we speculated that the IL-32γ-treated peripheral blood mononuclear cells produced and secreted an unknown antiviral factor. Using antibody neutralization assays, we identified the factor as interferon (IFN)-λ1 and not IFN-α. Further studies indicated that IL-32γ effectively inhibited HBV replication in a hydrodynamic injection mouse model. Clinical data showed that elevated levels of IFN-λ1 both in serum and liver tissue of HBV patients were positively correlated to the increased levels of IL-32. Our results demonstrate that elevated IL-32 levels during viral infection mediate antiviral effects by stimulating the expression of IFN-λ1. PMID:23729669

  15. Extension of platelet concentrate storage.

    Science.gov (United States)

    Simon, T L; Nelson, E J; Carmen, R; Murphy, S

    1983-01-01

    Extension of the storage time of platelet concentrates in a satellite bag which is part of a new blood bag system was studied by reinfusing autologous 51Cr-labeled platelets into normal volunteers, and measuring postinfusion platelet counts and bleeding times in patients requiring platelet transfusions. This satellite bag, made of polyvinylchloride plasticized with a new agent, was found to protect platelet concentrates against fall of pH better than other containers studied. This protection was felt to be due to the greater gas permeability of the new plastic. Mean in vivo recovery and half-life (greater than 31% and 3.3 days, respectively) of autologous reinfused platelets were satisfactory following 5 days of storage. Following 7 days of storage, mean recovery was 41 percent and half-life was 2.8 days. Peripheral platelet count increments in patients following platelet transfusions with concentrates stored 4 to 7 days in the new plastic were comparable to increments following transfusion of platelets stored 2 to 3 days in the other plastics studied. Bleeding times shortened in three of four patients receiving platelet concentrates stored from 4 to 6 days in the new plastic. Platelet concentrates stored in the new bag at 20 to 24 degrees C with flat-bed or elliptical agitation could be transfused for up to 5 days following phlebotomy with acceptable clinical results. The new plastic container is promising for storage of platelet concentrates for up to 7 days. Due to the higher pH of 50-ml platelet concentrates stored in bags made with the new plastic, the concentrates were superior at any storage interval to those stored in bags made of the other plastics studied.

  16. Extension Large Colon Resection in 12 Horses

    Science.gov (United States)

    Arighi, Mimi; Ducharme, Norman G.; Horney, F. Donald.; Livesey, Michael A.

    1987-01-01

    Extensive resection (50-75%) of the large colon was performed in 12 horses. Indications for resection were: loss of viability due to large colon volvulus (seven), thromboembolic episode (three), impairment of flow of ingesta due to adhesions (one), or congenital abnormalities (one). The time required to correct the primary cause of abdominal pain and complete the resection ranged from 2.5 to 4.75 hours. Three horses had severe musculoskeletal problems postoperatively and were euthanized in the recovery stall. Four other horses were euthanized early in the postoperative period because of: further large colon infarction (two), ileus (one), or small intestinal problems (one). Five horses survived with no apparent nutritional or metabolic problems during two to three weeks of hospitalization. Clinical data were obtained from these horses from nine months to eighteen months postoperatively and revealed no clinical or clinicopathological abnormalities in four of them; the fifth horse exhibited diarrhea and weight loss four months postoperatively but responded to diet change. PMID:17422768

  17. Knowledge and perception of extension workers towards ict utilization in agricultural extension service delivery in Gazipur district of Bangladesh

    Directory of Open Access Journals (Sweden)

    F.A. Prodhan

    2014-12-01

    Full Text Available The primary purpose of the study was to assess the extent of knowledge and perception of extension workers towards ICT utilization and to determine the relationship between the selected characteristics of the respondents and knowledge and perception of extension workers towards ICT utilization in extension service delivery. The study was conducted in Gazipur district and comprised proportionate random sample of 90 extension workers from five upazila of Gazipur district. A pre-tested interview schedule was used to collect data from the respondents. To measure the knowledge on ICT utilization 35 statements were selected regarding 7 ICT with five possible answer of each tools and a score of one was given to the right answer and zero to the wrong answer alternatively to measure the perception of the respondents rated each of 10 statements ICT utilization in agriculture on a 5-point Likert type scale and the total of these ratings formed perception index. The result of the study showed that out of seven ICT tools the knowledge of extension workers was highest in case of MS Word this was followed by internet/ web service and the lowest knowledge was found in case of Geographical Information System. It is observed that an overwhelming majority (88.9% of agricultural extension workers in the study area had low to medium knowledge towards ICT utilization. Findings reveal that the respondents had top most perception on the ICT utilization in respect of ‘Extension work can be greatly enhanced by ICT’ followed by on ‘The benefits of ICT use outweigh the financial burden involved’. The result also indicated that more than fourth-fifth (84.4% of the respondents had medium to high perception towards ICT utilization. There were significant relationship between service experience and use of the information sources of the respondents with their knowledge towards ICT utilization conversely innovativeness, cosmopoliteness and job satisfaction of the

  18. Extension systems in Southern African countries: A review | Oladele ...

    African Journals Online (AJOL)

    Global Approaches to Extension Practice: A Journal of Agricultural Extension ... programmes to improve rural areas, extensive grassroots coverage, use of ICT, high involvement of farmers in extension planning, potential for effective programme implementation, and effective setting of extension administration units.

  19. Extension of Mittag-Leffler function

    OpenAIRE

    Rahman, G.; K.S. Nisar; Mubeen, S; Arshad, M.

    2017-01-01

    In this paper, we present an extension of Mittag-Leffler function by using the extension of beta functions (\\"{O}zergin et al. in J. Comput. Appl. Math. 235 (2011), 4601-4610) and obtain some integral representation of this newly defined function. Also, we present the Mellin transform of this function in terms of Wright hypergeometric function. Furthermore, we show that the extended fractional derivative of the usual Mittag-Leffler function gives the extension of Mittag-Leffler function.

  20. Revealing the 1 nm/s Extensibility of Nanoscale Amorphous Carbon in a Scanning Electron Microscope

    DEFF Research Database (Denmark)

    Zhang, Wei

    2013-01-01

    In an ultra-high vacuum scanning electron microscope, the edged branches of amorphous carbon film (∼10 nm thickness) can be continuously extended with an eye-identifying speed (on the order of ∼1 nm/s) under electron beam. Such unusual mobility of amorphous carbon may be associated with deformati...... positive implications to explore some amorphous carbon as electron field emission device. SCANNING 35: 261-264, 2013. © 2012 Wiley Periodicals, Inc.......In an ultra-high vacuum scanning electron microscope, the edged branches of amorphous carbon film (∼10 nm thickness) can be continuously extended with an eye-identifying speed (on the order of ∼1 nm/s) under electron beam. Such unusual mobility of amorphous carbon may be associated with deformation...... promoted by the electric field, which resulted from an inner secondary electron potential difference from the main trunk of carbon film to the tip end of branches under electron beam. This result demonstrates importance of applying electrical effects to modify properties of carbon materials. It may have...

  1. Extensive Antibody Cross-reactivity among Infectious Gram-negative Bacteria Revealed by Proteome Microarray Analysis

    Science.gov (United States)

    2009-08-27

    DNA chip . One of four destination colonies that matched the expected insert size was selected and rearrayed into deep well plates with 2 yeast extract...Jagels, K., Karlyshev, A. V., Leather , S., Moule, S., Oyston, P. C., Quail, M., Rutherford, K., Simmonds, M., Skelton, J., Stevens, K., Whitehead, S...Snyder, M. (2001) Global analysis of protein activities using proteome chips . Science 293, 2101–2105 18. Schmid, K. E., Keasey, S. L., Pittman, P

  2. Sequencing wild and cultivated cassava and related species reveals extensive interspecific hybridization and genetic diversity.

    Science.gov (United States)

    Bredeson, Jessen V; Lyons, Jessica B; Prochnik, Simon E; Wu, G Albert; Ha, Cindy M; Edsinger-Gonzales, Eric; Grimwood, Jane; Schmutz, Jeremy; Rabbi, Ismail Y; Egesi, Chiedozie; Nauluvula, Poasa; Lebot, Vincent; Ndunguru, Joseph; Mkamilo, Geoffrey; Bart, Rebecca S; Setter, Tim L; Gleadow, Roslyn M; Kulakow, Peter; Ferguson, Morag E; Rounsley, Steve; Rokhsar, Daniel S

    2016-05-01

    Cassava (Manihot esculenta) provides calories and nutrition for more than half a billion people. It was domesticated by native Amazonian peoples through cultivation of the wild progenitor M. esculenta ssp. flabellifolia and is now grown in tropical regions worldwide. Here we provide a high-quality genome assembly for cassava with improved contiguity, linkage, and completeness; almost 97% of genes are anchored to chromosomes. We find that paleotetraploidy in cassava is shared with the related rubber tree Hevea, providing a resource for comparative studies. We also sequence a global collection of 58 Manihot accessions, including cultivated and wild cassava accessions and related species such as Ceará or India rubber (M. glaziovii), and genotype 268 African cassava varieties. We find widespread interspecific admixture, and detect the genetic signature of past cassava breeding programs. As a clonally propagated crop, cassava is especially vulnerable to pathogens and abiotic stresses. This genomic resource will inform future genome-enabled breeding efforts to improve this staple crop.

  3. Extensive homoeologous genome exchanges in allopolyploid crops revealed by mRNAseq-based visualization.

    Science.gov (United States)

    He, Zhesi; Wang, Lihong; Harper, Andrea L; Havlickova, Lenka; Pradhan, Akshay K; Parkin, Isobel A P; Bancroft, Ian

    2017-05-01

    Polyploidy, the possession of multiple sets of chromosomes, has been a predominant factor in the evolution and success of the angiosperms. Although artificially formed allopolyploids show a high rate of genome rearrangement, the genomes of cultivars and germplasm used for crop breeding were assumed stable and genome structural variation under the artificial selection process of commercial breeding has remained little studied. Here, we show, using a repurposed visualization method based on transcriptome sequence data, that genome structural rearrangement occurs frequently in varieties of three polyploid crops (oilseed rape, mustard rape and bread wheat), meaning that the extent of genome structural variation present in commercial crops is much higher than expected. Exchanges were found to occur most frequently where homoeologous chromosome segments are collinear to telomeres and in material produced as doubled haploids. The new insights into genome structural evolution enable us to reinterpret the results of recent studies and implicate homoeologous exchanges, not deletions, as being responsible for variation controlling important seed quality traits in rapeseed. Having begun to identify the extent of genome structural variation in polyploid crops, we can envisage new strategies for the global challenge of broadening crop genetic diversity and accelerating adaptation, such as the molecular identification and selection of genome deletions or duplications encompassing genes with trait-controlling dosage effects. © 2016 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

  4. Multiple ITS copies reveal extensive hybridization within Rheum (Polygonaceae), a genus that has undergone rapid radiation

    National Research Council Canada - National Science Library

    Wan, Dongshi; Sun, Yongshuai; Zhang, Xu; Bai, Xiaotao; Wang, Jun; Wang, Ailan; Milne, Richard

    2014-01-01

    During adaptive radiation events, characters can arise multiple times due to parallel evolution, but transfer of traits through hybridization provides an alternative explanation for the same character...

  5. Brown and polar bear Y chromosomes reveal extensive male-biased gene flow within brother lineages.

    Science.gov (United States)

    Bidon, Tobias; Janke, Axel; Fain, Steven R; Eiken, Hans Geir; Hagen, Snorre B; Saarma, Urmas; Hallström, Björn M; Lecomte, Nicolas; Hailer, Frank

    2014-06-01

    Brown and polar bears have become prominent examples in phylogeography, but previous phylogeographic studies relied largely on maternally inherited mitochondrial DNA (mtDNA) or were geographically restricted. The male-specific Y chromosome, a natural counterpart to mtDNA, has remained underexplored. Although this paternally inherited chromosome is indispensable for comprehensive analyses of phylogeographic patterns, technical difficulties and low variability have hampered its application in most mammals. We developed 13 novel Y-chromosomal sequence and microsatellite markers from the polar bear genome and screened these in a broad geographic sample of 130 brown and polar bears. We also analyzed a 390-kb-long Y-chromosomal scaffold using sequencing data from published male ursine genomes. Y chromosome evidence support the emerging understanding that brown and polar bears started to diverge no later than the Middle Pleistocene. Contrary to mtDNA patterns, we found 1) brown and polar bears to be reciprocally monophyletic sister (or rather brother) lineages, without signals of introgression, 2) male-biased gene flow across continents and on phylogeographic time scales, and 3) male dispersal that links the Alaskan ABC islands population to mainland brown bears. Due to female philopatry, mtDNA provides a highly structured estimate of population differentiation, while male-biased gene flow is a homogenizing force for nuclear genetic variation. Our findings highlight the importance of analyzing both maternally and paternally inherited loci for a comprehensive view of phylogeographic history, and that mtDNA-based phylogeographic studies of many mammals should be reevaluated. Recent advances in sequencing technology render the analysis of Y-chromosomal variation feasible, even in nonmodel organisms. © The Author 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  6. Analysis of patterns of bushmeat consumption reveals extensive exploitation of protected species in eastern Madagascar.

    Directory of Open Access Journals (Sweden)

    Richard K B Jenkins

    Full Text Available Understanding the patterns of wild meat consumption from tropical forests is important for designing approaches to address this major threat to biodiversity and mitigate potential pathways for transmission of emerging diseases. Bushmeat consumption has been particularly poorly studied in Madagascar, one of the world's hottest biodiversity hotspots. Studying bushmeat consumption is challenging as many species are protected and researchers must consider the incentives faced by informants. Using interviews with 1154 households in 12 communes in eastern Madagascar, as well as local monitoring data, we investigated the importance of socio-economic variables, taste preference and traditional taboos on consumption of 50 wild and domestic species. The majority of meals contain no animal protein. However, respondents consume a wide range of wild species and 95% of respondents have eaten at least one protected species (and nearly 45% have eaten more than 10. The rural/urban divide and wealth are important predictors of bushmeat consumption, but the magnitude and direction of the effect varies between species. Bushmeat species are not preferred and are considered inferior to fish and domestic animals. Taboos have provided protection to some species, particularly the Endangered Indri, but we present evidence that this taboo is rapidly eroding. By considering a variety of potential influences on consumption in a single study we have improved understanding of who is eating bushmeat and why. Evidence that bushmeat species are not generally preferred meats suggest that projects which increase the availability of domestic meat and fish may have success at reducing demand. We also suggest that enforcement of existing wildlife and firearm laws should be a priority, particularly in areas undergoing rapid social change. The issue of hunting as an important threat to biodiversity in Madagascar is only now being fully recognised. Urgent action is required to ensure that heavily hunted species are adequately protected.

  7. The organisation of Ebola virus reveals a capacity for extensive, modular polyploidy.

    Directory of Open Access Journals (Sweden)

    Daniel R Beniac

    Full Text Available BACKGROUND: Filoviruses, including Ebola virus, are unusual in being filamentous animal viruses. Structural data on the arrangement, stoichiometry and organisation of the component molecules of filoviruses has until now been lacking, partially due to the need to work under level 4 biological containment. The present study provides unique insights into the structure of this deadly pathogen. METHODOLOGY AND PRINCIPAL FINDINGS: We have investigated the structure of Ebola virus using a combination of cryo-electron microscopy, cryo-electron tomography, sub-tomogram averaging, and single particle image processing. Here we report the three-dimensional structure and architecture of Ebola virus and establish that multiple copies of the RNA genome can be packaged to produce polyploid virus particles, through an extreme degree of length polymorphism. We show that the helical Ebola virus inner nucleocapsid containing RNA and nucleoprotein is stabilized by an outer layer of VP24-VP35 bridges. Elucidation of the structure of the membrane-associated glycoprotein in its native state indicates that the putative receptor-binding site is occluded within the molecule, while a major neutralizing epitope is exposed on its surface proximal to the viral envelope. The matrix protein VP40 forms a regular lattice within the envelope, although its contacts with the nucleocapsid are irregular. CONCLUSIONS: The results of this study demonstrate a modular organization in Ebola virus that accommodates a well-ordered, symmetrical nucleocapsid within a flexible, tubular membrane envelope.

  8. The organisation of Ebola virus reveals a capacity for extensive, modular polyploidy.

    Science.gov (United States)

    Beniac, Daniel R; Melito, Pasquale L; Devarennes, Shauna L; Hiebert, Shannon L; Rabb, Melissa J; Lamboo, Lindsey L; Jones, Steven M; Booth, Timothy F

    2012-01-01

    Filoviruses, including Ebola virus, are unusual in being filamentous animal viruses. Structural data on the arrangement, stoichiometry and organisation of the component molecules of filoviruses has until now been lacking, partially due to the need to work under level 4 biological containment. The present study provides unique insights into the structure of this deadly pathogen. We have investigated the structure of Ebola virus using a combination of cryo-electron microscopy, cryo-electron tomography, sub-tomogram averaging, and single particle image processing. Here we report the three-dimensional structure and architecture of Ebola virus and establish that multiple copies of the RNA genome can be packaged to produce polyploid virus particles, through an extreme degree of length polymorphism. We show that the helical Ebola virus inner nucleocapsid containing RNA and nucleoprotein is stabilized by an outer layer of VP24-VP35 bridges. Elucidation of the structure of the membrane-associated glycoprotein in its native state indicates that the putative receptor-binding site is occluded within the molecule, while a major neutralizing epitope is exposed on its surface proximal to the viral envelope. The matrix protein VP40 forms a regular lattice within the envelope, although its contacts with the nucleocapsid are irregular. The results of this study demonstrate a modular organization in Ebola virus that accommodates a well-ordered, symmetrical nucleocapsid within a flexible, tubular membrane envelope.

  9. The complete genome sequence of Lactobacillus bulgaricus reveals extensive and ongoing reductive evolution.

    Science.gov (United States)

    van de Guchte, M; Penaud, S; Grimaldi, C; Barbe, V; Bryson, K; Nicolas, P; Robert, C; Oztas, S; Mangenot, S; Couloux, A; Loux, V; Dervyn, R; Bossy, R; Bolotin, A; Batto, J-M; Walunas, T; Gibrat, J-F; Bessières, P; Weissenbach, J; Ehrlich, S D; Maguin, E

    2006-06-13

    Lactobacillus delbrueckii ssp. bulgaricus (L. bulgaricus) is a representative of the group of lactic acid-producing bacteria, mainly known for its worldwide application in yogurt production. The genome sequence of this bacterium has been determined and shows the signs of ongoing specialization, with a substantial number of pseudogenes and incomplete metabolic pathways and relatively few regulatory functions. Several unique features of the L. bulgaricus genome support the hypothesis that the genome is in a phase of rapid evolution. (i) Exceptionally high numbers of rRNA and tRNA genes with regard to genome size may indicate that the L. bulgaricus genome has known a recent phase of important size reduction, in agreement with the observed high frequency of gene inactivation and elimination; (ii) a much higher GC content at codon position 3 than expected on the basis of the overall GC content suggests that the composition of the genome is evolving toward a higher GC content; and (iii) the presence of a 47.5-kbp inverted repeat in the replication termination region, an extremely rare feature in bacterial genomes, may be interpreted as a transient stage in genome evolution. The results indicate the adaptation of L. bulgaricus from a plant-associated habitat to the stable protein and lactose-rich milk environment through the loss of superfluous functions and protocooperation with Streptococcus thermophilus.

  10. Analysis of infantile fibrosarcoma reveals extensive T-cell responses within tumors: Implications for immunotherapy.

    Science.gov (United States)

    Zhu, Hua; Gu, Song; Yin, Minzhi; Shi, Min; Xin, Chao; Zhu, Jianmin; Wang, Jing; Huang, Siqi; Xie, Chenjie; Ma, Jing; Pan, Ci; Tang, Jingyan; Xu, Min; Bai, Xue-Feng

    2018-02-01

    Infantile fibrosarcoma (IFS) is a rare pediatric malignancy with relatively good prognosis, but the risk of progression or recurrence after therapy exists. To understand the immune microenvironment of IFS and determine if immunotherapy is a potential treatment, we analyzed T-cell responses in IFS tumors. IFS tumors were analyzed by immunohistochemistry and multicolor flow cytometry to characterize immune cell infiltration and function. Tumor infiltrating lymphocytes (TILs) were expanded in vitro and evaluated for recognition of autologous tumor cells. Real-time PCR was applied to evaluate tumor expression of chemokines/cytokines and tumor antigens. Significant infiltration of both CD4+ and CD8+ T cells was found in seven of 10 IFS but rarely found in age- and sex-matched rhabdomyosarcoma tumors. The TILs from recurrent IFS tumors expressed high levels of costimulatory molecules such as CD28, 4-1BB, and OX40, but little or no coinhibitory molecules such as PD-1 and CTLA4, Tim3, Lag3, and CD39. Upon activation, large portions of TILs produced IFN-γ and TNF-α. Eighteen out of 40 T cell lines generated from surgically removed tumors could recognize autologous tumor cells. Moreover, we found that IFS tumors expressed high levels of T-cell chemokines such as CXCL10 and CXCL16, and also classic tumor antigens such as CTAG2, GAGE, and NY-ESO-1, whose expression could be further enhanced by treatment with epigenetic modulator decitabine. IFS tumors are highly immunogenic and expansion of TILs followed by adoptive cell transfer could be a potential immunotherapy for IFS patients undergoing tumor recurrence. © 2017 Wiley Periodicals, Inc.

  11. Replication history of B lymphocytes reveals homeostatic proliferation and extensive antigen-induced B cell expansion

    NARCIS (Netherlands)

    M.C. van Zelm (Menno); T. Szczepanski (Tomasz); M. van der Burg (Mirjam); J.J.M. van Dongen (Jacques)

    2007-01-01

    textabstractThe contribution of proliferation to B lymphocyte homeostasis and antigen responses is largely unknown. We quantified the replication history of mouse and human B lymphocyte subsets by calculating the ratio between genomic coding joints and signal joints on kappa-deleting recombination

  12. Expanded target-chemical analysis reveals extensive mixed-organic-contaminant exposure in USA streams

    Science.gov (United States)

    Bradley, Paul M.; Journey, Celeste A.; Romanok, Kristin; Barber, Larry B.; Buxton, Herbert T.; Foreman, William; Furlong, Edward T.; Glassmeyer, Susan T.; Hladik, Michelle L.; Iwanowicz, Luke R.; Jones, Daniel K.; Kolpin, Dana W.; Kuivila, Kathryn M.; Loftin, Keith A.; Mills, Marc A.; Meyer, Michael T.; Orlando, James L.; Reilly, Timothy J.; Smalling, Kelly L.; Villeneuve, Daniel L.

    2017-01-01

    Surface water from 38 streams nationwide was assessed using 14 target-organic methods (719 compounds). Designed-bioactive anthropogenic contaminants (biocides, pharmaceuticals) comprised 57% of 406 organics detected at least once. The 10 most-frequently detected anthropogenic-organics included eight pesticides (desulfinylfipronil, AMPA, chlorpyrifos, dieldrin, metolachlor, atrazine, CIAT, glyphosate) and two pharmaceuticals (caffeine, metformin) with detection frequencies ranging 66–84% of all sites. Detected contaminant concentrations varied from less than 1 ng L–1 to greater than 10 μg L–1, with 77 and 278 having median detected concentrations greater than 100 ng L–1 and 10 ng L–1, respectively. Cumulative detections and concentrations ranged 4–161 compounds (median 70) and 8.5–102 847 ng L–1, respectively, and correlated significantly with wastewater discharge, watershed development, and toxic release inventory metrics. Log10 concentrations of widely monitored HHCB, triclosan, and carbamazepine explained 71–82% of the variability in the total number of compounds detected (linear regression; p-values: environment application (pesticides), designed-bioactive organics (median 41 per site at μg L–1 cumulative concentrations) in developed watersheds present aquatic health concerns, given their acknowledged potential for sublethal effects to sensitive species and lifecycle stages at low ng L–1.

  13. Transcriptome profiling of brown adipose tissue during cold exposure reveals extensive regulation of glucose metabolism

    DEFF Research Database (Denmark)

    Hao, Qin; Yadav, Rachita; Basse, Astrid L.

    2015-01-01

    We applied digital gene expression profiling to determine the transcriptome of brown and white adipose tissues (BAT and WAT, respectively) during cold exposure. Male C57BL/6J mice were exposed to cold for 2 or 4 days. A notable induction of genes related to glucose uptake, glycolysis, glycogen...... exposure, we propose a model for the intermediary glucose metabolism in activated BAT: 1) fluxes through glycolysis and the pentose phosphate pathway are induced, the latter providing reducing equivalents for de novo fatty acid synthesis; 2) glycerol synthesis from glucose is increased, facilitating...

  14. A large scale hearing loss screen reveals an extensive unexplored genetic landscape for auditory dysfunction

    DEFF Research Database (Denmark)

    Bowl, Michael R.; Simon, Michelle M.; Ingham, Neil J.

    2017-01-01

    The developmental and physiological complexity of the auditory system is likely reflected in the underlying set of genes involved in auditory function. In humans, over 150 non-syndromic loci have been identified, and there are more than 400 human genetic syndromes with a hearing loss component. O...

  15. Somatic Cell Fusions Reveal Extensive Heterogeneity in Basal-like Breast Cancer

    DEFF Research Database (Denmark)

    Su, Ying; Subedee, Ashim; Bloushtain-Qimron, Noga

    2015-01-01

    genetic and epigenetic (DNA methylation and chromatin) profiling. We found that the basal-like trait is generally dominant and is largely defined by epigenetic repression of luminal transcription factors. Definition of super-enhancers highlighted a core program common in luminal cells but a high degree...

  16. Biocytin Filling of Adult Gonadotropin-Releasing Hormone Neurons in Situ Reveals Extensive, Spiny, Dendritic Processes

    National Research Council Canada - National Science Library

    Campbell, Rebecca E; Han, Seong-Kyu; Herbison, Allan E

    2005-01-01

    .... Using acute brain slices prepared from transgenic GnRH-green fluorescent protein mice, individual fluorescing GnRH neurons were identified, patched, and filled with the small-molecular-weight dye biocytin...

  17. A Multiparameter Network Reveals Extensive Divergence between C. elegans bHLH Transcription Factors

    DEFF Research Database (Denmark)

    Grove, C.; De Masi, Federico; Newburger, Daniel

    2009-01-01

    parameters remain undetermined. We comprehensively identify dimerization partners, spatiotemporal expression patterns, and DNA-binding specificities for the C. elegans bHLH family of TFs, and model these data into an integrated network. This network displays both specificity and promiscuity, as some b...

  18. Phosphoproteome analysis of streptomyces development reveals extensive protein phosphorylation accompanying bacterial differentiation

    DEFF Research Database (Denmark)

    Manteca, Angel; Ye, Juanying; Sánchez, Jesús

    2011-01-01

    Streptomycetes are bacterial species that undergo a complex developmental cycle that includes programmed cell death (PCD) events and sporulation. They are widely used in biotechnology because they produce most clinically relevant secondary metabolites. Although Streptomyces coelicolor is one...... events were detected during the presporulation and sporulation stages (80%). Most of these phosphorylations were not reported before in Streptomyces, and included sporulation factors, transcriptional regulators, protein kinases and other regulatory proteins. Several of the identified phosphorylated...

  19. Seeing the Whole Elephant: Imaging Flow Cytometry Reveals Extensive Morphological Diversity within Blastocystis Isolates

    Science.gov (United States)

    Yason, John Anthony; Tan, Kevin Shyong Wei

    2015-01-01

    Blastocystis is a common protist isolated in humans and many animals. The parasite is a species complex composed of 19 subtypes, 9 of which have been found in humans. There are biological and molecular differences between Blastocystis subtypes although microscopy alone is unable to distinguish between these subtypes. Blastocystis isolates also display various morphological forms. Several of these forms, however, have not been properly evaluated on whether or not these play significant functions in the organism's biology. In this study, we used imaging flow cytometry to analyze morphological features of Blastocystis isolates representing 3 subtypes (ST1, ST4 and ST7). We also employed fluorescence dyes to discover new cellular features. The profiles from each of the subtypes exhibit considerable differences with the others in terms of shape, size and granularity. We confirmed that the classical vacuolar form comprises the majority in all three subtypes. We have also evaluated other morphotypes on whether these represent distinct life stages in the parasite. Irregularly-shaped cells were identified but all of them were found to be dying cells in one isolate. Granular forms were present as a continuum in both viable and non-viable populations, with non-viable forms displaying higher granularity. By analyzing the images, rare morphotypes such as multinucleated cells could be easily observed and quantified. These cells had low granularity and lower DNA content. Small structures containing nucleic acid were also identified. We discuss the possible biological implications of these unusual forms. PMID:26618361

  20. Tsallis non-extensive statistics and solar wind plasma complexity

    Science.gov (United States)

    Pavlos, G. P.; Iliopoulos, A. C.; Zastenker, G. N.; Zelenyi, L. M.; Karakatsanis, L. P.; Riazantseva, M. O.; Xenakis, M. N.; Pavlos, E. G.

    2015-03-01

    This article presents novel results revealing non-equilibrium phase transition processes in the solar wind plasma during a strong shock event, which took place on 26th September 2011. Solar wind plasma is a typical case of stochastic spatiotemporal distribution of physical state variables such as force fields (B → , E →) and matter fields (particle and current densities or bulk plasma distributions). This study shows clearly the non-extensive and non-Gaussian character of the solar wind plasma and the existence of multi-scale strong correlations from the microscopic to the macroscopic level. It also underlines the inefficiency of classical magneto-hydro-dynamic (MHD) or plasma statistical theories, based on the classical central limit theorem (CLT), to explain the complexity of the solar wind dynamics, since these theories include smooth and differentiable spatial-temporal functions (MHD theory) or Gaussian statistics (Boltzmann-Maxwell statistical mechanics). On the contrary, the results of this study indicate the presence of non-Gaussian non-extensive statistics with heavy tails probability distribution functions, which are related to the q-extension of CLT. Finally, the results of this study can be understood in the framework of modern theoretical concepts such as non-extensive statistical mechanics (Tsallis, 2009), fractal topology (Zelenyi and Milovanov, 2004), turbulence theory (Frisch, 1996), strange dynamics (Zaslavsky, 2002), percolation theory (Milovanov, 1997), anomalous diffusion theory and anomalous transport theory (Milovanov, 2001), fractional dynamics (Tarasov, 2013) and non-equilibrium phase transition theory (Chang, 1992).

  1. A lyapunov-based extension to particle swarm dynamics for continuous function optimization.

    Science.gov (United States)

    Bhattacharya, Sayantani; Konar, Amit; Das, Swagatam; Han, Sang Yong

    2009-01-01

    The paper proposes three alternative extensions to the classical global-best particle swarm optimization dynamics, and compares their relative performance with the standard particle swarm algorithm. The first extension, which readily follows from the well-known Lyapunov's stability theorem, provides a mathematical basis of the particle dynamics with a guaranteed convergence at an optimum. The inclusion of local and global attractors to this dynamics leads to faster convergence speed and better accuracy than the classical one. The second extension augments the velocity adaptation equation by a negative randomly weighted positional term of individual particle, while the third extension considers the negative positional term in place of the inertial term. Computer simulations further reveal that the last two extensions outperform both the classical and the first extension in terms of convergence speed and accuracy.

  2. Simultaneous RNA quantification of human and retroviral genomes reveals intact interferon signaling in HTLV-1-infected CD4+ T cell lines

    Directory of Open Access Journals (Sweden)

    Moens Britta

    2012-08-01

    Full Text Available Abstract Background IFN-α contributes extensively to host immune response upon viral infection through antiviral, pro-apoptotic, antiproliferative and immunomodulatory activities. Although extensively documented in various types of human cancers and viral infections, controversy exists in the exact mechanism of action of IFN-α in human immunodeficiency virus type 1 (HIV-1 and human T-lymphotropic virus type 1 (HTLV-1 retroviral infections. Results IFN-α displayed strong anti-HIV-1 effects in HIV-1/HTLV-1 co-infected MT-4 cells in vitro, demonstrated by the dose-dependent inhibition of the HIV-1-induced cytopathic effect (IC50 = 83.5 IU/ml, p 50 = 1.2 IU/ml, p  Conclusions Taken together, our results indicate that both the absence of in vitro antiproliferative and pro-apoptotic activity as well as the modest post-transcriptional antiviral activity of IFN-α against HTLV-1, were not due to a cell-intrinsic defect in IFN-α signalisation, but rather represents a retrovirus-specific phenomenon, considering the strong HIV-1 inhibition in co-infected cells.

  3. A Giant Guteal Schwannoma with extension into the Pelvis: A case ...

    African Journals Online (AJOL)

    RESULTS: Clinical examination revealed a 40cm by 60cm mass in the right gluteal region and continuous with a 25 cm by 15 cm pelvic mass. The ultrasound scan revealed a very complex (mixed solid and fluid containing) gluteal mass with extension to the pelvis. The CT scan showed a very large, well defined lobulated ...

  4. Towards professionalism in agricultural extension: The professional ...

    African Journals Online (AJOL)

    Towards professionalism in agricultural extension: The professional registration of Extensionists in South Africa – A dream or a reality? The role of the South African Society of Extensionists in South Africa – A dream or a reality? The role of the South African Society of Agricultural Extension (SASAE)

  5. Effective Use of Facebook for Extension Professionals

    Science.gov (United States)

    Mains, Mark; Jenkins-Howard, Brooke; Stephenson, Laura

    2013-01-01

    As the use of social media increases, Extension is challenged to stay relevant with cliental by using digital tools. This article illustrates how Facebook can be part of Extension's repertoire of methods for communication, program implementation, education, and marketing. This allows professionals to build social networking capacity with…

  6. Job satisfaction of extension agents towards innovation ...

    African Journals Online (AJOL)

    The study assessed job satisfaction of extension agents towards innovation dissemination to fish farmers in Lagos State, Nigeria. A simple random sampling technique was used to select 44 extension officers from which data were collected. A structured questionnaire consisting of 6 personal characteristics, 23 management ...

  7. Plagiarism within Extension: Origin and Current Effects

    Science.gov (United States)

    Rollins, Dora

    2011-01-01

    Extension publication editors from around the United States are finding cases of plagiarism within manuscripts that Extension educators submit as new public education materials. When editors confront such educators with the problem, some don't understand it as such, rationalizing that reproducing published information for a new purpose qualifies…

  8. Extension Sustainability Camp: Design, Implementation, and Evaluation

    Science.gov (United States)

    Brain, Roslynn; Upton, Sally; Tingey, Brett

    2015-01-01

    Sustainability Camps provide an opportunity for Extension educators to be in the forefront of sustainability outreach and to meet the growing demand for sustainability education. This article shares development, implementation, and evaluation of an Extension Sustainability Camp for youth, grades 4-6. Camp impact was measured via daily pre-and…

  9. Sound Type-Dependent Syntactic Language Extension

    NARCIS (Netherlands)

    Lorenzen, Florian; Erdweg, S.T.

    2016-01-01

    Syntactic language extensions can introduce new facilities into a programming language while requiring little implementation effort and modest changes to the compiler. It is typical to desugar language extensions in a distinguished compiler phase after parsing or type checking, not affecting any of

  10. Implementing socially responsive forestry extension programmes ...

    African Journals Online (AJOL)

    Following a literature review which pays particular attention to southern African references, a socially responsive forestry extension model is outlined. It is contended that the initial establishment of sustainable extension programmes rest upon the nature of the relations between the central-level office, the extensionist and ...

  11. Agricultural extension officers' perceptions of integrated pest ...

    African Journals Online (AJOL)

    The extension officers further believed that IPM has the potential to contribute effectively in pest management by the majority of small scale farmers in Kenya. The extension officers viewed crop rotation, a cultural practice, to be of priority use in pest management. Most of the other IPM practices were considered practical in ...

  12. Communication for Strengthening Agricultural Extension and Rural ...

    African Journals Online (AJOL)

    chrischisoni

    communication theories, methods, technologies and strategies. Yet they feel inadequately trained in these areas. Extension workers' views on decentralization. The government's policies on decentralization and pluralistic and demand-driven extension were introduced in 2000. This study was conducted almost a decade ...

  13. Farmer Experience of Pluralistic Agricultural Extension, Malawi

    Science.gov (United States)

    Chowa, Clodina; Garforth, Chris; Cardey, Sarah

    2013-01-01

    Purpose: Malawi's current extension policy supports pluralism and advocates responsiveness to farmer demand. We investigate whether smallholder farmers' experience supports the assumption that access to multiple service providers leads to extension and advisory services that respond to the needs of farmers. Design/methodology/approach: Within a…

  14. Subintegrality, invertible modules and Laurent polynomial extensions

    Indian Academy of Sciences (India)

    Let ⊆ be a commutative ring extension. Let I(, ) be the multiplicative group of invertible -submodules of . In this article, we extend a result of Sadhu and Singh by finding a necessary and sufficient condition on an integral birational extension ⊆ of integral domains with dim ≤ 1, so that the natural map I(, ...

  15. Perception of Commercialization of Agricultural Extension Service ...

    African Journals Online (AJOL)

    Public extension service delivery system has been unable to satisfactorily respond to the challenges of agricultural development, poverty eradication and rural transformation in Nigeria, resulting in continued calls for alternative systems, including commercialization of extension service. Because of their strategically ...

  16. Extension Learners' Use of Electronic Technology

    Science.gov (United States)

    Guenthner, Joseph F.; Swan, Benjamin G.

    2011-01-01

    Extension clientele use electronic technology for entertainment, communication, and business. Educational programs that use electronic technology can enhance learning. To learn more about use of electronic technology among Extension clientele, we surveyed 80 university students and 135 potato farmers. We found that the farmers were likely to use…

  17. Livestock extension practice and competency among agricultural ...

    African Journals Online (AJOL)

    The challenge of meeting the ever-increasing demand for animal products in Nigeria has become keen over the years. A major factor is low technology input by the bulk of animal producers. Because Extension has a crucial role to play, the purpose of this study was to investigate livestock extension (LE) activities and ...

  18. Job satisfaction amongst agricultural extension personnel in ...

    African Journals Online (AJOL)

    Job satisfaction broadly is considered to be as attitude of a person reflecting the degree to which his/her important needs are satisfied by this job. To study the job satisfaction level and factors associated with job satisfaction of Extension personnel, a sample of 74 extension personnel from Kurdistan province of Iran were ...

  19. Declarative language extensions for Prolog courses

    NARCIS (Netherlands)

    Neumerkel, U.; Triska, M.; Wielemaker, J.

    2008-01-01

    In this paper we present several extensions to support a more declarative view of programming in Prolog. These extensions enable introductory Prolog courses to concentrate on the pure parts of Prolog for longer periods than without. Even quite complex programs can now be written free of any

  20. Extensive Reading in Enhancing Lexical Chunks Acquisition

    Science.gov (United States)

    Pereyra, Nilsa

    2015-01-01

    The purpose of this action research was to investigate the effect of extensive reading and related activities on the acquisition of lexical chunks in EFL students. Seven adult EFL learners with an Intermediate level volunteered to take part in the 16 week project following Extensive Reading principles combined with tasks based on the Lexical…

  1. Extensive Reading Materials Produced by Learning Communities

    Science.gov (United States)

    Jacobs, G. M.

    2013-01-01

    This article advocates that students and teachers create some of their own extensive reading materials. Learning communities act as a means of motivating and sustaining student and teacher production of extensive reading materials. The article begins by explaining learning communities. The bulk of the article has two parts. The first part focuses…

  2. Extensive Reading: Students' Performance and Perception

    Science.gov (United States)

    Fernandez de Morgado, Nelly

    2009-01-01

    Reading is thought to be a crucial skill in the EFL learning process, and Extensive Reading a very useful strategy. However, very few teachers implement it on a regular basis. The process of introducing Extensive Reading (ER) is considered far too expensive, complicated, and time-consuming. One way to encourage its use would be to more deeply…

  3. Creating Teams Increases Extension Educator Productivity

    Science.gov (United States)

    Chalker-Scott, Linda; Daniels, Catherine H.; Martini, Nicole

    2016-01-01

    The Garden Team at Washington State University is a transdisciplinary group of faculty, staff, and students with expertise in applied plant and soil sciences and an interest in Extension education. The team's primary mission is to create current, relevant, and peer-reviewed materials as Extension publications for home gardeners. The average yearly…

  4. 77 FR 16022 - Agency Information Collection Extension

    Science.gov (United States)

    2012-03-19

    ... 1995. The information collection requests a three-year extension of its Better Buildings, Better Plants... and Regulatory Affairs, Office of Management and Budget, New Executive Office Building, Room 10102... of Energy Efficiency and Renewable Energy Agency Information Collection Extension AGENCY: Office of...

  5. User contributions and public extension delivery modes ...

    African Journals Online (AJOL)

    This study examined a number of extension communication channels through which farmers received farm management services/information from the public extension agent. The idea was, first, to find out the dominant channel(s) through which information/services were received and, second, to assess the willingness of ...

  6. Bilateral Wilms Tumor With Ureteral Extension.

    Science.gov (United States)

    Lockwood, Gina; Ferrer, Fernando; Makari, John

    2017-04-01

    Wilms tumor is the most common renal tumor in children. However, tumor extension into the ureter is exceedingly rare. We present a case of bilateral Wilms tumor with unilateral ureteral extension into the bladder. This case illustrates the importance of thoughtful diagnostic evaluation and surgical planning to obtain a good oncologic outcome while preserving renal function. Copyright © 2017 Elsevier Inc. All rights reserved.

  7. assessment of extension agents' communication methods

    African Journals Online (AJOL)

    USER

    ABSTRACT. The need to improve aquaculture production through enhanced technology transfer necessitated this study to assess extension agents' use of communication methods and its impact on linkage. A structured questionnaire was administered to 44 extension agents who were randomly selected from Lagos State ...

  8. Revitalizing Agricultural Extension Curriculum for Effective ...

    African Journals Online (AJOL)

    The authors argue that African agricultural universities and colleges must strengthen their capacities to develop and deliver responsive extension training programs in order to train extension staff to become critical thinkers and reflective practitioners. A framework is proposed to guide universities and colleges interested in ...

  9. Extension Service Delivery Of Agricultural Development ...

    African Journals Online (AJOL)

    The study was conducted to assess the extension service delivery within the Agricultural Development Programmes of Southwest Nigeria after the cessation of the World Bank funding between 1996 and 2013. Primary data were collected from 201 extension agents across 50% of the states in the area of study using ...

  10. Controleum - an independently extensible control system

    DEFF Research Database (Denmark)

    Jensen, Martin Lykke Rytter

    2014-01-01

    challenging kind of system to design for independent extension. This thesis presents two new software technologies that improve the extensibility of control systems: First, the concept of dynamic links is introduced and Decouplink – an implementation of dynamic links for Java - is presented. Dynamic links......While the extensibility of many software systems has been greatly improved during the past two decades, nontrivial control systems remain to be a category of software systems that are remarkably difficult for independent parties to extend. Support for independent extension is the ability...... is introduced, and an implementation is presented. The extensible controller is a component framework designed to automatically resolve conflicts among mutually unaware components in a control system. The solution is based on the idea that independent components implement different kinds of control concerns...

  11. Impact of invasive extranodal extension on the prognosis of patients with papillary thyroid carcinoma.

    Science.gov (United States)

    Moritani, Sueyoshi

    2014-12-01

    Although 20-50% of papillary thyroid carcinoma (PTC) patients initially present with lymph node metastases, prognosis is excellent. Thus, the significance of lymph node metastasis in PTC remains controversial. In this study, we examined the impact of extranodal extension to surrounding organs (invasive extranodal extension) on the prognosis for PTC patients. Medical records of PTC patients who underwent surgery as their initial treatment at our institution between 1981 and 2008 were retrospectively reviewed. Patients with or without invasive extranodal extension were selected. Our therapeutic strategy for PTC with invasive extranodal extension included complete resection and functional reconstruction. Intergroup comparison was performed using Student's t-test or the chi-square test as appropriate. Survival curves determined by the Kaplan-Meier method were compared for statistical significance using the log-rank test. A Cox-hazard regression model with the forward stepwise method was used for multivariate analysis. The study cohort included 60 (12.3%) patients with and 428 (87.7%) without invasive extranodal extension. The most common site of invasive extranodal extension in the central neck compartment was the recurrent laryngeal nerve, whereas the internal jugular vein was the most frequently invaded site in the lateral neck compartment. The locoregional recurrence rate did not differ significantly between patients with and without invasive extranodal extension, but the distant recurrence rate was higher for those with invasive extranodal extension. The 10-year disease-specific survival rate was significantly lower for patients with invasive extranodal extension than for those without invasive extranodal extension. Furthermore, multivariate analysis revealed that being aged ≥45 years, poor differentiation, and extrathyroidal extension were independent predictive factors for disease-specific death in PTC. Invasive extranodal extension had no effect on the

  12. Mixed periapical lesion: an atypical radicular cyst with extensive calcifications.

    Science.gov (United States)

    Ramos-Perez, Flávia Maria de Moraes; Pontual, Andréa dos Anjos; França, Talita Ribeiro Tenório de; Pontual, Maria Luiza dos Anjos; Beltrão, Ricardo Villar; Perez, Danyel Elias da Cruz

    2014-01-01

    The radicular cyst is an inflammatory odontogenic cyst of endodontic origin. Radiographically, the lesion appears as a periapical radiolucent image. This report describes a very rare case of a mixed periapical radiographic image diagnosed as a radicular cyst. A 37-year-old female patient presented a mixed, well-circumscribed image located in the periapical region of the left maxillary central incisor, which presented unsatisfactory endodontic treatment. Microscopic examination revealed a cavity lined by non-keratinized squamous epithelium and extensive calcifications in the cystic lumen and lining epithelium. Diagnosis of radicular cyst with extensive calcifications was established. Endodontic retreatment was performed and no radiographic signs of recurrence were observed 18 months after treatment. Although very rare, a radicular cyst should be considered in the differential diagnosis of a mixed periapical image associated to teeth with pulp necrosis.

  13. Identification of Current Proficiency Level of Extension Competencies and the Competencies Needed for Extension Agents to Be Successful in the 21st Century

    Directory of Open Access Journals (Sweden)

    Dona Lakai

    2014-02-01

    Full Text Available In this era of globalization, competency is an issue of concern to any field of professionals and their clients. Competency is an integrated set of skills, knowledge, and attitudes that allow one to effectively carry out the activities of a given work to the standards expected in the employment context. The purpose of this descriptive survey study was to determine the current proficiency level of North Carolina Cooperative Extension agents’ competencies and the other competencies they need to develop to be successful in Cooperative Extension. Findings indicate that the current proficiency level of competency for Extension agents in North Carolina Cooperative Extension varies from moderate to high in all 42 items listed in the survey. Multiple regression analysis confirmed that Extension agents’ years of Extension experience and age were major determinants of their overall proficiency level. Extension agents’ proficiency levels did not vary with gender, level of education, professional association affiliation, job position, or area of job responsibility. The research revealed that emotional intelligence, interpersonal skills, flexibility for adapting to changing environments, and ability to manage resources were the most significant other competencies needed for Extension agents to be successful in current context.

  14. A New Extension Model: The Memorial Middle School Agricultural Extension and Education Center

    Science.gov (United States)

    Skelton, Peter; Seevers, Brenda

    2010-01-01

    The Memorial Middle School Agricultural Extension and Education Center is a new model for Extension. The center applies the Cooperative Extension Service System philosophy and mission to developing public education-based programs. Programming primarily serves middle school students and teachers through agricultural and natural resource science…

  15. Extension Approach for an Effective Fisheries and Aquaculture Extension Service in India

    Science.gov (United States)

    Kumaran, M.; Vimala, D. Deboral; Chandrasekaran, V. S.; Alagappan, M.; Raja, S.

    2012-01-01

    Purpose: Public-funded fisheries extension services have been blamed as poor and responsible for the slow pace of aquaculture development in India. The present investigation aimed to find concrete interventions to streamline the extension service by understanding the research-extension-farmer linkage indirectly in terms of information sources of…

  16. Synthetic cannabinoids revealing adrenoleukodystrophy.

    Science.gov (United States)

    Fellner, Avi; Benninger, Felix; Djaldetti, Ruth

    2016-02-01

    We report a 41-year-old man who presented with a first generalized tonic-clonic seizure after recent consumption of a synthetic cannabinoid. MRI showed extensive bilateral, mainly frontal, white matter lesions. Blood analysis for very long chain fatty acids was compatible with adrenoleukodystrophy, and a missense mutation in the ABCD1 gene confirmed the diagnosis. We hypothesize that cannabinoid use might have contributed to metabolic decompensation with subacute worsening of the underlying condition. Copyright © 2015 Elsevier Ltd. All rights reserved.

  17. Extension versus Bending for Continuum Robots

    Directory of Open Access Journals (Sweden)

    George Grimes

    2008-11-01

    Full Text Available In this paper, we analyze the capabilities of a novel class of continuous-backbone ("continuum" robots. These robots are inspired by biological "trunks, and tentacles". However, the capabilities of established continuum robot designs, which feature controlled bending but not extension, fall short of those of their biological counterparts. In this paper, we argue that the addition of controlled extension provides dual and complementary functionality, and correspondingly enhanced performance, in continuum robots. We present an interval-based analysis to show how the inclusion of controllable extension significantly enhances the workspace and capabilities of continuum robots.

  18. abc: An Extensible AspectJ Compiler

    DEFF Research Database (Denmark)

    Avgustinov, Pavel; Christensen, Aske Simon; Hendren, Laurie J.

    2006-01-01

    checking and code generation, as well as data flow and control flow analyses. The AspectBench Compiler (abc) is an implementation of such a workbench. The base version of abc implements the full AspectJ language. Its front end is built using the Polyglot framework, as a modular extension of the Java...... overview of how to use abc to implement an extension. We illustrate the extension mechanisms of abc through a number of small, but nontrivial, examples. We then proceed to contrast the design goals of abc with those of the original AspectJ compiler, and how these different goals have led to different...

  19. Generalized extensions and blocking factors for FITS

    Science.gov (United States)

    Grosbol, P.; Harten, R. H.; Greisen, E. W.; Wells, D. C.

    1988-06-01

    A general design for extending the Flexible Image Transport System (FITS) tape format is proposed. The present design is shown to preserve compatibility with existing FITS tapes and software (including the 'random groups'), while being general enough to permit a wide variety of new extension files to be designed in the future. Rules are given for the blocking of FITS logical records. The rules for the generalized extension of FITS ensure that extensions can be located and decoded by standard routines without interfering with each other.

  20. 77 FR 58364 - Agency Information Collection Extension

    Science.gov (United States)

    2012-09-20

    ... Information Administration Agency Information Collection Extension AGENCY: Energy Information Administration... sent to Colleen Blessing, EI-40, Energy Information Administration, Department of Energy, 1000.... Both quantitative and qualitative studies are developed by EIA. Quantitative studies classify and count...

  1. Veld management: a challenge to agricultural extension ...

    African Journals Online (AJOL)

    Keywords: Adaptive research; Agricultural extension; agriculture; communication; Farmers; Knowledge diffusion; Knowledge generation; management; National Grazing Strategy; On-farm adaptive research; research; south africa; strategies; technology; Veld management. Journal of the Grassland Society of Southern Africa.

  2. Youth Development Agents' Needs: Challenges for Extension ...

    African Journals Online (AJOL)

    ... the areas of competencies. Regular training was therefore recommended for youth development agents to enable them update, improve and learn new strategies in the application of their competencies for extension service delivery. Keywords: Youth, Development, Agents' needs, Volunteer management, Competencies.

  3. Offshore extension of Gomati river, Dwarka

    Digital Repository Service at National Institute of Oceanography (India)

    Vora, K.H.; Naik, D.K.; Ganesan, P.; Moraes, C.

    information. Attempts have been made to identify the submerged extension of Gomati River by diving inspection and based on the results obtained such as findings like stone and iron anchors, circular bastions, etc. While many features reported earlier...

  4. ERP extension - Supply Chain Management (SCM

    Directory of Open Access Journals (Sweden)

    Vasile LUPSE

    2006-01-01

    Full Text Available This article presents an extension of a ERP (Enterprise Resource Planning, more precisely the Supply Chain Management (SCM, together with some personal considerations and contributions of the authors, regarding the presented concepts.

  5. Integrated Composite Rocket Nozzle Extension Project

    Data.gov (United States)

    National Aeronautics and Space Administration — ORBITEC proposes to develop and demonstrate an Integrated Composite Rocket Nozzle Extension (ICRNE) for use in rocket thrust chambers. The ICRNE will utilize an...

  6. 78 FR 13333 - Agency Information Collection Extension

    Science.gov (United States)

    2013-02-27

    ... energy resource reserves, production, demand, technology, and related economic and statistical... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY U.S. Energy Information Administration Agency Information Collection Extension AGENCY: U.S. Energy Information...

  7. Bandwidth extension of speech using perceptual criteria

    CERN Document Server

    Berisha, Visar; Liss, Julie

    2013-01-01

    Bandwidth extension of speech is used in the International Telecommunication Union G.729.1 standard in which the narrowband bitstream is combined with quantized high-band parameters. Although this system produces high-quality wideband speech, the additional bits used to represent the high band can be further reduced. In addition to the algorithm used in the G.729.1 standard, bandwidth extension methods based on spectrum prediction have also been proposed. Although these algorithms do not require additional bits, they perform poorly when the correlation between the low and the high band is weak. In this book, two wideband speech coding algorithms that rely on bandwidth extension are developed. The algorithms operate as wrappers around existing narrowband compression schemes. More specifically, in these algorithms, the low band is encoded using an existing toll-quality narrowband system, whereas the high band is generated using the proposed extension techniques. The first method relies only on transmitted high-...

  8. 77 FR 46750 - Agency Information Collection Extension

    Science.gov (United States)

    2012-08-06

    ... information collection, EIA-882T, ``Generic Clearance for Questionnaire Testing, Evaluation, and Research...: Generic Clearance for Questionnaire Testing, Evaluation, and Research; (3) Type of Request: Extension... questionnaires and validate EIA survey forms data quality, including conducting pretest ] surveys, pilot surveys...

  9. Generalized module extension Banach algebras: Derivations and ...

    African Journals Online (AJOL)

    Let A and X be Banach algebras and let X be an algebraic Banach A-module. Then the ℓ-1direct sum A x X equipped with the multiplication (a; x)(b; y) = (ab; ay + xb + xy) (a; b ∈ A; x; y ∈ X) is a Banach algebra, denoted by A ⋈ X, which will be called "a generalized module extension Banach algebra". Module extension ...

  10. Cooperative Extension as a Framework for Health Extension: The Michigan State University Model.

    Science.gov (United States)

    Dwyer, Jeffrey W; Contreras, Dawn; Eschbach, Cheryl L; Tiret, Holly; Newkirk, Cathy; Carter, Erin; Cronk, Linda

    2017-10-01

    The Affordable Care Act charged the Agency for Healthcare Research and Quality to create the Primary Care Extension Program, but did not fund this effort. The idea to work through health extension agents to support health care delivery systems was based on the nationally known Cooperative Extension System (CES). Instead of creating new infrastructure in health care, the CES is an ideal vehicle for increasing health-related research and primary care delivery. The CES, a long-standing component of the land-grant university system, features a sustained infrastructure for providing education to communities. The Michigan State University (MSU) Model of Health Extension offers another means of developing a National Primary Care Extension Program that is replicable in part because of the presence of the CES throughout the United States. A partnership between the MSU College of Human Medicine and MSU Extension formed in 2014, emphasizing the promotion and support of human health research. The MSU Model of Health Extension includes the following strategies: building partnerships, preparing MSU Extension educators for participation in research, increasing primary care patient referrals and enrollment in health programs, and exploring innovative funding. Since the formation of the MSU Model of Health Extension, researchers and extension professionals have made 200+ connections, and grants have afforded savings in salary costs. The MSU College of Human Medicine and MSU Extension partnership can serve as a model to promote health partnerships nationwide between CES services within land-grant universities and academic health centers or community-based medical schools.

  11. Initiation of diapirism by regional extension

    Energy Technology Data Exchange (ETDEWEB)

    Jackson, M.P.A.; Vendeville, B.C. (Univ. of Texas, Austin, TX (United States). Bureau of Economic Geology)

    1992-01-01

    Initiation of diapirism is one of the least understood aspects of salt tectonics. Sedimentary differential loading is a favorite explanation, but special conditions such as focused sedimentation are needed to trigger diapirism by differential loading. Compilation of published data from 18 of the world's salt-diapir provinces shows that salt upwelling is consistently linked in time with regional extension, whether thin-skinned or thick-skinned. Extended salt basins typically develop salt structures, whereas nonextended basins typically do not. In some basins containing thick salt (SW Iran), diapirism was delayed as long as 400 Ma until the basin was regionally extended. In other salt provinces (Maritime Alps), episodic growth of salt diapirs correlates with episodic regional extension during opening of the Neo-Tethys and Atlantic Oceans. Once initiated, salt diapirism can continue after regional extension is succeeded by contraction or quiescence. Thus even in salt basins overprinted by inversion or orogenic contraction (Morocco, Lusitania, Basque-Cantabrian, North Sea), the diapirs were initiated during extension on divergent continental margins or in intracontinental rifts. This observed temporal link between extension and diapirism is consistent with physical and numerical modeling, which demonstrates that extensional faulting of the overburden directly causes diapirism whether the salt was deposited before, during, or after rifting. Where the overburden is thinned by extension, pressurized salt wells up in response to the shifting positions of fault blocks.

  12. Android Emotions Revealed

    DEFF Research Database (Denmark)

    Vlachos, Evgenios; Schärfe, Henrik

    2012-01-01

    in which case an android robot like the Geminoid|DK –a duplicate of an Original person- reveals emotions convincingly; when following an empirical perspective, or when following a theoretical one. The methodology includes the processes of acquiring the empirical data, and gathering feedback on them. Our...

  13. Pituitary adenoma with extensive calcaficcations mimicking crainopharyngioma: a case report

    Energy Technology Data Exchange (ETDEWEB)

    Jin, Sung Chan; Lee, Seoung Ro; Kwon, Bae Ju; Moon, Won Jin; Jeon, Eui Yong [Hanyang Univ. College of Medicine, Seoul (Korea, Republic of)

    2001-01-01

    A 27-year-old man presented with complaints of headache and visual disturbance, first noted six months earlier. Simple radiographs of skull sellar widening and calcification. Brian CT revealed a 3 x 3 x 4 cm-sized sellar suprasellar mass with heavy calcification. T1-weighted MR images showed that the signal intencity of the mass was slightly lower than that of the gray matter, while T2-weighted images showed heterogeneous high signal intensity with centrl low-signal-intensity foci, suggesting calcification After contrast infusion, enancement was irregular. Surgery revealed a 4 x 5 cm sized, well-demarcated, lobulated mass adhering to the meninges. Papillary-type pituitary adenoma was histologically confirmed. We report the CT and MR findings of atypical pituitary adenoma with extensive internal calcification mimicking craniopharyngioma.

  14. Quantitative chromatin proteomics reveals a dynamic histone post-translational modification landscape that defines asexual and sexual Plasmodium falciparum parasites.

    Science.gov (United States)

    Coetzee, Nanika; Sidoli, Simone; van Biljon, Riëtte; Painter, Heather; Llinás, Manuel; Garcia, Benjamin A; Birkholtz, Lyn-Marie

    2017-04-04

    Gene expression in Plasmodia integrates post-transcriptional regulation with epigenetic marking of active genomic regions through histone post-translational modifications (PTMs). To generate insights into the importance of histone PTMs to the entire asexual and sexual developmental cycles of the parasite, we used complementary and comparative quantitative chromatin proteomics to identify and functionally characterise histone PTMs in 8 distinct life cycle stages of P. falciparum parasites. ~500 individual histone PTMs were identified of which 106 could be stringently validated. 46 individual histone PTMs and 30 co-existing PTMs were fully quantified with high confidence. Importantly, 15 of these histone PTMs are novel for Plasmodia (e.g. H3K122ac, H3K27me3, H3K56me3). The comparative nature of the data revealed a highly dynamic histone PTM landscape during life cycle development, with a set of histone PTMs (H3K4ac, H3K9me1 and H3K36me2) displaying a unique and conserved abundance profile exclusively during gametocytogenesis (P < 0.001). Euchromatic histone PTMs are abundant during schizogony and late gametocytes; heterochromatic PTMs mark early gametocytes. Collectively, this data provides the most accurate, complete and comparative chromatin proteomic analyses of the entire life cycle development of malaria parasites. A substantial association between histone PTMs and stage-specific transition provides insights into the intricacies characterising Plasmodial developmental biology.

  15. CLIP-seq of eIF4AIII reveals transcriptome-wide mapping of the human exon junction complex.

    Science.gov (United States)

    Saulière, Jérôme; Murigneux, Valentine; Wang, Zhen; Marquenet, Emélie; Barbosa, Isabelle; Le Tonquèze, Olivier; Audic, Yann; Paillard, Luc; Roest Crollius, Hugues; Le Hir, Hervé

    2012-11-01

    The exon junction complex (EJC) is a central effector of the fate of mRNAs, linking nuclear processing to mRNA transport, translation and surveillance. However, little is known about its transcriptome-wide targets. We used cross-linking and immunoprecipitation methods coupled to high-throughput sequencing (CLIP-seq) in human cells to identify the binding sites of the DEAD-box helicase eIF4AIII, an EJC core component. CLIP reads form peaks that are located mainly in spliced mRNAs. Most expressed exons harbor peaks either in the canonical EJC region, located ~24 nucleotides upstream of exonic junctions, or in other noncanonical regions. Notably, both of these types of peaks are preferentially associated with unstructured and purine-rich sequences containing the motif GAAGA, which is a potential binding site for EJC-associated factors. Therefore, EJC positions vary spatially and quantitatively between exons. This transcriptome-wide mapping of human eIF4AIII reveals unanticipated aspects of the EJC and broadens its potential impact on post-transcriptional regulation.

  16. Negative extensibility metamaterials: Occurrence and design-space topology

    Science.gov (United States)

    Karpov, Eduard G.; Danso, Larry A.; Klein, John T.

    2017-08-01

    A negative extensibility material structure pulls back and contracts when the external tensile load reaches a certain critical level. In this paper, we reveal basic mathematical features of the nonlinear strain energy function responsible for this unusual mechanical property. A systematic discussion leads to a comprehensive phase diagram in terms of design parameters for a simple unit cell structure that provides a panoramic view of all possible nonlinear mechanical behaviors. A negative extensibility region clearly is identified in the diagram. The sought property is seen to be rare, occurring only for a very narrow range of the design parameters. Nonetheless, due to the simplicity of the studied structure we suggest that the negative extensibility should be a more common phenomenon than previously thought. It can appear in simple bistable cells made of only several linearly elastic links, although at some peculiar combinations of their properties. These bistable unit cells can be used to design periodic mechanical metamaterials whose examples are shown as well as innovative architectural metastructures.

  17. An Educational Extension Service in India

    Science.gov (United States)

    Krichevsky, M. I.

    2001-12-01

    A strength of US education is interaction with the public under the Land Grant University program. The public benefits from outreach through extension services which evolved for communication with end users, e.g., farmers, homemakers, public health providers, schoolchildren and entrepreneurs i.e., the public with problems and the extension agents who advise on solutions. Further, the agents can seek specialized advice from university faculty. No such system exists in India. The University of Pune (UP), Bionomics International (BI), and WorldSpace Foundation (WSF) will use digital radio broadcasts to facilitate educational extension services. The UP (350,000 students, 250 campuses, among dispersed communities) is a useful institutional setting to demonstrate the value of an outreach system in India. The UP will coordinate development of the broadcast content and the teaching faculty. The campuses will be focal points for outreach. BI will consult on development of the extension structure. WSF will provide the facilities and technical expertise for use of the digital system under the terms of an agreement with Bionomics International. Digital radios (&$slash75-150 each) and PCs will be at each campus and community. The major components of the Extension Service are broadcast of 1) University lecture and examination material in many disciplines; 2) outreach to the general population with of "canned" presentations and talks, skits, songs, games. The steps are: 1) Enhance communication among the campuses by use of satellite digital audio and multimedia broadcasts with feedback by telephone, mail, fax, etc. 2) Develop course material for training of extension personnel. 3) Train extension personnel to interface between the faculty of the University and the local population. 4) Extend digital radio services to population centers for communication of locally useful information. 5) Utilize extension personnel for system maintenance, motivating use of the broadcast

  18. Metadata to Support Next-Generation Library Resource Discovery: Lessons from the eXtensible Catalog, Phase 1

    National Research Council Canada - National Science Library

    Jennifer Bowen

    2008-01-01

      The eXtensible Catalog (XC) Project at the University of Rochester will design and develop a set of open-source applications to provide libraries with an alternative way to reveal their collections to library users...

  19. Coral Cores for selected locations in the Pacific Ocean obtained to determine calcification and extension rates of Porites spp. corals

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Laboratory experiments reveal calcification and extension rates of corals are strongly correlated to seawater aragonite saturation state. Predictions of reduced...

  20. Timeability in Extensive-Form Games

    DEFF Research Database (Denmark)

    Jakobsen, Sune K.; Sørensen, Troels Bjerre; Conitzer, Vincent

    2016-01-01

    Extensive-form games constitute the standard representation scheme for games with a temporal component. But do all extensive-form games correspond to protocols that we can implement in the real world? We often rule out games with imperfect recall, which prescribe that an agent forget something...... that she knew before. In this paper, we show that even some games with perfect recall can be problematic to implement. Specifically, we show that if the agents have a sense of time passing (say, access to a clock), then some extensive-form games can no longer be implemented; no matter how we attempt...... to time the game, some information will leak to the agents that they are not supposed to have. We say such a game is not exactly timeable. We provide easy-to-check necessary and sufficient conditions for a game to be exactly timeable. Most of the technical depth of the paper concerns how to approximately...

  1. Mathematics for common entrance three (extension) answers

    CERN Document Server

    Alexander, Serena

    2015-01-01

    This book contains answers to all exercises featured in the accompanying textbook Mathematics for Common Entrance Three (Extension) , which provides essential preparation for Level 3 of the ISEB 13+ Mathematics exam, as well as for CASE and other scholarship exams. - Clean, clear layout for easy marking. - Includes examples of high-scoring answers with diagrams and workings. Also available to purchase from the Galore Park website www.galorepark.co.uk :. - Mathematics for Common Entrance Three (Extension). - Mathematics for Common Entrance One. - Mathematics for Common Entrance One Answers. - M

  2. Graded junction termination extensions for electronic devices

    Science.gov (United States)

    Merrett, J. Neil (Inventor); Isaacs-Smith, Tamara (Inventor); Sheridan, David C. (Inventor); Williams, John R. (Inventor)

    2007-01-01

    A graded junction termination extension in a silicon carbide (SiC) semiconductor device and method of its fabrication using ion implementation techniques is provided for high power devices. The properties of silicon carbide (SiC) make this wide band gap semiconductor a promising material for high power devices. This potential is demonstrated in various devices such as p-n diodes, Schottky diodes, bipolar junction transistors, thyristors, etc. These devices require adequate and affordable termination techniques to reduce leakage current and increase breakdown voltage in order to maximize power handling capabilities. The graded junction termination extension disclosed is effective, self-aligned, and simplifies the implementation process.

  3. Extensive keloidal healing of pemphigus vulgaris

    Directory of Open Access Journals (Sweden)

    Khanna Neena

    1997-01-01

    Full Text Available Bullae of pemphigus vulgaris heal without scarring. We here report a patient of pemphigus vulgaris whose lesions healed with a one-month history of extensive flaccid bullae and uninfected erosions on the trunk and extremities along with superficial erosions in the oral mucosa. The clinical suspicion of pemphigus vulgaris was confirmed by histopathological and immunohistological examination. Pulse therapy with monthly parenteral dexamethasone and cyclophosphamide pulse was instituted. The cutaneous lesions on healing formed extensive keloidal scars despite high dose of monthly corticosteroid therapy.

  4. Switchings, extensions, and reductions in central digraphs

    DEFF Research Database (Denmark)

    Kündgen, André; Leander, Gregor; Thomassen, Carsten

    2011-01-01

    A directed graph is called central if its adjacency matrix A satisfies the equation A2=J, where J is the matrix with a 1 in each entry. It has been conjectured that every central directed graph can be obtained from a standard example by a sequence of simple operations called switchings, and also ...... that it can be obtained from a smaller one by an extension. We disprove these conjectures and present a general extension result which, in particular, shows that each counterexample extends to an infinite family....

  5. Algomaster Platform Extension for Improved Usability

    Directory of Open Access Journals (Sweden)

    BENEJ Martin

    2017-05-01

    Full Text Available Visualizations of algorithms and data structures can be effectively used for supporting the teaching process. However, such visualization must be comprehensive for students and still semantically correct. Algomaster visualization platform offers effective visualization and simple extensibility. In this paper we describe major platform extensions we have implemented, including support for visualization of complex algorithms, features for real-time student testing and the tool for simplified development of new Algomaster plugins. These complex algorithms comprise visualization of operations with self-balancing trees and hashing algorithm. To enable the real-time student testing we have created a database and a separate tool for its management.

  6. Revealing the programming process

    DEFF Research Database (Denmark)

    Bennedsen, Jens; Caspersen, Michael Edelgaard

    2005-01-01

    One of the most important goals of an introductory programming course is that the students learn a systematic approach to the development of computer programs. Revealing the programming process is an important part of this; however, textbooks do not address the issue -- probably because...... the textbook medium is static and therefore ill-suited to expose the process of programming. We have found that process recordings in the form of captured narrated programming sessions are a simple, cheap, and efficient way of providing the revelation.We identify seven different elements of the programming...

  7. TypeScript revealed

    CERN Document Server

    Maharry, Dan

    2013-01-01

    TypeScript Revealed is a quick 100-page guide to Anders Hejlsberg's new take on JavaScript. With this brief, fast-paced introduction to TypeScript, .NET, Web and Windows 8 application developers who are already familiar with JavaScript will easily get up to speed with TypeScript and decide whether or not to start incorporating it into their own development. TypeScript is 'JavaScript for Application-scale development'; a superset of JavaScript that brings to it an additional object-oriented-like syntax familiar to .NET programmers that compiles down into simple, clean JavaScript that any browse

  8. Transcriptome and Functional Genomics Reveal the Participation of Adenine Phosphoribosyltransferase in Trypanosoma cruzi Resistance to Benznidazole.

    Science.gov (United States)

    García-Huertas, Paola; Mejía-Jaramillo, Ana María; González, Laura; Triana-Chávez, Omar

    2017-07-01

    Currently, the only available treatments for Trypanosoma cruzi are benznidazole (Bz) and nifurtimox (Nfx). The mechanisms of action and resistance to these drugs in this parasite are not complete known. In order to identify differentially expressed transcripts between sensitive and resistant parasites, a massive pyrosequencing of the T. cruzi transcriptome was carried out. Additionally, the 2D gel electrophoresis profile of sensitive and resistant parasites was analyzed and the data were supported with functional genomics. The results showed 133 differentially expressed genes in resistant parasites. The transcriptome analysis revealed the regulation of different genes with several functions and metabolic pathways, which could suggest that resistance in T. cruzi is a multigenic process. Additionally, using transcriptomics, one gene, adenine phosphoribosyltransferase (APRT), was found to be down-regulated in the resistant parasites and its expression profile was confirmed by 2D electrophoresis analysis. The role of this gene in the resistance to Bz was confirmed overexpressing it in sensitive and resistant parasites. Interestingly, both parasites became more sensitive to Bz and H 2 O 2 . This is the first RNA-seq study to identify regulated genes in T. cruzi associated with Bz resistance and to show the role of APRT in T. cruzi resistance. Although T. cruzi regulation is mainly post-transcriptional, the transcriptome analysis, supported by 2D gel analysis and functional genomic, provides an overall idea of the expression profiles of genes under resistance conditions. These results contribute essential information to further the understanding of the mechanisms of action and resistance to Bz in T. cruzi. J. Cell. Biochem. 118: 1936-1945, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  9. Systematic Analysis of Transcriptional and Post-transcriptional Regulation of Metabolism in Yeast.

    Directory of Open Access Journals (Sweden)

    Emanuel Gonçalves

    2017-01-01

    Full Text Available Cells react to extracellular perturbations with complex and intertwined responses. Systematic identification of the regulatory mechanisms that control these responses is still a challenge and requires tailored analyses integrating different types of molecular data. Here we acquired time-resolved metabolomics measurements in yeast under salt and pheromone stimulation and developed a machine learning approach to explore regulatory associations between metabolism and signal transduction. Existing phosphoproteomics measurements under the same conditions and kinase-substrate regulatory interactions were used to in silico estimate the enzymatic activity of signalling kinases. Our approach identified informative associations between kinases and metabolic enzymes capable of predicting metabolic changes. We extended our analysis to two studies containing transcriptomics, phosphoproteomics and metabolomics measurements across a comprehensive panel of kinases/phosphatases knockouts and time-resolved perturbations to the nitrogen metabolism. Changes in activity of transcription factors, kinases and phosphatases were estimated in silico and these were capable of building predictive models to infer the metabolic adaptations of previously unseen conditions across different dynamic experiments. Time-resolved experiments were significantly more informative than genetic perturbations to infer metabolic adaptation. This difference may be due to the indirect nature of the associations and of general cellular states that can hinder the identification of causal relationships. This work provides a novel genome-scale integrative analysis to propose putative transcriptional and post-translational regulatory mechanisms of metabolic processes.

  10. Members of a large retroposon family are determinants of post-transcriptional gene expression in Leishmania.

    Directory of Open Access Journals (Sweden)

    Frédéric Bringaud

    2007-09-01

    Full Text Available Trypanosomatids are unicellular protists that include the human pathogens Leishmania spp. (leishmaniasis, Trypanosoma brucei (sleeping sickness, and Trypanosoma cruzi (Chagas disease. Analysis of their recently completed genomes confirmed the presence of non-long-terminal repeat retrotransposons, also called retroposons. Using the 79-bp signature sequence common to all trypanosomatid retroposons as bait, we identified in the Leishmania major genome two new large families of small elements--LmSIDER1 (785 copies and LmSIDER2 (1,073 copies--that fulfill all the characteristics of extinct trypanosomatid retroposons. LmSIDERs are approximately 70 times more abundant in L. major compared to T. brucei and are found almost exclusively within the 3'-untranslated regions (3'UTRs of L. major mRNAs. We provide experimental evidence that LmSIDER2 act as mRNA instability elements and that LmSIDER2-containing mRNAs are generally expressed at lower levels compared to the non-LmSIDER2 mRNAs. The considerable expansion of LmSIDERs within 3'UTRs in an organism lacking transcriptional control and their role in regulating mRNA stability indicate that Leishmania have probably recycled these short retroposons to globally modulate the expression of a number of genes. To our knowledge, this is the first example in eukaryotes of the domestication and expansion of a family of mobile elements that have evolved to fulfill a critical cellular function.

  11. Post-transcriptional regulation of ethylene perception and signaling in Arabidopsis

    Energy Technology Data Exchange (ETDEWEB)

    Schaller, George Eric [Dartmouth College, Hanover, NH (United States)

    2014-03-19

    The simple gas ethylene functions as an endogenous regulator of plant growth and development, and modulates such energy relevant processes as photosynthesis and biomass accumulation. Ethylene is perceived in the plant Arabidopsis by a five-member family of receptors related to bacterial histidine kinases. Our data support a general model in which the receptors exist as parts of larger protein complexes. Our goals have been to (1) characterize physical interactions among members of the signaling complex; (2) the role of histidine-kinase transphosphorylation in signaling by the complex; and (3) the role of a novel family of proteins that regulate signal output by the receptors.

  12. UNR/CSDE1 Drives a Post-transcriptional Program to Promote Melanoma Invasion and Metastasis.

    Science.gov (United States)

    Wurth, Laurence; Papasaikas, Panagiotis; Olmeda, David; Bley, Nadine; Calvo, Guadalupe T; Guerrero, Santiago; Cerezo-Wallis, Daniela; Martinez-Useros, Javier; García-Fernández, María; Hüttelmaier, Stefan; Soengas, Maria S; Gebauer, Fátima

    2016-11-14

    RNA binding proteins (RBPs) modulate cancer progression through poorly understood mechanisms. Here we show that the RBP UNR/CSDE1 is overexpressed in melanoma tumors and promotes invasion and metastasis. iCLIP sequencing, RNA sequencing, and ribosome profiling combined with in silico studies unveiled sets of pro-metastatic factors coordinately regulated by UNR as part of RNA regulons. In addition to RNA steady-state levels, UNR was found to control many of its targets at the level of translation elongation/termination. Key pro-oncogenic targets of UNR included VIM and RAC1, as validated by loss- and gain-of-function studies. Our results identify UNR as an oncogenic modulator of melanoma progression, unravel the underlying molecular mechanisms, and identify potential targets for this therapeutically challenging malignancy. Copyright © 2016 Elsevier Inc. All rights reserved.

  13. Post-transcriptional inhibition of hepatitis C virus replication through small interference RNA

    Directory of Open Access Journals (Sweden)

    Rehman Sidra

    2011-03-01

    Full Text Available Abstract Background Hepatitis C Virus (HCV infection is a major health problem throughout world that causes acute and chronic infection which resulted in liver fibrosis, hepatocellular carcinoma and death. The only therapy currently available for HCV infection is the combination of pegylated interferon alpha (PEG-IFN α and ribavirin. This therapy can effectively clear the virus infection in only 50% of infected individuals. Hence, there is a dire need to develop antiviral agents against HCV. Results This study was design to examine the ability of exogenous small interfering RNAs (siRNAs to block the replication of HCV in human liver cells. In the present study six 21-bp siRNAs were designed against different regions of HCV non-structural genes (NS2, NS3 serine protease/helicase, NS4Band NS5B RNA dependent RNA polymerase. siRNAs were labeled as NS2si241, NS3si-229, NS3si-858, NS4Bsi-166, NS5Bsi-241 and NS5Bsi-1064. We found that siRNAs against HCV NS2- NS5B efficiently inhibit HCV replication in Huh-7 cells. Our results demonstrated that siRNAs directed against HCV NS3 (NS3si-229 and NS3si-858 showed 58% and 88% reduction in viral titer respectively. Moreover, NS4Bsi-166 and NS5Bsi-1064 exhibited a dramatic reduction in HCV viral RNA and resulted in greater than 90% inhibition at a 20 μM concentration, while NS2si-241 showed 27% reduction in viral titer. No significant inhibition was detected in cells transfected with the negative control siRNA. Conclusion Our results suggest that siRNAs targeting against HCV non-structural genes (NS2-NS5B efficiently inhibit HCV replication and combination of these siRNAs of different targets and interferon will be better option to treat HCV infection throughout the world.

  14. Synthesis of multiple Pseudomonas aeruginosa biofilm matrix exopolysaccharides is post-transcriptionally regulated.

    Science.gov (United States)

    Ma, Luyan; Wang, Juan; Wang, Shiwei; Anderson, Erin M; Lam, Joseph S; Parsek, Matthew R; Wozniak, Daniel J

    2012-08-01

    Exopolysaccharide is a critical biofilm matrix component, yet little is known about how the synthesis of multiple exopolysaccharides is regulated. Pseudomonas aeruginosa can produce several biofilm matrix exopolysaccharides that include alginate, Psl and Pel. Here we demonstrated that AlgC, a key enzyme that provides sugar precursors for the synthesis of alginate and lipopolysaccharides (LPS) is also required for both Psl and Pel production. We showed that forced-synthesis of Psl in alginate-producing mucoid bacteria reduced alginate production but this was not due to transcription of the alginate biosynthesis-operon. Likewise, when either alginate or Psl were overproduced, levels of B-band LPS decreased. Induction of Pel resulted in a reduction of Psl levels. Because the effects of reduced exopolysaccharide synthesis when another is overproduced didn't appear to be regulated at the transcriptional level, this suggests that the biosynthesis pathways of Psl, Pel, alginate, and LPS compete for common sugar precursors. As AlgC is the only enzyme that provides precursors for each of these exopolysaccharides, we propose that AlgC is a key checkpoint enzyme that coordinates the total amount of exopolysaccharide biosynthesis by controlling sugar precursor pool. Our data also provide a plausible strategy that P.aeruginosa utilizes to modulate its biofilm matrix exopolysaccharides. © 2012 Society for Applied Microbiology and Blackwell Publishing Ltd.

  15. Complex transcriptional and post-transcriptional regulation of an enzyme for Lipopolysaccharide modification

    OpenAIRE

    Moon, Kyung; Six, David A.; Lee, Hyun-Jung; Raetz, Christian R. H.; Gottesman, Susan

    2013-01-01

    The PhoQ/PhoP two-component system activates many genes for lipopolysaccharide (LPS) modification when cells are grown at low Mg2+ concentrations. An additional target of PhoQ and PhoP is MgrR, an Hfq-dependent small RNA that negatively regulates expression of eptB, also encoding a protein that carries out LPS modification. Examination of LPS confirmed that MgrR effectively silences EptB; the phosphoethanolamine modification associated with EptB is found in ΔmgrR::kan but not mgrR+ cells. Sig...

  16. Complex transcriptional and post-transcriptional regulation of an enzyme for lipopolysaccharide modification.

    Science.gov (United States)

    Moon, Kyung; Six, David A; Lee, Hyun-Jung; Raetz, Christian R H; Gottesman, Susan

    2013-07-01

    The PhoQ/PhoP two-component system activates many genes for lipopolysaccharide (LPS) modification when cells are grown at low Mg(2+) concentrations. An additional target of PhoQ and PhoP is MgrR, an Hfq-dependent small RNA that negatively regulates expression of eptB, also encoding a protein that carries out LPS modification. Examination of LPS confirmed that MgrR effectively silences EptB; the phosphoethanolamine modification associated with EptB is found in ΔmgrR::kan but not mgrR(+) cells. Sigma E has been reported to positively regulate eptB, although the eptB promoter does not have the expected Sigma E recognition motifs. The effects of Sigma E and deletion of mgrR on levels of eptB mRNA were independent, and the same 5' end was found in both cases. In vitro transcription and the behaviour of transcriptional and translational fusions demonstrate that Sigma E acts directly at the level of transcription initiation for eptB, from the same start point as Sigma 70. The results suggest that when Sigma E is active, synthesis of eptB transcript outstrips MgrR-dependent degradation; presumably the modification of LPS is important under these conditions. Adding to the complexity of eptB regulation is a second sRNA, ArcZ, which also directly and negatively regulates eptB. Published 2013. This article is a U.S. Government work and is in the public domain in the USA.

  17. Post-transcriptional regulation of thioredoxin by the stress inducible heterogenous ribonucleoprotein A18

    OpenAIRE

    Yang, Ruiqing; Weber, David J.; Carrier, France

    2006-01-01

    Thioredoxin (TRX) is a key protein of the cellular redox metabolism, which expression is increased in several tumors especially gastric tumors. Even though ultraviolet (UV) and hypoxia specifically induce TRX, the mechanisms that lead to increased TRX levels are still ill defined. Here, we show that the heterogenous ribonucleoprotein A18 (hnRNP A18) RNA Binding Domain (RBD) and the arginine, glycine (RGG) rich domain can bind TRX 3′-untranslated region (3′-UTR) independently but both domains ...

  18. Post-Transcriptional Regulation by the Csr Global Regulatory System in Escherichia coli

    OpenAIRE

    Suzuki, Kazushi; 鈴木, 一史

    2007-01-01

    In many species of bacteria, the Csr (carbon storage regulator) global regulatory system coordinates the expression of various genes. In Escherichia coli, the central component of this system, CsrA, is a RNA-binding protein. The CsrA is a homodimer and binds to leader segments of target mRNAs, affecting their translation and stability. CsrA activity is regulated by two small non-coding RNAs, CsrB and CsrC. These RNAs contain multiple CsrA-binding sequences and act by sequestering CsrA. In thi...

  19. Transcriptional and Post-transcriptional Gene Regulation by Long Non-coding RNA.

    Science.gov (United States)

    Dykes, Iain M; Emanueli, Costanza

    2017-06-01

    Advances in genomics technology over recent years have led to the surprising discovery that the genome is far more pervasively transcribed than was previously appreciated. Much of the newly-discovered transcriptome appears to represent long non-coding RNA (lncRNA), a heterogeneous group of largely uncharacterised transcripts. Understanding the biological function of these molecules represents a major challenge and in this review we discuss some of the progress made to date. One major theme of lncRNA biology seems to be the existence of a network of interactions with microRNA (miRNA) pathways. lncRNA has been shown to act as both a source and an inhibitory regulator of miRNA. At the transcriptional level, a model is emerging whereby lncRNA bridges DNA and protein by binding to chromatin and serving as a scaffold for modifying protein complexes. Such a mechanism can bridge promoters to enhancers or enhancer-like non-coding genes by regulating chromatin looping, as well as conferring specificity on histone modifying complexes by directing them to specific loci. Copyright © 2017 Beijing Institute of Genomics, Chinese Academy of Sciences and Genetics Society of China. Production and hosting by Elsevier B.V. All rights reserved.

  20. RNAi-directed post transcriptional gene silencing of an Arabidopsis Myb transgene in tobacco

    Science.gov (United States)

    The AtMyb90 gene encodes the 'production of anthocyanin pigment 2' (PAP2) transcription factor of Arabidopsis thaliana and is able to induce a visible hyper-pigmented phenotype when expressed in tobacco. Based upon this phenotype, we have used the AtMyb90 gene as a reporter gene to examine RNAi-dire...

  1. Post-transcriptional regulation of gene PA5507 controls PQS concentration in Pseudomonas aeruginosa

    OpenAIRE

    Tipton, Kyle A.; Coleman, James P.; Pesci, Everett C.

    2015-01-01

    Pseudomonas aeruginosa can sense and respond to a myriad of environmental signals and utilizes a system of small molecules to communicate through intercellular signaling. The small molecule 2-heptyl-3-hydroxy-4-quinolone (Pseudomonas Quinolone Signal [PQS]) is one of these signals and its synthesis is important for virulence. Previously, we identified an RpiR-type transcriptional regulator, QapR, that positively affects PQS production by repressing the qapR operon. An in-frame deletion of thi...

  2. Identification of Fhit as a post-transcriptional effector of Thymidine Kinase 1 expression.

    Science.gov (United States)

    Kiss, Daniel L; Waters, Catherine E; Ouda, Iman M; Saldivar, Joshua C; Karras, Jenna R; Amin, Zaynab A; Mahrous, Seham; Druck, Teresa; Bundschuh, Ralf A; Schoenberg, Daniel R; Huebner, Kay

    2017-03-01

    FHIT is a genome caretaker gene that is silenced in >50% of cancers. Loss of Fhit protein expression promotes accumulation of DNA damage, affects apoptosis and epithelial-mesenchymal transition, though molecular mechanisms underlying these alterations have not been fully elucidated. Initiation of genome instability directly follows Fhit loss and the associated reduced Thymidine Kinase 1 (TK1) protein expression. The effects on TK1 of Fhit knockdown and Fhit induction in the current study confirmed the role of Fhit in regulating TK1 expression. Changes in Fhit expression did not impact TK1 protein turnover or transcription from the TK1 promoter, nor steady-state levels of TK1 mRNA or turnover. Polysome profile analysis showed that up-regulated Fhit expression resulted in decreased TK1 RNA in non-translating messenger ribonucleoproteins and increased ribosome density on TK1 mRNA. Fhit does not bind RNA but its expression increased luciferase expression from a transgene bearing the TK1 5'-UTR. Fhit has been reported to act as a scavenger decapping enzyme, and a similar result with a mutant (H96) that binds but does not cleave nucleoside 5',5'-triphosphates suggests the impact on TK1 translation is due to its ability to modulate the intracellular level of cap-like molecules. Consistent with this, cells expressing Fhit mutants with reduced activity toward cap-like dinucleotides exhibit DNA damage resulting from TK1 deficiency, whereas cells expressing wild-type Fhit or the H96N mutant do not. The results have implications for the mechanism by which Fhit regulates TK1 mRNA, and more broadly, for its modulation of multiple functions as tumor suppressor/genome caretaker. Copyright © 2017 Elsevier B.V. All rights reserved.

  3. RNA N6-methyladenosine methylation in post-transcriptional gene expression regulation.

    Science.gov (United States)

    Yue, Yanan; Liu, Jianzhao; He, Chuan

    2015-07-01

    N(6)-methyladenosine (m(6)A) is the most prevalent and internal modification that occurs in the messenger RNAs (mRNA) of most eukaryotes, although its functional relevance remained a mystery for decades. This modification is installed by the m(6)A methylation "writers" and can be reversed by demethylases that serve as "erasers." In this review, we mainly summarize recent progress in the study of the m(6)A mRNA methylation machineries across eukaryotes and discuss their newly uncovered biological functions. The broad roles of m(6)A in regulating cell fates and embryonic development highlight the existence of another layer of epigenetic regulation at the RNA level, where mRNA is subjected to chemical modifications that affect protein expression. © 2015 Yue et al.; Published by Cold Spring Harbor Laboratory Press.

  4. Differential regulation of TGA transcription factors by post-transcriptional control.

    Science.gov (United States)

    Pontier, Dominique; Privat, Isabelle; Trifa, Youssef; Zhou, Jun-Ma; Klessig, Daniel F; Lam, Eric

    2002-12-01

    Transcription factors often belong to multigene families and their individual contribution in a particular regulatory network remains difficult to assess. We show here that specific members from a family of conserved Arabidopsis bZIP transcription factors, the TGA proteins, are regulated in their protein stability by developmental stage-specific proteolysis. Using GFP fusions of three different Arabidopsis TGA factors that represent members of distinct subclasses of the TGA factor family, we demonstrate that two of these TGA proteins are specifically targeted for proteolysis in mature leaf cells. Using a supershift gel mobility assay, we found evidence for similar regulation of the cognate proteins as compared to the GFP fusion proteins expressed under the cauliflower mosaic virus (CaMV) 35S promoter. Using various inhibitors, we showed that the expression of at least one of these three TGA factors could be stabilized by inhibition of proteasome-mediated proteolysis. This study indicates that TGA transcription factors may be regulated by distinct pathways of targeted proteolysis that can serve to modulate the contribution of specific members of a multigene family in complex regulatory pathways.

  5. Post-transcriptional control of the mammalian circadian clock: implications for health and disease

    OpenAIRE

    Preußner, Marco; Heyd, Florian

    2016-01-01

    Many aspects of human physiology and behavior display rhythmicity with a period of approximately 24 h. Rhythmic changes are controlled by an endogenous time keeper, the circadian clock, and include sleep-wake cycles, physical and mental performance capability, blood pressure, and body temperature. Consequently, many diseases, such as metabolic, sleep, autoimmune and mental disorders and cancer, are connected to the circadian rhythm. The development of therapies that take circadian biology int...

  6. Universal features of post-transcriptional gene regulation are critical for Plasmodium zygote development.

    NARCIS (Netherlands)

    Mair, G.R.; Lasonder, E.; Garver, L.S.; Franke-Fayard, B.; Carret, C.K.; Wiegant, J.C.; Dirks, R.W.; Dimopoulos, G.; Janse, C.J.; Waters, A.P.

    2010-01-01

    A universal feature of metazoan sexual development is the generation of oocyte P granules that withhold certain mRNA species from translation to provide coding potential for proteins during early post-fertilization development. Stabilisation of translationally quiescent mRNA pools in female

  7. Characteristics of Human Brain Activity during the Evaluation of Service-to-Service Brand Extension.

    Science.gov (United States)

    Yang, Taeyang; Lee, Seungji; Seomoon, Eunbi; Kim, Sung-Phil

    2018-01-01

    Brand extension is a marketing strategy to apply the previously established brand name into new goods or service. A number of studies have reported the characteristics of human event-related potentials (ERPs) in response to the evaluation of goods-to-goods brand extension. In contrast, human brain responses to the evaluation of service extension are relatively unexplored. The aim of this study was investigating cognitive processes underlying the evaluation of service-to-service brand extension with electroencephalography (EEG). A total of 56 text stimuli composed of service brand name (S1) followed by extended service name (S2) were presented to participants. The EEG of participants was recorded while participants were asked to evaluate whether a given brand extension was acceptable or not. The behavioral results revealed that participants could evaluate brand extension though they had little knowledge about the extended services, indicating the role of brand in the evaluation of the services. Additionally, we developed a method of grouping brand extension stimuli according to the fit levels obtained from behavioral responses, instead of grouping of stimuli a priori . The ERP analysis identified three components during the evaluation of brand extension: N2, P300, and N400. No difference in the N2 amplitude was found among the different levels of a fit between S1 and S2. The P300 amplitude for the low level of fit was greater than those for higher levels ( p < 0.05). The N400 amplitude was more negative for the mid- and high-level fits than the low level. The ERP results of P300 and N400 indicate that the early stage of brain extension evaluation might first detect low-fit brand extension as an improbable target followed by the late stage of the integration of S2 into S1. Along with previous findings, our results demonstrate different cognitive evaluation of service-to-service brand extension from goods-to-goods.

  8. Characteristics of Human Brain Activity during the Evaluation of Service-to-Service Brand Extension

    Directory of Open Access Journals (Sweden)

    Taeyang Yang

    2018-02-01

    Full Text Available Brand extension is a marketing strategy to apply the previously established brand name into new goods or service. A number of studies have reported the characteristics of human event-related potentials (ERPs in response to the evaluation of goods-to-goods brand extension. In contrast, human brain responses to the evaluation of service extension are relatively unexplored. The aim of this study was investigating cognitive processes underlying the evaluation of service-to-service brand extension with electroencephalography (EEG. A total of 56 text stimuli composed of service brand name (S1 followed by extended service name (S2 were presented to participants. The EEG of participants was recorded while participants were asked to evaluate whether a given brand extension was acceptable or not. The behavioral results revealed that participants could evaluate brand extension though they had little knowledge about the extended services, indicating the role of brand in the evaluation of the services. Additionally, we developed a method of grouping brand extension stimuli according to the fit levels obtained from behavioral responses, instead of grouping of stimuli a priori. The ERP analysis identified three components during the evaluation of brand extension: N2, P300, and N400. No difference in the N2 amplitude was found among the different levels of a fit between S1 and S2. The P300 amplitude for the low level of fit was greater than those for higher levels (p < 0.05. The N400 amplitude was more negative for the mid- and high-level fits than the low level. The ERP results of P300 and N400 indicate that the early stage of brain extension evaluation might first detect low-fit brand extension as an improbable target followed by the late stage of the integration of S2 into S1. Along with previous findings, our results demonstrate different cognitive evaluation of service-to-service brand extension from goods-to-goods.

  9. Mysterious Blob Galaxies Revealed

    Science.gov (United States)

    2005-01-01

    [figure removed for brevity, see original site] [figure removed for brevity, see original site] Figure 1Figure 2Figure 3 This image composite shows a giant galactic blob (red, figure 2) and the three merging galaxies NASA's Spitzer Space Telescope discovered within it (yellow, figure 3). Blobs are intensely glowing clouds of hot hydrogen gas that envelop faraway galaxies. They are about 10 times as large as the galaxies they surround. Visible-light images like the one shown in figure 2, reveal the vast extent of blobs, but don't provide much information about their host galaxies. Using its heat-seeking infrared eyes, Spitzer was able to see the dusty galaxies tucked inside one well-known blob located 11 billion light-years away. The findings reveal three monstrously bright galaxies, trillions of times brighter than the Sun, in the process of merging together (figure 3). Spitzer also observed three other blobs located in the same cosmic neighborhood, all of which were found to be glaringly bright. One of these blobs is also known to be a galactic merger, only between two galaxies instead of three. It remains to be seen whether the final two blobs studied also contain mergers. The Spitzer data were acquired by its multiband imaging photometer. The visible-light image was taken by the Blanco Telescope at the Cerro Tololo Inter-American Observatory, Chile.

  10. circTAIL-seq, a targeted method for deep analysis of RNA 3' tails, reveals transcript-specific differences by multiple metrics.

    Science.gov (United States)

    Gazestani, Vahid H; Hampton, Marshall; Abrahante, Juan E; Salavati, Reza; Zimmer, Sara L

    2016-03-01

    Post-transcriptionally added RNA 3' nucleotide extensions, or tails, impose numerous regulatory effects on RNAs, including effects on RNA turnover and translation. However, efficient methods for in-depth tail profiling of a transcript of interest are still lacking, hindering available knowledge particularly of tail populations that are highly heterogeneous. Here, we developed a targeted approach, termed circTAIL-seq, to quantify both major and subtle differences of heterogeneous tail populations. As proof-of-principle, we show that circTAIL-seq quantifies the differences in tail qualities between two selected Trypanosoma brucei mitochondrial transcripts. The results demonstrate the power of the developed method in identification, discrimination, and quantification of different tail states that the population of one transcript can possess. We further show that circTAIL-seq can detect the tail characteristics for variants of transcripts that are not easily detectable by conventional approaches, such as degradation intermediates. Our findings are not only well supported by previous knowledge, but they also expand this knowledge and provide experimental evidence for previous hypotheses. In the future, this approach can be used to determine changes in tail qualities in response to environmental or internal stimuli, or upon silencing of genes of interest in mRNA-processing pathways. In summary, circTAIL-seq is an effective tool for comparing nonencoded RNA tails, especially when the tails are extremely variable or transcript of interest is low abundance. © 2016 Gazestani et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  11. circTAIL-seq, a targeted method for deep analysis of RNA 3′ tails, reveals transcript-specific differences by multiple metrics

    Science.gov (United States)

    Gazestani, Vahid H.; Hampton, Marshall; Abrahante, Juan E.; Salavati, Reza; Zimmer, Sara L.

    2016-01-01

    Post-transcriptionally added RNA 3′ nucleotide extensions, or tails, impose numerous regulatory effects on RNAs, including effects on RNA turnover and translation. However, efficient methods for in-depth tail profiling of a transcript of interest are still lacking, hindering available knowledge particularly of tail populations that are highly heterogeneous. Here, we developed a targeted approach, termed circTAIL-seq, to quantify both major and subtle differences of heterogeneous tail populations. As proof-of-principle, we show that circTAIL-seq quantifies the differences in tail qualities between two selected Trypanosoma brucei mitochondrial transcripts. The results demonstrate the power of the developed method in identification, discrimination, and quantification of different tail states that the population of one transcript can possess. We further show that circTAIL-seq can detect the tail characteristics for variants of transcripts that are not easily detectable by conventional approaches, such as degradation intermediates. Our findings are not only well supported by previous knowledge, but they also expand this knowledge and provide experimental evidence for previous hypotheses. In the future, this approach can be used to determine changes in tail qualities in response to environmental or internal stimuli, or upon silencing of genes of interest in mRNA-processing pathways. In summary, circTAIL-seq is an effective tool for comparing nonencoded RNA tails, especially when the tails are extremely variable or transcript of interest is low abundance. PMID:26759453

  12. Confidence of Extension Staff in Akwa Ibom State Agricultural ...

    African Journals Online (AJOL)

    the extension agents (EAs), block extension agents (BEAs), block extension supervisors (BESs), and zonal extension officers (ZEOs) were sometimes satisfied with AKADEP as their organization. Age, household size, and years of extension experience of EAs were strong indicators of organizational confidence. Age, level of ...

  13. Expanding Agricultural and Rural Extension Roles for Sustainable ...

    African Journals Online (AJOL)

    Expanding Agricultural and Rural Extension Roles for Sustainable Extension Practice in Nigeria. ... The expanded scope could include marketing extension, non-farm rural micro enterprise development, service to farmers' associations, technical extension service and urban extension. These services should be provided at ...

  14. Global Approaches to Extension Practice: A Journal of Agricultural ...

    African Journals Online (AJOL)

    Global Approaches to Extension Practice (GAEP), A publication of the Department of Agricultural Extension, Federal University of Technology, Owerri, Imo State, Nigeria is an international journal which considers articles from all areas of Agricultural Extension: rural sociology, environmental extension, extension ...

  15. Particle Swarm Optimisation with Spatial Particle Extension

    DEFF Research Database (Denmark)

    Krink, Thiemo; Vesterstrøm, Jakob Svaneborg; Riget, Jacques

    2002-01-01

    In this paper, we introduce spatial extension to particles in the PSO model in order to overcome premature convergence in iterative optimisation. The standard PSO and the new model (SEPSO) are compared w.r.t. performance on well-studied benchmark problems. We show that the SEPSO indeed managed...... to keep diversity in the search space and yielded superior results....

  16. Longest Common Extensions in Sublinear Space

    DEFF Research Database (Denmark)

    Bille, Philip; Gørtz, Inge Li; Knudsen, Mathias Bæk Tejs

    2015-01-01

    The longest common extension problem (LCE problem) is to construct a data structure for an input string T of length n that supports LCE(i,j) queries. Such a query returns the length of the longest common prefix of the suffixes starting at positions i and j in T. This classic problem has a well...

  17. ANTLR Tree Grammar Generator and Extensions

    Science.gov (United States)

    Craymer, Loring

    2005-01-01

    A computer program implements two extensions of ANTLR (Another Tool for Language Recognition), which is a set of software tools for translating source codes between different computing languages. ANTLR supports predicated- LL(k) lexer and parser grammars, a notation for annotating parser grammars to direct tree construction, and predicated tree grammars. [ LL(k) signifies left-right, leftmost derivation with k tokens of look-ahead, referring to certain characteristics of a grammar.] One of the extensions is a syntax for tree transformations. The other extension is the generation of tree grammars from annotated parser or input tree grammars. These extensions can simplify the process of generating source-to-source language translators and they make possible an approach, called "polyphase parsing," to translation between computing languages. The typical approach to translator development is to identify high-level semantic constructs such as "expressions," "declarations," and "definitions" as fundamental building blocks in the grammar specification used for language recognition. The polyphase approach is to lump ambiguous syntactic constructs during parsing and then disambiguate the alternatives in subsequent tree transformation passes. Polyphase parsing is believed to be useful for generating efficient recognizers for C++ and other languages that, like C++, have significant ambiguities.

  18. Communication for Rural Innovation : rethinking agricultural extension

    NARCIS (Netherlands)

    Leeuwis, C.; Ban, van den A.W.

    2004-01-01

    This important book is the re-titled third edition of the extremely well received and widely used Agricultural Extension (van den Ban & Hawkins, 1988, 1996). Building on the previous editions, Communication for Rural Innovation maintains and adapts the insights and conceptual models of value

  19. Banana Algebra: Compositional Syntactic Language Extension

    DEFF Research Database (Denmark)

    Andersen, Jacob; Brabrand, Claus; Christiansen, David Raymond

    2013-01-01

    We propose an algebra of languages and transformations as a means of compositional syntactic language extension. The algebra provides a layer of high-level abstractions built on top of languages (captured by context-free grammars) and transformations (captured by constructive catamorphisms). The ...

  20. Equivalence relations of AF-algebra extensions

    Indian Academy of Sciences (India)

    In this paper, we consider equivalence relations of *-algebra extensions and describe the relationship between the isomorphism equivalence and the unitary equivalence. We also show that a certain group homomorphism is the obstruction for these equivalence relations to be the same.

  1. 78 FR 31885 - Patent Term Extension

    Science.gov (United States)

    2013-05-28

    ... Intellectual Property and Communications Omnibus Reform Act of 1999, require the USPTO to notify the applicant... 1995, Public Law 104-13 (44 U.S.C. 3506(c)(2)(A)). DATES: Written comments must be submitted on or... the extension provisions of 35 U.S.C. 156, the USPTO may in some cases extend the term of an original...

  2. Semi extensive methods - two main systems are

    African Journals Online (AJOL)

    next litter readily within a few days after weaning. It has long been ... terms of early growth and overall efficiency of conversion of ... 21-day Weaning. Semi extensive methods - two main systems are adopted, the first using arks with outside runs on pasture and the second using similar arks but fitted with slatted or weld mesh ...

  3. Seroprevalence Study Of Bovine Brucellosis In Extensive ...

    African Journals Online (AJOL)

    The prevalence of bovine brucellosis was measured in cross sectional study in Jimma zone, Western Ethiopia using Rose Bengal Plate Test (RBT) and CFT from October 2003 to April 2004. The study animals consisted of 1305 local breed found in extensive system in five districts of in the zone. The overall individual animal ...

  4. Stress: Professional Development Needs of Extension Faculty.

    Science.gov (United States)

    Place, Nick T.; Jacob, Steve

    2001-01-01

    Responses from 314 of 422 extension faculty showed a variety of levels of job stress, primarily from time pressures and overcommitment. Those who used formal planning and time management techniques had lower stress scores. Time with family was a common coping mechanism. (Contains 19 references.) (SK)

  5. Tools for Creating Mobile Applications for Extension

    Science.gov (United States)

    Drill, Sabrina L.

    2012-01-01

    Considerations and tools for developing mobile applications for Extension include evaluating the topic, purpose, and audience. Different computing platforms may be used, and apps designed as modified Web pages or implicitly programmed for a particular platform. User privacy is another important consideration, especially for data collection apps.…

  6. South African Journal of Agricultural Extension

    African Journals Online (AJOL)

    The South African Journal of Agricultural Extensionaims to: * advance and apply the science of extension and of rural development as scientific discipline by stimulating thought, study, research, discussion and the publication and exchange of knowledge both nationally and internationally. * promote the professionalism ...

  7. A Graph Library Extension of SVG

    DEFF Research Database (Denmark)

    Nørmark, Kurt

    2007-01-01

    be aggregated as a single node, and an entire graph can be embedded in a single node. In addition, a number of different graph animations are described. The starting point of the SVG extension is a library that provides an exact of mirror of SVG 1.1 in the functional programming language Scheme. Each element...

  8. On Touchard's continued fraction and extensions: combinatorices ...

    African Journals Online (AJOL)

    We give a direct and simple proof of Touchard's continued fraction, provide an extension of it, and transform it into similar expansions related to Motzkin and Schroder numbers. Another proof is then given that uses only induction. We use this machinery on two examples that appear in recent papers of Josuat-Verges; with an ...

  9. Emergency Food Programs: Untapped Opportunities for Extension?

    Science.gov (United States)

    Mobley, Amy R.

    2012-01-01

    This article reports results from a questionnaire that assessed the frequency and type of nutrition questions asked at emergency food programs to determine if Extension professionals need to increase direct outreach efforts. Emergency food program workers (n = 460) were recruited via mail to complete a self-administered survey. More than one-third…

  10. Equivalence relations of AF-algebra extensions

    Indian Academy of Sciences (India)

    Introduction. Brown, Douglas and Fillmore [3] gave the famous BDF theory to study essentially normal operators on an infinite dimensional Hilbert space and extensions of C∗. -algebra C(X) by. K in the 1970's, where X is a compact metric space and K is the C*-algebra of compact operators on an infinite dimensional ...

  11. Measuring Florida Extension Faculty's Agricultural Paradigmatic Preferences

    Science.gov (United States)

    Warner, Laura A.; Murphrey, Theresa Pesl; Lawver, David E.; Baker, Matt; Lindner, James R.

    2014-01-01

    The demand for sustainable agriculture has increased, and many institutions, including the University of Florida, have adopted agricultural sustainability as a major goal. Extension has been identified as a critical information source, important in disseminating sustainable agricultural growing techniques. However, research has demonstrated that…

  12. Assessment Of Shell Petroleum Development Company Extension ...

    African Journals Online (AJOL)

    The study assessed Shell Petroleum Development Company Extension Services in Etche Local Government Area of Rivers State, Nigeria. Data were gathered form four categories of respondents drawn from the Company\\'s staff and the communities. A total of 180 respondents participated in the study. means scores and ...

  13. assessment of shell petroleum development company extension ...

    African Journals Online (AJOL)

    ABSTRACT. The study assessed Shell Petroleum DeVelopment Company Extension. Services in Etche Local Government Area of Rivers State, Nigeria. Data were gathered form four categories of respondents drawn from the. Company's staff and the communities. A total of 180 respondents participated in the study. means ...

  14. Effectively Communicating Science to Extension Audiences

    Science.gov (United States)

    Robinson, Patrick

    2013-01-01

    This article discusses the concept of "framing" within the context of relevant communication and psychological research and considers its potential applicability to Extension science communication. Examples of research-based support for the framing of scientific issues are presented, along with a literature-based discussion of the…

  15. Matching Extension Service With Farmers' Needs: Towards ...

    African Journals Online (AJOL)

    of the farming family and the farm can better target its programs to meet farmers' needs. In this study 305 farm households, from two districts of northcentral Ethiopia are used as a case study, to examine key socio-economic and ecological indicators that affect effective use of extension services. Data was collected using the ...

  16. Improving Generation Y Volunteerism in Extension Programs

    Science.gov (United States)

    Andrews, Kevin B.; Lockett, Landry L.

    2013-01-01

    Members of Generation Y have many positive attributes that make them attractive to Extension volunteer administrators as a potential source of labor. However, they think differently, have unique needs, require new management styles, and have less tolerance for unpleasant working conditions than previous generations. Additionally, they are engaged…

  17. Integrating Reading and Writing through Extensive Reading

    Science.gov (United States)

    Park, Jeongyeon

    2016-01-01

    This study explores whether an extensive reading (ER) approach can enhance L2 learners' writing performance in an English for Academic Purposes context. Two classes were compared in terms of writing improvement after one semester: a 'traditional' writing class primarily focused on writing practice and grammar instruction, and an ER class in which…

  18. Does Extensive Reading Promote Reading Speed?

    Science.gov (United States)

    He, Mu

    2014-01-01

    Research has shown a wide range of learning benefits accruing from extensive reading. Not only is there improvement in reading, but also in a wide range of language uses and areas of language knowledge. However, few research studies have examined reading speed. The existing literature on reading speed focused on students' reading speed without…

  19. Definable maximal discrete sets in forcing extensions

    DEFF Research Database (Denmark)

    Törnquist, Asger Dag; Schrittesser, David

    2017-01-01

    that in the Sacks and Miller extensions there is a Π11 maximal orthogonal family ("mof") of Borel probability measures on Cantor space. A similar result is also obtained for Π11 mad families. By contrast, we show that if there is a Mathias real over L then there are no Σ12 mofs....

  20. 75 FR 9403 - Agency Information Collection Extension

    Science.gov (United States)

    2010-03-02

    ... Management and Budget (OMB) review; comment request. SUMMARY: The Department of Energy (DOE) has submitted an... 1995. The information collection requests a three-year extension of its Exchange/Sale Report, Excess... and Budget. DATES: Comments regarding this collection must be received on or before April 1, 2010. If...

  1. 78 FR 38305 - Agency Information Collection Extension

    Science.gov (United States)

    2013-06-26

    ... Budget (OMB) review; comment request. SUMMARY: The Department of Energy (DOE) has submitted an... 1995. The information collection requests a three-year extension of its Exchange/Sale Report, Excess... Management and Budget. DATES: Comments regarding this collection must be received on or before July 26, 2013...

  2. Catastrophic failure of polymer melts during extension

    DEFF Research Database (Denmark)

    Rasmussen, Henrik K.

    2013-01-01

    Numerical flow modeling has been applied to study the break of monodisperse polymer melts during extension. These continuum mechanical based computations are within the ideas of the microstructural ’interchain pressure’ theory. Calculated breaks, a result of small initial sample imperfections, ag...

  3. On an extension of a combinatorial identity

    Indian Academy of Sciences (India)

    On an extension of a combinatorial identity. M RANA and A K AGARWAL. Center for Advanced Study in Mathematics, Panjab University, Chandigarh 160 014,. India. E-mail: aka@pu.ac.in. MS received 22 August 2007. Abstract. Using Frobenius partitions we extend the main results of [4]. This leads to an infinite family of ...

  4. Entrepreneurial Extension Conducted via Social Media

    Science.gov (United States)

    Cornelisse, Sarah; Hyde, Jeffrey; Raines, Christopher; Kelley, Kathleen; Ollendyke, Dana; Remcheck, James

    2011-01-01

    The widespread availability of and access to the Internet have led to the development of new forms of communication. Collectively termed "social media," these new communication tools have created vast opportunities for Extension professionals in how they perform their work and how businesses interact with consumers. This article outlines currently…

  5. Extension of a theorem due to Ramanujan

    Directory of Open Access Journals (Sweden)

    Medhat A. Rakha

    2014-12-01

    Full Text Available The aim of this research paper is to establish an extension of a theorem due to Ramanujan. The result is obtained with the help of two terminating results for the series $_3F_{2}$ very recently obtained by Rakha et al. A few interesting special cases are also given.

  6. Livestock extension programmes participation and impact on ...

    African Journals Online (AJOL)

    In rural South Africa, the sustainability of cattle-based livelihoods is threatened by the competition for natural resources such as land and water. The central and provincial governments continue to invest funds in agricultural extension in order to uplift the productivity and safeguard the multifunctionality of cattle farming.

  7. Trials and Triumphs of Expanded Extension Programs.

    Science.gov (United States)

    Leavengood, Scott; Love, Bob

    1998-01-01

    Oregon extension faced challenges in presenting programs in the wood products industry. Several traditional tactics, revised to suit a new audience, have proved successful: personal coaching, building partnerships, and providing a high level of service. Newer methods, such as database marketing and distance learning, are also proving to be…

  8. Forestry Extension: An Indispensable Service for Sustainable ...

    African Journals Online (AJOL)

    Unfortunately human activities have depleted the forest through, uncontrolled lumbering, bush burning, charcoal production just to mention a few. ... is the premise on which the challenges facing effective forestry extension delivery in Nigeria and suggested solutions to the highlighted challenges is the focus of this write up.

  9. Developing Students' Reading Ability through Extensive Reading

    Science.gov (United States)

    Meng, Fanshao

    2009-01-01

    A good reading competence is a necessity for those studying English for academic and occupational purposes. Based on the results of previous research, theory and practice on L2 Extensive Reading, this paper analyses current situation for teaching and learning reading in our Chinese universities and proposes practical applications of extensive…

  10. Making Extensive Reading Even More Student Centered

    Science.gov (United States)

    Jacobs, George M.; Renandya, Willy A.

    2015-01-01

    This article begins by explaining the student centered learning paradigm. Next, the article explains various features of a student centered approach to education and how extensive reading (ER), as it is most often practiced, fits with those features. The bulk of the article suggests how ER might be implemented to make it even more learner centered.

  11. MAKING EXTENSIVE READING EVEN MORE STUDENT CENTERED

    Directory of Open Access Journals (Sweden)

    George Jacobs

    2015-01-01

    Full Text Available Abstract: This article begins by explaining the student centered learning paradigm.  Next, the article explains various features of a student centered approach to education and how extensive reading (ER, as it is most often practiced, fits with those features.  The bulk of the article suggests how ER might be implemented to make it even more learner centered.

  12. Some extensions and applications of Eisenstein Irreducibility ...

    Indian Academy of Sciences (India)

    Some extensions and applications of Eisenstein Irreducibility. Criterion. Sudesh Kaur Khanduja. Department of ... Suppose that there exists a prime number p such that. • a0 is not divisible by p,. • ai is divisible by p for .... + fn(xn) with complex coefficients is ir- reducible provided the degrees of f1. (x1. ), ..., fn(xn) have greatest ...

  13. Rhinoscleroma with orbital extension: CT and MRI

    Energy Technology Data Exchange (ETDEWEB)

    Le Hir, P. [Department of Radiology, CHU Saint-Antoine, 184 Rue du Faubourg Saint-Antoine, F-75012 Paris (France); Marsot-Dupuch, K. [Department of Radiology, CHU Saint-Antoine, 184 Rue du Faubourg Saint-Antoine, F-75012 Paris (France); Bigel, P. [Department of Pathology, CHU Saint-Antoine, Paris (France); Elbigourmie, T.M. [Department of Radiology, CHU Saint-Antoine, 184 Rue du Faubourg Saint-Antoine, F-75012 Paris (France); Jacquier, I. [ENT Department, CHU Saint-Antoine, Paris (France); Brunereau, L. [Department of Radiology, CHU Saint-Antoine, 184 Rue du Faubourg Saint-Antoine, F-75012 Paris (France); Tubiana, J.M. [Department of Radiology, CHU Saint-Antoine, 184 Rue du Faubourg Saint-Antoine, F-75012 Paris (France)

    1996-02-01

    We describe the MRI features of a rhinoscleroma with orbital extension. This benign bacterial and granulomatous lesion of the paranasal sinuses gave homogeneous low intensity on T2-weighted images and enhanced with gadolinium. It could simulate a malignant sinonasal tumour or a fungal sinusitis; the diagnosis must be considered in patients from endemic areas. (orig.). With 3 figs.

  14. 75 FR 20561 - Patent Term Extension

    Science.gov (United States)

    2010-04-20

    ... Patent and Trademark Office Patent Term Extension ACTION: Proposed collection; comment request. SUMMARY: The United States Patent and Trademark Office (USPTO), as part of its continuing effort to reduce... the Chief Information Officer, United States Patent and Trademark Office, P.O. Box 1450, Alexandria...

  15. Transforming agriculture through contracted extension service ...

    African Journals Online (AJOL)

    Transformation of small holder agriculture from subsistence farming to agribusiness focused systems, is paramount towards attainment of Kenya's vision 2030 and the Millennium Development Goals. This requires extension service delivery systems that focus on addressing challenges within agricultural product value ...

  16. Extensive Actinomyces naeslundii infection in a child.

    OpenAIRE

    Dobson, S R; Edwards, M. S.

    1987-01-01

    A case of extensive Actinomyces naeslundii infection in a globally retarded patient is reported. To our knowledge, this uncommon Actinomyces species has not previously been described as a cause of widespread disease. Mental retardation and thoracic scoliosis were identified as features predisposing to infection.

  17. abc: An extensible AspectJ compiler

    DEFF Research Database (Denmark)

    Avgustinov, Pavel; Christensen, Aske Simon; Hendren, Laurie

    2005-01-01

    checking and code generation, as well as data flow and control flow analyses. The AspectBench Compiler (abc) is an implementation of such a workbench. The base version of abc implements the full AspectJ language. Its frontend is built, using the Polyglot framework, as a modular extension of the Java...

  18. Transmural intrathoracic lipoma with intraspinal extension.

    Science.gov (United States)

    Jain, Vishesh; Singal, Arbinder K; Gupta, Arun K; Bhatnagar, Veereshwar

    2007-12-01

    A rare case of transmural dumbbell intrathoracic lipoma with intraspinal extension is reported. Preoperative diagnosis was possible with a computed tomographic scan and fine-needle aspiration cytology. Complete excision was curative. The chest wall defect was repaired with Prolene mesh. Only one similar case has been previously reported in the English literature.

  19. Professional extension support: A prerequisite for sustainable ...

    African Journals Online (AJOL)

    professionalism and reflects on the general perceptions for professional extension support in irrigation management perceived by small- scale and commercial irrigation farmers. It also portrays the findings on the assessment of the technical competence and knowledge of irrigation extensionists. Possible barriers why ...

  20. An Effective Aquaculture Extension System from Farmers ...

    African Journals Online (AJOL)

    Regionally, government extension system and reading materials also played a significant role in the diffusion of aquaculture information to peri-urban farmers, and were considered to be of high quality and very accessible. This study recommends that the aquaculture division should identify the institutional mechanism ...

  1. Communication for strengthening agricultural extension and rural ...

    African Journals Online (AJOL)

    This paper argues that extension workers need training in Communication for Development (C4D), an emerging body of knowledge for addressing problems, such as participation, integration and capacity building for them to relate more effectively with development partners. Thus, this paper proposes a C4D framework for ...

  2. Extension Procedures for Confirmatory Factor Analysis

    Science.gov (United States)

    Nagy, Gabriel; Brunner, Martin; Lüdtke, Oliver; Greiff, Samuel

    2017-01-01

    We present factor extension procedures for confirmatory factor analysis that provide estimates of the relations of common and unique factors with external variables that do not undergo factor analysis. We present identification strategies that build upon restrictions of the pattern of correlations between unique factors and external variables. The…

  3. Dialogic Reading Aloud to Promote Extensive Reading

    Science.gov (United States)

    Jacobs, George M.

    2016-01-01

    How can teachers motivate students to read extensively in a second language? One strategy is for teachers to read aloud to students to promote the joys of reading generally, to build students' language skills and to introduce students to specific authors, book series, genres, websites, etc. This article begins by discussing why teachers might want…

  4. Testing Extension Services through AKAP Models

    Science.gov (United States)

    De Rosa, Marcello; Bartoli, Luca; La Rocca, Giuseppe

    2014-01-01

    Purpose: The aim of the paper is to analyse the attitude of Italian farms in gaining access to agricultural extension services (AES). Design/methodology/approach: The ways Italian farms use AES are described through the AKAP (Awareness, Knowledge, Adoption, Product) sequence. This article investigated the AKAP sequence by submitting a…

  5. Journal of Environmental Extension: Editorial Policies

    African Journals Online (AJOL)

    Focus and Scope. Journal of Environmental Extension is to be published annually to generate ideas on formulation, packaging, dissemination and consequential impacts of ideas/policies relating to the quality and sustainability of the environment. Focus of the Journal is on: Health Agriculture Technology Waste ...

  6. Women Empowerment And Agricultural Extension Policy: The ...

    African Journals Online (AJOL)

    This paper examined the role and challenges of extension agents in empowering women in a bid to revamp the agricultural sector. The activities of women in agricultural production are reviewed against the backdrop of global shift to gender sensitivity, particularly the emphasis on the role of women in agriculture. The paper ...

  7. Ethics and morals in the extension work

    Directory of Open Access Journals (Sweden)

    Fátima Lourdes Morales Intriago

    2017-05-01

    Full Text Available One of the main discussions about agents that provide rural extension is the lack of adequate proposals for the reality of farmers. The exyensionists work according to ethics and morals. Was carried out a theoretical search by made analyzing concepts about these terms and that are applied by extension agents. In This paper discusses how agents act with respect to the aforementioned notions and the conflicts they can cause with rural communities. It was found that the extensionist’s behavior is based on its values, norms and sanctions formation that can be object, which determines the changes that occur in the communities served. On the other hand, farmers do not receive appropriate attention by organisms that facilitate the Rural Extension, ignoring their interests and priorities. In addition, agents, as servants of institutions that provide assistance and extension, lose autonomy during the contact with communities. It was concluded that agents act correctly according to morality, as well as what concerns to ethics, since lowing the rules of the institution to which they belong, which does not always match with what rural people pursued.

  8. Home Food Preservation Training for Extension Educators

    Science.gov (United States)

    Goard, Linnette Mizer; Hill, Melinda; Shumaker, Katharine; Warrix, Marisa

    2013-01-01

    During times of economic downturn, there has been an increased interest in home food preservation. As the primary resource for current research-based recommendations, a team of Extension Family and Consumer Sciences educators with specialization in food safety and food preservation responded to this demand by developing a standardized food…

  9. FISHERIES EXTENSION SERVICES IN OGUN STATE | Olopade ...

    African Journals Online (AJOL)

    The study attempts to assess the current trends, impact and constraints of fisheries extension services to artisanal fishers in Ogun Waterside Local Government Area of Ogun State. The survey approach was used to generate the needed data using 120 structured questionnaires. Simple statistical techniques such as means ...

  10. Tampa Bay Extension Agents’ Views of Urban Extension: Philosophy and Program Strategies

    Directory of Open Access Journals (Sweden)

    Amy Harder

    2017-06-01

    Full Text Available The purpose of this article was to explore the concept of urban Extension as perceived by Extension agents within the Tampa Bay area, one of Florida’s fastest growing metropolitan areas. From a theoretical perspective, it is critical to understand Extension agents’ beliefs about urban Extension because behaviors are directly related to attitudes (Ajzen, 2012. In 2016, a qualitative investigation was undertaken to explore the perspectives of 23 agents working within the Tampa Bay area. Results showed the majority of agents believed that context and client needs are unique for urban Extension, and that to a lesser extent, unique agent expertise is required. Further, these beliefs impacted how agents reported their approach to programming, with an emphasis on providing convenience and seeking partnerships. Difficulties were identified related to identifying the role of Extension in a resource-rich environment of service providers, which contributed to the existence of a perceived disconnect between urban audiences and Extension. Opportunities exist for Extension leadership to provide strategic organizational support that will enhance agents’ abilities to succeed in the metropolitan environment.

  11. Extension Study Group Members View Their Clubs and Extension Home Economists. ANREI Publication No. 28.

    Science.gov (United States)

    Miller, Mason E.

    The data presented in this report were selected from a 1972 study of Michigan Extension Study Group (ESG) members. Included are data descriptive of the women themselves and their situation (area and type of home, age, income, ESG experience, and especially their attitudes toward their ESG and their Extension Home Economists). Selected findings are…

  12. 78 FR 65242 - Occupational Exposure to Crystalline Silica; Extension of Comment Period; Extension of Period To...

    Science.gov (United States)

    2013-10-31

    ... Exposure to Crystalline Silica; Extension of Comment Period; Extension of Period To Submit Notices of... Notice of Proposed Rulemaking (NPRM) on Occupational Exposure to Crystalline Silica for an additional 47... occupational exposure to respirable crystalline silica (78 FR 56274). This notice requested written comments by...

  13. Tensor extension of the Poincar\\'e algebra

    OpenAIRE

    Soroka, Dmitrij V.; Soroka, Vyacheslav A.

    2004-01-01

    A tensor extension of the Poincar\\'e algebra is proposed for the arbitrary dimensions. Casimir operators of the extension are constructed. A possible supersymmetric generalization of this extension is also found in the dimensions $D=2,3,4$.

  14. Traumatic knee extension deficit (the locked knee)

    DEFF Research Database (Denmark)

    Helmark, I C; Neergaard, K; Krogsgaard, M R

    2007-01-01

    In the present study we investigated the validity of magnetic resonance imaging (MRI) and arthroscopy in knees with acute, traumatic extension deficit (the "locked knee"), and evaluated whether arthroscopy of knees with no mechanical pathology could be avoided by MRI evaluation. The study consisted...... of 50 patients who had an acute, traumatic extension deficit of the knee. All patients were submitted to MRI prior to arthroscopy. Following MRI and surgery, standardized forms were filled out, attempting to objectify the findings. The orthopaedic surgeon was not aware of the MRI result prior to surgery......, the following results were calculated for the overall appearance of a lesion able to cause locking: Positive predictive value = 0.85, negative predictive value = 0.77, sensitivity = 0.95, specificity = 0.53. Two knees were erroneously evaluated with no mechanical locking at MRI (one bucket-handle lesion and one...

  15. Army European Tour Extension: An Interdisciplinary Approach

    Science.gov (United States)

    1985-02-01

    Rollgleu Job -Family Enlisted Spousal Wellbeing Facilities Fit P.rceptin PerceptionCommunity of Familyr’. , Support Satisfacion Attend Religious...Extens+om Logit i model , . Family life -IFactor analysis) SIMOS .. . .% Economics Regressions, Job satisfaction."" ,. ,,~., ,l ’ .; " -C. 20. AUS ACT...amounts of the proposed extension bonuses as well as with increase in satis- Lam faction with job and family life. Smaller lump sum bonuses were (Continued

  16. Mathematical model of subscriber extension line

    OpenAIRE

    Petříková, Iva; Diviš, Zdeněk; Tesař, Zdeněk

    2012-01-01

    The paper focuses on measurement properties of metallic subscriber extension lines to build regression mathematical model for a symmetric pair cable. The regression model is compared with an analytical model based on a theoretical description of transfer parameters for this type of line. The output of the paper should demonstrate the impact of electromagnetic interference on the symmetric pair. The paper also describes the method to identify the interference sources and ...

  17. Extensions and degeneration of spectral triples

    DEFF Research Database (Denmark)

    Christensen, Erik; Ivan, Cristina

    2009-01-01

    To a compact non commutative metric space associated to a C*-algebra A and an extension E of A, we construct 2-parameter family of compact non commutative metric spaces associated to E. It is shown that under certain limits along paths in the parameter space the corresponding spaces converge...... in the quantum Gromov-Hausdorff metric towards either the given non commutative metric space or towards a compact non commutative metric space associated to the compact operators....

  18. Cauchy-Davenport theorem in group extensions

    CERN Document Server

    Karolyi, G

    2005-01-01

    Let A and B be nonempty subsets of a finite group G in which the order of the smallest nontrivial subgroup is not smaller than d=|A|+|B|-1. Then the product set AB has at least d elements. This extends a classical theorem of Cauchy and Davenport to noncommutative groups. We also generalize Vosper's inverse theorem in the same spirit, giving a complete description of the critical pairs. The proofs depend on the structure of group extensions.

  19. Stable Extensions with(out) Gravity

    DEFF Research Database (Denmark)

    Antipin, Oleg; Krog, Jens; Mojaza, Matin

    2014-01-01

    We investigate the vacuum stability as well as the gravitational corrections in extensions of the Standard Model featuring a new complex scalar, and two Dirac fermions for different choices of the hypercharge of the scalar and one of the two fermions. The neutral fermion acquires loop-induced mag...... and discover that the models can be compatible with the asymptotically safe gravity scenario at the price of a heavier Higgs and lighter top mass...

  20. Learning PrimeFaces extensions development

    CERN Document Server

    Jonna, Sudheer

    2014-01-01

    This book provides a step by step approach that explains the most important extension components and their features. All the major features are explained by using the JobHub application with supporting screenshots.If you are an intermediate to advanced level user (or developer) who already has a basic working knowledge of PrimeFaces, then this book is for you.The only thing you need to know is Java Server Faces(JSF).