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Herpesvirus Genome Recognition Induced Acetylation of Nuclear IFI16 Is Essential for Its Cytoplasmic Translocation, Inflammasome and IFN-β Responses.

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Mairaj Ahmed Ansari

2015-07-01

Full Text Available The IL-1β and type I interferon-β (IFN-β molecules are important inflammatory cytokines elicited by the eukaryotic host as innate immune responses against invading pathogens and danger signals. Recently, a predominantly nuclear gamma-interferon-inducible protein 16 (IFI16 involved in transcriptional regulation has emerged as an innate DNA sensor which induced IL-1β and IFN-β production through inflammasome and STING activation, respectively. Herpesvirus (KSHV, EBV, and HSV-1 episomal dsDNA genome recognition by IFI16 leads to IFI16-ASC-procaspase-1 inflammasome association, cytoplasmic translocation and IL-1β production. Independent of ASC, HSV-1 genome recognition results in IFI16 interaction with STING in the cytoplasm to induce interferon-β production. However, the mechanisms of IFI16-inflammasome formation, cytoplasmic redistribution and STING activation are not known. Our studies here demonstrate that recognition of herpesvirus genomes in the nucleus by IFI16 leads into its interaction with histone acetyltransferase p300 and IFI16 acetylation resulting in IFI16-ASC interaction, inflammasome assembly, increased interaction with Ran-GTPase, cytoplasmic redistribution, caspase-1 activation, IL-1β production, and interaction with STING which results in IRF-3 phosphorylation, nuclear pIRF-3 localization and interferon-β production. ASC and STING knockdowns did not affect IFI16 acetylation indicating that this modification is upstream of inflammasome-assembly and STING-activation. Vaccinia virus replicating in the cytoplasm did not induce nuclear IFI16 acetylation and cytoplasmic translocation. IFI16 physically associates with KSHV and HSV-1 genomes as revealed by proximity ligation microscopy and chromatin-immunoprecipitation studies which is not hampered by the inhibition of acetylation, thus suggesting that acetylation of IFI16 is not required for its innate sensing of nuclear viral genomes. Collectively, these studies identify the
Imaging analysis of nuclear antiviral factors through direct detection of incoming adenovirus genome complexes

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Komatsu, Tetsuro [Microbiologie Fondamentale et Pathogénicité, MFP CNRS UMR 5234, Université de Bordeaux, Bordeaux 33076 (France); Department of Infection Biology, Faculty of Medicine, University of Tsukuba, Tsukuba 305-8575 (Japan); Will, Hans [Department of Tumor Biology, University Hospital Hamburg-Eppendorf, 20246 Hamburg (Germany); Nagata, Kyosuke [Department of Infection Biology, Faculty of Medicine, University of Tsukuba, Tsukuba 305-8575 (Japan); Wodrich, Harald, E-mail: harald.wodrich@u-bordeaux.fr [Microbiologie Fondamentale et Pathogénicité, MFP CNRS UMR 5234, Université de Bordeaux, Bordeaux 33076 (France)

2016-04-22

Recent studies involving several viral systems have highlighted the importance of cellular intrinsic defense mechanisms through nuclear antiviral proteins that restrict viral propagation. These factors include among others components of PML nuclear bodies, the nuclear DNA sensor IFI16, and a potential restriction factor PHF13/SPOC1. For several nuclear replicating DNA viruses, it was shown that these factors sense and target viral genomes immediately upon nuclear import. In contrast to the anticipated view, we recently found that incoming adenoviral genomes are not targeted by PML nuclear bodies. Here we further explored cellular responses against adenoviral infection by focusing on specific conditions as well as additional nuclear antiviral factors. In line with our previous findings, we show that neither interferon treatment nor the use of specific isoforms of PML nuclear body components results in co-localization between incoming adenoviral genomes and the subnuclear domains. Furthermore, our imaging analyses indicated that neither IFI16 nor PHF13/SPOC1 are likely to target incoming adenoviral genomes. Thus our findings suggest that incoming adenoviral genomes may be able to escape from a large repertoire of nuclear antiviral mechanisms, providing a rationale for the efficient initiation of lytic replication cycle. - Highlights: • Host nuclear antiviral factors were analyzed upon adenovirus genome delivery. • Interferon treatments fail to permit PML nuclear bodies to target adenoviral genomes. • Neither Sp100A nor B targets adenoviral genomes despite potentially opposite roles. • The nuclear DNA sensor IFI16 does not target incoming adenoviral genomes. • PHF13/SPOC1 targets neither incoming adenoviral genomes nor genome-bound protein VII.
Imaging analysis of nuclear antiviral factors through direct detection of incoming adenovirus genome complexes

International Nuclear Information System (INIS)

Komatsu, Tetsuro; Will, Hans; Nagata, Kyosuke; Wodrich, Harald

2016-01-01

Recent studies involving several viral systems have highlighted the importance of cellular intrinsic defense mechanisms through nuclear antiviral proteins that restrict viral propagation. These factors include among others components of PML nuclear bodies, the nuclear DNA sensor IFI16, and a potential restriction factor PHF13/SPOC1. For several nuclear replicating DNA viruses, it was shown that these factors sense and target viral genomes immediately upon nuclear import. In contrast to the anticipated view, we recently found that incoming adenoviral genomes are not targeted by PML nuclear bodies. Here we further explored cellular responses against adenoviral infection by focusing on specific conditions as well as additional nuclear antiviral factors. In line with our previous findings, we show that neither interferon treatment nor the use of specific isoforms of PML nuclear body components results in co-localization between incoming adenoviral genomes and the subnuclear domains. Furthermore, our imaging analyses indicated that neither IFI16 nor PHF13/SPOC1 are likely to target incoming adenoviral genomes. Thus our findings suggest that incoming adenoviral genomes may be able to escape from a large repertoire of nuclear antiviral mechanisms, providing a rationale for the efficient initiation of lytic replication cycle. - Highlights: • Host nuclear antiviral factors were analyzed upon adenovirus genome delivery. • Interferon treatments fail to permit PML nuclear bodies to target adenoviral genomes. • Neither Sp100A nor B targets adenoviral genomes despite potentially opposite roles. • The nuclear DNA sensor IFI16 does not target incoming adenoviral genomes. • PHF13/SPOC1 targets neither incoming adenoviral genomes nor genome-bound protein VII.
Mitochondrial-nuclear genome interactions in nonalcoholic fatty liver disease in mice

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Betancourt, Angela M.; King, Adrienne L.; Fetterman, Jessica L.; Millender-Swain, Telisha; Finley, Rachel D.; Oliva, Claudia R.; Crowe, David Ralph; Ballinger, Scott W.; Bailey, Shannon M.

2014-01-01

Nonalcoholic fatty liver disease (NAFLD) involves significant changes in liver metabolism characterized by oxidative stress, lipid accumulation, and fibrogenesis. Mitochondrial dysfunction and bioenergetic defects also contribute to NAFLD. Herein, we examined whether differences in mtDNA influence NAFLD. To determine the role of mitochondrial and nuclear genomes in NAFLD, Mitochondrial-Nuclear eXchange (MNX) mice were fed an atherogenic diet. MNX mice have mtDNA from C57BL/6J mice on a C3H/HeN nuclear background and vice versa. Results from MNX mice were compared to wild-type C57BL/6J and C3H/HeN mice fed a control or atherogenic diet. Mice with the C57BL/6J nuclear genome developed more macrosteatosis, inflammation, and fibrosis compared with mice containing the C3H/HeN nuclear genome when fed the atherogenic diet. These changes were associated with parallel alterations in inflammation and fibrosis gene expression in wild-type mice, with intermediate responses in MNX mice. Mice with the C57BL/6J nuclear genome had increased State 4 respiration, whereas MNX mice had decreased State 3 respiration and RCR when fed the atherogenic diet. Complex IV activity and most mitochondrial biogenesis genes were increased in mice with the C57BL/6J nuclear or mitochondrial genome, or both fed the atherogenic diet. These results reveal new interactions between mitochondrial and nuclear genomes and support the concept that mtDNA influences mitochondrial function and metabolic pathways implicated in NAFLD. PMID:24758559
Mitochondrial-nuclear genome interactions in non-alcoholic fatty liver disease in mice.

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Betancourt, Angela M; King, Adrienne L; Fetterman, Jessica L; Millender-Swain, Telisha; Finley, Rachel D; Oliva, Claudia R; Crowe, David R; Ballinger, Scott W; Bailey, Shannon M

2014-07-15

NAFLD (non-alcoholic fatty liver disease) involves significant changes in liver metabolism characterized by oxidative stress, lipid accumulation and fibrogenesis. Mitochondrial dysfunction and bioenergetic defects also contribute to NAFLD. In the present study, we examined whether differences in mtDNA influence NAFLD. To determine the role of mitochondrial and nuclear genomes in NAFLD, MNX (mitochondrial-nuclear exchange) mice were fed an atherogenic diet. MNX mice have mtDNA from C57BL/6J mice on a C3H/HeN nuclear background and vice versa. Results from MNX mice were compared with wild-type C57BL/6J and C3H/HeN mice fed a control or atherogenic diet. Mice with the C57BL/6J nuclear genome developed more macrosteatosis, inflammation and fibrosis compared with mice containing the C3H/HeN nuclear genome when fed the atherogenic diet. These changes were associated with parallel alterations in inflammation and fibrosis gene expression in wild-type mice, with intermediate responses in MNX mice. Mice with the C57BL/6J nuclear genome had increased State 4 respiration, whereas MNX mice had decreased State 3 respiration and RCR (respiratory control ratio) when fed the atherogenic diet. Complex IV activity and most mitochondrial biogenesis genes were increased in mice with the C57BL/6J nuclear or mitochondrial genome, or both fed the atherogenic diet. These results reveal new interactions between mitochondrial and nuclear genomes and support the concept that mtDNA influences mitochondrial function and metabolic pathways implicated in NAFLD.
The Small Nuclear Genomes of Selaginella Are Associated with a Low Rate of Genome Size Evolution.

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Baniaga, Anthony E; Arrigo, Nils; Barker, Michael S

2016-06-03

The haploid nuclear genome size (1C DNA) of vascular land plants varies over several orders of magnitude. Much of this observed diversity in genome size is due to the proliferation and deletion of transposable elements. To date, all vascular land plant lineages with extremely small nuclear genomes represent recently derived states, having ancestors with much larger genome sizes. The Selaginellaceae represent an ancient lineage with extremely small genomes. It is unclear how small nuclear genomes evolved in Selaginella We compared the rates of nuclear genome size evolution in Selaginella and major vascular plant clades in a comparative phylogenetic framework. For the analyses, we collected 29 new flow cytometry estimates of haploid genome size in Selaginella to augment publicly available data. Selaginella possess some of the smallest known haploid nuclear genome sizes, as well as the lowest rate of genome size evolution observed across all vascular land plants included in our analyses. Additionally, our analyses provide strong support for a history of haploid nuclear genome size stasis in Selaginella Our results indicate that Selaginella, similar to other early diverging lineages of vascular land plants, has relatively low rates of genome size evolution. Further, our analyses highlight that a rapid transition to a small genome size is only one route to an extremely small genome. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
Hypothesis: Gene-rich plastid genomes in red algae may be an outcome of nuclear genome reduction.

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Qiu, Huan; Lee, Jun Mo; Yoon, Hwan Su; Bhattacharya, Debashish

2017-06-01

Red algae (Rhodophyta) putatively diverged from the eukaryote tree of life >1.2 billion years ago and are the source of plastids in the ecologically important diatoms, haptophytes, and dinoflagellates. In general, red algae contain the largest plastid gene inventory among all such organelles derived from primary, secondary, or additional rounds of endosymbiosis. In contrast, their nuclear gene inventory is reduced when compared to their putative sister lineage, the Viridiplantae, and other photosynthetic lineages. The latter is thought to have resulted from a phase of genome reduction that occurred in the stem lineage of Rhodophyta. A recent comparative analysis of a taxonomically broad collection of red algal and Viridiplantae plastid genomes demonstrates that the red algal ancestor encoded ~1.5× more plastid genes than Viridiplantae. This difference is primarily explained by more extensive endosymbiotic gene transfer (EGT) in the stem lineage of Viridiplantae, when compared to red algae. We postulate that limited EGT in Rhodophytes resulted from the countervailing force of ancient, and likely recurrent, nuclear genome reduction. In other words, the propensity for nuclear gene loss led to the retention of red algal plastid genes that would otherwise have undergone intracellular gene transfer to the nucleus. This hypothesis recognizes the primacy of nuclear genome evolution over that of plastids, which have no inherent control of their gene inventory and can change dramatically (e.g., secondarily non-photosynthetic eukaryotes, dinoflagellates) in response to selection acting on the host lineage. © 2017 Phycological Society of America.
Expression of a transferred nuclear gene in a mitochondrial genome

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Yichun Qiu

2014-08-01

Full Text Available Transfer of mitochondrial genes to the nucleus, and subsequent gain of regulatory elements for expression, is an ongoing evolutionary process in plants. Many examples have been characterized, which in some cases have revealed sources of mitochondrial targeting sequences and cis-regulatory elements. In contrast, there have been no reports of a nuclear gene that has undergone intracellular transfer to the mitochondrial genome and become expressed. Here we show that the orf164 gene in the mitochondrial genome of several Brassicaceae species, including Arabidopsis, is derived from the nuclear ARF17 gene that codes for an auxin responsive protein and is present across flowering plants. Orf164 corresponds to a portion of ARF17, and the nucleotide and amino acid sequences are 79% and 81% identical, respectively. Orf164 is transcribed in several organ types of Arabidopsis thaliana, as detected by RT-PCR. In addition, orf164 is transcribed in five other Brassicaceae within the tribes Camelineae, Erysimeae and Cardamineae, but the gene is not present in Brassica or Raphanus. This study shows that nuclear genes can be transferred to the mitochondrial genome and become expressed, providing a new perspective on the movement of genes between the genomes of subcellular compartments.
Instability of plastid DNA in the nuclear genome.

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Anna E Sheppard

2009-01-01

Full Text Available Functional gene transfer from the plastid (chloroplast and mitochondrial genomes to the nucleus has been an important driving force in eukaryotic evolution. Non-functional DNA transfer is far more frequent, and the frequency of such transfers from the plastid to the nucleus has been determined experimentally in tobacco using transplastomic lines containing, in their plastid genome, a kanamycin resistance gene (neo readymade for nuclear expression. Contrary to expectations, non-Mendelian segregation of the kanamycin resistance phenotype is seen in progeny of some lines in which neo has been transferred to the nuclear genome. Here, we provide a detailed analysis of the instability of kanamycin resistance in nine of these lines, and we show that it is due to deletion of neo. Four lines showed instability with variation between progeny derived from different areas of the same plant, suggesting a loss of neo during somatic cell division. One line showed a consistent reduction in the proportion of kanamycin-resistant progeny, suggesting a loss of neo during meiosis, and the remaining four lines were relatively stable. To avoid genomic enlargement, the high frequency of plastid DNA integration into the nuclear genome necessitates a counterbalancing removal process. This is the first demonstration of such loss involving a high proportion of recent nuclear integrants. We propose that insertion, deletion, and rearrangement of plastid sequences in the nuclear genome are important evolutionary processes in the generation of novel nuclear genes. This work is also relevant in the context of transgenic plant research and crop production, because similar processes to those described here may be involved in the loss of plant transgenes.
Actomyosin drives cancer cell nuclear dysmorphia and threatens genome stability.

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Takaki, Tohru; Montagner, Marco; Serres, Murielle P; Le Berre, Maël; Russell, Matt; Collinson, Lucy; Szuhai, Karoly; Howell, Michael; Boulton, Simon J; Sahai, Erik; Petronczki, Mark

2017-07-24

Altered nuclear shape is a defining feature of cancer cells. The mechanisms underlying nuclear dysmorphia in cancer remain poorly understood. Here we identify PPP1R12A and PPP1CB, two subunits of the myosin phosphatase complex that antagonizes actomyosin contractility, as proteins safeguarding nuclear integrity. Loss of PPP1R12A or PPP1CB causes nuclear fragmentation, nuclear envelope rupture, nuclear compartment breakdown and genome instability. Pharmacological or genetic inhibition of actomyosin contractility restores nuclear architecture and genome integrity in cells lacking PPP1R12A or PPP1CB. We detect actin filaments at nuclear envelope rupture sites and define the Rho-ROCK pathway as the driver of nuclear damage. Lamin A protects nuclei from the impact of actomyosin activity. Blocking contractility increases nuclear circularity in cultured cancer cells and suppresses deformations of xenograft nuclei in vivo. We conclude that actomyosin contractility is a major determinant of nuclear shape and that unrestrained contractility causes nuclear dysmorphia, nuclear envelope rupture and genome instability.
An Adenovirus DNA Replication Factor, but Not Incoming Genome Complexes, Targets PML Nuclear Bodies.

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Komatsu, Tetsuro; Nagata, Kyosuke; Wodrich, Harald

2016-02-01

Promyelocytic leukemia protein nuclear bodies (PML-NBs) are subnuclear domains implicated in cellular antiviral responses. Despite the antiviral activity, several nuclear replicating DNA viruses use the domains as deposition sites for the incoming viral genomes and/or as sites for viral DNA replication, suggesting that PML-NBs are functionally relevant during early viral infection to establish productive replication. Although PML-NBs and their components have also been implicated in the adenoviral life cycle, it remains unclear whether incoming adenoviral genome complexes target PML-NBs. Here we show using immunofluorescence and live-cell imaging analyses that incoming adenovirus genome complexes neither localize at nor recruit components of PML-NBs during early phases of infection. We further show that the viral DNA binding protein (DBP), an early expressed viral gene and essential DNA replication factor, independently targets PML-NBs. We show that DBP oligomerization is required to selectively recruit the PML-NB components Sp100 and USP7. Depletion experiments suggest that the absence of one PML-NB component might not affect the recruitment of other components toward DBP oligomers. Thus, our findings suggest a model in which an adenoviral DNA replication factor, but not incoming viral genome complexes, targets and modulates PML-NBs to support a conducive state for viral DNA replication and argue against a generalized concept that PML-NBs target incoming viral genomes. The immediate fate upon nuclear delivery of genomes of incoming DNA viruses is largely unclear. Early reports suggested that incoming genomes of herpesviruses are targeted and repressed by PML-NBs immediately upon nuclear import. Genome localization and/or viral DNA replication has also been observed at PML-NBs for other DNA viruses. Thus, it was suggested that PML-NBs may immediately sense and target nuclear viral genomes and hence serve as sites for deposition of incoming viral genomes and
Non-functional plastid ndh gene fragments are present in the nuclear genome of Norway spruce (Picea abies L. Karsch): insights from in silico analysis of nuclear and organellar genomes.

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Ranade, Sonali Sachin; García-Gil, María Rosario; Rosselló, Josep A

2016-04-01

Many genes have been lost from the prokaryote plastidial genome during the early events of endosymbiosis in eukaryotes. Some of them were definitively lost, but others were relocated and functionally integrated to the host nuclear genomes through serial events of gene transfer during plant evolution. In gymnosperms, plastid genome sequencing has revealed the loss of ndh genes from several species of Gnetales and Pinaceae, including Norway spruce (Picea abies). This study aims to trace the ndh genes in the nuclear and organellar Norway spruce genomes. The plastid genomes of higher plants contain 11 ndh genes which are homologues of mitochondrial genes encoding subunits of the proton-pumping NADH-dehydrogenase (nicotinamide adenine dinucleotide dehydrogenase) or complex I (electron transport chain). Ndh genes encode 11 NDH polypeptides forming the Ndh complex (analogous to complex I) which seems to be primarily involved in chloro-respiration processes. We considered ndh genes from the plastidial genome of four gymnosperms (Cryptomeria japonica, Cycas revoluta, Ginkgo biloba, Podocarpus totara) and a single angiosperm species (Arabidopsis thaliana) to trace putative homologs in the nuclear and organellar Norway spruce genomes using tBLASTn to assess the evolutionary fate of ndh genes in Norway spruce and to address their genomic location(s), structure, integrity and functionality. The results obtained from tBLASTn were subsequently analyzed by performing homology search for finding ndh specific conserved domains using conserved domain search. We report the presence of non-functional plastid ndh gene fragments, excepting ndhE and ndhG genes, in the nuclear genome of Norway spruce. Regulatory transcriptional elements like promoters, TATA boxes and enhancers were detected in the upstream regions of some ndh fragments. We also found transposable elements in the flanking regions of few ndh fragments suggesting nuclear rearrangements in those regions. These evidences
Genome-Nuclear Lamina Interactions Regulate Cardiac Stem Cell Lineage Restriction.

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Poleshko, Andrey; Shah, Parisha P; Gupta, Mudit; Babu, Apoorva; Morley, Michael P; Manderfield, Lauren J; Ifkovits, Jamie L; Calderon, Damelys; Aghajanian, Haig; Sierra-Pagán, Javier E; Sun, Zheng; Wang, Qiaohong; Li, Li; Dubois, Nicole C; Morrisey, Edward E; Lazar, Mitchell A; Smith, Cheryl L; Epstein, Jonathan A; Jain, Rajan

2017-10-19

Progenitor cells differentiate into specialized cell types through coordinated expression of lineage-specific genes and modification of complex chromatin configurations. We demonstrate that a histone deacetylase (Hdac3) organizes heterochromatin at the nuclear lamina during cardiac progenitor lineage restriction. Specification of cardiomyocytes is associated with reorganization of peripheral heterochromatin, and independent of deacetylase activity, Hdac3 tethers peripheral heterochromatin containing lineage-relevant genes to the nuclear lamina. Deletion of Hdac3 in cardiac progenitor cells releases genomic regions from the nuclear periphery, leading to precocious cardiac gene expression and differentiation into cardiomyocytes; in contrast, restricting Hdac3 to the nuclear periphery rescues myogenesis in progenitors otherwise lacking Hdac3. Our results suggest that availability of genomic regions for activation by lineage-specific factors is regulated in part through dynamic chromatin-nuclear lamina interactions and that competence of a progenitor cell to respond to differentiation signals may depend upon coordinated movement of responding gene loci away from the nuclear periphery. Copyright © 2017 Elsevier Inc. All rights reserved.
Nuclear-like Seq in mt Genome - RMG | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available ar-like Seq in mt Genome Data detail Data name Nuclear-like Seq in mt Genome DOI 10...e Site Policy | Contact Us Nuclear-like Seq in mt Genome - RMG | LSDB Archive ... ...switchLanguage; BLAST Search Image Search Home About Archive Update History Data List Contact us RMG Nucle
Nuclear fusion and genome encounter during yeast zygote formation.

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Tartakoff, Alan Michael; Jaiswal, Purnima

2009-06-01

When haploid cells of Saccharomyces cerevisiae are crossed, parental nuclei congress and fuse with each other. To investigate underlying mechanisms, we have developed assays that evaluate the impact of drugs and mutations. Nuclear congression is inhibited by drugs that perturb the actin and tubulin cytoskeletons. Nuclear envelope (NE) fusion consists of at least five steps in which preliminary modifications are followed by controlled flux of first outer and then inner membrane proteins, all before visible dilation of the waist of the nucleus or coalescence of the parental spindle pole bodies. Flux of nuclear pore complexes occurs after dilation. Karyogamy requires both the Sec18p/NSF ATPase and ER/NE luminal homeostasis. After fusion, chromosome tethering keeps tagged parental genomes separate from each other. The process of NE fusion and evidence of genome independence in yeast provide a prototype for understanding related events in higher eukaryotes.
Genome inventory and analysis of nuclear hormone receptors in ...

Indian Academy of Sciences (India)

Prakash

2006-12-20

Dec 20, 2006 ... progestins, as well as lipids, cholesterol metabolites, and. Genome ... Gene structure analysis shows strong conservation of exon structures among orthologoues. ..... earlier subfamily classification of NRs (Nuclear Receptors.
Conflicting Evolutionary Histories of the Mitochondrial and Nuclear Genomes in New World Myotis Bats.

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Platt, Roy N; Faircloth, Brant C; Sullivan, Kevin A M; Kieran, Troy J; Glenn, Travis C; Vandewege, Michael W; Lee, Thomas E; Baker, Robert J; Stevens, Richard D; Ray, David A

2018-03-01

The rapid diversification of Myotis bats into more than 100 species is one of the most extensive mammalian radiations available for study. Efforts to understand relationships within Myotis have primarily utilized mitochondrial markers and trees inferred from nuclear markers lacked resolution. Our current understanding of relationships within Myotis is therefore biased towards a set of phylogenetic markers that may not reflect the history of the nuclear genome. To resolve this, we sequenced the full mitochondrial genomes of 37 representative Myotis, primarily from the New World, in conjunction with targeted sequencing of 3648 ultraconserved elements (UCEs). We inferred the phylogeny and explored the effects of concatenation and summary phylogenetic methods, as well as combinations of markers based on informativeness or levels of missing data, on our results. Of the 294 phylogenies generated from the nuclear UCE data, all are significantly different from phylogenies inferred using mitochondrial genomes. Even within the nuclear data, quartet frequencies indicate that around half of all UCE loci conflict with the estimated species tree. Several factors can drive such conflict, including incomplete lineage sorting, introgressive hybridization, or even phylogenetic error. Despite the degree of discordance between nuclear UCE loci and the mitochondrial genome and among UCE loci themselves, the most common nuclear topology is recovered in one quarter of all analyses with strong nodal support. Based on these results, we re-examine the evolutionary history of Myotis to better understand the phenomena driving their unique nuclear, mitochondrial, and biogeographic histories.
Nuclear genome size analysis of Agave tequilana Weber

Czech Academy of Sciences Publication Activity Database

Palomino, G.; Doležel, Jaroslav; Méndez, I.; Rubluo, A.

2003-01-01

Roč. 56, č. 1 (2003), s. 37-46 ISSN 0008-7114 Grant - others:Itálie(IT) Z5038910 Institutional research plan: CEZ:AV0Z5038910 Keywords : Flow cytometry * nuclear genome size * Agave tequilana Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 0.337, year: 2003
Germline Genetic Modification and Identity: the Mitochondrial and Nuclear Genomes.

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Scott, Rosamund; Wilkinson, Stephen

2017-12-01

In a legal 'first', the UK removed a prohibition against modifying embryos in human reproduction, to enable mitochondrial replacement techniques (MRTs), a move the Government distanced from 'germline genetic modification', which it aligned with modifying the nuclear genome. This paper (1) analyzes the uses and meanings of this term in UK/US legal and policy debates; and (2) evaluates related ethical concerns about identity. It shows that, with respect to identity, MRTs and nuclear genome editing techniques such as CRISPR/Cas-9 (now a policy topic), are not as different as has been supposed. While it does not follow that the two should be treated exactly alike, one of the central reasons offered for treating MRTs more permissively than nuclear genetic modification, and for not regarding MRTs as 'germline genetic modification', is thereby in doubt. Identity cannot, by itself, do the work thus far assigned to it, explicitly or otherwise, in law and policy.
Somatic cell nuclear transfer: Infinite reproduction of a unique diploid genome

International Nuclear Information System (INIS)

Kishigami, Satoshi; Wakayama, Sayaka; Hosoi, Yoshihiko; Iritani, Akira; Wakayama, Teruhiko

2008-01-01

In mammals, a diploid genome of an individual following fertilization of an egg and a spermatozoon is unique and irreproducible. This implies that the generated unique diploid genome is doomed with the individual ending. Even as cultured cells from the individual, they cannot normally proliferate in perpetuity because of the 'Hayflick limit'. However, Dolly, the sheep cloned from an adult mammary gland cell, changes this scenario. Somatic cell nuclear transfer (SCNT) enables us to produce offspring without germ cells, that is, to 'passage' a unique diploid genome. Animal cloning has also proven to be a powerful research tool for reprogramming in many mammals, notably mouse and cow. The mechanism underlying reprogramming, however, remains largely unknown and, animal cloning has been inefficient as a result. More momentously, in addition to abortion and fetal mortality, some cloned animals display possible premature aging phenotypes including early death and short telomere lengths. Under these inauspicious conditions, is it really possible for SCNT to preserve a diploid genome? Delightfully, in mouse and recently in primate, using SCNT we can produce nuclear transfer ES cells (ntES) more efficiently, which can preserve the eternal lifespan for the 'passage' of a unique diploid genome. Further, new somatic cloning technique using histone-deacetylase inhibitors has been developed which can significantly increase the previous cloning rates two to six times. Here, we introduce SCNT and its value as a preservation tool for a diploid genome while reviewing aging of cloned animals on cellular and individual levels

Somatic cell nuclear transfer: infinite reproduction of a unique diploid genome.

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Kishigami, Satoshi; Wakayama, Sayaka; Hosoi, Yoshihiko; Iritani, Akira; Wakayama, Teruhiko

2008-06-10

In mammals, a diploid genome of an individual following fertilization of an egg and a spermatozoon is unique and irreproducible. This implies that the generated unique diploid genome is doomed with the individual ending. Even as cultured cells from the individual, they cannot normally proliferate in perpetuity because of the "Hayflick limit". However, Dolly, the sheep cloned from an adult mammary gland cell, changes this scenario. Somatic cell nuclear transfer (SCNT) enables us to produce offspring without germ cells, that is, to "passage" a unique diploid genome. Animal cloning has also proven to be a powerful research tool for reprogramming in many mammals, notably mouse and cow. The mechanism underlying reprogramming, however, remains largely unknown and, animal cloning has been inefficient as a result. More momentously, in addition to abortion and fetal mortality, some cloned animals display possible premature aging phenotypes including early death and short telomere lengths. Under these inauspicious conditions, is it really possible for SCNT to preserve a diploid genome? Delightfully, in mouse and recently in primate, using SCNT we can produce nuclear transfer ES cells (ntES) more efficiently, which can preserve the eternal lifespan for the "passage" of a unique diploid genome. Further, new somatic cloning technique using histone-deacetylase inhibitors has been developed which can significantly increase the previous cloning rates two to six times. Here, we introduce SCNT and its value as a preservation tool for a diploid genome while reviewing aging of cloned animals on cellular and individual levels.
Nuclear envelope and genome interactions in cell fate

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Talamas, Jessica A.; Capelson, Maya

2015-01-01

The eukaryotic cell nucleus houses an organism’s genome and is the location within the cell where all signaling induced and development-driven gene expression programs are ultimately specified. The genome is enclosed and separated from the cytoplasm by the nuclear envelope (NE), a double-lipid membrane bilayer, which contains a large variety of trans-membrane and associated protein complexes. In recent years, research regarding multiple aspects of the cell nucleus points to a highly dynamic and coordinated concert of efforts between chromatin and the NE in regulation of gene expression. Details of how this concert is orchestrated and how it directs cell differentiation and disease are coming to light at a rapid pace. Here we review existing and emerging concepts of how interactions between the genome and the NE may contribute to tissue specific gene expression programs to determine cell fate. PMID:25852741
Evidence for site-specific occupancy of the mitochondrial genome by nuclear transcription factors.

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Georgi K Marinov

Full Text Available Mitochondria contain their own circular genome, with mitochondria-specific transcription and replication systems and corresponding regulatory proteins. All of these proteins are encoded in the nuclear genome and are post-translationally imported into mitochondria. In addition, several nuclear transcription factors have been reported to act in mitochondria, but there has been no comprehensive mapping of their occupancy patterns and it is not clear how many other factors may also be found in mitochondria. Here we address these questions by using ChIP-seq data from the ENCODE, mouseENCODE and modENCODE consortia for 151 human, 31 mouse and 35 C. elegans factors. We identified 8 human and 3 mouse transcription factors with strong localized enrichment over the mitochondrial genome that was usually associated with the corresponding recognition sequence motif. Notably, these sites of occupancy are often the sites with highest ChIP-seq signal intensity within both the nuclear and mitochondrial genomes and are thus best explained as true binding events to mitochondrial DNA, which exist in high copy number in each cell. We corroborated these findings by immunocytochemical staining evidence for mitochondrial localization. However, we were unable to find clear evidence for mitochondrial binding in ENCODE and other publicly available ChIP-seq data for most factors previously reported to localize there. As the first global analysis of nuclear transcription factors binding in mitochondria, this work opens the door to future studies that probe the functional significance of the phenomenon.
The contribution of mitochondrial thymidylate synthesis in preventing the nuclear genome stress.

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Lee, Ming-Hsiang; Wang, Liya; Chang, Zee-Fen

2014-04-01

In quiescent fibroblasts, the expression levels of cytosolic enzymes for thymidine triphosphate (dTTP) synthesis are down-regulated, causing a marked reduction in the dTTP pool. In this study, we provide evidence that mitochondrial thymidylate synthesis via thymidine kinase 2 (TK2) is a limiting factor for the repair of ultraviolet (UV) damage in the nuclear compartment in quiescent fibroblasts. We found that TK2 deficiency causes secondary DNA double-strand breaks formation in the nuclear genome of quiescent cells at the late stage of recovery from UV damage. Despite slower repair of quiescent fibroblast deficient in TK2, DNA damage signals eventually disappeared, and these cells were capable of re-entering the S phase after serum stimulation. However, these cells displayed severe genome stress as revealed by the dramatic increase in 53BP1 nuclear body in the G1 phase of the successive cell cycle. Here, we conclude that mitochondrial thymidylate synthesis via TK2 plays a role in facilitating the quality repair of UV damage for the maintenance of genome integrity in the cells that are temporarily arrested in the quiescent state.
Responsability of nuclear industry

International Nuclear Information System (INIS)

Cadiz Deleito, J.C.

1985-01-01

Since the beginning of nuclear industry, civil responsibility with damages to the public health and properties was a critical problem, because the special conditions of this industry (nuclear accident, damages could be very high but probability of these events is very low). Legal precepts, universally accepted, in the first 60 years for all countries interested in nuclear energy are being revised, then 20 years of experience. The civil responsibility limited is being questioned and indemnities updated. (author)
A New Approach to Dissect Nuclear Organization: TALE-Mediated Genome Visualization (TGV).

Science.gov (United States)

Miyanari, Yusuke

2016-01-01

Spatiotemporal organization of chromatin within the nucleus has so far remained elusive. Live visualization of nuclear remodeling could be a promising approach to understand its functional relevance in genome functions and mechanisms regulating genome architecture. Recent technological advances in live imaging of chromosomes begun to explore the biological roles of the movement of the chromatin within the nucleus. Here I describe a new technique, called TALE-mediated genome visualization (TGV), which allows us to visualize endogenous repetitive sequence including centromeric, pericentromeric, and telomeric repeats in living cells.
Genome-wide identification of nuclear receptor (NR) superfamily genes in the copepod Tigriopus japonicus.

Science.gov (United States)

Hwang, Dae-Sik; Lee, Bo-Young; Kim, Hui-Su; Lee, Min Chul; Kyung, Do-Hyun; Om, Ae-Son; Rhee, Jae-Sung; Lee, Jae-Seong

2014-11-18

Nuclear receptors (NRs) are a large superfamily of proteins defined by a DNA-binding domain (DBD) and a ligand-binding domain (LBD). They function as transcriptional regulators to control expression of genes involved in development, homeostasis, and metabolism. The number of NRs differs from species to species, because of gene duplications and/or lineage-specific gene losses during metazoan evolution. Many NRs in arthropods interact with the ecdysteroid hormone and are involved in ecdysone-mediated signaling in arthropods. The nuclear receptor superfamily complement has been reported in several arthropods, including crustaceans, but not in copepods. We identified the entire NR repertoire of the copepod Tigriopus japonicus, which is an important marine model species for ecotoxicology and environmental genomics. Using whole genome and transcriptome sequences, we identified a total of 31 nuclear receptors in the genome of T. japonicus. Nomenclature of the nuclear receptors was determined based on the sequence similarities of the DNA-binding domain (DBD) and ligand-binding domain (LBD). The 7 subfamilies of NRs separate into five major clades (subfamilies NR1, NR2, NR3, NR4, and NR5/6). Although the repertoire of NR members in, T. japonicus was similar to that reported for other arthropods, there was an expansion of the NR1 subfamily in Tigriopus japonicus. The twelve unique nuclear receptors identified in T. japonicus are members of NR1L. This expansion may be a unique lineage-specific feature of crustaceans. Interestingly, E78 and HR83, which are present in other arthropods, were absent from the genomes of T. japonicus and two congeneric copepod species (T. japonicus and Tigriopus californicus), suggesting copepod lineage-specific gene loss. We identified all NR receptors present in the copepod, T. japonicus. Knowledge of the copepod nuclear receptor repertoire will contribute to a better understanding of copepod- and crustacean-specific NR evolution.
Mitochondrial-nuclear genome interactions in nonalcoholic fatty liver disease in mice

OpenAIRE

Betancourt, Angela M.; King, Adrienne L.; Fetterman, Jessica L.; Millender-Swain, Telisha; Finley, Rachel D.; Oliva, Claudia R.; Crowe, David Ralph; Ballinger, Scott W.; Bailey, Shannon M.

2014-01-01

Nonalcoholic fatty liver disease (NAFLD) involves significant changes in liver metabolism characterized by oxidative stress, lipid accumulation, and fibrogenesis. Mitochondrial dysfunction and bioenergetic defects also contribute to NAFLD. Herein, we examined whether differences in mtDNA influence NAFLD. To determine the role of mitochondrial and nuclear genomes in NAFLD, Mitochondrial-Nuclear eXchange (MNX) mice were fed an atherogenic diet. MNX mice have mtDNA from C57BL/6...
Unraveling the nuclear and chloroplast genomes of an agar producing red macroalga, Gracilaria changii (Rhodophyta, Gracilariales).

Science.gov (United States)

Ho, Chai-Ling; Lee, Wei-Kang; Lim, Ee-Leen

2018-03-01

Agar and agarose have wide applications in food and pharmaceutical industries. Knowledge on the genome of red seaweeds that produce them is still lacking. To fill the gap in genome analyses of these red algae, we have sequenced the nuclear and organellar genomes of an agarophyte, Gracilaria changii. The partial nuclear genome sequence of G. changii has a total length of 35.8Mb with 10,912 predicted protein coding sequences. Only 39.4% predicted proteins were found to have significant matches to protein sequences in SwissProt. The chloroplast genome of G. changii is 183,855bp with a total of 201 open reading frames (ORFs), 29 tRNAs and 3 rRNAs predicted. Five genes: ssrA, leuC and leuD CP76_p173 (orf139) and pbsA were absent in the chloroplast genome of G. changii. The genome information is valuable in accelerating functional studies of individual genes and resolving evolutionary relationship of red seaweeds. Copyright © 2017 Elsevier Inc. All rights reserved.
Nuclear genome size and genomic distribution of ribosomal DNA in Musa and Ensete (Musaceae): taxonomic implications

Czech Academy of Sciences Publication Activity Database

Bartoš, Jan; Alkhimova, Olena; Kubaláková, Marie; De Langhe, E.; Doležel, Jaroslav

2005-01-01

Roč. 109, - (2005), s. 50-57 ISSN 1424-8581 R&D Projects: GA AV ČR IAA6038204 Grant - others:IAEA Research Contract 12230/RBF Institutional research plan: CEZ:AV0Z50380511 Keywords : Musa and Ensete * nuclear genome size * FISH Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.076, year: 2005
Nuclear routing networks span between nuclear pore complexes and genomic DNA to guide nucleoplasmic trafficking of biomolecules

Science.gov (United States)

Malecki, Marek; Malecki, Bianca

2012-01-01

In health and disease, biomolecules, which are involved in gene expression, recombination, or reprogramming have to traffic through the nucleoplasm, between nuclear pore complexes (NPCs) and genomic DNA (gDNA). This trafficking is guided by the recently revealed nuclear routing networks (NRNs). In this study, we aimed to investigate, if the NRNs have established associations with the genomic DNA in situ and if the NRNs have capabilities to bind the DNA de novo. Moreover, we aimed to study further, if nucleoplasmic trafficking of the histones, rRNA, and transgenes’ vectors, between the NPCs and gDNA, is guided by the NRNs. We used Xenopus laevis oocytes as the model system. We engineered the transgenes’ DNA vectors equipped with the SV40 LTA nuclear localization signals (NLS) and/or HIV Rev nuclear export signals (NES). We purified histones, 5S rRNA, and gDNA. We rendered all these molecules superparamagnetic and fluorescent for detection with nuclear magnetic resonance (NMR), total reflection x-ray fluorescence (TXRF), energy dispersive x-ray spectroscopy (EDXS), and electron energy loss spectroscopy (EELS). The NRNs span between the NPCs and genomic DNA. They form firm bonds with the gDNA in situ. After complete digestion of the nucleic acids with the RNases and DNases, the newly added DNA - modified with the dNTP analogs, bonds firmly to the NRNs. Moreover, the NRNs guide the trafficking of the DNA transgenes’ vectors - modified with the SV40 LTA NLS, following their import into the nuclei through the NPCs. The pathway is identical to that of histones. The NRNs also guide the trafficking of the DNA transgenes’ vectors, modified with the HIV Rev NES, to the NPCs, followed by their export out of the nuclei. Ribosomal RNAs follow the same pathway. To summarize, the NRNs are the structures connecting the NPCs and the gDNA. They guide the trafficking of the biomolecules between the NPCs and the gDNA. PMID:23275893
Initial genomics of the human nucleolus.

Directory of Open Access Journals (Sweden)

Attila Németh

2010-03-01

Full Text Available We report for the first time the genomics of a nuclear compartment of the eukaryotic cell. 454 sequencing and microarray analysis revealed the pattern of nucleolus-associated chromatin domains (NADs in the linear human genome and identified different gene families and certain satellite repeats as the major building blocks of NADs, which constitute about 4% of the genome. Bioinformatic evaluation showed that NAD-localized genes take part in specific biological processes, like the response to other organisms, odor perception, and tissue development. 3D FISH and immunofluorescence experiments illustrated the spatial distribution of NAD-specific chromatin within interphase nuclei and its alteration upon transcriptional changes. Altogether, our findings describe the nature of DNA sequences associated with the human nucleolus and provide insights into the function of the nucleolus in genome organization and establishment of nuclear architecture.
Initial Genomics of the Human Nucleolus

Science.gov (United States)

Németh, Attila; Conesa, Ana; Santoyo-Lopez, Javier; Medina, Ignacio; Montaner, David; Péterfia, Bálint; Solovei, Irina; Cremer, Thomas; Dopazo, Joaquin; Längst, Gernot

2010-01-01

We report for the first time the genomics of a nuclear compartment of the eukaryotic cell. 454 sequencing and microarray analysis revealed the pattern of nucleolus-associated chromatin domains (NADs) in the linear human genome and identified different gene families and certain satellite repeats as the major building blocks of NADs, which constitute about 4% of the genome. Bioinformatic evaluation showed that NAD–localized genes take part in specific biological processes, like the response to other organisms, odor perception, and tissue development. 3D FISH and immunofluorescence experiments illustrated the spatial distribution of NAD–specific chromatin within interphase nuclei and its alteration upon transcriptional changes. Altogether, our findings describe the nature of DNA sequences associated with the human nucleolus and provide insights into the function of the nucleolus in genome organization and establishment of nuclear architecture. PMID:20361057
Human CST Facilitates Genome-wide RAD51 Recruitment to GC-Rich Repetitive Sequences in Response to Replication Stress.

Science.gov (United States)

Chastain, Megan; Zhou, Qing; Shiva, Olga; Fadri-Moskwik, Maria; Whitmore, Leanne; Jia, Pingping; Dai, Xueyu; Huang, Chenhui; Ye, Ping; Chai, Weihang

2016-08-02

The telomeric CTC1/STN1/TEN1 (CST) complex has been implicated in promoting replication recovery under replication stress at genomic regions, yet its precise role is unclear. Here, we report that STN1 is enriched at GC-rich repetitive sequences genome-wide in response to hydroxyurea (HU)-induced replication stress. STN1 deficiency exacerbates the fragility of these sequences under replication stress, resulting in chromosome fragmentation. We find that upon fork stalling, CST proteins form distinct nuclear foci that colocalize with RAD51. Furthermore, replication stress induces physical association of CST with RAD51 in an ATR-dependent manner. Strikingly, CST deficiency diminishes HU-induced RAD51 foci formation and reduces RAD51 recruitment to telomeres and non-telomeric GC-rich fragile sequences. Collectively, our findings establish that CST promotes RAD51 recruitment to GC-rich repetitive sequences in response to replication stress to facilitate replication restart, thereby providing insights into the mechanism underlying genome stability maintenance. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.
Transcriptional profiling in response to terminal drought stress reveals differential responses along the wheat genome

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Ferrari Francesco

2009-06-01

Full Text Available Abstract Background Water stress during grain filling has a marked effect on grain yield, leading to a reduced endosperm cell number and thus sink capacity to accumulate dry matter. The bread wheat cultivar Chinese Spring (CS, a Chinese Spring terminal deletion line (CS_5AL-10 and the durum wheat cultivar Creso were subjected to transcriptional profiling after exposure to mild and severe drought stress at the grain filling stage to find evidences of differential stress responses associated to different wheat genome regions. Results The transcriptome analysis of Creso, CS and its deletion line revealed 8,552 non redundant probe sets with different expression levels, mainly due to the comparisons between the two species. The drought treatments modified the expression of 3,056 probe sets. Besides a set of genes showing a similar drought response in Creso and CS, cluster analysis revealed several drought response features that can be associated to the different genomic structure of Creso, CS and CS_5AL-10. Some drought-related genes were expressed at lower level (or not expressed in Creso (which lacks the D genome or in the CS_5AL-10 deletion line compared to CS. The chromosome location of a set of these genes was confirmed by PCR-based mapping on the D genome (or the 5AL-10 region. Many clusters were characterized by different level of expression in Creso, CS and CS_AL-10, suggesting that the different genome organization of the three genotypes may affect plant adaptation to stress. Clusters with similar expression trend were grouped and functional classified to mine the biological mean of their activation or repression. Genes involved in ABA, proline, glycine-betaine and sorbitol pathways were found up-regulated by drought stress. Furthermore, the enhanced expression of a set of transposons and retrotransposons was detected in CS_5AL-10. Conclusion Bread and durum wheat genotypes were characterized by a different physiological reaction to water
The Nuclear and Mitochondrial Genomes of the Facultatively Eusocial Orchid Bee Euglossa dilemma

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Philipp Brand

2017-09-01

Full Text Available Bees provide indispensable pollination services to both agricultural crops and wild plant populations, and several species of bees have become important models for the study of learning and memory, plant–insect interactions, and social behavior. Orchid bees (Apidae: Euglossini are especially important to the fields of pollination ecology, evolution, and species conservation. Here we report the nuclear and mitochondrial genome sequences of the orchid bee Euglossa dilemma Bembé & Eltz. E. dilemma was selected because it is widely distributed, highly abundant, and it was recently naturalized in the southeastern United States. We provide a high-quality assembly of the 3.3 Gb genome, and an official gene set of 15,904 gene annotations. We find high conservation of gene synteny with the honey bee throughout 80 MY of divergence time. This genomic resource represents the first draft genome of the orchid bee genus Euglossa, and the first draft orchid bee mitochondrial genome, thus representing a valuable resource to the research community.
Isolation and analysis of high quality nuclear DNA with reduced organellar DNA for plant genome sequencing and resequencing

Directory of Open Access Journals (Sweden)

Zdepski Anna

2011-05-01

Full Text Available Abstract Background High throughput sequencing (HTS technologies have revolutionized the field of genomics by drastically reducing the cost of sequencing, making it feasible for individual labs to sequence or resequence plant genomes. Obtaining high quality, high molecular weight DNA from plants poses significant challenges due to the high copy number of chloroplast and mitochondrial DNA, as well as high levels of phenolic compounds and polysaccharides. Multiple methods have been used to isolate DNA from plants; the CTAB method is commonly used to isolate total cellular DNA from plants that contain nuclear DNA, as well as chloroplast and mitochondrial DNA. Alternatively, DNA can be isolated from nuclei to minimize chloroplast and mitochondrial DNA contamination. Results We describe optimized protocols for isolation of nuclear DNA from eight different plant species encompassing both monocot and eudicot species. These protocols use nuclei isolation to minimize chloroplast and mitochondrial DNA contamination. We also developed a protocol to determine the number of chloroplast and mitochondrial DNA copies relative to the nuclear DNA using quantitative real time PCR (qPCR. We compared DNA isolated from nuclei to total cellular DNA isolated with the CTAB method. As expected, DNA isolated from nuclei consistently yielded nuclear DNA with fewer chloroplast and mitochondrial DNA copies, as compared to the total cellular DNA prepared with the CTAB method. This protocol will allow for analysis of the quality and quantity of nuclear DNA before starting a plant whole genome sequencing or resequencing experiment. Conclusions Extracting high quality, high molecular weight nuclear DNA in plants has the potential to be a bottleneck in the era of whole genome sequencing and resequencing. The methods that are described here provide a framework for researchers to extract and quantify nuclear DNA in multiple types of plants.
Genome-wide deficiency screen for the genomic regions responsible for heat resistance in Drosophila melanogaster

Directory of Open Access Journals (Sweden)

Teramura Kouhei

2011-06-01

Full Text Available Abstract Background Temperature adaptation is one of the most important determinants of distribution and population size of organisms in nature. Recently, quantitative trait loci (QTL mapping and gene expression profiling approaches have been used for detecting candidate genes for heat resistance. However, the resolution of QTL mapping is not high enough to examine the individual effects of various genes in each QTL. Heat stress-responsive genes, characterized by gene expression profiling studies, are not necessarily responsible for heat resistance. Some of these genes may be regulated in association with the heat stress response of other genes. Results To evaluate which heat-responsive genes are potential candidates for heat resistance with higher resolution than previous QTL mapping studies, we performed genome-wide deficiency screen for QTL for heat resistance. We screened 439 isogenic deficiency strains from the DrosDel project, covering 65.6% of the Drosophila melanogaster genome in order to map QTL for thermal resistance. As a result, we found 19 QTL for heat resistance, including 3 novel QTL outside the QTL found in previous studies. Conclusion The QTL found in this study encompassed 19 heat-responsive genes found in the previous gene expression profiling studies, suggesting that they were strong candidates for heat resistance. This result provides new insights into the genetic architecture of heat resistance. It also emphasizes the advantages of genome-wide deficiency screen using isogenic deficiency libraries.
Using Partial Genomic Fosmid Libraries for Sequencing CompleteOrganellar Genomes

Energy Technology Data Exchange (ETDEWEB)

McNeal, Joel R.; Leebens-Mack, James H.; Arumuganathan, K.; Kuehl, Jennifer V.; Boore, Jeffrey L.; dePamphilis, Claude W.

2005-08-26

Organellar genome sequences provide numerous phylogenetic markers and yield insight into organellar function and molecular evolution. These genomes are much smaller in size than their nuclear counterparts; thus, their complete sequencing is much less expensive than total nuclear genome sequencing, making broader phylogenetic sampling feasible. However, for some organisms it is challenging to isolate plastid DNA for sequencing using standard methods. To overcome these difficulties, we constructed partial genomic libraries from total DNA preparations of two heterotrophic and two autotrophic angiosperm species using fosmid vectors. We then used macroarray screening to isolate clones containing large fragments of plastid DNA. A minimum tiling path of clones comprising the entire genome sequence of each plastid was selected, and these clones were shotgun-sequenced and assembled into complete genomes. Although this method worked well for both heterotrophic and autotrophic plants, nuclear genome size had a dramatic effect on the proportion of screened clones containing plastid DNA and, consequently, the overall number of clones that must be screened to ensure full plastid genome coverage. This technique makes it possible to determine complete plastid genome sequences for organisms that defy other available organellar genome sequencing methods, especially those for which limited amounts of tissue are available.
DNA damage response and spindle assembly checkpoint function throughout the cell cycle to ensure genomic integrity.

Directory of Open Access Journals (Sweden)

Katherine S Lawrence

2015-04-01

Full Text Available Errors in replication or segregation lead to DNA damage, mutations, and aneuploidies. Consequently, cells monitor these events and delay progression through the cell cycle so repair precedes division. The DNA damage response (DDR, which monitors DNA integrity, and the spindle assembly checkpoint (SAC, which responds to defects in spindle attachment/tension during metaphase of mitosis and meiosis, are critical for preventing genome instability. Here we show that the DDR and SAC function together throughout the cell cycle to ensure genome integrity in C. elegans germ cells. Metaphase defects result in enrichment of SAC and DDR components to chromatin, and both SAC and DDR are required for metaphase delays. During persistent metaphase arrest following establishment of bi-oriented chromosomes, stability of the metaphase plate is compromised in the absence of DDR kinases ATR or CHK1 or SAC components, MAD1/MAD2, suggesting SAC functions in metaphase beyond its interactions with APC activator CDC20. In response to DNA damage, MAD2 and the histone variant CENPA become enriched at the nuclear periphery in a DDR-dependent manner. Further, depletion of either MAD1 or CENPA results in loss of peripherally associated damaged DNA. In contrast to a SAC-insensitive CDC20 mutant, germ cells deficient for SAC or CENPA cannot efficiently repair DNA damage, suggesting that SAC mediates DNA repair through CENPA interactions with the nuclear periphery. We also show that replication perturbations result in relocalization of MAD1/MAD2 in human cells, suggesting that the role of SAC in DNA repair is conserved.

Accelerated evolution of mitochondrial but not nuclear genomes of Hymenoptera: new evidence from crabronid wasps.

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Martin Kaltenpoth

Full Text Available Mitochondrial genes in animals are especially useful as molecular markers for the reconstruction of phylogenies among closely related taxa, due to the generally high substitution rates. Several insect orders, notably Hymenoptera and Phthiraptera, show exceptionally high rates of mitochondrial molecular evolution, which has been attributed to the parasitic lifestyle of current or ancestral members of these taxa. Parasitism has been hypothesized to entail frequent population bottlenecks that increase rates of molecular evolution by reducing the efficiency of purifying selection. This effect should result in elevated substitution rates of both nuclear and mitochondrial genes, but to date no extensive comparative study has tested this hypothesis in insects. Here we report the mitochondrial genome of a crabronid wasp, the European beewolf (Philanthus triangulum, Hymenoptera, Crabronidae, and we use it to compare evolutionary rates among the four largest holometabolous insect orders (Coleoptera, Diptera, Hymenoptera, Lepidoptera based on phylogenies reconstructed with whole mitochondrial genomes as well as four single-copy nuclear genes (18S rRNA, arginine kinase, wingless, phosphoenolpyruvate carboxykinase. The mt-genome of P. triangulum is 16,029 bp in size with a mean A+T content of 83.6%, and it encodes the 37 genes typically found in arthropod mt genomes (13 protein-coding, 22 tRNA, and two rRNA genes. Five translocations of tRNA genes were discovered relative to the putative ancestral genome arrangement in insects, and the unusual start codon TTG was predicted for cox2. Phylogenetic analyses revealed significantly longer branches leading to the apocritan Hymenoptera as well as the Orussoidea, to a lesser extent the Cephoidea, and, possibly, the Tenthredinoidea than any of the other holometabolous insect orders for all mitochondrial but none of the four nuclear genes tested. Thus, our results suggest that the ancestral parasitic lifestyle of
Evolutionary analysis of a large mtDNA translocation (numt) into the nuclear genome of the Panthera genus species

OpenAIRE

Kim, Jae-Heup; Antunes, Agostinho; Luo, Shu-Jin; Menninger, Joan; Nash, William G.; O’Brien, Stephen J.; Johnson, Warren E.

2005-01-01

Translocation of cymtDNA into the nuclear genome, also referred to as numt, has been reported in many species, including several closely related to the domestic cat (Felis catus). We describe the recent transposition of 12,536 bp of the 17 kb mitochondrial genome into the nucleus of the common ancestor of the five Panthera genus species: tiger, P. tigris; snow leopard, P. uncia; jaguar, P. onca; leopard, P. pardus; and lion, P. leo. This nuclear integration, representing 74% of the mitochondr...
Moving through the Stressed Genome: Emerging Regulatory Roles for Transposons in Plant Stress Response.

Science.gov (United States)

Negi, Pooja; Rai, Archana N; Suprasanna, Penna

2016-01-01

The recognition of a positive correlation between organism genome size with its transposable element (TE) content, represents a key discovery of the field of genome biology. Considerable evidence accumulated since then suggests the involvement of TEs in genome structure, evolution and function. The global genome reorganization brought about by transposon activity might play an adaptive/regulatory role in the host response to environmental challenges, reminiscent of McClintock's original 'Controlling Element' hypothesis. This regulatory aspect of TEs is also garnering support in light of the recent evidences, which project TEs as "distributed genomic control modules." According to this view, TEs are capable of actively reprogramming host genes circuits and ultimately fine-tuning the host response to specific environmental stimuli. Moreover, the stress-induced changes in epigenetic status of TE activity may allow TEs to propagate their stress responsive elements to host genes; the resulting genome fluidity can permit phenotypic plasticity and adaptation to stress. Given their predominating presence in the plant genomes, nested organization in the genic regions and potential regulatory role in stress response, TEs hold unexplored potential for crop improvement programs. This review intends to present the current information about the roles played by TEs in plant genome organization, evolution, and function and highlight the regulatory mechanisms in plant stress responses. We will also briefly discuss the connection between TE activity, host epigenetic response and phenotypic plasticity as a critical link for traversing the translational bridge from a purely basic study of TEs, to the applied field of stress adaptation and crop improvement.
Moving through the Stressed Genome: Emerging Regulatory Roles for Transposons in Plant Stress Response

Science.gov (United States)

Negi, Pooja; Rai, Archana N.; Suprasanna, Penna

2016-01-01

The recognition of a positive correlation between organism genome size with its transposable element (TE) content, represents a key discovery of the field of genome biology. Considerable evidence accumulated since then suggests the involvement of TEs in genome structure, evolution and function. The global genome reorganization brought about by transposon activity might play an adaptive/regulatory role in the host response to environmental challenges, reminiscent of McClintock's original ‘Controlling Element’ hypothesis. This regulatory aspect of TEs is also garnering support in light of the recent evidences, which project TEs as “distributed genomic control modules.” According to this view, TEs are capable of actively reprogramming host genes circuits and ultimately fine-tuning the host response to specific environmental stimuli. Moreover, the stress-induced changes in epigenetic status of TE activity may allow TEs to propagate their stress responsive elements to host genes; the resulting genome fluidity can permit phenotypic plasticity and adaptation to stress. Given their predominating presence in the plant genomes, nested organization in the genic regions and potential regulatory role in stress response, TEs hold unexplored potential for crop improvement programs. This review intends to present the current information about the roles played by TEs in plant genome organization, evolution, and function and highlight the regulatory mechanisms in plant stress responses. We will also briefly discuss the connection between TE activity, host epigenetic response and phenotypic plasticity as a critical link for traversing the translational bridge from a purely basic study of TEs, to the applied field of stress adaptation and crop improvement. PMID:27777577
Emergency response and nuclear risk governance. Nuclear safety at nuclear power plant accidents

International Nuclear Information System (INIS)

Kuhlen, Johannes

2014-01-01

The present study entitled ''Emergency Response and Nuclear Risk Governance: nuclear safety at nuclear power plant accidents'' deals with issues of the protection of the population and the environment against hazardous radiation (the hazards of nuclear energy) and the harmful effects of radioactivity during nuclear power plant accidents. The aim of this study is to contribute to both the identification and remediation of shortcomings and deficits in the management of severe nuclear accidents like those that occurred at Chernobyl in 1986 and at Fukushima in 2011 as well as to the improvement and harmonization of plans and measures taken on an international level in nuclear emergency management. This thesis is divided into a theoretical part and an empirical part. The theoretical part focuses on embedding the subject in a specifically global governance concept, which includes, as far as Nuclear Risk Governance is concerned, the global governance of nuclear risks. Due to their characteristic features the following governance concepts can be assigned to these risks: Nuclear Safety Governance is related to safety, Nuclear Security Governance to security and NonProliferation Governance to safeguards. The subject of investigation of the present study is as a special case of the Nuclear Safety Governance, the Nuclear Emergency governance, which refers to off-site emergency response. The global impact of nuclear accidents and the concepts of security, safety culture and residual risk are contemplated in this context. The findings (accident sequences, their consequences and implications) from the analyses of two reactor accidents prior to Fukushima (Three Mile Iceland in 1979, Chernobyl in 1986) are examined from a historical analytical perspective and the state of the Nuclear Emergency governance and international cooperation aimed at improving nuclear safety after Chernobyl is portrayed by discussing, among other topics, examples of &apos
MACK/MACKLIB system for nuclear response functions

International Nuclear Information System (INIS)

Abdou, M.A.; Gohar, Y.M.

1978-01-01

The MACK computer program calculates energy pointwise and multigroup nuclear response functions from basic nuclear data in ENDF/B format. The new version of the program MACK-IV, incorporates major developments and improvements aimed at maximizing the utilization of available nuclear data and ensuring energy conservation in nuclear heating calculations. A new library, MACKLIB-IV, of nuclear response functions was generated in the CTR energy group structure of 171 neutron groups and 36 gamma groups. The library was prepared using MACK-IV and ENDF/B-IV and is suitable for fusion, fusion-fission hydrids, and fission applications
MACK/MACKLIB system for nuclear response functions

International Nuclear Information System (INIS)

Abdou, M.A.; Gohar, Y.

1978-01-01

The MACK computer program calculates energy pointwise and multigroup nuclear response functions from basic nuclear data in ENDF/B format. The new version of the program, MACK-IV, incorporates major developments and improvements aimed at maximizing the utilization of available nuclear data and ensuring energy conservation in nuclear heating calculations. A new library, MACKLIB-IV, of nuclear response functions was generated in the CTR energy group structure of 171 neutron groups and 36 gamma groups. The library was prepared using MACK-IV, and ENDF/B-IV, and is suitable for fusion, fusion--fission hybrids, and fission applications. 3 figures, 4 tables
MACK/MACKLIB system for nuclear response functions

Energy Technology Data Exchange (ETDEWEB)

Abdou, M.A.; Gohar, Y.M.

1978-03-15

The MACK computer program calculates energy pointwise and multigroup nuclear response functions from basic nuclear data in ENDF/B format. The new version of the program MACK-IV, incorporates major developments and improvements aimed at maximizing the utilization of available nuclear data and ensuring energy conservation in nuclear heating calculations. A new library, MACKLIB-IV, of nuclear response functions was generated in the CTR energy group structure of 171 neutron groups and 36 gamma groups. The library was prepared using MACK-IV and ENDF/B-IV and is suitable for fusion, fusion-fission hydrids, and fission applications.
Coevolution between Nuclear-Encoded DNA Replication, Recombination, and Repair Genes and Plastid Genome Complexity.

Science.gov (United States)

Zhang, Jin; Ruhlman, Tracey A; Sabir, Jamal S M; Blazier, John Chris; Weng, Mao-Lun; Park, Seongjun; Jansen, Robert K

2016-02-17

Disruption of DNA replication, recombination, and repair (DNA-RRR) systems has been hypothesized to cause highly elevated nucleotide substitution rates and genome rearrangements in the plastids of angiosperms, but this theory remains untested. To investigate nuclear-plastid genome (plastome) coevolution in Geraniaceae, four different measures of plastome complexity (rearrangements, repeats, nucleotide insertions/deletions, and substitution rates) were evaluated along with substitution rates of 12 nuclear-encoded, plastid-targeted DNA-RRR genes from 27 Geraniales species. Significant correlations were detected for nonsynonymous (dN) but not synonymous (dS) substitution rates for three DNA-RRR genes (uvrB/C, why1, and gyrA) supporting a role for these genes in accelerated plastid genome evolution in Geraniaceae. Furthermore, correlation between dN of uvrB/C and plastome complexity suggests the presence of nucleotide excision repair system in plastids. Significant correlations were also detected between plastome complexity and 13 of the 90 nuclear-encoded organelle-targeted genes investigated. Comparisons revealed significant acceleration of dN in plastid-targeted genes of Geraniales relative to Brassicales suggesting this correlation may be an artifact of elevated rates in this gene set in Geraniaceae. Correlation between dN of plastid-targeted DNA-RRR genes and plastome complexity supports the hypothesis that the aberrant patterns in angiosperm plastome evolution could be caused by dysfunction in DNA-RRR systems. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
Between Two Fern Genomes

Science.gov (United States)

2014-01-01

Ferns are the only major lineage of vascular plants not represented by a sequenced nuclear genome. This lack of genome sequence information significantly impedes our ability to understand and reconstruct genome evolution not only in ferns, but across all land plants. Azolla and Ceratopteris are ideal and complementary candidates to be the first ferns to have their nuclear genomes sequenced. They differ dramatically in genome size, life history, and habit, and thus represent the immense diversity of extant ferns. Together, this pair of genomes will facilitate myriad large-scale comparative analyses across ferns and all land plants. Here we review the unique biological characteristics of ferns and describe a number of outstanding questions in plant biology that will benefit from the addition of ferns to the set of taxa with sequenced nuclear genomes. We explain why the fern clade is pivotal for understanding genome evolution across land plants, and we provide a rationale for how knowledge of fern genomes will enable progress in research beyond the ferns themselves. PMID:25324969
The nuclear genome of Rhazya stricta and the evolution of alkaloid diversity in a medically relevant clade of Apocynaceae.

Science.gov (United States)

Sabir, Jamal S M; Jansen, Robert K; Arasappan, Dhivya; Calderon, Virginie; Noutahi, Emmanuel; Zheng, Chunfang; Park, Seongjun; Sabir, Meshaal J; Baeshen, Mohammed N; Hajrah, Nahid H; Khiyami, Mohammad A; Baeshen, Nabih A; Obaid, Abdullah Y; Al-Malki, Abdulrahman L; Sankoff, David; El-Mabrouk, Nadia; Ruhlman, Tracey A

2016-09-22

Alkaloid accumulation in plants is activated in response to stress, is limited in distribution and specific alkaloid repertoires are variable across taxa. Rauvolfioideae (Apocynaceae, Gentianales) represents a major center of structural expansion in the monoterpenoid indole alkaloids (MIAs) yielding thousands of unique molecules including highly valuable chemotherapeutics. The paucity of genome-level data for Apocynaceae precludes a deeper understanding of MIA pathway evolution hindering the elucidation of remaining pathway enzymes and the improvement of MIA availability in planta or in vitro. We sequenced the nuclear genome of Rhazya stricta (Apocynaceae, Rauvolfioideae) and present this high quality assembly in comparison with that of coffee (Rubiaceae, Coffea canephora, Gentianales) and others to investigate the evolution of genome-scale features. The annotated Rhazya genome was used to develop the community resource, RhaCyc, a metabolic pathway database. Gene family trees were constructed to identify homologs of MIA pathway genes and to examine their evolutionary history. We found that, unlike Coffea, the Rhazya lineage has experienced many structural rearrangements. Gene tree analyses suggest recent, lineage-specific expansion and diversification among homologs encoding MIA pathway genes in Gentianales and provide candidate sequences with the potential to close gaps in characterized pathways and support prospecting for new MIA production avenues.
Licensee responsibility for nuclear power plant safety

International Nuclear Information System (INIS)

Schneider, Horst

2010-01-01

Simple sentences easy to grasp are desirable in regulations and bans. However, in a legal system, their meaning must be unambiguous. Article 6, Paragraph 1 of the EURATOM Directive on a community framework for the nuclear safety of nuclear facilities of June 2009 states that 'responsibility for the nuclear safety of a nuclear facility is incumbent primarily on the licensee.' The draft 'Safety Criteria for Nuclear Power Plants, Revision D, April 2009' of the German Federal Ministry for the Environment, Nature Conservation, and Nuclear Safety (BMU) (A Module 1, 'Safety Criteria for Nuclear Power Plants: Basic Safety Criteria' / '0 Principles' Paragraph 2) reads: 'Responsibility for ensuring safety rests with the licensee. He shall give priority to compliance with the safety goal over the achievement of other operational objectives.' In addition, the existing rules and regulations, whose rank is equivalent to that of international regulations, assign priority to the safety goal to be pursued by the licensee over all other objectives of the company. The operator's responsibility for nuclear safety can be required and achieved only on the basis of permits granted, which must meet legal requirements. The operator's proximity to plant operation is the reason for his 'primary responsibility.' Consequently, verbatim incorporation of Article 6, Paragraph 1 of the EURATOM Directive would only be a superscript added to existing obligations of the operator - inclusive of a safety culture designed as an incentive to further 'the spirit of safety-related actions' - without any new legal contents and consequences. In the reasons of the regulation, this would have to be clarified in addition to the cryptic wording of 'responsibility.. primarily,' at the same time expressing that operators and authorities work together in a spirit of openness and trust. (orig.)
Unmanned Mobile Monitoring for Nuclear Emergency Response

Energy Technology Data Exchange (ETDEWEB)

Choi, YoungSoo; Park, JongWon; Kim, TaeWon; Jeong, KyungMin [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

2016-10-15

Severe accidents at nuclear power plant have led to significant consequences to the people, the environment or the facility. Therefore, the appropriate response is required for the mitigation of the accidents. In the past, most of responses were performed by human beings, but it was dangerous and risky. In this paper, we proposed unmanned mobile system for the monitoring of nuclear accident in order to response effectively. For the integrity of reactor cooling and containment building, reactor cooling pipe and hydrogen distribution monitoring with unmanned ground vehicle was designed. And, for the safety of workers, radiation distribution monitoring with unmanned aerial vehicle was designed. Unmanned mobile monitoring system was proposed to respond nuclear accidents effectively. Concept of reinforcing the integrity of RCS and containment building, and radiation distribution monitoring were described. RCS flow measuring, hydrogen distribution measuring and radiation monitoring deployed at unmanned vehicle were proposed. These systems could be a method for the preparedness of effective response of nuclear accidents.
The development of nuclear power and emergency response

International Nuclear Information System (INIS)

Pan Ziqiang

2007-01-01

Nuclear power is a safe, clean energy, which has been evidenced by the history of nuclear power development. Nuclear power is associated with very low risk but not equal to zero. Accident emergency response and preparedness is a final barrier necessary to reduce potential risks that may arise from nuclear power plants, which must be enhanced. In the course of accident emergency response and preparedness, it is highly necessary to draw domestic and foreign experiences and lessons. Lastly, the paper presents the discussions of some issues which merit attention with respect to emergency response and preparedness in China. (authors)
Some Qualitative Requirements for Testing of Nuclear Emergency Response Robots

International Nuclear Information System (INIS)

Eom, Heungseop; Cho, Jai Wan; Choi, Youngsoo; Jeong, Kyungmin

2014-01-01

Korea Atomic Energy Research Institute (KAERI) is carrying out the project 'Development of Core Technology for Remote Response in Nuclear Emergency Situation', and as a part of the project, we are studying the reliability and performance requirements of nuclear emergency response robots. In this paper, we described some qualitative requirements for testing of nuclear emergency response robots which are different to general emergency response robots. We briefly introduced test requirements of general emergency response robots and described some qualitative aspects of test requirements for nuclear emergency response robots. When considering an immature field-robot technology and variety of nuclear emergency situations, it seems hard to establish quantitative test requirements of these robots at this time. However, based on studies of nuclear severe accidents and the experience of Fukushima NPP accident, we can expect some test requirements including quantitative ones for nuclear emergency response robots
Incoming human papillomavirus 16 genome is lost in PML protein-deficient HaCaT keratinocytes.

Science.gov (United States)

Bienkowska-Haba, Malgorzata; Luszczek, Wioleta; Keiffer, Timothy R; Guion, Lucile G M; DiGiuseppe, Stephen; Scott, Rona S; Sapp, Martin

2017-05-01

Human papillomaviruses (HPVs) target promyelocytic leukemia (PML) nuclear bodies (NBs) during infectious entry and PML protein is important for efficient transcription of incoming viral genome. However, the transcriptional down regulation was shown to be promoter-independent in that heterologous promoters delivered by papillomavirus particles were also affected. To further investigate the role of PML protein in HPV entry, we used small hairpin RNA to knockdown PML protein in HaCaT keratinocytes. Confirming previous findings, PML knockdown in HaCaT cells reduced HPV16 transcript levels significantly following infectious entry without impairing binding and trafficking. However, when we quantified steady-state levels of pseudogenomes in interphase cells, we found strongly reduced genome levels compared with parental HaCaT cells. Because nuclear delivery was comparable in both cell lines, we conclude that viral pseudogenome must be removed after successful nuclear delivery. Transcriptome analysis by gene array revealed that PML knockdown in clonal HaCaT cells was associated with a constitutive interferon response. Abrogation of JAK1/2 signaling prevented genome loss, however, did not restore viral transcription. In contrast, knockdown of PML protein in HeLa cells did not affect HPV genome delivery and transcription. HeLa cells are transformed by HPV18 oncogenes E6 and E7, which have been shown to interfere with the JAK/Stat signaling pathway. Our data imply that PML NBs protect incoming HPV genomes. Furthermore, they provide evidence that PML NBs are key regulators of the innate immune response in keratinocytes. Promyelocytic leukemia nuclear bodies (PML NBs) are important for antiviral defense. Many DNA viruses target these subnuclear structures and reorganize them. Reorganization of PML NBs by viral proteins is important for establishment of infection. In contrast, HPVs require the presence of PML protein for efficient transcription of incoming viral genome. Our
Status and developing of nuclear emergency response techniques in China

International Nuclear Information System (INIS)

Jiangang, Zhang; Bing, Zhao; Rongyao, Tang; Xiaoxiao, Xu

2008-01-01

Full text: Nuclear Emergency preparedness and response in China is consistent with international basic principle of nuclear safety and emergency response. Nuclear emergency response techniques in China developed with nuclear power from 1980s. The status of nuclear emergency techniques in China are: 1) China have plentiful experiences and abilities in the fields of nuclear facility emergency planning and preparedness, nuclear accident consequence assessment, emergency monitoring, and emergency advisory; 2) Emergency assistance ability in China has a foundation, however it cannot satisfy national requirement; 3) Emergency planning and preparedness is not based on hazard assessment; 4) Remote monitoring and robot techniques in not adaptable to the requirements of nuclear emergency response; 5) A consistent emergency assessment system is lack in China. In this paper, it is analyzed what is the developing focal points of nuclear emergency response techniques in China, and it is proposed that the main points are: a) To develop the research of emergency preparedness on the base of hazard analysis; b) To improve remote monitoring and robot ability during nuclear emergency; c) To develop the response technique research with anti-terrorism. (author)
Understanding and exploiting the genomic response to hypoxia

International Nuclear Information System (INIS)

Giaccia, A.J.

2003-01-01

The tumor microenvironment influences both therapeutic outcome and malignant progression. Of the many factors that may be altered in the tumor microenvironment, changes in tumor oxygenation have been strongly associated with a lower probability of local tumor control and survival. In vitro studies indicate that cells exposed to a low oxygen environment exhibit multiple phenotypes, including cell-cycle arrest, increased expression of pro-angiogenic genes, increased invasive capacity, increased apoptosis, increased anaerobic metabolism and altered differentiation programs. While the mechanistic basis of hypoxia as an impediment to radiotherapy and chemotherapy is well understood, it is unclear what changes in the cellular phenotype are important in understanding how hypoxia modifies malignant progression. One insight into how hypoxia modulates malignant progression comes from understanding the critical transcriptional regulators of gene expression under hypoxic conditions such as hypoxia inducible factor 1 (HIF-1) as well as changes in gene expression in untransformed and transformed cells. Overall, about 1.5% of the genome is found to be transcriptionally responsive to changes in oxygenation. Most importantly, the coordinated changes in gene expression under hypoxic conditions underscore the physiologic basis for altering gene expression in response to a low oxygen environment. In addition, some hypoxia-induced genes exhibit increased expression after reoxygenation, suggesting that they are regulated both by hypoxia and oxidative stress. Analysis of the genomic response to hypoxia has several therapeutic uses. First, it allows one to ask the question of what the cellular consequences are to inhibition of the transcriptional response to hypoxia such as by targeting the HIF-1 transcription factor. While the effect of loss of HIF-1 in tumors leads to inhibition of tumor growth, it does not eliminate tumors. In fact, studies indicate that inhibition of HIF-1 leads to a
Plastid, nuclear and reverse transcriptase sequences in the mitochondrial genome of Oenothera: is genetic information transferred between organelles via RNA?

Science.gov (United States)

Schuster, W; Brennicke, A

1987-01-01

We describe an open reading frame (ORF) with high homology to reverse transcriptase in the mitochondrial genome of Oenothera. This ORF displays all the characteristics of an active plant mitochondrial gene with a possible ribosome binding site and 39% T in the third codon position. It is located between a sequence fragment from the plastid genome and one of nuclear origin downstream from the gene encoding subunit 5 of the NADH dehydrogenase. The nuclear derived sequence consists of 528 nucleotides from the small ribosomal RNA and contains an expansion segment unique to nuclear rRNAs. The plastid sequence contains part of the ribosomal protein S4 and the complete tRNA(Ser). The observation that only transcribed sequences have been found i more than one subcellular compartment in higher plants suggests that interorganellar transfer of genetic information may occur via RNA and subsequent local reverse transcription and genomic integration. PMID:14650433
The Insulator Protein SU(HW) Fine-Tunes Nuclear Lamina Interactions of the Drosophila Genome

NARCIS (Netherlands)

Van Bemmel, J.G.; Pagie, L.; Braunschweig, U.; Brugman, W.; Meuleman, W.; Kerkhoven, R.M.; Van Steensel, B.

2010-01-01

Specific interactions of the genome with the nuclear lamina (NL) are thought to assist chromosome folding inside the nucleus and to contribute to the regulation of gene expression. High-resolution mapping has recently identified hundreds of large, sharply defined lamina-associated domains (LADs) in

Nuclear alpha spectrin: Critical roles in DNA interstrand cross-link repair and genomic stability

OpenAIRE

Lambert, Muriel W

2016-01-01

Non-erythroid alpha spectrin (?IISp) is a structural protein which we have shown is present in the nucleus of human cells. It interacts with a number of nuclear proteins such as actin, lamin, emerin, chromatin remodeling factors, and DNA repair proteins. ?IISp?s interaction with DNA repair proteins has been extensively studied. We have demonstrated that nuclear ?IISp is critical in DNA interstrand cross-link (ICL) repair in S phase, in both genomic (non-telomeric) and telomeric DNA, and in ma...
Do nuclear engineering educators have a special responsibility

International Nuclear Information System (INIS)

Weinberg, A.M.

1977-01-01

Each 1000 MW(e) reactor in equilibrium contains 15 x 10 9 Ci of radioactivity. To handle this material safety requires an extremely high level of expertise and commitment - in many respects, an expertise that goes beyond what is demanded of any other technology. If one grants that nuclear engineering is more demanding than other engineering because the price of failure is greater, one must ask how can we inculcate into the coming generations of nuclear engineers a full sense of the responsibility they bear in practising their profession. Clearly a first requirement is that all elements of the nuclear community -utility executives, equipment engineers, operating engineers, nuclear engineers, administrators - must recognize and accept the idea that nuclear energy is something special, and that therefore its practitioners must be special. This sense must be instilled into young nuclear engineers during their education. A special responsibility therefore devolves upon nuclear engineering educators: first, to recognize the special character of their profession, and second, to convey this sense to their students. The possibility of institutionalizing this sense of responsibility by establishing a nuclear Hippocratic Oath or special canon of ethics for nuclear engineers ought to be discussed within the nuclear community. (author)
Symbiodinium genomes reveal adaptive evolution of functions related to symbiosis

KAUST Repository

Liu, Huanle; Stephens, Timothy G.; Gonzá lez-Pech, Raú l; Beltran, Victor H.; Lapeyre, Bruno; Bongaerts, Pim; Cooke, Ira; Bourne, David G.; Forê t, Sylvain; Miller, David John; van Oppen, Madeleine J. H.; Voolstra, Christian R.; Ragan, Mark A.; Chan, Cheong Xin

2017-01-01

Symbiosis between dinoflagellates of the genus Symbiodinium and reef-building corals forms the trophic foundation of the world's coral reef ecosystems. Here we present the first draft genome of Symbiodinium goreaui (Clade C, type C1: 1.03 Gbp), one of the most ubiquitous endosymbionts associated with corals, and an improved draft genome of Symbiodinium kawagutii (Clade F, strain CS-156: 1.05 Gbp), previously sequenced as strain CCMP2468, to further elucidate genomic signatures of this symbiosis. Comparative analysis of four available Symbiodinium genomes against other dinoflagellate genomes led to the identification of 2460 nuclear gene families that show evidence of positive selection, including genes involved in photosynthesis, transmembrane ion transport, synthesis and modification of amino acids and glycoproteins, and stress response. Further, we identified extensive sets of genes for meiosis and response to light stress. These draft genomes provide a foundational resource for advancing our understanding Symbiodinium biology and the coral-algal symbiosis.
Symbiodinium genomes reveal adaptive evolution of functions related to symbiosis

KAUST Repository

Liu, Huanle

2017-10-06

Symbiosis between dinoflagellates of the genus Symbiodinium and reef-building corals forms the trophic foundation of the world\\'s coral reef ecosystems. Here we present the first draft genome of Symbiodinium goreaui (Clade C, type C1: 1.03 Gbp), one of the most ubiquitous endosymbionts associated with corals, and an improved draft genome of Symbiodinium kawagutii (Clade F, strain CS-156: 1.05 Gbp), previously sequenced as strain CCMP2468, to further elucidate genomic signatures of this symbiosis. Comparative analysis of four available Symbiodinium genomes against other dinoflagellate genomes led to the identification of 2460 nuclear gene families that show evidence of positive selection, including genes involved in photosynthesis, transmembrane ion transport, synthesis and modification of amino acids and glycoproteins, and stress response. Further, we identified extensive sets of genes for meiosis and response to light stress. These draft genomes provide a foundational resource for advancing our understanding Symbiodinium biology and the coral-algal symbiosis.
Computations of nuclear response functions with MACK-IV

International Nuclear Information System (INIS)

Abdou, M.A.; Gohar, Y.

1978-01-01

The MACK computer program calculates energy pointwise and multigroup nuclear response functions from basic nuclear data in ENDF/B format. The new version of the program, MACK-IV, incorporates major developments and improvements aimed at maximizing the utilization of available nuclear data and ensuring energy conservation in nuclear heating calculations. A new library, MACKLIB-IV, of nuclear response functions was generated in the CTR energy group structure of 171 neutron groups and 36 gamma groups. The library was prepared using MACK-IV and ENDF/B-IV and is suitable for fusion, fusion-fission hybrids, and fission applications
Computations of nuclear response functions with MACK-IV

Energy Technology Data Exchange (ETDEWEB)

Abdou, M A; Gohar, Y

1978-01-01

The MACK computer program calculates energy pointwise and multigroup nuclear response functions from basic nuclear data in ENDF/B format. The new version of the program, MACK-IV, incorporates major developments and improvements aimed at maximizing the utilization of available nuclear data and ensuring energy conservation in nuclear heating calculations. A new library, MACKLIB-IV, of nuclear response functions was generated in the CTR energy group structure of 171 neutron groups and 36 gamma groups. The library was prepared using MACK-IV and ENDF/B-IV and is suitable for fusion, fusion-fission hybrids, and fission applications.
Identification and characterization of nuclear genes involved in photosynthesis in Populus

Science.gov (United States)

2014-01-01

Background The gap between the real and potential photosynthetic rate under field conditions suggests that photosynthesis could potentially be improved. Nuclear genes provide possible targets for improving photosynthetic efficiency. Hence, genome-wide identification and characterization of the nuclear genes affecting photosynthetic traits in woody plants would provide key insights on genetic regulation of photosynthesis and identify candidate processes for improvement of photosynthesis. Results Using microarray and bulked segregant analysis strategies, we identified differentially expressed nuclear genes for photosynthesis traits in a segregating population of poplar. We identified 515 differentially expressed genes in this population (FC ≥ 2 or FC ≤ 0.5, P photosynthesis by the nuclear genome mainly involves transport, metabolism and response to stimulus functions. Conclusions This study provides new genome-scale strategies for the discovery of potential candidate genes affecting photosynthesis in Populus, and for identification of the functions of genes involved in regulation of photosynthesis. This work also suggests that improving photosynthetic efficiency under field conditions will require the consideration of multiple factors, such as stress responses. PMID:24673936
Guidelines for nuclear plant response to an earthquake

International Nuclear Information System (INIS)

1989-12-01

Guidelines have been developed to assist nuclear plant personnel in the preparation of earthquake response procedures for nuclear power plants. The objectives of the earthquake response procedures are to determine (1) the immediate effects of an earthquake on the physical condition of the nuclear power plant, (2) if shutdown of the plant is appropriate based on the observed damage to the plant or because the OBE has been exceeded, and (3) the readiness of the plant to resume operation following shutdown due to an earthquake. Readiness of a nuclear power plant to restart is determined on the basis of visual inspections of nuclear plant equipment and structures, and the successful completion of surveillance tests which demonstrate that the limiting conditions for operation as defined in the plant Technical Specifications are met. The guidelines are based on information obtained from a review of earthquake response procedures from numerous US and foreign nuclear power plants, interviews with nuclear plant operations personnel, and a review of reports of damage to industrial equipment and structures in actual earthquakes. 7 refs., 4 figs., 4 tabs
Evolutionary analysis of a large mtDNA translocation (numt) into the nuclear genome of the Panthera genus species.

Science.gov (United States)

Kim, Jae-Heup; Antunes, Agostinho; Luo, Shu-Jin; Menninger, Joan; Nash, William G; O'Brien, Stephen J; Johnson, Warren E

2006-02-01

Translocation of cymtDNA into the nuclear genome, also referred to as numt, has been reported in many species, including several closely related to the domestic cat (Felis catus). We describe the recent transposition of 12,536 bp of the 17 kb mitochondrial genome into the nucleus of the common ancestor of the five Panthera genus species: tiger, P. tigris; snow leopard, P. uncia; jaguar, P. onca; leopard, P. pardus; and lion, P. leo. This nuclear integration, representing 74% of the mitochondrial genome, is one of the largest to be reported in eukaryotes. The Panthera genus numt differs from the numt previously described in the Felis genus in: (1) chromosomal location (F2-telomeric region vs. D2-centromeric region), (2) gene make up (from the ND5 to the ATP8 vs. from the CR to the COII), (3) size (12.5 vs. 7.9 kb), and (4) structure (single monomer vs. tandemly repeated in Felis). These distinctions indicate that the origin of this large numt fragment in the nuclear genome of the Panthera species is an independent insertion from that of the domestic cat lineage, which has been further supported by phylogenetic analyses. The tiger cymtDNA shared around 90% sequence identity with the homologous numt sequence, suggesting an origin for the Panthera numt at around 3.5 million years ago, prior to the radiation of the five extant Panthera species.
Explanation of procedure on site medical emergency response for nuclear accident

International Nuclear Information System (INIS)

Liu Yulong; Jiang Zhong

2012-01-01

National occupational health standard-Procedure on Site Medical Emergency Response for Nuclear Accident has been approved and issued by the Ministry of Health. This standard is formulated according to the Emergency Response Law of the People's Republic of China, Law of the People 's Republic of China on Prevention and Control of Occupational Diseases, Regulations on Emergency Measures for Nuclear Accidents at Nuclear Power Plants, and Health Emergency Plans for Nuclear and Radiological Accidents of Ministry of Health, supporting the use of On-site Medical Emergency Planning and Preparedness for Nuclear Accidents and Off-site Medical Emergency Planning and Preparedness for Nuclear Accidents. Nuclear accident on-site medical response procedure is a part of the on-site emergency plan. The standard specifies the basic content and requirements of the nuclear accident on-site medical emergency response procedures of nuclear facilities operating units to guide and regulate the work of nuclear accident on-site medical emergency response of nuclear facilities operating units. The criteria-related contents were interpreted in this article. (authors)
Genome-scale cold stress response regulatory networks in ten Arabidopsis thaliana ecotypes

DEFF Research Database (Denmark)

Barah, Pankaj; Jayavelu, Naresh Doni; Rasmussen, Simon

2013-01-01

available from Arabidopsis thaliana 1001 genome project, we further investigated sequence polymorphisms in the core cold stress regulon genes. Significant numbers of non-synonymous amino acid changes were observed in the coding region of the CBF regulon genes. Considering the limited knowledge about......BACKGROUND: Low temperature leads to major crop losses every year. Although several studies have been conducted focusing on diversity of cold tolerance level in multiple phenotypically divergent Arabidopsis thaliana (A. thaliana) ecotypes, genome-scale molecular understanding is still lacking....... RESULTS: In this study, we report genome-scale transcript response diversity of 10 A. thaliana ecotypes originating from different geographical locations to non-freezing cold stress (10°C). To analyze the transcriptional response diversity, we initially compared transcriptome changes in all 10 ecotypes...
The Nuclear Review: the Institution of Nuclear Engineers' response to the Review of Nuclear Power

International Nuclear Information System (INIS)

Anon.

1994-01-01

The United Kingdom Government's Nuclear Review currently underway, addresses whether and in what form nuclear power should continue to be part of the country's power generation capability. This article sets out the response of the Institution of Nuclear Engineers to the Nuclear Review. This pro-nuclear group emphasises the benefits to be gained from diversity of generation in the energy supply industry. The environmentally benign nature of nuclear power is emphasised, in terms of gaseous emissions. The industry's excellent safety record also argues in favour of nuclear power. Finally, as power demand increases globally, a health U.K. nuclear industry could generate British wealth through power exports and via the construction industry. The Institution's view on radioactive waste management is also set out. (UK)
The nucleolus: a raft adrift in the nuclear sea or the keystone in nuclear structure?

Science.gov (United States)

O'Sullivan, Justin M; Pai, Dave A; Cridge, Andrew G; Engelke, David R; Ganley, Austen R D

2013-06-01

The nucleolus is a prominent nuclear structure that is the site of ribosomal RNA (rRNA) transcription, and hence ribosome biogenesis. Cellular demand for ribosomes, and hence rRNA, is tightly linked to cell growth and the rRNA makes up the majority of all the RNA within a cell. To fulfill the cellular demand for rRNA, the ribosomal RNA (rDNA) genes are amplified to high copy number and transcribed at very high rates. As such, understanding the rDNA has profound consequences for our comprehension of genome and transcriptional organization in cells. In this review, we address the question of whether the nucleolus is a raft adrift the sea of nuclear DNA, or actively contributes to genome organization. We present evidence supporting the idea that the nucleolus, and the rDNA contained therein, play more roles in the biology of the cell than simply ribosome biogenesis. We propose that the nucleolus and the rDNA are central factors in the spatial organization of the genome, and that rapid alterations in nucleolar structure in response to changing conditions manifest themselves in altered genomic structures that have functional consequences. Finally, we discuss some predictions that result from the nucleolus having a central role in nuclear organization.
Emergency preparedness and response plan for nuclear facilities in Indonesia

International Nuclear Information System (INIS)

Nur Rahmah Hidayati; Pande Made Udiyani

2009-01-01

All nuclear facilities in Indonesia are owned and operated by the National Nuclear Energy Agency (BATAN). The programs and activities of emergency planning and preparedness in Indonesia are based on the existing nuclear facilities, i.e. research reactors, research reactor fuel fabrication plant, radioactive waste treatment installation and radioisotopes production installation. The assessment is conducted to learn of status of emergency preparedness and response plan for nuclear facilities in Indonesia and to support the preparation of future Nuclear Power Plant. The assessment is conducted by comparing the emergency preparedness and response system in Indonesia to the system in other countries such as Japan and Republic of Korea, since the countries have many Nuclear Power Plants and other nuclear facilities. As a result, emergency preparedness response plan for existing nuclear facility in Indonesia has been implemented in many activities such as environmental monitoring program, facility monitoring equipment, and the continuous exercise of emergency preparedness and response. However, the implementation need law enforcement for imposing the responsibility of the coordinators in National Emergency Preparedness Plan. It also needs some additional technical support systems which refer to the system in Japan or Republic of Korea. The systems must be completed with some real time monitors which will support the emergency preparedness and response organization. The system should be built in NPP site before the first NPP will be operated. The system should be connected to an Off Site Emergency Center under coordination of BAPETEN as the regulatory body which has responsibility to control of nuclear energy in Indonesia. (Author)
Multiscale fluctuations in nuclear response

International Nuclear Information System (INIS)

Lacroix, D.; Chomaz, Ph.

1999-01-01

The nuclear collective response is investigated in the framework of a doorway picture in which the spreading width of the collective emotion is described as a coupling to more and more complex configurations. It is shown that this coupling induces fluctuations of the observed strength. In the case of a hierarchy of overlapping decay channels, Ericson fluctuations are observed at different scales. Methods for extracting these scales and the related lifetimes are discussed. Finally, it is shown that the coupling of different states at one level of complexity to some common decay channels at the next level, may produce interference-like patterns in the nuclear response. This quantum effect leads to anew type of fluctuations with a typical width related to the level spacing. (author)
Multiscale fluctuations in nuclear response

Energy Technology Data Exchange (ETDEWEB)

Lacroix, D.; Chomaz, Ph

1999-01-01

The nuclear collective response is investigated in the framework of a doorway picture in which the spreading width of the collective emotion is described as a coupling to more and more complex configurations. It is shown that this coupling induces fluctuations of the observed strength. In the case of a hierarchy of overlapping decay channels, Ericson fluctuations are observed at different scales. Methods for extracting these scales and the related lifetimes are discussed. Finally, it is shown that the coupling of different states at one level of complexity to some common decay channels at the next level, may produce interference-like patterns in the nuclear response. This quantum effect leads to anew type of fluctuations with a typical width related to the level spacing. (author) 25 refs.
RAD-seq derived genome-wide nuclear markers resolve the phylogeny of tunas

KAUST Repository

Díaz-Arce, Natalia

2016-06-07

Although species from the genus Thunnus include some of the most commercially important and most severely overexploited fishes, the phylogeny of this genus is still unresolved, hampering evolutionary and traceability studies that could help improve conservation and management strategies for these species. Previous attempts based on mitochondrial and nuclear markers were unsuccessful in inferring a congruent and reliable phylogeny, probably due to mitochondrial introgression events and lack of enough phylogenetically informative markers. Here we infer the first genome-wide nuclear marker-based phylogeny of tunas using restriction site associated DNA sequencing (RAD-seq) data. Our results, derived from phylogenomic inferences obtained from 128 nucleotide matrices constructed using alternative data assembly procedures, support a single Thunnus evolutionary history that challenges previous assumptions based on morphological and molecular data.
Assembled Plastid and Mitochondrial Genomes, as well as Nuclear Genes, Place the Parasite Family Cynomoriaceae in the Saxifragales.

Science.gov (United States)

Bellot, Sidonie; Cusimano, Natalie; Luo, Shixiao; Sun, Guiling; Zarre, Shahin; Gröger, Andreas; Temsch, Eva; Renner, Susanne S

2016-08-03

Cynomoriaceae, one of the last unplaced families of flowering plants, comprise one or two species or subspecies of root parasites that occur from the Mediterranean to the Gobi Desert. Using Illumina sequencing, we assembled the mitochondrial and plastid genomes as well as some nuclear genes of a Cynomorium specimen from Italy. Selected genes were also obtained by Sanger sequencing from individuals collected in China and Iran, resulting in matrices of 33 mitochondrial, 6 nuclear, and 14 plastid genes and rDNAs enlarged to include a representative angiosperm taxon sampling based on data available in GenBank. We also compiled a new geographic map to discern possible discontinuities in the parasites' occurrence. Cynomorium has large genomes of 13.70-13.61 (Italy) to 13.95-13.76 pg (China). Its mitochondrial genome consists of up to 49 circular subgenomes and has an overall gene content similar to that of photosynthetic angiosperms, while its plastome retains only 27 of the normally 116 genes. Nuclear, plastid and mitochondrial phylogenies place Cynomoriaceae in Saxifragales, and we found evidence for several horizontal gene transfers from different hosts, as well as intracellular gene transfers. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
Analysis of nuclear and organellar genomes of Plasmodium knowlesi in humans reveals ancient population structure and recent recombination among host-specific subpopulations

KAUST Repository

Diez Benavente, Ernest

2017-09-18

The macaque parasite Plasmodium knowlesi is a significant concern in Malaysia where cases of human infection are increasing. Parasites infecting humans originate from genetically distinct subpopulations associated with the long-tailed (Macaca fascicularis (Mf)) or pig-tailed macaques (Macaca nemestrina (Mn)). We used a new high-quality reference genome to re-evaluate previously described subpopulations among human and macaque isolates from Malaysian-Borneo and Peninsular-Malaysia. Nuclear genomes were dimorphic, as expected, but new evidence of chromosomal-segment exchanges between subpopulations was found. A large segment on chromosome 8 originating from the Mn subpopulation and containing genes encoding proteins expressed in mosquito-borne parasite stages, was found in Mf genotypes. By contrast, non-recombining organelle genomes partitioned into 3 deeply branched lineages, unlinked with nuclear genomic dimorphism. Subpopulations which diverged in isolation have re-connected, possibly due to deforestation and disruption of wild macaque habitats. The resulting genomic mosaics reveal traits selected by host-vector-parasite interactions in a setting of ecological transition.
Analysis of nuclear and organellar genomes of Plasmodium knowlesi in humans reveals ancient population structure and recent recombination among host-specific subpopulations

KAUST Repository

Diez Benavente, Ernest; Florez de Sessions, Paola; Moon, Robert W.; Holder, Anthony A.; Blackman, Michael J.; Roper, Cally; Drakeley, Christopher J.; Pain, Arnab; Sutherland, Colin J.; Hibberd, Martin L.; Campino, Susana; Clark, Taane G.

2017-01-01

The macaque parasite Plasmodium knowlesi is a significant concern in Malaysia where cases of human infection are increasing. Parasites infecting humans originate from genetically distinct subpopulations associated with the long-tailed (Macaca fascicularis (Mf)) or pig-tailed macaques (Macaca nemestrina (Mn)). We used a new high-quality reference genome to re-evaluate previously described subpopulations among human and macaque isolates from Malaysian-Borneo and Peninsular-Malaysia. Nuclear genomes were dimorphic, as expected, but new evidence of chromosomal-segment exchanges between subpopulations was found. A large segment on chromosome 8 originating from the Mn subpopulation and containing genes encoding proteins expressed in mosquito-borne parasite stages, was found in Mf genotypes. By contrast, non-recombining organelle genomes partitioned into 3 deeply branched lineages, unlinked with nuclear genomic dimorphism. Subpopulations which diverged in isolation have re-connected, possibly due to deforestation and disruption of wild macaque habitats. The resulting genomic mosaics reveal traits selected by host-vector-parasite interactions in a setting of ecological transition.

Evolutionary gradient of predicted nuclear localization signals (NLS)-bearing proteins in genomes of family Planctomycetaceae.

Science.gov (United States)

Guo, Min; Yang, Ruifu; Huang, Chen; Liao, Qiwen; Fan, Guangyi; Sun, Chenghang; Lee, Simon Ming-Yuen

2017-04-04

The nuclear envelope is considered a key classification marker that distinguishes prokaryotes from eukaryotes. However, this marker does not apply to the family Planctomycetaceae, which has intracellular spaces divided by lipidic intracytoplasmic membranes (ICMs). Nuclear localization signal (NLS), a short stretch of amino acid sequence, destines to transport proteins from cytoplasm into nucleus, and is also associated with the development of nuclear envelope. We attempted to investigate the NLS motifs in Planctomycetaceae genomes to demonstrate the potential molecular transition in the development of intracellular membrane system. In this study, we identified NLS-like motifs that have the same amino acid compositions as experimentally identified NLSs in genomes of 11 representative species of family Planctomycetaceae. A total of 15 NLS types and 170 NLS-bearing proteins were detected in the 11 strains. To determine the molecular transformation, we compared NLS-bearing protein abundances in the 11 representative Planctomycetaceae genomes with them in genomes of 16 taxonomically varied microorganisms: nine bacteria, two archaea and five fungi. In the 27 strains, 29 NLS types and 1101 NLS-bearing proteins were identified, principal component analysis showed a significant transitional gradient from bacteria to Planctomycetaceae to fungi on their NLS-bearing protein abundance profiles. Then, we clustered the 993 non-redundant NLS-bearing proteins into 181 families and annotated their involved metabolic pathways. Afterwards, we aligned the ten types of NLS motifs from the 13 families containing NLS-bearing proteins among bacteria, Planctomycetaceae or fungi, considering their diversity, length and origin. A transition towards increased complexity from non-planctomycete bacteria to Planctomycetaceae to archaea and fungi was detected based on the complexity of the 10 types of NLS-like motifs in the 13 NLS-bearing proteins families. The results of this study reveal that
Computer Security Incident Response Planning at Nuclear Facilities

International Nuclear Information System (INIS)

2016-06-01

The purpose of this publication is to assist Member States in developing comprehensive contingency plans for computer security incidents with the potential to impact nuclear security and/or nuclear safety. It provides an outline and recommendations for establishing a computer security incident response capability as part of a computer security programme, and considers the roles and responsibilities of the system owner, operator, competent authority, and national technical authority in responding to a computer security incident with possible nuclear security repercussions
Confusion in practice: on nuclear safety responsibility subject of our nation

International Nuclear Information System (INIS)

Wang Jia

2014-01-01

Nuclear safety responsibility subject seems a unquestionable issue, but when I took part in the CNNC searching team of 'nuclear law legislation', I found that there are confusions on understanding of this concept and in application. The paper focuses on the content of nuclear safety responsibility, using legal and practical method to dig out the differences with the related and frequently confusing concepts, on which basis to analyze the situation of nuclear safety responsibility subject of our nation. In conclusion, I give suggestions on who shall be the nuclear safety responsibility subject. (author)
Adaptive response and genomic instability: allosteric response of genome to negative impact

International Nuclear Information System (INIS)

Sasaki, Masao S.

2010-01-01

Currently, there is an upsurge concern on the unique response of living cells to low dose ionizing radiation for its inconformity to the existing paradigm of the biological action of radiation and its impact on the current understanding of risk evaluation of health effect of radiation in our workplace and environment. For the allosteric response to have significance, the cells must have an excellent sensing mechanism to discriminate tolerable and intolerable signals. In a series of experiments with mammalian, including human, cells, we demonstrated a novel sensing and signaling mechanism in the low-dose irradiated cells that was mediated by a PKCα-p3BMAPK-PLCδ1 feedback regulatory loop. Upon irradiation, PKCα is immediately activated, which in turn activate p38MAPK. The activation of p38MAPK is feedbacked to the activation of PKCα via PLCδ1, which catalyzes the hydrolysis of PtdInsP2 to generate PKCα-directed second messengers DAG and lnsP3. At low doses, the PKCα and p38MAPK continue to be activated for long time through this feedback loop, but when the cells encounter the high dose (>10 cGy or equivalent), the feedback loop is immediately comes to shutdown by deprivation of PKCα protein, known as down-regulation of PKC signaling. Thus, PKCα plays a key role in the long lasting nature of adaptive response to low doses and a binary switch to the genomic instability by too much signals. Tumor suppressor protein, p53, is a downstream effecter
Active nuclear transcriptome analysis reveals inflammasome-dependent mechanism for early neutrophil response to Mycobacterium marinum.

Science.gov (United States)

Kenyon, Amy; Gavriouchkina, Daria; Zorman, Jernej; Napolitani, Giorgio; Cerundolo, Vincenzo; Sauka-Spengler, Tatjana

2017-07-26

The mechanisms governing neutrophil response to Mycobacterium tuberculosis remain poorly understood. In this study we utilise biotagging, a novel genome-wide profiling approach based on cell type-specific in vivo biotinylation in zebrafish to analyse the initial response of neutrophils to Mycobacterium marinum, a close genetic relative of M. tuberculosis used to model tuberculosis. Differential expression analysis following nuclear RNA-seq of neutrophil active transcriptomes reveals a significant upregulation in both damage-sensing and effector components of the inflammasome, including caspase b, NLRC3 ortholog (wu: fb15h11) and il1β. Crispr/Cas9-mediated knockout of caspase b, which acts by proteolytic processing of il1β, results in increased bacterial burden and less infiltration of macrophages to sites of mycobacterial infection, thus impairing granuloma development. We also show that a number of immediate early response genes (IEGs) are responsible for orchestrating the initial neutrophil response to mycobacterial infection. Further perturbation of the IEGs exposes egr3 as a key transcriptional regulator controlling il1β transcription.
The genomic view of genes responsive to the antagonistic phytohormones, abscisic acid, and gibberellin.

Science.gov (United States)

Yazaki, Junshi; Kikuchi, Shoshi

2005-01-01

We now have the various genomics tools for monocot (Oryza sativa) and a dicot (Arabidopsis thaliana) plant. Plant is not only a very important agricultural resource but also a model organism for biological research. It is important that the interaction between ABA and GA is investigated for controlling the transition from embryogenesis to germination in seeds using genomics tools. These studies have investigated the relationship between dormancy and germination using genomics tools. Genomics tools identified genes that had never before been annotated as ABA- or GA-responsive genes in plant, detected new interactions between genes responsive to the two hormones, comprehensively characterized cis-elements of hormone-responsive genes, and characterized cis-elements of rice and Arabidopsis. In these research, ABA- and GA-regulated genes have been classified as functional proteins (proteins that probably function in stress or PR tolerance) and regulatory proteins (protein factors involved in further regulation of signal transduction). Comparison between ABA and/or GA-responsive genes in rice and those in Arabidopsis has shown that the cis-element has specificity in each species. cis-Elements for the dehydration-stress response have been specified in Arabidopsis but not in rice. cis-Elements for protein storage are remarkably richer in the upstream regions of the rice gene than in those of Arabidopsis.
The insulator protein SU(HW fine-tunes nuclear lamina interactions of the Drosophila genome.

Directory of Open Access Journals (Sweden)

Joke G van Bemmel

Full Text Available Specific interactions of the genome with the nuclear lamina (NL are thought to assist chromosome folding inside the nucleus and to contribute to the regulation of gene expression. High-resolution mapping has recently identified hundreds of large, sharply defined lamina-associated domains (LADs in the human genome, and suggested that the insulator protein CTCF may help to demarcate these domains. Here, we report the detailed structure of LADs in Drosophila cells, and investigate the putative roles of five insulator proteins in LAD organization. We found that the Drosophila genome is also organized in discrete LADs, which are about five times smaller than human LADs but contain on average a similar number of genes. Systematic comparison to new and published insulator binding maps shows that only SU(HW binds preferentially at LAD borders and at specific positions inside LADs, while GAF, CTCF, BEAF-32 and DWG are mostly absent from these regions. By knockdown and overexpression studies we demonstrate that SU(HW weakens genome - NL interactions through a local antagonistic effect, but we did not obtain evidence that it is essential for border formation. Our results provide insights into the evolution of LAD organization and identify SU(HW as a fine-tuner of genome - NL interactions.
Common developmental genome deprogramming in schizophrenia - Role of Integrative Nuclear FGFR1 Signaling (INFS).

Science.gov (United States)

Narla, S T; Lee, Y-W; Benson, C A; Sarder, P; Brennand, K J; Stachowiak, E K; Stachowiak, M K

2017-07-01

The watershed-hypothesis of schizophrenia asserts that over 200 different mutations dysregulate distinct pathways that converge on an unspecified common mechanism(s) that controls disease ontogeny. Consistent with this hypothesis, our RNA-sequencing of neuron committed cells (NCCs) differentiated from established iPSCs of 4 schizophrenia patients and 4 control subjects uncovered a dysregulated transcriptome of 1349 mRNAs common to all patients. Data reveals a global dysregulation of developmental genome, deconstruction of coordinated mRNA networks, and the formation of aberrant, new coordinated mRNA networks indicating a concerted action of the responsible factor(s). Sequencing of miRNA transcriptomes demonstrated an overexpression of 16 miRNAs and deconstruction of interactive miRNA-mRNA networks in schizophrenia NCCs. ChiPseq revealed that the nuclear (n) form of FGFR1, a pan-ontogenic regulator, is overexpressed in schizophrenia NCCs and overtargets dysregulated mRNA and miRNA genes. The nFGFR1 targeted 54% of all human gene promoters and 84.4% of schizophrenia dysregulated genes. The upregulated genes reside within major developmental pathways that control neurogenesis and neuron formation, whereas downregulated genes are involved in oligodendrogenesis. Our results indicate (i) an early (preneuronal) genomic etiology of schizophrenia, (ii) dysregulated genes and new coordinated gene networks are common to unrelated cases of schizophrenia, (iii) gene dysregulations are accompanied by increased nFGFR1-genome interactions, and (iv) modeling of increased nFGFR1 by an overexpression of a nFGFR1 lead to up or downregulation of selected genes as observed in schizophrenia NCCs. Together our results designate nFGFR1 signaling as a potential common dysregulated mechanism in investigated patients and potential therapeutic target in schizophrenia. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.
Technical/institutional prerequisite for nuclear forensics response framework

International Nuclear Information System (INIS)

Tamai, Hiroshi; Okubo, Ayako; Kimura, Yoshiki; Kokaji, Lisa; Shinohara, Nobuo; Tomikawa, Hirofumi

2016-01-01

Nuclear Forensics capability has been developed under the international collaborations. For its effective function, technical development in analysis of seized nuclear materials as well as the institutional development in comprehensive response framework are required under individual national responsibility. In order to keep the “chain of custody” in the proper operation of sample collection at the event scene, radiological analysis at the laboratory, storage of the samples, and further inspection and trial, close cooperation and information sharing between relevant organisations are essential. IAEA issues the Implementing Guide to provide the model action plan and assists individual national development. Some countries at the advancing stage of national response framework, promote the international cooperation for the technical improvement and awareness cultivation. Examples in such national developments will be introduced and prospective technical/institutional prerequisite for nuclear forensics response framework will be studied. (author)
Pan-Cancer Analyses of the Nuclear Receptor Superfamily

Directory of Open Access Journals (Sweden)

Mark D. Long

2015-12-01

Full Text Available Nuclear receptors (NR act as an integrated conduit for environmental and hormonal signals to govern genomic responses, which relate to cell fate decisions. We review how their integrated actions with each other, shared co-factors and other transcription factors are disrupted in cancer. Steroid hormone nuclear receptors are oncogenic drivers in breast and prostate cancer and blockade of signaling is a major therapeutic goal. By contrast to blockade of receptors, in other cancers enhanced receptor function is attractive, as illustrated initially with targeting of retinoic acid receptors in leukemia. In the post-genomic era large consortia, such as The Cancer Genome Atlas, have developed a remarkable volume of genomic data with which to examine multiple aspects of nuclear receptor status in a pan-cancer manner. Therefore to extend the review of NR function we have also undertaken bioinformatics analyses of NR expression in over 3000 tumors, spread across six different tumor types (bladder, breast, colon, head and neck, liver and prostate. Specifically, to ask how the NR expression was distorted (altered expression, mutation and CNV we have applied bootstrapping approaches to simulate data for comparison, and also compared these NR findings to 12 other transcription factor families. Nuclear receptors were uniquely and uniformly downregulated across all six tumor types, more than predicted by chance. These approaches also revealed that each tumor type had a specific NR expression profile but these were most similar between breast and prostate cancer. Some NRs were down-regulated in at least five tumor types (e.g., NR3C2/MR and NR5A2/LRH-1 whereas others were uniquely down-regulated in one tumor (e.g., NR1B3/RARG. The downregulation was not driven by copy number variation or mutation and epigenetic mechanisms maybe responsible for the altered nuclear receptor expression.
Extension of responsibilities of the State Office for Nuclear Safety

International Nuclear Information System (INIS)

Hrehor, M.

1995-01-01

The responsibilities of the State Office for Nuclear Safety have been extended by Act No. 85/1995 to cover protection against ionizing radiation. The following responsibilities of the State Office for Nuclear Safety are defined by the Act: a) state surveillance over nuclear safety of nuclear facilities, and over radioactive waste and spent fuel management; b) state surveillance over nuclear materials, their record-keeping and accountancy; c) state surveillance over the safeguarding of nuclear facilities and nuclear materials; d) state surveillance over selected materials, facilities and technologies used in the nuclear field, as well as dual-purpose materials and facilities; e) state surveillance over protection against ionizing radiation; f) coordination of the performance of the Radiation Monitoring Network over the Czech Republic and responsibility for international exchange of data on the radiological situation. The Act is reproduced in full, and the organizational structure of the Office is shown in a chart. (J.B.)
Identification and insertion polymorphisms of short interspersed nuclear elements (SINEs) in Brassica genomes

International Nuclear Information System (INIS)

Nouroz, F.; Naveed, M.

2018-01-01

The non-LTR retrotransposons (retroposons) are abundant in plant genomes including members of Brassicaceae. Of the retroposons, long interspersed nuclear elements (LINEs) are more copious followed by short interspersed nuclear elements (SINEs) in sequenced eukaryotic genomes. The SINEs are short elements and ranged from 100-500 bps flanked by variable sized target site duplications, 5' tRNA region with polymerase III promoter, internal tRNA unrelated region, 3' LINEs derived region and a poly adenosine tail. Different computational approaches were used for the identification and characterization of SINEs, while PCR was used to detect the SINEs insertion polymorphisms in various Brassica genotypes. Ten previously unidentified families of SINEs were identified and characterized from Brassica genomes. The structural features of these SINEs were studied in detail, which showed typical SINE features displaying small sizes, target site duplications, head regions, internal regions (body) of variable sizes and a poly (A) tail at the 3' terminus. The elements from various families ranged from 206-558 bp, where BoSINE2 family displayed smallest SINE element (206 bp), while larger members belonged to BoSINE9 family (524-558 bp). The distribution and abundance of SINEs in various Brassica species and genotypes (40) at a particular site/locus were investigated by SINEs based PCR markers. Various SINE insertion polymorphisms were detected from different genotypes, where higher PCR bands amplified the SINE insertions, while lower bands amplified the pre-insertion sites (flanking regions). The analysis of Brassica SINEs copy numbers from 10 identified families revealed that around 860 and 1712 copies of SINEs were calculated from B. rapa and B. oleracea Whole-genome shotgun contigs (WGS) respectively. Analysis of insertion sites of Brassica SINEs revealed that the members from all 10 SINE families had shown an insertion preference in AT rich regions. The present
Analysis of high-identity segmental duplications in the grapevine genome

Directory of Open Access Journals (Sweden)

Carelli Francesco N

2011-08-01

Full Text Available Abstract Background Segmental duplications (SDs are blocks of genomic sequence of 1-200 kb that map to different loci in a genome and share a sequence identity > 90%. SDs show at the sequence level the same characteristics as other regions of the human genome: they contain both high-copy repeats and gene sequences. SDs play an important role in genome plasticity by creating new genes and modeling genome structure. Although data is plentiful for mammals, not much was known about the representation of SDs in plant genomes. In this regard, we performed a genome-wide analysis of high-identity SDs on the sequenced grapevine (Vitis vinifera genome (PN40024. Results We demonstrate that recent SDs (> 94% identity and >= 10 kb in size are a relevant component of the grapevine genome (85 Mb, 17% of the genome sequence. We detected mitochondrial and plastid DNA and genes (10% of gene annotation in segmentally duplicated regions of the nuclear genome. In particular, the nine highest copy number genes have a copy in either or both organelle genomes. Further we showed that several duplicated genes take part in the biosynthesis of compounds involved in plant response to environmental stress. Conclusions These data show the great influence of SDs and organelle DNA transfers in modeling the Vitis vinifera nuclear DNA structure as well as the impact of SDs in contributing to the adaptive capacity of grapevine and the nutritional content of grape products through genome variation. This study represents a step forward in the full characterization of duplicated genes important for grapevine cultural needs and human health.
Nuclear responses in INTOR plasma stabilization elements

International Nuclear Information System (INIS)

Gohar, Y.; Gilligan, J.; Jung, J.; Mattas, R.F.; Miley, G.H.; Wiffen, F.W.; Yang, S.

1985-01-01

Nuclear responses in the plasma stabilization elements were studied in a parametric fashion as a part of the transient electromagnetics critical issue C of ETR/INTOR activity. The main responses are neutron fluence and radiation dose in the insulator material, induced resistivity and atomic displacement in the conductor material, nuclear heating and life analysis for the elements. Copper and aluminum conductors with either MgAl 2 O 4 or MgO insulating material were investigated. Radiation damage and life analysis for these elements were also discussed
Vitamin D and the brain: Genomic and non-genomic actions.

Science.gov (United States)

Cui, Xiaoying; Gooch, Helen; Petty, Alice; McGrath, John J; Eyles, Darryl

2017-09-15

1,25(OH) 2 D 3 (vitamin D) is well-recognized as a neurosteroid that modulates multiple brain functions. A growing body of evidence indicates that vitamin D plays a pivotal role in brain development, neurotransmission, neuroprotection and immunomodulation. However, the precise molecular mechanisms by which vitamin D exerts these functions in the brain are still unclear. Vitamin D signalling occurs via the vitamin D receptor (VDR), a zinc-finger protein in the nuclear receptor superfamily. Like other nuclear steroids, vitamin D has both genomic and non-genomic actions. The transcriptional activity of vitamin D occurs via the nuclear VDR. Its faster, non-genomic actions can occur when the VDR is distributed outside the nucleus. The VDR is present in the developing and adult brain where it mediates the effects of vitamin D on brain development and function. The purpose of this review is to summarise the in vitro and in vivo work that has been conducted to characterise the genomic and non-genomic actions of vitamin D in the brain. Additionally we link these processes to functional neurochemical and behavioural outcomes. Elucidation of the precise molecular mechanisms underpinning vitamin D signalling in the brain may prove useful in understanding the role this steroid plays in brain ontogeny and function. Copyright © 2017 Elsevier B.V. All rights reserved.
Nigeria status on capabilities for response to nuclear or radiological emergency

International Nuclear Information System (INIS)

Sambo, I.; Elegba, S.B.; Ogharandukun, M.

2007-01-01

The use of nuclear technology has been widely employed and will continue to expand in use in Nigeria particularly in the health, industrial, mining, water resources, agriculture, manufacturing, education and research sectors. Incidents and emergencies cannot therefore be ruled out. Effective national response capabilities are essential to minimize the impacts from nuclear and radiological emergencies, and to build public trust in the safety and security of nuclear technology. The often discussed Nigeria's Nuclear Power Plant (NPP) project cannot occur without enhanced national capabilities to respond to an incidence or emergency. Moreover, increased concern over the use of nuclear or radioactive materials malevolent acts increases the need to broaden response capabilities. This paper examines Nigeria's status on capabilities for response to a nuclear and radiological emergency vis-a-vis international requirements for effective response capabilities
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.
Soviet medical response to the Chernobyl nuclear accident

International Nuclear Information System (INIS)

Linnemann, R.E.

1987-01-01

The nuclear accident at Chernobyl was the worst in the history of nuclear power. It tested the organized medical response to mass radiation casualties. This article reviews the Soviet response as reported at the 1986 postaccident review meeting in Vienna and as determined from interviews. The Soviets used three levels of care: rescue and first aid at the plant site; emergency treatment at regional hospitals; and definitive evaluation and treatment in Moscow. Diagnosis, triage, patient disposition, attendant exposure, and preventive actions are detailed. The United States would be well advised to organize its resources definitively to cope with future nonmilitary nuclear accidents
Nuclear Localization of Mitochondrial TCA Cycle Enzymes as a Critical Step in Mammalian Zygotic Genome Activation.

Science.gov (United States)

Nagaraj, Raghavendra; Sharpley, Mark S; Chi, Fangtao; Braas, Daniel; Zhou, Yonggang; Kim, Rachel; Clark, Amander T; Banerjee, Utpal

2017-01-12

Transcriptional control requires epigenetic changes directed by mitochondrial tricarboxylic acid (TCA) cycle metabolites. In the mouse embryo, global epigenetic changes occur during zygotic genome activation (ZGA) at the 2-cell stage. Pyruvate is essential for development beyond this stage, which is at odds with the low activity of mitochondria in this period. We now show that a number of enzymatically active mitochondrial enzymes associated with the TCA cycle are essential for epigenetic remodeling and are transiently and partially localized to the nucleus. Pyruvate is essential for this nuclear localization, and a failure of TCA cycle enzymes to enter the nucleus correlates with loss of specific histone modifications and a block in ZGA. At later stages, however, these enzymes are exclusively mitochondrial. In humans, the enzyme pyruvate dehydrogenase is transiently nuclear at the 4/8-cell stage coincident with timing of human embryonic genome activation, suggesting a conserved metabolic control mechanism underlying early pre-implantation development. Copyright © 2017 Elsevier Inc. All rights reserved.
10 CFR 1.46 - Office of Nuclear Security and Incident Response.

Science.gov (United States)

2010-01-01

... 10 Energy 1 2010-01-01 2010-01-01 false Office of Nuclear Security and Incident Response. 1.46... Headquarters Program Offices § 1.46 Office of Nuclear Security and Incident Response. The Office of Nuclear... evaluation and assessment of technical issues involving security at nuclear facilities, and is the agency...

The genomic analysis of lactic acidosis and acidosis response in human cancers.

Directory of Open Access Journals (Sweden)

Julia Ling-Yu Chen

2008-12-01

Full Text Available The tumor microenvironment has a significant impact on tumor development. Two important determinants in this environment are hypoxia and lactic acidosis. Although lactic acidosis has long been recognized as an important factor in cancer, relatively little is known about how cells respond to lactic acidosis and how that response relates to cancer phenotypes. We develop genome-scale gene expression studies to dissect transcriptional responses of primary human mammary epithelial cells to lactic acidosis and hypoxia in vitro and to explore how they are linked to clinical tumor phenotypes in vivo. The resulting experimental signatures of responses to lactic acidosis and hypoxia are evaluated in a heterogeneous set of breast cancer datasets. A strong lactic acidosis response signature identifies a subgroup of low-risk breast cancer patients having distinct metabolic profiles suggestive of a preference for aerobic respiration. The association of lactic acidosis response with good survival outcomes may relate to the role of lactic acidosis in directing energy generation toward aerobic respiration and utilization of other energy sources via inhibition of glycolysis. This "inhibition of glycolysis" phenotype in tumors is likely caused by the repression of glycolysis gene expression and Akt inhibition. Our study presents a genomic evaluation of the prognostic information of a lactic acidosis response independent of the hypoxic response. Our results identify causal roles of lactic acidosis in metabolic reprogramming, and the direct functional consequence of lactic acidosis pathway activity on cellular responses and tumor development. The study also demonstrates the utility of genomic analysis that maps expression-based findings from in vitro experiments to human samples to assess links to in vivo clinical phenotypes.
Cell Cycle Regulates Nuclear Stability of AID and Determines the Cellular Response to AID.

Directory of Open Access Journals (Sweden)

Quy Le

2015-09-01

Full Text Available AID (Activation Induced Deaminase deaminates cytosines in DNA to initiate immunoglobulin gene diversification and to reprogram CpG methylation in early development. AID is potentially highly mutagenic, and it causes genomic instability evident as translocations in B cell malignancies. Here we show that AID is cell cycle regulated. By high content screening microscopy, we demonstrate that AID undergoes nuclear degradation more slowly in G1 phase than in S or G2-M phase, and that mutations that affect regulatory phosphorylation or catalytic activity can alter AID stability and abundance. We directly test the role of cell cycle regulation by fusing AID to tags that destabilize nuclear protein outside of G1 or S-G2/M phases. We show that enforced nuclear localization of AID in G1 phase accelerates somatic hypermutation and class switch recombination, and is well-tolerated; while nuclear AID compromises viability in S-G2/M phase cells. We identify AID derivatives that accelerate somatic hypermutation with minimal impact on viability, which will be useful tools for engineering genes and proteins by iterative mutagenesis and selection. Our results further suggest that use of cell cycle tags to regulate nuclear stability may be generally applicable to studying DNA repair and to engineering the genome.
Nuclear targeting by fragmentation of the Potato spindle tuber viroid genome

International Nuclear Information System (INIS)

Abraitiene, Asta; Zhao Yan; Hammond, Rosemarie

2008-01-01

Transient expression of engineered reporter RNAs encoding an intron-containing green fluorescent protein (GFP) from a Potato virus X-based expression vector previously demonstrated the nuclear targeting capability of the 359 nucleotide Potato spindle tuber viroid (PSTVd) RNA genome. To further delimit the putative nuclear-targeting signal, PSTVd subgenomic fragments were embedded within the intron, and recombinant reporter RNAs were inoculated onto Nicotiana benthamiana plants. Appearance of green fluorescence in leaf tissue inoculated with PSTVd-fragment-containing constructs indicated shuttling of the RNA into the nucleus by fragments as short as 80 nucleotides in length. Plant-to-plant variation in the timing of intron removal and subsequent GFP fluorescence was observed; however, earliest and most abundant GFP expression was obtained with constructs containing the conserved hairpin I palindrome structure and embedded upper central conserved region. Our results suggest that this conserved sequence and/or the stem-loop structure it forms is sufficient for import of PSTVd into the nucleus
Nuclear genomic sequences reveal that polar bears are an old and distinct bear lineage.

Science.gov (United States)

Hailer, Frank; Kutschera, Verena E; Hallström, Björn M; Klassert, Denise; Fain, Steven R; Leonard, Jennifer A; Arnason, Ulfur; Janke, Axel

2012-04-20

Recent studies have shown that the polar bear matriline (mitochondrial DNA) evolved from a brown bear lineage since the late Pleistocene, potentially indicating rapid speciation and adaption to arctic conditions. Here, we present a high-resolution data set from multiple independent loci across the nuclear genomes of a broad sample of polar, brown, and black bears. Bayesian coalescent analyses place polar bears outside the brown bear clade and date the divergence much earlier, in the middle Pleistocene, about 600 (338 to 934) thousand years ago. This provides more time for polar bear evolution and confirms previous suggestions that polar bears carry introgressed brown bear mitochondrial DNA due to past hybridization. Our results highlight that multilocus genomic analyses are crucial for an accurate understanding of evolutionary history.
Russian Nuclear Power Response to the Fukushima Accident

International Nuclear Information System (INIS)

Asmolov, Vladimir G.

2011-01-01

Conclusions: 1. Nuclear safety is not based only on regulators. The prime responsibility for nuclear safety rests with operating organizations which have the necessary experience and knowledge. 2. Improvement in safety can be reached through better sharing of operation experience and improvements in technology. The IAEA is to increase interactions with utilities and nuclear industry. 3. The IAEA is to declare clearly the recognition of the role of operating organizations and nuclear industry in safe, efficacious and sustainable nuclear power development and to strengthen cooperation with them
Genomic instability: potential contributions to tumour and normal tissue response, and second tumours, after radiotherapy

International Nuclear Information System (INIS)

Hendry, Jolyon H.

2001-01-01

Purpose: Induced genomic instability generally refers to a type of damage which is transmissible down cell generations, and which results in a persistently enhanced frequency of de novo mutations, chromosomal abnormalities or lethality in a significant fraction of the descendant cell population. The potential contribution of induced genomic instability to tumour and normal tissue response, and second tumours, after radiotherapy, is explored. Results: The phenomenon of spontaneous genomic instability is well known in some rare genetic diseases (e.g. Gorlin's syndrome), and there is evidence in such cases that it can lead to a greater propensity for carcinogenesis (with shortened latency) which is enhanced after irradiation. It is unclear what role induced genomic instability plays in the response of normal individuals, but persistent chromosomal instability has been detected in vivo in lymphocytes and keratinocytes from irradiated normal individuals. Such induced genomic instability might play some role in tumour response in a subset of tumours with specific defects in damage response genes, but again its contribution to radiocurability in the majority of cancer patients is unclear. In normal tissues, genomic instability induced in wild-type cells leading to delayed cell death might contribute to more severe or prolonged early reactions as a consequence of increased cell loss, a longer time required for recovery, and greater residual injury. In tumours, induced genomic instability reflected in delayed reductions in clonogenic capacity might contribute to the radiosensitivity of primary tumours, and also to a lower incidence, longer latency and slower growth rate of recurrences and metastases. Conclusions: The evidence which is reviewed shows that there is little information at present to support these propositions, but what exists is consistent with their expectations. Also, it is not yet clear to what extent mutations associated with genomic instability
Responsibilities of the nuclear-weapon states

International Nuclear Information System (INIS)

Wang Jun

1994-01-01

The responsibilities of Nuclear Weapon States are presented by a straightforward analysis together with the ways in which they could fulfill them. The complete undertaking of all the commitments by the Nuclear Weapon States may take a long time. However they do not have a single excuse to neglect such a historic opportunity to do their best to provide a genuinely secure world environment for the international community, of which they too are members
Key Response Planning Factors for the Aftermath of Nuclear Terrorism

Energy Technology Data Exchange (ETDEWEB)

Buddemeier, B R; Dillon, M B

2009-01-21

Despite hundreds of above-ground nuclear tests and data gathered from Hiroshima and Nagasaki, the effects of a ground-level, low-yield nuclear detonation in a modern urban environment are still the subject of considerable scientific debate. Extensive review of nuclear weapon effects studies and discussions with nuclear weapon effects experts from various federal agencies, national laboratories, and technical organizations have identified key issues and bounded some of the unknowns required to support response planning for a low-yield, ground-level nuclear detonation in a modern U.S. city. This study, which is focused primarily upon the hazards posed by radioactive fallout, used detailed fallout predictions from the advanced suite of three-dimensional (3-D) meteorology and plume/fallout models developed at Lawrence Livermore National Laboratory (LLNL), including extensive global Key Response Planning Factors for the Aftermath of Nuclear Terrorism geographical and real-time meteorological databases to support model calculations. This 3-D modeling system provides detailed simulations that account for complex meteorology and terrain effects. The results of initial modeling and analysis were presented to federal, state, and local working groups to obtain critical, broad-based review and feedback on strategy and messaging. This effort involved a diverse set of communities, including New York City, National Capitol Regions, Charlotte, Houston, Portland, and Los Angeles. The largest potential for reducing casualties during the post-detonation response phase comes from reducing exposure to fallout radiation. This can be accomplished through early, adequate sheltering followed by informed, delayed evacuation.B The response challenges to a nuclear detonation must be solved through multiple approaches of public education, planning, and rapid response actions. Because the successful response will require extensive coordination of a large number of organizations, supplemented by
Legal responsibility in case of a nuclear accident

International Nuclear Information System (INIS)

Nabhane, M. F.

1988-01-01

Numerous laws have been elaborated in order to determine the legal responsibility in case of a nuclear accident. These laws were made necessary because of intervention of the factor 'error' in the nuclear accident. The legal definition of 'error' assumes that it results from non-respect or negligence of established norms on the part of the persons who manipulate the instruments of radioactive production. Nuclear research should not be undertaken in a country without the formal engagement of the central authorities to take the necessary dispositions to ensure the security and safety of the populations and their possessions. The world community should not admit a scientific activity in the nuclear field in the absence of guarantees for the safety and the security of man. The state that permits the production of nuclear energy is legally responsible for any failure that might result in radioactive spills. Considering the possibility of error and the dangers attached to the manipulation of radioactive material, the legislators have elaborated a series of laws, which take into consideration two principles: a)The inalienable right of man to life as conceived in the monotheistic religions and proclaimed by positive law; and b)The responsibility of the state for the safety and security of its citizens. Of course, error is human; but if man may make an error of judgement in ordinary normal life, he does not have the right to make the least miscalculation when this might lead to a nuclear disaster. (author)
Genome-Wide Association Study for Response to Eimeria maxima Challenge in Broilers

DEFF Research Database (Denmark)

Hamzic, Edin; Bed'hom, Bertrand; Hérault, Frédéric

Use of genetic tools for improvement of host’s response is considered as a promising complementary approach for coccidiosis control. Therefore, we performed genome wide association study (GWAS) for response to Eimeria maxima challenge in broilers. The challenge was done on 2024 Cobb500 broilers. We...
Rosatom's Crisis Response Centre within the national nuclear safety system

International Nuclear Information System (INIS)

Smirnov, S.N.; Komarovskij, A.V.; Moskalev, V.A.

2011-01-01

The Rosatom Corporation includes a number of subsidiaries associated with nuclear energy use as well as with the military, scientific, technological, nuclear and radiation safety management aspects. The Rosatom Corporation has a well-established and efficient industry-wide system of emergency prevention and response, whose purpose is to ensure safe functioning of the nuclear industry, protection of personnel, the public and nature from potential dangers; it is also a functional subsystem of the unified national system of emergency prevention and response. Overall management of the system is performed by Director General of the Rosatom Corporation, overall methodological management - by the Department of Licensing, Nuclear and Radiation Safety; everyday management of the emergency prevention and response system, round-the-clock monitoring and informational support - by the Rosatom Crisis and Response Centre (CRC). CRC acts as the national focal point for warning and communication in Russia, which provides continuous round-the-clock preparedness to cooperate with the IAEA's Incident and Emergency Centre using the formats of the ENATOM international emergency response system, similar national crisis response centres abroad [ru
The nuclear response function

International Nuclear Information System (INIS)

Bertsch, G.F.

1983-01-01

These lectures present the theory of the nuclear response in the Random Phase Approximation (RPA). In the first lecture, various relations are derived between densities and currents which give rise to the well-known sum rules. Then RPA is derived via the time-dependent Hartree theory. The various formulations of RPA are shown: the configuration space representation, the coordinate space representation, the Landau theory of infinite systems and the RPA for separable interactions constrained by consistency. The remarkable success of RPA in describing the collective density oscillations of closed shell nuclei is illustrated with a few examples. In the final lecture, the σtau response is discussed with the application of simple theoretical considerations to the empirical data. Finally, we point out several problems which remain in the response theory. (author)
DNA double-strand break response in stem cells: mechanisms to maintain genomic integrity.

Science.gov (United States)

Nagaria, Pratik; Robert, Carine; Rassool, Feyruz V

2013-02-01

Embryonic stem cells (ESCs) represent the point of origin of all cells in a given organism and must protect their genomes from both endogenous and exogenous genotoxic stress. DNA double-strand breaks (DSBs) are one of the most lethal forms of damage, and failure to adequately repair DSBs would not only compromise the ability of SCs to self-renew and differentiate, but will also lead to genomic instability and disease. Herein, we describe the mechanisms by which ESCs respond to DSB-inducing agents such as reactive oxygen species (ROS) and ionizing radiation, compared to somatic cells. We will also discuss whether the DSB response is fully reprogrammed in induced pluripotent stem cells (iPSCs) and the role of the DNA damage response (DDR) in the reprogramming of these cells. ESCs have distinct mechanisms to protect themselves against DSBs and oxidative stress compared to somatic cells. The response to damage and stress is crucial for the maintenance of self-renewal and differentiation capacity in SCs. iPSCs appear to reprogram some of the responses to genotoxic stress. However, it remains to be determined if iPSCs also retain some DDR characteristics of the somatic cells of origin. The mechanisms regulating the genomic integrity in ESCs and iPSCs are critical for its safe use in regenerative medicine and may shed light on the pathways and factors that maintain genomic stability, preventing diseases such as cancer. This article is part of a Special Issue entitled Biochemistry of Stem Cells. Copyright © 2012 Elsevier B.V. All rights reserved.
A nuclear engineer's ethical responsibility to society

International Nuclear Information System (INIS)

Kemeny, L.G.

1989-01-01

Chernobyl notwithstanding, this paper seeks to illustrate why, on numerous fronts, nuclear technology provides the safest, cleanest and most effective method of base-load power generation. In particular it seeks to demonstrate that, despite the strident rhetoric and media exposure given to the anti-nuclear lobby, the technology is fundamental to the quality of life and the equitable sharing of energy by the year 2000. Therefore, the safety and technological superiority of the nuclear fuel cycle together with its high technology peripheral benefits both societal and fiscal are viewed as an ever increasing challenge and motivation which constitutes a major part of the nuclear engineer's ethical responsibility to society
Improvements in the nuclear accident response system in Brazil

International Nuclear Information System (INIS)

Estrada, J.J.S.; Azevedo, E.M.; Knofel, T.M.J.; Recio, J.C.A.; Alves, R.N.

1998-01-01

The National Commission on Nuclear Energy has been making outstanding effort to improve its nuclear and radiological accident response systems since the tragic accident in Goiania. Most of this effort is related to nuclear area although the radiological accident has been also considered. This paper describes the improvements in the CNEN response system structure, discusses several topics involving those related to emergency planning and preparedness, and points out some deficiencies that need to be corrected also. The situation during the Goiania accident was more disadvantageous than nowadays, so it is believed that none of the actual deficiencies are sufficient to guess that the population and the environment will not be protected in case of a nuclear or radiological accident
The social responsibility of nuclear energy

International Nuclear Information System (INIS)

Mizuo, Junichi

2008-01-01

Interest in the concept of Social Responsibility (SR) has increased recently. Continuing advances in the pace of innovative science and information technology development, growing competition in the world's markets, economic globalization and harsh criticism from communities have all drawn attention to the behavior of different organizations. As a way of drawing global attention to the fulfillment of SR, the goal of coexistence assumes an increasingly significant role from the standpoint of sustainable development of organizations and society. This implies that SR involves two responsibilities: the primary responsibility being an obligation to society, and the secondary responsibility being a positive contribution to society. Seen from the same perspective, Nuclear Energy (NE) is expected to make a positive contribution to the advancement of society and to encourage a safety culture that prevents serious accidents while also encouraging the sound development of organizations and society. ('Society' includes the environment and the economy, with the same sense as a 'triple bottom line'.) Considering the Social Responsibility of Nuclear Energy (NSR) from these points-of-view, NE should coexist with multiple stakeholders. The purpose of this paper is to clarify the relationship between NE and society, to define a framework for problem-solving, and finally to suggest changes in NSR as a whole. (author)
Public's Cognitive and Emotional Responses to Nuclear Messages: Implications for Effective Nuclear Communication Programs

International Nuclear Information System (INIS)

Kim, Hyo Jung

2017-01-01

The public debate over the use of nuclear energy is not limited to the area of technology, and has become subject to the public's subjective perceptions and emotions regarding the issue. This study empirically demonstrated the advantage of loss framing in improving public's favorable responses toward nuclear energy messages. Such framing effect was found to be moderated by individuals' daily use of online news. The findings of this study suggest that public's cognitive and emotional responses toward nuclear messages should be carefully considered when planning effective nuclear communication program.
A prototype nuclear emergency response decision making expert system

International Nuclear Information System (INIS)

Chang, C.; Shih, C.; Hong, M.; Yu, W.; Su, M.; Wang, S.

1990-01-01

A prototype of emergency response expert system developed for nuclear power plants, has been fulfilled by Institute of Nuclear Energy Research. Key elements that have been implemented for emergency response include radioactive material dispersion assessment, dynamic transportation evacuation assessment, and meteorological parametric forecasting. A network system consists of five 80386 Personal Computers (PCs) has been installed to perform the system functions above. A further project is still continuing to achieve a more complicated and fanciful computer aid integral emergency response expert system
Nuclear vorticity and the low-energy nuclear response. Towards the neutron drip line

International Nuclear Information System (INIS)

Papakonstantinou, P.; Athens Univ.; Wambach, J.; Ponomarev, V.Y.; Mavrommatis, E.

2004-01-01

The transition density and current provide valuable insight into the nature of nuclear vibrations. Nuclear vorticity is a quantity related to the transverse transition current. In this work, we study the evolution of the strength distribution, related to density fluctuations, and the vorticity strength distribution, as the neutron drip line is approached. Our results on the isoscalar, natural-parity multipole response of Ni isotopes, obtained by using a self-consistent Skyrme-Hartree-Fock+continuum RPA model, indicate that, close to the drip line, the low-energy response is dominated by L > 1 vortical transitions. (orig.)
Latency Entry of Herpes Simplex Virus 1 Is Determined by the Interaction of Its Genome with the Nuclear Environment

Science.gov (United States)

Cohen, Camille; Streichenberger, Nathalie; Texier, Pascale; Takissian, Julie; Rousseau, Antoine; Poccardi, Nolwenn; Welsch, Jérémy; Corpet, Armelle; Schaeffer, Laurent; Labetoulle, Marc; Lomonte, Patrick

2016-01-01

Herpes simplex virus 1 (HSV-1) establishes latency in trigeminal ganglia (TG) sensory neurons of infected individuals. The commitment of infected neurons toward the viral lytic or latent transcriptional program is likely to depend on both viral and cellular factors, and to differ among individual neurons. In this study, we used a mouse model of HSV-1 infection to investigate the relationship between viral genomes and the nuclear environment in terms of the establishment of latency. During acute infection, viral genomes show two major patterns: replication compartments or multiple spots distributed in the nucleoplasm (namely “multiple-acute”). Viral genomes in the “multiple-acute” pattern are systematically associated with the promyelocytic leukemia (PML) protein in structures designated viral DNA-containing PML nuclear bodies (vDCP-NBs). To investigate the viral and cellular features that favor the acquisition of the latency-associated viral genome patterns, we infected mouse primary TG neurons from wild type (wt) mice or knock-out mice for type 1 interferon (IFN) receptor with wt or a mutant HSV-1, which is unable to replicate due to the synthesis of a non-functional ICP4, the major virus transactivator. We found that the inability of the virus to initiate the lytic program combined to its inability to synthesize a functional ICP0, are the two viral features leading to the formation of vDCP-NBs. The formation of the “multiple-latency” pattern is favored by the type 1 IFN signaling pathway in the context of neurons infected by a virus able to replicate through the expression of a functional ICP4 but unable to express functional VP16 and ICP0. Analyses of TGs harvested from HSV-1 latently infected humans showed that viral genomes and PML occupy similar nuclear areas in infected neurons, eventually forming vDCP-NB-like structures. Overall our study designates PML protein and PML-NBs to be major cellular components involved in the control of HSV-1 latency

Legal responsibility for damage caused by nuclear accidents

International Nuclear Information System (INIS)

Brink, J.J. van den.

1986-04-01

In this essay a treatment is given of the legal third-party risks of licencees of nuclear power plants. It is regarded to what extent the actual responsibility arrangements provide an adequate protection to the citizen against potential risks of a nuclear power plant. (Auth.)
[Compartmentalization of the cell nucleus and spatial organization of the genome].

Science.gov (United States)

Gavrilov, A A; Razin, S V

2015-01-01

The eukaryotic cell nucleus is one of the most complex cell organelles. Despite the absence of membranes, the nuclear space is divided into numerous compartments where different processes in- volved in the genome activity take place. The most important nuclear compartments include nucleoli, nuclear speckles, PML bodies, Cajal bodies, histone locus bodies, Polycomb bodies, insulator bodies, transcription and replication factories. The structural basis for the nuclear compartmentalization is provided by genomic DNA that occupies most of the nuclear volume. Nuclear compartments, in turn, guide the chromosome folding by providing a platform for the spatial interaction of individual genomic loci. In this review, we discuss fundamental principles of higher order genome organization with a focus on chromosome territories and chromosome domains, as well as consider the structure and function of the key nuclear compartments. We show that the func- tional compartmentalization of the cell nucleus and genome spatial organization are tightly interconnected, and that this form of organization is highly dynamic and is based on stochastic processes.
Bystander effects, adaptive response and genomic instability induced by prenatal irradiation

Energy Technology Data Exchange (ETDEWEB)

Streffer, Christian [Institute for Science and Ethics, University Duisburg-Essen, Auf dem Sutan 12, D-45239 Essen (Germany)]. E-mail: streffer.essen@t-online.de

2004-12-02

The developing human embryo and fetus undergo very radiosensitive stages during the prenatal development. It is likely that the induction of low dose related effects such as bystander effects, the adaptive response, and genomic instability would have profound effects on embryonic and fetal development. In this paper, I review what has been reported on the induction of these three phenomena in exposed embryos and fetuses. All three phenomena have been shown to occur in murine embryonic or fetal cells and structures, although the induction of an adaptive response (and also likely the induction of bystander effects) are limited in terms of when during development they can be induced and the dose or dose-rate used to treat animals in utero. In contrast, genomic instability can be induced throughout development, and the effects of radiation exposure on genome instability can be observed for long times after irradiation including through pre- and postnatal development and into the next generation of mice. There are clearly strain-specific differences in the induction of these phenomena and all three can lead to long-term detrimental effects. This is true for the adaptive response as well. While induction of an adaptive response can make fetuses more resistant to some gross developmental defects induced by a subsequent high dose challenge with ionizing radiation, the long-term effects of this low dose exposure are detrimental. The negative effects of all three phenomena reflect the complexity of fetal development, a process where even small changes in the timing of gene expression or suppression can have dramatic effects on the pattern of biological events and the subsequent development of the mammalian organism.
The possibility of nuclear war: Appraisal, coping and emotional response

International Nuclear Information System (INIS)

Kanofsky, S.

1989-01-01

This study used Lazarus and Folkman's (1984) model of appraisal and coping to explore people's emotional response to the possibility of nuclear war. Sixty-seven women and 49 men participated in a questionnaire study. The sample represented a cross-section of Americans by age and ethnic group but had more education and higher occupational status scores than is typical for the greater population. Sampling limitations and the political climate at the time of questionnaire administration suggested that the present findings be interpreted cautiously. Nevertheless, results suggested the importance of appraisal, defined in this study as the estimated probability of nuclear war and beliefs that citizen efforts to reduce the likelihood of nuclear war can be effective, and coping as factors in people's nuclear threat related emotional response. Six of the study's 11 hypotheses received at least partial confirmation. One or more measures of nuclear threat-related emotional distress were positively correlated with probability estimates of nuclear war, individual and collective response efficacy beliefs, and seeking social support in regard to the nuclear threat. Negative correlations were found between measures of threat-related distress and both trust in political leaders and distancing. Statistically significant relationships contrary to the other five hypotheses were also obtained. Measures of threat-related distress were positively, rather than negatively, correlated with escape avoidance and positive reappraisal coping efforts. Appraisal, coping, and emotion variables, acting together, predicted the extent of political activism regarding the nuclear arms race. It is useful to consider attitudes toward the nuclear arms race, distinguishing between intensity and frequency of emotional distress, and between measures of trait, state, and concept-specific emotionality in understanding emotional responses
International responsibility of using nuclear energy for peaceful purposes

International Nuclear Information System (INIS)

Ouenat, N.

2008-01-01

Although the stability of the idea of international responsibility in public international law, the international jurisprudence has not settled on a definition. The concept of international responsibility is no longer limited to the legal effects or consequences under international law to violate its provisions. The states recognized that the customary principles governing the international responsibility in public international law does not take into account the specificities of nuclear dangers, this sought to conclude a number of international conventions include a special system of nuclear liability not based on the wrongful act, but on the principle of keeping things, and it requires the existence of an international regime for nuclear liability in order to establish measures and procedures to achieve the implementation of the provisions for compensation unhindered by national legal systems. There is no doubt that the use of nuclear energy in time of peace falls within the scope of internationally prohibited acts. Atomic activities undertaken by the State within its borders for peaceful purposes are considered legitimate activities as long as they have taken necessary measures to avoid damage to neighboring countries. States has tended to conclude international agreements under which disputes that may result from the use of nuclear energy can be solved. The existing international legal framework on Civil Liability for Nuclear Damage consists of three major interrelated agreements: Paris Convention on civil liability in the field of nuclear energy, Vienna Convention on Civil Liability for civil damages and the Brussels Convention on Civil Liability in the Field of Maritime Carriage of Nuclear Materials.
Archaeal Genome Guardians Give Insights into Eukaryotic DNA Replication and Damage Response Proteins

Directory of Open Access Journals (Sweden)

David S. Shin

2014-01-01

Full Text Available As the third domain of life, archaea, like the eukarya and bacteria, must have robust DNA replication and repair complexes to ensure genome fidelity. Archaea moreover display a breadth of unique habitats and characteristics, and structural biologists increasingly appreciate these features. As archaea include extremophiles that can withstand diverse environmental stresses, they provide fundamental systems for understanding enzymes and pathways critical to genome integrity and stress responses. Such archaeal extremophiles provide critical data on the periodic table for life as well as on the biochemical, geochemical, and physical limitations to adaptive strategies allowing organisms to thrive under environmental stress relevant to determining the boundaries for life as we know it. Specifically, archaeal enzyme structures have informed the architecture and mechanisms of key DNA repair proteins and complexes. With added abilities to temperature-trap flexible complexes and reveal core domains of transient and dynamic complexes, these structures provide insights into mechanisms of maintaining genome integrity despite extreme environmental stress. The DNA damage response protein structures noted in this review therefore inform the basis for genome integrity in the face of environmental stress, with implications for all domains of life as well as for biomanufacturing, astrobiology, and medicine.
Nuclear response functions at large energy and momentum transfer

International Nuclear Information System (INIS)

Bertozzi, W.; Moniz, E.J.; Lourie, R.W.

1991-01-01

Quasifree nucleon processes are expected to dominate the nuclear electromagnetic response function for large energy and momentum transfers, i.e., for energy transfers large compared with nuclear single particle energies and momentum transfers large compared with typical nuclear momenta. Despite the evident success of the quasifree picture in providing the basic frame work for discussing and understanding the large energy, large momentum nuclear response, the limits of this picture have also become quite clear. In this article a selected set of inclusive and coincidence data are presented in order to define the limits of the quasifree picture more quantitatively. Specific dynamical mechanisms thought to be important in going beyond the quasifree picture are discussed as well. 75 refs, 37 figs
The complete genome sequence of Trueperella pyogenes UFV1 reveals a processing system involved in the quorumsensing signal response

DEFF Research Database (Denmark)

Duarte, Vinicius da Silva; Treu, Laura; Campanaro, Stefano

2017-01-01

We present here the complete genome sequence of Trueperella pyogenes UFV1. The 2.3-Mbp genome contains an extremely interesting AI-2 transporter and processing system related to the quorum-sensing signal response. This specific feature is described in this species for the first time and might be ...... be responsible for a new pathogenic behavior.......We present here the complete genome sequence of Trueperella pyogenes UFV1. The 2.3-Mbp genome contains an extremely interesting AI-2 transporter and processing system related to the quorum-sensing signal response. This specific feature is described in this species for the first time and might...
Genomic prediction in a nuclear population of layers using single-step models.

Science.gov (United States)

Yan, Yiyuan; Wu, Guiqin; Liu, Aiqiao; Sun, Congjiao; Han, Wenpeng; Li, Guangqi; Yang, Ning

2018-02-01

Single-step genomic prediction method has been proposed to improve the accuracy of genomic prediction by incorporating information of both genotyped and ungenotyped animals. The objective of this study is to compare the prediction performance of single-step model with a 2-step models and the pedigree-based models in a nuclear population of layers. A total of 1,344 chickens across 4 generations were genotyped by a 600 K SNP chip. Four traits were analyzed, i.e., body weight at 28 wk (BW28), egg weight at 28 wk (EW28), laying rate at 38 wk (LR38), and Haugh unit at 36 wk (HU36). In predicting offsprings, individuals from generation 1 to 3 were used as training data and females from generation 4 were used as validation set. The accuracies of predicted breeding values by pedigree BLUP (PBLUP), genomic BLUP (GBLUP), SSGBLUP and single-step blending (SSBlending) were compared for both genotyped and ungenotyped individuals. For genotyped females, GBLUP performed no better than PBLUP because of the small size of training data, while the 2 single-step models predicted more accurately than the PBLUP model. The average predictive ability of SSGBLUP and SSBlending were 16.0% and 10.8% higher than the PBLUP model across traits, respectively. Furthermore, the predictive abilities for ungenotyped individuals were also enhanced. The average improvements of prediction abilities were 5.9% and 1.5% for SSGBLUP and SSBlending model, respectively. It was concluded that single-step models, especially the SSGBLUP model, can yield more accurate prediction of genetic merits and are preferable for practical implementation of genomic selection in layers. © 2017 Poultry Science Association Inc.
Genetic divergence in nuclear genomes between populations of Fagus crenata along the Japan Sea and Pacific sides of Japan.

Science.gov (United States)

Hiraoka, Koichi; Tomaru, Nobuhiro

2009-05-01

Genetic diversity and structure in Fagus crenata were studied by analyzing 14 nuclear microsatellite loci in 23 populations distributed throughout the species' range. Although population differentiation was very low (F (ST) = 0.027; R (ST) = 0.041), both neighbor-joining tree and Bayesian clustering analyses provided clear evidence of genetic divergence between populations along the Japan Sea (Japan Sea lineage) and Pacific (Pacific lineage) sides of Japan, indicating that physical barriers to migration and gene flow, notably the mountain ranges separating the populations along the Japan Sea and Pacific sides, have promoted genetic divergence between these populations. The two lineages of the nuclear genome are generally consistent with those of the chloroplast genome detected in a previous study, with several discrepancies between the two genomes. Within-population genetic diversity was generally very high (average H (E) = 0.839), but decreased in a clinal fashion from southwest to northeast, largely among populations of the Japan Sea lineage. This geographical gradient may have resulted from the late-glacial and postglacial recolonization to the northeast, which led to a loss of within-population genetic diversity due to cumulative founder effects.
Nuclear fear and children: the impact of parental nuclear activism, responsivity, and fear

Energy Technology Data Exchange (ETDEWEB)

LaGuardia, M.R.

1986-01-01

This study examines the extent to which parental nuclear fear, parental activism, and parental responsivity is associated with children's (age 10) nuclear fear. Other associated variables investigated include: nuclear denial, general anxiety and fear, and the personal characteristics of sex, socio-economic status, and academic aptitude. Findings indicate that children attend to nuclear issues when their parents attend to a significant degree. Children's hopelessness about the arms race is increased as parents' worry about nuclear war increases. Children's fear about not surviving a nuclear war increases as parents' worry about survivability decreases. Children who have more general fears also indicated that they have a high level of hopelessness, pervasive worry, and much concern about being able to survive a nuclear war. Children with a high degree of general anxiety did not indicate high degrees of nuclear fears. Children with high academic aptitude were more knowledgeable about nuclear issues and expressed more fears about the nuclear threat. Boys demonstrated more knowledge about nuclear issues than girls, and girls expressed much more frequent fear and worry about the nuclear threat than boys. Parents of lower socio-economic statues (SES) expressed more denial about the nuclear threat and were more pro-military than the higher SES parents.
Cross-family translational genomics of abiotic stress-responsive genes between Arabidopsis and Medicago truncatula.

Directory of Open Access Journals (Sweden)

Daejin Hyung

Full Text Available Cross-species translation of genomic information may play a pivotal role in applying biological knowledge gained from relatively simple model system to other less studied, but related, genomes. The information of abiotic stress (ABS-responsive genes in Arabidopsis was identified and translated into the legume model system, Medicago truncatula. Various data resources, such as TAIR/AtGI DB, expression profiles and literatures, were used to build a genome-wide list of ABS genes. tBlastX/BlastP similarity search tools and manual inspection of alignments were used to identify orthologous genes between the two genomes. A total of 1,377 genes were finally collected and classified into 18 functional criteria of gene ontology (GO. The data analysis according to the expression cues showed that there was substantial level of interaction among three major types (i.e., drought, salinity and cold stress of abiotic stresses. In an attempt to translate the ABS genes between these two species, genomic locations for each gene were mapped using an in-house-developed comparative analysis platform. The comparative analysis revealed that fragmental colinearity, represented by only 37 synteny blocks, existed between Arabidopsis and M. truncatula. Based on the combination of E-value and alignment remarks, estimated translation rate was 60.2% for this cross-family translation. As a prelude of the functional comparative genomic approaches, in-silico gene network/interactome analyses were conducted to predict key components in the ABS responses, and one of the sub-networks was integrated with corresponding comparative map. The results demonstrated that core members of the sub-network were well aligned with previously reported ABS regulatory networks. Taken together, the results indicate that network-based integrative approaches of comparative and functional genomics are important to interpret and translate genomic information for complex traits such as abiotic stresses.
Nuclear emergency planning and response in the Netherlands after Chernobyl

International Nuclear Information System (INIS)

Bergman, L.J.W.M.; Kerkhoven, I.P.

1989-01-01

After Chernobyl an extensive project on nuclear emergency planning and response was started in the Netherlands. The objective of this project was to develop a (governmental) structure to cope with accidents with radioactive materials, that can threaten the Dutch community and neighbouring countries. The project has resulted in a new organizational structure for nuclear emergency response, that differs on major points from the existing plans and procedures. In this paper an outline of the new structure is given. Emphasis is placed on accidents with nuclear power plants
Mitochondrial genome evolution in the Saccharomyces sensu stricto complex.

Science.gov (United States)

Ruan, Jiangxing; Cheng, Jian; Zhang, Tongcun; Jiang, Huifeng

2017-01-01

Exploring the evolutionary patterns of mitochondrial genomes is important for our understanding of the Saccharomyces sensu stricto (SSS) group, which is a model system for genomic evolution and ecological analysis. In this study, we first obtained the complete mitochondrial sequences of two important species, Saccharomyces mikatae and Saccharomyces kudriavzevii. We then compared the mitochondrial genomes in the SSS group with those of close relatives, and found that the non-coding regions evolved rapidly, including dramatic expansion of intergenic regions, fast evolution of introns and almost 20-fold higher rearrangement rates than those of the nuclear genomes. However, the coding regions, and especially the protein-coding genes, are more conserved than those in the nuclear genomes of the SSS group. The different evolutionary patterns of coding and non-coding regions in the mitochondrial and nuclear genomes may be related to the origin of the aerobic fermentation lifestyle in this group. Our analysis thus provides novel insights into the evolution of mitochondrial genomes.
Impact of nuclear organization and chromatin structure on DNA repair and genome stability

International Nuclear Information System (INIS)

Batte, Amandine

2016-01-01

The non-random organization of the eukaryotic cell nucleus and the folding of genome in chromatin more or less condensed can influence many functions related to DNA metabolism, including genome stability. Double-strand breaks (DSBs) are the most deleterious DNA damages for the cells. To preserve genome integrity, eukaryotic cells thus developed DSB repair mechanisms conserved from yeast to human, among which homologous recombination (HR) that uses an intact homologous sequence to repair a broken chromosome. HR can be separated in two sub-pathways: Gene Conversion (GC) transfers genetic information from one molecule to its homologous and Break Induced Replication (BIR) establishes a replication fork than can proceed until the chromosome end. My doctorate work was focused on the contribution of the chromatin context and 3D genome organization on DSB repair. In S. cerevisiae, nuclear organization and heterochromatin spreading at sub-telomeres can be modified through the overexpression of the Sir3 or sir3A2Q mutant proteins. We demonstrated that reducing the physical distance between homologous sequences increased GC rates, reinforcing the notion that homology search is a limiting step for recombination. We also showed that hetero-chromatinization of DSB site fine-tunes DSB resection, limiting the loss of the DSB ends required to perform homology search and complete HR. Finally, we noticed that the presence of heterochromatin at the donor locus decreased both GC and BIR efficiencies, probably by affecting strand invasion. This work highlights new regulatory pathways of DNA repair. (author) [fr
Generation of floor response spectra for a model structure of nuclear power plant

International Nuclear Information System (INIS)

Vaidyanathan, C.V.; Kamatchi, P.; Ravichandran, R.; Lakshmanan, N.

2003-01-01

The importance of Nuclear power plants and the consequences of a nuclear accident require that the nuclear structures be designed for the most severe environmental conditions. Earthquakes constitutes major design consideration for the system, structures and equipment of a nuclear power plant. The design of structures on ground is based on the ground response spectra. Many important parts of a nuclear power plant facility are attached to the principal parts of the structure and respond in a manner determined by the structural response rather than by the general ground motion to which the structure is supported. Hence the seismic response of equipment is generally based on the response spectrum of the floor on which it is mounted. In this paper such floor response spectra have been generated at different nodes of a chosen model structure of a nuclear power plant. In the present study a detailed nonlinear time history analysis has been carried out on the mathematical model of the chosen Nuclear Power Plant model structure with the spectrum compatible time history. The acceleration response results of the time history analysis has been used in the spectral analysis and the response spectra are generated. Further peak broadening has been done to account for uncertainties in the material properties and soil characteristics. (author)
Response trees and expert systems for nuclear reactor operations

International Nuclear Information System (INIS)

Nelson, W.R.

1984-02-01

The United States Nuclear Regulatory Commission is sponsoring a project performed by EG and G Idaho, Inc., at the Idaho National Engineering Laboratory (INEL) to evaluate different display concepts for use in nuclear reactor control rooms. Included in this project is the evaluation of the response tree computer based decision aid and its associated displays. This report serves as an overview of the response tree methodology and how it has been implemented as a computer based decision aid utilizing color graphic displays. A qualitative assessment of the applicability of the response tree aid in the reactor control room is also made. Experience gained in evaluating the response tree aid is generalized to address a larger category of computer aids, those known as knowledge based expert systems. General characteristics of expert systems are discussed, as well as examples of their application in other domains. A survey of ongoing work on expert systems in the nuclear industry is presented, and an assessment of their potential applicability is made. Finally, recommendations for the design and evaluation of computer based decision aids are presented
Introducing PCTRAN as an evaluation tool for nuclear power plant emergency responses

International Nuclear Information System (INIS)

Cheng, Yi-Hsiang; Shih, Chunkuan; Chiang, Show-Chyuan; Weng, Tung-Li

2012-01-01

Highlights: ► PCTRAN is integrated with an atmospheric dispersion algorithm. ► The improved PCTRAN acts as an accident/incident simulator and a data exchange system. ► The software helps the responsible organizations decide the rescue and protective actions. ► The evaluation results show the nuclear power plant accident and its off-site dose consequences. ► The software can be used for nuclear power plant emergency responses. - Abstract: Protecting the public from radiation exposure is important if a nuclear power plant (NPP) accident occurs. Deciding appropriate protective actions in a timely and effective manner can be fulfilled by using an effective accident evaluation tool. In our earlier work, we have integrated PCTRAN (Personal Computer Transient Analyzer) with the off-site dose calculation model. In this study, we introduce PCTRAN as an evaluation tool for nuclear power plant emergency responses. If abnormal conditions in the plant are monitored or observed, the plant staffs can distinguish accident/incident initiation events. Thus, the responsible personnel can immediately operate PCTRAN and set up those accident/incident initiation events to simulate the nuclear power plant transient or accident in conjunction with off-site dose distributions. The evaluation results consequently help the responsible organizations decide the rescue and protective actions. In this study, we explain and demonstrate the capabilities of PCTRAN for nuclear emergency responses, through applying it to simulate the postulated nuclear power plant accident scenarios.
Planning for off-site response to radiation accidents in nuclear facilities

International Nuclear Information System (INIS)

1981-01-01

The purpose of this publication is to give guidance to those who are responsible for the protection of the public in the event of an accident occurring at a land-based nuclear facility. This guidance should assist in the advance preparation of emergency response plans and implementing procedures. Basic principles of protective measures along with their advantages and disadvantages are discussed. Other principles related to emergency planning and the operational response to an emergency are outlined. Although the guidance is primarily oriented towards land-based nuclear power facilities, the guidance does have general application to other types of nuclear facility
Planning for off-site response to radiation accidents in nuclear facilities

International Nuclear Information System (INIS)

1979-01-01

The purpose of this manual is to give guidance to those who are responsible for the protection of the public in the event of an accident occurring at a land-based nuclear facility. This guidance should assist in the advance preparation of emergency response plans and implementing procedures. Basic principles of protective measures along with their advantages and disadvantages are discussed. Other principles related to emergency planning and the operational response to an emergency are outlined. Although the guidance is primarily oriented toward land-based nuclear power facilities, the guidance does have general application to other types of nuclear facilities

Genome-wide association study of response to cognitive–behavioural therapy in children with anxiety disorders

Science.gov (United States)

Coleman, Jonathan R. I.; Lester, Kathryn J.; Keers, Robert; Roberts, Susanna; Curtis, Charles; Arendt, Kristian; Bögels, Susan; Cooper, Peter; Creswell, Cathy; Dalgleish, Tim; Hartman, Catharina A.; Heiervang, Einar R.; Hötzel, Katrin; Hudson, Jennifer L.; In-Albon, Tina; Lavallee, Kristen; Lyneham, Heidi J.; Marin, Carla E.; Meiser-Stedman, Richard; Morris, Talia; Nauta, Maaike H.; Rapee, Ronald M.; Schneider, Silvia; Schneider, Sophie C.; Silverman, Wendy K.; Thastum, Mikael; Thirlwall, Kerstin; Waite, Polly; Wergeland, Gro Janne; Breen, Gerome; Eley, Thalia C.

2016-01-01

Background Anxiety disorders are common, and cognitive–behavioural therapy (CBT) is a first-line treatment. Candidate gene studies have suggested a genetic basis to treatment response, but findings have been inconsistent. Aims To perform the first genome-wide association study (GWAS) of psychological treatment response in children with anxiety disorders (n = 980). Method Presence and severity of anxiety was assessed using semi-structured interview at baseline, on completion of treatment (post-treatment), and 3 to 12 months after treatment completion (follow-up). DNA was genotyped using the Illumina Human Core Exome-12v1.0 array. Linear mixed models were used to test associations between genetic variants and response (change in symptom severity) immediately post-treatment and at 6-month follow-up. Results No variants passed a genome-wide significance threshold (P = 5 × 10−8) in either analysis. Four variants met criteria for suggestive significance (P<5 × 10−6) in association with response post-treatment, and three variants in the 6-month follow-up analysis. Conclusions This is the first genome-wide therapygenetic study. It suggests no common variants of very high effect underlie response to CBT. Future investigations should maximise power to detect single-variant and polygenic effects by using larger, more homogeneous cohorts. PMID:26989097
Report of nuclear utility industry responses to Kemeny Commission recommendations

Energy Technology Data Exchange (ETDEWEB)

NONE

1989-02-15

The purpose of this paper is to provide a report of nuclear utility industry progress in responding to the recommendations of the President's Commission on the Accident at Three Mile Island (The Kemeny Commission). On April 11, 1979, in response to TMI, President Carter established a Commission to conduct '.... a comprehensive study and investigation of the recent accident involving the nuclear power facility on Three Mile Island in Pennsylvania'. The Commission was chaired by Dr. John G. Kemeny, then President of Dartmouth College. (A list of all members of The Kemeny Commission is provided in Attachment to the Appendix ). The report of the commission's findings and recommendations was transmitted to the President in October 1979. During this same period, the nuclear utility industry responded to TMI by creating the Institute of Nuclear Power Operations (INPO) with a mission to promote the highest levels of safety and reliability - to promote excellence - in the operation of nuclear electric generating plants. In addition, the Nuclear Safety Analysis Center (NSAC) was established at the Electric Power Research Institute (EPRI to evaluate the accident and assist in determining the best industry response. In a White House paper (and press release) of December 7 1979, the President announced that he agreed fully with the spirit and intent of al the Kemeny Commission recommendations and requested that the industry and The Nuclear Regulatory Commission (NRC) comply with the recommendations. The President also recognized the industry initiative in establishing INPO and called for several actions involving the Institute; the President directed the Department of Energy and other government agencies to provide assistance to INPO and the industry. An overall status of the nuclear utility industry responses to Kemeny Commission recommendations in the key areas directly related to nuclear plant operations is provided below. A more detailed status of industry responses to the
Report of nuclear utility industry responses to Kemeny Commission recommendations

International Nuclear Information System (INIS)

1989-02-01

The purpose of this paper is to provide a report of nuclear utility industry progress in responding to the recommendations of the President's Commission on the Accident at Three Mile Island (The Kemeny Commission). On April 11, 1979, in response to TMI, President Carter established a Commission to conduct '.... a comprehensive study and investigation of the recent accident involving the nuclear power facility on Three Mile Island in Pennsylvania'. The Commission was chaired by Dr. John G. Kemeny, then President of Dartmouth College. (A list of all members of The Kemeny Commission is provided in Attachment to the Appendix ). The report of the commission's findings and recommendations was transmitted to the President in October 1979. During this same period, the nuclear utility industry responded to TMI by creating the Institute of Nuclear Power Operations (INPO) with a mission to promote the highest levels of safety and reliability - to promote excellence - in the operation of nuclear electric generating plants. In addition, the Nuclear Safety Analysis Center (NSAC) was established at the Electric Power Research Institute (EPRI to evaluate the accident and assist in determining the best industry response. In a White House paper (and press release) of December 7 1979, the President announced that he agreed fully with the spirit and intent of al the Kemeny Commission recommendations and requested that the industry and The Nuclear Regulatory Commission (NRC) comply with the recommendations. The President also recognized the industry initiative in establishing INPO and called for several actions involving the Institute; the President directed the Department of Energy and other government agencies to provide assistance to INPO and the industry. An overall status of the nuclear utility industry responses to Kemeny Commission recommendations in the key areas directly related to nuclear plant operations is provided below. A more detailed status of industry responses to the
The Fukushima Daiichi Nuclear Power Plant Accident: OECD/NEA Nuclear Safety Response and Lessons Learnt

International Nuclear Information System (INIS)

2013-01-01

Following the March 2011 accident at the Fukushima Daiichi nuclear power plant, all NEA member countries took early action to ensure and confirm the continued safety of their nuclear power plants and the protection of the public. After these preliminary safety reviews, all countries with nuclear facilities carried out comprehensive safety reviews, often referred to as 'stress tests', which reassessed safety margins of nuclear facilities with a primary focus on challenges related to conditions experienced at the Fukushima Daiichi nuclear power plant, for example extreme external events and the loss of safety functions, or capabilities to cope with severe accidents. As appropriate, improvements are being made to safety and emergency response systems to ensure that nuclear power plants are capable of withstanding events that lead to loss of electrical power and/or cooling capability. In the weeks following the accident, the NEA immediately began establishing expert groups in the nuclear safety and radiological protection areas, as well as contributing to information exchange with the Japanese authorities and other international organisations. It promptly provided a forum for high-level decision makers and regulators within the G8-G20 frameworks. The NEA actions taken at the international level in response to the accident have been carried out primarily by the three NEA standing technical committees concerned with nuclear and radiation safety issues - the Committee on Nuclear Regulatory Activities (CNRA), the Committee on the Safety of Nuclear Installations (CSNI) and the Committee on Radiation Protection and Public Health (CRPPH) - under the leadership of the CNRA. More than two years following the accident, the NEA continues to assist the Japanese authorities in dealing with their nuclear safety and recovery efforts as well as to facilitate international co-operation on nuclear safety and radiological protection matters. It is strongly supporting the establishment of
Complete genome sequence and integrated protein localization and interaction map for alfalfa dwarf virus, which combines properties of both cytoplasmic and nuclear plant rhabdoviruses

Energy Technology Data Exchange (ETDEWEB)

Bejerman, Nicolás, E-mail: n.bejerman@uq.edu.au [Instituto de Patología Vegetal (IPAVE), Centro de Investigaciones Agropecuarias (CIAP), Instituto Nacional de Tecnología Agropecuaria INTA, Camino a 60 Cuadras k 5,5, Córdoba X5020ICA (Argentina); Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD 4072 (Australia); Giolitti, Fabián; Breuil, Soledad de; Trucco, Verónica; Nome, Claudia; Lenardon, Sergio [Instituto de Patología Vegetal (IPAVE), Centro de Investigaciones Agropecuarias (CIAP), Instituto Nacional de Tecnología Agropecuaria INTA, Camino a 60 Cuadras k 5,5, Córdoba X5020ICA (Argentina); Dietzgen, Ralf G. [Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD 4072 (Australia)

2015-09-15

Summary: We have determined the full-length 14,491-nucleotide genome sequence of a new plant rhabdovirus, alfalfa dwarf virus (ADV). Seven open reading frames (ORFs) were identified in the antigenomic orientation of the negative-sense, single-stranded viral RNA, in the order 3′-N-P-P3-M-G-P6-L-5′. The ORFs are separated by conserved intergenic regions and the genome coding region is flanked by complementary 3′ leader and 5′ trailer sequences. Phylogenetic analysis of the nucleoprotein amino acid sequence indicated that this alfalfa-infecting rhabdovirus is related to viruses in the genus Cytorhabdovirus. When transiently expressed as GFP fusions in Nicotiana benthamiana leaves, most ADV proteins accumulated in the cell periphery, but unexpectedly P protein was localized exclusively in the nucleus. ADV P protein was shown to have a homotypic, and heterotypic nuclear interactions with N, P3 and M proteins by bimolecular fluorescence complementation. ADV appears unique in that it combines properties of both cytoplasmic and nuclear plant rhabdoviruses. - Highlights: • The complete genome of alfalfa dwarf virus is obtained. • An integrated localization and interaction map for ADV is determined. • ADV has a genome sequence similarity and evolutionary links with cytorhabdoviruses. • ADV protein localization and interaction data show an association with the nucleus. • ADV combines properties of both cytoplasmic and nuclear plant rhabdoviruses.
Complete genome sequence and integrated protein localization and interaction map for alfalfa dwarf virus, which combines properties of both cytoplasmic and nuclear plant rhabdoviruses

International Nuclear Information System (INIS)

Bejerman, Nicolás; Giolitti, Fabián; Breuil, Soledad de; Trucco, Verónica; Nome, Claudia; Lenardon, Sergio; Dietzgen, Ralf G.

2015-01-01

Summary: We have determined the full-length 14,491-nucleotide genome sequence of a new plant rhabdovirus, alfalfa dwarf virus (ADV). Seven open reading frames (ORFs) were identified in the antigenomic orientation of the negative-sense, single-stranded viral RNA, in the order 3′-N-P-P3-M-G-P6-L-5′. The ORFs are separated by conserved intergenic regions and the genome coding region is flanked by complementary 3′ leader and 5′ trailer sequences. Phylogenetic analysis of the nucleoprotein amino acid sequence indicated that this alfalfa-infecting rhabdovirus is related to viruses in the genus Cytorhabdovirus. When transiently expressed as GFP fusions in Nicotiana benthamiana leaves, most ADV proteins accumulated in the cell periphery, but unexpectedly P protein was localized exclusively in the nucleus. ADV P protein was shown to have a homotypic, and heterotypic nuclear interactions with N, P3 and M proteins by bimolecular fluorescence complementation. ADV appears unique in that it combines properties of both cytoplasmic and nuclear plant rhabdoviruses. - Highlights: • The complete genome of alfalfa dwarf virus is obtained. • An integrated localization and interaction map for ADV is determined. • ADV has a genome sequence similarity and evolutionary links with cytorhabdoviruses. • ADV protein localization and interaction data show an association with the nucleus. • ADV combines properties of both cytoplasmic and nuclear plant rhabdoviruses
Some issues on nuclear and radiological emergency preparedness and response in China

International Nuclear Information System (INIS)

Pan Ziqiang

1999-01-01

The nuclear emergency preparedness and response have comprehensively been developed over ten years in China. In order to promote the sound development of emergency preparedness and response, it is useful to retrospect the process of emergency preparedness and response, to summarize the experiences and absorb the experiences from foreign countries. The main issues are as follows: 1) The preparedness and response to nuclear and radiological accident is basically the same as the response to any accident involving hazardous material. 2) The classification of emergency planning, not only for nuclear facilities, but also irradiation installation, etc. 3) The hazard assessment-- a top priority. 4) The emergency planning zones. 5) Psychological impact
Genomic selection improves response to selection in resilience by exploiting genotype by environment interactions

Directory of Open Access Journals (Sweden)

Han Mulder

2016-10-01

Full Text Available Genotype by environment interactions (GxE are very common in livestock and hamper genetic improvement. On the other hand, GxE is a source of genetic variation: genetic variation in response to environment, e.g. environmental perturbations such as heat stress or disease. In livestock breeding, there is tendency to ignore GxE because of increased complexity of models for genetic evaluations and lack of accuracy in extreme environments. GxE, however, creates opportunities to increase resilience of animals towards environmental perturbations. The main aim of the paper is to investigate to which extent GxE can be exploited with traditional and genomic selection methods. Furthermore, we investigated the benefit of reaction norm models compared to conventional methods ignoring GxE. The questions were addressed with selection index theory. GxE was modelled according to a linear reaction norm model in which the environmental gradient is the contemporary group mean. Economic values were based on linear and non-linear profit equations.Accuracies of environment-specific (GEBV were highest in intermediate environments and lowest in extreme environments. Reaction norm models had higher accuracies of (GEBV in extreme environments than conventional models ignoring GxE. Genomic selection always resulted in higher response to selection in all environments than sib or progeny testing schemes. The increase in response was with genomic selection between 9% and 140% compared to sib testing and between 11% and 114% compared to progeny testing when the reference population consisted of 1 million animals across all environments. When the aim was to decrease environmental sensitivity, the response in slope of the reaction norm model with genomic selection was between 1.09 and 319 times larger than with sib or progeny testing and in the right direction in contrast to sib and progeny testing that still increased environmental sensitivity. This shows that genomic selection
A biological-based model that links genomic instability, bystander effects, and adaptive response

International Nuclear Information System (INIS)

Scott, B.R.

2004-01-01

This paper links genomic instability, bystander effects, and adaptive response in mammalian cell communities via a novel biological-based, dose-response model called NEOTRANS 3 . The model is an extension of the NEOTRANS 2 model that addressed stochastic effects (genomic instability, mutations, and neoplastic transformation) associated with brief exposure to low radiation doses. With both models, ionizing radiation produces DNA damage in cells that can be associated with varying degrees of genomic instability. Cells with persistent problematic instability (PPI) are mutants that arise via misrepair of DNA damage. Progeny of PPI cells also have PPI and can undergo spontaneous neoplastic transformation. Unlike NEOTRANS 2 , with NEOTRANS 3 newly induced mutant PPI cells and their neoplastically transformed progeny can be suppressed via our previously introduced protective apoptosis-mediated (PAM) process, which can be activated by low linear energy transfer (LET) radiation. However, with NEOTRANS 3 (which like NEOTRANS 2 involves cross-talk between nongenomically compromised [e.g., nontransformed, nonmutants] and genomically compromised [e.g., mutants, transformants, etc.] cells), it is assumed that PAM is only activated over a relatively narrow, dose-rate-dependent interval (D PAM ,D off ); where D PAM is a small stochastic activation threshold, and D off is the stochastic dose above which PAM does not occur. PAM cooperates with activated normal DNA repair and with activated normal apoptosis in guarding against genomic instability. Normal repair involves both error-free repair and misrepair components. Normal apoptosis and the error-free component of normal repair protect mammals by preventing the occurrence of mutant cells. PAM selectively removes mutant cells arising via the misrepair component of normal repair, selectively removes existing neoplastically transformed cells, and probably selectively removes other genomically compromised cells when it is activated
The Glycolytic Versatility of Bacteroides uniformis CECT 7771 and Its Genome Response to Oligo and Polysaccharides

Directory of Open Access Journals (Sweden)

Alfonso Benítez-Páez

2017-08-01

Full Text Available Bacteroides spp. are dominant components of the phylum Bacteroidetes in the gut microbiota and prosper in glycan enriched environments. However, knowledge of the machinery of specific species isolated from humans (like Bacteroides uniformis contributing to the utilization of dietary and endogenous sources of glycans and their byproducts is limited. We have used the cutting-edge nanopore-based technology to sequence the genome of B. uniformis CECT 7771, a human symbiont with a proven pre-clinical efficacy on metabolic and immune dysfunctions in obesity animal models. We have also used massive sequencing approaches to distinguish the genome expression patterns in response to carbon sources of different complexity during growth. At genome-wide level, our analyses globally demonstrate that B. uniformis strains exhibit an expanded glycolytic capability when compared with other Bacteroides species. Moreover, by studying the growth and whole-genome expression of B. uniformis CECT 7771 in response to different carbon sources, we detected a differential growth fitness and expression patterns across the genome depending on the carbon source of the culture media. The dietary fibers used exerted different effects on B. uniformis CECT 7771 activating different molecular pathways and, therefore, allowing the production of different metabolite types with potential impact on gut health. The genome and transcriptome analysis of B. uniformis CECT 7771, in response to different carbon sources, shows its high versatility to utilize both dietary and endogenous glycans along with the production of potentially beneficial end products for both the bacterium and the host, pointing to a mechanistic basis of a mutualistic relationship.
Continued colonization of the human genome by mitochondrial DNA.

Directory of Open Access Journals (Sweden)

Miria Ricchetti

2004-09-01

Full Text Available Integration of mitochondrial DNA fragments into nuclear chromosomes (giving rise to nuclear DNA sequences of mitochondrial origin, or NUMTs is an ongoing process that shapes nuclear genomes. In yeast this process depends on double-strand-break repair. Since NUMTs lack amplification and specific integration mechanisms, they represent the prototype of exogenous insertions in the nucleus. From sequence analysis of the genome of Homo sapiens, followed by sampling humans from different ethnic backgrounds, and chimpanzees, we have identified 27 NUMTs that are specific to humans and must have colonized human chromosomes in the last 4-6 million years. Thus, we measured the fixation rate of NUMTs in the human genome. Six such NUMTs show insertion polymorphism and provide a useful set of DNA markers for human population genetics. We also found that during recent human evolution, Chromosomes 18 and Y have been more susceptible to colonization by NUMTs. Surprisingly, 23 out of 27 human-specific NUMTs are inserted in known or predicted genes, mainly in introns. Some individuals carry a NUMT insertion in a tumor-suppressor gene and in a putative angiogenesis inhibitor. Therefore in humans, but not in yeast, NUMT integrations preferentially target coding or regulatory sequences. This is indeed the case for novel insertions associated with human diseases and those driven by environmental insults. We thus propose a mutagenic phenomenon that may be responsible for a variety of genetic diseases in humans and suggest that genetic or environmental factors that increase the frequency of chromosome breaks provide the impetus for the continued colonization of the human genome by mitochondrial DNA.
Society response to nuclear energy

International Nuclear Information System (INIS)

Santamaria, N. C.

2007-01-01

Energy demand in the world is growing increasingly, among other factors due to economic development. Every way of producing electricity has got their own drawbacks and has implicit environmental impact. Among all the energy sources, nuclear energy is the most polemic because of the way it is presented by the mass media. This aspect provokes controversy to occidental societies which reject this kind of energy with arguments normally based on a wrong and insufficient knowledge of the matter. The antinuclear discourse, promoted late in the seventies, has gone deeply into the collective social unconscious and has undermined public acceptance of nuclear energy due to the fact, deeply exploited by antinuclear groups, of linking nuclear energy with the atomic bombing of Hiroshima and Nagasaki. In this sense, it is important to mention that in Japan there was a profound resentment and opposition to nuclear energy, because the memory of the nuclear bombings was permanently alive. However when the Japanese government told its people that this energy was necessary to boost their industrial development, Japanese citizens in an unprecedented attitude of patriotism overcame their most antagonist feelings, in order to contribute to the industrial development of their country. The result was that most of them voted in favour. Presently Japan gets 30% of its energy by means of 56 nuclear power plants and 1 more is under construction. Antinuclear groups took as their best emblem the accident of Chernobyl to justify their opposition to the nuclear power plants. The manipulation of this accident has been one of the most shameful in the nuclear history. It is widely known among the experts that the reactor used in Chernobyl was a type of military plutonium converter with a positive temperature reactivity coefficient, which made very dangerous its functioning. Any nuclear regulatory commission in democratic and responsible countries would have never authorized the use of this reactor
Molluscan Evolutionary Genomics

Energy Technology Data Exchange (ETDEWEB)

Simison, W. Brian; Boore, Jeffrey L.

2005-12-01

In the last 20 years there have been dramatic advances in techniques of high-throughput DNA sequencing, most recently accelerated by the Human Genome Project, a program that has determined the three billion base pair code on which we are based. Now this tremendous capability is being directed at other genome targets that are being sampled across the broad range of life. This opens up opportunities as never before for evolutionary and organismal biologists to address questions of both processes and patterns of organismal change. We stand at the dawn of a new 'modern synthesis' period, paralleling that of the early 20th century when the fledgling field of genetics first identified the underlying basis for Darwin's theory. We must now unite the efforts of systematists, paleontologists, mathematicians, computer programmers, molecular biologists, developmental biologists, and others in the pursuit of discovering what genomics can teach us about the diversity of life. Genome-level sampling for mollusks to date has mostly been limited to mitochondrial genomes and it is likely that these will continue to provide the best targets for broad phylogenetic sampling in the near future. However, we are just beginning to see an inroad into complete nuclear genome sequencing, with several mollusks and other eutrochozoans having been selected for work about to begin. Here, we provide an overview of the state of molluscan mitochondrial genomics, highlight a few of the discoveries from this research, outline the promise of broadening this dataset, describe upcoming projects to sequence whole mollusk nuclear genomes, and challenge the community to prepare for making the best use of these data.
Generic procedures for medical response during a nuclear or radiological emergency. Emergency preparedness and response

International Nuclear Information System (INIS)

2005-04-01

The aim of this publication is to serve as a practical resource for planning the medical response to a nuclear or radiological emergency. It fulfils in part functions assigned to the IAEA under Article 5.a(ii) of the Convention on Assistance in the Case of a Nuclear Accident or Radiological Emergency (Assistance Convention), namely, to collect and disseminate to States Parties and Member States information concerning methodologies, techniques and available results of research relating to such emergencies. Effective medical response is a necessary component of the overall response to nuclear or radiological (radiation) emergencies. In general, the medical response may represent a difficult challenge for the authorities due to the complexity of the situation, often requiring specialized expertise, and special organizational arrangements and materials. To be effective, adequate planning and preparedness are needed. This manual, if implemented, should help to contribute to coherent international response. The manual provides the practical tools and generic procedures for use by emergency medical personnel during an emergency situation. It also provides guidance to be used at the stage of preparedness for development of medical response capabilities. The manual also addresses mass casualty emergencies resulting from malicious acts involving radioactive material. This part was supported by the Nuclear Security Fund. The manual was developed based on a number of assumptions about national and local capabilities. Therefore, it must be reviewed and revised as part of the planning process to match the potential accidents, threats, local conditions and other unique characteristics of the facility where it may be used
Responsibility for safe management of spent nuclear fuel - a legal perspective

International Nuclear Information System (INIS)

Cramer, Per; Stendahl, Sara; Erhag, Thomas

2010-10-01

This study analyzes, based on Section 10 of the Swedish Nuclear Activities Act, the legal structures surrounding the issue of responsibility for safe management and final disposal of spent nuclear fuel. The purpose is to shed light on the legal aspects that must be considered in the future licensing process and thereby contribute to a better understanding of the importance of the legal structures for the decisions about final disposal that lie ahead of us. The overall question is thus future-oriented: What interpretation is it reasonable to assume will be given to the requirements of the Nuclear Activities Act on 'safe management and final disposal' of the spent nuclear fuel in the coming licensing process? The approach we take to this question is in part traditionally jurisprudential and based on a study of the travaux preparatoires (drafting history) of the Act and other legal sources. In addition, a study of legal practice is included where previous licensing processes are studied. One conclusion that can be drawn from this study is that the Swedish regulation of nuclear activities creates a legal basis for exacting far-reaching industrial responsibility from the reactor owners, but also for an extensive and interventionist state influence over the activities. Of central importance in the model for division of responsibility that was established via the Nuclear Activities Act in 1984 is the RDandD programme (Research, Development and Demonstration). The RDandD programme reflects the political will that the requirement of 'safe management' should be met through research. The statutory forms for how the programme is to be organized reflect an ambition to place great responsibility for execution and financing on the industry, but also, and not least, an ambition to retain instruments of control and influence in the hands of the state. It is difficult to judge whether the hopes of the 1980s regarding the influence of the public over this process have been fulfilled
Tropospheric response to a nuclear exchange

International Nuclear Information System (INIS)

Penner, J.E.

1983-10-01

The immediate effects of a full-scale nuclear war would be large and severe. The survivors of such a war would have to endure possible changes in the chemical structure of the atmosphere. These changes may come about as a result of changes caused by the nuclear explosions themselves (direct effects) or as a result of changes caused by fires that may start after the explosions (indirect effects). This paper focuses on the expected global-scale changes in the chemical structure of the atmosphere from both direct and indirect effects after a full-scale nuclear exchange. The immediate effects of a nuclear explosion include the creation of a hot mass of air or fireball which rises in the atmosphere to a level that depends on the yield of the explosion. Because the fireball is hot, it is able to dissociate atmospheric nitrogen, N 2 . As the fireball cools, nitrogen atoms recombine with oxygen to form nitrogen oxides, NO and NO 2 . In addition, dust and recondensed gases are swept up through the stem of the fireball and deposited at the same level to which the fireball rises. This paper focuses on the response of atmospheric ozone to a nuclear war
Costs for insurance of civil responsibility for nuclear damage during transportation of nuclear materials

International Nuclear Information System (INIS)

Amelina, M.E.; Arsent'ev, S.V.; Molchanov, A.S.

2009-01-01

The article considers the method of calculation of rates for insurance of civil responsibility for nuclear damage during transportation of nuclear materials, which can minimize the insurer's costs for this type of insurance in situation when there is no statistics available and it is not possible to calculate the insurance rate by the traditional means using the probability theory
Enhancing nuclear emergency response through international co-operation

International Nuclear Information System (INIS)

Ugletveit, F.; Aaltonen, H.

2003-01-01

Full text: A large number of different national plans and procedures have been established and substantial resources allocated world wide with varying comprehensiveness and quality depending an the national requirements and the possible threat scenarios considered. These national plans are only to a small degree harmonized. It is clear that it is the responsibility of the authorities in the respective countries or utilities under their jurisdiction, to decide upon and implement appropriate response actions to a nuclear emergency. The basic needs for responding properly are: infrastructure in terms of plans, procedures etc.; information regarding the accident, its development and consequences; resources in terms of expertise, man power and tools for acquiring and processing information, making assessments and decisions and carry out the actions. When a large number of countries are making assessments and decisions for their own country and providing the public with information, it is important that assessments, decisions and public information become correct, complete and consistent across boarders. In order to achieve this, they should all have access to the same information as basis for their actions. Lack of information or wrong information could easily lead to wrong assessments, wrong decisions and misleading information to the public. If there is a serious nuclear emergency somewhere that could potentially affect several or many States in one way or another, 'everyone' would like to know 'everything' that happens 'everywhere'. In this case, all States should have the obligation to share with the international community the relevant information they have available themselves and that could be of interest for other States responding to the situation. During a serious nuclear or radiological emergency, the demand for different kinds of resources is huge and could, in many countries, probably exceed national capabilities. Looking at the situation in a global
The mitochondrial gene encoding ribosomal protein S12 has been translocated to the nuclear genome in Oenothera.

Science.gov (United States)

Grohmann, L; Brennicke, A; Schuster, W

1992-01-01

The Oenothera mitochondrial genome contains only a gene fragment for ribosomal protein S12 (rps12), while other plants encode a functional gene in the mitochondrion. The complete Oenothera rps12 gene is located in the nucleus. The transit sequence necessary to target this protein to the mitochondrion is encoded by a 5'-extension of the open reading frame. Comparison of the amino acid sequence encoded by the nuclear gene with the polypeptides encoded by edited mitochondrial cDNA and genomic sequences of other plants suggests that gene transfer between mitochondrion and nucleus started from edited mitochondrial RNA molecules. Mechanisms and requirements of gene transfer and activation are discussed. Images PMID:1454526
Complete sequences of organelle genomes from the medicinal plant Rhazya stricta (Apocynaceae) and contrasting patterns of mitochondrial genome evolution across asterids.

Science.gov (United States)

Park, Seongjun; Ruhlman, Tracey A; Sabir, Jamal S M; Mutwakil, Mohammed H Z; Baeshen, Mohammed N; Sabir, Meshaal J; Baeshen, Nabih A; Jansen, Robert K

2014-05-28

Rhazya stricta is native to arid regions in South Asia and the Middle East and is used extensively in folk medicine to treat a wide range of diseases. In addition to generating genomic resources for this medicinally important plant, analyses of the complete plastid and mitochondrial genomes and a nuclear transcriptome from Rhazya provide insights into inter-compartmental transfers between genomes and the patterns of evolution among eight asterid mitochondrial genomes. The 154,841 bp plastid genome is highly conserved with gene content and order identical to the ancestral organization of angiosperms. The 548,608 bp mitochondrial genome exhibits a number of phenomena including the presence of recombinogenic repeats that generate a multipartite organization, transferred DNA from the plastid and nuclear genomes, and bidirectional DNA transfers between the mitochondrion and the nucleus. The mitochondrial genes sdh3 and rps14 have been transferred to the nucleus and have acquired targeting presequences. In the case of rps14, two copies are present in the nucleus; only one has a mitochondrial targeting presequence and may be functional. Phylogenetic analyses of both nuclear and mitochondrial copies of rps14 across angiosperms suggests Rhazya has experienced a single transfer of this gene to the nucleus, followed by a duplication event. Furthermore, the phylogenetic distribution of gene losses and the high level of sequence divergence in targeting presequences suggest multiple, independent transfers of both sdh3 and rps14 across asterids. Comparative analyses of mitochondrial genomes of eight sequenced asterids indicates a complicated evolutionary history in this large angiosperm clade with considerable diversity in genome organization and size, repeat, gene and intron content, and amount of foreign DNA from the plastid and nuclear genomes. Organelle genomes of Rhazya stricta provide valuable information for improving the understanding of mitochondrial genome evolution

Nuclear Energy Response in the EMF27 Study

International Nuclear Information System (INIS)

Kim, Son H.; Wada, Kenichi; Kurosawa, Atsushi; Roberts, Matthew

2014-01-01

The nuclear energy response for mitigating global climate change across eighteen participating models of the EMF27 study is investigated. Diverse perspectives on the future role of nuclear power in the global energy system are evident in the broad range of nuclear power contributions from participating models of the study. In the Baseline scenario without climate policy, nuclear electricity generation and shares span 0 - 66 EJ/ year and 0 - 25% in 2100 for all models, with a median nuclear electricity generation of 39 EJ/year (1,389 GWe at 90% capacity factor) and median share of 9%. The role of nuclear energy increased under the climate policy scenarios. The median of nuclear energy use across all models doubled in the 450 ppm CO2e scenario with a nuclear electricity generation of 67 EJ/year (2,352 GWe at 90% capacity factor) and share of 17% in 2100. The broad range of nuclear electricity generation (11 - 214 EJ/year) and shares (2 - 38%) in 2100 of the 450 ppm CO2e scenario reflect differences in the technology choice behavior, technology assumptions and competitiveness of low carbon technologies. Greater clarification of nuclear fuel cycle issues and risk factors associated with nuclear energy use are necessary for understanding the nuclear deployment constraints imposed in models and for improving the assessment of the nuclear energy potential in addressing climate change
Accuracy and responses of genomic selection on key traits in apple breeding

NARCIS (Netherlands)

Muranty, Hélène; Troggio, Michela; Sadok, Ben Inès; Rifaï, Al Mehdi; Auwerkerken, Annemarie; Banchi, E.; Velasco, Riccardo; Stevanato, P.; Weg, van de W.E.; Guardo, Di M.; Kumar, S.; Laurens, François; Bink, M.C.A.M.

2015-01-01

The application of genomic selection in fruit tree crops is expected to enhance breeding efficiency by increasing prediction accuracy, increasing selection intensity and decreasing generation interval. The objectives of this study were to assess the accuracy of prediction and selection response in
How the Nuclear Applications Laboratories Help in Strengthening Emergency Response

International Nuclear Information System (INIS)

2014-01-01

Safety is one of the most important considerations when engaging in highly advanced scientific and technological activities. In this respect, utilizing the potential of nuclear technology for peaceful purposes also involves risks, and nuclear techniques themselves can be useful in strengthening emergency response measures related to the use of nuclear technology. In the case of a nuclear incident, the rapid measurement and subsequent monitoring of radiation levels are top priorities as they help to determine the degree of risk faced by emergency responders and the general public. Instruments for the remote measurement of radioactivity are particularly important when there are potential health risks associated with entering areas with elevated radiation levels. The Nuclear Science and Instrumentation Laboratory (NSIL) — one of the eight laboratories of the Department of Nuclear Sciences and Applications (NA) in Seibersdorf, Austria — focuses on developing a variety of specialized analytical and diagnostic instruments and methods, and transferring knowledge to IAEA Member States. These include instruments capable of carrying out remote measurements. This emergency response work carried out by the NA laboratories supports health and safety in Member States and supports the IAEA’s mandate to promote the safe and peaceful use of nuclear energy
Genomic interrogation of mechanism(s) underlying cellular responses to toxicants

International Nuclear Information System (INIS)

Amin, Rupesh P.; Hamadeh, Hisham K.; Bushel, Pierre R.; Bennett, Lee; Afshari, Cynthia A.; Paules, Richard S.

2002-01-01

Assessment of the impact of xenobiotic exposure on human health and disease progression is complex. Knowledge of mode(s) of action, including mechanism(s) contributing to toxicity and disease progression, is valuable for evaluating compounds. Toxicogenomics, the subdiscipline which merges genomics with toxicology, holds the promise to contributing significantly toward the goal of elucidating mechanism(s) by studying genome-wide effects of xenobiotics. Global gene expression profiling, revolutionized by microarray technology and a crucial aspect of a toxicogenomic study, allows measuring transcriptional modulation of thousands of genes following exposure to a xenobiotic. We use our results from previous studies on compounds representing two different classes of xenobiotics (barbiturate and peroxisome proliferator) to discuss the application of computational approaches for analyzing microarray data to elucidate mechanism(s) underlying cellular responses to toxicants. In particular, our laboratory demonstrated that chemical-specific patterns of gene expression can be revealed using cDNA microarrays. Transcript profiling provides discrimination between classes of toxicants, as well as, genome-wide insight into mechanism(s) of toxicity and disease progression. Ultimately, the expectation is that novel approaches for predicting xenobiotic toxicity in humans will emerge from such information
National response plan - Major nuclear or radiological accidents

International Nuclear Information System (INIS)

2014-02-01

France has been implementing stringent radiation protection and nuclear safety and security measures for many years. However, this does not mean that the country is exempt from having to be prepared to deal with an emergency. Changes in France, Europe and other parts of the globe have made it necessary for France to reconsider how it responds to nuclear and radiological emergencies. As the potential impact of a nuclear or radiological accident can affect a wide range of activities, the plan described herein is based on a cross-sector and inter-ministerial approach to emergency response. The Chernobyl and Fukushima-Daiichi disasters are proof that the consequences of a major nuclear or radiological accident can affect all levels of society. These challenges are substantial and relate to: public health: An uncontrolled nuclear accident can have immediate consequences (death, injury, irradiation) as well as long-term consequences that can lead to increased risk of developing radiation-induced diseases (such as certain types of cancer); environmental quality: Radiation contamination can last for several decades and, in some cases, can result in an area being closed off permanently to the public; economic and social continuity: Nuclear accidents bring human activity to a halt in contaminated areas, disrupting the economic and social order of the entire country. It may therefore be necessary to adapt economic and social systems and carry out clean-up operations if people and businesses have been displaced; quality of international relations: Related to fulfillment of obligations to alert and inform European and international partners. This international dimension also covers the protection of French nationals present in countries stricken by a nuclear accident. This national plan provides reference information on how to prepare for a nuclear or radiological emergency and make the appropriate decisions in the event of an emergency. It covers the emergency phase (including
Conservation and divergence of chemical defense system in the tunicate Oikopleura dioica revealed by genome wide response to two xenobiotics

Directory of Open Access Journals (Sweden)

Yadetie Fekadu

2012-02-01

Full Text Available Abstract Background Animals have developed extensive mechanisms of response to xenobiotic chemical attacks. Although recent genome surveys have suggested a broad conservation of the chemical defensome across metazoans, global gene expression responses to xenobiotics have not been well investigated in most invertebrates. Here, we performed genome survey for key defensome genes in Oikopleura dioica genome, and explored genome-wide gene expression using high density tiling arrays with over 2 million probes, in response to two model xenobiotic chemicals - the carcinogenic polycyclic aromatic hydrocarbon benzo[a]pyrene (BaP the pharmaceutical compound Clofibrate (Clo. Results Oikopleura genome surveys for key genes of the chemical defensome suggested a reduced repertoire. Not more than 23 cytochrome P450 (CYP genes could be identified, and neither CYP1 family genes nor their transcriptional activator AhR was detected. These two genes were present in deuterostome ancestors. As in vertebrates, the genotoxic compound BaP induced xenobiotic biotransformation and oxidative stress responsive genes. Notable exceptions were genes of the aryl hydrocarbon receptor (AhR signaling pathway. Clo also affected the expression of many biotransformation genes and markedly repressed genes involved in energy metabolism and muscle contraction pathways. Conclusions Oikopleura has the smallest number of CYP genes among sequenced animal genomes and lacks the AhR signaling pathway. However it appears to have basic xenobiotic inducible biotransformation genes such as a conserved genotoxic stress response gene set. Our genome survey and expression study does not support a role of AhR signaling pathway in the chemical defense of metazoans prior to the emergence of vertebrates.
Response function of spin-isospin nuclear excitations

International Nuclear Information System (INIS)

Salvetti, A.R.

1986-01-01

The selected aspects of spin-isospir nuclear excitations are studied. The spreading width of M/ states in even Ca isotopes for the purpose of trying to understand the missing strenght specially in 44 Ca, was estimated. The doorway calculation, was used, considering the level of complexity next to the independent particle M/ state. Using a nuclear matter context, the system response function to a spin-isospin probe and verify how the response function behaves for free fermions and in the ring approximation was studied. Higher correlations to polarization propagation such as the induced interaction and self-energy corrections was introduced. The dopping of colletive effects by such collisions terms was verified. It was investigate how to estimate the short range term of the effective interaction in the spin-isospin channel and the possibility of detecting a difference between these short range terms in the longitudinal and the transverse channel, for understanding the absence of pior condensation precursor states and negative results in a recent attempt to detect differences between longitudinal and transverse response functions one naively expects theoretically. (author) [pt
Herbarium genomics

DEFF Research Database (Denmark)

Bakker, Freek T.; Lei, Di; Yu, Jiaying

2016-01-01

Herbarium genomics is proving promising as next-generation sequencing approaches are well suited to deal with the usually fragmented nature of archival DNA. We show that routine assembly of partial plastome sequences from herbarium specimens is feasible, from total DNA extracts and with specimens...... up to 146 years old. We use genome skimming and an automated assembly pipeline, Iterative Organelle Genome Assembly, that assembles paired-end reads into a series of candidate assemblies, the best one of which is selected based on likelihood estimation. We used 93 specimens from 12 different...... correlation between plastome coverage and nuclear genome size (C value) in our samples, but the range of C values included is limited. Finally, we conclude that routine plastome sequencing from herbarium specimens is feasible and cost-effective (compared with Sanger sequencing or plastome...
Genomic Characterization of Metformin Hepatic Response.

Directory of Open Access Journals (Sweden)

Marcelo R Luizon

2016-11-01

Full Text Available Metformin is used as a first-line therapy for type 2 diabetes (T2D and prescribed for numerous other diseases. However, its mechanism of action in the liver has yet to be characterized in a systematic manner. To comprehensively identify genes and regulatory elements associated with metformin treatment, we carried out RNA-seq and ChIP-seq (H3K27ac, H3K27me3 on primary human hepatocytes from the same donor treated with vehicle control, metformin or metformin and compound C, an AMP-activated protein kinase (AMPK inhibitor (allowing to identify AMPK-independent pathways. We identified thousands of metformin responsive AMPK-dependent and AMPK-independent differentially expressed genes and regulatory elements. We functionally validated several elements for metformin-induced promoter and enhancer activity. These include an enhancer in an ataxia telangiectasia mutated (ATM intron that has SNPs in linkage disequilibrium with a metformin treatment response GWAS lead SNP (rs11212617 that showed increased enhancer activity for the associated haplotype. Expression quantitative trait locus (eQTL liver analysis and CRISPR activation suggest that this enhancer could be regulating ATM, which has a known role in AMPK activation, and potentially also EXPH5 and DDX10, its neighboring genes. Using ChIP-seq and siRNA knockdown, we further show that activating transcription factor 3 (ATF3, our top metformin upregulated AMPK-dependent gene, could have an important role in gluconeogenesis repression. Our findings provide a genome-wide representation of metformin hepatic response, highlight important sequences that could be associated with interindividual variability in glycemic response to metformin and identify novel T2D treatment candidates.
Pilot program: NRC severe reactor accident incident response training manual: US Nuclear Regulatory Commission response

International Nuclear Information System (INIS)

Sakenas, C.A.; McKenna, T.J.; Perkins, K.; Miller, C.W.; Hively, L.M.; Sharpe, R.W.; Giitter, J.G.; Watkins, R.M.

1987-02-01

This pilot training manual has been written to fill the need for a general text on NRC response to reactor accidents. The manual is intended to be the foundation for a course for all NRC response personnel. US Nuclear Regulatory Commission Response is the fifth in a series of volumes that collectively summarize the US Nuclear Regulatory Commission (NRC) emergency response during severe power reactor accidents and provide necessary background information. This volume describes NRC response modes, organizations, and official positions; roles of other federal agencies are also described briefly. Each volume serves, respectively, as the text for a course of instruction in a series of courses for NRC response personnel. These materials do not provide guidance or license requirements for NRC licensees. Each volume is accompanied by an appendix of slides that can be used to present this material. The slides are called out in the text
Genomic treasure troves: complete genome sequencing of herbarium and insect museum specimens.

Science.gov (United States)

Staats, Martijn; Erkens, Roy H J; van de Vossenberg, Bart; Wieringa, Jan J; Kraaijeveld, Ken; Stielow, Benjamin; Geml, József; Richardson, James E; Bakker, Freek T

2013-01-01

Unlocking the vast genomic diversity stored in natural history collections would create unprecedented opportunities for genome-scale evolutionary, phylogenetic, domestication and population genomic studies. Many researchers have been discouraged from using historical specimens in molecular studies because of both generally limited success of DNA extraction and the challenges associated with PCR-amplifying highly degraded DNA. In today's next-generation sequencing (NGS) world, opportunities and prospects for historical DNA have changed dramatically, as most NGS methods are actually designed for taking short fragmented DNA molecules as templates. Here we show that using a standard multiplex and paired-end Illumina sequencing approach, genome-scale sequence data can be generated reliably from dry-preserved plant, fungal and insect specimens collected up to 115 years ago, and with minimal destructive sampling. Using a reference-based assembly approach, we were able to produce the entire nuclear genome of a 43-year-old Arabidopsis thaliana (Brassicaceae) herbarium specimen with high and uniform sequence coverage. Nuclear genome sequences of three fungal specimens of 22-82 years of age (Agaricus bisporus, Laccaria bicolor, Pleurotus ostreatus) were generated with 81.4-97.9% exome coverage. Complete organellar genome sequences were assembled for all specimens. Using de novo assembly we retrieved between 16.2-71.0% of coding sequence regions, and hence remain somewhat cautious about prospects for de novo genome assembly from historical specimens. Non-target sequence contaminations were observed in 2 of our insect museum specimens. We anticipate that future museum genomics projects will perhaps not generate entire genome sequences in all cases (our specimens contained relatively small and low-complexity genomes), but at least generating vital comparative genomic data for testing (phylo)genetic, demographic and genetic hypotheses, that become increasingly more horizontal
Emergency response and nuclear risk governance. Nuclear safety at nuclear power plant accidents; Notfallschutz und Risk Governance. Zur nuklearen Sicherheit bei Kernkraftwerksunfaellen

Energy Technology Data Exchange (ETDEWEB)

Kuhlen, Johannes

2014-07-01

The present study entitled ''Emergency Response and Nuclear Risk Governance: nuclear safety at nuclear power plant accidents'' deals with issues of the protection of the population and the environment against hazardous radiation (the hazards of nuclear energy) and the harmful effects of radioactivity during nuclear power plant accidents. The aim of this study is to contribute to both the identification and remediation of shortcomings and deficits in the management of severe nuclear accidents like those that occurred at Chernobyl in 1986 and at Fukushima in 2011 as well as to the improvement and harmonization of plans and measures taken on an international level in nuclear emergency management. This thesis is divided into a theoretical part and an empirical part. The theoretical part focuses on embedding the subject in a specifically global governance concept, which includes, as far as Nuclear Risk Governance is concerned, the global governance of nuclear risks. Due to their characteristic features the following governance concepts can be assigned to these risks: Nuclear Safety Governance is related to safety, Nuclear Security Governance to security and NonProliferation Governance to safeguards. The subject of investigation of the present study is as a special case of the Nuclear Safety Governance, the Nuclear Emergency governance, which refers to off-site emergency response. The global impact of nuclear accidents and the concepts of security, safety culture and residual risk are contemplated in this context. The findings (accident sequences, their consequences and implications) from the analyses of two reactor accidents prior to Fukushima (Three Mile Iceland in 1979, Chernobyl in 1986) are examined from a historical analytical perspective and the state of the Nuclear Emergency governance and international cooperation aimed at improving nuclear safety after Chernobyl is portrayed by discussing, among other topics, examples of &apos
Manual of functions, assignments, and responsibilities for nuclear safety: Revision 2

Energy Technology Data Exchange (ETDEWEB)

1994-10-15

The FAR Manual is a convenient easy-to-use collection of the functions, assignments, and responsibilities (FARs) of DOE nuclear safety personnel. Current DOE directives, including Orders, Secretary of Energy Notices, and other assorted policy memoranda, are the source of this information and form the basis of the FAR Manual. Today, the majority of FARs for DOE personnel are contained in DOE`s nuclear safety Orders. As these Orders are converted to rules in the Code of Federal Regulations, the FAR Manual will become the sole source for information relating to the functions, assignments, responsibilities of DOE nuclear safety personnel. The FAR Manual identifies DOE directives that relate to nuclear safety and the specific DOE personnel who are responsible for implementing them. The manual includes only FARs that have been extracted from active directives that have been approved in accordance with the procedures contained in DOE Order 1321.1B.
Response of base-isolated nuclear structures to extreme earthquake shaking

Energy Technology Data Exchange (ETDEWEB)

Kumar, Manish, E-mail: mkumar2@buffalo.edu; Whittaker, Andrew S.; Constantinou, Michael C.

2015-12-15

Highlights: • Response-history analysis of nuclear structures base-isolated using lead–rubber bearings is performed. • Advanced numerical model of lead–rubber bearing is used to capture behavior under extreme earthquake shaking. • Results of response-history analysis obtained using simplified and advanced model of lead–rubber bearings are compared. • Heating of the lead core and variation in buckling load and axial stiffness affect the response. - Abstract: Seismic isolation using low damping rubber and lead–rubber bearings is a viable strategy for mitigating the effects of extreme earthquake shaking on safety-related nuclear structures. The mechanical properties of these bearings are not expected to change substantially in design basis shaking. However, under shaking more intense than design basis, the properties of the lead cores in lead–rubber bearings may degrade due to heating associated with energy dissipation, some bearings in an isolation system may experience net tension, and the compression and tension stiffness may be affected by the lateral displacement of the isolation system. The effects of intra-earthquake changes in mechanical properties on the response of base-isolated nuclear power plants (NPPs) are investigated using an advanced numerical model of a lead–rubber bearing that has been verified and validated, and implemented in OpenSees. A macro-model is used for response-history analysis of base-isolated NPPs. Ground motions are selected and scaled to be consistent with response spectra for design basis and beyond design basis earthquake shaking at the site of the Diablo Canyon Nuclear Generating Station. Ten isolation systems of two periods and five characteristic strengths are analyzed. The responses obtained using simplified and advanced isolator models are compared. Strength degradation due to heating of lead cores and changes in buckling load most significantly affect the response of the base-isolated NPP.
Response of base-isolated nuclear structures to extreme earthquake shaking

International Nuclear Information System (INIS)

Kumar, Manish; Whittaker, Andrew S.; Constantinou, Michael C.

2015-01-01

Highlights: • Response-history analysis of nuclear structures base-isolated using lead–rubber bearings is performed. • Advanced numerical model of lead–rubber bearing is used to capture behavior under extreme earthquake shaking. • Results of response-history analysis obtained using simplified and advanced model of lead–rubber bearings are compared. • Heating of the lead core and variation in buckling load and axial stiffness affect the response. - Abstract: Seismic isolation using low damping rubber and lead–rubber bearings is a viable strategy for mitigating the effects of extreme earthquake shaking on safety-related nuclear structures. The mechanical properties of these bearings are not expected to change substantially in design basis shaking. However, under shaking more intense than design basis, the properties of the lead cores in lead–rubber bearings may degrade due to heating associated with energy dissipation, some bearings in an isolation system may experience net tension, and the compression and tension stiffness may be affected by the lateral displacement of the isolation system. The effects of intra-earthquake changes in mechanical properties on the response of base-isolated nuclear power plants (NPPs) are investigated using an advanced numerical model of a lead–rubber bearing that has been verified and validated, and implemented in OpenSees. A macro-model is used for response-history analysis of base-isolated NPPs. Ground motions are selected and scaled to be consistent with response spectra for design basis and beyond design basis earthquake shaking at the site of the Diablo Canyon Nuclear Generating Station. Ten isolation systems of two periods and five characteristic strengths are analyzed. The responses obtained using simplified and advanced isolator models are compared. Strength degradation due to heating of lead cores and changes in buckling load most significantly affect the response of the base-isolated NPP.
Plastome-Genome Interactions Affect Plastid Transmission in Oenothera

Science.gov (United States)

Chiu, W. L.; Sears, B. B.

1993-01-01

Plastids of Oenothera, the evening primrose, can be transmitted to the progeny from both parents. In a constant nuclear background, the frequency of biparental plastid transmission is determined by the types of plastid genomes (plastomes) involved in the crosses. In this study, the impact of nuclear genomes on plastid inheritance was analyzed. In general, the transmission efficiency of each plastome correlated strongly with its compatibility with the nuclear genome of the progeny, suggesting that plastome-genome interactions can influence plastid transmission by affecting the efficiency of plastid multiplication after fertilization. Lower frequencies of plastid transmission from the paternal side were observed when the pollen had poor vigor due to an incompatible plastome-genome combination, indicating that plastome-genome interactions may also affect the input of plastids at fertilization. Parental traits that affect the process of fertilization can also have an impact on plastid transmission. Crosses using maternal parents with long styles or pollen with relatively low growth capacity resulted in reduced frequencies of paternal plastid transmission. These observations suggest that degeneration of pollen plastids may occur as the time interval between pollination and fertilization is lengthened. PMID:8462856
Nuclear emergency preparedness and response in Germany

International Nuclear Information System (INIS)

Miska, H.

2009-01-01

Off-site nuclear emergency response in Germany is divided into disaster response under the responsibility of the Laender and measures for precautionary radiation protection pursuant to the Precautionary Radiation Protection Act under the lead of federal authorities. Early countermeasures at the regional level require a different management than long-term and comprehensive actions of precautionary radiation protection. As situations may arise in which measures of both approaches overlap with regard to place and time, it is essential to make thorough preparations in order to avoid problems with implementation. (orig.)
The directionality of the nuclear transport of the influenza A genome is driven by selective exposure of nuclear localization sequences on nucleoprotein

Directory of Open Access Journals (Sweden)

Panté Nelly

2009-06-01

Full Text Available Abstract Background Early in infection, the genome of the influenza A virus, consisting of eight complexes of RNA and proteins (termed viral ribonucleoproteins; vRNPs, enters the nucleus of infected cells for replication. Incoming vRNPs are imported into the nucleus of infected cells using at least two nuclear localization sequences on nucleoprotein (NP; NLS1 at the N terminus, and NLS2 in the middle of the protein. Progeny vRNP assembly occurs in the nucleus, and later in infection, these are exported from the nucleus to the cytoplasm. Nuclear-exported vRNPs are different from incoming vRNPs in that they are prevented from re-entering the nucleus. Why nuclear-exported vRNPs do not re-enter the nucleus is unknown. Results To test our hypothesis that the exposure of NLSs on the vRNP regulates the directionality of the nuclear transport of the influenza vRNPs, we immunolabeled the two NLSs of NP (NLS1 and NLS2 and analyzed their surface accessibility in cells infected with the influenza A virus. We found that the NLS1 epitope on NP was exposed throughout the infected cells, but the NLS2 epitope on NP was only exposed in the nucleus of the infected cells. Addition of the nuclear export inhibitor leptomycin B further revealed that NLS1 is no longer exposed in cytoplasmic NP and vRNPs that have already undergone nuclear export. Similar immunolabeling studies in the presence of leptomycin B and with cells transfected with the cDNA of NP revealed that the NLS1 on NP is hidden in nuclear exported-NP. Conclusion NLS1 mediates the nuclear import of newly-synthesized NP and incoming vRNPs. This NLS becomes hidden on nuclear-exported NP and nuclear-exported vRNPs. Thus the selective exposure of the NLS1 constitutes a critical mechanism to regulate the directionality of the nuclear transport of vRNPs during the influenza A viral life cycle.
Genomic responses to arsenic in the cyanobacterium Synechocystis sp. PCC 6803.

Directory of Open Access Journals (Sweden)

Ana María Sánchez-Riego

Full Text Available Arsenic is a ubiquitous contaminant and a toxic metalloid which presents two main redox states in nature: arsenite [As(III] and arsenate [As(V]. Arsenic resistance in Synechocystis sp. strain PCC 6803 is mediated by the arsBHC operon and two additional arsenate reductases encoded by the arsI1 and arsI2 genes. Here we describe the genome-wide responses to the presence of arsenate and arsenite in wild type and mutants in the arsenic resistance system. Both forms of arsenic produced similar responses in the wild type strain, including induction of several stress related genes and repression of energy generation processes. These responses were transient in the wild type strain but maintained in time in an arsB mutant strain, which lacks the arsenite transporter. In contrast, the responses observed in a strain lacking all arsenate reductases were somewhat different and included lower induction of genes involved in metal homeostasis and Fe-S cluster biogenesis, suggesting that these two processes are targeted by arsenite in the wild type strain. Finally, analysis of the arsR mutant strain revealed that ArsR seems to only control 5 genes in the genome. Furthermore, the arsR mutant strain exhibited hypersentivity to nickel, copper and cadmium and this phenotype was suppressed by mutation in arsB but not in arsC gene suggesting that overexpression of arsB is detrimental in the presence of these metals in the media.
Revealing less derived nature of cartilaginous fish genomes with their evolutionary time scale inferred with nuclear genes.

Directory of Open Access Journals (Sweden)

Adina J Renz

Full Text Available Cartilaginous fishes, divided into Holocephali (chimaeras and Elasmoblanchii (sharks, rays and skates, occupy a key phylogenetic position among extant vertebrates in reconstructing their evolutionary processes. Their accurate evolutionary time scale is indispensable for better understanding of the relationship between phenotypic and molecular evolution of cartilaginous fishes. However, our current knowledge on the time scale of cartilaginous fish evolution largely relies on estimates using mitochondrial DNA sequences. In this study, making the best use of the still partial, but large-scale sequencing data of cartilaginous fish species, we estimate the divergence times between the major cartilaginous fish lineages employing nuclear genes. By rigorous orthology assessment based on available genomic and transcriptomic sequence resources for cartilaginous fishes, we selected 20 protein-coding genes in the nuclear genome, spanning 2973 amino acid residues. Our analysis based on the Bayesian inference resulted in the mean divergence time of 421 Ma, the late Silurian, for the Holocephali-Elasmobranchii split, and 306 Ma, the late Carboniferous, for the split between sharks and rays/skates. By applying these results and other documented divergence times, we measured the relative evolutionary rate of the Hox A cluster sequences in the cartilaginous fish lineages, which resulted in a lower substitution rate with a factor of at least 2.4 in comparison to tetrapod lineages. The obtained time scale enables mapping phenotypic and molecular changes in a quantitative framework. It is of great interest to corroborate the less derived nature of cartilaginous fish at the molecular level as a genome-wide phenomenon.

Targeted identification of short interspersed nuclear element families shows their widespread existence and extreme heterogeneity in plant genomes.

Science.gov (United States)

Wenke, Torsten; Döbel, Thomas; Sörensen, Thomas Rosleff; Junghans, Holger; Weisshaar, Bernd; Schmidt, Thomas

2011-09-01

Short interspersed nuclear elements (SINEs) are non-long terminal repeat retrotransposons that are highly abundant, heterogeneous, and mostly not annotated in eukaryotic genomes. We developed a tool designated SINE-Finder for the targeted discovery of tRNA-derived SINEs. We analyzed sequence data of 16 plant genomes, including 13 angiosperms and three gymnosperms and identified 17,829 full-length and truncated SINEs falling into 31 families showing the widespread occurrence of SINEs in higher plants. The investigation focused on potato (Solanum tuberosum), resulting in the detection of seven different SolS SINE families consisting of 1489 full-length and 870 5' truncated copies. Consensus sequences of full-length members range in size from 106 to 244 bp depending on the SINE family. SolS SINEs populated related species and evolved separately, which led to some distinct subfamilies. Solanaceae SINEs are dispersed along chromosomes and distributed without clustering but with preferred integration into short A-rich motifs. They emerged more than 23 million years ago and were species specifically amplified during the radiation of potato, tomato (Solanum lycopersicum), and tobacco (Nicotiana tabacum). We show that tobacco TS retrotransposons are composite SINEs consisting of the 3' end of a long interspersed nuclear element integrated downstream of a nonhomologous SINE family followed by successfully colonization of the genome. We propose an evolutionary scenario for the formation of TS as a spontaneous event, which could be typical for the emergence of SINE families.
Hyb-Seq: Combining Target Enrichment and Genome Skimming for Plant Phylogenomics

Directory of Open Access Journals (Sweden)

Kevin Weitemier

2014-08-01

Full Text Available Premise of the study: Hyb-Seq, the combination of target enrichment and genome skimming, allows simultaneous data collection for low-copy nuclear genes and high-copy genomic targets for plant systematics and evolution studies. Methods and Results: Genome and transcriptome assemblies for milkweed (Asclepias syriaca were used to design enrichment probes for 3385 exons from 768 genes (>1.6 Mbp followed by Illumina sequencing of enriched libraries. Hyb-Seq of 12 individuals (10 Asclepias species and two related genera resulted in at least partial assembly of 92.6% of exons and 99.7% of genes and an average assembly length >2 Mbp. Importantly, complete plastomes and nuclear ribosomal DNA cistrons were assembled using off-target reads. Phylogenomic analyses demonstrated signal conflict between genomes. Conclusions: The Hyb-Seq approach enables targeted sequencing of thousands of low-copy nuclear exons and flanking regions, as well as genome skimming of high-copy repeats and organellar genomes, to efficiently produce genome-scale data sets for phylogenomics.
Analysis of emergency response to fukushima nuclear accident in Japan and suggestions for China's nuclear emergency management

International Nuclear Information System (INIS)

Li Wei; Ding Qihua; Wu Haosong

2014-01-01

On March 11, 2011, the Fukushima Dai-ichi Nuclear Power Station of the Tokyo Electric Power Company ('TEPCO') was hit and damaged by a magnitude 9 earthquake and accompanying tsunami. The accident is determined to be of the highest rating on the International Nuclear Event Scale. The Government of Japan and TEPCO have taken emergency response actions on-site and off-site at the accident. It became clear through the investigation that the accident had been initiated on the occasion of a natural disaster of an earthquake and tsunami, but there have been various complex problems behind this very serious and large scale accident. For an example, the then-available accident preventive measures and disaster preparedness of TEPCO were insufficient against tsunami and severe accidents; inadequate TEPCO emergency responses to the accident at the site were also identified. The accident rang the alarm for the nuclear safety of nuclear power plants. It also taught us a great of lessons in nuclear emergency management. (authors)
Nuclear emergency preparedness and response in Japan. Risk management and communication regarding nuclear events

International Nuclear Information System (INIS)

Sato, Hajime

2011-01-01

Severe accidents at nuclear plants can result in long-standing and large-scale disasters encompassing wide areas. The public may have special concerns regarding these plants and radiation-related health risks. It has therefore been argued that risk communications efforts, along with rigid safety management of nuclear plants, are imperative to prevent such accidents, mitigate their impacts, and alleviate public concerns. This article introduces a set of laws, acts, codes, and guidelines concerning nuclear safety in Japan. In addition, the preparedness and mitigation plans and programs for dealing with nuclear accidents and possible disasters are also discussed. Furthermore, the ongoing accidents at the Fukushima nuclear power plants following the Great East Japan Earthquake in 2011, and the government response to them are presented. A set of points regarding the management and communications of power plant accidents are discussed. (author)
Reflections at La Rabida: the responsibilities of the nuclear physicist for peace

International Nuclear Information System (INIS)

Hodgson, P.E.

1988-01-01

Atomic energy was first applied to war but it was successful in its aim of bringing about peace. Nuclear physicists have been responsible for many momentous changes in world history. Their continuing responsibility to see that the public debates on nuclear issues of both war and peace are conducted with due regard for the essential scientific facts. Attempts by nuclear scientists to influence political decisions, through Pugwash meetings and Non-Poliferation treaties are discussed in an historical context. It is concluded that the anti-nuclear activists have won the propaganda battle about nuclear power - scientists have lost the battle to convey the facts about nuclear physics and especially nuclear safety to the public. Risks from nuclear power are perceived as great whereas in fact they are very small. Wise decisions cannot be made until the facts are known. The media is saturated with false information. Those who know the facts are unable to make their voices heard. This is exceedingly dangerous for our society. (UK)
Transgenerational genomic instability in children of irradiated parents as a result of the Chernobyl Nuclear Accident

International Nuclear Information System (INIS)

Aghajanyan, Anna; Suskov, Igor

2009-01-01

The study of families irradiated as a result of the accident at the Chernobyl Nuclear Power Plant revealed significantly increased aberrant genomes frequencies (AGFs) not only in irradiated parents (n = 106, p 137 Cs) of peripheral blood samples from the children and their parents at doses of 0.1, 0.2 and 0.3 Gy. The spectrum and frequency of chromosome aberrations were studied in the 1st and 2nd cell generations. The average AGF was significantly increased at all doses (except 0.1 Gy) in children of irradiated parents, as compared to children born from non-irradiated parents. Amplification of cells with single-break chromosome aberrations in mitosis 2, as compared to mitosis 1, suggests the replication mechanism of realization of potential damage in DNA and the occurrence of genomic instability in succeeding cell generations.
Benchmarking nuclear models for Gamow–Teller response

International Nuclear Information System (INIS)

Litvinova, E.; Brown, B.A.; Fang, D.-L.; Marketin, T.; Zegers, R.G.T.

2014-01-01

A comparative study of the nuclear Gamow–Teller response (GTR) within conceptually different state-of-the-art approaches is presented. Three nuclear microscopic models are considered: (i) the recently developed charge-exchange relativistic time blocking approximation (RTBA) based on the covariant density functional theory, (ii) the shell model (SM) with an extended “jj77” model space and (iii) the non-relativistic quasiparticle random-phase approximation (QRPA) with a Brueckner G-matrix effective interaction. We study the physics cases where two or all three of these models can be applied. The Gamow–Teller response functions are calculated for 208 Pb, 132 Sn and 78 Ni within both RTBA and QRPA. The strengths obtained for 208 Pb are compared to data that enable a firm model benchmarking. For the nucleus 132 Sn, also SM calculations are performed within the model space truncated at the level of a particle–hole (ph) coupled to vibration configurations. This allows a consistent comparison to the RTBA where ph⊗phonon coupling is responsible for the spreading width and considerable quenching of the GTR. Differences between the models and perspectives of their future developments are discussed.
Benchmarking nuclear models for Gamow–Teller response

Energy Technology Data Exchange (ETDEWEB)

Litvinova, E., E-mail: elena.litvinova@wmich.edu [Department of Physics, Western Michigan University, Kalamazoo, MI 49008-5252 (United States); National Superconducting Cyclotron Laboratory, Michigan State University, East Lansing, MI 48824-1321 (United States); Brown, B.A. [Department of Physics and Astronomy, Michigan State University, East Lansing, MI 48824-1321 (United States); National Superconducting Cyclotron Laboratory, Michigan State University, East Lansing, MI 48824-1321 (United States); Fang, D.-L. [National Superconducting Cyclotron Laboratory, Michigan State University, East Lansing, MI 48824-1321 (United States); Joint Institute for Nuclear Astrophysics, Michigan State University, East Lansing, MI 48824-1321 (United States); Marketin, T. [Physics Department, Faculty of Science, University of Zagreb (Croatia); Zegers, R.G.T. [Department of Physics and Astronomy, Michigan State University, East Lansing, MI 48824-1321 (United States); National Superconducting Cyclotron Laboratory, Michigan State University, East Lansing, MI 48824-1321 (United States); Joint Institute for Nuclear Astrophysics, Michigan State University, East Lansing, MI 48824-1321 (United States)

2014-03-07

A comparative study of the nuclear Gamow–Teller response (GTR) within conceptually different state-of-the-art approaches is presented. Three nuclear microscopic models are considered: (i) the recently developed charge-exchange relativistic time blocking approximation (RTBA) based on the covariant density functional theory, (ii) the shell model (SM) with an extended “jj77” model space and (iii) the non-relativistic quasiparticle random-phase approximation (QRPA) with a Brueckner G-matrix effective interaction. We study the physics cases where two or all three of these models can be applied. The Gamow–Teller response functions are calculated for {sup 208}Pb, {sup 132}Sn and {sup 78}Ni within both RTBA and QRPA. The strengths obtained for {sup 208}Pb are compared to data that enable a firm model benchmarking. For the nucleus {sup 132}Sn, also SM calculations are performed within the model space truncated at the level of a particle–hole (ph) coupled to vibration configurations. This allows a consistent comparison to the RTBA where ph⊗phonon coupling is responsible for the spreading width and considerable quenching of the GTR. Differences between the models and perspectives of their future developments are discussed.
Integrated genomics of ovarian xenograft tumor progression and chemotherapy response

International Nuclear Information System (INIS)

Stuckey, Ashley; Brodsky, Alexander S; Fischer, Andrew; Miller, Daniel H; Hillenmeyer, Sara; Kim, Kyu K; Ritz, Anna; Singh, Rakesh K; Raphael, Benjamin J; Brard, Laurent

2011-01-01

Ovarian cancer is the most deadly gynecological cancer with a very poor prognosis. Xenograft mouse models have proven to be one very useful tool in testing candidate therapeutic agents and gene function in vivo. In this study we identify genes and gene networks important for the efficacy of a pre-clinical anti-tumor therapeutic, MT19c. In order to understand how ovarian xenograft tumors may be growing and responding to anti-tumor therapeutics, we used genome-wide mRNA expression and DNA copy number measurements to identify key genes and pathways that may be critical for SKOV-3 xenograft tumor progression. We compared SKOV-3 xenografts treated with the ergocalciferol derived, MT19c, to untreated tumors collected at multiple time points. Cell viability assays were used to test the function of the PPARγ agonist, Rosiglitazone, on SKOV-3 cell growth. These data indicate that a number of known survival and growth pathways including Notch signaling and general apoptosis factors are differentially expressed in treated vs. untreated xenografts. As tumors grow, cell cycle and DNA replication genes show increased expression, consistent with faster growth. The steroid nuclear receptor, PPARγ, was significantly up-regulated in MT19c treated xenografts. Surprisingly, stimulation of PPARγ with Rosiglitazone reduced the efficacy of MT19c and cisplatin suggesting that PPARγ is regulating a survival pathway in SKOV-3 cells. To identify which genes may be important for tumor growth and treatment response, we observed that MT19c down-regulates some high copy number genes and stimulates expression of some low copy number genes suggesting that these genes are particularly important for SKOV-3 xenograft growth and survival. We have characterized the time dependent responses of ovarian xenograft tumors to the vitamin D analog, MT19c. Our results suggest that PPARγ promotes survival for some ovarian tumor cells. We propose that a combination of regulated expression and copy number
Semiclassical theory for the nuclear response function

International Nuclear Information System (INIS)

Stroth, U.

1986-01-01

In the first part of this thesis it was demonstrated how on a semiclassical base a RPA theory is developed and applied to electron scattering. It was shown in which fields of nuclear physics this semiclassical theory can be applied and how it is to be understood. In this connection we dedicated an extensive discussion to the Fermi gas model. From the free response function we calculated the RPA response with a finite-range residual interaction which we completely antisymmetrize. In the second part of this thesis we studied with our theory (e,e') data for the separated response functions. (orig./HSI) [de
Genome reorganization in Nicotiana asymmetric somatic hybrids analysed by in situ hybridization

International Nuclear Information System (INIS)

Parokonny, A.S.; Kenton, A.Y.; Gleba, Y.Y.; Bennett, M.D.

1992-01-01

In situ hybridization was used to examine genome reorganization in asymmetric somatic hybrids between Nicotiana plumbaginifolia and Nicotiana sylvestris obtained by fusion of gamma-irradiated protoplasts from one of the parents (donor) with non-irradiated protoplasts from the other (recipient). Probing with biotinylated total genomic DNA from either the donor or the recipient species unequivocally identified genetic material from both parents in 31 regenerant plants, each originating from a different nuclear hybrid colony. This method, termed genomic in situ hybridization (GISH), allowed intergenomic translocations containing chromosome segments from both species to be recognized in four regenerants. A probe homologous to the consensus sequence of the Arabidopsis thaliana telomeric repeat (5'-TTTAGGG-3')n, identified telomeres on all chromosomes, including 'mini-chromosomes' originating from the irradiated donor genome. Genomic in situ hybridization to plant chromosomes provides a rapid and reliable means of screening for recombinant genotypes in asymmetric somatic hybrids. Used in combination with other DNA probes, it also contributes to a greater understanding of the events responsible for genomic recovery and restabilization following genetic manipulation in vitro
SINE_scan: an efficient tool to discover short interspersed nuclear elements (SINEs) in large-scale genomic datasets.

Science.gov (United States)

Mao, Hongliang; Wang, Hao

2017-03-01

Short Interspersed Nuclear Elements (SINEs) are transposable elements (TEs) that amplify through a copy-and-paste mode via RNA intermediates. The computational identification of new SINEs are challenging because of their weak structural signals and rapid diversification in sequences. Here we report SINE_Scan, a highly efficient program to predict SINE elements in genomic DNA sequences. SINE_Scan integrates hallmark of SINE transposition, copy number and structural signals to identify a SINE element. SINE_Scan outperforms the previously published de novo SINE discovery program. It shows high sensitivity and specificity in 19 plant and animal genome assemblies, of which sizes vary from 120 Mb to 3.5 Gb. It identifies numerous new families and substantially increases the estimation of the abundance of SINEs in these genomes. The code of SINE_Scan is freely available at http://github.com/maohlzj/SINE_Scan , implemented in PERL and supported on Linux. wangh8@fudan.edu.cn. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.
Genomic Microdiversity of Bifidobacterium pseudocatenulatum Underlying Differential Strain-Level Responses to Dietary Carbohydrate Intervention

Directory of Open Access Journals (Sweden)

Guojun Wu

2017-02-01

Full Text Available The genomic basis of the response to dietary intervention of human gut beneficial bacteria remains elusive, which hinders precise manipulation of the microbiota for human health. After receiving a dietary intervention enriched with nondigestible carbohydrates for 105 days, a genetically obese child with Prader-Willi syndrome lost 18.4% of his body weight and showed significant improvement in his bioclinical parameters. We obtained five isolates (C1, C15, C55, C62, and C95 of one of the most abundantly promoted beneficial species, Bifidobacterium pseudocatenulatum, from a postintervention fecal sample. Intriguingly, these five B. pseudocatenulatum strains showed differential responses during the dietary intervention. Two strains were largely unaffected, while the other three were promoted to different extents by the changes in dietary carbohydrate resources. The differential responses of these strains were consistent with their functional clustering based on the COGs (Clusters of Orthologous Groups, including those involved with the ABC-type sugar transport systems, suggesting that the strain-specific genomic variations may have contributed to the niche adaption. Particularly, B. pseudocatenulatum C15, which had the most diverse types and highest gene copy numbers of carbohydrate-active enzymes targeting plant polysaccharides, had the highest abundance after the dietary intervention. These studies show the importance of understanding genomic diversity of specific members of the gut microbiota if precise nutrition approaches are to be realized.
Intrinsic and extrinsic molecular determinants or modulators for epigenetic remodeling and reprogramming of somatic cell-derived genome in mammalian nuclear-transferred oocytes and resultant embryos.

Science.gov (United States)

Samiec, M; Skrzyszowska, M

2018-03-01

The efficiency of somatic cell cloning in mammals remains disappointingly low. Incomplete and aberrant reprogramming of epigenetic memory of somatic cell nuclei in preimplantation nuclear- transferred (NT) embryos is one of the most important factors that limit the cloning effectiveness. The extent of epigenetic genome-wide alterations, involving histone or DNA methylation and histone deacetylation, that are mediated by histone-lysine methyltransferases (HMTs) or DNA methyltransferases (DNMTs) and histone deacetylases (HDACs) can be modulated/reversed via exogenous inhibitors of these enzymes throughout in vitro culture of nuclear donor cells, nuclear recipient oocytes and/or cloned embryos. The use of the artificial modifiers of epigenomically-conditioned gene expression leads to inhibition of both chromatin condensation and transcriptional silencing the genomic DNA of somatic cells that provide a source of nuclear donors for reconstruction of enucleated oocytes and generation of cloned embryos. The onset of chromatin decondensation and gene transcriptional activity is evoked both through specific/selective inactivating HMTs by BIX-01294 and through non-specific/non-selective blocking the activity of either DNMTs by 5-aza-2'-deoxycytidine, zebularine, S-adenosylhomocysteine or HDACs by trichostatin A, valproic acid, scriptaid, oxamflatin, sodium butyrate, m-carboxycinnamic acid bishydroxamide, panobinostat, abexinostat, quisinostat, dacinostat, belinostat and psammaplin A. Epigenomic modulation of nuclear donor cells, nuclear recipient cells and/or cloned embryos may facilitate and accelerate the reprogrammability for gene expression of donor cell nuclei that have been transplanted into a host ooplasm and subsequently underwent dedifferentiating and re-establishing the epigenetically dependent status of their transcriptional activity during pre- and postimplantation development of NT embryos. Nevertheless, a comprehensive additional work is necessary to determine
Prevention and preparedness for response to nuclear and radiological threats

International Nuclear Information System (INIS)

Pradeepkumar, K.S.

2016-01-01

Challenges from smuggled or illegally transported radioactive sources with malevolent intention of causing potential threats to the society are much higher to those potential radiological emergencies from misplaced, orphan or lost radioactive sources. Large number of radioactive sources world over is transported for its application in various fields. The emergency preparedness and response system is less developed for potential radiological emergencies caused by them compared to those at nuclear facilities which are kept in readiness to respond to any kind of emergency. After the terrorist attack on WTC of 2001, there is significant concern world over about the malicious use of nuclear and other radioactive material. This calls for prevention of stealing/smuggling of radioactive materials and improving the emergency response system. Use of Radiological Dispersal Device (RDD) and Improvised Nuclear Device (IND) are considered as possible radiological and nuclear threats, can lead to large area contamination in addition to the injuries caused by blast and thermal effects. (author)
Regeneration of somatic hybrids in relation to the nuclear and cytoplasmic genomes of wheat and Setaria italica.

Science.gov (United States)

Xiang, Fengning; Xia, Guangmin; Zhi, Daying; Wang, Jing; Nie, Hui; Chen, Huimin

2004-08-01

Somatic hybridization via PEG (Polyethylene 6000)-mediated protoplast fusion was achieved between two different wheat culture lines (Triticum aestivum L., "Jinan"177, T1 and T2) and Setaria italica (L.) P. Beauv. The T1 recipient originated from non-regenerable long-term cell suspensions, while T2 was derived from embryogenic calli with a high regeneration capacity. Donor protoplasts were obtained from embryogenic calli of S. italica (S) (with low regeneration capacity) irradiated with different doses of ultraviolet light. Twenty-three putative hybrid cell lines were produced in fusion combinations with the donor protoplasts treated with UV light for 30 s (combination I) and 1 min (combination II), but only one (from combination II) differentiated into green plants. Three cell lines from combination I and five cell lines from combination II possessed the nuclear genomes of T1, T2, and S. italica as revealed by cytological, isozyme, RAPD, and 5S rDNA spacer sequence analyses. Genomic in situ hybridization (GISH) analysis showed that most hybrid cell lines had 22-36 wheat chromosomes, 0-2 S. italica chromosomes, and 1-6 wheat - S. italica recombinant chromosomes, whereas the regenerable cell line had 44-56 wheat chromosomes and 3-6 recombinant chromosomes, but no intact S. italica chromosomes. RFLP analysis of organellar DNA revealed that mitochondrial and chloroplast DNA of both parents coexisted in all hybrid cell lines and recombined in most hybrid cell lines. These results indicate that the regeneration of hybrid plants involves not only the integration of S. italica nuclear and organellar DNA, but also the genome complementation of T1 and T2.
GENOMIC PREDICTOR OF RESPONSE AND SURVIVAL FOLLOWING TAXANE-ANTHRACYCLINE CHEMOTHERAPY FOR INVASIVE BREAST CANCER

Science.gov (United States)

Hatzis, Christos; Pusztai, Lajos; Valero, Vicente; Booser, Daniel J.; Esserman, Laura; Lluch, Ana; Vidaurre, Tatiana; Holmes, Frankie; Souchon, Eduardo; Martin, Miguel; Cotrina, José; Gomez, Henry; Hubbard, Rebekah; Chacón, J. Ignacio; Ferrer-Lozano, Jaime; Dyer, Richard; Buxton, Meredith; Gong, Yun; Wu, Yun; Ibrahim, Nuhad; Andreopoulou, Eleni; Ueno, Naoto T.; Hunt, Kelly; Yang, Wei; Nazario, Arlene; DeMichele, Angela; O’Shaughnessy, Joyce; Hortobagyi, Gabriel N.; Symmans, W. Fraser

2017-01-01

CONTEXT Accurate prediction of who will (or won’t) have high probability of survival benefit from standard treatments is fundamental for individualized cancer treatment strategies. OBJECTIVE To develop a predictor of response and survival from chemotherapy for newly diagnosed invasive breast cancer. DESIGN Development of different predictive signatures for resistance and response to neoadjuvant chemotherapy (stratified according to estrogen receptor (ER) status) from gene expression microarrays of newly diagnosed breast cancer (310 patients). Then prediction of breast cancer treatment-sensitivity using the combination of signatures for: 1) sensitivity to endocrine therapy, 2) chemo-resistance, and 3) chemo-sensitivity. Independent validation (198 patients) and comparison with other reported genomic predictors of chemotherapy response. SETTING Prospective multicenter study to develop and test genomic predictors for neoadjuvant chemotherapy. PATIENTS Newly diagnosed HER2-negative breast cancer treated with chemotherapy containing sequential taxane and anthracycline-based regimens then endocrine therapy (if hormone receptor-positive). MAIN OUTCOME MEASURES Distant relapse-free survival (DRFS) if predicted treatment-sensitive and absolute risk reduction (ARR, difference in DRFS of the two predicted groups) at median follow-up (3 years), and their 95% confidence intervals (CI). RESULTS Patients in the independent validation cohort (99% clinical Stage II–III) who were predicted to be treatment-sensitive (28% of total) had DRFS of 92% (CI 85–100) and survival benefit compared to others (absolute risk reduction (ARR) 18%; CI 6–28). Predictions were accurate if breast cancer was ER-positive (30% predicted sensitive, DRFS 97%, CI 91–100; ARR 11%, CI 0.1–21) or ER-negative (26% predicted sensitive, DRFS 83%, CI 68–100; ARR 26%, CI 4–28), and were significant in multivariate analysis after adjusting for relevant clinical-pathologic characteristics. Other
Integrative Genomic and Proteomic Analysis of the Response of Lactobacillus casei Zhang to Glucose Restriction.

Science.gov (United States)

Yu, Jie; Hui, Wenyan; Cao, Chenxia; Pan, Lin; Zhang, Heping; Zhang, Wenyi

2018-03-02

Nutrient starvation is an important survival challenge for bacteria during industrial production of functional foods. As next-generation sequencing technology has greatly advanced, we performed proteomic and genomic analysis to investigate the response of Lactobacillus casei Zhang to a glucose-restricted environment. L. casei Zhang strains were permitted to evolve in glucose-restricted or normal medium from a common ancestor over a 3 year period, and they were sampled at 1000, 2000, 3000, 4000, 5000, 6000, 7000, and 8000 generations and subjected to proteomic and genomic analyses. Genomic resequencing data revealed different point mutations and other mutational events in each selected generation of L. casei Zhang under glucose restriction stress. The differentially expressed proteins induced by glucose restriction were mostly related to fructose and mannose metabolism, carbohydrate metabolic processes, lyase activity, and amino-acid-transporting ATPase activity. Integrative proteomic and genomic analysis revealed that the mutations protected L. casei Zhang against glucose starvation by regulating other cellular carbohydrate, fatty acid, and amino acid catabolism; phosphoenolpyruvate system pathway activation; glycogen synthesis; ATP consumption; pyruvate metabolism; and general stress-response protein expression. The results help reveal the mechanisms of adapting to glucose starvation and provide new strategies for enhancing the industrial utility of L. casei Zhang.
Protection against nuclear terrorism: the IAEA response

International Nuclear Information System (INIS)

Dodd, B.

2002-01-01

Full text: As a result of the events of 11 September 2001, the International Atomic Energy Agency (IAEA) identified possible threats from acts of nuclear terrorism. A report to the Board of Governors in November 2001 summarized the IAEA's ongoing work in areas relevant to the prevention and mitigation of the consequences of such acts and outlined proposals for a number of new and/or enhanced activities. Four main threats were addressed: theft of a nuclear weapon; acquisition of nuclear material; acquisition of other radioactive material; and violent acts against nuclear facilities. These proposals have been further refined and the new plan was approved in principle at the March 2002 board meeting. In the beginning, implementation will be dependent on member state contributions to a voluntary fund. Proposed new or enhanced activities are grouped into eight areas: I. Physical protection of nuclear material and nuclear facilities; II. Detection of malicious activities involving nuclear and other radioactive materials; III. State systems for nuclear material accountancy and control; IV. Security of radioactive material other than nuclear material; V. Assessment of safety/security related vulnerability of nuclear facilities; VI. Response to malicious acts, or threats thereof; VII. Adherence to and implementation of international agreements, guidelines and recommendations; VIII. Nuclear security co-ordination and information management. After an overview, this paper focuses on activity area IV, which deals with the radiological terrorism issues involving radioactive sources. A strategy for evaluation of the IAEA's role is presented, covering an analysis of the likely threats and possible scenarios. This leads to an assessment of the most desirable sources from a terrorist's viewpoint. The strategy then examines how terrorists might acquire such sources and attempts to determine the best ways to prevent their acquisition. Further activities are proposed to prevent the use
Hyb-Seq: Combining target enrichment and genome skimming for plant phylogenomics1

Science.gov (United States)

Weitemier, Kevin; Straub, Shannon C. K.; Cronn, Richard C.; Fishbein, Mark; Schmickl, Roswitha; McDonnell, Angela; Liston, Aaron

2014-01-01

• Premise of the study: Hyb-Seq, the combination of target enrichment and genome skimming, allows simultaneous data collection for low-copy nuclear genes and high-copy genomic targets for plant systematics and evolution studies. • Methods and Results: Genome and transcriptome assemblies for milkweed (Asclepias syriaca) were used to design enrichment probes for 3385 exons from 768 genes (>1.6 Mbp) followed by Illumina sequencing of enriched libraries. Hyb-Seq of 12 individuals (10 Asclepias species and two related genera) resulted in at least partial assembly of 92.6% of exons and 99.7% of genes and an average assembly length >2 Mbp. Importantly, complete plastomes and nuclear ribosomal DNA cistrons were assembled using off-target reads. Phylogenomic analyses demonstrated signal conflict between genomes. • Conclusions: The Hyb-Seq approach enables targeted sequencing of thousands of low-copy nuclear exons and flanking regions, as well as genome skimming of high-copy repeats and organellar genomes, to efficiently produce genome-scale data sets for phylogenomics. PMID:25225629

Non-genomic effects of the NR4A1/Nur77/TR3/NGFIB orphan nuclear receptor.

Science.gov (United States)

Pawlak, Alicja; Strzadala, Leon; Kalas, Wojciech

2015-03-01

The orphan nuclear receptor NR4A1/Nur77/TR3/NGFIB acts primarily as a transcription factor to regulate the expression of multiple genes. However, increasing research attention has recently been given to non-genomic activities of NR4A1. The first description of a non-genomic action of NR4A1 referred to the conversion of anti-apoptotic Bcl-2 into a pro-apoptotic protein by direct interaction with NR4A1. In response to certain apoptotic stimuli, NR4A1 translocates from the nucleus to the mitochondrial outer membrane (MOM) where it associates with Bcl-2 and thereby causes apoptosis. Afterwards, it appeared that NR4A1 could also bind and convert other anti-apoptotic Bcl-2 family members. The latest studies indicate a significant role of NR4A1 in the process of autophagy. For example, a new NR4A1-mediated pathway specific for melanoma cells has been described where NR4A1 interacts with the adenine nucleotide translocase 1 (ANT1) on the mitochondrial inner membrane (MIM) leading to induction of the autophagy pathway. Moreover, NR4A1 interaction with cytoplasmic p53 may also contribute to the induction of autophagy. In addition to mitochondria, NR4A1 could be translocated to the outer membrane of the endoplasmic reticulum (ER) and associate with Bcl-2 or translocon-associated protein subunit γ (TRAPγ) causing ER stress-induced apoptosis. NR4A1 also contributes to the proteasomal degradation of β-catenin in colon cancer cells in vitro and in vivo, as well as to the stabilization of hypoxia-inducible factor-1α (HIF-1α) under non-hypoxic conditions. This review summarizes research findings on non-genomic effects of NR4A1 in normal and cancer cells. Copyright © 2015 Elsevier Inc. All rights reserved.
Response to the accident at TEPCO's Fukushima Daiichi Nuclear Power Plants

International Nuclear Information System (INIS)

Nei, Hisanori

2012-01-01

This article was reading from the author's plenary lecture at the thermal and nuclear power generation convention 2011, which was summary of the author edited report of Japanese government to IAEA ministerial conference on nuclear safety. The article consisted of (1) outlines of occurrence and development of the accident at TEPCO's Fukushima Daiichi Nuclear Power Plants (NPPs), (2) comparison of Fukushima Daiichi NPPs with other NPPs (Fukushima Daini, Onagawa and Tokai Daini NPPs), (3) major countermeasures to settle the situation regarding the accident, (4) comprehensive safety evaluation of other NPPs as response to the accident and (5) lessons learned from the accident so far. It was highly important to ensure power supplies and robust cooling functions of reactors, pressure containment vessels and spent fuel pools. 28 lessons were categorized into five groups such as (1) strengthen preventive measures against a severe accident, (2) enhancement of response measures against severe accidents, (3) enhancement of nuclear emergency responses, (4) reinforcement of safety infrastructure and (5) thoroughness of safety culture. (T. Tanaka)
Genome wide analysis of stress responsive WRKY transcription factors in Arabidopsis thaliana

Directory of Open Access Journals (Sweden)

Shaiq Sultan

2016-04-01

Full Text Available WRKY transcription factors are a class of DNA-binding proteins that bind with a specific sequence C/TTGACT/C known as W-Box found in promoters of genes which are regulated by these WRKYs. From previous studies, 43 different stress responsive WRKY transcription factors in Arabidopsis thaliana, identified and then categorized in three groups viz., abiotic, biotic and both of these stresses. A comprehensive genome wide analysis including chromosomal localization, gene structure analysis, multiple sequence alignment, phylogenetic analysis and promoter analysis of these WRKY genes was carried out in this study to determine the functional homology in Arabidopsis. This analysis led to the classification of these WRKY family members into 3 major groups and subgroups and showed evolutionary relationship among these groups on the base of their functional WRKY domain, chromosomal localization and intron/exon structure. The proposed groups of these stress responsive WRKY genes and annotation based on their position on chromosomes can also be explored to determine their functional homology in other plant species in relation to different stresses. The result of the present study provides indispensable genomic information for the stress responsive WRKY transcription factors in Arabidopsis and will pave the way to explain the precise role of various AtWRKYs in plant growth and development under stressed conditions.
Preparedness for and response to a radiological or nuclear incident

International Nuclear Information System (INIS)

Norman Coleman, C.

2014-01-01

Public health and medical planning for a nuclear or radiological incident requires a complex, multi-faceted systematic approach involving federal, state and local governments, private sector organizations, academia, industry, international partners and individual experts and volunteers. The approach developed by the U.S. Department of Health and Human Services in collaboration with other U.S. Departments is the result of efforts from government and non-government experts that connect the available capabilities, resources, guidance tools, underlying concepts and science into the Nuclear Incident Medical Enterprise (NlME). It is a systems approach that can be used to support planning for, response to, and recovery from the effects of a nuclear incident. Experience is gained in exercises specific to radiation but also from other mass casualty incidents as there are many principles and components in common. Resilience and the ability to mitigate the consequences of a nuclear incident are enhanced by effective planning, preparation and training, timely response, clear communication, and continuous improvements based on new science, technology, experience and ideas. Recognizing that preparation for a radiological or nuclear incident will be a lower priority for healthcare workers and responders due to other demands, the Radiation Emergency Medical Management website has been developed with the National Library of Medicine. This includes tools for education and training, just-in-time medical management and triage among others. Most of the components of NIME are published in the peer review medical and disaster medicine literature to help ensure high quality and accessibility. While NIME is a continuous work-in-progress, the current status of the public health and medical preparedness and response for a nuclear incident is presented. (author)
Additional mitochondrial DNA influences the interactions between the nuclear and mitochondrial genomes in a bovine embryo model of nuclear transfer.

Science.gov (United States)

Srirattana, Kanokwan; St John, Justin C

2018-05-08

We generated cattle embryos using mitochondrial supplementation and somatic cell nuclear transfer (SCNT), named miNT, to determine how additional mitochondrial DNA (mtDNA) modulates the nuclear genome. To eliminate any confounding effects from somatic cell mtDNA in intraspecies SCNT, donor cell mtDNA was depleted prior to embryo production. Additional oocyte mtDNA did not affect embryo development rates but increased mtDNA copy number in blastocyst stage embryos. Moreover, miNT-derived blastocysts had different gene expression profiles when compared with SCNT-derived blastocysts. Additional mtDNA increased expression levels of genes involved in oxidative phosphorylation, cell cycle and DNA repair. Supplementing the embryo culture media with a histone deacetylase inhibitor, Trichostatin A (TSA), had no beneficial effects on the development of miNT-derived embryos, unlike SCNT-derived embryos. When compared with SCNT-derived blastocysts cultured in the presence of TSA, additional mtDNA alone had beneficial effects as the activity of glycolysis may increase and embryonic cell death may decrease. However, these beneficial effects were not found with additional mtDNA and TSA together, suggesting that additional mtDNA alone enhances reprogramming. In conclusion, additional mtDNA increased mtDNA copy number and expression levels of genes involved in energy production and embryo development in blastocyst stage embryos emphasising the importance of nuclear-mitochondrial interactions.
Supporting system in emergency response plan for nuclear material transport accidents

International Nuclear Information System (INIS)

Nakagome, Y.; Aoki, S.

1993-01-01

As aiming to provide the detailed information concerning nuclear material transport accidents and to supply it to the concerned organizations by an online computer, the Emergency Response Supporting System has been constructed in the Nuclear Safety Technology Center, Japan. The system consists of four subsystems and four data bases. By inputting initial information such as name of package and date of accident, one can obtain the appropriate initial response procedures and related information for the accident immediately. The system must be useful for protecting the public safety from nuclear material transport accidents. But, it is not expected that the system shall be used in future. (J.P.N.)
Targeted Identification of Short Interspersed Nuclear Element Families Shows Their Widespread Existence and Extreme Heterogeneity in Plant Genomes[W

Science.gov (United States)

Wenke, Torsten; Döbel, Thomas; Sörensen, Thomas Rosleff; Junghans, Holger; Weisshaar, Bernd; Schmidt, Thomas

2011-01-01

Short interspersed nuclear elements (SINEs) are non-long terminal repeat retrotransposons that are highly abundant, heterogeneous, and mostly not annotated in eukaryotic genomes. We developed a tool designated SINE-Finder for the targeted discovery of tRNA-derived SINEs. We analyzed sequence data of 16 plant genomes, including 13 angiosperms and three gymnosperms and identified 17,829 full-length and truncated SINEs falling into 31 families showing the widespread occurrence of SINEs in higher plants. The investigation focused on potato (Solanum tuberosum), resulting in the detection of seven different SolS SINE families consisting of 1489 full-length and 870 5′ truncated copies. Consensus sequences of full-length members range in size from 106 to 244 bp depending on the SINE family. SolS SINEs populated related species and evolved separately, which led to some distinct subfamilies. Solanaceae SINEs are dispersed along chromosomes and distributed without clustering but with preferred integration into short A-rich motifs. They emerged more than 23 million years ago and were species specifically amplified during the radiation of potato, tomato (Solanum lycopersicum), and tobacco (Nicotiana tabacum). We show that tobacco TS retrotransposons are composite SINEs consisting of the 3′ end of a long interspersed nuclear element integrated downstream of a nonhomologous SINE family followed by successfully colonization of the genome. We propose an evolutionary scenario for the formation of TS as a spontaneous event, which could be typical for the emergence of SINE families. PMID:21908723
[Non-LTR retrotransposons: LINEs and SINEs in plant genome].

Science.gov (United States)

Cheng, Xu-Dong; Ling, Hong-Qing

2006-06-01

Retrotransposons are one of the drivers of genome evolution. They include LTR (long terminal repeat) retrotransposons, which widespread in Eukaryotagenomes, show structural similarity to retroviruses. Non-LTR retrotransposons were first discovered in animal genomes and then identified as ubiquitous components of nuclear genomes in many species across the plant kingdom. They constitute a large fraction of the repetitive DNA. Non-LTR retrotransposons are divided into LINEs (long interspersed nuclear elements) and SINEs (short interspersed nuclear elements). Transposition of non-LTR retrotransposons is rarely observed in plants indicating that most of them are inactive and/or under regulation of the host genome. Transposition is poorly understood, but experimental evidence from other genetic systems shows that LINEs are able to transpose autonomously while non-autonomous SINEs depend on the reverse transcription machinery of other retrotransposons. Phylogenic analysis shows LINEs are probably the most ancient class of retrotransposons in plant genomes, while the origin of SINEs is unknown. This review sums up the above data and wants to show readers a clear picture of non-LTR retrotransposons.
Meta-analysis of genome-wide association studies of HDL cholesterol response to statins

NARCIS (Netherlands)

Postmus, Iris; Warren, Helen R.; Trompet, Stella; Arsenault, Benoit J.; Avery, Christy L.; Bis, Joshua C.; Chasman, Daniel I.; de Keyser, Catherine E.; Deshmukh, Harshal A.; Evans, Daniel S.; Feng, QiPing; Li, Xiaohui; Smit, Roelof A. J.; Smith, Albert V.; Sun, Fangui; Taylor, Kent D.; Arnold, Alice M.; Barnes, Michael R.; Barratt, Bryan J.; Betteridge, John; Boekholdt, S. Matthijs; Boerwinkle, Eric; Buckley, Brendan M.; Chen, Y.-D. Ida; de Craen, Anton J. M.; Cummings, Steven R.; Denny, Joshua C.; Dubé, Marie Pierre; Durrington, Paul N.; Eiriksdottir, Gudny; Ford, Ian; Guo, Xiuqing; Harris, Tamara B.; Heckbert, Susan R.; Hofman, Albert; Hovingh, G. Kees; Kastelein, John J. P.; Launer, Leonore J.; Liu, Ching-Ti; Liu, Yongmei; Lumley, Thomas; McKeigue, Paul M.; Munroe, Patricia B.; Neil, Andrew; Nickerson, Deborah A.; Nyberg, Fredrik; O'Brien, Eoin; O'Donnell, Christopher J.; Post, Wendy; Poulter, Neil; Vasan, Ramachandran S.; Rice, Kenneth; Rich, Stephen S.; Rivadeneira, Fernando; Sattar, Naveed; Sever, Peter; Shaw-Hawkins, Sue; Shields, Denis C.; Slagboom, P. Eline; Smith, Nicholas L.; Smith, Joshua D.; Sotoodehnia, Nona; Stanton, Alice; Stott, David J.; Stricker, Bruno H.; Stürmer, Til; Uitterlinden, André G.; Wei, Wei-Qi; Westendorp, Rudi G. J.; Whitsel, Eric A.; Wiggins, Kerri L.; Wilke, Russell A.; Ballantyne, Christie M.; Colhoun, Helen M.; Cupples, L. Adrienne; Franco, Oscar H.; Gudnason, Vilmundur; Hitman, Graham; Palmer, Colin N. A.; Psaty, Bruce M.; Ridker, Paul M.; Stafford, Jeanette M.; Stein, Charles M.; Tardif, Jean-Claude; Caulfield, Mark J.; Jukema, J. Wouter; Rotter, Jerome I.; Krauss, Ronald M.

2016-01-01

In addition to lowering low density lipoprotein cholesterol (LDL-C), statin therapy also raises high density lipoprotein cholesterol (HDL-C) levels. Inter-individual variation in HDL-C response to statins may be partially explained by genetic variation. We performed a meta-analysis of genome-wide
Initial operations in local nuclear emergency response headquarter

International Nuclear Information System (INIS)

2012-06-01

As a result of the Fukushima nuclear accident due to the Great East Japan Earthquake and the tsunami that occurred thereafter, local nuclear emergency response headquarters (local headquarters) was set up at off-site center (OFC). However, several obstacles such as the collapse of means of communication resulting from severed communication lines, food and fuel shortage resulting from stagnant physical distribution, and increasing radiation dose around the center significantly restricted originally intended operation of local headquarters. In such severe situation, the personnel gathered at the OFC from the government, local public bodies and electric companies from March 11 to 15 acted without sufficient food, sleep or rest and did all they could against successively occurring unexpected challenges by using limited means of communication. However, issues requiring further consideration were activities of each functional group, location of OFC and the functions of equipment, machines and materials and reflecting the consideration results into future protective measures and revision of the manual for nuclear emergency response were greatly important. This report described investigated results on initial operations in local headquarters such as situation of activities conducted by local headquarters and operations at functional groups. (T. Tanaka)
Update of the Nuclear Criticality Slide Rule for the Emergency Response to a Nuclear Criticality Accident

Science.gov (United States)

Duluc, Matthieu; Bardelay, Aurélie; Celik, Cihangir; Heinrichs, Dave; Hopper, Calvin; Jones, Richard; Kim, Soon; Miller, Thomas; Troisne, Marc; Wilson, Chris

2017-09-01

AWE (UK), IRSN (France), LLNL (USA) and ORNL (USA) began a long term collaboration effort in 2015 to update the nuclear criticality Slide Rule for the emergency response to a nuclear criticality accident. This document, published almost 20 years ago, gives order of magnitude estimates of key parameters, such as number of fissions and doses (neutron and gamma), useful for emergency response teams and public authorities. This paper will present, firstly the motivation and the long term objectives for this update, then the overview of the initial configurations for updated calculations and preliminary results obtained with modern 3D codes.
Update of the Nuclear Criticality Slide Rule for the Emergency Response to a Nuclear Criticality Accident

Directory of Open Access Journals (Sweden)

Duluc Matthieu

2017-01-01

Full Text Available AWE (UK, IRSN (France, LLNL (USA and ORNL (USA began a long term collaboration effort in 2015 to update the nuclear criticality Slide Rule for the emergency response to a nuclear criticality accident. This document, published almost 20 years ago, gives order of magnitude estimates of key parameters, such as number of fissions and doses (neutron and gamma, useful for emergency response teams and public authorities. This paper will present, firstly the motivation and the long term objectives for this update, then the overview of the initial configurations for updated calculations and preliminary results obtained with modern 3D codes.
Lophotrochozoan mitochondrial genomes

Energy Technology Data Exchange (ETDEWEB)

Valles, Yvonne; Boore, Jeffrey L.

2005-10-01

Progress in both molecular techniques and phylogeneticmethods has challenged many of the interpretations of traditionaltaxonomy. One example is in the recognition of the animal superphylumLophotrochozoa (annelids, mollusks, echiurans, platyhelminthes,brachiopods, and other phyla), although the relationships within thisgroup and the inclusion of some phyla remain uncertain. While much ofthis progress in phylogenetic reconstruction has been based on comparingsingle gene sequences, we are beginning to see the potential of comparinglarge-scale features of genomes, such as the relative order of genes.Even though tremendous progress is being made on the sequencedetermination of whole nuclear genomes, the dataset of choice forgenome-level characters for many animals across a broad taxonomic rangeremains mitochondrial genomes. We review here what is known aboutmitochondrial genomes of the lophotrochozoans and discuss the promisethat this dataset will enable insight into theirrelationships.
Salinity- and population-dependent genome regulatory response during osmotic acclimation in the killifish (Fundulus heteroclitus) gill.

Science.gov (United States)

Whitehead, Andrew; Roach, Jennifer L; Zhang, Shujun; Galvez, Fernando

2012-04-15

The killifish Fundulus heteroclitus is abundant in osmotically dynamic estuaries and it can quickly adjust to extremes in environmental salinity. We performed a comparative osmotic challenge experiment to track the transcriptomic and physiological responses to two salinities throughout a time course of acclimation, and to explore the genome regulatory mechanisms that enable extreme osmotic acclimation. One southern and one northern coastal population, known to differ in their tolerance to hypo-osmotic exposure, were used as our comparative model. Both populations could maintain osmotic homeostasis when transferred from 32 to 0.4 p.p.t., but diverged in their compensatory abilities when challenged down to 0.1 p.p.t., in parallel with divergent transformation of gill morphology. Genes involved in cell volume regulation, nucleosome maintenance, ion transport, energetics, mitochondrion function, transcriptional regulation and apoptosis showed population- and salinity-dependent patterns of expression during acclimation. Network analysis confirmed the role of cytokine and kinase signaling pathways in coordinating the genome regulatory response to osmotic challenge, and also posited the importance of signaling coordinated through the transcription factor HNF-4α. These genome responses support hypotheses of which regulatory mechanisms are particularly relevant for enabling extreme physiological flexibility.
An emergency response centre (ERC) for the preparedness and response to nuclear and radiological emergencies

International Nuclear Information System (INIS)

Pradeepkumar, K.S.; Sharma, D.N.; Abani, M.C.

2001-01-01

This paper discusses the requirement for a state of the art Emergency Response Centre (ERC) to be developed and kept in readiness for the quick response to any nuclear or radiological emergencies. For an effective response to any major nuclear emergency an ERC having the facilities of i) environmental dose rate monitoring network established using both mobile and fixed units ii) on-line meteorological data collection and information station iii) on-line computation and prediction of isodose curves in real time and iv) properly developed and tested monitoring methodologies are essential. Vehicles with on-line data transfer facility to the ERC and equipped with different type of monitoring systems can function as Mobile Monitoring Laboratories (MMLs) and can help in quick decision making even during a radiological emergency far away from the ERC. (author)
Evaluating droplet digital PCR for the quantification of human genomic DNA: converting copies per nanoliter to nanograms nuclear DNA per microliter.

Science.gov (United States)

Duewer, David L; Kline, Margaret C; Romsos, Erica L; Toman, Blaza

2018-05-01

The highly multiplexed polymerase chain reaction (PCR) assays used for forensic human identification perform best when used with an accurately determined quantity of input DNA. To help ensure the reliable performance of these assays, we are developing a certified reference material (CRM) for calibrating human genomic DNA working standards. To enable sharing information over time and place, CRMs must provide accurate and stable values that are metrologically traceable to a common reference. We have shown that droplet digital PCR (ddPCR) limiting dilution end-point measurements of the concentration of DNA copies per volume of sample can be traceably linked to the International System of Units (SI). Unlike values assigned using conventional relationships between ultraviolet absorbance and DNA mass concentration, entity-based ddPCR measurements are expected to be stable over time. However, the forensic community expects DNA quantity to be stated in terms of mass concentration rather than entity concentration. The transformation can be accomplished given SI-traceable values and uncertainties for the number of nucleotide bases per human haploid genome equivalent (HHGE) and the average molar mass of a nucleotide monomer in the DNA polymer. This report presents the considerations required to establish the metrological traceability of ddPCR-based mass concentration estimates of human nuclear DNA. Graphical abstract The roots of metrological traceability for human nuclear DNA mass concentration results. Values for the factors in blue must be established experimentally. Values for the factors in red have been established from authoritative source materials. HHGE stands for "haploid human genome equivalent"; there are two HHGE per diploid human genome.
Transient Genome-Wide Transcriptional Response to Low-Dose Ionizing Radiation In Vivo in Humans

International Nuclear Information System (INIS)

Berglund, Susanne R.; Rocke, David M.; Dai Jian; Schwietert, Chad W.; Santana, Alison; Stern, Robin L.; Lehmann, Joerg; Hartmann Siantar, Christine L.; Goldberg, Zelanna

2008-01-01

Purpose: The in vivo effects of low-dose low linear energy transfer ionizing radiation on healthy human skin are largely unknown. Using a patient-based tissue acquisition protocol, we have performed a series of genomic analyses on the temporal dynamics over a 24-hour period to determine the radiation response after a single exposure of 10 cGy. Methods and Materials: RNA from each patient tissue sample was hybridized to an Affymetrix Human Genome U133 Plus 2.0 array. Data analysis was performed on selected gene groups and pathways. Results: Nineteen gene groups and seven gene pathways that had been shown to be radiation responsive were analyzed. Of these, nine gene groups showed significant transient transcriptional changes in the human tissue samples, which returned to baseline by 24 hours postexposure. Conclusions: Low doses of ionizing radiation on full-thickness human skin produce a definable temporal response out to 24 hours postexposure. Genes involved in DNA and tissue remodeling, cell cycle transition, and inflammation show statistically significant changes in expression, despite variability between patients. These data serve as a reference for the temporal dynamics of ionizing radiation response following low-dose exposure in healthy full-thickness human skin
Generic Procedures for Response to a Nuclear or Radiological Emergency at Research Reactors

International Nuclear Information System (INIS)

2011-01-01

Under Article 5.a(ii) of the Convention on Assistance in the Case of a Nuclear Accident or Radiological Emergency (Assistance Convention), one function of the IAEA is to collect and disseminate to States Parties and Member States information concerning methodologies, techniques and results of research relating to response to nuclear or radiological emergencies. The IAEA publishes the Emergency Preparedness and Response Series to fulfil that function. This publication is part of that series. IAEA Safety Standards Series No. GS-R-2 Preparedness and Response for a Nuclear or Radiological Emergency, contains the following requirement: 'To ensure that arrangements are in place for a timely, managed, controlled, coordinated and effective response at the scene...'. The IAEA General Conference, in resolution GC(53)/RES/10, continues to encourage Member States '...to enhance, where necessary, their own preparedness and response capabilities for nuclear and radiological incidents and emergencies, by improving capabilities to prevent accidents, to respond to emergencies and to mitigate any harmful consequences...'. This publication is intended to assist Member States meet the requirements of GS-R-2 and enhance their preparedness by providing guidance on the response by facility personnel to emergencies at research reactor facilities.
Verifying a nuclear weapon`s response to radiation environments

Energy Technology Data Exchange (ETDEWEB)

Dean, F.F.; Barrett, W.H.

1998-05-01

The process described in the paper is being applied as part of the design verification of a replacement component designed for a nuclear weapon currently in the active stockpile. This process is an adaptation of the process successfully used in nuclear weapon development programs. The verification process concentrates on evaluating system response to radiation environments, verifying system performance during and after exposure to radiation environments, and assessing system survivability.
Sequencing of whole plastid genomes and nuclear ribosomal DNA of Diospyros species (Ebenaceae) endemic to New Caledonia: many species, little divergence.

Science.gov (United States)

Turner, Barbara; Paun, Ovidiu; Munzinger, Jérôme; Chase, Mark W; Samuel, Rosabelle

2016-06-01

Some plant groups, especially on islands, have been shaped by strong ancestral bottlenecks and rapid, recent radiation of phenotypic characters. Single molecular markers are often not informative enough for phylogenetic reconstruction in such plant groups. Whole plastid genomes and nuclear ribosomal DNA (nrDNA) are viewed by many researchers as sources of information for phylogenetic reconstruction of groups in which expected levels of divergence in standard markers are low. Here we evaluate the usefulness of these data types to resolve phylogenetic relationships among closely related Diospyros species. Twenty-two closely related Diospyros species from New Caledonia were investigated using whole plastid genomes and nrDNA data from low-coverage next-generation sequencing (NGS). Phylogenetic trees were inferred using maximum parsimony, maximum likelihood and Bayesian inference on separate plastid and nrDNA and combined matrices. The plastid and nrDNA sequences were, singly and together, unable to provide well supported phylogenetic relationships among the closely related New Caledonian Diospyros species. In the nrDNA, a 6-fold greater percentage of parsimony-informative characters compared with plastid DNA was found, but the total number of informative sites was greater for the much larger plastid DNA genomes. Combining the plastid and nuclear data improved resolution. Plastid results showed a trend towards geographical clustering of accessions rather than following taxonomic species. In plant groups in which multiple plastid markers are not sufficiently informative, an investigation at the level of the entire plastid genome may also not be sufficient for detailed phylogenetic reconstruction. Sequencing of complete plastid genomes and nrDNA repeats seems to clarify some relationships among the New Caledonian Diospyros species, but the higher percentage of parsimony-informative characters in nrDNA compared with plastid DNA did not help to resolve the phylogenetic tree

Genome sequence of the lager brewing yeast, an interspecies hybrid.

Science.gov (United States)

Nakao, Yoshihiro; Kanamori, Takeshi; Itoh, Takehiko; Kodama, Yukiko; Rainieri, Sandra; Nakamura, Norihisa; Shimonaga, Tomoko; Hattori, Masahira; Ashikari, Toshihiko

2009-04-01

This work presents the genome sequencing of the lager brewing yeast (Saccharomyces pastorianus) Weihenstephan 34/70, a strain widely used in lager beer brewing. The 25 Mb genome comprises two nuclear sub-genomes originating from Saccharomyces cerevisiae and Saccharomyces bayanus and one circular mitochondrial genome originating from S. bayanus. Thirty-six different types of chromosomes were found including eight chromosomes with translocations between the two sub-genomes, whose breakpoints are within the orthologous open reading frames. Several gene loci responsible for typical lager brewing yeast characteristics such as maltotriose uptake and sulfite production have been increased in number by chromosomal rearrangements. Despite an overall high degree of conservation of the synteny with S. cerevisiae and S. bayanus, the syntenies were not well conserved in the sub-telomeric regions that contain lager brewing yeast characteristic and specific genes. Deletion of larger chromosomal regions, a massive unilateral decrease of the ribosomal DNA cluster and bilateral truncations of over 60 genes reflect a post-hybridization evolution process. Truncations and deletions of less efficient maltose and maltotriose uptake genes may indicate the result of adaptation to brewing. The genome sequence of this interspecies hybrid yeast provides a new tool for better understanding of lager brewing yeast behavior in industrial beer production.
Congruent Deep Relationships in the Grape Family (Vitaceae) Based on Sequences of Chloroplast Genomes and Mitochondrial Genes via Genome Skimming.

Science.gov (United States)

Zhang, Ning; Wen, Jun; Zimmer, Elizabeth A

2015-01-01

Vitaceae is well-known for having one of the most economically important fruits, i.e., the grape (Vitis vinifera). The deep phylogeny of the grape family was not resolved until a recent phylogenomic analysis of 417 nuclear genes from transcriptome data. However, it has been reported extensively that topologies based on nuclear and organellar genes may be incongruent due to differences in their evolutionary histories. Therefore, it is important to reconstruct a backbone phylogeny of the grape family using plastomes and mitochondrial genes. In this study,next-generation sequencing data sets of 27 species were obtained using genome skimming with total DNAs from silica-gel preserved tissue samples on an Illumina NextSeq 500 instrument [corrected]. Plastomes were assembled using the combination of de novo and reference genome (of V. vinifera) methods. Sixteen mitochondrial genes were also obtained via genome skimming using the reference genome of V. vinifera. Extensive phylogenetic analyses were performed using maximum likelihood and Bayesian methods. The topology based on either plastome data or mitochondrial genes is congruent with the one using hundreds of nuclear genes, indicating that the grape family did not exhibit significant reticulation at the deep level. The results showcase the power of genome skimming in capturing extensive phylogenetic data: especially from chloroplast and mitochondrial DNAs.
Congruent Deep Relationships in the Grape Family (Vitaceae Based on Sequences of Chloroplast Genomes and Mitochondrial Genes via Genome Skimming.

Directory of Open Access Journals (Sweden)

Ning Zhang

Full Text Available Vitaceae is well-known for having one of the most economically important fruits, i.e., the grape (Vitis vinifera. The deep phylogeny of the grape family was not resolved until a recent phylogenomic analysis of 417 nuclear genes from transcriptome data. However, it has been reported extensively that topologies based on nuclear and organellar genes may be incongruent due to differences in their evolutionary histories. Therefore, it is important to reconstruct a backbone phylogeny of the grape family using plastomes and mitochondrial genes. In this study,next-generation sequencing data sets of 27 species were obtained using genome skimming with total DNAs from silica-gel preserved tissue samples on an Illumina NextSeq 500 instrument [corrected]. Plastomes were assembled using the combination of de novo and reference genome (of V. vinifera methods. Sixteen mitochondrial genes were also obtained via genome skimming using the reference genome of V. vinifera. Extensive phylogenetic analyses were performed using maximum likelihood and Bayesian methods. The topology based on either plastome data or mitochondrial genes is congruent with the one using hundreds of nuclear genes, indicating that the grape family did not exhibit significant reticulation at the deep level. The results showcase the power of genome skimming in capturing extensive phylogenetic data: especially from chloroplast and mitochondrial DNAs.
Understanding the Value of a Computer Emergency Response Capability for Nuclear Security

Energy Technology Data Exchange (ETDEWEB)

Gasper, Peter Donald [Idaho National Laboratory; Rodriguez, Julio Gallardo [Idaho National Laboratory

2015-06-01

The international nuclear community has a great understanding of the physical security needs relating to the prevention, detection, and response of malicious acts associated with nuclear facilities and radioactive material. International Atomic Energy Agency (IAEA) Nuclear Security Recommendations (INFCIRC_225_Rev 5) outlines specific guidelines and recommendations for implementing and maintaining an organization’s nuclear security posture. An important element for inclusion into supporting revision 5 is the establishment of a “Cyber Emergency Response Team (CERT)” focused on the international communities cybersecurity needs to maintain a comprehensive nuclear security posture. Cybersecurity and the importance of nuclear cybersecurity require that there be a specific focus on developing an International Nuclear CERT (NS-CERT). States establishing contingency plans should have an understanding of the cyber threat landscape and the potential impacts to systems in place to protect and mitigate malicious activities. This paper will outline the necessary components, discuss the relationships needed within the international community, and outline a process by which the NS-CERT identifies, collects, processes, and reports critical information in order to establish situational awareness (SA) and support decision-making
Trial application of guidelines for nuclear plant response to an earthquake

International Nuclear Information System (INIS)

Schmidt, W.; Oliver, R.; O'Connor, W.

1993-09-01

Guidelines have been developed to assist nuclear plant personnel in the preparation of earthquake response procedures for nuclear power plants. These guidelines are published in EPRI report NP-6695, ''Guidelines for Nuclear Plant Response to an Earthquake,'' dated December 1989. This report includes two sets of nuclear plant procedures which were prepared to implement the guidelines of EPRI report NP-6695. The first set were developed by the Toledo Edison Company Davis-Besse plant. Davis-Besse is a pressurized water reactor (PWR) and contains relatively standard seismic monitoring instrumentation typical of many domestic nuclear plants. The second set of procedures were prepared by Yankee Atomic Electric Company for the Vermont Yankee facility. This plant is a boiling water reactor (BWR) with state-of-the-art seismic monitoring and PC-based data processing equipment, software developed specifically to implement the OBE Exceedance Criterion presented in EPRI report NP-5930, ''A Criterion for Determining Exceedance of the operating Basis Earthquake.'' The two sets of procedures are intended to demonstrate how two different nuclear utilities have interpreted and applied the EPRI guidance given in report NP-6695
Validation of Infinite Impulse Response Multilayer Perceptron for Modelling Nuclear Dynamics

Directory of Open Access Journals (Sweden)

F. Cadini

2008-01-01

Full Text Available Artificial neural networks are powerful algorithms for constructing nonlinear empirical models from operational data. Their use is becoming increasingly popular in the complex modeling tasks required by diagnostic, safety, and control applications in complex technologies such as those employed in the nuclear industry. In this paper, the nonlinear modeling capabilities of an infinite impulse response multilayer perceptron (IIR-MLP for nuclear dynamics are considered in comparison to static modeling by a finite impulse response multilayer perceptron (FIR-MLP and a conventional static MLP. The comparison is made with respect to the nonlinear dynamics of a nuclear reactor as investigated by IIR-MLP in a previous paper. The superior performance of the locally recurrent scheme is demonstrated.
Critical seismic response of nuclear reactors

International Nuclear Information System (INIS)

Drenick, R.F.; Wang, P.C.; Yun, C.B.; Philappacopoulos, A.J.

1980-01-01

This paper deals with the problem of how to assess the seismic resistance of important structures, particularly of nuclear reactor structures. Most of the design procedures presently in use or under investigation are based on design response spectra obtained by statistical evaluation of past ground excitations assuming certain probability distributions (e.g., normal or lognormal) of response peaks. Artificial time histories generated from these spectra are also used. However, it is not clear whether these approaches lead to designs that can be relied upon on the confidence levels that are presumably desired for structures such as nuclear reactors whose integrity during an earthquake is of considerable importance. The trouble lies with the fact that the analysis of structural integrity seems highly sensitive to the assumptions regarding the nature of those probability distributions: small variations, especially in the tails of the distributions, can induce large changes in the desired results. This greatly weakens the reliance that can be placed in many assessments of earthquake resistance. In this paper, a new method is developed which has the potential of avoiding those weaknesses. It is more specifically based on assumptions that seem well supported by seismological observations but side-steps others, especially those regarding probability distribution of ground motions, which are more conjectural. (orig./RW)
Production of ABA responses requires both the nuclear and cytoplasmic functional involvement of PYR1

International Nuclear Information System (INIS)

Park, EunJoo; Kim, Tae-Houn

2017-01-01

Abscisic acid (ABA) enhances stress tolerant responses in plants against unfavorable environmental conditions. In Arabidopsis, ABA promotes interactions between PYR/PYL/RCARs and PP2C, thereby allowing SnRK2s to phosphorylate downstream components required for the regulation of gene expression or for gating ion channels. Because PYR1 is known to localize to nucleus and cytoplasm it is a question whether nuclear or cytoplasmic PYR1 confer different functions to the ABA signaling pathway, as has been previously shown for regulatory proteins. In order to answer this question, transgenic lines expressing nuclear PYR1 were generated in an ABA insensitive mutant background. Enforced nuclear expression of PYR1 was examined by confocal microscopy and western blot analysis. Physiological analyses of the transgenic lines demonstrated that nuclear PYR1 is sufficient to generate ABA responses, such as, the inhibition of seed germination, root growth inhibition, the induction of gene expression, and stomatal closing movement. However, for the full recovery of ABA responses in the mutant background cytoplasmic PYR1 was required. The study suggests both nuclear and cytoplasmic PYR1 participate in the control of ABA signal transduction. - Highlights: • Nuclear and cytoplasmic functions of PYR1 were studied in the mutant which lacked majority of ABA responses. • Nuclear PYR1 reconstituted partially the ABA responses during seed germination, root growth, and guard cell movement. • Both the nuclear and cytoplasmic functions of PYR1 were required for the full generation of ABA responses.
A DNMT3A2-HDAC2 Complex Is Essential for Genomic Imprinting and Genome Integrity in Mouse Oocytes

Directory of Open Access Journals (Sweden)

Pengpeng Ma

2015-11-01

Full Text Available Maternal genomic imprints are established during oogenesis. Histone deacetylases (HDACs 1 and 2 are required for oocyte development in mouse, but their role in genomic imprinting is unknown. We find that Hdac1:Hdac2−/− double-mutant growing oocytes exhibit global DNA hypomethylation and fail to establish imprinting marks for Igf2r, Peg3, and Srnpn. Global hypomethylation correlates with increased retrotransposon expression and double-strand DNA breaks. Nuclear-associated DNMT3A2 is reduced in double-mutant oocytes, and injecting these oocytes with Hdac2 partially restores DNMT3A2 nuclear staining. DNMT3A2 co-immunoprecipitates with HDAC2 in mouse embryonic stem cells. Partial loss of nuclear DNMT3A2 and HDAC2 occurs in Sin3a−/− oocytes, which exhibit decreased DNA methylation of imprinting control regions for Igf2r and Srnpn, but not Peg3. These results suggest seminal roles of HDAC1/2 in establishing maternal genomic imprints and maintaining genomic integrity in oocytes mediated in part through a SIN3A complex that interacts with DNMT3A2.
Ubiquitination of HTLV-I Tax in response to DNA damage regulates nuclear complex formation and nuclear export

Directory of Open Access Journals (Sweden)

Marriott Susan J

2007-12-01

Full Text Available Abstract Background The HTLV-I oncoprotein, Tax, is a pleiotropic protein whose activity is partially regulated by its ability to interact with, and perturb the functions of, numerous cellular proteins. Tax is predominantly a nuclear protein that localizes to nuclear foci known as Tax Speckled Structures (TSS. We recently reported that the localization of Tax and its interactions with cellular proteins are altered in response to various forms of genotoxic and cellular stress. The level of cytoplasmic Tax increases in response to stress and this relocalization depends upon the interaction of Tax with CRM1. Cellular pathways and signals that regulate the subcellular localization of Tax remain to be determined. However, post-translational modifications including sumoylation and ubiquitination are known to influence the subcellular localization of Tax and its interactions with cellular proteins. The sumoylated form of Tax exists predominantly in the nucleus while ubiquitinated Tax exists predominantly in the cytoplasm. Therefore, we hypothesized that post-translational modifications of Tax that occur in response to DNA damage regulate the localization of Tax and its interactions with cellular proteins. Results We found a significant increase in mono-ubiquitination of Tax in response to UV irradiation. Mutation of specific lysine residues (K280 and K284 within Tax inhibited DNA damage-induced ubiquitination. In contrast to wild-type Tax, which undergoes transient nucleocytoplasmic shuttling in response to DNA damage, the K280 and K284 mutants were retained in nuclear foci following UV irradiation and remained co-localized with the cellular TSS protein, sc35. Conclusion This study demonstrates that the localization of Tax, and its interactions with cellular proteins, are dynamic following DNA damage and depend on the post-translational modification status of Tax. Specifically, DNA damage induces the ubiquitination of Tax at K280 and K284
Genome digging: insight into the mitochondrial genome of Homo.

Directory of Open Access Journals (Sweden)

Igor V Ovchinnikov

2010-12-01

Full Text Available A fraction of the Neanderthal mitochondrial genome sequence has a similarity with a 5,839-bp nuclear DNA sequence of mitochondrial origin (numt on the human chromosome 1. This fact has never been interpreted. Although this phenomenon may be attributed to contamination and mosaic assembly of Neanderthal mtDNA from short sequencing reads, we explain the mysterious similarity by integration of this numt (mtAncestor-1 into the nuclear genome of the common ancestor of Neanderthals and modern humans not long before their reproductive split.Exploiting bioinformatics, we uncovered an additional numt (mtAncestor-2 with a high similarity to the Neanderthal mtDNA and indicated that both numts represent almost identical replicas of the mtDNA sequences ancestral to the mitochondrial genomes of Neanderthals and modern humans. In the proteins, encoded by mtDNA, the majority of amino acids distinguishing chimpanzees from humans and Neanderthals were acquired by the ancestral hominins. The overall rate of nonsynonymous evolution in Neanderthal mitochondrial protein-coding genes is not higher than in other lineages. The model incorporating the ancestral hominin mtDNA sequences estimates the average divergence age of the mtDNAs of Neanderthals and modern humans to be 450,000-485,000 years. The mtAncestor-1 and mtAncestor-2 sequences were incorporated into the nuclear genome approximately 620,000 years and 2,885,000 years ago, respectively.This study provides the first insight into the evolution of the mitochondrial DNA in hominins ancestral to Neanderthals and humans. We hypothesize that mtAncestor-1 and mtAncestor-2 are likely to be molecular fossils of the mtDNAs of Homo heidelbergensis and a stem Homo lineage. The d(N/d(S dynamics suggests that the effective population size of extinct hominins was low. However, the hominin lineage ancestral to humans, Neanderthals and H. heidelbergensis, had a larger effective population size and possessed genetic diversity
The elevation of radiation load on ecosystems and genome instability of organisms

International Nuclear Information System (INIS)

Gaziyev, A. I.; Bezlepkin, V.Q.

2002-01-01

prophylaxis of human disorders. Thus, it was found that the action of low-dose ionizing radiation on living organisms might induce an adaptive repair response in them aimed at decreasing the genetic consequences of the exposure. However, the potentialities of defense and repair systems of an organism are limited, so an increase in genome lesions may cause inheritable mutations, cancer and other pathologies, and death. DNA lesions caused by ionizing radiation in small and sublethal doses can essentially be repaired, whereas unrepaired lesions and errors of repair, replication, and recombination systems lead to formation of mutational changes in DNA sequences. These changes may be transmitted to daughter cells and induce genome instability in the progeny. Induced genome instability in survived somatic cells is characterized by persistence of a high level of acquired variability in many generations of these cells. Genome instability manifests itself as an increased frequency of karyotypic anomalies, chromosome and gene mutations, clonal heterogeneity, and malignant transformation in the progeny of cells exposed to DNA-damaging agents. Besides, cells with genome instability show increased amplification of genes and changes in their expression, as well as disturbances in their differentiation, delays in reproductive death and other phenotypic characters of abnormal development. Whereas some progress has been made towards knowledge of genome instability in the somatic cells of mammals, the radiation-induced genome instability in germ cells transmitted to individuals of the next generation is still not clearly understood. At the same time, evidence has been obtained which suggests that the transmission of genome instability to the somatic cells of the progeny from the germ cells of gamma - radiation-exposed parents is possible. This conclusion is based on the data on mutation frequency in the progeny of parents exposed to DNA-damaging agents. For instance, a significant increase in
BYSTANDER EFFECTS GENOMIC INSTABILITY, ADAPTIVE RESPONSE AND CANCER RISK ASSESSMENT FOR RADIAION AND CHEMICAL EXPOSURES

Science.gov (United States)

BYSTANDER EFFECTS, GENOMIC INSTABILITY, ADAPTIVE RESPONSE AND CANCER RISK ASSESSMENT FOR RADIATION AND CHEMICAL EXPOSURESR. Julian PrestonEnvironmental Carcinogenesis Division, U.S. Environmental Protection Agency, Research Triangle Park, N.C. 27711, USAThere ...
Initiating nuclear power programmes: Responsibilities and capabilities of owners and operators

International Nuclear Information System (INIS)

2009-01-01

There is an increasing interest in developing nuclear power due to growing energy needs, limitations on natural resources and concern for the environment. However, the introduction and development of nuclear power is a major undertaking. This requires building the necessary national infrastructure to construct and operate nuclear power plants in a safe, secure and technically sound manner. Many IAEA Member States that do not yet have nuclear power programmes have expressed their interest to the IAEA about the possibility of introducing nuclear power plants to help meet their energy needs. To assist these Member States, the IAEA is preparing a series of guides and reports. An overall description of the issues was presented by the IAEA in a brochure entitled Considerations to Launch a Nuclear Power Programme (GOV/INF/2007/2), which was targeted mainly at policy makers. A subsequent IAEA Nuclear Energy Series publication, Milestones in the Development of a National Infrastructure for Nuclear Power (NG-G-3.1), describes 19 infrastructure issues that should be addressed through the three phases of development outlined in the brochure, Considerations to Launch a Nuclear Power Programme. The IAEA is preparing a number of guides addressing these issues. Once a firm decision has been made by a government to proceed with the development of a nuclear programme, a number of organizations must be developed. A key organization for the successful construction and operation of the first nuclear power plant is the owner/operator, who provides ownership and management of the project. The owner/operator must clearly understand what must be done and how it has to act, who are partners and supporters and the corresponding interactions that have to be established. The owner or operator may be state owned or a private company. It may be an existing utility, or a specially established project organization. Its responsibilities include bidding, construction, licensing, commissioning
Long-term response to genomic selection: effects of estimation method and reference population structure for different genetic architectures.

Science.gov (United States)

Bastiaansen, John W M; Coster, Albart; Calus, Mario P L; van Arendonk, Johan A M; Bovenhuis, Henk

2012-01-24

Genomic selection has become an important tool in the genetic improvement of animals and plants. The objective of this study was to investigate the impacts of breeding value estimation method, reference population structure, and trait genetic architecture, on long-term response to genomic selection without updating marker effects. Three methods were used to estimate genomic breeding values: a BLUP method with relationships estimated from genome-wide markers (GBLUP), a Bayesian method, and a partial least squares regression method (PLSR). A shallow (individuals from one generation) or deep reference population (individuals from five generations) was used with each method. The effects of the different selection approaches were compared under four different genetic architectures for the trait under selection. Selection was based on one of the three genomic breeding values, on pedigree BLUP breeding values, or performed at random. Selection continued for ten generations. Differences in long-term selection response were small. For a genetic architecture with a very small number of three to four quantitative trait loci (QTL), the Bayesian method achieved a response that was 0.05 to 0.1 genetic standard deviation higher than other methods in generation 10. For genetic architectures with approximately 30 to 300 QTL, PLSR (shallow reference) or GBLUP (deep reference) had an average advantage of 0.2 genetic standard deviation over the Bayesian method in generation 10. GBLUP resulted in 0.6% and 0.9% less inbreeding than PLSR and BM and on average a one third smaller reduction of genetic variance. Responses in early generations were greater with the shallow reference population while long-term response was not affected by reference population structure. The ranking of estimation methods was different with than without selection. Under selection, applying GBLUP led to lower inbreeding and a smaller reduction of genetic variance while a similar response to selection was
Bicarbonate-responsive “soluble” adenylyl cyclase defines a nuclear cAMP microdomain

Science.gov (United States)

Zippin, Jonathan H.; Farrell, Jeanne; Huron, David; Kamenetsky, Margarita; Hess, Kenneth C.; Fischman, Donald A.; Levin, Lonny R.; Buck, Jochen

2004-01-01

Bicarbonate-responsive “soluble” adenylyl cyclase resides, in part, inside the mammalian cell nucleus where it stimulates the activity of nuclear protein kinase A to phosphorylate the cAMP response element binding protein (CREB). The existence of this complete and functional, nuclear-localized cAMP pathway establishes that cAMP signals in intracellular microdomains and identifies an alternate pathway leading to CREB activation. PMID:14769862
Response of high Tc superconducting Josephson junction to nuclear radiation

International Nuclear Information System (INIS)

Ding Honglin; Zhang Wanchang; Zhang Xiufeng

1992-10-01

The development of nuclear radiation detectors and research on high T c superconducting nuclear radiation detectors are introduced. The emphases are the principle of using thin-film and thick-film Josephson junctions (bridge junction) based on high T c YBCO superconductors to detect nuclear radiation, the fabrication of thin film and thick-film Josephson junction, and response of junction to low energy gamma-rays of 59.5 keV emitted from 241 Am and beta-rays of 546 keV. The results show that a detector for measuring nuclear radiation spectrum made of high T c superconducting thin-film or thick-film, especially, thick-film Josephson junction, certainly can be developed
Genome-Wide Host-Pathogen Interaction Unveiled by Transcriptomic Response of Diamondback Moth to Fungal Infection.

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Zhen-Jian Chu

Full Text Available Genome-wide insight into insect pest response to the infection of Beauveria bassiana (fungal insect pathogen is critical for genetic improvement of fungal insecticides but has been poorly explored. We constructed three pairs of transcriptomes of Plutella xylostella larvae at 24, 36 and 48 hours post treatment of infection (hptI and of control (hptC for insight into the host-pathogen interaction at genomic level. There were 2143, 3200 and 2967 host genes differentially expressed at 24, 36 and 48 hptI/hptC respectively. These infection-responsive genes (~15% of the host genome were enriched in various immune processes, such as complement and coagulation cascades, protein digestion and absorption, and drug metabolism-cytochrome P450. Fungal penetration into cuticle and host defense reaction began at 24 hptI, followed by most intensive host immune response at 36 hptI and attenuated immunity at 48 hptI. Contrastingly, 44% of fungal genes were differentially expressed in the infection course and enriched in several biological processes, such as antioxidant activity, peroxidase activity and proteolysis. There were 1636 fungal genes co-expressed during 24-48 hptI, including 116 encoding putative secretion proteins. Our results provide novel insights into the insect-pathogen interaction and help to probe molecular mechanisms involved in the fungal infection to the global pest.
Identification and characterisation of Short Interspersed Nuclear Elements in the olive tree (Olea europaea L.) genome.

Science.gov (United States)

Barghini, Elena; Mascagni, Flavia; Natali, Lucia; Giordani, Tommaso; Cavallini, Andrea

2017-02-01

Short Interspersed Nuclear Elements (SINEs) are nonautonomous retrotransposons in the genome of most eukaryotic species. While SINEs have been intensively investigated in humans and other animal systems, SINE identification has been carried out only in a limited number of plant species. This lack of information is apparent especially in non-model plants whose genome has not been sequenced yet. The aim of this work was to produce a specific bioinformatics pipeline for analysing second generation sequence reads of a non-model species and identifying SINEs. We have identified, for the first time, 227 putative SINEs of the olive tree (Olea europaea), that constitute one of the few sets of such sequences in dicotyledonous species. The identified SINEs ranged from 140 to 362 bp in length and were characterised with regard to the occurrence of the tRNA domain in their sequence. The majority of identified elements resulted in single copy or very lowly repeated, often in association with genic sequences. Analysis of sequence similarity allowed us to identify two major groups of SINEs showing different abundances in the olive tree genome, the former with sequence similarity to SINEs of Scrophulariaceae and Solanaceae and the latter to SINEs of Salicaceae. A comparison of sequence conservation between olive SINEs and LTR retrotransposon families suggested that SINE expansion in the genome occurred especially in very ancient times, before LTR retrotransposon expansion, and presumably before the separation of the rosids (to which Oleaceae belong) from the Asterids. Besides providing data on olive SINEs, our results demonstrate the suitability of the pipeline employed for SINE identification. Applying this pipeline will favour further structural and functional analyses on these relatively unknown elements to be performed also in other plant species, even in the absence of a reference genome, and will allow establishing general evolutionary patterns for this kind of repeats in
A concerted action towards improved international response to nuclear and radiological events

International Nuclear Information System (INIS)

Ugletveit, F.

2006-01-01

After the Chernobyl accident in 1986, two conventions, the Convention on Early Notification of a Nuclear Accident and the Convention on Assistance in the Case of a Nuclear Accident or Radiological Emergency, were established in order to provide a framework for enhanced international cooperation in the response to such events. It has however been widely recognised that a better practical implementation of these conventions could significantly enhance our response capabilities. In order to achieve this the IAEA Member States, their Competent Authorities and the IAEA Secretariat have developed an International Action Plan for Strengthening the International Preparedness and Response System for Nuclear and Radiological Emergencies, 2004-2009. This Action Plan has three main elements: International communication International assistance Sustainable infrastructure and Working Groups and Expert Groups have been established to carry out the work in accordance with the plan. The implementation of the Action Plan is managed jointly by the IAEA Secretariat and the National Competent Authority Coordinating Group, N.C.A.C.G.. Currently some 65 experts from about 30 different states and international organisations are taking part. Two of the main goals of this work are to develop standardised/harmonized response procedures necessary for efficient provision of international assistance and establishment of a common unified communication platform. A more detailed update on the development of the work will be given. The development and implementation of this Action Plan is an important milestone in nuclear and radiological emergency preparedness and response and will offer an opportunity for the international society to establish a better and more cost efficient response capability. The standardised procedures and the unified communication platform established will subsequently have to be adopted and implemented by states and international organisations. This may have significant

The C-terminal domain of the Bloom syndrome DNA helicase is essential for genomic stability

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Noonan James P

2001-07-01

Full Text Available Abstract Background Bloom syndrome is a rare cancer-prone disorder in which the cells of affected persons have a high frequency of somatic mutation and genomic instability. Bloom syndrome cells have a distinctive high frequency of sister chromatid exchange and quadriradial formation. BLM, the protein altered in BS, is a member of the RecQ DNA helicase family, whose members share an average of 40% identity in the helicase domain and have divergent N-terminal and C-terminal flanking regions of variable lengths. The BLM DNA helicase has been shown to localize to the ND10 (nuclear domain 10 or PML (promyelocytic leukemia nuclear bodies, where it associates with TOPIIIα, and to the nucleolus. Results This report demonstrates that the N-terminal domain of BLM is responsible for localization of the protein to the nuclear bodies, while the C-terminal domain directs the protein to the nucleolus. Deletions of the N-terminal domain of BLM have little effect on sister chromatid exchange frequency and chromosome stability as compared to helicase and C-terminal mutations which can increase SCE frequency and chromosome abnormalities. Conclusion The helicase activity and the C-terminal domain of BLM are critical for maintaining genomic stability as measured by the sister chromatid exchange assay. The localization of BLM into the nucleolus by the C-terminal domain appears to be more important to genomic stability than localization in the nuclear bodies.
Fukushima nuclear accident and the social responsibility of science

International Nuclear Information System (INIS)

Yoshioka, Hitoshi

2011-01-01

Five months had passed since Fukushima Daiichi Nuclear Power Plant (NPP) accident occurred but still there was no knowing when the accident ended. Released radioactivity seemed to be greater than one million terra Bq and if there occurred an explosive rupture of containment vessel due to the failure of containment vent or occurrence of steam explosion, the amount of released radioactivity might amount to be at least equivalent to or surpass that of Chernobyl NPP accident. There existed still a risk that overheating and meltdown of nuclear fuels might reoccur with loss of cooling due to a possible giant aftershock. This article described total views on significant disaster that the accident brought about on many neighboring residents or wide range of people. After a general discussion about what was social responsibility of scientists, social responsibility of scientists for Fukushima Daiichi NPP accident was discussed. Responsibility of omission was also argued. (T. Tanaka)
Human social genomics.

Directory of Open Access Journals (Sweden)

Steven W Cole

2014-08-01

Full Text Available A growing literature in human social genomics has begun to analyze how everyday life circumstances influence human gene expression. Social-environmental conditions such as urbanity, low socioeconomic status, social isolation, social threat, and low or unstable social status have been found to associate with differential expression of hundreds of gene transcripts in leukocytes and diseased tissues such as metastatic cancers. In leukocytes, diverse types of social adversity evoke a common conserved transcriptional response to adversity (CTRA characterized by increased expression of proinflammatory genes and decreased expression of genes involved in innate antiviral responses and antibody synthesis. Mechanistic analyses have mapped the neural "social signal transduction" pathways that stimulate CTRA gene expression in response to social threat and may contribute to social gradients in health. Research has also begun to analyze the functional genomics of optimal health and thriving. Two emerging opportunities now stand to revolutionize our understanding of the everyday life of the human genome: network genomics analyses examining how systems-level capabilities emerge from groups of individual socially sensitive genomes and near-real-time transcriptional biofeedback to empirically optimize individual well-being in the context of the unique genetic, geographic, historical, developmental, and social contexts that jointly shape the transcriptional realization of our innate human genomic potential for thriving.
Genome-wide association study for host response to bovine leukemia virus in Holstein cows.

Science.gov (United States)

Brym, P; Bojarojć-Nosowicz, B; Oleński, K; Hering, D M; Ruść, A; Kaczmarczyk, E; Kamiński, S

2016-07-01

The mechanisms of leukemogenesis induced by bovine leukemia virus (BLV) and the processes underlying the phenomenon of differential host response to BLV infection still remain poorly understood. The aim of the study was to screen the entire cattle genome to identify markers and candidate genes that might be involved in host response to bovine leukemia virus infection. A genome-wide association study was performed using Holstein cows naturally infected by BLV. A data set included 43 cows (BLV positive) and 30 cows (BLV negative) genotyped for 54,609 SNP markers (Illumina Bovine SNP50 BeadChip). The BLV status of cows was determined by serum ELISA, nested-PCR and hematological counts. Linear Regression Analysis with a False Discovery Rate and kinship matrix (computed on the autosomal SNPs) was calculated to find out which SNP markers significantly differentiate BLV-positive and BLV-negative cows. Nine markers reached genome-wide significance. The most significant SNPs were located on chromosomes 23 (rs41583098), 3 (rs109405425, rs110785500) and 8 (rs43564499) in close vicinity of a patatin-like phospholipase domain containing 1 (PNPLA1); adaptor-related protein complex 4, beta 1 subunit (AP4B1); tripartite motif-containing 45 (TRIM45) and cell division cycle associated 2 (CDCA2) genes, respectively. Furthermore, a list of 41 candidate genes was composed based on their proximity to significant markers (within a distance of ca. 1 Mb) and functional involvement in processes potentially underlying BLV-induced pathogenesis. In conclusion, it was demonstrated that host response to BLV infection involves nine sub-regions of the cattle genome (represented by 9 SNP markers), containing many genes which, based on the literature, could be involved to enzootic bovine leukemia progression. New group of promising candidate genes associated with the host response to BLV infection were identified and could therefore be a target for future studies. The functions of candidate genes
Genome wide analyses of metal responsive genes in Caenorhabditis elegans

Directory of Open Access Journals (Sweden)

Michael eAschner

2012-04-01

Full Text Available Metals are major contaminants that influence human health. Many metals have physiologic roles, but excessive levels can be harmful. Advances in technology have made toxicogenomic analyses possible to characterize the effects of metal exposure on the entire genome. Much of what is known about cellular responses to metals has come from mammalian systems; however the use of non-mammalian species is gaining wider attention. Caenorhabditis elegans (C. elegans is a small round worm whose genome has been fully sequenced and its development from egg to adult is well characterized. It is an attractive model for high throughput screens due to its short lifespan, ease of genetic mutability, low cost and high homology with humans. Research performed in C. elegans has led to insights in apoptosis, gene expression and neurodegeneration, all of which can be altered by metal exposure. Additionally, by using worms one can potentially study how the mechanisms that underline differential responses to metals in nematodes and humans, allowing for identification of novel pathways and therapeutic targets. In this review, toxicogenomic studies performed in C. elegans exposed to various metals will be discussed, highlighting how this non-mammalian system can be utilized to study cellular processes and pathways induced by metals. Recent work focusing on neurodegeneration in Parkinson’s disease will be discussed as an example of the usefulness of genetic screens in C. elegans and the novel findings that can be produced.
Consideration of vertical seismic response spectrum in nuclear safety review

International Nuclear Information System (INIS)

Sun Zaozhan; Huang Bingchen

2011-01-01

The basic requirements for civil nuclear installation are introduced in the article. Starting from the basic concept of seismic response spectrum, the authors analyze the site seismic response spectrum and the design seismic response spectrum that desire much consideration. By distinguishing the absolute seismic response spectrum and relative seismic response spectrum, the authors analyze the difference and relationship between the vertical seismic response spectrum and horizontal seismic response spectrum. The authors also bring forward some suggestions for determining the site vertical seismic response spectrum by considering the fact in our country. (authors)
Functional genomics and proteomics - the role of nuclear medicine

International Nuclear Information System (INIS)

Haberkorn, U.; Altmann, A.; Eisenhut, M.

2002-01-01

Now that the sequencing of the human genome has been completed, the basic challenges are finding the genes, locating their coding regions and predicting their functions. This will result in a new understanding of human biology as well as in the design of new molecular structures as potential novel diagnostic or drug discovery targets. The assessment of gene function may be performed using the tools of the genome program. These tools represent high-throughput methods used to evaluate changes in the expression of many or all genes of an organism at the same time in order to investigate genetic pathways for normal development and disease. This will lead to a shift in the scientific paradigm: In the pre-proteomics era, functional assignments were derived from hypothesis-driven experiments designed to understand specific cellular processes. The new tools describe proteins on a proteome-wide scale, thereby creating a new way of doing cell research which results in the determination of three-dimensional protein structures and the description of protein networks. These descriptions may then be used for the design of new hypotheses and experiments in the traditional physiological, biochemical and pharmacological sense. The evaluation of genetically manipulated animals or newly designed biomolecules will require a thorough understanding of physiology, biochemistry and pharmacology and the experimental approaches will involve many new technologies, including in vivo imaging with single-photon emission tomography and positron emission tomography. Nuclear medicine procedures may be applied for the determination of gene function and regulation using established and new tracers or using in vivo reporter genes such as enzymes, receptors, antigens or transporters. Pharmacogenomics will identify new surrogate markers for therapy monitoring which may represent potential new tracers for imaging. Also, drug distribution studies for new therapeutic biomolecules are needed, at least
Functional genomics and proteomics - the role of nuclear medicine

Energy Technology Data Exchange (ETDEWEB)

Haberkorn, U. [Heidelberg Univ. (Germany). Abt. fuer Klinische Nuklearmedizin; German Cancer Research Center, Heidelberg (Germany); Altmann, A. [German Cancer Research Center, Heidelberg (Germany); Eisenhut, M. [German Cancer Research Center, Heidelberg (Germany). Dept. of Radiopharmacy

2002-01-01

Now that the sequencing of the human genome has been completed, the basic challenges are finding the genes, locating their coding regions and predicting their functions. This will result in a new understanding of human biology as well as in the design of new molecular structures as potential novel diagnostic or drug discovery targets. The assessment of gene function may be performed using the tools of the genome program. These tools represent high-throughput methods used to evaluate changes in the expression of many or all genes of an organism at the same time in order to investigate genetic pathways for normal development and disease. This will lead to a shift in the scientific paradigm: In the pre-proteomics era, functional assignments were derived from hypothesis-driven experiments designed to understand specific cellular processes. The new tools describe proteins on a proteome-wide scale, thereby creating a new way of doing cell research which results in the determination of three-dimensional protein structures and the description of protein networks. These descriptions may then be used for the design of new hypotheses and experiments in the traditional physiological, biochemical and pharmacological sense. The evaluation of genetically manipulated animals or newly designed biomolecules will require a thorough understanding of physiology, biochemistry and pharmacology and the experimental approaches will involve many new technologies, including in vivo imaging with single-photon emission tomography and positron emission tomography. Nuclear medicine procedures may be applied for the determination of gene function and regulation using established and new tracers or using in vivo reporter genes such as enzymes, receptors, antigens or transporters. Pharmacogenomics will identify new surrogate markers for therapy monitoring which may represent potential new tracers for imaging. Also, drug distribution studies for new therapeutic biomolecules are needed, at least
Genomic priming of the antisecretory response to estrogen in rat distal colon throughout the estrous cycle.

LENUS (Irish Health Repository)

O'Mahony, Fiona

2009-11-01

The secretion of Cl(-) across distal colonic crypt cells provides the driving force for the movement of fluid into the luminal space. 17beta-Estradiol (E2) produces a rapid and sustained reduction in secretion in females, which is dependent on the novel protein kinase C delta (PKC delta) isozyme and PKA isoform I targeting of KCNQ1 channels. This sexual dimorphism in the E2 response is associated with a higher expression level of PKC delta in female compared with the male tissue. The present study revealed the antisecretory response is regulated throughout the female reproductive (estrous) cycle and is primed by genomic regulation of the kinases. E2 (1-10 nm) decreased cAMP-dependent secretion in colonic epithelia during the estrus, metestrus, and diestrus stages. A weak inhibition of secretion was demonstrated in the proestrus stage. The expression levels of PKC delta and PKA fluctuated throughout the estrous cycle and correlated with the potency of the antisecretory effect of E2. The expression of PKC delta and PKA were up-regulated by estrogen at a transcriptional level via a PKC delta-MAPK-cAMP response element-binding protein-regulated pathway indicating a genomic priming of the antisecretory response. PK Cdelta was activated by the membrane-impermeant E2-BSA, and this response was inhibited by the estrogen receptor antagonist ICI 182,780. The 66-kDa estrogen receptor-alpha isoform was present at the plasma membrane of female colonic crypt cells with a lower abundance found in male colonic crypts. The study demonstrates estrogen regulation of intestinal secretion both at a rapid and transcriptional level, demonstrating an interdependent relationship between both nongenomic and genomic hormone responses.
Functional Associations by Response Overlap (FARO), a functional genomics approach matching gene expression phenotypes

DEFF Research Database (Denmark)

Nielsen, Henrik Bjørn; Mundy, J.; Willenbrock, Hanni

2007-01-01

The systematic comparison of transcriptional responses of organisms is a powerful tool in functional genomics. For example, mutants may be characterized by comparing their transcript profiles to those obtained in other experiments querying the effects on gene expression of many experimental facto...
Planning guidance for emergency response to a hypothetical nuclear attack on Riyadh, Saudi Arabia

Science.gov (United States)

Shubayr, Nasser Ali M.

The threat of nuclear attack will remain imminent in an ever-advancing society. Saudi Arabia is not immune to this threat. This dissertation establishes planning guidance for response to a nuclear attack on Riyadh, the capital of Saudi Arabia, based on a hypothetical scenario of a nuclear detonation. A case scenario of a one-megaton thermonuclear bomb detonated at ground level over Riyadh is used to support the thesis. Previous nuclear tests and the Hiroshima and Nagasaki bombings have been used to present possible effects on Riyadh. US planning guidance and lessons learned from the Chernobyl and Fukushima nuclear plants accidents have been used to develop the emergency response guidance. The planning guidance outlines a rapid response to the nuclear detonation. Four damage zones have been identified; severe damage zone, moderate damage zone, light damage zone and dangerous fallout zone. Actions that are recommended, and those that should be avoided, have been determined for each zone. Shelter/ evacuation evaluation for blast-affected and fallout-affected areas is the basis for the recommendation that shelter in place is the best decision for the first hours to days after the attack. Guidelines for medical care response and population monitoring and decontamination are included to reduce the early and long-term effects of the attack. Recommendations to the Saudi Arabian authorities have been made to facilitate suitable preparedness and response for such an event.
Calcium and Nuclear Signaling in Prostate Cancer

Directory of Open Access Journals (Sweden)

Ivan V. Maly

2018-04-01

Full Text Available Recently, there have been a number of developments in the fields of calcium and nuclear signaling that point to new avenues for a more effective diagnosis and treatment of prostate cancer. An example is the discovery of new classes of molecules involved in calcium-regulated nuclear import and nuclear calcium signaling, from the G protein-coupled receptor (GPCR and myosin families. This review surveys the new state of the calcium and nuclear signaling fields with the aim of identifying the unifying themes that hold out promise in the context of the problems presented by prostate cancer. Genomic perturbations, kinase cascades, developmental pathways, and channels and transporters are covered, with an emphasis on nuclear transport and functions. Special attention is paid to the molecular mechanisms behind prostate cancer progression to the malignant forms and the unfavorable response to anti-androgen treatment. The survey leads to some new hypotheses that connect heretofore disparate results and may present a translational interest.
The diurnal logic of the expression of the chloroplast genome in Chlamydomonas reinhardtii.

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Adam D Idoine

Full Text Available Chloroplasts are derived from cyanobacteria and have retained a bacterial-type genome and gene expression machinery. The chloroplast genome encodes many of the core components of the photosynthetic apparatus in the thylakoid membranes. To avoid photooxidative damage and production of harmful reactive oxygen species (ROS by incompletely assembled thylakoid protein complexes, chloroplast gene expression must be tightly regulated and co-ordinated with gene expression in the nucleus. Little is known about the control of chloroplast gene expression at the genome-wide level in response to internal rhythms and external cues. To obtain a comprehensive picture of organelle transcript levels in the unicellular model alga Chlamydomonas reinhardtii in diurnal conditions, a qRT-PCR platform was developed and used to quantify 68 chloroplast, 21 mitochondrial as well as 71 nuclear transcripts in cells grown in highly controlled 12 h light/12 h dark cycles. Interestingly, in anticipation of dusk, chloroplast transcripts from genes involved in transcription reached peak levels first, followed by transcripts from genes involved in translation, and finally photosynthesis gene transcripts. This pattern matches perfectly the theoretical demands of a cell "waking up" from the night. A similar trend was observed in the nuclear transcripts. These results suggest a striking internal logic in the expression of the chloroplast genome and a previously unappreciated complexity in the regulation of chloroplast genes.
Spatial organization of the budding yeast genome in the cell nucleus and identification of specific chromatin interactions from multi-chromosome constrained chromatin model.

Science.gov (United States)

Gürsoy, Gamze; Xu, Yun; Liang, Jie

2017-07-01

Nuclear landmarks and biochemical factors play important roles in the organization of the yeast genome. The interaction pattern of budding yeast as measured from genome-wide 3C studies are largely recapitulated by model polymer genomes subject to landmark constraints. However, the origin of inter-chromosomal interactions, specific roles of individual landmarks, and the roles of biochemical factors in yeast genome organization remain unclear. Here we describe a multi-chromosome constrained self-avoiding chromatin model (mC-SAC) to gain understanding of the budding yeast genome organization. With significantly improved sampling of genome structures, both intra- and inter-chromosomal interaction patterns from genome-wide 3C studies are accurately captured in our model at higher resolution than previous studies. We show that nuclear confinement is a key determinant of the intra-chromosomal interactions, and centromere tethering is responsible for the inter-chromosomal interactions. In addition, important genomic elements such as fragile sites and tRNA genes are found to be clustered spatially, largely due to centromere tethering. We uncovered previously unknown interactions that were not captured by genome-wide 3C studies, which are found to be enriched with tRNA genes, RNAPIII and TFIIS binding. Moreover, we identified specific high-frequency genome-wide 3C interactions that are unaccounted for by polymer effects under landmark constraints. These interactions are enriched with important genes and likely play biological roles.
Nuclear-Cytoplasmic Conflict in Pea (Pisum sativum L.) Is Associated with Nuclear and Plastidic Candidate Genes Encoding Acetyl-CoA Carboxylase Subunits

Science.gov (United States)

Bogdanova, Vera S.; Zaytseva, Olga O.; Mglinets, Anatoliy V.; Shatskaya, Natalia V.; Kosterin, Oleg E.; Vasiliev, Gennadiy V.

2015-01-01

In crosses of wild and cultivated peas (Pisum sativum L.), nuclear-cytoplasmic incompatibility frequently occurs manifested as decreased pollen fertility, male gametophyte lethality, sporophyte lethality. High-throughput sequencing of plastid genomes of one cultivated and four wild pea accessions differing in cross-compatibility was performed. Candidate genes for involvement in the nuclear-plastid conflict were searched in the reconstructed plastid genomes. In the annotated Medicago truncatula genome, nuclear candidate genes were searched in the portion syntenic to the pea chromosome region known to harbor a locus involved in the conflict. In the plastid genomes, a substantial variability of the accD locus represented by nucleotide substitutions and indels was found to correspond to the pattern of cross-compatibility among the accessions analyzed. Amino acid substitutions in the polypeptides encoded by the alleles of a nuclear locus, designated as Bccp3, with a complementary function to accD, fitted the compatibility pattern. The accD locus in the plastid genome encoding beta subunit of the carboxyltransferase of acetyl-coA carboxylase and the nuclear locus Bccp3 encoding biotin carboxyl carrier protein of the same multi-subunit enzyme were nominated as candidate genes for main contribution to nuclear-cytoplasmic incompatibility in peas. Existence of another nuclear locus involved in the accD-mediated conflict is hypothesized. PMID:25789472
Nuclear-cytoplasmic conflict in pea (Pisum sativum L. is associated with nuclear and plastidic candidate genes encoding acetyl-CoA carboxylase subunits.

Directory of Open Access Journals (Sweden)

Vera S Bogdanova

Full Text Available In crosses of wild and cultivated peas (Pisum sativum L., nuclear-cytoplasmic incompatibility frequently occurs manifested as decreased pollen fertility, male gametophyte lethality, sporophyte lethality. High-throughput sequencing of plastid genomes of one cultivated and four wild pea accessions differing in cross-compatibility was performed. Candidate genes for involvement in the nuclear-plastid conflict were searched in the reconstructed plastid genomes. In the annotated Medicago truncatula genome, nuclear candidate genes were searched in the portion syntenic to the pea chromosome region known to harbor a locus involved in the conflict. In the plastid genomes, a substantial variability of the accD locus represented by nucleotide substitutions and indels was found to correspond to the pattern of cross-compatibility among the accessions analyzed. Amino acid substitutions in the polypeptides encoded by the alleles of a nuclear locus, designated as Bccp3, with a complementary function to accD, fitted the compatibility pattern. The accD locus in the plastid genome encoding beta subunit of the carboxyltransferase of acetyl-coA carboxylase and the nuclear locus Bccp3 encoding biotin carboxyl carrier protein of the same multi-subunit enzyme were nominated as candidate genes for main contribution to nuclear-cytoplasmic incompatibility in peas. Existence of another nuclear locus involved in the accD-mediated conflict is hypothesized.
Super-resolution imaging of a 2.5 kb non-repetitive DNA in situ in the nuclear genome using molecular beacon probes

Science.gov (United States)

Ni, Yanxiang; Cao, Bo; Ma, Tszshan; Niu, Gang; Huo, Yingdong; Huang, Jiandong; Chen, Danni; Liu, Yi; Yu, Bin; Zhang, Michael Q; Niu, Hanben

2017-01-01

High-resolution visualization of short non-repetitive DNA in situ in the nuclear genome is essential for studying looping interactions and chromatin organization in single cells. Recent advances in fluorescence in situ hybridization (FISH) using Oligopaint probes have enabled super-resolution imaging of genomic domains with a resolution limit of 4.9 kb. To target shorter elements, we developed a simple FISH method that uses molecular beacon (MB) probes to facilitate the probe-target binding, while minimizing non-specific fluorescence. We used three-dimensional stochastic optical reconstruction microscopy (3D-STORM) with optimized imaging conditions to efficiently distinguish sparsely distributed Alexa-647 from background cellular autofluorescence. Utilizing 3D-STORM and only 29–34 individual MB probes, we observed 3D fine-scale nanostructures of 2.5 kb integrated or endogenous unique DNA in situ in human or mouse genome, respectively. We demonstrated our MB-based FISH method was capable of visualizing the so far shortest non-repetitive genomic sequence in 3D at super-resolution. DOI: http://dx.doi.org/10.7554/eLife.21660.001 PMID:28485713
Proposal of new framework in nuclear emergency response based on problem in East Japan Great Earthquake

Energy Technology Data Exchange (ETDEWEB)

NONE

2013-08-15

In the nuclear emergency response activity in a East Japan great earthquake, the weakness the frame and the activity procedure (scheme) of the emergency response activity of our country that had been constructed after the accident of JCO became clear. Especially, it is necessary to recognize the importance of the enhancement of a prior plan after not only provision to response but also the damage to the environment occurs in the emergency for measures for restoration. Moreover, it is necessary to examine a concrete strategy about the management system strengthening of the radiation exposure at the accident. In this study, the experience and the finding in a East Japan great earthquake are arranged. The accident scenario that should be targeted is rearranged, and it proposes a new frame in the nuclear emergency response field through the requirement examinations such as the points of procedure, equipment, and the capital machine parts that lie a regulations frame of the nuclear emergency response, the activity frame of the nuclear emergency response, and materialized of the nuclear emergency response activity. (author)
Proposal of new framework in nuclear emergency response based on problem in East Japan Great Earthquake

International Nuclear Information System (INIS)

2013-01-01

In the nuclear emergency response activity in a East Japan great earthquake, the weakness the frame and the activity procedure (scheme) of the emergency response activity of our country that had been constructed after the accident of JCO became clear. Especially, it is necessary to recognize the importance of the enhancement of a prior plan after not only provision to response but also the damage to the environment occurs in the emergency for measures for restoration. Moreover, it is necessary to examine a concrete strategy about the management system strengthening of the radiation exposure at the accident. In this study, the experience and the finding in a East Japan great earthquake are arranged. The accident scenario that should be targeted is rearranged, and it proposes a new frame in the nuclear emergency response field through the requirement examinations such as the points of procedure, equipment, and the capital machine parts that lie a regulations frame of the nuclear emergency response, the activity frame of the nuclear emergency response, and materialized of the nuclear emergency response activity. (author)
Proposal of new framework in nuclear emergency response based on problem in East Japan Great Earthquake

International Nuclear Information System (INIS)

2012-01-01

In the nuclear emergency response activity in a East Japan great earthquake, the weakness the frame and the activity procedure (scheme) of the emergency response activity of our country that had been constructed after the accident of JCO became clear. Especially, it is necessary to recognize the importance of the enhancement of a prior plan after not only provision to response but also the damage to the environment occurs in the emergency for measures for restoration. Moreover, it is necessary to examine a concrete strategy about the management system strengthening of the radiation exposure at the accident. In this study, the experience and the finding in a East Japan great earthquake are arranged. The accident scenario that should be targeted is rearranged, and it proposes a new frame in the nuclear emergency response field through the requirement examinations such as the points of procedure, equipment, and the capital machine parts that lie a regulations frame of the nuclear emergency response, the activity frame of the nuclear emergency response, and materialized of the nuclear emergency response activity. (author)

Dynamical response of the nuclear 'pasta' in neutron star crusts

International Nuclear Information System (INIS)

Horowitz, C.J.; Perez-Garcia, M.A.; Berry, D.K.; Piekarewicz, J.

2005-01-01

The nuclear pasta - a novel state of matter having nucleons arranged in a variety of complex shapes - is expected to be found in the crust of neutron stars and in core-collapse supernovae at subnuclear densities of about 10 14 g/cm 3 . Owing to frustration, a phenomenon that emerges from the competition between short-range nuclear attraction and long-range Coulomb repulsion, the nuclear pasta displays a preponderance of unique low-energy excitations. These excitations could have a strong impact on many transport properties, such as neutrino propagation through stellar environments. The excitation spectrum of the nuclear pasta is computed via a molecular-dynamics simulation involving up to 100,000 nucleons. The dynamic response of the pasta displays a classical plasma oscillation in the 1- to 2-MeV region. In addition, substantial strength is found at low energies. Yet this low-energy strength is missing from a simple ion model containing a single-representative heavy nucleus. The low-energy strength observed in the dynamic response of the pasta is likely to be a density wave involving the internal degrees of freedom of the clusters
Whole Mitochondrial Genome Sequencing and Re-Examination of a Cytoplasmic Male Sterility-Associated Gene in Boro-Taichung-Type Cytoplasmic Male Sterile Rice.

Science.gov (United States)

Kazama, Tomohiko; Toriyama, Kinya

2016-01-01

Nuclear genome substitutions between subspecies can lead to cytoplasmic male sterility (CMS) through incompatibility between nuclear and mitochondrial genomes. Boro-Taichung (BT)-type CMS rice was obtained by substituting the nuclear genome of Oryza sativa subsp. indica cultivar Chinsurah Boro II with that of Oryza sativa subsp. japonica cultivar Taichung 65. In BT-type CMS rice, the mitochondrial gene orf79 is associated with male sterility. A complete sequence of the Boro-type mitochondrial genome responsible for BT-type CMS has not been determined to date. Here, we used pyrosequencing to construct the Boro-type mitochondrial genome. The contiguous sequences were assembled into five circular DNA molecules, four of which could be connected into a single circle. The two resulting subgenomic circles were unable to form a reliable master circle, as recombination between them was scarcely detected. We also found an unequal abundance of DNA molecules for the two loci of atp6. These results indicate the presence of multi-partite DNA molecules in the Boro-type mitochondrial genome. Expression patterns were investigated for Boro-type mitochondria-specific orfs, which were not found in the mitochondria from the standard japonica cultivar Nipponbare. Restorer of fertility 1 (RF1)-dependent RNA processing has been observed in orf79-containing RNA but was not detected in other Boro-type mitochondria-specific orfs, supporting the conclusion that orf79 is a unique CMS-associated gene in Boro-type mitochondria.
Nuclear Safety: Our Overriding Priority. EDF Group Report 2015 in response to FTSE4Good Nuclear Criteria

International Nuclear Information System (INIS)

Maillart, H.

2015-01-01

EDF is the world's leading nuclear operator with 74.8 GW of installed capacity in France, the United Kingdom and the United States, an EPR under construction in France, and 2 EPRs under construction in China through TNPJVC (EDF 30%), a joint venture with CGNPC. As such, EDF acts at all stages in the life of its power plants (design, construction, operation, decommissioning) to: - ensure rigorous operation of facilities; - prevent all incidents and accidents; - reduce the impact of any incidents or accidents that might nevertheless occur. The main safety measures were published in a single document in 2015 setting out the Group's nuclear safety policy. Each nuclear operating company inside the Group acts in compliance with the legal obligations and regulations specific to its host country. Each company works to ensure and continuously improve its safety performance with its own methods, skills and values. The EDF Group respects national differences. At the same time it frames common principles to deliver the highest level of incident prevention and protection of the public, workers and the environment. This policy applies to new projects (overall architecture, design and construction) and all existing plants (operation, maintenance, waste management, decommissioning and engineering). The Group works closely with its industrial partners to deliver these objectives. Each company is responsible for the proper operation of its nuclear activities, and delegates responsibilities appropriately to each level of management or operation. The Group guarantees the allocation of resources needed to ensure nuclear safety. An in-house independent nuclear safety function is in place at power plant level, company level and Group level. Each has a duty to alert senior management of inappropriate or inadequate line management response. Nuclear safety is the absolute priority for the EDF Group at every stage of the plant life-cycle. Each company is responsible for ensuring that its
Nuclear accident/radiological emergency assistance plan. NAREAP - edition 2000. Emergency preparedness and response

International Nuclear Information System (INIS)

2000-01-01

The purpose of the Nuclear Accident/Radiological Emergency Assistance Plan (NAREAP) is to describe the framework for systematic, integrated, co-ordinated, and effective preparedness and response for a nuclear accident or radiological emergency involving facilities or practices that may give rise to a threat to health, the environment or property. The purpose of the NAREAP is: to define the emergency response objectives of the Agency's staff in a nuclear accident or a radiological emergency; to assign responsibilities for performing the tasks and authorities for making the decisions that comprise the Agency staff's response to a nuclear accident or radiological emergency; to guide the Agency managers who must ensure that all necessary tasks are given the necessary support in discharging the Agency staff responsibilities and fulfilling its obligations in response to an emergency; to ensure that the development and maintenance of detailed and coherent response procedures are well founded; to act as a point of reference for individual Agency staff members on their responsibilities (as an individual or a team member) throughout a response; to identify interrelationships with other international intergovernmental Organizations; and to serve as a training aid to maintain readiness of personnel. The NAREAP refers to the arrangements of the International Atomic Energy Agency and of the United Nations Security and Safety Section at the Vienna International Centre (UNSSS-VIC) that may be necessary for the IAEA to respond to a nuclear accident or radiological emergency, as defined in the Early Notification and Assistance Conventions. It covers response arrangements for any situation that may have actual, potential or perceived radiological consequences and that could require a response from the IAEA, as well as the arrangements for developing, maintaining and exercising preparedness. The implementing procedures themselves are not included in the NAREAP, but they are required
Complete mitochondrial genomes and nuclear ribosomal RNA operons of two species of Diplostomum (Platyhelminthes: Trematoda): a molecular resource for taxonomy and molecular epidemiology of important fish pathogens.

Science.gov (United States)

Brabec, Jan; Kostadinova, Aneta; Scholz, Tomáš; Littlewood, D Timothy J

2015-06-19

The genus Diplostomum (Platyhelminthes: Trematoda: Diplostomidae) is a diverse group of freshwater parasites with complex life-cycles and global distribution. The larval stages are important pathogens causing eye fluke disease implicated in substantial impacts on natural fish populations and losses in aquaculture. However, the problematic species delimitation and difficulties in the identification of larval stages hamper the assessment of the distributional and host ranges of Diplostomum spp. and their transmission ecology. Total genomic DNA was isolated from adult worms and shotgun sequenced using Illumina MiSeq technology. Mitochondrial (mt) genomes and nuclear ribosomal RNA (rRNA) operons were assembled using established bioinformatic tools and fully annotated. Mt protein-coding genes and nuclear rRNA genes were subjected to phylogenetic analysis by maximum likelihood and the resulting topologies compared. We characterised novel complete mt genomes and nuclear rRNA operons of two closely related species, Diplostomum spathaceum and D. pseudospathaceum. Comparative mt genome assessment revealed that the cox1 gene and its 'barcode' region used for molecular identification are the most conserved regions; instead, nad4 and nad5 genes were identified as most promising molecular diagnostic markers. Using the novel data, we provide the first genome wide estimation of the phylogenetic relationships of the order Diplostomida, one of the two fundamental lineages of the Digenea. Analyses of the mitogenomic data invariably recovered the Diplostomidae as a sister lineage of the order Plagiorchiida rather than as a basal lineage of the Diplostomida as inferred in rDNA phylogenies; this was concordant with the mt gene order of Diplostomum spp. exhibiting closer match to the conserved gene order of the Plagiorchiida. Complete sequences of the mt genome and rRNA operon of two species of Diplostomum provide a valuable resource for novel genetic markers for species delineation and
Drosophila MOF controls Checkpoint protein2 and regulates genomic stability during early embryogenesis.

Science.gov (United States)

Pushpavalli, Sreerangam N C V L; Sarkar, Arpita; Ramaiah, M Janaki; Chowdhury, Debabani Roy; Bhadra, Utpal; Pal-Bhadra, Manika

2013-01-24

In Drosophila embryos, checkpoints maintain genome stability by delaying cell cycle progression that allows time for damage repair or to complete DNA synthesis. Drosophila MOF, a member of MYST histone acetyl transferase is an essential component of male X hyperactivation process. Until recently its involvement in G2/M cell cycle arrest and defects in ionizing radiation induced DNA damage pathways was not well established. Drosophila MOF is highly expressed during early embryogenesis. In the present study we show that haplo-insufficiency of maternal MOF leads to spontaneous mitotic defects like mitotic asynchrony, mitotic catastrophe and chromatid bridges in the syncytial embryos. Such abnormal nuclei are eliminated and digested in the yolk tissues by nuclear fall out mechanism. MOF negatively regulates Drosophila checkpoint kinase 2 tumor suppressor homologue. In response to DNA damage the checkpoint gene Chk2 (Drosophila mnk) is activated in the mof mutants, there by causing centrosomal inactivation suggesting its role in response to genotoxic stress. A drastic decrease in the fall out nuclei in the syncytial embryos derived from mof¹/+; mnkp⁶/+ females further confirms the role of DNA damage response gene Chk2 to ensure the removal of abnormal nuclei from the embryonic precursor pool and maintain genome stability. The fact that mof mutants undergo DNA damage has been further elucidated by the increased number of single and double stranded DNA breaks. mof mutants exhibited genomic instability as evidenced by the occurance of frequent mitotic bridges in anaphase, asynchronous nuclear divisions, disruption of cytoskeleton, inactivation of centrosomes finally leading to DNA damage. Our findings are consistent to what has been reported earlier in mammals that; reduced levels of MOF resulted in increased genomic instability while total loss resulted in lethality. The study can be further extended using Drosophila as model system and carry out the interaction of MOF
Drosophila MOF controls Checkpoint protein2 and regulates genomic stability during early embryogenesis

Directory of Open Access Journals (Sweden)

Pushpavalli Sreerangam NCVL

2013-01-01

Full Text Available Abstract Background In Drosophila embryos, checkpoints maintain genome stability by delaying cell cycle progression that allows time for damage repair or to complete DNA synthesis. Drosophila MOF, a member of MYST histone acetyl transferase is an essential component of male X hyperactivation process. Until recently its involvement in G2/M cell cycle arrest and defects in ionizing radiation induced DNA damage pathways was not well established. Results Drosophila MOF is highly expressed during early embryogenesis. In the present study we show that haplo-insufficiency of maternal MOF leads to spontaneous mitotic defects like mitotic asynchrony, mitotic catastrophe and chromatid bridges in the syncytial embryos. Such abnormal nuclei are eliminated and digested in the yolk tissues by nuclear fall out mechanism. MOF negatively regulates Drosophila checkpoint kinase 2 tumor suppressor homologue. In response to DNA damage the checkpoint gene Chk2 (Drosophila mnk is activated in the mof mutants, there by causing centrosomal inactivation suggesting its role in response to genotoxic stress. A drastic decrease in the fall out nuclei in the syncytial embryos derived from mof1/+; mnkp6/+ females further confirms the role of DNA damage response gene Chk2 to ensure the removal of abnormal nuclei from the embryonic precursor pool and maintain genome stability. The fact that mof mutants undergo DNA damage has been further elucidated by the increased number of single and double stranded DNA breaks. Conclusion mof mutants exhibited genomic instability as evidenced by the occurance of frequent mitotic bridges in anaphase, asynchronous nuclear divisions, disruption of cytoskeleton, inactivation of centrosomes finally leading to DNA damage. Our findings are consistent to what has been reported earlier in mammals that; reduced levels of MOF resulted in increased genomic instability while total loss resulted in lethality. The study can be further extended using
Communication with the Public in a Nuclear or Radiological Emergency. Emergency Preparedness and Response

International Nuclear Information System (INIS)

2012-05-01

The aim of this publication is to provide practical guidance for public information officers on the preparation for and response to a nuclear or radiological emergency, and to fulfil in part functions assigned to the IAEA in the Convention on Assistance in the Case of a Nuclear Accident or Radiological Emergency (Assistance Convention), as well as meeting requirements stated in IAEA Safety Standards Series No. SF-1, Fundamental Safety Principles, and in IAEA Safety Standards No. GS-R-2, Preparedness and Response for a Nuclear or Radiological Emergency. Under Article 5(a)(ii) of the Assistance Convention, one function of the IAEA is to collect and disseminate to States Parties and Member States information concerning methodologies, techniques and results of research relating to response to nuclear or radiological emergencies. IAEA Safety Standards Series No. GS-R-2 establishes the requirements for an adequate level of preparedness for and response to a nuclear or radiological emergency in any State, and specifies that 'All practicable steps shall be taken to provide the public with useful, timely, truthful, consistent and appropriate information throughout a nuclear or radiological emergency' in the response phase. It also requires 'responding to incorrect information and rumours; and responding to requests for information from the public and from the news and information media'. This publication provides guidance in the form of action guides and information sheets that can be easily applied by a State to build a basic capability to respond to a nuclear or radiological emergency. This guidance should be adapted to fit the user State's organizational arrangements, language, terminology, concept of operation and capabilities. This publication is published as part of the IAEA's Emergency Preparedness and Response series and complements the Manual for First Responders to a Radiological Emergency in the parts related to the tasks of public information officers. It takes
Protoparvovirus Knocking at the Nuclear Door.

Science.gov (United States)

Mäntylä, Elina; Kann, Michael; Vihinen-Ranta, Maija

2017-10-02

Protoparvoviruses target the nucleus due to their dependence on the cellular reproduction machinery during the replication and expression of their single-stranded DNA genome. In recent years, our understanding of the multistep process of the capsid nuclear import has improved, and led to the discovery of unique viral nuclear entry strategies. Preceded by endosomal transport, endosomal escape and microtubule-mediated movement to the vicinity of the nuclear envelope, the protoparvoviruses interact with the nuclear pore complexes. The capsids are transported actively across the nuclear pore complexes using nuclear import receptors. The nuclear import is sometimes accompanied by structural changes in the nuclear envelope, and is completed by intranuclear disassembly of capsids and chromatinization of the viral genome. This review discusses the nuclear import strategies of protoparvoviruses and describes its dynamics comprising active and passive movement, and directed and diffusive motion of capsids in the molecularly crowded environment of the cell.
Somatic Cell Nuclear Transfer Followed by CRIPSR/Cas9 Microinjection Results in Highly Efficient Genome Editing in Cloned Pigs

Directory of Open Access Journals (Sweden)

Timothy P. Sheets

2016-12-01

Full Text Available The domestic pig is an ideal “dual purpose” animal model for agricultural and biomedical research. With the availability of genome editing tools such as clustered regularly interspaced short palindromic repeat (CRISPR and associated nuclease Cas9 (CRISPR/Cas9, it is now possible to perform site-specific alterations with relative ease, and will likely help realize the potential of this valuable model. In this article, we investigated for the first time a combination of somatic cell nuclear transfer (SCNT and direct injection of CRISPR/Cas ribonucleoprotein complex targeting GRB10 into the reconstituted oocytes to generate GRB10 ablated Ossabaw fetuses. This strategy resulted in highly efficient (100% generation of biallelic modifications in cloned fetuses. By combining SCNT with CRISPR/Cas9 microinjection, genome edited animals can now be produced without the need to manage a founder herd, while simultaneously eliminating the need for laborious in vitro culture and screening. Our approach utilizes standard cloning techniques while simultaneously performing genome editing in the cloned zygotes of a large animal model for agriculture and biomedical applications.
Population Genomics of Infectious and Integrated Wolbachia pipientis Genomes in Drosophila ananassae

Science.gov (United States)

Choi, Jae Young; Bubnell, Jaclyn E.; Aquadro, Charles F.

2015-01-01

Coevolution between Drosophila and its endosymbiont Wolbachia pipientis has many intriguing aspects. For example, Drosophila ananassae hosts two forms of W. pipientis genomes: One being the infectious bacterial genome and the other integrated into the host nuclear genome. Here, we characterize the infectious and integrated genomes of W. pipientis infecting D. ananassae (wAna), by genome sequencing 15 strains of D. ananassae that have either the infectious or integrated wAna genomes. Results indicate evolutionarily stable maternal transmission for the infectious wAna genome suggesting a relatively long-term coevolution with its host. In contrast, the integrated wAna genome showed pseudogene-like characteristics accumulating many variants that are predicted to have deleterious effects if present in an infectious bacterial genome. Phylogenomic analysis of sequence variation together with genotyping by polymerase chain reaction of large structural variations indicated several wAna variants among the eight infectious wAna genomes. In contrast, only a single wAna variant was found among the seven integrated wAna genomes examined in lines from Africa, south Asia, and south Pacific islands suggesting that the integration occurred once from a single infectious wAna genome and then spread geographically. Further analysis revealed that for all D. ananassae we examined with the integrated wAna genomes, the majority of the integrated wAna genomic regions is represented in at least two copies suggesting a double integration or single integration followed by an integrated genome duplication. The possible evolutionary mechanism underlying the widespread geographical presence of the duplicate integration of the wAna genome is an intriguing question remaining to be answered. PMID:26254486
The nuclear response in extended RPA theories

International Nuclear Information System (INIS)

Wambach, J.

1991-01-01

Linear response theories for small-amplitude nuclear motion are discussed. A review is given of the Random-Phase-Approximation and its successes and shortcomings are pointed out. Systematic improvements are presented which include two-particle two-hole excitations and account for dissipative effects due to binary collisions of nucleons in the mean field. These improved theories describe inelastic scattering experiments satisfactorily over a wide kinematical range. (author)
Japanese Nuclear Accident and U.S. Response

International Nuclear Information System (INIS)

Douet, Randy

2011-01-01

U.S. Government response to the Fukushima accident: • Multi-agency task force (Nuclear Regulatory Commission, Department of Energy, Department of Defense) supporting Japan recovery efforts; • President Obama directed the NRC to perform a comprehensive review of U.S. reactors; • NRC established agency task force to develop lessons learned from Fukushima Daiichi accident to provide short-term and long-term analysis of the events
Genomic stability of lyophilized sheep somatic cells before and after nuclear transfer.

Directory of Open Access Journals (Sweden)

Domenico Iuso

Full Text Available The unprecedented decline of biodiversity worldwide is urging scientists to collect and store biological material from seriously threatened animals, including large mammals. Lyophilization is being explored as a low-cost system for storage in bio-banks of cells that might be used to expand or restore endangered or extinct species through the procedure of Somatic Cell Nuclear Transfer (SCNT. Here we report that the genome is intact in about 60% of lyophylized sheep lymphocytes, whereas DNA damage occurs randomly in the remaining 40%. Remarkably, lyophilized nuclei injected into enucleated oocytes are repaired by a robust DNA repairing activity of the oocytes, and show normal developmental competence. Cloned embryos derived from lyophylized cells exhibited chromosome and cellular composition comparable to those of embryos derived from fresh donor cells. These findings support the feasibility of lyophylization as a storage procedure of mammalian cells to be used for SCNT.
Genomic stability of lyophilized sheep somatic cells before and after nuclear transfer.

Science.gov (United States)

Iuso, Domenico; Czernik, Marta; Di Egidio, Fiorella; Sampino, Silvestre; Zacchini, Federica; Bochenek, Michal; Smorag, Zdzislaw; Modlinski, Jacek A; Ptak, Grazyna; Loi, Pasqualino

2013-01-01

The unprecedented decline of biodiversity worldwide is urging scientists to collect and store biological material from seriously threatened animals, including large mammals. Lyophilization is being explored as a low-cost system for storage in bio-banks of cells that might be used to expand or restore endangered or extinct species through the procedure of Somatic Cell Nuclear Transfer (SCNT). Here we report that the genome is intact in about 60% of lyophylized sheep lymphocytes, whereas DNA damage occurs randomly in the remaining 40%. Remarkably, lyophilized nuclei injected into enucleated oocytes are repaired by a robust DNA repairing activity of the oocytes, and show normal developmental competence. Cloned embryos derived from lyophylized cells exhibited chromosome and cellular composition comparable to those of embryos derived from fresh donor cells. These findings support the feasibility of lyophylization as a storage procedure of mammalian cells to be used for SCNT.
Cell-type-specific genome editing with a microRNA-responsive CRISPR–Cas9 switch

Science.gov (United States)

Hirosawa, Moe; Fujita, Yoshihiko; Parr, Callum J. C.; Hayashi, Karin; Kashida, Shunnichi; Hotta, Akitsu; Woltjen, Knut

2017-01-01

Abstract The CRISPR–Cas9 system is a powerful genome-editing tool useful in a variety of biotechnology and biomedical applications. Here we developed a synthetic RNA-based, microRNA (miRNA)-responsive CRISPR–Cas9 system (miR-Cas9 switch) in which the genome editing activity of Cas9 can be modulated through endogenous miRNA signatures in mammalian cells. We created miR-Cas9 switches by using a miRNA-complementary sequence in the 5΄-UTR of mRNA encoding Streptococcus pyogenes Cas9. The miR-21-Cas9 or miR-302-Cas9 switches selectively and efficiently responded to miR-21-5p in HeLa cells or miR-302a-5p in human induced pluripotent stem cells, and post-transcriptionally attenuated the Cas9 activity only in the target cells. Moreover, the miR-Cas9 switches could differentially control the genome editing by sensing endogenous miRNA activities within a heterogeneous cell population. Our miR-Cas9 switch system provides a promising framework for cell-type selective genome editing and cell engineering based on intracellular miRNA information. PMID:28525578
Global Developmental Gene Programing Involves a Nuclear Form of Fibroblast Growth Factor Receptor-1 (FGFR1.

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Christopher Terranova

Full Text Available Genetic studies have placed the Fgfr1 gene at the top of major ontogenic pathways that enable gastrulation, tissue development and organogenesis. Using genome-wide sequencing and loss and gain of function experiments the present investigation reveals a mechanism that underlies global and direct gene regulation by the nuclear form of FGFR1, ensuring that pluripotent Embryonic Stem Cells differentiate into Neuronal Cells in response to Retinoic Acid. Nuclear FGFR1, both alone and with its partner nuclear receptors RXR and Nur77, targets thousands of active genes and controls the expression of pluripotency, homeobox, neuronal and mesodermal genes. Nuclear FGFR1 targets genes in developmental pathways represented by Wnt/β-catenin, CREB, BMP, the cell cycle and cancer-related TP53 pathway, neuroectodermal and mesodermal programing networks, axonal growth and synaptic plasticity pathways. Nuclear FGFR1 targets the consensus sequences of transcription factors known to engage CREB-binding protein, a common coregulator of transcription and established binding partner of nuclear FGFR1. This investigation reveals the role of nuclear FGFR1 as a global genomic programmer of cell, neural and muscle development.
Mutation of a Conserved Nuclear Export Sequence in Chikungunya Virus Capsid Protein Disrupts Host Cell Nuclear Import.

Science.gov (United States)

Jacobs, Susan C; Taylor, Adam; Herrero, Lara J; Mahalingam, Suresh; Fazakerley, John K

2017-10-20

Transmitted by mosquitoes; chikungunya virus (CHIKV) is responsible for frequent outbreaks of arthritic disease in humans. CHIKV is an arthritogenic alphavirus of the Togaviridae family. Capsid protein, a structural protein encoded by the CHIKV RNA genome, is able to translocate to the host cell nucleus. In encephalitic alphaviruses nuclear translocation induces host cell shut off; however, the role of capsid protein nuclear localisation in arthritogenic alphaviruses remains unclear. Using replicon systems, we investigated a nuclear export sequence (NES) in the N-terminal region of capsid protein; analogous to that found in encephalitic alphavirus capsid but uncharacterised in CHIKV. The chromosomal maintenance 1 (CRM1) export adaptor protein mediated CHIKV capsid protein export from the nucleus and a region within the N-terminal part of CHIKV capsid protein was required for active nuclear targeting. In contrast to encephalitic alphaviruses, CHIKV capsid protein did not inhibit host nuclear import; however, mutating the NES of capsid protein (∆NES) blocked host protein access to the nucleus. Interactions between capsid protein and the nucleus warrant further investigation.
Community emergency response to nuclear power plant accidents: A selected and partially annotated bibliography

International Nuclear Information System (INIS)

Youngen, G.

1988-10-01

The role of responding to emergencies at nuclear power plants is often considered the responsibility of the personnel onsite. This is true for most, if not all, of the incidents that may happen during the course of the plant's operating lifetime. There is however, the possibility of a major accident occurring at anytime. Major nuclear accidents at Chernobyl and Three Mile Island have taught their respective countries and communities a significant lesson in local emergency preparedness and response. Through these accidents, the rest of the world can also learn a great deal about planning, preparing and responding to the emergencies unique to nuclear power. This bibliography contains books, journal articles, conference papers and government reports on emergency response to nuclear power plant accidents. It does not contain citations for ''onsite'' response or planning, nor does it cover the areas of radiation releases from transportation accidents. The compiler has attempted to bring together a sampling of the world's collective written experience on dealing with nuclear reactor accidents on the sate, local and community levels. Since the accidents at Three Mile Island and Chernobyl, that written experience has grown enormously
Community emergency response to nuclear power plant accidents: A selected and partially annotated bibliography

Energy Technology Data Exchange (ETDEWEB)

Youngen, G.

1988-10-01

The role of responding to emergencies at nuclear power plants is often considered the responsibility of the personnel onsite. This is true for most, if not all, of the incidents that may happen during the course of the plant`s operating lifetime. There is however, the possibility of a major accident occurring at anytime. Major nuclear accidents at Chernobyl and Three Mile Island have taught their respective countries and communities a significant lesson in local emergency preparedness and response. Through these accidents, the rest of the world can also learn a great deal about planning, preparing and responding to the emergencies unique to nuclear power. This bibliography contains books, journal articles, conference papers and government reports on emergency response to nuclear power plant accidents. It does not contain citations for ``onsite`` response or planning, nor does it cover the areas of radiation releases from transportation accidents. The compiler has attempted to bring together a sampling of the world`s collective written experience on dealing with nuclear reactor accidents on the sate, local and community levels. Since the accidents at Three Mile Island and Chernobyl, that written experience has grown enormously.

Effects of racial and ethnic group and health literacy on responses to genomic risk information in a medically underserved population.

Science.gov (United States)

Kaphingst, Kimberly A; Stafford, Jewel D; McGowan, Lucy D'Agostino; Seo, Joann; Lachance, Christina R; Goodman, Melody S

2015-02-01

Few studies have examined how individuals respond to genomic risk information for common, chronic diseases. This randomized study examined differences in responses by type of genomic information (genetic test/family history) and disease condition (diabetes/heart disease), and by race/ethnicity in a medically underserved population. 1,057 English-speaking adults completed a survey containing 1 of 4 vignettes (2-by-2 randomized design). Differences in dependent variables (i.e., interest in receiving genomic assessment, discussing with doctor or family, changing health habits) by experimental condition and race/ethnicity were examined using chi-squared tests and multivariable regression analysis. No significant differences were found in dependent variables by type of genomic information or disease condition. In multivariable models, Hispanics were more interested in receiving a genomic assessment than Whites (OR = 1.93; p literacy had greater interest than those with adequate health literacy. Blacks (OR = 1.78; p = .001) and Hispanics (OR = 1.85; p = .001) had greater interest in discussing information with family than Whites. Non-Hispanic Blacks (OR = 1.45; p = .04) had greater interest in discussing genomic information with a doctor than Whites. Blacks (β = -0.41; p literacy was negatively associated with number of health habits participants intended to change. Findings suggest that race/ethnicity may affect responses to genomic risk information. Additional research could examine how cognitive representations of this information differ across racial/ethnic groups. Health literacy is also critical to consider in developing approaches to communicating genomic information.
RPA spin-isospin nuclear response in the deep inelastic region

International Nuclear Information System (INIS)

Alberico, W.M.; Molinari, A.; De Pace, A.; Johnson, M.B.; Ericson, M.

1985-11-01

The spin-isospin volume responses of a finite nucleus are evaluated in the RPA frame, utilizing a harmonic oscillator basis. Particular emphasis is given to the mixing between the longitudinal and transverse couplings, which arise at the nuclear surface. We show that it reduces somewhat the contrast between the two spin responses. We compare the calculated transverse response with the experimental one extracted from deep inelastic electron scattering
SUMO Ligase Protein Inhibitor of Activated STAT1 (PIAS1) Is a Constituent Promyelocytic Leukemia Nuclear Body Protein That Contributes to the Intrinsic Antiviral Immune Response to Herpes Simplex Virus 1.

Science.gov (United States)

Brown, James R; Conn, Kristen L; Wasson, Peter; Charman, Matthew; Tong, Lily; Grant, Kyle; McFarlane, Steven; Boutell, Chris

2016-07-01

Aspects of intrinsic antiviral immunity are mediated by promyelocytic leukemia nuclear body (PML-NB) constituent proteins. During herpesvirus infection, these antiviral proteins are independently recruited to nuclear domains that contain infecting viral genomes to cooperatively promote viral genome silencing. Central to the execution of this particular antiviral response is the small ubiquitin-like modifier (SUMO) signaling pathway. However, the participating SUMOylation enzymes are not fully characterized. We identify the SUMO ligase protein inhibitor of activated STAT1 (PIAS1) as a constituent PML-NB protein. We show that PIAS1 localizes at PML-NBs in a SUMO interaction motif (SIM)-dependent manner that requires SUMOylated or SUMOylation-competent PML. Following infection with herpes simplex virus 1 (HSV-1), PIAS1 is recruited to nuclear sites associated with viral genome entry in a SIM-dependent manner, consistent with the SIM-dependent recruitment mechanisms of other well-characterized PML-NB proteins. In contrast to that of Daxx and Sp100, however, the recruitment of PIAS1 is enhanced by PML. PIAS1 promotes the stable accumulation of SUMO1 at nuclear sites associated with HSV-1 genome entry, whereas the accumulation of other evaluated PML-NB proteins occurs independently of PIAS1. We show that PIAS1 cooperatively contributes to HSV-1 restriction through mechanisms that are additive to those of PML and cooperative with those of PIAS4. The antiviral mechanisms of PIAS1 are counteracted by ICP0, the HSV-1 SUMO-targeted ubiquitin ligase, which disrupts the recruitment of PIAS1 to nuclear domains that contain infecting HSV-1 genomes through mechanisms that do not directly result in PIAS1 degradation. Adaptive, innate, and intrinsic immunity cooperatively and efficiently restrict the propagation of viral pathogens. Intrinsic immunity mediated by constitutively expressed cellular proteins represents the first line of intracellular defense against infection. PML
Evaluating nuclear power plant crew performance during emergency response drills

International Nuclear Information System (INIS)

Rabin, D.

1999-01-01

The Atomic Energy Control Board (AECB) is responsible for the regulation of the health, safety and environmental consequences of nuclear activities in Canada. Recently, the Human Factors Specialists of the AECB have become involved in the assessment of emergency preparedness and emergency response at nuclear facilities. One key contribution to existing AECB methodology is the introduction of Behaviourally Anchored Rating Scales (BARS) to measure crew interaction skills during emergency response drills. This report presents results of an on-going pilot study to determine if the BARS provide a reliable and valid means of rating the key dimensions of communications, openness, task coordination and adaptability under simulated emergency circumstances. To date, the objectivity of the BARS is supported by good inter-rater reliability while the validity of the BARS is supported by the agreement between ratings of crew interaction and qualitative and quantitative observations of crew performance. (author)
The mitochondrial genome of an aquatic plant, Spirodela polyrhiza.

Directory of Open Access Journals (Sweden)

Wenqin Wang

Full Text Available BACKGROUND: Spirodela polyrhiza is a species of the order Alismatales, which represent the basal lineage of monocots with more ancestral features than the Poales. Its complete sequence of the mitochondrial (mt genome could provide clues for the understanding of the evolution of mt genomes in plant. METHODS: Spirodela polyrhiza mt genome was sequenced from total genomic DNA without physical separation of chloroplast and nuclear DNA using the SOLiD platform. Using a genome copy number sensitive assembly algorithm, the mt genome was successfully assembled. Gap closure and accuracy was determined with PCR products sequenced with the dideoxy method. CONCLUSIONS: This is the most compact monocot mitochondrial genome with 228,493 bp. A total of 57 genes encode 35 known proteins, 3 ribosomal RNAs, and 19 tRNAs that recognize 15 amino acids. There are about 600 RNA editing sites predicted and three lineage specific protein-coding-gene losses. The mitochondrial genes, pseudogenes, and other hypothetical genes (ORFs cover 71,783 bp (31.0% of the genome. Imported plastid DNA accounts for an additional 9,295 bp (4.1% of the mitochondrial DNA. Absence of transposable element sequences suggests that very few nuclear sequences have migrated into Spirodela mtDNA. Phylogenetic analysis of conserved protein-coding genes suggests that Spirodela shares the common ancestor with other monocots, but there is no obvious synteny between Spirodela and rice mtDNAs. After eliminating genes, introns, ORFs, and plastid-derived DNA, nearly four-fifths of the Spirodela mitochondrial genome is of unknown origin and function. Although it contains a similar chloroplast DNA content and range of RNA editing as other monocots, it is void of nuclear insertions, active gene loss, and comprises large regions of sequences of unknown origin in non-coding regions. Moreover, the lack of synteny with known mitochondrial genomic sequences shed new light on the early evolution of monocot
Viral symbiosis and the holobiontic nature of the human genome.

Science.gov (United States)

Ryan, Francis Patrick

2016-01-01

The human genome is a holobiontic union of the mammalian nuclear genome, the mitochondrial genome and large numbers of endogenized retroviral genomes. This article defines and explores this symbiogenetic pattern of evolution, looking at the implications for human genetics, epigenetics, embryogenesis, physiology and the pathogenesis of inborn errors of metabolism and many other diseases. © 2016 APMIS. Published by John Wiley & Sons Ltd.
Impact of the allium genomes on plant breeding

Science.gov (United States)

An understanding of the structures and characteristics of the chloroplast, mitochondrial, and nuclear genomes have played significant roles in the genetic improvement of Allium crops. In this chapter I reflect upon the practical use of this genomic information for genetic improvement of the Alliums....
Genomic instability following irradiation

International Nuclear Information System (INIS)

Hacker-Klom, U.B.; Goehde, W.

2001-01-01

Ionising irradiation may induce genomic instability. The broad spectrum of stress reactions in eukaryontic cells to irradiation complicates the discovery of cellular targets and pathways inducing genomic instability. Irradiation may initiate genomic instability by deletion of genes controlling stability, by induction of genes stimulating instability and/or by activating endogeneous cellular viruses. Alternatively or additionally it is discussed that the initiation of genomic instability may be a consequence of radiation or other agents independently of DNA damage implying non nuclear targets, e.g. signal cascades. As a further mechanism possibly involved our own results may suggest radiation-induced changes in chromatin structure. Once initiated the process of genomic instability probably is perpetuated by endogeneous processes necessary for proliferation. Genomic instability may be a cause or a consequence of the neoplastic phenotype. As a conclusion from the data available up to now a new interpretation of low level radiation effects for radiation protection and in radiotherapy appears useful. The detection of the molecular mechanisms of genomic instability will be important in this context and may contribute to a better understanding of phenomenons occurring at low doses <10 cSv which are not well understood up to now. (orig.)
Nuclear law: organization and responsibilities

International Nuclear Information System (INIS)

Ha Vinh Phuong.

1986-01-01

The paper emphasizes the importance of a special legislation insuring the governmental control of nuclear applications and other related activities. This legislation must establish the authority in charge for the development of peaceful applications of nuclear energy and the specialized body legally competent to insure an independent control of nuclear activities, it must define the principles and the conditions for licensing nuclear activities insuring the physical protection of nuclear materials and installations and must establish the specific rules for nuclear liability in the case of a nuclear accident. A list of IAEA publications related to the safety of nuclear power plants is included
Genome-wide association study of response to cognitive-behavioural therapy in children with anxiety disorders

NARCIS (Netherlands)

Coleman, Jonathan R I; Lester, Kathryn J; Keers, Robert; Roberts, Susanna; Curtis, Charles; Arendt, Kristian; Bögels, Susan; Cooper, Peter; Creswell, Cathy; Dalgleish, Tim; Hartman, Catharina A; Heiervang, Einar R; Hötzel, Katrin; Hudson, Jennifer L; In-Albon, Tina; Lavallee, Kristen; Lyneham, Heidi J; Marin, Carla E; Meiser-Stedman, Richard; Morris, Talia; Nauta, Maaike H; Rapee, Ronald M; Schneider, Silvia; Schneider, Sophie C; Silverman, Wendy K; Thastum, Mikael; Thirlwall, Kerstin; Waite, Polly; Wergeland, Gro Janne; Breen, Gerome; Eley, Thalia C

2016-01-01

BACKGROUND: Anxiety disorders are common, and cognitive-behavioural therapy (CBT) is a first-line treatment. Candidate gene studies have suggested a genetic basis to treatment response, but findings have been inconsistent. AIMS: To perform the first genome-wide association study (GWAS) of
Medical Preparedness and Response for a Nuclear or Radiological Emergency. Training Materials

International Nuclear Information System (INIS)

2014-01-01

In almost all nuclear and radiological emergencies, local emergency services (e.g. local medical, law enforcement, and fire brigades) will have the most important role in the early response. Within hours, hospitals may also have an important role to play in the response at the local level. Since nuclear and radiological emergencies are rare, medical responders often have little or no experience in dealing with this type of emergency and inexperience may lead to an inadequate response. For this reason, training in medical preparedness and response for a nuclear or radiological emergency is an important aspect of preparedness and response activities. These materials are designed for use at a training course on medical preparedness and response for a nuclear or radiological emergency. They contain a wide range of lectures and supporting materials, which cover the basic topics and more specific areas of medical preparedness and response. Therefore, in planning their specific courses, organizers are encouraged to choose those lectures and supportive materials from the CD-ROM that best match their training priorities. Materials on the CD-ROM address the following areas: • Terrorism in Perspective; • Malicious Act Scenarios; • Providing Information to the Medical Community and the Public; • Medical Response to a Radiation Mass Casualty Event; • Handling of Contaminated Persons in Malicious Events; • Planning and Preparedness for Medical Response to Malicious Events with Radioactive Material; • Handling the Bodies of Decedents Contaminated with Radioactive Material; • Radiation Emergencies: Scope of the Problem; • Common Sources of Radiation; • Basic Concepts of Ionizing Radiation; • Basic Concepts of Radiation Protection; • Biological Effects of Ionizing Radiation – Basic Notions; • Basics of Radiopathology; • External Radioactive Contamination; • Internal Radioactive Contamination; • Acute Radiation Syndrome; • Cutaneous Radiation
Meteorological considerations in emergency response capability at nuclear power plant

International Nuclear Information System (INIS)

Fairobent, J.E.

1985-01-01

Meteorological considerations in emergency response at nuclear power plants are discussed through examination of current regulations and guidance documents, including discussion of the rationale for current regulatory requirements related to meteorological information for emergency response. Areas discussed include: major meteorological features important to emergency response; onsite meteorological measurements programs, including redundant and backup measurements; access to offsite sources of meteorological information; consideration of real-time and forecast conditions and atmospheric dispersion modeling
Genome-wide association study and biological pathway analysis of the Eimeria maxima response in broilers.

Science.gov (United States)

Hamzić, Edin; Buitenhuis, Bart; Hérault, Frédéric; Hawken, Rachel; Abrahamsen, Mitchel S; Servin, Bertrand; Elsen, Jean-Michel; Pinard-van der Laan, Marie-Hélène; Bed'Hom, Bertrand

2015-11-25

Coccidiosis is the most common and costly disease in the poultry industry and is caused by protozoans of the Eimeria genus. The current control of coccidiosis, based on the use of anticoccidial drugs and vaccination, faces serious obstacles such as drug resistance and the high costs for the development of efficient vaccines, respectively. Therefore, the current control programs must be expanded with complementary approaches such as the use of genetics to improve the host response to Eimeria infections. Recently, we have performed a large-scale challenge study on Cobb500 broilers using E. maxima for which we investigated variability among animals in response to the challenge. As a follow-up to this challenge study, we performed a genome-wide association study (GWAS) to identify genomic regions underlying variability of the measured traits in the response to Eimeria maxima in broilers. Furthermore, we conducted a post-GWAS functional analysis to increase our biological understanding of the underlying response to Eimeria maxima challenge. In total, we identified 22 single nucleotide polymorphisms (SNPs) with q value Eimeria maxima in broilers. Furthermore, the post-GWAS functional analysis indicates that biological pathways and networks involved in tissue proliferation and repair along with the primary innate immune response may play the most important role during the early stage of Eimeria maxima infection in broilers.
Modelling psychological responses to the Great East Japan earthquake and nuclear incident.

Directory of Open Access Journals (Sweden)

Robin Goodwin

Full Text Available The Great East Japan (Tōhoku/Kanto earthquake of March 2011 was followed by a major tsunami and nuclear incident. Several previous studies have suggested a number of psychological responses to such disasters. However, few previous studies have modelled individual differences in the risk perceptions of major events, or the implications of these perceptions for relevant behaviours. We conducted a survey specifically examining responses to the Great Japan earthquake and nuclear incident, with data collected 11-13 weeks following these events. 844 young respondents completed a questionnaire in three regions of Japan; Miyagi (close to the earthquake and leaking nuclear plants, Tokyo/Chiba (approximately 220 km from the nuclear plants, and Western Japan (Yamaguchi and Nagasaki, some 1000 km from the plants. Results indicated significant regional differences in risk perception, with greater concern over earthquake risks in Tokyo than in Miyagi or Western Japan. Structural equation analyses showed that shared normative concerns about earthquake and nuclear risks, conservation values, lack of trust in governmental advice about the nuclear hazard, and poor personal control over the nuclear incident were positively correlated with perceived earthquake and nuclear risks. These risk perceptions further predicted specific outcomes (e.g. modifying homes, avoiding going outside, contemplating leaving Japan. The strength and significance of these pathways varied by region. Mental health and practical implications of these findings are discussed in the light of the continuing uncertainties in Japan following the March 2011 events.
Modelling psychological responses to the Great East Japan earthquake and nuclear incident.

Science.gov (United States)

Goodwin, Robin; Takahashi, Masahito; Sun, Shaojing; Gaines, Stanley O

2012-01-01

The Great East Japan (Tōhoku/Kanto) earthquake of March 2011 was followed by a major tsunami and nuclear incident. Several previous studies have suggested a number of psychological responses to such disasters. However, few previous studies have modelled individual differences in the risk perceptions of major events, or the implications of these perceptions for relevant behaviours. We conducted a survey specifically examining responses to the Great Japan earthquake and nuclear incident, with data collected 11-13 weeks following these events. 844 young respondents completed a questionnaire in three regions of Japan; Miyagi (close to the earthquake and leaking nuclear plants), Tokyo/Chiba (approximately 220 km from the nuclear plants), and Western Japan (Yamaguchi and Nagasaki, some 1000 km from the plants). Results indicated significant regional differences in risk perception, with greater concern over earthquake risks in Tokyo than in Miyagi or Western Japan. Structural equation analyses showed that shared normative concerns about earthquake and nuclear risks, conservation values, lack of trust in governmental advice about the nuclear hazard, and poor personal control over the nuclear incident were positively correlated with perceived earthquake and nuclear risks. These risk perceptions further predicted specific outcomes (e.g. modifying homes, avoiding going outside, contemplating leaving Japan). The strength and significance of these pathways varied by region. Mental health and practical implications of these findings are discussed in the light of the continuing uncertainties in Japan following the March 2011 events.
Emergency Preparedness and Response at Nuclear Power Plants in Pakistan

Energy Technology Data Exchange (ETDEWEB)

Khan, L. A.; Qamar, M. A.; Liaquat, M.R., E-mail: samasl@yahoo.com [Pakistan Atomic Energy Commission, Islamabad (Pakistan)

2014-10-15

Emergency preparedness and response arrangements at Nuclear Power Plants (NPPs) in Pakistan have been reevaluated in the light of Fukushima Daiichi accident. Appropriate measures have been taken to strengthen and effectively implement the on-site and off-site emergency plans. Verification of these plans is conducted through regulatory review and by witnessing periodic emergency drills and exercises conducted by the NPPs in the fulfilment of the regulatory requirements. Emergency Planning Zones (EPZs) have been revised at NPPs. A multi discipline reserve force has been formed for assistance during severe accidents. Nuclear Emergency Management System (NEMS) has been established at the national level in order to make necessary arrangements for responding to nuclear and radiological emergencies. Training programs for first responders and medical professionals have been launched. Emergencies coordination centres have been established at national and corporate levels. Public awareness program has been initiated to ensure that the surrounding population is provided with appropriate information on emergency planning and response. To share national and international operational experience, Pakistan has arranged various workshops and developed a strong link with International Atomic Energy Agency (IAEA). (author)
A corporate social responsibility initiative in the field of nuclear power

International Nuclear Information System (INIS)

Stiopol, M.; Rizea, L.

2009-01-01

Societatea Nationala Nuclearelectrica SA is the operator of the Cernavoda nuclear power plant and the second largest energy producer in Romania, after Hidroelectrica, ensuring 18% of the internal energy demand. The production of nuclear power differs from other industrial activities through the risks it involves and through the legacy it leaves to the future generations, i.e. the nuclear waste. Taking into account these considerations, public acceptance represents a constant preoccupation for nuclear companies around the world. Corporate Social Responsibility (CSR) is a new practice in the nuclear industry. After a long tradition of involvement in the life of the local community through the Social Program for Cernavoda, Nuclearelectrica has initiated a CSR campaign with the theme 'Welcome a tree in your family', addressed to pupils and high school students from Cernavoda. By this campaign, we aimed at creating relevance, not just green lots and to launch a chain of reactions among the citizens of Cernavoda through 'word of mouth communication' so that our initiative may become a sustainable activity. In order to establish the basis of a long term program, the essential element was to change the attitude and behavior of the target population from lack of involvement to responsibility towards the environment. The ecological campaign developed in two phases of planting trees, has recorded significant results among the target population increasing the level of information and acceptance towards nuclear power. (authors)
Reflections on the emergency preparations and responses of China to Fukushima nuclear accident in Japan

International Nuclear Information System (INIS)

Chen Xiaoqiu; Li Bing; Yu Shaoqing

2012-01-01

This paper reviewed the emergency response of Japan in Fukushima nuclear accident, provided and discussed the issues should be of concern on emergency preparedness and response in future: (1) modifying the existing emergency preparedness and response system; (2) consolidating the concept of emergency preparedness as the ultimate level of defense-in-depth; (3) promoting the emergency response decision-making support capabilities; (4) valuing the information opening of involving nuclear news and radiation environmental information. (authors)
The discovery of nuclear fission and the responsibility of the scientist

International Nuclear Information System (INIS)

Staab, H.A.

1989-01-01

The history of the discovery of nuclear fission is placed in historical context and the responsibility of the scientists involved for the subsequent military uses is discussed. It is explained that the deep things in science are not found because they are useful; they are found because it is possible to find them. If Otto Hahn and his co-workers had not discovered nuclear fission someone else in the late 1930s or early 1940s would have done so. It was decisions outside science which set the course for the nuclear fission research once the basic principle had been understood. The question how far does the scientists responsibility extend for unknown and unintended consequences of research and for misuses of his findings by others is discussed. Scientists have a duty to understand the applications of their work and to warn of misuse or hazards, as did Otto Hahn. (UK)
Cell-type-specific genome editing with a microRNA-responsive CRISPR-Cas9 switch.

Science.gov (United States)

Hirosawa, Moe; Fujita, Yoshihiko; Parr, Callum J C; Hayashi, Karin; Kashida, Shunnichi; Hotta, Akitsu; Woltjen, Knut; Saito, Hirohide

2017-07-27

The CRISPR-Cas9 system is a powerful genome-editing tool useful in a variety of biotechnology and biomedical applications. Here we developed a synthetic RNA-based, microRNA (miRNA)-responsive CRISPR-Cas9 system (miR-Cas9 switch) in which the genome editing activity of Cas9 can be modulated through endogenous miRNA signatures in mammalian cells. We created miR-Cas9 switches by using a miRNA-complementary sequence in the 5΄-UTR of mRNA encoding Streptococcus pyogenes Cas9. The miR-21-Cas9 or miR-302-Cas9 switches selectively and efficiently responded to miR-21-5p in HeLa cells or miR-302a-5p in human induced pluripotent stem cells, and post-transcriptionally attenuated the Cas9 activity only in the target cells. Moreover, the miR-Cas9 switches could differentially control the genome editing by sensing endogenous miRNA activities within a heterogeneous cell population. Our miR-Cas9 switch system provides a promising framework for cell-type selective genome editing and cell engineering based on intracellular miRNA information. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Exercises for radiological and nuclear emergency response. Planing - performance - evaluation

International Nuclear Information System (INIS)

Bayer, A.; Faleschini, J.; Goelling, K.; Stapel, R.; Strobl, C.

2010-01-01

The report of the study group emergency response seminar covers the following topics: (A) purpose of exercises and exercise culture: fundamentals and appliances for planning, performance and evaluation; (B) exercises in nuclear facilities; (C) exercises of national authorities and aid organizations on nuclear scenarios; exercises of national authorities and aid organizations on other radiological scenarios; (D) exercises in industrial plants, universities, medical facilities and medical services, and research institutes; (E) transnational exercises, international exercises; (F): exercises on public information.
A Genome-Wide Landscape of Retrocopies in Primate Genomes.

Science.gov (United States)

Navarro, Fábio C P; Galante, Pedro A F

2015-07-29

Gene duplication is a key factor contributing to phenotype diversity across and within species. Although the availability of complete genomes has led to the extensive study of genomic duplications, the dynamics and variability of gene duplications mediated by retrotransposition are not well understood. Here, we predict mRNA retrotransposition and use comparative genomics to investigate their origin and variability across primates. Analyzing seven anthropoid primate genomes, we found a similar number of mRNA retrotranspositions (∼7,500 retrocopies) in Catarrhini (Old Word Monkeys, including humans), but a surprising large number of retrocopies (∼10,000) in Platyrrhini (New World Monkeys), which may be a by-product of higher long interspersed nuclear element 1 activity in these genomes. By inferring retrocopy orthology, we dated most of the primate retrocopy origins, and estimated a decrease in the fixation rate in recent primate history, implying a smaller number of species-specific retrocopies. Moreover, using RNA-Seq data, we identified approximately 3,600 expressed retrocopies. As expected, most of these retrocopies are located near or within known genes, present tissue-specific and even species-specific expression patterns, and no expression correlation to their parental genes. Taken together, our results provide further evidence that mRNA retrotransposition is an active mechanism in primate evolution and suggest that retrocopies may not only introduce great genetic variability between lineages but also create a large reservoir of potentially functional new genomic loci in primate genomes. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
Nuclear power plants in Germany. Recent developments in off-site nuclear emergency preparedness and response; Kernkraftwerke in Deutschland. Neue Entwicklungen im anlagenexternen Notfallschutz

Energy Technology Data Exchange (ETDEWEB)

Gering, Florian [Bundesamt fuer Strahlenschutz, Oberschleissheim/Neuherberg (Germany). Abt. SW 2.2 Entscheidungshilfesysteme, Lageermittlung und Kommunikation

2014-10-15

The reactor accident in Fukushima, Japan, in 2011 triggered a thorough review of the off-site emergency preparedness and response for nuclear power plants in Germany. ''Off-site emergency preparedness and response'' includes all actions to protect the public outside the fence of a nuclear power plant. This review resulted in several changes in off-site emergency preparedness and response, which are briefly described in this article. Additionally, several recent activities are described which may influence emergency preparedness and response in the future.
Responsibility, fairness and credibility - ethical dilemmas concerning nuclear waste

International Nuclear Information System (INIS)

Nilsson, Annika

1999-01-01

This book is written with the aim to stimulate discussion and studies on ethical aspects of nuclear waste management. It does not penetrate the technical details of the different stages of waste handling, but concentrates on questions such as our responsibility towards future generations etc
Identifying and training non-technical skills of nuclear emergency response teams

International Nuclear Information System (INIS)

Crichton, M.T.; Flin, R.

2004-01-01

Training of the non-technical (social and cognitive) skills that are crucial to safe and effective management by teams in emergency situations is an issue that is receiving increasing emphasis in many organisations, particularly in the nuclear power industry. As teams play a major role in emergency response organisations (ERO), effective functioning and interactions within, between and across teams is crucial, particularly as the management of an emergency situation often requires that teams are extended by members from various other sections and strategic groups throughout the company, as well as members of external agencies. A series of interviews was recently conducted with members of a UK nuclear emergency response organisation to identify the non-technical skills required by team members that would be required for managing an emergency. Critical skills have been identified as decision making and situation assessment, as well as communication, teamwork, and stress management. A number of training strategies are discussed which can be tailored to the roles and responsibilities of the team members and the team leader, based on the roles within the team being defined as either Decision Maker, Evaluator, or Implementor, according to Nuclear Energy Institute (NEI) classifications. It is anticipated that enhanced learning of the necessary non-technical skills, through experience and directed practice, will improve the skills of members of emergency response teams
Identifying and training non-technical skills of nuclear emergency response teams

Energy Technology Data Exchange (ETDEWEB)

Crichton, M.T. E-mail: m.crichton@abdn.ac.uk; Flin, R

2004-08-01

Training of the non-technical (social and cognitive) skills that are crucial to safe and effective management by teams in emergency situations is an issue that is receiving increasing emphasis in many organisations, particularly in the nuclear power industry. As teams play a major role in emergency response organisations (ERO), effective functioning and interactions within, between and across teams is crucial, particularly as the management of an emergency situation often requires that teams are extended by members from various other sections and strategic groups throughout the company, as well as members of external agencies. A series of interviews was recently conducted with members of a UK nuclear emergency response organisation to identify the non-technical skills required by team members that would be required for managing an emergency. Critical skills have been identified as decision making and situation assessment, as well as communication, teamwork, and stress management. A number of training strategies are discussed which can be tailored to the roles and responsibilities of the team members and the team leader, based on the roles within the team being defined as either Decision Maker, Evaluator, or Implementor, according to Nuclear Energy Institute (NEI) classifications. It is anticipated that enhanced learning of the necessary non-technical skills, through experience and directed practice, will improve the skills of members of emergency response teams.
Genome-wide analysis of ABA-responsive elements ABRE and CE3 reveals divergent patterns in Arabidopsis and rice

Directory of Open Access Journals (Sweden)

Riaño-Pachón Diego

2007-08-01

Full Text Available Abstract Background In plants, complex regulatory mechanisms are at the core of physiological and developmental processes. The phytohormone abscisic acid (ABA is involved in the regulation of various such processes, including stomatal closure, seed and bud dormancy, and physiological responses to cold, drought and salinity stress. The underlying tissue or plant-wide control circuits often include combinatorial gene regulatory mechanisms and networks that we are only beginning to unravel with the help of new molecular tools. The increasing availability of genomic sequences and gene expression data enables us to dissect ABA regulatory mechanisms at the individual gene expression level. In this paper we used an in-silico-based approach directed towards genome-wide prediction and identification of specific features of ABA-responsive elements. In particular we analysed the genome-wide occurrence and positional arrangements of two well-described ABA-responsive cis-regulatory elements (CREs, ABRE and CE3, in thale cress (Arabidopsis thaliana and rice (Oryza sativa. Results Our results show that Arabidopsis and rice use the ABA-responsive elements ABRE and CE3 distinctively. Earlier reports for various monocots have identified CE3 as a coupling element (CE associated with ABRE. Surprisingly, we found that while ABRE is equally abundant in both species, CE3 is practically absent in Arabidopsis. ABRE-ABRE pairs are common in both genomes, suggesting that these can form functional ABA-responsive complexes (ABRCs in Arabidopsis and rice. Furthermore, we detected distinct combinations, orientation patterns and DNA strand preferences of ABRE and CE3 motifs in rice gene promoters. Conclusion Our computational analyses revealed distinct recruitment patterns of ABA-responsive CREs in upstream sequences of Arabidopsis and rice. The apparent absence of CE3s in Arabidopsis suggests that another CE pairs with ABRE to establish a functional ABRC capable of
Genome-wide analysis of ABA-responsive elements ABRE and CE3 reveals divergent patterns in Arabidopsis and rice.

Science.gov (United States)

Gómez-Porras, Judith L; Riaño-Pachón, Diego Mauricio; Dreyer, Ingo; Mayer, Jorge E; Mueller-Roeber, Bernd

2007-08-01

In plants, complex regulatory mechanisms are at the core of physiological and developmental processes. The phytohormone abscisic acid (ABA) is involved in the regulation of various such processes, including stomatal closure, seed and bud dormancy, and physiological responses to cold, drought and salinity stress. The underlying tissue or plant-wide control circuits often include combinatorial gene regulatory mechanisms and networks that we are only beginning to unravel with the help of new molecular tools. The increasing availability of genomic sequences and gene expression data enables us to dissect ABA regulatory mechanisms at the individual gene expression level. In this paper we used an in-silico-based approach directed towards genome-wide prediction and identification of specific features of ABA-responsive elements. In particular we analysed the genome-wide occurrence and positional arrangements of two well-described ABA-responsive cis-regulatory elements (CREs), ABRE and CE3, in thale cress (Arabidopsis thaliana) and rice (Oryza sativa). Our results show that Arabidopsis and rice use the ABA-responsive elements ABRE and CE3 distinctively. Earlier reports for various monocots have identified CE3 as a coupling element (CE) associated with ABRE. Surprisingly, we found that while ABRE is equally abundant in both species, CE3 is practically absent in Arabidopsis. ABRE-ABRE pairs are common in both genomes, suggesting that these can form functional ABA-responsive complexes (ABRCs) in Arabidopsis and rice. Furthermore, we detected distinct combinations, orientation patterns and DNA strand preferences of ABRE and CE3 motifs in rice gene promoters. Our computational analyses revealed distinct recruitment patterns of ABA-responsive CREs in upstream sequences of Arabidopsis and rice. The apparent absence of CE3s in Arabidopsis suggests that another CE pairs with ABRE to establish a functional ABRC capable of interacting with transcription factors. Further studies will be
Genomic selection for the improvement of antibody response to Newcastle disease and avian influenza virus in chickens.

Directory of Open Access Journals (Sweden)

Tianfei Liu

Full Text Available Newcastle disease (ND and avian influenza (AI are the most feared diseases in the poultry industry worldwide. They can cause flock mortality up to 100%, resulting in a catastrophic economic loss. This is the first study to investigate the feasibility of genomic selection for antibody response to Newcastle disease virus (Ab-NDV and antibody response to Avian Influenza virus (Ab-AIV in chickens. The data were collected from a crossbred population. Breeding values for Ab-NDV and Ab-AIV were estimated using a pedigree-based best linear unbiased prediction model (BLUP and a genomic best linear unbiased prediction model (GBLUP. Single-trait and multiple-trait analyses were implemented. According to the analysis using the pedigree-based model, the heritability for Ab-NDV estimated from the single-trait and multiple-trait models was 0.478 and 0.487, respectively. The heritability for Ab-AIV estimated from the two models was 0.301 and 0.291, respectively. The estimated genetic correlation between the two traits was 0.438. A four-fold cross-validation was used to assess the accuracy of the estimated breeding values (EBV in the two validation scenarios. In the family sample scenario each half-sib family is randomly allocated to one of four subsets and in the random sample scenario the individuals are randomly divided into four subsets. In the family sample scenario, compared with the pedigree-based model, the accuracy of the genomic prediction increased from 0.086 to 0.237 for Ab-NDV and from 0.080 to 0.347 for Ab-AIV. In the random sample scenario, the accuracy was improved from 0.389 to 0.427 for Ab-NDV and from 0.281 to 0.367 for Ab-AIV. The multiple-trait GBLUP model led to a slightly higher accuracy of genomic prediction for both traits. These results indicate that genomic selection for antibody response to ND and AI in chickens is promising.
Genome-wide transcription responses to synchrotron microbeam radiotherapy.

Science.gov (United States)

Sprung, Carl N; Yang, Yuqing; Forrester, Helen B; Li, Jason; Zaitseva, Marina; Cann, Leonie; Restall, Tina; Anderson, Robin L; Crosbie, Jeffrey C; Rogers, Peter A W

2012-10-01

The majority of cancer patients achieve benefit from radiotherapy. A significant limitation of radiotherapy is its relatively low therapeutic index, defined as the maximum radiation dose that causes acceptable normal tissue damage to the minimum dose required to achieve tumor control. Recently, a new radiotherapy modality using synchrotron-generated X-ray microbeam radiotherapy has been demonstrated in animal models to ablate tumors with concurrent sparing of normal tissue. Very little work has been undertaken into the cellular and molecular mechanisms that differentiate microbeam radiotherapy from broad beam. The purpose of this study was to investigate and compare the whole genome transcriptional response of in vivo microbeam radiotherapy versus broad beam irradiated tumors. We hypothesized that gene expression changes after microbeam radiotherapy are different from those seen after broad beam. We found that in EMT6.5 tumors at 4-48 h postirradiation, microbeam radiotherapy differentially regulates a number of genes, including major histocompatibility complex (MHC) class II antigen gene family members, and other immunity-related genes including Ciita, Ifng, Cxcl1, Cxcl9, Indo and Ubd when compared to broad beam. Our findings demonstrate molecular differences in the tumor response to microbeam versus broad beam irradiation and these differences provide insight into the underlying mechanisms of microbeam radiotherapy and broad beam.
Selective recruitment of nuclear factors to productively replicating herpes simplex virus genomes.

Science.gov (United States)

Dembowski, Jill A; DeLuca, Neal A

2015-05-01

Much of the HSV-1 life cycle is carried out in the cell nucleus, including the expression, replication, repair, and packaging of viral genomes. Viral proteins, as well as cellular factors, play essential roles in these processes. Isolation of proteins on nascent DNA (iPOND) was developed to label and purify cellular replication forks. We adapted aspects of this method to label viral genomes to both image, and purify replicating HSV-1 genomes for the identification of associated proteins. Many viral and cellular factors were enriched on viral genomes, including factors that mediate DNA replication, repair, chromatin remodeling, transcription, and RNA processing. As infection proceeded, packaging and structural components were enriched to a greater extent. Among the more abundant proteins that copurified with genomes were the viral transcription factor ICP4 and the replication protein ICP8. Furthermore, all seven viral replication proteins were enriched on viral genomes, along with cellular PCNA and topoisomerases, while other cellular replication proteins were not detected. The chromatin-remodeling complexes present on viral genomes included the INO80, SWI/SNF, NURD, and FACT complexes, which may prevent chromatinization of the genome. Consistent with this conclusion, histones were not readily recovered with purified viral genomes, and imaging studies revealed an underrepresentation of histones on viral genomes. RNA polymerase II, the mediator complex, TFIID, TFIIH, and several other transcriptional activators and repressors were also affinity purified with viral DNA. The presence of INO80, NURD, SWI/SNF, mediator, TFIID, and TFIIH components is consistent with previous studies in which these complexes copurified with ICP4. Therefore, ICP4 is likely involved in the recruitment of these key cellular chromatin remodeling and transcription factors to viral genomes. Taken together, iPOND is a valuable method for the study of viral genome dynamics during infection and
Polar bears exhibit genome-wide signatures of bioenergetic adaptation to life in the arctic environment.

Science.gov (United States)

Welch, Andreanna J; Bedoya-Reina, Oscar C; Carretero-Paulet, Lorenzo; Miller, Webb; Rode, Karyn D; Lindqvist, Charlotte

2014-02-01

Polar bears (Ursus maritimus) face extremely cold temperatures and periods of fasting, which might result in more severe energetic challenges than those experienced by their sister species, the brown bear (U. arctos). We have examined the mitochondrial and nuclear genomes of polar and brown bears to investigate whether polar bears demonstrate lineage-specific signals of molecular adaptation in genes associated with cellular respiration/energy production. We observed increased evolutionary rates in the mitochondrial cytochrome c oxidase I gene in polar but not brown bears. An amino acid substitution occurred near the interaction site with a nuclear-encoded subunit of the cytochrome c oxidase complex and was predicted to lead to a functional change, although the significance of this remains unclear. The nuclear genomes of brown and polar bears demonstrate different adaptations related to cellular respiration. Analyses of the genomes of brown bears exhibited substitutions that may alter the function of proteins that regulate glucose uptake, which could be beneficial when feeding on carbohydrate-dominated diets during hyperphagia, followed by fasting during hibernation. In polar bears, genes demonstrating signatures of functional divergence and those potentially under positive selection were enriched in functions related to production of nitric oxide (NO), which can regulate energy production in several different ways. This suggests that polar bears may be able to fine-tune intracellular levels of NO as an adaptive response to control trade-offs between energy production in the form of adenosine triphosphate versus generation of heat (thermogenesis).
Assembly of the Complete Sitka Spruce Chloroplast Genome Using 10X Genomics' GemCode Sequencing Data.

Directory of Open Access Journals (Sweden)

Lauren Coombe

Full Text Available The linked read sequencing library preparation platform by 10X Genomics produces barcoded sequencing libraries, which are subsequently sequenced using the Illumina short read sequencing technology. In this new approach, long fragments of DNA are partitioned into separate micro-reactions, where the same index sequence is incorporated into each of the sequencing fragment inserts derived from a given long fragment. In this study, we exploited this property by using reads from index sequences associated with a large number of reads, to assemble the chloroplast genome of the Sitka spruce tree (Picea sitchensis. Here we report on the first Sitka spruce chloroplast genome assembled exclusively from P. sitchensis genomic libraries prepared using the 10X Genomics protocol. We show that the resulting 124,049 base pair long genome shares high sequence similarity with the related white spruce and Norway spruce chloroplast genomes, but diverges substantially from a previously published P. sitchensis- P. thunbergii chimeric genome. The use of reads from high-frequency indices enabled separation of the nuclear genome reads from that of the chloroplast, which resulted in the simplification of the de Bruijn graphs used at the various stages of assembly.
Development of national level preparedness for response to nuclear and radiological emergencies

International Nuclear Information System (INIS)

Pradeepkumar, K.S.

2014-01-01

In India, DAE being the nodal agency for technical support for response to any radiation emergency nuclear disaster and various nuclear and radiological emergency scenarios and their impacts are identified. To reduce their consequences development of methodologies for detection and quick impact assessment, trained First Responders and Quick Response Teams (QRTs), twenty two DAE Emergency Response Centers, mobile and aerial radiation monitoring systems, aerial and ground based validation trials etc. are carried out. Study related to radiological threats and simulated RDD experiments conducted using stable isotopes indicates that radiation levels for distances more than 50 m will not be very high as hotspots may be restricted to nearby area. The biggest challenge from an RDD explosion will be handling of the radioactive contamination and 'fear factor' compared to radiation exposure to public or First Responders. Level and pattern of radioactive contamination on ground following releases during nuclear accidents and minimum strength of orphan radioactive sources to be detected are taken into account for optimizing systems and monitoring methodology required for emergency preparedness
Integrity of nuclear genomic deoxyribonucleic acid in cooked meat: Implications for food traceability.

Science.gov (United States)

Aslan, O; Hamill, R M; Sweeney, T; Reardon, W; Mullen, A M

2009-01-01

It is essential to isolate high-quality DNA from muscle tissue for PCR-based applications in traceability of animal origin. We wished to examine the impact of cooking meat to a range of core temperatures on the quality and quantity of subsequently isolated genomic (specifically, nuclear) DNA. Triplicate steak samples were cooked in a water bath (100 degrees C) until their final internal temperature was 75, 80, 85, 90, 95, or 100 degrees C, and DNA was extracted. Deoxyribonucleic acid quantity was significantly reduced in cooked meat samples compared with raw (6.5 vs. 56.6 ng/microL; P 800 bp) were observed only when using DNA from raw meat and steak cooked to lower core temperatures. Small amplicons (food authentication, it is less abundant, and results suggest that analyses should be designed to use small amplicon sizes for meat cooked to high core temperatures.
Phytozome Comparative Plant Genomics Portal

Energy Technology Data Exchange (ETDEWEB)

Goodstein, David; Batra, Sajeev; Carlson, Joseph; Hayes, Richard; Phillips, Jeremy; Shu, Shengqiang; Schmutz, Jeremy; Rokhsar, Daniel

2014-09-09

The Dept. of Energy Joint Genome Institute is a genomics user facility supporting DOE mission science in the areas of Bioenergy, Carbon Cycling, and Biogeochemistry. The Plant Program at the JGI applies genomic, analytical, computational and informatics platforms and methods to: 1. Understand and accelerate the improvement (domestication) of bioenergy crops 2. Characterize and moderate plant response to climate change 3. Use comparative genomics to identify constrained elements and infer gene function 4. Build high quality genomic resource platforms of JGI Plant Flagship genomes for functional and experimental work 5. Expand functional genomic resources for Plant Flagship genomes
A simulator-based nuclear reactor emergency response training exercise.

Science.gov (United States)

Waller, Edward; Bereznai, George; Shaw, John; Chaput, Joseph; Lafortune, Jean-Francois

Training offsite emergency response personnel basic awareness of onsite control room operations during nuclear power plant emergency conditions was the primary objective of a week-long workshop conducted on a CANDU® virtual nuclear reactor simulator available at the University of Ontario Institute of Technology, Oshawa, Canada. The workshop was designed to examine both normal and abnormal reactor operating conditions, and to observe the conditions in the control room that may have impact on the subsequent offsite emergency response. The workshop was attended by participants from a number of countries encompassing diverse job functions related to nuclear emergency response. Objectives of the workshop were to provide opportunities for participants to act in the roles of control room personnel under different reactor operating scenarios, providing a unique experience for participants to interact with the simulator in real-time, and providing increased awareness of control room operations during accident conditions. The ability to "pause" the simulator during exercises allowed the instructors to evaluate and critique the performance of participants, and to provide context with respect to potential offsite emergency actions. Feedback from the participants highlighted (i) advantages of observing and participating "hands-on" with operational exercises, (ii) their general unfamiliarity with control room operational procedures and arrangements prior to the workshop, (iii) awareness of the vast quantity of detailed control room procedures for both normal and transient conditions, and (iv) appreciation of the increased workload for the operators in the control room during a transient from normal operations. Based upon participant feedback, it was determined that the objectives of the training had been met, and that future workshops should be conducted.
Proteomics approach to identify dehydration responsive nuclear proteins from chickpea (Cicer arietinum L.).

Science.gov (United States)

Pandey, Aarti; Chakraborty, Subhra; Datta, Asis; Chakraborty, Niranjan

2008-01-01

Dehydration or water-deficit is one of the most important environmental stress factors that greatly influences plant growth and development and limits crop productivity. Plants respond and adapt to such stress by altering their cellular metabolism and activating various defense machineries. Mechanisms that operate signal perception, transduction, and downstream regulatory events provide valuable information about the underlying pathways involved in environmental stress responses. The nuclear proteins constitute a highly organized, complex network that plays diverse roles during cellular development and other physiological processes. To gain a better understanding of dehydration response in plants, we have developed a comparative nuclear proteome in a food legume, chickpea (Cicer arietinum L.). Three-week-old chickpea seedlings were subjected to progressive dehydration by withdrawing water and the changes in the nuclear proteome were examined using two-dimensional gel electrophoresis. Approximately 205 protein spots were found to be differentially regulated under dehydration. Mass spectrometry analysis allowed the identification of 147 differentially expressed proteins, presumably involved in a variety of functions including gene transcription and replication, molecular chaperones, cell signaling, and chromatin remodeling. The dehydration responsive nuclear proteome of chickpea revealed a coordinated response, which involves both the regulatory as well as the functional proteins. This study, for the first time, provides an insight into the complex metabolic network operating in the nucleus during dehydration.
NRC/FEMA operational response procedures for response to a commercial nuclear reactor accident

International Nuclear Information System (INIS)

1983-11-01

Procedures have been developed by the US Nuclear Regulatory Commission (NRC) and the Federal Emergency Management Agency (FEMA) which provide the response teams of both agencies with the steps to be taken in responding to an emergency at a commercial nuclear power plant. The emphasis of these procedures is mainly on the interface between NRC and FEMA at their respective Headquarters and Regional Offices and at the various sites at which such an emergency could occur. Detailed procedures are presented that cover for both agencies, notification schemes and manner of activation, organizations at Headquaters and the site, interface procedures, coordination of onsite and offsite operations, the role of the Senior FEMA Official, and the cooperative efforts of each agency's public information staff
Selective recruitment of nuclear factors to productively replicating herpes simplex virus genomes.

Directory of Open Access Journals (Sweden)

Jill A Dembowski

2015-05-01

Full Text Available Much of the HSV-1 life cycle is carried out in the cell nucleus, including the expression, replication, repair, and packaging of viral genomes. Viral proteins, as well as cellular factors, play essential roles in these processes. Isolation of proteins on nascent DNA (iPOND was developed to label and purify cellular replication forks. We adapted aspects of this method to label viral genomes to both image, and purify replicating HSV-1 genomes for the identification of associated proteins. Many viral and cellular factors were enriched on viral genomes, including factors that mediate DNA replication, repair, chromatin remodeling, transcription, and RNA processing. As infection proceeded, packaging and structural components were enriched to a greater extent. Among the more abundant proteins that copurified with genomes were the viral transcription factor ICP4 and the replication protein ICP8. Furthermore, all seven viral replication proteins were enriched on viral genomes, along with cellular PCNA and topoisomerases, while other cellular replication proteins were not detected. The chromatin-remodeling complexes present on viral genomes included the INO80, SWI/SNF, NURD, and FACT complexes, which may prevent chromatinization of the genome. Consistent with this conclusion, histones were not readily recovered with purified viral genomes, and imaging studies revealed an underrepresentation of histones on viral genomes. RNA polymerase II, the mediator complex, TFIID, TFIIH, and several other transcriptional activators and repressors were also affinity purified with viral DNA. The presence of INO80, NURD, SWI/SNF, mediator, TFIID, and TFIIH components is consistent with previous studies in which these complexes copurified with ICP4. Therefore, ICP4 is likely involved in the recruitment of these key cellular chromatin remodeling and transcription factors to viral genomes. Taken together, iPOND is a valuable method for the study of viral genome dynamics

Limits on the experimental simulation of nuclear fuel rod response

International Nuclear Information System (INIS)

Hagar, R.C.

1980-01-01

The steady-state and transient effects of intrinxic geometric and material property differences between typical nuclear fuel pins and electric fuel pin simulators (FPSs) are identified. The effectiveness of varying the transient power supplied to the FPS in reducing the differences between the transient responses of nuclear fuel pins and FPSs is investigated. This effectiveness is shown to be limited by the heat capacity of the FPS, the allowed range of the power program, and different FPS power requirements at different positions on a full-length FPS
Mitochondrial genome sequences and comparative genomics ofPhytophthora ramorum and P. sojae

Energy Technology Data Exchange (ETDEWEB)

Martin, Frank N.; Douda, Bensasson; Tyler, Brett M.; Boore,Jeffrey L.

2007-01-01

The complete sequences of the mitochondrial genomes of theoomycetes of Phytophthora ramorum and P. sojae were determined during thecourse of their complete nuclear genome sequencing (Tyler, et al. 2006).Both are circular, with sizes of 39,314 bp for P. ramorum and 42,975 bpfor P. sojae. Each contains a total of 37 identifiable protein-encodinggenes, 25 or 26 tRNAs (P. sojae and P. ramorum, respectively)specifying19 amino acids, and a variable number of ORFs (7 for P. ramorum and 12for P. sojae) which are potentially additional functional genes.Non-coding regions comprise approximately 11.5 percent and 18.4 percentof the genomes of P. ramorum and P. sojae, respectively. Relative to P.sojae, there is an inverted repeat of 1,150 bp in P. ramorum thatincludes an unassigned unique ORF, a tRNA gene, and adjacent non-codingsequences, but otherwise the gene order in both species is identical.Comparisons of these genomes with published sequences of the P. infestansmitochondrial genome reveals a number of similarities, but the gene orderin P. infestans differs in two adjacent locations due to inversions.Sequence alignments of the three genomes indicated sequence conservationranging from 75 to 85 percent and that specific regions were morevariable than others.
Nuclear Genome Size: Are We Getting Closer?

Czech Academy of Sciences Publication Activity Database

Doležel, Jaroslav; Greilhuber, J.

77A, č. 7 (2010), s. 635-642 ISSN 1552-4922 R&D Projects : GA MŠk(CZ) LC06004 Institutional research plan: CEZ:AV0Z50380511 Keywords : cytometric techniques * reference standards * genome sequencing Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.749, year: 2010
Duties and responsibilities of the Nuclear Power Inspectorate and the National Radiation Protection Institute in connection with nuclear power plants

International Nuclear Information System (INIS)

Eckered, T.

1977-01-01

The two Swedish bodies competent for the control of nuclear energy are the Swedish Nuclear Power Inspectorate (SKI) and the National Swedish Institute on Radiation Protection (SSI). The duties of both bodies in respect of inspection stem from the provisions of the Atomic Energy Act and the Radiation Protection Act. The procedure to be followed for construction and operation of nuclear power plants is described from the viewpoint of the responsibilities entrusted to SKI and SSI. (NEA) [fr
Nuclear accident response and population protection in The Netherlands: philosophy, solutions, and problems

International Nuclear Information System (INIS)

Baas, J.L.; Bosnjakovic, B.F.M.

1981-01-01

The subject is dealt with under the headings: nuclear energy in the Netherlands; the philosophy underlying the existing organization of response to nuclear accidents and population protection; practical experiences and recent developments; dose estimates; data transmission and lines of communication; international cooperation. (U.K.)
Nuclear energy and the responsibilities of the Atomic Energy Board

International Nuclear Information System (INIS)

De Villiers, J.W.L.

1980-01-01

The paper discusses nuclear energy and the responsibilities of the previous Atomic Energy Board, (now the Atomic Energy Corporation) of South Africa in this respect. The paper starts by giving a brief introduction to the Atomic Energy Board, its organization and its functions. Research is undertaken in various fields such as the exploitation of nuclear fuels, radiobiology, radioisotopes, etc. Certain activities of the Board was also more directly related to Koeberg. The paper covers four of these areas, namely the early studies of the feasibility of introducing nuclear power in South Africa; the services involving the Board's special expertise in certain areas which Escom makes use of; the regulatory function and the preparation for handling and disposal of radioactive waste
The U.S. Department of Energy, National Nuclear Security Agency's Use of Geographic Information Systems for Nuclear Emergency Response Support

International Nuclear Information System (INIS)

Guber, A. L.

2001-01-01

The U.S, Department of Energy (DOE), National Nuclear Security Agency's (NNSA) Remote Sensing Laboratory (RSL) provides Geographic Information System (GIS) support during nuclear emergency response activities. As directed by the NNSA, the RSL GIS staff maintains databases and equipment for rapid field deployment during an emergency response. When on location, GIS operators provide information products to on-site emergency managers as well as to emergency managers at the DOE Headquarters (HQ) Emergency Operations Center (EOC) in Washington, D.C. Data products are derived from multiple information sources in the field including radiological prediction models, field measurements taken on the ground and from the air, and pertinent information researched on the Internet. The GIS functions as a central data hub where it supplies the information to response elements in the field, as well as to headquarters officials at HQ during emergency response activities
Short interspersed nuclear elements (SINEs) are abundant in Solanaceae and have a family-specific impact on gene structure and genome organization.

Science.gov (United States)

Seibt, Kathrin M; Wenke, Torsten; Muders, Katja; Truberg, Bernd; Schmidt, Thomas

2016-05-01

Short interspersed nuclear elements (SINEs) are highly abundant non-autonomous retrotransposons that are widespread in plants. They are short in size, non-coding, show high sequence diversity, and are therefore mostly not or not correctly annotated in plant genome sequences. Hence, comparative studies on genomic SINE populations are rare. To explore the structural organization and impact of SINEs, we comparatively investigated the genome sequences of the Solanaceae species potato (Solanum tuberosum), tomato (Solanum lycopersicum), wild tomato (Solanum pennellii), and two pepper cultivars (Capsicum annuum). Based on 8.5 Gbp sequence data, we annotated 82 983 SINE copies belonging to 10 families and subfamilies on a base pair level. Solanaceae SINEs are dispersed over all chromosomes with enrichments in distal regions. Depending on the genome assemblies and gene predictions, 30% of all SINE copies are associated with genes, particularly frequent in introns and untranslated regions (UTRs). The close association with genes is family specific. More than 10% of all genes annotated in the Solanaceae species investigated contain at least one SINE insertion, and we found genes harbouring up to 16 SINE copies. We demonstrate the involvement of SINEs in gene and genome evolution including the donation of splice sites, start and stop codons and exons to genes, enlargement of introns and UTRs, generation of tandem-like duplications and transduction of adjacent sequence regions. © 2016 The Authors The Plant Journal © 2016 John Wiley & Sons Ltd.
Research on the response of various persons to information about nuclear power generation

International Nuclear Information System (INIS)

Maruta, Katsuhiko

2014-01-01

The author surveyed blogs readily available on the Internet for three purposes: (1) to grasp the public response to nuclear problems after the accident at the Fukushima Daiichi Nuclear Power Station, (2) to determine changes in the number of blogs based on an article search, and (3) to identify the stance of bloggers on the necessity of nuclear power generation based on reading contribution contents. Furthermore the author conducted a questionnaire survey of public response in reference to the results of the blog survey. From the blog survey, it was found that immediately after the accident, the number of blogs which were negative toward nuclear power generation drastically increased, but as time has passed, blogs which are positive are increasing in number somewhat in expectation of stabilized economic and living conditions. The main results of the questionnaire survey are as follows. (1) Many persons want power generation that is non-nuclear; this is because they have good expectations for renewable energy sources or new thermal power generation as an alternative energy and they strongly feel anxious about the issue of disposal of spent nuclear fuel. (2) Because of the risk of negative impacts which electricity shortages bring on the economy and lifestyles, some persons do not want immediate decommissioning of nuclear power reactors, they favor a phase-out of nuclear power generation. Though public opinion about nuclear problems includes the expectation that one alternative energy can be selected, there is a possibility that this opinion will shift to find an optimum energy mix of plural energy sources. (author)
Implementing genomics and pharmacogenomics in the clinic: The National Human Genome Research Institute's genomic medicine portfolio.

Science.gov (United States)

Manolio, Teri A

2016-10-01

Increasing knowledge about the influence of genetic variation on human health and growing availability of reliable, cost-effective genetic testing have spurred the implementation of genomic medicine in the clinic. As defined by the National Human Genome Research Institute (NHGRI), genomic medicine uses an individual's genetic information in his or her clinical care, and has begun to be applied effectively in areas such as cancer genomics, pharmacogenomics, and rare and undiagnosed diseases. In 2011 NHGRI published its strategic vision for the future of genomic research, including an ambitious research agenda to facilitate and promote the implementation of genomic medicine. To realize this agenda, NHGRI is consulting and facilitating collaborations with the external research community through a series of "Genomic Medicine Meetings," under the guidance and leadership of the National Advisory Council on Human Genome Research. These meetings have identified and begun to address significant obstacles to implementation, such as lack of evidence of efficacy, limited availability of genomics expertise and testing, lack of standards, and difficulties in integrating genomic results into electronic medical records. The six research and dissemination initiatives comprising NHGRI's genomic research portfolio are designed to speed the evaluation and incorporation, where appropriate, of genomic technologies and findings into routine clinical care. Actual adoption of successful approaches in clinical care will depend upon the willingness, interest, and energy of professional societies, practitioners, patients, and payers to promote their responsible use and share their experiences in doing so. Published by Elsevier Ireland Ltd.
Application of geographical information system (GIS) for the preparedness for response to nuclear emergencies

International Nuclear Information System (INIS)

Chaudhury, Probal; Pradeepkumar, K.S.; Saindane, S.S.; Suri, M.M.K.; Sharma, D.N.

2005-01-01

As recommended by International Atomic Energy Agency (IAEA), preparedness for response to nuclear/radiological emergencies is essential for all nations including those not having nuclear facilities. Methodology and systems for quick assessment of radiological impact following any large scale radioactive release/contamination in the environment are already developed. Efforts are being made to provide Geographical Information System (GIS) support for enhancing the capability of quick decision making on the implementation of countermeasures and to strengthen the Emergency Preparedness Program. This requires development of the database of nuclear facilities, roads, buildings, agriculture land, population density and geolocating using geocoded addresses. GIS helps in the creation of custom maps that spatially show several data layers pertinent to the cities/area around the nuclear power plants. The GIS based software imports and spatially displays the predicted movement of radioactive plume and helps in the revision of emergency plans based on the periodic inputs from various systems and monitoring teams. These tools, allow the Emergency Response Centers to take decisions regarding the progress, success and future direction of response in large cities/complex sites. (author)
Meta-analysis of genome-wide association studies of HDL cholesterol response to statins

DEFF Research Database (Denmark)

Postmus, Iris; Warren, Helen R; Trompet, Stella

2016-01-01

BACKGROUND: In addition to lowering low density lipoprotein cholesterol (LDL-C), statin therapy also raises high density lipoprotein cholesterol (HDL-C) levels. Inter-individual variation in HDL-C response to statins may be partially explained by genetic variation. METHODS AND RESULTS: We performed...... a meta-analysis of genome-wide association studies (GWAS) to identify variants with an effect on statin-induced high density lipoprotein cholesterol (HDL-C) changes. The 123 most promising signals with p
Infectious diseases of marine molluscs and host responses as revealed by genomic tools

Science.gov (United States)

Ford, Susan E.

2016-01-01

More and more infectious diseases affect marine molluscs. Some diseases have impacted commercial species including MSX and Dermo of the eastern oyster, QPX of hard clams, withering syndrome of abalone and ostreid herpesvirus 1 (OsHV-1) infections of many molluscs. Although the exact transmission mechanisms are not well understood, human activities and associated environmental changes often correlate with increased disease prevalence. For instance, hatcheries and large-scale aquaculture create high host densities, which, along with increasing ocean temperature, might have contributed to OsHV-1 epizootics in scallops and oysters. A key to understanding linkages between the environment and disease is to understand how the environment affects the host immune system. Although we might be tempted to downplay the role of immunity in invertebrates, recent advances in genomics have provided insights into host and parasite genomes and revealed surprisingly sophisticated innate immune systems in molluscs. All major innate immune pathways are found in molluscs with many immune receptors, regulators and effectors expanded. The expanded gene families provide great diversity and complexity in innate immune response, which may be key to mollusc's defence against diverse pathogens in the absence of adaptive immunity. Further advances in host and parasite genomics should improve our understanding of genetic variation in parasite virulence and host disease resistance. PMID:26880838
Responsibilities and capabilities of a nuclear energy programme implementing organization

International Nuclear Information System (INIS)

2009-01-01

An appropriate infrastructure is essential for the efficient, safe, reliable and peaceful use of nuclear power. The IAEA was encouraged by its Member States to provide assistance to those considering the introduction of nuclear power. These countries face the challenge of building a national nuclear infrastructure to support a first nuclear power plant. The IAEA is responding to their needs through increased technical assistance, missions and workshops, and with new and updated technical publications in the IAEA Nuclear Energy Series. Milestones in the Development of a National Infrastructure for Nuclear Power, an IAEA Nuclear Energy Series publication (NG-G-3.1), provides detailed guidance on a holistic approach to national nuclear infrastructure development, over three phases. Nineteen issues are identified in this guide, ranging from development of a government's national position on nuclear power to planning for procurement related to the first NPP. An important element of the holistic approach is an entity that can help prepare the decision makers in a country to make a knowledgeable commitment to nuclear power, and then to coordinate infrastructure development efforts among various implementing organizations so that they arrive at the point of readiness to issue a bid tender at the same time. In the Milestones guide, this entity is called a nuclear energy programme implementing organization (NEPIO). As a growing number of Member States started to consider the nuclear power option, they asked for guidance from the IAEA on how to launch a nuclear power programme. In particular, Member States requested additional information on how to establish a NEPIO, especially in the earliest phases of a programme. This report has been prepared to provide information on the responsibilities and capabilities of a NEPIO, as well as to give an indication on how it relates to other key national organizations in the implementation of a nuclear power programme, such as the owner
Dynamic Response of AP1000 Nuclear Island Due to Safe Shutdown Earthquake Loading

Directory of Open Access Journals (Sweden)

Gan Buntara S.

2017-01-01

Full Text Available AP1000 is a standard nuclear power plant developed by Westinghouse and its partners by using an advanced passive safety feature. Among the five principle building structures, namely the nuclear island, turbine building, annex building, diesel generator building and radwaste building, the safety of the nuclear island building is the most concerned. This paper investigates the dynamic response of the nuclear island building of the AP1000 plant subjected to safe shutdown earthquake loadings. A finite element model for the building, which is assumed to be built in a hard-rock base, is developed and its dynamic response is computed with the aid of the commercial finite element package ANSYS. The dynamic characteristics, including the natural frequencies, the vibration modes, and the time histories for displacements, velocities, and accelerations of the building are obtained for two typical safe shutdown earthquakes, El Centro and Kobe earthquakes. The dynamic behavior of the building due to the earthquakes and its safety is examined and highlighted.
Considerations in Emergency Preparedness and Response for a State Embarking on a Nuclear Power Programme (Arabic Edition)

International Nuclear Information System (INIS)

2014-01-01

The aim of this publication is to provide a practical tool for emergency planning for States embarking on a nuclear power programme and to fulfil, in part, functions assigned to the IAEA in the Convention on Assistance in the Case of a Nuclear Accident or Radiological Emergency ('Assistance Convention'). Under Article 5.a (ii) of the Assistance Convention, one function of the IAEA is to collect and disseminate to State Parties and Member States information concerning methodologies, techniques and available results of research relating to such emergencies. As established in the publication Preparedness and Response for a Nuclear or Radiological Emergency (IAEA Safety Standards Series No. GS-R-2), the practical goal of emergency response is 'to ensure that arrangements are in place for a timely, managed, controlled, coordinated and effective response at the scene, and at the local, regional, national and international level, to any nuclear or radiological emergency'. In 2011 the IAEA General Conference, in resolution GC(55)/RES/9, encouraged States 'embarking on new nuclear power programmes to take timely and proactive steps, based upon gradual and systematic application of IAEA safety standards, to establish and sustain a strong safety culture'. It also 'emphasizes the importance for all Member States to implement emergency preparedness and response mechanisms and develop mitigation measures at a national level, consistent with the IAEA's Safety Standards, for improving emergency preparedness and response, facilitating communication in an emergency and contributing to harmonization of national criteria for protective and other actions'. This publication, issued in the IAEA Emergency Preparedness and Response Series, is intended to assist on steps to be taken by States embarking on a nuclear power programme to establish effective national capabilities and arrangements of preparedness for and response to a nuclear or radiological emergency (hereinafter referred to as
Considerations in Emergency Preparedness and Response for a State Embarking on a Nuclear Power Programme (Russian Edition)

International Nuclear Information System (INIS)

2013-01-01

The aim of this publication is to provide a practical tool for emergency planning for States embarking on a nuclear power programme and to fulfil, in part, functions assigned to the IAEA in the Convention on Assistance in the Case of a Nuclear Accident or Radiological Emergency ('Assistance Convention'). Under Article 5.a (ii) of the Assistance Convention, one function of the IAEA is to collect and disseminate to State Parties and Member States information concerning methodologies, techniques and available results of research relating to such emergencies. As established in the publication Preparedness and Response for a Nuclear or Radiological Emergency (IAEA Safety Standards Series No. GS-R-2), the practical goal of emergency response is 'to ensure that arrangements are in place for a timely, managed, controlled, coordinated and effective response at the scene, and at the local, regional, national and international level, to any nuclear or radiological emergency'. In 2011 the IAEA General Conference, in resolution GC(55)/RES/9, encouraged States 'embarking on new nuclear power programmes to take timely and proactive steps, based upon gradual and systematic application of IAEA safety standards, to establish and sustain a strong safety culture'. It also 'emphasizes the importance for all Member States to implement emergency preparedness and response mechanisms and develop mitigation measures at a national level, consistent with the IAEA's Safety Standards, for improving emergency preparedness and response, facilitating communication in an emergency and contributing to harmonization of national criteria for protective and other actions'. This publication, issued in the IAEA Emergency Preparedness and Response Series, is intended to assist on steps to be taken by States embarking on a nuclear power programme to establish effective national capabilities and arrangements of preparedness for and response to a nuclear or radiological emergency (hereinafter referred to as
Considerations in Emergency Preparedness and Response for a State Embarking on a Nuclear Power Programme (Spanish Edition)

International Nuclear Information System (INIS)

2014-01-01

The aim of this publication is to provide a practical tool for emergency planning for States embarking on a nuclear power programme and to fulfil, in part, functions assigned to the IAEA in the Convention on Assistance in the Case of a Nuclear Accident or Radiological Emergency ('Assistance Convention'). Under Article 5.a (ii) of the Assistance Convention, one function of the IAEA is to collect and disseminate to State Parties and Member States information concerning methodologies, techniques and available results of research relating to such emergencies. As established in the publication Preparedness and Response for a Nuclear or Radiological Emergency (IAEA Safety Standards Series No. GS-R-2), the practical goal of emergency response is 'to ensure that arrangements are in place for a timely, managed, controlled, coordinated and effective response at the scene, and at the local, regional, national and international level, to any nuclear or radiological emergency'. In 2011 the IAEA General Conference, in resolution GC(55)/RES/9, encouraged States 'embarking on new nuclear power programmes to take timely and proactive steps, based upon gradual and systematic application of IAEA safety standards, to establish and sustain a strong safety culture'. It also 'emphasizes the importance for all Member States to implement emergency preparedness and response mechanisms and develop mitigation measures at a national level, consistent with the IAEA's Safety Standards, for improving emergency preparedness and response, facilitating communication in an emergency and contributing to harmonization of national criteria for protective and other actions'. This publication, issued in the IAEA Emergency Preparedness and Response Series, is intended to assist on steps to be taken by States embarking on a nuclear power programme to establish effective national capabilities and arrangements of preparedness for and response to a nuclear or radiological emergency (hereinafter referred to as
Communication with the Public in a Nuclear or Radiological Emergency. Emergency Preparedness and Response (Chinese Edition)

International Nuclear Information System (INIS)

2013-01-01

The aim of this publication is to provide practical guidance for public information officers on the preparation for and response to a nuclear or radiological emergency, and to fulfil in part functions assigned to the IAEA in the Convention on Assistance in the Case of a Nuclear Accident or Radiological Emergency (Assistance Convention), as well as meeting requirements stated in IAEA Safety Standards Series No. SF-1, Fundamental Safety Principles, and in IAEA Safety Standards No. GS-R-2, Preparedness and Response for a Nuclear or Radiological Emergency. Under Article 5(a)(ii) of the Assistance Convention, one function of the IAEA is to collect and disseminate to States Parties and Member States information concerning methodologies, techniques and results of research relating to response to nuclear or radiological emergencies. IAEA Safety Standards Series No. GS-R-2 establishes the requirements for an adequate level of preparedness for and response to a nuclear or radiological emergency in any State, and specifies that 'All practicable steps shall be taken to provide the public with useful, timely, truthful, consistent and appropriate information throughout a nuclear or radiological emergency' in the response phase. It also requires 'responding to incorrect information and rumours; and responding to requests for information from the public and from the news and information media'. This publication provides guidance in the form of action guides and information sheets that can be easily applied by a State to build a basic capability to respond to a nuclear or radiological emergency. This guidance should be adapted to fit the user State's organizational arrangements, language, terminology, concept of operation and capabilities. This publication is published as part of the IAEA's Emergency Preparedness and Response series and complements the Manual for First Responders to a Radiological Emergency in the parts related to the tasks of public information officers. It takes
Communication with the Public in a Nuclear or Radiological Emergency. Emergency Preparedness and Response (French Edition)

International Nuclear Information System (INIS)

2013-01-01

The aim of this publication is to provide practical guidance for public information officers on the preparation for and response to a nuclear or radiological emergency, and to fulfil in part functions assigned to the IAEA in the Convention on Assistance in the Case of a Nuclear Accident or Radiological Emergency (Assistance Convention), as well as meeting requirements stated in IAEA Safety Standards Series No. SF-1, Fundamental Safety Principles, and in IAEA Safety Standards No. GS-R-2, Preparedness and Response for a Nuclear or Radiological Emergency. Under Article 5(a)(ii) of the Assistance Convention, one function of the IAEA is to collect and disseminate to States Parties and Member States information concerning methodologies, techniques and results of research relating to response to nuclear or radiological emergencies. IAEA Safety Standards Series No. GS-R-2 establishes the requirements for an adequate level of preparedness for and response to a nuclear or radiological emergency in any State, and specifies that 'All practicable steps shall be taken to provide the public with useful, timely, truthful, consistent and appropriate information throughout a nuclear or radiological emergency' in the response phase. It also requires 'responding to incorrect information and rumours; and responding to requests for information from the public and from the news and information media'. This publication provides guidance in the form of action guides and information sheets that can be easily applied by a State to build a basic capability to respond to a nuclear or radiological emergency. This guidance should be adapted to fit the user State's organizational arrangements, language, terminology, concept of operation and capabilities. This publication is published as part of the IAEA's Emergency Preparedness and Response series and complements the Manual for First Responders to a Radiological Emergency in the parts related to the tasks of public information officers. It takes

Communication with the Public in a Nuclear or Radiological Emergency. Emergency Preparedness and Response (Chinese Edition)

Energy Technology Data Exchange (ETDEWEB)

NONE

2013-09-01

The aim of this publication is to provide practical guidance for public information officers on the preparation for and response to a nuclear or radiological emergency, and to fulfil in part functions assigned to the IAEA in the Convention on Assistance in the Case of a Nuclear Accident or Radiological Emergency (Assistance Convention), as well as meeting requirements stated in IAEA Safety Standards Series No. SF-1, Fundamental Safety Principles, and in IAEA Safety Standards No. GS-R-2, Preparedness and Response for a Nuclear or Radiological Emergency. Under Article 5(a)(ii) of the Assistance Convention, one function of the IAEA is to collect and disseminate to States Parties and Member States information concerning methodologies, techniques and results of research relating to response to nuclear or radiological emergencies. IAEA Safety Standards Series No. GS-R-2 establishes the requirements for an adequate level of preparedness for and response to a nuclear or radiological emergency in any State, and specifies that 'All practicable steps shall be taken to provide the public with useful, timely, truthful, consistent and appropriate information throughout a nuclear or radiological emergency' in the response phase. It also requires 'responding to incorrect information and rumours; and responding to requests for information from the public and from the news and information media'. This publication provides guidance in the form of action guides and information sheets that can be easily applied by a State to build a basic capability to respond to a nuclear or radiological emergency. This guidance should be adapted to fit the user State's organizational arrangements, language, terminology, concept of operation and capabilities. This publication is published as part of the IAEA's Emergency Preparedness and Response series and complements the Manual for First Responders to a Radiological Emergency in the parts related to the tasks of public information officers. It takes
Communication with the Public in a Nuclear or Radiological Emergency. Emergency Preparedness and Response (Arabic Edition)

International Nuclear Information System (INIS)

2014-01-01

The aim of this publication is to provide practical guidance for public information officers on the preparation for and response to a nuclear or radiological emergency, and to fulfil in part functions assigned to the IAEA in the Convention on Assistance in the Case of a Nuclear Accident or Radiological Emergency (Assistance Convention), as well as meeting requirements stated in IAEA Safety Standards Series No. SF-1, Fundamental Safety Principles, and in IAEA Safety Standards No. GS-R-2, Preparedness and Response for a Nuclear or Radiological Emergency. Under Article 5(a)(ii) of the Assistance Convention, one function of the IAEA is to collect and disseminate to States Parties and Member States information concerning methodologies, techniques and results of research relating to response to nuclear or radiological emergencies. IAEA Safety Standards Series No. GS-R-2 establishes the requirements for an adequate level of preparedness for and response to a nuclear or radiological emergency in any State, and specifies that 'All practicable steps shall be taken to provide the public with useful, timely, truthful, consistent and appropriate information throughout a nuclear or radiological emergency' in the response phase. It also requires 'responding to incorrect information and rumours; and responding to requests for information from the public and from the news and information media'. This publication provides guidance in the form of action guides and information sheets that can be easily applied by a State to build a basic capability to respond to a nuclear or radiological emergency. This guidance should be adapted to fit the user State's organizational arrangements, language, terminology, concept of operation and capabilities. This publication is published as part of the IAEA's Emergency Preparedness and Response series and complements the Manual for First Responders to a Radiological Emergency in the parts related to the tasks of public information officers. It takes
Communication with the Public in a Nuclear or Radiological Emergency. Emergency Preparedness and Response (Russian Edition)

International Nuclear Information System (INIS)

2014-01-01

The aim of this publication is to provide practical guidance for public information officers on the preparation for and response to a nuclear or radiological emergency, and to fulfil in part functions assigned to the IAEA in the Convention on Assistance in the Case of a Nuclear Accident or Radiological Emergency (Assistance Convention), as well as meeting requirements stated in IAEA Safety Standards Series No. SF-1, Fundamental Safety Principles, and in IAEA Safety Standards No. GS-R-2, Preparedness and Response for a Nuclear or Radiological Emergency. Under Article 5(a)(ii) of the Assistance Convention, one function of the IAEA is to collect and disseminate to States Parties and Member States information concerning methodologies, techniques and results of research relating to response to nuclear or radiological emergencies. IAEA Safety Standards Series No. GS-R-2 establishes the requirements for an adequate level of preparedness for and response to a nuclear or radiological emergency in any State, and specifies that 'All practicable steps shall be taken to provide the public with useful, timely, truthful, consistent and appropriate information throughout a nuclear or radiological emergency' in the response phase. It also requires 'responding to incorrect information and rumours; and responding to requests for information from the public and from the news and information media'. This publication provides guidance in the form of action guides and information sheets that can be easily applied by a State to build a basic capability to respond to a nuclear or radiological emergency. This guidance should be adapted to fit the user State's organizational arrangements, language, terminology, concept of operation and capabilities. This publication is published as part of the IAEA's Emergency Preparedness and Response series and complements the Manual for First Responders to a Radiological Emergency in the parts related to the tasks of public information officers. It takes
Communication with the Public in a Nuclear or Radiological Emergency. Emergency Preparedness and Response (Spanish Edition)

International Nuclear Information System (INIS)

2013-01-01

The aim of this publication is to provide practical guidance for public information officers on the preparation for and response to a nuclear or radiological emergency, and to fulfil in part functions assigned to the IAEA in the Convention on Assistance in the Case of a Nuclear Accident or Radiological Emergency (Assistance Convention), as well as meeting requirements stated in IAEA Safety Standards Series No. SF-1, Fundamental Safety Principles, and in IAEA Safety Standards No. GS-R-2, Preparedness and Response for a Nuclear or Radiological Emergency. Under Article 5(a)(ii) of the Assistance Convention, one function of the IAEA is to collect and disseminate to States Parties and Member States information concerning methodologies, techniques and results of research relating to response to nuclear or radiological emergencies. IAEA Safety Standards Series No. GS-R-2 establishes the requirements for an adequate level of preparedness for and response to a nuclear or radiological emergency in any State, and specifies that 'All practicable steps shall be taken to provide the public with useful, timely, truthful, consistent and appropriate information throughout a nuclear or radiological emergency' in the response phase. It also requires 'responding to incorrect information and rumours; and responding to requests for information from the public and from the news and information media'. This publication provides guidance in the form of action guides and information sheets that can be easily applied by a State to build a basic capability to respond to a nuclear or radiological emergency. This guidance should be adapted to fit the user State's organizational arrangements, language, terminology, concept of operation and capabilities. This publication is published as part of the IAEA's Emergency Preparedness and Response series and complements the Manual for First Responders to a Radiological Emergency in the parts related to the tasks of public information officers. It takes
Genome-wide expression analysis offers new insights into the origin and evolution of Physcomitrella patens stress response

KAUST Repository

Khraiwesh, Basel

2015-11-30

Changes in the environment, such as those caused by climate change, can exert stress on plant growth, diversity and ultimately global food security. Thus, focused efforts to fully understand plant response to stress are urgently needed in order to develop strategies to cope with the effects of climate change. Because Physcomitrella patens holds a key evolutionary position bridging the gap between green algae and higher plants, and because it exhibits a well-developed stress tolerance, it is an excellent model for such exploration. Here, we have used Physcomitrella patens to study genome-wide responses to abiotic stress through transcriptomic analysis by a high-throughput sequencing platform. We report a comprehensive analysis of transcriptome dynamics, defining profiles of elicited gene regulation responses to abiotic stress-associated hormone Abscisic Acid (ABA), cold, drought, and salt treatments. We identified more than 20,000 genes expressed under each aforementioned stress treatments, of which 9,668 display differential expression in response to stress. The comparison of Physcomitrella patens stress regulated genes with unicellular algae, vascular and flowering plants revealed genomic delineation concomitant with the evolutionary movement to land, including a general gene family complexity and loss of genes associated with different functional groups.
Genome-wide annotation of the soybean WRKY family and functional characterization of genes involved in response to Phakopsora pachyrhizi infection.

Science.gov (United States)

Bencke-Malato, Marta; Cabreira, Caroline; Wiebke-Strohm, Beatriz; Bücker-Neto, Lauro; Mancini, Estefania; Osorio, Marina B; Homrich, Milena S; Turchetto-Zolet, Andreia Carina; De Carvalho, Mayra C C G; Stolf, Renata; Weber, Ricardo L M; Westergaard, Gastón; Castagnaro, Atílio P; Abdelnoor, Ricardo V; Marcelino-Guimarães, Francismar C; Margis-Pinheiro, Márcia; Bodanese-Zanettini, Maria Helena

2014-09-10

Many previous studies have shown that soybean WRKY transcription factors are involved in the plant response to biotic and abiotic stresses. Phakopsora pachyrhizi is the causal agent of Asian Soybean Rust, one of the most important soybean diseases. There are evidences that WRKYs are involved in the resistance of some soybean genotypes against that fungus. The number of WRKY genes already annotated in soybean genome was underrepresented. In the present study, a genome-wide annotation of the soybean WRKY family was carried out and members involved in the response to P. pachyrhizi were identified. As a result of a soybean genomic databases search, 182 WRKY-encoding genes were annotated and 33 putative pseudogenes identified. Genes involved in the response to P. pachyrhizi infection were identified using superSAGE, RNA-Seq of microdissected lesions and microarray experiments. Seventy-five genes were differentially expressed during fungal infection. The expression of eight WRKY genes was validated by RT-qPCR. The expression of these genes in a resistant genotype was earlier and/or stronger compared with a susceptible genotype in response to P. pachyrhizi infection. Soybean somatic embryos were transformed in order to overexpress or silence WRKY genes. Embryos overexpressing a WRKY gene were obtained, but they were unable to convert into plants. When infected with P. pachyrhizi, the leaves of the silenced transgenic line showed a higher number of lesions than the wild-type plants. The present study reports a genome-wide annotation of soybean WRKY family. The participation of some members in response to P. pachyrhizi infection was demonstrated. The results contribute to the elucidation of gene function and suggest the manipulation of WRKYs as a strategy to increase fungal resistance in soybean plants.
Preliminary Genomic Characterization of Ten Hardwood Tree Species from Multiplexed Low Coverage Whole Genome Sequencing.

Directory of Open Access Journals (Sweden)

Margaret Staton

Full Text Available Forest health issues are on the rise in the United States, resulting from introduction of alien pests and diseases, coupled with abiotic stresses related to climate change. Increasingly, forest scientists are finding genetic/genomic resources valuable in addressing forest health issues. For a set of ten ecologically and economically important native hardwood tree species representing a broad phylogenetic spectrum, we used low coverage whole genome sequencing from multiplex Illumina paired ends to economically profile their genomic content. For six species, the genome content was further analyzed by flow cytometry in order to determine the nuclear genome size. Sequencing yielded a depth of 0.8X to 7.5X, from which in silico analysis yielded preliminary estimates of gene and repetitive sequence content in the genome for each species. Thousands of genomic SSRs were identified, with a clear predisposition toward dinucleotide repeats and AT-rich repeat motifs. Flanking primers were designed for SSR loci for all ten species, ranging from 891 loci in sugar maple to 18,167 in redbay. In summary, we have demonstrated that useful preliminary genome information including repeat content, gene content and useful SSR markers can be obtained at low cost and time input from a single lane of Illumina multiplex sequence.
Quantitative analysis of polycomb response elements (PREs at identical genomic locations distinguishes contributions of PRE sequence and genomic environment

Directory of Open Access Journals (Sweden)

Okulski Helena

2011-03-01

Full Text Available Abstract Background Polycomb/Trithorax response elements (PREs are cis-regulatory elements essential for the regulation of several hundred developmentally important genes. However, the precise sequence requirements for PRE function are not fully understood, and it is also unclear whether these elements all function in a similar manner. Drosophila PRE reporter assays typically rely on random integration by P-element insertion, but PREs are extremely sensitive to genomic position. Results We adapted the ΦC31 site-specific integration tool to enable systematic quantitative comparison of PREs and sequence variants at identical genomic locations. In this adaptation, a miniwhite (mw reporter in combination with eye-pigment analysis gives a quantitative readout of PRE function. We compared the Hox PRE Frontabdominal-7 (Fab-7 with a PRE from the vestigial (vg gene at four landing sites. The analysis revealed that the Fab-7 and vg PREs have fundamentally different properties, both in terms of their interaction with the genomic environment at each site and their inherent silencing abilities. Furthermore, we used the ΦC31 tool to examine the effect of deletions and mutations in the vg PRE, identifying a 106 bp region containing a previously predicted motif (GTGT that is essential for silencing. Conclusions This analysis showed that different PREs have quantifiably different properties, and that changes in as few as four base pairs have profound effects on PRE function, thus illustrating the power and sensitivity of ΦC31 site-specific integration as a tool for the rapid and quantitative dissection of elements of PRE design.
Hope, connectedness, and action: responses of adolescents and young adults to the threat of nuclear war

Energy Technology Data Exchange (ETDEWEB)

Fernald, M.C.

1985-01-01

This study undertook to assess the degree to which a person's sense of interconnectedness with others may have a mediating effect on whether one reacts to the consciousness of nuclear threat with feelings of despair (helplessness and hopelessness) or with a sense of empowerment (hope, efficacy, and action for change). Subjects included 119 public high school students and 14 Friends' school students, ranging from 12-18 years of age; 58 university students ranging from 18-25 years of age; and 24 parents of public school students, 10 adult Friends, and 38 members of Physicians for Social Responsibility, ranging from 20-83 years of age. A self-rating questionnaire was administered to assess subjects' conscious level of concern about nuclear issues, feelings of connectedness with others in general and about nuclear concerns, feelings of hope and efficacy in general and with regard to nuclear issues, and participation in activities reflecting concerns about nuclear threat. Correlational analyses (multiple regression, Spearman Rho, Kendall's Tau) showed that general feelings of hope, level of activity, and feelings of connectedness about nuclear concerns were the best predictors of hope about nuclear concerns. Conscious level of concern and feelings of connectedness about nuclear concerns, along with age and SES were the best predictors of an active response to nuclear threat; additionally, parents' level of concern about nuclear issues was predictive of their children's degree of activity in response to nuclear threat. Adolescents' level of concern and degree of connectedness with others was predicted by their parents' degree of connectedness.
A 'joint venture' model of recontacting in clinical genomics: challenges for responsible implementation.

Science.gov (United States)

Dheensa, Sandi; Carrieri, Daniele; Kelly, Susan; Clarke, Angus; Doheny, Shane; Turnpenny, Peter; Lucassen, Anneke

2017-07-01

Advances in genomics often lead healthcare professionals (HCPs) to learn new information, e.g., about reinterpreted variants that could have clinical significance for patients seen previously. A question arises of whether HCPs should recontact these former patients. We present some findings interrogating the views of patients (or parents of patients) with a rare or undiagnosed condition about how such recontacting might be organised ethically and practically. Forty-one interviews were analysed thematically. Participants suggested a 'joint venture' model in which efforts to recontact are shared with HCPs. Some proposed an ICT-approach involving an electronic health record that automatically alerts them to potentially relevant updates. The need for rigorous privacy controls and transparency about who could access their data was emphasised. Importantly, these findings highlight that the lack of clarity about recontacting is a symptom of a wider problem: the lack of necessary infrastructure to pool genomic data responsibly, to aggregate it with other health data, and to enable patients/parents to receive updates. We hope that our findings will instigate a debate about the way responsibilities for recontacting under any joint venture model could be allocated, as well as the limitations and normative implications of using ICT as a solution to this intractable problem. As a first step to delineating responsibilities in the clinical setting, we suggest HCPs should routinely discuss recontacting with patients/parents, including the new information that should trigger a HCP to initiate recontact, as part of the consent process for genetic testing. Copyright © 2017 The Authors. Published by Elsevier Masson SAS.. All rights reserved.
Integration of mtDNA pseudogenes into the nuclear genome coincides with speciation of the human genus. A hypothesis.

Science.gov (United States)

Gunbin, Konstantin; Peshkin, Leonid; Popadin, Konstantin; Annis, Sofia; Ackermann, Rebecca R; Khrapko, Konstantin

2017-05-01

Fragments of mitochondrial DNA are known to get inserted into nuclear DNA to form NUMTs, i.e. nuclear pseudogenes of the mtDNA. The insertion of a NUMT is a rare event. Hundreds of pseudogenes have been cataloged in the human genome. NUMTs are, in essence, a special type of mutation with their own internal timer, which is synchronized with an established molecular clock, the mtDNA. Thus insertion of NUMTs can be timed with respect to evolution milestones such as the emergence of new species. We asked whether NUMTs were inserted uniformly over time or preferentially during certain periods of evolution, as implied by the "punctuated evolution" model. To our surprise, the NUMT insertion times do appear nonrandom with at least one cluster positioned at around 2.8 million years ago (Ma). Interestingly, 2.8Ma closely corresponds to the time of emergence of the genus Homo, and to a well-documented period of major climate change ca. 2.9-2.5Ma. It is tempting to hypothesize that the insertion of NUMTs is related to the speciation process. NUMTs could be either "riders", i.e., their insertion could be facilitated by the overall higher genome rearrangement activity during speciation, or "drivers", i.e. they may more readily get fixed in the population due to positive selection associated with speciation. If correct, the hypothesis would support the idea that evolution of our genus may have happened in a rapid, punctuated manner. Copyright © 2016 Elsevier B.V. and Mitochondria Research Society. All rights reserved.
No boundaries: genomes, organisms, and ecological interactions responsible for divergence and reproductive isolation.

Science.gov (United States)

Etges, William J

2014-01-01

Revealing the genetic basis of traits that cause reproductive isolation, particularly premating or sexual isolation, usually involves the same challenges as most attempts at genotype-phenotype mapping and so requires knowledge of how these traits are expressed in different individuals, populations, and environments, particularly under natural conditions. Genetic dissection of speciation phenotypes thus requires understanding of the internal and external contexts in which underlying genetic elements are expressed. Gene expression is a product of complex interacting factors internal and external to the organism including developmental programs, the genetic background including nuclear-cytotype interactions, epistatic relationships, interactions among individuals or social effects, stochasticity, and prevailing variation in ecological conditions. Understanding of genomic divergence associated with reproductive isolation will be facilitated by functional expression analysis of annotated genomes in organisms with well-studied evolutionary histories, phylogenetic affinities, and known patterns of ecological variation throughout their life cycles. I review progress and prospects for understanding the pervasive role of host plant use on genetic and phenotypic expression of reproductive isolating mechanisms in cactophilic Drosophila mojavensis and suggest how this system can be used as a model for revealing the genetic basis for species formation in organisms where speciation phenotypes are under the joint influences of genetic and environmental factors. © The American Genetic Association. 2014. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
Hyb-Seq: combining target enrichment and genome skimming for plant phylogenomics

Science.gov (United States)

Kevin Weitemier; Shannon C.K. Straub; Richard C. Cronn; Mark Fishbein; Roswitha Schmickl; Angela McDonnell; Aaron. Liston

2014-01-01

â¢ Premise of the study: Hyb-Seq, the combination of target enrichment and genome skimming, allows simultaneous data collection for low-copy nuclear genes and high-copy genomic targets for plant systematics and evolution studies. â¢ Methods and Results: Genome and transcriptome assemblies for milkweed ( Asclepias syriaca ) were used to design enrichment probes for 3385...
Identification of genetic loci in Lactobacillus plantarum that modulate the immune response of dendritic cells using comparative genome hybridization.

Directory of Open Access Journals (Sweden)

Marjolein Meijerink

Full Text Available BACKGROUND: Probiotics can be used to stimulate or regulate epithelial and immune cells of the intestinal mucosa and generate beneficial mucosal immunomodulatory effects. Beneficial effects of specific strains of probiotics have been established in the treatment and prevention of various intestinal disorders, including allergic diseases and diarrhea. However, the precise molecular mechanisms and the strain-dependent factors involved are poorly understood. METHODOLOGY/PRINCIPAL FINDINGS: In this study, we aimed to identify gene loci in the model probiotic organism Lactobacillus plantarum WCFS1 that modulate the immune response of host dendritic cells. The amounts of IL-10 and IL-12 secreted by dendritic cells (DCs after stimulation with 42 individual L. plantarum strains were measured and correlated with the strain-specific genomic composition using comparative genome hybridisation and the Random Forest algorithm. This in silico "gene-trait matching" approach led to the identification of eight candidate genes in the L. plantarum genome that might modulate the DC cytokine response to L. plantarum. Six of these genes were involved in bacteriocin production or secretion, one encoded a bile salt hydrolase and one encoded a transcription regulator of which the exact function is unknown. Subsequently, gene deletions mutants were constructed in L. plantarum WCFS1 and compared to the wild-type strain in DC stimulation assays. All three bacteriocin mutants as well as the transcription regulator (lp_2991 had the predicted effect on cytokine production confirming their immunomodulatory effect on the DC response to L. plantarum. Transcriptome analysis and qPCR data showed that transcript level of gtcA3, which is predicted to be involved in glycosylation of cell wall teichoic acids, was substantially increased in the lp_2991 deletion mutant (44 and 29 fold respectively. CONCLUSION: Comparative genome hybridization led to the identification of gene loci in L
Sum rule approach to the nuclear response in the isovector spin channel

International Nuclear Information System (INIS)

Alberico, W.M.; Ericson, M.; Molinari, A.

1982-01-01

We study the global features of the response of infinite nuclear matter in the spin-isospin channel through the energy weighted sum rules S 1 and Ssub(-) 1 . In particular we compare the outcome of the ring approximation with the exact RPA evaluation of the sum rules. We also investigate the influence of the collective character of the response, induced by the particle hole force for a longitudinal and transverse spin couplings. We show that S 1 is insensitive to the collectivity of the response, as long as the Δ degree of freedom is ignored. The inverse energy weighted sum rule on the other hand, which is linked to the paramagnetic susceptibility, always reflects the hardening or softening of the nuclear response, due to the repulsive or attractive character of the p-h force. This quantity is well suited to the comparison with the experiments, which we perform for 12 C and 56 Fe. (orig.)
Neutron dosimetry at commercial nuclear plants. Final report of Subtask B: dosimeter response

Energy Technology Data Exchange (ETDEWEB)

Cummings, F.M.; Endres, G.W.R.; Brackenbush, L.W.

1983-03-01

As part of a larger program to evaluate personnel neutron dosimetry at commercial nuclear power plants, this study was designed to characterize neutron dosimeter responses inside the containment structure of commercial nuclear plants. In order to characterize those responses, dosimeters were irradiated inside containment at 2 pressurized water reactors and at pipe penetrations outside the biological shield at two boiling water reactors. The reactors were operating at full power during the irradiations. Measurements were also performed with electronic instruments, the tissue equivalent proportional counter (TEPC), and portable remmeters, SNOOPY, RASCAL and PNR-4.
Neutron dosimetry at commercial nuclear plants. Final report of Subtask B: dosimeter response

International Nuclear Information System (INIS)

Cummings, F.M.; Endres, G.W.R.; Brackenbush, L.W.

1983-03-01

As part of a larger program to evaluate personnel neutron dosimetry at commercial nuclear power plants, this study was designed to characterize neutron dosimeter responses inside the containment structure of commercial nuclear plants. In order to characterize those responses, dosimeters were irradiated inside containment at 2 pressurized water reactors and at pipe penetrations outside the biological shield at two boiling water reactors. The reactors were operating at full power during the irradiations. Measurements were also performed with electronic instruments, the tissue equivalent proportional counter (TEPC), and portable remmeters, SNOOPY, RASCAL and PNR-4
Emergency Response Resources guide for nuclear power plant emergencies

International Nuclear Information System (INIS)

1992-07-01

On August 28 and September 18, 1990, the States of Louisiana and Mississippi, Gulf States Utilities, five local parishes, six Federal agencies, and the American Nuclear Insurers participated in a post-emergency TABLETOP exercise in Baton Rouge, Louisiana. One of the products developed from that experience was this guide for understanding the responsibilities and obtaining resources for specific needs from the various participants, particularly from those organizations within the Federal Government. This first revision of that guide broadens the focus of the original document. Also, new information defines the major Federal response facilities. This guide should assist State and local government organizations with identifying and obtaining those resources for the post-emergency response when their resources have been exhausted
First genomic insights into members of a candidate bacterial phylum responsible for wastewater bulking

Directory of Open Access Journals (Sweden)

Yuji Sekiguchi

2015-01-01

Full Text Available Filamentous cells belonging to the candidate bacterial phylum KSB3 were previously identified as the causative agent of fatal filament overgrowth (bulking in a high-rate industrial anaerobic wastewater treatment bioreactor. Here, we obtained near complete genomes from two KSB3 populations in the bioreactor, including the dominant bulking filament, using differential coverage binning of metagenomic data. Fluorescence in situ hybridization with 16S rRNA-targeted probes specific for the two populations confirmed that both are filamentous organisms. Genome-based metabolic reconstruction and microscopic observation of the KSB3 filaments in the presence of sugar gradients indicate that both filament types are Gram-negative, strictly anaerobic fermenters capable of non-flagellar based gliding motility, and have a strikingly large number of sensory and response regulator genes. We propose that the KSB3 filaments are highly sensitive to their surroundings and that cellular processes, including those causing bulking, are controlled by external stimuli. The obtained genomes lay the foundation for a more detailed understanding of environmental cues used by KSB3 filaments, which may lead to more robust treatment options to prevent bulking.
Genome-wide Escherichia coli stress response and improved tolerance towards industrially relevant chemicals

DEFF Research Database (Denmark)

Rau, Martin Holm; Calero Valdayo, Patricia; Lennen, Rebecca

2016-01-01

Economically viable biobased production of bulk chemicals and biofuels typically requires high product titers. During microbial bioconversion this often leads to product toxicity, and tolerance is therefore a critical element in the engineering of production strains. Here, a systems biology...... approach was employed to understand the chemical stress response of Escherichia coli, including a genome-wide screen for mutants with increased fitness during chemical stress. Twelve chemicals with significant production potential were selected, consisting of organic solvent-like chemicals (butanol......, hydroxy-γ-butyrolactone, 1,4-butanediol, furfural), organic acids (acetate, itaconic acid, levulinic acid, succinic acid), amino acids (serine, threonine) and membrane-intercalating chemicals (decanoic acid, geraniol). The transcriptional response towards these chemicals revealed large overlaps...

Radioactive waste: the Nuclear Industry's response to the Environment Committee's report

International Nuclear Information System (INIS)

1986-07-01

This paper represents the nuclear industry's response to the Environmental Committee's report on the handling and disposal of radioactive wastes. Topics covered include the historical aspects of the management of radioactive wastes, technical problems, comparisons with overseas management methods, liquid effluents, reprocessing problems, and public attitudes and perceptions of radioactive waste. Responses to the Environmental Committee's recommendations form an appendix. (U.K.)
Implementing genomics and pharmacogenomics in the clinic: The National Human Genome Research Institute’s genomic medicine portfolio

Science.gov (United States)

Manolio, Teri A.

2016-01-01

Increasing knowledge about the influence of genetic variation on human health and growing availability of reliable, cost-effective genetic testing have spurred the implementation of genomic medicine in the clinic. As defined by the National Human Genome Research Institute (NHGRI), genomic medicine uses an individual’s genetic information in his or her clinical care, and has begun to be applied effectively in areas such as cancer genomics, pharmacogenomics, and rare and undiagnosed diseases. In 2011 NHGRI published its strategic vision for the future of genomic research, including an ambitious research agenda to facilitate and promote the implementation of genomic medicine. To realize this agenda, NHGRI is consulting and facilitating collaborations with the external research community through a series of “Genomic Medicine Meetings,” under the guidance and leadership of the National Advisory Council on Human Genome Research. These meetings have identified and begun to address significant obstacles to implementation, such as lack of evidence of efficacy, limited availability of genomics expertise and testing, lack of standards, and diffficulties in integrating genomic results into electronic medical records. The six research and dissemination initiatives comprising NHGRI’s genomic research portfolio are designed to speed the evaluation and incorporation, where appropriate, of genomic technologies and findings into routine clinical care. Actual adoption of successful approaches in clinical care will depend upon the willingness, interest, and energy of professional societies, practitioners, patients, and payers to promote their responsible use and share their experiences in doing so. PMID:27612677
Task 4 Improvised Nuclear Device Response Curves

Energy Technology Data Exchange (ETDEWEB)

Alai, Maureen [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Neuscamman, Stephanie [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

2016-05-31

LLNL performed fallout and nuclear blast modeling for the 60 cities using the NARAC modeling system and predominant weather patterns determined in a previous Task 4 effort. LLNL performed model simulations and analyses to identify and provide response curves (expressed as two-dimensional contours) for radioactive fallout deposition, transport, population, and blast overpressure as a function of yield, weather, location and time. These contours can then be further combined and correlated with infrastructure and population databases to estimate city specific effects on KPFs such as impacted infrastructure and casualty rates.
The responsibility of nuclear suppliers in the international market

International Nuclear Information System (INIS)

Thiessen, C.W.; Cotton, J.D.; Tait, B.I.

1978-01-01

As a result of escalating oil prices, the developing countries are more and more turning to nuclear energy. As these countries become a more significant part of the international market, unique issues must be faced by the utility and country concerned and the nuclear supplier. A fundamental prerequisite of a successful supplier/customer relationship is a good relationship between their two governments. The supplier can fulfil an effective liaison function to ensure efficiency of communications in this area. In the preplanning phase the supplier can play a major role in supplying information relative to siting, unit size, system planning and plant economics. Once the nuclear choice is made, the pros and cons of purchasing plants on a turnkey versus non-turnkey basis must be weighed. The customer must balance his available resources and experience against his desires for acquisition of overall plant and systems knowledge. During the planning and procurement phase the subject of training, maintenance and service facilities can be an effective part of a comprehensive nuclear programme. In fact, local training and service centres could logically be the first step of a long-term localization effort. With respect to localization the supplier should be capable and experienced in developing this capability and willing to make a long-term commitment in this area. Through a clearer understanding of the responsibilities of the nuclear supplier and a clear delineation of his role, developing nations can more adequately assess the basis upon which to move forward on a nuclear programme. (author)
Demography or selection on linked cultural traits or genes? Investigating the driver of low mtDNA diversity in the sperm whale using complementary mitochondrial and nuclear genome analyses.

Science.gov (United States)

Morin, Phillip A; Foote, Andrew D; Baker, C Scott; Hancock-Hanser, Brittany L; Kaschner, Kristin; Mate, Bruce R; Mesnick, Sarah L; Pease, Victoria L; Rosel, Patricia E; Alexander, Alana

2018-04-19

Mitochondrial DNA has been heavily utilized in phylogeography studies for several decades. However, underlying patterns of demography and phylogeography may be misrepresented due to coalescence stochasticity, selection, variation in mutation rates, and cultural hitchhiking (linkage of genetic variation to culturally transmitted traits affecting fitness). Cultural hitchhiking has been suggested as an explanation for low genetic diversity in species with strong social structures, counteracting even high mobility, abundance and limited barriers to dispersal. One such species is the sperm whale, which shows very limited phylogeographic structure and low mtDNA diversity despite a worldwide distribution and large population. Here, we use analyses of 175 globally distributed mitogenomes and three nuclear genomes to evaluate hypotheses of a population bottleneck/expansion versus a selective sweep due to cultural-hitchhiking or selection on mtDNA as the mechanism contributing to low worldwide mitochondrial diversity in sperm whales. In contrast to mtDNA control region (CR) data, mitogenome haplotypes are largely ocean-specific, with only one of 80 shared between the Atlantic and Pacific. Demographic analyses of nuclear genomes suggest low mtDNA diversity is consistent with a global reduction in population size that ended approximately 125,000 years ago, correlated with the Eemian interglacial. Phylogeographic analysis suggests that extant sperm whales descend from maternal lineages endemic to the Pacific during the period of reduced abundance, and have subsequently colonized the Atlantic several times. Results highlight the apparent impact of past climate change, and suggest selection and hitchhiking are not the sole processes responsible for low mtDNA diversity in this highly social species. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.
mEBT: multiple-matching Evidence-based Translator of Murine Genomic Responses for Human Immunity Studies.

Science.gov (United States)

Tae, Donghyun; Seok, Junhee

2018-05-29

In this paper, we introduce multiple-matching Evidence-based Translator (mEBT) to discover genomic responses from murine expression data for human immune studies, which are significant in the given condition of mice and likely have similar responses in the corresponding condition of human. mEBT is evaluated over multiple data sets and shows improved inter-species agreement. mEBT is expected to be useful for research groups who use murine models to study human immunity. http://cdal.korea.ac.kr/mebt/. jseok14@korea.ac.kr. Supplementary data are available at Bioinformatics online.
Radio- and magnetobiology program GENOM at Nuclear Institute

Energy Technology Data Exchange (ETDEWEB)

Molchanov, E

1985-01-01

The five-year program called GENOM was adopted at OIYAI five years ago. The main task of this program has been the study of mechanisms that determine differences in the biological effectiveness of ionizing radiations with different stopping powers, as well as regularities involved in the action of magnetic fields. A unit called GENOM, which is controlled by a computer, was built at OIYAI. With this unit, living cells have been irradiated with charged particles of various energies, using the U-200. Magnetic-field generators and a unit which makes it possible to weaken the strength of the earth's magnetic field by a million times have been developed for magnetobiology research. DNA molecules, bacteria, yeasts, plant cells, normal and tumor cells of animals, and nerve cells of mollusks have been objects of research.
Genome-wide identification of soybean WRKY transcription factors in response to salt stress.

Science.gov (United States)

Yu, Yanchong; Wang, Nan; Hu, Ruibo; Xiang, Fengning

2016-01-01

Members of the large family of WRKY transcription factors are involved in a wide range of developmental and physiological processes, most particularly in the plant response to biotic and abiotic stress. Here, an analysis of the soybean genome sequence allowed the identification of the full complement of 188 soybean WRKY genes. Phylogenetic analysis revealed that soybean WRKY genes were classified into three major groups (I, II, III), with the second group further categorized into five subgroups (IIa-IIe). The soybean WRKYs from each group shared similar gene structures and motif compositions. The location of the GmWRKYs was dispersed over all 20 soybean chromosomes. The whole genome duplication appeared to have contributed significantly to the expansion of the family. Expression analysis by RNA-seq indicated that in soybean root, 66 of the genes responded rapidly and transiently to the imposition of salt stress, all but one being up-regulated. While in aerial part, 49 GmWRKYs responded, all but two being down-regulated. RT-qPCR analysis showed that in the whole soybean plant, 66 GmWRKYs exhibited distinct expression patterns in response to salt stress, of which 12 showed no significant change, 35 were decreased, while 19 were induced. The data present here provide critical clues for further functional studies of WRKY gene in soybean salt tolerance.
An Arabidopsis introgression zone studied at high spatio-temporal resolution: interglacial and multiple genetic contact exemplified using whole nuclear and plastid genomes.

Science.gov (United States)

Hohmann, Nora; Koch, Marcus A

2017-10-23

Gene flow between species, across ploidal levels, and even between evolutionary lineages is a common phenomenon in the genus Arabidopsis. However, apart from two genetically fully stabilized allotetraploid species that have been investigated in detail, the extent and temporal dynamics of hybridization are not well understood. An introgression zone, with tetraploid A. arenosa introgressing into A. lyrata subsp. petraea in the Eastern Austrian Forealps and subsequent expansion towards pannonical lowlands, was described previously based on morphological observations as well as molecular data using microsatellite and plastid DNA markers. Here we investigate the spatio-temporal context of this suture zone, making use of the potential of next-generation sequencing and whole-genome data. By utilizing a combination of nuclear and plastid genomic data, the extent, direction and temporal dynamics of gene flow are elucidated in detail and Late Pleistocene evolutionary processes are resolved. Analysis of nuclear genomic data significantly recognizes the clinal structure of the introgression zone, but also reveals that hybridization and introgression is more common and substantial than previously thought. Also tetraploid A. lyrata and A. arenosa subsp. borbasii from outside the previously defined suture zone show genomic signals of past introgression. A. lyrata is shown to serve usually as the maternal parent in these hybridizations, but one exception is identified from plastome-based phylogenetic reconstruction. Using plastid phylogenomics with secondary time calibration, the origin of A. lyrata and A. arenosa lineages is pre-dating the last three glaciation complexes (approx. 550,000 years ago). Hybridization and introgression followed during the last two glacial-interglacial periods (since approx. 300,000 years ago) with later secondary contact at the northern and southern border of the introgression zone during the Holocene. Footprints of adaptive introgression in the
Estimation of low-dose radiation-responsive proteins in the absence of genomic instability in normal human fibroblast cells.

Science.gov (United States)

Yim, Ji-Hye; Yun, Jung Mi; Kim, Ji Young; Nam, Seon Young; Kim, Cha Soon

2017-11-01

Low-dose radiation has various biological effects such as adaptive responses, low-dose hypersensitivity, as well as beneficial effects. However, little is known about the particular proteins involved in these effects. Here, we sought to identify low-dose radiation-responsive phosphoproteins in normal fibroblast cells. We assessed genomic instability and proliferation of fibroblast cells after γ-irradiation by γ-H2AX foci and micronucleus formation analyses and BrdU incorporation assay, respectively. We screened fibroblast cells 8 h after low-dose (0.05 Gy) γ-irradiation using Phospho Explorer Antibody Microarray and validated two differentially expressed phosphoproteins using Western blotting. Cell proliferation proceeded normally in the absence of genomic instability after low-dose γ-irradiation. Phospho antibody microarray analysis and Western blotting revealed increased expression of two phosphoproteins, phospho-NFκB (Ser536) and phospho-P70S6K (Ser418), 8 h after low-dose radiation. Our findings suggest that low-dose radiation of normal fibroblast cells activates the expression of phospho-NFκB (Ser536) and phospho-P70S6K (Ser418) in the absence of genomic instability. Therefore, these proteins may be involved in DNA damage repair processes.
The Nucleolus: In Genome Maintenance and Repair.

Science.gov (United States)

Tsekrekou, Maria; Stratigi, Kalliopi; Chatzinikolaou, Georgia

2017-07-01

The nucleolus is the subnuclear membrane-less organelle where rRNA is transcribed and processed and ribosomal assembly occurs. During the last 20 years, however, the nucleolus has emerged as a multifunctional organelle, regulating processes that go well beyond its traditional role. Moreover, the unique organization of rDNA in tandem arrays and its unusually high transcription rates make it prone to unscheduled DNA recombination events and frequent RNA:DNA hybrids leading to DNA double strand breaks (DSBs). If not properly repaired, rDNA damage may contribute to premature disease onset and aging. Deregulation of ribosomal synthesis at any level from transcription and processing to ribosomal subunit assembly elicits a stress response and is also associated with disease onset. Here, we discuss how genome integrity is maintained within nucleoli and how such structures are functionally linked to nuclear DNA damage response and repair giving an emphasis on the newly emerging roles of the nucleolus in mammalian physiology and disease.
Co-ordinate decrease in the expression of the mitochondrial genome and nuclear genes for mitochondrial proteins in the lactation-induced mitochondrial hypotrophy of rat brown fat.

Science.gov (United States)

Martin, I; Giralt, M; Viñas, O; Iglesias, R; Mampel, T; Villarroya, F

1995-01-01

The relative abundance of the mitochondrial-encoded mRNAs for cytochrome c oxidase subunit II and NADH dehydrogenase subunit I was lower in brown adipose tissue (BAT) from lactating rats than in virgin controls. This decrease was in parallel with a significant decrease in mitochondrial 16 S rRNA levels and in the relative content of mitochondrial DNA in the tissue. BAT from lactating rats showed lowered mRNA expression of the nuclear-encoded genes for the mitochondrial uncoupling protein, subunit IV of cytochrome c oxidase and the adenine nucleotide translocase isoforms ANT1 and ANT2, whereas mRNA levels for the ATP synthase beta-subunit were unchanged. However, the relative content of this last protein was lower in BAT mitochondria from lactating rats than in virgin controls. It is concluded that lactation-induced mitochondrial hypotrophy in BAT is associated with a co-ordinate decrease in the expression of the mitochondrial genome and nuclear genes for mitochondrial proteins. This decrease is caused by regulatory events acting at different levels, including pre- and post-transcriptional regulation. BAT appears to be a useful model with which to investigate the molecular mechanisms involved in the co-ordination of the expression of the mitochondrial and nuclear genomes during mitochondrial biogenesis. Images Figure 1 Figure 2 PMID:8948428
A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response. | Office of Cancer Genomics

Science.gov (United States)

Functional genomics efforts face tradeoffs between number of perturbations examined and complexity of phenotypes measured. We bridge this gap with Perturb-seq, which combines droplet-based single-cell RNA-seq with a strategy for barcoding CRISPR-mediated perturbations, allowing many perturbations to be profiled in pooled format. We applied Perturb-seq to dissect the mammalian unfolded protein response (UPR) using single and combinatorial CRISPR perturbations. Two genome-scale CRISPR interference (CRISPRi) screens identified genes whose repression perturbs ER homeostasis.
Nuclear and nuclear reprogramming during the first cell cycle in bovine nuclear transfer embryos

DEFF Research Database (Denmark)

Østrup, Olga; Petrovicova, Ida; Strejcek, Frantisek

2009-01-01

Abstract The immediate events of genomic reprogramming at somatic cell nuclear transfer (SCNT) are to high degree unknown. This study was designed to evaluate the nuclear and nucleolar changes during the first cell cycle. Bovine SCNT embryos were produced from starved bovine fibroblasts and fixed......, somatic cell nuclei introduced into enucleated oocytes displayed chromatin condensation, partial nuclear envelope breakdown, nucleolar desegregation and transcriptional quiescence already at 0.5 hpa. Somatic cell cytoplasm remained temporally attached to introduced nucleus and nucleolus was partially...... restored indicating somatic influence in the early SCNT phases. At 1-3 hpa, chromatin gradually decondensed toward the nucleus periphery and nuclear envelope reformed. From 4 hpa, the somatic cell nucleus gained a PN-like appearance and displayed NPBs suggesting ooplasmic control of development....
Information for nuclear emergency response: a case study based on ANGRA nuclear power plant emergency simulation exercises

International Nuclear Information System (INIS)

Carvalho, Paulo V.R. de

2008-01-01

Full text: Current nuclear emergency management procedures do not always satisfactorily address issues related to the information availability and to how people in emergency control centres use this information to respond to an nuclear accident. The lack of an adequate and prompt information may lead to a response that can be very different from what authorities recommend and thus create confusion, mistrust, and widespread uncertainty. This is a potentially serious problem for emergency planners. An adequate and prompt access to relevant information is a critical requirement that emergency teams face while they work towards reducing the undesired consequences of the emergency. There are three basic types of knowledge according to a conceptual framework developed to deal with emergency response: Previous Personal, Previous and, Current Contextual knowledge. Most decisions in emergency control centres require a dynamic combination of all types of knowledge, particularly the current contextual that comes from the emergency settings, including all information about the activities of other emergency teams. The aim of this paper is to describe the concepts and the structure of a system that aims at storing and disseminating the previous formal and contextual knowledge to help teams make the correct decisions during the evolution of an emergency. The elicitation of critical requirements are provided by a case study based on Cognitive Work Analysis and Naturalistic Decision Making methods, applied to a nuclear emergency response simulation. The framework and a prototype system were tested in a controlled experiment. The paper reports the results of this experiment. (author)
Endogenous viral elements in animal genomes.

Directory of Open Access Journals (Sweden)

Aris Katzourakis

2010-11-01

Full Text Available Integration into the nuclear genome of germ line cells can lead to vertical inheritance of retroviral genes as host alleles. For other viruses, germ line integration has only rarely been documented. Nonetheless, we identified endogenous viral elements (EVEs derived from ten non-retroviral families by systematic in silico screening of animal genomes, including the first endogenous representatives of double-stranded RNA, reverse-transcribing DNA, and segmented RNA viruses, and the first endogenous DNA viruses in mammalian genomes. Phylogenetic and genomic analysis of EVEs across multiple host species revealed novel information about the origin and evolution of diverse virus groups. Furthermore, several of the elements identified here encode intact open reading frames or are expressed as mRNA. For one element in the primate lineage, we provide statistically robust evidence for exaptation. Our findings establish that genetic material derived from all known viral genome types and replication strategies can enter the animal germ line, greatly broadening the scope of paleovirological studies and indicating a more significant evolutionary role for gene flow from virus to animal genomes than has previously been recognized.
Genome wide transcriptional response of Saccharomyces cerevisiae to stress-induced perturbations

Directory of Open Access Journals (Sweden)

Hilal eTaymaz-Nikerel

2016-02-01

Full Text Available Cells respond to environmental and/or genetic perturbations in order to survive and proliferate. Characterization of the changes after various stimuli at different -omics levels is crucial to comprehend the adaptation of cells to changing conditions. Genome wide quantification and analysis of transcript levels, the genes affected by perturbations, extends our understanding of cellular metabolism by pointing out the mechanisms that play role in sensing the stress caused by those perturbations and related signaling pathways, and in this way guides us to achieve endeavors such as rational engineering of cells or interpretation of disease mechanisms. Saccharomyces cerevisiae as a model system has been studied in response to different perturbations and corresponding transcriptional profiles were followed either statically or/and dynamically, short- and long- term. This review focuses on response of yeast cells to diverse stress inducing perturbations including nutritional changes, ionic stress, salt stress, oxidative stress, osmotic shock, as well as to genetic interventions such as deletion and over-expression of genes. It is aimed to conclude on common regulatory phenomena that allow yeast to organize its transcriptomic response after any perturbation under different external conditions.
Freedom and Responsibility in Synthetic Genomics: The Synthetic Yeast Project

OpenAIRE

Sliva, Anna; Yang, Huanming; Boeke, Jef D.; Mathews, Debra J. H.

2015-01-01

First introduced in 2011, the Synthetic Yeast Genome (Sc2.0) Project is a large international synthetic genomics project that will culminate in the first eukaryotic cell (Saccharomyces cerevisiae) with a fully synthetic genome. With collaborators from across the globe and from a range of institutions spanning from do-it-yourself biology (DIYbio) to commercial enterprises, it is important that all scientists working on this project are cognizant of the ethical and policy issues associated with...
Effects of non-uniform embedments on earthquake responses of nuclear reactor building

International Nuclear Information System (INIS)

Koyanagi, Y.; Okamoto, S.; Yoshida, K.; Inove, H.

1989-01-01

The nuclear reactor buildings have the portion embedded in soil. In the seismic design of such structures, it is essential to consider the effects of the embedment on the earthquake response. Most studies on these effects, however, assume the uniform embedment, i.e. the depth of the embedment is constant, which is convenient for the design and analysis. The behavior of the earthquake response considering the three-dimensional aspects of non-uniform embedment has not been made clear yet. In this paper, the authors evaluate the effects of the non-uniform embedment in an inclined ground surface on the earthquake response of a nuclear reactor building as illustrated. A typical PWR type reactor building is chosen as an analysis structure model. Four different types of embedment are set up for the comparison study. The three-dimensional analysis is carried out considering the geometry of embedment
Heat Shock Protein Genes Undergo Dynamic Alteration in Their Three-Dimensional Structure and Genome Organization in Response to Thermal Stress.

Science.gov (United States)

Chowdhary, Surabhi; Kainth, Amoldeep S; Gross, David S

2017-12-15

Three-dimensional (3D) chromatin organization is important for proper gene regulation, yet how the genome is remodeled in response to stress is largely unknown. Here, we use a highly sensitive version of chromosome conformation capture in combination with fluorescence microscopy to investigate Heat Shock Protein ( HSP ) gene conformation and 3D nuclear organization in budding yeast. In response to acute thermal stress, HSP genes undergo intense intragenic folding interactions that go well beyond 5'-3' gene looping previously described for RNA polymerase II genes. These interactions include looping between upstream activation sequence (UAS) and promoter elements, promoter and terminator regions, and regulatory and coding regions (gene "crumpling"). They are also dynamic, being prominent within 60 s, peaking within 2.5 min, and attenuating within 30 min, and correlate with HSP gene transcriptional activity. With similarly striking kinetics, activated HSP genes, both chromosomally linked and unlinked, coalesce into discrete intranuclear foci. Constitutively transcribed genes also loop and crumple yet fail to coalesce. Notably, a missense mutation in transcription factor TFIIB suppresses gene looping, yet neither crumpling nor HSP gene coalescence is affected. An inactivating promoter mutation, in contrast, obviates all three. Our results provide evidence for widespread, transcription-associated gene crumpling and demonstrate the de novo assembly and disassembly of HSP gene foci. Copyright © 2017 American Society for Microbiology.

Genomic and non-genomic effects of androgens in the cardiovascular system: clinical implications.

Science.gov (United States)

Lucas-Herald, Angela K; Alves-Lopes, Rheure; Montezano, Augusto C; Ahmed, S Faisal; Touyz, Rhian M

2017-07-01

The principle steroidal androgens are testosterone and its metabolite 5α-dihydrotestosterone (DHT), which is converted from testosterone by the enzyme 5α-reductase. Through the classic pathway with androgens crossing the plasma membrane and binding to the androgen receptor (AR) or via mechanisms independent of the ligand-dependent transactivation function of nuclear receptors, testosterone induces genomic and non-genomic effects respectively. AR is widely distributed in several tissues, including vascular endothelial and smooth muscle cells. Androgens are essential for many developmental and physiological processes, especially in male reproductive tissues. It is now clear that androgens have multiple actions besides sex differentiation and sexual maturation and that many physiological systems are influenced by androgens, including regulation of cardiovascular function [nitric oxide (NO) release, Ca 2+ mobilization, vascular apoptosis, hypertrophy, calcification, senescence and reactive oxygen species (ROS) generation]. This review focuses on evidence indicating that interplay between genomic and non-genomic actions of testosterone may influence cardiovascular function. © 2017 The Author(s). published by Portland Press Limited on behalf of the Biochemical Society.
Improved nuclear emergency management system reflecting lessons learned from the emergency response at Fukushima Daini Nuclear Power Station after the Great East Japan Earthquake

International Nuclear Information System (INIS)

Kawamura, Shinichi; Narabayashi, Tadashi

2016-01-01

Three nuclear reactors at Fukushima Daini Nuclear Power Station lost all their ultimate heat sinks owing to damage from the tsunami caused by the Great East Japan Earthquake on March 11, 2011. Water was injected into the reactors by alternate measures, damaged cooling systems were restored with promptly supplied substitute materials, and all the reactors were brought to a cold shutdown state within four days. Lessons learned from this experience were identified to improve emergency management, especially in the areas of strategic response planning, logistics, and functions supporting response activities continuing over a long period. It was found that continuous planning activities reflecting information from plant parameters and response action results were important, and that relevant functions in emergency response organizations should be integrated. Logistics were handled successfully but many difficulties were experienced. Therefore, their functions should be clearly established and improved by emergency response organizations. Supporting emergency responders in the aspects of their physical and mental conditions was important for sustaining continuous response. As a platform for improvement, the concept of the Incident Command System was applied for the first time to a nuclear emergency management system, with specific improvement ideas such as a phased approach in response planning and common operation pictures. (author)
Genome projects and the functional-genomic era.

Science.gov (United States)

Sauer, Sascha; Konthur, Zoltán; Lehrach, Hans

2005-12-01

The problems we face today in public health as a result of the -- fortunately -- increasing age of people and the requirements of developing countries create an urgent need for new and innovative approaches in medicine and in agronomics. Genomic and functional genomic approaches have a great potential to at least partially solve these problems in the future. Important progress has been made by procedures to decode genomic information of humans, but also of other key organisms. The basic comprehension of genomic information (and its transfer) should now give us the possibility to pursue the next important step in life science eventually leading to a basic understanding of biological information flow; the elucidation of the function of all genes and correlative products encoded in the genome, as well as the discovery of their interactions in a molecular context and the response to environmental factors. As a result of the sequencing projects, we are now able to ask important questions about sequence variation and can start to comprehensively study the function of expressed genes on different levels such as RNA, protein or the cell in a systematic context including underlying networks. In this article we review and comment on current trends in large-scale systematic biological research. A particular emphasis is put on technology developments that can provide means to accomplish the tasks of future lines of functional genomics.
Transposon domestication versus mutualism in ciliate genome rearrangements.

Directory of Open Access Journals (Sweden)

Alexander Vogt

Full Text Available Ciliated protists rearrange their genomes dramatically during nuclear development via chromosome fragmentation and DNA deletion to produce a trimmer and highly reorganized somatic genome. The deleted portion of the genome includes potentially active transposons or transposon-like sequences that reside in the germline. Three independent studies recently showed that transposase proteins of the DDE/DDD superfamily are indispensible for DNA processing in three distantly related ciliates. In the spirotrich Oxytricha trifallax, high copy-number germline-limited transposons mediate their own excision from the somatic genome but also contribute to programmed genome rearrangement through a remarkable transposon mutualism with the host. By contrast, the genomes of two oligohymenophorean ciliates, Tetrahymena thermophila and Paramecium tetraurelia, encode homologous PiggyBac-like transposases as single-copy genes in both their germline and somatic genomes. These domesticated transposases are essential for deletion of thousands of different internal sequences in these species. This review contrasts the events underlying somatic genome reduction in three different ciliates and considers their evolutionary origins and the relationships among their distinct mechanisms for genome remodeling.
Nuclear receptor 4a3 (nr4a3 regulates murine mast cell responses and granule content.

Directory of Open Access Journals (Sweden)

Gianni Garcia-Faroldi

Full Text Available Nuclear receptor 4a3 (Nr4a3 is a transcription factor implicated in various settings such as vascular biology and inflammation. We have recently shown that mast cells dramatically upregulate Nuclear receptor 4a3 upon activation, and here we investigated the functional impact of Nuclear receptor 4a3 on mast cell responses. We show that Nuclear receptor 4a3 is involved in the regulation of cytokine/chemokine secretion in mast cells following activation via the high affinity IgE receptor. Moreover, Nuclear receptor 4a3 negatively affects the transcript and protein levels of mast cell tryptase as well as the mast cell's responsiveness to allergen. Together, these findings identify Nuclear receptor 4a3 as a novel regulator of mast cell function.
Nuclear receptors and endocrine disruptors in fetal and neonatal testes: a gapped landscape.

Directory of Open Access Journals (Sweden)

Virginie eRouiller-Fabre

2015-05-01

Full Text Available During the last decades, many studies reported that male reproductive disorders are increasing among humans. It is currently acknowledged that these abnormalities can result from fetal exposure to environmental chemicals that are progressively becoming more concentrated and widespread in our environment. Among the chemicals present in the environment (air, water, food and many consumer products, several can act as endocrine disrupting compounds (EDCs, thus interfering with the endocrine system. Phthalates, bisphenol A (BPA and diethylstilbestrol (DES have been largely incriminated, particularly during the fetal and neonatal period, due to their estrogenic and/or anti-androgenic properties. Indeed, many epidemiological and experimental studies have highlighted their deleterious impact on fetal and neonatal testis development. As EDCs can affect many different genomic and non-genomic pathways, the mechanisms underlying the adverse effects of EDC exposure are difficult to elucidate. Using literature data and results from our laboratory, in the present review we discuss the role of classical nuclear receptors (genomic pathway in the fetal and neonatal testis response to EDC exposure, particularly to phthalates, BPA and DES. Among the nuclear receptors we focused on some of the most likely candidates, such as peroxisome-proliferator activated receptor (PPAR, androgen receptor (AR, estrogen receptors (ERα and β, liver X receptors (LXR and small heterodimer partner (SHP. First, we describe the expression and potential functions (based on data from studies using receptor agonists and mouse knockout models of these nuclear receptors in the developing testis. Then, for each EDC studied, we summarize the main evidences indicating that the reprotoxic effect of each EDC under study is mediated through a specific nuclear receptor(s. We also point-out the involvement of other receptors and nuclear receptor-independent pathways.
Legislative framework on establishing emergency response plan in the case of a nuclear accident

International Nuclear Information System (INIS)

Novosel, N.; Valcic, I.; Biscan, R.

2000-01-01

To give an overview of the legislative framework, which defined emergency planning in Croatia in the case of a nuclear accident, it's necessary to look at all international recommendations and obligations and the national legislation, acts and regulations. It has to be emphasized that Croatia signed three international conventions in this field, and by that took over some responsibilities and obligations. Beside that, it is also in Croatian interest to follow the recommendations of international institutions such as International Atomic Energy Agency (IAEA standards and technical documents). On the other hand, national legislation in this field consists of several laws, which cover nuclear safety measures, governmental organization, natural disasters and acts (decree, decisions) of responsible authority for emergency planning in the case of a nuclear accident (Ministry of Economy). This paper presents an overview of the international and Croatian legislation which influenced the emergency planning in the case of a nuclear accident. (author)
Response spectra for nuclear structures on rock sites considering the near-fault directivity effect

Institute of Scientific and Technical Information of China (English)

Xu Longiun; Yang Shengchao; Xie Lili

2010-01-01

Near-fault ground motions, potentially with large amplitude and typical velocity pulses, may significantly impact the performance of a wide range of structures. The current study is aimed at evaluating the safety implications of the near-fault effect on nuclear power plant facilities designed according to the Chinese code. To this end, a set of near-fault ground motions at rock sites with typical forward-directivity effect is examined with special emphasis on several key parameters and response spectra. Spectral comparison of the selected records with the Chinese and other code design spectra was conducted. The bi-normalized response spectra in terms of different comer periods are utilized to derive nuclear design spectra. It is concluded that nuclear design spectra on rock sites derived from typical rupture directivity records are significantly influenced both by the earthquake magnitude and the rupture distance. The nuclear design spectra specified in the code needs to be adjusted to reflect the near-fault directivity effect of large earthquakes.
Inactivating UBE2M impacts the DNA damage response and genome integrity involving multiple cullin ligases.

Directory of Open Access Journals (Sweden)

Scott Cukras

Full Text Available Protein neddylation is involved in a wide variety of cellular processes. Here we show that the DNA damage response is perturbed in cells inactivated with an E2 Nedd8 conjugating enzyme UBE2M, measured by RAD51 foci formation kinetics and cell based DNA repair assays. UBE2M knockdown increases DNA breakages and cellular sensitivity to DNA damaging agents, further suggesting heightened genomic instability and defective DNA repair activity. Investigating the downstream Cullin targets of UBE2M revealed that silencing of Cullin 1, 2, and 4 ligases incurred significant DNA damage. In particular, UBE2M knockdown, or defective neddylation of Cullin 2, leads to a blockade in the G1 to S progression and is associated with delayed S-phase dependent DNA damage response. Cullin 4 inactivation leads to an aberrantly high DNA damage response that is associated with increased DNA breakages and sensitivity of cells to DNA damaging agents, suggesting a DNA repair defect is associated. siRNA interrogation of key Cullin substrates show that CDT1, p21, and Claspin are involved in elevated DNA damage in the UBE2M knockdown cells. Therefore, UBE2M is required to maintain genome integrity by activating multiple Cullin ligases throughout the cell cycle.
Inactivating UBE2M impacts the DNA damage response and genome integrity involving multiple cullin ligases.

Science.gov (United States)

Cukras, Scott; Morffy, Nicholas; Ohn, Takbum; Kee, Younghoon

2014-01-01

Protein neddylation is involved in a wide variety of cellular processes. Here we show that the DNA damage response is perturbed in cells inactivated with an E2 Nedd8 conjugating enzyme UBE2M, measured by RAD51 foci formation kinetics and cell based DNA repair assays. UBE2M knockdown increases DNA breakages and cellular sensitivity to DNA damaging agents, further suggesting heightened genomic instability and defective DNA repair activity. Investigating the downstream Cullin targets of UBE2M revealed that silencing of Cullin 1, 2, and 4 ligases incurred significant DNA damage. In particular, UBE2M knockdown, or defective neddylation of Cullin 2, leads to a blockade in the G1 to S progression and is associated with delayed S-phase dependent DNA damage response. Cullin 4 inactivation leads to an aberrantly high DNA damage response that is associated with increased DNA breakages and sensitivity of cells to DNA damaging agents, suggesting a DNA repair defect is associated. siRNA interrogation of key Cullin substrates show that CDT1, p21, and Claspin are involved in elevated DNA damage in the UBE2M knockdown cells. Therefore, UBE2M is required to maintain genome integrity by activating multiple Cullin ligases throughout the cell cycle.
Helicosporidia: a genomic snapshot of an early transition to parasitism

Directory of Open Access Journals (Sweden)

Yukun Sun

2014-12-01

Full Text Available Helicosporidia are gut parasites of invertebrates. These achlorophyllous, non-photosynthetic green algae are the first reported to infect insects. Helicosporidia are members of the green algal class Trebouxiophyceae and are further related to the photosynthetic and non-photosynthetic genera Auxenochlorella and Prototheca, respectively, the latter of which can also turn to parasitism under opportunistic conditions. Molecular analyses suggest that Helicosporidia diverged from other photosynthetic trebouxiophytes less than 200 million years ago and that its adaptation to parasitism is therefore recent. In this minireview, we summarize the current knowledge of helicosporidian genomics. Unlike many well-known parasitic lineages, the Helicosporidium sp. organelle and nuclear genomes have lost surprisingly little in terms of coding content aside from photosynthesis-related genes. While the small size of its nuclear genome compared to other sequenced trebouxiophycean representatives suggests that Helicosporidium is going through a streamlining process, this scenario cannot be ascertained at this stage. Genome expansions and contractions have occurred independently multiple times in the green algae, and the small size of the Helicosporidium genome may reflect a lack of expansion from a lean ancestor state rather than a tendency towards reduction.
OxyGene: an innovative platform for investigating oxidative-response genes in whole prokaryotic genomes

Directory of Open Access Journals (Sweden)

Barloy-Hubler Frédérique

2008-12-01

Full Text Available Abstract Background Oxidative stress is a common stress encountered by living organisms and is due to an imbalance between intracellular reactive oxygen and nitrogen species (ROS, RNS and cellular antioxidant defence. To defend themselves against ROS/RNS, bacteria possess a subsystem of detoxification enzymes, which are classified with regard to their substrates. To identify such enzymes in prokaryotic genomes, different approaches based on similarity, enzyme profiles or patterns exist. Unfortunately, several problems persist in the annotation, classification and naming of these enzymes due mainly to some erroneous entries in databases, mistake propagation, absence of updating and disparity in function description. Description In order to improve the current annotation of oxidative stress subsystems, an innovative platform named OxyGene has been developed. It integrates an original database called OxyDB, holding thoroughly tested anchor-based signatures associated to subfamilies of oxidative stress enzymes, and a new anchor-driven annotator, for ab initio detection of ROS/RNS response genes. All complete Bacterial and Archaeal genomes have been re-annotated, and the results stored in the OxyGene repository can be interrogated via a Graphical User Interface. Conclusion OxyGene enables the exploration and comparative analysis of enzymes belonging to 37 detoxification subclasses in 664 microbial genomes. It proposes a new classification that improves both the ontology and the annotation of the detoxification subsystems in prokaryotic whole genomes, while discovering new ORFs and attributing precise function to hypothetical annotated proteins. OxyGene is freely available at: http://www.umr6026.univ-rennes1.fr/english/home/research/basic/software
Nuclear RNA sequencing of the mouse erythroid cell transcriptome.

Directory of Open Access Journals (Sweden)

Jennifer A Mitchell

Full Text Available In addition to protein coding genes a substantial proportion of mammalian genomes are transcribed. However, most transcriptome studies investigate steady-state mRNA levels, ignoring a considerable fraction of the transcribed genome. In addition, steady-state mRNA levels are influenced by both transcriptional and posttranscriptional mechanisms, and thus do not provide a clear picture of transcriptional output. Here, using deep sequencing of nuclear RNAs (nucRNA-Seq in parallel with chromatin immunoprecipitation sequencing (ChIP-Seq of active RNA polymerase II, we compared the nuclear transcriptome of mouse anemic spleen erythroid cells with polymerase occupancy on a genome-wide scale. We demonstrate that unspliced transcripts quantified by nucRNA-seq correlate with primary transcript frequencies measured by RNA FISH, but differ from steady-state mRNA levels measured by poly(A-enriched RNA-seq. Highly expressed protein coding genes showed good correlation between RNAPII occupancy and transcriptional output; however, genome-wide we observed a poor correlation between transcriptional output and RNAPII association. This poor correlation is due to intergenic regions associated with RNAPII which correspond with transcription factor bound regulatory regions and a group of stable, nuclear-retained long non-coding transcripts. In conclusion, sequencing the nuclear transcriptome provides an opportunity to investigate the transcriptional landscape in a given cell type through quantification of unspliced primary transcripts and the identification of nuclear-retained long non-coding RNAs.
Influence of individual differences in disease perception on consumer response to direct-to-consumer genomic testing.

Science.gov (United States)

Boeldt, D L; Schork, N J; Topol, E J; Bloss, C S

2015-03-01

Individuals who undergo multiplex direct-to-consumer (DTC) genomic testing receive genetic risk results for multiple conditions. To date, research has not investigated the influence of individual differences in disease perceptions among consumers on testing outcomes. A total of 2037 participants received DTC genomic testing and completed baseline and follow-up surveys assessing disease perceptions and health behaviors. Participants were asked to indicate their most feared disease of those tested. Perceived seriousness and controllability of the disease via lifestyle or medical intervention were assessed. Participants most frequently reported heart attack (19.1%) and Alzheimer's disease (18.6%) as their most feared disease. Perceived seriousness and control over the feared disease both influenced response to DTC genomic testing. Greater perceived seriousness and diminished perceived control were associated with higher, but not clinically significant levels of anxiety and distress. In some cases these associations were modified by genetic risk. No significant associations were observed for diet, exercise and screening behaviors. Individual differences in disease perceptions influence psychological outcomes following DTC genomic testing. Higher perceived seriousness may make a consumer more psychologically sensitive to test results and greater perceived control may protect against adverse psychological outcomes. Findings may inform development of educational and counseling services. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.
Nuclear scaffold attachment sites within ENCODE regions associate with actively transcribed genes.

Directory of Open Access Journals (Sweden)

Mignon A Keaton

2011-03-01

Full Text Available The human genome must be packaged and organized in a functional manner for the regulation of DNA replication and transcription. The nuclear scaffold/matrix, consisting of structural and functional nuclear proteins, remains after extraction of nuclei and anchors loops of DNA. In the search for cis-elements functioning as chromatin domain boundaries, we identified 453 nuclear scaffold attachment sites purified by lithium-3,5-iodosalicylate extraction of HeLa nuclei across 30 Mb of the human genome studied by the ENCODE pilot project. The scaffold attachment sites mapped predominately near expressed genes and localized near transcription start sites and the ends of genes but not to boundary elements. In addition, these regions were enriched for RNA polymerase II and transcription factor binding sites and were located in early replicating regions of the genome. We believe these sites correspond to genome-interactions mediated by transcription factors and transcriptional machinery immobilized on a nuclear substructure.
Seismic response analysis for a deeply embedded nuclear power plant

International Nuclear Information System (INIS)

Chen, W.W.H.; Chatterjee, M.; Day, S.M.

1979-01-01

One of the important aspect of the aseimic design of nuclear power plants is the evaluation of the seismic soil-structure interaction effect due to design earthquakes. The soil-structure interaction effect can initiate rocking and result in different soil motions compared to the free field motions, thus significantly affecting the structural response. Two methods are generally used to solve the seismic soil-structure interaction problems: the direct finite element method (FLUSH) and the substructure or impedance approach. This paper presents the results of the horizontal seismic soil-structure interaction analysis using the impedance aproach and the direct finite element method for a deeply embedded nuclear power plant. (orig.)
Genomes Behave as Social Entities: Alien Chromatin Minorities Evolve Through Specificities Reduction

Science.gov (United States)

Hybridization and chromosome doubling entailed by allopolyploidization requires genetic and epigenetic modifications, resulting in the adjustment of different genomes to the same nuclear environment. Recently, the main role of retrotransposon/microsatellite-rich regions of the genome in DNA sequenc...
The bad debt of nuclear responsibility

International Nuclear Information System (INIS)

Haverkamp, J.

2010-01-01

Nuclear regulation plays an important role in keeping the visible and invisible threats of radioactivity at bay. This article argues that the largest gains in nuclear safety can be made if nuclear activities with economically, socially and environmentally viable alternatives (such as nuclear energy and nuclear weapons) are phased out - similarly to what has been done for toxic substances. Unless this takes place, the legacy of radioactive waste for future generations will only increase. In this respect, the article highlights the importance of accountability, independence and transparency of nuclear regulators to contain the risks stemming from radioactivity. In the interest of safety, other uses of nuclear technology should, as a rule, apply the best available technology and the best regulatory practice. As is made clear in the article, the EURATOM Nuclear Safety Directive, adopted in 2009, hardly addresses any of these issues. The article ends on a set of demands from Greenpeace to meet the challenges posed by nuclear safety, concluding that there is still a long way to go before the sector can be considered even reasonably safe. (author)
Genomic predictors of the maximal O2 uptake response to standardized exercise training programs

Science.gov (United States)

Sarzynski, Mark A.; Rice, Treva K.; Kraus, William E.; Church, Timothy S.; Sung, Yun Ju; Rao, D. C.; Rankinen, Tuomo

2011-01-01

Low cardiorespiratory fitness is a powerful predictor of morbidity and cardiovascular mortality. In 473 sedentary adults, all whites, from 99 families of the Health, Risk Factors, Exercise Training, and Genetics (HERITAGE) Family Study, the heritability of gains in maximal O2 uptake (V̇o2max) after exposure to a standardized 20-wk exercise program was estimated at 47%. A genome-wide association study based on 324,611 single-nucleotide polymorphisms (SNPs) was undertaken to identify SNPs associated with improvements in V̇o2max Based on single-SNP analysis, 39 SNPs were associated with the gains with P HERITAGE whites were replicated in HERITAGE blacks (n = 247). These genomic predictors of the response of V̇o2max to regular exercise provide new targets for the study of the biology of fitness and its adaptation to regular exercise. Large-scale replication studies are warranted. PMID:21183627
Long-Term Protective Immune Response Elicited by Vaccination with an Expression Genomic Library of Toxoplasma gondii

OpenAIRE

Fachado, Alberto; Rodriguez, Alexandro; Molina, Judith; Silvério, Jaline C.; Marino, Ana P. M. P.; Pinto, Luzia M. O.; Angel, Sergio O.; Infante, Juan F.; Traub-Cseko, Yara; Amendoeira, Regina R.; Lannes-Vieira, Joseli

2003-01-01

Immunization of BALB/c mice with an expression genomic library of Toxoplasma gondii induces a Th1-type immune response, with recognition of several T. gondii proteins (21 to 117 kDa) and long-term protective immunity against a lethal challenge. These results support further investigations to achieve a multicomponent anti-T. gondii DNA vaccine.

Strains of bacterial species induce a greatly varied acute adaptive immune response: The contribution of the accessory genome.

Directory of Open Access Journals (Sweden)

Uri Sela

2018-01-01

Full Text Available A fundamental question in human susceptibility to bacterial infections is to what extent variability is a function of differences in the pathogen species or in individual humans. To focus on the pathogen species, we compared in the same individual the human adaptive T and B cell immune response to multiple strains of two major human pathogens, Staphylococcus aureus and Streptococcus pyogenes. We found wide variability in the acute adaptive immune response induced by various strains of a species, with a unique combination of activation within the two arms of the adaptive response. Further, this was also accompanied by a dramatic difference in the intensity of the specific protective T helper (Th response. Importantly, the same immune response differences induced by the individual strains were maintained across multiple healthy human donors. A comparison of isogenic phage KO strains, demonstrated that of the pangenome, prophages were the major contributor to inter-strain immune heterogeneity, as the T cell response to the remaining "core genome" was noticeably blunted. Therefore, these findings extend and modify the notion of an adaptive response to a pathogenic bacterium, by implying that the adaptive immune response signature of a bacterial species should be defined either per strain or alternatively to the species' 'core genome', common to all of its strains. Further, our results demonstrate that the acquired immune response variation is as wide among different strains within a single pathogenic species as it is among different humans, and therefore may explain in part the clinical heterogeneity observed in patients infected with the same species.
Design of a High Power Robotic Manipulator for Emergency Response to the Nuclear Accidents

International Nuclear Information System (INIS)

Park, Jongwon; Bae, Yeong-Geol; Kim, Myoung Ho; Choi, Young Soo

2016-01-01

An accident in a nuclear facility causes a great social cost. To prevent an unexpected nuclear accident from spreading to the catastrophic disaster, emergency response action in early stage is required. However, high radiation environment has been proved as a challenging obstacle for human workers to access to the accident site and take an action in previous accident cases. Therefore, emergency response robotic technology to be used in a nuclear accident site instead of human workers are actively conducted in domestically and internationally. Robots in an accident situation are required to carry out a variety of tasks depend on the types and patterns of accidents. An emergency response usually includes removing of debris, make an access road to a certain place and handling valves. These tasks normally involve high payload handling. A small sized high power robotic manipulator can be an appropriate candidate to deal with a wide spectrum of tasks in an emergency situation. In this paper, we discuss about the design of a high power robotic manipulator, which is capable of handling high payloads for an initial response action to the nuclear facility accident. In this paper, we presented a small sized high power robotic manipulator design. Actuator types of manipulator was selected and mechanical structure was discussed. In the future, the servo valve and hydraulic pump systems will be determined. Furthermore, control algorithms and test bed experiments will be also conducted
Design of a High Power Robotic Manipulator for Emergency Response to the Nuclear Accidents

Energy Technology Data Exchange (ETDEWEB)

Park, Jongwon; Bae, Yeong-Geol; Kim, Myoung Ho; Choi, Young Soo [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

2016-10-15

An accident in a nuclear facility causes a great social cost. To prevent an unexpected nuclear accident from spreading to the catastrophic disaster, emergency response action in early stage is required. However, high radiation environment has been proved as a challenging obstacle for human workers to access to the accident site and take an action in previous accident cases. Therefore, emergency response robotic technology to be used in a nuclear accident site instead of human workers are actively conducted in domestically and internationally. Robots in an accident situation are required to carry out a variety of tasks depend on the types and patterns of accidents. An emergency response usually includes removing of debris, make an access road to a certain place and handling valves. These tasks normally involve high payload handling. A small sized high power robotic manipulator can be an appropriate candidate to deal with a wide spectrum of tasks in an emergency situation. In this paper, we discuss about the design of a high power robotic manipulator, which is capable of handling high payloads for an initial response action to the nuclear facility accident. In this paper, we presented a small sized high power robotic manipulator design. Actuator types of manipulator was selected and mechanical structure was discussed. In the future, the servo valve and hydraulic pump systems will be determined. Furthermore, control algorithms and test bed experiments will be also conducted.
Carl Friedrich von Weizsaecker - a physicist and philosopher in the shade of the nuclear bomb. A conversation on nuclear weapons and the responsibility of nuclear scientists

International Nuclear Information System (INIS)

Schaaf, M.

1996-06-01

The 50th anniversary of the first nuclear explosion (16th July 1945) prompted the editor of this collection to look again at the part played by German physicists in the nuclear weapons issue. Carl Friedrich von Weizsaecker, one of the last surviving witnesses of this period, kindly agreed to give a comprehensive interview on the German nuclear programme and the responsibility of physicists. The interview is published here for the first time and forms the central part of this brochure. It is complemented by two statements by Edward Teller and two historical letters. The author, in preparing this compilation, had in mind to contribute towards science-historical discussion and to give younger colleagues a graphic idea of the conflict surrounding nuclear research. (orig.) [de
Comparison of Various Nuclear Localization Signal-Fused Cas9 Proteins and Cas9 mRNA for Genome Editing in Zebrafish.

Science.gov (United States)

Hu, Peinan; Zhao, Xueying; Zhang, Qinghua; Li, Weiming; Zu, Yao

2018-03-02

The clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system has been proven to be an efficient and precise genome editing technology in various organisms. However, the gene editing efficiencies of Cas9 proteins with a nuclear localization signal (NLS) fused to different termini and Cas9 mRNA have not been systematically compared. Here, we compared the ability of Cas9 proteins with NLS fused to the N-, C-, or both the N- and C-termini and N-NLS-Cas9-NLS-C mRNA to target two sites in the tyr gene and two sites in the gol gene related to pigmentation in zebrafish. Phenotypic analysis revealed that all types of Cas9 led to hypopigmentation in similar proportions of injected embryos. Genome analysis by T7 Endonuclease I (T7E1) assays demonstrated that all types of Cas9 similarly induced mutagenesis in four target sites. Sequencing results further confirmed that a high frequency of indels occurred in the target sites ( tyr1 > 66%, tyr2 > 73%, gol1 > 50%, and gol2 > 35%), as well as various types (more than six) of indel mutations observed in all four types of Cas9-injected embryos. Furthermore, all types of Cas9 showed efficient targeted mutagenesis on multiplex genome editing, resulting in multiple phenotypes simultaneously. Collectively, we conclude that various NLS-fused Cas9 proteins and Cas9 mRNAs have similar genome editing efficiencies on targeting single or multiple genes, suggesting that the efficiency of CRISPR/Cas9 genome editing is highly dependent on guide RNAs (gRNAs) and gene loci. These findings may help to simplify the selection of Cas9 for gene editing using the CRISPR/Cas9 system. Copyright © 2018 Hu et al.
A decade of understanding spatio-temporal regulation of DNA repair by the nuclear architecture.

Science.gov (United States)

Saad, Hicham; Cobb, Jennifer A

2016-10-01

The nucleus is a hub for gene expression and is a highly organized entity. The nucleoplasm is heterogeneous, owing to the preferential localization of specific metabolic factors, which lead to the definition of nuclear compartments or bodies. The genome is organized into chromosome territories, as well as heterochromatin and euchromatin domains. Recent observations have indicated that nuclear organization is important for maintaining genomic stability. For example, nuclear organization has been implicated in stabilizing damaged DNA, repair-pathway choice, and in preventing chromosomal rearrangements. Over the past decade, several studies have revealed that dynamic changes in the nuclear architecture are important during double-strand break repair. Stemming from work in yeast, relocation of a damaged site prior to repair appears to be at least partially conserved in multicellular eukaryotes. In this review, we will discuss genome and nucleoplasm architecture, particularly the importance of the nuclear periphery in genome stability. We will also discuss how the site of relocation regulates repair-pathway choice.
Analysis of genomic responses in a rat lung model treated with a humidifier sterilizer containing polyhexamethyleneguanidine phosphate.

Science.gov (United States)

Kim, Min-Seok; Jeong, Seok Won; Choi, Seong-Jin; Han, Jin-Young; Kim, Sung-Hwan; Yoon, Seokjoo; Oh, Jung-Hwa; Lee, Kyuhong

2017-02-15

The antimicrobial biocide polyhexamethyleneguanidine (PHMG) phosphate is the main ingredient in the commercially available humidifier disinfectant. PHMG phosphate-based humidifier disinfectants can cause pulmonary fibrosis and induce inflammatory and fibrotic responses both in vivo and in vitro. However, toxicological mechanisms including genomic alterations induced by inhalation exposure to PHMG phosphate have not been elucidated. Therefore, this study evaluated the toxicological effects of the PHMG phosphate-containing humidifier disinfectant. We used DNA microarray to identify global gene expression changes in rats treated with PHMG phosphate-containing humidifier disinfectant for 4 weeks and 10 weeks. Functional significance of differentially expressed genes (DEGs) was estimated by gene ontology (GO) analysis. Four weeks post-exposure, 320 and 392 DEGs were identified in female and male rats, respectively (>2-fold, pPHMG phosphate exposure. In addition, 21 genes were upregulated and 4 genes were downregulated in response to PHMG phosphate in a time-dependent manner. Thus, we predict that changes in genomic responses could be a significant molecular mechanism underlying PHMG phosphate toxicity. Further studies are required to determine the detailed mechanism of PHMG phosphate-induced pulmonary toxicity. Copyright © 2016. Published by Elsevier B.V.
Nuclear mitochondrial DNA activates replication in Saccharomyces cerevisiae.

Directory of Open Access Journals (Sweden)

Laurent Chatre

Full Text Available The nuclear genome of eukaryotes is colonized by DNA fragments of mitochondrial origin, called NUMTs. These insertions have been associated with a variety of germ-line diseases in humans. The significance of this uptake of potentially dangerous sequences into the nuclear genome is unclear. Here we provide functional evidence that sequences of mitochondrial origin promote nuclear DNA replication in Saccharomyces cerevisiae. We show that NUMTs are rich in key autonomously replicating sequence (ARS consensus motifs, whose mutation results in the reduction or loss of DNA replication activity. Furthermore, 2D-gel analysis of the mrc1 mutant exposed to hydroxyurea shows that several NUMTs function as late chromosomal origins. We also show that NUMTs located close to or within ARS provide key sequence elements for replication. Thus NUMTs can act as independent origins, when inserted in an appropriate genomic context or affect the efficiency of pre-existing origins. These findings show that migratory mitochondrial DNAs can impact on the replication of the nuclear region they are inserted in.
Post TMI-2 view on the responsibilities of nuclear engineering educators

International Nuclear Information System (INIS)

Long, R.L.

1980-01-01

The Three Mile Island (TMI) accident of March 28, 1979 was the result of a complex set of interactions involving design deficiencies, equipment failure and human error. Nuclear engineering educators may need to accept responsibility for some of the underlying, industry-wide causes leading to the event. The many detailed investigations and recommendations following the accident are certain to have a significant impact on nuclear engineering education. Areas of impact include changes in curricula, increased demand for graduates, heavier involvement in utility staff training and education, and new approaches to university, industry, and societal interactions
Deleterious mutation accumulation in organelle genomes.

Science.gov (United States)

Lynch, M; Blanchard, J L

1998-01-01

It is well established on theoretical grounds that the accumulation of mildly deleterious mutations in nonrecombining genomes is a major extinction risk in obligately asexual populations. Sexual populations can also incur mutational deterioration in genomic regions that experience little or no recombination, i.e., autosomal regions near centromeres, Y chromosomes, and organelle genomes. Our results suggest, for a wide array of genes (transfer RNAs, ribosomal RNAs, and proteins) in a diverse collection of species (animals, plants, and fungi), an almost universal increase in the fixation probabilities of mildly deleterious mutations arising in mitochondrial and chloroplast genomes relative to those arising in the recombining nuclear genome. This enhanced width of the selective sieve in organelle genomes does not appear to be a consequence of relaxed selection, but can be explained by the decline in the efficiency of selection that results from the reduction of effective population size induced by uniparental inheritance. Because of the very low mutation rates of organelle genomes (on the order of 10(-4) per genome per year), the reduction in fitness resulting from mutation accumulation in such genomes is a very long-term process, not likely to imperil many species on time scales of less than a million years, but perhaps playing some role in phylogenetic lineage sorting on time scales of 10 to 100 million years.
What would getting over with nuclear energy mean. Getting in on responsibility

International Nuclear Information System (INIS)

Haerle, W.

1986-01-01

In the current situation where the controversial debate in public about the further use or even enhancement of use of nuclear energy is carried on with ever growing vehemence and arguments lost in the flood of less transparent motivations, clear and down-to-earth information and sensible, convincing argumentation is badly needed. In his book the Professor of Systematic Theology at Marburg University tries to elaborate sensible answers to the puzzling questions, and to indicate ways and means of using one's own discernment. The problems involved are discussed under the following headings: Christian faith and political responsibility - Pros and cons of establishing the nuclear fuel reprocessing plant at Wackersdorf - Nuclear power seen from the point of view of economy and ecology - Nuclear power after Chernobyl - Energy policy concepts and their validation - The nuclear controversy as a challenge to political culture - The church and political culture. A documentation is given in an annex. (orig./HP) [de
Neutrino nuclear responses for double beta decays and astro neutrinos by charge exchange reactions

Science.gov (United States)

Ejiri, Hiroyasu

2014-09-01

Neutrino nuclear responses are crucial for neutrino studies in nuclei. Charge exchange reactions (CER) are shown to be used to study charged current neutrino nuclear responses associated with double beta decays(DBD)and astro neutrino interactions. CERs to be used are high energy-resolution (He3 ,t) reactions at RCNP, photonuclear reactions via IAR at NewSUBARU and muon capture reactions at MUSIC RCNP and MLF J-PARC. The Gamow Teller (GT) strengths studied by CERs reproduce the observed 2 neutrino DBD matrix elements. The GT and spin dipole (SD) matrix elements are found to be reduced much due to the nucleon spin isospin correlations and the non-nucleonic (delta isobar) nuclear medium effects. Impacts of the reductions on the DBD matrix elements and astro neutrino interactions are discussed.
Consequences of normalizing transcriptomic and genomic libraries of plant genomes using a duplex-specific nuclease and tetramethylammonium chloride.

Science.gov (United States)

Matvienko, Marta; Kozik, Alexander; Froenicke, Lutz; Lavelle, Dean; Martineau, Belinda; Perroud, Bertrand; Michelmore, Richard

2013-01-01

Several applications of high throughput genome and transcriptome sequencing would benefit from a reduction of the high-copy-number sequences in the libraries being sequenced and analyzed, particularly when applied to species with large genomes. We adapted and analyzed the consequences of a method that utilizes a thermostable duplex-specific nuclease for reducing the high-copy components in transcriptomic and genomic libraries prior to sequencing. This reduces the time, cost, and computational effort of obtaining informative transcriptomic and genomic sequence data for both fully sequenced and non-sequenced genomes. It also reduces contamination from organellar DNA in preparations of nuclear DNA. Hybridization in the presence of 3 M tetramethylammonium chloride (TMAC), which equalizes the rates of hybridization of GC and AT nucleotide pairs, reduced the bias against sequences with high GC content. Consequences of this method on the reduction of high-copy and enrichment of low-copy sequences are reported for Arabidopsis and lettuce.
Consequences of normalizing transcriptomic and genomic libraries of plant genomes using a duplex-specific nuclease and tetramethylammonium chloride.

Directory of Open Access Journals (Sweden)

Marta Matvienko

Full Text Available Several applications of high throughput genome and transcriptome sequencing would benefit from a reduction of the high-copy-number sequences in the libraries being sequenced and analyzed, particularly when applied to species with large genomes. We adapted and analyzed the consequences of a method that utilizes a thermostable duplex-specific nuclease for reducing the high-copy components in transcriptomic and genomic libraries prior to sequencing. This reduces the time, cost, and computational effort of obtaining informative transcriptomic and genomic sequence data for both fully sequenced and non-sequenced genomes. It also reduces contamination from organellar DNA in preparations of nuclear DNA. Hybridization in the presence of 3 M tetramethylammonium chloride (TMAC, which equalizes the rates of hybridization of GC and AT nucleotide pairs, reduced the bias against sequences with high GC content. Consequences of this method on the reduction of high-copy and enrichment of low-copy sequences are reported for Arabidopsis and lettuce.
Evolution of genome size and chromosome number in the carnivorous plant genus Genlisea (Lentibulariaceae), with a new estimate of the minimum genome size in angiosperms

Science.gov (United States)

Fleischmann, Andreas; Michael, Todd P.; Rivadavia, Fernando; Sousa, Aretuza; Wang, Wenqin; Temsch, Eva M.; Greilhuber, Johann; Müller, Kai F.; Heubl, Günther

2014-01-01

Background and Aims Some species of Genlisea possess ultrasmall nuclear genomes, the smallest known among angiosperms, and some have been found to have chromosomes of diminutive size, which may explain why chromosome numbers and karyotypes are not known for the majority of species of the genus. However, other members of the genus do not possess ultrasmall genomes, nor do most taxa studied in related genera of the family or order. This study therefore examined the evolution of genome sizes and chromosome numbers in Genlisea in a phylogenetic context. The correlations of genome size with chromosome number and size, with the phylogeny of the group and with growth forms and habitats were also examined. Methods Nuclear genome sizes were measured from cultivated plant material for a comprehensive sampling of taxa, including nearly half of all species of Genlisea and representing all major lineages. Flow cytometric measurements were conducted in parallel in two laboratories in order to compare the consistency of different methods and controls. Chromosome counts were performed for the majority of taxa, comparing different staining techniques for the ultrasmall chromosomes. Key Results Genome sizes of 15 taxa of Genlisea are presented and interpreted in a phylogenetic context. A high degree of congruence was found between genome size distribution and the major phylogenetic lineages. Ultrasmall genomes with 1C values of sections of the genus. The smallest known plant genomes were not found in G. margaretae, as previously reported, but in G. tuberosa (1C ≈ 61 Mbp) and some strains of G. aurea (1C ≈ 64 Mbp). Conclusions Genlisea is an ideal candidate model organism for the understanding of genome reduction as the genus includes species with both relatively large (∼1700 Mbp) and ultrasmall (∼61 Mbp) genomes. This comparative, phylogeny-based analysis of genome sizes and karyotypes in Genlisea provides essential data for selection of suitable species for comparative
Method for developing arrangements for response to a nuclear or radiological emergency. Updating IAEA-TECDOC-953. Emergency preparedness and response. Publication date: October 2003

International Nuclear Information System (INIS)

2003-09-01

In 1997 the IAEA compiled, consolidated and organized existing information, and published the TECDOC-953 'Method for Development of Emergency Response Preparedness for Nuclear or Radiological Accidents'. Subsequently this publication was used extensively by the IAEA for training and for evaluation of emergency response programmes. In November 1999 a technical committee meeting (TCM) with representatives of over 20 States reviewed and provided feedback on IAEA-TECDOC-953. In March 2002, the IAEA's Board of Governors approved a Safety Requirements publication, 'Preparedness and Response for a Nuclear or Radiological Emergency', jointly sponsored by seven international organizations, which establishes the requirements for an adequate level of preparedness and response for a nuclear or radiological emergency in any State. The IAEA General Conference in resolution GC(46)/RES/9 encouraged Member States to implement, if necessary, instruments for improving their own preparedness and response capabilities for nuclear and radiological incidents and accidents, including their arrangements for responding to acts involving the malicious use of nuclear or radioactive material and to threats of such acts, and has further encouraged them to implement the Safety Requirements for Preparedness and Response to a Nuclear or Radiological Emergency. The obligations, responsibilities and requirements for preparedness and response for radiation emergencies are set out in the safety standards, in particular the 1996 'International Basic Safety Standards for Protection against Ionizing Radiation and for the Safety of Radiation Sources'. Consensus information on relevant radiation protection criteria was established in 1994 and published in 'Intervention Criteria in a Nuclear or Radiation Emergency'. Several other guides and publications in the area of emergency preparedness and response had previously been issued. The present publication now being issued in the Emergency Preparedness and
National radiological emergency response to the Fukushima Daiichi Nuclear Power Plant accident

International Nuclear Information System (INIS)

Dela Rosa, Alumanda M.

2011-01-01

The Fukushima nuclear power plant accident occurred on March 11, 2011, when two natural disasters of unprecedented strengths, an earthquake with magnitude 9 followed one hour later by a powerful tsunami struck northeastern Japan and felled the external power supply and the emergency diesel generators of the Fukushima Daiichi nuclear power station, resulting in a loss of coolant accident. There were core meltdowns in three nuclear reactors with the release of radioactivity estimated to be 1/10 of what was released to the environment during the Chernobyl nuclear power plant accident in April 1986. The Fukushima nuclear accident tested the capability of the Philippine Nuclear Research Institute (PNRI) and the National Disaster Risk Reduction and Management Council (NDRRMC) in responding to such radiological emergency as a nuclear power plant accident. The PNRI and NDRRMC activated the RADPLAN for possible radiological emergency. The emergency response was calibrated to the status of the nuclear reactors on site and the environmental monitoring undertaken around the site and off-site, including the marine environment. This orchestrated effort enabled the PNRI and the national agencies concerned to reassure the public that the nuclear accident does not have a significant impact on the Philippines, both on the health and safety of the people and on the safety of the environment. National actions taken during the accident will be presented. The role played by the International Atomic Energy Agency as the central UN agency for nuclear matters will be discussed. (author)
Preparedness and Response for a Nuclear or Radiological Emergency. General Safety Requirements (Arabic Edition)

International Nuclear Information System (INIS)

2016-01-01

This publication, jointly sponsored by the FAO, IAEA, ICAO, ILO, IMO, INTERPOL, OECD/NEA, PAHO, CTBTO, UNEP, OCHA, WHO and WMO, is the new edition establishing the requirements for preparedness and response for a nuclear or radiological emergency which takes into account the latest experience and developments in the area. It supersedes the previous edition of the Safety Requirements for emergency preparedness and response, Safety Standards Series No. GS-R-2, which was published in 2002. This publication establishes the requirements for ensuring an adequate level of preparedness and response for a nuclear or radiological emergency, irrespective of its cause. These Safety Requirements are intended to be used by governments, emergency response organizations, other authorities at the local, regional and national levels, operating organizations and the regulatory body as well as by relevant international organizations at the international level.
Preparedness and Response for a Nuclear or Radiological Emergency. General Safety Requirements (Russian Edition)

International Nuclear Information System (INIS)

2016-01-01

This publication, jointly sponsored by the FAO, IAEA, ICAO, ILO, IMO, INTERPOL, OECD/NEA, PAHO, CTBTO, UNEP, OCHA, WHO and WMO, is the new edition establishing the requirements for preparedness and response for a nuclear or radiological emergency which takes into account the latest experience and developments in the area. It supersedes the previous edition of the Safety Requirements for emergency preparedness and response, Safety Standards Series No. GS-R-2, which was published in 2002. This publication establishes the requirements for ensuring an adequate level of preparedness and response for a nuclear or radiological emergency, irrespective of its cause. These Safety Requirements are intended to be used by governments, emergency response organizations, other authorities at the local, regional and national levels, operating organizations and the regulatory body as well as by relevant international organizations at the international level.
Preparedness and Response for a Nuclear or Radiological Emergency. General Safety Requirements (Chinese Edition)

International Nuclear Information System (INIS)

2016-01-01

This publication, jointly sponsored by the FAO, IAEA, ICAO, ILO, IMO, INTERPOL, OECD/NEA, PAHO, CTBTO, UNEP, OCHA, WHO and WMO, is the new edition establishing the requirements for preparedness and response for a nuclear or radiological emergency which takes into account the latest experience and developments in the area. It supersedes the previous edition of the Safety Requirements for emergency preparedness and response, Safety Standards Series No. GS-R-2, which was published in 2002. This publication establishes the requirements for ensuring an adequate level of preparedness and response for a nuclear or radiological emergency, irrespective of its cause. These Safety Requirements are intended to be used by governments, emergency response organizations, other authorities at the local, regional and national levels, operating organizations and the regulatory body as well as by relevant international organizations at the international level.

Genome-wide investigation reveals high evolutionary rates in annual model plants.

Science.gov (United States)

Yue, Jia-Xing; Li, Jinpeng; Wang, Dan; Araki, Hitoshi; Tian, Dacheng; Yang, Sihai

2010-11-09

Rates of molecular evolution vary widely among species. While significant deviations from molecular clock have been found in many taxa, effects of life histories on molecular evolution are not fully understood. In plants, annual/perennial life history traits have long been suspected to influence the evolutionary rates at the molecular level. To date, however, the number of genes investigated on this subject is limited and the conclusions are mixed. To evaluate the possible heterogeneity in evolutionary rates between annual and perennial plants at the genomic level, we investigated 85 nuclear housekeeping genes, 10 non-housekeeping families, and 34 chloroplast genes using the genomic data from model plants including Arabidopsis thaliana and Medicago truncatula for annuals and grape (Vitis vinifera) and popular (Populus trichocarpa) for perennials. According to the cross-comparisons among the four species, 74-82% of the nuclear genes and 71-97% of the chloroplast genes suggested higher rates of molecular evolution in the two annuals than those in the two perennials. The significant heterogeneity in evolutionary rate between annuals and perennials was consistently found both in nonsynonymous sites and synonymous sites. While a linear correlation of evolutionary rates in orthologous genes between species was observed in nonsynonymous sites, the correlation was weak or invisible in synonymous sites. This tendency was clearer in nuclear genes than in chloroplast genes, in which the overall evolutionary rate was small. The slope of the regression line was consistently lower than unity, further confirming the higher evolutionary rate in annuals at the genomic level. The higher evolutionary rate in annuals than in perennials appears to be a universal phenomenon both in nuclear and chloroplast genomes in the four dicot model plants we investigated. Therefore, such heterogeneity in evolutionary rate should result from factors that have genome-wide influence, most likely those
Rapid behavioral and genomic responses to social opportunity.

Directory of Open Access Journals (Sweden)

Sabrina S Burmeister

2005-11-01

Full Text Available From primates to bees, social status regulates reproduction. In the cichlid fish Astatotilapia (Haplochromis burtoni, subordinate males have reduced fertility and must become dominant to reproduce. This increase in sexual capacity is orchestrated by neurons in the preoptic area, which enlarge in response to dominance and increase expression of gonadotropin-releasing hormone 1 (GnRH1, a peptide critical for reproduction. Using a novel behavioral paradigm, we show for the first time that subordinate males can become dominant within minutes of an opportunity to do so, displaying dramatic changes in body coloration and behavior. We also found that social opportunity induced expression of the immediate-early gene egr-1 in the anterior preoptic area, peaking in regions with high densities of GnRH1 neurons, and not in brain regions that express the related peptides GnRH2 and GnRH3. This genomic response did not occur in stable subordinate or stable dominant males even though stable dominants, like ascending males, displayed dominance behaviors. Moreover, egr-1 in the optic tectum and the cerebellum was similarly induced in all experimental groups, showing that egr-1 induction in the anterior preoptic area of ascending males was specific to this brain region. Because egr-1 codes for a transcription factor important in neural plasticity, induction of egr-1 in the anterior preoptic area by social opportunity could be an early trigger in the molecular cascade that culminates in enhanced fertility and other long-term physiological changes associated with dominance.
Network of siren, public address and display system to preparedness and response for nuclear emergencies

International Nuclear Information System (INIS)

Joshi, G.H.; Padmanabhan, N.; Raman, N.; Pradeepkumar, K.S.; Sharma, D.N.; Abani, M.C.

2003-01-01

For an effective emergency response and implementation of counter measures, communication during a nuclear emergency is a very important aspect. The declaration of a nuclear emergency must be immediately conveyed to all those working in the plant and around the nuclear site. Besides this, the nature of emergency also needs to be conveyed unambiguously along with corresponding counter measures, such as stay in, evacuation or all clear signal for the relevant plants. This requirement has necessitated the need for a networked signaling system. Based on this requirement, a microcontroller based signaling and a telephone/wireless based communication and display system has been designed at Bhabha Atomic Research Centre. It is proposed to be used as a part of emergency preparedness and response programme at the nuclear facility sites. As per the design made for Bhabha Atomic Research Centre, Trombay site, each plant or area in the site is identified by a unique identification code. The main Site Emergency Control Centre/Emergency Response Centre at Mod. Labs. selectively calls the various plants and declares the nature of emergency to be followed In that plant/area through different siren signals along with display and announcement of instructions. This paper describes the details of the system that is designed for Bhabha Atomic Research Centre, Trombay site and proposed for other nuclear power plant sites. (author)
NRC/FEMA operational response procedures for response to a commercial nuclear reactor accident. Revision 1

International Nuclear Information System (INIS)

1985-02-01

Procedures have been developed by the US Nuclear Regulatory Commission (NRC) and the Federal Emergency Management Agency (FEMA) which provide the response teams of both agencies with the steps to be taken in responding to an emergency at a commercial nuclear power plant. The emphasis of these procedures is mainly on the interface between NRC and FEMA at their respective Headquarters and Regional Offices and at the various sites at which such an emergency could occur. Detailed procedures are presented that cover for both agencies, notification schemes and manner of activation, organizations at Headquarters and the site, interface procedures, coordination of onsite and offsite operations, the role of the Senior FEMA Official, and the cooperative efforts of each agency's public information staff
The yeast genome may harbor hypoxia response elements (HRE).

Science.gov (United States)

Ferreira, Túlio César; Hertzberg, Libi; Gassmann, Max; Campos, Elida Geralda

2007-01-01

The hypoxia-inducible factor-1 (HIF-1) is a heterodimeric transcription factor activated when cells are submitted to hypoxia. The heterodimer is composed of two subunits, HIF-1alpha and the constitutively expressed HIF-1beta. During normoxia, HIF-1alpha is degraded by the 26S proteasome, but hypoxia causes HIF-1alpha to be stabilized, enter the nucleus and bind to HIF-1beta, thus forming the active complex. The complex then binds to the regulatory sequences of various genes involved in physiological and pathological processes. The specific regulatory sequence recognized by HIF-1 is the hypoxia response element (HRE) that has the consensus sequence 5'BRCGTGVBBB3'. Although the basic transcriptional regulation machinery is conserved between yeast and mammals, Saccharomyces cerevisiae does not express HIF-1 subunits. However, we hypothesized that baker's yeast has a protein analogous to HIF-1 which participates in the response to changes in oxygen levels by binding to HRE sequences. In this study we screened the yeast genome for HREs using probabilistic motif search tools. We described 24 yeast genes containing motifs with high probability of being HREs (p-value<0.1) and classified them according to biological function. Our results show that S. cerevisiae may harbor HREs and indicate that a transcription factor analogous to HIF-1 may exist in this organism.
Early nongenomic events in aldosterone action in renal collecting duct cells: PKCalpha activation, mineralocorticoid receptor phosphorylation, and cross-talk with the genomic response.

Science.gov (United States)

Le Moëllic, Cathy; Ouvrard-Pascaud, Antoine; Capurro, Claudia; Cluzeaud, Francoise; Fay, Michel; Jaisser, Frederic; Farman, Nicolette; Blot-Chabaud, Marcel

2004-05-01

Effects of aldosterone on its target cells have long been considered to be mediated exclusively through the genomic pathway; however, evidence has been provided for rapid effects of the hormone that may involve nongenomic mechanisms. Whether an interaction exists between these two signaling pathways is not yet established. In this study, the authors show that aldosterone triggers both early nongenomic and late genomic increase in sodium transport in the RCCD(2) rat cortical collecting duct cell line. In these cells, the early (up to 2.5 h) aldosterone-induced increase in short-circuit current (Isc) is not blocked by the mineralocorticoid receptor (MR) antagonist RU26752, it does not require mRNA or protein synthesis, and it involves the PKCalpha signaling pathway. In addition, this early response is reproduced by aldosterone-BSA, which acts at the cell surface and presumably does not enter the cells (aldo-BSA is unable to trigger the late response). The authors also show that MR is rapidly phosphorylated on serine and threonine residues by aldosterone or aldosterone-BSA. In contrast, the late (4 to 24 h) aldosterone-induced increase in ion transport occurs through activation of the MR and requires mRNA and protein synthesis. Interestingly, nongenomic and genomic aldosterone actions appear to be interdependent. Blocking the PKCalpha pathway results in the inhibition of the late genomic response to aldosterone, as demonstrated by the suppression of aldosterone-induced increase in MR transactivation activity, alpha1 Na(+)/K(+)/ATPase mRNA, and Isc. These data suggest cross-talk between the nongenomic and genomic responses to aldosterone in renal cells and suggest that the aldosterone-MR mediated increase in mRNA/protein synthesis and ion transport depends, at least in part, upon PKCalpha activation. E-mail: marcel.blot-chabaud@pharmacie.univ-mrs.fr
Radiation and chemotherapy bystander effects induce early genomic instability events: telomere shortening and bridge formation coupled with mitochondrial dysfunction.

LENUS (Irish Health Repository)

Gorman, Sheeona

2012-02-01

The bridge breakage fusion cycle is a chromosomal instability mechanism responsible for genomic changes. Radiation bystander effects induce genomic instability; however, the mechanism driving this instability is unknown. We examined if radiation and chemotherapy bystander effects induce early genomic instability events such as telomere shortening and bridge formation using a human colon cancer explant model. We assessed telomere lengths, bridge formations, mitochondrial membrane potential and levels of reactive oxygen species in bystander cells exposed to medium from irradiated and chemotherapy-treated explant tissues. Bystander cells exposed to media from 2Gy, 5Gy, FOLFOX treated tumor and matching normal tissue showed a significant reduction in telomere lengths (all p values <0.018) and an increase in bridge formations (all p values <0.017) compared to bystander cells treated with media from unirradiated tissue (0Gy) at 24h. There was no significant difference between 2Gy and 5Gy treatments, or between effects elicited by tumor versus matched normal tissue. Bystander cells exposed to media from 2Gy irradiated tumor tissue showed significant depolarisation of the mitochondrial membrane potential (p=0.012) and an increase in reactive oxygen species levels. We also used bystander cells overexpressing a mitochondrial antioxidant manganese superoxide dismutase (MnSOD) to examine if this antioxidant could rescue the mitochondrial changes and subsequently influence nuclear instability events. In MnSOD cells, ROS levels were reduced (p=0.02) and mitochondrial membrane potential increased (p=0.04). These events were coupled with a decrease in percentage of cells with anaphase bridges and a decrease in the number of cells undergoing telomere length shortening (p values 0.01 and 0.028 respectively). We demonstrate that radiation and chemotherapy bystander responses induce early genomic instability coupled with defects in mitochondrial function. Restoring mitochondrial
Considerations in Emergency Preparedness and Response for a State Embarking on a Nuclear Power Programme. Publication Date: August 2012

Energy Technology Data Exchange (ETDEWEB)

NONE

2012-09-15

The aim of this publication is to provide a practical tool for emergency planning for States embarking on a nuclear power programme and to fulfil, in part, functions assigned to the IAEA in the Convention on Assistance in the Case of a Nuclear Accident or Radiological Emergency ('Assistance Convention'). Under Article 5.a (ii) of the Assistance Convention, one function of the IAEA is to collect and disseminate to State Parties and Member States information concerning methodologies, techniques and available results of research relating to such emergencies. As established in the publication Preparedness and Response for a Nuclear or Radiological Emergency (IAEA Safety Standards Series No. GS-R-2), the practical goal of emergency response is 'to ensure that arrangements are in place for a timely, managed, controlled, coordinated and effective response at the scene, and at the local, regional, national and international level, to any nuclear or radiological emergency'. In 2011 the IAEA General Conference, in resolution GC(55)/RES/9, encouraged States 'embarking on new nuclear power programmes to take timely and proactive steps, based upon gradual and systematic application of IAEA safety standards, to establish and sustain a strong safety culture'. It also 'emphasizes the importance for all Member States to implement emergency preparedness and response mechanisms and develop mitigation measures at a national level, consistent with the IAEA's Safety Standards, for improving emergency preparedness and response, facilitating communication in an emergency and contributing to harmonization of national criteria for protective and other actions'. This publication, issued in the IAEA Emergency Preparedness and Response Series, is intended to assist on steps to be taken by States embarking on a nuclear power programme to establish effective national capabilities and arrangements of preparedness for and response to a nuclear or radiological emergency (hereinafter referred to as
Considerations in Emergency Preparedness and Response for a State Embarking on a Nuclear Power Programme. Publication Date: August 2012

International Nuclear Information System (INIS)

2012-01-01

The aim of this publication is to provide a practical tool for emergency planning for States embarking on a nuclear power programme and to fulfil, in part, functions assigned to the IAEA in the Convention on Assistance in the Case of a Nuclear Accident or Radiological Emergency ('Assistance Convention'). Under Article 5.a (ii) of the Assistance Convention, one function of the IAEA is to collect and disseminate to State Parties and Member States information concerning methodologies, techniques and available results of research relating to such emergencies. As established in the publication Preparedness and Response for a Nuclear or Radiological Emergency (IAEA Safety Standards Series No. GS-R-2), the practical goal of emergency response is 'to ensure that arrangements are in place for a timely, managed, controlled, coordinated and effective response at the scene, and at the local, regional, national and international level, to any nuclear or radiological emergency'. In 2011 the IAEA General Conference, in resolution GC(55)/RES/9, encouraged States 'embarking on new nuclear power programmes to take timely and proactive steps, based upon gradual and systematic application of IAEA safety standards, to establish and sustain a strong safety culture'. It also 'emphasizes the importance for all Member States to implement emergency preparedness and response mechanisms and develop mitigation measures at a national level, consistent with the IAEA's Safety Standards, for improving emergency preparedness and response, facilitating communication in an emergency and contributing to harmonization of national criteria for protective and other actions'. This publication, issued in the IAEA Emergency Preparedness and Response Series, is intended to assist on steps to be taken by States embarking on a nuclear power programme to establish effective national capabilities and arrangements of preparedness for and response to a nuclear or radiological emergency (hereinafter referred to as
Evaluation of the nuclear and radiological emergency response system in Brazil; Visao critica do sistema de atendimento a emergencia radiologica e nuclear no Brasil

Energy Technology Data Exchange (ETDEWEB)

Estrada, Julio J.S.; Azevedo, Eduardo M.; Knoefel, Tom M.J. [Instituto de Radioprotecao e Dosimetria (IRD), Rio de Janeiro, RJ (Brazil)

1997-12-31

Brazilian Nuclear Energy Commission (CNEN) has made outstanding efforts to improve its nuclear and radiological accident response system since the tragic accident in Goiania, Brazil. Most of these efforts are related to nuclear emergency although radiological accidents are also considered. Several topics are discussed involving those related to planning and preparedness. Some deficiencies that need to be corrected or improved are pointed out 8 refs.
Functional role of a highly repetitive DNA sequence in anchorage of the mouse genome.

Science.gov (United States)

Neuer-Nitsche, B; Lu, X N; Werner, D

1988-09-12

The major portion of the eukaryotic genome consists of various categories of repetitive DNA sequences which have been studied with respect to their base compositions, organizations, copy numbers, transcription and species specificities; their biological roles, however, are still unclear. A novel quality of a highly repetitive mouse DNA sequence is described which points to a functional role: All copies (approximately 50,000 per haploid genome) of this DNA sequence reside on genomic Alu I DNA fragments each associated with nuclear polypeptides that are not released from DNA by proteinase K, SDS and phenol extraction. By this quality the repetitive DNA sequence is classified as a member of the sub-set of DNA sequences involved in tight DNA-polypeptide complexes which have been previously shown to be components of the subnuclear structure termed 'nuclear matrix'. From these results it has to be concluded that the repetitive DNA sequence characterized in this report represents or comprises a signal for a large number of site specific attachment points of the mouse genome in the nuclear matrix.
Dynamic association of NUP98 with the human genome.

Directory of Open Access Journals (Sweden)

Yun Liang

Full Text Available Faithful execution of developmental gene expression programs occurs at multiple levels and involves many different components such as transcription factors, histone-modification enzymes, and mRNA processing proteins. Recent evidence suggests that nucleoporins, well known components that control nucleo-cytoplasmic trafficking, have wide-ranging functions in developmental gene regulation that potentially extend beyond their role in nuclear transport. Whether the unexpected role of nuclear pore proteins in transcription regulation, which initially has been described in fungi and flies, also applies to human cells is unknown. Here we show at a genome-wide level that the nuclear pore protein NUP98 associates with developmentally regulated genes active during human embryonic stem cell differentiation. Overexpression of a dominant negative fragment of NUP98 levels decreases expression levels of NUP98-bound genes. In addition, we identify two modes of developmental gene regulation by NUP98 that are differentiated by the spatial localization of NUP98 target genes. Genes in the initial stage of developmental induction can associate with NUP98 that is embedded in the nuclear pores at the nuclear periphery. Alternatively, genes that are highly induced can interact with NUP98 in the nuclear interior, away from the nuclear pores. This work demonstrates for the first time that NUP98 dynamically associates with the human genome during differentiation, revealing a role of a nuclear pore protein in regulating developmental gene expression programs.
Membrane-initiated non-genomic signaling by estrogens in the hypothalamus: cross-talk with glucocorticoids with implications for behavior

Directory of Open Access Journals (Sweden)

Jennifer eRainville

2015-02-01

Full Text Available The estrogen receptor (ER and glucocorticoid receptor (GR are members of the nuclear receptor superfamily that can signal using both non-genomic and genomic transcriptional modes. Though genomic modes of signaling have been well characterized and several behaviors attributed to this signaling mechanism, the physiological significance of non-genomic modes of signaling has not been well understood. This has partly been due to the controversy regarding the identity of the membrane ER (mER or membrane GR (mGR that may mediate rapid, non-genomic signaling and the downstream signaling cascades that may result as a consequence of steroid ligands binding the mER or the mGR. Both estrogens and glucocorticoids exert a number of actions on the hypothalamus, including feedback. This review focuses on the various candidates for the mER or mGR in the hypothalamus and the contribution of non-genomic signaling to classical hypothalamically-driven behaviors and changes in neuronal morphology. It also attempts to categorize some of the possible functions of non-genomic signaling at both the cellular level and at the organismal level that are relevant for behavior, including some behaviors that are regulated by both estrogens and glucocorticoids in a potentially synergistic manner. Lastly, it attempts to show that steroid signaling via non-genomic modes may provide the organism with rapid behavioral responses to stimuli.
The Trichoplax Genome and the Nature of Placozoans

Energy Technology Data Exchange (ETDEWEB)

Srivastava, Mansi; Begovic, Emina; Chapman, Jarrod; Putnam, Nicholas H.; Hellsten, Uffe; Kawashima, Takeshi; Kuo, Alan; Mitros, Therese; Salamov, Asaf; Carpenter, Meredith L.; Signorovitch, Ana Y.; Moreno, Maria A.; Kamm, Kai; Grimwood, Jane; Schmutz, Jeremy; Shapiro, Harris; Grigoriev, Igor V.; Buss, Leo W.; Schierwater, Bernd; Dellaporta, Stephen L.; Rokhsar, Daniel S.

2008-08-01

Placozoans are arguably the simplest free-living animals, possibly evoking an early stage in metazoan evolution, yet their biology is poorly understood. Here we report the sequencing and analysis of the {approx}98 million base pair nuclear genome of the placozoan Trichoplax adhaerens. Whole genome phylogenetic analysis suggests that placozoans belong to a 'eumetazoan' clade that includes cnidarians and bilaterians, with sponges as the earliest diverging animals. The compact genome exhibits conserved gene content, gene structure, and synteny relative to the human and other complex eumetazoan genomes. Despite the apparent cellular and organismal simplicity of Trichoplax, its genome encodes a rich array of transcription factor and signaling pathway genes that are typically associated with diverse cell types and developmental processes in eumetazoans, motivating further searches for cryptic cellular complexity and/or as yet unobserved life history stages.
Chromatin dynamics in genome stability

DEFF Research Database (Denmark)

Nair, Nidhi; Shoaib, Muhammad; Sørensen, Claus Storgaard

2017-01-01

Genomic DNA is compacted into chromatin through packaging with histone and non-histone proteins. Importantly, DNA accessibility is dynamically regulated to ensure genome stability. This is exemplified in the response to DNA damage where chromatin relaxation near genomic lesions serves to promote...... access of relevant enzymes to specific DNA regions for signaling and repair. Furthermore, recent data highlight genome maintenance roles of chromatin through the regulation of endogenous DNA-templated processes including transcription and replication. Here, we review research that shows the importance...... of chromatin structure regulation in maintaining genome integrity by multiple mechanisms including facilitating DNA repair and directly suppressing endogenous DNA damage....
Integrative proteomics, genomics, and translational immunology approaches reveal mutated forms of Proteolipid Protein 1 (PLP1) and mutant-specific immune response in multiple sclerosis.

Science.gov (United States)

Qendro, Veneta; Bugos, Grace A; Lundgren, Debbie H; Glynn, John; Han, May H; Han, David K

2017-03-01

In order to gain mechanistic insights into multiple sclerosis (MS) pathogenesis, we utilized a multi-dimensional approach to test the hypothesis that mutations in myelin proteins lead to immune activation and central nervous system autoimmunity in MS. Mass spectrometry-based proteomic analysis of human MS brain lesions revealed seven unique mutations of PLP1; a key myelin protein that is known to be destroyed in MS. Surprisingly, in-depth genomic analysis of two MS patients at the genomic DNA and mRNA confirmed mutated PLP1 in RNA, but not in the genomic DNA. Quantification of wild type and mutant PLP RNA levels by qPCR further validated the presence of mutant PLP RNA in the MS patients. To seek evidence linking mutations in abundant myelin proteins and immune-mediated destruction of myelin, specific immune response against mutant PLP1 in MS patients was examined. Thus, we have designed paired, wild type and mutant peptide microarrays, and examined antibody response to multiple mutated PLP1 in sera from MS patients. Consistent with the idea of different patients exhibiting unique mutation profiles, we found that 13 out of 20 MS patients showed antibody responses against specific but not against all the mutant-PLP1 peptides. Interestingly, we found mutant PLP-directed antibody response against specific mutant peptides in the sera of pre-MS controls. The results from integrative proteomic, genomic, and immune analyses reveal a possible mechanism of mutation-driven pathogenesis in human MS. The study also highlights the need for integrative genomic and proteomic analyses for uncovering pathogenic mechanisms of human diseases. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Genome-Wide Distribution, Organisation and Functional Characterization of Disease Resistance and Defence Response Genes across Rice Species

Science.gov (United States)

Singh, Sangeeta; Chand, Suresh; Singh, N. K.; Sharma, Tilak Raj

2015-01-01

The resistance (R) genes and defense response (DR) genes have become very important resources for the development of disease resistant cultivars. In the present investigation, genome-wide identification, expression, phylogenetic and synteny analysis was done for R and DR-genes across three species of rice viz: Oryza sativa ssp indica cv 93-11, Oryza sativa ssp japonica and wild rice species, Oryza brachyantha. We used the in silico approach to identify and map 786 R -genes and 167 DR-genes, 672 R-genes and 142 DR-genes, 251 R-genes and 86 DR-genes in the japonica, indica and O. brachyanth a genomes, respectively. Our analysis showed that 60.5% and 55.6% of the R-genes are tandemly repeated within clusters and distributed over all the rice chromosomes in indica and japonica genomes, respectively. The phylogenetic analysis along with motif distribution shows high degree of conservation of R- and DR-genes in clusters. In silico expression analysis of R-genes and DR-genes showed more than 85% were expressed genes showing corresponding EST matches in the databases. This study gave special emphasis on mechanisms of gene evolution and duplication for R and DR genes across species. Analysis of paralogs across rice species indicated 17% and 4.38% R-genes, 29% and 11.63% DR-genes duplication in indica and Oryza brachyantha, as compared to 20% and 26% duplication of R-genes and DR-genes in japonica respectively. We found that during the course of duplication only 9.5% of R- and DR-genes changed their function and rest of the genes have maintained their identity. Syntenic relationship across three genomes inferred that more orthology is shared between indica and japonica genomes as compared to brachyantha genome. Genome wide identification of R-genes and DR-genes in the rice genome will help in allele mining and functional validation of these genes, and to understand molecular mechanism of disease resistance and their evolution in rice and related species. PMID:25902056
Resilience and Brittleness in a Nuclear Emergency Response Simulation: Focusing on Team Coordination Activity

International Nuclear Information System (INIS)

Costa, Wagner Schenkel; Buarque, Lia; Voshell, Martin; Branlat, Matthieu; Woods, David D.; Gomes, Jose Orlando

2008-01-01

The current work presents results from a cognitive task analysis (CTA) of a nuclear disaster simulation. Audio-visual records were collected from an emergency room team composed of individuals from 26 different agencies as they responded to multiple scenarios in a simulated nuclear disaster. This simulation was part of a national emergency response training activity for a nuclear power plant located in a developing country. The objectives of this paper are to describe sources of resilience and brittleness in these activities, identify cues of potential improvements for future emergency simulations, and leveraging the resilience of the emergency response System in case of a real disaster. Multiple CTA techniques were used to gain a better understanding of the cognitive dimensions of the activity and to identify team coordination and crisis management patterns that emerged from the simulation training. (authors)
Short Interspersed Nuclear Element (SINE) Sequences in the Genome of the Human Pathogenic Fungus Aspergillus fumigatus Af293.

Science.gov (United States)

Kanhayuwa, Lakkhana; Coutts, Robert H A

2016-01-01

Novel families of short interspersed nuclear element (SINE) sequences in the human pathogenic fungus Aspergillus fumigatus, clinical isolate Af293, were identified and categorised into tRNA-related and 5S rRNA-related SINEs. Eight predicted tRNA-related SINE families originating from different tRNAs, and nominated as AfuSINE2 sequences, contained target site duplications of short direct repeat sequences (4-14 bp) flanking the elements, an extended tRNA-unrelated region and typical features of RNA polymerase III promoter sequences. The elements ranged in size from 140-493 bp and were present in low copy number in the genome and five out of eight were actively transcribed. One putative tRNAArg-derived sequence, AfuSINE2-1a possessed a unique feature of repeated trinucleotide ACT residues at its 3'-terminus. This element was similar in sequence to the I-4_AO element found in A. oryzae and an I-1_AF long nuclear interspersed element-like sequence identified in A. fumigatus Af293. Families of 5S rRNA-related SINE sequences, nominated as AfuSINE3, were also identified and their 5'-5S rRNA-related regions show 50-65% and 60-75% similarity to respectively A. fumigatus 5S rRNAs and SINE3-1_AO found in A. oryzae. A. fumigatus Af293 contains five copies of AfuSINE3 sequences ranging in size from 259-343 bp and two out of five AfuSINE3 sequences were actively transcribed. Investigations on AfuSINE distribution in the fungal genome revealed that the elements are enriched in pericentromeric and subtelomeric regions and inserted within gene-rich regions. We also demonstrated that some, but not all, AfuSINE sequences are targeted by host RNA silencing mechanisms. Finally, we demonstrated that infection of the fungus with mycoviruses had no apparent effects on SINE activity.
Cytoplasmic ATR Activation Promotes Vaccinia Virus Genome Replication

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Antonio Postigo

2017-05-01

Full Text Available In contrast to most DNA viruses, poxviruses replicate their genomes in the cytoplasm without host involvement. We find that vaccinia virus induces cytoplasmic activation of ATR early during infection, before genome uncoating, which is unexpected because ATR plays a fundamental nuclear role in maintaining host genome integrity. ATR, RPA, INTS7, and Chk1 are recruited to cytoplasmic DNA viral factories, suggesting canonical ATR pathway activation. Consistent with this, pharmacological and RNAi-mediated inhibition of canonical ATR signaling suppresses genome replication. RPA and the sliding clamp PCNA interact with the viral polymerase E9 and are required for DNA replication. Moreover, the ATR activator TOPBP1 promotes genome replication and associates with the viral replisome component H5. Our study suggests that, in contrast to long-held beliefs, vaccinia recruits conserved components of the eukaryote DNA replication and repair machinery to amplify its genome in the host cytoplasm.

The response to a worst-case scenario - the national emergency plan for nuclear accidents

Energy Technology Data Exchange (ETDEWEB)

Cunningham D, John [Radiological Protection Inst. of Ireland (Ireland)

1996-10-01

The Chernobyl accident in 1986 highlighted many deficiencies in the preparedness of countries to deal with a major accident. It demonstrated how vulnerable countries are to transboundary contamination. Ireland had no emergency plan at the time of the accident and only minimal facilities with which to assess the consequences of the accident. Nonetheless, the then Nuclear Energy Board with the assistance of Government Departments and the Civil Defence organisation reacted quickly to assess the situation despite the complete lack of information about the accident from the then USSR. Even countries with advanced nuclear technologies faced similar difficulties. It was quickly recognised by Government that the national laboratory facilities were totally inadequate. The Nuclear Energy Board was provided with additional resources to assist it to cope in the short term with the very large demand for monitoring. In the longer term a new national radiation laboratory was provided and the Board was formally replaced by the Radiological Protection Institute of Ireland. It was given statutory responsibility to monitor radiation levels, to advise measures to be taken for the protection of the public and to provide information for the public. An emergency plan based on the Chernobyl experience was drafted in 1987, amended and published in 1992. Certain features of this plan were implemented from 1987 onwards, notably the classification of responsibilities and the installation of a national continuous radiation monitoring system. The paper outlines the responsibilities of those who could be involved in a response to a nuclear incident, the procedures used to evaluate its consequences and the provision of information for the public. The plan provides an integrated management system which has sufficient flexibility to enable a rapid response to be made to a major or minor crisis, either foreseen or unforeseen and whatever its cause.
Financing responsibility for nuclear waste disposal

International Nuclear Information System (INIS)

2004-01-01

The basic premise for financing arrangements for the disposal of nuclear waste is that the nuclear industry - not the taxpayer - must bear the costs. Present regulations, however, are imperfect in this regard. The Inquiry therefore proposes extending the financial liability of the nuclear industry and introducing new fee-setting arrangements. It is proposed that a new law be enacted to regulate these changes. The present financing system is regulated in the 'Financing Act' 1. Under this Act, the licensed owner and operator of a nuclear reactor is required to pay an annual fee and provide guarantees to the State. Four companies are reactor owners. These companies are wholly or partly owned by other companies according to various arrangements. Each reactor owner is responsible for its own dismantling costs and for its share of allocated common costs of disposal and related measures. If there is insufficient money in the funds, the nuclear industry will still be liable. The basic premise of the Inquiry is that the financing system should be designed so as to minimise the risk that the State (and taxpayers) will need to step in and pay. Although the nuclear industry is intended to have full liability for payment, in practice it does not. This is because the formal full liability for payment in the nuclear industry rests with the reactor companies and not where the industry's long-term ability to pay is to be found. Essentially, the present arrangements mean that: - Companies that cannot be expected to have any long-term ability to pay have unlimited liability, and - Companies that can be expected to have an ability to pay have very limited liability. The Inquiry therefore proposes that ability to pay and liability are brought into line by a formal assumption by owning companies of the sort of liability for payment that now rests solely with the reactor companies. This means that the owning company in each group that is best suited to bear the liability for payment
Carnivore-specific SINEs (Can-SINEs): distribution, evolution, and genomic impact.

Science.gov (United States)

Walters-Conte, Kathryn B; Johnson, Diana L E; Allard, Marc W; Pecon-Slattery, Jill

2011-01-01

Short interspersed nuclear elements (SINEs) are a type of class 1 transposable element (retrotransposon) with features that allow investigators to resolve evolutionary relationships between populations and species while providing insight into genome composition and function. Characterization of a Carnivora-specific SINE family, Can-SINEs, has, has aided comparative genomic studies by providing rare genomic changes, and neutral sequence variants often needed to resolve difficult evolutionary questions. In addition, Can-SINEs constitute a significant source of functional diversity with Carnivora. Publication of the whole-genome sequence of domestic dog, domestic cat, and giant panda serves as a valuable resource in comparative genomic inferences gleaned from Can-SINEs. In anticipation of forthcoming studies bolstered by new genomic data, this review describes the discovery and characterization of Can-SINE motifs as well as describes composition, distribution, and effect on genome function. As the contribution of noncoding sequences to genomic diversity becomes more apparent, SINEs and other transposable elements will play an increasingly large role in mammalian comparative genomics.
Public response to the Diablo Canyon Nuclear Generating Station

Energy Technology Data Exchange (ETDEWEB)

Pijawka, K D [Arizona State Univ., Tempe (USA)

1982-08-01

We examine the nature of the public response to the Diablo Canyon Nuclear Generating Station located in San Luis Obispo, California, from the early 1960s to the present. Four distinct phases of public intervention were discerned, based on change in both plant-related issues and in the nature of the antinuclear constituencies in the region. The level of public concern varied both geographically and temporally and is related to the area's social structure, environmental predispositions, and distribution of plant-related economic benefits. External events, such as the prolonged debate over the risk assessment of the seismic hazard and the Three Mile Island accident were found to be important factors in explaining variation in public concern and political response.
Response tree evaluation: experimental assessment of an expert system for nuclear reactor operators

International Nuclear Information System (INIS)

Nelson, W.R.; Blackman, H.S.

1985-09-01

The United States Nuclear Regulatory Commission (USNRC) sponsored a project performed by EG and G Idaho, Inc., at the Idaho National Engineering Laboratory (INEL) to evaluate different display concepts for use in nuclear reactor control rooms. Included in this project was the evaluation of the response tree computer-based decision aid and its associated displays. The response tree evaluation task was deisgned to (1) assess the merit of the response tree decision aid and (2) develop a technical basis for recommendations, guidelines, and criteria for the design and evaluation of computerized decision aids for use in reactor control rooms. Two major experiments have been conducted to evaluate the response tree system. This report emphasizes the conduct and results of the second experiment. An enhanced version of the response tree system, known as the automated response tree system, was used in a controlled experiment using trained reactor operators as test subjects. This report discusses the automated response tree system, the design of the evaluation experiment, and the quantitative results of the experiment. The results of the experiment are compared to the results of the previous experiment to provide an integrated perspective of the response tree evaluation project. In addition, a subjective assessment of the results addresses the implications for the use of advanced, ''intelligent'' decision aids in the reactor control room
Transcriptomics and molecular evolutionary rate analysis of the bladderwort (Utricularia, a carnivorous plant with a minimal genome

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Herrera-Estrella Alfredo

2011-06-01

digestion that were previously thought to be encoded by bacteria. Supporting physiological data, global gene expression analysis shows that traps significantly over-express genes involved in respiration and that phosphate uptake might occur mainly in traps, whereas nitrogen uptake could in part take place in vegetative parts. Expression of DNA repair and ROS detoxification enzymes may be indicative of a response to increased respiration. Finally, evidence from the bladderwort transcriptome, direct measurement of ROS in situ, and cross-species comparisons of organellar genomes and multiple nuclear genes supports the hypothesis that increased nucleotide substitution rates throughout the plant may be due to the mutagenic action of amplified ROS production.
Comparative scaffolding and gap filling of ancient bacterial genomes applied to two ancient Yersinia pestis genomes

Science.gov (United States)

Doerr, Daniel; Chauve, Cedric

2017-01-01

Yersinia pestis is the causative agent of the bubonic plague, a disease responsible for several dramatic historical pandemics. Progress in ancient DNA (aDNA) sequencing rendered possible the sequencing of whole genomes of important human pathogens, including the ancient Y. pestis strains responsible for outbreaks of the bubonic plague in London in the 14th century and in Marseille in the 18th century, among others. However, aDNA sequencing data are still characterized by short reads and non-uniform coverage, so assembling ancient pathogen genomes remains challenging and often prevents a detailed study of genome rearrangements. It has recently been shown that comparative scaffolding approaches can improve the assembly of ancient Y. pestis genomes at a chromosome level. In the present work, we address the last step of genome assembly, the gap-filling stage. We describe an optimization-based method AGapEs (ancestral gap estimation) to fill in inter-contig gaps using a combination of a template obtained from related extant genomes and aDNA reads. We show how this approach can be used to refine comparative scaffolding by selecting contig adjacencies supported by a mix of unassembled aDNA reads and comparative signal. We applied our method to two Y. pestis data sets from the London and Marseilles outbreaks, for which we obtained highly improved genome assemblies for both genomes, comprised of, respectively, five and six scaffolds with 95 % of the assemblies supported by ancient reads. We analysed the genome evolution between both ancient genomes in terms of genome rearrangements, and observed a high level of synteny conservation between these strains. PMID:29114402
Coordinated rates of evolution between interacting plastid and nuclear genes in Geraniaceae.

Science.gov (United States)

Zhang, Jin; Ruhlman, Tracey A; Sabir, Jamal; Blazier, J Chris; Jansen, Robert K

2015-03-01

Although gene coevolution has been widely observed within individuals and between different organisms, rarely has this phenomenon been investigated within a phylogenetic framework. The Geraniaceae is an attractive system in which to study plastid-nuclear genome coevolution due to the highly elevated evolutionary rates in plastid genomes. In plants, the plastid-encoded RNA polymerase (PEP) is a protein complex composed of subunits encoded by both plastid (rpoA, rpoB, rpoC1, and rpoC2) and nuclear genes (sig1-6). We used transcriptome and genomic data for 27 species of Geraniales in a systematic evaluation of coevolution between genes encoding subunits of the PEP holoenzyme. We detected strong correlations of dN (nonsynonymous substitutions) but not dS (synonymous substitutions) within rpoB/sig1 and rpoC2/sig2, but not for other plastid/nuclear gene pairs, and identified the correlation of dN/dS ratio between rpoB/C1/C2 and sig1/5/6, rpoC1/C2 and sig2, and rpoB/C2 and sig3 genes. Correlated rates between interacting plastid and nuclear sequences across the Geraniales could result from plastid-nuclear genome coevolution. Analyses of coevolved amino acid positions suggest that structurally mediated coevolution is not the major driver of plastid-nuclear coevolution. The detection of strong correlation of evolutionary rates between SIG and RNAP genes suggests a plausible explanation for plastome-genome incompatibility in Geraniaceae. © 2015 American Society of Plant Biologists. All rights reserved.
ATM signaling and genomic stability in response to DNA damage

International Nuclear Information System (INIS)

Lavin, Martin F.; Birrell, Geoff; Chen, Philip; Kozlov, Sergei; Scott, Shaun; Gueven, Nuri

2005-01-01

DNA double strand breaks represent the most threatening lesion to the integrity of the genome in cells exposed to ionizing radiation and radiomimetic chemicals. Those breaks are recognized, signaled to cell cycle checkpoints and repaired by protein complexes. The product of the gene (ATM) mutated in the human genetic disorder ataxia-telangiectasia (A-T) plays a central role in the recognition and signaling of DNA damage. ATM is one of an ever growing number of proteins which when mutated compromise the stability of the genome and predispose to tumour development. Mechanisms for recognising double strand breaks in DNA, maintaining genome stability and minimizing risk of cancer are discussed
Genomes and geography: genomic insights into the evolution and phylogeography of the genus Schistosoma

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Ironside Joe E

2011-07-01

Full Text Available Abstract Blood flukes within the genus Schistosoma still remain a major cause of disease in the tropics and subtropics and the study of their evolution has been an area of major debate and research. With the advent of modern molecular and genomic approaches deeper insights have been attained not only into the divergence and speciation of these worms, but also into the historic movement of these parasites from Asia into Africa, via migration and dispersal of definitive and snail intermediate hosts. This movement was subsequently followed by a radiation of Schistosoma species giving rise to the S. mansoni and S. haematobium groups, as well as the S. indicum group that reinvaded Asia. Each of these major evolutionary events has been marked by distinct changes in genomic structure evident in differences in mitochondrial gene order and nuclear chromosomal architecture between the species associated with Asia and Africa. Data from DNA sequencing, comparative molecular genomics and karyotyping are indicative of major constitutional genomic events which would have become fixed in the ancestral populations of these worms. Here we examine how modern genomic techniques may give a more in depth understanding of the evolution of schistosomes and highlight the complexity of speciation and divergence in this group.
The Population Genomics of Sunflowers and Genomic Determinants of Protein Evolution Revealed by RNAseq

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Loren H. Rieseberg

2012-10-01

Full Text Available Few studies have investigated the causes of evolutionary rate variation among plant nuclear genes, especially in recently diverged species still capable of hybridizing in the wild. The recent advent of Next Generation Sequencing (NGS permits investigation of genome wide rates of protein evolution and the role of selection in generating and maintaining divergence. Here, we use individual whole-transcriptome sequencing (RNAseq to refine our understanding of the population genomics of wild species of sunflowers (Helianthus spp. and the factors that affect rates of protein evolution. We aligned 35 GB of transcriptome sequencing data and identified 433,257 polymorphic sites (SNPs in a reference transcriptome comprising 16,312 genes. Using SNP markers, we identified strong population clustering largely corresponding to the three species analyzed here (Helianthus annuus, H. petiolaris, H. debilis, with one distinct early generation hybrid. Then, we calculated the proportions of adaptive substitution fixed by selection (alpha and identified gene ontology categories with elevated values of alpha. The “response to biotic stimulus” category had the highest mean alpha across the three interspecific comparisons, implying that natural selection imposed by other organisms plays an important role in driving protein evolution in wild sunflowers. Finally, we examined the relationship between protein evolution (dN/dS ratio and several genomic factors predicted to co-vary with protein evolution (gene expression level, divergence and specificity, genetic divergence [FST], and nucleotide diversity pi. We find that variation in rates of protein divergence was correlated with gene expression level and specificity, consistent with results from a broad range of taxa and timescales. This would in turn imply that these factors govern protein evolution both at a microevolutionary and macroevolutionary timescale. Our results contribute to a general understanding of the
Transposable element distribution, abundance and role in genome size variation in the genus Oryza.

Science.gov (United States)

Zuccolo, Andrea; Sebastian, Aswathy; Talag, Jayson; Yu, Yeisoo; Kim, HyeRan; Collura, Kristi; Kudrna, Dave; Wing, Rod A

2007-08-29

The genus Oryza is composed of 10 distinct genome types, 6 diploid and 4 polyploid, and includes the world's most important food crop - rice (Oryza sativa [AA]). Genome size variation in the Oryza is more than 3-fold and ranges from 357 Mbp in Oryza glaberrima [AA] to 1283 Mbp in the polyploid Oryza ridleyi [HHJJ]. Because repetitive elements are known to play a significant role in genome size variation, we constructed random sheared small insert genomic libraries from 12 representative Oryza species and conducted a comprehensive study of the repetitive element composition, distribution and phylogeny in this genus. Particular attention was paid to the role played by the most important classes of transposable elements (Long Terminal Repeats Retrotransposons, Long interspersed Nuclear Elements, helitrons, DNA transposable elements) in shaping these genomes and in their contributing to genome size variation. We identified the elements primarily responsible for the most strikingly genome size variation in Oryza. We demonstrated how Long Terminal Repeat retrotransposons belonging to the same families have proliferated to very different extents in various species. We also showed that the pool of Long Terminal Repeat Retrotransposons is substantially conserved and ubiquitous throughout the Oryza and so its origin is ancient and its existence predates the speciation events that originated the genus. Finally we described the peculiar behavior of repeats in the species Oryza coarctata [HHKK] whose placement in the Oryza genus is controversial. Long Terminal Repeat retrotransposons are the major component of the Oryza genomes analyzed and, along with polyploidization, are the most important contributors to the genome size variation across the Oryza genus. Two families of Ty3-gypsy elements (RIRE2 and Atlantys) account for a significant portion of the genome size variations present in the Oryza genus.
Genome-Wide Characterization and Expression Profiling of the AUXIN RESPONSE FACTOR (ARF) Gene Family in Eucalyptus grandis

Science.gov (United States)

Yu, Hong; Soler, Marçal; Mila, Isabelle; San Clemente, Hélène; Savelli, Bruno; Dunand, Christophe; Paiva, Jorge A. P.; Myburg, Alexander A.; Bouzayen, Mondher; Grima-Pettenati, Jacqueline; Cassan-Wang, Hua

2014-01-01

Auxin is a central hormone involved in a wide range of developmental processes including the specification of vascular stem cells. Auxin Response Factors (ARF) are important actors of the auxin signalling pathway, regulating the transcription of auxin-responsive genes through direct binding to their promoters. The recent availability of the Eucalyptus grandis genome sequence allowed us to examine the characteristics and evolutionary history of this gene family in a woody plant of high economic importance. With 17 members, the E. grandis ARF gene family is slightly contracted, as compared to those of most angiosperms studied hitherto, lacking traces of duplication events. In silico analysis of alternative transcripts and gene truncation suggested that these two mechanisms were preeminent in shaping the functional diversity of the ARF family in Eucalyptus. Comparative phylogenetic analyses with genomes of other taxonomic lineages revealed the presence of a new ARF clade found preferentially in woody and/or perennial plants. High-throughput expression profiling among different organs and tissues and in response to environmental cues highlighted genes expressed in vascular cambium and/or developing xylem, responding dynamically to various environmental stimuli. Finally, this study allowed identification of three ARF candidates potentially involved in the auxin-regulated transcriptional program underlying wood formation. PMID:25269088
Genome-wide characterization and expression profiling of the AUXIN RESPONSE FACTOR (ARF gene family in Eucalyptus grandis.

Directory of Open Access Journals (Sweden)

Hong Yu

Full Text Available Auxin is a central hormone involved in a wide range of developmental processes including the specification of vascular stem cells. Auxin Response Factors (ARF are important actors of the auxin signalling pathway, regulating the transcription of auxin-responsive genes through direct binding to their promoters. The recent availability of the Eucalyptus grandis genome sequence allowed us to examine the characteristics and evolutionary history of this gene family in a woody plant of high economic importance. With 17 members, the E. grandis ARF gene family is slightly contracted, as compared to those of most angiosperms studied hitherto, lacking traces of duplication events. In silico analysis of alternative transcripts and gene truncation suggested that these two mechanisms were preeminent in shaping the functional diversity of the ARF family in Eucalyptus. Comparative phylogenetic analyses with genomes of other taxonomic lineages revealed the presence of a new ARF clade found preferentially in woody and/or perennial plants. High-throughput expression profiling among different organs and tissues and in response to environmental cues highlighted genes expressed in vascular cambium and/or developing xylem, responding dynamically to various environmental stimuli. Finally, this study allowed identification of three ARF candidates potentially involved in the auxin-regulated transcriptional program underlying wood formation.
Comparative genome analysis of Bacillus cereus group genomes withBacillus subtilis

Energy Technology Data Exchange (ETDEWEB)

Anderson, Iain; Sorokin, Alexei; Kapatral, Vinayak; Reznik, Gary; Bhattacharya, Anamitra; Mikhailova, Natalia; Burd, Henry; Joukov, Victor; Kaznadzey, Denis; Walunas, Theresa; D' Souza, Mark; Larsen, Niels; Pusch,Gordon; Liolios, Konstantinos; Grechkin, Yuri; Lapidus, Alla; Goltsman,Eugene; Chu, Lien; Fonstein, Michael; Ehrlich, S. Dusko; Overbeek, Ross; Kyrpides, Nikos; Ivanova, Natalia

2005-09-14

Genome features of the Bacillus cereus group genomes (representative strains of Bacillus cereus, Bacillus anthracis and Bacillus thuringiensis sub spp israelensis) were analyzed and compared with the Bacillus subtilis genome. A core set of 1,381 protein families among the four Bacillus genomes, with an additional set of 933 families common to the B. cereus group, was identified. Differences in signal transduction pathways, membrane transporters, cell surface structures, cell wall, and S-layer proteins suggesting differences in their phenotype were identified. The B. cereus group has signal transduction systems including a tyrosine kinase related to two-component system histidine kinases from B. subtilis. A model for regulation of the stress responsive sigma factor sigmaB in the B. cereus group different from the well studied regulation in B. subtilis has been proposed. Despite a high degree of chromosomal synteny among these genomes, significant differences in cell wall and spore coat proteins that contribute to the survival and adaptation in specific hosts has been identified.
TRAIP promotes DNA damage response during genome replication and is mutated in primordial dwarfism.

Science.gov (United States)

Harley, Margaret E; Murina, Olga; Leitch, Andrea; Higgs, Martin R; Bicknell, Louise S; Yigit, Gökhan; Blackford, Andrew N; Zlatanou, Anastasia; Mackenzie, Karen J; Reddy, Kaalak; Halachev, Mihail; McGlasson, Sarah; Reijns, Martin A M; Fluteau, Adeline; Martin, Carol-Anne; Sabbioneda, Simone; Elcioglu, Nursel H; Altmüller, Janine; Thiele, Holger; Greenhalgh, Lynn; Chessa, Luciana; Maghnie, Mohamad; Salim, Mahmoud; Bober, Michael B; Nürnberg, Peter; Jackson, Stephen P; Hurles, Matthew E; Wollnik, Bernd; Stewart, Grant S; Jackson, Andrew P

2016-01-01

DNA lesions encountered by replicative polymerases threaten genome stability and cell cycle progression. Here we report the identification of mutations in TRAIP, encoding an E3 RING ubiquitin ligase, in patients with microcephalic primordial dwarfism. We establish that TRAIP relocalizes to sites of DNA damage, where it is required for optimal phosphorylation of H2AX and RPA2 during S-phase in response to ultraviolet (UV) irradiation, as well as fork progression through UV-induced DNA lesions. TRAIP is necessary for efficient cell cycle progression and mutations in TRAIP therefore limit cellular proliferation, providing a potential mechanism for microcephaly and dwarfism phenotypes. Human genetics thus identifies TRAIP as a component of the DNA damage response to replication-blocking DNA lesions.
Genomic resources for a unique, low-virulence Babesia taxon from China

Directory of Open Access Journals (Sweden)

Guiquan Guan

2016-10-01

Full Text Available Abstract Background Babesiosis is a socioeconomically important tick-borne disease of animals (including humans caused by haemoprotozoan parasites. The severity of babesiosis relates to host and parasite factors, particularly virulence/pathogenicity. Although Babesia bovis is a particularly pathogenic species of cattle, there are species of Babesia of ruminants that have limited pathogenicity. For instance, the operational taxonomic unit Babesia sp. Xinjiang (abbreviated here as Bx of sheep from China is substantially less virulent/pathogenic than B. bovis is in cattle. Although the reason for this distinctiveness is presently unknown, it is possible that Bx has a reduced ability to adhere to cells or evade/suppress immune responses, which might relate to particular proteins, such as the variant erythrocyte surface antigens (VESAs. Results We sequenced and annotated the 8.4 Mb nuclear draft genome of Bx and compared it with those of B. bovis and B. bigemina by synteny analysis; we also investigated the genetic relationship of Bx with selected Babesia species and related apicomplexans for which genomic datasets are available, and explored the VESA complement in Bx. Conclusions The availability of the Bx genome now provides unique opportunities to elucidate aspects of the molecular biology, biochemistry and physiology of Bx, and to explore the reason(s for its limited virulence and/or apparent ability to evade immune attack by the host animal. Moreover, the present genomic resource and an in vitro culture system for Bx raises the prospect of establishing a functional genomic platform to explore essential genes as new intervention targets against babesiosis.
Genomic resources for a unique, low-virulence Babesia taxon from China.

Science.gov (United States)

Guan, Guiquan; Korhonen, Pasi K; Young, Neil D; Koehler, Anson V; Wang, Tao; Li, Youquan; Liu, Zhijie; Luo, Jianxun; Yin, Hong; Gasser, Robin B

2016-10-27

Babesiosis is a socioeconomically important tick-borne disease of animals (including humans) caused by haemoprotozoan parasites. The severity of babesiosis relates to host and parasite factors, particularly virulence/pathogenicity. Although Babesia bovis is a particularly pathogenic species of cattle, there are species of Babesia of ruminants that have limited pathogenicity. For instance, the operational taxonomic unit Babesia sp. Xinjiang (abbreviated here as Bx) of sheep from China is substantially less virulent/pathogenic than B. bovis is in cattle. Although the reason for this distinctiveness is presently unknown, it is possible that Bx has a reduced ability to adhere to cells or evade/suppress immune responses, which might relate to particular proteins, such as the variant erythrocyte surface antigens (VESAs). We sequenced and annotated the 8.4 Mb nuclear draft genome of Bx and compared it with those of B. bovis and B. bigemina by synteny analysis; we also investigated the genetic relationship of Bx with selected Babesia species and related apicomplexans for which genomic datasets are available, and explored the VESA complement in Bx. The availability of the Bx genome now provides unique opportunities to elucidate aspects of the molecular biology, biochemistry and physiology of Bx, and to explore the reason(s) for its limited virulence and/or apparent ability to evade immune attack by the host animal. Moreover, the present genomic resource and an in vitro culture system for Bx raises the prospect of establishing a functional genomic platform to explore essential genes as new intervention targets against babesiosis.
Single HIV-1 Imaging Reveals Progression of Infection through CA-Dependent Steps of Docking at the Nuclear Pore, Uncoating, and Nuclear Transport.

Science.gov (United States)

Francis, Ashwanth C; Melikyan, Gregory B

2018-04-11

The HIV-1 core consists of capsid proteins (CA) surrounding viral genomic RNA. After virus-cell fusion, the core enters the cytoplasm and the capsid shell is lost through uncoating. CA loss precedes nuclear import and HIV integration into the host genome, but the timing and location of uncoating remain unclear. By visualizing single HIV-1 infection, we find that CA is required for core docking at the nuclear envelope (NE), whereas early uncoating in the cytoplasm promotes proteasomal degradation of viral complexes. Only docked cores exhibiting accelerated loss of CA at the NE enter the nucleus. Interestingly, a CA mutation (N74D) altering virus engagement of host factors involved in nuclear transport does not alter the uncoating site at the NE but reduces the nuclear penetration depth. Thus, CA protects HIV-1 complexes from degradation, mediates docking at the nuclear pore before uncoating, and determines the depth of nuclear penetration en route to integration. Copyright © 2018 Elsevier Inc. All rights reserved.
Genome-wide Differences in DNA Methylation Changes in Two Contrasting Rice Genotypes in Response to Drought Conditions

Directory of Open Access Journals (Sweden)

Wensheng Wang

2016-11-01

Full Text Available Differences in drought stress tolerance within diverse rice genotypes have been attributed to genetic diversity and epigenetic alterations. DNA methylation is an important epigenetic modification that influences diverse biological processes, but its effects on rice drought stress tolerance are poorly understood. In this study, methylated DNA immunoprecipitation sequencing and an Affymetrix GeneChip rice genome array were used to profile the DNA methylation patterns and transcriptomes of the drought-tolerant introgression line DK151 and its drought-sensitive recurrent parent IR64 under drought and control conditions. The introgression of donor genomic DNA induced genome-wide DNA methylation changes in DK151 plants. A total of 1190 differentially methylated regions (DMRs were detected between the two genotypes under normal growth conditions, and the DMR-associated genes in DK151 plants were mainly related to stress response, programmed cell death, and nutrient reservoir activity, which are implicated to constitutive drought stress tolerance. A comparison of the DNA methylation changes in the two genotypes under drought conditions indicated that DK151 plants have a more stable methylome, with only 92 drought-induced DMRs, than IR64 plants with 506 DMRs. Gene ontology analyses of the DMR-associated genes in drought-stressed plants revealed that changes to the DNA methylation status of genotype-specific genes are associated with the epigenetic regulation of drought stress responses. Transcriptome analysis further helped to identify a set of 12 and 23 DMR-associated genes that were differentially expressed in DK151 and IR64, respectively, under drought stress compared with respective controls. Correlation analysis indicated that DNA methylation has various effects on gene expression, implying that it affects gene expression directly or indirectly through diverse regulatory pathways. Our results indicate that drought-induced alterations to DNA

DNA Checkpoint and Repair Factors Are Nuclear Sensors for Intracellular Organelle Stresses—Inflammations and Cancers Can Have High Genomic Risks

Directory of Open Access Journals (Sweden)

Huihong Zeng

2018-05-01

Full Text Available Under inflammatory conditions, inflammatory cells release reactive oxygen species (ROS and reactive nitrogen species (RNS which cause DNA damage. If not appropriately repaired, DNA damage leads to gene mutations and genomic instability. DNA damage checkpoint factors (DDCF and DNA damage repair factors (DDRF play a vital role in maintaining genomic integrity. However, how DDCFs and DDRFs are modulated under physiological and pathological conditions are not fully known. We took an experimental database analysis to determine the expression of 26 DNA DDCFs and 42 DNA DDRFs in 21 human and 20 mouse tissues in physiological/pathological conditions. We made the following significant findings: (1 Few DDCFs and DDRFs are ubiquitously expressed in tissues while many are differentially regulated.; (2 the expression of DDCFs and DDRFs are modulated not only in cancers but also in sterile inflammatory disorders and metabolic diseases; (3 tissue methylation status, pro-inflammatory cytokines, hypoxia regulating factors and tissue angiogenic potential can determine the expression of DDCFs and DDRFs; (4 intracellular organelles can transmit the stress signals to the nucleus, which may modulate the cell death by regulating the DDCF and DDRF expression. Our results shows that sterile inflammatory disorders and cancers increase genomic instability, therefore can be classified as pathologies with a high genomic risk. We also propose a new concept that as parts of cellular sensor cross-talking network, DNA checkpoint and repair factors serve as nuclear sensors for intracellular organelle stresses. Further, this work would lead to identification of novel therapeutic targets and new biomarkers for diagnosis and prognosis of metabolic diseases, inflammation, tissue damage and cancers.
Virus Type and Genomic Load in Acute Bronchiolitis: Severity and Treatment Response With Inhaled Adrenaline.

Science.gov (United States)

Skjerven, Håvard O; Megremis, Spyridon; Papadopoulos, Nikolaos G; Mowinckel, Petter; Carlsen, Kai-Håkon; Lødrup Carlsen, Karin C

2016-03-15

Acute bronchiolitis frequently causes infant hospitalization. Studies on different viruses or viral genomic load and disease severity or treatment effect have had conflicting results. We aimed to investigate whether the presence or concentration of individual or multiple viruses were associated with disease severity in acute bronchiolitis and to evaluate whether detected viruses modified the response to inhaled racemic adrenaline. Nasopharyngeal aspirates were collected from 363 infants with acute bronchiolitis in a randomized, controlled trial that compared inhaled racemic adrenaline versus saline. Virus genome was identified and quantified by polymerase chain reaction analyses. Severity was assessed on the basis of the length of stay and the use of supportive care. Respiratory syncytial virus (83%) and human rhinovirus (34%) were most commonly detected. Seven other viruses were present in 8%-15% of the patients. Two or more viruses (maximum, 7) were detected in 61% of the infants. Virus type or coinfection was not associated with disease severity. A high genomic load of respiratory syncytial virus was associated with a longer length of stay and with an increased frequency of oxygen and ventilatory support use. Treatment effect of inhaled adrenaline was not modified by virus type, load or coinfection. In infants hospitalized with acute bronchiolitis, disease severity was not associated with specific viruses or the total number of viruses detected. A high RSV genomic load was associated with more-severe disease. NCT00817466 and EudraCT 2009-012667-34. © The Author 2015. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail journals.permissions@oup.com.
Genome size estimation: a new methodology

Science.gov (United States)

Álvarez-Borrego, Josué; Gallardo-Escárate, Crisitian; Kober, Vitaly; López-Bonilla, Oscar

2007-03-01

Recently, within the cytogenetic analysis, the evolutionary relations implied in the content of nuclear DNA in plants and animals have received a great attention. The first detailed measurements of the nuclear DNA content were made in the early 40's, several years before Watson and Crick proposed the molecular structure of the DNA. In the following years Hewson Swift developed the concept of "C-value" in reference to the haploid phase of DNA in plants. Later Mirsky and Ris carried out the first systematic study of genomic size in animals, including representatives of the five super classes of vertebrates as well as of some invertebrates. From these preliminary results it became evident that the DNA content varies enormously between the species and that this variation does not bear relation to the intuitive notion from the complexity of the organism. Later, this observation was reaffirmed in the following years as the studies increased on genomic size, thus denominating to this characteristic of the organisms like the "Paradox of the C-value". Few years later along with the no-codification discovery of DNA the paradox was solved, nevertheless, numerous questions remain until nowadays unfinished, taking to denominate this type of studies like the "C-value enigma". In this study, we reported a new method for genome size estimation by quantification of fluorescence fading. We measured the fluorescence intensity each 1600 milliseconds in DAPI-stained nuclei. The estimation of the area under the graph (integral fading) during fading period was related with the genome size.
Genomic Copy Number Dictates a Gene-Independent Cell Response to CRISPR/Cas9 Targeting | Office of Cancer Genomics

Science.gov (United States)

The CRISPR/Cas9 system enables genome editing and somatic cell genetic screens in mammalian cells. We performed genome-scale loss-of-function screens in 33 cancer cell lines to identify genes essential for proliferation/survival and found a strong correlation between increased gene copy number and decreased cell viability after genome editing. Within regions of copy-number gain, CRISPR/Cas9 targeting of both expressed and unexpressed genes, as well as intergenic loci, led to significantly decreased cell proliferation through induction of a G2 cell-cycle arrest.
Genomic Evolution of the Ascomycete Yeasts

Energy Technology Data Exchange (ETDEWEB)

Riley, Robert; Haridas, Sajeet; Salamov, Asaf; Boundy-Mills, Kyria; Goker, Markus; Hittinger, Chris; Klenk, Hans-Peter; Lopes, Mariana; Meir-Kolthoff, Jan P.; Rokas, Antonis; Rosa, Carlos; Scheuner, Carmen; Soares, Marco; Stielow, Benjamin; Wisecaver, Jennifer H.; Wolfe, Ken; Blackwell, Meredith; Kurtzman, Cletus; Grigoriev, Igor; Jeffries, Thomas

2015-03-16

Yeasts are important for industrial and biotechnological processes and show remarkable metabolic and phylogenetic diversity despite morphological similarities. We have sequenced the genomes of 16 ascomycete yeasts of taxonomic and industrial importance including members of Saccharomycotina and Taphrinomycotina. Phylogenetic analysis of these and previously published yeast genomes helped resolve the placement of species including Saitoella complicata, Babjeviella inositovora, Hyphopichia burtonii, and Metschnikowia bicuspidata. Moreover, we find that alternative nuclear codon usage, where CUG encodes serine instead of leucine, are monophyletic within the Saccharomycotina. Most of the yeasts have compact genomes with a large fraction of single exon genes, and a tendency towards more introns in early-diverging species. Analysis of enzyme phylogeny gives insights into the evolution of metabolic capabilities such as methanol utilization and assimilation of alternative carbon sources.
Resynthesized Brassica juncea lines with novel organellar genome ...

Indian Academy of Sciences (India)

To obtain shoot cultures, shoot apices were ... and culture, plant regeneration and hardening etc. are as described ... Hence two other media were tested for plant regeneration. .... genomes exert a strong influence on reorganization of nuclear.
Political pressure on nuclear - responsibility or business?

International Nuclear Information System (INIS)

Petrech, Rastislav; Holy, Robert

2001-01-01

Environmental Impact Assessment study prior to bringing the plant in a commercial operation - will change nothing. I believe that the outcomes will reinforce the arguments in favour of construction and commissioning of new sources of clean, safe, and reliable generation of electricity. Is it just diverting the public's attention from other problems or an attempt to gain a political capital? Is the political pressure on nuclear a real responsibility or a sheer business? Most politicians have no idea about the nuclear power, and if they do, it is only very misty one. It is necessary to invite them to visit plants, discuss with them and give them clear arguments. A clear statement of an energy policy and relying on the safe and economic advantageous nuclear power can also attract a large portion of electors in the future. We should try so that energy policy in post-communist countries got into election programmes of each political party, since the energy mix policy cannot be tailored only for one election period of a government, but for a time of 20 to 30 years in advance
Scale model study of the seismic response of a nuclear reactor core

International Nuclear Information System (INIS)

Dove, R.C.; Dunwoody, W.E.; Rhorer, R.L.

1983-01-01

The use of scale models to study the dynamics of a system of graphite core blocks used in certain nuclear reactor designs is described. Scaling laws, material selecton, model instrumentation to measure collision forces, and the response of several models to simulated seismic excitation are covered. The effects of Coulomb friction between the blocks and the clearance gaps between the blocks on the system response to seismic excitation are emphasized
Environmental Response and Genomic Regions Correlated with Rice Root Growth and Yield under Drought in the OryzaSNP Panel across Multiple Study Systems.

Directory of Open Access Journals (Sweden)

Len J Wade

Full Text Available The rapid progress in rice genotyping must be matched by advances in phenotyping. A better understanding of genetic variation in rice for drought response, root traits, and practical methods for studying them are needed. In this study, the OryzaSNP set (20 diverse genotypes that have been genotyped for SNP markers was phenotyped in a range of field and container studies to study the diversity of rice root growth and response to drought. Of the root traits measured across more than 20 root experiments, root dry weight showed the most stable genotypic performance across studies. The environment (E component had the strongest effect on yield and root traits. We identified genomic regions correlated with root dry weight, percent deep roots, maximum root depth, and grain yield based on a correlation analysis with the phenotypes and aus, indica, or japonica introgression regions using the SNP data. Two genomic regions were identified as hot spots in which root traits and grain yield were co-located; on chromosome 1 (39.7-40.7 Mb and on chromosome 8 (20.3-21.9 Mb. Across experiments, the soil type/ growth medium showed more correlations with plant growth than the container dimensions. Although the correlations among studies and genetic co-location of root traits from a range of study systems points to their potential utility to represent responses in field studies, the best correlations were observed when the two setups had some similar properties. Due to the co-location of the identified genomic regions (from introgression block analysis with QTL for a number of previously reported root and drought traits, these regions are good candidates for detailed characterization to contribute to understanding rice improvement for response to drought. This study also highlights the utility of characterizing a small set of 20 genotypes for root growth, drought response, and related genomic regions.
Carcinogen susceptibility is regulated by genome architecture and predicts cancer mutagenesis.

Science.gov (United States)

García-Nieto, Pablo E; Schwartz, Erin K; King, Devin A; Paulsen, Jonas; Collas, Philippe; Herrera, Rafael E; Morrison, Ashby J

2017-10-02

The development of many sporadic cancers is directly initiated by carcinogen exposure. Carcinogens induce malignancies by creating DNA lesions (i.e., adducts) that can result in mutations if left unrepaired. Despite this knowledge, there has been remarkably little investigation into the regulation of susceptibility to acquire DNA lesions. In this study, we present the first quantitative human genome-wide map of DNA lesions induced by ultraviolet (UV) radiation, the ubiquitous carcinogen in sunlight that causes skin cancer. Remarkably, the pattern of carcinogen susceptibility across the genome of primary cells significantly reflects mutation frequency in malignant melanoma. Surprisingly, DNase-accessible euchromatin is protected from UV, while lamina-associated heterochromatin at the nuclear periphery is vulnerable. Many cancer driver genes have an intrinsic increase in carcinogen susceptibility, including the BRAF oncogene that has the highest mutation frequency in melanoma. These findings provide a genome-wide snapshot of DNA injuries at the earliest stage of carcinogenesis. Furthermore, they identify carcinogen susceptibility as an origin of genome instability that is regulated by nuclear architecture and mirrors mutagenesis in cancer. © 2017 The Authors.
Fishing Fish Stem Cells and Nuclear Transplants

OpenAIRE

Hong, Yunhan

2011-01-01

Fish has been the subject of various research fields, ranging from ecology, evolution, physiology and toxicology to aquaculture. In the past decades fish has attracted considerable attention for functional genomics, cancer biology and developmental genetics, in particular nuclear transfer for understanding of cytoplasmic-nuclear relationship. This special issue reports on recent progress made in fish stem cells and nuclear transfer.
Floor Response Spectra of Nuclear Containment Building with Soil-Structure Interaction

Energy Technology Data Exchange (ETDEWEB)

Seo, Choon Gyo; Ryu, Jeong Soo [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

2008-10-15

This paper presents a seismic analysis technique for a 3D soil-structure interaction(SSI) system in frequency domain, based on the finite element formulation incorporating frequency-dependent dynamic infinite elements for the far field soil region. Earthquake input motions are regarded as traveling SV-wave which is vertically incident from a far-field soil region. In which, the equivalent earthquake forces in the frequency domain are calculated using the exterior rigid boundary method and the free field response analysis. For the application, floor response spectra analyses for nuclear containment building on a soil medium is carried out, the obtained results are compared with the free field response by other solution.
Phylogenetic relationships of rollers (Coraciidae) based on complete mitochondrial genomes and fifteen nuclear genes.

Science.gov (United States)

Johansson, Ulf S; Irestedt, Martin; Qu, Yanhua; Ericson, Per G P

2018-04-06

The rollers (Coraciidae) constitute a relative small avian family with ca. 12 species distributed in Africa, western and southern Eurasia, and eastern Australia. In this study we examine the phylogenetic relationships of all species currently recognized in the family, including two taxa whose taxonomic status is currently contested. By using shotgun sequencing on degraded DNA from museum study skins we have been able to recover complete mitochondrial genomes as well as 15 nuclear genes for in total 16 taxa. The gene sequences were analyzed both concatenated in a maximum likelihood framework as well in a species tree approach using MP-EST. The different analytical approaches yield similar, highly supported trees and support the current division of the rollers into two genera, Coracias and Eurystomus. The only conflict relates to the placement of the Blue-bellied Roller (C. cyanogaster), where the mitochondrial, and the concatenated nuclear and mitochondrial data set, place this taxon as sister to the other Coracias species, whereas nuclear data and the species tree analysis place it as the sister taxon of C. naevia and C. spatulatus. All analyses place the Eurasian roller (C. garrulus) with the two African species, Abyssinian Roller (C. abyssinica) and Liliac-breasted Roller (C. caudatus), and place this clade as the sister group to the Asian Coracias rollers. In addition, our results support a sister group relationship between the morphologically rather dissimilar Purple Roller (C. naevia) and Racquet-tailed Roller (C. spatulatus) and also support the division of Eurystomus in an African and an Asian clade. However, within the Asian clade the Azure Roller (E. azureus) from Halmahera appears to be nested within the Dollarbird (E. orientalis), indicating that that this taxon is a morphological divergent, but a rather recent offshoot, of the widespread Dollarbird. Similarly, the Purple-winged Roller (C. temminickii) from Sulawesi group together with C. benghalensis
Sirtuin 7 promotes cellular survival following genomic stress by attenuation of DNA damage, SAPK activation and p53 response

Energy Technology Data Exchange (ETDEWEB)

Kiran, Shashi; Oddi, Vineesha [Laboratory of Cancer Biology, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, 500001 (India); Ramakrishna, Gayatri, E-mail: gayatrirama1@gmail.com [Laboratory of Cancer Biology, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, 500001 (India); Laboratory of Cancer Cell Biology, Department of Research, Institute of Liver and Biliary Sciences, Delhi 110070 (India)

2015-02-01

Maintaining the genomic integrity is a constant challenge in proliferating cells. Amongst various proteins involved in this process, Sirtuins play a key role in DNA damage repair mechanisms in yeast as well as mammals. In the present work we report the role of one of the least explored Sirtuin viz., SIRT7, under conditions of genomic stress when treated with doxorubicin. Knockdown of SIRT7 sensitized osteosarcoma (U2OS) cells to DNA damage induced cell death by doxorubicin. SIRT7 overexpression in NIH3T3 delayed cell cycle progression by causing delay in G1 to S transition. SIRT7 overexpressing cells when treated with low dose of doxorubicin (0.25 µM) showed delayed onset of senescence, lesser accumulation of DNA damage marker γH2AX and lowered levels of growth arrest markers viz., p53 and p21 when compared to doxorubicin treated control GFP expressing cells. Resistance to DNA damage following SIRT7 overexpression was also evident by EdU incorporation studies where cellular growth arrest was significantly delayed. When treated with higher dose of doxorubicin (>1 µM), SIRT7 conferred resistance to apoptosis by attenuating stress activated kinases (SAPK viz., p38 and JNK) and p53 response thereby shifting the cellular fate towards senescence. Interestingly, relocalization of SIRT7 from nucleolus to nucleoplasm together with its co-localization with SAPK was an important feature associated with DNA damage. SIRT7 mediated resistance to doxorubicin induced apoptosis and senescence was lost when p53 level was restored by nutlin treatment. Overall, we propose SIRT7 attenuates DNA damage, SAPK activation and p53 response thereby promoting cellular survival under conditions of genomic stress. - Highlights: • Knockdown of SIRT7 sensitized cells to DNA damage induced apoptosis. • SIRT7 delayed onset of premature senescence by attenuating DNA damage response. • Overexpression of SIRT7 delayed cell cycle progression by delaying G1/S transition. • Upon DNA damage SIRT
Genomics technologies to study structural variations in the grapevine genome

Directory of Open Access Journals (Sweden)

Cardone Maria Francesca

2016-01-01

Full Text Available Grapevine is one of the most important crop plants in the world. Recently there was great expansion of genomics resources about grapevine genome, thus providing increasing efforts for molecular breeding. Current cultivars display a great level of inter-specific differentiation that needs to be investigated to reach a comprehensive understanding of the genetic basis of phenotypic differences, and to find responsible genes selected by cross breeding programs. While there have been significant advances in resolving the pattern and nature of single nucleotide polymorphisms (SNPs on plant genomes, few data are available on copy number variation (CNV. Furthermore association between structural variations and phenotypes has been described in only a few cases. We combined high throughput biotechnologies and bioinformatics tools, to reveal the first inter-varietal atlas of structural variation (SV for the grapevine genome. We sequenced and compared four table grape cultivars with the Pinot noir inbred line PN40024 genome as the reference. We detected roughly 8% of the grapevine genome affected by genomic variations. Taken into account phenotypic differences existing among the studied varieties we performed comparison of SVs among them and the reference and next we performed an in-depth analysis of gene content of polymorphic regions. This allowed us to identify genes showing differences in copy number as putative functional candidates for important traits in grapevine cultivation.
Radiological and nuclear emergency preparedness and response. How well are we prepared?

International Nuclear Information System (INIS)

Geick, Gunther H.G.; Herrmann, Andre R.; Koch, Doris; Meisenberg, Oliver; Rauber, Dominique; Stuerm, Rolf P.; Weiss, Wolfgang; Miska, Horst; Schoenhacker, Stefan

2011-01-01

The contributions to this topic are dealing, in a broad overview, with important aspects of Nuclear Emergency Preparedness and Response, like the influence of the new ICRP recommendations number 103 and number 109 on emergency preparedness and on planning for response, possible problems in installing and operating emergency care centres, experience from exercises as well as the training of response personnel in Austria and Germany. Finally, measures in emergency preparedness with regard to a dirty bomb attack are reported by means of an INEX-4-exercise in Switzerland. (orig.)
The Role of the International Atomic Energy Agency in a Response to Nuclear and Radiological Incidents and Emergencies

Energy Technology Data Exchange (ETDEWEB)

Buglova, E.; Baciu, F., E-mail: E.Buglova@iaea.org [International Atomic Energy Agency (IAEA), Department of Nuclear Safety and Security, Wagramer Strasse 5, P.O. Box 100, 1400 Vienna (Austria)

2014-10-15

Full text: The role of the International Atomic Energy Agency (IAEA) in a response to nuclear and radiological incidents and emergencies has been defined and further expanded through the IAEA Statute, the Convention on Early Notification of a Nuclear Accident, the Convention on Assistance in the Case of a Nuclear Accident or Radiological Emergency, the Convention on Physical Protection of Nuclear Material, IAEA safety standards, relevant decisions by Policy Making Organs of the IAEA, inter-agency agreements and other documents such as the IAEA Action Plan on Nuclear Safety. The IAEA Secretariat fulfils its roles through the Agency's Incident and Emergency System (IES) and the Incident and Emergency Centre (IEC). The IEC is the global focal point for international preparedness and response to nuclear and radiological safety or security related incidents, emergencies, threats or events of media interest and for coordination of International assistance. During a response the IEC performs and facilitates for Member States many specific functions which include: prompt notification; official information exchange; assessment of potential consequences; prognosis of emergency progression; provision, facilitation and coordination of International assistance; provision of timely, accurate and easily understandable public information; coordination of inter-agency response at the International level. Through officially designated contact points of Member States the IEC is able to communicate at any time with national authorities to ensure the prompt and successful sharing of information and resources. The IEC routinely performs internal exercising of all aspects of the IAEA response and in cooperation with Member States, the IAEA organizes and facilitates the conduct of large scale international exercises to practice cooperation and coordination. This presentation outlines in detail the specific functions of the IAEA IEC during a response. (author)
RadGenomics project

Energy Technology Data Exchange (ETDEWEB)

Iwakawa, Mayumi; Imai, Takashi; Harada, Yoshinobu [National Inst. of Radiological Sciences, Chiba (Japan). Frontier Research Center] [and others

2002-06-01

Human health is determined by a complex interplay of factors, predominantly between genetic susceptibility, environmental conditions and aging. The ultimate aim of the RadGenomics (Radiation Genomics) project is to understand the implications of heterogeneity in responses to ionizing radiation arising from genetic variation between individuals in the human population. The rapid progression of the human genome sequencing and the recent development of new technologies in molecular genetics are providing us with new opportunities to understand the genetic basis of individual differences in susceptibility to natural and/or artificial environmental factors, including radiation exposure. The RadGenomics project will inevitably lead to improved protocols for personalized radiotherapy and reductions in the potential side effects of such treatment. The project will contribute to future research into the molecular mechanisms of radiation sensitivity in humans and will stimulate the development of new high-throughput technologies for a broader application of biological and medical sciences. The staff members are specialists in a variety of fields, including genome science, radiation biology, medical science, molecular biology, and informatics, and have joined the RadGenomics project from various universities, companies, and research institutes. The project started in April 2001. (author)
RadGenomics project

International Nuclear Information System (INIS)

Iwakawa, Mayumi; Imai, Takashi; Harada, Yoshinobu

2002-01-01

Human health is determined by a complex interplay of factors, predominantly between genetic susceptibility, environmental conditions and aging. The ultimate aim of the RadGenomics (Radiation Genomics) project is to understand the implications of heterogeneity in responses to ionizing radiation arising from genetic variation between individuals in the human population. The rapid progression of the human genome sequencing and the recent development of new technologies in molecular genetics are providing us with new opportunities to understand the genetic basis of individual differences in susceptibility to natural and/or artificial environmental factors, including radiation exposure. The RadGenomics project will inevitably lead to improved protocols for personalized radiotherapy and reductions in the potential side effects of such treatment. The project will contribute to future research into the molecular mechanisms of radiation sensitivity in humans and will stimulate the development of new high-throughput technologies for a broader application of biological and medical sciences. The staff members are specialists in a variety of fields, including genome science, radiation biology, medical science, molecular biology, and informatics, and have joined the RadGenomics project from various universities, companies, and research institutes. The project started in April 2001. (author)
Comparative analysis of mitochondrial genomes between the hau cytoplasmic male sterility (CMS) line and its iso-nuclear maintainer line in Brassica juncea to reveal the origin of the CMS-associated gene orf288.

Science.gov (United States)

Heng, Shuangping; Wei, Chao; Jing, Bing; Wan, Zhengjie; Wen, Jing; Yi, Bin; Ma, Chaozhi; Tu, Jinxing; Fu, Tingdong; Shen, Jinxiong

2014-04-30

Cytoplasmic male sterility (CMS) is not only important for exploiting heterosis in crop plants, but also as a model for investigating nuclear-cytoplasmic interaction. CMS may be caused by mutations, rearrangement or recombination in the mitochondrial genome. Understanding the mitochondrial genome is often the first and key step in unraveling the molecular and genetic basis of CMS in plants. Comparative analysis of the mitochondrial genome of the hau CMS line and its maintainer line in B. juneca (Brassica juncea) may help show the origin of the CMS-associated gene orf288. Through next-generation sequencing, the B. juncea hau CMS mitochondrial genome was assembled into a single, circular-mapping molecule that is 247,903 bp in size and 45.08% in GC content. In addition to the CMS associated gene orf288, the genome contains 35 protein-encoding genes, 3 rRNAs, 25 tRNA genes and 29 ORFs of unknown function. The mitochondrial genome sizes of the maintainer line and another normal type line "J163-4" are both 219,863 bp and with GC content at 45.23%. The maintainer line has 36 genes with protein products, 3 rRNAs, 22 tRNA genes and 31 unidentified ORFs. Comparative analysis the mitochondrial genomes of the hau CMS line and its maintainer line allowed us to develop specific markers to separate the two lines at the seedling stage. We also confirmed that different mitotypes coexist substoichiometrically in hau CMS lines and its maintainer lines in B. juncea. The number of repeats larger than 100 bp in the hau CMS line (16 repeats) are nearly twice of those found in the maintainer line (9 repeats). Phylogenetic analysis of the CMS-associated gene orf288 and four other homologous sequences in Brassicaceae show that orf288 was clearly different from orf263 in Brassica tournefortii despite of strong similarity. The hau CMS mitochondrial genome was highly rearranged when compared with its iso-nuclear maintainer line mitochondrial genome. This study may be useful for studying the

Error-free versus mutagenic processing of genomic uracil--relevance to cancer.

Science.gov (United States)

Krokan, Hans E; Sætrom, Pål; Aas, Per Arne; Pettersen, Henrik Sahlin; Kavli, Bodil; Slupphaug, Geir

2014-07-01

Genomic uracil is normally processed essentially error-free by base excision repair (BER), with mismatch repair (MMR) as an apparent backup for U:G mismatches. Nuclear uracil-DNA glycosylase UNG2 is the major enzyme initiating BER of uracil of U:A pairs as well as U:G mismatches. Deficiency in UNG2 results in several-fold increases in genomic uracil in mammalian cells. Thus, the alternative uracil-removing glycosylases, SMUG1, TDG and MBD4 cannot efficiently complement UNG2-deficiency. A major function of SMUG1 is probably to remove 5-hydroxymethyluracil from DNA with general back-up for UNG2 as a minor function. TDG and MBD4 remove deamination products U or T mismatched to G in CpG/mCpG contexts, but may have equally or more important functions in development, epigenetics and gene regulation. Genomic uracil was previously thought to arise only from spontaneous cytosine deamination and incorporation of dUMP, generating U:G mismatches and U:A pairs, respectively. However, the identification of activation-induced cytidine deaminase (AID) and other APOBEC family members as DNA-cytosine deaminases has spurred renewed interest in the processing of genomic uracil. Importantly, AID triggers the adaptive immune response involving error-prone processing of U:G mismatches, but also contributes to B-cell lymphomagenesis. Furthermore, mutational signatures in a substantial fraction of other human cancers are consistent with APOBEC-induced mutagenesis, with U:G mismatches as prime suspects. Mutations can be caused by replicative polymerases copying uracil in U:G mismatches, or by translesion polymerases that insert incorrect bases opposite abasic sites after uracil-removal. In addition, kataegis, localized hypermutations in one strand in the vicinity of genomic rearrangements, requires APOBEC protein, UNG2 and translesion polymerase REV1. What mechanisms govern error-free versus error prone processing of uracil in DNA remains unclear. In conclusion, genomic uracil is an
Nitric oxide coordinates metabolism, growth, and development via the nuclear receptor E75

OpenAIRE

Cáceres, Lucía; Necakov, Aleksandar S.; Schwartz, Carol; Kimber, Sandra; Roberts, Ian J.H.; Krause, Henry M.

2011-01-01

Nitric oxide gas acts as a short-range signaling molecule in a vast array of important physiological processes, many of which include major changes in gene expression. How these genomic responses are induced, however, is poorly understood. Here, using genetic and chemical manipulations, we show that nitric oxide is produced in the Drosophila prothoracic gland, where it acts via the nuclear receptor ecdysone-induced protein 75 (E75), reversing its ability to interfere with its heterodimer part...
Public response to the Diablo Canyon Nuclear Generating Station

International Nuclear Information System (INIS)

Pijawka, K.D.

1982-01-01

The authors examine the nature of the public response to the Diablo Canyon Nuclear Generating Station located in San Luis Obispo, California, from the early 1960s to the present. Four distinct phases of public intervention were discerned, based on change in both plant-related issues and in the nature of the antinuclear constituencies in the region. The level of public concern varied both geographically and temporally and is related to the area's social structure, environmental predispositions, and distribution of plant-related economic benefits. External events, such as the prolonged debate over the risk assessment of the seismic hazard and the Three Mile Island accident were found to be important factors in explaining variation in public concern and political response
Public response to the Diablo Canyon Nuclear Generating Station

International Nuclear Information System (INIS)

Pijawka, K.D.

1982-01-01

We examine the nature of the public response to the Diablo Canyon Nuclear Generating Station located in San Luis Obispo, California, from the early 1960s to the present. Four distinct phases of public intervention were discerned, based on change in both plant-related issues and in the nature of the antinuclear constituencies in the region. The level of public concern varied both geographically and temporally and is related to the area's social structure, environmental predispositions, and distribution of plant-related economic benefits. External events, such as the prolonged debate over the risk assessment of the seismic hazard and the Three Mile Island accident were found to be important factors in explaining variation in public concern and political response. (author)
Deep sequencing of Brachypodium small RNAs at the global genome level identifies microRNAs involved in cold stress response

Directory of Open Access Journals (Sweden)

Chong Kang

2009-09-01

Full Text Available Abstract Background MicroRNAs (miRNAs are endogenous small RNAs having large-scale regulatory effects on plant development and stress responses. Extensive studies of miRNAs have only been performed in a few model plants. Although miRNAs are proved to be involved in plant cold stress responses, little is known for winter-habit monocots. Brachypodium distachyon, with close evolutionary relationship to cool-season cereals, has recently emerged as a novel model plant. There are few reports of Brachypodium miRNAs. Results High-throughput sequencing and whole-genome-wide data mining led to the identification of 27 conserved miRNAs, as well as 129 predicted miRNAs in Brachypodium. For multiple-member conserved miRNA families, their sizes in Brachypodium were much smaller than those in rice and Populus. The genome organization of miR395 family in Brachypodium was quite different from that in rice. The expression of 3 conserved miRNAs and 25 predicted miRNAs showed significant changes in response to cold stress. Among these miRNAs, some were cold-induced and some were cold-suppressed, but all the conserved miRNAs were up-regulated under cold stress condition. Conclusion Our results suggest that Brachypodium miRNAs are composed of a set of conserved miRNAs and a large proportion of non-conserved miRNAs with low expression levels. Both kinds of miRNAs were involved in cold stress response, but all the conserved miRNAs were up-regulated, implying an important role for cold-induced miRNAs. The different size and genome organization of miRNA families in Brachypodium and rice suggest that the frequency of duplication events or the selection pressure on duplicated miRNAs are different between these two closely related plant species.
Genome-wide analysis of WRKY gene family in the sesame genome and identification of the WRKY genes involved in responses to abiotic stresses.

Science.gov (United States)

Li, Donghua; Liu, Pan; Yu, Jingyin; Wang, Linhai; Dossa, Komivi; Zhang, Yanxin; Zhou, Rong; Wei, Xin; Zhang, Xiurong

2017-09-11

Sesame (Sesamum indicum L.) is one of the world's most important oil crops. However, it is susceptible to abiotic stresses in general, and to waterlogging and drought stresses in particular. The molecular mechanisms of abiotic stress tolerance in sesame have not yet been elucidated. The WRKY domain transcription factors play significant roles in plant growth, development, and responses to stresses. However, little is known about the number, location, structure, molecular phylogenetics, and expression of the WRKY genes in sesame. We performed a comprehensive study of the WRKY gene family in sesame and identified 71 SiWRKYs. In total, 65 of these genes were mapped to 15 linkage groups within the sesame genome. A phylogenetic analysis was performed using a related species (Arabidopsis thaliana) to investigate the evolution of the sesame WRKY genes. Tissue expression profiles of the WRKY genes demonstrated that six SiWRKY genes were highly expressed in all organs, suggesting that these genes may be important for plant growth and organ development in sesame. Analysis of the SiWRKY gene expression patterns revealed that 33 and 26 SiWRKYs respond strongly to waterlogging and drought stresses, respectively. Changes in the expression of 12 SiWRKY genes were observed at different times after the waterlogging and drought treatments had begun, demonstrating that sesame gene expression patterns vary in response to abiotic stresses. In this study, we analyzed the WRKY family of transcription factors encoded by the sesame genome. Insight was gained into the classification, evolution, and function of the SiWRKY genes, revealing their putative roles in a variety of tissues. Responses to abiotic stresses in different sesame cultivars were also investigated. The results of our study provide a better understanding of the structures and functions of sesame WRKY genes and suggest that manipulating these WRKYs could enhance resistance to waterlogging and drought.
Social response to nuclear power and alternative energy systems

International Nuclear Information System (INIS)

Savellano, R.A.; Bulaon, C.A.

1986-01-01

Phase I of this study analyzed attitudes and beliefs of respondents drawn from Metro Manila. The second phase utilized a sample drawn from residents near a geothermal power plant site in the Southern Philippines. Four dimensions of beliefs (psychological environmental risks, technological benefits/development, economic benefits/implications, and socio-political/implications/benefit) were identified through factor analysis of beliefs items on nuclear energy and refined empirically to determine perceptions of respondents about all other energy systems. Identification of the relationship between dimensions provided insight into the shared perceptions about each energy system held by the various groups of respondents. The overall attitude of the respondents towards energy systems (nuclear, solar, hydro, geothermal and oil) was determined using three attitude measures: the Fishbein model, Osgood's semantic differential technique, and direct response to unfavorability/favorability scale. The belief dimensions were correlated with the attitude measures to determine the degree of contribution to attitude. A comparative analysis was made to different attitudes and beliefs held by the PRO and CON nuclear groups and by the subsamples: university students, science teachers and barangay leaders of Metro Manila sample. Attitudes and beliefs relating to the demographic variables were also examined for the two samples. (author)
Raison d'etat and popular response: the resumption of French nuclear testing in the South Pacific

International Nuclear Information System (INIS)

Wooler, Derek.

1995-01-01

This Current Issues Brief highlights the issues surrounding several aspects of resumed French nuclear testing series. The French perspective, and the nature of French nuclear weapons program, are discussed, as is the impact of test explosions on the ecology of the Mururoa test site. Also discussed are the development of testing, the pressures that have led to its resumption following the suspension in 1992 and the French position regarding the nuclear weapons control regime; the development of attitudes to French testing in regional countries and the response of their governments to the resumption; the scope for, and restrictions on, as well as the use of trade sanctions as a response in the regulatory environment under the World Trade Organisation. The two appendices give a summary of all known nuclear tests since 1945 as well as details of all French tests. 36 refs., 1 tab
Analysis of the Complete Mitochondrial Genome Sequence of the Diploid Cotton Gossypium raimondii by Comparative Genomics Approaches

Directory of Open Access Journals (Sweden)

Changwei Bi

2016-01-01

Full Text Available Cotton is one of the most important economic crops and the primary source of natural fiber and is an important protein source for animal feed. The complete nuclear and chloroplast (cp genome sequences of G. raimondii are already available but not mitochondria. Here, we assembled the complete mitochondrial (mt DNA sequence of G. raimondii into a circular genome of length of 676,078 bp and performed comparative analyses with other higher plants. The genome contains 39 protein-coding genes, 6 rRNA genes, and 25 tRNA genes. We also identified four larger repeats (63.9 kb, 10.6 kb, 9.1 kb, and 2.5 kb in this mt genome, which may be active in intramolecular recombination in the evolution of cotton. Strikingly, nearly all of the G. raimondii mt genome has been transferred to nucleus on Chr1, and the transfer event must be very recent. Phylogenetic analysis reveals that G. raimondii, as a member of Malvaceae, is much closer to another cotton (G. barbadense than other rosids, and the clade formed by two Gossypium species is sister to Brassicales. The G. raimondii mt genome may provide a crucial foundation for evolutionary analysis, molecular biology, and cytoplasmic male sterility in cotton and other higher plants.
Considerations in Emergency Preparedness and Response for a State Embarking on a Nuclear Power Programme, Training Materials

International Nuclear Information System (INIS)

2013-01-01

The aim of these training materials is to provide a practical tool for emergency planning for a State embarking on a nuclear power programme, and to fulfil, in part, functions assigned to the IAEA under the Convention on Assistance in the Case of a Nuclear Accident or Radiological Emergency (the Assistance Convention). Under Article 5.a(ii) of the Assistance Convention, one function of the IAEA is to collect and disseminate to States Parties and Member States information concerning methodologies, techniques and available results of research relating to such emergencies. One of the concerns associated with nuclear power is the possibility that a State embarking on a nuclear power programme might not have sufficient capabilities and therefore would not be adequately prepared to respond to a radiation emergency caused by severe accident conditions. Protecting the public, the environment and property in the event of a failure of any level of defence in depth is the most important safety objective. A robust framework for emergency preparedness and response to a radiation emergency forms the last level of defence in depth and, as such, must be developed and implemented by any State embarking on a nuclear power programme, using best international practices. The establishment of capabilities and arrangements for emergency preparedness and response to severe accident conditions is one of the principal tasks in the development of a national infrastructure for nuclear power. State of the art emergency preparedness and response is a key element in achieving overall plant safety. This training course complements the IAEA publication 'Considerations in Emergency Preparedness and Response for a State Embarking on a Nuclear Power Programme' (EPR-Embarking 2012). These materials are designed to help States apply the guidance in EPR-Embarking 2012, in order to develop the capability to adequately prepare for and respond to a radiation emergency after the commissioning and start of
Population Genomics of Paramecium Species.

Science.gov (United States)

Johri, Parul; Krenek, Sascha; Marinov, Georgi K; Doak, Thomas G; Berendonk, Thomas U; Lynch, Michael

2017-05-01

Population-genomic analyses are essential to understanding factors shaping genomic variation and lineage-specific sequence constraints. The dearth of such analyses for unicellular eukaryotes prompted us to assess genomic variation in Paramecium, one of the most well-studied ciliate genera. The Paramecium aurelia complex consists of ∼15 morphologically indistinguishable species that diverged subsequent to two rounds of whole-genome duplications (WGDs, as long as 320 MYA) and possess extremely streamlined genomes. We examine patterns of both nuclear and mitochondrial polymorphism, by sequencing whole genomes of 10-13 worldwide isolates of each of three species belonging to the P. aurelia complex: P. tetraurelia, P. biaurelia, P. sexaurelia, as well as two outgroup species that do not share the WGDs: P. caudatum and P. multimicronucleatum. An apparent absence of global geographic population structure suggests continuous or recent dispersal of Paramecium over long distances. Intergenic regions are highly constrained relative to coding sequences, especially in P. caudatum and P. multimicronucleatum that have shorter intergenic distances. Sequence diversity and divergence are reduced up to ∼100-150 bp both upstream and downstream of genes, suggesting strong constraints imposed by the presence of densely packed regulatory modules. In addition, comparison of sequence variation at non-synonymous and synonymous sites suggests similar recent selective pressures on paralogs within and orthologs across the deeply diverging species. This study presents the first genome-wide population-genomic analysis in ciliates and provides a valuable resource for future studies in evolutionary and functional genetics in Paramecium. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
Yeast Toxicogenomics: genome-wide responses to chemical stresses with impact in Environmental Health, Pharmacology and Biotechnology

Directory of Open Access Journals (Sweden)

Sandra Costa dos Santos

2012-04-01

Full Text Available The emerging transdisciplinary field of Toxicogenomics aims to study the cell response to a given toxicant at the genome, transcriptome, proteome and metabolome levels. This approach is expected to provide earlier and more sensitive biomarkers of toxicological responses and help in the delineation of regulatory risk assessment. The use of model organisms to gather such genomic information, through the exploitation of Omics and Bioinformatics approaches and tools, together with more focused molecular and cellular biology studies are rapidly increasing our understanding and providing an integrative view on how cells interact with their environment. The use of the model eukaryote Saccharomyces cerevisiae in the field of Toxicogenomics is discussed in this review. Despite the limitations intrinsic to the use of such a simple single cell experimental model, S. cerevisiae appears to be very useful as a first screening tool, limiting the use of animal models. Moreover, it is also one of the most interesting systems to obtain a truly global understanding of the toxicological response and resistance mechanisms, being in the frontline of systems biology research and developments. The impact of the knowledge gathered in the yeast model, through the use of Toxicogenomics approaches, is highlighted here by its use in prediction of toxicological outcomes of exposure to pesticides and pharmaceutical drugs, but also by its impact in biotechnology, namely in the development of more robust crops and in the improvement of yeast strains as cell factories.
Bread wheat progenitors: Aegilops tauschii (DD genome) and Triticum dicoccoides (AABB genome) reveal differential antioxidative response under water stress.

Science.gov (United States)

Suneja, Yadhu; Gupta, Anil Kumar; Bains, Navtej Singh

2017-01-01

Antioxidant enzymes are known to play a significant role in scavenging reactive oxygen species and maintaining cellular homeostasis. Activity of four antioxidant enzymes viz., superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase (APX) and glutathione reductase (GR) was examined in the flag leaves of nine Aegilops tauschii and three Triticum dicoccoides accessions along with two bread wheat cultivars under irrigated and rain-fed conditions. These accessions were shortlisted from a larger set on the basis of field performance for a set of morpho-physiological traits. At anthesis, significant differences were observed in enzyme activities in two environments. A 45% elevation in average GR activity was observed under rain-fed conditions. Genotypic variation was evident within each environment as well as in terms of response to stress environment. Aegilops tauschii accession 3769 (86% increase in SOD, 41% in CAT, 72% in APX, 48% in GR activity) and acc. 14096 (37% increase in SOD, 32% CAT, 25% APX, 42% GR) showed up-regulation in the activity of all the four studied antioxidant enzymes. Aegilops tauschii accessions-9809, 14189 and 14113 also seemed to have strong induction mechanism as elevated activity of at least three enzymes was observed in them under rain-fed conditions. T. dicoccoides , on the other hand, maintained active antioxidative machinery under irrigated condition with relatively lower induction under stress. A significant positive correlation (r = 0.760) was identified between change in the activity of CAT and GR under stress. Changes in plant height, spike length and grain weight were recorded under stress and non-stress conditions on the basis of which a cumulative tolerance index was deduced and accessions were ranked for drought tolerance. Overall, Ae. tauschii accession 3769, 14096, 14113 (DD-genome) and T. dicoccoides accession 7054 (AABB-genome) may be used as donors to combine beneficial stress adaptive traits of all the three sub-genomes
Responsibility for safe management of spent nuclear fuel - a legal perspective; Ansvarstagande i kaernbraenslecykelns slutsteg - ett raettsligt perspektiv

Energy Technology Data Exchange (ETDEWEB)

Cramer, Per; Stendahl, Sara; Erhag, Thomas (Dept. of Law, Univ. of Goeteborg, Goeteborg (Sweden))

2010-10-15

This study analyzes, based on Section 10 of the Swedish Nuclear Activities Act, the legal structures surrounding the issue of responsibility for safe management and final disposal of spent nuclear fuel. The purpose is to shed light on the legal aspects that must be considered in the future licensing process and thereby contribute to a better understanding of the importance of the legal structures for the decisions about final disposal that lie ahead of us. The overall question is thus future-oriented: What interpretation is it reasonable to assume will be given to the requirements of the Nuclear Activities Act on 'safe management and final disposal' of the spent nuclear fuel in the coming licensing process? The approach we take to this question is in part traditionally jurisprudential and based on a study of the travaux preparatoires (drafting history) of the Act and other legal sources. In addition, a study of legal practice is included where previous licensing processes are studied. One conclusion that can be drawn from this study is that the Swedish regulation of nuclear activities creates a legal basis for exacting far-reaching industrial responsibility from the reactor owners, but also for an extensive and interventionist state influence over the activities. Of central importance in the model for division of responsibility that was established via the Nuclear Activities Act in 1984 is the RDandD programme (Research, Development and Demonstration). The RDandD programme reflects the political will that the requirement of 'safe management' should be met through research. The statutory forms for how the programme is to be organized reflect an ambition to place great responsibility for execution and financing on the industry, but also, and not least, an ambition to retain instruments of control and influence in the hands of the state. It is difficult to judge whether the hopes of the 1980s regarding the influence of the public over this process
The Front Line of Genomic Translation

International Nuclear Information System (INIS)

O'Neill, C. S.; McBride, C. M.; Koehly, L. M.; Bryan, A. D.; Wideroff, L.

2012-01-01

Cancer prevention, detection, and treatment represent the front line of genomic translation. Increasingly, new genomic knowledge is being used to inform personalized cancer prevention recommendations and treatment [1-3]. Genomic applications proposed and realized span the full cancer continuum, from cancer prevention and early detection vis a vis genomic risk profiles to motivate behavioral risk reduction and adherence [4] to screening and prophylactic prevention recommendations for high-risk families [5-7], to enhancing cancer survivorship by using genomic tumor profiles to inform treatment decisions and targeted cancer therapies [8, 9]. Yet the utility for many of these applications is as yet unclear and will be influenced heavily by the public’s, patients’, and health care providers’ responses and in numerous other factors, such as health care delivery models [3]. The contributors to this special issue consider various target groups’ responses and contextual factors. To reflect the cancer continuum, the special issue is divided into three broad, overlapping themes-primary prevention, high risk families and family communication and clinical translation.
Preparedness and response for a nuclear or radiological emergency. Safety requirements

International Nuclear Information System (INIS)

2004-01-01

This Safety Requirements publication establishes the requirements for an adequate level of preparedness and response for a nuclear or radiological emergency in any State. Their implementation is intended to minimize the consequences for people, property and the environment of any nuclear or radiological emergency. The fulfilment of these requirements will also contribute to the harmonization of arrangements in the event of a transnational emergency. These requirements are intended to be applied by authorities at the national level by means of adopting legislation, establishing regulations and assigning responsibilities. The requirements apply to all those practices and sources that have the potential for causing radiation exposure or environmental radioactive contamination warranting an emergency intervention and that are: (a) Used in a State that chooses to adopt the requirements or that requests any of the sponsoring organizations to provide for the application of the requirements. (B) Used by States with the assistance of the FAO, IAEA, ILO, PAHO, OCHA or WHO in compliance with applicable national rules and regulations. (C) Used by the IAEA or which involve the use of materials, services, equipment, facilities and non-published information made available by the IAEA or at its request or under its control or supervision. Or (d) Used under any bilateral or multilateral arrangement whereby the parties request the IAEA to provide for the application of the requirements. The requirements also apply to the off-site jurisdictions that may need to make an emergency intervention in a State that adopts the requirements. The types of practices and sources covered by these requirements include: fixed and mobile nuclear reactors. Facilities for the mining and processing of radioactive ores. Facilities for fuel reprocessing and other fuel cycle facilities. Facilities for the management of radioactive waste. The transport of radioactive material. Sources of radiation used in
The tiger genome and comparative analysis with lion and snow leopard genomes.

Science.gov (United States)

Cho, Yun Sung; Hu, Li; Hou, Haolong; Lee, Hang; Xu, Jiaohui; Kwon, Soowhan; Oh, Sukhun; Kim, Hak-Min; Jho, Sungwoong; Kim, Sangsoo; Shin, Young-Ah; Kim, Byung Chul; Kim, Hyunmin; Kim, Chang-Uk; Luo, Shu-Jin; Johnson, Warren E; Koepfli, Klaus-Peter; Schmidt-Küntzel, Anne; Turner, Jason A; Marker, Laurie; Harper, Cindy; Miller, Susan M; Jacobs, Wilhelm; Bertola, Laura D; Kim, Tae Hyung; Lee, Sunghoon; Zhou, Qian; Jung, Hyun-Ju; Xu, Xiao; Gadhvi, Priyvrat; Xu, Pengwei; Xiong, Yingqi; Luo, Yadan; Pan, Shengkai; Gou, Caiyun; Chu, Xiuhui; Zhang, Jilin; Liu, Sanyang; He, Jing; Chen, Ying; Yang, Linfeng; Yang, Yulan; He, Jiaju; Liu, Sha; Wang, Junyi; Kim, Chul Hong; Kwak, Hwanjong; Kim, Jong-Soo; Hwang, Seungwoo; Ko, Junsu; Kim, Chang-Bae; Kim, Sangtae; Bayarlkhagva, Damdin; Paek, Woon Kee; Kim, Seong-Jin; O'Brien, Stephen J; Wang, Jun; Bhak, Jong

2013-01-01

Tigers and their close relatives (Panthera) are some of the world's most endangered species. Here we report the de novo assembly of an Amur tiger whole-genome sequence as well as the genomic sequences of a white Bengal tiger, African lion, white African lion and snow leopard. Through comparative genetic analyses of these genomes, we find genetic signatures that may reflect molecular adaptations consistent with the big cats' hypercarnivorous diet and muscle strength. We report a snow leopard-specific genetic determinant in EGLN1 (Met39>Lys39), which is likely to be associated with adaptation to high altitude. We also detect a TYR260G>A mutation likely responsible for the white lion coat colour. Tiger and cat genomes show similar repeat composition and an appreciably conserved synteny. Genomic data from the five big cats provide an invaluable resource for resolving easily identifiable phenotypes evident in very close, but distinct, species.
The tiger genome and comparative analysis with lion and snow leopard genomes

Science.gov (United States)

Cho, Yun Sung; Hu, Li; Hou, Haolong; Lee, Hang; Xu, Jiaohui; Kwon, Soowhan; Oh, Sukhun; Kim, Hak-Min; Jho, Sungwoong; Kim, Sangsoo; Shin, Young-Ah; Kim, Byung Chul; Kim, Hyunmin; Kim, Chang-uk; Luo, Shu-Jin; Johnson, Warren E.; Koepfli, Klaus-Peter; Schmidt-Küntzel, Anne; Turner, Jason A.; Marker, Laurie; Harper, Cindy; Miller, Susan M.; Jacobs, Wilhelm; Bertola, Laura D.; Kim, Tae Hyung; Lee, Sunghoon; Zhou, Qian; Jung, Hyun-Ju; Xu, Xiao; Gadhvi, Priyvrat; Xu, Pengwei; Xiong, Yingqi; Luo, Yadan; Pan, Shengkai; Gou, Caiyun; Chu, Xiuhui; Zhang, Jilin; Liu, Sanyang; He, Jing; Chen, Ying; Yang, Linfeng; Yang, Yulan; He, Jiaju; Liu, Sha; Wang, Junyi; Kim, Chul Hong; Kwak, Hwanjong; Kim, Jong-Soo; Hwang, Seungwoo; Ko, Junsu; Kim, Chang-Bae; Kim, Sangtae; Bayarlkhagva, Damdin; Paek, Woon Kee; Kim, Seong-Jin; O’Brien, Stephen J.; Wang, Jun; Bhak, Jong

2013-01-01

Tigers and their close relatives (Panthera) are some of the world’s most endangered species. Here we report the de novo assembly of an Amur tiger whole-genome sequence as well as the genomic sequences of a white Bengal tiger, African lion, white African lion and snow leopard. Through comparative genetic analyses of these genomes, we find genetic signatures that may reflect molecular adaptations consistent with the big cats’ hypercarnivorous diet and muscle strength. We report a snow leopard-specific genetic determinant in EGLN1 (Met39>Lys39), which is likely to be associated with adaptation to high altitude. We also detect a TYR260G>A mutation likely responsible for the white lion coat colour. Tiger and cat genomes show similar repeat composition and an appreciably conserved synteny. Genomic data from the five big cats provide an invaluable resource for resolving easily identifiable phenotypes evident in very close, but distinct, species. PMID:24045858
The relationship between early ego strength and adolescent responses to the threat of nuclear war

International Nuclear Information System (INIS)

Andrekus, N.J.

1989-01-01

Ego resiliency and ego control, measured when subjects were 3 or 4 years old, were related to expectation of war, concern for the future, and activism in response to the threat of nuclear war, measured when subjects were 18 years old. Data from 92 participants in a longitudinal study of ego and cognitive development conducted by Jeanne and Jack Block at the University of California, Berkeley were used to test hypotheses. Assessments with the California Child Q-set, composited across multiple independent observers, provide measures of ego resiliency and ego control. Adolescent interviews regarding the perception of likelihood of nuclear war, how this affects their future, and their antinuclear and general political activism were scaled and rated. Early ego resiliency and ego under control were hypothesized to account for the variance in adolescent nuclear responses and activism. The only significant longitudinal relationships were in the female sample, where ego under control was found to be a significant predictor of both general political activism (p<.01) and ideas of the future being affected by the nuclear threat (p<.05). Among males, the relationship between early ego resiliency and adolescent antinuclear activism approached significance (p<.10). Adolescent personality was significantly related to several measures of nuclear response. In girls, adolescent ego under control related to perception of likelihood of nuclear war (p<.05) and antinuclear activism (p<.05), and the interaction of ego resiliency and ego under control predicted general political activism (p<.0005). In boys, adolescent ego resiliency correlated with antinuclear activism (p<.05). These findings were discussed in terms of antecedent parenting styles, and conceptual links were drawn between children's ego resiliency and security of attachment, perspective taking, and moral development
The relationship between early ego strength and adolescent responses to the threat of nuclear war

Energy Technology Data Exchange (ETDEWEB)

Andrekus, N.J.

1989-01-01

Ego resiliency and ego control, measured when subjects were 3 or 4 years old, were related to expectation of war, concern for the future, and activism in response to the threat of nuclear war, measured when subjects were 18 years old. Data from 92 participants in a longitudinal study of ego and cognitive development conducted by Jeanne and Jack Block at the University of California, Berkeley were used to test hypotheses. Assessments with the California Child Q-set, composited across multiple independent observers, provide measures of ego resiliency and ego control. Adolescent interviews regarding the perception of likelihood of nuclear war, how this affects their future, and their antinuclear and general political activism were scaled and rated. Early ego resiliency and ego under control were hypothesized to account for the variance in adolescent nuclear responses and activism. The only significant longitudinal relationships were in the female sample, where ego under control was found to be a significant predictor of both general political activism (p<.01) and ideas of the future being affected by the nuclear threat (p<.05). Among males, the relationship between early ego resiliency and adolescent antinuclear activism approached significance (p<.10). Adolescent personality was significantly related to several measures of nuclear response. In girls, adolescent ego under control related to perception of likelihood of nuclear war (p<.05) and antinuclear activism (p<.05), and the interaction of ego resiliency and ego under control predicted general political activism (p<.0005). In boys, adolescent ego resiliency correlated with antinuclear activism (p<.05). These findings were discussed in terms of antecedent parenting styles, and conceptual links were drawn between children's ego resiliency and security of attachment, perspective taking, and moral development.

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