WorldWideScience

Sample records for mosaic arabidopsis epigenomes

  1. Transposable elements, a treasure trove to decipher epigenetic variation: insights from Arabidopsis and crop epigenomes.

    Science.gov (United States)

    Mirouze, Marie; Vitte, Clémentine

    2014-06-01

    In the past decade, plant biologists and breeders have developed a growing interest in the field of epigenetics, which is defined as the study of heritable changes in gene expression that cannot be explained by changes in the DNA sequence. Epigenetic marks can be responsive to the environment, and evolve faster than genetic changes. Therefore, epigenetic diversity may represent an unexplored resource of natural variation that could be used in plant breeding programmes. On the other hand, crop genomes are largely populated with transposable elements (TEs) that are efficiently targeted by epigenetic marks, and part of the epigenetic diversity observed might be explained by TE polymorphisms. Characterizing the degree to which TEs influence epigenetic variation in crops is therefore a major goal to better use epigenetic variation. To date, epigenetic analyses have been mainly focused on the model plant Arabidopsis thaliana, and have provided clues on epigenome features, components that silence pathways, and effects of silencing impairment. But to what extent can Arabidopsis be used as a model for the epigenomics of crops? In this review, we discuss the similarities and differences between the epigenomes of Arabidopsis and crops. We explore the relationship between TEs and epigenomes, focusing on TE silencing control and escape, and the impact of TE mobility on epigenomic variation. Finally, we provide insights into challenges to tackle, and future directions to take in the route towards using epigenetic diversity in plant breeding programmes. © The Author 2014. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  2. Infection and RNA recombination of Brome mosaic virus in Arabidopsis thaliana

    International Nuclear Information System (INIS)

    Dzianott, Aleksandra; Bujarski, Jozef J.

    2004-01-01

    Ecotypes of Arabidopsis thaliana supported the replication and systemic spread of Brome mosaic virus (BMV) RNAs. Infection was induced either by manual inoculation with viral RNA or by BMV virions, demonstrating that virus disassembly did not prevent infection. When in vitro-transcribed BMV RNAs 1-3 were used, production of subgenomic RNA4 was observed, showing that BMV RNA replication and transcription had occurred. Furthermore, inoculations of the transgenic Arabidopsis line that expressed a suppressor of RNA interference (RNAi) pathway markedly increased the BMV RNA concentrations. Inoculations with designed BMV RNA3 recombination vectors generated both homologous and nonhomologous BMV RNA-RNA recombinants. Thus, all cellular factors essential for BMV RNA replication, transcription, and RNA recombination were shown to be present in Arabidopsis. The current scope of understanding of the model Arabidopsis plant system should facilitate the identification of these factors governing the BMV life cycle

  3. GOLDEN2-LIKE transcription factors coordinate the tolerance to Cucumber mosaic virus in Arabidopsis

    Energy Technology Data Exchange (ETDEWEB)

    Han, Xue-Ying; Li, Peng-Xu; Zou, Li-Juan; Tan, Wen-rong; Zheng, Ting; Zhang, Da-Wei, E-mail: yuanmiao1892@163.com; Lin, Hong-Hui, E-mail: hhlin@scu.edu.cn

    2016-09-02

    Arabidopsis thaliana GOLDEN2-LIKE (GLKs) transcription factors play important roles in regulation of photosynthesis-associated nuclear genes, as well as participate in chloroplast development. However, the involvement of GLKs in plants resistance to virus remains largely unknown. Here, the relationship between GLKs and Cucumber mosaic virus (CMV) stress response was investigated. Our results showed that the Arabidopsis glk1glk2 double-mutant was more susceptible to CMV infection and suffered more serious damages (such as higher oxidative damages, more compromised in PSII photochemistry and more reactive oxygen species accumulation) when compared with the wild-type plants. Interestingly, there was little difference between single mutant (glk1 or glk2) and wild-type plants in response to CMV infection, suggesting GLK1 and GLK2 might function redundant in virus resistance in Arabidopsis. Furthermore, the induction of antioxidant system and defense-associated genes expression in the double mutant were inhibited when compared with single mutant or wild-type plants after CMV infection. Further evidences showed that salicylic acid (SA) and jasmonic acid (JA) might be involved in GLKs-mediated virus resistance, as SA or JA level and synthesis-related genes transcription were impaired in glk1glk2 mutant. Taken together, our results indicated that GLKs played a positively role in virus resistance in Arabidopsis. - Highlights: • GLKs play a positive role in CMV resistance in Arabidopsis. • Defective of GLKs suffered more ROS accumulation. • Arabidopsis lacking GLKs have damaged photosynthesis. • Arabidopsis lacking GLKs show low SA and JA accumulation.

  4. GOLDEN2-LIKE transcription factors coordinate the tolerance to Cucumber mosaic virus in Arabidopsis

    International Nuclear Information System (INIS)

    Han, Xue-Ying; Li, Peng-Xu; Zou, Li-Juan; Tan, Wen-rong; Zheng, Ting; Zhang, Da-Wei; Lin, Hong-Hui

    2016-01-01

    Arabidopsis thaliana GOLDEN2-LIKE (GLKs) transcription factors play important roles in regulation of photosynthesis-associated nuclear genes, as well as participate in chloroplast development. However, the involvement of GLKs in plants resistance to virus remains largely unknown. Here, the relationship between GLKs and Cucumber mosaic virus (CMV) stress response was investigated. Our results showed that the Arabidopsis glk1glk2 double-mutant was more susceptible to CMV infection and suffered more serious damages (such as higher oxidative damages, more compromised in PSII photochemistry and more reactive oxygen species accumulation) when compared with the wild-type plants. Interestingly, there was little difference between single mutant (glk1 or glk2) and wild-type plants in response to CMV infection, suggesting GLK1 and GLK2 might function redundant in virus resistance in Arabidopsis. Furthermore, the induction of antioxidant system and defense-associated genes expression in the double mutant were inhibited when compared with single mutant or wild-type plants after CMV infection. Further evidences showed that salicylic acid (SA) and jasmonic acid (JA) might be involved in GLKs-mediated virus resistance, as SA or JA level and synthesis-related genes transcription were impaired in glk1glk2 mutant. Taken together, our results indicated that GLKs played a positively role in virus resistance in Arabidopsis. - Highlights: • GLKs play a positive role in CMV resistance in Arabidopsis. • Defective of GLKs suffered more ROS accumulation. • Arabidopsis lacking GLKs have damaged photosynthesis. • Arabidopsis lacking GLKs show low SA and JA accumulation.

  5. Towards annotating the plant epigenome: the Arabidopsis thaliana small RNA locus map.

    Science.gov (United States)

    Hardcastle, Thomas J; Müller, Sebastian Y; Baulcombe, David C

    2018-04-20

    Based on 98 public and internal small RNA high throughput sequencing libraries, we mapped small RNAs to the genome of the model organism Arabidopsis thaliana and defined loci based on their expression using an empirical Bayesian approach. The resulting loci were subsequently classified based on their genetic and epigenetic context as well as their expression properties. We present the results of this classification, which broadly conforms to previously reported divisions between transcriptional and post-transcriptional gene silencing small RNAs, and to PolIV and PolV dependencies. However, we are able to demonstrate the existence of further subdivisions in the small RNA population of functional significance. Moreover, we present a framework for similar analyses of small RNA populations in all species.

  6. Chitosan oligosaccharide induces resistance to Tobacco mosaic virus in Arabidopsis via the salicylic acid-mediated signalling pathway.

    Science.gov (United States)

    Jia, Xiaochen; Meng, Qingshan; Zeng, Haihong; Wang, Wenxia; Yin, Heng

    2016-05-18

    Chitosan is one of the most abundant carbohydrate biopolymers in the world, and chitosan oligosaccharide (COS), which is prepared from chitosan, is a plant immunity regulator. The present study aimed to validate the effect of COS on inducing resistance to tobacco mosaic virus (TMV) in Arabidopsis and to investigate the potential defence-related signalling pathways involved. Optimal conditions for the induction of TMV resistance in Arabidopsis were COS pretreatment at 50 mg/L for 1 day prior to inoculation with TMV. Multilevel indices, including phenotype data, and TMV coat protein expression, revealed that COS induced TMV resistance in wild-type and jasmonic acid pathway- deficient (jar1) Arabidopsis plants, but not in salicylic acid pathway deficient (NahG) Arabidopsis plants. Quantitative-PCR and analysis of phytohormone levels confirmed that COS pretreatment enhanced the expression of the defence-related gene PR1, which is a marker of salicylic acid signalling pathway, and increased the amount of salicylic acid in WT and jar1, but not in NahG plants. Taken together, these results confirm that COS induces TMV resistance in Arabidopsis via activation of the salicylic acid signalling pathway.

  7. Genetic and histological studies on the delayed systemic movement of Tobacco Mosaic Virus in Arabidopsis thaliana

    Directory of Open Access Journals (Sweden)

    Matus José

    2008-09-01

    Full Text Available Abstract Background Viral infections and their spread throughout a plant require numerous interactions between the host and the virus. While new functions of viral proteins involved in these processes have been revealed, current knowledge of host factors involved in the spread of a viral infection is still insufficient. In Arabidopsis thaliana, different ecotypes present varying susceptibilities to Tobacco mosaic virus strain U1 (TMV-U1. The rate of TMV-U1 systemic movement is delayed in ecotype Col-0 when compared with other 13 ecotypes. We followed viral movement through vascular tissue in Col-0 plants by electronic microscopy studies. In addition, the delay in systemic movement of TMV-U1 was genetically studied. Results TMV-U1 reaches apical leaves only after 18 days post rosette inoculation (dpi in Col-0, whereas it is detected at 9 dpi in the Uk-4 ecotype. Genetic crosses between Col-0 and Uk-4 ecotypes, followed by analysis of viral movement in F1 and F2 populations, revealed that this delayed movement correlates with a recessive, monogenic and nuclear locus. The use of selected polymorphic markers showed that this locus, denoted DSTM1 (Delayed Systemic Tobamovirus Movement 1, is positioned on the large arm of chromosome II. Electron microscopy studies following the virion's route in stems of Col-0 infected plants showed the presence of curved structures, instead of the typical rigid rods of TMV-U1. This was not observed in the case of TMV-U1 infection in Uk-4, where the observed virions have the typical rigid rod morphology. Conclusion The presence of defectively assembled virions observed by electron microscopy in vascular tissue of Col-0 infected plants correlates with a recessive delayed systemic movement trait of TMV-U1 in this ecotype.

  8. Expression of Cucumber mosaic virus suppressor 2b alters FWA methylation and its siRNA accumulation in Arabidopsis thaliana

    Directory of Open Access Journals (Sweden)

    Sadia Hamera

    2016-11-01

    Full Text Available The Cucumber mosaic virus (CMV suppressor 2b co-localizes with AGO4 in cytoplasmic and nuclear fractions of Arabidopsis thaliana. Biochemical fractionation of A. thaliana cellular extracts revealed that 2b and AGO4 coexist in multiple size exclusions. 2b transgenic A. thaliana exhibited an enhanced accumulation of 24nt siRNAs from flowering wageningen (FWA and other heterochromatic loci. These plants also exhibited hypo-methylation of an endogenous- as well as transgene-FWA promoter at non-CG sites. In corroboration, both transgenic 2b and CMV infection affected the regulation of transposons which mimics the ago4 phenotype. In conclusion, 2b perturbs plant defense by interfering with AGO4-regulated transcriptional gene silencing.

  9. Identification of an Arabidopsis thaliana protein that binds to tomato mosaic virus genomic RNA and inhibits its multiplication

    International Nuclear Information System (INIS)

    Fujisaki, Koki; Ishikawa, Masayuki

    2008-01-01

    The genomic RNAs of positive-strand RNA viruses carry RNA elements that play positive, or in some cases, negative roles in virus multiplication by interacting with viral and cellular proteins. In this study, we purified Arabidopsis thaliana proteins that specifically bind to 5' or 3' terminal regions of tomato mosaic virus (ToMV) genomic RNA, which contain important regulatory elements for translation and RNA replication, and identified these proteins by mass spectrometry analyses. One of these host proteins, named BTR1, harbored three heterogeneous nuclear ribonucleoprotein K-homology RNA-binding domains and preferentially bound to RNA fragments that contained a sequence around the initiation codon of the 130K and 180K replication protein genes. The knockout and overexpression of BTR1 specifically enhanced and inhibited, respectively, ToMV multiplication in inoculated A. thaliana leaves, while such effect was hardly detectable in protoplasts. These results suggest that BTR1 negatively regulates the local spread of ToMV

  10. Study on radiation-responsive epigenomes

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Jin Hong; Lee, Seung Sik; Bae, Hyung Woo; Kim, Ji Hong; Kim, Ji Eun; Cho, Eun Ju; Lee, Min Hee; Moon, Yu Ran [KAERI, Daejeon (Korea, Republic of)

    2012-01-15

    The purpose of this project is development of world-class headspring techniques of biological science for application of plant genomes/epigenomes through study on radiation- responsive epigenomes and improvement of the national competitiveness in the field of fundamental technology for biological science and industry. Research scope includes 1) Investigation of radiation-responsive epigenomes and elucidation of their relation with phenotypes, 2) Elucidation of interaction and transcription control of epigenomes and epigenetic regulators using IR, 3) Investigation of epigenome-mediated traits in plant development, differentiation and antioxidant defense using IR, and 4) Development of application techniques of radiation-responsive epigenomes for eco-monitoring and molecular breeding. Main results are as follow: practical application of ChIP in GR-treated Arabidopsis using anti-histone antibodies: mapping of DNA methylomes associated with GR-responsive transcriptomes: setup of methylated DNA quantification using HPLC: elucidation of aberrations in epigenetic regulation induced by low-dose GR using gamma phytotron: comparison of gene expression of histone-modifying enzymes after treatment of GR: elucidation of transcriptomes and physiological alterations associated with delayed senescence of drd1-6 mutant: comparison of gene expression of DNA methylation-related enzymes in GR-treated rice callus and Arabidopsis: investigation of germination capacity, low-temperature, salinity and drought stress-resistance in drd1-6 epigenetic mutant: investigation of aberrations in DNA methylation depending on dose rates of gamma radiation

  11. Study on radiation-responsive epigenomes

    International Nuclear Information System (INIS)

    Kim, Jin Hong; Lee, Seung Sik; Bae, Hyung Woo; Kim, Ji Hong; Kim, Ji Eun; Cho, Eun Ju; Lee, Min Hee; Moon, Yu Ran

    2012-01-01

    The purpose of this project is development of world-class headspring techniques of biological science for application of plant genomes/epigenomes through study on radiation- responsive epigenomes and improvement of the national competitiveness in the field of fundamental technology for biological science and industry. Research scope includes 1) Investigation of radiation-responsive epigenomes and elucidation of their relation with phenotypes, 2) Elucidation of interaction and transcription control of epigenomes and epigenetic regulators using IR, 3) Investigation of epigenome-mediated traits in plant development, differentiation and antioxidant defense using IR, and 4) Development of application techniques of radiation-responsive epigenomes for eco-monitoring and molecular breeding. Main results are as follow: practical application of ChIP in GR-treated Arabidopsis using anti-histone antibodies: mapping of DNA methylomes associated with GR-responsive transcriptomes: setup of methylated DNA quantification using HPLC: elucidation of aberrations in epigenetic regulation induced by low-dose GR using gamma phytotron: comparison of gene expression of histone-modifying enzymes after treatment of GR: elucidation of transcriptomes and physiological alterations associated with delayed senescence of drd1-6 mutant: comparison of gene expression of DNA methylation-related enzymes in GR-treated rice callus and Arabidopsis: investigation of germination capacity, low-temperature, salinity and drought stress-resistance in drd1-6 epigenetic mutant: investigation of aberrations in DNA methylation depending on dose rates of gamma radiation

  12. The relationship between host lifespan and pathogen reservoir potential: an analysis in the system Arabidopsis thaliana--cucumber mosaic virus.

    Directory of Open Access Journals (Sweden)

    Jean Michel Hily

    2014-11-01

    Full Text Available Identification of the determinants of pathogen reservoir potential is central to understand disease emergence. It has been proposed that host lifespan is one such determinant: short-lived hosts will invest less in costly defenses against pathogens, so that they will be more susceptible to infection, more competent as sources of infection and/or will sustain larger vector populations, thus being effective reservoirs for the infection of long-lived hosts. This hypothesis is sustained by analyses of different hosts of multihost pathogens, but not of different genotypes of the same host species. Here we examined this hypothesis by comparing two genotypes of the plant Arabidopsis thaliana that differ largely both in life-span and in tolerance to its natural pathogen Cucumber mosaic virus (CMV. Experiments with the aphid vector Myzus persicae showed that both genotypes were similarly competent as sources for virus transmission, but the short-lived genotype was more susceptible to infection and was able to sustain larger vector populations. To explore how differences in defense against CMV and its vector relate to reservoir potential, we developed a model that was run for a set of experimentally-determined parameters, and for a realistic range of host plant and vector population densities. Model simulations showed that the less efficient defenses of the short-lived genotype resulted in higher reservoir potential, which in heterogeneous host populations may be balanced by the longer infectious period of the long-lived genotype. This balance was modulated by the demography of both host and vector populations, and by the genetic composition of the host population. Thus, within-species genetic diversity for lifespan and defenses against pathogens will result in polymorphisms for pathogen reservoir potential, which will condition within-population infection dynamics. These results are relevant for a better understanding of host-pathogen co-evolution, and of

  13. Study on radiation-responsive epigenomes

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Seung Sik; Lee, Seung Sik; Chung, Byung Yeoup; and others

    2013-01-15

    The purpose of this project is development of world-class head spring techniques of biological science for application of plant genomes/epigenomes through study on radiation-responsive epigenomes and improvement of the national competitiveness in the field of fundamental technology for biological science and industry. Research scope includes 1) Investigation of radiation-responsive epigenomes and elucidation of their relation with phenotypes, 2) Elucidation of interaction and transcription control of epigenomes and epigenetic regulators using IR, 3) Investigation of epigenome-mediated traits in plant development, differentiation and antioxidant defense using IR, and 4) Development of application techniques of radiation-responsive epigenomes for eco-monitoring and molecular breeding. Main results are as follow: investigation of the expression level of histone-modifying enzymes by IR; elucidation of the structural and functional changes of chaperone protein by IR; development of transgenic plant (DRD1-6); investigation of transcription control of epigenetic regulators by IR; investigation of relevance between DNA methylation and miRNA; comparison of gene expression in wild type and cmt mutant from Arabidopsis using gene chip; investigation control of epigenetic regulators in drd1-6 mutant by drought stress; development of transgenic plant using epigenetic regulators.

  14. The USC Epigenome Center.

    Science.gov (United States)

    Laird, Peter W

    2009-10-01

    The University of Southern California (USC, CA, USA) has a long tradition of excellence in epigenetics. With the recent explosive growth and technological maturation of the field of epigenetics, it became clear that a dedicated high-throughput epigenomic data production facility would be needed to remain at the forefront of epigenetic research. To address this need, USC launched the USC Epigenome Center as the first large-scale center in academics dedicated to epigenomic research. The Center is providing high-throughput data production for large-scale genomic and epigenomic studies, and developing novel analysis tools for epigenomic research. This unique facility promises to be a valuable resource for multidisciplinary research, education and training in genomics, epigenomics, bioinformatics, and translational medicine.

  15. Time for the epigenome

    CERN Multimedia

    2010-01-01

    The complexity of genetic regulation is one of the great wonders of nature, but it represents a daunting challenge to unravel. The International Human Epigenome Consortium is an appropriate response. ( 1 page)

  16. The Aging Epigenome

    Science.gov (United States)

    Booth, Lauren N.

    2016-01-01

    During aging, the mechanisms that normally maintain health and stress resistance strikingly decline, resulting in decrepitude, frailty, and ultimately death. Exactly when and how this decline occurs is unknown. Changes in transcriptional networks and chromatin state lie at the heart of age-dependent decline. These epigenomic changes are not only observed during aging but also profoundly affect cellular function and stress resistance, thereby contributing to the progression of aging. We propose that the dysregulation of transcriptional and chromatin networks is a crucial component of aging. Understanding age-dependent epigenomic changes will yield key insights into how aging begins and progresses and should lead to the development of new therapeutics that delay or even reverse aging and age-related diseases. PMID:27259204

  17. Epigenomics in cancer management

    International Nuclear Information System (INIS)

    Costa, Fabricio F

    2010-01-01

    The identification of all epigenetic modifications implicated in gene expression is the next step for a better understanding of human biology in both normal and pathological states. This field is referred to as epigenomics, and it is defined as epigenetic changes (ie, DNA methylation, histone modifications and regulation by noncoding RNAs such as microRNAs) on a genomic scale rather than a single gene. Epigenetics modulate the structure of the chromatin, thereby affecting the transcription of genes in the genome. Different studies have already identified changes in epigenetic modifications in a few genes in specific pathways in cancers. Based on these epigenetic changes, drugs against different types of tumors were developed, which mainly target epimutations in the genome. Examples include DNA methylation inhibitors, histone modification inhibitors, and small molecules that target chromatin-remodeling proteins. However, these drugs are not specific, and side effects are a major problem; therefore, new DNA sequencing technologies combined with epigenomic tools have the potential to identify novel biomarkers and better molecular targets to treat cancers. The purpose of this review is to discuss current and emerging epigenomic tools and to address how these new technologies may impact the future of cancer management

  18. The International Human Epigenome Consortium

    DEFF Research Database (Denmark)

    Stunnenberg, Hendrik G; Hirst, Martin

    2016-01-01

    The International Human Epigenome Consortium (IHEC) coordinates the generation of a catalog of high-resolution reference epigenomes of major primary human cell types. The studies now presented (see the Cell Press IHEC web portal at http://www.cell.com/consortium/IHEC) highlight the coordinated ac...

  19. A systemic increase in the recombination frequency upon local infection of Arabidopsis thaliana plants with oilseed rape mosaic virus depends on plant age, the initial inoculum concentration and the time for virus replication

    Directory of Open Access Journals (Sweden)

    Youli eYao

    2013-03-01

    Full Text Available In the past, we showed that local infection of tobacco leaves with either Tobacco mosaic virus (TMV or Oilseed rape mosaic virus (ORMV resulted in a systemic increase in the homologous recombination frequency (HRF. Later on, we showed that a similar phenomenon occurs in Arabidopsis thaliana plants infected with ORMV. Here, we tested whether the time of removing the infected leaves as well as viral titer have any effect on the degree of changes in HRF in systemic tissues. An increase in HRF in systemic non-infected tissues was more pronounced when the infected leaves were detached from the infected plants at 60-96 hours post infection, rather than at earlier time. Next, we found that exposure to higher concentrations of inoculum was much more efficient in triggering an increase in HRF than exposure to lower concentrations. Finally, we showed that older plants exhibited a higher increase in HRF than younger plants. We found that an increase in genome instability in systemic tissues of locally infected plants depends on plant age, the concentration of initial inoculums and the time of viral replication.

  20. Reconstructing ancient genomes and epigenomes

    DEFF Research Database (Denmark)

    Orlando, Ludovic Antoine Alexandre; Gilbert, M. Thomas P.; Willerslev, Eske

    2015-01-01

    DNA studies have now progressed to whole-genome sequencing for an increasing number of ancient individuals and extinct species, as well as to epigenomic characterization. Such advances have enabled the sequencing of specimens of up to 1 million years old, which, owing to their extensive DNA damage...... and contamination, were previously not amenable to genetic analyses. In this Review, we discuss these varied technical challenges and solutions for sequencing ancient genomes and epigenomes....

  1. Study on radiation-responsive epigenomes

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Jin Hong; Chung, Byung Yeop; Lee, Seung Sik; Moon, Yu Ran; Lee, Min Hee; Kim, Ji Hong [KAERI, Daejeon (Korea, Republic of)

    2011-01-15

    The purpose of this project is development of world-class headspring techniques of biological science for application of plant genomes/epigenomes through study on radiation- responsive epigenomes and improvement of the national competitiveness in the field of fundamental technology for biological science and industry. Research scope includes 1) Investigation of radiation-responsive epigenomes and elucidation of their relation with phenotypes, 2) Elucidation of interaction and transcription control of epigenomes and epigenetic regulators using ionizing radiation (IR), 3) Investigation of epigenome-mediated traits in plant development, differentiation and antioxidant defense using IR, and 4) Development of application techniques of radiation-responsive epigenomes for eco-monitoring and molecular breeding. Main results are as follow: Setup of conditions for chromatin immunoprecipitation in irradiated plants: investigation of aberrations in DNA methylation after treatment with different IR: elucidation of responses of epigenetic regulators to gamma rays (GR): investigation of aberrations in GR-responsive epigenetic regulators at different developmental stages: elucidation of interactive aberrations of epigenomes and epigenetic regulators after treatment of GR: comparison of functional genomes after treatment of GR or H{sub 2}O{sub 2}: elucidation of relation of epigenomes with GR-induced delay in senescence: elucidation of relation of epigenomes with GR-induced aberrations in pigment metabolism: comparison of antioxidant defense in epigenetic mutants: investigation of senescence-associated changes in epigenomes: investigation of senescence-associated changes in epigenetic regulators: comparison of aberrations in epigenomes at different dose of GR for mutation.

  2. Study on radiation-responsive epigenomes

    International Nuclear Information System (INIS)

    Kim, Jin Hong; Chung, Byung Yeop; Lee, Seung Sik; Moon, Yu Ran; Lee, Min Hee; Kim, Ji Hong

    2011-01-01

    The purpose of this project is development of world-class headspring techniques of biological science for application of plant genomes/epigenomes through study on radiation- responsive epigenomes and improvement of the national competitiveness in the field of fundamental technology for biological science and industry. Research scope includes 1) Investigation of radiation-responsive epigenomes and elucidation of their relation with phenotypes, 2) Elucidation of interaction and transcription control of epigenomes and epigenetic regulators using ionizing radiation (IR), 3) Investigation of epigenome-mediated traits in plant development, differentiation and antioxidant defense using IR, and 4) Development of application techniques of radiation-responsive epigenomes for eco-monitoring and molecular breeding. Main results are as follow: Setup of conditions for chromatin immunoprecipitation in irradiated plants: investigation of aberrations in DNA methylation after treatment with different IR: elucidation of responses of epigenetic regulators to gamma rays (GR): investigation of aberrations in GR-responsive epigenetic regulators at different developmental stages: elucidation of interactive aberrations of epigenomes and epigenetic regulators after treatment of GR: comparison of functional genomes after treatment of GR or H 2 O 2 : elucidation of relation of epigenomes with GR-induced delay in senescence: elucidation of relation of epigenomes with GR-induced aberrations in pigment metabolism: comparison of antioxidant defense in epigenetic mutants: investigation of senescence-associated changes in epigenomes: investigation of senescence-associated changes in epigenetic regulators: comparison of aberrations in epigenomes at different dose of GR for mutation

  3. Sleep Deprivation and the Epigenome

    Directory of Open Access Journals (Sweden)

    Marie E. Gaine

    2018-02-01

    Full Text Available Sleep deprivation disrupts the lives of millions of people every day and has a profound impact on the molecular biology of the brain. These effects begin as changes within a neuron, at the DNA and RNA level, and result in alterations in neuronal plasticity and dysregulation of many cognitive functions including learning and memory. The epigenome plays a critical role in regulating gene expression in the context of memory storage. In this review article, we begin by describing the effects of epigenetic alterations on the regulation of gene expression, focusing on the most common epigenetic mechanisms: (i DNA methylation; (ii histone modifications; and (iii non-coding RNAs. We then discuss evidence suggesting that sleep loss impacts the epigenome and that these epigenetic alterations might mediate the changes in cognition seen following disruption of sleep. The link between sleep and the epigenome is only beginning to be elucidated, but clear evidence exists that epigenetic alterations occur following sleep deprivation. In the future, these changes to the epigenome could be utilized as biomarkers of sleep loss or as therapeutic targets for sleep-related disorders.

  4. Sleep Deprivation and the Epigenome.

    Science.gov (United States)

    Gaine, Marie E; Chatterjee, Snehajyoti; Abel, Ted

    2018-01-01

    Sleep deprivation disrupts the lives of millions of people every day and has a profound impact on the molecular biology of the brain. These effects begin as changes within a neuron, at the DNA and RNA level, and result in alterations in neuronal plasticity and dysregulation of many cognitive functions including learning and memory. The epigenome plays a critical role in regulating gene expression in the context of memory storage. In this review article, we begin by describing the effects of epigenetic alterations on the regulation of gene expression, focusing on the most common epigenetic mechanisms: (i) DNA methylation; (ii) histone modifications; and (iii) non-coding RNAs. We then discuss evidence suggesting that sleep loss impacts the epigenome and that these epigenetic alterations might mediate the changes in cognition seen following disruption of sleep. The link between sleep and the epigenome is only beginning to be elucidated, but clear evidence exists that epigenetic alterations occur following sleep deprivation. In the future, these changes to the epigenome could be utilized as biomarkers of sleep loss or as therapeutic targets for sleep-related disorders.

  5. Auxin and Cytokinin Metabolism and Root Morphological Modifications in Arabidopsis thaliana Seedlings Infected with Cucumber mosaic virus (CMV or Exposed to Cadmium

    Directory of Open Access Journals (Sweden)

    Adriano Sofo

    2013-03-01

    Full Text Available Arabidopsis thaliana L. is a model plant but little information is available about morphological root changes as part of a phytohormonal common response against both biotic and abiotic stressors. For this purpose, two-week-old Arabidopsis seedlings were treated with 10 µM CdSO4 or infected with CMV. After 12 days the entire aerial parts and the root system were analyzed, and the presence of CMV or the accumulation of Cd were detected. Microscopic analysis revealed that both CMV and Cd influenced root morphology by a marked development in the length of root hairs and an intense root branching if compared to controls. Among the three treatments, Cd-treated seedlings showed a shorter root axis length and doubled their lateral root diameter, while the lateral roots of CMV-infected seedlings were the longest. The root growth patterns were accompanied by significant changes in the levels of indole-3-acetic acid, trans-zeatin riboside, dihydrozeatin riboside, as a probable consequence of the regulation of some genes involved in their biosynthesis/degradation. The opposite role on root development played by the phythormones studied is discussed in detail. The results obtained could provide insights into novel strategies for plant defense against pathogens and plant protection against pollutants.

  6. Auxin and cytokinin metabolism and root morphological modifications in Arabidopsis thaliana seedlings infected with Cucumber mosaic virus (CMV) or exposed to cadmium.

    Science.gov (United States)

    Vitti, Antonella; Nuzzaci, Maria; Scopa, Antonio; Tataranni, Giuseppe; Remans, Tony; Vangronsveld, Jaco; Sofo, Adriano

    2013-03-26

    Arabidopsis thaliana L. is a model plant but little information is available about morphological root changes as part of a phytohormonal common response against both biotic and abiotic stressors. For this purpose, two-week-old Arabidopsis seedlings were treated with 10 µM CdSO4 or infected with CMV. After 12 days the entire aerial parts and the root system were analyzed, and the presence of CMV or the accumulation of Cd were detected. Microscopic analysis revealed that both CMV and Cd influenced root morphology by a marked development in the length of root hairs and an intense root branching if compared to controls. Among the three treatments, Cd-treated seedlings showed a shorter root axis length and doubled their lateral root diameter, while the lateral roots of CMV-infected seedlings were the longest. The root growth patterns were accompanied by significant changes in the levels of indole-3-acetic acid, trans-zeatin riboside, dihydrozeatin riboside, as a probable consequence of the regulation of some genes involved in their biosynthesis/degradation. The opposite role on root development played by the phythormones studied is discussed in detail. The results obtained could provide insights into novel strategies for plant defense against pathogens and plant protection against pollutants.

  7. Prospects for discovery by epigenome comparison

    Science.gov (United States)

    Milosavljevic, Aleksandar

    2010-01-01

    Epigenomic analysis efforts have so far focused on the multiple layers of epigenomic information within individual cell types. With the rapidly increasing diversity of epigenomically mapped cell types, unprecedented opportunities for comparative analysis of epigenomes are opening up. One such opportunity is to map the bifurcating tree of cellular differentiation. Another is to understand the epigenomically mediated effects of mutations, environmental influences, and disease processes. Comparative analysis of epigenomes therefore has the potential to provide wide-ranging fresh insights into basic biology and human disease. The realization of this potential will critically depend on availability of a cyberinfrastructure that will scale with the volume of data and diversity of applications and a number of other computational challenges. PMID:20944597

  8. Sleep Deprivation and the Epigenome

    OpenAIRE

    Marie E. Gaine; Snehajyoti Chatterjee; Ted Abel

    2018-01-01

    Sleep deprivation disrupts the lives of millions of people every day and has a profound impact on the molecular biology of the brain. These effects begin as changes within a neuron, at the DNA and RNA level, and result in alterations in neuronal plasticity and dysregulation of many cognitive functions including learning and memory. The epigenome plays a critical role in regulating gene expression in the context of memory storage. In this review article, we begin by describing the effects of e...

  9. Chromatin replication and epigenome maintenance

    DEFF Research Database (Denmark)

    Alabert, Constance; Groth, Anja

    2012-01-01

    Stability and function of eukaryotic genomes are closely linked to chromatin structure and organization. During cell division the entire genome must be accurately replicated and the chromatin landscape reproduced on new DNA. Chromatin and nuclear structure influence where and when DNA replication...... initiates, whereas the replication process itself disrupts chromatin and challenges established patterns of genome regulation. Specialized replication-coupled mechanisms assemble new DNA into chromatin, but epigenome maintenance is a continuous process taking place throughout the cell cycle. If DNA...

  10. Mosaic Messages

    Science.gov (United States)

    Baldauf, Annemarie

    2012-01-01

    Through the generosity of a Lowes Toolbox for Education Grant and a grant from the Bill Graham Foundation, an interdisciplinary mosaic mural was created and installed at Riverview Middle School in Bay Point, California. The actual mural, which featured a theme of nurturing students through music, art, sports, science, and math, took about three…

  11. Perspectives of International Human Epigenome Consortium

    Directory of Open Access Journals (Sweden)

    Jae-Bum Bae

    2013-03-01

    Full Text Available As the International Human Epigenome Consortium (IHEC launched officially at the 2010 Washington meeting, a giant step toward the conquest of unexplored regions of the human genome has begun. IHEC aims at the production of 1,000 reference epigenomes to the international scientific community for next 7-10 years. Seven member institutions, including South Korea, Korea National Institute of Health (KNIH, will produce 25-200 reference epigenomes individually, and the produced data will be publically available by using a data center. Epigenome data will cover from whole genome bisulfite sequencing, histone modification, and chromatin access information to miRNA-seq. The final goal of IHEC is the production of reference maps of human epigenomes for key cellular status relevant to health and disease.

  12. Epigenomics

    Science.gov (United States)

    ... Care Genomic Medicine Working Group New Horizons and Research Patient Management Policy and Ethics Issues Quick Links for Patient Care Education All About the Human Genome Project Fact Sheets Genetic Education Resources for ...

  13. The International Human Epigenome Consortium Data Portal.

    Science.gov (United States)

    Bujold, David; Morais, David Anderson de Lima; Gauthier, Carol; Côté, Catherine; Caron, Maxime; Kwan, Tony; Chen, Kuang Chung; Laperle, Jonathan; Markovits, Alexei Nordell; Pastinen, Tomi; Caron, Bryan; Veilleux, Alain; Jacques, Pierre-Étienne; Bourque, Guillaume

    2016-11-23

    The International Human Epigenome Consortium (IHEC) coordinates the production of reference epigenome maps through the characterization of the regulome, methylome, and transcriptome from a wide range of tissues and cell types. To define conventions ensuring the compatibility of datasets and establish an infrastructure enabling data integration, analysis, and sharing, we developed the IHEC Data Portal (http://epigenomesportal.ca/ihec). The portal provides access to >7,000 reference epigenomic datasets, generated from >600 tissues, which have been contributed by seven international consortia: ENCODE, NIH Roadmap, CEEHRC, Blueprint, DEEP, AMED-CREST, and KNIH. The portal enhances the utility of these reference maps by facilitating the discovery, visualization, analysis, download, and sharing of epigenomics data. The IHEC Data Portal is the official source to navigate through IHEC datasets and represents a strategy for unifying the distributed data produced by international research consortia. Crown Copyright © 2016. Published by Elsevier Inc. All rights reserved.

  14. Epigenomic programing: a future way to health?

    Directory of Open Access Journals (Sweden)

    Boris A. Shenderov

    2014-05-01

    Full Text Available It is now generally accepted that the ‘central genome dogma’ (i.e. a causal chain going from DNA to RNA to proteins and downstream to biological functions should be replaced by the ‘fluid genome dogma’, that is, complex feed-forward and feed-back cycles that interconnect organism and environment by epigenomic programing – and reprograming – throughout life and at all levels, sometimes also down the generations. The epigenomic programing is the net sum of interactions derived from own metabolism and microbiota as well as external factors such as diet, pharmaceuticals, environmental compounds, and so on. It is a growing body of results indicating that many chronic metabolic and degenerative disorders and diseases – often called ‘civilization diseases’ – are initiated and/or influenced upon by non-optimal epigenomic programing, often taking place early in life. In this context, the first 1,000 days of life – from conception into early infancy – is often called the most important period of life. The following sections present some major mechanisms for epigenomic programing as well as some factors assumed to be of importance. The need for more information about own genome and metagenome, as well as a substantial lack of adequate information regarding dietary and environmental databases are also commented upon. However, the mere fact that we can influence epigenomic health programing opens up the way for prophylactic and therapeutic interventions. The authors underline the importance of creating a ‘Human Gut Microbiota and Epigenomic Platform’ in order to facilitate interdisciplinary collaborations among scientists and clinicians engaged in host microbial ecology, nutrition, metagenomics, epigenomics and metabolomics as well as in disease epidemiology, prevention and treatment.

  15. Epigenomic programing: a future way to health?

    Science.gov (United States)

    Shenderov, Boris A; Midtvedt, Tore

    2014-01-01

    It is now generally accepted that the 'central genome dogma' (i.e. a causal chain going from DNA to RNA to proteins and downstream to biological functions) should be replaced by the 'fluid genome dogma', that is, complex feed-forward and feed-back cycles that interconnect organism and environment by epigenomic programing - and reprograming - throughout life and at all levels, sometimes also down the generations. The epigenomic programing is the net sum of interactions derived from own metabolism and microbiota as well as external factors such as diet, pharmaceuticals, environmental compounds, and so on. It is a growing body of results indicating that many chronic metabolic and degenerative disorders and diseases - often called 'civilization diseases' - are initiated and/or influenced upon by non-optimal epigenomic programing, often taking place early in life. In this context, the first 1,000 days of life - from conception into early infancy - is often called the most important period of life. The following sections present some major mechanisms for epigenomic programing as well as some factors assumed to be of importance. The need for more information about own genome and metagenome, as well as a substantial lack of adequate information regarding dietary and environmental databases are also commented upon. However, the mere fact that we can influence epigenomic health programing opens up the way for prophylactic and therapeutic interventions. The authors underline the importance of creating a 'Human Gut Microbiota and Epigenomic Platform' in order to facilitate interdisciplinary collaborations among scientists and clinicians engaged in host microbial ecology, nutrition, metagenomics, epigenomics and metabolomics as well as in disease epidemiology, prevention and treatment.

  16. Epigenetics and Epigenomics of Plants.

    Science.gov (United States)

    Yadav, Chandra Bhan; Pandey, Garima; Muthamilarasan, Mehanathan; Prasad, Manoj

    2018-01-23

    The genetic material DNA in association with histone proteins forms the complex structure called chromatin, which is prone to undergo modification through certain epigenetic mechanisms including cytosine DNA methylation, histone modifications, and small RNA-mediated methylation. Alterations in chromatin structure lead to inaccessibility of genomic DNA to various regulatory proteins such as transcription factors, which eventually modulates gene expression. Advancements in high-throughput sequencing technologies have provided the opportunity to study the epigenetic mechanisms at genome-wide levels. Epigenomic studies using high-throughput technologies will widen the understanding of mechanisms as well as functions of regulatory pathways in plant genomes, which will further help in manipulating these pathways using genetic and biochemical approaches. This technology could be a potential research tool for displaying the systematic associations of genetic and epigenetic variations, especially in terms of cytosine methylation onto the genomic region in a specific cell or tissue. A comprehensive study of plant populations to correlate genotype to epigenotype and to phenotype, and also the study of methyl quantitative trait loci (QTL) or epiGWAS, is possible by using high-throughput sequencing methods, which will further accelerate molecular breeding programs for crop improvement. Graphical Abstract.

  17. Enabling interspecies epigenomic comparison with CEpBrowser.

    Science.gov (United States)

    Cao, Xiaoyi; Zhong, Sheng

    2013-05-01

    We developed the Comparative Epigenome Browser (CEpBrowser) to allow the public to perform multi-species epigenomic analysis. The web-based CEpBrowser integrates, manages and visualizes sequencing-based epigenomic datasets. Five key features were developed to maximize the efficiency of interspecies epigenomic comparisons. CEpBrowser is a web application implemented with PHP, MySQL, C and Apache. URL: http://www.cepbrowser.org/.

  18. The Epigenomic Analysis of Human Obesity.

    Science.gov (United States)

    Bell, Christopher G

    2017-09-01

    Analysis of the epigenome-the chemical modifications and packaging of the genome that can influence or indicate its activity-enables molecular insight into cell type-specific machinery. It can, therefore, reveal the pathophysiological mechanisms at work in disease. Detected changes can also represent physiological responses to adverse environmental exposures, thus enabling the epigenetic mark of DNA methylation to act as an epidemiological biomarker, even in surrogate tissue. This makes epigenomic analysis an attractive prospect to further understand the pathobiology and epidemiological aspects of obesity. Furthermore, integrating epigenomic data with known obesity-associated common genetic variation can aid in deciphering their molecular mechanisms. This review primarily examines epidemiological or population-based studies of epigenetic modifications in relation to adiposity traits, as opposed to animal or cell models. It discusses recent work exploring the epigenome with respect to human obesity, which to date has predominately consisted of array-based studies of DNA methylation in peripheral blood. It is of note that highly replicated BMI DNA methylation associations are not causal, but strongly driven by coassociations for more precisely measured intertwined outcomes and factors, such as hyperlipidemia, hyperglycemia, and inflammation. Finally, the potential for the future exploration of the epigenome in obesity and related disorders is considered. © 2017 The Obesity Society.

  19. DeepBlue epigenomic data server: programmatic data retrieval and analysis of epigenome region sets.

    Science.gov (United States)

    Albrecht, Felipe; List, Markus; Bock, Christoph; Lengauer, Thomas

    2016-07-08

    Large amounts of epigenomic data are generated under the umbrella of the International Human Epigenome Consortium, which aims to establish 1000 reference epigenomes within the next few years. These data have the potential to unravel the complexity of epigenomic regulation. However, their effective use is hindered by the lack of flexible and easy-to-use methods for data retrieval. Extracting region sets of interest is a cumbersome task that involves several manual steps: identifying the relevant experiments, downloading the corresponding data files and filtering the region sets of interest. Here we present the DeepBlue Epigenomic Data Server, which streamlines epigenomic data analysis as well as software development. DeepBlue provides a comprehensive programmatic interface for finding, selecting, filtering, summarizing and downloading region sets. It contains data from four major epigenome projects, namely ENCODE, ROADMAP, BLUEPRINT and DEEP. DeepBlue comes with a user manual, examples and a well-documented application programming interface (API). The latter is accessed via the XML-RPC protocol supported by many programming languages. To demonstrate usage of the API and to enable convenient data retrieval for non-programmers, we offer an optional web interface. DeepBlue can be openly accessed at http://deepblue.mpi-inf.mpg.de. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  20. CLEMENTINE HIRES MOSAIC

    Data.gov (United States)

    National Aeronautics and Space Administration — This CD contains portions of the Clementine HiRes Lunar Mosaic, a geometrically controlled, calibrated mosaic compiled from non-uniformity corrected, 750 nanometer...

  1. Epigenomic programing: a future way to health?

    OpenAIRE

    Shenderov, Boris A.; Midtvedt, Tore

    2014-01-01

    It is now generally accepted that the ‘central genome dogma’ (i.e. a causal chain going from DNA to RNA to proteins and downstream to biological functions) should be replaced by the ‘fluid genome dogma’, that is, complex feed-forward and feed-back cycles that interconnect organism and environment by epigenomic programing – and reprograming – throughout life and at all levels, sometimes also down the generations. The epigenomic programing is the net sum of interactions derived from own metabol...

  2. The epigenomics of embryonic stem cell differentiation.

    Science.gov (United States)

    Kraushaar, Daniel C; Zhao, Keji

    2013-01-01

    Embryonic stem cells (ESCs) possess an open and highly dynamic chromatin landscape, which underlies their plasticity and ultimately maintains ESC pluripotency. The ESC epigenome must not only maintain the transcription of pluripotency-associated genes but must also, through gene priming, facilitate rapid and cell type-specific activation of developmental genes upon lineage commitment. Trans-generational inheritance ensures that the ESC chromatin state is stably transmitted from one generation to the next; yet at the same time, epigenetic marks are highly dynamic, reversible and responsive to extracellular cues. Once committed to differentiation, the ESC epigenome is remodeled and resolves into a more compact chromatin state. A thorough understanding of the role of chromatin modifiers in ESC fate and differentiation will be important if they are to be used for therapeutic purposes. Recent technical advances, particularly in next-generation sequencing technologies, have provided a genome-scale view of epigenetic marks and chromatin modifiers. More affordable and faster sequencing platforms have led to a comprehensive characterization of the ESC epigenome and epigenomes of differentiated cell types. In this review, we summarize and discuss the recent progress that has highlighted the central role of histone modifications, histone variants, DNA methylation and chromatin modifiers in ESC pluripotency and ESC fate. We provide a detailed and comprehensive discussion of genome-wide studies that are pertinent to our understanding of mammalian development.

  3. Keystone Symposia on Epigenomics and Chromatin Dynamics

    DEFF Research Database (Denmark)

    Ravnskjær, Kim

    2012-01-01

    Keystone Symposia kicked off the start of 2012 with two joint meetings on Epigenomics and Chromatin Dynamics and a star-studded list of speakers. Held in Keystone, CO, January 17-22, and organized by Steven Jacobsen and Steven Henikoff and by Bradley Cairns and Geneviève Almouzni, respectively...

  4. Epigenomics of cancer – emerging new concepts

    Science.gov (United States)

    Hassler, Melanie R.; Egger, Gerda

    2012-01-01

    The complexity of the mammalian genome is regulated by heritable epigenetic mechanisms, which provide the basis for differentiation, development and cellular homeostasis. These mechanisms act on the level of chromatin, by modifying DNA, histone proteins and nucleosome density/composition. During the last decade it became clear that cancer is defined by a variety of epigenetic changes, which occur in early stages of disease and parallel genetic mutations. With the advent of new technologies we are just starting to unravel the cancer epigenome and latest mechanistic findings provide the first clue as to how altered epigenetic patterns might occur in different cancers. Here we review latest findings on chromatin related mechanisms and hypothesize how their impairment might contribute to the altered epigenome of cancer cells. PMID:22609632

  5. New approaches to manipulating the epigenome.

    Science.gov (United States)

    Day, Jeremy J

    2014-09-01

    Cellular processes that control transcription of genetic information are critical for cellular function, and are often implicated in psychiatric and neurological disease states. Among the most critical of these processes are epigenetic mechanisms, which serve to link the cellular environment with genomic material. Until recently our understanding of epigenetic mechanisms has been limited by the lack of tools that can selectively manipulate the epigenome with genetic, cellular, and temporal precision, which in turn diminishes the potential impact of epigenetic processes as therapeutic targets. This review highlights an emerging suite of tools that enable robust yet selective interrogation of the epigenome. In addition to allowing site-specific epigenetic editing, these tools can be paired with optogenetic approaches to provide temporal control over epigenetic processes, allowing unparalleled insight into the function of these mechanisms. This improved control promises to revolutionize our understanding of epigenetic modifications in human health and disease states.

  6. Rice epigenomics and epigenetics: challenges and opportunities.

    Science.gov (United States)

    Chen, Xiangsong; Zhou, Dao-Xiu

    2013-05-01

    During recent years rice genome-wide epigenomic information such as DNA methylation and histone modifications, which are important for genome activity has been accumulated. The function of a number of rice epigenetic regulators has been studied, many of which are found to be involved in a diverse range of developmental and stress-responsive pathways. Analysis of epigenetic variations among different rice varieties indicates that epigenetic modification may lead to inheritable phenotypic variation. Characterizing phenotypic consequences of rice epigenomic variations and the underlining chromatin mechanism and identifying epialleles related to important agronomic traits may provide novel strategies to enhance agronomically favorable traits and grain productivity in rice. Copyright © 2013 Elsevier Ltd. All rights reserved.

  7. The Einstein Center for Epigenomics: studying the role of epigenomic dysregulation in human disease.

    Science.gov (United States)

    McLellan, Andrew S; Dubin, Robert A; Jing, Qiang; Maqbool, Shahina B; Olea, Raul; Westby, Gael; Broin, Pilib Ó; Fazzari, Melissa J; Zheng, Deyou; Suzuki, Masako; Greally, John M

    2009-10-01

    There is increasing interest in the role of epigenetic and transcriptional dysregulation in the pathogenesis of a range of human diseases, not just in the best-studied example of cancer. It is, however, quite difficult for an individual investigator to perform these studies, as they involve genome-wide molecular assays combined with sophisticated computational analytical approaches of very large datasets that may be generated from various resources and technologies. In 2008, the Albert Einstein College of Medicine in New York, USA established a Center for Epigenomics to facilitate the research programs of its investigators, providing shared resources for genome-wide assays and for data analysis. As a result, several avenues of research are now expanding, with cancer epigenomics being complemented by studies of the epigenomics of infectious disease and a neuroepigenomics program.

  8. Mosaic epigenetic dysregulation of ectodermal cells in autism spectrum disorder.

    Directory of Open Access Journals (Sweden)

    Esther R Berko

    Full Text Available DNA mutational events are increasingly being identified in autism spectrum disorder (ASD, but the potential additional role of dysregulation of the epigenome in the pathogenesis of the condition remains unclear. The epigenome is of interest as a possible mediator of environmental effects during development, encoding a cellular memory reflected by altered function of progeny cells. Advanced maternal age (AMA is associated with an increased risk of having a child with ASD for reasons that are not understood. To explore whether AMA involves covert aneuploidy or epigenetic dysregulation leading to ASD in the offspring, we tested a homogeneous ectodermal cell type from 47 individuals with ASD compared with 48 typically developing (TD controls born to mothers of ≥35 years, using a quantitative genome-wide DNA methylation assay. We show that DNA methylation patterns are dysregulated in ectodermal cells in these individuals, having accounted for confounding effects due to subject age, sex and ancestral haplotype. We did not find mosaic aneuploidy or copy number variability to occur at differentially-methylated regions in these subjects. Of note, the loci with distinctive DNA methylation were found at genes expressed in the brain and encoding protein products significantly enriched for interactions with those produced by known ASD-causing genes, representing a perturbation by epigenomic dysregulation of the same networks compromised by DNA mutational mechanisms. The results indicate the presence of a mosaic subpopulation of epigenetically-dysregulated, ectodermally-derived cells in subjects with ASD. The epigenetic dysregulation observed in these ASD subjects born to older mothers may be associated with aging parental gametes, environmental influences during embryogenesis or could be the consequence of mutations of the chromatin regulatory genes increasingly implicated in ASD. The results indicate that epigenetic dysregulatory mechanisms may complement

  9. The influence of DNA sequence on epigenome-induced pathologies

    Directory of Open Access Journals (Sweden)

    Meagher Richard B

    2012-07-01

    Full Text Available Abstract Clear cause-and-effect relationships are commonly established between genotype and the inherited risk of acquiring human and plant diseases and aberrant phenotypes. By contrast, few such cause-and-effect relationships are established linking a chromatin structure (that is, the epitype with the transgenerational risk of acquiring a disease or abnormal phenotype. It is not entirely clear how epitypes are inherited from parent to offspring as populations evolve, even though epigenetics is proposed to be fundamental to evolution and the likelihood of acquiring many diseases. This article explores the hypothesis that, for transgenerationally inherited chromatin structures, “genotype predisposes epitype”, and that epitype functions as a modifier of gene expression within the classical central dogma of molecular biology. Evidence for the causal contribution of genotype to inherited epitypes and epigenetic risk comes primarily from two different kinds of studies discussed herein. The first and direct method of research proceeds by the examination of the transgenerational inheritance of epitype and the penetrance of phenotype among genetically related individuals. The second approach identifies epitypes that are duplicated (as DNA sequences are duplicated and evolutionarily conserved among repeated patterns in the DNA sequence. The body of this article summarizes particularly robust examples of these studies from humans, mice, Arabidopsis, and other organisms. The bulk of the data from both areas of research support the hypothesis that genotypes predispose the likelihood of displaying various epitypes, but for only a few classes of epitype. This analysis suggests that renewed efforts are needed in identifying polymorphic DNA sequences that determine variable nucleosome positioning and DNA methylation as the primary cause of inherited epigenome-induced pathologies. By contrast, there is very little evidence that DNA sequence directly

  10. From forensic epigenetics to forensic epigenomics: Broadening DNA investigative intelligence

    NARCIS (Netherlands)

    A. Vidaki (Athina); M.H. Kayser (Manfred)

    2017-01-01

    textabstractHuman genetic variation is a major resource in forensics, but does not allow all forensically relevant questions to be answered. Some questions may instead be addressable via epigenomics, as the epigenome acts as an interphase between the fixed genome and the dynamic environment. We

  11. Characteristics of rose mosaic diseases

    Directory of Open Access Journals (Sweden)

    Marek S. Szyndel

    2013-12-01

    Full Text Available Presented review of rose diseases, associated with the mosaic symptoms, includes common and yellow rose mosaic, rose ring pattern, rose X disease, rose line pattern, yellow vein mosaic and rose mottle mosaic disease. Based on symptomatology and graft transmissibility of causing agent many of those rose disorders are called "virus-like diseases" since the pathogen has never been identified. However, several viruses were detected and identified in roses expressing mosaic symptoms. Currently the most prevalent rose viruses are Prunus necrotic ringspot virus - PNRSV, Apple mosaic virus - ApMV (syn. Rose mosaic virus and Arabis mosaic virus - ArMV Symptoms and damages caused by these viruses are described. Tomato ringspot virus, Tobacco ringspot virus and Rose mottle mosaic virus are also mentioned as rose pa thogcns. Methods of control of rose mosaic diseases are discussed.

  12. Genomic and Epigenomic Alterations in Cancer.

    Science.gov (United States)

    Chakravarthi, Balabhadrapatruni V S K; Nepal, Saroj; Varambally, Sooryanarayana

    2016-07-01

    Multiple genetic and epigenetic events characterize tumor progression and define the identity of the tumors. Advances in high-throughput technologies, like gene expression profiling, next-generation sequencing, proteomics, and metabolomics, have enabled detailed molecular characterization of various tumors. The integration and analyses of these high-throughput data have unraveled many novel molecular aberrations and network alterations in tumors. These molecular alterations include multiple cancer-driving mutations, gene fusions, amplification, deletion, and post-translational modifications, among others. Many of these genomic events are being used in cancer diagnosis, whereas others are therapeutically targeted with small-molecule inhibitors. Multiple genes/enzymes that play a role in DNA and histone modifications are also altered in various cancers, changing the epigenomic landscape during cancer initiation and progression. Apart from protein-coding genes, studies are uncovering the critical regulatory roles played by noncoding RNAs and noncoding regions of the genome during cancer progression. Many of these genomic and epigenetic events function in tandem to drive tumor development and metastasis. Concurrent advances in genome-modulating technologies, like gene silencing and genome editing, are providing ability to understand in detail the process of cancer initiation, progression, and signaling as well as opening up avenues for therapeutic targeting. In this review, we discuss some of the recent advances in cancer genomic and epigenomic research. Copyright © 2016 American Society for Investigative Pathology. Published by Elsevier Inc. All rights reserved.

  13. THEMIS Global Mosaics

    Science.gov (United States)

    Gorelick, N. S.; Christensen, P. R.

    2005-12-01

    We have developed techniques to make seamless, controlled global mosaics from the more than 50,000 multi-spectral infrared images of the Mars returned by the THEMIS instrument aboard the Mars Odyssey spacecraft. These images cover more than 95% of the surface at 100m/pixel resolution at both day and night local times. Uncertainties in the position and pointing of the spacecraft, varying local time, and imaging artifacts make creating well-registered mosaics from these datasets a challenging task. In preparation for making global mosaics, many full-resolution regional mosaics have been made. These mosaics typically cover an area 10x10 degrees or smaller, and are constructed from only a few hundred images. To make regional mosaics, individual images are geo-rectified using the USGS ISIS software. This dead-reckoning is sufficient to approximate position to within 400m in cases where the SPICE information was downlinked. Further coregistration of images is handled in two ways: grayscale differences minimization in overlapping regions through integer pixel shifting, or through automatic tie-point generation using a radial symmetry transformation (RST). The RST identifies points within an image that exhibit 4-way symmetry. Martian craters tend to to be very radially symmetric, and the RST can pin-point a crater center to sub-pixel accuracy in both daytime and nighttime images, independent of lighting, time of day, or seasonal effects. Additionally, the RST works well on visible-light images, and in a 1D application, on MOLA tracks, to provide precision tie-points across multiple data sets. The RST often finds many points of symmetry that aren't related to surface features. These "false-hits" are managed using a clustering algorithm that identifies constellations of points that occur in multiple images, independent of scaling or other affine transformations. This technique is able to make use of data in which the "good" tie-points comprise even less than 1% of total

  14. From forensic epigenetics to forensic epigenomics: broadening DNA investigative intelligence.

    Science.gov (United States)

    Vidaki, Athina; Kayser, Manfred

    2017-12-21

    Human genetic variation is a major resource in forensics, but does not allow all forensically relevant questions to be answered. Some questions may instead be addressable via epigenomics, as the epigenome acts as an interphase between the fixed genome and the dynamic environment. We envision future forensic applications of DNA methylation analysis that will broaden DNA-based forensic intelligence. Together with genetic prediction of appearance and biogeographic ancestry, epigenomic lifestyle prediction is expected to increase the ability of police to find unknown perpetrators of crime who are not identifiable using current forensic DNA profiling.

  15. Nutritional epigenomics: a portal to disease prevention.

    Science.gov (United States)

    Choi, Sang-Woon; Claycombe, Kate J; Martinez, J Alfredo; Friso, Simonetta; Schalinske, Kevin L

    2013-09-01

    Epigenetics can be defined as inheritable and reversible phenomena that affect gene expression without altering the underlying base pair sequence. Epigenomics is the study of genome-wide epigenetic modifications. Because gene expression changes are critical in both normal development and disease progression, epigenetics is widely applicable to many aspects of biological research. The influences of nutrients and bioactive food components on epigenetic phenomena such as DNA methylation and various types of histone modifications have been extensively investigated. Because an individual's epigenetic patterns are established during early gestation and are changed and personalized by environmental factors during our lifetime, epigenetic mechanisms are quite important in the development of transgenerational and adult obesity as well as in the development of diabetes mellitus. Aging and cancer demonstrate profound genome-wide DNA methylation changes, suggesting that nutrition may affect the aging process and cancer development through epigenetic mechanisms.

  16. Epigenomic Adaptation to Low Dose Radiation

    Energy Technology Data Exchange (ETDEWEB)

    Gould, Michael N. [Univ. of Wisconsin, Madison, WI (United States)

    2015-06-30

    The overall hypothesis of this grant application is that the adaptive responses elicited by low dose ionizing radiation (LDIR) result in part from heritable DNA methylation changes in the epigenome. In the final budget period at the University of Wisconsin-Madison, we will specifically address this hypothesis by determining if the epigenetically labile, differentially methylated regions (DMRs) that regulate parental-specific expression of imprinted genes are deregulated in agouti mice by low dose radiation exposure during gestation. This information is particularly important to ascertain given the 1) increased human exposure to medical sources of radiation; 2) increased number of people predicted to live and work in space; and 3) enhanced citizen concern about radiation exposure from nuclear power plant accidents and terrorist ‘dirty bombs.’

  17. Evolutionary relationship of alfalfa mosaic virus with cucumber mosaic virus and brome mosaic virus

    OpenAIRE

    Savithri, HS; Murthy, MRN

    1983-01-01

    The amino acid sequences of the non-structural protein (molecular weight 35,000; 3a protein) from three plant viruses - cucumber mosaic, brome mosaic and alfalfa mosaic have been systematically compared using the partial genomic sequences for these three viruses already available. The 3a protein of cucumber mosaic virus has an amino acid sequence homology of 33.7% with the corresponding protein of brome mosaic virus. A similar protein from alfalfa mosaic virus has a homology of 18.2% and 14.2...

  18. Designing Epigenome Editors: Considerations of Biochemical and Locus Specificities.

    Science.gov (United States)

    Sen, Dilara; Keung, Albert J

    2018-01-01

    The advent of locus-specific protein recruitment technologies has enabled a new class of studies in chromatin biology. Epigenome editors enable biochemical modifications of chromatin at almost any specific endogenous locus. Their locus specificity unlocks unique information including the functional roles of distinct modifications at specific genomic loci. Given the growing interest in using these tools for biological and translational studies, there are many specific design considerations depending on the scientific question or clinical need. Here we present and discuss important design considerations and challenges regarding the biochemical and locus specificities of epigenome editors. These include how to account for the complex biochemical diversity of chromatin; control for potential interdependency of epigenome editors and their resultant modifications; avoid sequestration effects; quantify the locus specificity of epigenome editors; and improve locus specificity by considering concentration, affinity, avidity, and sequestration effects.

  19. Infantile spasms and pigmentary mosaicism

    DEFF Research Database (Denmark)

    Hansen, Lars K; Bygum, Anette; Krogh, Lotte N

    2010-01-01

    Summary We present a 3-year-old boy with pigmentary mosaicism and persistent intractable infantile spasms due to mosaicism of chromosome 7. Getting the diagnosis of pigmentary mosaicism in a child with infantile spasms may not be easy, as most diagnostic work-up is done in infancy, at a time when...

  20. IMAGE-2006 Mosaic: Product Description

    OpenAIRE

    SOILLE Pierre; BIELSKI Conrad

    2008-01-01

    This report describes the IMAGE-2006 mosaic products. Each product consists of a range of information layers grouped into three categories: base layers, mosaic layers, and quality layers. A mosaic product is available for each coverage and data/country region of interest combination.

  1. Pepino mosaic virus

    NARCIS (Netherlands)

    Vlugt, van der R.A.A.

    2009-01-01

    Pepino mosaic virus (PepMV) is a relatively new plant virus that has become a signifi cant agronomical problem in a relatively short period of time. It is a member of the genus Potexvirus within the family Flexiviridae and is readily mechanically transmissible. It is capable of infecting tomato

  2. Apple mosaic virus

    Science.gov (United States)

    Apple mosaic virus (ApMV), a member of the ilarvirus group, naturally infects Betula, Aesculus, Humulus, and several crop genera in the family Rosaceae (Malus, Prunus, Rosa and Rubus). ApMV was first reported in Rubus in several blackberry and raspberry cultivars in the United States and subsequentl...

  3. Epigenomic Views of Innate Lymphoid Cells.

    Science.gov (United States)

    Sciumè, Giuseppe; Shih, Han-Yu; Mikami, Yohei; O'Shea, John J

    2017-01-01

    The discovery of innate lymphoid cells (ILCs) with selective production of cytokines typically attributed to subsets of T helper cells forces immunologists to reassess the mechanisms by which selective effector functions arise. The parallelism between ILCs and T cells extends beyond these two cell types and comprises other innate-like T lymphocytes. Beyond the recognition of specialized effector functionalities in diverse lymphocytes, features typical of T cells, such as plasticity and memory, are also relevant for innate lymphocytes. Herein, we review what we have learned in terms of the molecular mechanisms underlying these shared functions, focusing on insights provided by next generation sequencing technologies. We review data on the role of lineage-defining- and signal-dependent transcription factors (TFs). ILC regulomes emerge developmentally whereas the much of the open chromatin regions of T cells are generated acutely, in an activation-dependent manner. And yet, these regions of open chromatin in T cells and ILCs have remarkable overlaps, suggesting that though accessibility is acquired by distinct modes, the end result is that convergent signaling pathways may be involved. Although much is left to be learned, substantial progress has been made in understanding how TFs and epigenomic status contribute to ILC biology in terms of differentiation, specification, and plasticity.

  4. Are we Genomic Mosaics? Variations of the Genome of Somatic Cells can Contribute to Diversify our Phenotypes.

    Science.gov (United States)

    Astolfi, P A; Salamini, F; Sgaramella, V

    2010-09-01

    Theoretical and experimental evidences support the hypothesis that the genomes and the epigenomes may be different in the somatic cells of complex organisms. In the genome, the differences range from single base substitutions to chromosome number; in the epigenome, they entail multiple postsynthetic modifications of the chromatin. Somatic genome variations (SGV) may accumulate during development in response both to genetic programs, which may differ from tissue to tissue, and to environmental stimuli, which are often undetected and generally irreproducible. SGV may jeopardize physiological cellular functions, but also create novel coding and regulatory sequences, to be exposed to intraorganismal Darwinian selection. Genomes acknowledged as comparatively poor in genes, such as humans', could thus increase their pristine informational endowment. A better understanding of SGV will contribute to basic issues such as the "nature vs nurture" dualism and the inheritance of acquired characters. On the applied side, they may explain the low yield of cloning via somatic cell nuclear transfer, provide clues to some of the problems associated with transdifferentiation, and interfere with individual DNA analysis. SGV may be unique in the different cells types and in the different developmental stages, and thus explain the several hundred gaps persisting in the human genomes "completed" so far. They may compound the variations associated to our epigenomes and make of each of us an "(epi)genomic" mosaic. An ensuing paradigm is the possibility that a single genome (the ephemeral one assembled at fertilization) has the capacity to generate several different brains in response to different environments.

  5. Selective interaction between Chloroplast B ATPase and TGB1 retards severe symptoms caused by Alternanthera mosaic virus infection

    Science.gov (United States)

    The multifunctional triple gene block protein 1 (TGB1) of the Potexvirus Alternanthera mosaic virus (AltMV) has been reported to have silencing suppressor, cell-to-cell movement, and helicase functions. Yeast two hybrid screening using an Arabidopsis thaliana cDNA library with TGB1 as bait, and co-p...

  6. Generation of TALE-Based Designer Epigenome Modifiers.

    Science.gov (United States)

    Nitsch, Sandra; Mussolino, Claudio

    2018-01-01

    Manipulation of gene expression can be facilitated by editing the genome or the epigenome. Precise genome editing is traditionally achieved by using designer nucleases which are generally exploited to eliminate a specific gene product. Upon the introduction of a site-specific DNA double-strand break (DSB) by the nuclease, endogenous DSB repair mechanisms are in turn harnessed to induce DNA sequence changes that can result in target gene inactivation. Minimal off-target effects can be obtained by endowing designer nucleases with the highly specific DNA-binding domain (DBD) derived from transcription activator-like effectors (TALEs). In contrast, epigenome editing allows gene expression control without inducing changes in the DNA sequence by specifically altering epigenetic marks, as histone tails modifications or DNA methylation patterns within promoter or enhancer regions. Importantly, this approach allows both up- and downregulation of the target gene expression, and the effect is generally reversible. TALE-based designer epigenome modifiers combine the high specificity of TALE-derived DBDs with the power of epigenetic modifier domains to induce fast and long-lasting changes in the epigenetic landscape of a target gene and control its expression. Here we provide a detailed description for the generation of TALE-based designer epigenome modifiers and of a suitable reporter cell line to easily monitor their activity.

  7. Integration and Visualization of Epigenome and Mobilome Data in Crops

    OpenAIRE

    Robakowska Hyzorek, Dagmara; Mirouze, Marie; Larmande, Pierre

    2016-01-01

    International audience; In the coming years, the study of the interaction between the epigenome and the mobilome is likely to give insights on the role of TEs on genome stability and evolution. In the present project we have created tools to collect epigenetic datasets from different laboratories and databases and translate them to a standard format to be integrated, analyzed and finally visualized.

  8. Breast Cancer Methylomes Establish an Epigenomic Foundation for Metastasis

    Science.gov (United States)

    Fang, Fang; Turcan, Sevin; Rimner, Andreas; Kaufman, Andrew; Giri, Dilip; Morris, Luc G. T.; Shen, Ronglai; Seshan, Venkatraman; Mo, Qianxing; Heguy, Adriana; Baylin, Stephen B.; Ahuja, Nita; Viale, Agnes; Massague, Joan; Norton, Larry; Vahdat, Linda T.; Moynahan, Mary Ellen; Chan, Timothy A.

    2011-01-01

    Cancer-specific alterations in DNA methylation are hallmarks of human malignancies; however, the nature of the breast cancer epigenome and its effects on metastatic behavior remain obscure. To address this issue, we used genome-wide analysis to characterize the methylomes of breast cancers with diverse metastatic behavior. Groups of breast tumors were characterized by the presence or absence of coordinate hypermethylation at a large number of genes, demonstrating a breast CpG island methylator phenotype (B-CIMP). The B-CIMP provided a distinct epigenomic profile and was a strong determinant of metastatic potential. Specifically, the presence of the B-CIMP in tumors was associated with low metastatic risk and survival, and the absence of the B-CIMP was associated with high metastatic risk and death. B-CIMP loci were highly enriched for genes that make up the metastasis transcriptome. Methylation at B-CIMP genes accounted for much of the transcriptomal diversity between breast cancers of varying prognosis, indicating a fundamental epigenomic contribution to metastasis. Comparison of the loci affected by the B-CIMP with those affected by the hypermethylator phenotype in glioma and colon cancer revealed that the CIMP signature was shared by multiple human malignancies. Our data provide a unifying epigenomic framework linking breast cancers with varying outcome and transcriptomic changes underlying metastasis. These findings significantly enhance our understanding of breast cancer oncogenesis and aid the development of new prognostic biomarkers for this common malignancy. PMID:21430268

  9. Association between the degree of mosaicism and the severity of syndrome in Turner mosaics and Klinefelter mosaics.

    Science.gov (United States)

    Sarkar, R; Marimuthu, K M

    1983-12-01

    This study, based on the investigations carried on 82 cases of Turners of which 50 of them were mosaics and 85 cases of Klinefelters of which 70 of them were mosaics, is an attempt to explain the vast range of clinical variations observed in cytogenetically established Turner mosaics (45,X/46,XX) and Klinefelter mosaics (47,XXY/46,XY) in the light of the degree of mosaicism present in them. It was observed that the severity of the syndrome in Turner mosaics and Klinefelter mosaics increased with the relative increase in the abnormal cell line population.

  10. Advances in epigenetics and epigenomics for neurodegenerative diseases.

    Science.gov (United States)

    Qureshi, Irfan A; Mehler, Mark F

    2011-10-01

    In the post-genomic era, epigenetic factors-literally those that are "over" or "above" genetic ones and responsible for controlling the expression and function of genes-have emerged as important mediators of development and aging; gene-gene and gene-environmental interactions; and the pathophysiology of complex disease states. Here, we provide a brief overview of the major epigenetic mechanisms (ie, DNA methylation, histone modifications and chromatin remodeling, and non-coding RNA regulation). We highlight the nearly ubiquitous profiles of epigenetic dysregulation that have been found in Alzheimer's and other neurodegenerative diseases. We also review innovative methods and technologies that enable the characterization of individual epigenetic modifications and more widespread epigenomic states at high resolution. We conclude that, together with complementary genetic, genomic, and related approaches, interrogating epigenetic and epigenomic profiles in neurodegenerative diseases represent important and increasingly practical strategies for advancing our understanding of and the diagnosis and treatment of these disorders.

  11. Genomic and epigenomic heterogeneity in chronic lymphocytic leukemia

    OpenAIRE

    Guièze, Romain; Wu, Catherine J.

    2015-01-01

    Defining features of chronic lymphocytic leukemia (CLL) are not only its immunophenotype of CD19+CD5+CD23+sIgdim expressing clonal mature B cells but also its highly variable clinical course. In recent years, advances in massively parallel sequencing technologies have led to rapid progress in our understanding of the CLL genome and epigenome. Overall, these studies have clearly demarcated not only the vast degree of genetic and epigenetic heterogeneity among individuals with CLL but also even...

  12. ALEA: a toolbox for allele-specific epigenomics analysis.

    Science.gov (United States)

    Younesy, Hamid; Möller, Torsten; Heravi-Moussavi, Alireza; Cheng, Jeffrey B; Costello, Joseph F; Lorincz, Matthew C; Karimi, Mohammad M; Jones, Steven J M

    2014-04-15

    The assessment of expression and epigenomic status using sequencing based methods provides an unprecedented opportunity to identify and correlate allelic differences with epigenomic status. We present ALEA, a computational toolbox for allele-specific epigenomics analysis, which incorporates allelic variation data within existing resources, allowing for the identification of significant associations between epigenetic modifications and specific allelic variants in human and mouse cells. ALEA provides a customizable pipeline of command line tools for allele-specific analysis of next-generation sequencing data (ChIP-seq, RNA-seq, etc.) that takes the raw sequencing data and produces separate allelic tracks ready to be viewed on genome browsers. The pipeline has been validated using human and hybrid mouse ChIP-seq and RNA-seq data. The package, test data and usage instructions are available online at http://www.bcgsc.ca/platform/bioinfo/software/alea CONTACT: : mkarimi1@interchange.ubc.ca or sjones@bcgsc.ca Supplementary information: Supplementary data are available at Bioinformatics online. © The Author 2013. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  13. CpG island mapping by epigenome prediction.

    Directory of Open Access Journals (Sweden)

    Christoph Bock

    2007-06-01

    Full Text Available CpG islands were originally identified by epigenetic and functional properties, namely, absence of DNA methylation and frequent promoter association. However, this concept was quickly replaced by simple DNA sequence criteria, which allowed for genome-wide annotation of CpG islands in the absence of large-scale epigenetic datasets. Although widely used, the current CpG island criteria incur significant disadvantages: (1 reliance on arbitrary threshold parameters that bear little biological justification, (2 failure to account for widespread heterogeneity among CpG islands, and (3 apparent lack of specificity when applied to the human genome. This study is driven by the idea that a quantitative score of "CpG island strength" that incorporates epigenetic and functional aspects can help resolve these issues. We construct an epigenome prediction pipeline that links the DNA sequence of CpG islands to their epigenetic states, including DNA methylation, histone modifications, and chromatin accessibility. By training support vector machines on epigenetic data for CpG islands on human Chromosomes 21 and 22, we identify informative DNA attributes that correlate with open versus compact chromatin structures. These DNA attributes are used to predict the epigenetic states of all CpG islands genome-wide. Combining predictions for multiple epigenetic features, we estimate the inherent CpG island strength for each CpG island in the human genome, i.e., its inherent tendency to exhibit an open and transcriptionally competent chromatin structure. We extensively validate our results on independent datasets, showing that the CpG island strength predictions are applicable and informative across different tissues and cell types, and we derive improved maps of predicted "bona fide" CpG islands. The mapping of CpG islands by epigenome prediction is conceptually superior to identifying CpG islands by widely used sequence criteria since it links CpG island detection to

  14. CpG island mapping by epigenome prediction.

    Science.gov (United States)

    Bock, Christoph; Walter, Jörn; Paulsen, Martina; Lengauer, Thomas

    2007-06-01

    CpG islands were originally identified by epigenetic and functional properties, namely, absence of DNA methylation and frequent promoter association. However, this concept was quickly replaced by simple DNA sequence criteria, which allowed for genome-wide annotation of CpG islands in the absence of large-scale epigenetic datasets. Although widely used, the current CpG island criteria incur significant disadvantages: (1) reliance on arbitrary threshold parameters that bear little biological justification, (2) failure to account for widespread heterogeneity among CpG islands, and (3) apparent lack of specificity when applied to the human genome. This study is driven by the idea that a quantitative score of "CpG island strength" that incorporates epigenetic and functional aspects can help resolve these issues. We construct an epigenome prediction pipeline that links the DNA sequence of CpG islands to their epigenetic states, including DNA methylation, histone modifications, and chromatin accessibility. By training support vector machines on epigenetic data for CpG islands on human Chromosomes 21 and 22, we identify informative DNA attributes that correlate with open versus compact chromatin structures. These DNA attributes are used to predict the epigenetic states of all CpG islands genome-wide. Combining predictions for multiple epigenetic features, we estimate the inherent CpG island strength for each CpG island in the human genome, i.e., its inherent tendency to exhibit an open and transcriptionally competent chromatin structure. We extensively validate our results on independent datasets, showing that the CpG island strength predictions are applicable and informative across different tissues and cell types, and we derive improved maps of predicted "bona fide" CpG islands. The mapping of CpG islands by epigenome prediction is conceptually superior to identifying CpG islands by widely used sequence criteria since it links CpG island detection to their characteristic

  15. Highest Resolution Gaspra Mosaic

    Science.gov (United States)

    1992-01-01

    This picture of asteroid 951 Gaspra is a mosaic of two images taken by the Galileo spacecraft from a range of 5,300 kilometers (3,300 miles), some 10 minutes before closest approach on October 29, 1991. The Sun is shining from the right; phase angle is 50 degrees. The resolution, about 54 meters/pixel, is the highest for the Gaspra encounter and is about three times better than that in the view released in November 1991. Additional images of Gaspra remain stored on Galileo's tape recorder, awaiting playback in November. Gaspra is an irregular body with dimensions about 19 x 12 x 11 kilometers (12 x 7.5 x 7 miles). The portion illuminated in this view is about 18 kilometers (11 miles) from lower left to upper right. The north pole is located at upper left; Gaspra rotates counterclockwise every 7 hours. The large concavity on the lower right limb is about 6 kilometers (3.7 miles) across, the prominent crater on the terminator, center left, about 1.5 kilometers (1 mile). A striking feature of Gaspra's surface is the abundance of small craters. More than 600 craters, 100-500 meters (330-1650 feet) in diameter are visible here. The number of such small craters compared to larger ones is much greater for Gaspra than for previously studied bodies of comparable size such as the satellites of Mars. Gaspra's very irregular shape suggests that the asteroid was derived from a larger body by nearly catastrophic collisions. Consistent with such a history is the prominence of groove-like linear features, believed to be related to fractures. These linear depressions, 100-300 meters wide and tens of meters deep, are in two crossing groups with slightly different morphology, one group wider and more pitted than the other. Grooves had previously been seen only on Mars's moon Phobos, but were predicted for asteroids as well. Gaspra also shows a variety of enigmatic curved depressions and ridges in the terminator region at left. The Galileo project, whose primary mission is the

  16. Gaspra - Highest Resolution Mosaic

    Science.gov (United States)

    1992-01-01

    This picture of asteroid 951 Gaspra is a mosaic of two images taken by the Galileo spacecraft from a range of 5,300 kilometers (3,300 miles), some 10 minutes before closest approach on October 29, 1991. The Sun is shining from the right; phase angle is 50 degrees. The resolution, about 54 meters/pixel, is the highest for the Gaspra encounter and is about three times better than that in the view released in November 1991. Additional images of Gaspra remain stored on Galileo's tape recorder, awaiting playback in November. Gaspra is an irregular body with dimensions about 19 x 12 x 11 kilometers (12 x 7.5 x 7 miles). The portion illuminated in this view is about 18 kilometers (11 miles) from lower left to upper right. The north pole is located at upper left; Gaspra rotates counterclockwise every 7 hours. The large concavity on the lower right limb is about 6 kilometers (3.7 miles) across, the prominent crater on the terminator, center left, about 1.5 kilometers (1 mile). A striking feature of Gaspra's surface is the abundance of small craters. More than 600 craters, 100-500 meters (330-1650 feet) in diameter are visible here. The number of such small craters compared to larger ones is much greater for Gaspra than for previously studied bodies of comparable size such as the satellites of Mars. Gaspra's very irregular shape suggests that the asteroid was derived from a larger body by nearly catastrophic collisions. Consistent with such a history is the prominence of groove-like linear features, believed to be related to fractures. These linear depressions, 100-300 meters wide and tens of meters deep, are in two crossing groups with slightly different morphology, one group wider and more pitted than the other. Grooves had previously been seen only on Mars's moon Phobos, but were predicted for asteroids as well. Gaspra also shows a variety of enigmatic curved depressions and ridges in the terminator region at left. The Galileo project, whose primary mission is the

  17. Epigenomic annotation-based interpretation of genomic data: from enrichment analysis to machine learning.

    Science.gov (United States)

    Dozmorov, Mikhail G

    2017-10-15

    One of the goals of functional genomics is to understand the regulatory implications of experimentally obtained genomic regions of interest (ROIs). Most sequencing technologies now generate ROIs distributed across the whole genome. The interpretation of these genome-wide ROIs represents a challenge as the majority of them lie outside of functionally well-defined protein coding regions. Recent efforts by the members of the International Human Epigenome Consortium have generated volumes of functional/regulatory data (reference epigenomic datasets), effectively annotating the genome with epigenomic properties. Consequently, a wide variety of computational tools has been developed utilizing these epigenomic datasets for the interpretation of genomic data. The purpose of this review is to provide a structured overview of practical solutions for the interpretation of ROIs with the help of epigenomic data. Starting with epigenomic enrichment analysis, we discuss leading tools and machine learning methods utilizing epigenomic and 3D genome structure data. The hierarchy of tools and methods reviewed here presents a practical guide for the interpretation of genome-wide ROIs within an epigenomic context. mikhail.dozmorov@vcuhealth.org. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

  18. Systems considerations in mosaic focal planes

    Science.gov (United States)

    White, K. P., III

    1983-08-01

    Two key reasons for pursuing the development of mosaic focal planes are reviewed and it is shown that rapid frame repetition rate is the only requirement that can be solved no other way than through mosaic focal planes. With the view that spaceborne mosaic focal plane sensors are necessarily 'smart sensors' requiring a lot of onboard processing just to function, it is pointed out that various artificial intelligence techniques may be the most appropriate to incorporate in the data processing. Finally, a novel mosaic focal plane design is proposed, termed a virtual mosaic focal plane, in response to other system constraints.

  19. Genomic and Epigenomic Insights into Nutrition and Brain Disorders

    Directory of Open Access Journals (Sweden)

    Margaret Joy Dauncey

    2013-03-01

    Full Text Available Considerable evidence links many neuropsychiatric, neurodevelopmental and neurodegenerative disorders with multiple complex interactions between genetics and environmental factors such as nutrition. Mental health problems, autism, eating disorders, Alzheimer’s disease, schizophrenia, Parkinson’s disease and brain tumours are related to individual variability in numerous protein-coding and non-coding regions of the genome. However, genotype does not necessarily determine neurological phenotype because the epigenome modulates gene expression in response to endogenous and exogenous regulators, throughout the life-cycle. Studies using both genome-wide analysis of multiple genes and comprehensive analysis of specific genes are providing new insights into genetic and epigenetic mechanisms underlying nutrition and neuroscience. This review provides a critical evaluation of the following related areas: (1 recent advances in genomic and epigenomic technologies, and their relevance to brain disorders; (2 the emerging role of non-coding RNAs as key regulators of transcription, epigenetic processes and gene silencing; (3 novel approaches to nutrition, epigenetics and neuroscience; (4 gene-environment interactions, especially in the serotonergic system, as a paradigm of the multiple signalling pathways affected in neuropsychiatric and neurological disorders. Current and future advances in these four areas should contribute significantly to the prevention, amelioration and treatment of multiple devastating brain disorders.

  20. Epigenetic diet: impact on the epigenome and cancer

    Science.gov (United States)

    Hardy, Tabitha M; Tollefsbol, Trygve O

    2011-01-01

    A number of bioactive dietary components are of particular interest in the field of epigenetics. Many of these compounds display anticancer properties and may play a role in cancer prevention. Numerous studies suggest that a number of nutritional compounds have epigenetic targets in cancer cells. Importantly, emerging evidence strongly suggests that consumption of dietary agents can alter normal epigenetic states as well as reverse abnormal gene activation or silencing. Epigenetic modifications induced by bioactive dietary compounds are thought to be beneficial. Substantial evidence is mounting proclaiming that commonly consumed bioactive dietary factors act to modify the epigenome and may be incorporated into an ‘epigenetic diet’. Bioactive nutritional components of an epigenetic diet may be incorporated into one’s regular dietary regimen and used therapeutically for medicinal or chemopreventive purposes. This article will primarily focus on dietary factors that have been demonstrated to influence the epigenome and that may be used in conjunction with other cancer prevention and chemotherapeutic therapies. PMID:22022340

  1. How to stomach an epigenetic insult: the gastric cancer epigenome.

    Science.gov (United States)

    Padmanabhan, Nisha; Ushijima, Toshikazu; Tan, Patrick

    2017-08-01

    Gastric cancer is a deadly malignancy afflicting close to a million people worldwide. Patient survival is poor and largely due to late diagnosis and suboptimal therapies. Disease heterogeneity is a substantial obstacle, underscoring the need for precision treatment strategies. Studies have identified different subgroups of gastric cancer displaying not just genetic, but also distinct epigenetic hallmarks. Accumulating evidence suggests that epigenetic abnormalities in gastric cancer are not mere bystander events, but rather promote carcinogenesis through active mechanisms. Epigenetic aberrations, induced by pathogens such as Helicobacter pylori, are an early component of gastric carcinogenesis, probably preceding genetic abnormalities. This Review summarizes our current understanding of the gastric cancer epigenome, highlighting key advances in recent years in both tumours and pre-malignant lesions, made possible through targeted and genome-wide technologies. We focus on studies related to DNA methylation and histone modifications, linking these findings to potential therapeutic opportunities. Lessons learned from the gastric cancer epigenome might also prove relevant for other gastrointestinal cancers.

  2. [Folates and fetal programming: role of epigenetics and epigenomics].

    Science.gov (United States)

    Guéant, Jean-Louis; Daval, Jean-Luc; Vert, Paul; Nicolas, Jean-Pierre

    2012-12-01

    Folates are needed for synthesis of methionine, the precursor of S-adenosyl methionine (SAM). They play therefore a key role in nutrition and epigenomics by fluxing monocarbons towards synthesis or methylation of DNA and RNA, and methylation of gene transregulators, respectively. The deficiency produces intrauterine growth retardation and birth dejects. Folate deficiency deregulates epigenomic mechanisms related to fetal programming through decreased cellular availability of SAM. Epigenetic mechanisms of folate deficiency are illustrated by inheritance of coat colour of agouti mice model and altered expression of Igf2/H19 imprinting genes. Dietary exposure to fumonisin FB1 acts synergistically with folate deficiency on alterations of heterochromatin assembly. Deficiency in folate and vitamin B12 produces impaired fatty acid oxidation in liver and heart through imbalanced methylation and acetylation of PGC1-alpha and decreased expression of SIRT1, and long-lasting cognitive disabilities through impaired hippocampal cell proliferation, differentiation and plasticity and atrophy of hippocampal CA1. Deciphering these mechanisms will help understand the discordances between experimental models and population studies on folate supplementation.

  3. ENCODE: A Sourcebook of Epigenomes and Chromatin Language

    Directory of Open Access Journals (Sweden)

    Maryam Yavartanoo

    2013-03-01

    Full Text Available Until recently, since the Human Genome Project, the general view has been that the majority of the human genome is composed of junk DNA and has little or no selective advantage to the organism. Now we know that this conclusion is an oversimplification. In April 2003, the National Human Genome Research Institute (NHGRI launched an international research consortium called Encyclopedia of DNA Elements (ENCODE to uncover non-coding functional elements in the human genome. The result of this project has identified a set of new DNA regulatory elements, based on novel relationships among chromatin accessibility, histone modifications, nucleosome positioning, DNA methylation, transcription, and the occupancy of sequence-specific factors. The project gives us new insights into the organization and regulation of the human genome and epigenome. Here, we sought to summarize particular aspects of the ENCODE project and highlight the features and data that have recently been released. At the end of this review, we have summarized a case study we conducted using the ENCODE epigenome data.

  4. Mosaic HIV envelope immunogenic polypeptides

    Science.gov (United States)

    Korber, Bette T. M.; Gnanakaran, S.; Perkins, Simon; Sodroski, Joseph; Haynes, Barton

    2018-01-02

    Disclosed herein are mosaic HIV envelope (Env) polypeptides that can elicit an immune response to HIV (such as cytotoxic T cell (CTL), helper T cell, and/or humoral responses). Also disclosed are sets of the disclosed mosaic Env polypeptides, which include two or more (for example, three) of the polypeptides. Also disclosed herein are methods for treating or inhibiting HIV in a subject including administering one or more of the disclosed immunogenic polypeptides or compositions to a subject infected with HIV or at risk of HIV infection. In some embodiments, the methods include inducing an immune response to HIV in a subject comprising administering to the subject at least one (such as two, three, or more) of the immunogenic polypeptides or at least one (such as two, three, or more) nucleic acids encoding at least one of the immunogenic polypeptides disclosed herein.

  5. NaviSE: superenhancer navigator integrating epigenomics signal algebra.

    Science.gov (United States)

    Ascensión, Alex M; Arrospide-Elgarresta, Mikel; Izeta, Ander; Araúzo-Bravo, Marcos J

    2017-06-06

    Superenhancers are crucial structural genomic elements determining cell fate, and they are also involved in the determination of several diseases, such as cancer or neurodegeneration. Although there are pipelines which use independent pieces of software to predict the presence of superenhancers from genome-wide chromatin marks or DNA-interaction protein binding sites, there is not yet an integrated software tool that processes automatically algebra combinations of raw data sequencing into a comprehensive final annotated report of predicted superenhancers. We have developed NaviSE, a user-friendly streamlined tool which performs a fully-automated parallel processing of genome-wide epigenomics data from sequencing files into a final report, built with a comprehensive set of annotated files that are navigated through a graphic user interface dynamically generated by NaviSE. NaviSE also implements an 'epigenomics signal algebra' that allows the combination of multiple activation and repression epigenomics signals. NaviSE provides an interactive chromosomal landscaping of the locations of superenhancers, which can be navigated to obtain annotated information about superenhancer signal profile, associated genes, gene ontology enrichment analysis, motifs of transcription factor binding sites enriched in superenhancers, graphs of the metrics evaluating the superenhancers quality, protein-protein interaction networks and enriched metabolic pathways among other features. We have parallelised the most time-consuming tasks achieving a reduction up to 30% for a 15 CPUs machine. We have optimized the default parameters of NaviSE to facilitate its use. NaviSE allows different entry levels of data processing, from sra-fastq files to bed files; and unifies the processing of multiple replicates. NaviSE outperforms the more time-consuming processes required in a non-integrated pipeline. Alongside its high performance, NaviSE is able to provide biological insights, predicting cell

  6. Identification of virus isolates inducing mosaic of sugarcane in ...

    African Journals Online (AJOL)

    Sugarcane mosaic disease caused by sugarcane mosaic virus (SCMV), Johnsongrass mosaic virus (JGMV), maize dwarf mosaic virus (MDMV) and sorghum mosaic Virus (SrMV) is an economically important viral disease of sugarcane worldwide. Field survey was conducted to assess the presence of the viruses involve in ...

  7. Nutritional Epigenomics: A Portal to Disease Prevention12

    Science.gov (United States)

    Choi, Sang-Woon; Claycombe, Kate J.; Martinez, J. Alfredo; Friso, Simonetta; Schalinske, Kevin L.

    2013-01-01

    Epigenetics can be defined as inheritable and reversible phenomena that affect gene expression without altering the underlying base pair sequence. Epigenomics is the study of genome-wide epigenetic modifications. Because gene expression changes are critical in both normal development and disease progression, epigenetics is widely applicable to many aspects of biological research. The influences of nutrients and bioactive food components on epigenetic phenomena such as DNA methylation and various types of histone modifications have been extensively investigated. Because an individual’s epigenetic patterns are established during early gestation and are changed and personalized by environmental factors during our lifetime, epigenetic mechanisms are quite important in the development of transgenerational and adult obesity as well as in the development of diabetes mellitus. Aging and cancer demonstrate profound genome-wide DNA methylation changes, suggesting that nutrition may affect the aging process and cancer development through epigenetic mechanisms. PMID:24038247

  8. The epigenome as a therapeutic target in prostate cancer.

    Science.gov (United States)

    Perry, Antoinette S; Watson, R William G; Lawler, Mark; Hollywood, Donal

    2010-12-01

    During cancer development and progression, tumor cells undergo abnormal epigenetic modifications, including DNA methylation, histone deacetylation and nucleosome remodeling. Collectively, these aberrations promote genomic instability and lead to silencing of tumor-suppressor genes and reactivation of oncogenic retroviruses. Epigenetic modifications, therefore, provide exciting new avenues for prostate cancer research. Promoter hypermethylation is widespread during neoplastic transformation of prostate cells, which suggests that restoration of a 'normal' epigenome through treatment with inhibitors of the enzymes involved could be clinically beneficial. Global patterns of histone modifications are also being defined and have been associated with clinical and pathologic predictors of prostate cancer outcome. Although treatment for localized prostate cancer can be curative, the development of successful therapies for the management of castration-resistant metastatic disease is urgently needed. Reactivation of tumor-suppressor genes by demethylating agents and histone deacetylase inhibitors could be a potential treatment option for patients with advanced disease.

  9. Epigenomics, gestational programming and risk of metabolic syndrome.

    Science.gov (United States)

    Desai, M; Jellyman, J K; Ross, M G

    2015-04-01

    Epigenetic mechanisms are emerging as mediators linking early environmental exposures during pregnancy with programmed changes in gene expression that alter offspring growth and development. There is irrefutable evidence from human and animal studies that nutrient and environmental agent exposures (for example, endocrine disruptors) during pregnancy may affect fetal/newborn development resulting in offspring obesity and obesity-associated metabolic abnormalities (metabolic syndrome). This concept of 'gestational programming' is associated with alterations to the epigenome (nongenomic) rather than changes in the DNA sequence (genomic). Epigenetic alterations induced by suboptimal maternal nutrition/endocrine factors include DNA methylation, histone modifications, chromatin remodeling and/or regulatory feedback by microRNAs, all of which have the ability to modulate gene expression and promote the metabolic syndrome phenotype. Recent studies have shown tissue-specific transcriptome patterns and phenotypes not only in the exposed individual, but also in subsequent progeny. Notably, the transmission of gestational programming effects to subsequent generations occurs in the absence of continued adverse environmental exposures, thus propagating the cycle of obesity and metabolic syndrome. This phenomenon may be attributed to an extrinsic process resulting from the maternal phenotype and the associated nutrient alterations occurring within each pregnancy. In addition, epigenetic inheritance may occur through somatic cells or through the germ line involving both maternal and paternal lineages. Since epigenetic gene modifications may be reversible, understanding how epigenetic mechanisms contribute to transgenerational transmission of obesity and metabolic dysfunction is crucial for the development of novel early detection and prevention strategies for programmed metabolic syndrome. In this review we discuss the evidence in human and animal studies for the role of

  10. ePIANNO: ePIgenomics ANNOtation tool.

    Directory of Open Access Journals (Sweden)

    Chia-Hsin Liu

    Full Text Available Recently, with the development of next generation sequencing (NGS, the combination of chromatin immunoprecipitation (ChIP and NGS, namely ChIP-seq, has become a powerful technique to capture potential genomic binding sites of regulatory factors, histone modifications and chromatin accessible regions. For most researchers, additional information including genomic variations on the TF binding site, allele frequency of variation between different populations, variation associated disease, and other neighbour TF binding sites are essential to generate a proper hypothesis or a meaningful conclusion. Many ChIP-seq datasets had been deposited on the public domain to help researchers make new discoveries. However, researches are often intimidated by the complexity of data structure and largeness of data volume. Such information would be more useful if they could be combined or downloaded with ChIP-seq data. To meet such demands, we built a webtool: ePIgenomic ANNOtation tool (ePIANNO, http://epianno.stat.sinica.edu.tw/index.html. ePIANNO is a web server that combines SNP information of populations (1000 Genomes Project and gene-disease association information of GWAS (NHGRI with ChIP-seq (hmChIP, ENCODE, and ROADMAP epigenomics data. ePIANNO has a user-friendly website interface allowing researchers to explore, navigate, and extract data quickly. We use two examples to demonstrate how users could use functions of ePIANNO webserver to explore useful information about TF related genomic variants. Users could use our query functions to search target regions, transcription factors, or annotations. ePIANNO may help users to generate hypothesis or explore potential biological functions for their studies.

  11. Multichannel Image Mosaicing of Stem Cells

    OpenAIRE

    Alessandro Bevilacqua; Alessandro Gherardi; Filippo Piccinini

    2010-01-01

    Image mosaicing techniques are usually employed to offer researchers a wider field of view of microscopic image of biological samples. a mosaic is commonly achieved using automated microscopes and often with one “color" channel, whether it refers to natural or fluorescent analysis. In this work we present a method to achieve three subsequent mosaics of the same part of a stem cell culture analyzed in phase contrast and in fluorescence, with a common non-automated inverted microscope. The mosa...

  12. High-fat diet reprograms the epigenome of rat spermatozoa and transgenerationally affects metabolism of the offspring

    Directory of Open Access Journals (Sweden)

    Thais de Castro Barbosa

    2016-03-01

    Conclusion: Our results provide insight into mechanisms by which HFD transgenerationally reprograms the epigenome of sperm cells, thereby affecting metabolic tissues of offspring throughout two generations.

  13. Occurrence of Cucumber mosaic virus on vanilla

    Indian Academy of Sciences (India)

    Cucumber mosaic virus (CMV) causing mosaic, leaf distortion and stunting of vanilla (Vanilla planifolia Andrews) in India was characterized on the basis of biological and coat protein (CP) nucleotide sequence properties. In mechanical inoculation tests, the virus was found to infect members of Chenopodiaceae, ...

  14. Web Map Services (WMS) Global Mosaic

    Science.gov (United States)

    Percivall, George; Plesea, Lucian

    2003-01-01

    The WMS Global Mosaic provides access to imagery of the global landmass using an open standard for web mapping. The seamless image is a mosaic of Landsat 7 scenes; geographically-accurate with 30 and 15 meter resolutions. By using the OpenGIS Web Map Service (WMS) interface, any organization can use the global mosaic as a layer in their geospatial applications. Based on a trade study, an implementation approach was chosen that extends a previously developed WMS hosting a Landsat 5 CONUS mosaic developed by JPL. The WMS Global Mosaic supports the NASA Geospatial Interoperability Office goal of providing an integrated digital representation of the Earth, widely accessible for humanity's critical decisions.

  15. Rapid and reversible epigenome editing by endogenous chromatin regulators.

    Science.gov (United States)

    Braun, Simon M G; Kirkland, Jacob G; Chory, Emma J; Husmann, Dylan; Calarco, Joseph P; Crabtree, Gerald R

    2017-09-15

    Understanding the causal link between epigenetic marks and gene regulation remains a central question in chromatin biology. To edit the epigenome we developed the FIRE-Cas9 system for rapid and reversible recruitment of endogenous chromatin regulators to specific genomic loci. We enhanced the dCas9-MS2 anchor for genome targeting with Fkbp/Frb dimerizing fusion proteins to allow chemical-induced proximity of a desired chromatin regulator. We find that mSWI/SNF (BAF) complex recruitment is sufficient to oppose Polycomb within minutes, leading to activation of bivalent gene transcription in mouse embryonic stem cells. Furthermore, Hp1/Suv39h1 heterochromatin complex recruitment to active promoters deposits H3K9me3 domains, resulting in gene silencing that can be reversed upon washout of the chemical dimerizer. This inducible recruitment strategy provides precise kinetic information to model epigenetic memory and plasticity. It is broadly applicable to mechanistic studies of chromatin in mammalian cells and is particularly suited to the analysis of endogenous multi-subunit chromatin regulator complexes.Understanding the link between epigenetic marks and gene regulation requires the development of new tools to directly manipulate chromatin. Here the authors demonstrate a Cas9-based system to recruit chromatin remodelers to loci of interest, allowing rapid, reversible manipulation of epigenetic states.

  16. Epigenome profiling and editing of neocortical progenitor cells during development.

    Science.gov (United States)

    Albert, Mareike; Kalebic, Nereo; Florio, Marta; Lakshmanaperumal, Naharajan; Haffner, Christiane; Brandl, Holger; Henry, Ian; Huttner, Wieland B

    2017-09-01

    The generation of neocortical neurons from neural progenitor cells (NPCs) is primarily controlled by transcription factors binding to DNA in the context of chromatin. To understand the complex layer of regulation that orchestrates different NPC types from the same DNA sequence, epigenome maps with cell type resolution are required. Here, we present genomewide histone methylation maps for distinct neural cell populations in the developing mouse neocortex. Using different chromatin features, we identify potential novel regulators of cortical NPCs. Moreover, we identify extensive H3K27me3 changes between NPC subtypes coinciding with major developmental and cell biological transitions. Interestingly, we detect dynamic H3K27me3 changes on promoters of several crucial transcription factors, including the basal progenitor regulator Eomes We use catalytically inactive Cas9 fused with the histone methyltransferase Ezh2 to edit H3K27me3 at the Eomes locus in vivo , which results in reduced Tbr2 expression and lower basal progenitor abundance, underscoring the relevance of dynamic H3K27me3 changes during neocortex development. Taken together, we provide a rich resource of neocortical histone methylation data and outline an approach to investigate its contribution to the regulation of selected genes during neocortical development. © 2017 The Authors.

  17. Manipulating the epigenome for the treatment of urological malignancies.

    LENUS (Irish Health Repository)

    O'Rourke, Colm J

    2013-05-01

    Urological malignancies (cancers of the prostate, bladder, kidney and testes) account for 15% of all human cancers and more than 500,000 deaths worldwide each year. This group of malignancies is spread across multiple generations, affecting the young (testicular) through middle and old-age (kidney, prostate and bladder). Like most human cancers, urological cancers are characterized by widespread epigenetic insult, causing changes in DNA hypermethylation and histone modifications leading to silencing of tumor suppressor genes and genomic instability. The inherent stability yet dynamic plasticity of the epigenome lends itself well to therapeutic manipulation. Epigenetic changes are amongst the earliest lesions to occur during carcinogenesis and are essentially reversible (unlike mutations). For this reason, much attention has been placed over the past two decades on deriving pharmacological compounds that can specifically target and reverse such epi-mutations, either halting cancer on its developmental trajectory or reverting fully formed cancers to a more clinically manageable state. This review discusses DNA methyltransferase and histone deacetylase inhibitors that have been extensively studied in preclinical models and clinical trials for advanced and metastatic urological cancers.

  18. Epigenome-Wide Association Study of Tic Disorders.

    Science.gov (United States)

    Zilhão, Nuno R; Padmanabhuni, Shanmukha S; Pagliaroli, Luca; Barta, Csaba; Smit, Dirk J A; Cath, Danielle; Nivard, Michel G; Baselmans, Bart M L; van Dongen, Jenny; Paschou, Peristera; Boomsma, Dorret I

    2015-12-01

    Tic disorders are moderately heritable common psychiatric disorders that can be highly troubling, both in childhood and in adulthood. In this study, we report results obtained in the first epigenome-wide association study (EWAS) of tic disorders. The subjects are participants in surveys at the Netherlands Twin Register (NTR) and the NTR biobank project. Tic disorders were measured with a self-report version of the Yale Global Tic Severity Scale Abbreviated version (YGTSS-ABBR), included in the 8th wave NTR data collection (2008). DNA methylation data consisted of 411,169 autosomal methylation sites assessed by the Illumina Infinium HumanMethylation450 BeadChip Kit (HM450k array). Phenotype and DNA methylation data were available in 1,678 subjects (mean age = 41.5). No probes reached genome-wide significance (p tic disorders. The top significantly enriched gene ontology (GO) terms among higher ranking methylation sites included anatomical structure morphogenesis (GO:0009653, p = 4.6 × 10-(15)) developmental process (GO:0032502, p = 2.96 × 10(-12)), and cellular developmental process (GO:0048869, p = 1.96 × 10(-12)). Overall, these results provide a first insight into the epigenetic mechanisms of tic disorders. This first study assesses the role of DNA methylation in tic disorders, and it lays the foundations for future work aiming to unravel the biological mechanisms underlying the architecture of this disorder.

  19. Epidaurus: aggregation and integration analysis of prostate cancer epigenome.

    Science.gov (United States)

    Wang, Liguo; Huang, Haojie; Dougherty, Gregory; Zhao, Yu; Hossain, Asif; Kocher, Jean-Pierre A

    2015-01-01

    Integrative analyses of epigenetic data promise a deeper understanding of the epigenome. Epidaurus is a bioinformatics tool used to effectively reveal inter-dataset relevance and differences through data aggregation, integration and visualization. In this study, we demonstrated the utility of Epidaurus in validating hypotheses and generating novel biological insights. In particular, we described the use of Epidaurus to (i) integrate epigenetic data from prostate cancer cell lines to validate the activation function of EZH2 in castration-resistant prostate cancer and to (ii) study the mechanism of androgen receptor (AR) binding deregulation induced by the knockdown of FOXA1. We found that EZH2's noncanonical activation function was reaffirmed by its association with active histone markers and the lack of association with repressive markers. More importantly, we revealed that the binding of AR was selectively reprogramed to promoter regions, leading to the up-regulation of hundreds of cancer-associated genes including EGFR. The prebuilt epigenetic dataset from commonly used cell lines (LNCaP, VCaP, LNCaP-Abl, MCF7, GM12878, K562, HeLa-S3, A549, HePG2) makes Epidaurus a useful online resource for epigenetic research. As standalone software, Epidaurus is specifically designed to process user customized datasets with both efficiency and convenience. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  20. Chromosome mosaicism in hypomelanosis of Ito.

    Science.gov (United States)

    Ritter, C L; Steele, M W; Wenger, S L; Cohen, B A

    1990-01-01

    Our finding of chromosome mosaicism with a ring 22 in a retarded black boy with hypomelanosis of Ito prompted a review of this "syndrome." Most patients have a variety of non-dermal defects, particularly those affecting CNS function. Among karyotyped patients, most are chromosome mosaics of one sort or another. Hypomelanosis of Ito turns out to be a causable non-specific phenotype, i.e., a clinical marker for chromosome mosaicism of all different types in individuals with a dark enough skin to show lighter patches. Consequently, cytogenetic evaluation is indicated in all patients with this skin finding.

  1. Trisomy 9 Mosaicism Diagnosed In Utero

    Directory of Open Access Journals (Sweden)

    Hironori Takahashi

    2010-01-01

    Full Text Available We present three cases of trisomy 9 mosaicism diagnosed by amniocentesis with ongoing pregnancies after referral to our center due to fetal abnormalities. Two cases were associated with severe fetal growth restriction (FGR, each of which resulted in an intrauterine fetal demise (IUFD in the third trimester. The other case involved mild FGR with a congenital diaphragmatic hernia and resulted in a live birth with severe development delay. A major prenatal finding of trisomy 9 mosaicism is FGR. Fetuses with trisomy 9 mosaicism can rarely survive in the case of severe FGR.

  2. High-Resolution Mapping of Chromatin Conformation in Cardiac Myocytes Reveals Structural Remodeling of the Epigenome in Heart Failure

    NARCIS (Netherlands)

    M. Rosa-Garrido (Manuel); Chapski, D.J. (Douglas J.); Schmitt, A.D. (Anthony D.); Kimball, T.H. (Todd H.); Karbassi, E. (Elaheh); Monte, E. (Emma); Balderas, E. (Enrique); Pellegrini, M. (Matteo); Shih, T.-T. (Tsai-Ting); Soehalim, E. (Elizabeth); D.A. Liem (David); Ping, P. (Peipei); N.J. Galjart (Niels); Ren, S. (Shuxun); Wang, Y. (Yibin); Ren, B. (Bing); Vondriska, T.M. (Thomas M.)

    2017-01-01

    textabstractBACKGROUND: Cardiovascular disease is associated with epigenomic changes in the heart; however, the endogenous structure of cardiac myocyte chromatin has never been determined.METHODS: To investigate the mechanisms of epigenomic function in the heart, genome-wide chromatin conformation

  3. Genomic and Epigenomic Aberrations in Esophageal Squamous Cell Carcinoma and Implications for Patients

    Science.gov (United States)

    Lin, De-Chen; Wang, Ming-Rong; Koeffler, H. Phillip

    2018-01-01

    Esophageal squamous cell carcinoma (ESCC) is a common malignancy without effective therapy. The exomes of more than 600 ESCCs have been sequenced in the past 4 years, and numerous key aberrations have been identified. Recently, researchers reported both inter- and intratumor heterogeneity. Although these are interesting observations, their clinical implications are unclear due to the limited number of samples profiled. Epigenomic alterations, such as changes in DNA methylation, histone acetylation, and RNA editing, also have been observed in ESCCs. However, it is not clear what proportion of ESCC cells carry these epigenomic aberrations or how they contribute to tumor development. We review the genomic and epigenomic characteristics of ESCCs, with a focus on emerging themes. We discuss their clinical implications and future research directions. PMID:28757263

  4. A Decade of Exploring the Mammalian Sperm Epigenome: Paternal Epigenetic and Transgenerational Inheritance

    Directory of Open Access Journals (Sweden)

    Alexandre Champroux

    2018-05-01

    Full Text Available The past decade has seen a tremendous increase in interest and progress in the field of sperm epigenetics. Studies have shown that chromatin regulation during male germline development is multiple and complex, and that the spermatozoon possesses a unique epigenome. Its DNA methylation profile, DNA-associated proteins, nucleo-protamine distribution pattern and non-coding RNA set up a unique epigenetic landscape which is delivered, along with its haploid genome, to the oocyte upon fertilization, and therefore can contribute to embryogenesis and to the offspring health. An emerging body of compelling data demonstrates that environmental exposures and paternal lifestyle can change the sperm epigenome and, consequently, may affect both the embryonic developmental program and the health of future generations. This short review will attempt to provide an overview of what is currently known about sperm epigenome and the existence of transgenerational epigenetic inheritance of paternally acquired traits that may contribute to the offspring phenotype.

  5. Prenatal Diagnosis and Genetic Counseling for Mosaic Trisomy 13

    Directory of Open Access Journals (Sweden)

    Chih-Ping Chen

    2010-03-01

    Full Text Available Counseling parents of a fetus with trisomy 13 mosaicism remains difficult because of the phenotypic variability associated with the condition; some patients exhibit the typical phenotype of complete trisomy 13 with neonatal death, while others have few dysmorphic features and prolonged survival. This article provides a comprehensive review of the prenatal diagnosis and genetic counseling for mosaic trisomy 13, including confined placental mosaicism 13, mosaic trisomy 13 diagnosed at amniocentesis, and phylloid hypomelanosis in association with mosaic trisomy 13.

  6. Endocrine Disrupters: the new players able to affect the epigenome.

    Directory of Open Access Journals (Sweden)

    Lavinia eCasati

    2015-06-01

    Full Text Available Epigenetics represents the way by which the environment is able to program the genome; there are three main levels of epigenetic control on genome: DNA methylation, post-translational histone modification and microRNA expression. The term Epigenetics has been widened by NIH to include both heritable changes in gene activity and expression but also stable, long-term alterations in the transcriptional potential of a cell that are not necessarily heritable. These changes might be produced mostly by the early life environment and might affect health influencing the susceptibility to develop diseases, from cancer to mental disorder, during the entire life span. The most studied environmental influences acting on epigenome are diet, infections, wasting, child care, smoking and environmental pollutants, in particular endocrine disrupters (EDs. These are environmental xenobiotics able to interfere with the normal development of the male and female reproductive systems of wildlife, of experimental animals and possibly of humans, disrupting the normal reproductive functions. Data from literature indicate that EDs can act at different levels of epigenetic control, in some cases transgenerationally, in particular when the exposure to these compounds occurs during the prenatal and earliest period of life. Some of the best characterized EDs will be considered in this review. Among the EDs, vinclozolin (VZ and methoxychlor (MXC promote epigenetic transgenerational effects. Polychlorinated biphenils (PCBs, the most widespread environmental EDs, affect histone post-translational modifications in a dimorphic way, possibly as the result of an alteration of gene expression of the enzymes involved in histone modification, as the demethylase Jarid1b, an enzyme also involved in regulating the interaction of androgens with their receptor.

  7. CAUSEL: an epigenome- and genome-editing pipeline for establishing function of noncoding GWAS variants

    DEFF Research Database (Denmark)

    Spisák, Sándor; Lawrenson, Kate; Fu, Yanfang

    2015-01-01

    a general pipeline in which candidate functional SNPs are first evaluated by fine mapping, epigenomic profiling, and epigenome editing, and then interrogated for causal function by using genome editing to create isogenic cell lines followed by phenotypic characterization. To validate this approach, we......me2 histone mark at the rs339331 region compared to lines homozygous for the 'C' protective allele. The cell lines also differed in cellular morphology and adhesion, and pathway analysis of differentially expressed genes suggested an influence of androgens. In summary, we have developed and validated...

  8. Epigenome remodelling in breast cancer: insights from an early in vitro model of carcinogenesis.

    Science.gov (United States)

    Locke, Warwick J; Clark, Susan J

    2012-11-15

    Epigenetic gene regulation has influence over a diverse range of cellular functions, including the maintenance of pluripotency, differentiation, and cellular identity, and is deregulated in many diseases, including cancer. Whereas the involvement of epigenetic dysregulation in cancer is well documented, much of the mechanistic detail involved in triggering these changes remains unclear. In the current age of genomics, the development of new sequencing technologies has seen an influx of genomic and epigenomic data and drastic improvements in both resolution and coverage. Studies in cancer cell lines and clinical samples using next-generation sequencing are rapidly delivering spectacular insights into the nature of the cancer genome and epigenome. Despite these improvements in technology, the timing and relationship between genetic and epigenetic changes that occur during the process of carcinogenesis are still unclear. In particular, what changes to the epigenome are playing a driving role during carcinogenesis and what influence the temporal nature of these changes has on cancer progression are not known. Understanding the early epigenetic changes driving breast cancer has the exciting potential to provide a novel set of therapeutic targets or early-disease biomarkers or both. Therefore, it is important to find novel systems that permit the study of initial epigenetic events that potentially occur during the first stages of breast cancer. Non-malignant human mammary epithelial cells (HMECs) provide an exciting in vitro model of very early breast carcinogenesis. When grown in culture, HMECs are able to temporarily escape senescence and acquire a pre-malignant breast cancer-like phenotype (variant HMECs, or vHMECs). Cultured HMECs are composed mainly of cells from the basal breast epithelial layer. Therefore, vHMECs are considered to represent the basal-like subtype of breast cancer. The transition from HMECs to vHMECs in culture recapitulates the epigenomic

  9. Mutants of alfalfa mosaic virus

    International Nuclear Information System (INIS)

    Roosien, J.

    1983-01-01

    In this thesis the isolation and characterization of a number of mutants of alfalfa mosaic virus, a plant virus with a coat protein dependent genome, is described. Thermo-sensitive (ts) mutants were selected since, at least theoretically, ts mutations can be present in all virus coded functions. It was found that a high percentage of spontaneous mutants, isolated because of their aberrant symptoms, were ts. The majority of these isolates could grow at the non-permissive temperature in the presence of a single wild type (wt) component. To increase the mutation rate virus preparations were treated with several mutagens. After nitrous acid treatment or irradiation with ultraviolet light, an increase in the level of mutations was observed. UV irradiation was preferred since it did not require large amounts of purified viral components. During the preliminary characterization of potential ts mutants the author also obtained one structural and several symptom mutants which were analysed further (chapter 7, 8 and 9). The properties of the ts mutants are described in chapter 3-7. (Auth.)

  10. Tubule-forming capacity of the movement proteins of alfalfa mosaic virus and brome mosaic virus

    NARCIS (Netherlands)

    Kasteel, D. T.; van der Wel, N. N.; Jansen, K. A.; Goldbach, R. W.; van Lent, J. W.

    1997-01-01

    The structural phenotype of the movement proteins (MPs) of two representatives of the Bromoviridae, alfalfa mosaic virus (AMV) and brome mosaic virus (BMV), was studied in protoplasts. Immunofluorescence microscopy showed that the MPs of these viruses, for which there has been no evidence of a

  11. The Arabidopsis synaptotagmin SYTA regulates the cell-to-cell movement of diverse plant viruses

    Directory of Open Access Journals (Sweden)

    Asako eUchiyama

    2014-11-01

    Full Text Available Synaptotagmins are a large gene family in animals that have been extensively characterized due to their role as calcium sensors to regulate synaptic vesicle exocytosis and endocytosis in neurons, and dense core vesicle exocytosis for hormone secretion from neuroendocrine cells. Thought to be exclusive to animals, synaptotagmins have recently been characterized in Arabidopsis thaliana, in which they comprise a five gene family. Using infectivity and leaf-based functional assays, we have shown that Arabidopsis SYTA regulates endocytosis and marks an endosomal vesicle recycling pathway to regulate movement protein-mediated trafficking of the Begomovirus Cabbage leaf curl virus (CaLCuV and the Tobamovirus Tobacco mosaic virus (TMV through plasmodesmata (Lewis and Lazarowitz, 2010. To determine whether SYTA has a central role in regulating the cell-to-cell trafficking of a wider range of diverse plant viruses, we extended our studies here to examine the role of SYTA in the cell-to-cell movement of additional plant viruses that employ different modes of movement, namely the Potyvirus Turnip mosaic virus (TuMV, the Caulimovirus Cauliflower mosaic virus (CaMV and the Tobamovirus Turnip vein clearing virus (TVCV, which in contrast to TMV does efficiently infect Arabidopsis. We found that both TuMV and TVCV systemic infection, and the cell-to-cell trafficking of the their movement proteins, were delayed in the Arabidopsis Col-0 syta-1 knockdown mutant. In contrast, CaMV systemic infection was not inhibited in syta-1. Our studies show that SYTA is a key regulator of plant virus intercellular movement, being necessary for the ability of diverse cell-to-cell movement proteins encoded by Begomoviruses (CaLCuV MP, Tobamoviruses (TVCV and TMV 30K protein and Potyviruses (TuMV P3N-PIPO to alter PD and thereby mediate virus cell-to-cell spread.

  12. Arabidopsis thaliana peroxidase N

    DEFF Research Database (Denmark)

    Mirza, Osman Asghar; Henriksen, A; Ostergaard, L

    2000-01-01

    The structure of the neutral peroxidase from Arabidopsis thaliana (ATP N) has been determined to a resolution of 1.9 A and a free R value of 20.5%. ATP N has the expected characteristic fold of the class III peroxidases, with a C(alpha) r.m.s.d. of 0.82 A when compared with horseradish peroxidase C...

  13. eFORGE : A Tool for Identifying Cell Type-Specific Signal in Epigenomic Data

    NARCIS (Netherlands)

    Breeze, Charles E.; Paul, Dirk S.; van Dongen, Jenny; Butcher, Lee M.; Ambrose, John C.; Barrett, James E.; Lowe, Robert; Rakyan, Vardhman K.; Iotchkova, Valentina; Frontini, Mattia; Downes, Kate; Ouwehand, Willem H.; Laperle, Jonathan; Jacques, Pierre-ETienne; Bourque, Guillaume; Bergmann, Anke K.; Siebert, Reiner; Vellenga, Edo; Saeed, Sadia; Matarese, Filomena; Martens, Joost H. A.; Stunnenberg, Hendrik G.; Teschendorff, Andrew E.; Herrero, Javier; Birney, Ewan; Dunham, Ian; Beck, Stephan

    2016-01-01

    Epigenome-wide association studies (EWAS) provide an alternative approach for studying human disease through consideration of non-genetic variants such as altered DNA methylation. To advance the complex interpretation of EWAS, we developed eFORGE (http://eforge.cs.ucl.ac.uk/), a new stand-alone and

  14. Quantitative ChIP-Seq Normalization Reveals Global Modulation of the Epigenome

    Directory of Open Access Journals (Sweden)

    David A. Orlando

    2014-11-01

    Full Text Available Epigenomic profiling by chromatin immunoprecipitation coupled with massively parallel DNA sequencing (ChIP-seq is a prevailing methodology used to investigate chromatin-based regulation in biological systems such as human disease, but the lack of an empirical methodology to enable normalization among experiments has limited the precision and usefulness of this technique. Here, we describe a method called ChIP with reference exogenous genome (ChIP-Rx that allows one to perform genome-wide quantitative comparisons of histone modification status across cell populations using defined quantities of a reference epigenome. ChIP-Rx enables the discovery and quantification of dynamic epigenomic profiles across mammalian cells that would otherwise remain hidden using traditional normalization methods. We demonstrate the utility of this method for measuring epigenomic changes following chemical perturbations and show how reference normalization of ChIP-seq experiments enables the discovery of disease-relevant changes in histone modification occupancy.

  15. Comparative epigenomics: an emerging field with breakthrough potential to understand evolution of epigenetic regulation

    Directory of Open Access Journals (Sweden)

    Janine E. Deakin

    2014-12-01

    Full Text Available Epigenetic mechanisms regulate gene expression, thereby mediating the interaction between environment, genotype and phenotype. Changes to epigenetic regulation of genes may be heritable, permitting rapid adaptation of a species to environmental cues. However, most of the current understanding of epigenetic gene regulation has been gained from studies of mice and humans, with only a limited understanding of the conservation of epigenetic mechanisms across divergent taxa. The relative ease at which genome sequence data is now obtained and the advancements made in epigenomics techniques for non-model species provides a basis for carrying out comparative epigenomic studies across a wider range of species, making it possible to start unraveling the evolution of epigenetic mechanisms. We review the current knowledge of epigenetic mechanisms obtained from studying model organisms, give an example of how comparative epigenomics using non-model species is helping to trace the evolutionary history of X chromosome inactivation in mammals and explore the opportunities to study comparative epigenomics in biological systems displaying adaptation between species, such as the immune system and sex determination.

  16. Not all biofluids are created equal: chewing over salivary diagnostics and the epigenome.

    Science.gov (United States)

    Wren, Michael E; Shirtcliff, Elizabeth A; Drury, Stacy S

    2015-03-01

    This article describes progress to date in the characterization of the salivary epigenome and considers the importance of previous work in the salivary microbiome, proteome, endocrine analytes, genome, and transcriptome. PubMed and Web of Science were used to extensively search the existing literature (original research and reviews) related to salivary diagnostics and biomarker development, of which 125 studies were examined. This article was derived from the most relevant 74 sources highlighting the recent state of the evolving field of salivary epigenomics and contributing significantly to the foundational work in saliva-based research. Validation of any new saliva-based diagnostic or analyte will require comparison to previously accepted standards established in blood. Careful attention to the collection, processing, and analysis of salivary analytes is critical for the development and implementation of newer applications that include genomic, transcriptomic, and epigenomic markers. All these factors must be integrated into initial study design. This commentary highlights the appeal of the salivary epigenome for translational applications and its utility in future studies of development and the interface among environment, disease, and health. Copyright © 2015 Elsevier HS Journals, Inc. All rights reserved.

  17. CRISPR Epigenome Editing of AKAP150 in DRG Neurons Abolishes Degenerative IVD-Induced Neuronal Activation.

    Science.gov (United States)

    Stover, Joshua D; Farhang, Niloofar; Berrett, Kristofer C; Gertz, Jason; Lawrence, Brandon; Bowles, Robby D

    2017-09-06

    Back pain is a major contributor to disability and has significant socioeconomic impacts worldwide. The degenerative intervertebral disc (IVD) has been hypothesized to contribute to back pain, but a better understanding of the interactions between the degenerative IVD and nociceptive neurons innervating the disc and treatment strategies that directly target these interactions is needed to improve our understanding and treatment of back pain. We investigated degenerative IVD-induced changes to dorsal root ganglion (DRG) neuron activity and utilized CRISPR epigenome editing as a neuromodulation strategy. By exposing DRG neurons to degenerative IVD-conditioned media under both normal and pathological IVD pH levels, we demonstrate that degenerative IVDs trigger interleukin (IL)-6-induced increases in neuron activity to thermal stimuli, which is directly mediated by AKAP and enhanced by acidic pH. Utilizing this novel information on AKAP-mediated increases in nociceptive neuron activity, we developed lentiviral CRISPR epigenome editing vectors that modulate endogenous expression of AKAP150 by targeted promoter histone methylation. When delivered to DRG neurons, these epigenome-modifying vectors abolished degenerative IVD-induced DRG-elevated neuron activity while preserving non-pathologic neuron activity. This work elucidates the potential for CRISPR epigenome editing as a targeted gene-based pain neuromodulation strategy. Copyright © 2017 The American Society of Gene and Cell Therapy. Published by Elsevier Inc. All rights reserved.

  18. Editing the Epigenome : Overview, Open Questions, and Directions of Future Development

    NARCIS (Netherlands)

    Rots, Marianne G; Jeltsch, Albert

    2018-01-01

    The introduction of CRISPR/Cas has resulted in a strong impulse for the field of gene-targeted epigenome reprogramming. In this approach EpiEditors are applied in cells, which consist of a DNA-binding part for targeting and a functional part to induce chromatin modifications at targeted genome loci.

  19. Mosaic convergence of rodent dentitions.

    Directory of Open Access Journals (Sweden)

    Vincent Lazzari

    Full Text Available BACKGROUND: Understanding mechanisms responsible for changes in tooth morphology in the course of evolution is an area of investigation common to both paleontology and developmental biology. Detailed analyses of molar tooth crown shape have shown frequent homoplasia in mammalian evolution, which requires accurate investigation of the evolutionary pathways provided by the fossil record. The necessity of preservation of an effective occlusion has been hypothesized to functionally constrain crown morphological changes and to also facilitate convergent evolution. The Muroidea superfamily constitutes a relevant model for the study of molar crown diversification because it encompasses one third of the extant mammalian biodiversity. METHODOLOGY/PRINCIPAL FINDINGS: Combined microwear and 3D-topographic analyses performed on fossil and extant muroid molars allow for a first quantification of the relationships between changes in crown morphology and functionality of occlusion. Based on an abundant fossil record and on a well resolved phylogeny, our results show that the most derived functional condition associates longitudinal chewing and non interlocking of cusps. This condition has been reached at least 7 times within muroids via two main types of evolutionary pathways each respecting functional continuity. In the first type, the flattening of tooth crown which induces the removal of cusp interlocking occurs before the rotation of the chewing movement. In the second type however, flattening is subsequent to rotation of the chewing movement which can be associated with certain changes in cusp morphology. CONCLUSION/SIGNIFICANCE: The reverse orders of the changes involved in these different pathways reveal a mosaic evolution of mammalian dentition in which direction of chewing and crown shape seem to be partly decoupled. Either can change in respect to strong functional constraints affecting occlusion which thereby limit the number of the possible

  20. Genome and Epigenome Editing in Mechanistic Studies of Human Aging and Aging-Related Disease.

    Science.gov (United States)

    Lau, Cia-Hin; Suh, Yousin

    2017-01-01

    The recent advent of genome and epigenome editing technologies has provided a new paradigm in which the landscape of the human genome and epigenome can be precisely manipulated in their native context. Genome and epigenome editing technologies can be applied to many aspects of aging research and offer the potential to develop novel therapeutics against age-related diseases. Here, we discuss the latest technological advances in the CRISPR-based genome and epigenome editing toolbox, and provide insight into how these synthetic biology tools could facilitate aging research by establishing in vitro cell and in vivo animal models to dissect genetic and epigenetic mechanisms underlying aging and age-related diseases. We discuss recent developments in the field with the aims to precisely modulate gene expression and dynamic epigenetic landscapes in a spatial and temporal manner in cellular and animal models, by complementing the CRISPR-based editing capability with conditional genetic manipulation tools including chemically inducible expression systems, optogenetics, logic gate genetic circuits, tissue-specific promoters, and the serotype-specific adeno-associated virus. We also discuss how the combined use of genome and epigenome editing tools permits investigators to uncover novel molecular pathways involved in the pathophysiology and etiology conferred by risk variants associated with aging and aging-related disease. A better understanding of the genetic and epigenetic regulatory mechanisms underlying human aging and age-related disease will significantly contribute to the developments of new therapeutic interventions for extending health span and life span, ultimately improving the quality of life in the elderly populations. © 2016 S. Karger AG, Basel.

  1. GENERATION OF GEOMETRIC ORNAMENTS IN ANCIENT MOSAIC ART

    Directory of Open Access Journals (Sweden)

    SASS Ludmila

    2015-06-01

    Full Text Available The paper examines geometrical ornaments from ancient mosaic.We studied the geometric generation by using Computer Aided Graphics for three examples of ancient mosaic: a mosaic of Ancient Corinth, a mosaic of the sacred geometry Flower of Life (exposed in the National Museum of Israel and a mosaic of fortress Masada - Israel. The technique of drawing ancient mosaic is recomposed using computer aided graphics. A program has been developed that can help draw a petal-type arc (semicircle of the mosaic that is the Byzantine church of Masada. Based on these mosaics, other variants of aesthetic images in monochrome or black and white and polychrome were drawn, all of which can be materialized in decorative art to embellish various surfaces: walls, floors, pools, fountains, etc.

  2. MONOCLONAL ANTIBODIES TO IDENTIFY TOMATO MOSAIC TOBAMOVIRUS (TOMV

    Directory of Open Access Journals (Sweden)

    Duarte Keila M.R.

    2001-01-01

    Full Text Available Monoclonal antibodies were obtained against Tomato mosaic tobamovirus (ToMV isolated in Brazil. One antibody (8G7G2 isotyped as IgG2b (kappa light chain showed strong specificity and very low cross reaction with the Tobacco mosaic virus (TMV. It can be used in identification of tomato mosaic virus (ToMV.

  3. Evaluation of the minimal replication time of Cauliflower mosaic virus in different hosts

    International Nuclear Information System (INIS)

    Khelifa, Mounia; Masse, Delphine; Blanc, Stephane; Drucker, Martin

    2010-01-01

    Though the duration of a single round of replication is an important biological parameter, it has been determined for only few viruses. Here, this parameter was determined for Cauliflower mosaic virus (CaMV) in transfected protoplasts from different hosts: the highly susceptible Arabidopsis and turnip, and Nicotiana benthamiana, where CaMV accumulates only slowly. Four methods of differing sensitivity were employed: labelling of (1) progeny DNA and (2) capsid protein, (3) immunocapture PCR,, and (4) progeny-specific PCR. The first progeny virus was detected about 21 h after transfection. This value was confirmed by all methods, indicating that our estimate was not biased by the sensitivity of the detection method, and approximated the actual time required for one round of CaMV replication. Unexpectedly, the replication kinetics were similar in the three hosts; suggesting that slow accumulation of CaMV in Nicotiana plants is determined by non-optimal interactions in other steps of the infection cycle.

  4. Genetics Home Reference: mosaic variegated aneuploidy syndrome

    Science.gov (United States)

    ... In MVA syndrome, growth before birth is slow (intrauterine growth restriction). After birth, affected individuals continue to grow at ... InfoSearch: Warburton Anyane Yeboa syndrome KidsHealth from Nemours: Intrauterine Growth Restriction ... mosaic variegated aneuploidy syndrome 1 MalaCards: ...

  5. Retro reflective glass mosaic; Mosaico Vitreo Retrorreflectante

    Energy Technology Data Exchange (ETDEWEB)

    Belda, A.; Orts, M. J.; Viciano, F.; Lucas, F.

    2012-07-01

    Salquisa and Alttoglass have developed a very innovative product : the retro reflective glass mosaic. This new product can be used in both horizontal and vertical signposting and also in interior design and architecture. This particular product has many advantages compare to the traditional methods used for signposting, design or architecture. One of them is that the product is mainly made of glass therefore it can last much longer than paints for example. The used of glass mosaic for civil engineering it is opened up especially for signposting and it contributes to improve visibility at night not only in standard conditions but also in the hard ones such as wind, fog or rain at nighttimes. Higher visibility = higher security. We should remember that a high percentage of accidents occur under rain conditions at night. The glass mosaic is presented in a mesh which allows the use in both plane and curve surfaces in signposting, interior design and architecture. The retro reflective effect last under the water therefore the mosaic can be fixed in ornamental and decorative fountains, swimming pools, etc. Furthermore, the retro reflective effect can also be applied on big size ceramic tiles. This project was developed along with the Institute of Ceramic Technology (ITC), it was supported by the Center for Industrial Technological Development (CDTI) and it is also patented. (Author)

  6. Multicultural Mosaic: A Family Book Club.

    Science.gov (United States)

    Dias-Mitchell, Laurie; Harris, Elizabeth

    2001-01-01

    Authors, a library media specialist and a literature/language arts teacher, both recipients of Theodore R. Sizer Fellowships, describe their joint project, "Multicultural Mosaic: A Family Book Club." Their proposal was to strengthen the home-school connection by establishing a book club accessible to all middle and high school students…

  7. Educating Multicultural Citizens: Melting Pot or Mosaic?

    Science.gov (United States)

    Entwistle, Harold

    2000-01-01

    Explores the educational metaphors of the melting pot (immigrants must assimilate into the mainstream culture) and the cultural mosaic (immigrants should retain their cultural identifies). Focuses on such issues as multiculturalism and justice for immigrants, social cohesion, the notion of cultural relativism, and differing conceptions of culture.…

  8. Document image mosaicing: A novel approach

    Indian Academy of Sciences (India)

    R. Narasimhan (Krishtel eMaging) 1461 1996 Oct 15 13:05:22

    MS received 28 April 2003; revised 22 July 2003. Abstract. ... Hence, document image mosaicing is the process of merging split ..... Case 2: Algorithm 2 is an improved version of algorithm 1 which eliminates the drawbacks of ... One of the authors (PS) thanks the All India Council for Technical Education, New Delhi for.

  9. Disruption of Ethylene Responses by Turnip mosaic virus Mediates Suppression of Plant Defense against the Green Peach Aphid Vector.

    Science.gov (United States)

    Casteel, Clare L; De Alwis, Manori; Bak, Aurélie; Dong, Haili; Whitham, Steven A; Jander, Georg

    2015-09-01

    Plants employ diverse responses mediated by phytohormones to defend themselves against pathogens and herbivores. Adapted pathogens and herbivores often manipulate these responses to their benefit. Previously, we demonstrated that Turnip mosaic virus (TuMV) infection suppresses callose deposition, an important plant defense induced in response to feeding by its aphid vector, the green peach aphid (Myzus persicae), and increases aphid fecundity compared with uninfected control plants. Further, we determined that production of a single TuMV protein, Nuclear Inclusion a-Protease (NIa-Pro) domain, was responsible for changes in host plant physiology and increased green peach aphid reproduction. To characterize the underlying molecular mechanisms of this phenomenon, we examined the role of three phytohormone signaling pathways, jasmonic acid, salicylic acid, and ethylene (ET), in TuMV-infected Arabidopsis (Arabidopsis thaliana), with or without aphid herbivory. Experiments with Arabidopsis mutants ethylene insensitive2 and ethylene response1, and chemical inhibitors of ET synthesis and perception (aminoethoxyvinyl-glycine and 1-methylcyclopropene, respectively), show that the ET signaling pathway is required for TuMV-mediated suppression of Arabidopsis resistance to the green peach aphid. Additionally, transgenic expression of NIa-Pro in Arabidopsis alters ET responses and suppresses aphid-induced callose formation in an ET-dependent manner. Thus, disruption of ET responses in plants is an additional function of NIa-Pro, a highly conserved potyvirus protein. Virus-induced changes in ET responses may mediate vector-plant interactions more broadly and thus represent a conserved mechanism for increasing transmission by insect vectors across generations. © 2015 American Society of Plant Biologists. All Rights Reserved.

  10. The openness of pluripotent epigenome - Defining the genomic integrity of stemness for regenerative medicine

    Directory of Open Access Journals (Sweden)

    Xuejun H Parsons

    2014-02-01

    Full Text Available This article is an editorial, and it doesn't include an abstract. Full text of this article is available in HTML and PDF.Cite this article as: Parsons XH. The openness of pluripotent epigenome - Defining the genomic Integrity of stemness for regenerative medicine. Int J Cancer Ther Oncol 2014; 2(1:020114.DOI: http://dx.doi.org/10.14319/ijcto.0201.14

  11. Prader-Willi Syndrome: The Disease that Opened up Epigenomic-Based Preemptive Medicine

    Directory of Open Access Journals (Sweden)

    Takeo Kubota

    2016-03-01

    Full Text Available Prader-Willi syndrome (PWS is a congenital neurodevelopmental disorder caused by loss of function of paternally expressed genes on chromosome 15 due to paternal deletion of 15q11–q13, maternal uniparental disomy for chromosome 15, or an imprinting mutation. We previously developed a DNA methylation-based PCR assay to identify each of these three genetic causes of PWS. The assay enables straightforward and rapid diagnosis during infancy and therefore allows early intervention such as nutritional management, physical therapy, or growth hormone treatment to prevent PWS patients from complications such as obesity and type 2 diabetes. It is known that various environmental factors induce epigenomic changes during the perinatal period, which increase the risk of adult diseases such as type 2 diabetes and intellectual disabilities. Therefore, a similar preemptive approach as used in PWS would also be applicable to acquired disorders and would make use of environmentally-introduced “epigenomic signatures” to aid development of early intervention strategies that take advantage of “epigenomic reversibility”.

  12. Distinct epigenomic landscapes of pluripotent and lineage-committed human cells.

    Science.gov (United States)

    Hawkins, R David; Hon, Gary C; Lee, Leonard K; Ngo, Queminh; Lister, Ryan; Pelizzola, Mattia; Edsall, Lee E; Kuan, Samantha; Luu, Ying; Klugman, Sarit; Antosiewicz-Bourget, Jessica; Ye, Zhen; Espinoza, Celso; Agarwahl, Saurabh; Shen, Li; Ruotti, Victor; Wang, Wei; Stewart, Ron; Thomson, James A; Ecker, Joseph R; Ren, Bing

    2010-05-07

    Human embryonic stem cells (hESCs) share an identical genome with lineage-committed cells, yet possess the remarkable properties of self-renewal and pluripotency. The diverse cellular properties in different cells have been attributed to their distinct epigenomes, but how much epigenomes differ remains unclear. Here, we report that epigenomic landscapes in hESCs and lineage-committed cells are drastically different. By comparing the chromatin-modification profiles and DNA methylomes in hESCs and primary fibroblasts, we find that nearly one-third of the genome differs in chromatin structure. Most changes arise from dramatic redistributions of repressive H3K9me3 and H3K27me3 marks, which form blocks that significantly expand in fibroblasts. A large number of potential regulatory sequences also exhibit a high degree of dynamics in chromatin modifications and DNA methylation. Additionally, we observe novel, context-dependent relationships between DNA methylation and chromatin modifications. Our results provide new insights into epigenetic mechanisms underlying properties of pluripotency and cell fate commitment.

  13. Chapter 4 genomics, transcriptomics, and epigenomics in traumatic brain injury research.

    Science.gov (United States)

    Puccio, Ava M; Alexander, Sheila

    2015-01-01

    The long-term effects and significant impact of the full spectrum of traumatic brain injury (TBI) has received increased attention in recent years. Despite increased research efforts, there has been little movement toward improving outcomes for the survivors of TBI. TBI is a heterogeneous condition with a complex biological response, and significant variability in human recovery contributes to the difficulty in identifying therapeutics that improve outcomes. Personalized medicine, identifying the best course of treatment for a given individual based on individual characteristics, has great potential to improve recovery for TBI survivors. The advances in medical genetics and genomics over the past 20 years have increased our understanding of many biological processes. A substantial amount of research has focused on the genomic, transcriptomic, and epigenomic profiles in many health and disease states, including recovery from TBI. The focus of this review chapter is to describe the current state of the science in genomic, transcriptomic, and epigenomic research in the TBI population. There have been some advancements toward understanding the genomic, transcriptomic, and epigenomic processes in humans, but much of this work remains at the preclinical stage. This current evidence does improve our understanding of TBI recovery, but also serves as an excellent platform upon which to build further study toward improved outcomes for this population.

  14. Epigenome engineering in cancer: fairytale or a realistic path to the clinic?

    Directory of Open Access Journals (Sweden)

    Fahimeh eFalahi

    2015-02-01

    Full Text Available Epigenetic modifications such as histone post-transcriptional modifications and DNA methylation organize the DNA in the nucleus of eukaryotic cells and are critical for the spatio-temporal regulation of gene expression. These epigenetic modifications are reversible and precisely regulated by epigenetic enzymes. In addition to genetic mutations, epigenetic modifications are highly disrupted in cancer relative to normal tissues. Many epigenetic alterations (epi-mutations are associated with aberrations in the expression and/or activity of epigenetic enzymes. Thus, epigenetic regulators have emerged as prime targets for cancer therapy. Currently, several inhibitors of epigenetic enzymes (epi-drugs have been approved for use in the clinic to treat cancer patients with hematological malignancies. However, one potential disadvantage of epi-drugs is their lack of locus-selective specificity, which may result in the over-expression of undesirable parts of the genome. The emerging and rapidly growing field of epigenome engineering has opened new grounds for improving epigenetic therapy in view of reducing the genome-wide off-target effects of the treatment. In the current review, we will first describe the language of epigenetic modifications and their involvement in cancer. Next, we will overview the current strategies for engineering of artificial DNA binding domains in order to manipulate and ultimately normalize the aberrant landscape of the cancer epigenome (epigenome engineering. Lastly, the potential clinical applications of these emerging genome-engineering approaches will be discussed.

  15. Transitioning from genotypes to epigenotypes: why the time has come for medulloblastoma epigenomics.

    Science.gov (United States)

    Batora, N V; Sturm, D; Jones, D T W; Kool, M; Pfister, S M; Northcott, P A

    2014-04-04

    Recent advances in genomic technologies have allowed for tremendous progress in our understanding of the biology underlying medulloblastoma, a malignant childhood brain tumor. Consensus molecular subgroups have been put forth by the pediatric neuro-oncology community and next-generation genomic studies have led to an improved description of driver genes and pathways somatically altered in these subgroups. In contrast to the impressive pace at which advances have been made at the level of the medulloblastoma genome, comparable studies of the epigenome have lagged behind. Complementary data yielded from genomic sequencing and copy number profiling have verified frequent targeting of chromatin modifiers in medulloblastoma, highly suggestive of prominent epigenetic deregulation in the disease. Past studies of DNA methylation-dependent gene silencing and microRNA expression analyses further support the concept of medulloblastoma as an epigenetic disease. In this Review, we aim to summarize the key findings of past reports pertaining to medulloblastoma epigenetics as well as recent and ongoing genomic efforts linking somatic alterations of the genome with inferred deregulation of the epigenome. In addition, we predict what is on the horizon for medulloblastoma epigenetics and how aberrant changes in the medulloblastoma epigenome might serve as an attractive target for future therapies. Copyright © 2013 IBRO. Published by Elsevier Ltd. All rights reserved.

  16. An Arabidopsis callose synthase

    DEFF Research Database (Denmark)

    Ostergaard, Lars; Petersen, Morten; Mattsson, Ole

    2002-01-01

    in the Arabidopsis mpk4 mutant which exhibits systemic acquired resistance (SAR), elevated beta-1,3-glucan synthase activity, and increased callose levels. In addition, AtGsl5 is a likely target of salicylic acid (SA)-dependent SAR, since AtGsl5 mRNA accumulation is induced by SA in wild-type plants, while...... expression of the nahG salicylate hydroxylase reduces AtGsl5 mRNA levels in the mpk4 mutant. These results indicate that AtGsl5 is likely involved in callose synthesis in flowering tissues and in the mpk4 mutant....

  17. Matrix metalloproteinases operate redundantly in Arabidopsis immunity against necrotrophic and biotrophic fungal pathogens.

    Directory of Open Access Journals (Sweden)

    Puyan Zhao

    Full Text Available Matrix metalloproteinases (MMPs are evolutionarily conserved and multifunctional effector molecules playing pivotal roles in development and homeostasis. In this study we explored the involvement of the five Arabidopsis thaliana At-MMPs in plant defence against microbial pathogens. Expression of At2-MMP was most responsive to inoculation with fungi and a bacterial pathogen followed by At3-MMP and At5-MMP, while At1-MMP and At4-MMP were non-responsive to these biotic stresses. Loss-of-function mutants for all tested At-MMPs displayed increased susceptibility to the necrotrophic fungus Botrytis cinerea and double mutant at2,3-mmp and triple mutant at2,3,5-mmp plants developed even stronger symptoms. Consistent with this, transgenic Arabidopsis plants that expressed At2-MMP constitutively under the Cauliflower mosaic virus 35S promoter showed enhanced resistance to the necrotrophic pathogen. Similarly, resistance to the biotrophic Arabidopsis powdery mildew fungus Golovinomyces orontii was also compromised particularly in the at2,3-mmp / at2,3,5-mmp multiplex mutants, and increased in At2-MMP overexpressor plants. The degree of disease resistance of at-mmp mutants and At2-MMP overexpressor plants also correlated positively with the degree of MAMP-triggered callose deposition in response to the bacterial flagellin peptide flg22, suggesting that matrix metalloproteinases contribute to pattern-triggered immunity (PTI in interactions of Arabidopsis with necrotrophic and biotrophic pathogens.

  18. Towards Luminescence Dating Of Mosaic Glass

    Science.gov (United States)

    Galli, A.; Martini, M.; Sibila, E.; Villa, I.

    The possibility of dating archaeological glass by means of luminescent techniques has been investigated in recent years, despite the difficulties of this application, mainly linked to the amorphous structure of the material. We focused in particular on mosaic glass, after the encouraging results obtained on byzantine and medieval samples. Further studies were devoted to the comprehension of the luminescent mechanisms in silica glasses, and to the investigation of the relationships between luminescence, colouring or opacifier ions and crystalline phase of the vitreous matrix. The results of a study on the dosimetric characteristics of thermoluminescence (TL) and Optically Stimulated Luminescence (OSL) of a few medieval blue-green mosaic glasses from the San Lorenzo church (Milan) are presented, and the experimental protocols established to identify their suitability for dating are discussed.

  19. Mosaic Turner syndrome and hyperinsulinaemic hypoglycaemia

    DEFF Research Database (Denmark)

    Alkhayyat, H.; Christesen, Henrik Thybo; Steer, J.

    2006-01-01

    BACKGROUND: A common and well recognised feature of Turner's syndrome (partial or total monosomy X) is impaired glucose tolerance or type 2 diabetes mellitus. A small percentage of patients with Turner's syndrome have a complex mosaic karyotype with atypical clinical features and mental retardation....... METHODS/PATIENT: We report the first case of a child with a complex mosaic Turner genotype and hyperinsulinaemic hypoglycaemia responsive to diazoxide therapy. RESULTS: Cytogenetic analysis showed four cell lines: one with 45,X; the others with an additional small ring chromosome, a small marker...... chromosome, and both the ring and marker chromosomes, respectively. FISH studies showed the abnormal chromosomes to originate from an X. The X inactivation locus (XIST) was present in the ring, but not in the marker chromosome. CONCLUSIONS: The recognition of hypoglycaemia in children with atypical Turner...

  20. Mosaic Turner syndrome associated with schizophrenia.

    Science.gov (United States)

    Jung, Sook Young; Park, Joo Won; Kim, Dong Hyun; Jun, Yong Hoon; Lee, Jeong Seop; Lee, Ji Eun

    2014-03-01

    Turner syndrome is a sex-chromosome disorder; occurring in 1 in 2,500 female births. There are sporadic few case reports of concomitant Turner syndrome with schizophrenia worldwide. Most Turner females had a 45,X monosomy, whereas the majority of comorbidity between Turner syndrome and schizophrenia had a mosaic karyotype (45,X/46,XX). We present a case of a 21-year-old woman with Turner syndrome, mosaic karyotype (45,X/46,XX), showing mental retardation, hypothyroidism, and schizophrenia. HOPA gene within Xq13 is related to mental retardation, hypothyroidism, and schizophrenia. Our case may be a potential clue which supports the hypothesis for involvement of genes on X chromosome in development of schizophrenia. Further studies including comorbid cases reports are need in order to discern the cause of schizophrenia in patients having Turner syndrome.

  1. Distribution of Fig Mosaic in Jordan

    OpenAIRE

    Khalil I. Al-Mughrabi; Ghandi H. Anfoka

    2000-01-01

    Fig mosaic (FM) is one of the most important diseases of figs in Jordan. A nationwide survey was conducted to determine the incidence and severity of this disease in trees and in seedlings propagated by cuttings in orchards and nurseries in 13 provinces and cities all over the country. Cultivars surveyed included Khdari, Mwazi, Zraki, Khartamani, Dafoori, Turki, Hamari, Esaili, Ajlouni, in addition to an Italian and a French cultivar. Disease severity varied from moderately severe...

  2. Photorepair mutants of Arabidopsis

    International Nuclear Information System (INIS)

    Jiang, C.Z.; Yee, J.; Mitchell, D.L.; Britt, A.B.

    1997-01-01

    UV radiation induces two major DNA damage products, the cyclobutane pyrimidine dimer (CPD) and, at a lower frequency, the pyrimidine (6-4) pyrimidinone dimer (6-4 product). Although Escherichia coli and Saccharomyces cerevisiae produce a CPD-specific photolyase that eliminates only this class of dimer, Arabidopsis thaliana, Drosophila melanogaster, Crotalus atrox, and Xenopus laevis have recently been shown to photoreactivate both CPDs and 6-4 products. We describe the isolation and characterization of two new classes of mutants of Arabidopsis, termed uvr2 and uvr3, that are defective in the photoreactivation of CPDs and 6-4 products, respectively. We demonstrate that the CPD photolyase mutation is genetically linked to a DNA sequence encoding a type II (metazoan) CPD photolyase. In addition, we are able to generate plants in which only CPDs or 6-4 products are photoreactivated in the nuclear genome by exposing these mutants to UV light and then allowing them to repair one or the other class of dimers. This provides us with a unique opportunity to study the biological consequences of each of these two major UV-induced photoproducts in an intact living system

  3. Arabidopsis peroxisome proteomics

    Directory of Open Access Journals (Sweden)

    John D. Bussell

    2013-04-01

    Full Text Available The analytical depth of investigation of the peroxisomal proteome of the model plant Arabidopsis thaliana has not yet reached that of other major cellular organelles such as chloroplasts or mitochondria. This is primarily due to the difficulties associated with isolating and obtaining purified samples of peroxisomes from Arabidopsis. So far only a handful of research groups have been successful in obtaining such fractions. To make things worse, enriched peroxisome fractions frequently suffer from significant organellar contamination, lowering confidence in localization assignment of the identified proteins. As with other cellular compartments, identification of peroxisomal proteins forms the basis for investigations of the dynamics of the peroxisomal proteome. It is therefore not surprising that, in terms of functional analyses by proteomic means, there remains a considerable gap between peroxisomes and chloroplasts or mitochondria. Alternative strategies are needed to overcome the obstacle of hard-to-obtain organellar fractions. This will help to close the knowledge gap between peroxisomes and other organelles and provide a full picture of the physiological pathways shared between organelles. In this review we briefly summarize the status quo and discuss some of the methodological alternatives to classic organelle proteomic approaches.

  4. KARAKTERISASICYMBIDIUM MOSAIC VIRUS (CYMMV PADA TANAMAN ANGGREK

    Directory of Open Access Journals (Sweden)

    KHAMDAN KHALIMI

    2012-11-01

    Full Text Available Characterization ofCymbidium mosaic virus (CymMV on Orchid Plant Orchids are affected by more virus disease problems than most crops, reducing their commercial values considerably. Orchid viruses are widespread in cultivated orchids, withCymbidium mosaic potexvirus (CymMV being the most prevalent. CymMV high incidence in cultivated orchids has been attributed to the stability and ease of transmission of this virus through cultural practices. CymMV induces floral and foliar necrosis. The virus also reduce plant vigor and lower flower quality, which affect their economic value. The objective of the research is to characterize the virus causing mosaic or chlorotic and necrotic on orchids in West Java. A reverse transcription-polymerase chain reaction (RT- PCR assays using oligonucleotide primers specific to CymMV were also successfully amplified the regions of the coat protein (CP gene of the virus. Analysis by using sodium dodecyl sulphate- polyacrylamide gel electrophoresis (SDS-PAGE revealed that the virus have a major structural protein with an estimated molecular weight of 28 kDa. Aligments of partial nucleotide sequences of the CP gene displayed 86 to 92% homology to CymMV isolates from other countries.

  5. Reassessing Jacob Strauss and the Mosaic Code

    Directory of Open Access Journals (Sweden)

    Joel McDurmon

    2012-01-01

    Full Text Available This article reviewed claims made by modern scholars Ford Lewis Battles, G.H. Williams, and Theodore Tappert concerning the views of Jacob Strauss (1480–1530, court preacher at Eisenach, particularly in regard to the imposition of Mosaic Law upon the civil realm. Most pointedly, Battles claims Strauss proposed to replace European civil law completely with the ‘entire Mosaic code’. This study examined Strauss’s relevant writings to determine his position on Mosaic Law and civil law and demonstrated that the claims of Battles, Williams, and Tappert were not supported by the primary source evidence. Selections from Strauss’ 51 theses on usury are translated into English for the first time. To a much lesser degree, this study addressed the issue in regard to the Weimar court preacher Wolfgang Stein, against whom the same claims were made. A paucity of evidence rendered those claims dubious in his case. In the end we were left only with unsubstantiated second-hand claims against these men.

  6. Transgenic Arabidopsis Gene Expression System

    Science.gov (United States)

    Ferl, Robert; Paul, Anna-Lisa

    2009-01-01

    The Transgenic Arabidopsis Gene Expression System (TAGES) investigation is one in a pair of investigations that use the Advanced Biological Research System (ABRS) facility. TAGES uses Arabidopsis thaliana, thale cress, with sensor promoter-reporter gene constructs that render the plants as biomonitors (an organism used to determine the quality of the surrounding environment) of their environment using real-time nondestructive Green Fluorescent Protein (GFP) imagery and traditional postflight analyses.

  7. The genome of Arabidopsis thaliana.

    OpenAIRE

    Goodman, H M; Ecker, J R; Dean, C

    1995-01-01

    Arabidopsis thaliana is a small flowering plant that is a member of the family cruciferae. It has many characteristics--diploid genetics, rapid growth cycle, relatively low repetitive DNA content, and small genome size--that recommend it as the model for a plant genome project. The current status of the genetic and physical maps, as well as efforts to sequence the genome, are presented. Examples are given of genes isolated by using map-based cloning. The importance of the Arabidopsis project ...

  8. Efficient Plastid Transformation in Arabidopsis.

    Science.gov (United States)

    Yu, Qiguo; Lutz, Kerry Ann; Maliga, Pal

    2017-09-01

    Plastid transformation is routine in tobacco ( Nicotiana tabacum ) but 100-fold less frequent in Arabidopsis ( Arabidopsis thaliana ), preventing its use in plastid biology. A recent study revealed that null mutations in ACC2 , encoding a plastid-targeted acetyl-coenzyme A carboxylase, cause hypersensitivity to spectinomycin. We hypothesized that plastid transformation efficiency should increase in the acc2 background, because when ACC2 is absent, fatty acid biosynthesis becomes dependent on translation of the plastid-encoded ACC β-carboxylase subunit. We bombarded ACC2 -defective Arabidopsis leaves with a vector carrying a selectable spectinomycin resistance ( aadA ) gene and gfp , encoding the green fluorescence protein GFP. Spectinomycin-resistant clones were identified as green cell clusters on a spectinomycin medium. Plastid transformation was confirmed by GFP accumulation from the second open reading frame of a polycistronic messenger RNA, which would not be translated in the cytoplasm. We obtained one to two plastid transformation events per bombarded sample in spectinomycin-hypersensitive Slavice and Columbia acc2 knockout backgrounds, an approximately 100-fold enhanced plastid transformation frequency. Slavice and Columbia are accessions in which plant regeneration is uncharacterized or difficult to obtain. A practical system for Arabidopsis plastid transformation will be obtained by creating an ACC2 null background in a regenerable Arabidopsis accession. The recognition that the duplicated ACCase in Arabidopsis is an impediment to plastid transformation provides a rational template to implement plastid transformation in related recalcitrant crops. © 2017 American Society of Plant Biologists. All Rights Reserved.

  9. Constitutional trisomy 8 mosaicism syndrome: case report and review.

    Science.gov (United States)

    Udayakumar, Achandira M; Al-Kindy, Adila

    2013-12-01

    Trisomy 8 mosaicism (Warkany syndrome) is a rare viable condition with variable phenotypes, ranging from mild dysmorphic features to severe malformations. Karyotyping and fluorescence in-situ hybridization potentially help detecting this low mosaic clone to confirm the diagnosis of patients with classical and unusual clinical presentations. This report reviews few previous cases to describe our case - a boy who had trisomy 8 mosaicism with severe dysmorphic features, born to a consanguineous Arabic couple. This study concludes that careful cytogenetic diagnoses of trisomy 8 mosaicism is essential for appropriate management and follow up of this rare disorder.

  10. The Contribution of Mosaic Variants to Autism Spectrum Disorder.

    Science.gov (United States)

    Freed, Donald; Pevsner, Jonathan

    2016-09-01

    De novo mutation is highly implicated in autism spectrum disorder (ASD). However, the contribution of post-zygotic mutation to ASD is poorly characterized. We performed both exome sequencing of paired samples and analysis of de novo variants from whole-exome sequencing of 2,388 families. While we find little evidence for tissue-specific mosaic mutation, multi-tissue post-zygotic mutation (i.e. mosaicism) is frequent, with detectable mosaic variation comprising 5.4% of all de novo mutations. We identify three mosaic missense and likely-gene disrupting mutations in genes previously implicated in ASD (KMT2C, NCKAP1, and MYH10) in probands but none in siblings. We find a strong ascertainment bias for mosaic mutations in probands relative to their unaffected siblings (p = 0.003). We build a model of de novo variation incorporating mosaic variants and errors in classification of mosaic status and from this model we estimate that 33% of mosaic mutations in probands contribute to 5.1% of simplex ASD diagnoses (95% credible interval 1.3% to 8.9%). Our results indicate a contributory role for multi-tissue mosaic mutation in some individuals with an ASD diagnosis.

  11. The Contribution of Mosaic Variants to Autism Spectrum Disorder.

    Directory of Open Access Journals (Sweden)

    Donald Freed

    2016-09-01

    Full Text Available De novo mutation is highly implicated in autism spectrum disorder (ASD. However, the contribution of post-zygotic mutation to ASD is poorly characterized. We performed both exome sequencing of paired samples and analysis of de novo variants from whole-exome sequencing of 2,388 families. While we find little evidence for tissue-specific mosaic mutation, multi-tissue post-zygotic mutation (i.e. mosaicism is frequent, with detectable mosaic variation comprising 5.4% of all de novo mutations. We identify three mosaic missense and likely-gene disrupting mutations in genes previously implicated in ASD (KMT2C, NCKAP1, and MYH10 in probands but none in siblings. We find a strong ascertainment bias for mosaic mutations in probands relative to their unaffected siblings (p = 0.003. We build a model of de novo variation incorporating mosaic variants and errors in classification of mosaic status and from this model we estimate that 33% of mosaic mutations in probands contribute to 5.1% of simplex ASD diagnoses (95% credible interval 1.3% to 8.9%. Our results indicate a contributory role for multi-tissue mosaic mutation in some individuals with an ASD diagnosis.

  12. Identification of histone modifications in biomedical text for supporting epigenomic research.

    Science.gov (United States)

    Kolárik, Corinna; Klinger, Roman; Hofmann-Apitius, Martin

    2009-01-30

    Posttranslational modifications of histones influence the structure of chromatine and in such a way take part in the regulation of gene expression. Certain histone modification patterns, distributed over the genome, are connected to cell as well as tissue differentiation and to the adaption of organisms to their environment. Abnormal changes instead influence the development of disease states like cancer. The regulation mechanisms for modifying histones and its functionalities are the subject of epigenomics investigation and are still not completely understood. Text provides a rich resource of knowledge on epigenomics and modifications of histones in particular. It contains information about experimental studies, the conditions used, and results. To our knowledge, no approach has been published so far for identifying histone modifications in text. We have developed an approach for identifying histone modifications in biomedical literature with Conditional Random Fields (CRF) and for resolving the recognized histone modification term variants by term standardization. For the term identification F1 measures of 0.84 by 10-fold cross-validation on the training corpus and 0.81 on an independent test corpus have been obtained. The standardization enabled the correct transformation of 96% of the terms from training and 98% from test the corpus. Due to the lack of terminologies exhaustively covering specific histone modification types, we developed a histone modification term hierarchy for use in a semantic text retrieval system. The developed approach highly improves the retrieval of articles describing histone modifications. Since text contains context information about performed studies and experiments, the identification of histone modifications is the basis for supporting literature-based knowledge discovery and hypothesis generation to accelerate epigenomic research.

  13. Epigenetic transgenerational actions of vinclozolin on promoter regions of the sperm epigenome.

    Directory of Open Access Journals (Sweden)

    Carlos Guerrero-Bosagna

    2010-09-01

    Full Text Available Previous observations have demonstrated that embryonic exposure to the endocrine disruptor vinclozolin during gonadal sex determination promotes transgenerational adult onset disease such as male infertility, kidney disease, prostate disease, immune abnormalities and tumor development. The current study investigates genome-wide promoter DNA methylation alterations in the sperm of F3 generation rats whose F0 generation mother was exposed to vinclozolin. A methylated DNA immunoprecipitation with methyl-cytosine antibody followed by a promoter tilling microarray (MeDIP-Chip procedure was used to identify 52 different regions with statistically significant altered methylation in the sperm promoter epigenome. Mass spectrometry bisulfite analysis was used to map the CpG DNA methylation and 16 differential DNA methylation regions were confirmed, while the remainder could not be analyzed due to bisulfite technical limitations. Analysis of these validated regions identified a consensus DNA sequence (motif that associated with 75% of the promoters. Interestingly, only 16.8% of a random set of 125 promoters contained this motif. One candidate promoter (Fam111a was found to be due to a copy number variation (CNV and not a methylation change, suggesting initial alterations in the germline epigenome may promote genetic abnormalities such as induced CNV in later generations. This study identifies differential DNA methylation sites in promoter regions three generations after the initial exposure and identifies common genome features present in these regions. In addition to primary epimutations, a potential indirect genetic abnormality was identified, and both are postulated to be involved in the epigenetic transgenerational inheritance observed. This study confirms that an environmental agent has the ability to induce epigenetic transgenerational changes in the sperm epigenome.

  14. Epigenetic transgenerational actions of vinclozolin on promoter regions of the sperm epigenome.

    Science.gov (United States)

    Guerrero-Bosagna, Carlos; Settles, Matthew; Lucker, Ben; Skinner, Michael K

    2010-09-30

    Previous observations have demonstrated that embryonic exposure to the endocrine disruptor vinclozolin during gonadal sex determination promotes transgenerational adult onset disease such as male infertility, kidney disease, prostate disease, immune abnormalities and tumor development. The current study investigates genome-wide promoter DNA methylation alterations in the sperm of F3 generation rats whose F0 generation mother was exposed to vinclozolin. A methylated DNA immunoprecipitation with methyl-cytosine antibody followed by a promoter tilling microarray (MeDIP-Chip) procedure was used to identify 52 different regions with statistically significant altered methylation in the sperm promoter epigenome. Mass spectrometry bisulfite analysis was used to map the CpG DNA methylation and 16 differential DNA methylation regions were confirmed, while the remainder could not be analyzed due to bisulfite technical limitations. Analysis of these validated regions identified a consensus DNA sequence (motif) that associated with 75% of the promoters. Interestingly, only 16.8% of a random set of 125 promoters contained this motif. One candidate promoter (Fam111a) was found to be due to a copy number variation (CNV) and not a methylation change, suggesting initial alterations in the germline epigenome may promote genetic abnormalities such as induced CNV in later generations. This study identifies differential DNA methylation sites in promoter regions three generations after the initial exposure and identifies common genome features present in these regions. In addition to primary epimutations, a potential indirect genetic abnormality was identified, and both are postulated to be involved in the epigenetic transgenerational inheritance observed. This study confirms that an environmental agent has the ability to induce epigenetic transgenerational changes in the sperm epigenome.

  15. Reference: 783 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available xpression of the Arabidopsis 10-kilodalton acyl-coenzyme A-binding protein ACBP6 en...phospholipid metabolism in Arabidopsis, including the possibility of ACBP6 in the cytosolic trafficking of phosphatidylcholine. Overe

  16. Reference: 774 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available an essential gene, the disruption of which causes embryonic lethality. Plants carrying a hypomorphic smg7 mu...e progression from anaphase to telophase in the second meiotic division in Arabidopsis. Arabidopsis SMG7 is

  17. JERS-1 Synthetic Aperture Radar, 1- km Mosaic, Amazon Basin: 1995-1996

    Data.gov (United States)

    National Aeronautics and Space Administration — ABSTRACT: This data set contains two image mosaics of L-band radar backscatter and two image mosaics of first order texture. The two backscatter images are mosaics...

  18. Ovarian cancer plasticity and epigenomics in the acquisition of a stem-like phenotype

    Directory of Open Access Journals (Sweden)

    Berry Nicholas B

    2008-11-01

    Full Text Available Abstract Aggressive epithelial ovarian cancer (EOC is genetically and epigenetically distinct from normal ovarian surface epithelial cells (OSE and early neoplasia. Co-expression of epithelial and mesenchymal markers in EOC suggests an involvement of epithelial-mesenchymal transition (EMT in cancer initiation and progression. This phenomenon is often associated with acquisition of a stem cell-like phenotype and chemoresistance that correlate with the specific gene expression patterns accompanying transformation, revealing a plasticity of the ovarian cancer cell genome during disease progression. Differential gene expressions between normal and transformed cells reflect the varying mechanisms of regulation including genetic changes like rearrangements within the genome, as well as epigenetic changes such as global genomic hypomethylation with localized promoter CpG island hypermethylation. The similarity of gene expression between ovarian cancer cells and the stem-like ovarian cancer initiating cells (OCIC are surprisingly also correlated with epigenetic mechanisms of gene regulation in normal stem cells. Both normal and cancer stem cells maintain genetic flexibility by co-placement of activating and/or repressive epigenetic modifications on histone H3. The co-occupancy of such opposing histone marks is believed to maintain gene flexibility and such bivalent histones have been described as being poised for transcriptional activation or epigenetic silencing. The involvement of both-microRNA (miRNA mediated epigenetic regulation, as well as epigenetic-induced changes in miRNA expression further highlight an additional complexity in cancer stem cell epigenomics. Recent advances in array-based whole-genome/epigenome analyses will continue to further unravel the genomes and epigenomes of cancer and cancer stem cells. In order to illuminate phenotypic signatures that delineate ovarian cancer from their associated cancer stem cells, a priority must lie

  19. Epigenome-wide association studies without the need for cell-type composition.

    Science.gov (United States)

    Zou, James; Lippert, Christoph; Heckerman, David; Aryee, Martin; Listgarten, Jennifer

    2014-03-01

    In epigenome-wide association studies, cell-type composition often differs between cases and controls, yielding associations that simply tag cell type rather than reveal fundamental biology. Current solutions require actual or estimated cell-type composition--information not easily obtainable for many samples of interest. We propose a method, FaST-LMM-EWASher, that automatically corrects for cell-type composition without the need for explicit knowledge of it, and then validate our method by comparison with the state-of-the-art approach. Corresponding software is available from http://www.microsoft.com/science/.

  20. Modulation of the Genome and Epigenome of Individuals Susceptible to Autism by Environmental Risk Factors

    Directory of Open Access Journals (Sweden)

    Costas Koufaris

    2015-04-01

    Full Text Available Diverse environmental factors have been implicated with the development of autism spectrum disorders (ASD. Genetic factors also underlie the differential vulnerability to environmental risk factors of susceptible individuals. Currently the way in which environmental risk factors interact with genetic factors to increase the incidence of ASD is not well understood. A greater understanding of the metabolic, cellular, and biochemical events involved in gene x environment interactions in ASD would have important implications for the prevention and possible treatment of the disorder. In this review we discuss various established and more alternative processes through which environmental factors implicated in ASD can modulate the genome and epigenome of genetically-susceptible individuals.

  1. Mosaic crystal algorithm for Monte Carlo simulations

    CERN Document Server

    Seeger, P A

    2002-01-01

    An algorithm is presented for calculating reflectivity, absorption, and scattering of mosaic crystals in Monte Carlo simulations of neutron instruments. The algorithm uses multi-step transport through the crystal with an exact solution of the Darwin equations at each step. It relies on the kinematical model for Bragg reflection (with parameters adjusted to reproduce experimental data). For computation of thermal effects (the Debye-Waller factor and coherent inelastic scattering), an expansion of the Debye integral as a rapidly converging series of exponential terms is also presented. Any crystal geometry and plane orientation may be treated. The algorithm has been incorporated into the neutron instrument simulation package NISP. (orig.)

  2. Identification of virus isolates inducing mosaic of sugarcane in ...

    African Journals Online (AJOL)

    SAM

    2014-03-19

    Mar 19, 2014 ... (JGMV), maize dwarf mosaic virus (MDMV) and sorghum mosaic Virus (SrMV) is an economically important viral disease of sugarcane ... race (“Bahausa”) and the least infected was the white land race (“fararkwama”). ... stripes symptoms on leaf blade and white stripe on stem in infected sugarcane and are ...

  3. Chromosomal mosaicism in human preimplantation embryos: a systematic review.

    NARCIS (Netherlands)

    Echten-Arends, J. van; Mastenbroek, S.; Sikkema-Raddatz, B.; Korevaar, J.C.; Heineman, M.J.; Veen, F. van der; Repping, S.

    2011-01-01

    BACKGROUND: Although chromosomal mosaicism in human preimplantation embryos has been described for almost two decades, its exact prevalence is still unknown. The prevalence of mosaicism is important in the context of preimplantation genetic screening in which the chromosomal status of an embryo is

  4. Chromosomal mosaicism in human preimplantation embryos : a systematic review

    NARCIS (Netherlands)

    van Echten-Arends, Jannie; Mastenbroek, Sebastiaan; Sikkema-Raddatz, Birgit; Korevaar, Johanna C.; Heineman, Maas Jan; van der Veen, Fulco; Repping, Sjoerd

    2011-01-01

    BACKGROUND: Although chromosomal mosaicism in human preimplantation embryos has been described for almost two decades, its exact prevalence is still unknown. The prevalence of mosaicism is important in the context of preimplantation genetic screening in which the chromosomal status of an embryo is

  5. Status of cassava mosaic disease and whitefly population in Zambia ...

    African Journals Online (AJOL)

    Cassava mosaic disease is the most important disease affecting cassava in Zambia. A study was conducted through a survey to determine the status of cassava mosaic disease incidence, severity and whitefly abundance in farmers' fields in six provinces: Lusaka, Northern, North-Western, Luapula, Eastern and Western ...

  6. Sex mosaics in a male dimorphic ant Cardiocondyla kagutsuchi

    Science.gov (United States)

    Yoshizawa, Juri; Mimori, Kohei; Yamauchi, Katsusuke; Tsuchida, Koji

    2009-01-01

    Gynandromorphy, or the development of organisms with a combination of male and female morphological features, is common in Hymenoptera. The underlying mechanism is likely associated with the sex-determination system, and studying this phenomenon should lead to a deeper understanding of both embryonic development and sex determination. The reproductive capabilities of gynandromorphs (hereafter, sex mosaics) remain unclear. We studied gynandromorphy in the Malaysian ant Cardiocondyla kagutsuchi, which has sex mosaics of queens (gynandromorphs; mosaic of queens and winged male) and workers (ergatandromorphs; mosaic of worker and wingless ergatoid male). These sex mosaics were classified into seven morphological categories. Most individuals had more male than female body areas. Behavioral observations revealed that sex mosaics behave more in accordance with the “sex” of their brain than that of the reproductive organs (gaster). Relative DNA quantities showed that both female and male regions contained haploid and diploid nuclei, irrespective of their phenotypic appearance, indicating that external appearance did not reflect internal tissues. Nearly one third of the adults were sex mosaics and they were not infected with Wolbachia. Our results suggest that the production of sex mosaics in this species does not pose a substantial cost to colonies and that the underlying causes are therefore not strongly selected against.

  7. Mosaic model for sensorimotor learning and control.

    Science.gov (United States)

    Haruno, M; Wolpert, D M; Kawato, M

    2001-10-01

    Humans demonstrate a remarkable ability to generate accurate and appropriate motor behavior under many different and often uncertain environmental conditions. We previously proposed a new modular architecture, the modular selection and identification for control (MOSAIC) model, for motor learning and control based on multiple pairs of forward (predictor) and inverse (controller) models. The architecture simultaneously learns the multiple inverse models necessary for control as well as how to select the set of inverse models appropriate for a given environment. It combines both feedforward and feedback sensorimotor information so that the controllers can be selected both prior to movement and subsequently during movement. This article extends and evaluates the MOSAIC architecture in the following respects. The learning in the architecture was implemented by both the original gradient-descent method and the expectation-maximization (EM) algorithm. Unlike gradient descent, the newly derived EM algorithm is robust to the initial starting conditions and learning parameters. Second, simulations of an object manipulation task prove that the architecture can learn to manipulate multiple objects and switch between them appropriately. Moreover, after learning, the model shows generalization to novel objects whose dynamics lie within the polyhedra of already learned dynamics. Finally, when each of the dynamics is associated with a particular object shape, the model is able to select the appropriate controller before movement execution. When presented with a novel shape-dynamic pairing, inappropriate activation of modules is observed followed by on-line correction.

  8. Considering Maternal Dietary Modulators for Epigenetic Regulation and Programming of the Fetal Epigenome

    Directory of Open Access Journals (Sweden)

    Abalo Chango

    2015-04-01

    Full Text Available Fetal life is characterized by a tremendous plasticity and ability to respond to various environmental and lifestyle factors, including maternal nutrition. Identification of the role of dietary factors that can modulate and reshape the cellular epigenome during development, including methyl group donors (e.g., folate, choline and bioactive compounds (e.g., polyphenols is of great importance; however, there is insufficient knowledge of a particular effect of each type of modulator and/or their combination on fetal life. To enhance the quality and safety of food products for proper fetal health and disease prevention in later life, a better understanding of the underlying mechanisms of dietary epigenetic modulators during the critical prenatal period is necessary. This review focuses on the influence of maternal dietary components on DNA methylation, histone modification, and microRNAs, and summarizes current knowledge of the effect and importance of dietary components on epigenetic mechanisms that control the proper expression of genetic information. Evidence reveals that some components in the maternal diet can directly or indirectly affect epigenetic mechanisms. Understanding the underlying mechanisms of how early-life nutritional environment affects the epigenome during development is of great importance for the successful prevention of adult chronic diseases through optimal maternal nutrition.

  9. Considering maternal dietary modulators for epigenetic regulation and programming of the fetal epigenome.

    Science.gov (United States)

    Chango, Abalo; Pogribny, Igor P

    2015-04-14

    Fetal life is characterized by a tremendous plasticity and ability to respond to various environmental and lifestyle factors, including maternal nutrition. Identification of the role of dietary factors that can modulate and reshape the cellular epigenome during development, including methyl group donors (e.g., folate, choline) and bioactive compounds (e.g., polyphenols) is of great importance; however, there is insufficient knowledge of a particular effect of each type of modulator and/or their combination on fetal life. To enhance the quality and safety of food products for proper fetal health and disease prevention in later life, a better understanding of the underlying mechanisms of dietary epigenetic modulators during the critical prenatal period is necessary. This review focuses on the influence of maternal dietary components on DNA methylation, histone modification, and microRNAs, and summarizes current knowledge of the effect and importance of dietary components on epigenetic mechanisms that control the proper expression of genetic information. Evidence reveals that some components in the maternal diet can directly or indirectly affect epigenetic mechanisms. Understanding the underlying mechanisms of how early-life nutritional environment affects the epigenome during development is of great importance for the successful prevention of adult chronic diseases through optimal maternal nutrition.

  10. Integrated Transcriptomic and Epigenomic Analysis of Primary Human Lung Epithelial Cell Differentiation

    Science.gov (United States)

    Marconett, Crystal N.; Zhou, Beiyun; Rieger, Megan E.; Selamat, Suhaida A.; Dubourd, Mickael; Fang, Xiaohui; Lynch, Sean K.; Stueve, Theresa Ryan; Siegmund, Kimberly D.; Berman, Benjamin P.

    2013-01-01

    Elucidation of the epigenetic basis for cell-type specific gene regulation is key to gaining a full understanding of how the distinct phenotypes of differentiated cells are achieved and maintained. Here we examined how epigenetic changes are integrated with transcriptional activation to determine cell phenotype during differentiation. We performed epigenomic profiling in conjunction with transcriptomic profiling using in vitro differentiation of human primary alveolar epithelial cells (AEC). This model recapitulates an in vivo process in which AEC transition from one differentiated cell type to another during regeneration following lung injury. Interrogation of histone marks over time revealed enrichment of specific transcription factor binding motifs within regions of changing chromatin structure. Cross-referencing of these motifs with pathways showing transcriptional changes revealed known regulatory pathways of distal alveolar differentiation, such as the WNT and transforming growth factor beta (TGFB) pathways, and putative novel regulators of adult AEC differentiation including hepatocyte nuclear factor 4 alpha (HNF4A), and the retinoid X receptor (RXR) signaling pathways. Inhibition of the RXR pathway confirmed its functional relevance for alveolar differentiation. Our incorporation of epigenetic data allowed specific identification of transcription factors that are potential direct upstream regulators of the differentiation process, demonstrating the power of this approach. Integration of epigenomic data with transcriptomic profiling has broad application for the identification of regulatory pathways in other models of differentiation. PMID:23818859

  11. 40 CFR 174.514 - Coat Protein of Watermelon Mosaic Virus-2 and Zucchini Yellow Mosaic Virus; exemption from the...

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 23 2010-07-01 2010-07-01 false Coat Protein of Watermelon Mosaic Virus-2 and Zucchini Yellow Mosaic Virus; exemption from the requirement for a tolerance. 174.514 Section 174.514 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) PESTICIDE PROGRAMS PROCEDURES AND REQUIREMENTS FOR PLANT-INCORPORATED...

  12. Arabidopsis thaliana peroxidase N

    DEFF Research Database (Denmark)

    Mirza, Osman Asghar; Henriksen, A; Ostergaard, L

    2000-01-01

    The structure of the neutral peroxidase from Arabidopsis thaliana (ATP N) has been determined to a resolution of 1.9 A and a free R value of 20.5%. ATP N has the expected characteristic fold of the class III peroxidases, with a C(alpha) r.m.s.d. of 0.82 A when compared with horseradish peroxidase C...... (HRP C). HRP C is 54% identical to ATP N in sequence. When the structures of four class III plant peroxidases are superimposed, the regions with structural differences are non-randomly distributed; all are located in one half of the molecule. The architecture of the haem pocket of ATP N is very similar...... to that of HRP C, in agreement with the low small-molecule substrate specificity of all class III peroxidases. The structure of ATP N suggests that the pH dependence of the substrate turnover will differ from that of HRP C owing to differences in polarity of the residues in the substrate-access channel. Since...

  13. An epigenome-wide association study in whole blood of measures of adiposity among Ghanaians: the RODAM study

    NARCIS (Netherlands)

    Meeks, Karlijn A. C.; Henneman, Peter; Venema, Andrea; Burr, Tom; Galbete, Cecilia; Danquah, Ina; Schulze, Matthias B.; Mockenhaupt, Frank P.; Owusu-Dabo, Ellis; Rotimi, Charles N.; Addo, Juliet; Smeeth, Liam; Bahendeka, Silver; Spranger, Joachim; Mannens, Marcel M. A. M.; Zafarmand, Mohammad H.; Agyemang, Charles; Adeyemo, Adebowale

    2017-01-01

    Background: Epigenome-wide association studies (EWAS) have identified DNA methylation loci involved in adiposity. However, EWAS on adiposity in sub-Saharan Africans are lacking despite the high burden of adiposity among African populations. We undertook an EWAS for anthropometric indices of

  14. Sensitive radioimmunosorbent assay for the detection of plant viruses. [Cauliflower mosaic virus, lettuce mosaic virus

    Energy Technology Data Exchange (ETDEWEB)

    Ghabrial, S A; Shepherd, R J [Kentucky Univ., Lexington (USA); California Univ., Davis (USA))

    1980-06-01

    A simple and highly sensitive radioimmunosorbent assay (RISA) for the detection of plant viruses is described. The RISA procedure is a microplate method based on the principle of 'double-antibody sandwich' and follows essentially the protocol of the enzyme-linked immunosorbent assay (ELISA) (Clark and Adams, 1977), with the exception that /sup 125/I-labelled ..gamma..-globulin is substituted for the ..gamma..-globulin enzyme conjugate; the bound /sup 125/I-..gamma..-globulin is dissociated by acidification from the double-antibody sandwich. The radioactivity is proportional to virus concentration, and cauliflower mosaic virus (CaMV) and lettuce mosaic virus (LMV) could be detected at concentrations as low as 5 and 2 ng/ml, respectively. Direct evidence of the adverse effects of conjugation with enzyme on the binding abilities of antibodies is presented. The RISA procedure should prove valuable with viruses for which the ELISA values are too low to be dependable.

  15. High-Resolution Mapping of Chromatin Conformation in Cardiac Myocytes Reveals Structural Remodeling of the Epigenome in Heart Failure.

    Science.gov (United States)

    Rosa-Garrido, Manuel; Chapski, Douglas J; Schmitt, Anthony D; Kimball, Todd H; Karbassi, Elaheh; Monte, Emma; Balderas, Enrique; Pellegrini, Matteo; Shih, Tsai-Ting; Soehalim, Elizabeth; Liem, David; Ping, Peipei; Galjart, Niels J; Ren, Shuxun; Wang, Yibin; Ren, Bing; Vondriska, Thomas M

    2017-10-24

    Cardiovascular disease is associated with epigenomic changes in the heart; however, the endogenous structure of cardiac myocyte chromatin has never been determined. To investigate the mechanisms of epigenomic function in the heart, genome-wide chromatin conformation capture (Hi-C) and DNA sequencing were performed in adult cardiac myocytes following development of pressure overload-induced hypertrophy. Mice with cardiac-specific deletion of CTCF (a ubiquitous chromatin structural protein) were generated to explore the role of this protein in chromatin structure and cardiac phenotype. Transcriptome analyses by RNA-seq were conducted as a functional readout of the epigenomic structural changes. Depletion of CTCF was sufficient to induce heart failure in mice, and human patients with heart failure receiving mechanical unloading via left ventricular assist devices show increased CTCF abundance. Chromatin structural analyses revealed interactions within the cardiac myocyte genome at 5-kb resolution, enabling examination of intra- and interchromosomal events, and providing a resource for future cardiac epigenomic investigations. Pressure overload or CTCF depletion selectively altered boundary strength between topologically associating domains and A/B compartmentalization, measurements of genome accessibility. Heart failure involved decreased stability of chromatin interactions around disease-causing genes. In addition, pressure overload or CTCF depletion remodeled long-range interactions of cardiac enhancers, resulting in a significant decrease in local chromatin interactions around these functional elements. These findings provide a high-resolution chromatin architecture resource for cardiac epigenomic investigations and demonstrate that global structural remodeling of chromatin underpins heart failure. The newly identified principles of endogenous chromatin structure have key implications for epigenetic therapy. © 2017 The Authors.

  16. Tissue differences in fragile X mosaics: Mosaicism in blood cells may differ greatly from skin

    Energy Technology Data Exchange (ETDEWEB)

    Dobkin, C.S.; Nolin, S.L.; Cohen, I. [NYS Institute for Basic Research in Developmental Disabilities, Staten Island, NY (United States)] [and others

    1996-08-09

    The fragile X mutation is diagnosed from the structure of the FMR1 gene in blood cell DNA. An estimated 12 to 41% of affected males are mosaics who carry both a {open_quotes}full mutation{close_quotes} allele from which there is no gene expression and a {open_quotes}premutation{close_quotes} allele which has normal gene expression. We compared the DNA in blood cells and skin fibroblasts from four mosaic fragile X males to see if there was a difference in the relative amounts of premutation and full mutation alleles within the tissues of these individuals. Two of these males showed striking differences in the ratio of premutation to full mutation in different tissues while the other two showed only slight differences. These observations conform with the widely accepted hypothesis that the fragile X CGG repeat is unstable in somatic tissue during early embryogenesis. Accordingly, the mosaicism in brain and skin, which are both ectodermal in origin, may be similar to each other but different from blood which is not ectodermal in origin. Thus, the ratio of full mutation to premutation allele in skin fibroblasts might be a better indicator of psychological impairment than the ratio in blood cells. 24 refs., 4 figs., 1 tab.

  17. Solar Mosaic Inc. Mosaic Home Solar Loan SunShot 9 Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Walsh, Colin James [Solar Mosaic Inc., Oakland, CA (United States)

    2017-02-09

    The 6686 Mosaic SunShot award has helped Solar Mosaic Inc to progress from an early stage startup focused on commercial crowdfunding to a leading multi-state residential solar lender. The software platform is now used by the majority of the nation's top solar installers and offers a variety of simple home solar loans. Mosaic is has originated approximately $1Bil in solar loans to date to put solar on over 35k rooftops. The company now lends to homeowners with a wide range of credit scores across multiple states and mitigates boundaries preventing them from profiting from ownership of a home solar system. The project included milestones in 5 main categories: 1. Lending to homeowners outside of CA 2. Lending to homeowners with FICO scores under 700 3. Packaging O&M with the home solar loan 4. Allowing residential installers to process home solar loans via API 5. Lowering customer acquisition costs below $1500 This report includes a detailed review of the final results achieved and key findings.

  18. SPECIFICITY OF THE PRECIPITIN REACTION IN TOBACCO MOSAIC DISEASE.

    Science.gov (United States)

    Beale, H P

    1931-09-30

    1. Leaf extracts of Sudan grass, Hippeastrum equestre Herb., lily, and Abutilon striatum Dicks. (A. Thompsoni hort.), each affected with its respective mosaic disease, and peach affected with yellows disease, were tested for their ability to precipitate antiserum for virus extract of tobacco mosaic disease. No precipitate occurred. 2. Nicotiana glutinosa L., N. rustica L., and Martynia louisiana Mill. were added to the list of hosts of tobacco mosaic virus which have been tested with antiserum for the same virus in N. tabacum L. var. Turkish. The object was to determine the presence or absence of material reacting with the specific precipitins such as that already demonstrated in extracts of tomato, pepper, and petunia affected with the same virus. The presence of specific substances was demonstrated in every case. 3. The viruses of ringspot and cucumber mosaic diseases were multiplied in Turkish tobacco and leaf extracts of the affected plants were used in turn as antigens in precipitin tests with antiserum for tobacco mosaic virus extract of Turkish tobacco. A slight precipitation resulted in the tubes containing undiluted antiserum and virus extract such as occurs when juice from normal tobacco is used with undiluted antiserum. No precipitate was demonstrable that was specific for virus extracts of tobacco affected with either ringspot or cucumber mosaic disease. 4. The results favor the interpretation that the specific antigenic substance in virus extract of tobacco mosaic disease is foreign antigenic material, possibly virus itself, not altered host protein.

  19. Maternal XX/X chromosome mosaicism in donor oocyte in vitro fertilization (IVF

    Directory of Open Access Journals (Sweden)

    Paul R. Brezina

    2012-06-01

    Results: The rates of maternal X chromosome mosaicism noted in the cycles from women with miscarriages (3%, 4%, 4%, and 6% were not statistically different from cycles in TS-Mosaic women with normal deliveries (3% and 11%. These data suggest that the rate of maternal X chromosome mosaicism does not affect pregnancy loss rates in TS-Mosaic women undergoing donor oocyte IVF.

  20. Exploiting natural variation in Arabidopsis

    NARCIS (Netherlands)

    Molenaar, J.A.; Keurentjes, J.J.B.; Sanchez-Serrano, J.J.; Salinas, J.

    2014-01-01

    Natural variation for many traits is present within the species Arabidopsis thaliana. This chapter describes the use of natural variation to elucidate genes underlying the regulation of quantitative traits. It deals with the development and use of mapping populations, the detection and handling of

  1. Epigenomic strategies at the interface of genetic and environmental risk factors for autism.

    Science.gov (United States)

    LaSalle, Janine M

    2013-07-01

    Autism spectrum disorders (ASD) have been increasing in prevalence over the last two decades, primarily because of increased awareness and diagnosis. However, autism is clearly a complex human genetic disorder that involves interactions between genes and environment. Epigenetic mechanisms, such as DNA methylation, act at the interface of genetic and environmental risk and protective factors. Advancements in genome-wide sequencing has broadened the view of the human methylome and revealed the organization of the human genome into large-scale methylation domains that footprint over neurologically important genes involved in embryonic development. Future integrative epigenomic analyses of genetic risk factors with environmental exposures and methylome analyses are expected to be important for understanding the complex etiology of ASD.

  2. Epigenome-Wide Association Study of Cognitive Functioning in Middle-Aged Monozygotic Twins

    DEFF Research Database (Denmark)

    Starnawska, Anna; Tan, Qihua; McGue, Matt

    2017-01-01

    As the world's population ages, the age-related cognitive decline presents a great challenge to world's healthcare systems. One of the molecular mechanisms implicated in cognitive ageing is DNA methylation, an epigenetic modification known to be a key player in memory formation, maintenance......, and synaptic plasticity. Using the twin design we performed an epigenome-wide association study (EWAS) in a population of 486 middle-aged monozygotic twins (mean age at follow-up 65.9, SD = 6.1) and correlated their blood DNA methylation to their level (cross-sectional analysis) and change in cognitive...... abilities over 10 years (longitudinal analysis). We identified several CpG sites where cross-sectional cognitive functioning was associated with DNA methylation levels. The top identified loci were located in ZBTB46 (p = 5.84 × 10-7), and TAF12 (p = 4.91 × 10-7). KEGG's enrichment analyses of the most...

  3. New insights and updated guidelines for epigenome-wide association studies

    Directory of Open Access Journals (Sweden)

    Lisa H. Chadwick

    2015-01-01

    Full Text Available Epigenetic dysregulation in disease is increasingly studied as a potential mediator of pathophysiology. The epigenetic events are believed to occur in somatic cells, but the limited changes of DNA methylation in studies to date indicate that only subsets of the cells tested undergo epigenetic dysregulation. The recognition of this subpopulation effect indicates the need for care in design and execution of epigenome-wide association studies (EWASs, paying particular attention to confounding sources of variability. To maximize the sensitivity of the EWASs, ideally, the cell type mediating the disease should be tested, which is not always practical or ethical in human subjects. The value of using accessible cells as surrogates for the target, disease-mediating cell type has not been rigorously tested to date. In this review, participants in a workshop convened by the National Institutes of Health update EWAS design and execution guidelines to reflect new insights in the field.

  4. Toward understanding the evolution of vertebrate gene regulatory networks: comparative genomics and epigenomic approaches.

    Science.gov (United States)

    Martinez-Morales, Juan R

    2016-07-01

    Vertebrates, as most animal phyla, originated >500 million years ago during the Cambrian explosion, and progressively radiated into the extant classes. Inferring the evolutionary history of the group requires understanding the architecture of the developmental programs that constrain the vertebrate anatomy. Here, I review recent comparative genomic and epigenomic studies, based on ChIP-seq and chromatin accessibility, which focus on the identification of functionally equivalent cis-regulatory modules among species. This pioneer work, primarily centered in the mammalian lineage, has set the groundwork for further studies in representative vertebrate and chordate species. Mapping of active regulatory regions across lineages will shed new light on the evolutionary forces stabilizing ancestral developmental programs, as well as allowing their variation to sustain morphological adaptations on the inherited vertebrate body plan. © The Author 2015. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  5. Epigenetic transgenerational inheritance of vinclozolin induced mouse adult onset disease and associated sperm epigenome biomarkers.

    Science.gov (United States)

    Guerrero-Bosagna, Carlos; Covert, Trevor R; Haque, Md M; Settles, Matthew; Nilsson, Eric E; Anway, Matthew D; Skinner, Michael K

    2012-12-01

    The endocrine disruptor vinclozolin has previously been shown to promote epigenetic transgenerational inheritance of adult onset disease in the rat. The current study was designed to investigate the transgenerational actions of vinclozolin on the mouse. Transient exposure of the F0 generation gestating female during gonadal sex determination promoted transgenerational adult onset disease in F3 generation male and female mice, including spermatogenic cell defects, testicular abnormalities, prostate abnormalities, kidney abnormalities and polycystic ovarian disease. Pathology analysis demonstrated 75% of the vinclozolin lineage animals developed disease with 34% having two or more different disease states. Interestingly, the vinclozolin induced transgenerational disease was observed in the outbred CD-1 strain, but not the inbred 129 mouse strain. Analysis of the F3 generation sperm epigenome identified differential DNA methylation regions that can potentially be utilized as epigenetic biomarkers for transgenerational exposure and disease. Copyright © 2012 Elsevier Inc. All rights reserved.

  6. Cauliflower mosaic virus protein P6 inhibits signaling responses to salicylic acid and regulates innate immunity.

    Directory of Open Access Journals (Sweden)

    Andrew J Love

    Full Text Available Cauliflower mosaic virus (CaMV encodes a multifunctional protein P6 that is required for translation of the 35S RNA and also acts as a suppressor of RNA silencing. Here we demonstrate that P6 additionally acts as a pathogenicity effector of an unique and novel type, modifying NPR1 (a key regulator of salicylic acid (SA- and jasmonic acid (JA-dependent signaling and inhibiting SA-dependent defence responses We find that that transgene-mediated expression of P6 in Arabidopsis and transient expression in Nicotiana benthamiana has profound effects on defence signaling, suppressing expression of representative SA-responsive genes and increasing expression of representative JA-responsive genes. Relative to wild-type Arabidopsis P6-expressing transgenics had greatly reduced expression of PR-1 following SA-treatment, infection by CaMV or inoculation with an avirulent bacterial pathogen Pseudomonas syringae pv tomato (Pst. Similarly transient expression in Nicotiana benthamiana of P6 (including a mutant form defective in translational transactivation activity suppressed PR-1a transcript accumulation in response to Agrobacterium infiltration and following SA-treatment. As well as suppressing the expression of representative SA-regulated genes, P6-transgenic Arabidopsis showed greatly enhanced susceptibility to both virulent and avirulent Pst (titres elevated 10 to 30-fold compared to non-transgenic controls but reduced susceptibility to the necrotrophic fungus Botrytis cinerea. Necrosis following SA-treatment or inoculation with avirulent Pst was reduced and delayed in P6-transgenics. NPR1 an important regulator of SA/JA crosstalk, was more highly expressed in the presence of P6 and introduction of the P6 transgene into a transgenic line expressing an NPR1:GFP fusion resulted in greatly increased fluorescence in nuclei even in the absence of SA. Thus in the presence of P6 an inactive form of NPR1 is mislocalized in the nucleus even in uninduced plants

  7. Meta-analysis of epigenome-wide association studies of cognitive abilities.

    Science.gov (United States)

    Marioni, Riccardo E; McRae, Allan F; Bressler, Jan; Colicino, Elena; Hannon, Eilis; Li, Shuo; Prada, Diddier; Smith, Jennifer A; Trevisi, Letizia; Tsai, Pei-Chien; Vojinovic, Dina; Simino, Jeannette; Levy, Daniel; Liu, Chunyu; Mendelson, Michael; Satizabal, Claudia L; Yang, Qiong; Jhun, Min A; Kardia, Sharon L R; Zhao, Wei; Bandinelli, Stefania; Ferrucci, Luigi; Hernandez, Dena G; Singleton, Andrew B; Harris, Sarah E; Starr, John M; Kiel, Douglas P; McLean, Robert R; Just, Allan C; Schwartz, Joel; Spiro, Avron; Vokonas, Pantel; Amin, Najaf; Ikram, M Arfan; Uitterlinden, Andre G; van Meurs, Joyce B J; Spector, Tim D; Steves, Claire; Baccarelli, Andrea A; Bell, Jordana T; van Duijn, Cornelia M; Fornage, Myriam; Hsu, Yi-Hsiang; Mill, Jonathan; Mosley, Thomas H; Seshadri, Sudha; Deary, Ian J

    2018-01-08

    Cognitive functions are important correlates of health outcomes across the life-course. Individual differences in cognitive functions are partly heritable. Epigenetic modifications, such as DNA methylation, are susceptible to both genetic and environmental factors and may provide insights into individual differences in cognitive functions. Epigenome-wide meta-analyses for blood-based DNA methylation levels at ~420,000 CpG sites were performed for seven measures of cognitive functioning using data from 11 cohorts. CpGs that passed a Bonferroni correction, adjusting for the number of CpGs and cognitive tests, were assessed for: longitudinal change; being under genetic control (methylation QTLs); and associations with brain health (structural MRI), brain methylation and Alzheimer's disease pathology. Across the seven measures of cognitive functioning (meta-analysis n range: 2557-6809), there were epigenome-wide significant (P cognitive function (cg21450381, P = 1.6 × 10 -8 ), and phonemic verbal fluency (cg12507869, P = 2.5 × 10 -9 ). The CpGs are located in an intergenic region on chromosome 12 and the INPP5A gene on chromosome 10, respectively. Both probes have moderate correlations (~0.4) with brain methylation in Brodmann area 20 (ventral temporal cortex). Neither probe showed evidence of longitudinal change in late-life or associations with white matter brain MRI measures in one cohort with these data. A methylation QTL analysis suggested that rs113565688 was a cis methylation QTL for cg12507869 (P = 5 × 10 -5 and 4 × 10 -13 in two lookup cohorts). We demonstrate a link between blood-based DNA methylation and measures of phonemic verbal fluency and global cognitive ability. Further research is warranted to understand the mechanisms linking genomic regulatory changes with cognitive function to health and disease.

  8. Distribution and molecular detection of apple mosaic virus in apple ...

    African Journals Online (AJOL)

    SAM

    2014-07-30

    Jul 30, 2014 ... Apple mosaic virus (ApMV) is one of the most important diseases limiting the production of hazelnut and apple in Turkey ... success of those programs depends on specific and sensitive ..... Applied Biostatistics Inc. Rott ME ...

  9. 1935 15' Quad #004 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  10. NEPR World View 2 Satellite Mosaic - NOAA TIFF Image

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This GeoTiff is a mosaic of World View 2 panchromatic satellite imagery of Northeast Puerto Rico that contains the shallow water area (0-35m deep) surrounding...

  11. 1935 15' Quad #009 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  12. 1935 15' Quad #062 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  13. 1935 15' Quad #127 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  14. 1935 15' Quad #350 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  15. 1935 15' Quad #387 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  16. 1935 15' Quad #243 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  17. 1935 15' Quad #155 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  18. 1935 15' Quad #129 Aerial Photo Mosaic Index - NM

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  19. 1935 15' Quad #059 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  20. 1935 15' Quad #221 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  1. 1935 15' Quad #266 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  2. 1935 15' Quad #130 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  3. 1935 15' Quad #410 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  4. 1935 15' Quad #368 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  5. 1935 15' Quad #180 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  6. 1935 15' Quad #349 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  7. 1935 15' Quad #063 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  8. 1935 15' Quad #147 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  9. 1935 15' Quad #032 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  10. 1935 15' Quad #056 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  11. 1935 15' Quad #222 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  12. 1935 15' Quad #122 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  13. 1935 15' Quad #265 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  14. 1935 15' Quad #202 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  15. 2010 NOAA Ortho-rectified Mosaic of Lake Champlain, Vermont

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data set contains ortho-rectified mosaic tiles, created as a product from the NOAA Integrated Ocean and Coastal Mapping (IOCM) initiative. The source imagery...

  16. Viral protein synthesis in cowpea mosaic virus infected protoplasts

    International Nuclear Information System (INIS)

    Rottier, P.

    1980-01-01

    Some aspects of cowpea mosaic virus (CPMV) multiplication in cowpea mesophyll protoplasts were studied. The detection and characterization of proteins whose synthesis is induced or is stimulated upon virus infection was performed with the aid of radioactive labelling. (Auth.)

  17. 1935 15' Quad #364 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  18. 1935 15' Quad #292 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  19. 1935 15' Quad #246 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  20. 1935 15' Quad #371 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  1. Counselling considerations for chromosomal mosaicism detected by preimplantation genetic screening.

    Science.gov (United States)

    Besser, Andria G; Mounts, Emily L

    2017-04-01

    The evolution of preimplantation genetic screening (PGS) for aneuploidy to blastocyst biopsy and more sensitive 24-chromosome screening techniques has resulted in a new diagnostic category of PGS results: those classified as mosaic. This diagnosis presents significant challenges for clinicians in developing policies regarding transfer and storage of such embryos, as well as in providing genetic counselling for patients prior to and following PGS. Given the high frequency of mosaic PGS results and the wide range of possible associated outcomes, there is an urgent need to understand how to appropriately counsel patients regarding such embryos. This is the first commentary to thoroughly address pre- and post-test genetic counselling recommendations, as well as considerations regarding prenatal screening and diagnosis. Current data on mosaic PGS results are summarized along with embryo selection considerations and potential outcomes of embryos diagnosed as mosaic. Copyright © 2017 Reproductive Healthcare Ltd. Published by Elsevier Ltd. All rights reserved.

  2. 1935 15' Quad #223 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  3. 1935 15' Quad #370 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  4. 1935 15' Quad #319 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  5. 1935 15' Quad #181 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  6. 1935 15' Quad #173 Aerial Photo Mosaic Index - NM

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  7. 1935 15' Quad #345 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  8. 1935 15' Quad #272 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  9. 1935 15' Quad #417 Aerial Photo Mosaic Index - AZ

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  10. 1935 15' Quad #339 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  11. 1935 15' Quad #490 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  12. 1935 15' Quad #270 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  13. 1935 15' Quad #219 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  14. 1935 15' Quad #145 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  15. 1935 15' Quad #227 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  16. 1935 15' Quad #132 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  17. 1935 15' Quad #298 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  18. 1935 15' Quad #100 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  19. 1935 15' Quad #152 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  20. 1935 15' Quad #226 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  1. 1935 15' Quad #361 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  2. 1935 15' Quad #126 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  3. 1935 15' Quad #037 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  4. 1935 15' Quad #297 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  5. 1935 15' Quad #124 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  6. Immunogenic compositions comprising human immunodeficiency virus (HIV) mosaic Nef proteins

    Science.gov (United States)

    Korber, Bette T [Los Alamos, NM; Perkins, Simon [Los Alamos, NM; Bhattacharya, Tanmoy [Los Alamos, NM; Fischer, William M [Los Alamos, NM; Theiler, James [Los Alamos, NM; Letvin, Norman [Boston, MA; Haynes, Barton F [Durham, NC; Hahn, Beatrice H [Birmingham, AL; Yusim, Karina [Los Alamos, NM; Kuiken, Carla [Los Alamos, NM

    2012-02-21

    The present invention relates to mosaic clade M HIV-1 Nef polypeptides and to compositions comprising same. The polypeptides of the invention are suitable for use in inducing an immune response to HIV-1 in a human.

  7. 1935 15' Quad #388 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  8. 2012 NOAA Ortho-rectified Color Mosaic of Astoria, Oregon

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data set contains ortho-rectified mosaic tiles, created as a product from the NOAA Integrated Ocean and Coastal Mapping (IOCM) initiative. The source imagery...

  9. 2011 NOAA Ortho-rectified Mosaic of Intracoastal Waterway, Texas

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data set contains ortho-rectified mosaic tiles, created as a product from the NOAA Integrated Ocean and Coastal Mapping (IOCM) initiative. The source imagery...

  10. Antiviral activities of streptomycetes against tobacco mosaic virus ...

    African Journals Online (AJOL)

    Mahera Shinwari

    2012-01-26

    Jan 26, 2012 ... Key words: Antiviral activity, tobacco mosaic virus, actinomycetes, Streptomyces, Datura metel ... have received less attention than those caused by fungal .... leaves were divided in to three partitions each containing triplicates.

  11. 1935 15' Quad #267 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  12. 1935 15' Quad #386 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  13. 1935 15' Quad #259 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  14. 1935 15' Quad #195 Aerial Photo Mosaic Index - NM

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  15. 1935 15' Quad #373 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  16. 1935 15' Quad #172 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  17. 1935 15' Quad #197 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  18. Crystal mosaic spread determination by slow neutron scattering

    International Nuclear Information System (INIS)

    Adib, M.; Naguib, K.; Abdel Kawy, A.; Ashry, A.; Abbas, Y.; Wahba, M.; Maayouf, M.A.

    1988-01-01

    A method has been established for determination of the crystal mosaic spread. The method is based on recording all neutron-reflected, under bragg condition, from a certain crystal plane. A computer code was developed especially in order to fit the measured wavelength's distribution of the reflected neutrons with the calculated one, assuming that the crystal mosaic spread has a Gaussian shape. The code accounts for the parameters of the time of flight spectrometer used during the present measurements, as well as divergence of the incident neutron beam. The developed method has been applied for determination of the mosaic spread of both zinc and pyrolytic graphite (P.G.) crystals. The mosaic spread values deduced from the present measurements, are 10'+-6' and 3.60 0 +-0.16 0 respectively for Zn and P.G. crystals

  19. 2011 NOAA Ortho-rectified Mosaic of Galveston, Texas

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data set contains ortho-rectified mosaic tiles, created as a product from the NOAA Integrated Ocean and Coastal Mapping (IOCM) initiative. The source imagery...

  20. 1935 15' Quad #179 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  1. 1935 15' Quad #269 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  2. 1935 15' Quad #242 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  3. 1935 15' Quad #049 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  4. 1935 15' Quad #084 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  5. 1935 15' Quad #054 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  6. 1935 15' Quad #057 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  7. 1935 15' Quad #086 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  8. 1935 15' Quad #010 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  9. 1935 15' Quad #079 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  10. 1935 15' Quad #055 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  11. 1935 15' Quad #083 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  12. 1935 15' Quad #035 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  13. 1935 15' Quad #033 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  14. 1935 15' Quad #012 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  15. 1935 15' Quad #008 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  16. 1935 15' Quad #013 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  17. 1935 15' Quad #110 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  18. 1935 15' Quad #011 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  19. 1935 15' Quad #078 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  20. 1935 15' Quad #109 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  1. 1935 15' Quad #036 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  2. 1935 15' Quad #105 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  3. 1935 15' Quad #085 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  4. 1935 15' Quad #007 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  5. 1935 15' Quad #080 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  6. 1935 15' Quad #201 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  7. 1935 15' Quad #082 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  8. 1935 15' Quad #061 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  9. 1935 15' Quad #106 Aerial Photo Mosaic Index - NM

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  10. 1935 15' Quad #006 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  11. 1935 15' Quad #058 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  12. 1935 15' Quad #108 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  13. 1935 15' Quad #060 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  14. 1935 15' Quad #030 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  15. 1935 15' Quad #075 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  16. 1935 15' Quad #074 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  17. 1935 15' Quad #176 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  18. 1935 15' Quad #316 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  19. 1935 15' Quad #415 Aerial Photo Mosaic Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Aerial Photo Reference Mosaics contain aerial photographs that are retrievable on a frame by frame basis. The inventory contains imagery from various sources that...

  20. Different myrosinase and idioblast distribution in Arabidopsis and Brassica napus

    DEFF Research Database (Denmark)

    Andreasson, Erik; Jørgensen, Lise Bolt; Höglund, Anna-Stina

    2001-01-01

    Arabidopsis, Brassica napus, Myrosinase, Myrosinase Binding Protein, Glucosinolates, Myrosin Cell, Immunocytochemistry......Arabidopsis, Brassica napus, Myrosinase, Myrosinase Binding Protein, Glucosinolates, Myrosin Cell, Immunocytochemistry...

  1. Mosaic trisomy 8 detected by fibroblasts cultured of skin

    Science.gov (United States)

    Gómez, Ana M; Mora, Lina; Suarez-Obando, Fernando; Moreno, Olga

    2016-01-01

    Introduction: Mosaic trisomy 8 or "Warkany's Syndrome" is a chromosomopathy with an estimated prevalance of 1:25,000 to 1:50,000, whose clinical presentation has a wide phenotypic variability. Case Description: Patient aged 14 years old with antecedents of global retardation of development, moderate cognitive deficit and hypothyroidism of possible congenital origin. Clinical Findings: Physical examination revealed palpebral ptosis, small corneas and corectopia, hypoplasia of the upper maxilla and prognathism, dental crowding, high-arched palate, anomalies of the extremities such as digitalization of the thumbs, clinodactyly and bilateral shortening of the fifth finger, shortening of the right femur, columnar deviation and linear brown blotches that followed Blaschko's lines. Cerebral nuclear magnetic resonance revealed type 1 Chiari's malformation and ventriculomegaly. Although the karyotype was normal in peripheral blood (46,XY), based on the finding of cutaneous mosaicism the lesions were biopsied and cytogenetic analysis demonstrated mosaic trisomy 8: mos 47,XY,+8[7]/46,XY[93]. Clinical Relevance: Trisomy 8 is clinically presented as a mosaic, universal cases being unfailingly lethal. In this particular case, cutaneous lesions identified the mosaic in tissue, although the karyotype was normal in peripheral blood. The cutaneous mosaicism represented by brown linear blotches which follow Blaschko's lines is a clinical finding that has not previously been described in Warkany's syndrome. PMID:27546932

  2. Behavioral Variability and Somatic Mosaicism: A Cytogenomic Hypothesis.

    Science.gov (United States)

    Vorsanova, Svetlana G; Zelenova, Maria A; Yurov, Yuri B; Iourov, Ivan Y

    2018-04-01

    Behavioral sciences are inseparably related to genetics. A variety of neurobehavioral phenotypes are suggested to result from genomic variations. However, the contribution of genetic factors to common behavioral disorders (i.e. autism, schizophrenia, intellectual disability) remains to be understood when an attempt to link behavioral variability to a specific genomic change is made. Probably, the least appreciated genetic mechanism of debilitating neurobehavioral disorders is somatic mosaicism or the occurrence of genetically diverse (neuronal) cells in an individual's brain. Somatic mosaicism is assumed to affect directly the brain being associated with specific behavioral patterns. As shown in studies of chromosome abnormalities (syndromes), genetic mosaicism is able to change dynamically the phenotype due to inconsistency of abnormal cell proportions. Here, we hypothesize that brain-specific postzygotic changes of mosaicism levels are able to modulate variability of behavioral phenotypes. More precisely, behavioral phenotype variability in individuals exhibiting somatic mosaicism might correlate with changes in the amount of genetically abnormal cells throughout the lifespan. If proven, the hypothesis can be used as a basis for therapeutic interventions through regulating levels of somatic mosaicism to increase functioning and to improve overall condition of individuals with behavioral problems.

  3. Further applications for mosaic pixel FPA technology

    Science.gov (United States)

    Liddiard, Kevin C.

    2011-06-01

    In previous papers to this SPIE forum the development of novel technology for next generation PIR security sensors has been described. This technology combines the mosaic pixel FPA concept with low cost optics and purpose-designed readout electronics to provide a higher performance and affordable alternative to current PIR sensor technology, including an imaging capability. Progressive development has resulted in increased performance and transition from conventional microbolometer fabrication to manufacture on 8 or 12 inch CMOS/MEMS fabrication lines. A number of spin-off applications have been identified. In this paper two specific applications are highlighted: high performance imaging IRFPA design and forest fire detection. The former involves optional design for small pixel high performance imaging. The latter involves cheap expendable sensors which can detect approaching fire fronts and send alarms with positional data via mobile phone or satellite link. We also introduce to this SPIE forum the application of microbolometer IR sensor technology to IoT, the Internet of Things.

  4. ViralEpi v1.0: a high-throughput spectrum of viral epigenomic methylation profiles from diverse diseases.

    Science.gov (United States)

    Khan, Mohd Shoaib; Gupta, Amit Kumar; Kumar, Manoj

    2016-01-01

    To develop a computational resource for viral epigenomic methylation profiles from diverse diseases. Methylation patterns of Epstein-Barr virus and hepatitis B virus genomic regions are provided as web platform developed using open source Linux-Apache-MySQL-PHP (LAMP) bundle: programming and scripting languages, that is, HTML, JavaScript and PERL. A comprehensive and integrated web resource ViralEpi v1.0 is developed providing well-organized compendium of methylation events and statistical analysis associated with several diseases. Additionally, it also facilitates 'Viral EpiGenome Browser' for user-affable browsing experience using JavaScript-based JBrowse. This web resource would be helpful for research community engaged in studying epigenetic biomarkers for appropriate prognosis and diagnosis of diseases and its various stages.

  5. High-fat diet reprograms the epigenome of rat spermatozoa and transgenerationally affects metabolism of the offspring

    DEFF Research Database (Denmark)

    de Castro Barbosa, Thais; Ingerslev, Lars R; Alm, Petter S

    2016-01-01

    OBJECTIVES: Chronic and high consumption of fat constitutes an environmental stress that leads to metabolic diseases. We hypothesized that high-fat diet (HFD) transgenerationally remodels the epigenome of spermatozoa and metabolism of the offspring. METHODS: F0-male rats fed either HFD or chow diet......1 male offspring showed common DNA methylation and small non-coding RNA expression signatures. Altered expression of sperm miRNA let-7c was passed down to metabolic tissues of the offspring, inducing a transcriptomic shift of the let-7c predicted targets. CONCLUSION: Our results provide insight...... into mechanisms by which HFD transgenerationally reprograms the epigenome of sperm cells, thereby affecting metabolic tissues of offspring throughout two generations....

  6. Transcriptional provirus silencing as a crosstalk of de novo DNA methylation and epigenomic features at the integration site

    Czech Academy of Sciences Publication Activity Database

    Šenigl, Filip; Auxt, Miroslav; Hejnar, Jiří

    2012-01-01

    Roč. 40, č. 12 (2012), s. 5298-5312 ISSN 0305-1048 R&D Projects: GA ČR GP301/09/P667; GA ČR GAP502/11/2207 Institutional research plan: CEZ:AV0Z50520514 Keywords : retrovirus integration * provirus silencing * epigenomics Subject RIV: EB - Genetic s ; Molecular Biology Impact factor: 8.278, year: 2012

  7. Environmentally induced epigenetic transgenerational inheritance of altered Sertoli cell transcriptome and epigenome: molecular etiology of male infertility.

    Directory of Open Access Journals (Sweden)

    Carlos Guerrero-Bosagna

    Full Text Available Environmental toxicants have been shown to induce the epigenetic transgenerational inheritance of adult onset disease, including testis disease and male infertility. The current study was designed to determine the impact of an altered sperm epigenome on the subsequent development of an adult somatic cell (Sertoli cell that influences the onset of a specific disease (male infertility. A gestating female rat (F0 generation was exposed to the agriculture fungicide vinclozolin during gonadal sex determination and then the subsequent F3 generation progeny used for the isolation of Sertoli cells and assessment of testis disease. As previously observed, enhanced spermatogenic cell apoptosis was observed. The Sertoli cells provide the physical and nutritional support for the spermatogenic cells. Over 400 genes were differentially expressed in the F3 generation control versus vinclozolin lineage Sertoli cells. A number of specific cellular pathways were identified to be transgenerationally altered. One of the key metabolic processes affected was pyruvate/lactate production that is directly linked to spermatogenic cell viability. The Sertoli cell epigenome was also altered with over 100 promoter differential DNA methylation regions (DMR modified. The genomic features and overlap with the sperm DMR were investigated. Observations demonstrate that the transgenerational sperm epigenetic alterations subsequently alters the development of a specific somatic cell (Sertoli cell epigenome and transcriptome that correlates with adult onset disease (male infertility. The environmentally induced epigenetic transgenerational inheritance of testis disease appears to be a component of the molecular etiology of male infertility.

  8. Epigenome-Wide Association Study Identifies Cardiac Gene Patterning and a Novel Class of Biomarkers for Heart Failure.

    Science.gov (United States)

    Meder, Benjamin; Haas, Jan; Sedaghat-Hamedani, Farbod; Kayvanpour, Elham; Frese, Karen; Lai, Alan; Nietsch, Rouven; Scheiner, Christina; Mester, Stefan; Bordalo, Diana Martins; Amr, Ali; Dietrich, Carsten; Pils, Dietmar; Siede, Dominik; Hund, Hauke; Bauer, Andrea; Holzer, Daniel Benjamin; Ruhparwar, Arjang; Mueller-Hennessen, Matthias; Weichenhan, Dieter; Plass, Christoph; Weis, Tanja; Backs, Johannes; Wuerstle, Maximilian; Keller, Andreas; Katus, Hugo A; Posch, Andreas E

    2017-10-17

    Biochemical DNA modification resembles a crucial regulatory layer among genetic information, environmental factors, and the transcriptome. To identify epigenetic susceptibility regions and novel biomarkers linked to myocardial dysfunction and heart failure, we performed the first multi-omics study in myocardial tissue and blood of patients with dilated cardiomyopathy and controls. Infinium human methylation 450 was used for high-density epigenome-wide mapping of DNA methylation in left-ventricular biopsies and whole peripheral blood of living probands. RNA deep sequencing was performed on the same samples in parallel. Whole-genome sequencing of all patients allowed exclusion of promiscuous genotype-induced methylation calls. In the screening stage, we detected 59 epigenetic loci that are significantly associated with dilated cardiomyopathy (false discovery corrected P ≤0.05), with 3 of them reaching epigenome-wide significance at P ≤5×10 -8 . Twenty-seven (46%) of these loci could be replicated in independent cohorts, underlining the role of epigenetic regulation of key cardiac transcription regulators. Using a staged multi-omics study design, we link a subset of 517 epigenetic loci with dilated cardiomyopathy and cardiac gene expression. Furthermore, we identified distinct epigenetic methylation patterns that are conserved across tissues, rendering these CpGs novel epigenetic biomarkers for heart failure. The present study provides to our knowledge the first epigenome-wide association study in living patients with heart failure using a multi-omics approach. © 2017 American Heart Association, Inc.

  9. On the Origin of De Novo Genes in Arabidopsis thaliana Populations.

    Science.gov (United States)

    Li, Zi-Wen; Chen, Xi; Wu, Qiong; Hagmann, Jörg; Han, Ting-Shen; Zou, Yu-Pan; Ge, Song; Guo, Ya-Long

    2016-08-03

    De novo genes, which originate from ancestral nongenic sequences, are one of the most important sources of protein-coding genes. This origination process is crucial for the adaptation of organisms. However, how de novo genes arise and become fixed in a population or species remains largely unknown. Here, we identified 782 de novo genes from the model plant Arabidopsis thaliana and divided them into three types based on the availability of translational evidence, transcriptional evidence, and neither transcriptional nor translational evidence for their origin. Importantly, by integrating multiple types of omics data, including data from genomes, epigenomes, transcriptomes, and translatomes, we found that epigenetic modifications (DNA methylation and histone modification) play an important role in the origination process of de novo genes. Intriguingly, using the transcriptomes and methylomes from the same population of 84 accessions, we found that de novo genes that are transcribed in approximately half of the total accessions within the population are highly methylated, with lower levels of transcription than those transcribed at other frequencies within the population. We hypothesized that, during the origin of de novo gene alleles, those neutralized to low expression states via DNA methylation have relatively high probabilities of spreading and becoming fixed in a population. Our results highlight the process underlying the origin of de novo genes at the population level, as well as the importance of DNA methylation in this process. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  10. Distribution of Fig Mosaic in Jordan

    Directory of Open Access Journals (Sweden)

    Khalil I. Al-Mughrabi

    2000-08-01

    Full Text Available Fig mosaic (FM is one of the most important diseases of figs in Jordan. A nationwide survey was conducted to determine the incidence and severity of this disease in trees and in seedlings propagated by cuttings in orchards and nurseries in 13 provinces and cities all over the country. Cultivars surveyed included Khdari, Mwazi, Zraki, Khartamani, Dafoori, Turki, Hamari, Esaili, Ajlouni, in addition to an Italian and a French cultivar. Disease severity varied from moderately severe to extremely severe with leaf malformation and fruit drop FM was found in all provinces. Incidence of FM, averaged over trees of all cultivars and all age categories, was 95.3%. Fig trees 3 years and older had the highest disease incidence, ranging from 93.3% to 100% in the different orchards. The Esaili cultivar had the lowest incidence ranging between 50% and100%, with an average of 76.5%. The highest FM incidence was on Dafoori. Of the most common cultivars, Khdari was the most susceptible. Jerash province had the highest percentage (12.5% of fig seedlings and trees in the most severe disease category. The highest percentage (27.8% of healthy fig seedlings and trees was in Irbid province. This paper reports the incidence of FM in various local and imported fig cultivars of different ages, and relates the spread of the disease to the method of fig propagation practiced in Jordan. Suggested solutions for the problem, which include the introduction of disease and pest free fig seedlings derived from tissue culture and the establishment of new rules and regulations to prevent the spread of the disease are discussed.

  11. Interfering Satellite RNAs of Bamboo mosaic virus

    Directory of Open Access Journals (Sweden)

    Kuan-Yu Lin

    2017-05-01

    Full Text Available Satellite RNAs (satRNAs are sub-viral agents that may interact with their cognate helper virus (HV and host plant synergistically and/or antagonistically. SatRNAs totally depend on the HV for replication, so satRNAs and HV usually evolve similar secondary or tertiary RNA structures that are recognized by a replication complex, although satRNAs and HV do not share an appreciable sequence homology. The satRNAs of Bamboo mosaic virus (satBaMV, the only satRNAs of the genus Potexvirus, have become one of the models of how satRNAs can modulate HV replication and virus-induced symptoms. In this review, we summarize the molecular mechanisms underlying the interaction of interfering satBaMV and BaMV. Like other satRNAs, satBaMV mimics the secondary structures of 5′- and 3′-untranslated regions (UTRs of BaMV as a molecular pretender. However, a conserved apical hairpin stem loop (AHSL in the 5′-UTR of satBaMV was found as the key determinant for downregulating BaMV replication. In particular, two unique nucleotides (C60 and C83 in the AHSL of satBaMVs determine the satBaMV interference ability by competing for the replication machinery. Thus, transgenic plants expressing interfering satBaMV could confer resistance to BaMV, and interfering satBaMV could be used as biological-control agent. Unlike two major anti-viral mechanisms, RNA silencing and salicylic acid-mediated immunity, our findings in plants by in vivo competition assay and RNA deep sequencing suggested replication competition is involved in this transgenic satBaMV-mediated BaMV interference. We propose how a single nucleotide of satBaMV can make a great change in BaMV pathogenicity and the underlying mechanism.

  12. Using "Arabidopsis" Genetic Sequences to Teach Bioinformatics

    Science.gov (United States)

    Zhang, Xiaorong

    2009-01-01

    This article describes a new approach to teaching bioinformatics using "Arabidopsis" genetic sequences. Several open-ended and inquiry-based laboratory exercises have been designed to help students grasp key concepts and gain practical skills in bioinformatics, using "Arabidopsis" leucine-rich repeat receptor-like kinase (LRR…

  13. Reference: 255 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available ases, AtIPK1 and AtIPK2beta, for the later steps of phytate synthesis in Arabidopsis thaliana. Coincident disruption...olyphosphate kinases in phosphate signaling biology. Generation of phytate-free seeds in Arabidopsis through disruption

  14. Arabidopsis CDS blastp result: AK108458 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK108458 002-143-D05 At4g35000.1 L-ascorbate peroxidase 3 (APX3) identical to ascorbat...e peroxidase 3 [Arabidopsis thaliana] GI:2444019, L-ascorbate peroxidase [Arabidopsis thaliana] gi|152379...1|emb|CAA66926; similar to ascorbate peroxidase [Gossypium hirsutum] gi|1019946|gb|AAB52954 2e-35 ...

  15. Arabidopsis CDS blastp result: AK070842 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK070842 J023074O14 At4g35000.1 L-ascorbate peroxidase 3 (APX3) identical to ascorbat...e peroxidase 3 [Arabidopsis thaliana] GI:2444019, L-ascorbate peroxidase [Arabidopsis thaliana] gi|1523791...|emb|CAA66926; similar to ascorbate peroxidase [Gossypium hirsutum] gi|1019946|gb|AAB52954 1e-112 ...

  16. Integration of microbiome and epigenome to decipher the pathogenesis of autoimmune diseases.

    Science.gov (United States)

    Chen, Beidi; Sun, Luxi; Zhang, Xuan

    2017-09-01

    The interaction between genetic predisposition and environmental factors are of great significance in the pathogenesis and development of autoimmune diseases (AIDs). The human mucosa is the most frequent site that interacts with the exterior environment, and commensal microbiota at the gut and other human mucosal cavities play a crucial role in the regulation of immune system. Growing evidence has shown that the compositional and functional changes of mucosal microbiota are closely related to AIDs. Gut dysbiosis not only influence the expression level of Toll-like receptors (TLRs) of antigen presenting cells, but also contribute to Th17/Treg imbalance. Epigenetic modifications triggered by environmental factors is an important mechanism that leads to altered gene expression. Researches addressing the role of DNA methylation, histone modification and non-coding RNA in AIDs have been increasing in recent years. Furthermore, studies showed that human microbiota and their metabolites can regulate immune cells and cytokines via epigenomic modifications. For example, short-chain fatty acids (SCFAs) produced by gut microbiota promote the differentiation of naïve T cell into Treg by suppressing histone deacetylases (HDACs). Therefore, we propose that dysbiosis and resulting metabolites may cause aberrant immune responses via epigenetic modifications, and lead to AIDs. With the development of high-throughput sequencing, metagenome analysis has been applied to investigate the dysbiosis in AIDs patients. We have tested the fecal, dental and salivary samples from treatment-naïve rheumatoid arthritis (RA) individuals by metagenomic shotgun sequencing and a metagenome-wide association study. Dysbiosis was detected in the gut and oral microbiomes of RA patients, but it was partially restored after treatment. We also found functional changes of microbiota and molecular mimicry of human antigens in RA individuals. By integrating the analysis of multi-omics of microbiome and

  17. Meaning of visualizing retinal cone mosaic on adaptive optics images.

    Science.gov (United States)

    Jacob, Julie; Paques, Michel; Krivosic, Valérie; Dupas, Bénédicte; Couturier, Aude; Kulcsar, Caroline; Tadayoni, Ramin; Massin, Pascale; Gaudric, Alain

    2015-01-01

    To explore the anatomic correlation of the retinal cone mosaic on adaptive optics images. Retrospective nonconsecutive observational case series. A retrospective review of the multimodal imaging charts of 6 patients with focal alteration of the cone mosaic on adaptive optics was performed. Retinal diseases included acute posterior multifocal placoid pigment epitheliopathy (n = 1), hydroxychloroquine retinopathy (n = 1), and macular telangiectasia type 2 (n = 4). High-resolution retinal images were obtained using a flood-illumination adaptive optics camera. Images were recorded using standard imaging modalities: color and red-free fundus camera photography; infrared reflectance scanning laser ophthalmoscopy, fluorescein angiography, indocyanine green angiography, and spectral-domain optical coherence tomography (OCT) images. On OCT, in the marginal zone of the lesions, a disappearance of the interdigitation zone was observed, while the ellipsoid zone was preserved. Image recording demonstrated that such attenuation of the interdigitation zone co-localized with the disappearance of the cone mosaic on adaptive optics images. In 1 case, the restoration of the interdigitation zone paralleled that of the cone mosaic after a 2-month follow-up. Our results suggest that the interdigitation zone could contribute substantially to the reflectance of the cone photoreceptor mosaic. The absence of cones on adaptive optics images does not necessarily mean photoreceptor cell death. Copyright © 2015 Elsevier Inc. All rights reserved.

  18. Mosaic boreal landscapes with open and forested wetlands

    International Nuclear Information System (INIS)

    Sjoeberg, K.; Ericson, L.

    1997-01-01

    We review patterns and processes important for biodiversity in the Fennoscandian boreal forest, describe man's past and present impact and outline a strategy for conservation. The boreal landscape was earlier characterized by a mosaic of open and forested wetlands and forests. Drainage and felling operation have largely changed that pattern. Several organisms depend upon the landscape mosaic. Natural ecotones between mire and forest provide food resources predictable in space and time contrasting to unpredictable edges in the silvicultured landscape. The mosaic is also a prerequisite for organisms dependent on non-substitutable resources in the landscape. The importance of swamp forests has increased as they function as refugia for earlier more widespread old-growth species. Programmes for maintaining biodiversity in the boreal landscape should include the following points. First, the natural mosaic with open and forested wetlands must be maintained. Second, swamp forests must receive a general protection as they often constitute the only old-growth patches in the landscape. Third, we need to restore earlier disturbance regimes. Present strategy plans for conservation are insufficient, as they imply that a too large proportion of boreal organisms will not be able to survive outside protected areas. Instead, we need to focus more on how to preserve organisms in the man-influenced landscape. As a first step we need to understand how organisms are distributed in landscapes at various spatial scales. We need studies in landscapes where the original mosaic has faced various degrees of fragmentation. (au) 124 refs

  19. Efisiensi Tular Benih Squash mosaic virus pada Cucurbitaceae

    Directory of Open Access Journals (Sweden)

    Susanti Mugi Lestari

    2014-09-01

    Full Text Available Infection of viruses on Cucurbitaceae may cause high yield and economic losses. Squash mosaic virus is a seed borne virus and among the most important virus infecting Cucurbitaceae. The aims of these research was to detect infection of several viruses on Cucurbitaceae and to examine seed transmission efficiency of SqMV. Detection of Cucumber mosaic virus (CMV, Squash mosaic virus (SqMV, Watermelon mosaic virus-2 (WMV-2, Zucchini yellow mosaic virus (ZYMV, and Tobacco ringspot virus (TRSV from field samples and seeds was conducted using Indirect-ELISA method. Infection of CMV, SqMV and ZYMV was detected from field samples. Seed transmission of SqMV on commercial seeds of bottle gourd, watermelon, zucchini, cabocha, cucumber, and melon was 13, 13, 33, 73, 100, and 100%, respectively. Seed transmission of ZYMV was only occurred on bottle gourd and zucchini, i.e. 13.3% and 26.67%, respectively. Infection of SqMV through F2 seed was determined from cucumber, bottle gourd, and melon, i.e. 93, 100, and 100%, respectively. Therefore, the status of SqMV as quarantine pest should be evaluated since SqMV was already found in West Java.

  20. LBA-ECO LC-15 JERS-1 Synthetic Aperture Radar, 1- km Mosaic, Amazon Basin: 1995-1996

    Data.gov (United States)

    National Aeronautics and Space Administration — This data set contains two image mosaics of L-band radar backscatter and two image mosaics of first order texture. The two backscatter images are mosaics of L-band...

  1. The Arabidopsis eukaryotic initiation factor (iso)4E is dispensable for plant growth but required for susceptibility to potyviruses.

    Science.gov (United States)

    Duprat, Anne; Caranta, Carole; Revers, Frédéric; Menand, Benoît; Browning, Karen S; Robaglia, Christophe

    2002-12-01

    An Arabidopsis thaliana line bearing a transposon insertion in the gene coding for the isozyme form of the plant-specific cap-binding protein, eukaryotic initiation factor (iso) 4E (eIF (iso) 4E), has been isolated. This mutant line completely lacks both eIF(iso)4E mRNA and protein, but was found to have a phenotype and fertility indistinguishable from wild-type plants under standard laboratory conditions. In contrast, the amount of the related eIF4E protein was found to increase in seedling extracts. Furthermore, polysome analysis shows that the mRNA encoding eIF4E was being translated at increased levels. Given the known interaction between cap-binding proteins and potyviral genome-linked proteins (VPg), this plant line was challenged with two potyviruses, Turnip mosaic virus (TuMV) and Lettuce mosaic virus (LMV) and was found resistant to both, but not to the Nepovirus, Tomato black ring virus (TBRV) and the Cucumovirus, Cucumber mosaic virus (CMV). Together with previous data showing that the VPg-eIF4E interaction is necessary for virus infectivity and upregulates genome amplification, this shows that the eIF4E proteins are specifically recruited for the replication cycle of potyviruses.

  2. Epigenomic mechanisms of early adversity and HPA dysfunction: Considerations for PTSD research

    Directory of Open Access Journals (Sweden)

    Patrick O McGowan

    2013-09-01

    Full Text Available Childhood adversity can have life-long consequences for the response to stressful events later in life. Abuse or severe neglect are well known risk factors for post-traumatic stress disorder (PTSD, at least in part via changes in neural systems mediating the endocrine response to stress. Determining the biological signatures of risk for stress-related mental disorders such as PTSD is important for identifying homogenous subgroups and improving treatment options. This review will focus on epigenetic regulation in early life by adversity and parental care – prime mediators of offspring neurodevelopment - in order to address several questions: (1 what have studies of humans and analogous animal models taught us about molecular mechanisms underlying changes in stress-sensitive physiological systems in response to early life trauma? (2 What are the considerations for studies relating early adversity and PTSD risk, going forward? I will summarize studies in animals and humans that address the epigenetic response to early adversity in the brain and in peripheral tissues. In so doing, I will describe work on the Glucocorticoid Receptor (GR and other well-characterized genes within the stress response pathway and then turn to genomic studies to illustrate the use of increasingly powerful high-throughput approaches to the study of epigenomic mechanisms.

  3. Epigenome-wide association study of DNA methylation in narcolepsy: an integrated genetic and epigenetic approach.

    Science.gov (United States)

    Shimada, Mihoko; Miyagawa, Taku; Toyoda, Hiromi; Tokunaga, Katsushi; Honda, Makoto

    2018-04-01

    Narcolepsy with cataplexy, which is a hypersomnia characterized by excessive daytime sleepiness and cataplexy, is a multifactorial disease caused by both genetic and environmental factors. Several genetic factors including HLA-DQB1*06:02 have been identified; however, the disease etiology is still unclear. Epigenetic modifications, such as DNA methylation, have been suggested to play an important role in the pathogenesis of complex diseases. Here, we examined DNA methylation profiles of blood samples from narcolepsy and healthy control individuals and performed an epigenome-wide association study (EWAS) to investigate methylation loci associated with narcolepsy. Moreover, data from the EWAS and a previously performed narcolepsy genome-wide association study were integrated to search for methylation loci with causal links to the disease. We found that (1) genes annotated to the top-ranked differentially methylated positions (DMPs) in narcolepsy were associated with pathways of hormone secretion and monocarboxylic acid metabolism. (2) Top-ranked narcolepsy-associated DMPs were significantly more abundant in non-CpG island regions and more than 95 per cent of such sites were hypomethylated in narcolepsy patients. (3) The integrative analysis identified the CCR3 region where both a single methylation site and multiple single-nucleotide polymorphisms were found to be associated with the disease as a candidate region responsible for narcolepsy. The findings of this study suggest the importance of future replication studies, using methylation technologies with wider genome coverage and/or larger number of samples, to confirm and expand on these results.

  4. An epigenomics approach to individual differences and its translation to neuropsychiatric conditions.

    Science.gov (United States)

    Sweatt, J David; Tamminga, Carol A

    2016-09-01

    This review concerns epigenetic mechanisms and their roles in conferring interindividual differences, especially as related to experientially acquired and genetically driven changes in central nervous system (CNS) function. In addition, the review contains commentary regarding the possible ways in which epigenomic changes may contribute to neuropsychiatric conditions and disorders and ways in which epigenotyping might be cross-correlated with clinical phenotyping in the context of precision medicine. The review begins with a basic description of epigenetic marking in the CNS and how these changes are powerful regulators of gene readout. Means for characterizing the individual epigenotype are briefly described, with a focus on DNA cytosine methylation as a readily measurable, stable epigenetic mark. This background enables a discussion of how "epigenotyping" might be integrated along with genotyping and deep phenotyping as a means of implementing advanced precision medicine. Finally, the commentary addresses two exemplars when considering how epigenotype may correlate with and modulate cognitive and behavioral phenotype: schizophrenia and Rett syndrome. These two disorders provide an interesting compare-and-contrast example regarding possible epigenotypic regulation of behavior: whereas Rett syndrome is clearly established as being caused by disruption of the function of an epigenetic "reader" of the DNA cytosine methylome-methyl-CpG-binding protein 2 (MeCP2)-the case for a role for epigenetic mechanisms in schizophrenia is still quite speculative.

  5. Naked Mole Rat Cells Have a Stable Epigenome that Resists iPSC Reprogramming

    Directory of Open Access Journals (Sweden)

    Li Tan

    2017-11-01

    Full Text Available Naked mole rat (NMR is a valuable model for aging and cancer research due to its exceptional longevity and cancer resistance. We observed that the reprogramming efficiency of NMR fibroblasts in response to OSKM was drastically lower than that of mouse fibroblasts. Expression of SV40 LargeT antigen (LT dramatically improved reprogramming of NMR fibroblasts. Inactivation of Rb alone, but not p53, was sufficient to improve reprogramming efficiency, suggesting that NMR chromatin may be refractory to reprogramming. Analysis of the global histone landscape revealed that NMR had higher levels of repressive H3K27 methylation marks and lower levels of activating H3K27 acetylation marks than mouse. ATAC-seq revealed that in NMR, promoters of reprogramming genes were more closed than mouse promoters, while expression of LT led to massive opening of the NMR promoters. These results suggest that NMR displays a more stable epigenome that resists de-differentiation, contributing to the cancer resistance and longevity of this species.

  6. Epigenomic Regulation of Androgen Receptor Signaling: Potential Role in Prostate Cancer Therapy

    Directory of Open Access Journals (Sweden)

    Vito Cucchiara

    2017-01-01

    Full Text Available Androgen receptor (AR signaling remains the major oncogenic pathway in prostate cancer (PCa. Androgen-deprivation therapy (ADT is the principle treatment for locally advanced and metastatic disease. However, a significant number of patients acquire treatment resistance leading to castration resistant prostate cancer (CRPC. Epigenetics, the study of heritable and reversible changes in gene expression without alterations in DNA sequences, is a crucial regulatory step in AR signaling. We and others, recently described the technological advance Chem-seq, a method to identify the interaction between a drug and the genome. This has permitted better understanding of the underlying regulatory mechanisms of AR during carcinogenesis and revealed the importance of epigenetic modifiers. In screening for new epigenomic modifiying drugs, we identified SD-70, and found that this demethylase inhibitor is effective in CRPC cells in combination with current therapies. The aim of this review is to explore the role of epigenetic modifications as biomarkers for detection, prognosis, and risk evaluation of PCa. Furthermore, we also provide an update of the recent findings on the epigenetic key processes (DNA methylation, chromatin modifications and alterations in noncoding RNA profiles involved in AR expression and their possible role as therapeutic targets.

  7. Epigenomic profiling of DNA methylation in paired prostate cancer versus adjacent benign tissue.

    Science.gov (United States)

    Geybels, Milan S; Zhao, Shanshan; Wong, Chao-Jen; Bibikova, Marina; Klotzle, Brandy; Wu, Michael; Ostrander, Elaine A; Fan, Jian-Bing; Feng, Ziding; Stanford, Janet L

    2015-12-01

    Aberrant DNA methylation may promote prostate carcinogenesis. We investigated epigenome-wide DNA methylation profiles in prostate cancer (PCa) compared to adjacent benign tissue to identify differentially methylated CpG sites. The study included paired PCa and adjacent benign tissue samples from 20 radical prostatectomy patients. Epigenetic profiling was done using the Infinium HumanMethylation450 BeadChip. Linear models that accounted for the paired study design and False Discovery Rate Q-values were used to evaluate differential CpG methylation. mRNA expression levels of the genes with the most differentially methylated CpG sites were analyzed. In total, 2,040 differentially methylated CpG sites were identified in PCa versus adjacent benign tissue (Q-value Cancer Genome Atlas (TCGA) data provided confirmatory evidence for our findings. This study of PCa versus adjacent benign tissue showed many differentially methylated CpGs and regions in and outside gene promoter regions, which may potentially be used for the development of future epigenetic-based diagnostic tests or as therapeutic targets. © 2015 Wiley Periodicals, Inc.

  8. Real-time image mosaicing for medical applications.

    Science.gov (United States)

    Loewke, Kevin E; Camarillo, David B; Jobst, Christopher A; Salisbury, J Kenneth

    2007-01-01

    In this paper we describe the development of a robotically-assisted image mosaicing system for medical applications. The processing occurs in real-time due to a fast initial image alignment provided by robotic position sensing. Near-field imaging, defined by relatively large camera motion, requires translations as well as pan and tilt orientations to be measured. To capture these measurements we use 5-d.o.f. sensing along with a hand-eye calibration to account for sensor offset. This sensor-based approach speeds up the mosaicing, eliminates cumulative errors, and readily handles arbitrary camera motions. Our results have produced visually satisfactory mosaics on a dental model but can be extended to other medical images.

  9. A List of Astronomical Meetings Available via Mosaic

    Science.gov (United States)

    Bryson, E.; Crabtree, D.

    We have been making a list of astronomical and related meetings available electronically for a number of years. Recently, several meeting organizers have made information about their meetings available via anonymous ftp or even NCSA Mosaic. We have produced a new version of our electronic meeting list available via NCSA Mosaic which provides links to the information being provided electronically. Depending upon the amount of information being provided for an individual meeting, it may be possible for a user browsing the list of meetings to click on the meeting of interest, fill out a registration form, download maps, browse abstracts, etc. We hope the availability of this service will encourage other meeting organizers to make information about their meetings available electronically and to take advantage of new technology such as NCSA Mosaic. URL: http:// cadcwww.dao.nrc.calmeetings/meetings.html

  10. Mosaic serine proteases in the mammalian central nervous system.

    Science.gov (United States)

    Mitsui, Shinichi; Watanabe, Yoshihisa; Yamaguchi, Tatsuyuki; Yamaguchi, Nozomi

    2008-01-01

    We review the structure and function of three kinds of mosaic serine proteases expressed in the mammalian central nervous system (CNS). Mosaic serine proteases have several domains in the proenzyme fragment, which modulate proteolytic function, and a protease domain at the C-terminus. Spinesin/TMPRSS5 is a transmembrane serine protease whose presynaptic distribution on motor neurons in the spinal cord suggests that it is significant for neuronal plasticity. Cell type-specific alternative splicing gives this protease diverse functions by modulating its intracellular localization. Motopsin/PRSS12 is a mosaic protease, and loss of its function causes mental retardation. Recent reports indicate the significance of this protease for cognitive function. We mention the fibrinolytic protease, tissue plasminogen activator (tPA), which has physiological and pathological functions in the CNS.

  11. Image Mosaic Method Based on SIFT Features of Line Segment

    Directory of Open Access Journals (Sweden)

    Jun Zhu

    2014-01-01

    Full Text Available This paper proposes a novel image mosaic method based on SIFT (Scale Invariant Feature Transform feature of line segment, aiming to resolve incident scaling, rotation, changes in lighting condition, and so on between two images in the panoramic image mosaic process. This method firstly uses Harris corner detection operator to detect key points. Secondly, it constructs directed line segments, describes them with SIFT feature, and matches those directed segments to acquire rough point matching. Finally, Ransac method is used to eliminate wrong pairs in order to accomplish image mosaic. The results from experiment based on four pairs of images show that our method has strong robustness for resolution, lighting, rotation, and scaling.

  12. Extended image differencing for change detection in UAV video mosaics

    Science.gov (United States)

    Saur, Günter; Krüger, Wolfgang; Schumann, Arne

    2014-03-01

    Change detection is one of the most important tasks when using unmanned aerial vehicles (UAV) for video reconnaissance and surveillance. We address changes of short time scale, i.e. the observations are taken in time distances from several minutes up to a few hours. Each observation is a short video sequence acquired by the UAV in near-nadir view and the relevant changes are, e.g., recently parked or moved vehicles. In this paper we extend our previous approach of image differencing for single video frames to video mosaics. A precise image-to-image registration combined with a robust matching approach is needed to stitch the video frames to a mosaic. Additionally, this matching algorithm is applied to mosaic pairs in order to align them to a common geometry. The resulting registered video mosaic pairs are the input of the change detection procedure based on extended image differencing. A change mask is generated by an adaptive threshold applied to a linear combination of difference images of intensity and gradient magnitude. The change detection algorithm has to distinguish between relevant and non-relevant changes. Examples for non-relevant changes are stereo disparity at 3D structures of the scene, changed size of shadows, and compression or transmission artifacts. The special effects of video mosaicking such as geometric distortions and artifacts at moving objects have to be considered, too. In our experiments we analyze the influence of these effects on the change detection results by considering several scenes. The results show that for video mosaics this task is more difficult than for single video frames. Therefore, we extended the image registration by estimating an elastic transformation using a thin plate spline approach. The results for mosaics are comparable to that of single video frames and are useful for interactive image exploitation due to a larger scene coverage.

  13. First Complete Genome Sequence of a Watermelon Mosaic Virus Isolated from Watermelon in the United States

    OpenAIRE

    Rajbanshi, Naveen; Ali, Akhtar

    2016-01-01

    Watermelon mosaic virus was first reported in 1965 from the Rio Grande Valley, TX. We report here the first complete genome sequence of a watermelon mosaic virus isolate from watermelon collected from the Rio Grande Valley of Texas.

  14. Turner syndrome and 45,X/47,XXX mosaicism.

    Science.gov (United States)

    Akbas, E; Mutluhan, H; Savasoglu, K; Soylemez, F; Ozturk, I; Yazici, G

    2009-01-01

    The occurrence of double aneuploidy is a relatively rare phenomenon. We report on a 17-year-old woman with short stature, minimal pubic and axillar hair and short hands. In cultured lymphocyte a double aneuploidy mosaicism was detected, consisting of a cell line with trisomy for X chromosome and a cell line with monosomy for the X-chromosome and no cell line with a normal karyotype. To our knowledge, this is the first case of mosaic 45,X/47,XXX in Turkey.

  15. Prenatal diagnosis and gonadal findings in X/XXX mosaicism.

    Science.gov (United States)

    Kohn, G; Cohen, M M; Beyth, Y; Ornoy, A

    1977-01-01

    Prenatal diagnosis of a case of X/XXX mosaicism is presented. In spite of the fact that over 50% of the cells cultured from both ovaries were trisomic for the X chromosome, fetal öocytes were rarely found. This case illustrates that the presence of a triple-X cell line, even in a relatively high percentage of ovarian cells, does not necessarily protect the ovary from 'aöogenesis'. This observation might prove useful in the counselling of future cases involving the prenatal detection of sex chromosome mosaicism. Images PMID:856232

  16. Expression of artificial microRNAs in transgenic Arabidopsis thaliana confers virus resistance.

    Science.gov (United States)

    Niu, Qi-Wen; Lin, Shih-Shun; Reyes, Jose Luis; Chen, Kuan-Chun; Wu, Hui-Wen; Yeh, Shyi-Dong; Chua, Nam-Hai

    2006-11-01

    Plant microRNAs (miRNAs) regulate the abundance of target mRNAs by guiding their cleavage at the sequence complementary region. We have modified an Arabidopsis thaliana miR159 precursor to express artificial miRNAs (amiRNAs) targeting viral mRNA sequences encoding two gene silencing suppressors, P69 of turnip yellow mosaic virus (TYMV) and HC-Pro of turnip mosaic virus (TuMV). Production of these amiRNAs requires A. thaliana DICER-like protein 1. Transgenic A. thaliana plants expressing amiR-P69(159) and amiR-HC-Pro(159) are specifically resistant to TYMV and TuMV, respectively. Expression of amiR-TuCP(159) targeting TuMV coat protein sequences also confers specific TuMV resistance. However, transgenic plants that express both amiR-P69(159) and amiR-HC-Pro(159) from a dimeric pre-amiR-P69(159)/amiR-HC-Pro(159) transgene are resistant to both viruses. The virus resistance trait is displayed at the cell level and is hereditable. More important, the resistance trait is maintained at 15 degrees C, a temperature that compromises small interfering RNA-mediated gene silencing. The amiRNA-mediated approach should have broad applicability for engineering multiple virus resistance in crop plants.

  17. A plant small polypeptide is a novel component of DNA-binding protein phosphatase 1-mediated resistance to plum pox virus in Arabidopsis.

    Science.gov (United States)

    Castelló, María José; Carrasco, Jose Luis; Navarrete-Gómez, Marisa; Daniel, Jacques; Granot, David; Vera, Pablo

    2011-12-01

    DNA-binding protein phosphatases (DBPs) have been identified as a novel class of plant-specific regulatory factors playing a role in plant-virus interactions. NtDBP1 from tobacco (Nicotiana tabacum) was shown to participate in transcriptional regulation of gene expression in response to virus infection in compatible interactions, and AtDBP1, its closest relative in the model plant Arabidopsis (Arabidopsis thaliana), has recently been found to mediate susceptibility to potyvirus, one of the most speciose taxa of plant viruses. Here, we report on the identification of a novel family of highly conserved small polypeptides that interact with DBP1 proteins both in tobacco and Arabidopsis, which we have designated DBP-interacting protein 2 (DIP2). The interaction of AtDIP2 with AtDBP1 was demonstrated in vivo by bimolecular fluorescence complementation, and AtDIP2 was shown to functionally interfere with AtDBP1 in yeast. Furthermore, reducing AtDIP2 gene expression leads to increased susceptibility to the potyvirus Plum pox virus and to a lesser extent also to Turnip mosaic virus, whereas overexpression results in enhanced resistance. Therefore, we describe a novel family of conserved small polypeptides in plants and identify AtDIP2 as a novel host factor contributing to resistance to potyvirus in Arabidopsis.

  18. Functional Characterization of the Apple RING E3 Ligase MdMIEL1 in Transgenic Arabidopsis

    Directory of Open Access Journals (Sweden)

    Jianping AN

    2017-03-01

    Full Text Available E3 ubiquitin ligases are involved in various physiological processes, and they play pivotal roles in growth and development. In this study, we identified a previously unknown gene in the apple fruit (Malus × domestica and named it MdMIEL1. The MdMIEL1 gene encoded a protein that contained a zinc-finger domain at its N-terminus and a RING-finger motif at its C-terminus. To investigate MdMIEL1 functions, we generated transgenic Arabidopsis lines expressing the MdMIEL1 gene under the control of the Cauliflower mosaic virus 35S promoter. Interestingly, ectopic expression of MdMIEL1 in Arabidopsis produced multiple phenotypes, including early germination, early flowering and a lateral root number increase relative to wild-type plants. Further analysis indicated that MdMIEL1 regulated lateral root initiation by increasing auxin accumulation in the roots. In a word, these results suggest that, MdMIEL1 as a novel RING-finger ubiquitin ligase influences plant growth and development, and highlight that MdMIEL1 regulates lateral root growth.

  19. First report of Apple necrotic mosaic virus infecting apple trees in Korea

    Science.gov (United States)

    In September 2016, two apple trees (Malus domestica Borkh) cv. Shinano Sweet showing bright cream spot and mosaic patterns on leaves were observed in Pocheon, South Korea. Mosaic symptoms are common on leaves of apple trees infected with Apple mosaic virus (ApMV). Symptomatic leaves were tested by e...

  20. Health Profiles of Mosaic Versus Non-mosaic FMR1 Premutation Carrier Mothers of Children With Fragile X Syndrome

    Directory of Open Access Journals (Sweden)

    Marsha R. Mailick

    2018-05-01

    Full Text Available The FMR1 premutation is of increasing interest to the FXS community, as questions about a primary premutation phenotype warrant research attention. 100 FMR1 premutation carrier mothers (mean age = 58; 67–138 CGG repeats of adults with fragile X syndrome were studied with respect to their physical and mental health, motor, and neurocognitive characteristics. We explored the correlates of CGG repeat mosaicism in women with expanded alleles. Mothers provided buccal swabs from which DNA was extracted and the FMR1 CGG genotyping was performed (Amplidex Kit, Asuragen. Mothers were categorized into three groups: Group 1: premutation non-mosaic (n = 45; Group 2: premutation mosaic (n = 41, and Group 3: premutation/full mutation mosaic (n = 14. Group 2 mothers had at least two populations of cells with different allele sizes in the premutation range besides their major expanded allele. Group 3 mothers had a very small population of cells in the full mutation range (>200 CGGs in addition to one or multiple populations of cells with different allele sizes in the premutation range. Machine learning (random forest was used to identify symptoms and conditions that correctly classified mothers with respect to mosaicism; follow-up comparisons were made to characterize the three groups. In categorizing mosaicism, the random forest yielded significantly better classification than random classification, with overall area under the receiver operating characteristic curve (AUROC of 0.737. Among the most important symptoms and conditions that contributed to the classification were anxiety, menopause symptoms, executive functioning limitations, and difficulty walking several blocks, with the women who had full mutation mosaicism (Group 3 unexpectedly having better health. Although only 14 premutation carrier mothers in the present sample also had a small population of full mutation cells, their profile of comparatively better health, mental health, and executive

  1. [Epigenome: what we learned from Rett syndrome, a neurological disease caused by mutation of a methyl-CpG binding protein].

    Science.gov (United States)

    Kubota, Takeo

    2013-01-01

    Epigenome is defined as DNA and histone modification-dependent gene regulation system. Abnormalities in this system are known to cause various neuro-developmental diseases. We recently reported that neurological symptoms of Rett syndrome, which is an autistic disorder caused by mutations in methyl-CpG binding protein 2 (MeCP2), was associated with failure of epigenomic gene regulation in neuronal cells, and that clinical differences in the identical twins with Rett syndrome in the differences in DNA methylation in neuronal genes, but not caused by DNA sequence differences. Since central nervus system requires precise gene regulation, neurological diseases including Alzheimer and Parkinson diseases may be caused by acquired DNA modification (epigenomic) changes that results in aberrant gene regulation as well as DNA sequence changes congenitally occurred (mutation).

  2. Production of yam mosaic virus monoclonal antibodies in mice ...

    African Journals Online (AJOL)

    Administrator

    2011-09-19

    Sep 19, 2011 ... 4AVRDC-The World Vegetable Center, Shanhua, Taiwan. Accepted 11 August, 2011. Yam mosaic virus (YMV) ... leaves and non-infected tissue culture yam leaves. The antibody produced had a titre of ... systems for in-vitro production of monoclonal antibodies, such as standard tissue culture techniques,.

  3. Distribution and molecular detection of apple mosaic virus in apple ...

    African Journals Online (AJOL)

    ... pair for real time polymerase chain reaction (RT-PCR) detection of coat protein gene for Turkish ApMV isolates. Apple mosaic virus isolates were collected in 2007 to 2010 and the presence of the pathogen was detected by double antibody sandwich enzyme-linked immunosorbent assay (DAS-ELISA) and RT-PCR tests.

  4. Research of x-ray automatic image mosaic method

    Science.gov (United States)

    Liu, Bin; Chen, Shunan; Guo, Lianpeng; Xu, Wanpeng

    2013-10-01

    Image mosaic has widely applications value in the fields of medical image analysis, and it is a technology that carries on the spatial matching to a series of image which are overlapped with each other, and finally builds a seamless and high quality image which has high resolution and big eyeshot. In this paper, the method of grayscale cutting pseudo-color enhancement was firstly used to complete the mapping transformation from gray to the pseudo-color, and to extract SIFT features from the images. And then by making use of a similar measure of NCC (normalized cross correlation - Normalized cross-correlation), the method of RANSAC (Random Sample Consensus) was used to exclude the pseudofeature points right in order to complete the exact match of feature points. Finally, seamless mosaic and color fusion were completed by using wavelet multi-decomposition. The experiment shows that the method we used can effectively improve the precision and automation of the medical image mosaic, and provide an effective technical approach for automatic medical image mosaic.

  5. Mosaic protein and nucleic acid vaccines against hepatitis C virus

    Science.gov (United States)

    Yusim, Karina; Korber, Bette T. M.; Kuiken, Carla L.; Fischer, William M.

    2013-06-11

    The invention relates to immunogenic compositions useful as HCV vaccines. Provided are HCV mosaic polypeptide and nucleic acid compositions which provide higher levels of T-cell epitope coverage while minimizing the occurrence of unnatural and rare epitopes compared to natural HCV polypeptides and consensus HCV sequences.

  6. Purification and properties of cowpea mosaic virus RNA replicase

    NARCIS (Netherlands)

    Zabel, P.

    1978-01-01

    This thesis concerns the partial purification and properties of an RNA-dependent RNA polymerase (RNA replicase) produced upon infection of Vigna unguiculata plants with Cowpea Mosaic Virus (CPMV). The enzyme is believed to be coded, at least in part, by the virus genome and to

  7. Potential of marker-assisted selection for Tobacco mosaic ...

    African Journals Online (AJOL)

    Tobacco mosaic tobamovirus (TMV) is one of the most destructive virus threatening worldwide tobacco production. Use of host resistance is the best method of control. The N-gene was introgressed into tobacco from Nicotiana glutinosa to confer hypersensitive resistance to TMV. Phenotypic selection of TMV resistant ...

  8. Coat protein sequence shows that Cucumber mosaic virus isolate

    Indian Academy of Sciences (India)

    A viral disease was identified on geraniums (Pelargonium spp.) grown in a greenhouse at the Institute of Himalayan Bioresource Technology (IHBT), Palampur, exhibiting mild mottling and stunting. The causal virus (Cucumber mosaic virus, CMV) was identified and characterized on the basis of host range, aphid ...

  9. Variability in alternanthera mosaic virus isolates from different hosts

    Science.gov (United States)

    We have determined the complete genome sequences of Alternanthera mosaic virus phlox isolate PA (AltMV-PA) and four infectious clone variants derived from AltMV-SP, as well as partial sequences of other isolates from various types of phlox, and from portulaca, nandina, and cineraria. Phylogenetic co...

  10. Simultaneous detection of Apple mosaic virus in cultivated hazelnuts ...

    African Journals Online (AJOL)

    The most economically damaging ilarvirus affecting hazelnut on a worldwide scale is the related apple mosaic virus (ApMV). Attempts were made to isolate the virus RNA from hazelnut tissues using different extraction methods. The most suitable extraction method that could detect the virus occurring naturally in hazelnut by ...

  11. Orthophoto Mosaic (2012) for Coral Bay, St. John

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This 0.3x0.3 meter imagery mosaic of Coral Bay, St. John in the U.S. Virgin Islands was created by the National Oceanic and Atmospheric Administration (NOAA) using a...

  12. Orthophoto Mosaic (2012) of the St. Thomas East End Reserve

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This 0.3x0.3 meter imagery mosaic of the St. Thomas East End Reserve (STEER), St. Thomas in the U.S. Virgin Islands was created by the National Oceanic and...

  13. Turner/Down mosaicism: A case report | Jansen | South African ...

    African Journals Online (AJOL)

    A 45,X/47,XX, +21 mosaicism (80%:20%) in a young girl with clinical features of Down syndrome is reported. The proportion of 45,X:47,XX, +21 cells present in peripheral lymphocytes does not necessarily have a profound effect on the phenotype. A possible explanation for the occurrence of double aneuploidy is given.

  14. Transmission of Switchgrass mosaic virus by Graminella aureovitatta

    Science.gov (United States)

    Switchgrass mosaic virus (SwMV) was identified in switchgrass (Panicum virgatum) and was proposed as a new marafivirus based on its genome sequence and comparison with its closest relative, Maize rayado fino virus (MRFV), a type member of the genus, Marafivirus. MRFV only infects maize (Zea mays) an...

  15. The use of biolistic inoculation of cassava mosaic begomoviruses in ...

    African Journals Online (AJOL)

    These cassava cultivars were challenged with both DNA A and B components of the infectious clones named above using particle gun bombardment. The cassava cultivars showed varying degrees of susceptibility/resistance to the two infectious clones used. All symptoms of Cassava Mosaic Disease (CMD) observed were ...

  16. Neutron diffraction on a large block mosaic crystal

    International Nuclear Information System (INIS)

    Kim Chir Sen; Nitts, V.V.

    1985-01-01

    The neutron diffraction by the mosaic single crystal with size of crystallites sufficient to achieve the primary extinction saturation is considered. Two cases where the proportionality between the reflection intensity and the structure amplitude is performed are analysed. Such a dependence is convenient for structure investigations. The difficulties connected with the accounting of the extinction are eliminated considerably

  17. Proteins synthesized in tobacco mosaic virus infected protoplasts

    NARCIS (Netherlands)

    Huber, R.

    1979-01-01

    The study described here concerns the proteins, synthesized as a result of tobacco mosaic virus (TMV) multiplication in tobacco protoplasts and in cowpea protoplasts. The identification of proteins involved in the TMV infection, for instance in the virus RNA replication, helps to elucidate

  18. Familial recurrences of FOXG1-related disorder: Evidence for mosaicism.

    Science.gov (United States)

    McMahon, Kelly Q; Papandreou, Apostolos; Ma, Mandy; Barry, Brenda J; Mirzaa, Ghayda M; Dobyns, William B; Scott, Richard H; Trump, Natalie; Kurian, Manju A; Paciorkowski, Alex R

    2015-12-01

    FOXG1-related disorders are caused by heterozygous mutations in FOXG1 and result in a spectrum of neurodevelopmental phenotypes including postnatal microcephaly, intellectual disability with absent speech, epilepsy, chorea, and corpus callosum abnormalities. The recurrence risk for de novo mutations in FOXG1-related disorders is assumed to be low. Here, we describe three unrelated sets of full siblings with mutations in FOXG1 (c.515_577del63, c.460dupG, and c.572T > G), representing familial recurrence of the disorder. In one family, we have documented maternal somatic mosaicism for the FOXG1 mutation, and all of the families presumably represent parental gonadal (or germline) mosaicism. To our knowledge, mosaicism has not been previously reported in FOXG1-related disorders. Therefore, this report provides evidence that germline mosaicism for FOXG1 mutations is a likely explanation for familial recurrence and should be considered during recurrence risk counseling for families of children with FOXG1-related disorders. © 2015 Wiley Periodicals, Inc.

  19. Protection of melon plants against Cucumber mosaic virus infection ...

    African Journals Online (AJOL)

    This study was carried out to characterize a virus causing severe mosaic, yellowing, stunting and leaf deformation on melon (Cucumis melo L.), and evaluate the capacity of Pseudomonas fluorescens as biofertilizer to improve plant growth and restrict the accumulation of the virus in the plant. The virus was identified as an ...

  20. Introduction to the World Wide Web and Mosaic

    Science.gov (United States)

    Youngblood, Jim

    1994-01-01

    This tutorial provides an introduction to some of the terminology related to the use of the World Wide Web and Mosaic. It is assumed that the user has some prior computer experience. References are included to other sources of additional information.

  1. Bemisia tabaci : the whitefly vector of cassava mosaic geminiviruses ...

    African Journals Online (AJOL)

    The ecology of the Bemisia tabaci/cassava/African cassava mosaic virus (ACMV) pathosystem is reviewed briefly with special attention given to the parameters affecting the pattern of population development of B. tabaci. Significant gaps in our understanding of this system remain, particularly concerning the importance of ...

  2. gmos: Rapid Detection of Genome Mosaicism over Short Evolutionary Distances.

    Science.gov (United States)

    Domazet-Lošo, Mirjana; Domazet-Lošo, Tomislav

    2016-01-01

    Prokaryotic and viral genomes are often altered by recombination and horizontal gene transfer. The existing methods for detecting recombination are primarily aimed at viral genomes or sets of loci, since the expensive computation of underlying statistical models often hinders the comparison of complete prokaryotic genomes. As an alternative, alignment-free solutions are more efficient, but cannot map (align) a query to subject genomes. To address this problem, we have developed gmos (Genome MOsaic Structure), a new program that determines the mosaic structure of query genomes when compared to a set of closely related subject genomes. The program first computes local alignments between query and subject genomes and then reconstructs the query mosaic structure by choosing the best local alignment for each query region. To accomplish the analysis quickly, the program mostly relies on pairwise alignments and constructs multiple sequence alignments over short overlapping subject regions only when necessary. This fine-tuned implementation achieves an efficiency comparable to an alignment-free tool. The program performs well for simulated and real data sets of closely related genomes and can be used for fast recombination detection; for instance, when a new prokaryotic pathogen is discovered. As an example, gmos was used to detect genome mosaicism in a pathogenic Enterococcus faecium strain compared to seven closely related genomes. The analysis took less than two minutes on a single 2.1 GHz processor. The output is available in fasta format and can be visualized using an accessory program, gmosDraw (freely available with gmos).

  3. Pepino mosaic virus isolates and differential symptomatology in tomato

    NARCIS (Netherlands)

    Hanssen, I.M.; Paeleman, A.; Vandewoestijne, E.; Bergen, Van L.; Bragard, C.; Lievens, B.; Vanachter, A.C.R.C.; Thomma, B.P.H.J.

    2009-01-01

    Based on a survey conducted in commercial tomato production in Belgium in 2006, four Pepino mosaic virus (PepMV) isolates that differed in symptom expression in the crop of origin were selected for greenhouse trials. The selected isolates were inoculated onto tomato plants grown in four separate

  4. Orthophoto Mosaic (2012) for Fish Bay, St. John

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This 0.3x0.3 meter imagery mosaic of Fish Bay, St. John in the U.S. Virgin Islands was created by the National Oceanic and Atmospheric Administration (NOAA) using a...

  5. Revertant mosaicism in epidermolysis bullosa caused by mitotic gene conversion

    NARCIS (Netherlands)

    Jonkman, MF; Scheffer, H; Stulp, R; Pas, HH; Nijenhuis, Albertine; Heeres, K; Owaribe, K; Pulkkinen, L; Uitto, J

    1997-01-01

    Mitotic gene conversion acting as reverse mutation has not been previously demonstrated in human. We report here that the revertant mosaicism of a compound heterozygous proband with an autosomal recessive genodermatosis, generalized atrophic benign epidermolysis bullosa, is caused by mitotic gene

  6. Protocol for cost effective detection of cassava mosaic virus ...

    African Journals Online (AJOL)

    Early detection of cassava mosaic disease (CMD) is an extremely important step in containing the spread of the disease in Africa. Many nucleic acid based detection tools have been developed for CMD diagnosis but although these methods are specific and sensitive for their target DNA, they are not fast, cost effective, can't ...

  7. Controlled transmission of African cassava mosaic virus (ACMV) by ...

    African Journals Online (AJOL)

    Jatropha curcas, a plant with great biodiesel potential is also used to reduce the population of whiteflies, Bemisia tabaci on cassava fields when planted as a hedge. We therefore, investigated the transmission of African cassava mosaic virus (ACMV) by the whitefly vector from cassava to seedlings of 10 accessions of J.

  8. Cowpea mosaic virus: effects on host cell processes

    NARCIS (Netherlands)

    Pouwels, J.; Carette, J.E.; Lent, van J.; Wellink, J.E.

    2002-01-01

    Taxonomy: Cowpea mosaic virus (CPMV) is the type member of the Comoviridae and bears a strong resemblance to animal picornaviruses, both in gene organization and in the amino acid sequence of replication proteins. Little systematic work has been done to compare isolates of the virus from different

  9. ENG mutational mosaicism in a family with hereditary hemorrhagic telangiectasia

    DEFF Research Database (Denmark)

    Tørring, Pernille M; Kjeldsen, Anette D; Ousager, Lilian Bomme

    2018-01-01

    mutation using Sanger sequencing. Analyzing her DNA by NGS HHT panel sequencing when extracted from both peripheral blood leukocytes, and cheek swabs, identified the familial ENG mutation at low levels. CONCLUSION: We provide evidence of ENG mutational mosaicism in an individual presenting with clinical...

  10. 181 Farmers Adoption Scenarios for the Control of Cassava Mosaic ...

    African Journals Online (AJOL)

    Journal Seek, Scientific Commons, http://journal.aesonnigeria. ... the Cassava Enterprise Development Project in Enugu State, Nigeria ... emptive management of the cassava mosaic disease in the eleven cassava growing states of the ..... facilitators. Therefore, for farmers to adopt this innovation, adequate sustainable plan.

  11. Recent characterization of cowpea aphid-borne mosaic virus ...

    African Journals Online (AJOL)

    Woodiness disease is the most important disorder of passion fruit worldwide. The causal agent in Brazil is the Cowpea aphid-borne mosaic virus (CABMV), and despite the economic relevance of passion fruit for agriculture there have been recently very few studies about this virus in Brazil and worldwide. This work reveals ...

  12. CARM1 modulators affect epigenome of stem cells and change morphology of nucleoli.

    Science.gov (United States)

    Franek, M; Legartová, S; Suchánková, J; Milite, C; Castellano, S; Sbardella, G; Kozubek, S; Bártová, E

    2015-01-01

    CARM1 interacts with numerous transcription factors to mediate cellular processes, especially gene expression. This is important for the maintenance of ESC pluripotency or intervention to tumorigenesis. Here, we studied epigenomic effects of two potential CARM1 modulators: an activator (EML159) and an inhibitor (ellagic acid dihydrate, EA). We examined nuclear morphology in human and mouse embryonic stem cells (hESCs, mESCs), as well as in iPS cells. The CARM1 modulators did not function similarly in all cell types. EA decreased the levels of the pluripotency markers, OCT4 and NANOG, particularly in iPSCs, whereas the levels of these proteins increased after EML159 treatment. EML159 treatment of mouse ESCs led to decreased levels of OCT4 and NANOG, which was accompanied by an increased level of Endo-A. The same trend was observed for NANOG and Endo-A in hESCs affected by EML159. Interestingly, EA mainly changed epigenetic features of nucleoli because a high level of arginine asymmetric di-methylation in the nucleoli of hESCs was reduced after EA treatment. ChIP-PCR of ribosomal genes confirmed significantly reduced levels of H3R17me2a, in both the promoter region of ribosomal genes and rDNA encoding 28S rRNA, after EA addition. Moreover, EA treatment changed the nuclear pattern of AgNORs (silver-stained nucleolus organizer regions) in all cell types studied. In EA-treated ESCs, AgNOR pattern was similar to the pattern of AgNORs after inhibition of RNA pol I by actinomycin D. Together, inhibitory effect of EA on arginine methylation and effect on related morphological parameters was especially observed in compartment of nucleoli.

  13. Imprinted genes and transpositions: epigenomic targets for low dose radiation effects. Final report

    International Nuclear Information System (INIS)

    Jirtle, Randy L.

    2012-01-01

    The overall hypothesis of this grant application is that low dose ionizing radiation (LDIR) elicits adaptive responses in part by causing heritable DNA methylation changes in the epigenome. This novel postulate was tested by determining if the level of DNA methylation at the Agouti viable yellow (A vy ) metastable locus is altered, in a dose-dependent manner, by low dose radiation exposure ( vy locus in a sex-specific manner (p=0.004). Average DNA methylation was significantly increased in male offspring exposed to doses between 0.7 cGy and 7.6 cGy with maximum effects at 1.4 cGy and 3.0 cGy (p<0.01). Offspring coat color was concomitantly shifted towards pseudoagouti (p<0.01). Maternal dietary antioxidant supplementation mitigated both the DNA methylation changes and coat color shift in the irradiated offspring (p<0.05). Thus, LDIR exposure during gestation elicits epigenetic alterations that lead to positive adaptive phenotypic changes that are negated with antioxidants, indicating they are mediated in part by oxidative stress. These findings provide evidence that in the isogenic Avy mouse model epigenetic alterations resulting from LDIR play a role in radiation hormesis, bringing into question the assumption that every dose of radiation is harmful. Our findings not only have significant implications concerning the mechanism of hormesis, but they also emphasize the potential importance of this phenomenon in determining human risk at low radiation doses. Since the epigenetic regulation of genes varies markedly between species, the effect of LDIR on other epigenetically labile genes (e.g. imprinted genes) in animals and humans needs to be defined

  14. Stage-specific histone modification profiles reveal global transitions in the Xenopus embryonic epigenome.

    Directory of Open Access Journals (Sweden)

    Tobias D Schneider

    Full Text Available Vertebrate embryos are derived from a transitory pool of pluripotent cells. By the process of embryonic induction, these precursor cells are assigned to specific fates and differentiation programs. Histone post-translational modifications are thought to play a key role in the establishment and maintenance of stable gene expression patterns underlying these processes. While on gene level histone modifications are known to change during differentiation, very little is known about the quantitative fluctuations in bulk histone modifications during development. To investigate this issue we analysed histones isolated from four different developmental stages of Xenopus laevis by mass spectrometry. In toto, we quantified 59 modification states on core histones H3 and H4 from blastula to tadpole stages. During this developmental period, we observed in general an increase in the unmodified states, and a shift from histone modifications associated with transcriptional activity to transcriptionally repressive histone marks. We also compared these naturally occurring patterns with the histone modifications of murine ES cells, detecting large differences in the methylation patterns of histone H3 lysines 27 and 36 between pluripotent ES cells and pluripotent cells from Xenopus blastulae. By combining all detected modification transitions we could cluster their patterns according to their embryonic origin, defining specific histone modification profiles (HMPs for each developmental stage. To our knowledge, this data set represents the first compendium of covalent histone modifications and their quantitative flux during normogenesis in a vertebrate model organism. The HMPs indicate a stepwise maturation of the embryonic epigenome, which may be causal to the progressing restriction of cellular potency during development.

  15. Hereditary kidney cancer syndromes: Genetic disorders driven by alterations in metabolism and epigenome regulation.

    Science.gov (United States)

    Hasumi, Hisashi; Yao, Masahiro

    2018-03-01

    Although hereditary kidney cancer syndrome accounts for approximately five percent of all kidney cancers, the mechanistic insight into tumor development in these rare conditions has provided the foundation for the development of molecular targeting agents currently used for sporadic kidney cancer. In the late 1980s, the comprehensive study for hereditary kidney cancer syndrome was launched in the National Cancer Institute, USA and the first kidney cancer-associated gene, VHL, was identified through kindred analysis of von Hippel-Lindau (VHL) syndrome in 1993. Subsequent molecular studies on VHL function have elucidated that the VHL protein is a component of E3 ubiquitin ligase complex for hypoxia-inducible factor (HIF), which provided the basis for the development of tyrosine kinase inhibitors targeting the HIF-VEGF/PDGF pathway. Recent whole-exome sequencing analysis of sporadic kidney cancer exhibited the recurrent mutations in chromatin remodeling genes and the later study has revealed that several chromatin remodeling genes are altered in kidney cancer kindred at the germline level. To date, more than 10 hereditary kidney cancer syndromes together with each responsible gene have been characterized and most of the causative genes for these genetic disorders are associated with either metabolism or epigenome regulation. In this review article, we describe the molecular mechanisms of how an alteration of each kidney cancer-associated gene leads to renal tumorigenesis as well as denote therapeutic targets elicited by studies on hereditary kidney cancer. © 2018 The Authors. Cancer Science published by John Wiley & Sons Australia, Ltd on behalf of Japanese Cancer Association.

  16. Common Altered Epigenomic Domains in Cancer Cells: Characterization and Subtle Variations

    International Nuclear Information System (INIS)

    Tsai, Yi-Chien; Chiao, Chun-Hui; Chang, Ian Yi-Feng; Chen, Dow-Tien; Liu, Tze-Tze; Hua, Kate; Chang, Chuan-Hsiung; Hsu, Ming-Ta

    2011-01-01

    We have previously identified large megabase-sized hypomethylated zones in the genome of the breast cancer cell line MCF-7 using the TspRI-ExoIII technique. In this report, we used a more convenient high throughput method for mapping the hypomethylated zones in a number of human tumor genomes simultaneously. The method was validated by the bisulfite sequencing of 39 randomly chosen sites in a demethylated domain and by bisulfite genome-wide sequencing of the MCF-7 genome. This showed that the genomes of the various tumor cell lines, as well as some primary tumors, exhibit common hypomethylated domains. Interestingly, these hypomethylated domains are correlated with low CpG density distribution genome-wide, together with the histone H3K27Me3 landscape. Furthermore, they are inversely correlated with the H3K9Ac landscape and gene expression as measured in MCF-7 cells. Treatment with drugs resulted in en-bloc changes to the methylation domains. A close examination of the methylation domains found differences between non-invasive and invasive tumors with respect to tumorigenesis related genes. Taken together these results suggest that the human genome is organized in epigenomic domains that contain various different types of genes and imply that there are cis- and trans-regulators that control these domain-wide epigenetic changes and hence gene expression in the human genome. The hypomethylated domains are located in gene deserts that contain mainly tissue-specific genes and therefore we hypothesize that tumor cells keep these regions demethylated and silenced in order to save energy and resources and allow higher levels of cell proliferation and better survival (a thrifty tumor genome hypothesis)

  17. Epigenomic diversity of colorectal cancer indicated by LINE-1 methylation in a database of 869 tumors

    Directory of Open Access Journals (Sweden)

    Schernhammer Eva S

    2010-05-01

    Full Text Available Abstract Background Genome-wide DNA hypomethylation plays a role in genomic instability and carcinogenesis. LINE-1 (L1 retrotransposon constitutes a substantial portion of the human genome, and LINE-1 methylation correlates with global DNA methylation status. LINE-1 hypomethylation in colon cancer has been strongly associated with poor prognosis. However, whether LINE-1 hypomethylators constitute a distinct cancer subtype remains uncertain. Recent evidence for concordant LINE-1 hypomethylation within synchronous colorectal cancer pairs suggests the presence of a non-stochastic mechanism influencing tumor LINE-1 methylation level. Thus, it is of particular interest to examine whether its wide variation can be attributed to clinical, pathologic or molecular features. Design Utilizing a database of 869 colorectal cancers in two prospective cohort studies, we constructed multivariate linear and logistic regression models for LINE-1 methylation (quantified by Pyrosequencing. Variables included age, sex, body mass index, family history of colorectal cancer, smoking status, tumor location, stage, grade, mucinous component, signet ring cells, tumor infiltrating lymphocytes, CpG island methylator phenotype (CIMP, microsatellite instability, expression of TP53 (p53, CDKN1A (p21, CTNNB1 (β-catenin, PTGS2 (cyclooxygenase-2, and FASN, and mutations in KRAS, BRAF, and PIK3CA. Results Tumoral LINE-1 methylation ranged from 23.1 to 90.3 of 0-100 scale (mean 61.4; median 62.3; standard deviation 9.6, and distributed approximately normally except for extreme hypomethylators [LINE-1 methylation Conclusions LINE-1 extreme hypomethylators appear to constitute a previously-unrecognized, distinct subtype of colorectal cancers, which needs to be confirmed by additional studies. Our tumor LINE-1 methylation data indicate enormous epigenomic diversity of individual colorectal cancers.

  18. Reference: 21 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available ication of a number of mutant lines with altered Chl fluorescence characteristics. Analysis of photosynthesis...cation of mutants of Arabidopsis defective in acclimation of photosynthesis to th

  19. Reference: 789 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available ylakoid membranes. Microarray analysis of the chl27-t mutant showed repression of numerous nuclear genes involved in photosynthesis...d CHL27 proteins. Role of Arabidopsis CHL27 protein for photosynthesis, chloroplast development and gene exp

  20. Reference: 306 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available of the endoreduplication cycle in Arabidopsis requires a plant homologue of archaeal DNA topoisomerase (topo) VI. To further understa...nd how DNA is endoreduplicated and how this process is r

  1. Reference: 150 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available ridization, Pht1;4 was found mainly expressed in inorgan...physiological characterization of Arabidopsis pht1;4 high affinity phosphate transporter mutants. Using GUS-gene trap and in situ hyb

  2. Arabidopsis CDS blastp result: AK099152 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK099152 J023070H02 At4g01900.1 P II nitrogen sensing protein (GLB I) identical to P II nitrogen... sensing protein GLB I (GI:7268574) [Arabidopsis thaliana]; similar to nitrogen regulatory prot

  3. Arabidopsis CDS blastp result: AK068407 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK068407 J013149B08 At4g01900.1 P II nitrogen sensing protein (GLB I) identical to P II nitrogen... sensing protein GLB I (GI:7268574) [Arabidopsis thaliana]; similar to nitrogen regulatory prot

  4. Arabidopsis CDS blastp result: AK241043 [KOME

    Lifescience Database Archive (English)

    Full Text Available upted by a stop codon, creating non-consensus donor and acceptor splice sites. 2e-41 ... ...tical to SP|P92997 Germin-like protein subfamily 1 member 13 precursor {Arabidopsis thaliana}; exon 2 interr

  5. Arabidopsis CDS blastp result: AK243135 [KOME

    Lifescience Database Archive (English)

    Full Text Available upted by a stop codon, creating non-consensus donor and acceptor splice sites. 7e-43 ... ...tical to SP|P92997 Germin-like protein subfamily 1 member 13 precursor {Arabidopsis thaliana}; exon 2 interr

  6. Reference: 346 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available th a function in purine turnover in Arabidopsis. To our knowledge this is the fir...ock in allantoate catabolism. AtAAH transcript was detected in all tissues examined by RT-PCR, consistent wi

  7. Reference: 510 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available in support of PSII activity, whereas the interaction of PsbO2 with PSII regulates the turnover... its degradation. The Arabidopsis PsbO2 protein regulates dephosphorylation and turnover of the photosystem

  8. Reference: 278 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available functional ERA1 gene, which encodes the beta-subunit of protein farnesyltransferase (PFT), exhibit pleiotropic effects...gnaling and meristem development. Here, we report the effects of T-DNA insertion mutations in the Arabidopsi

  9. Arabidopsis CDS blastp result: AK287673 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK287673 J065121E18 At4g37750.1 68417.m05344 ovule development protein aintegumenta... (ANT) identical to ovule development protein aintegumenta (ANT) (GI:1244708) ) [Arabidopsis thaliana] 6e-17 ...

  10. Arabidopsis CDS blastp result: AK241272 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK241272 J065132I19 At4g37750.1 68417.m05344 ovule development protein aintegumenta... (ANT) identical to ovule development protein aintegumenta (ANT) (GI:1244708) ) [Arabidopsis thaliana] 1e-88 ...

  11. Arabidopsis CDS blastp result: AK241712 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK241712 J065197H24 At4g37750.1 68417.m05344 ovule development protein aintegumenta... (ANT) identical to ovule development protein aintegumenta (ANT) (GI:1244708) ) [Arabidopsis thaliana] 6e-27 ...

  12. Arabidopsis CDS blastp result: AK106306 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK106306 002-101-C10 At4g37750.1 ovule development protein aintegumenta (ANT) ident...ical to ovule development protein aintegumenta (ANT) (GI:1244708) ) [Arabidopsis thaliana] 3e-89 ...

  13. Arabidopsis CDS blastp result: AK287726 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK287726 J065138E17 At4g37750.1 68417.m05344 ovule development protein aintegumenta... (ANT) identical to ovule development protein aintegumenta (ANT) (GI:1244708) ) [Arabidopsis thaliana] 1e-88 ...

  14. Arabidopsis CDS blastp result: AK109848 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK109848 002-148-F05 At4g37750.1 ovule development protein aintegumenta (ANT) ident...ical to ovule development protein aintegumenta (ANT) (GI:1244708) ) [Arabidopsis thaliana] 5e-73 ...

  15. Arabidopsis CDS blastp result: AK242387 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK242387 J080051E14 At4g37750.1 68417.m05344 ovule development protein aintegumenta... (ANT) identical to ovule development protein aintegumenta (ANT) (GI:1244708) ) [Arabidopsis thaliana] 2e-45 ...

  16. Arabidopsis CDS blastp result: AK240892 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK240892 J065030K10 At4g37750.1 68417.m05344 ovule development protein aintegumenta... (ANT) identical to ovule development protein aintegumenta (ANT) (GI:1244708) ) [Arabidopsis thaliana] 5e-88 ...

  17. Arabidopsis CDS blastp result: AK242957 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK242957 J090089I15 At4g37750.1 68417.m05344 ovule development protein aintegumenta... (ANT) identical to ovule development protein aintegumenta (ANT) (GI:1244708) ) [Arabidopsis thaliana] 1e-28 ...

  18. Arabidopsis CDS blastp result: AK287621 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK287621 J065066I09 At4g37750.1 68417.m05344 ovule development protein aintegumenta... (ANT) identical to ovule development protein aintegumenta (ANT) (GI:1244708) ) [Arabidopsis thaliana] 5e-85 ...

  19. Reference: 627 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available omal processing protease (GPP) from the fat-storing cotyledons of watermelon (Citrullus vulgaris) by column ...ptidase, and a Lon-protease. Specific antibodies against the peroxisomal Deg-protease from Arabidopsis (Deg15) identify the watermelo

  20. Arabidopsis CDS blastp result: AK242585 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK242585 J090010M20 At3g03050.1 68416.m00301 cellulose synthase family protein (CslD3) similar to cellulose... synthase catalytic subunit gi:2827143 from [Arabidopsis thaliana], cellulose syntha

  1. Arabidopsis CDS blastp result: AK242601 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK242601 J090014G03 At3g03050.1 68416.m00301 cellulose synthase family protein (CslD3) similar to cellulose... synthase catalytic subunit gi:2827143 from [Arabidopsis thaliana], cellulose syntha

  2. Arabidopsis CDS blastp result: AK110467 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK110467 002-166-G08 At3g03050.1 cellulose synthase family protein (CslD3) similar to cellulose... synthase catalytic subunit gi:2827143 from [Arabidopsis thaliana], cellulose synthase-7 (gi:962

  3. Arabidopsis CDS blastp result: AK066835 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK066835 J013087I16 At5g16910.1 cellulose synthase family protein similar to gi:2827143 cellulose... synthase catalytic subunit, Arabidopsis thaliana, gi:9622886 cellulose synthase-7 from Zea mays 1e-171 ...

  4. Arabidopsis CDS blastp result: AK102695 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK102695 J033103F21 At5g16910.1 cellulose synthase family protein similar to gi:2827143 cellulose... synthase catalytic subunit, Arabidopsis thaliana, gi:9622886 cellulose synthase-7 from Zea mays 0.0 ...

  5. Arabidopsis CDS blastp result: AK242890 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK242890 J090079L19 At3g03050.1 68416.m00301 cellulose synthase family protein (CslD3) similar to cellulose... synthase catalytic subunit gi:2827143 from [Arabidopsis thaliana], cellulose syntha

  6. Arabidopsis CDS blastp result: AK100523 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK100523 J023100P04 At5g16910.1 cellulose synthase family protein similar to gi:2827143 cellulose... synthase catalytic subunit, Arabidopsis thaliana, gi:9622886 cellulose synthase-7 from Zea mays 0.0 ...

  7. Arabidopsis CDS blastp result: AK065259 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK065259 J013002J18 At5g16910.1 cellulose synthase family protein similar to gi:2827143 cellulose... synthase catalytic subunit, Arabidopsis thaliana, gi:9622886 cellulose synthase-7 from Zea mays 0.0 ...

  8. Arabidopsis CDS blastp result: AK102134 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK102134 J033085F12 At5g16910.1 cellulose synthase family protein similar to gi:2827143 cellulose... synthase catalytic subunit, Arabidopsis thaliana, gi:9622886 cellulose synthase-7 from Zea mays 0.0 ...

  9. The fifth international conference on Arabidopsis research

    Energy Technology Data Exchange (ETDEWEB)

    Hangarter, R.; Scholl, R.; Davis, K.; Feldmann, K.

    1993-12-31

    This volume contains abstracts of oral and poster presentations made in conjunction with the Fifth International Conference on Arabidopsis Research held August 19--22, 1993 at the Ohio State University, Columbus, Ohio.

  10. Characterization of Large Structural Genetic Mosaicism in Human Autosomes

    Science.gov (United States)

    Machiela, Mitchell J.; Zhou, Weiyin; Sampson, Joshua N.; Dean, Michael C.; Jacobs, Kevin B.; Black, Amanda; Brinton, Louise A.; Chang, I-Shou; Chen, Chu; Chen, Constance; Chen, Kexin; Cook, Linda S.; Crous Bou, Marta; De Vivo, Immaculata; Doherty, Jennifer; Friedenreich, Christine M.; Gaudet, Mia M.; Haiman, Christopher A.; Hankinson, Susan E.; Hartge, Patricia; Henderson, Brian E.; Hong, Yun-Chul; Hosgood, H. Dean; Hsiung, Chao A.; Hu, Wei; Hunter, David J.; Jessop, Lea; Kim, Hee Nam; Kim, Yeul Hong; Kim, Young Tae; Klein, Robert; Kraft, Peter; Lan, Qing; Lin, Dongxin; Liu, Jianjun; Le Marchand, Loic; Liang, Xiaolin; Lissowska, Jolanta; Lu, Lingeng; Magliocco, Anthony M.; Matsuo, Keitaro; Olson, Sara H.; Orlow, Irene; Park, Jae Yong; Pooler, Loreall; Prescott, Jennifer; Rastogi, Radhai; Risch, Harvey A.; Schumacher, Fredrick; Seow, Adeline; Setiawan, Veronica Wendy; Shen, Hongbing; Sheng, Xin; Shin, Min-Ho; Shu, Xiao-Ou; VanDen Berg, David; Wang, Jiu-Cun; Wentzensen, Nicolas; Wong, Maria Pik; Wu, Chen; Wu, Tangchun; Wu, Yi-Long; Xia, Lucy; Yang, Hannah P.; Yang, Pan-Chyr; Zheng, Wei; Zhou, Baosen; Abnet, Christian C.; Albanes, Demetrius; Aldrich, Melinda C.; Amos, Christopher; Amundadottir, Laufey T.; Berndt, Sonja I.; Blot, William J.; Bock, Cathryn H.; Bracci, Paige M.; Burdett, Laurie; Buring, Julie E.; Butler, Mary A.; Carreón, Tania; Chatterjee, Nilanjan; Chung, Charles C.; Cook, Michael B.; Cullen, Michael; Davis, Faith G.; Ding, Ti; Duell, Eric J.; Epstein, Caroline G.; Fan, Jin-Hu; Figueroa, Jonine D.; Fraumeni, Joseph F.; Freedman, Neal D.; Fuchs, Charles S.; Gao, Yu-Tang; Gapstur, Susan M.; Patiño-Garcia, Ana; Garcia-Closas, Montserrat; Gaziano, J. Michael; Giles, Graham G.; Gillanders, Elizabeth M.; Giovannucci, Edward L.; Goldin, Lynn; Goldstein, Alisa M.; Greene, Mark H.; Hallmans, Goran; Harris, Curtis C.; Henriksson, Roger; Holly, Elizabeth A.; Hoover, Robert N.; Hu, Nan; Hutchinson, Amy; Jenab, Mazda; Johansen, Christoffer; Khaw, Kay-Tee; Koh, Woon-Puay; Kolonel, Laurence N.; Kooperberg, Charles; Krogh, Vittorio; Kurtz, Robert C.; LaCroix, Andrea; Landgren, Annelie; Landi, Maria Teresa; Li, Donghui; Liao, Linda M.; Malats, Nuria; McGlynn, Katherine A.; McNeill, Lorna H.; McWilliams, Robert R.; Melin, Beatrice S.; Mirabello, Lisa; Peplonska, Beata; Peters, Ulrike; Petersen, Gloria M.; Prokunina-Olsson, Ludmila; Purdue, Mark; Qiao, You-Lin; Rabe, Kari G.; Rajaraman, Preetha; Real, Francisco X.; Riboli, Elio; Rodríguez-Santiago, Benjamín; Rothman, Nathaniel; Ruder, Avima M.; Savage, Sharon A.; Schwartz, Ann G.; Schwartz, Kendra L.; Sesso, Howard D.; Severi, Gianluca; Silverman, Debra T.; Spitz, Margaret R.; Stevens, Victoria L.; Stolzenberg-Solomon, Rachael; Stram, Daniel; Tang, Ze-Zhong; Taylor, Philip R.; Teras, Lauren R.; Tobias, Geoffrey S.; Viswanathan, Kala; Wacholder, Sholom; Wang, Zhaoming; Weinstein, Stephanie J.; Wheeler, William; White, Emily; Wiencke, John K.; Wolpin, Brian M.; Wu, Xifeng; Wunder, Jay S.; Yu, Kai; Zanetti, Krista A.; Zeleniuch-Jacquotte, Anne; Ziegler, Regina G.; de Andrade, Mariza; Barnes, Kathleen C.; Beaty, Terri H.; Bierut, Laura J.; Desch, Karl C.; Doheny, Kimberly F.; Feenstra, Bjarke; Ginsburg, David; Heit, John A.; Kang, Jae H.; Laurie, Cecilia A.; Li, Jun Z.; Lowe, William L.; Marazita, Mary L.; Melbye, Mads; Mirel, Daniel B.; Murray, Jeffrey C.; Nelson, Sarah C.; Pasquale, Louis R.; Rice, Kenneth; Wiggs, Janey L.; Wise, Anastasia; Tucker, Margaret; Pérez-Jurado, Luis A.; Laurie, Cathy C.; Caporaso, Neil E.; Yeager, Meredith; Chanock, Stephen J.

    2015-01-01

    Analyses of genome-wide association study (GWAS) data have revealed that detectable genetic mosaicism involving large (>2 Mb) structural autosomal alterations occurs in a fraction of individuals. We present results for a set of 24,849 genotyped individuals (total GWAS set II [TGSII]) in whom 341 large autosomal abnormalities were observed in 168 (0.68%) individuals. Merging data from the new TGSII set with data from two prior reports (the Gene-Environment Association Studies and the total GWAS set I) generated a large dataset of 127,179 individuals; we then conducted a meta-analysis to investigate the patterns of detectable autosomal mosaicism (n = 1,315 events in 925 [0.73%] individuals). Restricting to events >2 Mb in size, we observed an increase in event frequency as event size decreased. The combined results underscore that the rate of detectable mosaicism increases with age (p value = 5.5 × 10−31) and is higher in men (p value = 0.002) but lower in participants of African ancestry (p value = 0.003). In a subset of 47 individuals from whom serial samples were collected up to 6 years apart, complex changes were noted over time and showed an overall increase in the proportion of mosaic cells as age increased. Our large combined sample allowed for a unique ability to characterize detectable genetic mosaicism involving large structural events and strengthens the emerging evidence of non-random erosion of the genome in the aging population. PMID:25748358

  11. Reference: 398 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available modulate the photosynthetic potential of plant cells. Identification of genes required for light-induced chloroplast movement... is beginning to define the molecular machinery that controls these movement...s. In this work, we describe plastid movement impaired 2 (pmi2), a mutant in Arabidopsis (Arabi...dopsis thaliana) that displays attenuated chloroplast movements under intermediate and high light intensitie...s while maintaining a normal movement response under low light intensities. In wi

  12. Reference: 170 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available rice A et al. 2005 Mar. Plant Cell 17(3):791-803. Environmental time cues, such as photocycles (light/dark) and thermocycles...h is known about entrainment of the Arabidopsis thaliana clock to photocycles, th...e determinants of thermoperception and entrainment to thermocycles are not known. The Arabidopsis PSEUDO-RES... an oscillation after entrainment to thermocycles and to reset its clock in response to cold pulses and thus

  13. Intracellular localization of Arabidopsis sulfurtransferases.

    Science.gov (United States)

    Bauer, Michael; Dietrich, Christof; Nowak, Katharina; Sierralta, Walter D; Papenbrock, Jutta

    2004-06-01

    Sulfurtransferases (Str) comprise a group of enzymes widely distributed in archaea, eubacteria, and eukaryota which catalyze the transfer of a sulfur atom from suitable sulfur donors to nucleophilic sulfur acceptors. In all organisms analyzed to date, small gene families encoding Str proteins have been identified. The gene products were localized to different compartments of the cells. Our interest concerns the localization of Str proteins encoded in the nuclear genome of Arabidopsis. Computer-based prediction methods revealed localization in different compartments of the cell for six putative AtStrs. Several methods were used to determine the localization of the AtStr proteins experimentally. For AtStr1, a mitochondrial localization was demonstrated by immunodetection in the proteome of isolated mitochondria resolved by one- and two-dimensional gel electrophoresis and subsequent blotting. The respective mature AtStr1 protein was identified by mass spectrometry sequencing. The same result was obtained by transient expression of fusion constructs with the green fluorescent protein in Arabidopsis protoplasts, whereas AtStr2 was exclusively localized to the cytoplasm by this method. Three members of the single-domain AtStr were localized in the chloroplasts as demonstrated by transient expression of green fluorescent protein fusions in protoplasts and stomata, whereas the single-domain AtStr18 was shown to be cytoplasmic. The remarkable subcellular distribution of AtStr15 was additionally analyzed by transmission electron immunomicroscopy using a monospecific antibody against green fluorescent protein, indicating an attachment to the thylakoid membrane. The knowledge of the intracellular localization of the members of this multiprotein family will help elucidate their specific functions in the organism.

  14. Epigenomic maintenance through dietary intervention can facilitate DNA repair process to slow down the progress of premature aging.

    Science.gov (United States)

    Ghosh, Shampa; Sinha, Jitendra Kumar; Raghunath, Manchala

    2016-09-01

    DNA damage caused by various sources remains one of the most researched topics in the area of aging and neurodegeneration. Increased DNA damage causes premature aging. Aging is plastic and is characterised by the decline in the ability of a cell/organism to maintain genomic stability. Lifespan can be modulated by various interventions like calorie restriction, a balanced diet of macro and micronutrients or supplementation with nutrients/nutrient formulations such as Amalaki rasayana, docosahexaenoic acid, resveratrol, curcumin, etc. Increased levels of DNA damage in the form of double stranded and single stranded breaks are associated with decreased longevity in animal models like WNIN/Ob obese rats. Erroneous DNA repair can result in accumulation of DNA damage products, which in turn result in premature aging disorders such as Hutchinson-Gilford progeria syndrome. Epigenomic studies of the aging process have opened a completely new arena for research and development of drugs and therapeutic agents. We propose here that agents or interventions that can maintain epigenomic stability and facilitate the DNA repair process can slow down the progress of premature aging, if not completely prevent it. © 2016 IUBMB Life, 68(9):717-721, 2016. © 2016 International Union of Biochemistry and Molecular Biology.

  15. An obesity-associated gut microbiome reprograms the intestinal epigenome and leads to altered colonic gene expression.

    Science.gov (United States)

    Qin, Yufeng; Roberts, John D; Grimm, Sara A; Lih, Fred B; Deterding, Leesa J; Li, Ruifang; Chrysovergis, Kaliopi; Wade, Paul A

    2018-01-23

    The gut microbiome, a key constituent of the colonic environment, has been implicated as an important modulator of human health. The eukaryotic epigenome is postulated to respond to environmental stimuli through alterations in chromatin features and, ultimately, gene expression. How the host mediates epigenomic responses to gut microbiota is an emerging area of interest. Here, we profile the gut microbiome and chromatin characteristics in colon epithelium from mice fed either an obesogenic or control diet, followed by an analysis of the resultant changes in gene expression. The obesogenic diet shapes the microbiome prior to the development of obesity, leading to altered bacterial metabolite production which predisposes the host to obesity. This microbiota-diet interaction leads to changes in histone modification at active enhancers that are enriched for binding sites for signal responsive transcription factors. These alterations of histone methylation and acetylation are associated with signaling pathways integral to the development of colon cancer. The transplantation of obesogenic diet-conditioned microbiota into germ free mice, combined with an obesogenic diet, recapitulates the features of the long-term diet regimen. The diet/microbiome-dependent changes are reflected in both the composition of the recipient animals' microbiome as well as in the set of transcription factor motifs identified at diet-influenced enhancers. These findings suggest that the gut microbiome, under specific dietary exposures, stimulates a reprogramming of the enhancer landscape in the colon, with downstream effects on transcription factors. These chromatin changes may be associated with those seen during colon cancer development.

  16. CRISPR-Cas9 epigenome editing enables high-throughput screening for functional regulatory elements in the human genome.

    Science.gov (United States)

    Klann, Tyler S; Black, Joshua B; Chellappan, Malathi; Safi, Alexias; Song, Lingyun; Hilton, Isaac B; Crawford, Gregory E; Reddy, Timothy E; Gersbach, Charles A

    2017-06-01

    Large genome-mapping consortia and thousands of genome-wide association studies have identified non-protein-coding elements in the genome as having a central role in various biological processes. However, decoding the functions of the millions of putative regulatory elements discovered in these studies remains challenging. CRISPR-Cas9-based epigenome editing technologies have enabled precise perturbation of the activity of specific regulatory elements. Here we describe CRISPR-Cas9-based epigenomic regulatory element screening (CERES) for improved high-throughput screening of regulatory element activity in the native genomic context. Using dCas9 KRAB repressor and dCas9 p300 activator constructs and lentiviral single guide RNA libraries to target DNase I hypersensitive sites surrounding a gene of interest, we carried out both loss- and gain-of-function screens to identify regulatory elements for the β-globin and HER2 loci in human cells. CERES readily identified known and previously unidentified regulatory elements, some of which were dependent on cell type or direction of perturbation. This technology allows the high-throughput functional annotation of putative regulatory elements in their native chromosomal context.

  17. Impact of body size, nutrition and socioeconomic position in early life on the epigenome: a systematic review protocol.

    Science.gov (United States)

    Maddock, Jane; Wulaningsih, Wahyu; Hardy, Rebecca

    2017-07-05

    Body size, nutrition and socioeconomic position (SEP) in early life have been associated with a range of later life health outcomes. Epigenetic regulation is one mechanism through which these early life factors may impact later life health. The aim of this review protocol is to outline procedures to document the influence of body size, nutrition and SEP in early life on the epigenome. MEDLINE, Embase and BIOSIS will be systematically searched using pre-defined keywords. Additional studies will be identified through manual searching of reference lists. Two independent researchers will assess the eligibility and quality of each study, with disagreements being resolved through discussion or a third reviewer. Studies will be included if they have epigenetic markers measured either at the same time as, or after, the early life exposure and, have a measure of body size, nutrition or SEP in early life (up to 12 years), are in the English language and are from a sample of community-dwelling participants. This protocol will be used to collate the evidence for the effect of early life factors on the epigenome. Findings will form a component of a wider research study examining epigenetic responses to exposures in early life and over the life course and its impact on healthy ageing using data from population-based cohort studies. PROSPERO CRD42016050193.

  18. Piecing together cis-regulatory networks: insights from epigenomics studies in plants.

    Science.gov (United States)

    Huang, Shao-Shan C; Ecker, Joseph R

    2018-05-01

    5-Methylcytosine, a chemical modification of DNA, is a covalent modification found in the genomes of both plants and animals. Epigenetic inheritance of phenotypes mediated by DNA methylation is well established in plants. Most of the known mechanisms of establishing, maintaining and modifying DNA methylation have been worked out in the reference plant Arabidopsis thaliana. Major functions of DNA methylation in plants include regulation of gene expression and silencing of transposable elements (TEs) and repetitive sequences, both of which have parallels in mammalian biology, involve interaction with the transcriptional machinery, and may have profound effects on the regulatory networks in the cell. Methylome and transcriptome dynamics have been investigated in development and environmental responses in Arabidopsis and agriculturally and ecologically important plants, revealing the interdependent relationship among genomic context, methylation patterns, and expression of TE and protein coding genes. Analyses of methylome variation among plant natural populations and species have begun to quantify the extent of genetic control of methylome variation vs. true epimutation, and model the evolutionary forces driving methylome evolution in both short and long time scales. The ability of DNA methylation to positively or negatively modulate binding affinity of transcription factors (TFs) provides a natural link from genome sequence and methylation changes to transcription. Technologies that allow systematic determination of methylation sensitivities of TFs, in native genomic and methylation context without confounding factors such as histone modifications, will provide baseline datasets for building cell-type- and individual-specific regulatory networks that underlie the establishment and inheritance of complex traits. This article is categorized under: Laboratory Methods and Technologies > Genetic/Genomic Methods Biological Mechanisms > Regulatory Biology. © 2017 Wiley

  19. The Epigenome of Schistosoma mansoni Provides Insight about How Cercariae Poise Transcription until Infection

    Science.gov (United States)

    Freitag, Michael; Parrinello, Hugues; Groth, Marco; Emans, Rémi; Cosseau, Céline; Grunau, Christoph

    2015-01-01

    Background Chromatin structure can control gene expression and can define specific transcription states. For example, bivalent methylation of histone H3K4 and H3K27 is linked to poised transcription in vertebrate embryonic stem cells (ESC). It allows them to rapidly engage specific developmental pathways. We reasoned that non-vertebrate metazoans that encounter a similar developmental constraint (i.e. to quickly start development into a new phenotype) might use a similar system. Schistosomes are parasitic platyhelminthes that are characterized by passage through two hosts: a mollusk as intermediate host and humans or rodents as definitive host. During its development, the parasite undergoes drastic changes, most notable immediately after infection of the definitive host, i.e. during the transition from the free-swimming cercariae into adult worms. Methodology/Principal Findings We used Chromatin Immunoprecipitation followed by massive parallel sequencing (ChIP-Seq) to analyze genome-wide chromatin structure of S. mansoni on the level of histone modifications (H3K4me3, H3K27me3, H3K9me3, and H3K9ac) in cercariae, schistosomula and adults (available at http://genome.univ-perp.fr). We saw striking differences in chromatin structure between the developmental stages, but most importantly we found that cercariae possess a specific combination of marks at the transcription start sites (TSS) that has similarities to a structure found in ESC. We demonstrate that in cercariae no transcription occurs, and we provide evidences that cercariae do not possess large numbers of canonical stem cells. Conclusions/Significance We describe here a broad view on the epigenome of a metazoan parasite. Most notably, we find bivalent histone H3 methylation in cercariae. Methylation of H3K27 is removed during transformation into schistosomula (and stays absent in adults) and transcription is activated. In addition, shifts of H3K9 methylation and acetylation occur towards upstream and

  20. The Epigenome of Schistosoma mansoni Provides Insight about How Cercariae Poise Transcription until Infection.

    Directory of Open Access Journals (Sweden)

    David Roquis

    Full Text Available Chromatin structure can control gene expression and can define specific transcription states. For example, bivalent methylation of histone H3K4 and H3K27 is linked to poised transcription in vertebrate embryonic stem cells (ESC. It allows them to rapidly engage specific developmental pathways. We reasoned that non-vertebrate metazoans that encounter a similar developmental constraint (i.e. to quickly start development into a new phenotype might use a similar system. Schistosomes are parasitic platyhelminthes that are characterized by passage through two hosts: a mollusk as intermediate host and humans or rodents as definitive host. During its development, the parasite undergoes drastic changes, most notable immediately after infection of the definitive host, i.e. during the transition from the free-swimming cercariae into adult worms.We used Chromatin Immunoprecipitation followed by massive parallel sequencing (ChIP-Seq to analyze genome-wide chromatin structure of S. mansoni on the level of histone modifications (H3K4me3, H3K27me3, H3K9me3, and H3K9ac in cercariae, schistosomula and adults (available at http://genome.univ-perp.fr. We saw striking differences in chromatin structure between the developmental stages, but most importantly we found that cercariae possess a specific combination of marks at the transcription start sites (TSS that has similarities to a structure found in ESC. We demonstrate that in cercariae no transcription occurs, and we provide evidences that cercariae do not possess large numbers of canonical stem cells.We describe here a broad view on the epigenome of a metazoan parasite. Most notably, we find bivalent histone H3 methylation in cercariae. Methylation of H3K27 is removed during transformation into schistosomula (and stays absent in adults and transcription is activated. In addition, shifts of H3K9 methylation and acetylation occur towards upstream and downstream of the transcriptional start site (TSS. We conclude

  1. Same-day genomic and epigenomic diagnosis of brain tumors using real-time nanopore sequencing.

    Science.gov (United States)

    Euskirchen, Philipp; Bielle, Franck; Labreche, Karim; Kloosterman, Wigard P; Rosenberg, Shai; Daniau, Mailys; Schmitt, Charlotte; Masliah-Planchon, Julien; Bourdeaut, Franck; Dehais, Caroline; Marie, Yannick; Delattre, Jean-Yves; Idbaih, Ahmed

    2017-11-01

    Molecular classification of cancer has entered clinical routine to inform diagnosis, prognosis, and treatment decisions. At the same time, new tumor entities have been identified that cannot be defined histologically. For central nervous system tumors, the current World Health Organization classification explicitly demands molecular testing, e.g., for 1p/19q-codeletion or IDH mutations, to make an integrated histomolecular diagnosis. However, a plethora of sophisticated technologies is currently needed to assess different genomic and epigenomic alterations and turnaround times are in the range of weeks, which makes standardized and widespread implementation difficult and hinders timely decision making. Here, we explored the potential of a pocket-size nanopore sequencing device for multimodal and rapid molecular diagnostics of cancer. Low-pass whole genome sequencing was used to simultaneously generate copy number (CN) and methylation profiles from native tumor DNA in the same sequencing run. Single nucleotide variants in IDH1, IDH2, TP53, H3F3A, and the TERT promoter region were identified using deep amplicon sequencing. Nanopore sequencing yielded ~0.1X genome coverage within 6 h and resulting CN and epigenetic profiles correlated well with matched microarray data. Diagnostically relevant alterations, such as 1p/19q codeletion, and focal amplifications could be recapitulated. Using ad hoc random forests, we could perform supervised pan-cancer classification to distinguish gliomas, medulloblastomas, and brain metastases of different primary sites. Single nucleotide variants in IDH1, IDH2, and H3F3A were identified using deep amplicon sequencing within minutes of sequencing. Detection of TP53 and TERT promoter mutations shows that sequencing of entire genes and GC-rich regions is feasible. Nanopore sequencing allows same-day detection of structural variants, point mutations, and methylation profiling using a single device with negligible capital cost. It

  2. Imprinted genes and transpositions: epigenomic targets for low dose radiation effects. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Jirtle, Randy L.

    2012-10-11

    The overall hypothesis of this grant application is that low dose ionizing radiation (LDIR) elicits adaptive responses in part by causing heritable DNA methylation changes in the epigenome. This novel postulate was tested by determining if the level of DNA methylation at the Agouti viable yellow (A{sup vy}) metastable locus is altered, in a dose-dependent manner, by low dose radiation exposure (<10 cGy) during early gestation. This information is particularly important to ascertain given the increased use of CT scans in disease diagnosis, increased number of people predicted to live and work in space, and the present concern about radiological terrorism. We showed for the first time that LDIR significantly increased DNA methylation at the A{sup vy} locus in a sex-specific manner (p=0.004). Average DNA methylation was significantly increased in male offspring exposed to doses between 0.7 cGy and 7.6 cGy with maximum effects at 1.4 cGy and 3.0 cGy (p<0.01). Offspring coat color was concomitantly shifted towards pseudoagouti (p<0.01). Maternal dietary antioxidant supplementation mitigated both the DNA methylation changes and coat color shift in the irradiated offspring (p<0.05). Thus, LDIR exposure during gestation elicits epigenetic alterations that lead to positive adaptive phenotypic changes that are negated with antioxidants, indicating they are mediated in part by oxidative stress. These findings provide evidence that in the isogenic Avy mouse model epigenetic alterations resulting from LDIR play a role in radiation hormesis, bringing into question the assumption that every dose of radiation is harmful. Our findings not only have significant implications concerning the mechanism of hormesis, but they also emphasize the potential importance of this phenomenon in determining human risk at low radiation doses. Since the epigenetic regulation of genes varies markedly between species, the effect of LDIR on other epigenetically labile genes (e.g. imprinted genes) in

  3. Photoreactivation of DNA-containing cauliflower mosaic virus and tobacco mosaic virus RNA on Datura

    International Nuclear Information System (INIS)

    Towill, L.; Huang, C.W.; Gordon, M.P.

    1977-01-01

    Datura stramonium L. is a local lesion host for TMV-RNA and DNA-containing cauliflower mosaic virus (CAMV). Datura can photorepair UV-damaged TMV-RNA and CAMV, giving photoreactivation sectors of 0.40 and 0.33, respectively. Dose response curves for photoreactivation of TMV-RNA and CAMV showed that 45 to 60 min of cool white light (15 W.m -2 ) was required for maximum photoreactivation. Blue light and near UV were equally effective in photoreactivating UV-irradiated TMV-RNA, whereas near UV was initially more effective than blue light for the photorepair of UV-inactivated CAMV. Higher doses of near UV apparently inactivated the CAMV photorepair system. In the case of CAMV, photoreactivating light had to be applied immediately after inoculation with the virus. Two to three hours of incubation in the dark after inoculation resulted in complete loss of response to photoreactivating irradiation. In contrast, limited photoreactivation of TMV-RNA occurred even after 4 h of dark incubation after inoculation, although photoreactivating irradiation was most effective when applied immediately after inoculation. Light was required for the maintenance of photoreactivation for both TMV-RNA and CAMV. Daturas placed in the dark for six days lost their ability to photoreactivate. Recovery of the TMV-RNA photorepair system was rapid; complete recovery attained with 90 or more min of white light (15 W.m -2 ). Recovery of CAMV photorepair system was slow; 90% recovery attained after only 20 h of light. However, full recovery could be induced by as little as 6 h of light when CAMV was inoculated 24 h after the onset of illumination. These results suggest two photorepair systems are present in Datura. (author)

  4. Multiple loci condition seed transmission of soybean mosaic virus (SMV) and SMV-induced seed coat mottling in soybean.

    Science.gov (United States)

    Domier, Leslie L; Hobbs, Houston A; McCoppin, Nancy K; Bowen, Charles R; Steinlage, Todd A; Chang, Sungyul; Wang, Yi; Hartman, Glen L

    2011-06-01

    Infection of soybean plants with Soybean mosaic virus (SMV), which is transmitted by aphids and through seed, can cause significant reductions in seed production and quality. Because seedborne infections are the primary sources of inoculum for SMV infections in North America, host-plant resistance to seed transmission can limit the pool of plants that can serve as sources of inoculum. To examine the inheritance of SMV seed transmission in soybean, crosses were made between plant introductions (PIs) with high (PI88799), moderate (PI60279), and low (PI548391) rates of transmission of SMV through seed. In four F(2) populations, SMV seed transmission segregated as if conditioned by two or more genes. Consequently, a recombinant inbred line population was derived from a cross between PIs 88799 and 548391 and evaluated for segregation of SMV seed transmission, seed coat mottling, and simple sequence repeat markers. Chromosomal regions on linkage groups C1 and C2 were significantly associated with both transmission of isolate SMV 413 through seed and SMV-induced seed coat mottling, and explained ≈42.8 and 46.4% of the variability in these two traits, respectively. Chromosomal regions associated with seed transmission and seed coat mottling contained homologues of Arabidopsis genes DCL3 and RDR6, which encode enzymes involved in RNA-mediated transcriptional and posttranscriptional gene silencing.

  5. Capsicum annuum WRKY transcription factor d (CaWRKYd) regulates hypersensitive response and defense response upon Tobacco mosaic virus infection.

    Science.gov (United States)

    Huh, Sung Un; Choi, La Mee; Lee, Gil-Je; Kim, Young Jin; Paek, Kyung-Hee

    2012-12-01

    WRKY transcription factors regulate biotic, abiotic, and developmental processes. In terms of plant defense, WRKY factors have important roles as positive and negative regulators via transcriptional regulation or protein-protein interaction. Here, we report the characterization of the gene encoding Capsicum annuum WRKY transcription factor d (CaWRKYd) isolated from microarray analysis in the Tobacco mosaic virus (TMV)-P(0)-inoculated hot pepper plants. CaWRKYd belongs to the WRKY IIa group, a very small clade in the WRKY subfamily, and WRKY IIa group has positive/negative regulatory roles in Arabidopsis and rice. CaWRKYd transcripts were induced by various plant defense-related hormone treatments and TMV-P(0) inoculation. Silencing of CaWRKYd affected TMV-P(0)-mediated hypersensitive response (HR) cell death and accumulation of TMV-P(0) coat protein in local and systemic leaves. Furthermore, expression of some pathogenesis-related (PR) genes and HR-related genes was reduced in the CaWRKYd-silenced plants compared with TRV2 vector control plants upon TMV-P(0) inoculation. CaWRKYd was confirmed to bind to the W-box. Thus CaWRKYd is a newly identified Capsicum annuum WRKY transcription factor that appears to be involved in TMV-P(0)-mediated HR cell death by regulating downstream gene expression. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

  6. Heat shock 70 protein interaction with Turnip mosaic virus RNA-dependent RNA polymerase within virus-induced membrane vesicles

    International Nuclear Information System (INIS)

    Dufresne, Philippe J.; Thivierge, Karine; Cotton, Sophie; Beauchemin, Chantal; Ide, Christine; Ubalijoro, Eliane; Laliberte, Jean-Francois; Fortin, Marc G.

    2008-01-01

    Tandem affinity purification was used in Arabidopsis thaliana to identify cellular interactors of Turnip mosaic virus (TuMV) RNA-dependent RNA polymerase (RdRp). The heat shock cognate 70-3 (Hsc70-3) and poly(A)-binding (PABP) host proteins were recovered and shown to interact with the RdRp in vitro. As previously shown for PABP, Hsc70-3 was redistributed to nuclear and membranous fractions in infected plants and both RdRp interactors were co-immunoprecipitated from a membrane-enriched extract using RdRp-specific antibodies. Fluorescently tagged RdRp and Hsc70-3 localized to the cytoplasm and the nucleus when expressed alone or in combination in Nicotiana benthamiana. However, they were redistributed to large perinuclear ER-derived vesicles when co-expressed with the membrane binding 6K-VPg-Pro protein of TuMV. The association of Hsc70-3 with the RdRp could possibly take place in membrane-derived replication complexes. Thus, Hsc70-3 and PABP2 are potentially integral components of the replicase complex and could have important roles to play in the regulation of potyviral RdRp functions

  7. Alfalfa mosaic virus replicase proteins, P1 and P2, localize to the tonoplast in the presence of virus RNA

    International Nuclear Information System (INIS)

    Ibrahim, Amr; Hutchens, Heather M.; Howard Berg, R.; Sue Loesch-Fries, L.

    2012-01-01

    To identify the virus components important for assembly of the Alfalfa mosaic virus replicase complex, we used live cell imaging of Arabidopsis thaliana protoplasts that expressed various virus cDNAs encoding native and GFP-fusion proteins of P1 and P2 replicase proteins and full-length virus RNAs. Expression of P1-GFP alone resulted in fluorescent vesicle-like bodies in the cytoplasm that colocalized with FM4-64, an endocytic marker, and RFP-AtVSR2, RabF2a/Rha1-mCherry, and RabF2b/Ara7-mCherry, all of which localize to multivesicular bodies (MVBs), which are also called prevacuolar compartments, that mediate traffic to the lytic vacuole. GFP-P2 was driven from the cytosol to MVBs when expressed with P1 indicating that P1 recruited GFP-P2. P1-GFP localized on the tonoplast, which surrounds the vacuole, in the presence of infectious virus RNA, replication competent RNA2, or P2 and replication competent RNA1 or RNA3. This suggests that a functional replication complex containing P1, P2, and a full-length AMV RNA assembles on MVBs to traffic to the tonoplast.

  8. Alfalfa mosaic virus replicase proteins, P1 and P2, localize to the tonoplast in the presence of virus RNA

    Energy Technology Data Exchange (ETDEWEB)

    Ibrahim, Amr [Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907 (United States); Present address: Genomics Facility, Agricultural Genetic Engineering Research Institute, Agricultural Research Center, Giza 12619 (Egypt); Hutchens, Heather M. [Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907 (United States); Howard Berg, R. [Integrated Microscopy Facility, Donald Danforth Plant Science Center, Saint Louis, MO 63132 (United States); Sue Loesch-Fries, L., E-mail: loeschfr@purdue.edu [Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907 (United States)

    2012-11-25

    To identify the virus components important for assembly of the Alfalfa mosaic virus replicase complex, we used live cell imaging of Arabidopsis thaliana protoplasts that expressed various virus cDNAs encoding native and GFP-fusion proteins of P1 and P2 replicase proteins and full-length virus RNAs. Expression of P1-GFP alone resulted in fluorescent vesicle-like bodies in the cytoplasm that colocalized with FM4-64, an endocytic marker, and RFP-AtVSR2, RabF2a/Rha1-mCherry, and RabF2b/Ara7-mCherry, all of which localize to multivesicular bodies (MVBs), which are also called prevacuolar compartments, that mediate traffic to the lytic vacuole. GFP-P2 was driven from the cytosol to MVBs when expressed with P1 indicating that P1 recruited GFP-P2. P1-GFP localized on the tonoplast, which surrounds the vacuole, in the presence of infectious virus RNA, replication competent RNA2, or P2 and replication competent RNA1 or RNA3. This suggests that a functional replication complex containing P1, P2, and a full-length AMV RNA assembles on MVBs to traffic to the tonoplast.

  9. An epigenome-wide study of obesity in African American youth and young adults : novel findings, replication in neutrophils, and relationship with gene expression

    NARCIS (Netherlands)

    Wang, Xiaoling; Pan, Yue; Zhu, Haidong; Hao, Guang; Huang, Yisong; Barnes, Vernon; Shi, Huidong; Snieder, Harold; Pankow, James; North, Kari; Grove, Megan; Guan, Weihua; Demerath, Ellen; Dong, Yanbin; Su, Shaoyong

    2018-01-01

    Background: We conducted an epigenome-wide association study (EWAS) on obesity in healthy youth and young adults and further examined to what extent identified signals influenced gene expression and were independent of cell type composition and obesity-related cardio-metabolic risk factors.

  10. Association of a cucumber mosaic virus strain with mosaic disease of banana, Musa paradisiaca--an evidence using immuno/nucleic acid probe.

    Science.gov (United States)

    Srivastava, A; Raj, S K; Haq, Q M; Srivastava, K M; Singh, B P; Sane, P V

    1995-12-01

    Virus causing severe chlorosis/mosaic disease of banana was identified as a strain of cucumber mosaic virus (CMV). Association of CMV with the disease was established by Western immunoblot using polyclonal antibodies to CMV-T and slot blot hybridization with nucleic acid probe of CMV-P genome.

  11. 45,X/47,XXX Mosaicism and Short Stature.

    Science.gov (United States)

    Everest, Erica; Tsilianidis, Laurie A; Haider, Anzar; Rogers, Douglas G; Raissouni, Nouhad; Schweiger, Bahareh

    2015-01-01

    We describe the case of a ten-year-old girl with short stature and 45,X/47,XXX genotype. She also suffered from vesicoureteric reflux and kidney dysfunction prior to having surgery on her ureters. Otherwise, she does not have any of the characteristics of Turner nor Triple X syndrome. It has been shown that this mosaic condition as well as other varieties creates a milder phenotype than typical Turner syndrome, which is what we mostly see in our patient. However, this patient is a special case, because she is exceptionally short. Overall, one cannot predict the resultant phenotype in these mosaic conditions. This creates difficulty in counseling parents whose children or fetuses have these karyotypes.

  12. A new ophiovirus is associated with blueberry mosaic disease.

    Science.gov (United States)

    Thekke-Veetil, Thanuja; Ho, Thien; Keller, Karen E; Martin, Robert R; Tzanetakis, Ioannis E

    2014-08-30

    Blueberry mosaic disease (BMD) was first described more than 60 years ago and is caused by a yet unidentified graft transmissible agent. A combination of traditional methods and next generation sequencing disclosed the presence of a new ophiovirus in symptomatic plants. The virus was detected in all BMD samples collected from several production areas of North America and was thus named blueberry mosaic associated virus. Phylogenetic analysis, supported by high bootstrap values, places the virus within the family Ophioviridae. The genome organization resembles that of citrus psorosis virus, the type member of the genus Ophiovirus. The implications of this discovery in BMD control and blueberry virus certification schemes are also discussed. Copyright © 2014 Elsevier B.V. All rights reserved.

  13. Mosaic VSGs and the scale of Trypanosoma brucei antigenic variation.

    Directory of Open Access Journals (Sweden)

    James P J Hall

    Full Text Available A main determinant of prolonged Trypanosoma brucei infection and transmission and success of the parasite is the interplay between host acquired immunity and antigenic variation of the parasite variant surface glycoprotein (VSG coat. About 0.1% of trypanosome divisions produce a switch to a different VSG through differential expression of an archive of hundreds of silent VSG genes and pseudogenes, but the patterns and extent of the trypanosome diversity phenotype, particularly in chronic infection, are unclear. We applied longitudinal VSG cDNA sequencing to estimate variant richness and test whether pseudogenes contribute to antigenic variation. We show that individual growth peaks can contain at least 15 distinct variants, are estimated computationally to comprise many more, and that antigenically distinct 'mosaic' VSGs arise from segmental gene conversion between donor VSG genes or pseudogenes. The potential for trypanosome antigenic variation is probably much greater than VSG archive size; mosaic VSGs are core to antigenic variation and chronic infection.

  14. Ion Transport through Diffusion Layer Controlled by Charge Mosaic Membrane

    Directory of Open Access Journals (Sweden)

    Akira Yamauchi

    2012-01-01

    Full Text Available The kinetic transport behaviors in near interface of the membranes were studied using commercial anion and cation exchange membrane and charge mosaic membrane. Current-voltage curve gave the limiting current density that indicates the ceiling of conventional flux. From chronopotentiometry above the limiting current density, the transition time was estimated. The thickness of boundary layer was derived with conjunction with the conventional limiting current density and the transition time from steady state flux. On the other hand, the charge mosaic membrane was introduced in order to examine the ion transport on the membrane surface in detail. The concentration profile was discussed by the kinetic transport number with regard to the water dissociation (splitting on the membrane surface.

  15. Visualization and interaction tools for aerial photograph mosaics

    Science.gov (United States)

    Fernandes, João Pedro; Fonseca, Alexandra; Pereira, Luís; Faria, Adriano; Figueira, Helder; Henriques, Inês; Garção, Rita; Câmara, António

    1997-05-01

    This paper describes the development of a digital spatial library based on mosaics of digital orthophotos, called Interactive Portugal, that will enable users both to retrieve geospatial information existing in the Portuguese National System for Geographic Information World Wide Web server, and to develop local databases connected to the main system. A set of navigation, interaction, and visualization tools are proposed and discussed. They include sketching, dynamic sketching, and navigation capabilities over the digital orthophotos mosaics. Main applications of this digital spatial library are pointed out and discussed, namely for education, professional, and tourism markets. Future developments are considered. These developments are related to user reactions, technological advancements, and projects that also aim at delivering and exploring digital imagery on the World Wide Web. Future capabilities for site selection and change detection are also considered.

  16. A systemic identification approach for primary transcription start site of Arabidopsis miRNAs from multidimensional omics data.

    Science.gov (United States)

    You, Qi; Yan, Hengyu; Liu, Yue; Yi, Xin; Zhang, Kang; Xu, Wenying; Su, Zhen

    2017-05-01

    The 22-nucleotide non-coding microRNAs (miRNAs) are mostly transcribed by RNA polymerase II and are similar to protein-coding genes. Unlike the clear process from stem-loop precursors to mature miRNAs, the primary transcriptional regulation of miRNA, especially in plants, still needs to be further clarified, including the original transcription start site, functional cis-elements and primary transcript structures. Due to several well-characterized transcription signals in the promoter region, we proposed a systemic approach integrating multidimensional "omics" (including genomics, transcriptomics, and epigenomics) data to improve the genome-wide identification of primary miRNA transcripts. Here, we used the model plant Arabidopsis thaliana to improve the ability to identify candidate promoter locations in intergenic miRNAs and to determine rules for identifying primary transcription start sites of miRNAs by integrating high-throughput omics data, such as the DNase I hypersensitive sites, chromatin immunoprecipitation-sequencing of polymerase II and H3K4me3, as well as high throughput transcriptomic data. As a result, 93% of refined primary transcripts could be confirmed by the primer pairs from a previous study. Cis-element and secondary structure analyses also supported the feasibility of our results. This work will contribute to the primary transcriptional regulatory analysis of miRNAs, and the conserved regulatory pattern may be a suitable miRNA characteristic in other plant species.

  17. Cucurbits depicted in Byzantine mosaics from Israel, 350–600 ce

    Science.gov (United States)

    Avital, Anat; Paris, Harry S.

    2014-01-01

    Background and Aims Thousands of floor mosaics were produced in lands across the Roman and Byzantine empires. Some mosaics contain depictions of agricultural produce, potentially providing useful information concerning the contemporary presence and popularity of crop plants in a particular geographical region. Hundreds of floor mosaics produced in Israel during the Byzantine period have survived. The objective of the present work was to search these mosaics for Cucurbitaceae in order to obtain a more complete picture of cucurbit crop history in the eastern Mediterranean region. Results and Conclusions Twenty-three mosaics dating from 350–600 ce were found that had images positively identifiable as cucurbits. The morphological diversity of the cucurbit fruits in the mosaics of Israel is greater than that appearing in mosaics from any other Roman or Byzantine provincial area. The depicted fruits vary in shape from oblate to extremely long, and some are furrowed, others are striped and others lack definite markings. The cucurbit taxa depicted in the mosaics are Cucumis melo (melon), Citrullus lanatus (watermelon), Luffa aegyptiaca (sponge gourd) and Lagenaria siceraria (bottle gourd). Cucumis melo is the most frequently found taxon in the mosaics and is represented by round dessert melons and long snake melons. Fruits of at least two cultivars of snake melons and of watermelons are represented. To our knowledge, images of sponge gourds have not been found in Roman and Byzantine mosaics elsewhere. Indeed, the mosaics of Israel contain what are probably the oldest depictions of Luffa aegyptiaca in Mediterranean lands. Sponge gourds are depicted often, in 11 of the mosaics at eight localities, and the images include both mature fruits, which are useful for cleaning and washing, and immature fruits, which are edible. Only one mosaic has images positively identifiable as of bottle gourds, and these were round–pyriform and probably used as vessels. PMID:24948671

  18. Cucurbits depicted in Byzantine mosaics from Israel, 350-600 ce.

    Science.gov (United States)

    Avital, Anat; Paris, Harry S

    2014-08-01

    Thousands of floor mosaics were produced in lands across the Roman and Byzantine empires. Some mosaics contain depictions of agricultural produce, potentially providing useful information concerning the contemporary presence and popularity of crop plants in a particular geographical region. Hundreds of floor mosaics produced in Israel during the Byzantine period have survived. The objective of the present work was to search these mosaics for Cucurbitaceae in order to obtain a more complete picture of cucurbit crop history in the eastern Mediterranean region. Twenty-three mosaics dating from 350-600 ce were found that had images positively identifiable as cucurbits. The morphological diversity of the cucurbit fruits in the mosaics of Israel is greater than that appearing in mosaics from any other Roman or Byzantine provincial area. The depicted fruits vary in shape from oblate to extremely long, and some are furrowed, others are striped and others lack definite markings. The cucurbit taxa depicted in the mosaics are Cucumis melo (melon), Citrullus lanatus (watermelon), Luffa aegyptiaca (sponge gourd) and Lagenaria siceraria (bottle gourd). Cucumis melo is the most frequently found taxon in the mosaics and is represented by round dessert melons and long snake melons. Fruits of at least two cultivars of snake melons and of watermelons are represented. To our knowledge, images of sponge gourds have not been found in Roman and Byzantine mosaics elsewhere. Indeed, the mosaics of Israel contain what are probably the oldest depictions of Luffa aegyptiaca in Mediterranean lands. Sponge gourds are depicted often, in 11 of the mosaics at eight localities, and the images include both mature fruits, which are useful for cleaning and washing, and immature fruits, which are edible. Only one mosaic has images positively identifiable as of bottle gourds, and these were round-pyriform and probably used as vessels. © The Author 2014. Published by Oxford University Press on behalf of

  19. Both the constitutive Cauliflower Mosaic Virus 35S and tissue-specific AGAMOUS enhancers activate transcription autonomously in Arabidopsis thaliana

    Science.gov (United States)

    The presence of multiple enhancers and promoters within a single vector often provokes complicated mutual interaction and crosstalk, thereby, altering promoter specificity, which causes serious problems for precisely engineering gene function and agronomic traits in transgenic plants. Enhancer elem...

  20. A Mole's Eye View: Marcellus as Mosaic by Rachel Sager

    Science.gov (United States)

    Sager, R.

    2013-12-01

    I am an artist living and working in the energy vortex of Southwestern Pennsylvania and am watching great upheaval, both good and bad, happen to my land and its citizens due to the phenomenon caused by our particular geologic formation; the Marcellus Shale. My work embraces the earth itself through the medium of mosaic, and I have found it to be a great communicator to many groups of people: landowners, gas industry workers, environmentalists. I tell the story of how I came to be so dependent on my native stone, coming from a long line of coal miners and farmers who taught me to be aware of what lies beneath my feet. With my stone hammer, I chop up shale, sandstone, limestone, and coal, transforming it into tiny, expressive pieces that tell stories and help people to grasp geologic concepts that can otherwise be overwhelming and mysterious. I address the industry itself by representing the controversial enterprise of fracking, but also delve intimately into building relationships with the stone that I gather, wash, categorize, cut, and lay into mortar. By depicting these layers of earth, I am building touchable, organic images of geologic time that are highly accessible to the human brain and sensibility. There is something personal and immediate about standing in front of one of these mosaics, being able to touch it that gives the viewer power over an idea that often leaves them feeling in the dark. As a classically trained mosaic artist, I bring back the skills, culture, and tradition of a Euro-centered art form and weave it into my North American geology. Through a highly detailed and dynamic PowerPoint presentation of my work, I help people to see the earth beneath their feet with new eyes. Rachel Sager, artist www.rachelsagermosaics.com Contemporary Art in a Geologic Medium: Rachel Sager Mosaics

  1. Integrity of the cone photoreceptor mosaic in oligocone trichromacy

    DEFF Research Database (Denmark)

    Michaelides, Michel; Rha, Jungtae; Dees, Elise W

    2011-01-01

    Oligocone trichromacy (OT) is an unusual cone dysfunction syndrome characterized by reduced visual acuity, mild photophobia, reduced amplitude of the cone electroretinogram with normal rod responses, normal fundus appearance, and normal or near-normal color vision. It has been proposed that these...... that these patients have a reduced number of normal functioning cones (oligocone). This paper has sought to evaluate the integrity of the cone photoreceptor mosaic in four patients previously described as having OT....

  2. Radiation of ultrarelativistic particles passing through ideal and mosaic crystals

    International Nuclear Information System (INIS)

    Afanas'ev, A.M.

    1977-01-01

    When a charged particle passes through an ideal crystal, then besides the transition radiation, a new kind of radiation, connected with the periodic structure of the crystal is produced. The influence of mosaic structure of a crystal on the intensity of this radiation is considered. Simple analytical expressions for the integral intensity of this radiation for the case of an ideal crystal are obtained. The results show, that the integral radiation intensity depends weakly on the degree of crystal perfection

  3. New Multibeam Bathymetry Mosaic at NOAA/NCEI

    Science.gov (United States)

    Varner, J. D.; Cartwright, J.; Rosenberg, A. M.; Amante, C.; Sutherland, M.; Jencks, J. H.

    2017-12-01

    NOAA's National Centers for Environmental Information (NCEI) maintains an ever-growing archive of multibeam bathymetric data acquired from U.S. and international government and academic sources. The data are partitioned in the individual survey files in which they were originally received, and are stored in various formats not directly accessible by popular analysis and visualization tools. In order to improve the discoverability and accessibility of the data, NCEI created a new Multibeam Bathymetry Mosaic. Each survey was gridded at 3 arcsecond cell size and organized in an ArcGIS mosaic dataset, which was published as a set of standards-based web services usable in desktop GIS and web clients. In addition to providing a "seamless" grid of all surveys, a filter can be applied to isolate individual surveys. Both depth values in meters and shaded relief visualizations are available. The product represents the current state of the archive; no QA/QC was performed on the data before being incorporated, and the mosaic will be updated incrementally as new surveys are added to the archive. We expect the mosaic will address customer needs for visualization/extraction that existing tools (e.g. NCEI's AutoGrid) are unable to meet, and also assist data managers in identifying problem surveys, missing data, quality control issues, etc. This project complements existing efforts such as the Global Multi-Resolution Topography Data Synthesis (GMRT) at LDEO. Comprehensive visual displays of bathymetric data holdings are invaluable tools for seafloor mapping initiatives, such as Seabed 2030, that will aid in minimizing data collection redundancies and ensuring that valuable data are made available to the broadest community.

  4. Protein synthesis directed by cowpea mosaic virus RNAs

    International Nuclear Information System (INIS)

    Stuik, E.

    1979-01-01

    The thesis concerns the proteins synthesized under direction of Cowpea mosaic virus RNAs. Sufficient radioactive labelling of proteins was achieved when 35 S as sulphate was administered to intact Vigna plants, cultivated in Hoagland solution. The large polypeptides synthesized under direction of B- and M-RNA are probably precursor molecules from which the coat proteins are generated by a mechanism of posttranslational cleavage. (Auth.)

  5. Proteins synthesized in tobacco mosaic virus infected protoplasts

    International Nuclear Information System (INIS)

    Huber, R.

    1979-01-01

    The author deals with research on the multiplication of tobacco mosaic virus (TMV) in leaf cell protoplasts. An attempt is made to answer three questions: (1) Which proteins are synthesized in TMV infected protoplasts as a result of TMV multiplication. (2) Which of the synthesized proteins are made under the direction of the TMV genome and, if any, which of the proteins are host specific. (3) In which functions are these proteins involved. (Auth.)

  6. Concurrent insulinoma with mosaic Turner syndrome: A case report.

    Science.gov (United States)

    Wang, Shaoyun; Yang, Lijuan; Li, Jie; Mu, Yiming

    2015-03-01

    Turner syndrome is a chromosomal abnormality in which the majority of patients have a 45XO karyotype, while a small number have a 45XO/47XXX karyotype. Congenital adrenal hyperplasia has been previously reported in patients with Turner syndrome. Although insulinomas are the most common type of functioning pancreatic neuroendocrine tumor and have been reported in patients with multiple endocrine neoplasias, the tumors have not been reported in patients with mosaic Turner syndrome. The present study reports the first case of an insulinoma in a patient with 45XO/47XXX mosaic Turner syndrome. The patient suffered from recurrent hypoglycemia, which was relieved following ingestion of glucose or food. A 5-h glucose tolerance test was performed and the levels of glucose, C-Peptide and insulin were detected. In addition, computed tomography (CT) and ultrasound scanning were performed to evaluate the possibility of an insulinoma. Pathological examination and karyotyping were performed on a surgical specimen and a whole blood sample, respectively. The patient was found to suffer from premature ovarian failure, and a physical examination was consistent with a diagnosis of Turner syndrome. An ultrasound scan demonstrated streak ovaries and the patient was found to have a 45XO/47XXX karyotype. Furthermore, a lesion was detected in the pancreas following CT scanning, which was identified as an insulinoma following surgical removal and histological examination. In conclusion, the present study reports the first case of an insulinoma in a patient with mosaic Turner syndrome. Since mosaic Turner syndrome and insulinoma are rare diseases, an association may exist that has not been previously identified.

  7. gmos: Rapid Detection of Genome Mosaicism over Short Evolutionary Distances.

    Directory of Open Access Journals (Sweden)

    Mirjana Domazet-Lošo

    Full Text Available Prokaryotic and viral genomes are often altered by recombination and horizontal gene transfer. The existing methods for detecting recombination are primarily aimed at viral genomes or sets of loci, since the expensive computation of underlying statistical models often hinders the comparison of complete prokaryotic genomes. As an alternative, alignment-free solutions are more efficient, but cannot map (align a query to subject genomes. To address this problem, we have developed gmos (Genome MOsaic Structure, a new program that determines the mosaic structure of query genomes when compared to a set of closely related subject genomes. The program first computes local alignments between query and subject genomes and then reconstructs the query mosaic structure by choosing the best local alignment for each query region. To accomplish the analysis quickly, the program mostly relies on pairwise alignments and constructs multiple sequence alignments over short overlapping subject regions only when necessary. This fine-tuned implementation achieves an efficiency comparable to an alignment-free tool. The program performs well for simulated and real data sets of closely related genomes and can be used for fast recombination detection; for instance, when a new prokaryotic pathogen is discovered. As an example, gmos was used to detect genome mosaicism in a pathogenic Enterococcus faecium strain compared to seven closely related genomes. The analysis took less than two minutes on a single 2.1 GHz processor. The output is available in fasta format and can be visualized using an accessory program, gmosDraw (freely available with gmos.

  8. Hellenistic mosaic glass vessels in Bohemia and Moravia

    Czech Academy of Sciences Publication Activity Database

    Venclová, Natalie; Hulínský, V.; Jonášová, Šárka; Frána, Jaroslav; Fikrle, Marek; Vaculovič, T.

    2015-01-01

    Roč. 67, č. 2 (2015), s. 213-238 ISSN 0323-1267 R&D Projects: GA ČR(CZ) GA14-25396S Grant - others:GA MŠk(CZ) ED1.1.00/02.0068 Program:ED Institutional support: RVO:67985912 ; RVO:67985831 ; RVO:61389005 Keywords : mosaic glass vessels * Late La Tène period * Mediterranean imports Subject RIV: AC - Archeology, Anthropology, Ethnology

  9. Detectable clonal mosaicism and its relationship to aging and cancer

    Science.gov (United States)

    Jacobs, Kevin B; Yeager, Meredith; Zhou, Weiyin; Wacholder, Sholom; Wang, Zhaoming; Rodriguez-Santiago, Benjamin; Hutchinson, Amy; Deng, Xiang; Liu, Chenwei; Horner, Marie-Josephe; Cullen, Michael; Epstein, Caroline G; Burdett, Laurie; Dean, Michael C; Chatterjee, Nilanjan; Sampson, Joshua; Chung, Charles C; Kovaks, Joseph; Gapstur, Susan M; Stevens, Victoria L; Teras, Lauren T; Gaudet, Mia M; Albanes, Demetrius; Weinstein, Stephanie J; Virtamo, Jarmo; Taylor, Philip R; Freedman, Neal D; Abnet, Christian C; Goldstein, Alisa M; Hu, Nan; Yu, Kai; Yuan, Jian-Min; Liao, Linda; Ding, Ti; Qiao, You-Lin; Gao, Yu-Tang; Koh, Woon-Puay; Xiang, Yong-Bing; Tang, Ze-Zhong; Fan, Jin-Hu; Aldrich, Melinda C; Amos, Christopher; Blot, William J; Bock, Cathryn H; Gillanders, Elizabeth M; Harris, Curtis C; Haiman, Christopher A; Henderson, Brian E; Kolonel, Laurence N; Le Marchand, Loic; McNeill, Lorna H; Rybicki, Benjamin A; Schwartz, Ann G; Signorello, Lisa B; Spitz, Margaret R; Wiencke, John K; Wrensch, Margaret; Wu, Xifeng; Zanetti, Krista A; Ziegler, Regina G; Figueroa, Jonine D; Garcia-Closas, Montserrat; Malats, Nuria; Marenne, Gaelle; Prokunina-Olsson, Ludmila; Baris, Dalsu; Schwenn, Molly; Johnson, Alison; Landi, Maria Teresa; Goldin, Lynn; Consonni, Dario; Bertazzi, Pier Alberto; Rotunno, Melissa; Rajaraman, Preetha; Andersson, Ulrika; Freeman, Laura E Beane; Berg, Christine D; Buring, Julie E; Butler, Mary A; Carreon, Tania; Feychting, Maria; Ahlbom, Anders; Gaziano, J Michael; Giles, Graham G; Hallmans, Goran; Hankinson, Susan E; Hartge, Patricia; Henriksson, Roger; Inskip, Peter D; Johansen, Christoffer; Landgren, Annelie; McKean-Cowdin, Roberta; Michaud, Dominique S; Melin, Beatrice S; Peters, Ulrike; Ruder, Avima M; Sesso, Howard D; Severi, Gianluca; Shu, Xiao-Ou; Visvanathan, Kala; White, Emily; Wolk, Alicja; Zeleniuch-Jacquotte, Anne; Zheng, Wei; Silverman, Debra T; Kogevinas, Manolis; Gonzalez, Juan R; Villa, Olaya; Li, Donghui; Duell, Eric J; Risch, Harvey A; Olson, Sara H; Kooperberg, Charles; Wolpin, Brian M; Jiao, Li; Hassan, Manal; Wheeler, William; Arslan, Alan A; Bas Bueno-de-Mesquita, H; Fuchs, Charles S; Gallinger, Steven; Gross, Myron D; Holly, Elizabeth A; Klein, Alison P; LaCroix, Andrea; Mandelson, Margaret T; Petersen, Gloria; Boutron-Ruault, Marie-Christine; Bracci, Paige M; Canzian, Federico; Chang, Kenneth; Cotterchio, Michelle; Giovannucci, Edward L; Goggins, Michael; Bolton, Judith A Hoffman; Jenab, Mazda; Khaw, Kay-Tee; Krogh, Vittorio; Kurtz, Robert C; McWilliams, Robert R; Mendelsohn, Julie B; Rabe, Kari G; Riboli, Elio; Tjønneland, Anne; Tobias, Geoffrey S; Trichopoulos, Dimitrios; Elena, Joanne W; Yu, Herbert; Amundadottir, Laufey; Stolzenberg-Solomon, Rachael Z; Kraft, Peter; Schumacher, Fredrick; Stram, Daniel; Savage, Sharon A; Mirabello, Lisa; Andrulis, Irene L; Wunder, Jay S; García, Ana Patiño; Sierrasesúmaga, Luis; Barkauskas, Donald A; Gorlick, Richard G; Purdue, Mark; Chow, Wong-Ho; Moore, Lee E; Schwartz, Kendra L; Davis, Faith G; Hsing, Ann W; Berndt, Sonja I; Black, Amanda; Wentzensen, Nicolas; Brinton, Louise A; Lissowska, Jolanta; Peplonska, Beata; McGlynn, Katherine A; Cook, Michael B; Graubard, Barry I; Kratz, Christian P; Greene, Mark H; Erickson, Ralph L; Hunter, David J; Thomas, Gilles; Hoover, Robert N; Real, Francisco X; Fraumeni, Joseph F; Caporaso, Neil E; Tucker, Margaret; Rothman, Nathaniel; Pérez-Jurado, Luis A; Chanock, Stephen J

    2012-01-01

    In an analysis of 31,717 cancer cases and 26,136 cancer-free controls drawn from 13 genome-wide association studies (GWAS), we observed large chromosomal abnormalities in a subset of clones from DNA obtained from blood or buccal samples. Mosaic chromosomal abnormalities, either aneuploidy or copy-neutral loss of heterozygosity, of size >2 Mb were observed in autosomes of 517 individuals (0.89%) with abnormal cell proportions between 7% and 95%. In cancer-free individuals, the frequency increased with age; 0.23% under 50 and 1.91% between 75 and 79 (p=4.8×10−8). Mosaic abnormalities were more frequent in individuals with solid-tumors (0.97% versus 0.74% in cancer-free individuals, OR=1.25, p=0.016), with a stronger association for cases who had DNA collected prior to diagnosis or treatment (OR=1.45, p=0.0005). Detectable clonal mosaicism was common in individuals for whom DNA was collected at least one year prior to diagnosis of leukemia compared to cancer-free individuals (OR=35.4, p=3.8×10−11). These findings underscore the importance of the role and time-dependent nature of somatic events in the etiology of cancer and other late-onset diseases. PMID:22561519

  10. Enabling Large Focal Plane Arrays Through Mosaic Hybridization

    Science.gov (United States)

    Miller, Timothy M.; Jhabvala, Christine A.; Leong, Edward; Costen, Nicholas P.; Sharp, Elmer; Adachi, Tomoko; Benford, Dominic J.

    2012-01-01

    We have demonstrated advances in mosaic hybridization that will enable very large format far-infrared detectors. Specifically we have produced electrical detector models via mosaic hybridization yielding superconducting circuit paths by hybridizing separately fabricated sub-units onto a single detector unit. The detector model was made on a 100mm diameter wafer while four model readout quadrant chips were made from a separate 100mm wafer. The individually fabricated parts were hybridized using a flip-chip bonder to assemble the detector-readout stack. Once all of the hybridized readouts were in place, a single, large and thick silicon substrate was placed on the stack and attached with permanent epoxy to provide strength and a Coefficient of Thermal Expansion match to the silicon components underneath. Wirebond pads on the readout chips connect circuits to warm readout electronics; and were used to validate the successful superconducting electrical interconnection of the model mosaic-hybrid detector. This demonstration is directly scalable to 150 mm diameter wafers, enabling pixel areas over ten times the area currently available.

  11. LANDSAT M. S. S. IMAGE MOSAIC OF TUNISIA.

    Science.gov (United States)

    Boswell-Thomas, J. C.; ,

    1984-01-01

    The Landsat mosaic of Tunisia funded by USAID for the Remote Sensing Laboratory, Soils Division, Ministry of Agriculture, Tunisia, was completed by the USGS in September 1983. It is a mixed mosaic associating digital corrections and enhancements to manual mosaicking and corresponding to the Tunisian request for high resolution and the limited available funds. The scenes were processed by the Environmental Research Institute of Michigan, resampling the data geodesically corrected to fit the Universal Transverse Mercator projection using control points from topographic maps at 1:50,000 and 1:100,000 scales available in the U. S. The mosaicking was done in the Eastern Mapping Center under the supervision of the Graphic Arts System Section. The three black and white mosaics were made at the 1:1,000,000 scale and various products generated. They included color film positives at 1:2,000,000 and 1:4,000,000 scales reproducible in the Remote Sensing Laboratory in Tunis and corresponding color prints as well as tricolor prints at various scales from 1:500,000 to 1:2,000,000.

  12. Origin of nondisjunction in trisomy 8 and trisomy 8 mosaicism.

    Science.gov (United States)

    Karadima, G; Bugge, M; Nicolaidis, P; Vassilopoulos, D; Avramopoulos, D; Grigoriadou, M; Albrecht, B; Passarge, E; Annerén, G; Blennow, E; Clausen, N; Galla-Voumvouraki, A; Tsezou, A; Kitsiou-Tzeli, S; Hahnemann, J M; Hertz, J M; Houge, G; Kuklík, M; Macek, M; Lacombe, D; Miller, K; Moncla, A; López Pajares, I; Patsalis, P C; Petersen, M B

    1998-01-01

    Causes of chromosomal nondisjunction is one of the remaining unanswered questions in human genetics. In order to increase our understanding of the mechanisms underlying nondisjunction we have performed a molecular study on trisomy 8 and trisomy 8 mosaicism. We report the results on analyses of 26 probands (and parents) using 19 microsatellite DNA markers mapping along the length of chromosome 8. The 26 cases represented 20 live births, four spontaneous abortions, and two prenatal diagnoses (CVS). The results of the nondisjunction studies show that 20 cases (13 maternal, 7 paternal) were probably due to mitotic (postzygotic) duplication as reduction to homozygosity of all informative markers was observed and as no third allele was ever detected. Only two cases from spontaneous abortions were due to maternal meiotic nondisjunction. In four cases we were not able to detect the extra chromosome due to a low level of mosaicism. These results are in contrast to the common autosomal trisomies (including mosaics), where the majority of cases are due to errors in maternal meiosis.

  13. Mining the active proteome of Arabidopsis thaliana

    Directory of Open Access Journals (Sweden)

    Renier A. L. Van Der Hoorn

    2011-11-01

    Full Text Available Assigning functions to the >30.000 proteins encoded by the Arabidopsis genome is a challenging task of the Arabidopsis Functional Genomics Network. Although genome-wide technologies like proteomics and transcriptomics have generated a wealth of information that significantly accelerated gene annotation, protein activities are poorly predicted by transcript or protein levels as protein activities are post-translationally regulated. To directly display protein activities in Arabidopsis proteomes, we developed and applied Activity-based Protein Profiling (ABPP. ABPP is based on the use of small molecule probes that react with the catalytic residues of distinct protein classes in an activity-dependent manner. Labeled proteins are separated and detected from proteins gels and purified and identified by mass spectrometry. Using probes of six different chemotypes we have displayed of activities of 76 Arabidopsis proteins. These proteins represent over ten different protein classes that contain over 250 Arabidopsis proteins, including cysteine- serine- and metallo-proteases, lipases, acyltransferases, and the proteasome. We have developed methods for identification of in vivo labeled proteins using click-chemistry and for in vivo imaging with fluorescent probes. In vivo labeling has revealed novel protein activities and unexpected subcellular activities of the proteasome. Labeling of extracts displayed several differential activities e.g. of the proteasome during immune response and methylesterases during infection. These studies illustrate the power of ABPP to display the functional proteome and testify to a successful interdisciplinary collaboration involving chemical biology, organic chemistry and proteomics.

  14. Bioavailability of nanoparticulate hematite to Arabidopsis thaliana

    International Nuclear Information System (INIS)

    Marusenko, Yevgeniy; Shipp, Jessie; Hamilton, George A.; Morgan, Jennifer L.L.; Keebaugh, Michael; Hill, Hansina; Dutta, Arnab; Zhuo, Xiaoding; Upadhyay, Nabin; Hutchings, James; Herckes, Pierre; Anbar, Ariel D.; Shock, Everett; Hartnett, Hilairy E.

    2013-01-01

    The environmental effects and bioavailability of nanoparticulate iron (Fe) to plants are currently unknown. Here, plant bioavailability of synthesized hematite Fe nanoparticles was evaluated using Arabidopsis thaliana (A. thaliana) as a model. Over 56-days of growing wild-type A. thaliana, the nanoparticle-Fe and no-Fe treatments had lower plant biomass, lower chlorophyll concentrations, and lower internal Fe concentrations than the Fe-treatment. Results for the no-Fe and nanoparticle-Fe treatments were consistently similar throughout the experiment. These results suggest that nanoparticles (mean diameter 40.9 nm, range 22.3–67.0 nm) were not taken up and therefore not bioavailable to A. thaliana. Over 14-days growing wild-type and transgenic (Type I/II proton pump overexpression) A. thaliana, the Type I plant grew more than the wild-type in the nanoparticle-Fe treatment, suggesting Type I plants cope better with Fe limitation; however, the nanoparticle-Fe and no-Fe treatments had similar growth for all plant types. -- Highlights: ► Iron nanoparticles were synthesized and assessed for bioavailability to Arabidopsis. ► Arabidopsis grew better in the presence of EDTA-bound iron than nanoparticulate iron. ► Arabidopsis grew the same in the presence of nanoparticulate iron compared to no iron. -- Synthesized iron nanoparticles were not bioavailable to Arabidopsis thaliana in agar nutrient media

  15. Velvet bean severe mosaic virus: a distinct begomovirus species causing severe mosaic in Mucuna pruriens (L.) DC.

    Science.gov (United States)

    Zaim, Mohammad; Kumar, Yogesh; Hallan, Vipin; Zaidi, A A

    2011-08-01

    Velvet bean [Mucuna pruriens (L.) DC] is one of the most important medicinal plants. It is used to treat many ailments, but is widely used for the treatment especially for Parkinson's disease because of the presence of 3,4-dihydroxyphenylalanine (L-dopa) in it. It was noticed in last 5 years that the plants in the field showed severe mosaic, downward curling of the leaves, stunting, etc. This is consistently observed over the years in India. The disease was transmitted by whiteflies and by grafting and the causal agent was found to be a bipartite begomovirus. The whole genome was amplified by rolling circle amplification (RCA) using ϕ-29 DNA polymerase and characterized. DNA-A and DNA-B shared a 124-nucleotide (nt) long highly conserved (98%) common region (CR). Comparisons with other begomovirus showed that DNA-A sequence has highest identity (76%) with an isolate of Mungbean yellow mosaic India virus (MYMIV; AY937195) reported from India. This data suggested that the present isolate is a new species of genus Begomovirus for which the name "Velvet bean severe mosaic virus" (VbSMV) is proposed. DNA-B has a maximum sequence identity of 49% with an isolate of Horsegram yellow mosaic virus (HgYMV; AM932426) reported from India. Infectious clones consisting of a 1.7 mer partial tandem repeat of DNA-A and a dimer of DNB-B were constructed and agro-inoculated to Macuna pruriens (L.) DC plants, which showed field observed symptoms 24 days post-infiltration (dpi). In phylogenetic analysis, DNA-A and DNA-B of the present isolate grouped with DNA-A of different begomoviruses reported from fabaceous crops. The study presents first ever molecular evidence of any disease in velvet bean and whole genome analysis of the causative virus which is a distinct bipartite species of Begomovirus.

  16. Left-sided congenital heart lesions in mosaic Turner syndrome.

    Science.gov (United States)

    Bouayed Abdelmoula, Nouha; Abdelmoula, Balkiss; Smaoui, Walid; Trabelsi, Imen; Louati, Rim; Aloulou, Samir; Aloulou, Wafa; Abid, Fatma; Kammoun, Senda; Trigui, Khaled; Bedoui, Olfa; Denguir, Hichem; Mallek, Souad; Ben Aziza, Mustapha; Dammak, Jamila; Kaabi, Oldez; Abdellaoui, Nawel; Turki, Fatma; Kaabi, Asma; Kamoun, Wafa; Jabeur, Jihen; Ltaif, Wided; Chaker, Kays; Fourati, Haytham; M'rabet, Samir; Ben Ameur, Hedi; Gouia, Naourez; Mhiri, Mohamed Nabil; Rebai, Tarek

    2018-04-01

    In the era of the diseasomes and interactome networks, linking genetics with phenotypic traits in Turner syndrome should be studied thoroughly. As a part of this stratagem, mosaicism of both X and Y chromosome which is a common finding in TS and an evaluation of congenital heart diseases in the different situations of mosaic TS types, can be helpful in the identification of disturbed sex chromosomes, genes and signaling pathway actors. Here we report the case of a mosaic TS associated to four left-sided CHD, including BAV, COA, aortic aneurysms and dissections at an early age. The mosaicism included two cell lines, well-defined at the cytogenetic and molecular levels: a cell line which is monosomic for Xp and Xq genes (45,X) and another which is trisomic for pseudoautosomal genes that are present on the X and Y chromosomes and escape X inactivation: 45,X[8]/46,X,idic(Y)(pter→q11.2::q11.2→pter)[42]. This case generates two hypotheses about the contribution of genes linked to the sex chromosomes and the signaling pathways involving these genes, in left-sided heart diseases. The first hypothesis suggests the interaction between X chromosome and autosomal genes or loci of aortic development, possibly dose-dependent, and which could be in the framework of TGF-β-SMAD signaling pathways. The second implies that left-sided congenital heart lesions involve sex chromosomes loci. The reduced dosage of X chromosome gene(s), escaping X inactivation during development, contributes to this type of CHD. Regarding our case, these X chromosome genes may have homologues at the Y chromosome, but the process of inactivation of the centromeres of the isodicentric Y spreads to the concerned Y chromosome genes. Therefore, this case emerges as an invitation to consider the mosaics of Turner syndrome and to study their phenotypes in correlation with their genotypes to discover the underlying developmental and genetic mechanisms, especially the ones related to sex chromosomes.

  17. Chromosomal Mosaicism in Human Feto-Placental Development: Implications for Prenatal Diagnosis

    Directory of Open Access Journals (Sweden)

    Francesca Romana Grati

    2014-07-01

    Full Text Available Chromosomal mosaicism is one of the primary interpretative issues in prenatal diagnosis. In this review, the mechanisms underlying feto-placental chromosomal mosaicism are presented. Based on the substantial retrospective diagnostic experience with chorionic villi samples (CVS of a prenatal diagnosis laboratory the following items are discussed: (i The frequency of the different types of mosaicism (confined placental, CPM, and true fetal mosaicisms, TFM; (ii The risk of fetal confirmation after the detection of a mosaic in CVS stratified by chromosome abnormality and placental tissue involvement; (iii The frequency of uniparental disomy for imprinted chromosomes associated with CPM; (iv The incidence of false-positive and false-negative results in CVS samples analyzed by only (semi-direct preparation or long term culture; and (v The implications of the presence of a feto-placental mosaicism for microarray analysis of CVS and non-invasive prenatal screening (NIPS.

  18. Effect of medicinal plants extracts on the incidence of mosaic disease caused by cucumber mosaic virus and growth of chili

    Science.gov (United States)

    Hamidson, H.; Damiri, N.; Angraini, E.

    2018-01-01

    This research was conducted to study the effect of the application of several extracts of medicinal plants on the incidence of mosaic disease caused by Cucumber Mosaic Virus infection on the chili (Capsicum annuum L.) plantation. A Randomized Block Design with eight treatments including control was used throughout the experiment. Treatments consisted of Azadiracta indica (A), Piper bitle (B), Cymbopogon citrates (C), Curcuma domestica (D), Averroa bilimbi (E), Datura stramonium (F), Annona Muricata (G) and control (H). Each treatment consist of three replications. The parameters observed were the incidence of mosaic attack due to CMV, disease severity, plant height, wet and dry weight and production (number of fruits and the weight of total fruits) each plant. Results showed that the application of medicinal plant extracts reduced the disease severity due to CMV. Extracts of Annona muricata and Datura stramonium were most effective in suppressing disease severity caused by the virus as they significantly different from control and from a number of treatment. The plants medicinal extracts were found to have increased the plant height and total weight of the plant, fruit amount and fruit weight. Extracts of Curcuma domestica, Piper bitle and Cymbopogon citrates were the third highest in fruit amount and weight and significantly different from the control.

  19. The arabidopsis cyclic nucleotide interactome

    KAUST Repository

    Donaldson, Lara Elizabeth

    2016-05-11

    Background Cyclic nucleotides have been shown to play important signaling roles in many physiological processes in plants including photosynthesis and defence. Despite this, little is known about cyclic nucleotide-dependent signaling mechanisms in plants since the downstream target proteins remain unknown. This is largely due to the fact that bioinformatics searches fail to identify plant homologs of protein kinases and phosphodiesterases that are the main targets of cyclic nucleotides in animals. Methods An affinity purification technique was used to identify cyclic nucleotide binding proteins in Arabidopsis thaliana. The identified proteins were subjected to a computational analysis that included a sequence, transcriptional co-expression and functional annotation analysis in order to assess their potential role in plant cyclic nucleotide signaling. Results A total of twelve cyclic nucleotide binding proteins were identified experimentally including key enzymes in the Calvin cycle and photorespiration pathway. Importantly, eight of the twelve proteins were shown to contain putative cyclic nucleotide binding domains. Moreover, the identified proteins are post-translationally modified by nitric oxide, transcriptionally co-expressed and annotated to function in hydrogen peroxide signaling and the defence response. The activity of one of these proteins, GLYGOLATE OXIDASE 1, a photorespiratory enzyme that produces hydrogen peroxide in response to Pseudomonas, was shown to be repressed by a combination of cGMP and nitric oxide treatment. Conclusions We propose that the identified proteins function together as points of cross-talk between cyclic nucleotide, nitric oxide and reactive oxygen species signaling during the defence response.

  20. Mosaic Down syndrome and acute lymphoblastic B cell-leukemia. Case report

    Directory of Open Access Journals (Sweden)

    Parra-Baltazar, Isabel Mónica

    2016-10-01

    Full Text Available Down syndrome (DS or trisomy 21 is a constitutional chromosomal abnormality, which may be mosaic in 1 % to 4 % of cases. DS mosaic diagnosis is difficult because most patients have a normal phenotype and show no significant clinical abnormalities. Patients with DS have a higher risk of developing acute leukemia such as acute lymphoblastic leukemia (ALL. We report the case of a 19-year old woman with mosaic trisomy 21 and ALL.

  1. Self-standing quasi-mosaic crystals for focusing hard X-rays

    International Nuclear Information System (INIS)

    Camattari, Riccardo; Guidi, Vincenzo; Bellucci, Valerio; Neri, Ilaria; Frontera, Filippo; Jentschel, Michael

    2013-01-01

    A quasi mosaic bent crystal for high-resolution diffraction of X and γ rays has been realized. A net curvature was imprinted to the crystal thanks to a series of superficial grooves to keep the curvature without external devices. The crystal highlights very high diffraction efficiency due to quasi mosaic curvature. Quasi mosaic crystals of this kind are proposed for the realization of a high-resolution focusing Laue lens for hard X-rays.

  2. Breeding of new variety Yangfumai 4 with high resistance to wheat yellow mosaic disease

    International Nuclear Information System (INIS)

    He Zhentian; Chen Xiulan; Zhang Rong; Wang Jianhua; Wang Jinrong; Liu Jian

    2011-01-01

    To control the infection of wheat yellow mosaic disease,new wheat variety with high-yield, disease-resistant was selected. Ningmai 9, which carries yellow mosaic disease resistant genes, was used as original material. Combination of conventional breeding technique and radiation methods, a new wheat variety Yangfumai 4 was developed during 1996-2007, and registered in 2008. The new wheat variety with high yield and resistance to yellow mosaic disease is suitable to plant in the Yangtze River region. (authors)

  3. Glufosinate ammonium selection of transformed Arabidopsis.

    Science.gov (United States)

    Weigel, Detlef; Glazebrook, Jane

    2006-12-01

    INTRODUCTIONOne of the most commonly used markers for the selection of transgenic Arabidopsis is resistance to glufosinate ammonium, an herbicide that is sold under a variety of trade names including Basta and Finale. Resistance to glufosinate ammonium is conferred by the bacterial bialophos resistance gene (BAR) encoding the enzyme phosphinotricin acetyl transferase (PAT). This protocol describes the use of glufosinate ammonium to select transformed Arabidopsis plants. The major advantage of glufosinate ammonium selection is that it can be performed on plants growing in soil and does not require the use of sterile techniques.

  4. A New Waveform Mosaic Algorithm in the Vectorization of Paper Seismograms

    Directory of Open Access Journals (Sweden)

    Maofa Wang

    2014-11-01

    Full Text Available History paper seismograms are very important information for earthquake monitoring and prediction, and the vectorization of paper seismograms is a very import problem to be resolved. In this paper, a new waveform mosaic algorithm in the vectorization of paper seismograms is presented. We also give out the technological process to waveform mosaic, and a waveform mosaic system used to vectorize analog seismic record has been accomplished independently. Using it, we can precisely and speedy accomplish waveform mosaic for vectorizing analog seismic records.

  5. Female chromosome X mosaicism is age-related and preferentially affects the inactivated X chromosome

    Science.gov (United States)

    Machiela, Mitchell J.; Zhou, Weiyin; Karlins, Eric; Sampson, Joshua N.; Freedman, Neal D.; Yang, Qi; Hicks, Belynda; Dagnall, Casey; Hautman, Christopher; Jacobs, Kevin B.; Abnet, Christian C.; Aldrich, Melinda C.; Amos, Christopher; Amundadottir, Laufey T.; Arslan, Alan A.; Beane-Freeman, Laura E.; Berndt, Sonja I.; Black, Amanda; Blot, William J.; Bock, Cathryn H.; Bracci, Paige M.; Brinton, Louise A.; Bueno-de-Mesquita, H Bas; Burdett, Laurie; Buring, Julie E.; Butler, Mary A.; Canzian, Federico; Carreón, Tania; Chaffee, Kari G.; Chang, I-Shou; Chatterjee, Nilanjan; Chen, Chu; Chen, Constance; Chen, Kexin; Chung, Charles C.; Cook, Linda S.; Crous Bou, Marta; Cullen, Michael; Davis, Faith G.; De Vivo, Immaculata; Ding, Ti; Doherty, Jennifer; Duell, Eric J.; Epstein, Caroline G.; Fan, Jin-Hu; Figueroa, Jonine D.; Fraumeni, Joseph F.; Friedenreich, Christine M.; Fuchs, Charles S.; Gallinger, Steven; Gao, Yu-Tang; Gapstur, Susan M.; Garcia-Closas, Montserrat; Gaudet, Mia M.; Gaziano, J. Michael; Giles, Graham G.; Gillanders, Elizabeth M.; Giovannucci, Edward L.; Goldin, Lynn; Goldstein, Alisa M.; Haiman, Christopher A.; Hallmans, Goran; Hankinson, Susan E.; Harris, Curtis C.; Henriksson, Roger; Holly, Elizabeth A.; Hong, Yun-Chul; Hoover, Robert N.; Hsiung, Chao A.; Hu, Nan; Hu, Wei; Hunter, David J.; Hutchinson, Amy; Jenab, Mazda; Johansen, Christoffer; Khaw, Kay-Tee; Kim, Hee Nam; Kim, Yeul Hong; Kim, Young Tae; Klein, Alison P.; Klein, Robert; Koh, Woon-Puay; Kolonel, Laurence N.; Kooperberg, Charles; Kraft, Peter; Krogh, Vittorio; Kurtz, Robert C.; LaCroix, Andrea; Lan, Qing; Landi, Maria Teresa; Marchand, Loic Le; Li, Donghui; Liang, Xiaolin; Liao, Linda M.; Lin, Dongxin; Liu, Jianjun; Lissowska, Jolanta; Lu, Lingeng; Magliocco, Anthony M.; Malats, Nuria; Matsuo, Keitaro; McNeill, Lorna H.; McWilliams, Robert R.; Melin, Beatrice S.; Mirabello, Lisa; Moore, Lee; Olson, Sara H.; Orlow, Irene; Park, Jae Yong; Patiño-Garcia, Ana; Peplonska, Beata; Peters, Ulrike; Petersen, Gloria M.; Pooler, Loreall; Prescott, Jennifer; Prokunina-Olsson, Ludmila; Purdue, Mark P.; Qiao, You-Lin; Rajaraman, Preetha; Real, Francisco X.; Riboli, Elio; Risch, Harvey A.; Rodriguez-Santiago, Benjamin; Ruder, Avima M.; Savage, Sharon A.; Schumacher, Fredrick; Schwartz, Ann G.; Schwartz, Kendra L.; Seow, Adeline; Wendy Setiawan, Veronica; Severi, Gianluca; Shen, Hongbing; Sheng, Xin; Shin, Min-Ho; Shu, Xiao-Ou; Silverman, Debra T.; Spitz, Margaret R.; Stevens, Victoria L.; Stolzenberg-Solomon, Rachael; Stram, Daniel; Tang, Ze-Zhong; Taylor, Philip R.; Teras, Lauren R.; Tobias, Geoffrey S.; Van Den Berg, David; Visvanathan, Kala; Wacholder, Sholom; Wang, Jiu-Cun; Wang, Zhaoming; Wentzensen, Nicolas; Wheeler, William; White, Emily; Wiencke, John K.; Wolpin, Brian M.; Wong, Maria Pik; Wu, Chen; Wu, Tangchun; Wu, Xifeng; Wu, Yi-Long; Wunder, Jay S.; Xia, Lucy; Yang, Hannah P.; Yang, Pan-Chyr; Yu, Kai; Zanetti, Krista A.; Zeleniuch-Jacquotte, Anne; Zheng, Wei; Zhou, Baosen; Ziegler, Regina G.; Perez-Jurado, Luis A.; Caporaso, Neil E.; Rothman, Nathaniel; Tucker, Margaret; Dean, Michael C.; Yeager, Meredith; Chanock, Stephen J.

    2016-01-01

    To investigate large structural clonal mosaicism of chromosome X, we analysed the SNP microarray intensity data of 38,303 women from cancer genome-wide association studies (20,878 cases and 17,425 controls) and detected 124 mosaic X events >2 Mb in 97 (0.25%) women. Here we show rates for X-chromosome mosaicism are four times higher than mean autosomal rates; X mosaic events more often include the entire chromosome and participants with X events more likely harbour autosomal mosaic events. X mosaicism frequency increases with age (0.11% in 50-year olds; 0.45% in 75-year olds), as reported for Y and autosomes. Methylation array analyses of 33 women with X mosaicism indicate events preferentially involve the inactive X chromosome. Our results provide further evidence that the sex chromosomes undergo mosaic events more frequently than autosomes, which could have implications for understanding the underlying mechanisms of mosaic events and their possible contribution to risk for chronic diseases. PMID:27291797

  6. The coat protein of Alfalfa mosaic virus interacts and interferes with the transcriptional activity of the bHLH transcription factor ILR3 promoting salicylic acid-dependent defence signalling response.

    Science.gov (United States)

    Aparicio, Frederic; Pallás, Vicente

    2017-02-01

    During virus infection, specific viral component-host factor interaction elicits the transcriptional reprogramming of diverse cellular pathways. Alfalfa mosaic virus (AMV) can establish a compatible interaction in tobacco and Arabidopsis hosts. We show that the coat protein (CP) of AMV interacts directly with transcription factor (TF) ILR3 of both species. ILR3 is a basic helix-loop-helix (bHLH) family member of TFs, previously proposed to participate in diverse metabolic pathways. ILR3 has been shown to regulate NEET in Arabidopsis, a critical protein in plant development, senescence, iron metabolism and reactive oxygen species (ROS) homeostasis. We show that the AMV CP-ILR3 interaction causes a fraction of this TF to relocate from the nucleus to the nucleolus. ROS, pathogenesis-related protein 1 (PR1) mRNAs, salicylic acid (SA) and jasmonic acid (JA) contents are increased in healthy Arabidopsis loss-of-function ILR3 mutant (ilr3.2) plants, which implicates ILR3 in the regulation of plant defence responses. In AMV-infected wild-type (wt) plants, NEET expression is reduced slightly, but is induced significantly in ilr3.2 mutant plants. Furthermore, the accumulation of SA and JA is induced in Arabidopsis wt-infected plants. AMV infection in ilr3.2 plants increases JA by over 10-fold, and SA is reduced significantly, indicating an antagonist crosstalk effect. The accumulation levels of viral RNAs are decreased significantly in ilr3.2 mutants, but the virus can still systemically invade the plant. The AMV CP-ILR3 interaction may down-regulate a host factor, NEET, leading to the activation of plant hormone responses to obtain a hormonal equilibrium state, where infection remains at a level that does not affect plant viability. © 2016 BSPP AND JOHN WILEY & SONS LTD.

  7. Nucleotide sequence of Hungarian grapevine chrome mosaic nepovirus RNA1.

    OpenAIRE

    Le Gall, O; Candresse, T; Brault, V; Dunez, J

    1989-01-01

    The nucleotide sequence of the RNA1 of hungarian grapevine chrome mosaic virus, a nepovirus very closely related to tomato black ring virus, has been determined from cDNA clones. It is 7212 nucleotides in length excluding the 3' terminal poly(A) tail and contains a large open reading frame extending from nucleotides 216 to 6971. The presumably encoded polyprotein is 2252 amino acids in length with a molecular weight of 250 kDa. The primary structure of the polyprotein was compared with that o...

  8. In-Situ Mosaic Production at JPL/MIPL

    Science.gov (United States)

    Deen, Bob

    2012-01-01

    Multimission Image Processing Lab (MIPL) at JPL is responsible for (among other things) the ground-based operational image processing of all the recent in-situ Mars missions: (1) Mars Pathfinder (2) Mars Polar Lander (3) Mars Exploration Rovers (MER) (4) Phoenix (5) Mars Science Lab (MSL) Mosaics are probably the most visible products from MIPL (1) Generated for virtually every rover position at which a panorama is taken (2) Provide better environmental context than single images (3) Valuable to operations and science personnel (4) Arguably the signature products for public engagement

  9. Grandpaternal mosaicism in a family with isolated haemophilia A.

    Science.gov (United States)

    Casey, G J; Rodgers, S E; Hall, J R; Rudzki, Z; Lloyd, J V

    1999-12-01

    About one third of cases of haemophilia A have no family history of the disorder, and 20% are thought to be due to a new mutation. In the family reported here, a 3 bp deletion was detected in DNA from the proband at the 3' end of exon 15. Direct sequencing of genomic DNA prepared from blood and buccal cells of the grandfather revealed both normal and mutant sequences, suggesting that he is a mosaic for this mutation. This highlights the usefulness of mutation detection, both for accurate genetic counselling and to determine the origin of new mutations of haemophilia.

  10. Arabidopsis CDS blastp result: AK288349 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK288349 J090023P19 At2g46590.1 68415.m05811 Dof zinc finger protein DAG2 / Dof affecting germination... 2 (DAG2) identical to SP|Q9ZPY0 DOF zinc finger protein DAG2 (Dof affecting germination 2) {Arabidopsis thaliana} 1e-23 ...

  11. Arabidopsis CDS blastp result: AK241364 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK241364 J065152E11 At2g46590.1 68415.m05811 Dof zinc finger protein DAG2 / Dof affecting germination... 2 (DAG2) identical to SP|Q9ZPY0 DOF zinc finger protein DAG2 (Dof affecting germination 2) {Arabidopsis thaliana} 2e-20 ...

  12. Reference: 439 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available or IID (TFIID) complex. Overexpression of atTAF10 under the control of the 35S promoter in Arabidopsis impro...is TATA box-binding protein (TBP)-associated factor 10 (atTAF10), which constitutes the transcriptional fact

  13. Arabidopsis CDS blastp result: AK064663 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK064663 002-115-A10 At2g34450.1 high mobility group (HMG1/2) family protein simila...r to HMG protein [Arabidopsis thaliana] GI:2832361; contains Pfam profile PF00505: HMG (high mobility group) box 2e-27 ...

  14. Divergent regulation of Arabidopsis SAUR genes

    NARCIS (Netherlands)

    Mourik, van Hilda; Dijk, van Aalt D.J.; Stortenbeker, Niek; Angenent, Gerco C.; Bemer, Marian

    2017-01-01

    Background: Small Auxin-Upregulated RNA (SAUR) genes encode growth regulators that induce cell elongation. Arabidopsis contains more than 70 SAUR genes, of which the growth-promoting function has been unveiled in seedlings, while their role in other tissues remained largely unknown. Here, we

  15. Arabidopsis CDS blastp result: AK120871 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK120871 J023026D19 At1g48900.1 signal recognition particle 54 kDa protein 3 / SRP5...4 (SRP-54C) identical to SP|P49967 Signal recognition particle 54 kDa protein 3 (SRP54) {Arabidopsis thaliana} 0.0 ...

  16. Arabidopsis CDS blastp result: AK071661 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK071661 J023105D07 At5g37770.1 touch-responsive protein / calmodulin-related protein 2, touch...-induced (TCH2) identical to calmodulin-related protein 2,touch-induced SP:P25070 from [Arabidopsis thaliana] 3e-33 ...

  17. Arabidopsis CDS blastp result: AK242428 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK242428 J080089P09 At5g37770.1 68418.m04547 touch-responsive protein / calmodulin-related protein 2, touch...-induced (TCH2) identical to calmodulin-related protein 2,touch-induced SP:P25070 from [Arabidopsis thaliana] 9e-19 ...

  18. Arabidopsis CDS blastp result: AK242428 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK242428 J080089P09 At2g41100.1 68415.m05076 touch-responsive protein / calmodulin-related protein 3, touch...-induced (TCH3) identical to calmodulin-related protein 3, touch-induced SP:P25071 from [Arabidopsis thaliana] 8e-18 ...

  19. Arabidopsis CDS blastp result: AK241786 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK241786 J065207F05 At5g37770.1 68418.m04547 touch-responsive protein / calmodulin-related protein 2, touch...-induced (TCH2) identical to calmodulin-related protein 2,touch-induced SP:P25070 from [Arabidopsis thaliana] 1e-19 ...

  20. Arabidopsis CDS blastp result: AK242346 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK242346 J080012M07 At2g41100.1 68415.m05076 touch-responsive protein / calmodulin-related protein 3, touch...-induced (TCH3) identical to calmodulin-related protein 3, touch-induced SP:P25071 from [Arabidopsis thaliana] 8e-44 ...

  1. Arabidopsis CDS blastp result: AK242428 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK242428 J080089P09 At2g41100.1 68415.m05076 touch-responsive protein / calmodulin-related protein 3, touch...-induced (TCH3) identical to calmodulin-related protein 3, touch-induced SP:P25071 from [Arabidopsis thaliana] 2e-14 ...

  2. Arabidopsis CDS blastp result: AK242428 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK242428 J080089P09 At2g41100.2 68415.m05077 touch-responsive protein / calmodulin-related protein 3, touch...-induced (TCH3) identical to calmodulin-related protein 3, touch-induced SP:P25071 from [Arabidopsis thaliana] 3e-16 ...

  3. Arabidopsis CDS blastp result: AK242346 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK242346 J080012M07 At5g37770.1 68418.m04547 touch-responsive protein / calmodulin-related protein 2, touch...-induced (TCH2) identical to calmodulin-related protein 2,touch-induced SP:P25070 from [Arabidopsis thaliana] 2e-11 ...

  4. Arabidopsis CDS blastp result: AK108506 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK108506 002-143-H11 At5g37770.1 touch-responsive protein / calmodulin-related protein 2, touch...-induced (TCH2) identical to calmodulin-related protein 2,touch-induced SP:P25070 from [Arabidopsis thaliana] 7e-14 ...

  5. Arabidopsis CDS blastp result: AK242346 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK242346 J080012M07 At2g41100.1 68415.m05076 touch-responsive protein / calmodulin-related protein 3, touch...-induced (TCH3) identical to calmodulin-related protein 3, touch-induced SP:P25071 from [Arabidopsis thaliana] 4e-41 ...

  6. Arabidopsis CDS blastp result: AK242346 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK242346 J080012M07 At5g37770.1 68418.m04547 touch-responsive protein / calmodulin-related protein 2, touch...-induced (TCH2) identical to calmodulin-related protein 2,touch-induced SP:P25070 from [Arabidopsis thaliana] 2e-25 ...

  7. Arabidopsis CDS blastp result: AK242346 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK242346 J080012M07 At2g41100.2 68415.m05077 touch-responsive protein / calmodulin-related protein 3, touch...-induced (TCH3) identical to calmodulin-related protein 3, touch-induced SP:P25071 from [Arabidopsis thaliana] 3e-26 ...

  8. Arabidopsis CDS blastp result: AK243656 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK243656 J100088L22 At2g41100.1 68415.m05076 touch-responsive protein / calmodulin-related protein 3, touch...-induced (TCH3) identical to calmodulin-related protein 3, touch-induced SP:P25071 from [Arabidopsis thaliana] 1e-19 ...

  9. Arabidopsis CDS blastp result: AK243656 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK243656 J100088L22 At2g41100.2 68415.m05077 touch-responsive protein / calmodulin-related protein 3, touch...-induced (TCH3) identical to calmodulin-related protein 3, touch-induced SP:P25071 from [Arabidopsis thaliana] 5e-20 ...

  10. Arabidopsis CDS blastp result: AK242346 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK242346 J080012M07 At2g41100.2 68415.m05077 touch-responsive protein / calmodulin-related protein 3, touch...-induced (TCH3) identical to calmodulin-related protein 3, touch-induced SP:P25071 from [Arabidopsis thaliana] 3e-44 ...

  11. Arabidopsis CDS blastp result: AK243656 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK243656 J100088L22 At2g41100.1 68415.m05076 touch-responsive protein / calmodulin-related protein 3, touch...-induced (TCH3) identical to calmodulin-related protein 3, touch-induced SP:P25071 from [Arabidopsis thaliana] 2e-17 ...

  12. Arabidopsis CDS blastp result: AK062711 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK062711 001-106-C02 At5g37770.1 touch-responsive protein / calmodulin-related protein 2, touch...-induced (TCH2) identical to calmodulin-related protein 2,touch-induced SP:P25070 from [Arabidopsis thaliana] 9e-34 ...

  13. Arabidopsis CDS blastp result: AK288095 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK288095 J075191E21 At2g41100.1 68415.m05076 touch-responsive protein / calmodulin-related protein 3, touch...-induced (TCH3) identical to calmodulin-related protein 3, touch-induced SP:P25071 from [Arabidopsis thaliana] 2e-16 ...

  14. Arabidopsis CDS blastp result: AK242346 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK242346 J080012M07 At2g41100.1 68415.m05076 touch-responsive protein / calmodulin-related protein 3, touch...-induced (TCH3) identical to calmodulin-related protein 3, touch-induced SP:P25071 from [Arabidopsis thaliana] 3e-26 ...

  15. Arabidopsis CDS blastp result: AK288095 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK288095 J075191E21 At2g41100.2 68415.m05077 touch-responsive protein / calmodulin-related protein 3, touch...-induced (TCH3) identical to calmodulin-related protein 3, touch-induced SP:P25071 from [Arabidopsis thaliana] 2e-15 ...

  16. Arabidopsis CDS blastp result: AK068893 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK068893 J023001G24 At4g15090.1 far-red impaired response protein (FAR1) / far-red impai...red responsive protein (FAR1) identical to far-red impaired response protein FAR1 [Arabidopsis thaliana] gi|5764395|gb|AAD51282; contains Pfam:PF03101 domain: FAR1 family 1e-39 ...

  17. Reference: 359 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available 359 http://metadb.riken.jp/db/SciNetS_ria224i/cria224u4ria224u16531491i Cnops Gerda...leaf development in Arabidopsis thaliana. 4 852-66 16531491 2006 Apr The Plant cell Azmi Abdelkrim|Cnops Gerda

  18. Reference: 749 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available former mutant had decreased electron transport rates, a lower DeltapH gradient across the grana membranes, r...the PSII particles of these plants were organized in unusual two-dimensional arrays in the grana membranes. ...d the electron transport rate in grana membranes of Arabidopsis. 4 1012-28 18381925 2008 Apr The Plant cell

  19. Arabidopsis CDS blastp result: AK241679 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK241679 J065193F24 At3g29410.1 68416.m03695 terpene synthase/cyclase family protein similar to terpene... synthase GB:CAA72074 from [Arabidopsis thaliana], contains Pfam profile: PF01397 terpene synthase family 5e-65 ...

  20. Arabidopsis CDS blastp result: AK242212 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK242212 J075171E13 At3g29410.1 68416.m03695 terpene synthase/cyclase family protein similar to terpene... synthase GB:CAA72074 from [Arabidopsis thaliana], contains Pfam profile: PF01397 terpene synthase family 1e-21 ...