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Sample records for fork head gene

  1. Human brain factor 1, a new member of the fork head gene family

    Energy Technology Data Exchange (ETDEWEB)

    Murphy, D.B.; Wiese, S.; Burfeind, P. [Institut fuer Humangenetik, Goettingen (Germany)] [and others

    1994-06-01

    Analysis of cDNA clones that cross-hybridized with the fork head domain of the rat HNF-3 gene family revealed 10 cDNAs from human fetal brain and human testis cDNA libraries containing this highly conserved DNA-binding domain. Three of these cDNAs (HFK1, HFK2, and HFK3) were further analyzed. The cDNA HFK1 has a length of 2557 nucleotides and shows strong homology at the nucleotide level (91.2%) to brain factor 1 (BF-1) from rat. The HFK1 cDNA codes for a putative 476 amino acid protein. The homology to BF-1 from rat in the coding region at the amino acid level is 87.5%. The fork head homologous region includes 111 amino acids starting at amino acid 160 and has a 97.5% homology to BF-1. Southern hybridization revealed that HFK1 is highly conserved among mammalian species and possibly birds. Northern analysis with total RNA from human tissues and poly(A)-rich RNA from mouse revealed a 3.2-kb transcript that is present in human and mouse fetal brain and in adult mouse brain. In situ hybridization with sections of mouse embryo and human fetal brain reveals that HFK1 expression is restricted to the neuronal cells in the telencepthalon, with strong expression being observed in the developing dentate gyrus and hippocampus. HFK1 was chromosomally localized by in situ hybridization to 14q12. The cDNA clones HFK2 and HFK3 were analyzed by restriction analysis and sequencing. HFK2 and HFK3 were found to be closely related but different from HFK1. Therefore, it would appear that HFK1, HFK2, HFK3, and BF-1 form a new fork head related subfamily. 33 refs., 6 figs.

  2. Structural and functional characterisation of the fork head transcription factor-encoding gene, Hc-daf-16, from the parasitic nematode Haemonchus contortus (Strongylida)

    OpenAIRE

    2009-01-01

    Despite their phylogenetic diversity, parasitic nematodes share attributes of longevity and developmental arrest (=hypobiosis) with free-living nematodes at key points in their life cycles, particularly in larval stages responsible for establishing infection in the host. Insulin-like signalling plays crucial roles in the regulation of life span and arrest (=dauer formation) in the free-living nematode, Caenorhabditis elegans. Insulin-like signalling in C. elegans negatively regulates the fork...

  3. Computer Aided Design of the Link-Fork Head-Piston Assembly of the Kaplan Turbine with Solidworks

    Directory of Open Access Journals (Sweden)

    Camelia Jianu

    2010-10-01

    Full Text Available The paper presents the steps for 3D computer aided design (CAD of the link-fork head-piston assembly of the Kaplan turbine made in SolidWorks.The present paper is a tutorial for a Kaplan turbine assembly 3D geometry, which is dedicated to the Assembly design and Drawing Geometry and Drawing Annotation.

  4. An overview of gene therapy in head and neck cancer.

    Science.gov (United States)

    Bali, Amit; Bali, Deepika; Sharma, Ashutosh

    2013-07-01

    Gene therapy is a new treatment modality in which new gene is introduced or existing gene is manipulated to cause cancer cell death or slow the growth of the tumor. In this review, we have discussed the different treatment approaches for cancer gene therapy; gene addition therapy, immunotherapy, gene therapy using oncolytic viruses, antisense ribonucleic acid (RNA) and RNA interference-based gene therapy. Clinical trials to date in head and neck cancer have shown evidence of gene transduction and expression, mediation of apoptosis and clinical response including pathological complete responses. The objective of this article is to provide an overview of the current available gene therapies for head and neck cancer.

  5. An overview of gene therapy in head and neck cancer

    OpenAIRE

    2013-01-01

    Gene therapy is a new treatment modality in which new gene is introduced or existing gene is manipulated to cause cancer cell death or slow the growth of the tumor. In this review, we have discussed the different treatment approaches for cancer gene therapy; gene addition therapy, immunotherapy, gene therapy using oncolytic viruses, antisense ribonucleic acid (RNA) and RNA interference-based gene therapy. Clinical trials to date in head and neck cancer have shown evidence of gene transduction...

  6. [Genetic basis of head and neck cancers and gene therapy].

    Science.gov (United States)

    Özel, Halil Erdem; Özkırış, Mahmut; Gencer, Zeliha Kapusuz; Saydam, Levent

    2013-01-01

    Surgery and combinations of traditional treatments are not successful enough particularly for advanced stage head and neck cancer. The major disadvantages of chemotherapy and radiation therapy are the lack of specificity for the target tissue and toxicity to the patient. As a result, gene therapy may offer a more specific approach. The aim of gene therapy is to present therapeutic genes into cancer cells which selectively eliminate malignant cells with no systemic toxicity to the patient. This article reviews the genetic basis of head and neck cancers and important concepts in cancer gene therapy: (i) inhibition of oncogenes; (ii) tumor suppressor gene replacement; (iii) regulation of immune response against malignant cells; (iv) genetic prodrug activation; and (v) antiangiogenic gene therapy. Currently, gene therapy is not sufficient to replace the traditional treatments of head and neck cancers, however there is no doubt that it will have an important role in the near future.

  7. Mitochondrial retrograde regulation tuning fork in nuclear genes expressions of higher plants

    Institute of Scientific and Technical Information of China (English)

    Jinghua Yang; Mingfang Zhang; Jingquan Yu

    2008-01-01

    In plant cells, there are three organelles: the nucleus, chloroplast, and mitochondria that store genetic information. The nucleus possesses the majority of genetic information and controls most aspects of organelles gene expression, growth, and development. In return,organdies also send signals back to regulate nuclear gene expression, a process defined as retrograde regulation. The best studies of organelles to nucleus retrograde regulation exist in plant chloroplast-to-nuclear regulation and yeast mitochondria-to-nuclear regulation. In this review, we summarize the recent understanding of mitochondrial retrograde regulation in higher plant, which involves multiple potential signaling pathway in relation to cytoplasmic male-sterility, biotic stress, and abiotie stress. With respect to mitochondrial retrograde regulation signal pathways involved in cytoplasmic male-sterility, we consider that nuclear transcriptional factor genes are the targeted genes regulated by mitoehondria to determine the abnormal reproductive development, and the MAPK signaling pathway may be involved in this regulation in Brassica juncea. When plants suffer biotic and abiotie stress, plant cells will initiate cell death or other events directed toward recovering from stress. During this process, we propose that mitochondria may determine how plant cell responds to a given stress through retrograde regulation. Meanwhile, several transducer molecules have also been discussed here. In particular, thePaepe research group reported that leaf mitochondrial modulated whole cell redox homeostasis, set antioxidant capacity, and determinedstress resistance through altered signaling and diurnal regulation, which is an indication of plant mitochondria with more active function than ever.

  8. An overview of gene therapy in head and neck cancer

    Directory of Open Access Journals (Sweden)

    Amit Bali

    2013-01-01

    Full Text Available Gene therapy is a new treatment modality in which new gene is introduced or existing gene is manipulated to cause cancer cell death or slow the growth of the tumor. In this review, we have discussed the different treatment approaches for cancer gene therapy; gene addition therapy, immunotherapy, gene therapy using oncolytic viruses, antisense ribonucleic acid (RNA and RNA interference-based gene therapy. Clinical trials to date in head and neck cancer have shown evidence of gene transduction and expression, mediation of apoptosis and clinical response including pathological complete responses. The objective of this article is to provide an overview of the current available gene therapies for head and neck cancer.

  9. Genes affecting heading date in cocksfoot (Dactylis glomerata)

    Science.gov (United States)

    Several genes cause well known effects on heading date in cool-season forages: Vrn1, Constans, and FloweringTime. Vrn1 is a MADs box transcription factor that is induced upon vernalization and necessary for flowering. Constans genes are induced upon long days in cool-season grasses and induce exp...

  10. Mating alters gene expression patterns in Drosophila melanogaster male heads

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    Ellis Lisa L

    2010-10-01

    Full Text Available Abstract Background Behavior is a complex process resulting from the integration of genetic and environmental information. Drosophila melanogaster rely on multiple sensory modalities for reproductive success, and mating causes physiological changes in both sexes that affect reproductive output or behavior. Some of these effects are likely mediated by changes in gene expression. Courtship and mating alter female transcript profiles, but it is not known how mating affects male gene expression. Results We used Drosophila genome arrays to identify changes in gene expression profiles that occur in mated male heads. Forty-seven genes differed between mated and control heads 2 hrs post mating. Many mating-responsive genes are highly expressed in non-neural head tissues, including an adipose tissue called the fat body. One fat body-enriched gene, female-specific independent of transformer (fit, is a downstream target of the somatic sex-determination hierarchy, a genetic pathway that regulates Drosophila reproductive behaviors as well as expression of some fat-expressed genes; three other mating-responsive loci are also downstream components of this pathway. Another mating-responsive gene expressed in fat, Juvenile hormone esterase (Jhe, is necessary for robust male courtship behavior and mating success. Conclusions Our study demonstrates that mating causes changes in male head gene expression profiles and supports an increasing body of work implicating adipose signaling in behavior modulation. Since several mating-induced genes are sex-determination hierarchy target genes, additional mating-responsive loci may be downstream components of this pathway as well.

  11. The contribution of cis-regulatory elements to head-to-head gene pairs’ co-expression pattern

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    Transcription regulation is one of the most critical pipelines in biological process,in which cis-elements play the role as gene expression regulators.We attempt to deduce the principles underlying the co-expression of "head-to-head" gene pairs by analyzing activities or behaviors of the shared cis-elements.A network component analysis was performed to estimate the impact of cis-elements on gene promoters and their activities under different conditions.Our discoveries reveal how biological system uses those regulatory elements to control the expression pattern of "head-to-head" gene pairs and the whole transcription regulation system.

  12. Eukaryotic DNA Replication Fork.

    Science.gov (United States)

    Burgers, Peter M J; Kunkel, Thomas A

    2017-06-20

    This review focuses on the biogenesis and composition of the eukaryotic DNA replication fork, with an emphasis on the enzymes that synthesize DNA and repair discontinuities on the lagging strand of the replication fork. Physical and genetic methodologies aimed at understanding these processes are discussed. The preponderance of evidence supports a model in which DNA polymerase ε (Pol ε) carries out the bulk of leading strand DNA synthesis at an undisturbed replication fork. DNA polymerases α and δ carry out the initiation of Okazaki fragment synthesis and its elongation and maturation, respectively. This review also discusses alternative proposals, including cellular processes during which alternative forks may be utilized, and new biochemical studies with purified proteins that are aimed at reconstituting leading and lagging strand DNA synthesis separately and as an integrated replication fork.

  13. Replication Termination: Containing Fork Fusion-Mediated Pathologies in Escherichia coli

    Directory of Open Access Journals (Sweden)

    Juachi U. Dimude

    2016-07-01

    Full Text Available Duplication of bacterial chromosomes is initiated via the assembly of two replication forks at a single defined origin. Forks proceed bi-directionally until they fuse in a specialised termination area opposite the origin. This area is flanked by polar replication fork pause sites that allow forks to enter but not to leave. The precise function of this replication fork trap has remained enigmatic, as no obvious phenotypes have been associated with its inactivation. However, the fork trap becomes a serious problem to cells if the second fork is stalled at an impediment, as replication cannot be completed, suggesting that a significant evolutionary advantage for maintaining this chromosomal arrangement must exist. Recently, we demonstrated that head-on fusion of replication forks can trigger over-replication of the chromosome. This over-replication is normally prevented by a number of proteins including RecG helicase and 3’ exonucleases. However, even in the absence of these proteins it can be safely contained within the replication fork trap, highlighting that multiple systems might be involved in coordinating replication fork fusions. Here, we discuss whether considering the problems associated with head-on replication fork fusion events helps us to better understand the important role of the replication fork trap in cellular metabolism.

  14. Mutations in two nonhomologous genes in a head-to-head configuration cause Ellis-van Creveld syndrome.

    NARCIS (Netherlands)

    Ruiz-Perez, V.L.; Tompson, S.W.; Blair, H.J.; Espinoza-Valdez, C.; Lapunzina, P.; Silva, E.O.; Hamel, B.C.J.; Gibbs, J.L.; Young, I.D.; Wright, M.J.; Goodship, J.A.

    2003-01-01

    Ellis-van Creveld syndrome (EvC) is an autosomal recessive skeletal dysplasia. Elsewhere, we described mutations in EVC in patients with this condition (Ruiz-Perez et al. 2000). We now report that mutations in EVC2 also cause EvC. These two genes lie in a head-to-head configuration that is conserved

  15. The potential for tumor suppressor gene therapy in head and neck cancer.

    Science.gov (United States)

    Birkeland, Andrew C; Ludwig, Megan L; Spector, Matthew E; Brenner, J Chad

    2016-01-01

    Head and neck squamous cell carcinoma remains a highly morbid and fatal disease. Importantly, genomic sequencing of head and neck cancers has identified frequent mutations in tumor suppressor genes. While targeted therapeutics increasingly are being investigated in head and neck cancer, the majority of these agents are against overactive/overexpressed oncogenes. Therapy to restore lost tumor suppressor gene function remains a key and under-addressed niche in trials for head and neck cancer. Recent advances in gene editing have captured the interest of both the scientific community and the public. As our technology for gene editing and gene expression modulation improves, addressing lost tumor suppressor gene function in head and neck cancers is becoming a reality. This review will summarize new techniques, challenges to implementation, future directions, and ethical ramifications of gene therapy in head and neck cancer.

  16. Duplication of OsHAP family genes and their association with heading date in rice.

    Science.gov (United States)

    Li, Qiuping; Yan, Wenhao; Chen, Huaxia; Tan, Cong; Han, Zhongmin; Yao, Wen; Li, Guangwei; Yuan, Mengqi; Xing, Yongzhong

    2016-03-01

    Heterotrimeric Heme Activator Protein (HAP) family genes are involved in the regulation of flowering in plants. It is not clear how many HAP genes regulate heading date in rice. In this study, we identified 35 HAP genes, including seven newly identified genes, and performed gene duplication and candidate gene-based association analyses. Analyses showed that segmental duplication and tandem duplication are the main mechanisms of HAP gene duplication. Expression profiling and functional identification indicated that duplication probably diversifies the functions of HAP genes. A nucleotide diversity analysis revealed that 13 HAP genes underwent selection. A candidate gene-based association analysis detected four HAP genes related to heading date. An investigation of transgenic plants or mutants of 23 HAP genes confirmed that overexpression of at least four genes delayed heading date under long-day conditions, including the previously cloned Ghd8/OsHAP3H. Our results indicate that the large number of HAP genes in rice was mainly produced by gene duplication, and a few HAP genes function to regulate heading date. Selection of HAP genes is probably caused by their diverse functions rather than regulation of heading.

  17. Parallel Domestication of the Heading Date 1 Gene in Cereals.

    Science.gov (United States)

    Liu, Huanhuan; Liu, Hangqin; Zhou, Leina; Zhang, Zhihai; Zhang, Xuan; Wang, Mingli; Li, Haixia; Lin, Zhongwei

    2015-10-01

    Flowering time is one of the key determinants of crop adaptation to local environments during domestication. However, the genetic basis underlying flowering time is yet to be elucidated in most cereals. Although staple cereals, such as rice, maize, wheat, barley, and sorghum, have spread and adapted to a wide range of ecological environments during domestication, it is yet to be determined whether they have a common genetic basis for flowering time. In this study, we show, through map-based cloning, that flowering time in sorghum is controlled by a major quantitative trait locus (QTL) Heading Date 1 (HD1), located on chromosome 10. The causal gene encodes the CONSTANS gene family which contains a CCT domain. A 5-bp deletion of a minor allele present in the coding sequence leads to a gene frameshift that delays flowering in sorghum. In contrast, in foxtail millet, association mapping of HD1 showed a common causal site with a splicing variant from "GT" to "AT" that was highly correlated with flowering time. In addition, the rice HD1 gene is known to harbor several causal variants controlling flowering time. These data indicate that the major flowering time QTL HD1 was under parallel domestication in sorghum, foxtail millet, and rice. The pattern of common mixed minor, or even rare, causal alleles in HD1 across different species may be representative of the genetic basis of the domestication syndrome. Furthermore, large DNA sequence analysis of HD1 revealed multiple origins for domesticated sorghum and a single origin for domesticated foxtail millet.

  18. SC tuning fork

    CERN Multimedia

    The tuning fork used to modulate the radiofrequency system of the synchro cyclotron (SC) from 1957 to 1973. This piece is an unused spare part. The SC was the 1st accelerator built at CERN. It operated from August 1957 until it was closed down at the end of 1990. In the SC the magnetic field did not change with time, and the particles were accelerated in successive pulses by a radiofrequency voltage of some 20kV which varied in frequency as they spiraled outwards towards the extraction radius. The frequency varied from 30MHz to about 17Mz in each pulse. The tuning fork vibrated at 55MHz in vacuum in an enclosure which formed a variable capacitor in the tuning circuit of the RF system, allowing the RF to vary over the appropriate range to accelerate protons from the centre of the macine up to 600Mev at extraction radius. In operation the tips of the tuning fork blade had an amplitude of movement of over 1 cm. The SC accelerator underwent extensive improvements from 1973 to 1975, including the installation of a...

  19. Comparative Study of Transcriptome Profiles of Mouse Livers and Skins Infected by Fork-Tailed or Non-Fork-Tailed Schistosoma japonicum

    Directory of Open Access Journals (Sweden)

    Yan Yang

    2017-08-01

    Full Text Available Schistosoma japonicum (S. japonicum is a worldwide spread pathogen which penetrates host skin and then induces several diseases in infected host, such as fibrosis, formation of granulomas, hepatocirrhosis, and hepatomegaly. In present study, for the first time, transcriptomic profiles of mouse livers and skins infected by fork-tailed S. japonicum cercaria or non-fork-tailed S. japonicum cercaria were analyzed by using RNA-seq. The present findings demonstrated that transcriptomic landscapes of livers and skins infected by fork-tailed S. japonicum cercaria or non-fork-tailed S. japonicum cercaria were different. S. japonicum has great influence on hepatic metabolic processes. Fork-tailed S. japonicum cercaria upregulated hepatic metabolic processes, while non-fork-tailed S. japonicum cercaria downregulated hepatic metabolic processes. For the metabolism process or the metabolism enzyme expressional change, the pharmacokinetics of host could be changed during S. japonicum infection, regardless the biotypes of S. japonicum cercariae. The changes of infected skins focused on upregulation of immune response. During the S. japonicum skin infection period, fork-tailed S. japonicum cercaria infection induced stronger immune response comparing with that immune response triggered by non-fork-tailed S. japonicum cercaria. The transcription factor enrichment analysis showed that Irf7, Stat1 and Stat2 could play important roles in gene regulation during fork-tailed S. japonicum cercaria infection.

  20. Sequence analysis of the phage 21 genes for prohead assembly and head completion.

    Science.gov (United States)

    Smith, M P; Feiss, M

    1993-04-15

    Phage 21 is a temperate lambdoid coliphage, and its head-encoding genes, as well as those of phage lambda, are descended from a common ancestral phage. The head protein-encoding genes of phage 21 have been sequenced, confirming earlier genetic studies indicating that the head-encoding genes of 21 and lambda are analogous in location, size, and function. The phage 21 head-encoding genes identified (and their lambda analogues) include: 3(W), 4(B), 5(C), 6(Nu3), shp (D), 7(E), and 8(FII), respectively. An open reading frame, orf1, is analogous in position and shares some sequence identity with FI, a phage lambda gene involved in DNA packaging. The phage 21 major head protein, gp7, is predicted to have strong sequence identity (65%) with the lambda major capsid protein, gpE, including amino acids known to be important for capsid form determination. The nested genes 5/6 of phage 21 and C/Nu3 of lambda differ by several rearrangements including deletions and a triplication. The possibility that lambda genes C/Nu3 evolved from ancestal nested genes containing a triplication is discussed.

  1. On non-forking spectra

    CERN Document Server

    Chernikov, Artem; Shelah, Saharon

    2012-01-01

    Non-forking is one of the most important notions in modern model theory capturing the idea of a generic extension of a type (which is a far-reaching generalization of the concept of a generic point of a variety). To a countable first-order theory we associate its non-forking spectrum - a function of two cardinals kappa and lambda giving the supremum of the possible number of types over a model of size lambda that do not fork over a sub-model of size kappa. This is a natural generalization of the stability function of a theory. We make progress towards classifying the non-forking spectra. On the one hand, we show that the possible values a non-forking spectrum may take are quite limited. On the other hand, we develop a general technique for constructing theories with a prescribed non-forking spectrum, thus giving a number of examples. In particular, we answer negatively a question of Adler whether NIP is equivalent to bounded non-forking. In addition, we answer a question of Keisler regarding the number of cut...

  2. Discrimination method of forked larch trees

    Institute of Scientific and Technical Information of China (English)

    Li Wen-bin; Sun Ren-shan; Liu Xu-hua; Liu Yong

    2006-01-01

    For the demands of automatíc pruning, an effective discrimination rule of the forked and non-forked larch trees is established. First, information of trunk and branch diameters of a larch plantations was collected from the west mountain of Beijing. The growth characteristics of the forked and non-forked trees were studied. Given the statistical characteristics of the trunk and branch diameters, a discriminant function of the forked branch and non-forked larch trees was established statistically. Excellent discrimination results were obtained by the function and the rule. The study presents an effective discrimination rule to separate forked trees from straight trees for automatic pruning.

  3. Tuning fork tests: forgotten art.

    Science.gov (United States)

    Girgis, T F; Shambaugh, G E

    1988-01-01

    Four examples are cited in which tuning fork tests helped in proper selection of patients for surgery, after audiometric air and bone tests were equivocal or gave the wrong diagnostic and prognostic indication.

  4. BRCA1 controls homologous recombination at Tus/Ter-stalled mammalian replication forks.

    Science.gov (United States)

    Willis, Nicholas A; Chandramouly, Gurushankar; Huang, Bin; Kwok, Amy; Follonier, Cindy; Deng, Chuxia; Scully, Ralph

    2014-06-26

    Replication fork stalling can promote genomic instability, predisposing to cancer and other diseases. Stalled replication forks may be processed by sister chromatid recombination (SCR), generating error-free or error-prone homologous recombination (HR) outcomes. In mammalian cells, a long-standing hypothesis proposes that the major hereditary breast/ovarian cancer predisposition gene products, BRCA1 and BRCA2, control HR/SCR at stalled replication forks. Although BRCA1 and BRCA2 affect replication fork processing, direct evidence that BRCA gene products regulate homologous recombination at stalled chromosomal replication forks is lacking, due to a dearth of tools for studying this process. Here we report that the Escherichia coli Tus/Ter complex can be engineered to induce site-specific replication fork stalling and chromosomal HR/SCR in mouse cells. Tus/Ter-induced homologous recombination entails processing of bidirectionally arrested forks. We find that the Brca1 carboxy (C)-terminal tandem BRCT repeat and regions of Brca1 encoded by exon 11-two Brca1 elements implicated in tumour suppression-control Tus/Ter-induced homologous recombination. Inactivation of either Brca1 or Brca2 increases the absolute frequency of 'long-tract' gene conversions at Tus/Ter-stalled forks, an outcome not observed in response to a site-specific endonuclease-mediated chromosomal double-strand break. Therefore, homologous recombination at stalled forks is regulated differently from homologous recombination at double-strand breaks arising independently of a replication fork. We propose that aberrant long-tract homologous recombination at stalled replication forks contributes to genomic instability and breast/ovarian cancer predisposition in BRCA mutant cells.

  5. Sex-biased gene expression during head development in a sexually dimorphic stalk-eyed fly.

    Science.gov (United States)

    Wilkinson, Gerald S; Johns, Philip M; Metheny, Jackie D; Baker, Richard H

    2013-01-01

    Stalk-eyed flies (family Diopsidae) are a model system for studying sexual selection due to the elongated and sexually dimorphic eye-stalks found in many species. These flies are of additional interest because their X chromosome is derived largely from an autosomal arm in other flies. To identify candidate genes required for development of dimorphic eyestalks and investigate how sex-biased expression arose on the novel X, we compared gene expression between males and females using oligonucleotide microarrays and RNA from developing eyestalk tissue or adult heads in the dimorphic diopsid, Teleopsis dalmanni. Microarray analysis revealed sex-biased expression for 26% of 3,748 genes expressed in eye-antennal imaginal discs and concordant sex-biased expression for 86 genes in adult heads. Overall, 415 female-biased and 482 male-biased genes were associated with dimorphic eyestalk development but not differential expression in the adult head. Functional analysis revealed that male-biased genes are disproportionately associated with growth and mitochondrial function while female-biased genes are associated with cell differentiation and patterning or are novel transcripts. With regard to chromosomal effects, dosage compensation occurs by elevated expression of X-linked genes in males. Genes with female-biased expression were more common on the X and less common on autosomes than expected, while male-biased genes exhibited no chromosomal pattern. Rates of protein evolution were lower for female-biased genes but higher for genes that moved on or off the novel X chromosome. These findings cannot be due to meiotic sex chromosome inactivation or by constraints associated with dosage compensation. Instead, they could be consistent with sexual conflict in which female-biased genes on the novel X act primarily to reduce eyespan in females while other genes increase eyespan in both sexes. Additional information on sex-biased gene expression in other tissues and related sexually

  6. Sex-biased gene expression during head development in a sexually dimorphic stalk-eyed fly.

    Directory of Open Access Journals (Sweden)

    Gerald S Wilkinson

    Full Text Available Stalk-eyed flies (family Diopsidae are a model system for studying sexual selection due to the elongated and sexually dimorphic eye-stalks found in many species. These flies are of additional interest because their X chromosome is derived largely from an autosomal arm in other flies. To identify candidate genes required for development of dimorphic eyestalks and investigate how sex-biased expression arose on the novel X, we compared gene expression between males and females using oligonucleotide microarrays and RNA from developing eyestalk tissue or adult heads in the dimorphic diopsid, Teleopsis dalmanni. Microarray analysis revealed sex-biased expression for 26% of 3,748 genes expressed in eye-antennal imaginal discs and concordant sex-biased expression for 86 genes in adult heads. Overall, 415 female-biased and 482 male-biased genes were associated with dimorphic eyestalk development but not differential expression in the adult head. Functional analysis revealed that male-biased genes are disproportionately associated with growth and mitochondrial function while female-biased genes are associated with cell differentiation and patterning or are novel transcripts. With regard to chromosomal effects, dosage compensation occurs by elevated expression of X-linked genes in males. Genes with female-biased expression were more common on the X and less common on autosomes than expected, while male-biased genes exhibited no chromosomal pattern. Rates of protein evolution were lower for female-biased genes but higher for genes that moved on or off the novel X chromosome. These findings cannot be due to meiotic sex chromosome inactivation or by constraints associated with dosage compensation. Instead, they could be consistent with sexual conflict in which female-biased genes on the novel X act primarily to reduce eyespan in females while other genes increase eyespan in both sexes. Additional information on sex-biased gene expression in other tissues and

  7. Vascular endothelial growth factor gene transfection to enhance the repair of avascular necrosis of the femoral head of rabbit

    Institute of Scientific and Technical Information of China (English)

    杨操; 杨述华; 杜靖远; 李进; 许伟华; 熊宇芳

    2003-01-01

    Objective To explore a new method for the therapy of avascular necrosis of the femoral head.Methods The recombinant plasmid pCD-hVEGF165 was mixed with collagen and was implanted in the necrotic femoral head. The expression of vascular endothelial growth factor (VEGF) was examined by RNA dot hybridization and immunohistochemical techniques. Repair of the femoral head was observed by histological and histomorphometric analysis.Results The expression of VEGF was detected in the femoral head transfected with the VEGF gene. The femoral head transfected with the VEGF gene showed a significant increase in angiogenesis 2 and 4 weeks after gene transfection and a significant increase in bone formation 6 and 8 weeks after gene transfection on histomorphometric analysis (P<0.01).Conclusions Transfection of the VEGF gene enhances bone tissue angiogenesis. Repair of osteonecrosis could be accelerated accordingly, thus providing a potential method for therapy of osteonecrosis.

  8. Differential gene expression in the honeybee head after a bacterial challenge.

    Science.gov (United States)

    Scharlaken, Bieke; de Graaf, Dirk C; Goossens, Karen; Peelman, Luc J; Jacobs, Frans J

    2008-01-01

    Bidirectional interactions between the immune and nervous systems are well established in vertebrates. Insects show similar neuro-immune-behavioral interactions to those seen in vertebrates. Using quantitative real-time PCR, we present evidence that gene expression in the honeybee head is influenced by activation of the immune system 8h after a bacterial challenge with Escherichia coli. Seven genes were selected for quantitative analysis in order to cover both typical functions of the head such as exocrine secretion (mrjp3 and mrjp4) and olfactory processes (obp17) as well as more general processes such as structural functions (mlc2 and paramyosin), stress response (ERp60) and energy housekeeping (enolase). In this way, we show at the molecular level that the immune system functions as a sensory organ in insects -- as it does in vertebrates -- which signals to the head that a bacterial infection is present, and leads to regulation of expression of several genes in the head by a yet unidentified mechanism.

  9. Over one-half billion years of head conservation? Expression of an ems class gene in Hydractinia symbiolongicarpus (Cnidaria: Hydrozoa)

    Science.gov (United States)

    Mokady, Ofer; Dick, Matthew H.; Lackschewitz, Dagmar; Schierwater, Bernd; Buss, Leo W.

    1998-01-01

    We report the isolation of an empty spiracles class homeodomain-containing gene, Cn-ems, from the hydrozoan Hydractinia symbiolongicarpus, the first gene of this class characterized in a lower metazoan. Cn-ems was found to be expressed in the head of gastrozooids, specifically in endodermal epithelial cells of the taeniolae of the hypostome. Cn-ems is not expressed in gonozooids, which lack taeniolae. Experimental conversion of the posterior region of the planula larva into head structures up-regulates expression of the gene. These findings establish that the association of ems-class genes with head structures preceded the evolution of bilateral symmetry. PMID:9520424

  10. Grainy head and its target genes in epithelial morphogenesis and wound healing.

    Science.gov (United States)

    Wang, Shenqiu; Samakovlis, Christos

    2012-01-01

    The Grainy head (Grh) family of transcription factors is characterized by a unique DNA-binding domain that binds to a conserved consensus sequence. Nematodes and flies have a single grh gene, whereas mice and humans have evolved three genes encoding Grainy head-like (Grhl) factors. We review the biological function of Grh in different animals and the mechanisms modulating its activity. grh and grhl genes play a remarkably conserved role in epithelial organ development and extracellular barrier repair after tissue damage. Recent studies in flies and vertebrates suggest that Grh factors may be primary determinants of cell adhesion and epithelial tissue formation. Grh proteins can dimerize and act as activators or repressors in different developmental contexts. In flies, tissue-specific, alternative splicing generates different Grh isoforms with different DNA-binding specificities and functions. Grh activity is also modulated by receptor tyrosine kinases: it is phosphorylated by extracellular signal regulated kinase, and this phosphorylation is selectively required for epidermal barrier repair. Two mechanisms have been proposed to explain the repressive function of Grh on target gene transcription. First, Grh can target the Polycomb silencing complex to specific response elements. Second, it can directly compete for DNA binding with transcriptional activators. Understanding the molecular mechanisms of gene regulation by Grh factors is likely to elucidate phylogenetically conserved mechanisms of epithelial cell morphogenesis and regeneration upon tissue damage.

  11. Gene Expression Changes in Femoral Head Necrosis of Human Bone Tissue

    Directory of Open Access Journals (Sweden)

    Bernadett Balla

    2011-01-01

    Full Text Available Osteonecrosis of the femoral head (ONFH is the result of an interruption of the local circulation and the injury of vascular supply of bone. Multiple factors have been implicated in the development of the disease. However the mechanism of ischemia and necrosis in non-traumatic ONFH is not clear. The aim of our investigation was to identify genes that are differently expressed in ONFH vs. non-ONFH human bone and to describe the relationships between these genes using multivariate data analysis. Six bone tissue samples from ONFH male patients and 8 bone tissue samples from non-ONFH men were examined. The expression differences of selected 117 genes were analyzed by TaqMan probe-based quantitative real-time RT-PCR system. The significance test indicated marked differences in the expression of nine genes between ONFH and non-ONFH individuals. These altered genes code for collagen molecules, an extracellular matrix digesting metalloproteinase, a transcription factor, an adhesion molecule, and a growth factor. Canonical variates analysis demonstrated that ONFH and non-ONFH bone tissues can be distinguished by the multiple expression profile analysis of numerous genes controlled via canonical TGFB pathway as well as genes coding for extracellular matrix composing collagen type molecules. The markedly altered gene expression profile observed in the ONFH of human bone tissue may provide further insight into the pathogenetic process of osteonecrotic degeneration of bone.

  12. A New Class of SINEs with snRNA Gene-Derived Heads.

    Science.gov (United States)

    Kojima, Kenji K

    2015-05-27

    Eukaryotic genomes are colonized by various transposons including short interspersed elements (SINEs). The 5' region (head) of the majority of SINEs is derived from one of the three types of RNA genes--7SL RNA, transfer RNA (tRNA), or 5S ribosomal RNA (rRNA)--and the internal promoter inside the head promotes the transcription of the entire SINEs. Here I report a new group of SINEs whose heads originate from either the U1 or U2 small nuclear RNA gene. These SINEs, named SINEU, are distributed among crocodilians and classified into three families. The structures of the SINEU-1 subfamilies indicate the recurrent addition of a U1- or U2-derived sequence onto the 5' end of SINEU-1 elements. SINEU-1 and SINEU-3 are ancient and shared among alligators, crocodiles, and gharials, while SINEU-2 is absent in the alligator genome. SINEU-2 is the only SINE family that was active after the split of crocodiles and gharials. All SINEU families, especially SINEU-3, are preferentially inserted into a family of Mariner DNA transposon, Mariner-N4_AMi. A group of Tx1 non-long terminal repeat retrotransposons designated Tx1-Mar also show target preference for Mariner-N4_AMi, indicating that SINEU was mobilized by Tx1-Mar. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  13. Leafy head formation of the progenies of transgenic plants of Chinese cabbage with exogenous auxin genes

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    The experiment was performed to evaluate the progenies of plant lines transgenic for auxin synthesis genes derived from Ri T-DNA. Four lines of the transgenic plants were self-crossed and the foreign auxin genes in plants of T5 generation were confirmed by Southern hybridization. Two lines, D1232 and D1653, showed earlier folding of expanding leaves than untransformed line and therefore had early initiation of leafy head. Leaf cuttings derived from plant of transgenic line D1653 produced more adventitious roots than the control whereas the cuttings from folding leaves had much more roots than rosette leaves at folding stage, and the cuttings from head leaves had more roots than rosette leaves at heading stage. It is demonstrated that early folding of transgenic leaf may be caused by the relatively higher concentration of auxin. These plant lines with auxin transgenes can be used for the study of hormonal regulation in differentiation and development of plant organs and for the breeding of new variety with rapid growth trait.

  14. Leafy head formation of the progenies of transgenic plants of Chinese cabbage with exogenous auxin genes

    Institute of Scientific and Technical Information of China (English)

    HEYUKE; WANXINXUE; 等

    2000-01-01

    The experiment was performed to evaluate the progenies of plant lines transgenic for auxin synthesis genes derived from Ri T-DNA.Four lines of the transgenic plants were self-crossed and the foreign auxin genes in plants of T5 generation were confirmed by Southern hybridization.Two lines,D1232 and D1653,showed earlier folding of expanding leaves than untransformed line and therefore had early initiation of leafy head.Leaf cuttings derived from plant of transgenic line D1653 produced more adventitious roots than the control whereas the cuttings from folding leaves had much more roots than rosette leaves at folding stage,and the cuttings from head leaves had more roots than rosette leaves at heading stage.It is demonstrated that early folding of transgenic leaf may be caused by the relatively higher concentration of auxin.These plant lines with auxin transgenes can be used for the study of hormonal regulation in differentiation and development of plant orgens and for the breeding of new variety with rapid growth trait.

  15. ING Genes Work as Tumor Suppressor Genes in the Carcinogenesis of Head and Neck Squamous Cell Carcinoma.

    Science.gov (United States)

    Li, Xiaohan; Kikuchi, Keiji; Takano, Yasuo

    2011-01-01

    Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer in the world. The evolution and progression of HNSCC are considered to result from multiple stepwise alterations of cellular and molecular pathways in squamous epithelium. Recently, inhibitor of growth gene (ING) family consisting of five genes, ING1 to ING5, was identified as a new tumor suppressor gene family that was implicated in the downregulation of cell cycle and chromatin remodeling. In contrast, it has been shown that ING1 and ING2 play an oncogenic role in some cancers, this situation being similar to TGF-β. In HNSCC, the ING family has been reported to be downregulated, and ING translocation from the nucleus to the cytoplasm may be a critical event for carcinogenesis. In this paper, we describe our recent results and briefly summarize current knowledge regarding the biologic functions of ING in HNSCC.

  16. PAMP INDUCED EXPRESSION OF IMMUNE RELEVANT GENES IN HEAD KIDNEY LEUKOCYTES OF RAINBOW TROUT (ONCORHYNCHUS MYKISS)

    DEFF Research Database (Denmark)

    Chettri, Jiwan Kumar; Holten-Andersen, Lars; Kania, Per Walter

    Host immune responses elicited by invading pathogens depend on recognition of the pathogen by specific receptors present on phagocytic cells. However, the response to viral, bacterial, parasitic and fungal pathogens vary according to the pathogen-associated molecular patterns (PAMPs) on the surface...... of the invader. Phagocytic cells are known to initiate a respiratory burst following an exposure to the pathogen, but the underlying and associated specific elements are poorly elucidated in fish. The present study describes the differential response of head kidney leukocytes from rainbow trout (Oncorhynchus...... moderate reactions. In contrast, IFN-¿ expression was significantly higher in the poly I:C stimulated group compared to LPS group. When head kidney cells were exposed to zymosan or ß-glucan, genes encoding IL-1ß, TNF-a, IL-6 and IL-10 became up-regulated. Their level of up-regulation was comparable to LPS...

  17. Altered Gene Expression Profiles of Wheat Genotypes against Fusarium Head Blight

    Directory of Open Access Journals (Sweden)

    Ayumi Kosaka

    2015-02-01

    Full Text Available Fusarium graminearum is responsible for Fusarium head blight (FHB, which is a destructive disease of wheat that makes its quality unsuitable for end use. To understand the temporal molecular response against this pathogen, microarray gene expression analysis was carried out at two time points on three wheat genotypes, the spikes of which were infected by Fusarium graminearum. The greatest number of genes was upregulated in Nobeokabouzu-komugi followed by Sumai 3, whereas the minimum expression in Gamenya was at three days after inoculation (dai. In Nobeokabouzu-komugi, high expression of detoxification genes, such as multidrug-resistant protein, multidrug resistance-associated protein, UDP-glycosyltransferase and ABC transporters, in addition to systemic defense-related genes, were identified at the early stage of infection. This early response of the highly-resistant genotype implies a different resistance response from the other resistant genotype, Sumai 3, primarily containing local defense-related genes, such as cell wall defense genes. In Gamenya, the expression of all three functional groups was minimal. The differences in these molecular responses with respect to the time points confirmed the variation in the genotypes. For the first time, we report the nature of gene expression in the FHB-highly resistant cv. Nobeokabouzu-komugi during the disease establishment stage and the possible underlying molecular response.

  18. FBH1 Catalyzes Regression of Stalled Replication Forks

    DEFF Research Database (Denmark)

    Fugger, Kasper; Mistrik, Martin; Neelsen, Kai J

    2015-01-01

    DNA replication fork perturbation is a major challenge to the maintenance of genome integrity. It has been suggested that processing of stalled forks might involve fork regression, in which the fork reverses and the two nascent DNA strands anneal. Here, we show that FBH1 catalyzes regression...... a model whereby FBH1 promotes early checkpoint signaling by remodeling of stalled DNA replication forks....... of a model replication fork in vitro and promotes fork regression in vivo in response to replication perturbation. Cells respond to fork stalling by activating checkpoint responses requiring signaling through stress-activated protein kinases. Importantly, we show that FBH1, through its helicase activity...

  19. Altered expression of SIRT gene family in head and neck squamous cell carcinoma.

    Science.gov (United States)

    Lai, Chi-Chih; Lin, Pai-Mei; Lin, Sheng-Fung; Hsu, Cheng-Hsien; Lin, Hsin-Ching; Hu, Ming-Luen; Hsu, Cheng-Ming; Yang, Ming-Yu

    2013-06-01

    Head and neck squamous cell carcinoma (HNSCC) include a group of malignant neoplasms that arise from the upper aerodigestive tract and represent the seventh most common cause of cancer-related death. The overall 5-year survival rates have not significantly improved for decades in spite of the advances in the field of oncology and surgery, encouraging further research on factors that might modify disease prognosis. The silent information regulator (SIR) genes (Sirtuins) play key roles in cellular stress and are associated with aging-related diseases including cancer. Currently, seven human sirtuin (SIRT1-7) genes have been identified, but the roles of SIRT genes in HNSCC are still uncertain. Therefore, in this study, we used real-time quantitative reverse transcription-polymerase chain reaction to investigate the expressions of the seven SIRT genes in human HNSCC tissues to assess the changes in cancerous and noncancerous parts and the correlation with different tumor behaviors. Our results demonstrated that the expression levels of SIRT1, SIRT2, SIRT3, SIRT5, SIRT6, and SIRT7 were significantly downregulated in cancerous tissues compared with noncancerous tissues (all pSIRT1, SIRT2, SIRT3, SIRT5, and SIRT7 showed downregulation in advanced stages in respect to early stages (pSIRT genes expression may contribute to the development of cancer and trigger the neoplastic disease to more advanced stages. Our study indicates that SIRT genes expression could help in the diagnosis and represent a prognostic biomarker in HNSCC.

  20. Fine Mapping and Cloning of Leafy Head Mutant Gene pla1-5 in Rice

    Directory of Open Access Journals (Sweden)

    Gong-neng FENG

    2013-09-01

    Full Text Available We identified a leafy head mutant pla1-5 (plastochron 1-5 from the progeny of japonica rice cultivar Taipei 309 treated with 60Co-γ ray irradiation. The pla1-5 mutant has a dwarf phenotype and small leaves. Compared with its wild type, pla1-5 has more leaves and fewer tillers, and it fails to produce normal panicles at the maturity stage. Genetic analysis showed that the pla1-5 phenotype is controlled by a single recessive nuclear gene. Using the map-based cloning strategy, we narrowed down the location of the target gene to a 58-kb region between simple sequence repeat markers CHR1027 and CHR1030 on the long arm of chromosome 10. The target gene cosegregated with molecular markers CHR1028 and CHR1029. There were five predicted genes in the mapped region. The results from sequencing analysis revealed that there was one base deletion in the first exon of LOC_Os10g26340 encoding cytochrome P450 CYP78A11 in the pla1-5 mutant, which might result in a downstream frame shift and premature termination. These results suggest that the P450 CYP78A11 gene is the candidate gene of PLA1-5.

  1. Genes for wheat resistance ad susceptibility to Fusarium head blight and Septoria tritici blotch disease of wheat

    Science.gov (United States)

    Septoria tritici blotch (STB) and Fusarium head blight (FHB) are two of the most devastating diseases of wheat. Breeding for host resistance is an important component of integrated strategies for STB and FHB control. We identify genes and functional gene markers that can be used to expedite the proc...

  2. Replication fork stability confers chemoresistance in BRCA-deficient cells

    DEFF Research Database (Denmark)

    Chaudhuri, Arnab Ray; Callen, Elsa; Ding, Xia;

    2016-01-01

    Cells deficient in the Brca1 and Brca2 genes have reduced capacity to repair DNA double-strand breaks by homologous recombination and consequently are hypersensitive to DNA-damaging agents, including cisplatin and poly(ADP-ribose) polymerase (PARP) inhibitors. Here we show that loss of the MLL3....../4 complex protein, PTIP, protects Brca1/2-deficient cells from DNA damage and rescues the lethality of Brca2-deficient embryonic stem cells. However, PTIP deficiency does not restore homologous recombination activity at double-strand breaks. Instead, its absence inhibits the recruitment of the MRE11...... nuclease to stalled replication forks, which in turn protects nascent DNA strands from extensive degradation. More generally, acquisition of PARP inhibitors and cisplatin resistance is associated with replication fork protection in Brca2-deficient tumour cells that do not develop Brca2 reversion mutations...

  3. Analysis of Saliva Gene Expression during Head and Neck Cancer Radiotherapy: A Pilot Study.

    Science.gov (United States)

    Lacombe, Jerome; Brooks, Carla; Hu, Chengcheng; Menashi, Emmanuel; Korn, Ronald; Yang, Farley; Zenhausern, Frederic

    2017-07-01

    Saliva, a biological fluid, is a promising candidate for novel approaches to prognosis, clinical diagnosis, monitoring and management of patients with both oral and systemic diseases. However, to date, saliva has not been widely investigated as a biomarker for radiation exposure. Since white blood cells are also present in saliva, it should theoretically be possible to investigate the transcriptional biomarkers of radiation exposure classically studied in whole blood. Therefore, we collected whole blood and saliva samples from eight head and neck cancer patients before the start of radiation treatment, at mid-treatment and after treatment. We then used a panel of five genes: BAX, BBC3, CDKN1A, DDB2 and MDM2, designated for assessing radiation dose in whole blood to evaluate gene expression changes that can occur during radiotherapy. The results revealed that the expression of the five genes did not change in whole blood. However, in saliva, CDKN1A and DDB2 were significantly overexpressed at the end, compared to the start, of radiotherapy, and MDM2 was significantly underexpressed between mid-treatment and at the end of treatment. Interestingly, CDKN1A and DDB2 expressions also showed an increasing monotonic relationship with total radiation dose received during radiotherapy. To our knowledge, these results show for the first time the ability to detect gene expression changes in saliva after head and neck cancer radiotherapy, and pave the way for further promising studies validating saliva as a minimally invasive means of biofluid collection to directly measure radiation dose escalation during treatment.

  4. The rice HGW gene encodes a ubiquitin-associated (UBA domain protein that regulates heading date and grain weight.

    Directory of Open Access Journals (Sweden)

    Juan Li

    Full Text Available Heading date and grain weight are two determining agronomic traits of crop yield. To date, molecular factors controlling both heading date and grain weight have not been identified. Here we report the isolation of a hemizygous mutation, heading and grain weight (hgw, which delays heading and reduces grain weight in rice. Analysis of hgw mutant phenotypes indicate that the hemizygous hgw mutation decreases latitudinal cell number in the lemma and palea, both composing the spikelet hull that is known to determine the size and shape of brown grain. Molecular cloning and characterization of the HGW gene showed that it encodes a novel plant-specific ubiquitin-associated (UBA domain protein localized in the cytoplasm and nucleus, and functions as a key upstream regulator to promote expressions of heading date- and grain weight-related genes. Moreover, co-expression analysis in rice and Arabidopsis indicated that HGW and its Arabidopsis homolog are co-expressed with genes encoding various components of ubiquitination machinery, implying a fundamental role for the ubiquitination pathway in heading date and grain weight control.

  5. Polymorphisms in human DNA repair genes and head and neck squamous cell carcinoma

    Indian Academy of Sciences (India)

    Rim Khlifi; Ahmed Rebai; Amel Hamza-Chaffai

    2012-12-01

    Genetic polymorphisms in some DNA repair proteins are associated with a number of malignant transformations like head and neck squamous cell carcinoma (HNSCC). Xeroderma pigmentosum group D (XPD) and X-ray repair cross-complementing proteins 1 (XRCC1) and 3 (XRCC3) genes are involved in DNA repair and were found to be associated with HNSCC in numerous studies. To establish our overall understanding of possible relationships between DNA repair gene polymorphisms and development of HNSCC, we surveyed the literature on epidemiological studies that assessed potential associations with HNSCC risk in terms of gene–environment interactions, genotype-induced functional defects in enzyme activity and/or protein expression, and the influence of ethnic origin on these associations.We conclude that large, well-designed studies of common polymorphisms in DNA repair genes are needed. Such studies may benefit from analysis of multiple genes or polymorphisms and from the consideration of relevant exposures that may influence the likelihood of HNSCC when DNA repair capacity is reduced.

  6. Tyrosine kinase domain mutations of EGFR gene in head and neck squamous cell carcinoma

    Science.gov (United States)

    Vatte, Chittibabu; Al Amri, Ali M; Cyrus, Cyril; Chathoth, Shahanas; Acharya, Sadananda; Hashim, Tariq Mohammad; Al Ali, Zhara; Alshreadah, Saleh Tawfeeq; Alsayyah, Ahmed; Al-Ali, Amein K

    2017-01-01

    Background Epidermal growth factor receptor (EGFR) is a commonly altered gene that is identified in various cancers, including head and neck squamous cell carcinoma (HNSCC). Therefore, EGFR is a promising molecular marker targeted by monoclonal antibodies and small molecule inhibitors targeting the tyrosine kinase (TK) domain. Objective The objective of this study was to investigate the spectrum of mutations in exons 18, 19, 20, and 21 of the EGFR gene in HNSCC patients. Materials and methods This retrospective study included 47 confirmed HNSCC cases. Mutations in the TK domain, exons 18, 19, 20, and 21 of the EGFR gene, were detected by Scorpion® chemistry and ARMS® technologies on Rotor-Gene Q real-time polymerase chain reaction. Results The tumors exhibited EGFR-TK domain mutations in 57% of cases. Four cases of T790M mutations were reported for the first time among HNSCC patients. Out of the total mutations, L861Q (exon 21), exon 20 insertions and deletions of exon 19 accounted for the majority of mutations (21%, 19%, and 17%, respectively). EGFR mutation status was correlated with the higher grade (P=0.026) and advanced stage (P=0.034) of HNSCC tumors. Conclusion Higher frequency of EGFR-TK domain mutations together with the presence of the T790M mutation suggests that identification of these mutations might streamline the therapy and provide a better prognosis in HNSCC cases. PMID:28352186

  7. Functional analysis of a wheat pleiotropic drug resistance gene involved in Fusarium head blight resistance

    Institute of Scientific and Technical Information of China (English)

    WANG Gui-ping; KONG Ling-rang; HOU Wen-qian; ZHANG Lei; WU Hong-yan; ZHAO Lan-fei; DU Xu-ye; MA Xin; LI An-fei; WANG Hong-wei

    2016-01-01

    The pleiotropic drug resistance (PDR) sub-family of adenosine triphosphate (ATP)-binding cassette (ABC) transporter had been reported to participate in diverse biological processes of plant. In this study, we cloned three novelPDR genes in Fusarium head blight (FHB) resistant wheat cultivar Ning 7840, which were located on wheat chromosomes 6A, 6B and 6D. In phylogeny, these genes were members of cluster I together with AePDR7 andBdPDR7. Subcelular localization analysis showed thatTaPDR7 was expressed on the plasmalemma. The quantitative real time PCR (RT-PCR) analysis showed that this gene and its probable orthologues in chromosomes 6B and 6D were both up-regulated sharply at 48 h after infected byFusarium graminearum and trichothecene deoxynivalenol (DON) in spike. When knocking down the transcripts of alTaPDR7 members by barely stripe mosaic virus-induced gene silencing (BSMV-VIGS) system, it could promote the F. graminearum hyphae growth and made larger pathogen inoculation points in Ning 7840, which suggested that TaPDR7 might play an important role in response toF. graminearum. Although salicylic acid (SA), methyl jasmonate (MeJA) and abscisic acid (ABA) had been reported to possibly regulate wheat FHB resistance, here, we found that the three members ofTaPDR7 were negatively regulated by these three hormones but positively regulated by indoleacetic acid (IAA).

  8. South Fork Holston River basin 1988 biomonitoring

    Energy Technology Data Exchange (ETDEWEB)

    Saylor, C.F.; Ahlstedt, S.A.

    1990-06-01

    There is concern over the effects of shifts in land use use practices on the aquatic fauna of streams in the South Fork Holston River basin in northwestern North Carolina and southwestern Virginia. Trout reproduction has noticeably declined in the Watauga River subbasin. The Watauga River and Elk River subbasins have been subjected to commercial and resort development. The Middle fork Holston River and the upper South Fork Holston River subbasins have been affected by agricultural and mining activities, respectively (Cox, 1986). To aid reclamation and management of the South Fork Holston basin, Tennessee Valley Authority (TVA) biologists conducted biomonitoring--including index of biotic integrity and macroinvertebrate sampling--on the Middle Fork Holston, South Fork Holston, Watauga, and Elk Rivers to assess cumulative impairment related to changes in habitat and pollutant loading in these subbasins. Biomonitoring can detect environmental degradation, help document problem areas, and assist in development of strategies for managing water quality. This report discusses the methods and materials and results of the biomonitoring of South Fork Holston River Basin. 13 refs., 5 figs., 12 tabs.

  9. Identification of Heading Date Six (Hd6 Gene Derived from Rice Mutant Varieties

    Directory of Open Access Journals (Sweden)

    Aryanti Aryanti

    2017-04-01

    Full Text Available Genes which were associated with flowering time to indicate the early maturity is known as heading date (Hd. Heading date six (Hd6 gene was identified from rice mutant varieties were Atomita 2, Atomita 3, Atomita 4, Bestari, Cilosari, Diah Suci, Sidenuk, Kahayan, Mayang, Meraoke, Mira-1, Pandan Putri, Superwin, Suluttan Unsrat 1, Suluttan Unsrat 2, Winongo, Woyla, Yuwono, while the rice var. Nipponbare was used as a positive control. All of rice mutant varieties derived from mutation induction by the dose of 0.2 kGy. The aim of this experiment was to find out the data base of mutant varieties which could be used as parent material with earlier maturity trait genetically. To obtain the DNA of plants, young leaves of each variety were extracted by liquid nitrogen, and then lysis and extracted by Kit Plant Genomic DNA. The amplification of DNA with 7 primers of Hd6 conducted of 40 cycles by PCR and were continues to separated by 1 % agarose. The results were shown that the rice Mira-1 and Bestari varieties obtained from mutation of Cisantana highly different from one to another on 7 primers of Hd6 used. Mayang variety from mutation of cross breeding between Cilosari and IR64, Pandan putri from Pandan wangi and Woyla from mutation of cross breeding from Atomita 2 and IR64 were highly different with those of their parents. Identification of Hd6 gene on Sidenuk variety was shown the same bands pattern with Nipponbare as control positive toward all primers used, this variety would be better for earlier maturity parent material compared to others. The information could be useful for breeding programs aiming to develop early maturing widely adaptive and high yielding rice cultivars.

  10. Stalled replication forks within heterochromatin require ATRX for protection.

    Science.gov (United States)

    Huh, M S; Ivanochko, D; Hashem, L E; Curtin, M; Delorme, M; Goodall, E; Yan, K; Picketts, D J

    2016-05-12

    Expansive growth of neural progenitor cells (NPCs) is a prerequisite to the temporal waves of neuronal differentiation that generate the six-layered neocortex, while also placing a heavy burden on proteins that regulate chromatin packaging and genome integrity. This problem is further reflected by the growing number of developmental disorders caused by mutations in chromatin regulators. ATRX gene mutations cause a severe intellectual disability disorder (α-thalassemia mental retardation X-linked (ATRX) syndrome; OMIM no. 301040), characterized by microcephaly, urogenital abnormalities and α-thalassemia. Although the ATRX protein is required for the maintenance of repetitive DNA within heterochromatin, how this translates to disease pathogenesis remain poorly understood and was a focus of this study. We demonstrate that Atrx(FoxG1Cre) forebrain-specific conditional knockout mice display poly(ADP-ribose) polymerase-1 (Parp-1) hyperactivation during neurogenesis and generate fewer late-born Cux1- and Brn2-positive neurons that accounts for the reduced cortical size. Moreover, DNA damage, induced Parp-1 and Atm activation is elevated in progenitor cells and contributes to their increased level of cell death. ATRX-null HeLa cells are similarly sensitive to hydroxyurea-induced replication stress, accumulate DNA damage and proliferate poorly. Impaired BRCA1-RAD51 colocalization and PARP-1 hyperactivation indicated that stalled replication forks are not efficiently protected. DNA fiber assays confirmed that MRE11 degradation of stalled replication forks was rampant in the absence of ATRX or DAXX. Indeed, fork degradation in ATRX-null cells could be attenuated by treatment with the MRE11 inhibitor mirin, or exacerbated by inhibiting PARP-1 activity. Taken together, these results suggest that ATRX is required to limit replication stress during cellular proliferation, whereas upregulation of PARP-1 activity functions as a compensatory mechanism to protect stalled forks

  11. PAMP induced expression of immune relevant genes in head kidney leukocytes of rainbow trout (Oncorhynchus mykiss)

    DEFF Research Database (Denmark)

    Chettri, Jiwan Kumar; Raida, Martin Kristian; Holten-Andersen, Lars

    2011-01-01

    Host immune responses elicited by invading pathogens depend on recognition of the pathogen by specific receptors present on phagocytic cells. However, the reactions to viral, bacterial, parasitic and fungal pathogens vary according to the pathogen-associated molecular patterns (PAMPs) on the surf......Host immune responses elicited by invading pathogens depend on recognition of the pathogen by specific receptors present on phagocytic cells. However, the reactions to viral, bacterial, parasitic and fungal pathogens vary according to the pathogen-associated molecular patterns (PAMPs......) on the surface of the invader. Phagocytic cells are known to initiate a respiratory burst following an exposure to the pathogen, but the underlying and associated specific elements are poorly elucidated in fish. The present study describes the differential response of head kidney leukocytes from rainbow trout...... merely moderate reactions. In contrast, IFN-¿ expression was significantly higher in the poly I:C stimulated group compared to the LPS group. When head kidney cells were exposed to zymosan or ß-glucan, genes encoding IL-1ß, TNF-a, IL-6 and IL-10 became up-regulated. Their level of up...

  12. A wheat homologue of PHYTOCLOCK 1 is a candidate gene conferring the early heading phenotype to einkorn wheat.

    Science.gov (United States)

    Mizuno, Nobuyuki; Nitta, Miyuki; Sato, Kazuhiro; Nasuda, Shuhei

    2012-01-01

    An X-ray mutant showing an early flowering phenotype has been identified in einkorn wheat (Triticum monococcum L.), for which a major QTL for heading time was previously mapped in the telomeric region on the long arm of chromosome 3A. Recent advances in Triticeae genomics revealed that the gene order in this region is highly conserved between wheat and barley. Thus, we adopted a hypothetical gene order in barley, the so-called GenomeZipper, to develop DNA markers for fine mapping the target gene in wheat. We identified three genes tightly linked to the early heading phenotype. PCR analysis revealed that early-flowering is associated with the deletion of two genes in the mutant. Of the two deleted genes, one is an ortholog of the LUX ARRHYTHMO (LUX)/PHYTOCLOCK 1 (PCL1) gene found in Arabidopsis, which regulates the circadian clock and flowering time. We found distorted expression patterns of two clock genes (TOC1 and LHY) in the einkorn pcl1 deletion mutant as was reported for the Arabidopsis lux mutant. Transcript accumulation levels of photoperiod-response related genes, a photoperiod sensitivity gene (Ppd-1) and two wheat CONSTANS-like genes (WCO1 and TaHd1), were significantly higher in the einkorn wheat mutant. In addition, transcripts of the wheat florigen gene (WFT) accumulated temporally under short-day conditions in the einkorn wheat mutant. These results suggest that deletion of WPCL1 leads to abnormally higher expression of Ppd-1, resulting in the accumulation of WFT transcripts that triggers flowering even under short-day conditions. Our observations from gene mapping, gene deletions, and expression levels of flowering related genes strongly suggest that WPCL1 is the most likely candidate gene for controlling the early flowering phenotype in the einkorn wheat mutant.

  13. Validation of reference genes for real-time quantitative PCR normalisation in non-heading Chinese cabbage

    NARCIS (Netherlands)

    Xiao, D.; Zhang, N.; Jianjun Zhao, Jianjun; Bonnema, A.B.; Hou, X.L.

    2012-01-01

    Non-heading Chinese cabbage is an important vegetable crop that includes pak choi, caixin and several Japanese vegetables like mizuna, mibuna and komatsuna. Gene expression studies are frequently used to unravel the genetics of complex traits and in such studies the proper selection of reference gen

  14. Relationship between gene polymorphism and milk production traits in Teleorman Black Head sheep breed

    Directory of Open Access Journals (Sweden)

    Gras MA

    2015-12-01

    Full Text Available Objective. This study is a preliminary step of a larger national program aimed to develop a strategy for “in situ” preservation of Teleorman Black Head sheep population. In this paper we estimated the effect of β-lactoglobulin, casein and prolactin on some quantitative and qualitative milk traits in this local sheep population. Material and methods. Genotyping methodology included PCR for CSN3 (A and B alleles and PCR-RFLP for LGB (A and B alleles and PRL (T and C alleles, respectively. Repeated milking and milk composition analysis were used for the polymorphism effect estimation. Results. No association between CSN3 polymorphism and milk traits was found. Effect of LGB on production traits was quite constant. Genotype AA performed better than BB. PRL marker effect showed small differences than LGB. Concerning milk, fat and protein yield, AA genotype for PRL had a smaller positive impact than AA genotype for LGB. Regarding fat and protein content, PRL showed a negative effect for AA and positive for BB genotype, respectively. Conclusions. Positive association between LGB and milk yield and composition recommend this candidate gene like marker for a future MAS program. Although PRL gene is also associated with an increased milk quantity, inverse response over milk composition must be considered in MAS strategy. Our study demonstrated that both LGB and PRL markers could became an advent of MAS utilization in Romanian dairy sheep breeding industry.

  15. Rad53-Mediated Regulation of Rrm3 and Pif1 DNA Helicases Contributes to Prevention of Aberrant Fork Transitions under Replication Stress

    Directory of Open Access Journals (Sweden)

    Silvia Emma Rossi

    2015-10-01

    Full Text Available Replication stress activates the Mec1ATR and Rad53 kinases. Rad53 phosphorylates nuclear pores to counteract gene gating, thus preventing aberrant transitions at forks approaching transcribed genes. Here, we show that Rrm3 and Pif1, DNA helicases assisting fork progression across pausing sites, are detrimental in rad53 mutants experiencing replication stress. Rrm3 and Pif1 ablations rescue cell lethality, chromosome fragmentation, replisome-fork dissociation, fork reversal, and processing in rad53 cells. Through phosphorylation, Rad53 regulates Rrm3 and Pif1; phospho-mimicking rrm3 mutants ameliorate rad53 phenotypes following replication stress without affecting replication across pausing elements under normal conditions. Hence, the Mec1-Rad53 axis protects fork stability by regulating nuclear pores and DNA helicases. We propose that following replication stress, forks stall in an asymmetric conformation by inhibiting Rrm3 and Pif1, thus impeding lagging strand extension and preventing fork reversal; conversely, under unperturbed conditions, the peculiar conformation of forks encountering pausing sites would depend on active Rrm3 and Pif1.

  16. Target genes of microsatellite sequences in head and neck squamous cell carcinoma: mononucleotide repeats are not detected.

    Science.gov (United States)

    Wang, Yimin; Liu, Xuejuan; Li, Yulin

    2012-09-10

    Microsatellite instability (MSI) is detected in a wide variety of tumors. It is thought that mismatch repair gene mutation or inactivation is the major cause of MSI. Microsatellite sequences are predominantly distributed in intergenic or intronic DNA. However, MSI is found in the exonic sequences of some genes, causing their inactivation. In this report, we searched GenBank for candidate genes containing potential MSI sequences in exonic regions. Twenty seven target genes were selected for MSI analysis. Instability was found in 70% of these genes (14/20) with head and neck squamous cell carcinoma (HNSCC). Interestingly, no instability was detected in mononucleotide repeats in genes or in intergenic sequences. We conclude that instability of mononucleotide repeats is a rare event in HNSCC. High MSI phenotype in young HNSCC patients is limited to noncoding regions only. MSI percentage in HNSCC tumor is closely related to the repeat type, repeat location and patient's age.

  17. Mammalian RAD52 Functions in Break-Induced Replication Repair of Collapsed DNA Replication Forks

    DEFF Research Database (Denmark)

    Sotiriou, Sotirios K; Kamileri, Irene; Lugli, Natalia

    2016-01-01

    Human cancers are characterized by the presence of oncogene-induced DNA replication stress (DRS), making them dependent on repair pathways such as break-induced replication (BIR) for damaged DNA replication forks. To better understand BIR, we performed a targeted siRNA screen for genes whose depl...

  18. Tyrosine kinase domain mutations of EGFR gene in head and neck squamous cell carcinoma

    Directory of Open Access Journals (Sweden)

    Vatte C

    2017-03-01

    Full Text Available Chittibabu Vatte,1 Ali M Al Amri,2 Cyril Cyrus,1 Shahanas Chathoth,1 Sadananda Acharya,3 Tariq Mohammad Hashim,4 Zhara Al Ali,2 Saleh Tawfeeq Alshreadah,2 Ahmed Alsayyah,4 Amein K Al-Ali5 1Department of Genetic Research, Institute for Research and Medical Consultation, University of Dammam, Dammam, 2Department of Internal Medicine, King Fahd Hospital of the University, University of Dammam, Al-Khobar, 3Department of Stemcell Research, Institute for Research and Medical Consultation, 4Department of Pathology, King Fahd Hospital of the University, University of Dammam, Al-Khobar, 5Department of Biochemistry, College of Medicine, University of Dammam, Dammam, Kingdom of Saudi Arabia Background: Epidermal growth factor receptor (EGFR is a commonly altered gene that is identified in various cancers, including head and neck squamous cell carcinoma (HNSCC. Therefore, EGFR is a promising molecular marker targeted by monoclonal antibodies and small molecule inhibitors targeting the tyrosine kinase (TK domain. Objective: The objective of this study was to investigate the spectrum of mutations in exons 18, 19, 20, and 21 of the EGFR gene in HNSCC patients. Materials and methods: This retrospective study included 47 confirmed HNSCC cases. Mutations in the TK domain, exons 18, 19, 20, and 21 of the EGFR gene, were detected by Scorpion® chemistry and ARMS® technologies on Rotor-Gene Q real-time polymerase chain reaction.Results: The tumors exhibited EGFR-TK domain mutations in 57% of cases. Four cases of T790M mutations were reported for the first time among HNSCC patients. Out of the total mutations, L861Q (exon 21, exon 20 insertions and deletions of exon 19 accounted for the majority of mutations (21%, 19%, and 17%, respectively. EGFR mutation status was correlated with the higher grade (P=0.026 and advanced stage (P=0.034 of HNSCC tumors.Conclusion: Higher frequency of EGFR-TK domain mutations together with the presence of the T790M mutation suggests

  19. FBH1 Catalyzes Regression of Stalled Replication Forks

    Directory of Open Access Journals (Sweden)

    Kasper Fugger

    2015-03-01

    Full Text Available DNA replication fork perturbation is a major challenge to the maintenance of genome integrity. It has been suggested that processing of stalled forks might involve fork regression, in which the fork reverses and the two nascent DNA strands anneal. Here, we show that FBH1 catalyzes regression of a model replication fork in vitro and promotes fork regression in vivo in response to replication perturbation. Cells respond to fork stalling by activating checkpoint responses requiring signaling through stress-activated protein kinases. Importantly, we show that FBH1, through its helicase activity, is required for early phosphorylation of ATM substrates such as CHK2 and CtIP as well as hyperphosphorylation of RPA. These phosphorylations occur prior to apparent DNA double-strand break formation. Furthermore, FBH1-dependent signaling promotes checkpoint control and preserves genome integrity. We propose a model whereby FBH1 promotes early checkpoint signaling by remodeling of stalled DNA replication forks.

  20. 5-Methyltetrahydrofolate-homocysteine methyltransferase gene polymorphism (MTR and risk of head and neck cancer

    Directory of Open Access Journals (Sweden)

    A.L.S. Galbiatti

    2010-05-01

    Full Text Available The functional effect of the A>G transition at position 2756 on the MTR gene (5-methyltetrahydrofolate-homocysteine methyltransferase, involved in folate metabolism, may be a risk factor for head and neck squamous cell carcinoma (HNSCC. The frequency of MTR A2756G (rs1805087 polymorphism was compared between HNSCC patients and individuals without history of neoplasias. The association of this polymorphism with clinical histopathological parameters was evaluated. A total of 705 individuals were included in the study. The polymerase chain reaction-restriction fragment length polymorphism technique was used to genotype the polymorphism. For statistical analysis, the chi-square test (univariate analysis was used for comparisons between groups and multiple logistic regression (multivariate analysis was used for interactions between the polymorphism and risk factors and clinical histopathological parameters. Using univariate analysis, the results did not show significant differences in allelic or genotypic distributions. Multivariable analysis showed that tobacco and alcohol consumption (P < 0.05, AG genotype (P = 0.019 and G allele (P = 0.028 may be predictors of the disease and a higher frequency of the G polymorphic allele was detected in men with HNSCC compared to male controls (P = 0.008. The analysis of polymorphism regarding clinical histopathological parameters did not show any association with the primary site, aggressiveness, lymph node involvement or extension of the tumor. In conclusion, our data provide evidence that supports an association between the polymorphism and the risk of HNSCC.

  1. Deproteinized bone with VEGF gene transfer to facilitate the repair of early avascular necrosis of femoral head of rabbit

    Institute of Scientific and Technical Information of China (English)

    CAO Kai; HUANG Wei; AN Hong; JIANG Dian-ming; SHU Yong; HAN Zhi-min

    2009-01-01

    Objective: To explore a new method for early avascular necrosis of femoral head (AVNFH) therapy.Methods: Sixty-nine AVNFH New Zealand adult rabbits were randomly divided into three groups with equal number. In Group A, deproteinized bone (DPB) that absorbed with recombinant plasmid pcDNA3.1-hVEGF165 was implanted into the drilled tunnel of necrotic femoral head. In Group B, only DPB was implanted. In Group C, only tunnel was drilled without DPB or plasmid implanted. Femoral head specimens were obtained at postoperative 1, 2, 4, 8, 16 weeks. The expression of VEGF165 and collagen I was detected by immunohistochemistry. Bone formation was detected generally by X-ray. Angiogenesis and the repair of the femoral head were observed histologically.Results: The expression of VEGF 165 could be detected 2 weeks after implantation in Group A, but it was not observed in other groups. The result of collagen I expression had a significantly difference 2, 4 and 8 weeks after operation in Group A from those in other groups (P<0.01).X-ray results indicated that there was more bone formation in Group A than in other groups. The regenerated capillary vessels staining result of necrotic femoral head in Group A was significantly different from those in other groups at postoperative 2 and 4 weeks (P<0.01).Conclusions: Transfection ofhVEGF165 gene enhances local angiogenesis and DPB-VEGF compound improves the repair of necrotic femoral head. Deproteinized bone grafting with VEGF gene transfer provides a potential method for the treatment of osteonecrosis.

  2. Sequencing and analysis of the prolate-headed lactococcal bacteriophage c2 genome and identification of the structural genes.

    Science.gov (United States)

    Lubbers, M W; Waterfield, N R; Beresford, T P; Le Page, R W; Jarvis, A W

    1995-12-01

    The 22,163-bp genome of the lactococcal prolate-headed phage c2 was sequenced. Thirty-nine open reading frames (ORFs), early and late promoters, and a putative transcription terminator were identified. Twenty-two ORFs were in the early gene region, and 17 were in the late gene region. Putative genes for a DNA polymerase, a recombination protein, a sigma factor protein, a transcription regulatory protein, holin proteins, and a terminase were identified. Transcription of the early and late genes proceeded divergently from a noncoding 611-bp region. A 521-bp fragment contained within the 611-bp intergenic region could act as an origin of replication in Lactococcus lactis. Three major structural proteins, with sizes of 175, 90, and 29 kDa, and eight minor proteins, with sizes of 143, 82, 66, 60, 44, 42, 32, and 28 kDa, were identified. Several of these proteins appeared to be posttranslationally modified by proteolytic cleavage. The 175- and 90-kDa proteins were identified as the major phage head proteins, and the 29- and 60-kDa proteins were identified as the major tail protein and (possibly) the tail adsorption protein, respectively. The head proteins appeared to be covalently linked multimers of the same 30-kDa gene product. Phage c2 and prolate-headed lactococcal phage bIL67 (C. Schouler, S. D. Ehrlich, and M.-C. Chopin, Microbiology 140:3061-3069, 1994) shared 80% nucleotide sequence identity. However, several DNA deletions or insertions which corresponded to the loss or acquisition of specific ORFs, respectively, were noted. The identification of direct nucleotide repeats flanking these sequences indicated that recombination may be important in the evolution of these phages.(ABSTRACT TRUNCATED AT 250 WORDS)

  3. Grand Forks - East Grand Forks Urban Water Resources Study. Wastewater Management Appendix.

    Science.gov (United States)

    1981-07-01

    denitrification or clinoptilolite ion exchange is required to meet the ammonia and total nitrogen levels. The effluent from these unit processes would be filtered...32 45 Dissolved Oxygen (mg/1) At Grand Forks 6.0 7.0 8.6 i0.0 12.1 At East Grand Forks 6.5 7.4 9.0 11.4 12.7 Ammonia Nitrogen (mg/i) At Grand Forks...Concentration (mg/i) Total Solids 700 Dissolved Solids 500 Suspended Solids 200 BOD5 200 COD 500 Total Nitrogen 40 Organic Nitrogen 15 Ammonia Nitrogen

  4. Head Transcriptomes of Two Closely Related Species of Fruit Flies of the Anastrepha fraterculus Group Reveals Divergent Genes in Species with Extensive Gene Flow

    Directory of Open Access Journals (Sweden)

    Victor Borges Rezende

    2016-10-01

    Full Text Available Several fruit flies species of the Anastrepha fraterculus group are of great economic importance for the damage they cause to a variety of fleshy fruits. Some species in this group have diverged recently, with evidence of introgression, showing similar morphological attributes that render their identification difficult, reinforcing the relevance of identifying new molecular markers that may differentiate species. We investigated genes expressed in head tissues from two closely related species: A. obliqua and A. fraterculus, aiming to identify fixed single nucleotide polymorphisms (SNPs and highly differentiated transcripts, which, considering that these species still experience some level of gene flow, could indicate potential candidate genes involved in their differentiation process. We generated multiple libraries from head tissues of these two species, at different reproductive stages, for both sexes. Our analyses indicate that the de novo transcriptome assemblies are fairly complete. We also produced a hybrid assembly to map each species’ reads, and identified 67,470 SNPs in A. fraterculus, 39,252 in A. obliqua, and 6386 that were common to both species. We identified 164 highly differentiated unigenes that had a mean interspecific index (D¯ of at least 0.94. We selected unigenes that had Ka/Ks higher than 0.5, or had at least three or more highly differentiated SNPs as potential candidate genes for species differentiation. Among these candidates, we identified proteases, regulators of redox homeostasis, and an odorant-binding protein (Obp99c, among other genes. The head transcriptomes described here enabled the identification of thousands of genes hitherto unavailable for these species, and generated a set of candidate genes that are potentially important to genetically identify species and understand the speciation process in the presence of gene flow of A. obliqua and A. fraterculus.

  5. Forks impacts and motivations in free and open source projects

    Directory of Open Access Journals (Sweden)

    R. Viseur

    2012-02-01

    Full Text Available Forking is a mechanism of splitting in a community and is typically found in the free and open source software field. As a failure of cooperation in a context of open innovation, forking is a practical and informative subject of study. In-depth researches concerning the fork phenomenon are uncommon. We therefore conducted a detailed study of 26 forks from popular free and open source projects. We created fact sheets, highlighting the impact and motivations to fork. We particularly point to the fact that the desire for greater technical differentiation and problems of project governance are major sources of conflict.

  6. Ground-Tracking With a Forked Tongue

    Institute of Scientific and Technical Information of China (English)

    1995-01-01

    Scientists since Aristotle’s day have wondered why the tongues of snakes and many lizards——are forked, a trait that dates from at least the Cretaceous,more than 65 million years ago.Now Kurt Schwenk,a University of Connecticut evolutionary biologist, thinks he knows the answer. "It gives them the abil-

  7. Homologous Recombination as a Replication Fork Escort: Fork-Protection and Recovery

    Directory of Open Access Journals (Sweden)

    Audrey Costes

    2012-12-01

    Full Text Available Homologous recombination is a universal mechanism that allows DNA repair and ensures the efficiency of DNA replication. The substrate initiating the process of homologous recombination is a single-stranded DNA that promotes a strand exchange reaction resulting in a genetic exchange that promotes genetic diversity and DNA repair. The molecular mechanisms by which homologous recombination repairs a double-strand break have been extensively studied and are now well characterized. However, the mechanisms by which homologous recombination contribute to DNA replication in eukaryotes remains poorly understood. Studies in bacteria have identified multiple roles for the machinery of homologous recombination at replication forks. Here, we review our understanding of the molecular pathways involving the homologous recombination machinery to support the robustness of DNA replication. In addition to its role in fork-recovery and in rebuilding a functional replication fork apparatus, homologous recombination may also act as a fork-protection mechanism. We discuss that some of the fork-escort functions of homologous recombination might be achieved by loading of the recombination machinery at inactivated forks without a need for a strand exchange step; as well as the consequence of such a model for the stability of eukaryotic genomes.

  8. Homologous recombination as a replication fork escort: fork-protection and recovery.

    Science.gov (United States)

    Costes, Audrey; Lambert, Sarah A E

    2012-12-27

    Homologous recombination is a universal mechanism that allows DNA repair and ensures the efficiency of DNA replication. The substrate initiating the process of homologous recombination is a single-stranded DNA that promotes a strand exchange reaction resulting in a genetic exchange that promotes genetic diversity and DNA repair. The molecular mechanisms by which homologous recombination repairs a double-strand break have been extensively studied and are now well characterized. However, the mechanisms by which homologous recombination contribute to DNA replication in eukaryotes remains poorly understood. Studies in bacteria have identified multiple roles for the machinery of homologous recombination at replication forks. Here, we review our understanding of the molecular pathways involving the homologous recombination machinery to support the robustness of DNA replication. In addition to its role in fork-recovery and in rebuilding a functional replication fork apparatus, homologous recombination may also act as a fork-protection mechanism. We discuss that some of the fork-escort functions of homologous recombination might be achieved by loading of the recombination machinery at inactivated forks without a need for a strand exchange step; as well as the consequence of such a model for the stability of eukaryotic genomes.

  9. Identification and expression profile analysis of odorant binding protein and chemosensory protein genes in Bemisia tabaci MED by head transcriptome

    Science.gov (United States)

    Zhang, Wei; Zhang, Xiaoman; Qu, Cheng; Tetreau, Guillaume; Sun, Lujuan; Zhou, Jingjiang

    2017-01-01

    Odorant binding proteins (OBPs) and chemosensory proteins (CSPs) of arthropods are thought to be involved in chemical recognition which regulates pivotal behaviors including host choice, copulation and reproduction. In insects, OBPs and CSPs located mainly in the antenna but they have not been systematically characterized yet in Bemisia tabaci which is a cryptic species complex and could damage more than 600 plant species. In this study, among the 106,893 transcripts in the head assembly, 8 OBPs and 13 CSPs were identified in B. tabaci MED based on head transcriptomes of adults. Phylogenetic analyses were conducted to investigate the relationships of B. tabaci OBPs and CSPs with those from several other important Hemipteran species, and the motif-patterns between Hemiptera OBPs and CSPs were also compared by MEME. The expression profiles of the OBP and CSP genes in different tissues of B. tabaci MED adults were analyzed by real-time qPCR. Seven out of the 8 OBPs found in B. tabaci MED were highly expressed in the head. Conversely, only 4 CSPs were enriched in the head, while the other nine CSPs were specifically expressed in other tissues. Our findings pave the way for future research on chemical recognition of B. tabaci at the molecular level. PMID:28166541

  10. The gene expression profile of inflammatory, hypoxic and metabolic genes predicts the metastatic spread of human head and neck squamous cell carcinoma.

    Science.gov (United States)

    Clatot, Florian; Gouérant, Sophie; Mareschal, Sylvain; Cornic, Marie; Berghian, Anca; Choussy, Olivier; El Ouakif, Faissal; François, Arnaud; Bénard, Magalie; Ruminy, Philippe; Picquenot, Jean-Michel; Jardin, Fabrice

    2014-03-01

    To assess the prognostic value of the expression profile of the main genes implicated in hypoxia, glucose and lactate metabolism, inflammation, angiogenesis and extracellular matrix interactions for the metastatic spread of head and neck squamous cell carcinoma. Using a high-throughput qRT-PCR, we performed an unsupervised clustering analysis based on the expression of 42 genes for 61 patients. Usual prognostic factors and clustering analysis results were related to metastasis free survival. With a median follow-up of 48months, 19 patients died from a metastatic evolution of their head and neck squamous cell carcinoma and one from a local recurrence. The unsupervised clustering analysis distinguished two groups of genes that were related to metastatic evolution. A capsular rupture (p=0.005) and the "cluster CXCL12 low" (p=0.002) were found to be independent prognostic factors for metastasis free survival. Using a Linear Predictive Score methodology, we established a 9-gene model (VHL, PTGER4, HK1, SLC16A4, DLL4, CXCL12, CXCR4, PTGER3 and CA9) that was capable of classifying the samples into the 2 clusters with 90% accuracy. In this cohort, our clustering analysis underlined the independent prognostic value of the expression of a panel of genes involved in hypoxia and tumor environment. It allowed us to define a 9-gene model which can be applied routinely to classify newly diagnosed head and neck squamous cell carcinoma. If confirmed by an independent prospective study, this approach may help future clinical management of these aggressive tumors. Copyright © 2013 Elsevier Ltd. All rights reserved.

  11. No evidence that polymorphisms of brain regulator genes Microcephalin and ASPM are associated with general mental ability, head circumference or altruism

    OpenAIRE

    Rushton, J. Philippe; Vernon, Philip A; Bons, Trudy Ann

    2007-01-01

    We test the hypothesis that polymorphisms of the brain regulator genes MCPH1 and ASPM contribute to variations in human brain size and its correlates. We measured general mental ability, head circumference and social intelligence in 644 Canadian adults (496 Caucasians, 36 Orientals, 84 Mixed Race/Other and 28 Blacks; 257 men and 387 women). The gene polymorphisms were assessed from buccal DNA; mental ability by Wonderlic Personnel Test and Multidimensional Aptitude Battery; head circumference...

  12. Q36R polymorphism of KiSS-1 gene in Brazilian head and neck cancer patients.

    Science.gov (United States)

    Ruiz, Mariângela Torreglosa; Galbiatti, Ana Lívia Silva; Pavarino, Erika Cristina; Maniglia, José Victor; Goloni-Bertollo, Eny Maria

    2012-05-01

    The KiSS-1 metastasis-suppressor gene (KiSS-1) product (metastin, kisspeptin) is reported to act after binding with the natural ligand of a G-protein coupled receptor and this gene product inhibits chemotaxis, invasion, and metastasis of cells. The aim of this study was to evaluate the Q36R polymorphism of KiSS-1 in patients with head and neck cancer and to compare the results with healthy individuals and its association with clinicopathological parameters. Gender, age, smoking and alcohol consumption were analyzed for 744 individual (252 head and neck cancer patients and in 522 control individuals). The molecular analysis of these individuals was made after extraction of genomic DNA using the SSCP-PCR technique. This study did not reveal any significant differences in genotype frequencies between healthy individuals and patients with head and neck cancer or with the clinical parameters. This study showed an increase frequency of the Q36R polymorphism in pharyngeal cancer.

  13. Stable Binding of the Conserved Transcription Factor Grainy Head to its Target Genes Throughout Drosophila melanogaster Development.

    Science.gov (United States)

    Nevil, Markus; Bondra, Eliana R; Schulz, Katharine N; Kaplan, Tommy; Harrison, Melissa M

    2017-02-01

    It has been suggested that transcription factor binding is temporally dynamic, and that changes in binding determine transcriptional output. Nonetheless, this model is based on relatively few examples in which transcription factor binding has been assayed at multiple developmental stages. The essential transcription factor Grainy head (Grh) is conserved from fungi to humans, and controls epithelial development and barrier formation in numerous tissues. Drosophila melanogaster, which possess a single grainy head (grh) gene, provide an excellent system to study this conserved factor. To determine whether temporally distinct binding events allow Grh to control cell fate specification in different tissue types, we used a combination of ChIP-seq and RNA-seq to elucidate the gene regulatory network controlled by Grh during four stages of embryonic development (spanning stages 5-17) and in larval tissue. Contrary to expectations, we discovered that Grh remains bound to at least 1146 genomic loci over days of development. In contrast to this stable DNA occupancy, the subset of genes whose expression is regulated by Grh varies. Grh transitions from functioning primarily as a transcriptional repressor early in development to functioning predominantly as an activator later. Our data reveal that Grh binds to target genes well before the Grh-dependent transcriptional program commences, suggesting it sets the stage for subsequent recruitment of additional factors that execute stage-specific Grh functions. Copyright © 2017 by the Genetics Society of America.

  14. Characterization of head transcriptome and analysis of gene expression involved in caste differentiation and aggression in Odontotermes formosanus (Shiraki.

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    Qiuying Huang

    Full Text Available BACKGROUND: The subterranean termite Odontotermes formosanus (Shiraki is a serious insect pest of trees and dams in China. To date, very little is known about genomic or transcriptomic data for caste differentiation and aggression in O. formosanus. Hence, studies on transcriptome and gene expression profiling are helpful to better understand molecular basis underlying caste differentiation and aggressive behavior in O. formosanus. METHODOLOGY AND PRINCIPAL FINDINGS: Using the Illumina sequencing, we obtained more than 57 million sequencing reads derived from the heads of O. formosanus. These reads were assembled into 116,885 unique sequences (mean size  =  536 bp. Of the unigenes, 30,646 (26.22% had significant similarity with proteins in the NCBI nonredundant protein database and Swiss-Prot database (E-value<10(-5. Of these annotated unigenes, 10,409 and 9,009 unigenes were assigned to gene ontology categories and clusters of orthologous groups, respectively. In total, 19,611 (25.52% unigenes were mapped onto 242 pathways using the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG. A total of 11,661 simple sequence repeats (SSRs were predicted from the current transcriptome database. Moreover, we detected seven putative genes involved in caste differentiation and six putative genes involved in aggression. The qPCR analysis showed that there were significant differences in the expression levels of the three putative genes hexamerin 2, β-glycosidase and bicaudal D involved in caste differentiation and one putative gene Cyp6a20 involved in aggression among workers, soldiers and larvae of O. formosanus. CONCLUSIONS: To our knowledge, this is the first study to characterize the complete head transcriptome of a higher fungus-cultivating termite using high-throughput sequencing. Our study has provided the comprehensive sequence resources available for elucidating molecular basis underlying caste differentiation and aggressive

  15. Stress associated gene expression in blood cells is related to outcome in radiotherapy treated head and neck cancer patients

    Directory of Open Access Journals (Sweden)

    Bøhn Siv K

    2012-09-01

    Full Text Available Abstract Background We previously observed that a radiotherapy-induced biochemical response in plasma was associated with favourable outcome in head and neck squamous carcinoma cancer (HNSCC patients. The aim of the present study was to compare stress associated blood cell gene expression between two sub-groups of HNSCC patients with different biochemical responses to radiotherapy. Methods Out of 87 patients (histologically verified, 10 biochemical ‘responders’ having a high relative increase in plasma oxidative damage and a concomitant decrease in plasma antioxidants during radiotherapy and 10 ‘poor-responders’ were selected for gene-expression analysis and compared using gene set enrichment analysis. Results There was a significant induction of stress-relevant gene-sets in the responders following radiotherapy compared to the poor-responders. The relevance of the involvement of similar stress associated gene expression for HNSCC cancer and radioresistance was verified using two publicly available data sets of 42 HNSCC cases and 14 controls (GEO GSE6791, and radiation resistant and radiation sensitive HNSCC xenografts (E-GEOD-9716. Conclusions Radiotherapy induces a systemic stress response, as revealed by induction of stress relevant gene expression in blood cells, which is associated to favourable outcome in a cohort of 87 HNSCC patients. Whether these changes in gene expression reflects a systemic effect or are biomarkers of the tumour micro-environmental status needs further study. Trial registration Raw data are available at ArrayExpress under accession number E-MEXP-2460.

  16. Heading date gene, dth3 controlled late flowering in O. Glaberrima Steud. by down-regulating Ehd1.

    Science.gov (United States)

    Bian, X F; Liu, X; Zhao, Z G; Jiang, L; Gao, H; Zhang, Y H; Zheng, M; Chen, L M; Liu, S J; Zhai, H Q; Wan, J M

    2011-12-01

    Heading date in rice is an important agronomic trait controlled by several genes. In this study, flowering time of variety Dianjingyou 1 (DJY1) was earlier than a near-isogenic line (named NIL) carried chromosome segment from African rice on chromosome 3S, when grown in both long-day (LD) and short-day (SD) conditions. By analyzing a large F2 population from NIL × DJY1, the locus DTH3 (QTL for days to heading on chromosome 3) controlling early heading date in DJY1 was fine mapped to a 64-kb segment which contained only one annotated gene, a MIKC-type MADS-box protein. We detected a 6-bp deletion and a single base substitution in the C-domain by sequencing DTH3 in DJY1 compared with dth3 in NIL, and overexpression of DTH3 caused early flowering in callus. Quantitative real-time PCR revealed that the transcript level of dth3 in NIL was lower than that DTH3 in DJY1 in both LD and SD conditions. The Early heading date 1 (Ehd1) which promotes the RFT1, was up-regulated by DTH3 in both LD and SD conditions. Based on Indel and dCAPs marker analysis, the dth3 allele was only present in African rice accessions. A phylogenetic analysis based on microsatellite genotyping suggested that African rice had a close genetic relationship to O. rufipogon and O. latifolia, and was similar to japonica cultivars. DTH3 affected flowering time and had no significant effect on the main agronomic traits.

  17. Mapping of Ppd-B1, a Major Candidate Gene for Late Heading on Wild Emmer Chromosome Arm 2BS and Assessment of Its Interactions with Early Heading QTLs on 3AL.

    Directory of Open Access Journals (Sweden)

    Wei Zhou

    Full Text Available Wheat heading date is an important agronomic trait determining maturation time and yield. A set of common wheat (Triticum aestivum var. Chinese Spring; CS-wild emmer (T. turgidum L. subsp. dicoccoides (TDIC chromosome arm substitution lines (CASLs was used to identify and allocate QTLs conferring late or early spike emergence by examining heading date. Genetic loci accelerating heading were found on TDIC chromosome arms 3AL and 7BS, while loci delaying heading were located on 4AL and 2BS. To map QTLs conferring late heading on 2BS, F2 populations derived from two cross combinations of CASL2BS × CS and CASL3AL × CASL2BS were developed and each planted at two times, constituting four F2 mapping populations. Heading date varied continuously among individuals of these four populations, suggesting quantitative characteristics. A genetic map of 2BS, consisting of 23 SSR and one single-stranded conformation polymorphism (SSCP marker(s, was constructed using these F2 populations. This map spanned a genetic length of 53.2 cM with average marker density of 2.3 cM. The photoperiod-sensitivity gene Ppd-B1 was mapped to chromosome arm 2BS as a SSCP molecular marker, and was validated as tightly linked to a major QTL governing late heading of CASL2BS in all mapping populations. A significant dominance by additive effect of Ppd-B1 with the LUX gene located on 3AL was also detected. CS had more copies of Ppd-B1 than CASL2BS, implying that increased copy number could elevate the expression of Ppd-1 in CS, also increasing expression of LUX and FT genes and causing CS to have an earlier heading date than CASL2BS in long days.

  18. Code Forking, Governance, and Sustainability in Open Source Software

    Directory of Open Access Journals (Sweden)

    Juho Lindman

    2013-01-01

    Full Text Available The right to fork open source code is at the core of open source licensing. All open source licenses grant the right to fork their code, that is to start a new development effort using an existing code as its base. Thus, code forking represents the single greatest tool available for guaranteeing sustainability in open source software. In addition to bolstering program sustainability, code forking directly affects the governance of open source initiatives. Forking, and even the mere possibility of forking code, affects the governance and sustainability of open source initiatives on three distinct levels: software, community, and ecosystem. On the software level, the right to fork makes planned obsolescence, versioning, vendor lock-in, end-of-support issues, and similar initiatives all but impossible to implement. On the community level, forking impacts both sustainability and governance through the power it grants the community to safeguard against unfavourable actions by corporations or project leaders. On the business-ecosystem level forking can serve as a catalyst for innovation while simultaneously promoting better quality software through natural selection. Thus, forking helps keep open source initiatives relevant and presents opportunities for the development and commercialization of current and abandoned programs.

  19. Quartz tuning fork based microwave impedance microscopy

    Science.gov (United States)

    Cui, Yong-Tao; Ma, Eric Yue; Shen, Zhi-Xun

    2016-06-01

    Microwave impedance microscopy (MIM), a near-field microwave scanning probe technique, has become a powerful tool to characterize local electrical responses in solid state samples. We present the design of a new type of MIM sensor based on quartz tuning fork and electrochemically etched thin metal wires. Due to a higher aspect ratio tip and integration with tuning fork, such design achieves comparable MIM performance and enables easy self-sensing topography feedback in situations where the conventional optical feedback mechanism is not available, thus is complementary to microfabricated shielded stripline-type probes. The new design also enables stable differential mode MIM detection and multiple-frequency MIM measurements with a single sensor.

  20. The forked flap repair for hypospadias

    Directory of Open Access Journals (Sweden)

    Anil Chadha

    2012-01-01

    Full Text Available Context: Despite the abundance of techniques for the repair of Hypospadias, its problems still persist and a satisfactory design to correct the penile curvature with the formation of neourethra from the native urethral tissue or genital or extragenital tissues, with minimal postoperative complications has yet to evolve. Aim: Persisting with such an endeavor, a new technique for the repair of distal and midpenile hypospadias is described. Materials and Methods: The study has been done in 70 cases over the past 11 years. The "Forked-Flap" repair is a single stage method for the repair of such Hypospadias with chordee. It takes advantage of the rich vascular communication at the corona and capitalizes on the established reliability of the meatal based flip-flap. The repair achieves straightening of the curvature of the penis by complete excision of chordee tissue from the ventral surface of the penis beneath the urethral plate. The urethra is reconstructed using the native plate with forked flap extensions and genital tissue relying on the concept of meatal based flaps. Water proofing by dartos tissue and reinforcement by Nesbit′s prepucial tissue transfer completes the one stage procedure. Statistical Analysis: An analysis of 70 cases of this single stage technique of repair of penile hypospadias with chordee, operated at 3 to 5 years of age over the past 11 years is presented. Results and Conclusion: The Forked Flap gives comparable and replicable results; except for a urethrocutaneous fistula rate of 4% no other complications were observed.

  1. Candidate gene screen in the red flour beetle Tribolium reveals six3 as ancient regulator of anterior median head and central complex development.

    Directory of Open Access Journals (Sweden)

    Nico Posnien

    2011-12-01

    Full Text Available Several highly conserved genes play a role in anterior neural plate patterning of vertebrates and in head and brain patterning of insects. However, head involution in Drosophila has impeded a systematic identification of genes required for insect head formation. Therefore, we use the red flour beetle Tribolium castaneum in order to comprehensively test the function of orthologs of vertebrate neural plate patterning genes for a function in insect head development. RNAi analysis reveals that most of these genes are indeed required for insect head capsule patterning, and we also identified several genes that had not been implicated in this process before. Furthermore, we show that Tc-six3/optix acts upstream of Tc-wingless, Tc-orthodenticle1, and Tc-eyeless to control anterior median development. Finally, we demonstrate that Tc-six3/optix is the first gene known to be required for the embryonic formation of the central complex, a midline-spanning brain part connected to the neuroendocrine pars intercerebralis. These functions are very likely conserved among bilaterians since vertebrate six3 is required for neuroendocrine and median brain development with certain mutations leading to holoprosencephaly.

  2. Head and neck squamous cell carcinoma susceptibility genes in the HLA region

    NARCIS (Netherlands)

    Reinders, Judith

    2006-01-01

    The Human Leukocyte Antigen (HLA) region on the short arm of chromosome 6 includes the classical HLA genes and in addition HLA-related and non-HLA related genes. The majority of the genes located in this region are directly or indirectly involved in the immune response. The polymorphic HLA molecules

  3. Needs assessment for the Greenway Grand Forks-East Grand Forks development and public education

    Science.gov (United States)

    Munski, Laura

    Following the flood of 1997, the U.S. Army Corps of Engineers included the Greenway Grand Forks---East Grand Forks (the Greenway) as a flood control measure for Grand Forks, North Dakota and East Grand Forks, Minnesota. It extends along both the Red River of the North and the Red Lake River, encompassing 2200 acres of land. The cities of Grand Forks and East Grand Forks hired consultants to assist with the postflood planning process. The planning process culminated with the Red River of the North Greenway Final Report (Flink, 1998). The purpose of this study was to determine if the development of the Greenway addressed the objectives of the planning report. The history of the land adjacent to the rivers was reviewed to document the progression of riverfront development. Anecdotal evidence was collected, field observations were made, city council minutes were reviewed, Greenway Technical Committee members were interviewed, Greenway Technical Committee minutes were reviewed, and the Greenway Grand Forks---East Grand Forks survey results were reviewed to determine if the objectives of the Red River of the North Greenway Final Report were addressed. A cross section survey was designed by Laura Munski for this dissertation research. The survey was approved by the Greenway Technical Committee. The survey collected both quantitative and qualitative data from the community. The purpose of the survey portion of the research project was to ascertain how residents were kept informed of activities on the Greenway and what amenities residents were using on the Greenway and to solicit their comments regarding the Greenway. The results of the survey research were used in both marketing and event planning for the Greenway. The singular qualitative survey question gave respondents an opportunity to share their comments regarding the Greenway. The qualitative data analysis provided insight to the amenities and educational programs desired by respondents, their concerns regarding the

  4. Heavy alcohol drinking downregulates ALDH2 gene expression but heavy smoking up-regulates SOD2 gene expression in head and neck squamous cell carcinoma.

    Science.gov (United States)

    Lee, Dong Jin; Lee, Hyung Min; Kim, Jin Hwan; Park, Ii Seok; Rho, Young Soo

    2017-08-25

    This study aims to determine the relationship between expression levels of ALDH2 and SOD2 genes and clinical parameters such as alcohol drinking, tobacco smoking, primary site of HNSCC, and human papilloma virus (HPV) state. Gene expression data were obtained from gene expression omnibus (GEO accession number: GSE65858). Clinical data (N = 270) including survival result, gender, age, TNM stage, primary site of HNSCC, HPV status, alcohol drinking, and tobacco smoking habit were analyzed according to gene expression pattern. ALDH2 gene was expressed in low levels in patients with heavy alcohol consumption. It was expressed in high (p = 0.01) levels in patients with no or light alcohol consumption. ALDH2 gene was also expressed in low levels in patients with oral cavity cancers or hypopharynx cancers. However, ALDH2 gene was expressed in high (p = 0.03) levels in patients with oropharyngeal cancers or laryngeal cancers. HPV-positive patients were found to have high (p = 0.02) expression levels of ALDH2. SOD2 gene was expressed in high (p = 0.005) levels in patients who had greater mean pack-year of tobacco smoking. Based on log rank test, the group of patients with high expression of ALDH2 showed better (p = 0.002) clinical results than those with low expression of ALDH2. Difference of survival results between ALDH2 high-expressed group and ALDH2 low-expressed group was validated in another cohort (GSE39368, N = 138). Heavy alcohol drinking downregulates ALDH2 gene expression level. Heavy smoking up-regulates SOD2 gene expression level in patients with head and neck squamous cell carcinoma. The group of patients with low expression levels of ALDH2 showed significantly poorer survival results compared to those with high expression levels of ALDH2.

  5. Code forking in open-source software: a requirements perspective

    CERN Document Server

    Ernst, Neil A; Mylopoulos, John

    2010-01-01

    To fork a project is to copy the existing code base and move in a direction different than that of the erstwhile project leadership. Forking provides a rapid way to address new requirements by adapting an existing solution. However, it can also create a plethora of similar tools, and fragment the developer community. Hence, it is not always clear whether forking is the right strategy. In this paper, we describe a mixed-methods exploratory case study that investigated the process of forking a project. The study concerned the forking of an open-source tool for managing software projects, Trac. Trac was forked to address differing requirements in an academic setting. The paper makes two contributions to our understanding of code forking. First, our exploratory study generated several theories about code forking in open source projects, for further research. Second, we investigated one of these theories in depth, via a quantitative study. We conjectured that the features of the OSS forking process would allow new...

  6. Evolution of tail fork depth in genus Hirundo.

    Science.gov (United States)

    Hasegawa, Masaru; Arai, Emi; Kutsukake, Nobuyuki

    2016-02-01

    A classic example of a sexually selected trait, the deep fork tail of the barn swallow Hirundo rustica is now claimed to have evolved and be maintained mainly via aerodynamic advantage rather than sexually selected advantage. However, this aerodynamic advantage hypothesis does not clarify which flight habits select for/against deep fork tails, causing diversity of tail fork depth in hirundines. Here, by focusing on the genus Hirundo, we investigated whether the large variation in tail fork depth could be explained by the differential flight habits. Using a phylogenetic comparative approach, we found that migrant species had deeper fork tails, but less colorful plumage, than the other species, indicating that migration favors a specific trait, deep fork tails. At the same time, tail fork depth but not plumage coloration decreased with increasing bill size - a proxy of prey size, suggesting that foraging on larger prey items favors shallower fork tails. Variation of tail fork depth in the genus Hirundo may be explained by differential flight habits, even without assuming sexual selection.

  7. A fragile lattice: replacing bacteriophage lambda's head stability gene D with the shp gene of phage 21 generates the Mg2+-dependent virus, lambda shp.

    Science.gov (United States)

    Wendt, Jennifer L; Feiss, Michael

    2004-08-15

    Phage lambda DNA packaging is accompanied by prohead expansion, due to structural changes in gpE, the major capsid protein. Rearrangement of the gpE lattice creates binding sites for trimers of gpD, the head stabilization protein. lambda-Like phage 21's shp gene is homologous to lambda's D gene. gpD and gpShp share 49% amino acid identity. To ask whether gpShp could stabilize the lambda head shell, we replaced lambda's D gene with shp, creating lambda shp. Unlike lambda or 21, lambda shp was strictly dependent on the presence of 10(-2) M Mg2+, and lambda shp virions were very sensitive to chelating agents. Density gradient studies indicated that the lambda gpE lattice was underpopulated with gpShp. gpD's N-terminus has been proposed to contact gpE, and we found that lambda D/shp, which produces a chimeric protein with the N-terminus of gpD and the C-terminus of gpShp, was Mg2+-independent and more stable than lambda shp.

  8. The complete mitochondrial genome and novel gene arrangement of the unique-headed bug Stenopirates sp. (Hemiptera: Enicocephalidae.

    Directory of Open Access Journals (Sweden)

    Hu Li

    Full Text Available Many of true bugs are important insect pests to cultivated crops and some are important vectors of human diseases, but few cladistic analyses have addressed relationships among the seven infraorders of Heteroptera. The Enicocephalomorpha and Nepomorpha are consider the basal groups of Heteroptera, but the basal-most lineage remains unresolved. Here we report the mitochondrial genome of the unique-headed bug Stenopirates sp., the first mitochondrial genome sequenced from Enicocephalomorpha. The Stenopirates sp. mitochondrial genome is a typical circular DNA molecule of 15, 384 bp in length, and contains 37 genes and a large non-coding fragment. The gene order differs substantially from other known insect mitochondrial genomes, with rearrangements of both tRNA genes and protein-coding genes. The overall AT content (82.5% of Stenopirates sp. is the highest among all the known heteropteran mitochondrial genomes. The strand bias is consistent with other true bugs with negative GC-skew and positive AT-skew for the J-strand. The heteropteran mitochondrial atp8 exhibits the highest evolutionary rate, whereas cox1 appears to have the lowest rate. Furthermore, a negative correlation was observed between the variation of nucleotide substitutions and the GC content of each protein-coding gene. A microsatellite was identified in the putative control region. Finally, phylogenetic reconstruction suggests that Enicocephalomorpha is the sister group to all the remaining Heteroptera.

  9. Mechanism of chromosomal DNA replication initiation and replication fork stabilization in eukaryotes.

    Science.gov (United States)

    Wu, LiHong; Liu, Yang; Kong, DaoChun

    2014-05-01

    Chromosomal DNA replication is one of the central biological events occurring inside cells. Due to its large size, the replication of genomic DNA in eukaryotes initiates at hundreds to tens of thousands of sites called DNA origins so that the replication could be completed in a limited time. Further, eukaryotic DNA replication is sophisticatedly regulated, and this regulation guarantees that each origin fires once per S phase and each segment of DNA gets duplication also once per cell cycle. The first step of replication initiation is the assembly of pre-replication complex (pre-RC). Since 1973, four proteins, Cdc6/Cdc18, MCM, ORC and Cdt1, have been extensively studied and proved to be pre-RC components. Recently, a novel pre-RC component called Sap1/Girdin was identified. Sap1/Girdin is required for loading Cdc18/Cdc6 to origins for pre-RC assembly in the fission yeast and human cells, respectively. At the transition of G1 to S phase, pre-RC is activated by the two kinases, cyclindependent kinase (CDK) and Dbf4-dependent kinase (DDK), and subsequently, RPA, primase-polα, PCNA, topoisomerase, Cdc45, polδ, and polɛ are recruited to DNA origins for creating two bi-directional replication forks and initiating DNA replication. As replication forks move along chromatin DNA, they frequently stall due to the presence of a great number of replication barriers on chromatin DNA, such as secondary DNA structures, protein/DNA complexes, DNA lesions, gene transcription. Stalled forks must require checkpoint regulation for their stabilization. Otherwise, stalled forks will collapse, which results in incomplete DNA replication and genomic instability. This short review gives a concise introduction regarding the current understanding of replication initiation and replication fork stabilization.

  10. SUMO modification regulates BLM and RAD51 interaction at damaged replication forks.

    Directory of Open Access Journals (Sweden)

    Karen J Ouyang

    2009-12-01

    Full Text Available The gene mutated in Bloom's syndrome, BLM, is important in the repair of damaged replication forks, and it has both pro- and anti-recombinogenic roles in homologous recombination (HR. At damaged forks, BLM interacts with RAD51 recombinase, the essential enzyme in HR that catalyzes homology-dependent strand invasion. We have previously shown that defects in BLM modification by the small ubiquitin-related modifier (SUMO cause increased gamma-H2AX foci. Because the increased gamma-H2AX could result from defective repair of spontaneous DNA damage, we hypothesized that SUMO modification regulates BLM's function in HR repair at damaged forks. To test this hypothesis, we treated cells that stably expressed a normal BLM (BLM+ or a SUMO-mutant BLM (SM-BLM with hydroxyurea (HU and examined the effects of stalled replication forks on RAD51 and its DNA repair functions. HU treatment generated excess gamma-H2AX in SM-BLM compared to BLM+ cells, consistent with a defect in replication-fork repair. SM-BLM cells accumulated increased numbers of DNA breaks and were hypersensitive to DNA damage. Importantly, HU treatment failed to induce sister-chromatid exchanges in SM-BLM cells compared to BLM+ cells, indicating a specific defect in HR repair and suggesting that RAD51 function could be compromised. Consistent with this hypothesis, RAD51 localization to HU-induced repair foci was impaired in SM-BLM cells. These data suggested that RAD51 might interact noncovalently with SUMO. We found that in vitro RAD51 interacts noncovalently with SUMO and that it interacts more efficiently with SUMO-modified BLM compared to unmodified BLM. These data suggest that SUMOylation controls the switch between BLM's pro- and anti-recombinogenic roles in HR. In the absence of BLM SUMOylation, BLM perturbs RAD51 localization at damaged replication forks and inhibits fork repair by HR. Conversely, BLM SUMOylation relieves its inhibitory effects on HR, and it promotes RAD51 function.

  11. Human ribonuclease H1 resolves R-loops and thereby enables progression of the DNA replication fork.

    Science.gov (United States)

    Parajuli, Shankar; Teasley, Daniel C; Murali, Bhavna; Jackson, Jessica; Vindigni, Alessandro; Stewart, Sheila A

    2017-09-15

    Faithful DNA replication is essential for genome stability. To ensure accurate replication, numerous complex and redundant replication and repair mechanisms function in tandem with the core replication proteins to ensure DNA replication continues even when replication challenges are present that could impede progression of the replication fork. A unique topological challenge to the replication machinery is posed by RNA-DNA hybrids, commonly referred to as R-loops. Although R-loops play important roles in gene expression and recombination at immunoglobulin sites, their persistence is thought to interfere with DNA replication by slowing or impeding replication fork progression. Therefore, it is of interest to identify DNA-associated enzymes that help resolve replication-impeding R-loops. Here, using DNA fiber analysis, we demonstrate that human ribonuclease H1 (RNH1) plays an important role in replication fork movement in the mammalian nucleus by resolving R-loops. We found that RNH1 depletion results in accumulation of RNA-DNA hybrids, slowing of replication forks, and increased DNA damage. Our data uncovered a role for RNH1 in global DNA replication in the mammalian nucleus. Because accumulation of RNA-DNA hybrids is linked to various human cancers and neurodegenerative disorders, our study raises the possibility that replication fork progression might be impeded, adding to increased genomic instability and contributing to disease. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  12. Grand Forks - East Grand Forks Urban Water Resources Study. Social and Environmental Inventory.

    Science.gov (United States)

    1979-01-01

    character- ized by wide variations in temperature, light to moderate precipitation, plentiful sunshine and nearly continuous air movement. Weather patterns...Forks Bicentennial Committee for its photo of the University of North Dakota’s Eternal Flame Memorial. 2. To Mr. Dan Metz for the use of his wildlife

  13. Host-induced gene silencing of an essential chitin synthase gene confers durable resistance to Fusarium head blight and seedling blight in wheat.

    Science.gov (United States)

    Cheng, Wei; Song, Xiu-Shi; Li, He-Ping; Cao, Le-Hui; Sun, Ke; Qiu, Xiao-Li; Xu, Yu-Bin; Yang, Peng; Huang, Tao; Zhang, Jing-Bo; Qu, Bo; Liao, Yu-Cai

    2015-12-01

    Fusarium head blight (FHB) and Fusarium seedling blight (FSB) of wheat, caused by Fusarium pathogens, are devastating diseases worldwide. We report the expression of RNA interference (RNAi) sequences derived from an essential Fusarium graminearum (Fg) virulence gene, chitin synthase (Chs) 3b, as a method to enhance resistance of wheat plants to fungal pathogens. Deletion of Chs3b was lethal to Fg; disruption of the other Chs gene family members generated knockout mutants with diverse impacts on Fg. Comparative expression analyses revealed that among the Chs gene family members, Chs3b had the highest expression levels during Fg colonization of wheat. Three hairpin RNAi constructs corresponding to the different regions of Chs3b were found to silence Chs3b in transgenic Fg strains. Co-expression of these three RNAi constructs in two independent elite wheat cultivar transgenic lines conferred high levels of stable, consistent resistance (combined type I and II resistance) to both FHB and FSB throughout the T3 to T5 generations. Confocal microscopy revealed profoundly restricted mycelia in Fg-infected transgenic wheat plants. Presence of the three specific short interfering RNAs in transgenic wheat plants was confirmed by Northern blotting, and these RNAs efficiently down-regulated Chs3b in the colonizing Fusarium pathogens on wheat seedlings and spikes. Our results demonstrate that host-induced gene silencing of an essential fungal chitin synthase gene is an effective strategy for enhancing resistance in crop plants under field test conditions.

  14. Matrix Metalloproteinases: The Gene Expression Signatures of Head and Neck Cancer Progression

    Energy Technology Data Exchange (ETDEWEB)

    Iizuka, Shinji [Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037 (United States); Ishimaru, Naozumi; Kudo, Yasusei, E-mail: yasusei@tokushima-u.ac.jp [Department of Oral Molecular Pathology, Institute of Health Biosciences, The University of Tokushima Graduate School, 3-8-15 Kuramoto, Tokushima 770-8504 (Japan)

    2014-02-13

    Extracellular matrix degradation by matrix metalloproteinases (MMPs) plays a pivotal role in cancer progression by promoting motility, invasion and angiogenesis. Studies have shown that MMP expression is increased in head and neck squamous cell carcinomas (HNSCCs), one of the most common cancers in the world, and contributes to poor outcome. In this review, we examine the expression pattern of MMPs in HNSCC by microarray datasets and summarize the current knowledge of MMPs, specifically MMP-1, -3, -7 -10, -12, -13, 14 and -19, that are highly expressed in HNSCCs and involved cancer invasion and angiogenesis.

  15. Expression microarray analysis reveals alternative splicing of LAMA3 and DST genes in head and neck squamous cell carcinoma.

    Directory of Open Access Journals (Sweden)

    Ryan Li

    Full Text Available Prior studies have demonstrated tumor-specific alternative splicing events in various solid tumor types. The role of alternative splicing in the development and progression of head and neck squamous cell carcinoma (HNSCC is unclear. Our study queried exon-level expression to implicate splice variants in HNSCC tumors.We performed a comparative genome-wide analysis of 44 HNSCC tumors and 25 uvulopalatopharyngoplasty (UPPP tissue samples at an exon expression level. In our comparison we ranked genes based upon a novel score-the Maximum-Minimum Exon Score (MMES--designed to predict the likelihood of an alternative splicing event occurring. We validated predicted alternative splicing events using quantitative RT-PCR on an independent cohort.After MMES scoring of 17,422 genes, the top 900 genes with the highest scores underwent additional manual inspection of expression patterns in a graphical analysis. The genes LAMA3, DST, VEGFC, SDHA, RASIP1, and TP63 were selected for further validation studies because of a high frequency of alternative splicing suggested in our graphical analysis, and literature review showing their biological relevance and known splicing patterns. We confirmed TP63 as having dominant expression of the short DeltaNp63 isoform in HNSCC tumor samples, consistent with prior reports. Two of the six genes (LAMA3 and DST validated by quantitative RT-PCR for tumor-specific alternative splicing events (Student's t test, P<0.001.Alternative splicing events of oncologically relevant proteins occur in HNSCC. The number of genes expressing tumor-specific splice variants needs further elucidation, as does the functional significance of selective isoform expression.

  16. Integrated Metabolo-Transcriptomics Reveals Fusarium Head Blight Candidate Resistance Genes in Wheat QTL-Fhb2.

    Directory of Open Access Journals (Sweden)

    Dhananjay Dhokane

    Full Text Available Fusarium head blight (FHB caused by Fusarium graminearum not only causes severe losses in yield, but also reduces quality of wheat grain by accumulating mycotoxins. Breeding for host plant resistance is considered as the best strategy to manage FHB. Resistance in wheat to FHB is quantitative in nature, involving cumulative effects of many genes governing resistance. The poor understanding of genetics and lack of precise phenotyping has hindered the development of FHB resistant cultivars. Though more than 100 QTLs imparting FHB resistance have been reported, none discovered the specific genes localized within the QTL region, nor the underlying mechanisms of resistance.In our study recombinant inbred lines (RILs carrying resistant (R-RIL and susceptible (S-RIL alleles of QTL-Fhb2 were subjected to metabolome and transcriptome profiling to discover the candidate genes. Metabolome profiling detected a higher abundance of metabolites belonging to phenylpropanoid, lignin, glycerophospholipid, flavonoid, fatty acid, and terpenoid biosynthetic pathways in R-RIL than in S-RIL. Transcriptome analysis revealed up-regulation of several receptor kinases, transcription factors, signaling, mycotoxin detoxification and resistance related genes. The dissection of QTL-Fhb2 using flanking marker sequences, integrating metabolomic and transcriptomic datasets, identified 4-Coumarate: CoA ligase (4CL, callose synthase (CS, basic Helix Loop Helix (bHLH041 transcription factor, glutathione S-transferase (GST, ABC transporter-4 (ABC4 and cinnamyl alcohol dehydrogenase (CAD as putative resistance genes localized within the QTL-Fhb2 region.Some of the identified genes within the QTL region are associated with structural resistance through cell wall reinforcement, reducing the spread of pathogen through rachis within a spike and few other genes that detoxify DON, the virulence factor, thus eventually reducing disease severity. In conclusion, we report that the wheat

  17. 33 CFR 207.370 - Big Fork River, Minn.; logging.

    Science.gov (United States)

    2010-07-01

    ... 33 Navigation and Navigable Waters 3 2010-07-01 2010-07-01 false Big Fork River, Minn.; logging. 207.370 Section 207.370 Navigation and Navigable Waters CORPS OF ENGINEERS, DEPARTMENT OF THE ARMY, DEPARTMENT OF DEFENSE NAVIGATION REGULATIONS § 207.370 Big Fork River, Minn.; logging. (a) During the season of navigation, parties engaged in...

  18. Epigenetic and Genetic Alterations Affect the WWOX Gene in Head and Neck Squamous Cell Carcinoma

    Science.gov (United States)

    Ekizoglu, Seda; Bulut, Pelin; Karaman, Emin; Kilic, Erkan; Buyru, Nur

    2015-01-01

    Different types of genetic and epigenetic changes are associated with HNSCC. The molecular mechanisms of HNSCC carcinogenesis are still undergoing intensive investigation. WWOX gene expression is altered in many cancers and in a recent work reduced WWOX expression has been associated with miR-134 expression in HNSCC. In this study we investigated the WWOX messenger RNA expression levels in association with the promoter methylation of the WWOX gene and miR-134 expression levels in 80 HNSCC tumor and non-cancerous tissue samples. Our results show that WWOX expression is down-regulated especially in advanced-stage tumor samples or in tumors with SCC. This down-regulation was associated with methylation of the WWOX promoter region but not with miR-134 expression. There was an inverse correlation between the expression level and promoter methylation. We also analyzed whole exons and exon/intron boundries of the WWOX gene by direct sequencing. In our study group we observed 10 different alterations in the coding sequences and 18 different alterations in the non-coding sequences of the WWOX gene in HNSCC tumor samples. These results indicate that the WWOX gene can be functionally inactivated by promoter methylation, epigenetically or by mutations affecting the sequences coding for the enzymatic domain of the gene, functionally. We conclude that inactivation of WWOX gene contributes to the progression of HNSCC. PMID:25612104

  19. Gene Drive for Mosquito Control: Where Did It Come from and Where Are We Headed?

    Science.gov (United States)

    Macias, Vanessa M; Ohm, Johanna R; Rasgon, Jason L

    2017-09-02

    Mosquito-borne pathogens place an enormous burden on human health. The existing toolkit is insufficient to support ongoing vector-control efforts towards meeting disease elimination and eradication goals. The perspective that genetic approaches can potentially add a significant set of tools toward mosquito control is not new, but the recent improvements in site-specific gene editing with CRISPR/Cas9 systems have enhanced our ability to both study mosquito biology using reverse genetics and produce genetics-based tools. Cas9-mediated gene-editing is an efficient and adaptable platform for gene drive strategies, which have advantages over innundative release strategies for introgressing desirable suppression and pathogen-blocking genotypes into wild mosquito populations; until recently, an effective gene drive has been largely out of reach. Many considerations will inform the effective use of new genetic tools, including gene drives. Here we review the lengthy history of genetic advances in mosquito biology and discuss both the impact of efficient site-specific gene editing on vector biology and the resulting potential to deploy new genetic tools for the abatement of mosquito-borne disease.

  20. Epidermal differentiation complex (locus 1q21) gene expression in head and neck cancer and normal mucosa.

    Science.gov (United States)

    Tyszkiewicz, Tomasz; Jarzab, Michal; Szymczyk, Cezary; Kowal, Monika; Krajewska, Jolanta; Jaworska, Magdalena; Fraczek, Marcin; Krajewska, Anna; Hadas, Ewa; Swierniak, Michal; Markowski, Jaroslaw; Lange, Dariusz; Poltorak, Stanislaw; Wiench, Malgorzata; Krecicki, Tomasz; Jarzab, Jerzy; Maciejewski, Adam

    2014-01-01

    Epidermal differentiation complex (EDC) comprises a number of genes associated with human skin diseases including psoriasis, atopic dermatitis and hyperkeratosis. These genes have also been linked to numerous cancers, among them skin, gastric, colorectal, lung, ovarian and renal carcinomas. The involvement of EDC components encoding S100 proteins, small proline-rich proteins (SPRRs) and other genes in the tumorigenesis of head and neck squamous cell cancer (HNSCC) has been previously suggested. The aim of the study was to systematically analyze the expression of EDC components on the transcript level in HNSCC. Tissue specimens from 93 patients with HNC of oral cavity and 87 samples from adjacent or distant grossly normal oral mucosawere analyzed. 48 samples (24 tumor and 24 corresponding surrounding tissue) were hybridized to Affymetrix GeneChip Human 1.0 ST Arrays. For validation by quantitative real-time PCR (QPCR) the total RNA from all180 samples collected in the study was analyzed with Real-Time PCR system and fluorescent amplicon specific-probes. Additional set of samples from 14 patients with laryngeal carcinoma previously obtained by HG-U133 Plus 2.0 microarray was also included in the analyses. The expression of analyzed EDC genes was heterogeneous. Two transcripts (S100A1 and S100A4) were significantly down-regulated in oral cancer when compared to normal mucosa (0.69 and 0.36-fold change, respectively), showing an opposite pattern of expression to the remaining S100 genes. Significant up-regulation in tumors was found for S100A11, S100A7, LCE3D, S100A3 and S100A2 genes. The increased expression of S100A7 was subsequently validated by QPCR, confirming significant differences. The remaining EDC genes, including all encoding SPRR molecules, did not show any differences between oral cancer and normal mucosa. The observed differences were also assessed in the independent set of laryngeal cancer samples, confirming the role of S100A3 and LCE3D transcripts in

  1. Acute MUS81 depletion leads to replication fork slowing and a constitutive DNA damage response

    DEFF Research Database (Denmark)

    Xing, Meichun; Wang, Xiaohui; Palmai-Pallag, Timea;

    2015-01-01

    The MUS81 protein belongs to a conserved family of DNA structure-specific nucleases that play important roles in DNA replication and repair. Inactivation of the Mus81 gene in mice has no major deleterious consequences for embryonic development, although cancer susceptibility has been reported. We...... have investigated the role of MUS81 in human cells by acutely depleting the protein using shRNAs. We found that MUS81 depletion from human fibroblasts leads to accumulation of ssDNA and a constitutive DNA damage response that ultimately activates cellular senescence. Moreover, we show that MUS81...... is required for efficient replication fork progression during an unperturbed S-phase, and for recovery of productive replication following replication stalling. These results demonstrate essential roles for the MUS81 nuclease in maintenance of replication fork integrity....

  2. Outlier Analysis Defines Zinc Finger Gene Family DNA Methylation in Tumors and Saliva of Head and Neck Cancer Patients.

    Directory of Open Access Journals (Sweden)

    Daria A Gaykalova

    Full Text Available Head and Neck Squamous Cell Carcinoma (HNSCC is the fifth most common cancer, annually affecting over half a million people worldwide. Presently, there are no accepted biomarkers for clinical detection and surveillance of HNSCC. In this work, a comprehensive genome-wide analysis of epigenetic alterations in primary HNSCC tumors was employed in conjunction with cancer-specific outlier statistics to define novel biomarker genes which are differentially methylated in HNSCC. The 37 identified biomarker candidates were top-scoring outlier genes with prominent differential methylation in tumors, but with no signal in normal tissues. These putative candidates were validated in independent HNSCC cohorts from our institution and TCGA (The Cancer Genome Atlas. Using the top candidates, ZNF14, ZNF160, and ZNF420, an assay was developed for detection of HNSCC cancer in primary tissue and saliva samples with 100% specificity when compared to normal control samples. Given the high detection specificity, the analysis of ZNF DNA methylation in combination with other DNA methylation biomarkers may be useful in the clinical setting for HNSCC detection and surveillance, particularly in high-risk patients. Several additional candidates identified through this work can be further investigated toward future development of a multi-gene panel of biomarkers for the surveillance and detection of HNSCC.

  3. Anomalous altered expressions of downstream gene-targets in TP53-miRNA pathways in head and neck cancer.

    Science.gov (United States)

    Mitra, Sanga; Mukherjee, Nupur; Das, Smarajit; Das, Pijush; Panda, Chinmay Kumar; Chakrabarti, Jayprokas

    2014-01-01

    The prevalence of head and neck squamous cell carcinoma, HNSCC, continues to grow. Change in the expression of TP53 in HNSCC affects its downstream miRNAs and their gene targets, anomalously altering the expressions of the five genes, MEIS1, AGTR1, DTL, TYMS and BAK1. These expression alterations follow the repression of TP53 that upregulates miRNA-107, miRNA- 215, miRNA-34 b/c and miRNA-125b, but downregulates miRNA-155. The above five so far unreported genes are the targets of these miRNAs. Meta-analyses of microarray and RNA-Seq data followed by qRT-PCR validation unravel these new ones in HNSCC. The regulatory roles of TP53 on miRNA-155 and miRNA-125b differentiate the expressions of AGTR1 and BAK1in HNSCC vis-à-vis other carcinogenesis. Expression changes alter cell cycle regulation, angiogenic and blood cell formation, and apoptotic modes in affliction. Pathway analyses establish the resulting systems-level functional and mechanistic insights into the etiology of HNSCC.

  4. Association of Complement Receptor 2 Gene Polymorphisms with Susceptibility to Osteonecrosis of the Femoral Head in Systemic Lupus Erythematosus

    Directory of Open Access Journals (Sweden)

    Tae-Ho Kim

    2016-01-01

    Full Text Available Osteonecrosis of the femoral head (ONFH is a complex and multifactorial disease that is influenced by a number of genetic factors in addition to environmental factors. Some autoimmune disorders, including systemic lupus erythematosus (SLE, rheumatoid arthritis (RA, and inflammatory bowel disease (IBD, are associated with the development of ONFH. Complement receptor type 2 (CR2 is membrane glycoprotein which binds C3 degradation products generated during complement activation. CR2 has many important functions in normal immunity and is assumed to play a role in the development of autoimmune disease. We investigated whether CR2 gene polymorphisms are associated with risk of ONFH in SLE patients. Eight polymorphisms in the CR2 gene were genotyped using TaqMan™ assays in 150 SLE patients and 50 ONFH in SLE patients (SLE_ONFH. The association analysis of genotyped SNPs and haplotypes was performed with ONFH. It was found that three SNPs, rs3813946 in 5′-UTR (untranslated region, rs311306 in intron 1, and rs17615 in exon 10 (nonsynonymous SNP; G/A, Ser639Asn of the CR2 gene, were associated with an increased risk of ONFH under recessive model (P values; 0.004~0.016. Haplotypes were also associated with an increased risk (OR; 3.73~ of ONFH in SLE patients. These findings may provide evidences that CR2 contributes to human ONFH susceptibility in Korean SLE patients.

  5. Anomalous altered expressions of downstream gene-targets in TP53-miRNA pathways in head and neck cancer

    Science.gov (United States)

    Mitra, Sanga; Mukherjee, Nupur; Das, Smarajit; Das, Pijush; Panda, Chinmay Kumar; Chakrabarti, Jayprokas

    2014-01-01

    The prevalence of head and neck squamous cell carcinoma, HNSCC, continues to grow. Change in the expression of TP53 in HNSCC affects its downstream miRNAs and their gene targets, anomalously altering the expressions of the five genes, MEIS1, AGTR1, DTL, TYMS and BAK1. These expression alterations follow the repression of TP53 that upregulates miRNA-107, miRNA- 215, miRNA-34 b/c and miRNA-125b, but downregulates miRNA-155. The above five so far unreported genes are the targets of these miRNAs. Meta-analyses of microarray and RNA-Seq data followed by qRT-PCR validation unravel these new ones in HNSCC. The regulatory roles of TP53 on miRNA-155 and miRNA-125b differentiate the expressions of AGTR1 and BAK1in HNSCC vis-à-vis other carcinogenesis. Expression changes alter cell cycle regulation, angiogenic and blood cell formation, and apoptotic modes in affliction. Pathway analyses establish the resulting systems-level functional and mechanistic insights into the etiology of HNSCC. PMID:25186767

  6. Development of Tuning Fork Based Probes for Atomic Force Microscopy

    Science.gov (United States)

    Jalilian, Romaneh; Yazdanpanah, Mehdi M.; Torrez, Neil; Alizadeh, Amirali; Askari, Davood

    2014-03-01

    This article reports on the development of tuning fork-based AFM/STM probes in NaugaNeedles LLC for use in atomic force microscopy. These probes can be mounted on different carriers per customers' request. (e.g., RHK carrier, Omicron carrier, and tuning fork on a Sapphire disk). We are able to design and engineer tuning forks on any type of carrier used in the market. We can attach three types of tips on the edge of a tuning fork prong (i.e., growing Ag2Ga nanoneedles at any arbitrary angle, cantilever of AFM tip, and tungsten wire) with lengths from 100-500 μm. The nanoneedle is located vertical to the fork. Using a suitable insulation and metallic coating, we can make QPlus sensors that can detect tunneling current during the AFM scan. To make Qplus sensors, the entire quartz fork will be coated with an insulating material, before attaching the nanoneedle. Then, the top edge of one prong is coated with a thin layer of conductive metal and the nanoneedle is attached to the fork end of the metal coated prong. The metal coating provides electrical connection to the tip for tunneling current readout and to the electrodes and used to read the QPlus current. Since the amount of mass added to the fork is minimal, the resonance frequency spectrum does not change and still remains around 32.6 KHz and the Q factor is around 1,200 in ambient condition. These probes can enhance the performance of tuning fork based atomic microscopy.

  7. Msx genes define a population of mural cell precursors required for head blood vessel maturation.

    Science.gov (United States)

    Lopes, Miguel; Goupille, Olivier; Saint Cloment, Cécile; Lallemand, Yvan; Cumano, Ana; Robert, Benoît

    2011-07-01

    Vessels are primarily formed from an inner endothelial layer that is secondarily covered by mural cells, namely vascular smooth muscle cells (VSMCs) in arteries and veins and pericytes in capillaries and veinules. We previously showed that, in the mouse embryo, Msx1(lacZ) and Msx2(lacZ) are expressed in mural cells and in a few endothelial cells. To unravel the role of Msx genes in vascular development, we have inactivated the two Msx genes specifically in mural cells by combining the Msx1(lacZ), Msx2(lox) and Sm22α-Cre alleles. Optical projection tomography demonstrated abnormal branching of the cephalic vessels in E11.5 mutant embryos. The carotid and vertebral arteries showed an increase in caliber that was related to reduced vascular smooth muscle coverage. Taking advantage of a newly constructed Msx1(CreERT2) allele, we demonstrated by lineage tracing that the primary defect lies in a population of VSMC precursors. The abnormal phenotype that ensues is a consequence of impaired BMP signaling in the VSMC precursors that leads to downregulation of the metalloprotease 2 (Mmp2) and Mmp9 genes, which are essential for cell migration and integration into the mural layer. Improper coverage by VSMCs secondarily leads to incomplete maturation of the endothelial layer. Our results demonstrate that both Msx1 and Msx2 are required for the recruitment of a population of neural crest-derived VSMCs.

  8. Wireless tuning fork gyroscope for biomedical applications

    Science.gov (United States)

    Abraham, Jose K.; Varadan, Vijay K.; Whitchurch, Ashwin K.; Sarukesi, K.

    2003-07-01

    This paper presents the development of a Bluetooth enabled wireless tuning fork gyroscope for the biomedical applications, including gait phase detection system, human motion analysis and physical therapy. This gyroscope is capable of measuring rotation rates between -90 and 90 and it can read the rotation information using a computer. Currently, the information from a gyroscope can trigger automobile airbag deployment during rollover, improve the accuracy and reliability of GPS navigation systems and stabilize moving platforms such as automobiles, airplanes, robots, antennas, and industrial equipment. Adding wireless capability to the existing gyroscope could help to expand its applications in many areas particularly in biomedical applications, where a continuous patient monitoring is quite difficult. This wireless system provides information on several aspects of activities of patients for real-time monitoring in hospitals.

  9. Chemical and biological sensing using tuning forks

    Science.gov (United States)

    Tao, Nongjian; Boussaad, Salah

    2012-07-10

    A device for sensing a chemical analyte is disclosed. The device is comprised of a vibrating structure having first and second surfaces and having an associated resonant frequency and a wire coupled between the first and second surfaces of the vibrating structure, wherein the analyte interacts with the wire and causes a change in the resonant frequency of the vibrating structure. The vibrating structure can include a tuning fork. The vibrating structure can be comprised of quartz. The wire can be comprised of polymer. A plurality of vibrating structures are arranged in an array to increase confidence by promoting a redundancy of measurement or to detect a plurality of chemical analytes. A method of making a device for sensing a chemical analyte is also disclosed.

  10. The TALE class homeobox gene Smed-prep defines the anterior compartment for head regeneration.

    Directory of Open Access Journals (Sweden)

    Daniel A Felix

    2010-04-01

    Full Text Available Planaria continue to blossom as a model system for understanding all aspects of regeneration. They provide an opportunity to understand how the replacement of missing tissues from preexisting adult tissue is orchestrated at the molecular level. When amputated along any plane, planaria are capable of regenerating all missing tissue and rescaling all structures to the new size of the animal. Recently, rapid progress has been made in understanding the developmental pathways that control planarian regeneration. In particular Wnt/beta-catenin signaling is central in promoting posterior fates and inhibiting anterior identity. Currently the mechanisms that actively promote anterior identity remain unknown. Here, Smed-prep, encoding a TALE class homeodomain, is described as the first gene necessary for correct anterior fate and patterning during planarian regeneration. Smed-prep is expressed at high levels in the anterior portion of whole animals, and Smed-prep(RNAi leads to loss of the whole brain during anterior regeneration, but not during lateral regeneration or homeostasis in intact worms. Expression of markers of different anterior fated cells are greatly reduced or lost in Smed-prep(RNAi animals. We find that the ectopic anterior structures induced by abrogation of Wnt signaling also require Smed-prep to form. We use double knockdown experiments with the S. mediterranea ortholog of nou-darake (that when knocked down induces ectopic brain formation to show that Smed-prep defines an anterior fated compartment within which stem cells are permitted to assume brain fate, but is not required directly for this differentiation process. Smed-prep is the first gene clearly implicated as being necessary for promoting anterior fate and the first homeobox gene implicated in establishing positional identity during regeneration. Together our results suggest that Smed-prep is required in stem cell progeny as they form the anterior regenerative blastema and is

  11. The TALE class homeobox gene Smed-prep defines the anterior compartment for head regeneration.

    Science.gov (United States)

    Felix, Daniel A; Aboobaker, A Aziz

    2010-04-22

    Planaria continue to blossom as a model system for understanding all aspects of regeneration. They provide an opportunity to understand how the replacement of missing tissues from preexisting adult tissue is orchestrated at the molecular level. When amputated along any plane, planaria are capable of regenerating all missing tissue and rescaling all structures to the new size of the animal. Recently, rapid progress has been made in understanding the developmental pathways that control planarian regeneration. In particular Wnt/beta-catenin signaling is central in promoting posterior fates and inhibiting anterior identity. Currently the mechanisms that actively promote anterior identity remain unknown. Here, Smed-prep, encoding a TALE class homeodomain, is described as the first gene necessary for correct anterior fate and patterning during planarian regeneration. Smed-prep is expressed at high levels in the anterior portion of whole animals, and Smed-prep(RNAi) leads to loss of the whole brain during anterior regeneration, but not during lateral regeneration or homeostasis in intact worms. Expression of markers of different anterior fated cells are greatly reduced or lost in Smed-prep(RNAi) animals. We find that the ectopic anterior structures induced by abrogation of Wnt signaling also require Smed-prep to form. We use double knockdown experiments with the S. mediterranea ortholog of nou-darake (that when knocked down induces ectopic brain formation) to show that Smed-prep defines an anterior fated compartment within which stem cells are permitted to assume brain fate, but is not required directly for this differentiation process. Smed-prep is the first gene clearly implicated as being necessary for promoting anterior fate and the first homeobox gene implicated in establishing positional identity during regeneration. Together our results suggest that Smed-prep is required in stem cell progeny as they form the anterior regenerative blastema and is required for

  12. The role of odd-skipped family genes in the Drosophila head development

    OpenAIRE

    Pereira, Catarina Brás

    2008-01-01

    Tese de doutoramento em Bioquímica (Biologia Molecular) apresentada à Fac. de Ciências e Tecnologia da Univ. de Coimbra O desenvolvimento de organismos multicelulares requer uma coordenação correcta entre a proliferação e a especificação das células. As mesmas vias de sinalização extracelular que controlam a especificação da identidade das células também regulam a proliferação das mesmas. O principal objectivo desta tese foi compreender o papel da família de genes odd durante a...

  13. Clusterin is a Gene Specific Target of MicroRNA-21 in Head and Neck Squamous Cell Carcinoma

    Science.gov (United States)

    Mydlarz, Wojciech; Uemura, Mamoru; Ahn, Sun; Hennessey, Patrick; Chang, Steven; Demokan, Semra; Sun, Wenyue; Shao, Chunbo; Bishop, Justin; Krosting, Julie; Mambo, Elizabeth; Westra, William; Ha, Patrick; Sidransky, David; Califano, Joseph

    2014-01-01

    Purpose: MicroRNA-21 (miRNA-21) has proto-oncogenic properties, though no miRNA-21 specific targets have been found in head and neck squamous cell carcinoma (HNSCC). Further study of miRNA-21 and its specific targets is essential to understanding HNSCC biology. Experimental Design: miRNA expression profiles of 10 HNSCC and 10 normal mucosa samples were investigated using a custom miRNA microarray. 13 HNSCC and 5 normal mucosa primary tissue specimens underwent mRNA expression microarray analysis. To identify miRNA-21 downstream targets, oral keratinocyte cells were subjected to microarray analysis after miRNA-21 transient transfection. miRNA and mRNA expression were validated by RT-qPCR in a separate cohort of 16 HNSCC and 15 normal mucosal samples. Microarray and bioinformatics analyses were integrated to identify potential gene targets. In vitro assays looked at the function and interaction of miRNA-21 and its specific gene targets. Results: miRNA-21 was upregulated in HNSCC and stimulated cell growth. Integrated analyses identified Clusterin (CLU) as a potential miRNA-21 gene target. CLU was downregulated after forced expression of miRNA-21 in normal and HNSCC cell lines. The activity of a luciferase construct containing the 3’UTR of CLU was repressed by the ectopic expression of miRNA-21. CLU was also downregulated in primary HNSCC and correlated with miRNA-21 over-expression. CLU variant 1 (CLU-1) was the predominant splice variant in HNSCC, and showed growth suppression function that was reversed by miRNA-21 over-expression. Conclusions: CLU is a specific, functional target of oncogenic miRNA-21 in HNSCC. CLU-1 isoform is the predominant growth suppressive variant targeted by miRNA-21. PMID:24327270

  14. The Trail Inventory of Deep Fork NWR [Cycle 2

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — The purpose of this report is to create a baseline inventory of all non-motorized trails on Deep Fork National Wildlife Refuge. Trails in this inventory are eligible...

  15. Regulation of replication fork progression through histone supply and demand

    DEFF Research Database (Denmark)

    Groth, Anja; Corpet, Armelle; Cook, Adam J L

    2007-01-01

    DNA replication in eukaryotes requires nucleosome disruption ahead of the replication fork and reassembly behind. An unresolved issue concerns how histone dynamics are coordinated with fork progression to maintain chromosomal stability. Here, we characterize a complex in which the human histone...... chaperone Asf1 and MCM2-7, the putative replicative helicase, are connected through a histone H3-H4 bridge. Depletion of Asf1 by RNA interference impedes DNA unwinding at replication sites, and similar defects arise from overproduction of new histone H3-H4 that compromises Asf1 function. These data link Asf......1 chaperone function, histone supply, and replicative unwinding of DNA in chromatin. We propose that Asf1, as a histone acceptor and donor, handles parental and new histones at the replication fork via an Asf1-(H3-H4)-MCM2-7 intermediate and thus provides a means to fine-tune replication fork...

  16. Inventory and Monitoring Plan for Deep Fork National Wildlife Refuge

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This Inventory and Monitoring Plan (IMP) is prepared to document the inventory and monitoring surveys that will, or could be conducted at Deep Fork National Wildlife...

  17. Assembly of Slx4 signaling complexes behind DNA replication forks.

    Science.gov (United States)

    Balint, Attila; Kim, TaeHyung; Gallo, David; Cussiol, Jose Renato; Bastos de Oliveira, Francisco M; Yimit, Askar; Ou, Jiongwen; Nakato, Ryuichiro; Gurevich, Alexey; Shirahige, Katsuhiko; Smolka, Marcus B; Zhang, Zhaolei; Brown, Grant W

    2015-08-13

    Obstructions to replication fork progression, referred to collectively as DNA replication stress, challenge genome stability. In Saccharomyces cerevisiae, cells lacking RTT107 or SLX4 show genome instability and sensitivity to DNA replication stress and are defective in the completion of DNA replication during recovery from replication stress. We demonstrate that Slx4 is recruited to chromatin behind stressed replication forks, in a region that is spatially distinct from that occupied by the replication machinery. Slx4 complex formation is nucleated by Mec1 phosphorylation of histone H2A, which is recognized by the constitutive Slx4 binding partner Rtt107. Slx4 is essential for recruiting the Mec1 activator Dpb11 behind stressed replication forks, and Slx4 complexes are important for full activity of Mec1. We propose that Slx4 complexes promote robust checkpoint signaling by Mec1 by stably recruiting Dpb11 within a discrete domain behind the replication fork, during DNA replication stress.

  18. An inventory of wildlife resources, Marsh Fork, summer 1973

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — The Bureau of Sport Fisheries and Wildlife contracted us to do a wildlife resource inventory of the Marsh Fork in summer, 1973. We had planned the inventory in two...

  19. Combining eicosapentaenoic acid, decosahexaenoic acid and arachidonic acid, using a fully crossed design, affect gene expression and eicosanoid secretion in salmon head kidney cells in vitro.

    Science.gov (United States)

    Holen, Elisabeth; He, Juyun; Espe, Marit; Chen, Liqiou; Araujo, Pedro

    2015-08-01

    Future feed for farmed fish are based on untraditional feed ingredients, which will change nutrient profiles compared to traditional feed based on marine ingredients. To understand the impact of oils from different sources on fish health, n-6 and n-3 polyunsaturated fatty acids (PUFAs) were added to salmon head kidney cells, in a fully crossed design, to monitor their individual and combined effects on gene expression. Exposing salmon head kidney cells to single fatty acids, arachidonic acid (AA) or decosahexaenoic acid (DHA), resulted in down-regulation of cell signaling pathway genes and specific fatty acid metabolism genes as well as reduced prostaglandin E2 (PGE2) secretion. Eicosapentaenoic acid (EPA) had no impact on gene transcription in this study, but reduced the cell secretion of PGE2. The combined effect of AA + EPA resulted in up-regulation of eicosanoid pathway genes and the pro-inflammatory cytokine, tumor necrosis factor alpha (TNF-α), Bclx (an inducer of apoptosis) and fatty acid translocase (CD36) as well as increased cell secretion of PGE2 into the media. Adding single fatty acids to salmon head kidney cells decreased inflammation markers in this model. The combination AA + EPA acted differently than the rest of the fatty acid combinations by increasing the inflammation markers in these cells. The concentration of fatty acid used in this experiment did not induce any lipid peroxidation responses.

  20. Environmental Assessment: Demolish 452 at Grand Forks Air Force Base

    Science.gov (United States)

    2005-12-01

    Preserve” has been developed to restore a part of the native tallgrass prairie that once was dominant in this region. Plants thriving in this...native wildflower species. The Grand Forks AFB Natural Resources Manager installed a butterfly garden in the Prairie View Nature 32 Preserve in the...characterized as typical prairie potholes found within the northern plains ecoregion. 31 Wetlands on Grand Forks AFB occur frequently in drainage

  1. Fascin, may the Forked be with you.

    Science.gov (United States)

    Okenve-Ramos, Pilar; Llimargas, Marta

    2014-01-01

    The FGFR pathway triggers a wide range of key biological responses. Among others, the Breathless (Btl, Drosophila FGFR1) receptor cascade promotes cell migration during embryonic tracheal system development. However, how the actin cytoskeleton responds to Btl pathway activation to induce cell migration has remained largely unclear. Our recent results shed light into this issue by unveiling a link between the actin-bundling protein Singed (Sn) and the Btl pathway. We showed that the Btl pathway regulates sn, which leads to the stabilization of the actin bundles required for filopodia formation and actin cytoskeleton rearrangement. This regulation contributes to tracheal migration, tracheal branch fusion and tracheal cell elongation. Parallel actin bundles (PABs) are usually cross-linked by more than one actin-bundling protein. Accordingly, we have also shown that sn synergistically interacts with forked (f), another actin crosslinker. In this Extra View we extend f analysis and hypothesize how both actin-bundling proteins may act together to regulate the PABs during tracheal embryonic development. Although both proteins are required for similar tracheal events, we suggest that Sn is essential for actin bundle initiation and stiffening, while F is required for the lengthening and further stabilization of the PABs.

  2. Evaluation of Aegilops tauschii for Heading Date and Its Gene Location in a Re-synthesized Hexaploid Wheat

    Institute of Scientific and Technical Information of China (English)

    XIANG Zhi-guo; ZHANG Lian-quan; NING Shun-zong; ZHENG You-Liang; LIU Deng-cai

    2009-01-01

    The successful worldwide cultivation of hexaploid wheat in a diverse range of environments is because of, in part, breeding and selection for appropriate heading date. To adjust and fine-tune the heading time of hexaploid wheat to particular geographical regions and specific environment within these, there is an urgent need to evaluate and use alternative alleles for heading time. Aegilops tauschii, the donor species of D-genome of hexaploid wheat, has a wide geographic distribution. The present study revealed a wide variation for heading time among 56 Ae. tauschii accessions. All the accessions with short heading dates belonged to the ssp. tauschii, whereas most of ssp. strangulata accessions showed very long heading date. The heading date was also related to distribution of this species. The monotelosomic and monosomic analysis of a synthetic hexaploid wheat showed that chromosome 2D derived from ssp. tauschii accession AS60 had a major effect on promoting heading time with a reduction of more than 5 days. It is postulated that this Ae. tauschii genotype possess the allele Ppd-Dt1 responsible for the insensitivity to photoperiod. This allele is probably different from Ppd-D1 existing in hexaploid wheat. The new allele Ppd-Dt1 derived from Ae. tauschii might be used as a source for hexaploid wheat breeding on photoperiod response.

  3. Association of mutations in the zona pellucida binding protein 1 (ZPBP1) gene with abnormal sperm head morphology in infertile men

    Science.gov (United States)

    Yatsenko, Alexander N.; O'Neil, Derek S.; Roy, Angshumoy; Arias-Mendoza, Paola A.; Chen, Ruihong; Murthy, Lata J.; Lamb, Dolores J.; Matzuk, Martin M.

    2012-01-01

    Nearly 7% of men are afflicted by male infertility worldwide, and genetic factors are suspected to play a significant role in the majority of these patients. Although sperm morphology is an important parameter measured in the semen analysis, only a few genetic causes of teratozoospermia are currently known. The objective of this study was to define the association between alterations in the genes encoding the Golgi-associated PDZ- and coiled-coil motif containing protein (GOPC), the protein interacting with C kinase 1 (PICK1) and the acrosomal protein zona pellucida binding protein 1 (ZPBP1/sp38) with abnormal sperm head morphology in infertile men. Previous reports demonstrated that mice lacking Gopc, Pick1 and Zpbp1 are infertile due to abnormal head morphology. Herein, using our validated RNA-based method, we studied spermatozoal cDNA encoding the human GOPC, PICK1 and ZPBP1 genes in 381 teratozoospermic and 240 controls patients via direct sequencing. Among these genes, we identified missense and splicing mutations in the sperm cDNA encoding ZPBP1 in 3.9% (15/381) of men with abnormal sperm head morphology. These mutations were not observed in 240 matched controls and the dbSNP database (χ2 = 9.3, P = 0.002). In contrast, statistically significant and functionally relevant mutations were not discovered in the GOPC and PICK1 genes. In our study ZPBP1 mutations are associated with abnormal sperm head morphology, defined according to strict criteria, resembling the mouse Zpbp1 null phenotype. We hypothesize that missense mutations exert a dominant-negative effect due to altered ZPBP1 protein folding and protein:protein interactions in the acrosome. PMID:21911476

  4. More forks on the road to replication stress recovery

    Institute of Scientific and Technical Information of China (English)

    Chris Allen; Amanda K. Ashley; Robert Hromas; Jac A. Nickoloff

    2011-01-01

    High-fidelity replication of DNA, and its accurate segregation to daughter cells, is critical for maintaining genome stability and suppressing cancer. DNA replication forks are stalled by many DNA lesions, activating checkpoint proteins that stabilize stalled forks.Stalled forks may eventually collapse, producing a broken DNA end. Fork restart is typically mediated by proteins initially identified by their rotes in homologous recombination repair of DNA double-strand breaks (DSBs). In recent years, several proteins involved in DSB repair by non-homologous end joining (NHEJ) have been implicated in the replication stress response, including DNA-PKcs, Ku,DNA Ligase IV-XRCC4, Artemis, XLF and Metnase. It is currently unclear whether NHEJ proteins are involved in the replication stress response through indirect (signaling) roles, and/or direct roles involving DNA end joining. Additional complexity in the replication stress response centers around RPA, which undergoes significant post-translational modification after stress, and RAD52, a conserved HR protein whose role in DSB repair may have shifted to another protein in higher eukaryotes, such as BRCA2, but retained its rote in fork restart. Most cancer therapeutic strategies create DNA reputation stress. Thus, it is imperative to gain a better understanding of replication stress response proteins and pathways to improve cancer therapy.

  5. OK - Establishing a mussel monitoring program to evaluate point-source discharges into Deep Fork NWR

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — A study incorporating several investigative methods was conducted at the Deep Fork River, Okmulgee, Oklahoma in and near the Deep Fork National Wildlife Refuge. The...

  6. Effects of Blood-Activating and Stasis-Removing Drugs Combined with VEGF Gene Transfer on Angiogenesis in Ischemic Necrosis of the Femoral Head

    Institute of Scientific and Technical Information of China (English)

    LI Jun-hui; WU Ya-ling; YE Jian-hong; NING Ya-gong; YU Hai-ying; PENG Zhong-jie; LUAN Xiao-wen

    2009-01-01

    Objective:To observe the promoting effects of blood-activating and stasis-removing Chinese drugs combined with vascular endothelial growth factor (VEGF) gene transfer on angiogenesis in ischemic necrosis of the femoral head.Methods:Forty Japanese giant-ear rabbits were randomly divided into a control group, a model group, a Chinese drug group, a gene group, and a combined group.After 8 weeks of treatment, the rate of VEGF positive cell expression in the synovium of the femoral head was measured using the immunohistochemical method, and the number of blood vessels in the femoral head was measured by digital subtraction angiography.Results:The rate of VEGF positive cell expression in the model group was significantly lower than that in the Chinese drug group (P<0.05) and very significantly lower than those in other groups (P<0.01);but in the combined group it was significantly higher than in the Chinese drug group (P<0.05).The differences in the number of blood vessels in area A between the model group and other groups were not statistically significant.However, in area B, the number of blood vessels significantly increased in the control group, the gene group and the combined group as compared with the model group (P<0.05), and in the combined group the number of blood vessels was significantly more than in the gene group (P<0.05);but in the Chinese drug group it was not significantly different than the model group P>0.05).Conelusion:Either the blood-activating and stasis-removing Chinese drugs or VEGF gene transfer can promote the angiogenesis and building of collateral circulation for femoral head ischemic necrosis, and the combined therapy with Chinese drugs or VEGF gene transfer may show a better therapeutic effect.The present study provides an experimental basis for clinical application of the combined therapy with the blood-activating and stasis-removing Chinese drugs and VEGF gene transfer.

  7. Mapping of Hd6-f1 Gene on Rice Heading Date%水稻抽穗期基因 Hd6-f1的定位

    Institute of Scientific and Technical Information of China (English)

    周鹏飞; 柳絮; 张华; 宣宁; 李军; 杨永义; 李广贤; 姚方印; 刘开启

    2015-01-01

    本试验以明恢63(供体)/早熟豫6(受体)的BC4 F2分离群体为材料,采用BSA ( Bulked segrega-tion analysis)法,对控制水稻抽穗期分离的基因进行SSR分子标记定位。 BC4 F2出现抽穗期分离,早抽穗植株为253株,晚抽穗植株为657株,χ2=3.66<P0.05=3.84,符合1∶3的孟德尔分离比,表明F2群体的抽穗期分离受一对等位基因控制,晚抽穗性状为显性。以明恢63×早熟豫6的BC4 F2分离群体的253株隐性单株为定位群体,将该抽穗基因(暂时命名为Hd6-f1)定位在水稻第6染色体分子标记RM19771与RM527之间,遗传距离分别为0.2 cM和2.9 cM,与RM19780共分离。%Using the BC4F2 segregation populations of Minghui 63(donor) and Zaoshuyu 6(receptor) as materials, the SSR markers were located for the gene on rice heading date by the bulked segregation analysis (BSA).The BC4F2 population had 253 early heading plants and 657 late heading plants( χ2 =3.66heading date was controlled by a pair of alleles and the late heading character was dominant .Using the 253 early heading plants of BC 4 F2 population as mapping population , the gene on heading date named Hd6-f1 was mapped on chromosome 6 between SSR markers RM19771 and RM527 with the genetic distances as 0.2 cM and 2.9 cM respectively, and co-segregated with RM19780 .

  8. A Multi-Fork Z-Axis Quartz Micromachined Gyroscope

    Directory of Open Access Journals (Sweden)

    Aiying Yang

    2013-09-01

    Full Text Available A novel multi-fork z-axis gyroscope is presented in this paper. Different from traditional quartz gyroscopes, the lateral electrodes of the sense beam can be arranged in simple patterns; as a result, the fabrication is simplified. High sensitivity is achieved by the multi-fork design. The working principles are introduced, while the finite element method (FEM is used to simulate the modal and sensitivity. A quartz fork is fabricated, and a prototype is assembled. Impedance testing shows that the drive frequency and sense frequency are similar to the simulations, and the quality factor is approximately 10,000 in air. The scale factor is measured to be 18.134 mV/(°/s and the nonlinearity is 0.40% in a full-scale input range of ±250 °/s.

  9. New histone supply regulates replication fork speed and PCNA unloading

    DEFF Research Database (Denmark)

    Mejlvang, Jakob; Feng, Yunpeng; Alabert, Constance;

    2014-01-01

    Correct duplication of DNA sequence and its organization into chromatin is central to genome function and stability. However, it remains unclear how cells coordinate DNA synthesis with provision of new histones for chromatin assembly to ensure chromosomal stability. In this paper, we show...... that replication fork speed is dependent on new histone supply and efficient nucleosome assembly. Inhibition of canonical histone biosynthesis impaired replication fork progression and reduced nucleosome occupancy on newly synthesized DNA. Replication forks initially remained stable without activation...... of conventional checkpoints, although prolonged histone deficiency generated DNA damage. PCNA accumulated on newly synthesized DNA in cells lacking new histones, possibly to maintain opportunity for CAF-1 recruitment and nucleosome assembly. Consistent with this, in vitro and in vivo analysis showed that PCNA...

  10. A multi-fork z-axis quartz micromachined gyroscope.

    Science.gov (United States)

    Feng, Lihui; Zhao, Ke; Sun, Yunan; Cui, Jianmin; Cui, Fang; Yang, Aiying

    2013-01-01

    A novel multi-fork z-axis gyroscope is presented in this paper. Different from traditional quartz gyroscopes, the lateral electrodes of the sense beam can be arranged in simple patterns; as a result, the fabrication is simplified. High sensitivity is achieved by the multi-fork design. The working principles are introduced, while the finite element method (FEM) is used to simulate the modal and sensitivity. A quartz fork is fabricated, and a prototype is assembled. Impedance testing shows that the drive frequency and sense frequency are similar to the simulations, and the quality factor is approximately 10,000 in air. The scale factor is measured to be 18.134 mV/(°/s) and the nonlinearity is 0.40% in a full-scale input range of ±250 °/s.

  11. Geometric Metasurface Fork Gratings for Vortex Beam Generation and Manipulation

    CERN Document Server

    Chen, Shumei; Li, Guixin; Zhang, Shuang; Cheah, Kok Wai

    2016-01-01

    In recent years, optical vortex beams possessing orbital angular momentum have caught much attention due to their potential for high capacity optical communications. This capability arises from the unbounded topological charges of orbital angular momentum (OAM) that provides infinite freedoms for encoding information. The two most common approaches for generating vortex beams are through fork diffraction gratings and spiral phase plates. While realization of conventional spiral phase plate requires complicated 3D fabrication, the emerging field of metasurfaces has provided a planar and facile solution for generating vortex beams of arbitrary orbit angular momentum. Here we realize a novel type of geometric metasurface fork grating that seamlessly combine the functionality of a metasurface phase plate for vortex beam generation, and that of a linear phase gradient metasurface for controlling the wave propagation direction. The metasurface fork grating is therefore capable of simultaneously controlling both the...

  12. Elm Fork of the Trinity River Floodplain Management Study

    OpenAIRE

    Tickle, Greg; Clary, Melinda

    2001-01-01

    Wendy Lopez and Associates, Inc. (WLA) was asked to provide a conservation and ecological restoration overview for the City of Dallas as part of an Elm Fork Floodplain Management Study. This study encompasses a unique portion of the main stem of the Elm Fork of the Trinity River, Dallas County, Dallas, Texas. The project area includes approximately 8.5 square miles, half of which lie within a 100-year floodplain. Approximately 15% of the project area is mature bottomland hardwood forest and s...

  13. Forked and Integrated Variants In An Open-Source Firmware Project

    DEFF Research Database (Denmark)

    Stanciulescu, Stefan; Schulze, Sandro; Wasowski, Andrzej

    2015-01-01

    and interactive source management platforms such as Github. We study advantages and disadvantages of forking using the case of Marlin, an open source firmware for 3D printers. We find that many problems and advantages of cloning do translate to forking. Interestingly, the Marlin community uses both forking...

  14. The CAG repeat polymorphism in the androgen receptor gene (AR) and its relationship to head and neck cancer.

    Science.gov (United States)

    dos Santos, M L; Sibov, T T; Nishimoto, I N; Kowalski, L P; Miracca, E C; Nagai, M A

    2004-02-01

    Sex hormones may play an important role in the tumorigenic process of the head and neck. The aim of our work was to investigate whether the androgen receptor (AR) CAG repeat polymorphism is associated with an increased relative risk for head and neck cancer. Genomic DNA from 103 male patients with head and neck carcinomas and 100 male controls were analyzed for the AR CAG polymorphism by PCR amplification and direct sequencing or denaturing polyacrilamide gel electrophoresis. Logistic regression analysis showed a significant association between CAG repeat length and risk of head and neck cancer in individuals with more than 20 CAG repeats [OR=2.54 (95% CI, 1.3-4.8)]. For the group of individuals with oral and laryngeal cancer the estimated relative risk was increased to 2.79 (95% CI, 1.2-6.3) and 3.06 (95% CI, 1.0-9.6), respectively, in men with CAG repeat length >20. These results suggest, for the first time, that shorter AR CAG repeat alleles have a protective effect for head and neck cancer development.

  15. Loss of Mitochondrial Tumor Suppressor Genes Expression Is Associated with Unfavorable Clinical Outcome in Head and Neck Squamous Cell Carcinoma: Data from Retrospective Study.

    Directory of Open Access Journals (Sweden)

    Ishrat Mahjabeen

    Full Text Available Mitochondrial genes play important roles in cellular energy metabolism, free radical generation, and apoptosis. Dysregulation of these genes have long been suspected to contribute to the generation of reactive oxygen species (ROS, increased proliferation and progression of cancer. A family of orthologues of yeast silent information regulator 3 (SIRT3, 4 (SIRT4 and mitochondrial tumor suppressor 1 (MTUS1 are important mitochondrial tumor suppressor genes which play an important role in the progression of multiple cancers. However, their role in the development of oxidative stress, enhanced proliferation and progression of head and neck squamous cell carcinoma (HNSCC has not yet been studied. In this study we aimed to test the association between reduced mitochondrial tumor suppressor genes' activities and enhancement in tissue oxidative stress and cell proliferation in HNSCC cases. The expression of mitochondrial tumor suppressor genes (SIRT3, SIRT4 and MTUS1, mitochondrial DNA repair gene (OGG1-2a and a proliferation marker (Ki-67 was studied in a study cohort of 120 HNSCC patients and controls with reverse transcriptase polymerase chain reaction (RT-PCR and real-time PCR (qPCR in order to determine the potential prognostic significance of these genes. A statistically significant downregulation of SIRT3 (p<0.001, SIRT4 (p<0.0001, MTUS1 (p<0.002 and OGG1 (p<0.0001 was observed in HNSCC compared to control samples. Ki-67 was also overexpressed (p<0.0001 in HNSCC versus control samples. Additionally, to explore gene-gene relationship, we observed a positive spearmen correlation between SIRT3 versus SIRT4 (r = 0.523***, p<0.0001, SIRT3 versus MTUS1 (r = 0.273***, p<0.001, SIRT3 versus OGG1-2a (r = 0.213*, p<0.03, SIRT4 versus OGG1 (r = 0.338***, p<0.0001 and MTUS1 versus OGG1-2a (r = 0.215*, p<0.03 in HNSCC cases. A negative spearman correlation was observed between OGG1 versus Ki-67 (r = -0.224**, p<0.01 and OGG1-2a versus Ki-67 (r = -0.224**, p<0

  16. cDNA-AFLP analysis reveals differential gene expression in incompatible interaction between infected non-heading Chinese cabbage and Hyaloperonospora parasitica.

    Science.gov (United States)

    Xiao, Dong; Liu, Shi-Tuo; Wei, Yan-Ping; Zhou, Dao-Yun; Hou, Xi-Lin; Li, Ying; Hu, Chun-Mei

    2016-01-01

    Non-heading Chinese cabbage (Brassica rapa ssp. chinensis) is one of the main green leafy vegetables in the world, especially in China, with significant economic value. Hyaloperonospora parasitica is a fungal pathogen responsible for causing downy mildew disease in Chinese cabbage, which greatly affects its production. The objective of this study was to identify transcriptionally regulated genes during incompatible interactions between non-heading Chinese cabbage and H. parasitica using complementary DNA-amplified fragment length polymorphism (cDNA-AFLP). We obtained 129 reliable differential transcript-derived fragments (TDFs) in a resistant line 'Suzhou Qing'. Among them, 121 upregulated TDFs displayed an expression peak at 24-48 h post inoculation (h.p.i.). Fifteen genes were further selected for validation of cDNA-AFLP expression patterns using quantitative reverse transcription PCR. Results confirmed the altered expression patterns of 13 genes (86.7%) revealed by the cDNA-AFLP. We identified four TDFs related to fungal resistance among the 15 TDFs. Furthermore, comparative analysis of four TDFs between resistant line 'Suzhou Qing' and susceptible line 'Aijiao Huang' showed that transcript levels of TDF14 (BcLIK1_A01) peaked at 48 h.p.i. and 25.1-fold increased in the resistant line compared with the susceptible line. Similarly, transcript levels of the other three genes, TDF42 (BcCAT3_A07), TDF75 (BcAAE3_A06) and TDF88 (BcAMT2_A05) peaked at 24, 48 and 24 h.p.i. with 25.1-, 100- and 15.8-fold increases, respectively. The results suggested that the resistance genes tended to transcribe at higher levels in the resistance line than in the susceptible line, which may provide resistance against pathogen infections. The present study might facilitate elucidating the molecular basis of the infection process and identifying candidate genes for resistance improvement of susceptible cultivars.

  17. Ten Things You Should Do with a Tuning Fork

    Science.gov (United States)

    Lincoln, James

    2013-01-01

    Tuning forks are wonderful tools for teaching physics. Every physics classroom should have several and every physics student should be taught how to use them. In this article, I highlight 10 enriching demonstrations that most teachers might not know, as well as provide tips to enhance the demonstrations teachers might already be doing. Some of…

  18. Accurate aging of juvenile salmonids using fork lengths

    Science.gov (United States)

    Sethi, Suresh; Gerken, Jonathon; Ashline, Joshua

    2017-01-01

    Juvenile salmon life history strategies, survival, and habitat interactions may vary by age cohort. However, aging individual juvenile fish using scale reading is time consuming and can be error prone. Fork length data are routinely measured while sampling juvenile salmonids. We explore the performance of aging juvenile fish based solely on fork length data, using finite Gaussian mixture models to describe multimodal size distributions and estimate optimal age-discriminating length thresholds. Fork length-based ages are compared against a validation set of juvenile coho salmon, Oncorynchus kisutch, aged by scales. Results for juvenile coho salmon indicate greater than 95% accuracy can be achieved by aging fish using length thresholds estimated from mixture models. Highest accuracy is achieved when aged fish are compared to length thresholds generated from samples from the same drainage, time of year, and habitat type (lentic versus lotic), although relatively high aging accuracy can still be achieved when thresholds are extrapolated to fish from populations in different years or drainages. Fork length-based aging thresholds are applicable for taxa for which multiple age cohorts coexist sympatrically. Where applicable, the method of aging individual fish is relatively quick to implement and can avoid ager interpretation bias common in scale-based aging.

  19. OsBBX14 delays heading date by repressing florigen gene expression under long and short-day conditions in rice.

    Science.gov (United States)

    Bai, Bo; Zhao, Jie; Li, Yaping; Zhang, Fang; Zhou, Jinjun; Chen, Fan; Xie, Xianzhi

    2016-06-01

    B-box (BBX) proteins are zinc finger proteins containing B-box domains, which have roles in Arabidopsis growth and development. However, little is known concerning rice BBXs. Herein, we identified a rice BBX protein, Oryza sativa BBX14 (OsBBX14). OsBBX14 is highly expressed in flag leaf blades. OsBBX14 expression shows a diurnal rhythm under photoperiodic conditions and subsequent continuous white light. OsBBX14 is located in the nucleus and has transcriptional activation potential. OsBBX14-overexpression (OsBBX14-OX) lines exhibited delayed heading date under long-day (LD) and short-day (SD) conditions, whereas RNAi lines of OsBBX14 lines had similar heading dates to the WT. The florigen genes, Hd3a and RFT1, were downregulated in the OsBBX14-OX lines under LD and SD conditions. Under LD conditions, Hd1 was expressed higher in the OsBBX14-OX lines than in the wild type (WT), and the rhythmic expression of circadian clock genes, OsLHY and OsPRR1, was changed in OsBBX14-OX lines. Thus, OsBBX14 acts as a floral repressor by promoting Hd1 expression under LD conditions, probably because of crosstalk with the circadian clock. Under SD conditions, Ehd1 expression was reduced in OsBBX14-OX lines, but Hd1 and circadian clock gene expressions were unaffected, indicating that OsBBX14 acts as a repressor of Ehd1. Our findings suggested that OsBBX14 regulates heading date differently under LD and SD conditions.

  20. Fork rotation and DNA precatenation are restricted during DNA replication to prevent chromosomal instability.

    Science.gov (United States)

    Schalbetter, Stephanie A; Mansoubi, Sahar; Chambers, Anna L; Downs, Jessica A; Baxter, Jonathan

    2015-08-18

    Faithful genome duplication and inheritance require the complete resolution of all intertwines within the parental DNA duplex. This is achieved by topoisomerase action ahead of the replication fork or by fork rotation and subsequent resolution of the DNA precatenation formed. Although fork rotation predominates at replication termination, in vitro studies have suggested that it also occurs frequently during elongation. However, the factors that influence fork rotation and how rotation and precatenation may influence other replication-associated processes are unknown. Here we analyze the causes and consequences of fork rotation in budding yeast. We find that fork rotation and precatenation preferentially occur in contexts that inhibit topoisomerase action ahead of the fork, including stable protein-DNA fragile sites and termination. However, generally, fork rotation and precatenation are actively inhibited by Timeless/Tof1 and Tipin/Csm3. In the absence of Tof1/Timeless, excessive fork rotation and precatenation cause extensive DNA damage following DNA replication. With Tof1, damage related to precatenation is focused on the fragile protein-DNA sites where fork rotation is induced. We conclude that although fork rotation and precatenation facilitate unwinding in hard-to-replicate contexts, they intrinsically disrupt normal chromosome duplication and are therefore restricted by Timeless/Tipin.

  1. A resistance-like gene identified by EST mapping and its association with a QTL controlling Fusarium head blight infection on wheat chromosome 3BS.

    Science.gov (United States)

    Shen, Xiaorong; Francki, Michael G; Ohm, Herbert W

    2006-06-01

    Fusarium head blight (FHB) is a major disease in the wheat growing regions of the world. A quantitative trait locus (QTL) on the short arm of chromosome 3B controls much of the variation for resistance. The cloning of candidate disease-resistance genes for FHB QTLs on chromosome 3B can provide further elucidation of the mechanisms that control resistance. However, rearrangements and divergence during plant genome evolution often hampers the identification of sequences with similarity to known disease-resistance genes. This study focuses on the use of wheat expressed sequence tags (ESTs) that map to the region on chromosome 3B containing the QTL for FHB resistance and low-stringency BLAST searching to identify sequences with similarity to known disease-resistance genes. One EST rich with leucine repeats and low similarity to a protein kinase domain of the barley Rpg1 gene was identified. Genetic mapping using a Ning894037 x Alondra recombinant inbred (RI) population showed that this EST mapped to the QTL on the short arm of chromosome 3B and may represent a portion of a newly diverged gene contributing to FHB resistance. The EST is a new marker suitable for marker-assisted selection and provides a starting point to begin map-based cloning for chromosome walking and investigate new diverged genes at this locus.

  2. Structure of eukaryotic CMG helicase at a replication fork and implications to replisome architecture and origin initiation.

    Science.gov (United States)

    Georgescu, Roxana; Yuan, Zuanning; Bai, Lin; de Luna Almeida Santos, Ruda; Sun, Jingchuan; Zhang, Dan; Yurieva, Olga; Li, Huilin; O'Donnell, Michael E

    2017-01-31

    The eukaryotic CMG (Cdc45, Mcm2-7, GINS) helicase consists of the Mcm2-7 hexameric ring along with five accessory factors. The Mcm2-7 heterohexamer, like other hexameric helicases, is shaped like a ring with two tiers, an N-tier ring composed of the N-terminal domains, and a C-tier of C-terminal domains; the C-tier contains the motor. In principle, either tier could translocate ahead of the other during movement on DNA. We have used cryo-EM single-particle 3D reconstruction to solve the structure of CMG in complex with a DNA fork. The duplex stem penetrates into the central channel of the N-tier and the unwound leading single-strand DNA traverses the channel through the N-tier into the C-tier motor, 5'-3' through CMG. Therefore, the N-tier ring is pushed ahead by the C-tier ring during CMG translocation, opposite the currently accepted polarity. The polarity of the N-tier ahead of the C-tier places the leading Pol ε below CMG and Pol α-primase at the top of CMG at the replication fork. Surprisingly, the new N-tier to C-tier polarity of translocation reveals an unforeseen quality-control mechanism at the origin. Thus, upon assembly of head-to-head CMGs that encircle double-stranded DNA at the origin, the two CMGs must pass one another to leave the origin and both must remodel onto opposite strands of single-stranded DNA to do so. We propose that head-to-head motors may generate energy that underlies initial melting at the origin.

  3. Termination of DNA replication forks: "Breaking up is hard to do".

    Science.gov (United States)

    Bailey, Rachael; Priego Moreno, Sara; Gambus, Agnieszka

    2015-01-01

    To ensure duplication of the entire genome, eukaryotic DNA replication initiates from thousands of replication origins. The replication forks move through the chromatin until they encounter forks from neighboring origins. During replication fork termination forks converge, the replisomes disassemble and topoisomerase II resolves the daughter DNA molecules. If not resolved efficiently, terminating forks result in genomic instability through the formation of pathogenic structures. Our recent findings shed light onto the mechanism of replisome disassembly upon replication fork termination. We have shown that termination-specific polyubiquitylation of the replicative helicase component - Mcm7, leads to dissolution of the active helicase in a process dependent on the p97/VCP/Cdc48 segregase. The inhibition of terminating helicase disassembly resulted in a replication termination defect. In this extended view we present hypothetical models of replication fork termination and discuss remaining and emerging questions in the DNA replication termination field.

  4. Differences in expression of oncogenes and tumor suppressor genes in different sites of head and neck squamous cell

    NARCIS (Netherlands)

    Takes, R P; Baatenburg de Jong, R J; Schuuring, E; Litvinov, S V; Hermans, J; Van Krieken, J H

    1999-01-01

    BACKGROUND: In most studies concerning chromosomal changes or protein expression in head and neck squamous cell carcinomas (HNSCC) no distinction is made between the sites within this area. The behaviour of tumors arising in one site or the other, however, differs significantly, suggesting different

  5. Identification of a tachykinin-related neuropeptide from the honeybee brain using direct MALDI-TOF MS and its gene expression in worker, queen and drone heads.

    Science.gov (United States)

    Takeuchi, H; Yasuda, A; Yasuda-Kamatani, Y; Kubo, T; Nakajima, T

    2003-06-01

    Using a combination of MALDI-TOF and on-line capillary HPLC/Q-Tof mass spectroscopy, we identified and determined the amino acid sequence of a novel neuropeptide in the brain of the honeybee Apis mellifera L., termed AmTRP peptide (Apis mellifera tachykinin-related peptide), related to insect tachykinin. A cDNA for a prepro-protein (prepro-AmTRP) of AmTRP was isolated and determined to encode seven AmTRPs 1-7. Northern blot analysis indicated that the prepro-AmTRP gene is expressed differentially in the nurse bee, forager, queen and drone heads. Strong expression was detected in the queen and forager heads, while weak and almost no significant expression was detected in the nurse and drone heads, respectively. These results suggest that AmTRP peptide functions as a neuromodulator and/or hormone, associated with sex-specific or age/division of labour-selective behaviour and/or physiology of the honeybees.

  6. A single administration of the peptide NAP induces long-term protective changes against the consequences of head injury: gene Atlas array analysis.

    Science.gov (United States)

    Romano, Jacob; Beni-Adani, Liana; Nissenbaum, Orlev Levy; Brenneman, Douglas E; Shohami, Esther; Gozes, Illana

    2002-01-01

    The femtomolar-acting eight-amino-acid peptide (NAP), derived from activity-dependent neuroprotective protein (ADNP), provides long-term protection against the deleterious effects of closed head injury (CHI) in mice. Fifteen minutes after injury, mice were divided into two groups, control and NAP-treated and a single subcutaneous injection of NAP or vehicle was administered. A third group served as sham-treated (not subjected to head trauma). Each mouse was assessed for its clinical function, using neurological severity score, at various time intervals following CHI, up to 30-45 d. Total cerebral cortex RNA was prepared from the site of injury of CHI mice, and from parallel regions in peptide-treated and sham brains. RNA was then reversed transcribed to yield radioactive cDNA preparations that were hybridized to Atlas array membranes containing 1200 cDNAs spots. Comparison of sham-treated individual mice showed differential expression levels of at least 15 mRNA species. Furthermore, results indicated that one of the genes that did not change among individuals but specifically increased after CHI and decreased after NAP treatment was the cell surface glycoprotein Mac-1 (CD11B antigen). Thus, Mac-1 is suggested as a marker for the long-term outcome of head injury and as a potential target for NAP protective actions.

  7. Bull Trout (Salvelinus Confluentus) Population and Habitat Surveys in the McKenzie and Middle Fork Willamette Basins, 2000 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    Taylor, Greg

    2000-11-28

    Prior to 1978, Dolly Varden Salvelinus malma were classified into an anadromous and interior form. Cavender (1978) classified the interior form as a distinct species, Salvelinus confluentus, the bull trout. Bull trout are large char weighing up to 18 kg and growing to over one meter in length (Goetz 1989). They are distinguished by a broad flat head, large downward curving maxillaries that extend beyond the eye, a well developed fleshy knob and a notch in the lower terminus of the snout, and light colored spots normally smaller than the pupil of the eye (Cavender 1978). Bull trout are found throughout northwestern North America from lat. 41{sup o}N to lat. 60{sup o}N. In Oregon, bull trout were once distributed throughout 12 basins in the Klamath and Columbia River systems including the Clackamas, Santiam, McKenzie and Middle Fork Willamette sub-basins west of the Cascades (Buchanan et al. 1997). However, it is believed bull trout have been extirpated from west of the Cascades with the exception of the McKenzie sub-basin. Before 1963, bull trout in the McKenzie sub-basin were a contiguous population from the mouth to Tamolitch Falls. Following the construction of Cougar and Trail Bridge Reservoirs there are three isolated populations: (1) mainstem McKenzie and tributaries from the mouth to Trail Bridge Reservoir. (2) mainstem McKenzie and tributaries above Trail Bridge Reservoir to Tamolitch Falls. (3) South Fork McKenzie and tributaries above Cougar Reservoir. The study area includes the three aforementioned McKenzie populations, and the Middle Fork Willamette and tributaries above Hills Creek Reservoir. We monitored bull trout populations in the McKenzie and Middle Fork Willamette basins using a combination of sampling techniques including: spawning surveys, standard pool counts, juvenile trapping, radio tracking, electronic fish counters, and a modified Hankin and Reeves protocol to estimate juvenile abundance and density. In addition, we continued to

  8. The Impact of Gross Anatomy on the Future Head and Neck Surgeon

    Science.gov (United States)

    Archibald, David J.; Carlson, Matthew L.

    2009-01-01

    Gross anatomy is not only a rite of passage for medical students as they enter the world of practicing medicine but may also be an unrecognized fork in the road in their pursuit of choosing a medical specialty. Otolaryngology: head and neck surgery tends to be poorly represented in medical school curriculum, often only offered as an elective…

  9. Avoidance of Linkage Drag Between Blast Resistance Gene and the QTL Conditioning Spikelet Fertility Based on Genotype Selection Against Heading Date in Rice

    Institute of Scientific and Technical Information of China (English)

    LIU Wen-qiang; FAN Ye-yang; CHEN Jie; SHI Yong-feng; WU Jian-li

    2009-01-01

    Previous study showed that a linkage drag between a blast resistance gene Pi25(t) and QTLs conditioning spikelet fertility (qSF-6) and number of filled grains per panicle (qNFGP-6) was detected on the short arm of chromosome 6. A larger population was used for further verification, and the results confirmed the linkage drag between the blast resistance gene and QTL conditioning spikelet fertility, other than QTL conditioning number of filled grains per panicle. Breakdown or avoidance of the linkage drag could be achieved by selection against the genotype background of a heading-date gene (qHD-7) that resided in the region between RM2 and RM214 on chromosome 7. For further validation, two lines with almost identical genotypes on all chromosomal regions except the Pi25(t) region on chromosome 6 were chosen to develop a new population. The results showed that qSF-6 could be further subdivided into qSF-6-1 and qSF-6-2. When the genotype of the region between RM2 and RM214 was from rice variety Zhong 156, the linkage drag between Pi25(t) and qSF-6-2 was detected and the allele of qSF-6-2 from rice variety Gumei 2 reduced the spikelet fertility. When the genotype of the region between RM2 and RM214 was from Gumei 2, no linkage drag was detected. This indicates that the linkage drag between the blast resistance gene and the QTL conditioning spikelet fertility could be broken down or avoided under a certain background genotype selection against heading-date and provides a marker aided solution for high level of blast resistance and yield breeding in rice and other crops as well.

  10. Thyroid active agents T3 and PTU differentially affect immune gene transcripts in the head kidney of rainbow trout (Oncorynchus mykiss).

    Science.gov (United States)

    Quesada-García, Alba; Encinas, Paloma; Valdehita, Ana; Baumann, Lisa; Segner, Helmut; Coll, Julio M; Navas, José M

    2016-05-01

    In mammals, numerous reports describe an immunomodulating effect of thyroid-active compounds. In contrast, only few reports have been published on this subject in fish. We previously demonstrated that immune cells of rainbow trout (Oncorhynchus mykiss) possess thyroid hormone receptors (THRs) and that exposure of trout to the thyroid hormone 3,3',5-triiodo-l-thyronine (T3) or the antithyroid drug propylthiouracil (PTU) alters immune cell transcript levels of THR and several immune genes. The present study aims to further characterize the immunomodulating action of thyroid-active compounds in trout immune cells. We report here the use of a custom-designed 60-mer oligo immune-targeted microarray for rainbow trout to analyze the gene expression profiles induced in the head kidney by T3 and PTU. Morphometric analyses of the thyroid showed that PTU exposure increased the size of the epithelial cells, whereas T3 induced no significant effects. Both T3 and PTU had diverse and partly contrasting effects on immune transcript profiles. The strongest differential effects of T3 and PTU on gene expressions were those targeting the Mitogen Associated Protein Kinase (MAPK), NFkB, Natural Killer (NK) and Toll-Like Receptor (TLR) pathways, a number of multipath genes (MPG) such as those encoding pleiotropic transcription factors (atf1, junb, myc), as well as important pro-inflammatory genes (tnfa, tnf6, il1b) and interferon-related genes (ifng, irf10). With these results we show for the first time in a fish species that the in vivo thyroidal status modulates a diversity of immune genes and pathways. This knowledge provides the basis to investigate both mechanisms and consequences of thyroid hormone- and thyroid disruptor-mediated immunomodulation for the immunocompetence of fish.

  11. RNAi analysis of Deformed, proboscipedia and Sex combs reduced in the milkweed bug Oncopeltus fasciatus: novel roles for Hox genes in the hemipteran head.

    Science.gov (United States)

    Hughes, C L; Kaufman, T C

    2000-09-01

    Insects have evolved a large variety of specialized feeding strategies, with a corresponding variability in mouthpart morphology. We have, however, little understanding of the developmental mechanisms that underlie this diversity. Until recently it was difficult to perform any analysis of gene function outside of the genetic model insects Drosophila melanogaster and Tribolium castaneum. In this paper, we report the use of dsRNA-mediated interference (RNAi) to dissect gene function in the development of the milkweed bug Oncopeltus fasciatus, which has specialized suctorial mouthparts. The Hox genes Deformed (Dfd), proboscipedia (pb) and Sex combs reduced (Scr) have previously been shown to be expressed in the gnathal appendages of this species. Strikingly, the milkweed bug was found to have an unusual expression pattern of pb. Here, by analyzing single and combination RNAi depletions, we find that Dfd, pb and Scr are used in the milkweed bug to specify the identity of the mouthparts. The exact roles of the genes, however, are different from what is known in the two genetic model insects. The maxillary appendages in the bug are determined by the activities of the genes Dfd and Scr, rather than Dfd and pb as in the fly and beetle. The mandibular appendages are specified by Dfd, but their unique morphology in Oncopeltus suggests that Dfd's target genes are different. As in flies and beetles, the labium is specified by the combined activities of pb and Scr, but again, the function of pb appears to be different. Additionally, the regulatory control of pb by the other two genes seems to be different in the bug than in either of the other species. These novelties in Hox function, expression pattern and regulatory relationships may have been important for the evolution of the unique Hemipteran head.

  12. Arrays of optical vortices formed by "fork" holograms

    CERN Document Server

    Bekshaev, A Ya; Mohammed, K A

    2014-01-01

    Singular light beams with optical vortices (OV) are often generated by means of thin binary gratings with groove bifurcation ("fork holograms") that produce a set of diffracted beams with different OV charges. Usually, only single separate beams are used and investigated; here we consider the whole set of diffracted OV beams that, at certain conditions, are involved in efficient mutual interference to form a characteristic pattern where the ring-like structure of separate OV beams is replaced by series of bright and dark lines between adjacent diffraction orders. This pattern, well developed for high diffraction orders, reflects the main spatial properties of the diffracted beams as well as of the fork grating used for their generation. In particular, it confirms the theoretical model for the diffracted beams (Kummer beam model) and enables to determine the sign and the absolute value of the phase singularity embedded in the hologram.

  13. Replication-Coupled Recruitment of Viral and Cellular Factors to Herpes Simplex Virus Type 1 Replication Forks for the Maintenance and Expression of Viral Genomes

    Science.gov (United States)

    Dembowski, Jill A.

    2017-01-01

    Herpes simplex virus type 1 (HSV-1) infects over half the human population. Much of the infectious cycle occurs in the nucleus of cells where the virus has evolved mechanisms to manipulate host processes for the production of virus. The genome of HSV-1 is coordinately expressed, maintained, and replicated such that progeny virions are produced within 4–6 hours post infection. In this study, we selectively purify HSV-1 replication forks and associated proteins from virus-infected cells and identify select viral and cellular replication, repair, and transcription factors that associate with viral replication forks. Pulse chase analyses and imaging studies reveal temporal and spatial dynamics between viral replication forks and associated proteins and demonstrate that several DNA repair complexes and key transcription factors are recruited to or near replication forks. Consistent with these observations we show that the initiation of viral DNA replication is sufficient to license late gene transcription. These data provide insight into mechanisms that couple HSV-1 DNA replication with transcription and repair for the coordinated expression and maintenance of the viral genome. PMID:28095497

  14. Genome-wide localization of Rrm3 and Pif1 DNA helicases at stalled active and inactive DNA replication forks of Saccharomyces cerevisiae

    Directory of Open Access Journals (Sweden)

    Silvia Emma Rossi

    2016-03-01

    Full Text Available The genome of the budding yeast Saccharomyces cerevisiae is sequenced and the location and dynamic of activation of DNA replication origins are known. G1 synchronized yeast cells can be released into S-phase in the presence of hydroxyurea (HU (1, which slows down DNA replication and retains replication forks in proximity of DNA replication origins. In this condition, the Chromatin Immuno-Precipitation on chip (ChIP on chip (2–4 of replisome components allows the precise localization of all active DNA replication forks. This analysis can be coupled with the ssDNA-BromodeoxyUridine (ssDNA-BrdU Immuno-Precipitation on chip (ssDNA-BrdU IP on chip technique (5–7, which detects the location of newly synthesized DNA. Comparison of binding and BrdU incorporation profiles allows to locate a factor of interest at DNA replication forks genome wide. We present datasets deposited in the gene expression omnibus (GEO database under accession number GSE68214, which show how the DNA helicases Rrm3 and Pif1 (8 associate to active and inactive DNA replication forks.

  15. Association of single nucleotide polymorphic sites in candidate genes with aggressiveness and deoxynivalenol production in Fusarium graminearum causing wheat head blight

    Directory of Open Access Journals (Sweden)

    Talas Firas

    2012-03-01

    Full Text Available Abstract Background Fusarium graminearum sensu stricto (s.s. is an ubiquitous pathogen of cereals. The economic impact of Fusarium head blight (FHB is characterized by crop losses and mycotoxin contamination. Our objective was to associate SNP diversity within candidate genes with phenotypic traits. A total of 77 F. graminearum s.s. isolates was tested for severity of fungal infection (= aggressiveness and deoxynivalenol (DON production in an inoculated field experiment at two locations in each of two years. For seven genes known to control fungal growth (MetAP1, Erf2 or DON production (TRI1, TRI5, TRI6 TRI10 and TRI14 single nucleotides polymorphic sites (SNPs were determined and evaluated for the extent of linkage disequilibrium (LD. Associations of SNPs with both phenotypic traits were tested using linear mixed models. Results Decay of LD was in most instances fast. Two neighboring SNPs in MetAP1 and one SNP in Erf2 were significantly (P pG of 25.6%, 0.5%, and 13.1%, respectively. One SNP in TRI1 was significantly associated with DON production (pG = 4.4. Conclusions We argue that using the published sequence information of Fusarium graminearum as a template to amplify comparative sequence parts of candidate genes is an effective method to detect quantitative trait loci. Our findings underline the potential of candidate gene association mapping approaches to identify functional SNPs underlying aggressiveness and DON production for F. graminearum s.s populations.

  16. Environmental Assessment: Demolish 934 of Grand Forks Air Force Base

    Science.gov (United States)

    2006-03-01

    the “ Prairie View Nature Preserve” has been developed to restore a part of the native tallgrass prairie that once was dominant in this region...buffalo grass, and many native wildflower species. The Grand Forks AFB Natural Resources Manager installed a butterfly garden in the Prairie View...identified as jurisdictional. Vegetation is robust at GFAFB wetlands, and they are characterized as typical prairie potholes found within the

  17. Environmental Assessment - Demolish 934 of Grand Forks Air Force Base

    Science.gov (United States)

    2006-03-01

    in the “ Prairie View Nature Preserve” has been developed to restore a part of the native tallgrass prairie that once was dominant in this region...buffalo grass, and many native wildflower species. The Grand Forks AFB Natural Resources Manager installed a butterfly garden in the Prairie View...identified as jurisdictional. Vegetation is robust at GFAFB wetlands, and they are characterized as typical prairie potholes found within the

  18. South Fork Clearwater River Habitat Enhancement, Nez Perce National Forest.

    Energy Technology Data Exchange (ETDEWEB)

    Siddall, Phoebe

    1992-04-01

    In 1984, the Nez Perce National forest and the Bonneville Power Administration entered into a contractual agreement which provided for improvement of spring chinook salmon and summer steelhead trout habitat in south Fork Clearwater River tributaries. Project work was completed in seven main locations: Crooked River, Red River, Meadow Creek Haysfork Gloryhole, Cal-Idaho Gloryhole, Fisher Placer and Leggett Placer. This report describes restoration activities at each of these sites.

  19. 68erne – en forkælet generation?

    DEFF Research Database (Denmark)

    Jørgensen, Thomas Ekman; L. B. Jensen, Steven

    2007-01-01

    Kronikken gennemgår beskyldningerne mod 1968erne for at være en forkælet generation, der sidder på magten og pengene i Danmark. De væsentligste argumenter er, at de samfundsændringer, '1968' afstedkom, gav gode chancer for højtuddannede fra alle generationer. Til gengæld har de forringet chancerne...

  20. Environmental Assessment Housing Transfer at Grand Forks AFB, North Dakota

    Science.gov (United States)

    2005-01-27

    of grasses, legumes, and wild herbaceous plants. Included in the grasses and legumes vegetation species are tall wheat grass, brome grass, Kentucky ...little bluestem, Indian grass, switchgrass, blue gramma, buffalo grass, and many native wildflower species. 35 Two hundred and fifty five taxa...were identified in the ND Natural Heritage Inventory and the BS Bioserve biological inventory update for Grand Forks Air Force Base. Two rare orchid

  1. Environmental Assessment Tent City at Grand Forks AFB, North Dakota

    Science.gov (United States)

    2004-11-15

    legumes, and wild herbaceous plants. Included in the grasses and legumes vegetation species are tall wheat grass, brome grass, Kentucky bluegrass, sweet...bluestem, Indian grass, switchgrass, blue gramma, buffalo grass, and many native wildflower species. Two hundred and fifty five taxa were...identified in the ND Natural Heritage Inventory and the BS Bioserve biological inventory update for Grand Forks Air Force Base. Two rare orchid species are

  2. Molecular clock fork phylogenies: closed form analytic maximum likelihood solutions.

    Science.gov (United States)

    Chor, Benny; Snir, Sagi

    2004-12-01

    Maximum likelihood (ML) is increasingly used as an optimality criterion for selecting evolutionary trees, but finding the global optimum is a hard computational task. Because no general analytic solution is known, numeric techniques such as hill climbing or expectation maximization (EM) are used in order to find optimal parameters for a given tree. So far, analytic solutions were derived only for the simplest model-three-taxa, two-state characters, under a molecular clock. Quoting Ziheng Yang, who initiated the analytic approach,"this seems to be the simplest case, but has many of the conceptual and statistical complexities involved in phylogenetic estimation."In this work, we give general analytic solutions for a family of trees with four-taxa, two-state characters, under a molecular clock. The change from three to four taxa incurs a major increase in the complexity of the underlying algebraic system, and requires novel techniques and approaches. We start by presenting the general maximum likelihood problem on phylogenetic trees as a constrained optimization problem, and the resulting system of polynomial equations. In full generality, it is infeasible to solve this system, therefore specialized tools for the molecular clock case are developed. Four-taxa rooted trees have two topologies-the fork (two subtrees with two leaves each) and the comb (one subtree with three leaves, the other with a single leaf). We combine the ultrametric properties of molecular clock fork trees with the Hadamard conjugation to derive a number of topology dependent identities. Employing these identities, we substantially simplify the system of polynomial equations for the fork. We finally employ symbolic algebra software to obtain closed formanalytic solutions (expressed parametrically in the input data). In general, four-taxa trees can have multiple ML points. In contrast, we can now prove that each fork topology has a unique(local and global) ML point.

  3. Timing, coordination, and rhythm: Acrobatics at the DNA replication fork

    KAUST Repository

    Hamdan, Samir

    2010-04-09

    In DNA replication, the antiparallel nature of the parental duplex imposes certain constraints on the activity of the DNA polymerases that synthesize new DNA. The leading-strand polymerase advances in a continuous fashion, but the lagging-strand polymerase is forced to restart at short intervals. In several prokaryotic systems studied so far, this problem is solved by the formation of a loop in the lagging strand of the replication fork to reorient the lagging-strand DNA polymerase so that it advances in parallel with the leading-strand polymerase. The replication loop grows and shrinks during each cycle of Okazaki fragment synthesis. The timing of Okazaki fragment synthesis and loop formation is determined by a subtle interplay of enzymatic activities at the fork. Recent developments in single-molecule techniques have enabled the direct observation of these processes and have greatly contributed to a better understanding of the dynamic nature of the replication fork. Here, we will review recent experimental advances, present the current models, and discuss some of the exciting developments in the field. 2010 by The American Society for Biochemistry and Molecular Biology, Inc.

  4. Ku stabilizes replication forks in the absence of Brc1.

    Directory of Open Access Journals (Sweden)

    Arancha Sánchez

    Full Text Available DNA replication errors are a major source of genome instability in all organisms. In the fission yeast Schizosaccharomyces pombe, the DNA damage response protein Brc1 binds phospho-histone H2A (γH2A-marked chromatin during S-phase, but how Brc1 protects genome integrity remains unclear. Here we report that the non-homologous end-joining (NHEJ protein Ku becomes critical for survival of replication stress in brc1∆ cells. Ku's protective activity in brc1∆ cells does not involve its canonical NHEJ function or its roles in protecting telomeres or shielding DNA ends from Exo1 exonuclease. In brc1∆ pku80∆ cells, nuclear foci of Rad52 homologous recombination (HR protein increase and Mus81-Eme1 Holliday junction resolvase becomes critical, indicating increased replication fork instability. Ku's localization at a ribosomal DNA replication fork barrier associated with frequent replisome-transcriptosome collisions increases in brc1∆ cells and increased collisions correlate with an enhanced requirement for Brc1. These data indicate that Ku stabilizes replication forks in the absence of Brc1.

  5. Heat-shock responsive genes identified and validated in Atlantic cod (Gadus morhua liver, head kidney and skeletal muscle using genomic techniques

    Directory of Open Access Journals (Sweden)

    Kimball Jennifer

    2010-01-01

    Full Text Available Abstract Background Daily and seasonal changes in temperature are challenges that fish within aquaculture settings cannot completely avoid, and are known to elicit complex organismal and cellular stress responses. We conducted a large-scale gene discovery and transcript expression study in order to better understand the genes that are potentially involved in the physiological and cellular aspects of stress caused by heat-shock. We used suppression subtractive hybridization (SSH cDNA library construction and characterization to identify transcripts that were dysregulated by heat-shock in liver, skeletal muscle and head kidney of Atlantic cod. These tissues were selected due to their roles in metabolic regulation, locomotion and growth, and immune function, respectively. Fish were exposed for 3 hours to an 8°C elevation in temperature, and then allowed to recover for 24 hours at the original temperature (i.e. 10°C. Tissue samples obtained before heat-shock (BHS, at the cessation of heat-shock (CS, and 3, 12, and 24 hours after the cessation of heat-shock (ACS, were used for reciprocal SSH library construction and quantitative reverse transcription - polymerase chain reaction (QPCR analysis of gene expression using samples from a group that was transferred but not heat-shocked (CT as controls. Results We sequenced and characterized 4394 ESTs (1524 from liver, 1451 from head kidney and 1419 from skeletal muscle from three "forward subtracted" libraries (enriched for genes up-regulated by heat-shock and 1586 from the liver "reverse subtracted" library (enriched for genes down-regulated by heat-shock, for a total of 5980 ESTs. Several cDNAs encoding putative chaperones belonging to the heat-shock protein (HSP family were found in these libraries, and "protein folding" was among the gene ontology (GO terms with the highest proportion in the libraries. QPCR analysis of HSP90α and HSP70-1 (synonym: HSPA1A mRNA expression showed significant up

  6. Integrative miRNA-Gene Expression Analysis Enables Refinement of Associated Biology and Prediction of Response to Cetuximab in Head and Neck Squamous Cell Cancer

    Directory of Open Access Journals (Sweden)

    Loris De Cecco

    2017-01-01

    Full Text Available This paper documents the process by which we, through gene and miRNA expression profiling of the same samples of head and neck squamous cell carcinomas (HNSCC and an integrative miRNA-mRNA expression analysis, were able to identify candidate biomarkers of progression-free survival (PFS in patients treated with cetuximab-based approaches. Through sparse partial least square–discriminant analysis (sPLS-DA and supervised analysis, 36 miRNAs were identified in two components that clearly separated long- and short-PFS patients. Gene set enrichment analysis identified a significant correlation between the miRNA first-component and EGFR signaling, keratinocyte differentiation, and p53. Another significant correlation was identified between the second component and RAS, NOTCH, immune/inflammatory response, epithelial–mesenchymal transition (EMT, and angiogenesis pathways. Regularized canonical correlation analysis of sPLS-DA miRNA and gene data combined with the MAGIA2 web-tool highlighted 16 miRNAs and 84 genes that were interconnected in a total of 245 interactions. After feature selection by a smoothed t-statistic support vector machine, we identified three miRNAs and five genes in the miRNA-gene network whose expression result was the most relevant in predicting PFS (Area Under the Curve, AUC = 0.992. Overall, using a well-defined clinical setting and up-to-date bioinformatics tools, we are able to give the proof of principle that an integrative miRNA-mRNA expression could greatly contribute to the refinement of the biology behind a predictive model.

  7. Jasmonate and ethylene dependent defence gene expression and suppression of fungal virulence factors: two essential mechanisms of Fusarium head blight resistance in wheat?

    Directory of Open Access Journals (Sweden)

    Gottwald Sven

    2012-08-01

    Full Text Available Abstract Background Fusarium head blight (FHB caused by Fusarium species like F. graminearum is a devastating disease of wheat (Triticum aestivum worldwide. Mycotoxins such as deoxynivalenol produced by the fungus affect plant and animal health, and cause significant reductions of grain yield and quality. Resistant varieties are the only effective way to control this disease, but the molecular events leading to FHB resistance are still poorly understood. Transcriptional profiling was conducted for the winter wheat cultivars Dream (moderately resistant and Lynx (susceptible. The gene expressions at 32 and 72 h after inoculation with Fusarium were used to trace possible defence mechanisms and associated genes. A comparative qPCR was carried out for selected genes to analyse the respective expression patterns in the resistant cultivars Dream and Sumai 3 (Chinese spring wheat. Results Among 2,169 differentially expressed genes, two putative main defence mechanisms were found in the FHB-resistant Dream cultivar. Both are defined base on their specific mode of resistance. A non-specific mechanism was based on several defence genes probably induced by jasmonate and ethylene signalling, including lipid-transfer protein, thionin, defensin and GDSL-like lipase genes. Additionally, defence-related genes encoding jasmonate-regulated proteins were up-regulated in response to FHB. Another mechanism based on the targeted suppression of essential Fusarium virulence factors comprising proteases and mycotoxins was found to be an essential, induced defence of general relevance in wheat. Moreover, similar inductions upon fungal infection were frequently observed among FHB-responsive genes of both mechanisms in the cultivars Dream and Sumai 3. Conclusions Especially ABC transporter, UDP-glucosyltransferase, protease and protease inhibitor genes associated with the defence mechanism against fungal virulence factors are apparently active in different resistant

  8. Cytochrome P450 1B1, a new keystone in gene-environment interactions related to human head and neck cancer?

    Energy Technology Data Exchange (ETDEWEB)

    Thier, R. [Dept. Physiology and Pharmacology, Univ. of Queensland, St. Lucia, Qld. (Australia); Bruening, T. [Berufsgenossenschaftliches Forschungsinstitut fuer Arbeitsmedizin (BGFA), Bochum (Germany); Roos, P.H.; Bolt, H.M. [Inst. fuer Arbeitsphysiologie an der Univ. Dortmund (IfADo), Dortmund (Germany)

    2002-06-01

    Alcohol consumption and tobacco smoking are major causes of head and neck cancers, and regional differences point to the importance of research into gene-environment interactions. Much interest has been focused on polymorphisms of CYP1A1 and of GSTM1 and GSTT1, but a number of studies have not demonstrated significant effects. This has mostly been ascribed to small sample sizes. In general, the impact of polymorphisms of metabolic enzymes appears inconsistent, with some reports of weak-to-moderate associations, and with other of no elevation of risks. The classical cytochrome P450 isoenzyme considered for metabolic activation of polycyclic aromatic hydrocarbons (PAH) is CYP1A1. A new member of CYP1 family, CYP1B1, was cloned in 1994, currently representing the only member of the CYP1B subfamily. A number of single nucleotide polymorphisms of the CYP1B1 gene have been reported. The amino acid substitutions Val432Leu (CYP1B1*3) and Asn453Ser (CYP1B1*4), located in the heme binding domain of CYP1B1, appear as likely candidates to be linked with biological effects. CYP1B1 activates a wide range of PAH, aromatic and heterocyclic amines. Very recently, the CYP1B1 codon 432 polymorphism (CYP1B1*3) has been identified as a susceptibility factor in smoking-related head-and-neck squamous cell cancer. The impact of this polymorphic variant of CYP1B1 on cancer risk was also reflected by an association with the frequency of somatic mutations of the p53 gene. Combined genotype analysis of CYP1B1 and the glutathione transferases GSTM1 or GSTT1 has pointed to interactive effects. This provides new molecular evidence that tobacco smoke-specific compounds relevant to head and neck carcinogenesis are metabolically activated through CYP1B1 and is consistent with a major pathogenetic relevance of PAH as ingredients of tobacco smoke. (orig.)

  9. A Network of Multi-Tasking Proteins at the DNA Replication Fork Preserves Genome Stability.

    Directory of Open Access Journals (Sweden)

    2005-12-01

    Full Text Available To elucidate the network that maintains high fidelity genome replication, we have introduced two conditional mutant alleles of DNA2, an essential DNA replication gene, into each of the approximately 4,700 viable yeast deletion mutants and determined the fitness of the double mutants. Fifty-six DNA2-interacting genes were identified. Clustering analysis of genomic synthetic lethality profiles of each of 43 of the DNA2-interacting genes defines a network (consisting of 322 genes and 876 interactions whose topology provides clues as to how replication proteins coordinate regulation and repair to protect genome integrity. The results also shed new light on the functions of the query gene DNA2, which, despite many years of study, remain controversial, especially its proposed role in Okazaki fragment processing and the nature of its in vivo substrates. Because of the multifunctional nature of virtually all proteins at the replication fork, the meaning of any single genetic interaction is inherently ambiguous. The multiplexing nature of the current studies, however, combined with follow-up supporting experiments, reveals most if not all of the unique pathways requiring Dna2p. These include not only Okazaki fragment processing and DNA repair but also chromatin dynamics.

  10. A network of multi-tasking proteins at the DNA replication fork preserves genome stability.

    Directory of Open Access Journals (Sweden)

    Martin E Budd

    2005-12-01

    Full Text Available To elucidate the network that maintains high fidelity genome replication, we have introduced two conditional mutant alleles of DNA2, an essential DNA replication gene, into each of the approximately 4,700 viable yeast deletion mutants and determined the fitness of the double mutants. Fifty-six DNA2-interacting genes were identified. Clustering analysis of genomic synthetic lethality profiles of each of 43 of the DNA2-interacting genes defines a network (consisting of 322 genes and 876 interactions whose topology provides clues as to how replication proteins coordinate regulation and repair to protect genome integrity. The results also shed new light on the functions of the query gene DNA2, which, despite many years of study, remain controversial, especially its proposed role in Okazaki fragment processing and the nature of its in vivo substrates. Because of the multifunctional nature of virtually all proteins at the replication fork, the meaning of any single genetic interaction is inherently ambiguous. The multiplexing nature of the current studies, however, combined with follow-up supporting experiments, reveals most if not all of the unique pathways requiring Dna2p. These include not only Okazaki fragment processing and DNA repair but also chromatin dynamics.

  11. Reduced rate of DNA replication fork movement in megaloblastic anemia.

    Science.gov (United States)

    Wickremasinghe, R G; Hoffbrand, A V

    1980-01-01

    Chromatography on benzoylated naphthoylated DEAE-cellulose has been used to fractionate fully double-stranded from partially single-stranded DNA molecules. DNA was extracted from phytohemagglutinin-stimulated lymphocytes from patients with megaloblastic anemia resulting from vitamin B12 or folate deficiency after pulse-labeling the cells with [3H]thymidine for 5 min and chasing in unlabeled medium for 24 h. No gross accumulation of partially single-stranded material was observed in the DNA of these cells when compared with DNA from similarly labeled control cells obtained by the addition of 5-formyl tetrahydrofolic acid to the culture medium. When DNA from lymphocytes labeled with a 5-min pulse of [3H]thymidine and sheared to fragments of an average length of 18 micrometer was chromatographed on benzoylated naphthoylated DEAE-cellulose, approximately 80% of the label was recovered in the partially single-stranded fraction. After chasing in unlabeled medium the label was progressively transferred to the double-stranded fraction over a period of 2--3 h. The rate of transfer was slower in megaloblastic lymphocytes than in controls. The difference in rate suggested a slower rate of replication fork movement in megaloblastic lymphocytes and so the density shift technique of Painter and schaeffer (J. Mol. Biol. 45: 467--479, 1969) was used to measure the fork rate directly. [3H]Deoxycytidine was used as the labeled nucleoside to avoid possible complications arising from [3H]thymidine labeling of megaloblastic cells. Investigations on the lymphocytes from four patients showed that the replication fork rate in vitamin-treated control lyphocytes was about 1 micrometer/min. The fork rates in the corresponding untreated cells were invariably lower and rates ranging from 40 to 92% of those of controls were observed. Normal lymphocytes treated with the deoxynucleotide pool-depleting drugs methotrexate or hydroxyurea displayed defects in DNA synthesis similar to those of

  12. Take It Slow: can feedback from a smart fork reduce eating speed?

    Directory of Open Access Journals (Sweden)

    Sander Hermsen

    2015-09-01

    The present study examines the efficacy of a smart fork that helps people to eat more slowly. This adapted fork records eating speed and delivers vibrotactile feedback if users eat too quickly. In two studies, we tested the acceptability and user experience of the fork (Study 1, and its effect on eating rate and satiety levels in a controlled lab-setting (Study 2. Method: In study 1, 11 participants (all self-reported fast eaters ate a meal using the fork in our laboratory and used the fork for three consecutive days in their home setting. Participants took part in semi-structured interviews after the first meal and upon returning the fork, covering perceived effect on eating rate, comfort of use, accuracy, and motivational and social aspects of fork use. Interviews were coded and a thematic classification analysis was performed. In study 2, 128 participants (all self-reported fast eaters ate a standardized meal using the fork in our laboratory. We used a between-participants design with 2 conditions; participants ate their meal either with vibrotactile feedback from the fork (experimental condition or ate their meal without vibrotactile feedback (control condition. Eating rate, meal duration, error rate (number of bites taken faster than 10 seconds after previous bite, total food intake, and satiety were recorded for every participant. Results: Study 1: All participants felt that the feedback was generally accurate and consistent. Fork size, weight, and intensity of the feedback were seen as comfortable and acceptable. All participants reported a heightened awareness of eating rate and all but one participant reported eating more slowly with the fork. Study 2: Participants in the experimental condition ate significantly slower, and with a lower error rate than those in the control condition. Feedback did not significantly affect the amount of food eaten. Conclusions: Our findings suggest that this smart fork is an acceptable and effective tool to disrupt and

  13. The fork and the kinase: a DNA replication tale from a CHK1 perspective.

    Science.gov (United States)

    González Besteiro, Marina A; Gottifredi, Vanesa

    2015-01-01

    Replication fork progression is being continuously hampered by exogenously introduced and naturally occurring DNA lesions and other physical obstacles. Checkpoint kinase 1 (Chk1) is activated at replication forks that encounter damaged DNA. Subsequently, Chk1 inhibits the initiation of new replication factories and stimulates the firing of dormant origins (those in the vicinity of stalled forks). Chk1 also avoids fork collapse into DSBs (double strand breaks) and promotes fork elongation. At the molecular level, the current model considers stalled forks as the site of Chk1 activation and the nucleoplasm as the location where Chk1 phosphorylates target proteins. This model certainly serves to explain how Chk1 modulates origin firing, but how Chk1 controls the fate of stalled forks is less clear. Interestingly, recent reports demonstrating that Chk1 phosphorylates chromatin-bound proteins and even holds kinase-independent functions might shed light on how Chk1 contributes to the elongation of damaged DNA. Indeed, such findings have unveiled a puzzling connection between Chk1 and DNA lesion bypass, which might be central to promoting fork elongation and checkpoint attenuation. In summary, Chk1 is a multifaceted and versatile signaling factor that acts at ongoing forks and replication origins to determine the extent and quality of the cellular response to replication stress.

  14. Molecular subtypes in head and neck cancer exhibit distinct patterns of chromosomal gain and loss of canonical cancer genes.

    Directory of Open Access Journals (Sweden)

    Vonn Walter

    Full Text Available Head and neck squamous cell carcinoma (HNSCC is a frequently fatal heterogeneous disease. Beyond the role of human papilloma virus (HPV, no validated molecular characterization of the disease has been established. Using an integrated genomic analysis and validation methodology we confirm four molecular classes of HNSCC (basal, mesenchymal, atypical, and classical consistent with signatures established for squamous carcinoma of the lung, including deregulation of the KEAP1/NFE2L2 oxidative stress pathway, differential utilization of the lineage markers SOX2 and TP63, and preference for the oncogenes PIK3CA and EGFR. For potential clinical use the signatures are complimentary to classification by HPV infection status as well as the putative high risk marker CCND1 copy number gain. A molecular etiology for the subtypes is suggested by statistically significant chromosomal gains and losses and differential cell of origin expression patterns. Model systems representative of each of the four subtypes are also presented.

  15. Genetic analysis and gene mapping of leafy head (lhd), a mutant blocking the differentiation of rachis branches in rice (Oryza sativa L.)

    Institute of Scientific and Technical Information of China (English)

    DUAN Yuanlin; MAO Damei; LI Weiming; XUE Yongbiao; WU Weiren; LIU Huaqing; ZHANG Danfeng; ZHOU Yuanchang; PAN Runsheng; LIN Lihui; CHEN Zhiwei; GUAN Huazhong

    2003-01-01

    A rice mutant called leafy head (lhd), in which the differentiation of rachis branches is blocked, was identified in a doubled haploid (DH) population derived through F1 anther culture from a cross between rice (Oryza sativa L.) indica cultivar Gui-630 and japonica cultivar Taiwanjing. The mutant is shorter in plant height, possessing smaller and clumpy leaves, and always stays at the vegetative growth stage. Genetic analysis suggests that lhd is controlled by a single recessive gene, which is temporarily named lhd(t). The phenotype of the mutant suggests that LHD(t) is a key gene controlling the differentiation of rachis branches. In order to map the gene, two F2 populations were constructed by crossing the lhd heterozygote with varieties Minghui-77 (indica) and Jinghua-8 (japonica). In the F2 of lhd heterozygote ( Jinghua-8, some mutant plants appeared as the "medium type", suggesting that the lhd phenotype could be influenced by genetic backgrounds. With the published SSR markers of RM series and additional SSR markers developed by ourselves and using the methods of bulked segregant analysis (BSA) and mutant analysis (with 498 mutant plants in total), LHD(t) gene was mapped onto the distal region of the long arm of chromosome 10. Markers SSR1, RM269, RM258, RM304 and RM171 were located on one side with distances of 6.4, 16.6, 18.4, 22.2 and 26.3 cM to LHD(t); whereas markers SSR4 and SSR5 were on the other side with distances of 0.6 and 2.2 cM to LHD(t). The results will facilitate the positional cloning and functional study of the LHD(t) gene.

  16. Analysis of a homologue of the adducin head gene which is a potential target for the Dictyostelium STAT protein Dd-STATa.

    Science.gov (United States)

    Aoshima, Ryota; Hiraoka, Rieko; Shimada, Nao; Kawata, Takefumi

    2006-01-01

    A Dd-STATa-null mutant, which is defective in expression of a Dictyostelium homologue of the metazoan STAT (signal transducers and activators of transcription) proteins, fails to culminate and this phenotype correlates with the loss of expression of various prestalk (pst) genes. An EST clone, SSK395, encodes a close homologue of the adducin amino-terminal head domain and harbors a putative actin-binding domain. We fused promoter fragments of the cognate gene, ahhA (adducin head homologue A), to a lacZ reporter and determined their expression pattern. The proximal promoter region is necessary for the expression of ahhA at an early (pre-aggregative) stage of development and this expression is Dd-STATa independent. The distal promoter region is necessary for expression at later stages of development in pstA cells, of the slug and in upper cup and pstAB cells during culmination. The distal region is partly Dd-STATa-dependent. The ahhA-null mutant develops almost normally until culmination, but it forms slanting culminants that tend to collapse on to the substratum. The mutant also occasionally forms fruiting bodies with swollen papillae and with constrictions in the prestalk region. The AhhA protein localizes to the stalk tube entrance and also to the upper cup cells and in cells at or near to the constricted region where an F-actin ring is localized. These findings suggest that Dd-STATa regulates culmination and may be necessary for straight downward elongation of the stalk, via the putative actin-binding protein AhhA.

  17. Bull Trout (Salvelinus Confluentus) Population and Habitat Surveys in the McKenzie and Middle Fork Willamette Basins, 2001 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    Taylor, Greg

    2003-02-01

    Prior to 1978, bull trout were commonly known as dolly varden (Salvelinus malma) and were classified into an anadromous and interior form. Cavender (1978) described the interior form as a distinct species, classifying it as Salvelinus confluentus, the bull trout. Bull trout are large char weighing up to 18 kg and growing to over one meter in length (Goetz 1994). They are distinguished by a broad flat head, large downward curving maxillaries that extend beyond the eye, a fleshy knob and a notch in the lower terminus of the snout, and light colored spots normally smaller than the pupil of the eye (Cavender 1978). Bull trout are found throughout northwestern North America from latitude 41{sup o}N to 60{sup o}N. In Oregon, bull trout were once distributed throughout 12 basins in the Klamath and Columbia River systems including the Clackamas, Santiam, McKenzie and Middle Fork Willamette subbasins west of the Cascades (Buchanan et al. 1997). However, it is likely that bull trout have been extirpated from west of the Cascades with the exception of the McKenzie sub-basin. McKenzie River bull trout were a contiguous population from the mouth to Tamolitch Falls prior to 1963. Three populations were isolated following the construction of Cougar and Trail Bridge Reservoirs which include the mainstem McKenzie and tributaries from the mouth to Trail Bridge Reservoir, mainstem McKenzie and tributaries above Trail Bridge Reservoir to Tamolitch Falls, and the South Fork McKenzie and tributaries above Cougar Reservoir. On June 10, 1998 the U.S. Fish and Wildlife Service (USFWS) listed the Columbia River bull trout population segment as Threatened under the federal Endangered Species Act and Buchanan et al. (1997) listed the bull trout population in the mainstem McKenzie as ''of special concern'', the South Fork McKenzie population as ''high risk of extinction,'' and the population above Trail Bridge Reservoir as ''high risk of

  18. Head Injuries

    Science.gov (United States)

    ... object that's stuck in the wound. previous continue Concussions Concussions — the temporary loss of normal brain function due ... also a type of internal head injury. Repeated concussions can permanently damage the brain. In many cases, ...

  19. Head Tilt

    Science.gov (United States)

    ... Healthy Living Healthy Living Healthy Living Nutrition Fitness Sports Oral Health Emotional Wellness Growing Healthy Sleep Safety & ... When this happens, the neck muscles go into spasm, causing the head to tilt to one side. ...

  20. Head Injuries

    Science.gov (United States)

    ... ATV) Safety Balance Disorders Knowing Your Child's Medical History First Aid: Falls First Aid: Head Injuries Preventing Children's Sports Injuries Getting Help: Know the Numbers Concussions Stay Safe: Baseball Concussions Concussions: Getting Better Sports and Concussions Dealing ...

  1. Head MRI

    Science.gov (United States)

    ... heart valves Heart defibrillator or pacemaker Inner ear (cochlear) implants Kidney disease or dialysis (you may not ... to: Abnormal blood vessels in the brain ( arteriovenous malformations of the head ) Tumor of the nerve that ...

  2. Identification of genetic polymorphisms in DNA repair xenoderma pigmentosum group D gene and its association with head and neck cancer susceptibility in rural Indian population: a hospital based case-control study from south-western Maharashtra, India

    Directory of Open Access Journals (Sweden)

    Kailas D. Datkhile

    2016-06-01

    Conclusions: This study indicates that polymorphisms in cd199 of XPD gene could play a role in modifying genetic susceptibility of individual to head and neck cancer in Maharashtra patients. Thus, the case-control study suggest that selected DNA repair genes represent genetic determinants in oral carcinogenesis along with other risk factors in the rural Indian population. [Int J Res Med Sci 2016; 4(6.000: 1997-2005

  3. Implementing farm-to-fork traceability in Tanzania

    CSIR Research Space (South Africa)

    Van Dyk, FE

    2005-08-01

    Full Text Available .csir.co.za Implementing farm-to-fork traceability in Tanzania Esbeth van Dyk CSIR Centre for Logistics ORSSA/SAIIE August 2005 Copyright @ CSIR 2005 www.csir.co.za Structure • Why traceability? • Legislation • Tanzania project • Recordkeeping in coffee...” Copyright @ CSIR 2005 www.csir.co.za Tanzania project Copyright @ CSIR 2005 www.csir.co.za Tanzania project • DANIDA funded (Danish government) • Business Sector Programme Support II • 4 components: Improved access to markets • 3 sub-components...

  4. Ideal synchronizer for marked pairs in fork-join network

    CERN Document Server

    Vyshenski, S V; Dubenskaya, Yu Yu

    2008-01-01

    We introduce a new functional element (synchronizer for marked pairs) meant to join results of parallel processing in two-branch fork-join queueing network. Approximations for distribution of sojourn time at the synchronizer are derived along with a validity domain. Calculations are performed assuming that: arrivals to the network form a Poisson process, each branch operates like an M/M/N queueing system. It is shown that a mean quantity of jobs in the synchronizer is bounded below by the value, defined by parameters of the network (which contains the synchronizer) and does not depend upon performance and particular properties of the synchronizer.

  5. Analysis of polymorphism in the survivin gene promoter as a potential risk factor for head and neck cancers development

    Directory of Open Access Journals (Sweden)

    Kostić Marija

    2013-01-01

    Full Text Available Introduction. Association studies have shown that gene polymorphisms in various classes of genes can modulate cancer risk. The -31G/C polymorphism in the promoter of survivin gene, affects the expression of the anti-apoptotic protein survivin which in turn may predispose an individual to some types of cancer. Objective. The aim of the study was to determine whether the survivin promoter -31G/C polymorphism could be a susceptibility factor for squamous cell carcinoma (SCC of the oral cavity and basal cell carcinoma (BCC of the skin. Methods. The DNA obtained from 88 patients with SCC, 60 patients with BCC and 111 healthy individuals was subjected to polymerase chain reaction-restriction fragment length polymorphism analysis (PCR- RFLP in order to determine genotype and allele frequencies in patients and control groups. Logistic regression was used for cancer risk assessment. Results. The following distribution of genotypes was obtained: CC genotype 15% in the SCC group, 13% in the BCC group and 12% in controls; CG genotype 41% in SCCs, 35% in BCCs, 48% in controls; GG genotype 44% in SCCs, 52% in BCCs and 40% in controls. Allelic frequencies were as follows: G allele 0.65 in SCCs, 0.69 in BCCs and 0.64 in the control group; C allele 0.35 in SCCs, 0.31 in BCCs and 0.36 in the control group. There was no statistically significant difference in allele or genotype frequencies between the patients and controls (p>0.05. Conclusion. In Serbian population, -31G/C polymorphism in the promoter of the survivin gene cannot be considered as a risk factor for oral squamous cell carcinoma and skin basal cell carcinoma. [Projekat Ministarstva nauke Republike Srbije, br. 175075

  6. Influence of G308A polymorphism of tumor necrosis factor-alpha gene on inflammatory markers in postsurgical head and neck cancer patients with early enteral nutrition.

    Science.gov (United States)

    de Luis, Daniel Antonio; Sagrado, Manue Gonzalez; Vallejo, Luis Angel; Carcedo, Luis María Gil; Izaola, Olatz; Cuellar, Luis; Terroba, María Concepción; Aller, Rocío

    2007-01-01

    Although immune dysfunction in patients with cancer could be multifactorial, the immune system may be modulated by nutritional substrates and genetic background. Our study evaluated the effect of G308A polymorphism of the tumor necrosis factor-alpha (TNF-alpha) gene on inflammatory markers in patients after surgery for head and neck cancer who received early enteral nutrition. A population of 60 patients with oral and laryngeal cancer was enrolled. At surgery patients were treated with a hyperproteic enteral diet. Perioperatively and on postoperative day 6 the following parameters were evaluated: serum values of prealbumin, transferrin, total number of lymphocytes, interleukin-6, TNF-alpha, and C-reactive protein. In addition, genotyping of G308A gene polymorphism was assessed. Patients' mean age was 61.1 +/- 14.6 y (four women, 56 men) with a body mass index of 25.4 +/- 5.2 kg/m(2) and a previous weight loss of 0.35 +/- 0.2 kg. Forty patients (37 men, 3 women; 66.6%) had the genotype G308/G308 (wild group) and 20 patients (19 men, 1 woman; 23.4%) had the genotype G308/A308 (mutant group). A significant increase in prealbumin and transferrin levels was detected in both groups. C-reactive protein decreased in both groups (wild group: 105.1 +/- 60 versus 53.8 +/- 62.3 mg/dL, P < 0.05; mutant group: 99.5 +/- 46 versus 43.9 +/- 51.9 mg/dL, P < 0.05). Interleukin-6 decreased in both groups (wild group: 20.1 +/- 22 versus 6.2 +/- 4.1 pg/mL, P < 0.05; mutant group: 22.3 +/- 38 versus 9.2 +/- 7.4 pg/mL, P = NS). Lymphocytes increased in both groups (wild group: 1102 +/- 468 versus 1600 +/- 537 10(3)/mL, P = NS; mutant group: 1441 +/- 739 10(3)/mL versus 1669 +/- 614 10(6)/mL, P = NS). TNF-alpha showed no changes. The G308A polymorphism of the TNF-alpha gene did not affect levels of inflammatory markers in patients after surgery for head and neck cancer who were treated with early enteral nutrition.

  7. Water-power resources in upper Carson River basin, California-Nevada, A discussion of potential development of power and reservoir sites on east and west forks, Carson River

    Science.gov (United States)

    Pumphrey, Harold L.

    1955-01-01

    West Fork Carson River offers the best opportunity for power development in the Carson River basin. The Hope Valley reservoir site could be developed to provide adequate storage regulation and concentration of fall would permit utilization of 1,400 feet of head in 51h miles below the clam site, or 1,900 feet of head in about 972 miles below the dam site; however, the average annual runoff susceptible of development is only about 70,000 acre-feet which limits the power that could be developed continuously in an average year with regulation to about 8,700 kilowatts utilizing 1,400 feet of head, or 12,000 kilowatts utilizing 1,900 feet of head. The method and degree of development will be determined to large extent by the method devised to supplement regulated flows from the Hope Valley reservoir to supply the water already appropriated for irrigation. If the Hope Valley site and the Watasheamu site on East Fork Carson River were developed coordinately water could be transferred to the West Fork for distribution through canals leading from that stream thus satisfying the deficiency due to regulation at Hope Valley and release of stored water on a power schedule. This would permit utilization of the entire 1,900 feet of fall. Independent development of the West Fork for optimum power production would require re-regulation of releases from Hope Valley reservoir and storage of a considerable part of the fall and winter flow for use during the irrigation season. Adequate storage capacity is apparently not available on the West Fork below Hope Valley; but offstream storage may be available in Diamond Valley which could be utilized by diversion from the West Fork near Woodfords. This would limit the utilization of the stream for power purposes to the development of the 1,400 feet of head between the Hope Valley dam site and Wood fords. In a year of average discharge East Fork Carson River and three of its principal tributaries could be developed to produce about 13

  8. Atomic Steps with tuning-fork-based noncontact atomic force microscopy

    NARCIS (Netherlands)

    Rensen, W.H.J.; Hulst, van N.F.; Ruiter, A.G.T.; West, P.E.

    1999-01-01

    Tuning forks as tip-sample distance detectors are a promising and versatile alternative to conventional cantilevers with optical beam deflection in noncontact atomic force microscopy (AFM). Both theory and experiments are presented to make a comparison between conventional and tuning-fork-based AFM.

  9. 76 FR 35909 - Temporary Concession Contract for Big South Fork National Recreation Area, TN/KY

    Science.gov (United States)

    2011-06-20

    ... National Recreation Area, TN/KY. SUMMARY: Pursuant to 36 CFR 51.24, public notice is hereby given that the...] Temporary Concession Contract for Big South Fork National Recreation Area, TN/KY AGENCY: National Park... visitor services within Big South Fork National Recreation Area, Tennessee and Kentucky, for a term not...

  10. 76 FR 6114 - Lincoln National Forest, New Mexico, North Fork Eagle Creek Wells Special Use Authorization

    Science.gov (United States)

    2011-02-03

    ... Forest Service Lincoln National Forest, New Mexico, North Fork Eagle Creek Wells Special Use... Ruidoso (the applicant) for continued operation of their municipal water supply wells on the North Fork of... portion of their water rights for these wells to locations off of National Forest System land; and...

  11. Imaging soft samples in liquid with tuning fork based shear force microscopy

    NARCIS (Netherlands)

    Rensen, W.H.J.; van Hulst, N.F.; Kammer, S.B.

    2000-01-01

    We present a study of the dynamic behavior of tuning forks and the application of tuning fork based shear force microscopy o­n soft samples in liquid. A shift in resonance frequency and a recovery of the tip vibration amplitude have been observed upon immersion into liquid. Conservation of the

  12. Precise excision of the retrotransposon gypsy from the forked and cut loci in a genetically unstable D. melanogaster strain.

    Science.gov (United States)

    Kuzin, A B; Lyubomirskaya, N V; Khudaibergenova, B M; Ilyin, Y V; Kim, A I

    1994-11-11

    The genetically unstable Mutator Strain of D. melanogaster is characterised by a high frequency of spontaneous mutations and their reversions. Three forked mutants were obtained independently and several reversions arose spontaneously with frequency of 10(-3)-10(-4). The sites of integration and excision of the gypsy retrotransposon were analysed by Southern blot analysis and sequencing of PCR fragments. In all cases gypsy had inserted at the end of the third exon of the major transcript of the forked gene, causing the duplication of TCCA target sequence. All the reversions resulted from precise excision of the gypsy. A double mutant containing ct6 and f1, caused by gypsy insertions into untranslated regions of the corresponding genes, was constructed. Two spontaneous ct6f+ revertants as well as one ct+f1 revertant were obtained from this line. Sequence analysis of gypsy integration and excision sites revealed that in all cases gypsy excision was also precise. These experiments constitute the first demonstration of precise excision of LTR-containing elements from their host genomes.

  13. Dynamics of quartz tuning fork force sensors used in standoff photoacoustic detection

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Zhouqiang; Jia, Shuhai; Ma, Binshan; Chen, Hualing [Xi' an Jiao tong University, Xi' an (China); Wei, Yuan [Harbin Institute of Technology, Harbin (Korea, Republic of)

    2015-08-15

    In this paper, a two-degrees-of-freedom model with two coupled oscillators is established to study the dynamics of quartz tuning fork force sensors. Air squeeze-film damping is considered in this model. When the laser power is 40 mW and the distance between the tuning fork and detected objects is approximately 0.5 m, the resonance amplitude of the tuning fork under the electromagnetic radiation pressure of the laser can reach 0.22 pm. Electromagnetic radiation pressure and resonance amplitude have the tendency to exponentially decay along with the distance between the tuning fork and detected objects. The influence of laser power and distance between the tuning fork and detected objects on electromagnetic radiation pressure is also considered. Lastly, an experimental device is set up to verify the calculation result of the model. Analysis shows that the experimental data are in good agreement with the theoretical calculation results.

  14. 59 FR- Prohibited Acts in West Little and North Fork Owyhee National Wild and Scenic River Area

    Science.gov (United States)

    1994-12-15

    ... INTERIOR [OR-030-03-1220-04: GS-043] Prohibited Acts in West Little and North Fork Owyhee National Wild and... and restrictions within the boundaries of the West Little and North Fork Owyhee Rivers as established in the Main, West Little and North Fork Owyhee National Wild and Scenic Rivers Management...

  15. MRX protects fork integrity at protein–DNA barriers, and its absence causes checkpoint activation dependent on chromatin context

    DEFF Research Database (Denmark)

    Bentsen, Iben Bach; Nielsen, Ida; Lisby, Michael

    2013-01-01

    To address how eukaryotic replication forks respond to fork stalling caused by strong non-covalent protein–DNA barriers, we engineered the controllable Fob-block system in Saccharomyces cerevisiae. This system allows us to strongly induce and control replication fork barriers (RFB) at their natural...

  16. Temperature Regulation in Critical Salmon Habitat of the Middle Fork of the John Day River, Oregon.

    Science.gov (United States)

    Buskirk, B. A.; Selker, J. S.

    2016-12-01

    Flow and temperature within the Middle Fork of the John Day River, an arid Eastern Oregon river, is dominated primarily by contributions from groundwater fed tributaries. The hydrology of arid streams is an important metric for understanding the critical environment in which salmon spawn and salmonids reside. The regulation of temperature within these streams is considered the primary metric for survival rates of these fish. Since 2007 Oregon State University has conducted stream monitoring efforts on the Middle Fork of the John Day River at the Oxbow and Forrest Conservation Areas. These sites were chosen through collaborative effort with the Confederated Tribes of the Warm Springs Reservation of Oregon, who have been restoring remnant mining canals back to their natural sinuous river pattern. The John Day River is also one of the few undammed reaches in which salmon runs occur. Efforts have focused on fiber optic distributed temperature sensing (DTS), groundwater gradient, stream discharge, bed permeability, GPS location and stream bathymetry across the conservation sites. During the peak of summer, stream temperature exhibits a strong diurnal cycle ranging from 9° C to 23° C depending on the daily maximum observed within the reach. Salmon have been found to be sensitive to stream temperatures above 15° C and are unable to survive temperatures above 24° C (Bell et al, 1991). The synthesis of temperature and stream flow data we collected show that very little groundwater is contributing to flow and temperature in the main channel of our study site while tributaries provide a constant, typically 0.5 to 2° C cooler, input of water to the main river channel and significant source of flow (0.01 - 0.1 m3/s). Due to the minimal rain fall in this arid environment, snow melt infiltration is likely the primary annual source of recharge into the head waters of the tributaries while also providing temperature regulation through input of near 0° C water. This cold water

  17. VIBRATION MEASUREMENT OF DOUBLE-ENDED TUNING FORKS RESONATOR

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    To enhance the coherence and reliability of the double-ended tuning fork (DETF) resonator, a measurement system of resonator vibration is presented to check its dynamic characteristics. Laser Doppler techniques are utilized and the relation between DETF vibration velocity and output current of photodetector is obtained. Resonator vibration equation is also analyzed and its driving power only depends on the direct current bias voltage and the amplitude of alternative voltage. Furthermore, a special resonator driving control circuit based on measurement is designed. The amplitude and frequency of circuit is controlled by a computer so that highly stable and strong driving signal can be output. Experiments on driving and measuring double-ended tuning fork have been done. The frequency of driving signal is 8 kHz and the peak-to-peak value of driving voltage is 140 V. Experimental results indicate resonator can be drived stably by driving control circuit and dynamic characteristics of DETF may be measured in real time.

  18. Environment of deposition of Clear Fork Formation: Yoakum County, Texas

    Energy Technology Data Exchange (ETDEWEB)

    Moore, B.K.

    1987-05-01

    The Clear Fork Formation is Permian (Leonardian) in age and constitutes a major oil-bearing unit in the Permian basin of west Texas. In Yoakum County, west Texas, the upper Clear Fork carbonates record a subtidal upward-shoaling sequence of deposition. A small bryozoan-algal patch reef is situated within these carbonates near the southern edge of the North Basin platform. The reef is completely dolomitized, but paramorphic replacement has facilitated a study of the paleoecology, lateral variations, and community succession within this buildup. Build-ups of this type are scarcely known in strata of Permian age. The reef was apparently founded on a coquina horizon at the base of the buildup. The reef apparently had a low-relief, dome-shaped morphology. The trapping and binding of sediment by bryozoa appear to have been the main constructional process. A significant role was also played by encrusting forams and the early precipitation of submarine cements, both of which added rigidity to the structure. The reef also contains a low-diversity community of other invertebrates. Algal constituents predominate at the basinward edge of the buildup. The reef was formed entirely subaqueously on a broad, relatively shallow tropical marine carbonate shelf environment. An understanding of the lithofacies distribution and paragenesis within this sequence will provide information on porosity variations and the nature and distribution of permeability barriers. Such information is useful in reservoir modeling studies and for secondary recovery techniques in shelf-edge carbonate reservoirs of this type.

  19. Identification of SSR markers closely linked to the yellow seed coat color gene in heading Chinese cabbage (Brassica rapa L. ssp. pekinensis)

    Science.gov (United States)

    Ren, Yanjing; Wu, Junqing; Zhao, Jing; Hao, Lingyu

    2017-01-01

    ABSTRACT Research on the yellow-seeded variety of heading Chinese cabbage will aid in broadening its germplasm resources and lay a foundation for AA genome research in Brassica crops. Here, an F2 segregating population of 1575 individuals was constructed from two inbred lines (brown-seeded ‘92S105’ and yellow-seeded ‘91-125’). This population was used to identify the linkage molecular markers of the yellow seed coat trait using simple sequence repeat (SSR) techniques combined with a bulk segregant analysis (BSA). Of the 144 SSR primer pairs on the A01-A10 chromosomes from the Brassica database (http://brassicadb.org/brad/), two pairs located on the A06 chromosome showed polymorphic bands between the bulk DNA pools of eight brown-seeded and eight yellow-seeded F2 progeny. Based on the genome sequence, 454 SSR markers were designed to A06 to detect these polymorphic bands and were synthesized. Six SSR markers linked to the seed coat color gene were successfully selected for fine linkage genetic map construction, in which the two closest flanking markers, SSR449a and SSR317, mapped the Brsc-ye gene to a 40.2 kb region with distances of 0.07 and 0.06 cM, respectively. The molecular markers obtained in this report will assist in the marker-assisted selection and breeding of yellow-seeded lines in Brassica rapa L. and other close species. PMID:28069590

  20. Replication forks reverse at high frequency upon replication stress in Physarum polycephalum.

    Science.gov (United States)

    Maric, Chrystelle; Bénard, Marianne

    2014-12-01

    The addition of hydroxyurea after the onset of S phase allows replication to start and permits the successive detecting of replication-dependent joint DNA molecules and chicken foot structures in the synchronous nuclei of Physarum polycephalum. We find evidence for a very high frequency of reversed replication forks upon replication stress. The formation of these reversed forks is dependent on the presence of joint DNA molecules, the impediment of the replication fork progression by hydroxyurea, and likely on the propensity of some replication origins to reinitiate replication to counteract the action of this compound. As hydroxyurea treatment enables us to successively detect the appearance of joint DNA molecules and then of reversed replication forks, we propose that chicken foot structures are formed both from the regression of hydroxyurea-frozen joint DNA molecules and from hydroxyurea-stalled replication forks. These experiments underscore the transient nature of replication fork regression, which becomes detectable due to the hydroxyurea-induced slowing down of replication fork progression.

  1. DNA content and methylation of p16, DAPK and RASSF1A gene in tumour and distant, normal mucosal tissue of head and neck squamous cell carcinoma patients.

    Science.gov (United States)

    Laytragoon-Lewin, Nongnit; Chen, Fu; Castro, Juan; Elmberger, Göran; Rutqvist, Lars Erik; Lewin, Freddi; Turesson, Ingela; Lundgren, Jan

    2010-11-01

    Long-term survival of head and neck squamous cell carcinoma (HNSCC) patients has not improved significantly during the last 20 years and recurrent disease is frequently observed. In this study, the potential presence of pre-malignant cells or rare malignant cells at the time of diagnosis in HNSCC was investigated. Fifty-nine biopsies obtained from 41 HNSCC patients were analysed. Eighteen of these biopsies were normal mucosal tissue, located at least 5 cm from the tumour margin. DNA content and DNA methylation of p16, DAPK and RASSF1A was examined. Thirty-nine out of 41 (95%) tumour biopsies showed p16 methylation and 21 (51%) of them displayed aneuploidy. Of 18 distant normal mucosal biopsies, 6 (33%) of these showed evidence of aneuploidy and 15(83%) of them showed methylated p16 genes. Among paired samples, the highest frequencies of DNA methylation were found in tumours with aneuploidy. Regardless of DNA content, methylation at DAPK, RASSF1A or p16 were found in the corresponding distant mucosal biopsies. The cells with abnormal DNA content or DNA methylation in mucosal tissue were not detected clinically or by pathological macroscopic and microscopic examination. Thus, distant mucosal tissue DNA content and DNA methylation analyses in combination with histopathology will provide a better prognostic base for the evaluation and treatment of HNSCC patients.

  2. Head Start.

    Science.gov (United States)

    Greenman, Geri

    2000-01-01

    Discusses an art project in which students created drawings of mop heads. Explains that the approach of drawing was more important than the subject. States that the students used the chiaroscuro technique, used by Rembrandt and Caravaggio, in which light appears out of the darkness. (CMK)

  3. MicroRNA genes diversity analysis between bone tissue of alcohol avascular necrosis femoral head and normal femoral head%酒精性与正常股骨头骨组织中微小RNA基因的多态性分析

    Institute of Scientific and Technical Information of China (English)

    杨玉宝; 刘省臣; 宋扬; 高忠礼; 李林; 阚金庆

    2013-01-01

    目的 观察微小RNA(miRNA)在酒精缺血坏死性与正常股骨头骨组织的表达变化,探讨miRNA基因在两者中的变化关系.方法 分别对5例酒精性股骨头与5例正常股骨头骨组织进行miRNA基因芯片检测,可见有上调基因has-miR-29a-st和下调基因has-miR-486-5p-st,分别对上调和下调基因行逆转录-聚合酶链反应(RT-PCR).结果 miRNA基因芯片共检测酒精缺血坏死性与正常股骨头骨组织400条基因,对明显上调has-miR-29a-st和下调has-miR-486-5p-st基因片段行RT-PCR检测,正常股骨头和酒精坏死性股骨头上调基因的2-△△Ct平均值为1.06±0.09和1.93±1.12,下调基因的2-△△Ct平均值为1.88±25.37和1.70 ±0.98(变化>2倍且P<0.05).结论 酒精缺血坏死性与正常股骨头骨组织存在明显miRNA变化,其可能在股骨头坏死发生过程中可能起着重要的调控作用.%Objective To observe expression variation of microRNA (miRNA) between bone tissue of alcohol avascular necrosis femoral head and normal femoral head and discuss miRNA change relation between them.Methods It is tested for miRNA for five normal femoral head tissue and alcohol avascular necrosis femoral head tissue.it is thus clear that there are up regulation has-miR-29a-st and downregulation genes has-miR-486-5p-st.they are went on reverse transcriptase-polymerase chain reaction (RT-PCR).Results Four hundred genes were analysed between between bone tissue of alcohol avascular necrosis femoral head and normal femoral head with miRNA gene chip.clear down regulation has-miR-486-5p-st and up regulation has-miR-29a-st were went on PCR,the average value of has-miR-29a-st 2-~Ct is 1.06 ±0.09 and 1.93 ± 1.12 for bone tissue of alcohol avascular necrosis femoral head and normal femoral head; the average value of has-miR-486-5p-st2-~Ct is 1.88 ± 25.37 and 1.70 ± 0.98 (variation > 2 times moreover P < 0.05).Conclusion There is obvious up regulation and down regulation miRNA genes

  4. Oligodeoxynucleotide binding to (CTG) · (CAG) microsatellite repeats inhibits replication fork stalling, hairpin formation, and genome instability.

    Science.gov (United States)

    Liu, Guoqi; Chen, Xiaomi; Leffak, Michael

    2013-02-01

    (CTG)(n) · (CAG)(n) trinucleotide repeat (TNR) expansion in the 3' untranslated region of the dystrophia myotonica protein kinase (DMPK) gene causes myotonic dystrophy type 1. However, a direct link between TNR instability, the formation of noncanonical (CTG)(n) · (CAG)(n) structures, and replication stress has not been demonstrated. In a human cell model, we found that (CTG)(45) · (CAG)(45) causes local replication fork stalling, DNA hairpin formation, and TNR instability. Oligodeoxynucleotides (ODNs) complementary to the (CTG)(45) · (CAG)(45) lagging-strand template eliminated DNA hairpin formation on leading- and lagging-strand templates and relieved fork stalling. Prolonged cell culture, emetine inhibition of lagging-strand synthesis, or slowing of DNA synthesis by low-dose aphidicolin induced (CTG)(45) · (CAG)(45) expansions and contractions. ODNs targeting the lagging-strand template blocked the time-dependent or emetine-induced instability but did not eliminate aphidicolin-induced instability. These results show directly that TNR replication stalling, replication stress, hairpin formation, and instability are mechanistically linked in vivo.

  5. Hydrolyzed fish proteins modulates both inflammatory and antioxidant gene expression as well as protein expression in a co culture model of liver and head kidney cells isolated from Atlantic salmon (Salmo salar).

    Science.gov (United States)

    Holen, Elisabeth; He, Juyun; Araujo, Pedro; Seliussen, Jørgen; Espe, Marit

    2016-07-01

    Hydrolyzed fish proteins (H-pro) contain high concentrations of free amino acids and low molecular peptides that potentially may benefit fish health. The following study aimed to test whether the water-soluble phase of H-pro could attenuate lipopolysaccharide (LPS) provoked inflammation in liver cells and head kidney cells isolated from Atlantic salmon. Cells were grown as mono cultures or co cultures to assess possible crosstalk between immune cells and metabolic cells during treatments. Cells were added media with or without H-pro for 2 days before LPS exposure and harvested 24 h post LPS exposure. Respective cells without H-pro and LPS were used as controls. H-pro alone could affect expression of proteins directly as H-pro increased catalase protein expression in head kidney- and liver cells, regardless of culturing methods and LPS treatment. Leukotriene B4 (LTB4) production was also increased by H-pro in head kidney cells co cultured with liver cells. H-pro increased LPS induced interleukin 1β (IL-1β) transcription in liver cells co cultured with head kidney cells. All cultures of head kidney cells showed a significant increase in IL-1β transcription when treated with H-pro + LPS. H-pro decreased caspase-3 transcription in liver cells cultured co cultured with head kidney cells. Peroxisome proliferator activated receptor α (PPAR α) was upregulated, regardless of treatment, in liver cells co cultured with head kidney cells clearly showing that culturing method alone affected gene transcription. H-pro alone and together with LPS as an inflammation inducer, affect both antioxidant and inflammatory responses.

  6. Wavelike movement of bedload sediment, East Fork River, Wyoming

    Science.gov (United States)

    Meade, R.H.

    1985-01-01

    Bedload is moved down the East Fork River in distinct wavelike pulses that have the form of composite dune fields The moving material consists mostly of coarse sand and fine gravel The wavelengths of the pulses are about 500-600 m, a distance that is predetermined by the pattern of stoage of bed sediment in the river during low water As the river discharge increases, the bed sediment is scoured from the storage areas, and it is moved onto and across the interventing riffles As the river discharge decreases, the bed sediment is scoured off the riffles and moved into the next storage area downstream Each successive pulse of water discharge sets into motion a wave of bedload that continues to move unitil it reaches the next storage area ?? 1985 Springer-Verlag New York Inc.

  7. Education, tobacco smoking, alcohol consumption, and IL-2 and IL-6 gene polymorphisms in the survival of head and neck cancer

    Directory of Open Access Journals (Sweden)

    R.V.M. López

    2011-10-01

    Full Text Available The association of education, tobacco smoking, alcohol consumption, and interleukin-2 (IL-2 +114 and -384 and -6 (IL-6 -174 DNA polymorphisms with head and neck squamous cell carcinoma (HNSCC was investigated in a cohort study of 445 subjects. IL-2 and IL-6 genotypes were determined by real-time PCR. Cox regression was used to estimate hazard ratios (HR and 95% confidence intervals (95%CI of disease-specific survival according to anatomical sites of the head and neck. Mean age was 56 years and most patients were males (87.6%. Subjects with 5 or more years of schooling had better survival in larynx cancer. Smoking had no effect on HNSCC survival, but alcohol consumption had a statistically significant effect on larynx cancer. IL-2 gene +114 G/T (HR = 0.52; 95%CI = 0.15-1.81 and T/T (HR = 0.22; 95%CI = 0.02-3.19 genotypes were associated with better survival in hypopharynx cancer. IL-2 +114 G/T was a predictor of poor survival in oral cavity/oropharynx cancer and larynx cancer (HR = 1.32; 95%CI = 0.61-2.85. IL-2 -384 G/T was associated with better survival in oral cavity/oropharynx cancer (HR = 0.80; 95%CI = 0.45-1.42 and hypopharynx cancer (HR = 0.68; 95%CI = 0.21-2.20, but an inverse relationship was observed for larynx cancer. IL-6 -174 G/C was associated with better survival in hypopharynx cancer (HR = 0.68; 95%CI = 0.26-1.78 and larynx cancer (HR = 0.93; 95%CI = 0.42-2.07, and C/C reduced mortality in larynx cancer. In general, our results are similar to previous reports on the value of education, smoking, alcohol consumption, and IL-2 and IL-6 genetic polymorphisms for the prognosis of HNSCC, but the risks due to these variables are small and estimates imprecise.

  8. Pfh1 Is an Accessory Replicative Helicase that Interacts with the Replisome to Facilitate Fork Progression and Preserve Genome Integrity.

    Directory of Open Access Journals (Sweden)

    Karin R McDonald

    2016-09-01

    Full Text Available Replicative DNA helicases expose the two strands of the double helix to the replication apparatus, but accessory helicases are often needed to help forks move past naturally occurring hard-to-replicate sites, such as tightly bound proteins, RNA/DNA hybrids, and DNA secondary structures. Although the Schizosaccharomyces pombe 5'-to-3' DNA helicase Pfh1 is known to promote fork progression, its genomic targets, dynamics, and mechanisms of action are largely unknown. Here we address these questions by integrating genome-wide identification of Pfh1 binding sites, comprehensive analysis of the effects of Pfh1 depletion on replication and DNA damage, and proteomic analysis of Pfh1 interaction partners by immunoaffinity purification mass spectrometry. Of the 621 high confidence Pfh1-binding sites in wild type cells, about 40% were sites of fork slowing (as marked by high DNA polymerase occupancy and/or DNA damage (as marked by high levels of phosphorylated H2A. The replication and integrity of tRNA and 5S rRNA genes, highly transcribed RNA polymerase II genes, and nucleosome depleted regions were particularly Pfh1-dependent. The association of Pfh1 with genomic integrity at highly transcribed genes was S phase dependent, and thus unlikely to be an artifact of high transcription rates. Although Pfh1 affected replication and suppressed DNA damage at discrete sites throughout the genome, Pfh1 and the replicative DNA polymerase bound to similar extents to both Pfh1-dependent and independent sites, suggesting that Pfh1 is proximal to the replication machinery during S phase. Consistent with this interpretation, Pfh1 co-purified with many key replisome components, including the hexameric MCM helicase, replicative DNA polymerases, RPA, and the processivity clamp PCNA in an S phase dependent manner. Thus, we conclude that Pfh1 is an accessory DNA helicase that interacts with the replisome and promotes replication and suppresses DNA damage at hard

  9. Effect of dietary glutamine on growth performance, non-specific immunity, expression of cytokine genes, phosphorylation of target of rapamycin (TOR), and anti-oxidative system in spleen and head kidney of Jian carp (Cyprinus carpio var. Jian).

    Science.gov (United States)

    Hu, Kai; Zhang, Jing-Xiu; Feng, Lin; Jiang, Wei-Dan; Wu, Pei; Liu, Yang; Jiang, Jun; Zhou, Xiao-Qiu

    2015-06-01

    This study was designed to investigate the effects of dietary glutamine on the growth performance, cytokines, target of rapamycin (TOR), and antioxidant-related parameters in the spleen and head kidney of juvenile Jian carp (Cyprinus carpio var. Jian). Fish were fed the basal (control) and glutamine-supplemented (12.0 g glutamine kg(-1) diet) diets for 6 weeks. Results indicated that the dietary glutamine supplementation improved the growth performance, spleen protein content, serum complement 3 content, and lysozyme activity in fish. In the spleen, glutamine down-regulated the expression of the interleukin 1 and interleukin 10 genes, and increased the level of phosphorylation of TOR protein. In the head kidney, glutamine down-regulated the tumor necrosis factor α and interleukin 10 gene expressions, phosphorylated and total TOR protein levels, while up-regulated the transforming growth factor β2 gene expression. Furthermore, the protein carbonyl content was decreased in the spleen of fish fed glutamine-supplemented diet; conversely, the anti-hydroxyl radical capacity and glutathione content in the spleen were increased by glutamine. However, diet supplemented with glutamine did not affect the lipid peroxidation, anti-superoxide anion capacity, and antioxidant enzyme activities in the spleen. Moreover, all of these antioxidant parameters in the head kidney were not affected by glutamine. Results from the present experiment showed the importance of dietary supplementation of glutamine in benefaction of the growth performance and several components of the innate immune system, and the deferential role in cytokine gene expression, TOR kinase activity, and antioxidant status between the spleen and head kidney of juvenile Jian carp.

  10. Physical Habitat Characteristics on the North Fork Shenandoah River, VA in 2002-2003

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — This dataset was collected with a PLGR government-issue GPS, and through manual measurement in the field. Points were gathered while canoeing along the North Fork...

  11. Geographic distribution of mercury in asiatic clams, Corbicuia plumihea, from the North Fork Holston River, Virginia

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — A study was conducted quantifying mercury concentrations in the Asiatic clam, Corbicula fluminea, from the North Fork Holston River, Virginia. The purpose of this...

  12. Assessment of contaminant loads at the Deep Fork National Wildlife Refuge

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Fish, sediment, and benthic macroinvertebrate communities were sampled on and near the Deep Fork National Wildlife Refuge, Okmulgee County, Oklahoma. Collections...

  13. The Frequency Dependence of the Added Mass of Quartz Tuning Fork Immersed in He II

    Science.gov (United States)

    Gritsenko, I.; Klokol, K.; Sokolov, S.; Sheshin, G.

    2016-11-01

    We measured the dependences of the resonance frequency of tuning forks immersed in liquid helium at T = 0.365 K in the pressure interval from saturated vapor pressure to 24.8 atm. The quartz tuning forks have been studied with different resonance frequencies of 6.65, 8.46, 12.1, 25.0 and 33.6 kHz in vacuum. The measurements were taken in the laminar flow regime. The experimental data allow us to determine the added mass of a quartz tuning fork in He II. It was found that the added mass per unit length of the prong fork is frequency dependent. Some possible qualitative explanations for such dependence are proposed. In addition, we observed, at T = 0.365 K, the changes in added mass with pressure according to the pressure dependence of He II density.

  14. The DNA helicase Pfh1 promotes fork merging at replication termination sites to ensure genome stability

    Science.gov (United States)

    Steinacher, Roland; Osman, Fekret; Dalgaard, Jacob Z.; Lorenz, Alexander; Whitby, Matthew C.

    2012-01-01

    Bidirectionally moving DNA replication forks merge at termination sites composed of accidental or programmed DNA–protein barriers. If merging fails, then regions of unreplicated DNA can result in the breakage of DNA during mitosis, which in turn can give rise to genome instability. Despite its importance, little is known about the mechanisms that promote the final stages of fork merging in eukaryotes. Here we show that the Pif1 family DNA helicase Pfh1 plays a dual role in promoting replication fork termination. First, it facilitates replication past DNA–protein barriers, and second, it promotes the merging of replication forks. A failure of these processes in Pfh1-deficient cells results in aberrant chromosome segregation and heightened genome instability. PMID:22426535

  15. Theoretical model and optimization of a novel temperature sensor based on quartz tuning fork resonators

    Science.gov (United States)

    Jun, Xu; Bo, You; Xin, Li; Juan, Cui

    2007-12-01

    To accurately measure temperatures, a novel temperature sensor based on a quartz tuning fork resonator has been designed. The principle of the quartz tuning fork temperature sensor is that the resonant frequency of the quartz resonator changes with the variation in temperature. This type of tuning fork resonator has been designed with a new doubly rotated cut work at flexural vibration mode as temperature sensor. The characteristics of the temperature sensor were evaluated and the results sufficiently met the target of development for temperature sensor. The theoretical model for temperature sensing has been developed and built. The sensor structure was analysed by finite element method (FEM) and optimized, including tuning fork geometry, tine electrode pattern and the sensor's elements size. The performance curve of output versus measured temperature is given. The results from theoretical analysis and experiments indicate that the sensor's sensitivity can reach 60 ppm °C-1 with the measured temperature range varying from 0 to 100 °C.

  16. Deep Fork National Wildlife Refuge: Comprehensive Conservation Plan 1999-2009 and Environmental Assessment

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This Comprehensive Conservation Plan (CCP) was written to guide management on Deep Fork NWR for the next 15 years. This plan outlines the Refuge vision and purpose...

  17. Complex rearrangements in patients with duplications of MECP2 can occur by fork stalling and template switching

    Science.gov (United States)

    Carvalho, Claudia M.B.; Zhang, Feng; Liu, Pengfei; Patel, Ankita; Sahoo, Trilochan; Bacino, Carlos A.; Shaw, Chad; Peacock, Sandra; Pursley, Amber; Tavyev, Y. Jane; Ramocki, Melissa B.; Nawara, Magdalena; Obersztyn, Ewa; Vianna-Morgante, Angela M.; Stankiewicz, Pawel; Zoghbi, Huda Y.; Cheung, Sau Wai; Lupski, James R.

    2009-01-01

    Duplication at the Xq28 band including the MECP2 gene is one of the most common genomic rearrangements identified in neurodevelopmentally delayed males. Such duplications are non-recurrent and can be generated by a non-homologous end joining (NHEJ) mechanism. We investigated the potential mechanisms for MECP2 duplication and examined whether genomic architectural features may play a role in their origin using a custom designed 4-Mb tiling-path oligonucleotide array CGH assay. Each of the 30 patients analyzed showed a unique duplication varying in size from ∼250 kb to ∼2.6 Mb. Interestingly, in 77% of these non-recurrent duplications, the distal breakpoints grouped within a 215 kb genomic interval, located 47 kb telomeric to the MECP2 gene. The genomic architecture of this region contains both direct and inverted low-copy repeat (LCR) sequences; this same region undergoes polymorphic structural variation in the general population. Array CGH revealed complex rearrangements in eight patients; in six patients the duplication contained an embedded triplicated segment, and in the other two, stretches of non-duplicated sequences occurred within the duplicated region. Breakpoint junction sequencing was achieved in four duplications and identified an inversion in one patient, demonstrating further complexity. We propose that the presence of LCRs in the vicinity of the MECP2 gene may generate an unstable DNA structure that can induce DNA strand lesions, such as a collapsed fork, and facilitate a Fork Stalling and Template Switching event producing the complex rearrangements involving MECP2. PMID:19324899

  18. Computed Tomography (CT) -- Head

    Medline Plus

    Full Text Available ... Professions Site Index A-Z Computed Tomography (CT) - Head Computed tomography (CT) of the head uses special ... the Head? What is CT Scanning of the Head? Computed tomography, more commonly known as a CT ...

  19. Head injury management guidelines for general practitioners

    Directory of Open Access Journals (Sweden)

    Jeremy C Ganz

    2011-01-01

    Full Text Available A complete examination of a head injured patient in the hospital requires a number of instruments. These include a stethoscope, sphygmomanometer, ophthalmoscope, otoscope, cotton wool, safety pin, tuning fork, reflex hammer and a small key to test the plantar response. Few of these are required at the accident scene. This is because, in the hospital, the aim is optimal definitive treatment. At the accident scene, the aim is prevention of secondary injury, rapid recording of the most important findings and safe efficient transport to the hospital. This short paper reviews how the local doctor should undertake a neurosurgical assessment of traumatic brain injury patients. Moreover, the primary management at accident scenes is described and the rationale behind the approach is outlined

  20. Head injury management guidelines for general practitioners.

    Science.gov (United States)

    Ganz, Jeremy C

    2011-07-01

    A complete examination of a head injured patient in the hospital requires a number of instruments. These include a stethoscope, sphygmomanometer, ophthalmoscope, otoscope, cotton wool, safety pin, tuning fork, reflex hammer and a small key to test the plantar response. Few of these are required at the accident scene. This is because, in the hospital, the aim is optimal definitive treatment. At the accident scene, the aim is prevention of secondary injury, rapid recording of the most important findings and safe efficient transport to the hospital. This short paper reviews how the local doctor should undertake a neurosurgical assessment of traumatic brain injury patients. Moreover, the primary management at accident scenes is described and the rationale behind the approach is outlined.

  1. Gene silencing with siRNA targeting E6/E7 as a therapeutic intervention against head and neck cancer-containing HPV16 cell lines.

    Science.gov (United States)

    Adhim, Zainal; Otsuki, Naoki; Kitamoto, Junko; Morishita, Naoya; Kawabata, Masato; Shirakawa, Toshiro; Nibu, Ken-Ichi

    2013-07-01

    Our results indicate that siRNA E6 and/or E7 may have potential as a gene-specific therapy for human papillomavirus (HPV) type 16 (HPV16)-related squamous cell carcinoma of the head and neck (HNSCC). To evaluate the effectiveness of siRNA targeting E6 and/or E7 on the in vitro and in vivo growth suppression of HPV16-related HNSCC. HPV16-related HNSCC (UM-SCC47) cell lines were used for the present study. Expression of HPV viral oncogenes E6 and/or E7 and their cellular targets, p53 and pRb, was evaluated by real-time PCR, Western blotting, and immunofluorescence staining. To study the effect of siRNA on tumor growth in vivo, we developed animal models. Representative tumors harvested from each group were processed for apoptosis analyses (TUNEL assay) and immunofluorescence staining for p53 and pRb. E6 and E7 oncogenes of HPV16 were down-regulated by E6 and/or E7 targeting siRNAs, respectively. The expression of p53 and pRb proteins in both the E6 siRNA group and E7 siRNA group was up-regulated compared with those of control groups. The cellular proliferation and apoptosis indexes of E6 and/or E7 siRNA groups were higher than those of controls. In vivo studies showed significant inhibitory effect of E6 and/or E7 siRNA compared with those of control groups, which was consistent with in vitro studies.

  2. Dose dependent activation of retinoic acid-inducible gene-I promotes both proliferation and apoptosis signals in human head and neck squamous cell carcinoma.

    Directory of Open Access Journals (Sweden)

    Jingzhou Hu

    Full Text Available The retinoic-acid-inducible gene (RIG-like receptor (RLR family proteins are major pathogen reorganization receptors (PRR responsible for detection of viral RNA, which initiates antiviral response. Here, we evaluated the functional role of one RLR family member, RIG-I, in human head and neck squamous cell carcinoma (HNSCC. RIG-I is abundantly expressed both in poorly-differentiated primary cancer and lymph node metastasis, but not in normal adjacent tissues. Activation of RIG-I by transfection with low dose of 5'-triphosphate RNA (3p-RNA induces low levels of interferon and proinflammatory cytokines and promotes NF-κB- and Akt-dependent cell proliferation, migration and invasion. In contrast, activation of RIG-I by a high dose of 3p-RNA induces robust mitochondria-derived apoptosis accompanied by decreased activation of Akt, which is independent of the interferon and TNFα receptor, but can be rescued by over-expression of constitutively active Akt. Furthermore, co-immunoprecipitation experiments indicate that the CARD domain of RIG-I is essential for inducing apoptosis by interacting with caspase-9. Together, our results reveal a dual role of RIG-I in HNSCC through regulating activation of Akt, in which RIG-I activation by low-dose viral dsRNA increases host cell survival, whereas higher level of RIG-I activation leads to apoptosis. These findings highlight the therapeutic potential of dsRNA mediated RIG-I activation in the treatment of HNSCC.

  3. Vascular endothelial growth factor (VEGF) gene polymorphisms and risk of head and neck cancer: a meta-analysis involving 2,444 individuals.

    Science.gov (United States)

    Leng, Wei-Dong; He, Mei-Ni; Chen, Qi-Lin; Gong, Heng; Zhang, Li; Zeng, Xian-Tao

    2013-10-01

    The association between vascular endothelial growth factor (VEGF) gene polymorphisms and risk of head and neck cancer (HNC) were investigated in many published studies; however, the currently available results are inconclusive. Therefore, we conducted this meta-analysis for deriving a more precise estimation of association between VEGF polymorphisms and the risk of HNC. Finally, we yield eight case-control studies involving six polymorphisms contain 2,444 individuals from PubMed, Embase, and CNKI up to January 30, 2013 (last updated on May 4, 2013). The results of meta-analysis showed that all the six polymorphisms of VEGF were not associated with risk of HNC [OR 1.25, 95 % CI (0.60-1.58) for TT vs. CC for 936 C/T; OR 1.41, 95 % CI (0.79-2.52) for GG vs. AA for -1,154 A/G; OR 0.97, 95 % CI (0.38-2.50) for CC vs. GG for 405 G/C; OR 1.44, 95 % CI (0.80-2.61) for AA vs. CC for 2,578 C/A; OR 1.27, 95 % CI (0.77-3.72) for TT vs. CC for -460 C/T; and OR 0.87, 95 % CI (0.37-2.06) for GG vs. CC for -634 G/C]. When performed subgroup analysis according to ethnicity for VEGF 936 C/T, the results suggested that it was not associated with the risk of HNC for either Asians [OR 0.84, 95 % CI (0.27-2.56) for TT vs. CC] or Caucasians [OR 2.10, 95 % CI (0.82-5.37) for TT vs. CC]. However, due to the limitations of this meta-analysis, more well designed, larger sample size, and adjusted risk factors studies are suggested to further assess the findings.

  4. Environmental Assessment: Demolish CASS Switch Stations Buildings 644, 645, 646 at Grand Forks Air Force Base

    Science.gov (United States)

    2006-06-01

    Prairie View Nature Preserve” has been developed to restore a part of the native tallgrass prairie that once was dominant in this region. Plants...grass, and many native wildflower species. The Grand Forks AFB Natural Resources Manager and volunteers installed a butterfly garden in the Prairie ...are characterized as typical prairie potholes found within the northern plains ecoregion. Wetlands on Grand Forks AFB occur frequently in

  5. Environmental Assessment: Demolish Buildings 212, 218, 819, 820 at Grand Forks Air Force Base

    Science.gov (United States)

    2007-01-31

    View Nature Preserve” has been developed to restore a part of the native tallgrass prairie that once was dominant in this region. Plants thriving in...and many native wildflower species. The Grand Forks AFB Natural Resources Manager and volunteers installed a butterfly garden in the Prairie View...characterized as typical prairie potholes found within the northern plains ecoregion. Wetlands on Grand Forks AFB occur frequently in drainage

  6. Take It Slow: can feedback from a smart fork reduce eating speed?

    OpenAIRE

    Sander Hermsen

    2015-01-01

    Background: Reductions in eating rate have been recommended as potential behavioural strategies to prevent and treat overweight [1–4]. Unfortunately, eating rate is difficult to modify, due to its highly automatic nature [5]. Training people to eat more slowly in everyday eating contexts, therefore, requires creative and engaging solutions. Aim: The present study examines the efficacy of a smart fork that helps people to eat more slowly. This adapted fork records eating speed ...

  7. Environmental Assessment: Construct Miscellaneous Services Recreation Area at Grand Forks AFB, North Dakota

    Science.gov (United States)

    2004-03-15

    DATA OS Nov03 1ST AJ< ’IT"’"< ~.CL~ "VVI GRANO FORKS AFB, NORTH DAKOTA A TV Trainin /Misc. Services Recreation/ Land Use Chan e/Mass Parkin NA N...PF(AMC) FY 2004 MILITARY CONSTRUCTION DATA 05 Nov03 AS!" .IlLlA TIONNO lCCAliOH GRANO FORKS AFB. NORTH DAKOTA ATV Trainin /Misc. Services

  8. Environmental Assessment: Armory Addition to CATM with Parking at Grand Forks AFB, North Dakota

    Science.gov (United States)

    2005-07-01

    are tall wheat grass, brome grass, Kentucky bluegrass, sweet clover, and alfalfa. Herbaceous plants include little bluestem, goldenrod, green... wildflower species. Two hundred and fifty five taxa were identified in the ND Natural Heritage Inventory and the BS Bioserve biological inventory update...for Grand Forks Air Force Base. Two rare orchid species are known to exist on Grand Forks AFB, the Large and Small Yellow Lady’s Slipper, identified

  9. The Sound Field around a Tuning Fork and the Role of a Resonance Box

    Science.gov (United States)

    Bogacz, Bogdan F.; Pedziwiatr, Antoni T.

    2015-01-01

    Atypical two-tine tuning fork is barely audible when held vibrating at an arm's length. It is enough, however, to touch its base to a table or, better, to a resonance box and the emitted sound becomes much louder. An inquiring student may pose questions: (1) Why is a bare tuning fork such a weak emitter of sound? (2) What is the role of the…

  10. Environmental Assessment: Construct a CDC Main Entry Addition at Grand Forks Air Force Base

    Science.gov (United States)

    2006-03-01

    Forks County. Pastures, meadows, and other non- cultivated areas create a prairie-land mosaic of grasses, legumes, and wild herbaceous plants...Included in the grasses and legumes vegetation species are tall wheat grass, brome grass, Kentucky bluegrass, sweet clover, and alfalfa . Herbaceous...LAND USE Land use in Grand Forks County consists primarily of cultivated crops with remaining land used for pasture and hay, urban development

  11. Environmental Assessment: Construct Airfield Lighting Vault and Demolish Building 531 at Grand Forks Air Force Base

    Science.gov (United States)

    2007-08-01

    Forks County. Pastures, meadows, and other non- cultivated areas create a prairie-land mosaic of grasses, legumes, and wild herbaceous plants. Included...in the grasses and legumes vegetation species are tall wheat grass, brome grass, Kentucky bluegrass, sweet clover, and alfalfa . Herbaceous plants...These are buildings 313, 606, 703, 704, 705, 706, 707, and 714. 3.9 LAND USE Land use in Grand Forks County consists primarily of cultivated crops

  12. Fabrication of SMD 32.768 kHz tuning fork-type crystals: photolithography and selective etching of an array of quartz tuning fork resonators

    Energy Technology Data Exchange (ETDEWEB)

    Lee, S. [Dept. of Molecular Science and Technology, Ajou Univ., Suwon (Korea); Lee, J.Y.; Park, T.S. [Research and Development Center, Samsung Electro-Mechanics Co., Ltd., Suwon (Korea)

    2001-09-01

    Negative photoresist photolithography was used to etch array of quartz tuning forks for use in Qualcomm trademark mobile station modem (MSM)-3000{sup TM} central processing unit (CPU) chips of code division multiple access (CDMA), personal communication system (PCS), and global system for mobile communication (GSM) units. It was found superior to positive photoresist photolithography. Quartz tuning fork blanks with optimum shock-resistant characteristics were designed using finite element method (FEM) and processing condition was devised for reproducible precision etching of Z-cut quartz wafer into array of tuning forks. Tuning fork pattern was transferred via ordinary photolithographical chromium/quartz glass template using a standard single-sided aligner and subsequent negative photoresist development. Tightly adhering and pinhole-free 600/2000 A chromium/gold mask is coated over the developed photoresist pattern which was subsequently stripped in acetone. This procedure was repeated on the backside of the wafer. With protective metallization area of tuning fork geometry thus formed, etching through quartz wafer was done at 80 C in a {+-} 1.5 C controlled bath containing concentrated solution of ammonium bifluoride to remove unwanted area of the quartz wafer. Surface finish of quartz wafer prior to etching and the quality of quartz crystals used primarily affected the quality of quartz wafer surface finish after quartz etching. At 80 C, selective etching of 100 {mu}m quartz wafer could be effected within 90 min. Reproducible precision selective etching method has thus been established and enables mass production of miniature tuning fork resonators photolithographically. (orig.)

  13. Genome-wide association of functional traits linked with Campylobacter jejuni survival from farm to fork.

    Science.gov (United States)

    Yahara, Koji; Méric, Guillaume; Taylor, Aidan J; de Vries, Stefan P W; Murray, Susan; Pascoe, Ben; Mageiros, Leonardos; Torralbo, Alicia; Vidal, Ana; Ridley, Anne; Komukai, Sho; Wimalarathna, Helen; Cody, Alison J; Colles, Frances M; McCarthy, Noel; Harris, David; Bray, James E; Jolley, Keith A; Maiden, Martin C J; Bentley, Stephen D; Parkhill, Julian; Bayliss, Christopher D; Grant, Andrew; Maskell, Duncan; Didelot, Xavier; Kelly, David J; Sheppard, Samuel K

    2017-01-01

    Campylobacter jejuni is a major cause of bacterial gastroenteritis worldwide, primarily associated with the consumption of contaminated poultry. C. jejuni lineages vary in host range and prevalence in human infection, suggesting differences in survival throughout the poultry processing chain. From 7343 MLST-characterised isolates, we sequenced 600 C. jejuni and C. coli isolates from various stages of poultry processing and clinical cases. A genome-wide association study (GWAS) in C. jejuni ST-21 and ST-45 complexes identified genetic elements over-represented in clinical isolates that increased in frequency throughout the poultry processing chain. Disease-associated SNPs were distinct in these complexes, sometimes organised in haplotype blocks. The function of genes containing associated elements was investigated, demonstrating roles for cj1377c in formate metabolism, nuoK in aerobic survival and oxidative respiration, and cj1368-70 in nucleotide salvage. This work demonstrates the utility of GWAS for investigating transmission in natural zoonotic pathogen populations and provides evidence that major C. jejuni lineages have distinct genotypes associated with survival, within the host specific niche, from farm to fork. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

  14. ruvA Mutants that resolve Holliday junctions but do not reverse replication forks.

    Science.gov (United States)

    Baharoglu, Zeynep; Bradley, Alison Sylvia; Le Masson, Marie; Tsaneva, Irina; Michel, Bénédicte

    2008-03-07

    RuvAB and RuvABC complexes catalyze branch migration and resolution of Holliday junctions (HJs) respectively. In addition to their action in the last steps of homologous recombination, they process HJs made by replication fork reversal, a reaction which occurs at inactivated replication forks by the annealing of blocked leading and lagging strand ends. RuvAB was recently proposed to bind replication forks and directly catalyze their conversion into HJs. We report here the isolation and characterization of two separation-of-function ruvA mutants that resolve HJs, based on their capacity to promote conjugational recombination and recombinational repair of UV and mitomycin C lesions, but have lost the capacity to reverse forks. In vivo and in vitro evidence indicate that the ruvA mutations affect DNA binding and the stimulation of RuvB helicase activity. This work shows that RuvA's actions at forks and at HJs can be genetically separated, and that RuvA mutants compromised for fork reversal remain fully capable of homologous recombination.

  15. ruvA Mutants that resolve Holliday junctions but do not reverse replication forks.

    Directory of Open Access Journals (Sweden)

    Zeynep Baharoglu

    2008-03-01

    Full Text Available RuvAB and RuvABC complexes catalyze branch migration and resolution of Holliday junctions (HJs respectively. In addition to their action in the last steps of homologous recombination, they process HJs made by replication fork reversal, a reaction which occurs at inactivated replication forks by the annealing of blocked leading and lagging strand ends. RuvAB was recently proposed to bind replication forks and directly catalyze their conversion into HJs. We report here the isolation and characterization of two separation-of-function ruvA mutants that resolve HJs, based on their capacity to promote conjugational recombination and recombinational repair of UV and mitomycin C lesions, but have lost the capacity to reverse forks. In vivo and in vitro evidence indicate that the ruvA mutations affect DNA binding and the stimulation of RuvB helicase activity. This work shows that RuvA's actions at forks and at HJs can be genetically separated, and that RuvA mutants compromised for fork reversal remain fully capable of homologous recombination.

  16. Mutations in DONSON disrupt replication fork stability and cause microcephalic dwarfism.

    Science.gov (United States)

    Reynolds, John J; Bicknell, Louise S; Carroll, Paula; Higgs, Martin R; Shaheen, Ranad; Murray, Jennie E; Papadopoulos, Dimitrios K; Leitch, Andrea; Murina, Olga; Tarnauskaitė, Žygimantė; Wessel, Sarah R; Zlatanou, Anastasia; Vernet, Audrey; von Kriegsheim, Alex; Mottram, Rachel M A; Logan, Clare V; Bye, Hannah; Li, Yun; Brean, Alexander; Maddirevula, Sateesh; Challis, Rachel C; Skouloudaki, Kassiani; Almoisheer, Agaadir; Alsaif, Hessa S; Amar, Ariella; Prescott, Natalie J; Bober, Michael B; Duker, Angela; Faqeih, Eissa; Seidahmed, Mohammed Zain; Al Tala, Saeed; Alswaid, Abdulrahman; Ahmed, Saleem; Al-Aama, Jumana Yousuf; Altmüller, Janine; Al Balwi, Mohammed; Brady, Angela F; Chessa, Luciana; Cox, Helen; Fischetto, Rita; Heller, Raoul; Henderson, Bertram D; Hobson, Emma; Nürnberg, Peter; Percin, E Ferda; Peron, Angela; Spaccini, Luigina; Quigley, Alan J; Thakur, Seema; Wise, Carol A; Yoon, Grace; Alnemer, Maha; Tomancak, Pavel; Yigit, Gökhan; Taylor, A Malcolm R; Reijns, Martin A M; Simpson, Michael A; Cortez, David; Alkuraya, Fowzan S; Mathew, Christopher G; Jackson, Andrew P; Stewart, Grant S

    2017-04-01

    To ensure efficient genome duplication, cells have evolved numerous factors that promote unperturbed DNA replication and protect, repair and restart damaged forks. Here we identify downstream neighbor of SON (DONSON) as a novel fork protection factor and report biallelic DONSON mutations in 29 individuals with microcephalic dwarfism. We demonstrate that DONSON is a replisome component that stabilizes forks during genome replication. Loss of DONSON leads to severe replication-associated DNA damage arising from nucleolytic cleavage of stalled replication forks. Furthermore, ATM- and Rad3-related (ATR)-dependent signaling in response to replication stress is impaired in DONSON-deficient cells, resulting in decreased checkpoint activity and the potentiation of chromosomal instability. Hypomorphic mutations in DONSON substantially reduce DONSON protein levels and impair fork stability in cells from patients, consistent with defective DNA replication underlying the disease phenotype. In summary, we have identified mutations in DONSON as a common cause of microcephalic dwarfism and established DONSON as a critical replication fork protein required for mammalian DNA replication and genome stability.

  17. Head Position and Internally Headed Relative Clauses.

    Science.gov (United States)

    Basilico, David

    1996-01-01

    Examines "Head Movement" in internally headed relative clauses (IHRCs). The article shows that in some cases, head movement to an external position need not take place and demonstrates that this movement of the head to a sentence-internal position results from the quantificational nature of IHRCs and Diesing's mapping hypothesis (1990, 1992). (56…

  18. Ultrasonic superlensing jets and acoustic-fork sheets

    Energy Technology Data Exchange (ETDEWEB)

    Mitri, F.G., E-mail: F.G.Mitri@ieee.org

    2017-05-18

    Focusing acoustical (and optical) beams beyond the diffraction limit has remained a major challenge in imaging instruments and systems, until recent advances on “hyper” or “super” lensing and higher-resolution imaging techniques have shown the counterintuitive violation of this rule under certain circumstances. Nonetheless, the proposed technologies of super-resolution acoustical focusing beyond the diffraction barrier require complex tools such as artificially engineered metamaterials, and other hardware equipment that may not be easily synthesized or manufactured. The present contribution therefore suggests a simple and reliable method of using a sound-penetrable circular cylinder lens illuminated by a nonparaxial Gaussian acoustical sheet (i.e. finite beam in 2D) to produce non-evanescent ultrasonic superlensing jets (or bullets) and acoustical ‘snail-fork’ shaped wavefronts with limited diffraction. The generalized (near-field) scattering theory for acoustical sheets of arbitrary wavefronts and incidence is utilized to synthesize the incident beam based upon the angular spectrum decomposition method and the multipole expansion method in cylindrical wave functions to compute the scattered pressure around the cylinder with particular emphasis on its physical properties. The results show that depending on the beam and lens parameters, a tight focusing (with dimensions much smaller than the beam waist) can be achieved. Subwavelength resolution can be also achieved by selecting a lens material with a speed of sound exceeding that of the host fluid medium. The ultrasonic superlensing jets provide the impetus to develop improved subwavelength microscopy and acoustical image-slicing systems, cell lysis and surgery, and photoacoustic imaging to name a few examples. Moreover, an acoustical fork-sheet generation may open innovative avenues in reconfigurable on-chip micro/nanoparticle tweezers and surface acoustic waves devices. - Highlights: • Ultrasonic

  19. Niosomes based on synthetic cationic lipids for gene delivery: the influence of polar head-groups on the transfection efficiency in HEK-293, ARPE-19 and MSC-D1 cells.

    Science.gov (United States)

    Ojeda, E; Puras, G; Agirre, M; Zárate, J; Grijalvo, S; Pons, R; Eritja, R; Martinez-Navarrete, G; Soto-Sanchez, C; Fernández, E; Pedraz, J L

    2015-01-28

    We designed niosomes based on three lipids that differed only in the polar-head group to analyze their influence on the transfection efficiency. These lipids were characterized by small-angle X-ray scattering before being incorporated into the niosomes which were characterized in terms of pKa, size, zeta potential, morphology and physical stability. Nioplexes were obtained upon the addition of a plasmid. Different ratios (w/w) were selected to analyze the influence of this parameter on size, charge and the ability to condense, release and protect the DNA. In vitro transfection experiments were performed in HEK-293, ARPE-19 and MSC-D1 cells. Our results show that the chemical composition of the cationic head-group clearly affects the physicochemical parameters of the niosomes and especially the transfection efficiency. Only niosomes based on cationic lipids with a dimethyl amino head group (lipid 3) showed a transfection capacity when compared with their counterparts amino (lipid 1) and tripeptide head-groups (lipid 2). Regarding cell viability, we clearly observed that nioplexes based on the cationic lipid 3 had a more deleterious effect than their counterparts, especially in ARPE-19 cells at 20/1 and 30/1 ratios. Similar studies could be extended to other series of cationic lipids in order to progress in the research on safe and efficient non-viral vectors for gene delivery purposes.

  20. Growth Data - Captive Broodstock Gene Rescue Program for Odd Year Class Elwha River Pink Salmon

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Conduct captive brood stock gene rescue program for Elwha River odd-year class pink salmon. The fork length to the nearest mm and weight to the nearest gram of a...

  1. 基因治疗非创伤性股骨头坏死的研究进展%Research progress of gene therapy in the treatment of non-traumatic osteonecrosis of femoral head

    Institute of Scientific and Technical Information of China (English)

    周明旺; 李盛华; 郭铁峰

    2012-01-01

    There are many methods of conservative treatment for early non-traumatic osteonecrosis of femoral head, but still lack of a mature and effective treatment. Gene therapy is a new treatment method for non-traumatic osteonecrosis of femoral head in recent years. This article showed that the non-traumatic osteonecrosis of femoral head related to progress and problems on pathogenesy,molecular biology foundation,exogenous theoretical gene,carrier selection and so on,discussed some problems and countermeasure and future applications.%非创伤性股骨头坏死早期保守治疗方法甚多,但尚缺乏一种成熟有效的治疗方法.基因治疗非创伤性股骨头坏死是近年来新型的治疗方法,本文就该病的发病机制、分子生物学基础、外源性治疗基因与载体选择等方面研究的相关进展及存在问题展开综述,讨论了研究的有关问题及对策,并就研究前景进行了展望.

  2. BIOLOGICAL MONITORING PROGRAM FOR EAST FORK POPLAR CREEK

    Energy Technology Data Exchange (ETDEWEB)

    ADAMS, S.M.; BEATY, T.W.; BRANDT, C.C.; CHRISTENSEN, S.W.; CICERONE, D.S.

    1998-09-09

    In May 1985, a National Pollutant Discharge Elimination System (NPDES) permit was issued for the Oak Ridge Y-12 Plant. As a condition of the permit, a Biological Monitoring and Abatement Program (BMAP) was developed to demonstrate that the effluent limitations established for the Y-12 Plant protect the classified uses of the receiving stream (East Fork Poplar Creek; EFPC), in particular, the growth and propagation of aquatic life (Lear et al. 1989). A second objective of the BMAP is to document the ecological effects resulting from the implementation of a water pollution control program designed to eliminate direct discharges of wastewaters to EFPC and to minimize the inadvertent release of pollutants to the environment. Because of the complex nature of the discharges to EFPC and the temporal and spatial variability in the composition of the discharges, a comprehensive, integrated approach to biological monitoring was developed. A new permit was issued to the Y-12 Plant on April 28, 1995 and became effective on July 1, 1995. Biological monitoring continues to be required under the new permit. The BMAP consists of four major tasks that reflect different but complementary approaches to evaluating the effects of the Y-12 Plant discharges on the aquatic integrity of EFPC. These tasks are (1) toxicity monitoring, (2) biological indicator studies, (3) bioaccumulation studies, and (4) ecological surveys of the periphyton, benthic macroinvertebrate, and fish communities.

  3. Soil Investigation of Lower East Fork Poplar Creek

    Energy Technology Data Exchange (ETDEWEB)

    Dickson, Johnbull O [ORNL; Mayes, Melanie [ORNL; Earles, Jennifer E [ORNL; Mehlhorn, Tonia L [ORNL; Lowe, Kenneth Alan [ORNL; Peterson, Mark J [ORNL; Pierce, Eric M [ORNL

    2017-03-01

    Mercury is regarded by the US Department of Energy (DOE) Oak Ridge Office of Environmental Management as a priority contaminant on the Oak Ridge Reservation because of the environmental risks associated with substantial losses from buildings, soils, and surface waters at the Y-12 National Security Complex (Y-12). As a result of historical releases of mercury from Y-12 primarily in the 1950s and early 1960s, the lower East Fork Poplar Creek (LEFPC) stream channel and bank soil margins are contaminated with mercury (Brooks and Southworth 2011; Tennessee Valley Authority 1985b, a). A Mercury Remediation Technology Development project is underway to evaluate the nature of downstream mercury contamination and to develop targeted site-specific remedial technologies that can mitigate mercury release and biological uptake. It is known that mercury concentration varies longitudinally and with depth in LEFPC bank soils; however, soil types and soil physical properties are not well known, especially relative to the zones of mercury contamination. Moreover, there are no soil maps for the downstream reaches of LEFPC in Roane County (i.e. from the Chestnut Hill Road downstream) and this work represents the first ever soil mapping along this section of LEFPC.

  4. BIOLOGICAL MONITORING PROGRAM FOR EAST FORK POPLAR CREEK

    Energy Technology Data Exchange (ETDEWEB)

    ADAMS, S.M.; ASHWOOD, T.L.; BEATY, T.W.; BRANDT, C.C.

    1997-10-24

    In May 1985, a National Pollutant Discharge Elimination System (NPDES) permit was issued for the Oak Ridge Y-12 Plant. As a condition of the permit a Biological Monitoring and Abatement Program (BMAP) was developed to demonstrate that the effluent limitations established for the Y- 12 Plant protect the classified uses of the receiving stream (East Fork Poplar Creek; EFPC), in particular, the growth and propagation of aquatic life (Lear et al. 1989). A second objective of the BMAP is to document the ecological effects resulting from the implementation of a water pollution control program designed to eliminate direct discharges of wastewaters to EFPC and to minimize the inadvertent release of pollutants to the environment. Because of the complex nature of the discharges to EFPC and the temporal and spatial variability in the composition of the discharges, a comprehensive, integrated approach to biological monitoring was developed. A new permit was issued to the Y-12 Plant on April 28, 1995 and became effective on July 1, 1995. Biological monitoring continues to be required under the new permit. The BMAP consists of four major tasks that reflect different but complementary approaches to evaluating the effects of the Y-12 Plant discharges on the aquatic integrity of EFPC. These tasks are (1) toxicity monitoring, (2) biological indicator studies, (3) bioaccumulation studies, and (4) ecological surveys of the periphyton, benthic macroinvertebrate, and fish communities.

  5. Failure analysis of axle shaft of a fork lift

    Directory of Open Access Journals (Sweden)

    Souvik Das

    2015-04-01

    Full Text Available An axle shaft of fork lift failed at operation within 296 h of service. The shaft transmits torque from discrepancy to wheel through planetary gear arrangement. A section of fractured axle shaft made of induction-hardened steel was analyzed to determine the root cause of the failure. Optical microscopies as well as field emission gun scanning electron microscopy (FEG-SEM along with energy dispersive spectroscopy (EDS were carried out to characterize the microstructure. Hardness profile throughout the cross-section was evaluated by micro-hardness measurements. Chemical analysis indicated that the shaft was made of 42CrMo4 steel grade as per specification. Microstructural analysis and micro-hardness profile revealed that the shaft was improperly heat treated resulting in a brittle case, where crack was found to initiate from the case in a brittle mode in contrast to ductile mode within the core. This behaviour was related to differences in microstructure, which was observed to be martensitic within the case with a micro-hardness equivalent to 735 HV, and a mixture of non-homogeneous structure of pearlite and ferrite within the core with a hardness of 210 HV. The analysis suggests that the fracture initiated from the martensitic case as brittle mode due to improper heat treatment process (high hardness. Moreover the inclusions along the hot working direction i.e. in the longitudinal axis made the component more susceptible to failure.

  6. A Tuning Fork with a Short Fibre Probe Sensor for a Near-FieldScanning Optical Microscope

    Institute of Scientific and Technical Information of China (English)

    王沛; 鲁拥华; 章江英; 明海; 谢建平; 黄建文; 高宗圣; 蔡定平

    2002-01-01

    We report on a tapping-mode tuning fork with a short fibre probe sensor for a near-field scanning optical microscope. The method demonstrates how to fabricate the short fibre probe. This tapping-mode tuning fork with a short fibre probe can provide stable and high Q at the tapping frequency of the tuning fork, and can give high-quality near-field scanning optical microscope and atomic force microscope images of samples. We present the results of using the tapping-mode tuning fork with a short fibre probe sensor for a near-field scanning optical microscope performed on an eight-channel silica waveguide.

  7. Is HEADS in our heads?

    DEFF Research Database (Denmark)

    Boisen, Kirsten A; Hertz, Pernille Grarup; Blix, Charlotte

    2016-01-01

    BACKGROUND: Outpatient clinic visits are a window of opportunity to address health risk behaviors and promote a healthier lifestyle among young people. The HEADS (Home, Education, Eating, Activities, Drugs [i.e. substance use including tobacco, alcohol, and illegal drugs], Sexuality [including...... care professionals participated. We found only small reported differences between staff and young patients regarding whether home, education, and activity were addressed. However, staff reported twice the rate of addressing smoking, alcohol, illegal drugs, sexuality, and contraception compared to young...... patients. Young patients reported that smoking, alcohol, illegal drugs, sexuality, and contraception were addressed significantly more at adult clinics in comparison to pediatric clinics. After controlling for age, gender and duration of illness, according to young patients, adjusted odds ratios...

  8. Molecular recognition imaging using tuning fork-based transverse dynamic force microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Hofer, Manuel; Adamsmaier, Stefan [University of Linz, Institute for Biophysics, Altenbergerstr. 69, 4040 Linz (Austria); Zanten, Thomas S. van [IBEC-Institute for Bioengineering of Catalonia and CIBER-Bbn, Baldiri i Reixac 15-21, Barcelona 08028 (Spain); Chtcheglova, Lilia A. [University of Linz, Institute for Biophysics, Altenbergerstr. 69, 4040 Linz (Austria); Manzo, Carlo [IBEC-Institute for Bioengineering of Catalonia and CIBER-Bbn, Baldiri i Reixac 15-21, Barcelona 08028 (Spain); Duman, Memed [University of Linz, Institute for Biophysics, Altenbergerstr. 69, 4040 Linz (Austria); Mayer, Barbara [Christian Doppler Laboratory for Nanoscopic Methods in Biophysics, Institute for Biophysics, University of Linz, Altenbergerstr. 69, 4040 Linz (Austria); Ebner, Andreas [University of Linz, Institute for Biophysics, Altenbergerstr. 69, 4040 Linz (Austria); Christian Doppler Laboratory for Nanoscopic Methods in Biophysics, Institute for Biophysics, University of Linz, Altenbergerstr. 69, 4040 Linz (Austria); Moertelmaier, Manuel; Kada, Gerald [Agilent Technologies Austria GmbH, Aubrunnerweg 11, 4040 Linz (Austria); Garcia-Parajo, Maria F. [IBEC-Institute for Bioengineering of Catalonia and CIBER-Bbn, Baldiri i Reixac 15-21, Barcelona 08028 (Spain); ICREA-Institucio Catalana de Recerca i Estudis Avancats, 08010 Barcelona (Spain); Hinterdorfer, Peter, E-mail: peter.hinterdorfer@jku.at [University of Linz, Institute for Biophysics, Altenbergerstr. 69, 4040 Linz (Austria); Christian Doppler Laboratory for Nanoscopic Methods in Biophysics, Institute for Biophysics, University of Linz, Altenbergerstr. 69, 4040 Linz (Austria); Kienberger, Ferry [Agilent Technologies Austria GmbH, Aubrunnerweg 11, 4040 Linz (Austria)

    2010-05-15

    We demonstrate simultaneous transverse dynamic force microscopy and molecular recognition imaging using tuning forks as piezoelectric sensors. Tapered aluminum-coated glass fibers were chemically functionalized with biotin and anti-lysozyme molecules and attached to one of the prongs of a 32 kHz tuning fork. The lateral oscillation amplitude of the tuning fork was used as feedback signal for topographical imaging of avidin aggregates and lysozyme molecules on mica substrate. The phase difference between the excitation and detection signals of the tuning fork provided molecular recognition between avidin/biotin or lysozyme/anti-lysozyme. Aggregates of avidin and lysozyme molecules appeared as features with heights of 1-4 nm in the topographic images, consistent with single molecule atomic force microscopy imaging. Recognition events between avidin/biotin or lysozyme/anti-lysozyme were detected in the phase image at high signal-to-noise ratio with phase shifts of 1-2{sup o}. Because tapered glass fibers and shear-force microscopy based on tuning forks are commonly used for near-field scanning optical microscopy (NSOM), these results open the door to the exciting possibility of combining optical, topographic and biochemical recognition at the nanometer scale in a single measurement and in liquid conditions.

  9. South Fork Snake River/Palisades Wildlife Mitigation Project: Environmental assessment

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1995-09-01

    BPA proposes to fund the implementation of the South Fork Snake River Programmatic Management Plan to compensate for losses of wildlife and wildlife habitat due to hydroelectric development at Palisades Dam. The Idaho Department of Fish and Game drafted the plan, which was completed in May 1993. This plan recommends land and conservation easement acquisition and wildlife habitat enhancement measures. These measures would be implemented on selected lands along the South Fork of the Snake River between Palisades Dam and the confluence with the Henry`s Fork, and on portions of the Henry`s Fork located in Bonneville, Madison, and Jefferson Counties, Idaho. BPA has prepared an Environmental Assessment evaluating the proposed project. The EA also incorporates by reference the analyses in the South Fork Snake River Activity/Operations Plan and EA prepared jointly in 1991 by the Bureau of Land Management and the Forest Service. Based on the analysis in the EA, BPA has determined that the proposed action is not a major Federal action significantly affecting the quality of the human environment within the meaning of the National Environmental Policy Act (NEPA) of 1969. Therefore, the preparation of an Environmental Impact Statement (EIS) is not required and BPA is issuing this FONSI.

  10. RECOVERY FOLLOWING SUBARACHNOID BLOCK : EVALUATION USING 128 HZ TUNING FORK

    Directory of Open Access Journals (Sweden)

    Goyal

    2014-07-01

    Full Text Available BACKGROUND: Following spinal anesthesia it is very important to see complete recovery before ambulation and discharge of the patient. Conventional methods to see recovery from spinal block use different types of motor power tests like Bromage score or the Formal motor power test system. MATERIAL AND METHODS: A total of one hundred and fifty patients of ASA grade I and II, presenting for lower segment caesarean section under spinal anesthesia were taken up for the study. We compared the use of a 128-Hz tuning fork with the results of conventional evaluation of block recovery. Conventional block recovery testing included Bromage score, Formal muscle power testing according to the British Medical Research Council, pinprick testing, and warm/cold testing. After obtaining base line values, a subarachnoid block was performed and patients were tested every 15 minutes after surgery, till the vibration score of one less than the baseline was achieved. Statistical analysis was performed to compare the results of the different methods to the time at which baseline values of vibration sense were reached. RESULTS: At the time vibration sense testing returned to baseline, 100% of the patients had attained Bromage score of 0 with no residual motor block. 98% of the patients regained foot extension and foot flexion strength completely while 92% of the patients showed complete recovery of the quadriceps strength. CONCLUSION: Recovery of vibration sense corresponds with recovery of motor block after spinal anesthesia and may serve as an easy means of documenting recovery with a single test before discharge.

  11. A nucleotide substitution at the 5′splice site of intron 1 of rice HEADING DATE 1 (HD1) gene homolog in foxtail millet, broadly found in landraces from Europe and Asia

    Institute of Scientific and Technical Information of China (English)

    Kenji Fukunaga; Naoko Izuka; Takehiro Hachiken; Satoshi Mizuguchi; Hidemi Ito; Katsuyuki Ichitani

    2015-01-01

    We investigated genetic variation of a rice HEADING DATE 1(HD1) homolog in foxtail millet. First, we searched for a rice HD1 homolog in a foxtail millet genome sequence and designed primers to amplify the entire coding sequence of the gene. We compared full HD1 gene sequences of 11 accessions (including Yugu 1, a Chinese cultivar used for genome sequencing) from various regions in Europe and Asia, found a nucleotide substitution at a putative splice site of intron 1, and designated the accessions with the nucleotide substitution as carrying a splicing variant. We verified by RT-PCR that this single nucleotide substitution causes aberrant splicing of intron 1. We investigated the geographical distribution of the splicing variant in 480 accessions of foxtail millet from various regions of Europe and Asia and part of Africa by dCAPS and found that the splicing variant is broadly distributed in Europe and Asia. Differences of heading times between accessions with wild type allele of the HD1 gene and those with the splicing variant allele were unclear. We also investigated variation in 13 accessions of ssp. viridis, the wild ancestor, and the results suggested that the wild type is predominant in the wild ancestor.

  12. A nucleotide substitution at the 5′ splice site of intron 1 of rice HEADING DATE 1(HD1) gene homolog in foxtail millet, broadly found in landraces from Europe and Asia

    Institute of Scientific and Technical Information of China (English)

    Kenji Fukunaga; Naoko Izuka; Takehiro Hachiken; Satoshi Mizuguchi; Hidemi Ito; Katsuyuki Ichitani

    2015-01-01

    We investigated genetic variation of a rice HEADING DATE 1(HD1) homolog in foxtail millet.First, we searched for a rice HD1 homolog in a foxtail millet genome sequence and designed primers to amplify the entire coding sequence of the gene. We compared full HD1 gene sequences of 11 accessions(including Yugu 1, a Chinese cultivar used for genome sequencing) from various regions in Europe and Asia, found a nucleotide substitution at a putative splice site of intron 1, and designated the accessions with the nucleotide substitution as carrying a splicing variant. We verified by RT-PCR that this single nucleotide substitution causes aberrant splicing of intron 1. We investigated the geographical distribution of the splicing variant in 480 accessions of foxtail millet from various regions of Europe and Asia and part of Africa by d CAPS and found that the splicing variant is broadly distributed in Europe and Asia. Differences of heading times between accessions with wild type allele of the HD1 gene and those with the splicing variant allele were unclear. We also investigated variation in 13 accessions of ssp. viridis, the wild ancestor, and the results suggested that the wild type is predominant in the wild ancestor.

  13. Computed Tomography (CT) -- Head

    Medline Plus

    Full Text Available ... of the Head? What is CT Scanning of the Head? Computed tomography, more commonly known as a ... of page What are some common uses of the procedure? CT scanning of the head is typically ...

  14. Computed Tomography (CT) -- Head

    Medline Plus

    Full Text Available ... of the Head? What is CT Scanning of the Head? Computed tomography, more commonly known as a ... of page What are some common uses of the procedure? CT scanning of the head is typically ...

  15. Movements of fluvial Bonneville cutthroat trout in the Thomas Fork of the Bear River, Idaho-Wyoming

    Science.gov (United States)

    Colyer, W.T.; Kershner, J.L.; Hilderbrand, R.H.

    2005-01-01

    The majority of interior subspecies of cutthroat trout Oncorhynchus clarkii have been extirpated from large rivers by anthropogenic activities that have fragmented habitats and introduced nonnative competitors. Selective pressures against migratory behaviors and main-stem river occupation, coupled with conservation strategies that isolate genetically pure populations above barriers, have restricted gene flow and prevented expression of the fluvial life history in many populations. Existing knowledge about the movements and home range requirements of fluvial cutthroat trout is, therefore, limited. Our objectives in this study were to (1) determine the extent of seasonal home ranges and mobility of Bonneville cutthroat trout O. c. utah (BCT) in the Thomas Fork and main-stem Bear River and (2) evaluate the role of a water diversion structure functioning as a seasonal migration barrier to fish movement. We implanted 55 BCT in the Thomas Fork of the Bear River, Idaho, with radio transmitters and located them bimonthly in 1999–2000 and weekly in 2000–2001. We found fish to be more mobile than previously reported. Individuals above the diversion barrier occupied substantially larger home ranges than those below the barrier (analysis of variance: P = 0.0003; median = 2,225 m above barrier; median = 500 m below barrier) throughout our study, and they moved more frequently (mean, 0.89 movements/contact; range, 0.57–1.00) from October 2000 through March 2001 than fish below the barrier (mean, 0.45 movements/contact; range, 0.00–1.00). During the spring of both years, we located radio-tagged fish in both upstream and neighboring tributaries as far as 86 km away from our study site. Our results document the existence of a fluvial component of BCT in the Bear River and its tributaries and suggest that successful efforts at conservation of these fish must focus on main-stem habitats and the maintenance of seasonal migration corridors.

  16. Determining the order of resistance genes against Stagonospora nodorum blotch, Fusarium head blight and stem rust on wheat chromosome 3BS

    Science.gov (United States)

    Fungal diseases of wheat occur every year in the U.S., leading to significant grain yield losses. Stagonospora nodorum blotch (SNB), Fusarium head blight (FHB) and stem rust (SR) are caused by the fungi Stagonospora nodorum, Fusarium graminearum and Puccinia graminis, respectively. These leaf and he...

  17. Head Impact Laboratory (HIL)

    Data.gov (United States)

    Federal Laboratory Consortium — The HIL uses testing devices to evaluate vehicle interior energy attenuating (EA) technologies for mitigating head injuries resulting from head impacts during mine/...

  18. The DNA damage checkpoint response to replication stress: A Game of Forks.

    Directory of Open Access Journals (Sweden)

    Rachel eJossen

    2013-03-01

    Full Text Available Conditions challenging replication fork progression, collectively referred to as replication stress, represent a major source of genomic instability and are associated to cancer onset. The replication checkpoint, a specialized branch of the DNA damage checkpoint, monitors fork problems and triggers a cellular response aimed at preserving genome integrity. Here, we review the mechanisms by which the replication checkpoint monitors and responds to replication stress, focusing on the checkpoint-mediated pathways contributing to protect replication fork integrity. We discuss how cells achieve checkpoint signaling inactivation once replication stress is overcome and how a failure to timely revert checkpoint-mediated changes in cellular physiology might impact on replication dynamics and genome integrity. We also highlight the checkpoint function as an anti-cancer barrier preventing cells malignant transformation following oncogene-induced replication stress.

  19. The Coefficient of the Voltage Induced Frequency Shift Measurement on a Quartz Tuning Fork

    Directory of Open Access Journals (Sweden)

    Yubin Hou

    2014-11-01

    Full Text Available We have measured the coefficient of the voltage induced frequency shift (VIFS of a 32.768 KHz quartz tuning fork. Three vibration modes were studied: one prong oscillating, two prongs oscillating in the same direction, and two prongs oscillating in opposite directions. They all showed a parabolic dependence of the eigen-frequency shift on the bias voltage applied across the fork, due to the voltage-induced internal stress, which varies as the fork oscillates. The average coefficient of the VIFS effect is as low as several hundred nano-Hz per millivolt, implying that fast-response voltage-controlled oscillators and phase-locked loops with nano-Hz resolution can be built.

  20. Multiple critical velocities in oscillatory flow of superfluid 4He due to quartz tuning forks

    Science.gov (United States)

    Schmoranzer, D.; Jackson, M. J.; Tsepelin, V.; Poole, M.; Woods, A. J.; Človečko, M.; Skrbek, L.

    2016-12-01

    We report recent investigations into the transition to turbulence in superfluid 4He, realized experimentally by measuring the drag forces acting on two custom-made quartz tuning forks with fundamental resonances at 6.5 kHz and 55.5 kHz, in the temperature range 10 mK to 2.17 K. In pure superfluid in the zero temperature limit, three distinct critical velocities were observed with both tuning forks. We discuss the significance of all critical velocities and associate the third critical velocity reported here with the development of large vortical structures in the flow, which thus starts to mimic turbulence in classical fluids. The interpretation of our results is directly linked to previous experimental work with oscillators such as tuning forks, grids, and vibrating wires, focusing on the behavior of purely superfluid 4He at very low temperatures.

  1. Pathological Changes of von Economo Neuron and Fork Neuron in Neuropsychiatric Diseases.

    Science.gov (United States)

    Liu, Jia; Wang, Lu-ning; Arzberger, Thomas; Zhu, Ming-wei

    2016-02-01

    von Economo neuron (VEN) is a bipolar neuron characterized by a large spindle-shaped soma. VEN is generally distributed in the layer V of anterior insular lobe and anterior cingulate cortex. Fork neuron is another featured bipolar neuron. In recent years,many studies have illustrated that VEN and fork neurons are correlated with complicated cognition such as self-consciousness and social emotion. Studies in the development and morpholigies of these two neurons as well as their pathological changes in various neurological and psychiatric disorders have found that the abnormal number and functions of VEN can cause corresponding dysfunctions in social recognition and emotions both during the neuro-developmental stages of childhood and during the nerve degeneration in old age stage. Therefore, more attentions should be paid on the research of VEN and fork neurons in neuropsychiatric diseases.

  2. Replication Fork Protection Factors Controlling R-Loop Bypass and Suppression.

    Science.gov (United States)

    Chang, Emily Yun-Chia; Stirling, Peter C

    2017-01-14

    Replication-transcription conflicts have been a well-studied source of genome instability for many years and have frequently been linked to defects in RNA processing. However, recent characterization of replication fork-associated proteins has revealed that defects in fork protection can directly or indirectly stabilize R-loop structures in the genome and promote transcription-replication conflicts that lead to genome instability. Defects in essential DNA replication-associated activities like topoisomerase, or the minichromosome maintenance (MCM) helicase complex, as well as fork-associated protection factors like the Fanconi anemia pathway, both appear to mitigate transcription-replication conflicts. Here, we will highlight recent advances that support the concept that normal and robust replisome function itself is a key component of mitigating R-loop coupled genome instability.

  3. 77 FR 66865 - Record of Decision for the Oil and Gas Management Plan, Big South Fork National River and...

    Science.gov (United States)

    2012-11-07

    ... National Park Service Record of Decision for the Oil and Gas Management Plan, Big South Fork National River....C. 4332(2)(C), the National Park Service (NPS) announces the availability of the Record of Decision (ROD) for the Oil and Gas Management Plan (Plan) for Big South Fork National River and Recreation Area...

  4. 76 FR 50171 - Notice of Intent To Prepare an Environmental Impact Statement for the Henrys Fork Salinity...

    Science.gov (United States)

    2011-08-12

    ... the Henrys Fork Salinity Control Project Plan, Sweetwater and Uinta Counties, WY; Daggett and Summit... Statement (EIS) for the Henrys Fork Salinity Control Project Plan (SCPP). The NRCS will be the lead agency... Improvements'' alternative assumes a salinity control project will be implemented. Existing financial...

  5. 33 CFR 165.552 - Security Zone; Oyster Creek Generation Station, Forked River, Ocean County, New Jersey.

    Science.gov (United States)

    2010-07-01

    ... 33 Navigation and Navigable Waters 2 2010-07-01 2010-07-01 false Security Zone; Oyster Creek... Coast Guard District § 165.552 Security Zone; Oyster Creek Generation Station, Forked River, Ocean... the Forked River in the vicinity of the Oyster Creek Generation Station, bounded by a line...

  6. Recombination occurs within minutes of replication blockage by RTS1 producing restarted forks that are prone to collapse

    Science.gov (United States)

    Nguyen, Michael O; Jalan, Manisha; Morrow, Carl A; Osman, Fekret; Whitby, Matthew C

    2015-01-01

    The completion of genome duplication during the cell cycle is threatened by the presence of replication fork barriers (RFBs). Following collision with a RFB, replication proteins can dissociate from the stalled fork (fork collapse) rendering it incapable of further DNA synthesis unless recombination intervenes to restart replication. We use time-lapse microscopy and genetic assays to show that recombination is initiated within ∼10 min of replication fork blockage at a site-specific barrier in fission yeast, leading to a restarted fork within ∼60 min, which is only prevented/curtailed by the arrival of the opposing replication fork. The restarted fork is susceptible to further collapse causing hyper-recombination downstream of the barrier. Surprisingly, in our system fork restart is unnecessary for maintaining cell viability. Seemingly, the risk of failing to complete replication prior to mitosis is sufficient to warrant the induction of recombination even though it can cause deleterious genetic change. DOI: http://dx.doi.org/10.7554/eLife.04539.001 PMID:25806683

  7. Heading and head injuries in soccer.

    Science.gov (United States)

    Kirkendall, D T; Jordan, S E; Garrett, W E

    2001-01-01

    In the world of sports, soccer is unique because of the purposeful use of the unprotected head for controlling and advancing the ball. This skill obviously places the player at risk of head injury and the game does carry some risk. Head injury can be a result of contact of the head with another head (or other body parts), ground, goal post, other unknown objects or even the ball. Such impacts can lead to contusions, fractures, eye injuries, concussions or even, in rare cases, death. Coaches, players, parents and physicians are rightly concerned about the risk of head injury in soccer. Current research shows that selected soccer players have some degree of cognitive dysfunction. It is important to determine the reasons behind such deficits. Purposeful heading has been blamed, but a closer look at the studies that focus on heading has revealed methodological concerns that question the validity of blaming purposeful heading of the ball. The player's history and age (did they play when the ball was leather and could absorb significant amounts of water), alcohol intake, drug intake, learning disabilities, concussion definition and control group use/composition are all factors that cloud the ability to blame purposeful heading. What does seem clear is that a player's history of concussive episodes is a more likely explanation for cognitive deficits. While it is likely that the subconcussive impact of purposeful heading is a doubtful factor in the noted deficits, it is unknown whether multiple subconcussive impacts might have some lingering effects. In addition, it is unknown whether the noted deficits have any affect on daily life. Proper instruction in the technique is critical because if the ball contacts an unprepared head (as in accidental head-ball contacts), the potential for serious injury is possible. To further our understanding of the relationship of heading, head injury and cognitive deficits, we need to: learn more about the actual impact of a ball on the

  8. Multiple genetic pathways for restarting DNA replication forks in Escherichia coli K-12.

    OpenAIRE

    Sandler, S J

    2000-01-01

    In Escherichia coli, the primosome assembly proteins, PriA, PriB, PriC, DnaT, DnaC, DnaB, and DnaG, are thought to help to restart DNA replication forks at recombinational intermediates. Redundant functions between priB and priC and synthetic lethality between priA2::kan and rep3 mutations raise the possibility that there may be multiple pathways for restarting replication forks in vivo. Herein, it is shown that priA2::kan causes synthetic lethality when placed in combination with either Delt...

  9. Reconnaissance for radioactive deposits in the Nixon Fork mining district, Medfra Quadrangle, central Alaska, 1949

    Science.gov (United States)

    White, Max G.; Stevens, John M.

    1953-01-01

    Reconnaissance for radioactive deposits in the Nixon Fork mining district, Medfra quadrangle, central Alaska, in 1949 disclosed the occurrence of allanite in sampled containing as much as 0.05 percent equivalent uranium from the dump of the Whalen mine; the presence of radioactive parisite (a rare-earth fluocarbonate) in a highly altered limestone containing about 0.025 percent equivalent uranium near the Whalen shaft; and radioactive idocrase in samples of altered garnet rock with about 0.025 percent equivalent uranium, form the Crystal shaft of the Nixon Fork mine. This radioactivity is due mostly to thorium rather than uranium. Placer concentrates

  10. Genomic structure of the human mitochondrial chaperonin genes: Hsp60 and Hsp10 are localised head to head on chromosome 2 separated by a bidirectional promoter

    DEFF Research Database (Denmark)

    Hansen, J.J.; Bross, P.; Westergaard, M.;

    2003-01-01

    are not known to express any member of the platelet-derived growth factor receptor family. In order to study if epidermis may be genetically transformed to a platelet-derived growth factor sensitive compartment we aimed to introduce the gene encoding human platelet-derived growth factor receptor beta (PDGF beta...... at the air-liquid interface on devitalized dermis, we were able to establish a multilayered epithelium showing histologic similarities to that evolved from native keratinocytes or keratinocytes transduced with the reporter gene encoding enhanced green fluorescent protein. Receptor-modified epidermal tissue...... cultured for 6 days and examined by immunofluorescence microscopy was shown to contain PDGF beta R-expressing keratinocytes distributed in all layers of living epidermis. By continued tissue culture in serum-containing medium, the epidermis became increasingly cornified although receptor-positive cells...

  11. Genome-wide association study suggests common variants within RP11-634B7.4 gene influencing severe pre-treatment pain in head and neck cancer patients

    Science.gov (United States)

    Reyes-Gibby, Cielito C.; Wang, Jian; Silvas, Mary Rose T.; Yu, Robert K.; Hanna, Ehab Y.; Shete, Sanjay

    2016-01-01

    Pain is often one of the first signs of squamous cell carcinoma of the head and neck (HNSCC). Pain at diagnosis is an important prognostic marker for the development of chronic pain, and importantly, for the overall survival time. To identify variants influencing severe pre-treatment pain in 1,368 patients newly diagnosed with HNSCC, we conducted a genome-wide association study based on 730,525 tagging SNPs. The patients were all previously untreated for cancer. About 15% of the patients had severe pre-treatment pain, defined as pain score ≥7 (0 = “no pain” and 10 = “worst pain”). We identified 3 common genetic variants in high linkage disequilibrium for severe pre-treatment pain, representing one genomic region at 1q44 (rs3862188, P = 3.45 × 10−8; rs880143, P = 3.45 × 10−8; and rs7526880, P = 4.92 × 10−8), which maps to the RP11-634B7.4 gene, a novel antisense gene to three olfactory receptor genes. Olfactory receptor genes, upstream effectors of the MAPK signaling cascade, might be novel target genes for pain in HNSCC patients. Future experimental validation to explore biological mechanisms will be key to defining the role of the intronic variants and non-coding RNA for pain in patients with HNSCC. PMID:27670397

  12. Chrysanthemyl diphosphate synthase: Isolation of the gene and characterization of the recombinant non-head-to-tail monoterpene synthase from Chrysanthemum cinerariaefolium

    OpenAIRE

    Rivera, Susan B.; Swedlund, Bradley D.; King, Gretchen J.; Bell, Russell N.; Hussey, Charles E.; Shattuck-Eidens, Donna M.; Wrobel, Wislawa M.; Peiser, Galen D.; Poulter, C. Dale

    2001-01-01

    Chrysanthemyl diphosphate synthase (CPPase) catalyzes the condensation of two molecules of dimethylallyl diphosphate to produce chrysanthemyl diphosphate (CPP), a monoterpene with a non-head-to-tail or irregular c1′-2-3 linkage between isoprenoid units. Irregular monoterpenes are common in Chrysanthemum cinerariaefolium and related members of the Asteraceae family. In C. cinerariaefolium, CPP is an intermediate in the biosynthesis of the pyrethrin ester insecticides. CPPa...

  13. Characterization of four nr5a genes and gene expression profiling for testicular steroidogenesis-related genes and their regulatory factors in response to bisphenol A in rare minnow Gobiocypris rarus.

    Science.gov (United States)

    Zhang, Yingying; Yuan, Cong; Hu, Guojun; Li, Meng; Zheng, Yao; Gao, Jiancao; Yang, Yanping; Zhou, Ying; Wang, Zaizhao

    2013-12-01

    Bisphenol A (BPA) widely used in the manufacture of numerous products is ubiquitous in aquatic environment. To explore the mechanisms of BPA-mediated actions, male rare minnow Gobiocypris rarus were exposed to BPA at concentrations of 5, 15, and 50 μg/L for 14 and 35 days in the present study. Four subtypes of nr5a gene encoding important transcription factors for steroidogenesis were characterized, and tissue distribution analysis demonstrated distinct expression profiling of the four genes in G. rarus. BPA at environmentally relevant concentration (5 μg/L) caused increase of gonadosomatic index (GSI) of male fish. In response to BPA, no obvious changes on the testis development were observed. Modulation of vtg mRNA expression by BPA suggests estrogenic and/or anti-estrogenic effects of BPA were dependent on exposed duration (14 or 35 days). Gene expression profiling for testicular steroidogenesis-related genes, sexual steroid receptors, gonadotropin receptors, and transcription factors indicates differential regulation was dependent on exposure duration and dose of BPA. The correlation analysis at mRNA level demonstrates that the BPA-mediated actions on testicular steroidogenesis might involve sex steroid hormone receptor signaling, gonadotropin/gonadotropin receptor pathway, and transcription factors such as nuclear receptor subfamily 5, group A (Nr5a), fork head box protein L2 (Foxl2).

  14. 76 FR 46721 - Salmon-Challis National Forest, ID; Upper North Fork HFRA Ecosystem Restoration Project...

    Science.gov (United States)

    2011-08-03

    ... this project area to improve the health of the ecosystem and reach the desired future condition. DATES...; ] DEPARTMENT OF AGRICULTURE Forest Service Salmon-Challis National Forest, ID; Upper North Fork HFRA Ecosystem... the potential for large-scale, high-intensity wildfires that threaten human life, property, and...

  15. Numerical performance analysis of quartz tuning fork-based force sensors

    Science.gov (United States)

    Dagdeviren, Omur E.; Schwarz, Udo D.

    2017-01-01

    Quartz tuning fork-based force sensors where one prong is immobilized onto a holder while the other one is allowed to oscillate freely (‘qPlus’ configuration) are in widespread use for high-resolution scanning probe microscopy applications. Due to the small size of the tuning forks (≈3 mm) and the complexity of the sensor assemblies, the reliable and repeatable manufacturing of the sensors has been challenging. In this paper, we investigate the contribution of the amount and location of the epoxy glue used to attach the tuning fork to its holder on the sensor’s performance. Towards this end, we use finite element analysis to model the entire sensor assembly and to perform static and dynamic numerical simulations. Our analysis reveals that increasing the thickness of the epoxy layer between prong and holder results in a decrease of the sensor’s spring constant, eigenfrequency, and quality factor while showing an increasing deviation from oscillation in its primary modal shape. Adding epoxy at the sides of the tuning fork also leads to a degradation of the quality factor even though in this case, spring constant and eigenfrequency rise in tandem with a lessening of the deviation from its ideal modal shape.

  16. 16 CFR Figure 1 to Part 1512 - Bicycle Front Fork Cantilever Bending Test Rig

    Science.gov (United States)

    2010-01-01

    ... 16 Commercial Practices 2 2010-01-01 2010-01-01 false Bicycle Front Fork Cantilever Bending Test Rig 1 Figure 1 to Part 1512 Commercial Practices CONSUMER PRODUCT SAFETY COMMISSION FEDERAL HAZARDOUS SUBSTANCES ACT REGULATIONS REQUIREMENTS FOR BICYCLES Pt. 1512, Fig. 1 Figure 1 to Part 1512—Bicycle...

  17. 77 FR 71611 - Land Acquisitions; North Fork Rancheria of Mono Indians of California

    Science.gov (United States)

    2012-12-03

    ... Tribe's current government headquarters, which are located in the town of North Fork, Madera County, California, described as: Real property in the City of UNINCORPORATED AREA, County of Madera, State of..., AND 8 of PARCEL MAP 3426 IN THE UNINCORPORATED AREA OF THE COUNTY OF MADERA, STATE OF CALIFORNIA, AS...

  18. From farm to fork and further. Research tackling the grand challenge of food safety in Europe

    NARCIS (Netherlands)

    Ridder, M. de; Polchar, J.; Gehem, M.

    2012-01-01

    The study From Farm to Fork and Further shows how, as traditional causes of food safety problems such as basic hygiene are successfully dealt with, future food safety risks become ever harder to manage. European countries may have the highest food safety standards, however the trends that go hand in

  19. Environmental Assessment, Demolition of Alpha Ramp Grand Forks Air Force Base, North Dakota

    Science.gov (United States)

    2007-01-01

    support active cultivation of grass and alfalfa hay, and other areas are undergoing rehabilitation for future haying operations. Any cropping practices...January 2004). 3.10 Land Use Land use in Grand Forks County consists primarily of cultivated crops, including spring wheat, barley, sunflowers

  20. Final Environmental Assessment Demolition of Alpha Ramp, Grand Forks Air Force Base, North Dakota

    Science.gov (United States)

    2007-01-01

    unimproved areas at GFAFB have been used to support active cultivation of grass and alfalfa hay, and other areas are undergoing rehabilitation for...Native American areas of concern on GFAFB (USAF, January 2004). 3.10 Land Use Land use in Grand Forks County consists primarily of cultivated crops

  1. Bending Forks and Wagging Dogs--It's about the DNA 3' Tail.

    Science.gov (United States)

    Tsutakawa, Susan E; Tainer, John A

    2015-06-18

    Protecting, reversing, and remodeling stalled replication forks are critical to genome stability and require coordinating DNA replication, remodeling, and repair. In this issue, Kile et al. (2015) find that unexpected HLTF specificity for DNA's 3'-hydroxyl tail helps control these biological functions. Copyright © 2015 Elsevier Inc. All rights reserved.

  2. Bending forks and wagging dogs – it’s about the DNA 3′ tail

    Science.gov (United States)

    Tsutakawa, Susan E.; Tainer, John A.

    2017-01-01

    Protecting, reversing, and remodeling stalled replication forks are critical to genome stability and require coordinating DNA replication, remodeling, and repair. In this issue, Kile et al. (2015) find unexpected HLTF specificity for DNA’s 3′-hydroxyl tail helps control these biological functions. PMID:26091346

  3. MediaMill: Fast and effective video search using the ForkBrowser

    NARCIS (Netherlands)

    de Rooij, O.; Snoek, C.G.M.; Worring, M.

    2008-01-01

    In this technical demonstration we showcase the MediaMill ForkBrowser for video retrieval. It embeds multiple query methods into a single browsing environment. We show that users can switch query methods on demand without the need to adapt to a different interface. This allows for fast and effective

  4. Genomic structure of the human mitochondrial chaperonin genes: Hsp60 and Hsp10 are localised head to head on chromosome 2 separated by a bidirectional promoter

    DEFF Research Database (Denmark)

    Hansen, J.J.; Bross, P.; Westergaard, M.

    2003-01-01

    Platelet-derived growth factor is a major proliferative and migratory stimulus for connective tissue cells during the initiation of skin repair processes. In response to injury, locally produced platelet-derived growth factor is secreted by a diversity of cutaneous cell types whereas target...... R) into epidermal keratinocytes using a retrovirus-derived vector. Successful gene transfer to primary cells was confirmed by immunofluorescence staining, southern blotting, and ligand-induced receptor autophosphorylation. By culturing a mixture of PDGF beta R-transduced and unmodified keratinocytes...... cultured for 6 days and examined by immunofluorescence microscopy was shown to contain PDGF beta R-expressing keratinocytes distributed in all layers of living epidermis. By continued tissue culture in serum-containing medium, the epidermis became increasingly cornified although receptor-positive cells...

  5. Force-gradient-induced mechanical dissipation of quartz tuning fork force sensors used in atomic force microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Castellanos-Gomez, A. [Departamento de Fisica de la Materia Condensada (C-III), Universidad Autonoma de Madrid, Campus de Cantoblanco, 28049 Madrid (Spain); Agrait, N. [Departamento de Fisica de la Materia Condensada (C-III), Universidad Autonoma de Madrid, Campus de Cantoblanco, 28049 Madrid (Spain); Instituto Universitario de Ciencia de Materiales ' Nicolas Cabrera' , Universidad Autonoma de Madrid, Campus de Cantoblanco, 28049 Madrid (Spain); Instituto Madrileno de Estudios Avanzados en Nanociencia, IMDEA-Nanociencia, 28049 Madrid (Spain); Rubio-Bollinger, G., E-mail: gabino.rubio@uam.es [Departamento de Fisica de la Materia Condensada (C-III), Universidad Autonoma de Madrid, Campus de Cantoblanco, 28049 Madrid (Spain); Instituto Universitario de Ciencia de Materiales ' Nicolas Cabrera' , Universidad Autonoma de Madrid, Campus de Cantoblanco, 28049 Madrid (Spain)

    2011-02-15

    We have studied the dynamics of quartz tuning fork resonators used in atomic force microscopy taking into account the mechanical energy dissipation through the attachment of the tuning fork base. We find that the tuning fork resonator quality factor changes even in the case of a purely elastic sensor-sample interaction. This is due to the effective mechanical imbalance of the tuning fork prongs induced by the sensor-sample force gradient, which in turn has an impact on dissipation through the attachment of the resonator base. This effect may yield a measured dissipation signal that can be different from the one exclusively related to the dissipation between the sensor and the sample. We also find that there is a second-order term in addition to the linear relationship between the sensor-sample force gradient and the resonance frequency shift of the tuning fork that is significant even for force gradients usually present in atomic force microscopy, which are in the range of tens of N/m. -- Research Highlights: {yields} Dynamics of miniature tuning fork force sensors: a mechanical model. {yields} Non-linear relationship between resonance frequency shift and applied force gradient. {yields} An apparent mechanical dissipation channel opens even for purely conservative tip-sample interactions. {yields} qPlus tuning forks configuration has lower Q factor but straightforward dynamics.

  6. Evaluation of Lower East Fork Poplar Creek Mercury Sources

    Energy Technology Data Exchange (ETDEWEB)

    Watson, David B. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Brooks, Scott C. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Mathews, Teresa J. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Bevelhimer, Mark S. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); DeRolph, Chris [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Brandt, Craig C. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Peterson, Mark J. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Ketelle, Richard [East Tennessee Technology Park (ETTP), Oak Ridge, TN (United States)

    2016-06-01

    This report summarizes a 3-year research project undertaken to better understand the nature and magnitude of mercury (Hg) fluxes in East Fork Poplar Creek (EFPC). This project addresses the requirements of Action Plan 1 in the 2011 Oak Ridge Reservation-wide Comprehensive Environmental Response, Compensation, and Liability Act Five Year Review (FYR). The Action Plan is designed to address a twofold 2011 FYR issue: (1) new information suggests mobilization of mercury from the upper and lower EFPC streambeds and stream banks is the primary source of mercury export during high-flow conditions, and (2) the current Record of Decision did not address the entire hydrologic system and creek bank or creek bed sediments. To obtain a more robust watershed-scale understanding of mercury sources and processes in lower EFPC (LEFPC), new field and laboratory studies were coupled with existing data from multiple US Department of Energy programs to develop a dynamic watershed and bioaccumulation model. LEFPC field studies for the project focused primarily on quantification of streambank erosion and an evaluation of mercury dynamics in shallow groundwater adjacent to LEFPC and potential connection to the surface water. The approach to the stream bank study was innovative in using imagery from kayak floats’ surveys from the headwaters to the mouth of EFPC to estimate erosion, coupled with detailed bank soil mercury analyses. The goal of new field assessments and modeling was to generate a more holistic and quantitative understanding of the watershed and the sources, flux, concentration, transformation, and bioaccumulation of inorganic mercury (IHg) and methylmercury (MeHg). Model development used a hybrid approach that dynamically linked a spreadsheet-based physical and chemical watershed model to a systems dynamics, mercury bioaccumulation model for key fish species. The watershed model tracks total Hg and MeHg fluxes and concentrations by examining upstream inputs, floodplain

  7. Polymorphisms of the DNMT3b gene and risk of squamous cell carcinoma of the head and neck: a case-control study

    OpenAIRE

    Liu, Zhensheng; Wang, Luo; Wang, Li-E; Sturgis, Erich E.; Wei, Qingyi

    2008-01-01

    DNA-methyltransferase-3B (DNMT3B) may play an oncogenic role during tumorigenesis, and its genetic variants have been reportedly to be associated with risk of several cancers, but few studies have investigated their roles in head and neck cancer. Here we report a hospital-based case-control study with 832 SCCHN patients and 843 cancer-free controls of non-Hispanic whites that evaluated the association between two DNMT3B single nucleotide polymorphisms (SNPs) DNMT3B-149C>T (rs2424913) and DNMT...

  8. Unligated Okazaki Fragments Induce PCNA Ubiquitination and a Requirement for Rad59-Dependent Replication Fork Progression.

    Directory of Open Access Journals (Sweden)

    Hai Dang Nguyen

    Full Text Available Deficiency in DNA ligase I, encoded by CDC9 in budding yeast, leads to the accumulation of unligated Okazaki fragments and triggers PCNA ubiquitination at a non-canonical lysine residue. This signal is crucial to activate the S phase checkpoint, which promotes cell cycle delay. We report here that a pol30-K107 mutation alleviated cell cycle delay in cdc9 mutants, consistent with the idea that the modification of PCNA at K107 affects the rate of DNA synthesis at replication forks. To determine whether PCNA ubiquitination occurred in response to nicks or was triggered by the lack of PCNA-DNA ligase interaction, we complemented cdc9 cells with either wild-type DNA ligase I or a mutant form, which fails to interact with PCNA. Both enzymes reversed PCNA ubiquitination, arguing that the modification is likely an integral part of a novel nick-sensory mechanism and not due to non-specific secondary mutations that could have occurred spontaneously in cdc9 mutants. To further understand how cells cope with the accumulation of nicks during DNA replication, we utilized cdc9-1 in a genome-wide synthetic lethality screen, which identified RAD59 as a strong negative interactor. In comparison to cdc9 single mutants, cdc9 rad59Δ double mutants did not alter PCNA ubiquitination but enhanced phosphorylation of the mediator of the replication checkpoint, Mrc1. Since Mrc1 resides at the replication fork and is phosphorylated in response to fork stalling, these results indicate that Rad59 alleviates nick-induced replication fork slowdown. Thus, we propose that Rad59 promotes fork progression when Okazaki fragment processing is compromised and counteracts PCNA-K107 mediated cell cycle arrest.

  9. 用于微机电系统的叉形微铰链%Micro Fork Hinge for MEMS Devices

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Flexible beams are often used for rotation in MEMS (Micro Electro Mechanical Systems) devices to avoid the friction problems associated with hinge. However, the rotation angle of flexible beam is very limited and not enough for many applications. In this paper, we introduce a quasi hinge structure named as Fork Hinge, which has a larger equivalent rotation angle (e.g.10 times lager) and is more stable than the flexible hinge, while keeping its interesting properties. We develop an analytical model and simulate the Fork hinge behavior with FEM analysis. We find a good correlation with Fork Hinges fabricated using a SOI (Silicon on Insulator) wafer and DRIE (Deep Reactive Ion Etching).

  10. Computed Tomography (CT) -- Head

    Medline Plus

    Full Text Available ... limitations of CT Scanning of the Head? What is CT Scanning of the Head? Computed tomography, more ... the body being studied. top of page How is the procedure performed? The technologist begins by positioning ...

  11. Cytogenetic mapping of a major locus for resistance to Fusarium head blight and crown rot of wheat on Thinopyrum elongatum 7EL and its pyramiding with valuable genes from a Th. ponticum homoeologous arm onto bread wheat 7DL.

    Science.gov (United States)

    Ceoloni, Carla; Forte, Paola; Kuzmanović, Ljiljana; Tundo, Silvio; Moscetti, Ilaria; De Vita, Pasquale; Virili, Maria Elena; D'Ovidio, Renato

    2017-06-27

    A major locus for resistance to different Fusarium diseases was mapped to the most distal end of Th. elongatum 7EL and pyramided with Th. ponticum beneficial genes onto wheat 7DL. Perennial Triticeae species of the Thinopyrum genus are among the richest sources of valuable genes/QTL for wheat improvement. One notable and yet unexploited attribute is the exceptionally effective resistance to a major wheat disease worldwide, Fusarium head blight, associated with the long arm of Thinopyrum elongatum chromosome 7E (7EL). We targeted the transfer of the temporarily designated Fhb-7EL locus into bread wheat, pyramiding it with a Th. ponticum 7el1L segment stably inserted into the 7DL arm of wheat line T4. Desirable genes/QTL mapped along the T4 7el1L segment determine resistance to wheat rusts (Lr19, Sr25) and enhancement of yield-related traits. Mapping of the Fhb-7EL QTL, prerequisite for successful pyramiding, was established here on the basis of a bioassay with Fusarium graminearum of different 7EL-7el1L bread wheat recombinant lines. These were obtained without resorting to any genetic pairing promotion, but relying on the close 7EL-7el1L homoeology, resulting in 20% pairing frequency between the two arms. Fhb-7EL resided in the telomeric portion and resistant recombinants could be isolated with useful combinations of more proximally located 7el1L genes/QTL. The transferred Fhb-7EL locus was shown to reduce disease severity and fungal biomass in grains of infected recombinants by over 95%. The same Fhb-7EL was, for the first time, proved to be effective also against F. culmorum and F. pseudograminearum, predominant agents of crown rot. Prebreeding lines possessing a suitable 7EL-7el1L gene/QTL assembly showed very promising yield performance in preliminary field tests.

  12. Evaluation of Lower East Fork Poplar Creek Mercury Sources

    Energy Technology Data Exchange (ETDEWEB)

    Watson, David B. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Brooks, Scott C. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Mathews, Teresa J. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Bevelhimer, Mark S. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); DeRolph, Chris [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Brandt, Craig C. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Peterson, Mark J. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Ketelle, Richard [East Tennessee Technology Park (ETTP), Oak Ridge, TN (United States)

    2016-06-01

    This report summarizes a 3-year research project undertaken to better understand the nature and magnitude of mercury (Hg) fluxes in East Fork Poplar Creek (EFPC). This project addresses the requirements of Action Plan 1 in the 2011 Oak Ridge Reservation-wide Comprehensive Environmental Response, Compensation, and Liability Act Five Year Review (FYR). The Action Plan is designed to address a twofold 2011 FYR issue: (1) new information suggests mobilization of mercury from the upper and lower EFPC streambeds and stream banks is the primary source of mercury export during high-flow conditions, and (2) the current Record of Decision did not address the entire hydrologic system and creek bank or creek bed sediments. To obtain a more robust watershed-scale understanding of mercury sources and processes in lower EFPC (LEFPC), new field and laboratory studies were coupled with existing data from multiple US Department of Energy programs to develop a dynamic watershed and bioaccumulation model. LEFPC field studies for the project focused primarily on quantification of streambank erosion and an evaluation of mercury dynamics in shallow groundwater adjacent to LEFPC and potential connection to the surface water. The approach to the stream bank study was innovative in using imagery from kayak floats’ surveys from the headwaters to the mouth of EFPC to estimate erosion, coupled with detailed bank soil mercury analyses. The goal of new field assessments and modeling was to generate a more holistic and quantitative understanding of the watershed and the sources, flux, concentration, transformation, and bioaccumulation of inorganic mercury (IHg) and methylmercury (MeHg). Model development used a hybrid approach that dynamically linked a spreadsheet-based physical and chemical watershed model to a systems dynamics, mercury bioaccumulation model for key fish species. The watershed model tracks total Hg and MeHg fluxes and concentrations by examining upstream inputs, floodplain

  13. Interleukin-1-mediated effects of normal oral keratinocytes and head and neck squamous carcinoma cells on extracellular matrix related gene expression in fibroblasts.

    Science.gov (United States)

    Hakelius, Malin; Koskela, Anita; Reyhani, Vahid; Ivarsson, Mikael; Grenman, Reidar; Rubin, Kristofer; Gerdin, Bengt; Nowinski, Daniel

    2012-12-01

    The composition of tumor stroma and the activity of tumor associated fibroblasts are important for tumor growth. Interactions between carcinoma cells and fibroblasts regulate the turnover of extracellular matrix (ECM). Here, the in vitro effects of oral squamous cell carcinoma (SCC) cells (UT-SCC-30 and UT-SCC-87) on fibroblast expression of genes for ECM components and connective tissue growth factor (CTGF/CCN2), were compared to those of normal oral keratinocytes (NOK). Cocultures with fibroblasts in collagen gels and keratinocytes with the two cell types separated by a semi permeable membrane were used, and relative gene expression was measured with real-time PCR. All investigated genes were regulated by NOK and the SCCs. The downregulation of pro-collagens α1(I) and α1(III) was more pronounced in cocultures with NOK, while the expression of CCN2 and fibronectin was downregulated by both NOK and the SCCs to a similar extent. UT-SCC-87, but not UT-SCC-30, secreted significantly more IL-1α than NOK. A recombinant interleukin-1 receptor antagonist reversed many of the observed effects on fibroblast gene expression suggesting involvement of IL-1 in cocultures with NOK as well as with SCCs. The observed differential effects on fibroblast gene expression suggest that NOK are more antifibrotic compared to UT-SCC-30 and UT-SCC-87. These findings may contribute to a better understanding of the mechanisms behind ECM turnover in tumors. Copyright © 2012 Elsevier Ltd. All rights reserved.

  14. Status of fork-tailed and Leach's storm-petrel populations at St. Lazaria Island during the summer of 1985

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — The purposes of this study were to (1) continue monitoring on Leach's forktail (Oceanadroma furcata) and on fork-tailed storm petrels (Oceanodroma leucorhoa); (2)...

  15. Using Caffeine as a Water Quality Indicator in the Ambient Monitoring Program for Third Fork Creek Watershed, Durham, North Carolina.

    Science.gov (United States)

    Spence, Porché L

    2015-01-01

    Caffeine has been suggested as a chemical indicator for domestic wastewater in freshwater systems, although it is not included in water quality monitoring programs. The Third Fork Creek watershed in Durham, NC, is highly urbanized, with a history of receiving untreated wastewater from leaking and overflowing sanitary sewers. The poor water quality originating in the Third Fork Creek watershed threatens its intended uses and jeopardizes drinking water, aquatic life, and recreational activities provided by Jordan Lake. Organic waste contaminants have been detected in both Third Fork Creek watershed and Jordan Lake; however, the sampling periods were temporary, resulting in a few samples collected during nonstorm periods. It is recommended that (1) the concentration of caffeine and other organic waste contaminants are determined during storm and nonstorm periods and (2) caffeine is monitored regularly with traditional water quality indicators to evaluate the health of Third Fork Creek watershed.

  16. Calibration of piezoelectric positioning actuators using a reference voltage-to-displacement transducer based on quartz tuning forks

    CERN Document Server

    Castellanos-Gomez, Andres; Agraït, Nicolás; Rubio-Bollinger, Gabino; 10.1017/S1431927611012839

    2012-01-01

    We use a piezoelectric quartz tuning fork to calibrate the displacement of ceramic piezoelectric scanners which are widely employed in scanning probe microscopy. We measure the static piezoelectric response of a quartz tuning fork and find it to be highly linear, non-hysteretic and with negligible creep. These performance characteristics, close to those of an ideal transducer, make quartz transducers superior to ceramic piezoelectric actuators. Furthermore, quartz actuators in the form of a tuning fork have the advantage of yielding static displacements comparable to those of local probe microscope scanners. We use the static displacement of a quartz tuning fork as a reference to calibrate the three axis displacement of a ceramic piezoelectric scanner. Although this calibration technique is a non-traceable method, it can be more versatile than using calibration grids because it enables to characterize the linear and non-linear response of a piezoelectric scanner in a broad range of displacements, spanning fro...

  17. Physical Habitat Characteristics on the North and South Forks of the Shenandoah River, VA in 2002-2007

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — The layers within this geodataset describe physical habitat characteristics in the North and South Fork Shenandoah rivers. They represent conditions during summer...

  18. Inhibition of p38 MAPK during cellular activation modulate gene expression of head kidney leukocytes isolated from Atlantic salmon (Salmo salar) fed soy bean oil or fish oil based diets.

    Science.gov (United States)

    Holen, E; Winterthun, S; Du, Z-Y; Krøvel, A V

    2011-01-01

    Head kidney leukocytes isolated from Atlantic salmon fed either a diet based on fish oil (FO) or soy bean oil (VO) were used in order to evaluate if different lipid sources could contribute to cellular activation of the salmon innate immune system. A specific inhibitor of p38 MAPK, SB202190, was used to investigate the effect of lipopolysaccharide (LPS) signalling in the head kidney leukocytes. The results show that LPS up regulate IL-1β, TNF-α, Cox2 expression in leukocytes isolated from fish fed either diet. The p38 MAPK inhibitor, SB202190, reduced the LPS induced expression of these genes in both dietary groups. In LPS stimulated leukocytes isolated from VO fed fish, SB202190 showed a clear dose dependent inhibitory effect on IL-1β, TNF-α and Cox2 expression. This effect was also observed for Cox2 in leukocytes isolated from FO fed fish. Furthermore, there was a stronger mean induction of Cox2 in LPS stimulated leucocytes isolated from the VO-group compared to LPS stimulated leukocytes isolated from the FO-group. In both dietary groups, LPS stimulation of salmon head kidney leukocytes increased the induction of CD83, a dendrite cell marker, while the inhibitor reduced CD83 expression in the VO fed fish only. The inhibitor also clearly reduced hsp27 expression in VO fed fish. Indicating a p38 MAPK feedback loop, LPS significantly inhibited the expression of p38MAPK itself in both diets, while SB202190 increased p38MAPK expression especially in the VO diet group. hsp70 expression was not affected by any treatment or feed composition. There were also differences in p38MAPK protein phosphorylation comparing treatment groups but no obvious difference comparing the two dietary groups. The results indicate that dietary fatty acids have the ability to modify signalling through p38 MAPK which may have consequences for the fish's ability to handle infections and stress. Signalling through p38MAPK is ligand dependent and affects gene and protein expression differently.

  19. Using Caffeine as a Water Quality Indicator in the Ambient Monitoring Program for Third Fork Creek Watershed, Durham, North Carolina

    OpenAIRE

    2015-01-01

    Caffeine has been suggested as a chemical indicator for domestic wastewater in freshwater systems, although it is not included in water quality monitoring programs. The Third Fork Creek watershed in Durham, NC, is highly urbanized, with a history of receiving untreated wastewater from leaking and overflowing sanitary sewers. The poor water quality originating in the Third Fork Creek watershed threatens its intended uses and jeopardizes drinking water, aquatic life, and recreational activities...

  20. Magnetic Resonance Imaging (MRI) -- Head

    Medline Plus

    Full Text Available ... Site Index A-Z Magnetic Resonance Imaging (MRI) - Head Magnetic resonance imaging (MRI) of the head uses ... of the Head? What is MRI of the Head? Magnetic resonance imaging (MRI) is a noninvasive medical ...

  1. The RecQ DNA helicase Rqh1 constrains Exonuclease 1-dependent recombination at stalled replication forks.

    Science.gov (United States)

    Osman, Fekret; Ahn, Jong Sook; Lorenz, Alexander; Whitby, Matthew C

    2016-03-09

    DNA double-strand break (DSB) repair by homologous recombination (HR) involves resection of the break to expose a 3' single-stranded DNA tail. In budding yeast, resection occurs in two steps: initial short-range resection, performed by Mre11-Rad50-Xrs2 and Sae2; and long-range resection catalysed by either Exo1 or Sgs1-Dna2. Here we use genetic assays to investigate the importance of Exo1 and the Sgs1 homologue Rqh1 for DNA repair and promotion of direct repeat recombination in the fission yeast Schizosaccharomyces pombe. We find that Exo1 and Rqh1 function in alternative redundant pathways for promoting survival following replication fork breakage. Exo1 promotes replication fork barrier-induced direct repeat recombination but intriguingly limits recombination induced by fork breakage. Direct repeat recombination induced by ultraviolet light depends on either Exo1 or Rqh1. Finally, we show that Rqh1 plays a major role in limiting Exo1-dependent direct repeat recombination induced by replication fork stalling but only a minor role in constraining recombination induced by fork breakage. The implications of our findings are discussed in the context of the benefits that long-range resection may bring to processing perturbed replication forks.

  2. Applications of the quartz tuning fork in classical and superfluid hydrodynamics

    Directory of Open Access Journals (Sweden)

    La Mantia Marco

    2012-04-01

    Full Text Available We present a short review of the multitude of applications of the commercially produced quartz tuning fork in cryogenic fluid dynamics, using cold gaseous, normal liquid and superfluid 4He as working fluids with extraordinary, but well-known and tunable physical properties. While the central focus of this work is the use of the tuning fork as a detector of classical and quantum turbulence, we also report other studies and applications, mainly on cavitation, pressure-, thermo- and viscosimetry. Finally, we mention briefly our recent studies of the acoustic emission due to these high-Q oscillators and its effect on the characteristics of their resonance.

  3. Carbon fibre tips for scanning probe microscopy based on quartz tuning fork force sensors

    Energy Technology Data Exchange (ETDEWEB)

    Castellanos-Gomez, A; Agrait, N; Rubio-Bollinger, G, E-mail: gabino.rubio@uam.es [Departamento de Fisica de la Materia Condensada (C-III), Universidad Autonoma de Madrid, Campus de Cantoblanco, 28049 Madrid (Spain)

    2010-04-09

    We report the fabrication and the characterization of carbon fibre tips for use in combined scanning tunnelling and force microscopy based on piezoelectric quartz tuning fork force sensors. We find that the use of carbon fibre tips results in a minimum impact on the dynamics of quartz tuning fork force sensors, yielding a high quality factor and, consequently, a high force gradient sensitivity. This high force sensitivity, in combination with high electrical conductivity and oxidation resistance of carbon fibre tips, make them very convenient for combined and simultaneous scanning tunnelling microscopy and atomic force microscopy measurements. Interestingly, these tips are quite robust against occasionally occurring tip crashes. An electrochemical fabrication procedure to etch the tips is presented that produces a sub-100-nm apex radius in a reproducible way which can yield high resolution images.

  4. Turbo Charge CPU Utilization in Fork/Join Using the ManagedBlocker

    CERN Document Server

    CERN. Geneva

    2017-01-01

    Fork/Join is a framework for parallelizing calculations using recursive decomposition, also called divide and conquer. These algorithms occasionally end up duplicating work, especially at the beginning of the run. We can reduce wasted CPU cycles by implementing a reserved caching scheme. Before a task starts its calculation, it tries to reserve an entry in the shared map. If it is successful, it immediately begins. If not, it blocks until the other thread has finished its calculation. Unfortunately this might result in a significant number of blocked threads, decreasing CPU utilization. In this talk we will demonstrate this issue and offer a solution in the form of the ManagedBlocker. Combined with the Fork/Join, it can keep parallelism at the desired level.

  5. Z-Axis Micromachined Tuning Fork Gyroscope with Low Air Damping

    Directory of Open Access Journals (Sweden)

    Minh Ngoc Nguyen

    2017-02-01

    Full Text Available This paper reports on the design and fabrication of a z-axis tuning fork gyroscope which has a freestanding architecture. In order to improve the performance of the tuning fork gyroscope by eliminating the influence of the squeeze-film air damping, the driving and sensing parts of the gyroscope were designed to oscillate in-plane. Furthermore, by removing the substrate underneath the device, the slide-film air damping in the gap between the proof masses and the substrate was eliminated. The proposed architecture was analyzed by the finite element method using ANSYS software. The simulated frequencies of the driving and sensing modes were 9.788 and 9.761 kHz, respectively. The gyroscope was fabricated using bulk micromachining technology. The quality factor and sensitivity of the gyroscope operating in atmospheric conditions were measured to be 111.2 and 11.56 mV/°/s, respectively.

  6. Gaussian Random Fields Methods for Fork-Join Network with Synchronization Constraints

    Science.gov (United States)

    2014-12-22

    research papers, under review in Mathematics of Operations Research (minor revision) and Annals of Applied Probability. One paper was on the finalist...2.00 1.00 Hongyuan Lu, Guodong Pang. Heavy Traffic Limits for A Fork-Join Network In the Halfin-Whitt Regime, Annals of Applied Probability (11 2014...fellowships for further studies in science , mathematics, engineering or technology fields: Student Metrics This section only applies to graduating

  7. Nested Fork-Join Queuing Networks and Their Application to Mobility Airfield Operations Analysis.

    Science.gov (United States)

    1997-03-01

    Method. The accuracy of this approximation is similar to that of its single-class counterpart. A similar approach is used by Di Mascolo, Frein , Baynat and...et en Automatique , 1985. [9] Baccelli, F. and Z. Liu. "On the execution of parallel programs on multipro- cessor systems-a queuing theory approach...Le Chesnay, France: Institut National de Recherche en Informatique et en Automatique , 1986. [16] Baccelli, F., and others. "Acyclic fork-join

  8. New species of Triplocania Roesler with forewing M3 forked (Psocodea: 'Psocoptera': Ptiloneuridae), from Brazil.

    Science.gov (United States)

    Da Silva Neto, Alberto Moreira; Rafael, José Albertino; Aldrete, Alfonso N García

    2014-07-16

    Four new Brazilian species of Triplocania with forewing M3 forked are described and illustrated based on male specimens, namely: Triplocania lamasi n.sp. (Mato Grosso: Brazil), Triplocania mariateresae n.sp. (Rio de Janeiro: Brazil), Triplocania newi n.sp. (Tocantins: Brazil) and Triplocania plaumanni n.sp. (Santa Catarina: Brasil). They differ from all the other species in the genus, in which the males are known, by the hypandrium and phallosome structures.

  9. Chromatin dynamics at the replication fork: there's more to life than histones.

    Science.gov (United States)

    Whitehouse, Iestyn; Smith, Duncan J

    2013-04-01

    Before each division, eukaryotic cells face the daunting task of completely and accurately replicating a heterogeneous, chromatinized genome and repackaging both resulting daughters. Because replication requires strand separation, interactions between the DNA and its many associated proteins--including histones--must be transiently broken to allow the passage of the replication fork. Here, we will discuss the disruption and re-establishment of chromatin structure during replication, and the consequences of these processes for epigenetic inheritance. Published by Elsevier Ltd.

  10. Slow Replication Fork Velocity of Homologous Recombination-Defective Cells Results from Endogenous Oxidative Stress.

    Science.gov (United States)

    Wilhelm, Therese; Ragu, Sandrine; Magdalou, Indiana; Machon, Christelle; Dardillac, Elodie; Técher, Hervé; Guitton, Jérôme; Debatisse, Michelle; Lopez, Bernard S

    2016-05-01

    Replications forks are routinely hindered by different endogenous stresses. Because homologous recombination plays a pivotal role in the reactivation of arrested replication forks, defects in homologous recombination reveal the initial endogenous stress(es). Homologous recombination-defective cells consistently exhibit a spontaneously reduced replication speed, leading to mitotic extra centrosomes. Here, we identify oxidative stress as a major endogenous source of replication speed deceleration in homologous recombination-defective cells. The treatment of homologous recombination-defective cells with the antioxidant N-acetyl-cysteine or the maintenance of the cells at low O2 levels (3%) rescues both the replication fork speed, as monitored by single-molecule analysis (molecular combing), and the associated mitotic extra centrosome frequency. Reciprocally, the exposure of wild-type cells to H2O2 reduces the replication fork speed and generates mitotic extra centrosomes. Supplying deoxynucleotide precursors to H2O2-exposed cells rescued the replication speed. Remarkably, treatment with N-acetyl-cysteine strongly expanded the nucleotide pool, accounting for the replication speed rescue. Remarkably, homologous recombination-defective cells exhibit a high level of endogenous reactive oxygen species. Consistently, homologous recombination-defective cells accumulate spontaneous γH2AX or XRCC1 foci that are abolished by treatment with N-acetyl-cysteine or maintenance at 3% O2. Finally, oxidative stress stimulated homologous recombination, which is suppressed by supplying deoxynucleotide precursors. Therefore, the cellular redox status strongly impacts genome duplication and transmission. Oxidative stress should generate replication stress through different mechanisms, including DNA damage and nucleotide pool imbalance. These data highlight the intricacy of endogenous replication and oxidative stresses, which are both evoked during tumorigenesis and senescence initiation

  11. Environmental Assessment: Landscape Multiple Areas at Grand Forks Air Force Base

    Science.gov (United States)

    2006-03-01

    and other non- cultivated areas create a prairie-land mosaic of grasses, legumes, and wild herbaceous plants. Included in the grasses and legumes...vegetation species are tall wheat grass, brome grass, Kentucky bluegrass, sweet clover, and alfalfa . Herbaceous plants include little bluestem...Grand Forks County consists primarily of cultivated crops with remaining land used for pasture and hay, urban development, recreation, and wildlife

  12. An Archeological Survey in the Gypsum Breaks on the Elm Fork of the Red River,

    Science.gov (United States)

    1979-01-01

    Hughes (1973). One of the known sites was reported by James Shaeffer in 1960. The Hughes survey was based on an earlier plan to dam Fish Creek, and he...limits. Artifacts recovered include Trinity, Ensor , Darl, Ellis, Gary, Meserve, Frio, and Abasolo projectile points, Clear Fork gouges, burins and...Marcos, Ensor , Palmillas and Trinity. From the material of these four sites an estimated range of dates was proposed at 2000 B.C. to 1000 A.D. Eight

  13. Environmental Assessment: Replace Sanitary Sewer from Building 801 to Lagoons at Grand Forks AFB, North Dakota

    Science.gov (United States)

    2010-09-01

    for Grand Forks AFB include Marsh Milkweed , Bottlebrush Sedge, Prairie Cordgrass, Wooly Sedge, Awl- Fruit Sedge, Baltic Rush, Wool-Grass, Soft-stem...AFB has a humid continental climate that is characterized by frequent and drastic weather changes. The summers are short and humid with frequent...Vegetation is robust at GFAFB wetlands and many are characterized as typical prairie potholes found within the northern plains ecoregion. Wetlands

  14. Nanocharacterization of Soft Biological Samples in Shear Mode with Quartz Tuning Fork Probes

    OpenAIRE

    Manel Puig-Vidal; Laura Gonzalez; Jorge Otero

    2012-01-01

    Quartz tuning forks are extremely good resonators and their use is growing in scanning probe microscopy. Nevertheless, only a few studies on soft biological samples have been reported using these probes. In this work, we present the methodology to develop and use these nanosensors to properly work with biological samples. The working principles, fabrication and experimental setup are presented. The results in the nanocharacterization of different samples in different ambients are presented by...

  15. Noncontact atomic force microscopy in liquid environment with quartz tuning fork and carbon nanotube probe

    DEFF Research Database (Denmark)

    Kageshima, M.; Jensenius, Henriette; Dienwiebel, M.

    2002-01-01

    A force sensor for noncontact atomic force microscopy in liquid environment was developed by combining a multiwalled carbon nanotube (MWNT) probe with a quartz tuning fork. Solvation shells of octamethylcyclotetrasiloxane surface were detected both in the frequency shift and dissipation. Due...... to the high aspect ratio of the CNT probe, the long-range background force was barely detectable in the solvation region. (C) 2002 Elsevier Science B.V. All rights reserved....

  16. Continuous hydrologic simulation of runoff for the Middle Fork and South Fork of the Beargrass Creek basin in Jefferson County, Kentucky

    Science.gov (United States)

    Jarrett, G. Lynn; Downs, Aimee C.; Grace-Jarrett, Patricia A.

    1998-01-01

    The Hydrological Simulation Pro-gram-FORTRAN (HSPF) was applied to an urban drainage basin in Jefferson County, Ky to integrate the large amounts of information being collected on water quantity and quality into an analytical framework that could be used as a management and planning tool. Hydrologic response units were developed using geographic data and a K-means analysis to characterize important hydrologic and physical factors in the basin. The Hydrological Simulation Program FORTRAN Expert System (HSPEXP) was used to calibrate the model parameters for the Middle Fork Beargrass Creek Basin for 3 years (June 1, 1991, to May 31, 1994) of 5-minute streamflow and precipitation time series, and 3 years of hourly pan-evaporation time series. The calibrated model parameters were applied to the South Fork Beargrass Creek Basin for confirmation. The model confirmation results indicated that the model simulated the system within acceptable tolerances. The coefficient of determination and coefficient of model-fit efficiency between simulated and observed daily flows were 0.91 and 0.82, respectively, for model calibration and 0.88 and 0.77, respectively, for model confirmation. The model is most sensitive to estimates of the area of effective impervious land in the basin; the spatial distribution of rain-fall; and the lower-zone evapotranspiration, lower-zone nominal storage, and infiltration-capacity parameters during recession and low-flow periods. The error contribution from these sources varies with season and antecedent conditions.

  17. Vibration amplitude of a tip-loaded quartz tuning fork during shear force microscopy scanning

    Science.gov (United States)

    Sandoz, P.; Friedt, J.-M.; Carry, É.

    2008-08-01

    This Note reports on experimental results obtained with a recently published vision method for in-plane vibration measurement [Sandoz et al., Rev. Sci. Instrum. 78, 023706 (2007)]. The latter is applied to a tip-loaded quartz tuning fork frequently used in scanning probe microscopy for shear-force monitoring of the tip-sample distance. The vibration amplitude of the tip-loaded prong is compared to that of the free one and the damping induced by tip-surface interactions is measured. The tuning-fork behavior is characterized during approaches from free space to surface contact. Tip-surface contact is clearly identified by a drastic reduction in the prong vibration amplitude. However, no differences were observed between hydrophilic and hydrophobic surfaces. Experiments reported here show that the vibration amplitude of the quartz tuning fork in free space is a good estimate of the vibration amplitude of the tip interacting with the sample surface during shear force sample-tip feedback. The experimental setup for measuring the amplitude is easily integrated in an inverted microscope setup on which the shear force microscope is installed for simultaneous scanning probe and optical microscopy analysis of the sample.

  18. A secure and efficient cryptographic hash function based on NewFORK-256

    Directory of Open Access Journals (Sweden)

    Harshvardhan Tiwari

    2012-11-01

    Full Text Available Cryptographic hash functions serve as a fundamental building block of information security and are used in numerous security applications and protocols such as digital signature schemes, construction of MAC and random number generation, for ensuring data integrity and data origin authentication. Researchers have noticed serious security flaws and vulnerabilities in most widely used MD and SHA family hash functions. As a result hash functions from FORK family with longer digest value were considered as good alternatives for MD5 and SHA-1, but recent attacks against these hash functions have highlighted their weaknesses. In this paper we propose a dedicated hash function MNF-256 based on the design principle of NewFORK-256. It takes 512 bit message blocks and generates 256 bit hash value. A random sequence is added as an additional input to the compression function of MNF-256. Three branch parallel structure and secure compression function make MNF-256 an efficient, fast and secure hash function. Various simulation results indicate that MNF-256 is immune to common cryptanalytic attacks and faster than NewFORK-256.

  19. A tip-attached tuning fork sensor for the control of DNA translocation through a nanopore

    Science.gov (United States)

    Hyun, Changbae; Kaur, Harpreet; Huang, Tao; Li, Jiali

    2017-02-01

    In this work, we demonstrate that a tuning fork can be used as a force detecting sensor for manipulating DNA molecules and for controlling the DNA translocation rate through a nanopore. One prong of a tuning fork is glued with a probe tip which DNA molecules can be attached to. To control the motion and position of the tip, the tuning fork is fixed to a nanopositioning system which has sub-nanometer position control. A fluidic chamber is designed to fulfill many requirements for the experiment: for the access of a DNA-attached tip approaching to a nanopore, for housing a nanopore chip, and for measuring ionic current through a solid-state nanopore with a pair of electrodes. The location of a nanopore is first observed by transmission electron microscopy, and then is determined inside the liquid chambers with an optical microscope combined with local scanning the probe tip on the nanopore surface. When a DNA-immobilized tip approaches a membrane surface near a nanopore, free ends of the immobilized DNA strings can be pulled and trapped into the pore by an applied voltage across the nanopore chip, resulting in an ionic current reduction through the nanopore. The trapped DNA molecules can be lifted up from the nanopore at a user controlled speed. This integrated apparatus allows manipulation of biomolecules (DNA, RNA, and proteins) attached to a probe tip with sub-nanometer precision, and simultaneously allows measurement of the biomolecules by a nanopore device.

  20. On Bandwidth Characteristics of Tuning Fork Micro-Gyroscope with Mechanically Coupled Sense Mode

    Directory of Open Access Journals (Sweden)

    Yunfang Ni

    2014-07-01

    Full Text Available The bandwidth characteristics of a tuning fork micro-gyroscope with mechanically coupled sense mode were investigated in this paper to provide some references for mechanical bandwidth design. The concept of sense mode mechanical coupling is introduced first. Theoretical frequency response analyses were then carried out on the mechanical part of the gyroscope. Equations representing the relationships between the differential output signal and the frequency of the input angular rate were deduced in full frequency range and further simplified in low frequency range. Based on these equations, bandwidth characteristics under ideal and non-ideal conditions are discussed. Analytical results show that under ideal conditions, the bandwidth characteristics of a tuning fork micro-gyroscope are similar to those of a single mass micro-gyroscope, but under non-ideal conditions, especially when sense mass and/or stiffness are asymmetric, the bandwidth characteristics would be quite different because the in-phase mode would participate in the anti-phase vibration response. Experimental verifications were carried out on two micro-gyroscope prototypes designed in our laboratory. The deduced equations and analytical results can be used in guiding the mechanical bandwidth design of tuning fork micro-gyroscopes with mechanically coupled sense mode.

  1. On bandwidth characteristics of tuning fork micro-gyroscope with mechanically coupled sense mode.

    Science.gov (United States)

    Ni, Yunfang; Li, Hongsheng; Huang, Libin; Ding, Xukai; Wang, Haipeng

    2014-01-01

    The bandwidth characteristics of a tuning fork micro-gyroscope with mechanically coupled sense mode were investigated in this paper to provide some references for mechanical bandwidth design. The concept of sense mode mechanical coupling is introduced first. Theoretical frequency response analyses were then carried out on the mechanical part of the gyroscope. Equations representing the relationships between the differential output signal and the frequency of the input angular rate were deduced in full frequency range and further simplified in low frequency range. Based on these equations, bandwidth characteristics under ideal and non-ideal conditions are discussed. Analytical results show that under ideal conditions, the bandwidth characteristics of a tuning fork micro-gyroscope are similar to those of a single mass micro-gyroscope, but under non-ideal conditions, especially when sense mass and/or stiffness are asymmetric, the bandwidth characteristics would be quite different because the in-phase mode would participate in the anti-phase vibration response. Experimental verifications were carried out on two micro-gyroscope prototypes designed in our laboratory. The deduced equations and analytical results can be used in guiding the mechanical bandwidth design of tuning fork micro-gyroscopes with mechanically coupled sense mode.

  2. Novel mutation in forkhead box G1 (FOXG1) gene in an Indian patient with Rett syndrome.

    Science.gov (United States)

    Das, Dhanjit Kumar; Jadhav, Vaishali; Ghattargi, Vikas C; Udani, Vrajesh

    2014-03-15

    Rett syndrome (RTT) is a severe neurodevelopmental disorder characterized by the progressive loss of intellectual functioning, fine and gross motor skills and communicative abilities, deceleration of head growth, and the development of stereotypic hand movements, occurring after a period of normal development. The classic form of RTT involves mutation in MECP2 while the involvement of CDKL5 and FOXG1 genes has been identified in atypical RTT phenotype. FOXG1 gene encodes for a fork-head box protein G1, a transcription factor acting primarily as transcriptional repressor through DNA binding in the embryonic telencephalon as well as a number of other neurodevelopmental processes. In this report we have described the molecular analysis of FOXG1 gene in Indian patients with Rett syndrome. FOXG1 gene mutation analysis was done in a cohort of 34 MECP2/CDKL5 mutation negative RTT patients. We have identified a novel mutation (p. D263VfsX190) in FOXG1 gene in a patient with congenital variant of Rett syndrome. This mutation resulted into a frameshift, thereby causing an alteration in the reading frames of the entire coding sequence downstream of the mutation. The start position of the frameshift (Asp263) and amino acid towards the carboxyl terminal end of the protein was found to be well conserved across species using multiple sequence alignment. Since the mutation is located at forkhead binding domain, the resultant mutation disrupts the secondary structure of the protein making it non-functional. This is the first report from India showing mutation in FOXG1 gene in Rett syndrome.

  3. "承载丸"对股骨头坏死大鼠细胞黏附分子基因的影响%Effect of Chengzai pill on the genes of cell adhesion molecules in rats with femoral head necrosis

    Institute of Scientific and Technical Information of China (English)

    黄克勤; 陈燕平; 薛延; 郎风萍; 黄宏; 黄辉; 黄永勋; 张景辰

    2009-01-01

    strength and rigidity, it also reverses the low levels of estrogen. OBJECTIVE: To explore the effect of Chengzai pill on the genes of cell adhesion molecules on bone cells of steroid-induced ostaonecrotic rats, and to understand the role to resume normal blood transport in femoral head of steroid-induced osteonecrosis. DESIGN, TIME AND SETTING: Grouping controlled observation was performed in the Pharmacological Laboratory of Wangjing Hospital of China Academy of Chinese Medical Sciences and laboratory of CapitalBio Corporation between March and August in 2006. MATERIALS: Six male SD rats of 6 months old and weighing (280:1:20) g were used in this study. Chengzai pill was consisted of 22 Chinese medicines, such as Chinese Angelica, Eucommia Bark, Milkvetch Root, Barbary Wolfberry Fruit, Degelatined Deer-hom, Desertliving Cistanche, Eupolyphaga seu Steleophaga, Leech, Danshen Root and Himalayan Teasel Root, which were offered by Beijing Boran Pharmaceutical Co., Ltd. METHODS: The lipopolysaccharide and methylprednisolone were applied to prepare a rat model of steroid-induced osteonecrosis of femoral head. Six rats were divided into model group and Chengzai pill group at random with 3 rats in each group. The rats in the Chengzai pill group were administrated with methylprednisolone for the first time and then 1.5 g/kg Chengzai pill solution, once a day, totally for 6 weeks. The total RNA was extracted from femoral head in all rata 6 weeks later and then gene expression profiling was analyzed. MAIN OUTCOME MEASURES: Gene action pathway of cell adhesion molecules in gene expression profile. RESULTS: Compared with model rats, there were totally 8 downregulated genes of cell adhesion molecules which changed by a minimum of 1.5 folds in cell adhesion molecules pathway of Chengzai pill group, three rats were present with 633 genes (506 down-regulated and 127 up-regulated), 883 genes (640 down-regulated and 243 up-regulated) and 593 genes (408 down-regulated and 185 up

  4. Polymorphisms of the DNMT3B gene and risk of squamous cell carcinoma of the head and neck: a case-control study.

    Science.gov (United States)

    Liu, Zhensheng; Wang, Luo; Wang, Li-E; Sturgis, Erich M; Wei, Qingyi

    2008-09-08

    DNA-methyltransferase-3B (DNMT3B) may play an oncogenic role during tumorigenesis, and its genetic variants have been reportedly to be associated with risk of several cancers, but few studies have investigated their roles in squamous cell carcinoma of the head and neck cancer (SCCHN). Here we report a hospital-based case-control study with 832 SCCHN patients and 843 cancer-free controls of non-Hispanic whites that evaluated the association between two DNMT3B single nucleotide polymorphisms (SNPs) DNMT3B -149C>T (rs2424913) and DNMT3B -579G>T (rs2424909) in the promoter region and risk of SCCHN. We found that compared with C-allele carriers, the DNMT3B -149 TT genotype was statistically significantly associated with increased risk of SCCHN (adjusted OR, 1.35, 95% CI, 1.01-1.80, P=0.043), whereas the DNMT3B -579 TT genotype showed only a non-statistically significant risk compared with G-allele carriers. Further analysis of the effects of combined genotypes suggested that subjects with either DNMT3B -149 TT or DNMT3B -579 TT homozygous genotypes had statistically significantly increased risk of SCCHN (adjusted OR=1.36, 95% CI=1.07-1.73, P=0.013). Stratification analysis showed a more profound risk in the subgroups of the young (DNMT3B variants and SCCHN risk in non-Hispanic whites, and our findings are consistent with that of previously reported cancer case-control studies of other cancers. Further mechanistic studies are needed to unravel the underlying molecular mechanisms.

  5. Nuclear insulin-like growth factor 1 receptor phosphorylates proliferating cell nuclear antigen and rescues stalled replication forks after DNA damage.

    Science.gov (United States)

    Waraky, Ahmed; Lin, Yingbo; Warsito, Dudi; Haglund, Felix; Aleem, Eiman; Larsson, Olle

    2017-09-18

    We have previously shown that the insulin like growth factor 1 receptor (IGF1R) translocates to the cell nucleus, where it binds to enhancer like regions and increases gene transcription. Further studies have demonstrated that nuclear IGF1R (nIGF1R) physically and functionally interacts with some nuclear proteins, i.e. the lymphoid enhancer binding factor 1 (Lef1), histone H3, and Brahma related gene 1 proteins. In the present study, we identified the proliferating cell nuclear antigen (PCNA) as a nIGF1R binding partner. PCNA is a pivotal component of the replication fork machinery and a main regulator of the DNA damage tolerance (DDT) pathway. We found that IGF1R interacts with and phosphorylates PCNA in human embryonic stem cells and other cell lines. In vitro MS analysis of PCNA coincubated with the IGF1R kinase indicated tyrosine residues 60, 133, and 250 in PCNA as IGF1R targets, and PCNA phosphorylation was followed by mono and poly ubiquitination. Coimmunoprecipitation experiments suggested that these ubiquitination events may be mediated by DDT dependent E2/E3 ligases (e.g. RAD18 and SHPRH/HLTF). Absence of IGF1R or mutation of Tyr60, Tyr133, or Tyr250 in PCNA abrogated its ubiquitination. Unlike in cells expressing IGF1R, externally induced DNA damage in IGF1R negative cells caused G1 cell cycle arrest and S phase fork stalling. Taken together, our results suggest a role of IGF1R in DDT. Copyright © 2017, The American Society for Biochemistry and Molecular Biology.

  6. Flood-inundation maps for the East Fork White River near Bedford, Indiana

    Science.gov (United States)

    Fowler, Kathleen K.

    2014-01-01

    Digital flood-inundation maps for an 1.8-mile reach of the East Fork White River near Bedford, Indiana (Ind.) were created by the U.S. Geological Survey (USGS) in cooperation with the Indiana Department of Transportation. The inundation maps, which can be accessed through the USGS Flood Inundation Mapping Science Web site at http://water.usgs.gov/osw/flood_inundation/ depict estimates of the areal extent and depth of flooding corresponding to selectedwater levels (stages) at USGS streamgage 03371500, East Fork White River near Bedford, Ind. Current conditions for estimating near-real-time areas of inundation using USGS streamgage information may be obtained on the Internet at http://waterdata.usgs.gov/in/nwis/uv?site_no=03371500. In addition, information has been provided to the National Weather Service (NWS) for incorporation into their Advanced Hydrologic Prediction Service (AHPS) flood warning system (http://water.weather.gov/ahps/). The NWS forecasts flood hydrographs at many places that are often colocated with USGS streamgages, including the East Fork White River near Bedford, Ind. NWS-forecasted peak-stage information may be used in conjunction with the maps developed in this study to show predicted areas of flood inundation. For this study, flood profiles were computed for the East Fork White River reach by means of a one-dimensional step-backwater model. The hydraulic model was calibrated by using the most current stage-discharge relations at USGS streamgage 03371500, East Fork White River near Bedford, Ind., and documented high-water marks from the flood of June 2008. The calibrated hydraulic model was then used to determine 20 water-surface profiles for flood stages at 1-foot intervals referenced to the streamgage datum and ranging from bankfull to the highest stage of the current stage-discharge rating curve. The simulated water-surface profiles were then combined with a geographic information system (GIS) digital elevation model (DEM, derived from

  7. Flood-inundation maps for the East Fork White River at Shoals, Indiana

    Science.gov (United States)

    Boldt, Justin A.

    2016-05-06

    Digital flood-inundation maps for a 5.9-mile reach of the East Fork White River at Shoals, Indiana (Ind.), were created by the U.S. Geological Survey (USGS) in cooperation with the Indiana Office of Community and Rural Affairs. The flood-inundation maps, which can be accessed through the USGS Flood Inundation Mapping Science Web site at http://water.usgs.gov/osw/flood_inundation/ depict estimates of the areal extent and depth of flooding corresponding to selected water levels (stages) at the USGS streamgage on the East Fork White River at Shoals, Ind. (USGS station number 03373500). Near-real-time stages at this streamgage may be obtained on the Internet from the USGS National Water Information System at http://waterdata.usgs.gov/ or the National Weather Service (NWS) Advanced Hydrologic Prediction Service (AHPS) at http://water.weather.gov/ahps/, which also forecasts flood hydrographs at this site (NWS AHPS site SHLI3). NWS AHPS forecast peak stage information may be used in conjunction with the maps developed in this study to show predicted areas of flood inundation.Flood profiles were computed for the East Fork White River reach by means of a one-dimensional, step-backwater model developed by the U.S. Army Corps of Engineers. The hydraulic model was calibrated by using the current stage-discharge relation (USGS rating no. 43.0) at USGS streamgage 03373500, East Fork White River at Shoals, Ind. The calibrated hydraulic model was then used to compute 26 water-surface profiles for flood stages at 1-foot (ft) intervals referenced to the streamgage datum and ranging from approximately bankfull (10 ft) to the highest stage of the current stage-discharge rating curve (35 ft). The simulated water-surface profiles were then combined with a geographic information system (GIS) digital elevation model (DEM), derived from light detection and ranging (lidar) data, to delineate the area flooded at each water level. The areal extent of the 24-ft flood-inundation map was

  8. Head and Neck

    DEFF Research Database (Denmark)

    Højgaard, Liselotte; Berthelsen, Anne Kiil; Loft, Annika

    2014-01-01

    Positron emission tomography (PET)/computed tomography with FDG of the head and neck region is mainly used for the diagnosis of head and neck cancer, for staging, treatment evaluation, relapse, and planning of surgery and radio therapy. This article is a practical guide of imaging techniques......, including a detailed protocol for FDG PET in head and neck imaging, physiologic findings, and pitfalls in selected case stories....

  9. The Werner and Bloom syndrome proteins help resolve replication blockage by converting (regressed) holliday junctions to functional replication forks.

    Science.gov (United States)

    Machwe, Amrita; Karale, Rajashree; Xu, Xioahua; Liu, Yilun; Orren, David K

    2011-08-16

    Cells cope with blockage of replication fork progression in a manner that allows DNA synthesis to be completed and genomic instability minimized. Models for resolution of blocked replication involve fork regression to form Holliday junction structures. The human RecQ helicases WRN and BLM (deficient in Werner and Bloom syndromes, respectively) are critical for maintaining genomic stability and thought to function in accurate resolution of replication blockage. Consistent with this notion, WRN and BLM localize to sites of blocked replication after certain DNA-damaging treatments and exhibit enhanced activity on replication and recombination intermediates. Here we examine the actions of WRN and BLM on a special Holliday junction substrate reflective of a regressed replication fork. Our results demonstrate that, in reactions requiring ATP hydrolysis, both WRN and BLM convert this Holliday junction substrate primarily to a four-stranded replication fork structure, suggesting they target the Holliday junction to initiate branch migration. In agreement, the Holliday junction binding protein RuvA inhibits the WRN- and BLM-mediated conversion reactions. Importantly, this conversion product is suitable for replication with its leading daughter strand readily extended by DNA polymerases. Furthermore, binding to and conversion of this Holliday junction are optimal at low MgCl(2) concentrations, suggesting that WRN and BLM preferentially act on the square planar (open) conformation of Holliday junctions. Our findings suggest that, subsequent to fork regression events, WRN and/or BLM could re-establish functional replication forks to help overcome fork blockage. Such a function is highly consistent with phenotypes associated with WRN- and BLM-deficient cells.

  10. Effects of controlled burning of chaparral on streamflow and sediment characteristics, East Fork Sycamore Creek, central Arizona

    Science.gov (United States)

    Baldys, Stanley; Hjalmarson, H.W.

    1994-01-01

    The effects of controlled burning of part of a chaparral-covered drainage basin on streamflow and sediment characteristics were studied in the upper reaches of the Sycamore Creek basin in central Arizona. A paired-watershed method was used to analyze data collected in two phases separated by the controlled burning of 45 percent of the East Fork Sycamore Creek drainage basin by the U.S. Forest Service on October 31, 1981. Statistically significant increases in streamflow in East Fork occurred from October 26, 1982, through August 25, 1984. Streamflow for August 26, 1984, through the end of data collection for the study on May 31, 1986, was generally at or less than preburn levels. An increase in the percentage of time that flow occurred in East Fork was noted for water years 1983 and 1984. No increase in the magnitude of instantaneous peak flows as a result of the burn was discernable at statistically significant levels. Suspended-sediment yields computed for data collected during water year 1983 were significantly greater in the East Fork drainage basin, 546 tons per square mile, than in the West Fork drainage basin, 22.6 tons per square mile. Suspended-sediment yields computed for East Fork and West Fork for water year 1985, 38.3 and 13.3 tons per square mile, respectively, were much closer in yield. These more uniform yields indicate a possible return to preburn conditions. Data collection did not begin until 11 months after the burn; therefore, the largest increases in streamflow and sediment yields, which commonly occur during the year after a burn, may not have been measured. During the second through fourth years after the burn, smaller increases in stream- flow and sediment yields were found in this study than were found in similar studies in this region.

  11. Development of CE-QUAL-W2 models for the Middle Fork Willamette and South Santiam Rivers, Oregon

    Science.gov (United States)

    Buccola, Norman L.; Stonewall, Adam J.; Sullivan, Annett B.; Kim, Yoonhee; Rounds, Stewart A.

    2013-01-01

    Hydrodynamic (CE-QUAL-W2) models of Hills Creek Lake (HCL), Lookout Point Lake (LOP), and Dexter Lake (DEX) on the Middle Fork Willamette River (MFWR), and models of Green Peter Lake and Foster Lake on the South Santiam River systems in western Oregon were updated and recalibrated for a wide range of flow and meteorological conditions. These CE-QUAL-W2 models originally were developed by West Consultants, Inc., for the U.S. Army Corps of Engineers. This study by the U.S. Geological Survey included a reassessment of the models’ calibration in more recent years—2002, 2006, 2008, and 2011—categorized respectively as low, normal, high, and extremely high flow calendar years. These years incorporated current dam-operation practices and more available data than the time period used in the original calibration. Modeled water temperatures downstream of both HCL and LOP-DEX on the MFWR were within an average of 0.68 degree Celsius (°C) of measured values; modeled temperatures downstream of Foster Dam on the South Santiam River were within an average of 0.65°C of measured values. A new CE-QUAL-W2 model was developed and calibrated for the riverine MFWR reach between Hills Creek Dam and the head of LOP, allowing an evaluation of the flow and temperature conditions in the entire MFWR system from HCL to Dexter Dam. The complex bathymetry and long residence time of HCL, combined with the relatively deep location of the power and regulating outlet structures at Hills Creek Dam, led to a HCL model that was highly sensitive to several outlet and geometric parameters related to dam structures (STR TOP, STR BOT, STR WIDTH). Release temperatures from HCL were important and often persisted downstream as they were incorporated in the MFWR model and the LOP-DEX model (downstream of MFWR). The models tended to underpredict the measured temperature of water releases from Dexter Dam during the late-September-through-December drawdown period in 2002, and again (to a lesser extent) in

  12. An Optimal Scheduling Algorithm for Fork-Join Task Graphs%一个调度Fork-Join任务图的最优算法

    Institute of Scientific and Technical Information of China (English)

    李庆华; 阮幼林; 刘干; 蒋盛益; 杨世达

    2005-01-01

    The Fork-Join structure is one of the basic modeling structures for parallel processing. Although some algorithms are able to find an optimal schedule under certain conditions, they ignore to economize processors and minimize the total completion time. This paper presents a Task Duplication based Balance Scheduling(TDBS)algorithm which can generate an optimal schedule for fork-join task graph with a complexity of O(vq+vlogv), where v and q are the number of tasks and processors respectively. By considering workload and idle time slots of the used processors, TDBS algorithm tries to assign tasks to scheduled processors and maximize their utilization. Simulation results show that TDBS algorithm has better speedup and efficiency than other compared algorithms. Therefore,TDBS algorithm is a viable option for practical high performance applications.%Fork-Join任务图是一种并行处理的基本结构.虽然许多算法在任务满足某些条件时能产生最优调度,但往往没有考虑节省处理器个数和减少任务集的总完成时间,从而降低算法的加速比和效率.因此,提出一种基于任务复制的平衡调度算法,其时间复杂度为O(vq+vlogv),v和q分别表示任务集中任务的个数和使用的处理器个数.通过分析已用处理器的负载和空闲时间段,把任务尽量分配到已用的处理器上以均衡负载,从而提高其利用率.实验结果表明,该算法的加速比和总体效率优于其他算法.因此,该算法对于高性能应用程序的调度是一个较好的选择.

  13. Gene

    Data.gov (United States)

    U.S. Department of Health & Human Services — Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes,...

  14. Development of SMD 32.768 kHz tuning fork-type crystals using photolithography and selective etching process. Pt. I. Selective etching of an array of quartz tuning fork resonators

    Energy Technology Data Exchange (ETDEWEB)

    Lee, S. [Samsung Electro-Mechanics Co., Ltd., Suwon City (Korea); Kang, K.M. [National Univ. of Technology, Seoul (Korea). Dept. of Materials Engineering

    2001-05-01

    Negative photoresist photolithography was found superior to previously used positive photoresist photolithography to etch array of quartz tuning forks for use in Qualcomm trademark mobile station modem (MSM), 3000{sup TM} central processing unit (CPU), chips of code division multiple access (CDMA), personal communication system (PCS), and global system for mobile communication (GSM) units. Optimum processing condition was devised for reproducible precision etching of Z-cut quartz wafer into array of tuning forks. Tuning fork pattern was transferred via ordinary photolithographical chromium/quartz glass template using a standard single-sided aligner and subsequent negative photoresist development. A tightly adhering and pinhole-free 600/2000 A chromium/gold mask is coated over the developed photoresist pattern which was subsequently stripped in acetone. This procedure was repeated on the backside of the wafer. With protective metallization area of tuning fork geometry thus formed, etching through quartz wafer was done at 80 C in a {+-} 1.5 C controlled bath containing concentrated solution of ammonium bifluoride to remove unwanted area of the quartz wafer. The quality of quartz wafer surface finish after quartz etching depended primarily on the surface finish of quartz wafer prior to etching and the quality of quartz crystals used. At 80 C, selective etching of 100 {mu}m quartz wafer could be effected within 90 min. Reproducible precision selective etching method has thus been established and enables mass production of miniature tuning fork resonators with electrode patterns on them photolithographically. (orig.)

  15. Downhill exercise-induced changes in gene expression related with macrophage polarization and myogenic cells in the triceps long head of rats.

    Science.gov (United States)

    Minari, André Luis Araujo; Oyama, Lila Missae; Dos Santos, Ronaldo Vagner Thomatieli

    2015-02-01

    Macrophages are one of the most heterogenic immune cells involved in skeletal muscle regeneration. After skeletal muscle damage, M1 phenotypes exhibit pro-inflammatory reaction. In a later stage, they are converted to M2 phenotypes with anti-inflammatory properties. To study when gene expressions of macrophage polarization are changed after damage induced by downhill exercise to exhaustion is the objective of this paper. Before (CTRL) and 0 h (G0), 24 h (G24), 48 h (G48) and 72 h (G72) after 18 bouts of downhill exercise, the animals were euthanised, and the triceps were dissected. We measured gene expression of macrophages (CD68 and CD163), myogenic cells (MyoD and myogenin) and quantified cytokine secretion (interleukin (IL)-6, IL-10 and tumour necrosis factor alpha (TNF-α)). The CD68 expression was lower in G72 compared with G24 (P = 0.005) while CD163 was higher in G48 compared with G24 (P = 0.04). The MyoD expression was higher in G72 compared with G0 (P = 0.04). The myogenin expression was lower in G24 compared with CTRL (P = 0.01) and restored in G72 compared with G24 (P = 0.007). The TNF-α was significantly higher at all times after 24 h (all compared with CTRL, with P = 0.03). The CD68 and CD163 expressions behaved distinctly after exercise, which indicates macrophage polarization between 24 and 48 h. The distinct expression of myogenin, concomitantly with MyoD elevation in G72, indicates that myogenic cell differentiation and the significant change of TNF-α level show an important role of this cytokine in these processes.

  16. Polimorfismos do gene da interleucina-13 nas posições -1055 C/T e +2044 G/A em pacientes com carcinoma espinocelular de cabeça e pescoço Interleukin-13 gene polymorphisms at -1055 C/T and +2044 G/A positions in patients with squamous cell carcinoma of head and neck

    Directory of Open Access Journals (Sweden)

    Bijan Khademi

    2012-10-01

    Full Text Available O carcinoma espinocelular (CEC é a neoplasia mais comum do trato aerodigestivo superior. A interleucina-13 (IL-13 é uma citocina imunorreguladora com polimorfismos relatados para seu gene associados com a mesma doença, especialmente asma e alergia. O presente estudo investigou se os polimorfismos do gene da IL-13 (posições 1055C/T no gene promotor da 1L-13 e +2044G/T exon 4 podem distinguir os pacientes com CEC de cabeça e pescoço de controles saudáveis. MÉTODO: O estudo analisou pacientes com CEC de cabeça e pescoço (n = 137 pareados por idade e sexo com um grupo de controles saudáveis (n = 127. A genotipagem do polimorfismo do gene da IL-13 foi executada pelo método de polimorfismo no comprimento de fragmentos de restrição baseado em reação em cadeia da polimerase. RESULTADOS: Não foram identificadas diferenças estatisticamente significativas nas frequências dos genótipos e alelos entre pacientes e controles em ambas as posições (p = 0,16. Além disso, não foi observada associação entre os genótipos investigados e outros fatores prognósticos, como idade, sexo, localização do tumor primário, tamanho do tumor e tabagismo. CONCLUSÃO: O presente estudo sugere que não há associação entre os polimorfismos do gene da IL-13 (nas posições -1055C/T e +2044GI A e suscetibilidade dos pacientes a CEC de cabeça e pescoço.Squamous cell carcinoma (SCC is the most common malignancy that involves the upper aerodigestive tract. Interleukin-13 (IL-13 is an immunoregulatory cytokine that has been reported to have some polymorphisms in it gene associated with same disease especially asthma and allergy. The present study aimed to investigate whether the polymorphisms of IL-13 gene (at positions of 1055C/T in the promoter of1L-13 gene and +2044G/T exon-4 differ in patients with head and neck SCC from healthy controls. METHODS: This study was investigated in patient with head and neck SCC (n = 137 and age- and sex

  17. Hydrology of the North Fork of the Right Fork of Miller Creek, Carbon County, Utah, before, during, and after underground coal mining

    Science.gov (United States)

    Slaughter, C.B.; Freethey, G.W.; Spangler, L.E.

    1995-01-01

    From 1988-92 the U.S. Geological Survey, in cooperation with the Utah Division of Oil, Gas, and Mining, studied the effects of underground coal mining and the resulting subsidence on the hydrologic system near the North Fork of the Right Fork of Miller Creek, Carbon County, Utah. The subsidence caused open fractures at land surface, debris slides, and rockfalls in the canyon above the mined area. Land surface subsided and moved several feet horizontally. The perennial stream and a tributary upstream from the mined area were diverted below the ground by surface fractures where the overburden thickness above the Wattis coal seam is 300 to 500 feet. The reach downstream was dry but flow resumed where the channel traversed the Star Point Sandstone, which forms the aquifer below the coal seams where ground-water discharge provides new base flow. Concentrations of dissolved constituents in the stream water sampled just downstream from the mined area increased from about 300 mg/L (milligrams per liter) to more than 1,500 mg/L, and the water changed from primarily a magnesium calcium bicarbonate to primarily a magnesium sulfate type. Monitored water levels in two wells completed in the perched aquifer(s) above the mine indicate that fractures from subsidence- related deformation drained the perched aquifer in the Blackhawk Formation. The deformation also could have contributed to the decrease in discharge of three springs above the mined area, but discharge from other springs in the area did not change ubstantially; thus, the relation between subsidence and spring discharge, if any, is not clear. No significant changes in the chemical character of water discharging from springs were detected, but the dissolved-solids concentration in water collected from a perched sandstone aquifer overlying the mined coal seams increased during mining activity.

  18. Calibration of quartz tuning fork spring constants for non-contact atomic force microscopy: direct mechanical measurements and simulations

    Directory of Open Access Journals (Sweden)

    Jens Falter

    2014-04-01

    Full Text Available Quartz tuning forks are being increasingly employed as sensors in non-contact atomic force microscopy especially in the “qPlus” design. In this study a new and easily applicable setup has been used to determine the static spring constant at several positions along the prong of the tuning fork. The results show a significant deviation from values calculated with the beam formula. In order to understand this discrepancy the complete sensor set-up has been digitally rebuilt and analyzed by using finite element method simulations. These simulations provide a detailed view of the strain/stress distribution inside the tuning fork. The simulations show quantitative agreement with the beam formula if the beam origin is shifted to the position of zero stress onset inside the tuning fork base and torsional effects are also included. We further found significant discrepancies between experimental calibration values and predictions from the shifted beam formula, which are related to a large variance in tip misalignment during the tuning fork assembling process.

  19. Replication fork progression is paused in two large chromosomal zones flanking the DNA replication origin in Escherichia coli.

    Science.gov (United States)

    Akiyama, Masahiro Tatsumi; Oshima, Taku; Chumsakul, Onuma; Ishikawa, Shu; Maki, Hisaji

    2016-08-01

    Although the speed of nascent DNA synthesis at individual replication forks is relatively uniform in bacterial cells, the dynamics of replication fork progression on the chromosome are hampered by a variety of natural impediments. Genome replication dynamics can be directly measured from an exponentially growing cell population by sequencing newly synthesized DNA strands that were specifically pulse-labeled with the thymidine analogue 5-bromo-2'-deoxyuridine (BrdU). However, a short pulse labeling with BrdU is impracticable for bacteria because of poor incorporation of BrdU into the cells, and thus, the genomewide dynamics of bacterial DNA replication remain undetermined. Using a new thymidine-requiring Escherichia coli strain, eCOMB, and high-throughput sequencing, we succeeded in determining the genomewide replication profile in bacterial cells. We also found that fork progression is paused in two ~200-kb chromosomal zones that flank the replication origin in the growing cells. This origin-proximal obstruction to fork progression was overcome by an increased thymidine concentration in the culture medium and enhanced by inhibition of transcription. These indicate that DNA replication near the origin is sensitive to the impediments to fork progression, namely a scarcity of the DNA precursor deoxythymidine triphosphate and probable conflicts between replication and transcription machineries.

  20. Silicon carbide resonant tuning fork for microsensing applications in high-temperature and high G-shock environments

    Institute of Scientific and Technical Information of China (English)

    David R Myers; Kan Bun Cheng; Babak Jamshidi; Robert G Azevedo; Debbie G Senesky; Li Chen; Mehran Mehregany; Muthu B J Wijesundara; Albert P Pisano

    2012-01-01

    We present the fabrication and testing of a silicon carbide (SiC) balanced mass doublended tuning fork that survives harsh environments without compromising the device strain sensitivity and resolution bandwidth. The device features a material stack that survives corrosive environments and enables high-temperature operation. To perform hightemperature testing, a specialized setup was constructed that allows the tuning fork to be characterized using traditional silicon electronics. The tuning fork has been operated at 600°C in the presence of dry steam for short durations. This tuning fork has also been tested to 64 000 G using a hard-launch, soft-catch shock implemented with a light gas gun. However, the device still has a strain sensitivity of 66 Hz/μe and strain resolution of 0. 045 μe in a 10 kHz bandwidth. As such, this balanced-mass double-ended tuning fork can be used to create a variety of different sensors including strain gauges, accelerometers, gyroscopes, and pressure transducers. Given the adaptable fabrication process flow, this device could be useful to micro-electro-mechanical systems (MEMS) designers creating sensors for a variety of different applications.

  1. Head Injuries in Children

    Science.gov (United States)

    Pennington, Nicole

    2010-01-01

    School nurses play a crucial role in injury prevention and initial treatment when injuries occur at school. The role of school nurses includes being knowledgeable about the management of head injuries, including assessment and initial treatment. The school nurse must be familiar with the outcomes of a head injury and know when further evaluation…

  2. Water-quality trends and constituent-transport analysis for selected sampling sites in the Milltown Reservoir/Clark Fork River Superfund Site in the upper Clark Fork Basin, Montana, water years 1996–2015

    Science.gov (United States)

    Sando, Steven K.; Vecchia, Aldo V.

    2016-07-20

    During the extended history of mining in the upper Clark Fork Basin in Montana, large amounts of waste materials enriched with metallic contaminants (cadmium, copper, lead, and zinc) and the metalloid trace element arsenic were generated from mining operations near Butte and milling and smelting operations near Anaconda. Extensive deposition of mining wastes in the Silver Bow Creek and Clark Fork channels and flood plains had substantial effects on water quality. Federal Superfund remediation activities in the upper Clark Fork Basin began in 1983 and have included substantial remediation near Butte and removal of the former Milltown Dam near Missoula. To aid in evaluating the effects of remediation activities on water quality, the U.S. Geological Survey began collecting streamflow and water-quality data in the upper Clark Fork Basin in the 1980s.Trend analysis was done on specific conductance, selected trace elements (arsenic, copper, and zinc), and suspended sediment for seven sampling sites in the Milltown Reservoir/Clark Fork River Superfund Site for water years 1996–2015. The most upstream site included in trend analysis is Silver Bow Creek at Warm Springs, Montana (sampling site 8), and the most downstream site is Clark Fork above Missoula, Montana (sampling site 22), which is just downstream from the former Milltown Dam. Water year is the 12-month period from October 1 through September 30 and is designated by the year in which it ends. Trend analysis was done by using a joint time-series model for concentration and streamflow. To provide temporal resolution of changes in water quality, trend analysis was conducted for four sequential 5-year periods: period 1 (water years 1996–2000), period 2 (water years 2001–5), period 3 (water years 2006–10), and period 4 (water years 2011–15). Because of the substantial effect of the intentional breach of Milltown Dam on March 28, 2008, period 3 was subdivided into period 3A (October 1, 2005–March 27, 2008

  3. In-Field Performance Testing of the Fork Detector for Quantitative Spent Fuel Verification

    Energy Technology Data Exchange (ETDEWEB)

    Gauld, Ian C. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Hu, Jianwei [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); De Baere, P. [European Commission (Luxembourg). DG Energy, Directorate Nuclear Safeguards; Vaccaro, S. [European Commission (Luxembourg). DG Energy, Directorate Nuclear Safeguards; Schwalbach, P. [European Commission (Luxembourg). DG Energy, Directorate Nuclear Safeguards; Liljenfeldt, Henrik [Swedish Nuclear Fuel and Waste Management Company (Sweden); Tobin, Stephen [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2015-01-01

    Expanding spent fuel dry storage activities worldwide are increasing demands on safeguards authorities that perform inspections. The European Atomic Energy Community (EURATOM) and the International Atomic Energy Agency (IAEA) require measurements to verify declarations when spent fuel is transferred to difficult-to-access locations, such as dry storage casks and the repositories planned in Finland and Sweden. EURATOM makes routine use of the Fork detector to obtain gross gamma and total neutron measurements during spent fuel inspections. Data analysis is performed by modules in the integrated Review and Analysis Program (iRAP) software, developed jointly by EURATOM and the IAEA. Under the framework of the US Department of Energy–EURATOM cooperation agreement, a module for automated Fork detector data analysis has been developed by Oak Ridge National Laboratory (ORNL) using the ORIGEN code from the SCALE code system and implemented in iRAP. EURATOM and ORNL recently performed measurements on 30 spent fuel assemblies at the Swedish Central Interim Storage Facility for Spent Nuclear Fuel (Clab), operated by the Swedish Nuclear Fuel and Waste Management Company (SKB). The measured assemblies represent a broad range of fuel characteristics. Neutron count rates for 15 measured pressurized water reactor assemblies are predicted with an average relative standard deviation of 4.6%, and gamma signals are predicted on average within 2.6% of the measurement. The 15 measured boiling water reactor assemblies exhibit slightly larger deviations of 5.2% for the gamma signals and 5.7% for the neutron count rates, compared to measurements. These findings suggest that with improved analysis of the measurement data, existing instruments can provide increased verification of operator declarations of the spent fuel and thereby also provide greater ability to confirm integrity of an assembly. These results support the application of the Fork detector as a fully quantitative spent fuel

  4. Photo-thermal quartz tuning fork excitation for dynamic mode atomic force microscope

    Energy Technology Data Exchange (ETDEWEB)

    Bontempi, Alexia; Teyssieux, Damien; Thiery, Laurent; Hermelin, Damien; Vairac, Pascal [FEMTO-ST Institute UMR 6174, Université de Franche-Comté, CNRS, ENSMM, UTBM, 32 Avenue de l' Observatoire, F-25044 Besançon (France); Friedt, Jean-Michel [SENSeOR SAS, Besançon (France)

    2014-10-13

    A photo-thermal excitation of a Quartz Tuning Fork (QTF) for topographic studies is introduced. The non-invasive photo-thermal excitation presents practical advantages compared to QTF mechanical and electrical excitations, including the absence of the anti-resonance and its associated phase rotation. Comparison between our theoretical model and experiments validate that the optical transduction mechanism is a photo-thermal rather than photo-thermoacoustic phenomenon. Topographic maps in the context of near-field microscopy distance control have been achieved to demonstrate the performance of the system.

  5. Performance Characteristics and Temperature Compensation Method of Fluid Property Sensor Based on Tuning-Fork Technology

    Directory of Open Access Journals (Sweden)

    Yuan Chen

    2016-01-01

    Full Text Available Fluid property sensor (FPS based on tuning-fork technology is applied to the measurement of the contaminant level of lubricant oil. The measuring principle of FPS sensor is derived and proved together with its resolution. The performance characteristics of the FPS sensor, such as sensitivity coefficient, resolution, and quality factor, are analyzed. A temperature compensation method is proposed to eliminate the temperature-dependence of the measuring parameters, and its validity is investigated by numerical simulation of sensitivity, oscillating frequency, and dielectric constant. The values of purification efficiency obtained using microwave and without microwave are compared experimentally.

  6. South Fork Zumbro River Stage 1B, Rochester, Minnesota. Design Memorandum Number 2, Flood Control Project

    Science.gov (United States)

    1987-02-01

    Softb AMuchy, lack G M S, Very Dense, Block /00 Bo. 970 =_ Loose, Black-Gray 001, Very Dense, Tan -Gray 20 Very SofC Block TeO of Bedrock 2 , •MI P/a...Env cae,•,+,"’ epd ~-TaP ay. Dwq. 86 -1034e /0 May 49S6 :WS 9743 1 Water I To- of Bedrok -970 3 A/oaes: J .960 I/ ..Fork Zunbro River eev. 974.3: 2. ft

  7. Best management practices plan for the Lower East Fork Poplar Creek Operable Unit, Oak Ridge, Tennessee

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1996-04-01

    This plan was prepared in support of the Phase II Remedial Design Report (DOE/OR/01-1449&D1) and in accordance with requirements under CERCLA to present the plan for best management practices to be followed during the remediation. This document provides the Environmental Restoration Program with information about spill prevention and control, water quality monitoring, good housekeeping practices, sediment and erosion control measures, and inspections and environmental compliance practices to be used during Phase II of the remediation project for the Lower East Fork Poplar Creek Operable Unit.

  8. Thermoelastic investigation of a quartz tuning fork used in infrared spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Spajer, M., E-mail: michel.spajer@univ-fcomte.fr; Cavallier, B.; Euphrasie, S.; Matten, G.; Vacheret, X.; Vairac, P.; Vernier, D. [Institut FEMTO-ST, Université de Franche-Comté, CNRS, ENSMM, UTBM, 32 avenue de l' Observatoire, F-25044 Besançon cedex (France); Jalocha, A. [CILAS, Département de Photonique, 8 avenue Buffon, BP 6319, F-45000 Orléans (France)

    2013-11-11

    The performances of quartz tuning forks (QTF) used in infrared spectroscopy for pollutant detection are investigated. The transduction between light and QTF vibration is elucidated, thanks to QTF encapsulation under vacuum. From the sensitivity enhancement which is obtained, we conclude that their interaction is photo-thermoelastic rather than photo-thermoacoustic. A mapping of the local sensitivity of the QTF is obtained by scanning its faces with the excitation probe beam. The comparison between the signal mapping and the theoretical strain mapping indicates that the most efficient areas of the QTF correspond to the areas where the strain or stress is the highest.

  9. Monitoring the spatiotemporal dynamics of proteins at replication forks and in assembled chromatin using isolation of proteins on nascent DNA.

    Science.gov (United States)

    Sirbu, Bianca M; Couch, Frank B; Cortez, David

    2012-03-01

    Understanding the processes of DNA replication, chromatin assembly and maturation, and the replication stress response requires the ability to monitor protein dynamics at active and damaged replication forks. Detecting protein accumulation at replication forks or damaged sites has primarily relied on immunofluorescence imaging, which is limited in resolution and antibody sensitivity. Here we describe a procedure to isolate proteins on nascent DNA (iPOND) that permits a high-resolution spatiotemporal analysis of proteins at replication forks or on chromatin following DNA replication in cultured cells. iPOND relies on labeling of nascent DNA with the nucleoside analog 5-ethynyl-2'-deoxyuridine (EdU). Biotin conjugation to EdU-labeled DNA using click chemistry facilitates a single-step streptavidin purification of proteins bound to the nascent DNA. iPOND permits an interrogation of any cellular process linked to DNA synthesis using a 3- to 4-d protocol.

  10. Magnetic Resonance Imaging (MRI) -- Head

    Medline Plus

    Full Text Available ... MRI of the Head? What is MRI of the Head? Magnetic resonance imaging (MRI) is a noninvasive ... of page What are some common uses of the procedure? MR imaging of the head is performed ...

  11. Magnetic Resonance Imaging (MRI) -- Head

    Medline Plus

    Full Text Available ... MRI of the Head? What is MRI of the Head? Magnetic resonance imaging (MRI) is a noninvasive ... of page What are some common uses of the procedure? MR imaging of the head is performed ...

  12. Ulnar head replacement.

    Science.gov (United States)

    Herbert, Timothy J; van Schoonhoven, Joerg

    2007-03-01

    Recent years have seen an increasing awareness of the anatomical and biomechanical significance of the distal radioulnar joint (DRUJ). With this has come a more critical approach to surgical management of DRUJ disorders and a realization that all forms of "excision arthroplasty" can only restore forearm rotation at the expense of forearm stability. This, in turn, has led to renewed interest in prosthetic replacement of the ulnar head, a procedure that had previously fallen into disrepute because of material failures with early implants, in particular, the Swanson silicone ulnar head replacement. In response to these early failures, a new prosthesis was developed in the early 1990s, using materials designed to withstand the loads across the DRUJ associated with normal functional use of the upper limb. Released onto the market in 1995 (Herbert ulnar head prosthesis), clinical experience during the last 10 years has shown that this prosthesis is able to restore forearm function after ulnar head excision and that the materials (ceramic head and noncemented titanium stem), even with normal use of the limb, are showing no signs of failure in the medium to long term. As experience with the use of an ulnar head prosthesis grows, so does its acceptance as a viable and attractive alternative to more traditional operations, such as the Darrach and Sauve-Kapandji procedures. This article discusses the current indications and contraindications for ulnar head replacement and details the surgical procedure, rehabilitation, and likely outcomes.

  13. SIR2016-5029_cfwgoshor_8: Flood Inundation Depth for a Flow of 62,300 cfs at the Gage Coast Fork Willamette River at Goshen, Oregon

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — The domain of the model is as follows: Row River from Dorena dam to the confluence with the Coast Fork; Coast Fork from Cottage Grove dam to the confluence with the...

  14. SIR2016-5029_cfwgoshor_4: Flood Inundation Depth for a Flow of 27,900 cfs at the Gage Coast Fork Willamette River at Goshen, Oregon

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — The domain of the model is as follows: Row River from Dorena dam to the confluence with the Coast Fork; Coast Fork from Cottage Grove dam to the confluence with the...

  15. SIR2016-5029_cfwgoshor_7: Flood Inundation Depth for a Flow of 46,800 cfs at the Gage Coast Fork Willamette River at Goshen, Oregon

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — The domain of the model is as follows: Row River from Dorena dam to the confluence with the Coast Fork; Coast Fork from Cottage Grove dam to the confluence with the...

  16. SIR2016-5029_cfwgoshor_6: Flood Inundation Depth for a Flow of 39,900 at the Gage Coast Fork Willamette River at Goshen, Oregon

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — The domain of the model is as follows: Row River from Dorena dam to the confluence with the Coast Fork; Coast Fork from Cottage Grove dam to the confluence with the...

  17. SIR2016-5029_cfwgoshor_3: Flood Inundation Depth for a Flow of 21,450 cfs at the Gage Coast Fork Willamette River at Goshen, Oregon

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — The domain of the model is as follows: Row River from Dorena dam to the confluence with the Coast Fork; Coast Fork from Cottage Grove dam to the confluence with the...

  18. SIR2016-5029_cfwgoshor_5: Flood Inundation Depth for a Flow of 33,900 cfs at the Gage Coast Fork Willamette River at Goshen, Oregon

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — The domain of the model is as follows: Row River from Dorena dam to the confluence with the Coast Fork; Coast Fork from Cottage Grove dam to the confluence with the...

  19. SIR2016-5029_cfwgoshor_1: Flood Inundation Depth for a Flow of 12,000 cfs at the Gage Coast Fork Willamette River at Goshen, Oregon

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — The domain of the model is as follows: Row River from Dorena dam to the confluence with the Coast Fork; Coast Fork from Cottage Grove dam to the confluence with the...

  20. SIR2016-5029_cfwgoshor_2: Flood Inundation Depth for a Flow of 15,000 cfs at the Gage Coast Fork Willamette River at Goshen, Oregon

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — The domain of the model is as follows: Row River from Dorena dam to the confluence with the Coast Fork; Coast Fork from Cottage Grove dam to the confluence with the...

  1. Stream-Sediment Geochemistry in Mining-Impacted Drainages of the Yankee Fork of the Salmon River, Custer County, Idaho

    Science.gov (United States)

    Frost, Thomas P.; Box, Stephen E.

    2009-01-01

    This reconnaissance study was undertaken at the request of the USDA Forest Service, Region 4, to assess the geochemistry, in particular the mercury and selenium contents, of mining-impacted sediments in the Yankee Fork of the Salmon River in Custer County Idaho. The Yankee Fork has been the site of hard-rock and placer mining, primarily for gold and silver, starting in the 1880s. Major dredge placer mining from the 1930s to 1950s in the Yankee Fork disturbed about a 10-kilometer reach. Mercury was commonly used in early hard-rock mining and placer operations for amalgamation and recovery of gold. During the late 1970s, feasibility studies were done on cyanide-heap leach recovery of gold from low-grade ores of the Sunbeam and related deposits. In the mid-1990s a major open-pit bulk-vat leach operation was started at the Grouse Creek Mine. This operation shut down when gold values proved to be lower than expected. Mercury in stream sediments in the Yankee Fork ranges from below 0.02 ppm to 7 ppm, with the highest values associated with old mill locations and lode and placer mines. Selenium ranges from below the detection limit for this study of 0.2 ppm to 4 ppm in Yankee Fork sediment samples. The generally elevated selenium content in the sediment samples reflect the generally high selenium contents in the volcanic rocks that underlie the Yankee Fork and the presence of gold and silver selenides in some of the veins that were exploited in the early phases of mining.

  2. Photolithography and Selective Etching of an Array of Quartz Tuning Fork Resonators with Improved Impact Resistance Characteristics

    Science.gov (United States)

    Lee, Sungkyu

    2001-08-01

    Quartz tuning fork blanks with improved impact-resistant characteristics for use in Qualcomm mobile station modem (MSM)-3000 central processing unit (CPU) chips for code division multiple access (CDMA), personal communication system (PCS), and global system for mobile communication (GSM) systems were designed using finite element method (FEM) analysis and suitable processing conditions were determined for the reproducible precision etching of a Z-cut quartz wafer into an array of tuning forks. Negative photoresist photolithography for the additive process was used in preference to positive photoresist photolithography for the subtractive process to etch the array of quartz tuning forks. The tuning fork pattern was transferred via a conventional photolithographical chromium/quartz glass template using a standard single-sided aligner and subsequent negative photoresist development. A tightly adhering and pinhole-free 600/2000 Å chromium/gold mask was coated over the developed photoresist pattern which was subsequently stripped in acetone. This procedure was repeated on the back surface of the wafer. With the protective metallization area of the tuning fork geometry thus formed, etching through the quartz wafer was performed at 80°C in a ± 1.5°C controlled bath containing a concentrated solution of ammonium bifluoride to remove the unwanted areas of the quartz wafer. The quality of the quartz wafer surface finish after quartz etching depended primarily on the surface finish of the quartz wafer prior to etching and the quality of quartz crystals used. Selective etching of a 100 μm quartz wafer could be achieved within 90 min at 80°C. A selective etching procedure with reproducible precision has thus been established and enables the photolithographic mass production of miniature tuning fork resonators.

  3. 头颈部鳞癌中TP53基因的调控网络分析%TP53-related gene regulatory network analysis on head and neck squamous carcinoma

    Institute of Scientific and Technical Information of China (English)

    徐明义; 郑艳秋; 孙娟; 胡文良; 王亚平; 崔晓波; 李玲香

    2016-01-01

    Objective To find out the TP53-related mechanism underlying head and neck squamous cell carcinoma.Methods We used cbioportal to analyse the expression of TP53 and identify the co-expressed genes of TP53 in 279 samples from head and neck squamous cell carcinoma in TCGA database.We used String and DAVID database to establish the co-expression network of TP53 and analyze its func-tion.We used lncRNA2target and StarBase database to screen the microRNA,lncRNA and ceRNA that regulate TP53.Finally,Cytoscape soft-ware was used to establish TP53-related ceRNA network.Results In the 279 samples,77%samples were abnormal expression,and the sur-vival rate of patients with abnormal expression of TP53 was significantly lower than that of normal expression of TP53.Besides,we found 288 TP53-related co-expressed gene.(Spearman score and Pearson score>0.3)The functions of these genes were mainly transcription regulation, cell apoptosis,propagation and immune response.Gene regulatory network revealed that 43 microRNAs (i.g.,has-miR-186-5p and has-miR-202-3p),6 lncRNAs (e.g.,MEG1,TUG1 and MALAT1)and 56 ceRNAs (e.g.,PHC2,FZD4 and TUB)could regulate TP53.Conclusion We established TP53-related gene regulatory network and identified microRNA,lncRNA and ceRNA that regulate TP53.The data generated from this study could provide a new pointcut in research and treatment of head and neck squamous cell carcinoma.%目的:挖掘隐藏在头颈部鳞癌中抑癌基因TP53表达异常的机制。方法从TCGA数据库中选取279例头颈部鳞癌样本的测序数据,利用cbioportal获得TP53基因在头颈部鳞癌中的表达情况及其对患者生存的影响,并筛选样本中与TP53存在共表达关系的基因。利用String和DAVID数据库,建立TP53的共表达网络并分析网络功能,通过lncRNA2target和StarBase数据库,筛选出能够调控TP53的短链非编码RNA(microRNA),长链非编码RNA(lncRNA)和竞争性内源性RNA(ceRNA

  4. Maneuvering impact boring head

    Science.gov (United States)

    Zollinger, W. Thor; Reutzel, Edward W.

    1998-01-01

    An impact boring head may comprise a main body having an internal cavity with a front end and a rear end. A striker having a head end and a tail end is slidably mounted in the internal cavity of the main body so that the striker can be reciprocated between a forward position and an aft position in response to hydraulic pressure. A compressible gas contained in the internal cavity between the head end of the striker and the front end of the internal cavity returns the striker to the aft position upon removal of the hydraulic pressure.

  5. The Model Analysis of a Complex Tuning Fork Probe and Its Application in Bimodal Atomic Force Microscopy

    Directory of Open Access Journals (Sweden)

    Zhichao Wu

    2017-01-01

    Full Text Available A new electromechanical coupling model was built to quantitatively analyze the tuning fork probes, especially the complex ones. A special feature of a novel, soft tuning fork probe, that the second eigenfrequency of the probe was insensitive to the effective force gradient, was found and used in a homemade bimodal atomic force microscopy to measure power dissipation quantitatively. By transforming the mechanical parameters to the electrical parameters, a monotonous and concise method without using phase to calculate the power dissipation was proposed.

  6. Shear Force Detection Using Single-Tine Oscillating Tuning Fork for Scanning Near-Field Optical Microscopy

    Institute of Scientific and Technical Information of China (English)

    谭晓靖; 孙家林; 刘晟; 郭继华; 孙红三

    2003-01-01

    We propose a new method to detect near-field by using a single-tine oscillating tuning fork with mechanically asymmetric excitation that exhibits the sensitivity and stability better than that by using a double-tine oscillating one. Comparison of shear forces for the two methods demonstrate that the single-tine oscillating tuning fork provides a simpler and more sensitive method for near-field measurements. A theoretical analysis is presented for explanation to the greater sensitivity. The method is demonstrated by imaging a sparse-packed layer of micro-spheres in size of 200 nm.

  7. Early Head Start Evaluation

    Data.gov (United States)

    U.S. Department of Health & Human Services — Longitudinal information from an evaluation where children were randomly assigned to Early Head Start or community services as usual;direct assessments and...

  8. Computed Tomography (CT) -- Head

    Medline Plus

    Full Text Available ... you! Do you have a personal story about radiology? Share your patient story here Images × Image Gallery ... Pregnancy Head and Neck Cancer X-ray, Interventional Radiology and Nuclear Medicine Radiation Safety Images related to ...

  9. Head and face reconstruction

    Science.gov (United States)

    ... work together. Head and neck surgeons also perform craniofacial reconstruction operations. The surgery is done while you are deep asleep and pain-free (under general anesthesia ). The surgery may take ...

  10. Computed Tomography (CT) -- Head

    Medline Plus

    Full Text Available ... headaches, dizziness, and other symptoms of aneurysm, bleeding, stroke and brain tumors. It also helps your doctor ... scanning provides more detailed information on head injuries, stroke , brain tumors and other brain diseases than regular ...

  11. Computed Tomography (CT) -- Head

    Medline Plus

    Full Text Available ... a stroke, especially with a new technique called Perfusion CT. brain tumors. enlarged brain cavities (ventricles) in ... X-Ray and CT Exams Blood Clots CT Perfusion of the Head CT Angiography (CTA) Stroke Brain ...

  12. Computed Tomography (CT) -- Head

    Medline Plus

    Full Text Available ... traditional x-rays, particularly of soft tissues and blood vessels. CT scanning provides more detailed information on head injuries, stroke , brain tumors and other brain diseases than ...

  13. Computed Tomography (CT) -- Head

    Medline Plus

    Full Text Available ... special x-ray equipment to help assess head injuries, severe headaches, dizziness, and other symptoms of aneurysm, ... cancer. In emergency cases, it can reveal internal injuries and bleeding quickly enough to help save lives. ...

  14. Computed Tomography (CT) -- Head

    Medline Plus

    Full Text Available ... headaches, dizziness, and other symptoms of aneurysm, bleeding, stroke and brain tumors. It also helps your doctor ... scanning provides more detailed information on head injuries, stroke , brain tumors and other brain diseases than regular ...

  15. Computed Tomography (CT) -- Head

    Medline Plus

    Full Text Available ... images of internal organs, bones, soft tissue and blood vessels provide greater detail than traditional x-rays, particularly of soft tissues and blood vessels. CT scanning provides more detailed information on head ...

  16. Head CT scan

    Science.gov (United States)

    Brain CT; Cranial CT; CT scan - skull; CT scan - head; CT scan - orbits; CT scan - sinuses; Computed tomography - cranial; CAT scan - brain ... hold your breath for short periods. A complete scan usually take only 30 seconds to a few ...

  17. Head Start Impact Study

    Data.gov (United States)

    U.S. Department of Health & Human Services — Nationally representative, longitudinal information from an evaluation where children were randomly assigned to Head Start or community services as usual;direct...

  18. Computed Tomography (CT) -- Head

    Medline Plus

    Full Text Available ... special x-ray equipment to help assess head injuries, severe headaches, dizziness, and other symptoms of aneurysm, ... cancer. In emergency cases, it can reveal internal injuries and bleeding quickly enough to help save lives. ...

  19. Quartz Tuning Fork Pressure Gauge for High-Pressure Liquid Helium

    Science.gov (United States)

    Botimer, J.; Velasco, A.; Taborek, P.

    2017-01-01

    We have measured the quality factor Q and the frequency f of a 32-kHz quartz tuning fork immersed in liquid ^4He between 0.9 and 3.0 K, over pressures ranging from the saturated vapor pressure to ≈ 25 atm. At constant pressure, as a function of temperature, the quality factor and frequency have strong features related to the temperature dependence of the superfluid fraction. At constant temperature, Q depends on the superfluid fraction, while the frequency is a smooth function of pressure. The behavior is explained using a simple hydrodynamic model. The liquid helium viscosity is obtained from measured values of Q, and together with tabulated values of the helium density as a function of pressure and temperature, the frequency shift can be parameterized as a function of temperature and pressure. The observed sensitivity is ≈ 7.8 Hz/atm. The quartz tuning fork provides a compact low power method of measuring the pressure in the bulk liquid.

  20. A paleomagnetic study of the Prince William terrane and Nixon Fork terrane, Alaska

    Science.gov (United States)

    Plumley, P. W.

    1984-12-01

    The mean paleomagnetic inclination of Paleocene volcanics from two regions on Kodiak Island in the Ghost Rocks Formation suggests that the Prince William terrance originated at mid latitudes, about 25 deg south of its expected Alaskan latitude in Paleocene time. The mean declinations of the two regions, however, differ by approximately 120 deg, suggesting they have rotated with respect to each other, perhaps during emplacement. It is suggested that, despite the lack of evidence for a major Tertiary suture zone between the Prince William terrane and central Alaska, the Prince William and perhaps adjacent terranes may have lain substantially south of their present position in the early Tertiary. Paleomagnetic data from early Ordovician to early Tertiary rocks of the Nixon Fork terrane, central Alaska, provide evidence toward a better understanding of the tectonic evolution of the continental margin of northwestern America. The Nixon fork terrane, a Paleozoic continental margin assemblage, is bordered on the south by proven allochthonous terranes and to the North by provinces with oceanic affinities far younger in age. Paleomagnetic analysis of the Ordovician limestone sections (Lower Ordovician Novi Mountain and Middle to Upper Ordovican Telsitna Formation) are interpreted as having three components of magnetization.

  1. Lentiform fork sign: a magnetic resonance finding in a case of acute metabolic acidosis.

    Science.gov (United States)

    Grasso, Daniela; Borreggine, Carmela; Perfetto, Francesco; Bertozzi, Vincenzo; Trivisano, Marina; Specchio, Luigi Maria; Grilli, Gianpaolo; Macarini, Luca

    2014-06-01

    We report a 33 year-old woman addicted to chronic unspecified solvents abuse with stupor, respiratory disorders, tetraplegia and severe metabolic acidosis. On admission an unenhanced cranial CT scan showed symmetrical hypodensities of both lentiform nuclei. MR imaging performed 12 hours after stupor demonstrates bilateral putaminal hemorrhagic necrosis, bilateral external capsule, corona radiata and deep cerebellar hyperintensities with right cingulate cortex involvement. DWI reflected bilateral putaminal hyperintensities with restricted water diffusion as to citotoxic edema and development of vasogenic edema in the external capsule recalling a fork. On day twenty, after specific treatments MRI demonstrated a bilateral putaminal marginal enhancement. Bilateral putaminal necrosis is a characteristic but non-specific radiological finding of methanol poisoning. Lentiform Fork sign is a rare MRI finding reported in literature in 22 patients with various conditions characterized by metabolic acidosis. Vasogenic edema may be due to the differences in metabolic vulnerability between neurons and astrocytes. We postulate that metabolic acidosis could have an important role to generate this sign.

  2. The forked tongue and edge detection in snakes (Crotalus oreganus): an experimental test.

    Science.gov (United States)

    Parker, M Rockwell; Young, Bruce A; Kardong, Kenneth V

    2008-02-01

    Many stimulus-detection systems are lateralized to allow for simultaneous comparison of paired stimuli. It has been hypothesized that the deeply forked tongue of snakes and some derived lizards functions as a chemical edge detector where cues gathered by each tine are kept separate to provide two points of lateral odor assessment by the central nervous system via vomeronasal input. While following a chemical trail, one time can be on the trail, the other off, and such differential information prompts the snake to turn back to the trail. The authors tested this hypothesis in rattlesnakes within a predatory context by unilaterally severing the vomeronasal nerves. If edge detection is used by snakes during prey trailing, then unilateral denervation should disrupt trailing ability. The authors found no change in the seven separate trailing parameters measured. Therefore, they found no support for the edge detection hypothesis as it applies to prey trailing behavior. Instead, the deeply forked tongue may represent a chemosensory specialization to increase odor-sampling area, with snakes and derived lizards detecting only the concentration of chemical trails. (c) 2008 APA.

  3. ETAA1 acts at stalled replication forks to maintain genome integrity.

    Science.gov (United States)

    Bass, Thomas E; Luzwick, Jessica W; Kavanaugh, Gina; Carroll, Clinton; Dungrawala, Huzefa; Glick, Gloria G; Feldkamp, Michael D; Putney, Reid; Chazin, Walter J; Cortez, David

    2016-11-01

    The ATR checkpoint kinase coordinates cellular responses to DNA replication stress. Budding yeast contain three activators of Mec1 (the ATR orthologue); however, only TOPBP1 is known to activate ATR in vertebrates. We identified ETAA1 as a replication stress response protein in two proteomic screens. ETAA1-deficient cells accumulate double-strand breaks, sister chromatid exchanges, and other hallmarks of genome instability. They are also hypersensitive to replication stress and have increased frequencies of replication fork collapse. ETAA1 contains two RPA-interaction motifs that localize ETAA1 to stalled replication forks. It also interacts with several DNA damage response proteins including the BLM/TOP3α/RMI1/RMI2 and ATR/ATRIP complexes. It binds ATR/ATRIP directly using a motif with sequence similarity to the TOPBP1 ATR-activation domain; and like TOPBP1, ETAA1 acts as a direct ATR activator. ETAA1 functions in parallel to the TOPBP1/RAD9/HUS1/RAD1 pathway to regulate ATR and maintain genome stability. Thus, vertebrate cells contain at least two ATR-activating proteins.

  4. Resonance frequency-retuned quartz tuning fork as a force sensor for noncontact atomic force microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Ooe, Hiroaki; Sakuishi, Tatsuya; Arai, Toyoko, E-mail: arai@staff.kanazawa-u.ac.jp [Natural Science and Technology, Kanazawa University, Kanazawa, Ishikawa 920-1192 (Japan); Nogami, Makoto; Tomitori, Masahiko [Japan Advanced Institute of Science and Technology, Nomi, Ishikawa 923-1292 (Japan)

    2014-07-28

    Based on a two-prong type quartz tuning fork, a force sensor with a high Q factor, which we call a retuned fork sensor, was developed for non-contact atomic force microscopy (nc-AFM) with atomic resolution. By cutting a small notch and attaching an AFM tip to one prong, its resonance frequency can be retuned to that of the other intact prong. In balancing the two prongs in this manner, a high Q factor (>50 000 in ultrahigh vacuum) is obtained for the sensor. An atomic resolution image of the Si(111)-7 × 7 surface was demonstrated using an nc-AFM with the sensor. The dependence of the Q factor on resonance frequency of the sensor and the long-range force between tip and sample were measured and analyzed in view of the various dissipation channels. Dissipation in the signal detection circuit turned out to be mainly limited by the total Q factor of the nc-AFM system.

  5. The Oak Ridge Y-12 Plant biological monitoring and abatement program for East Fork Poplar Creek

    Energy Technology Data Exchange (ETDEWEB)

    Loar, J.M.; Adams, S.M.; Allison, L.J.; Giddings, J.M.; McCarthy, J.F.; Southworth, G.R.; Smith, J.G.; Stewart, A.J. (Oak Ridge National Lab., TN (USA); Springborn Bionomics, Inc., Wareham, MA (USA); Oak Ridge National Lab., TN (USA))

    1989-10-01

    In May 1985, a National Pollutant Discharge Elimination System permit was issued for the Oak Ridge Y-12 Plant, a nuclear weapons components production facility located in Oak Ridge, Tennessee, and operated by Martin Marietta Energy Systems, Inc., for the US Department of Energy. As a condition of the permit, a Biological Monitoring and Abatement Program (BMAP) was developed to demonstrate that the effluent limitations established for the Oak Ridge Y-12 Plant protect the classified uses of the receiving stream (East Fork Poplar Creek), in particular, the growth and propagation of fish and aquatic life, as designated by the Tennessee Department of Health and Environment. A second purpose for the BMAP is to document the ecological effects resulting from implementation of a water pollution control program that will include construction of nine new wastewater treatment facilities over the next 4 years. Because of the complex nature of the effluent discharged to East Fork Poplar Creek and the temporal and spatial variability in the composition of the effluent (i.e., temporal variability related to various pollution abatement measures that will be implemented over the next several years and spatial variability caused by pollutant inputs downstream of the Oak Ridge Y-12 Plant), a comprehensive, integrated approach to biological monitoring was developed for the BMAP. 39 refs., 5 figs., 8 tabs.

  6. The ammonoids from the Three Forks Shale (Late Devonian of Montana

    Directory of Open Access Journals (Sweden)

    D. Korn

    2006-08-01

    Full Text Available The ammonoid fauna from the Late Devonian Three Forks Shale of Montana is revised. Six taxa were recognised, which belong to the genera Tornoceras, Pernoceras, Raymondiceras, Platyclymenia, Pleuroclymenia, and Carinoclymenia. The ammonoid assemblage suggests a stratigraphic position within the middle Famennian, most probably the Platyclymenia annulata Zone. The ammonoids display extreme septal crowding in intermediate as well as adult growth stages, which can be regarded as evidence for instable palaeoecological conditions during lifetime of the animals. Die Ammonoideenfauna aus dem oberdevonischen Three Forks Shale von Montana wird revidiert. Sechs Taxa werden unterschieden; sie gehören zu den Gattungen Tornoceras, Pernoceras, Raymondiceras, Platyclymenia, Pleuroclymenia und Carinoclymenia. Die Ammonoideen-Vergesellschaftung spricht für eine stratigraphische Position im mittleren Famennium, wahrscheinlich in der Platyclymenia annulata Zone. Die Ammonoideen zeigen auffällige Drängung der Septen in intermediären und adulten Wachstumsstadien, die als Hinweis auf instabile Lebensbedingungen für die Tiere gewertet werden kann. doi:10.1002/mmng.200600008

  7. Head and neck teratomas

    OpenAIRE

    Shah, Ajaz; Latoo, Suhail; Ahmed, Irshad; Malik, Altaf H

    2009-01-01

    Teratomas are complex lesions composed of diverse tissues from all 3 germinal cell layers and may exhibit variable levels of maturity. Head and neck teratomas are most commonly cervical with the oropharynx (epignathus) being the second commonest location. In this article, clinical presentation, behaviour and associated significance of head and neck teratomas have been highlightened. Because of their obscure origin, bizarre microscopic appearance, unpredictable behaviour and often dramatic cli...

  8. Análise do gene TAX1BP1 em pacientes com câncer de cabeça e pescoço Analysis of the TAX1BP1 gene in head and neck cancer patients

    Directory of Open Access Journals (Sweden)

    Mariangela Torreglosa Ruiz

    2010-04-01

    Full Text Available No Brasil foram estimados 14.160 casos novos de câncer e cabeça e pescoço para o ano de 2008. O tabagismo e o etilismo são os principais fatores de riscos estabelecidos na etiologia dessa doença. OBJETIVO: Avaliar o polimorfismo T → A do gene TAX1BP1 (leu306ile em pacientes com câncer de cabeça e pescoço e em uma população controle. CASUÍSTICA E MÉTODOS: Estudo retrospectivo onde foram avaliados o sexo, idade, tabagismo e etilismo de 191 pacientes com câncer de cabeça e pescoço e de 200 indivíduos sem história de neoplasia. A análise molecular foi realizada após extração de DNA genômico pela técnica de PCR-RFLP. RESULTADOS: Há predominância de pacientes do sexo masculino (84,82%, tabagistas (91,1% e etilistas (77,49%. A avaliação molecular não mostrou diferença estatisticamente significante entre os dois grupos (p =0,32. A análise dos parâmetros clínicos e polimorfismos mostrou uma associação com câncer na cavidade oral (OR:2,38; IC 95%: 1,18-4,78; p = 0,01, os demais parâmetros não mostraram associação com o polimorfismo. CONCLUSÃO: Há evidências de associação entre o polimorfismo do gene TAX1BP1 e câncer de cavidade oral. Para os demais parâmetros analisados os resultados não sugerem uma associação com o polimorfismo do gene TAX1BP1.In Brazil, there were 14,160 new estimated cases of head and neck cancer for the year of 2008. Smoking and drinking are the main risk factors established in the etiology of this disease. AIM: to assess the T → A polymorphism in gene TAX1BP1 (leu306ile in patients with head and neck cancer and a control population. SERIES AND METHODS: a retrospective study in which we assessed the gender, age, smoking and drinking habits of 191 patients with head and neck cancer and 200 individuals without history of neoplasia. The molecular analysis was carried out after genomic DNA extraction by the PCR-RFLP method. RESULTS: there is a predominance of males (84.82%, smokers (91

  9. Organ-specific gene expression: the bHLH protein Sage provides tissue specificity to Drosophila FoxA.

    Science.gov (United States)

    Fox, Rebecca M; Vaishnavi, Aria; Maruyama, Rika; Andrew, Deborah J

    2013-05-01

    FoxA transcription factors play major roles in organ-specific gene expression, regulating, for example, glucagon expression in the pancreas, GLUT2 expression in the liver, and tyrosine hydroxylase expression in dopaminergic neurons. Organ-specific gene regulation by FoxA proteins is achieved through cooperative regulation with a broad array of transcription factors with more limited expression domains. Fork head (Fkh), the sole Drosophila FoxA family member, is required for the development of multiple distinct organs, yet little is known regarding how Fkh regulates tissue-specific gene expression. Here, we characterize Sage, a bHLH transcription factor expressed exclusively in the Drosophila salivary gland (SG). We show that Sage is required for late SG survival and normal tube morphology. We find that many Sage targets, identified by microarray analysis, encode SG-specific secreted cargo, transmembrane proteins, and the enzymes that modify these proteins. We show that both Sage and Fkh are required for the expression of Sage target genes, and that co-expression of Sage and Fkh is sufficient to drive target gene expression in multiple cell types. Sage and Fkh drive expression of the bZip transcription factor Senseless (Sens), which boosts expression of Sage-Fkh targets, and Sage, Fkh and Sens colocalize on SG chromosomes. Importantly, expression of Sage-Fkh target genes appears to simply add to the tissue-specific gene expression programs already established in other cell types, and Sage and Fkh cannot alter the fate of most embryonic cell types even when expressed early and continuously.

  10. Magnetic Resonance Imaging (MRI) -- Head

    Medline Plus

    Full Text Available ... News Physician Resources Professions Site Index A-Z Magnetic Resonance Imaging (MRI) - Head Magnetic resonance imaging (MRI) of the head ... limitations of MRI of the Head? What is MRI of the Head? Magnetic resonance imaging (MRI) is ...

  11. Missouri: Early Head Start Initiative

    Science.gov (United States)

    Center for Law and Social Policy, Inc. (CLASP), 2012

    2012-01-01

    Missouri's Early Head Start/Child Care Partnership Project expands access to Early Head Start (EHS) services for children birth to age 3 by developing partnerships between federal Head Start, EHS contractors, and child care providers. Head Start and EHS contractors that participate in the initiative provide services through community child care…

  12. Magnetic Resonance Imaging (MRI) -- Head

    Medline Plus

    Full Text Available ... News Physician Resources Professions Site Index A-Z Magnetic Resonance Imaging (MRI) - Head Magnetic resonance imaging (MRI) of the head uses a powerful ... the Head? What is MRI of the Head? Magnetic resonance imaging (MRI) is a noninvasive medical test that ...

  13. Economics of head injuries

    Directory of Open Access Journals (Sweden)

    Singh Manmohan

    2006-01-01

    Full Text Available Summary: Head injuries account for significant proportion of neurosurgical admissions and bed occupancy. Patients with head injuries also consume significant proportions of neurosurgical resources. A prospective 6-month study has been carried out to evaluate the expenditure incurred on head injury patients in a modern neurosurgical center equipped with state of the art infrastructure. Costing areas included wages / salaries of health care personnel, cost of medicines / surgical items / crystalloids, general store items, stationary, all investigation charges, equipment cost, overhead building cost, maintenance cost, electricity and water charges and cost of medical gases, air conditioning and operation theatre expenses. Expenditure in each area was calculated and apportioned to each bed. The statistical analysis was done using X2 test. The cost of stay in ward was found to be Rs. 1062 / bed / day and in neurosurgical ICU Rs. 3082 / bed / day. The operation theatre cost for each surgery was Rs. 11948. The cost of hospital stay per day for minor, moderate and severe head injury group was found to be Rs. 1921, Rs. 2569 and Rs. 2713 respectively. The patients who developed complications, the cost of stay per day in the hospital were Rs. 2867. In the operative group, the cost of hospital stay per day was Rs. 3804. The total expenditure in minor head injury was Rs. 7800 per patient, in moderate head injury was Rs. 22172 per patient, whereas in severe head injury, it was found to be Rs. 32852 per patient. Patients who underwent surgery, the total cost incurred was Rs. 33100 per operated patient.

  14. Fork2Farmer: Enabling Success of Small Farms through Partnerships with Well-Known Chefs and the Tourism Sector

    Science.gov (United States)

    Morais, Duarte; Jakes, Susan; Bowen, Becky; Lelekacs, Joanna Massey

    2017-01-01

    A team of economic development, local foods, and tourism specialists from North Carolina Cooperative Extension is pursuing an initiative titled Fork2Farmer. The goal is to increase visits to local farms and diversify farm income by leveraging the high visibility of well-known farm-to-table chefs who support local small farms. To do this, those…

  15. 77 FR 26733 - Uinta-Wasatch-Cache National Forest; Evanston-Mountain View Ranger District; Utah; Smiths Fork...

    Science.gov (United States)

    2012-05-07

    ... appeal process found at 36 CFR part 215. Rather, it is subject to the predecisional administrative review... environmental impact statement is expected November 2012. ADDRESSES: Send written comments to: Smiths Fork... hand delivered Monday through Friday 8 a.m. to 4:30 p.m. at the following physical address: 1565...

  16. Environmental Assessment - Construct a Ground-to-Air Transmitter and Receiver (GATR) Facility at Grand Forks Air Force Base

    Science.gov (United States)

    2006-06-06

    for wildlife in Grand Forks County. Pastures, meadows, and other non- cultivated areas create a prairie-land mosaic of grasses, legumes, and wild... alfalfa . Herbaceous plants include little bluestem, goldenrod, green needle grass, western wheat grass, and bluegrama. Shrubs such as Juneberry...consists primarily of cultivated crops with remaining land used for pasture and hay, urban development, recreation, and wildlife habitat. Principal

  17. Reliability and responsiveness of a graduated tuning fork in immune mediated polyneuropathies. The Inflammatory Neuropathy Cause and Treatment (INCAT) Group

    NARCIS (Netherlands)

    I.S.J. Merkies (Ingemar); P.I.M. Schmitz (Paul); F.G.A. van der Meché (Frans); P.A. van Doorn (Pieter)

    2000-01-01

    textabstractThe interobserver and intraobserver reliability of the Rydel-Seiffer (RS) graduated tuning fork was evaluated in 113 patients with a clinically stable immune mediated polyneuropathy (83 patients who had had Guillain-Barre syndrome (GBS) in the past, 22 with

  18. Water-quality trends and constituent-transport analysis for selected sampling sites in the Milltown Reservoir/Clark Fork River Superfund Site in the upper Clark Fork Basin, Montana, water years 1996–2015

    Science.gov (United States)

    Sando, Steven K.; Vecchia, Aldo V.

    2016-07-20

    During the extended history of mining in the upper Clark Fork Basin in Montana, large amounts of waste materials enriched with metallic contaminants (cadmium, copper, lead, and zinc) and the metalloid trace element arsenic were generated from mining operations near Butte and milling and smelting operations near Anaconda. Extensive deposition of mining wastes in the Silver Bow Creek and Clark Fork channels and flood plains had substantial effects on water quality. Federal Superfund remediation activities in the upper Clark Fork Basin began in 1983 and have included substantial remediation near Butte and removal of the former Milltown Dam near Missoula. To aid in evaluating the effects of remediation activities on water quality, the U.S. Geological Survey began collecting streamflow and water-quality data in the upper Clark Fork Basin in the 1980s.Trend analysis was done on specific conductance, selected trace elements (arsenic, copper, and zinc), and suspended sediment for seven sampling sites in the Milltown Reservoir/Clark Fork River Superfund Site for water years 1996–2015. The most upstream site included in trend analysis is Silver Bow Creek at Warm Springs, Montana (sampling site 8), and the most downstream site is Clark Fork above Missoula, Montana (sampling site 22), which is just downstream from the former Milltown Dam. Water year is the 12-month period from October 1 through September 30 and is designated by the year in which it ends. Trend analysis was done by using a joint time-series model for concentration and streamflow. To provide temporal resolution of changes in water quality, trend analysis was conducted for four sequential 5-year periods: period 1 (water years 1996–2000), period 2 (water years 2001–5), period 3 (water years 2006–10), and period 4 (water years 2011–15). Because of the substantial effect of the intentional breach of Milltown Dam on March 28, 2008, period 3 was subdivided into period 3A (October 1, 2005–March 27, 2008

  19. Hydrologic and hydraulic analyses for the Black Fork Mohican River Basin in and near Shelby, Ohio

    Science.gov (United States)

    Huitger, Carrie A.; Ostheimer, Chad J.; Koltun, G.F.

    2016-05-06

    Hydrologic and hydraulic analyses were done for selected reaches of five streams in and near Shelby, Richland County, Ohio. The U.S. Geological Survey (USGS), in cooperation with the Muskingum Watershed Conservancy District, conducted these analyses on the Black Fork Mohican River and four tributaries: Seltzer Park Creek, Seltzer Park Tributary, Tuby Run, and West Branch. Drainage areas of the four stream reaches studied range from 0.51 to 60.3 square miles. The analyses included estimation of the 10-, 2-, 1-, and 0.2-percent annual-exceedance probability (AEP) flood-peak discharges using the USGS Ohio StreamStats application. Peak discharge estimates, along with cross-sectional and hydraulic structure geometries, and estimates of channel roughness coefficients were used as input to step-backwater models. The step-backwater water models were used to determine water-surface elevation profiles of four flood-peak discharges and a regulatory floodway. This study involved the installation of, and data collection at, a streamflow-gaging station (Black Fork Mohican River at Shelby, Ohio, 03129197), precipitation gage (Rain gage at Reservoir Number Two at Shelby, Ohio, 405209082393200), and seven submersible pressure transducers on six selected river reaches. Two precipitation-runoff models, one for the winter events and one for nonwinter events for the headwaters of the Black Fork Mohican River, were developed and calibrated using the data collected. With the exception of the runoff curve numbers, all other parameters used in the two precipitation-runoff models were identical. The Nash-Sutcliffe model efficiency coefficients were 0.737, 0.899, and 0.544 for the nonwinter events and 0.850 and 0.671 for the winter events. Both of the precipitation-runoff models underestimated the total volume of water, with residual runoff ranging from -0.27 inches to -1.53 inches. The results of this study can be used to assess possible mitigation options and define flood hazard areas that

  20. Pediatric head injury.

    Science.gov (United States)

    Tulipan, N

    1998-01-01

    Pediatric head injury is a public health problem that exacts a high price from patients, their families and society alike. While much of the brain damage in head-injured patients occurs at the moment of impact, secondary injuries can be prevented by aggressive medical and surgical intervention. Modern imaging devices have simplified the task of diagnosing intracranial injuries. Recent advances in monitoring technology have made it easier to assess the effectiveness of medical therapy. These include intracranial pressure monitoring devices that are accurate and safe, and jugular bulb monitoring which provides a continuous, qualitative measure of cerebral blood flow. The cornerstones of treatment remain hyperventilation and osmotherapy. Despite maximal treatment, however, the mortality and morbidity associated with pediatric head injury remains high. Reduction of this mortality and morbidity will likely depend upon prevention rather than treatment.

  1. Hydrogeology and simulated groundwater flow and availability in the North Fork Red River aquifer, southwest Oklahoma, 1980–2013

    Science.gov (United States)

    Smith, S. Jerrod; Ellis, John H.; Wagner, Derrick L.; Peterson, Steven M.

    2017-09-28

    On September 8, 1981, the Oklahoma Water Resources Board established regulatory limits on the maximum annual yield of groundwater (343,042 acre-feet per year) and equal-proportionate-share (EPS) pumping rate (1.0 acre-foot per acre per year) for the North Fork Red River aquifer. The maximum annual yield and EPS were based on a hydrologic investigation that used a numerical groundwater-flow model to evaluate the effects of potential groundwater withdrawals on groundwater availability in the North Fork Red River aquifer. The Oklahoma Water Resources Board is statutorily required (every 20 years) to update the hydrologic investigation on which the maximum annual yield and EPS were based. Because 20 years have elapsed since the final order was issued, the U.S. Geological Survey, in cooperation with the Oklahoma Water Resources Board, conducted an updated hydrologic investigation and evaluated the effects of potential groundwater withdrawals on groundwater flow and availability in the North Fork Red River aquifer in Oklahoma. This report describes a hydrologic investigation of the North Fork Red River aquifer that includes an updated summary of the aquifer hydrogeology. As part of this investigation, groundwater flow and availability were simulated by using a numerical groundwater-flow model.The North Fork Red River aquifer in Beckham, Greer, Jackson, Kiowa, and Roger Mills Counties in Oklahoma is composed of about 777 square miles (497,582 acres) of alluvium and terrace deposits along the North Fork Red River and tributaries, including Sweetwater Creek, Elk Creek, Otter Creek, and Elm Fork Red River. The North Fork Red River is the primary source of surface-water inflow to Lake Altus, which overlies the North Fork Red River aquifer. Lake Altus is a U.S. Bureau of Reclamation reservoir with the primary purpose of supplying irrigation water to the Lugert-Altus Irrigation District.A hydrogeologic framework was developed for the North Fork Red River aquifer and included a

  2. Head First Statistics

    CERN Document Server

    Griffiths, Dawn

    2009-01-01

    Wouldn't it be great if there were a statistics book that made histograms, probability distributions, and chi square analysis more enjoyable than going to the dentist? Head First Statistics brings this typically dry subject to life, teaching you everything you want and need to know about statistics through engaging, interactive, and thought-provoking material, full of puzzles, stories, quizzes, visual aids, and real-world examples. Whether you're a student, a professional, or just curious about statistical analysis, Head First's brain-friendly formula helps you get a firm grasp of statistics

  3. Head first Ajax

    CERN Document Server

    Riordan, Rebecca M

    2008-01-01

    Ajax is no longer an experimental approach to website development, but the key to building browser-based applications that form the cornerstone of Web 2.0. Head First Ajax gives you an up-to-date perspective that lets you see exactly what you can do -- and has been done -- with Ajax. With it, you get a highly practical, in-depth, and mature view of what is now a mature development approach. Using the unique and highly effective visual format that has turned Head First titles into runaway bestsellers, this book offers a big picture overview to introduce Ajax, and then explores the use of ind

  4. Rocket injector head

    Science.gov (United States)

    Green, C. W., Jr. (Inventor)

    1968-01-01

    A high number of liquid oxygen and gaseous hydrogen orifices per unit area are provided in an injector head designed to give intimate mixing and more thorough combustion. The injector head comprises a main body portion, a cooperating plate member as a flow chamber for one propellant, a cooperating manifold portion for the second propellant, and an annular end plate for enclosing an annular propellant groove formed around the outer edge of the body. All the openings for one propellant are located at the same angle with respect to a radial plane to permit a short combustion chamber.

  5. Water-quality, bed-sediment, and biological data (October 2013 through September 2014) and statistical summaries of data for streams in the Clark Fork Basin, Montana

    Science.gov (United States)

    Dodge, Kent A.; Hornberger, Michelle I.

    2015-12-24

    Water, bed sediment, and biota were sampled in streams from Butte to near Missoula, Montana, as part of a monitoring program in the upper Clark Fork Basin of western Montana. The sampling program was led by the U.S. Geological Survey, in cooperation with the U.S. Environmental Protection Agency, to characterize aquatic resources in the Clark Fork Basin, with emphasis on trace elements associated with historic mining and smelting activities. Sampling sites were located on the Clark Fork and selected tributaries. Water samples were collected periodically at 20 sites from October 2013 through September 2014. Bed-sediment and biota samples were collected once at 14 sites during August 2014.

  6. Water-quality, bed-sediment, and biological data (October 2012 through September 2013) and statistical summaries of data for streams in the Clark Fork Basin, Montana

    Science.gov (United States)

    Dodge, Kent A.; Hornberger, Michelle I.; Dyke, Jessica

    2014-01-01

    Water, bed sediment, and biota were sampled in streams from Butte to near Missoula, Montana, as part of a monitoring program in the upper Clark Fork Basin of western Montana. The sampling program was led by the U.S. Geological Survey in cooperation with the U.S. Environmental Protection Agency to characterize aquatic resources in the Clark Fork Basin, with emphasis on trace elements associated with historic mining and smelting activities. Sampling sites were located on the Clark Fork and selected tributaries. Water samples were collected periodically at 20 sites from October 2012 through September 2013. Bed-sediment and biota samples were collected once at 13 sites during August 2013.

  7. Design and simulation of a tuning fork micromachined gyroscope with slide film damping

    Institute of Scientific and Technical Information of China (English)

    CHE Lu-feng; XIONG Bin; JIAO Ji-wei; WANG Yue-lin

    2005-01-01

    A novel tuning fork micromachined gyroscope, based on slide-film damping, is presented. The electrostatic driving gyroscope consists of two driving masses each of which supports one sensitive mass. The angular rate is sensed by the differential capacitances consisted of movable bar electrodes and fixed bar electrodes located on the glass wafer. The gyroscope can operate at atmospheric pressure with slide film damping in the driving and sensing directions, eliminate vacuum packaging and restrain cross-axis acceleration signal. The results of design and simulation show that the driving and sensing mode frequencies are 3 106 Hz and 3 175 Hz,respectively, and the Q-values in driving and sensitive modes are 1 721 and 1 450 respectively. The design resolution is 0.025°/s.

  8. Optimizing Data Locality for Fork/Join Programs Using Constrained Work Stealing

    Energy Technology Data Exchange (ETDEWEB)

    Lifflander, Jonathan; Krishnamoorthy, Sriram; Kale, Laxmikant

    2014-11-16

    We present an approach to improving data locality across different phases of fork/join programs scheduled using work stealing. The approach consists of: (1) user-specified and automated approaches to constructing a steal tree, the schedule of steal operations and (2) constrained work stealing algorithms that constrain the actions of the scheduler to mirror a given steal tree. These are combined to construct work stealing schedules that maximize data locality across computation phases while ensuring load balance within each phase. These algorithms are also used to demonstrate dynamic coarsening, an optimization to improve spatial locality and sequential overheads by combining many finer-grained tasks into coarser tasks while ensuring sufficient concurrency for locality-optimized load balance. Implementation and evaluation in Cilk demonstrate performance improvements of up to 2.5x on 80 cores. We also demonstrate that dynamic coarsening can combine the performance benefits of coarse task specification with the adaptability of finer tasks.

  9. South Fork Salmon River Watershed Restoration, 2008-2009 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    Reaney, Mark D. [Nez Perce Tribe Department of Fisheries Resource Management

    2009-04-15

    The watershed restoration work elements within the project area, the South Fork Salmon River Watershed, follow the watershed restoration approach adopted by the Nez Perce Tribe Department of Fisheries Resource Management (DFRM) - Watershed Division. The vision of the Nez Perce Tribe DFRM-Watershed Division focuses on protecting, restoring, and enhancing watersheds and treaty resources within the ceded territory of the Nez Perce Tribe under the Treaty of 1855 with the United States Federal Government. The program uses a holistic approach, which encompasses entire watersheds, ridge top to ridge top, emphasizing all cultural aspects and strategies that rely on natural fish production and healthy river ecosystems. The Nez Perce Tribe DFRM-Watershed Division strives towards maximizing historic ecosystem productivity and health for the restoration of anadromous and resident fish populations and the habitat on which all depend on for future generations Originally, this project was funded to create a step/pool stream channel that was appropriate to restore fish passage where the 'Glory Hole Cascade' is currently located at the Stibnite Mine. Due to unforeseen circumstances at the time, the project is unable to move forward as planned and a request for a change in scope of the project and an expansion of the geographic area in which to complete project work was submitted. No additional funds were being requested. The ultimate goal of this project is to work with the holistic, ridge top to ridge top approach to protect and restore the ecological and biological functions of the South Fork Salmon River Watershed to assist in the recovery of threatened and endangered anadromous and resident fish species. FY 2008 Work Elements included two aquatic organism passage (AOP) projects to restore habitat connectivity to two fish-bearing tributaries to the East Fork South Fork Salmon River, Salt and Profile Creeks. The Work Elements also included road survey and assessment

  10. Quartz enhanced photoacoustic spectroscopy based trace gas sensors using different quartz tuning forks.

    Science.gov (United States)

    Ma, Yufei; Yu, Guang; Zhang, Jingbo; Yu, Xin; Sun, Rui; Tittel, Frank K

    2015-03-27

    A sensitive trace gas sensor platform based on quartz-enhanced photoacoustic spectroscopy (QEPAS) is reported. A 1.395 μm continuous wave (CW), distributed feedback pigtailed diode laser was used as the excitation source and H2O was selected as the target analyte. Two kinds of quartz tuning forks (QTFs) with a resonant frequency (f0) of 30.72 kHz and 38 kHz were employed for the first time as an acoustic wave transducer, respectively for QEPAS instead of a standard QTF with a f0 of 32.768 kHz. The QEPAS sensor performance using the three different QTFs was experimentally investigated and theoretically analyzed. A minimum detection limit of 5.9 ppmv and 4.3 ppmv was achieved for f0 of 32.768 kHz and 30.72 kHz, respectively.

  11. Mercury Remediation Technology Development for Lower East Fork Poplar Creek - FY 2015 Progress Report

    Energy Technology Data Exchange (ETDEWEB)

    Peterson, Mark J. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Environmental Sciences Division; Brooks, Scott C. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Environmental Sciences Division; Mathews, Teresa J. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Environmental Sciences Division; Mayes, Melanie [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Environmental Sciences Division; Johs, Alexander [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Environmental Sciences Division; Watson, David B. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Environmental Sciences Division; Poteat, Monica D. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Smith, John [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Environmental Sciences Division; Mehlhorn, Tonia [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Environmental Sciences Division; Lester, Brian [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Environmental Sciences Division; Morris, Jesse [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Environmental Sciences Division; Lowe, Kenneth [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Environmental Sciences Division; Dickson, Johnbull O. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Eller, Virginia [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); DeRolph, Christopher R. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Environmental Sciences Division

    2016-04-01

    Mercury remediation is a high priority for the US Department of Energy (DOE) Oak Ridge Office of Environmental Management (OREM) because of large historical losses of mercury within buildings and to soils and surface waters at the Y-12 National Security Complex (Y-12). Because of the extent of mercury losses and the complexities of mercury transport and fate in the downstream environment, the success of conventional options for mercury remediation in lower East Fork Poplar Creek (EFPC) is uncertain. A phased, adaptive management approach to remediation of surface water includes mercury treatment actions at Y-12 in the short-term and research and technology development (TD) to evaluate longer-term solutions in the downstream environment (US Department of Energy 2014b).

  12. Chronology of Deformation Near the Iditarod-Nixon Fork Fault, West-Central Alaska

    Science.gov (United States)

    Perttu, B. K.; Wallace, W. K.; Newberry, R. J.; Layer, P. W.

    2010-12-01

    The Nixon Fork Mine is a Cu-Au deposit located 7 km south of the Iditarod-Nixon Fork (I-NF) fault. This fault strikes at ~060°, and can be traced for ~400 km, with a minimum dextral displacement of ~90 km. Proximity to the I-NF fault suggests it would be a dominant influence on deformation of the deposit, but the extent and timing of disruption are unknown. In order to reconstruct strain history and eventually understand structural evolution, we analyzed the orientations of geologic structures and dated representative K-bearing minerals and rocks. Felsic dikes, with 40Ar/39Ar ages of 69.6 ± 0.5 Ma and arc-type signatures, are cut by faults apparently related to the I-NF fault, but do not obviously cut such faults. Since no dikes are seen to cut faults, we know of no local fault motion prior to their intrusion. The northeast strike of the felsic dikes (n = 102; mean = 034° ± 10° ) requires σ3 oriented ~124°, at odds with the ~0° orientation inferred from the strike of the I-NF fault (~60°). The Nixon Fork pluton has approximately the same age and an overall elongation compatible with the felsic dikes. Mafic dikes, with 40Ar/39Ar ages of 62.8 ± 0.6 Ma, have within-plate signatures (average TiO2 = 2.48 wt%, Zr = 172 ppm, Nb = 58 ppm, Y = 25 ppm) and require a change in overall tectonic regime. Additionally, their north strike (n = 44; mean = 013° ± 10°) requires σ3 oriented ~103°, which is not compatible with σ3 (~0°) inferred from the right-lateral I-NF fault, and requires a different extension direction from the felsic dikes. We observed mafic dikes cut by faults with orientations compatible with right-lateral motion on the I-NF fault, and we propose that right-lateral motion on the I-NF fault began after mafic dike emplacement. Outcrop-scale fold axes trend north (n = 136; mean = 355° ± 10°). They are preferentially aligned perpendicular to the σ1 inferred for right-lateral motion on the I-NF fault and so are plausibly related to the I-NF fault

  13. Study on digital correlation demodulation technology of micro quartz tuning fork gyroscope

    Science.gov (United States)

    Zhang, Zhixiong; Feng, Lihui; Sun, Yu-Nan

    2010-11-01

    A signal demodulation scheme for micro quartz tuning fork gyroscope based on digital correlation demodulation technology is proposed. In the operation of quartz gyroscope the reference signal should be in the resonance state with steady amplitude and the reference signal should be in-phase and has the same frequency with the driving signal. The quartz gyroscope signal processing platform is designed on the foundation of DEC6713 DSP development board successfully. The adaptive algorithm including the reference signal frequency tacking, the amplitude automatic gain controlling, the reference signal phase locking, and complex correlation demodulation are devised, and the algorithm is programmed. It is proved that the digital signal process scheme is feasible by means of experimentation.

  14. Streaming flow due to a quartz tuning fork oscillating in normal and superfluid 4He

    Science.gov (United States)

    Duda, D.; La Mantia, M.; Skrbek, L.

    2017-07-01

    We visualize the streaming flow due to a rapidly oscillating quartz tuning fork, in both normal He I and superfluid He II, by following the flow-induced motions of relatively small particles suspended in the liquid. Over the investigated temperature range, between 1.2 and 2.3 K, at the experimentally probed length scales, the streaming patterns observed in He II appear identical to those seen in He I and are very similar to those reported to occur in water, outside the Stokes boundary layer. The outcome strongly supports the view that, at scales larger than the quantum length scale of the flow, the mean distance between quantized vortices, mechanically forced turbulent coflows of He II behave classically, due to the dynamical locking of the two components of superfluid 4He by the action of the mutual friction force.

  15. Water quality and streamflow data for the West Fork Trinity River in Forth Worth, Texas

    Science.gov (United States)

    McCutcheon, S.C.

    1985-01-01

    Water-quality data were collected on a 13.6-mile reach of the West Fork Trinity River in Fort Worth, Texas to test a dynamic Lagrangian model. Flow was steady. Loads of dissolved constituents varied with time at the beginning of the study reach and in the reach, primarily because of photosynthesis. River quality was fairly good despite low dissolved oxygen measured in the headwaters and the significant sewage load from the tributaries. Diel and longitudinal trends were defined by sampling at fixed sites and by following dyed parcels of water. Nitrification, deoxygenation, reaeration, and photosynthesis affected the dissolved oxygen balance. Independent estimates of some of the rate coefficients were 0.1 to 0.2, 0.8, and 0 to 3.6 , all per day, for deoxygenation, nitrification, and reaeration, respectively. (USGS)

  16. Flow regimes of the superfluid helium caused by oscillating quartz tuning fork

    Energy Technology Data Exchange (ETDEWEB)

    Chagovets, V; Gritsenko, I; Rudavskii, E; Sheshin, G; Zadorozhko, A; Verkin, B [Institute for Low Temperature Physics and Engineering 47 Lenin Ave., Kharkov 61103 (Ukraine)], E-mail: sheshin@ilt.kharkov.ua

    2009-02-01

    The laminar-turbulent flow transition in HeII was studied with an oscillating quartz tuning fork. At temperatures from 200 mK to 3.0 K a current-voltage characteristic were recorded with varying driving voltage from 10{sup -5} to 10 V. A resonance frequency and a width of the resonance curve were also registered. It is found that at temperatures below {approx} 0.8 K the laminar-turbulent transition proceeds through an intermediate region clearly seen in the current - voltage characteristic curves. In this case the resonance curve changes in its shape - there appears a plateau near the maximum. An increase in the resonance curve width suggests the existence of excess dissipation related to the generation of quantized vortices in HeII in the vicinity of the oscillating surface. Estimation of the possible size of the vortices may suggest that these are generated on the oscillating surface roughness.

  17. Ultrafine anaphase bridges, broken DNA and illegitimate recombination induced by a replication fork barrier

    Science.gov (United States)

    Sofueva, Sevil; Osman, Fekret; Lorenz, Alexander; Steinacher, Roland; Castagnetti, Stefania; Ledesma, Jennifer; Whitby, Matthew C.

    2011-01-01

    Most DNA double-strand breaks (DSBs) in S- and G2-phase cells are repaired accurately by Rad51-dependent sister chromatid recombination. However, a minority give rise to gross chromosome rearrangements (GCRs), which can result in disease/death. What determines whether a DSB is repaired accurately or inaccurately is currently unclear. We provide evidence that suggests that perturbing replication by a non-programmed protein–DNA replication fork barrier results in the persistence of replication intermediates (most likely regions of unreplicated DNA) into mitosis, which results in anaphase bridge formation and ultimately to DNA breakage. However, unlike previously characterised replication-associated DSBs, these breaks are repaired mainly by Rad51-independent processes such as single-strand annealing, and are therefore prone to generate GCRs. These data highlight how a replication-associated DSB can be predisposed to give rise to genome rearrangements in eukaryotes. PMID:21576223

  18. Nanocharacterization of soft biological samples in shear mode with quartz tuning fork probes.

    Science.gov (United States)

    Otero, Jorge; Gonzalez, Laura; Puig-Vidal, Manel

    2012-01-01

    Quartz tuning forks are extremely good resonators and their use is growing in scanning probe microscopy. Nevertheless, only a few studies on soft biological samples have been reported using these probes. In this work, we present the methodology to develop and use these nanosensors to properly work with biological samples. The working principles, fabrication and experimental setup are presented. The results in the nanocharacterization of different samples in different ambients are presented by using different working modes: amplitude modulation with and without the use of a Phase-Locked Loop (PLL) and frequency modulation. Pseudomonas aeruginosa bacteria are imaged in nitrogen using amplitude modulation. Microcontact printed antibodies are imaged in buffer using amplitude modulation with a PLL. Finally, metastatic cells are imaged in air using frequency modulation.

  19. Nanocharacterization of Soft Biological Samples in Shear Mode with Quartz Tuning Fork Probes

    Directory of Open Access Journals (Sweden)

    Manel Puig-Vidal

    2012-04-01

    Full Text Available Quartz tuning forks are extremely good resonators and their use is growing in scanning probe microscopy. Nevertheless, only a few studies on soft biological samples have been reported using these probes. In this work, we present the methodology to develop and use these nanosensors to properly work with biological samples. The working principles, fabrication and experimental setup are presented. The results in the nanocharacterization of different samples in different ambients are presented by using different working modes: amplitude modulation with and without the use of a Phase-Locked Loop (PLL and frequency modulation. Pseudomonas aeruginosa bacteria are imaged in nitrogen using amplitude modulation. Microcontact printed antibodies are imaged in buffer using amplitude modulation with a PLL. Finally, metastatic cells are imaged in air using frequency modulation.

  20. Waste management plan for the Lower East Fork Poplar Creek Operable Unit, Oak Ridge, Tennessee

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1996-04-01

    The Lower East Fork Poplar Creek (LEFPC) Remedial Action project will remove mercury-contaminated soils from the floodplain of LEFPC, dispose of these soils at the Y-12 Plant Landfill V, and restore the affected floodplain. The waste management plan addresses management and disposition of all wastes generated during the LEFPC remedial action. Most of the solid wastes will be sanitary or construction/demolition wastes and will be disposed of at existing Y- 12 facilities. Some small amounts of hazardous waste are anticipated, along with possible low-level or mixed wastes (> 35 pCi/g). Liquid wastes will be generated which will be sanitary and capable of being disposed of at the Oak Ridge Sewage Treatment Plant, except sanitary sewage.

  1. 水稻类树状突变体s2-21的遗传分析与精细定位%Genetic Analysis and Gene Fine Mapping of Rice Leafy Head Mutant s2-21

    Institute of Scientific and Technical Information of China (English)

    王海凤; 高洁; 孙伟; 张士永; 赵庆雷; 尹亮; 赵金凤; 李学勇; 袁守江

    2014-01-01

    叶序和出叶间隔期是叶片生长发育的基本生物学特性和水稻的重要农艺性状之一。对叶序或出叶间隔期突变体的研究,可以帮助我们了解叶片的形成机制。本研究通过甲基磺酸乙酯(EMS)诱变粳稻品种日本晴,获得一个稳定遗传的类树状突变体s2-21。该突变体出叶间隔期变短、节间缩短、植株矮化、分蘖数减少、叶片数增加、不能正常进行生殖生长。将该突变体与籼稻品种Dular杂交,遗传分析表明该突变体性状受1对隐性基因控制。通过InDel分子标记对s2-21/Dular F2群体进行遗传定位,将该基因初步定位在第1染色体InDel标记C1-15和S1-17之间。利用本实验已测序的籼稻品种Dular全基因组序列与NCBI (http://www.ncbi.nlm.nih.gov/)上提供的粳稻品种日本晴基因组序列比对,开发了6个新的InDel标记,最终将该基因定位在W25和W26之间约88 kb的区间内。测序结果表明该突变体中PLA2基因的第4个内含子的第5位碱基由G突变为A。%Phyllotaxy and plastochron are basic aspects of leaf development and the important agronomic traits of rice. The study of phyllotaxy or plastochron mutant will help us to understand the mechanism of leaf formation. In this study, a leafy head mutant s2-21 was isolated from an EMS (ethyl methane sulfonate) mutagenized japonica cultivar Nipponbare. It was characterized by shorter intervals between leaves, shortened internodes, dwarf plants, decreased tiller number, and increased leaf number. It was also unable to transit from vegetative to reproductive growth. Genetic analysis with a F2 population of the mutant and an indica cultivar Dular showed that this trait is controlled by a single recessive nucleus gene, which was primarily mapped between two insertion-deletion (InDel) markers C1-15 and S1-17 on chromosome 1. For the fine mapping, new InDel markers were designed by utilizing information of genomic sequences from

  2. Constraints to microbial food safety policy: opinions from stakeholder groups along the farm to fork continuum.

    Science.gov (United States)

    Sargeant, J M; Ramsingh, B; Wilkins, A; Travis, R G; Gavrus, D; Snelgrove, J W

    2007-01-01

    This exploratory qualitative study was conducted to identify constraints to microbial food safety policy in Canada and the USA from the perspective of stakeholder groups along the farm to fork continuum. Thirty-seven stakeholders participated in interviews or a focus group where semi-structured questions were used to facilitate discussion about constraints to policy development and implementation. An emergent grounded theory approach was used to determine themes and concepts that arose from the data (versus fitting the data to a hypothesis or a priori classification). Despite the plurality of stakeholders and the range of content expertise, participant perceptions emerged into five common themes, although, there were often disagreements as to the positive or negative attributes of specific concepts. The five themes included challenges related to measurement and objectives of microbial food safety policy goals, challenges arising from lack of knowledge, or problems with communication of knowledge coupled with current practices, beliefs and traditions; the complexity of the food system and the plurality of stakeholders; the economics of producing safe food and the limited resources to address the problem; and, issues related to decision-making and policy, including ownership of the problem and inappropriate inputs to the decision-making process. Responsibilities for food safety and for food policy failure were attributed to all stakeholders along the farm to fork continuum. While challenges regarding the biology of food safety were identified as constraints, a broader range of policy inputs encompassing social, economic and political considerations were also highlighted as critical to the development and implementation of effective food safety policy. Strategies to address these other inputs may require new, transdisciplinary approaches as an adjunct to the traditional science-based risk assessment model.

  3. Characterization of ecological risks at the Milltown Reservoir-Clark Fork River Sediments Superfund Site, Montana

    Science.gov (United States)

    Pascoe, Gary A.; Blanchet, Richard J.; Linder, Greg L.; Palawski, Don; Brumbaugh, William G.; Canfield, Tim J.; Kemble, Nile E.; Ingersoll, Chris G.; Farag, Aïda M.; DalSoglio, Julie A.

    1994-01-01

    A comprehensive field and laboratory approach to the ecological risk assessment for the Milltown Reservoir-Clark Fork River Sediments Site, a Superfund site in the Rocky Mountains of Montana, has been described in the preceding reports of this series. The risk assessment addresses concerns over the ecological impacts of upstream releases of mining wastes to fisheries of the upper Clark Fork River (CFR) and the benthic and terrestrial habitats further downstream in Milltown Reservoir. The risk characterization component of the process integrated results from a triad of information sources: (a) chemistry studies of environmental media to identify and quantify exposures of terrestrial and aquatic organisms to site-related contaminants; (b) ecological or population studies of terrestrial vegetation, birds, benthic communities, and fish; and (c) in situ and laboratory toxicity studies with terrestrial and aquatic invertebrates and plants, small mammals, amphibians, and fish exposed to contaminated surface water, sediments, wetland soils, and food sources. Trophic transfer studies were performed on waterfowl, mammals, and predatory birds using field measurement data on metals concentrations in environmental media and lower trophic food sources. Studies with sediment exposures were incorporated into the Sediment Quality Triad approach to evaluate risks to benthic ecology. Overall results of the wetland and terrestrial studies suggested that acute adverse biological effects were largely absent from the wetland; however, adverse effects to reproductive, growth, and physiological end points of various terrestrial and aquatic species were related to metals exposures in more highly contaminated depositional areas. Feeding studies with contaminated diet collected from the upper CFR indicated that trout are at high risk from elevated metals concentrations in surface water, sediment, and aquatic invertebrates. Integration of chemical analyses with toxicological and ecological

  4. Orbital angular momentum generation and mode transformation with high efficiency using forked polarization gratings.

    Science.gov (United States)

    Li, Yanming; Kim, Jihwan; Escuti, Michael J

    2012-12-01

    We present a novel optical element that efficiently generates orbital angular momentum (OAM) of light and transforms light between OAM modes based on a polarization grating with a fork-shaped singularity. This forked polarization grating (FPG) is composed of liquid crystalline materials, and can be made either static or switchable with high diffraction efficiency (i.e., 100% theoretically) into a single order. By spatially varying the Pancharatnam-Berry phase, FPGs shape the wavefront and thus control the OAM mode. We demonstrate theoretically and empirically that a charge l(g) FPG creates helical modes with OAM charge ±l(g) when a gaussian beam is input, and more generally, transforms the incident helical mode with OAM charge l(in) into output modes with OAM charge l(in)±l(g). We also show for the first time that this conversion into a single mode can be very efficient (i.e., ∼95% experimentally) at visible wavelengths, and the relative power between the two possible output modes is polarization-controllable from 0% to ∼100%. We developed a fabrication method that substantially improves FPG quality and efficiency over prior work. We also successfully fabricated switchable FPGs, which can be electrically switched between an OAM generating/transforming state and a transmissive state. Our experimental results showed >92% conversion efficiency for both configurations at 633 nm. These holographically fabricated elements are compact (i.e., thin glass plates), lightweight, and easily optimized for nearly any wavelength from ultraviolet to infrared, for a wide range of OAM charge, and for large or small clear apertures. They are ideal elements for enhanced control of OAM, e.g., in optical trapping and high-capacity information.

  5. Tectonic controls on large landslide complex: Williams Fork Mountains near Dillon, Colorado

    Science.gov (United States)

    Kellogg, K.S.

    2001-01-01

    An extensive (~ 25 km2) landslide complex covers a large area on the west side of the Williams Fork Mountains in central Colorado. The complex is deeply weathered and incised, and in most places geomorphic evidence of sliding (breakaways, hummocky topography, transverse ridges, and lobate distal zones) are no longer visible, indicating that the main mass of the slide has long been inactive. However, localized Holocene reactivation of the landslide deposits is common above the timberline (at about 3300 m) and locally at lower elevations. Clasts within the complex, as long as several tens of meters, are entirely of crystalline basement (Proterozoic gneiss and granitic rocks) from the hanging wall of the Laramide (Late Cretaceous to Early Tertiary), west-directed Williams Range thrust, which forms the western structural boundary of the Colorado Front Range. Late Cretaceous shale and sandstone compose most footwall rocks. The crystalline hanging-wall rocks are pervasively fractured or shattered, and alteration to clay minerals is locally well developed. Sackung structures (trenches or small-scale grabens and upslope-facing scarps) are common near the rounded crest of the range, suggesting gravitational spreading of the fractured rocks and oversteepening of the mountain flanks. Late Tertiary and Quaternary incision of the Blue River Valley, just west of the Williams Fork Mountains, contributed to the oversteepening. Major landslide movement is suspected during periods of deglaciation when abundant meltwater increased pore-water pressure in bedrock fractures. A fault-flexure model for the development of the widespread fracturing and weakening of the Proterozoic basement proposes that the surface of the Williams Range thrust contains a concave-downward flexure, the axis of which coincides approximately with the contact in the footwall between Proterozoic basement and mostly Cretaceous rocks. Movement of brittle, hanging-wall rocks through the flexure during Laramide

  6. Heading in soccer: dangerous play?

    Science.gov (United States)

    Spiotta, Alejandro M; Bartsch, Adam J; Benzel, Edward C

    2012-01-01

    Soccer is the world's most popular sport and unique in that players use their unprotected heads to intentionally deflect, stop, or redirect the ball for both offensive and defensive strategies. Headed balls travel at high velocity pre- and postimpact. Players, coaches, parents, and physicians are justifiably concerned with soccer heading injury risk. Furthermore, risk of long-term neurocognitive and motor deficits caused by repetitively heading a soccer ball remains unknown. We review the theoretical concerns, the results of biomechanical laboratory experiments, and the available clinical data regarding the effects of chronic, subconcussive head injury during heading in soccer.

  7. Computed Tomography (CT) -- Head

    Medline Plus

    Full Text Available ... are present in the paranasal sinuses. plan radiation therapy for cancer of the brain or other tissues. guide the ... RTAnswers.org Radiation Therapy for Brain Tumors Radiation Therapy for Head and Neck Cancer Others American Stroke Association National Stroke Association top ...

  8. Head space analysis

    NARCIS (Netherlands)

    Stekelenburg, G.J. van; Koorevaar, G.

    Additional analytical information is given about the method of head space analysis. From the data presented it can be concluded that this technique may be advantageous for enzyme kinetic studies in turbid solutions, provided a volatile organic substance is involved in the chemical reaction. Also

  9. Sculpting Ceramic Heads.

    Science.gov (United States)

    Sapiro, Maurice

    1983-01-01

    Clay sculpture is difficult to produce because of the requirements of kiln firing. The problems can be overcome by modeling the original manikin head and making a plaster mold, pressing molding slabs of clay into the plaster mold to form the hollow clay armature, and sculpting on the armature. (IS)

  10. Lubricating the swordfish head

    NARCIS (Netherlands)

    Videler, John J.; Haydar, Deniz; Snoek, Roelant; Hoving, Henk-Jan T.; Szabo, Ben G.

    2016-01-01

    The swordfish is reputedly the fastest swimmer on Earth. The concave head and iconic sword are unique characteristics, but how they contribute to its speed is still unknown. Recent computed tomography scans revealed a poorly mineralised area near the base of the rostrum. Here we report, using magnet

  11. Prognosis in head injury.

    Science.gov (United States)

    Jane, J A; Rimel, R W

    1982-01-01

    The prognosis of head injury when viewed from the perspective of the Glasgow Coma Scale confirms the utility of this measure. In particular, decrease in mortality is associated with an increase in GCS. In addition, the motor score portion of the GCS was of predictive value when taken alone. The outcome of patients in coma (GCS less than 8) was closely related to three preventable or treatable factors, namely, hypoxia, shock, and increased intracranial pressure. These three factors, when considered in combination, powerfully predicted mortality. Of considerable interest was the finding that moderate head injury (GCS 9-12) was associated with a small but perhaps preventable mortality. The morbidity was intermediate between that of severe and minor and was surprisingly high. Minor head injury, while not associated with significant mortality, also resulted in considerable morbidity. Neuropsychological evaluation of the patients and an experimental study suggests that an organic component may be involved even in this group. To deal with head injury, distinctions must be made between grades of severity. The Glasgow Coma Scale is suited for this task. Nonetheless, the recognition of this basic continuity should elicit the further recognition that different health providers may be involved in the case of, say, severe, as opposed to mild, injury, and that different outcome measures are suitable for one group but not another.

  12. Mass loading of selected major and trace elements in Lake Fork Creek near Leadville, Colorado, September-October 2001

    Science.gov (United States)

    Walton-Day, Katherine; Flynn, Jennifer L.; Kimball, Briant A.; Runkel, Robert L.

    2005-01-01

    A mass-loading study of Lake Fork Creek of the Arkansas River between Sugarloaf Dam and the mouth was completed in September-October 2001 to help ascertain the following: (1) variation of pH and aqueous constituent concentrations (calcium, sulfate, alkalinity, aluminum, cadmium, copper, iron, manganese, lead, and zinc) and their relation to toxicity standards along the study reach; (2) location and magnitude of sources of metal loading to Lake Fork Creek; (3) amount and locations of metal attenuation; (4) the effect of streamside wetlands on metal transport from contributing mine tunnels; and (5) the effect of organic-rich inflow from the Leadville National Fish Hatchery on water quality in Lake Fork Creek. The study was done in cooperation with the Bureau of Land Management, U.S. Department of Agriculture Forest Service, and U.S. Fish and Wildlife Service. Constituent concentrations and pH showed variable patterns over the study reach. Hardness-based acute and chronic toxicity standards were exceeded for some inflows and some constituents. However, stream concentrations did not exceed standards except for zinc starting in the upper parts of the study reach and extending to just downstream from the inflow from the Leadville National Fish Hatchery. Dilution from that inflow lowered stream zinc concentrations to less than acute and chronic toxicity standards. The uppermost 800 meters of the study reach that contained inflow from the Bartlett, Dinero, and Nelson mine tunnels and the Dinero wetland was the greatest source of loading for manganese and zinc. A middle section of the study reach that extended approximately 2 kilometers upstream from the National Fish Hatchery inflow to just downstream from that inflow was the largest source of aluminum, copper, iron, and lead loading. The loading was partially from the National Fish Hatchery inflow but also from unknown sources upstream from that inflow, possibly ground water. The largest sources for calcium and sulfate

  13. Water-quality trends for selected sampling sites in the upper Clark Fork Basin, Montana, water years 1996-2010

    Science.gov (United States)

    Sando, Steven K.; Vecchia, Aldo V.; Lorenz, David L.; Barnhart, Elliott P.

    2014-01-01

    A large-scale trend analysis was done on specific conductance, selected trace elements (arsenic, cadmium, copper, iron, lead, manganese, and zinc), and suspended-sediment data for 22 sites in the upper Clark Fork Basin for water years 1996–2010. Trend analysis was conducted by using two parametric methods: a time-series model (TSM) and multiple linear regression on time, streamflow, and season (MLR). Trend results for 1996–2010 indicate moderate to large decreases in flow-adjusted concentrations (FACs) and loads of copper (and other metallic elements) and suspended sediment in Silver Bow Creek upstream from Warm Springs. Deposition of metallic elements and suspended sediment within Warm Springs Ponds substantially reduces the downstream transport of those constituents. However, mobilization of copper and suspended sediment from floodplain tailings and stream banks in the Clark Fork reach from Galen to Deer Lodge is a large source of metallic elements and suspended sediment, which also affects downstream transport of those constituents. Copper and suspended-sediment loads mobilized from within this reach accounted for about 40 and 20 percent, respectively, of the loads for Clark Fork at Turah Bridge (site 20); whereas, streamflow contributed from within this reach only accounted for about 8 percent of the streamflow at Turah Bridge. Minor changes in FACs and loads of copper and suspended sediment are indicated for this reach during 1996–2010. Clark Fork reaches downstream from Deer Lodge are relatively smaller sources of metallic elements than the reach from Galen to Deer Lodge. In general, small decreases in loads and FACs of copper and suspended sediment are indicated for Clark Fork sites downstream from Deer Lodge during 1996–2010. Thus, although large decreases in FACs and loads of copper and suspended sediment are indicated for Silver Bow Creek upstream from Warm Springs, those large decreases are not translated to the more downstream reaches largely

  14. Head injuries, heading, and the use of headgear in soccer.

    Science.gov (United States)

    Niedfeldt, Mark W

    2011-01-01

    Soccer has more than 265 million players around the world and is the only contact sport with purposeful use of the head for controlling and advancing the ball. Head contact in soccer has the potential to cause acute traumatic brain injury including concussion or, potentially, a pattern of chronic brain injury. Although early retrospective research on the effects of soccer heading seemed to suggest that purposeful heading may contribute to long-term cognitive impairment, prospective controlled studies do not support this and, in fact, suggest that purposeful heading may not be a risk factor for cognitive impairment. Headgear has not been shown to be effective in reducing ball impact but may be helpful in reducing the force of non-ball-related impacts to the head. There are concerns that universal use of headgear may cause more aggressive heading and head challenges, leading to increased risk of injury.

  15. Análise dos genes GSTM1 e GSTT1 em pacientes com câncer de cabeça e pescoço GSTM1 and GSTT1 genes analysis in head and neck cancer patients

    Directory of Open Access Journals (Sweden)

    Cássia Veridiana Dourado Leme

    2010-01-01

    Full Text Available OBJETIVO: Estabelecer o perfil clínico e demográfico bem como identificar os fatores de risco entre os pacientes com câncer de cabeça e pescoço e relacioná-los ao polimorfismo dos genes GSTT1 e GSTM1. MÉTODOS: Foram estudados 100 pacientes com carcinoma espinocelular de cabeça e pescoço e 100 indivíduos sem história de neoplasia. A análise molecular foi realizada pela técnica de PCR multiplex. Para a análise estatística, os dados foram tabulados e comparados pelo teste exato de Fisher. Foi também utilizado o teste do Qui quadrado e de regressão logística múltipla. RESULTADOS: Há predomínio de indivíduos tabagistas (OR= 5,32; IC95%= 2,04-13,86; p=0,0006, etilistas (OR= 5,04; IC95%= 2,19-11,59; p= 0,0001 em pacientes com neoplasia de cabeça e pescoço. Foi identificado genótipo nulo do gene GSTT1 em 47% dos pacientes e 41% dos controles (OR= 0,67; IC 95%= 0,34-1,35; p= 0,2648. Da mesma forma, identificou-se o genótipo nulo do gene GSTM1 em 66% dos pacientes e 75% dos controles (OR= 2,25; IC95%= 1,05-4,84; p= 0,0368. A análise dos genótipos combinados demonstrou associação entre GSTM1*0/GSTT1 e a ocorrência de carcinoma de cabeça e pescoço (OR= 7,64; IC 95%= 1,72-34,04; p= 0,0076. A análise dos parâmetros clínicos mostrou que é possível identificar associação entre genótipo GSTT1 nulo e neoplasia na laringe, o inverso ocorrendo com este genótipo e a faringe. CONCLUSÃO: Em nosso estudo foi possível estabelecer a associação entre a nulidade do genótipo GSTM1 e dos genótipos combinados GSTT1/GSTM1 *0 ([ ] / [-] a ocorrência de câncer de cabeça e pescoço.OBJECTIVE: To establish the clinical and demographic profile and identify risk factors among patients with head and neck cancer and relate them to the polymorphism of GSTT1 and GSTM1. METHODS: One hundred patients with head and neck cancer and 100 control group individuals without history of neoplasm were analyzed. . The molecular analysis were made by

  16. SIR2016-5029_cfwgoshOR: Flood-Inundation Maps for the Coast Fork Willamette River from Creswell, Oregon to Goshen, Oregon

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — This feature class represents inundated area for the Coast Fork of the Willamette River, the Row River and Silk Creek (west of Cottage Grove, OR) for eight different...

  17. sir2016-5029_Low_Res_Extents: Flood-Inundation Maps for the Coast Fork Willamette River from Creswell, Oregon to Goshen, Oregon

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — The Digital Elevation Model (DEM) utilized for this Willamette FIS submittal was produced by combining multiple overlapping topographic surveys for the Middle Fork...

  18. Analysis of white-tailed deer (Odocoileus virginianus) camera survey data on Deep Fork National Wildlife Refuge, 2012-2103 final report

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report summarizes justification, methods, and results for white-tailed deer camera surveys conducted on Deep Fork National Wildlife Refuge during late summer of...

  19. sir2016-5029_Hi_Res_Extents: Flood-Inundation Maps for the Coast Fork Willamette River from Creswell, Oregon to Goshen, Oregon

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — The Digital Elevation Model (DEM) utilized for this Willamette FIS submittal was produced by combining multiple overlapping topographic surveys for the Middle Fork...

  20. SIR2016-5029_cfwgoshOR_breach: Flood-Inundation Maps for the Coast Fork Willamette River from Creswell, Oregon to Goshen, Oregon (Area of Uncertainty)

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — This feature class represents inundated area for the Coast Fork of the Willamette River, the Row River and Silk Creek (west of Cottage Grove, OR) for eight different...

  1. Magnetic Resonance Imaging (MRI) -- Head

    Medline Plus

    Full Text Available ... content. Related Articles and Media MR Angiography (MRA) Magnetic Resonance, Functional (fMRI) - Brain Head and Neck Cancer Treatment Brain Tumor Treatment Magnetic Resonance Imaging (MRI) Safety Alzheimer's Disease Head Injury Brain ...

  2. Head Lice: Prevention and Control

    Science.gov (United States)

    ... Diseases Laboratory Diagnostic Assistance [DPDx] Parasites Home Prevention & Control Language: English Español (Spanish) Recommend on Facebook Tweet ... that can be taken to help prevent and control the spread of head lice: Avoid head-to- ...

  3. Head and Neck Cancer Treatment

    Science.gov (United States)

    ... Professions Site Index A-Z Head and Neck Cancer Treatment Head and neck cancer overview What are my ... and neck cancer. For updated information on new cancer treatments that are available, you should discuss these issues ...

  4. Magnetic Resonance Imaging (MRI) -- Head

    Medline Plus

    Full Text Available ... to remain perfectly still and follow breath-holding instructions while the images are being recorded. If you ... Images related to Magnetic Resonance Imaging (MRI) - Head Videos related to Magnetic Resonance Imaging (MRI) - Head Sponsored ...

  5. Magnetic Resonance Imaging (MRI) -- Head

    Medline Plus

    Full Text Available ... the limitations of MRI of the Head? What is MRI of the Head? Magnetic resonance imaging (MRI) ... ray, CT and ultrasound. top of page How is the procedure performed? MRI examinations may be performed ...

  6. Head and Neck Cancer Treatment

    Science.gov (United States)

    ... oncologist will listen to the history of your problem and perform a physical examination. Consultations with other members of the head and neck team, such as the head and neck surgeon, pathologist, ...

  7. Sports-related Head Injury

    Science.gov (United States)

    ... difficulty expressing words or thoughts; dysarthric speech Head Injury Prevention Tips Buy and use helmets or protective head gear approved by the ASTM for specific sports 100 percent of the time. The ASTM has ...

  8. Preventing head injuries in children

    Science.gov (United States)

    Concussion - preventing in children; Traumatic brain injury - preventing in children; TBI - children; Safety - preventing head injury ... Helmets help to prevent head injuries. Your child should wear a ... sports or activities: Playing contact sports, such as lacrosse, ...

  9. Water temperature effects from simulated dam operations and structures in the Middle Fork Willamette River, western Oregon

    Science.gov (United States)

    Buccola, Norman L.; Turner, Daniel F.; Rounds, Stewart A.

    2016-09-14

    Significant FindingsStreamflow and water temperature in the Middle Fork Willamette River (MFWR), western Oregon, have been regulated and altered since the construction of Lookout Point, Dexter, and Hills Creek Dams in 1954 and 1961, respectively. Each year, summer releases from the dams typically are cooler than pre-dam conditions, with the reverse (warmer than pre-dam conditions) occurring in autumn. This pattern has been detrimental to habitat of endangered Upper Willamette River (UWR) Chinook salmon (Oncorhynchus tshawytscha) and UWR winter steelhead (O. mykiss) throughout multiple life stages. In this study, scenarios testing different dam-operation strategies and hypothetical dam-outlet structures were simulated using CE-QUAL-W2 hydrodynamic/temperature models of the MFWR system from Hills Creek Lake (HCR) to Lookout Point (LOP) and Dexter (DEX) Lakes to explore and understand the efficacy of potential flow and temperature mitigation options.Model scenarios were run in constructed wet, normal, and dry hydrologic calendar years, and designed to minimize the effects of Hills Creek and Lookout Point Dams on river temperature by prioritizing warmer lake surface releases in May–August and cooler, deep releases in September–December. Operational scenarios consisted of a range of modified release rate rules, relaxation of power-generation constraints, variations in the timing of refill and drawdown, and maintenance of different summer maximum lake levels at HCR and LOP. Structural scenarios included various combinations of hypothetical floating outlets near the lake surface and hypothetical new outlets at depth. Scenario results were compared to scenarios using existing operational rules that give temperature management some priority (Base), scenarios using pre-2012 operational rules that prioritized power generation over temperature management (NoBlend), and estimated temperatures from a without-dams condition (WoDams).Results of the tested model scenarios led

  10. "Head versus heart"

    Directory of Open Access Journals (Sweden)

    Paul Rozin

    2007-08-01

    Full Text Available Most American respondents give ``irrational,'' magical responses in a variety of situations that exemplify the sympathetic magical laws of similarity and contagion. In most of these cases, respondents are aware that their responses (usually rejections, as of fudge crafted to look like dog feces, or a food touched by a sterilized, dead cockroach are not ``scientifically'' justified, but they are willing to avow them. We interpret this, in some sense, as ``heart over head.'' We report in this study that American adults and undergraduates are substantially less likely to acknowledge magical effects when the judgments involve money (amount willing to pay to avoid an ``unpleasant'' magical contact than they are when using preference or rating measures. We conclude that in ``head-heart'' conflicts of this type, money tips the balance towards the former, or, in other words, that money makes the mind less magical.

  11. "Head versus heart"

    OpenAIRE

    2007-01-01

    Most American respondents give ``irrational,'' magical responses in a variety of situations that exemplify the sympathetic magical laws of similarity and contagion. In most of these cases, respondents are aware that their responses (usually rejections, as of fudge crafted to look like dog feces, or a food touched by a sterilized, dead cockroach) are not ``scientifically'' justified, but they are willing to avow them. We interpret this, in some sense, as ``heart over head.'' We report in this ...

  12. Dissection of Genetic Mechanism of Abnormal Heading in Hybrid Rice

    Institute of Scientific and Technical Information of China (English)

    ZHANG Hong-jun; QU Li-jun; XIANG Chao; WANG Hui; XIA Jia-fa; LI Ze-fu; GAO Yong-ming; SHI Ying-yao

    2014-01-01

    Abnormal heading in hybrid rice production has caused great economic loss in recent years, but the genetic basis of this phenomenon remains elusive. In this study, we developed four testcross populations using 38 introgression lines (ILs) from Shuhui 527 (SH527)/Fuhui 838 (FH838)//SH527 population as male parents and four male sterile lines (MSLs; namely II-32A, Xieqingzao A, Gang 46A and Jin 23A) as female parents. Progeny testing allowed us to identify 55 abnormal heading combinations in Hefei, but had late heading date in Hangzhou and Guangzhou of China. By one-and two-way analysis of variance, a total of 21 QTLs and 31 pairs of epistatic QTLs associated with photosensitivity were identified in the four populations, respectively. Genotypic analysis showed that the IL parent of most abnormal heading combinations showed some introgressions at markers RM331 and RM3395 on chromosome 8 (strongly associated with the known genes OsHAP3H/DTH8/Ghd8/LHD1) of donor FH838 alleles, and these two markers were also identified as affecting photosensitivity. The observation that the recipient parent (SH527), donor parent (FH838), their testcross combinations with four MSLs, and the IL parents of abnormal heading combinations had normal heading date in Hefei suggested that OsHAP3H/DTH8/Ghd8/LHD1 showed no independent regulation on abnormal heading in the abnormal heading combinations. It is noteworthy that complex epistasis among RM331 or RM3395 with other loci, including dominant × additive, additive × dominant, and dominant × dominant epistases, were identified only in the four testcross populations of the current study, but not in the SH527/FH838//SH527 population, suggesting the cause of abnormal heading in abnormal heading combinations in Hefei and delayed heading in Hangzhou and Guangzhou.

  13. Environmental settings of the South Fork Iowa River basin, Iowa, and the Bogue Phalia basin, Mississippi, 2006-10

    Science.gov (United States)

    McCarthy, Kathleen A.; Rose, Claire E.; Kalkhoff, Stephen J.

    2012-01-01

    Studies of the transport and fate of agricultural chemicals in different environmental settings were conducted by the U.S. Geological Survey (USGS) National Water-Quality Assessment (NAWQA) Program's Agricultural Chemicals Team (ACT) at seven sites across the Nation, including the South Fork Iowa River basin in central Iowa and the Bogue Phalia basin in northwestern Mississippi. The South Fork Iowa River basin is representative of midwestern agriculture, where corn and soybeans are the predominant crops and a large percentage of the cultivated land is underlain by artificial drainage. The Bogue Phalia basin is representative of corn, soybean, cotton, and rice cropping in the humid, subtropical southeastern United States. Details of the environmental settings of these basins and the data-collection activities conducted by the USGS ACT over the 2006-10 study period are described in this report.

  14. Excess Cdt1 inhibits nascent strand elongation by repressing the progression of replication forks in Xenopus egg extracts.

    Science.gov (United States)

    Nakazaki, Yuta; Tsuyama, Takashi; Seki, Masayuki; Takahashi, Mikiko; Enomoto, Takemi; Tada, Shusuke

    2016-02-01

    Cdt1 is a protein essential for initiation of DNA replication; it recruits MCM helicase, a core component of the replicative DNA helicase, onto replication origins. In our previous study, we showed that addition of excess Cdt1 inhibits nascent strand elongation during DNA replication in Xenopus egg extracts. In the present study, we investigated the mechanism behind the inhibitory effect of Cdt1. We found that addition of recombinant Cdt1 inhibited nascent DNA synthesis in a reinitiation-independent manner. To identify the mechanism by which Cdt1 inhibits nascent strand elongation, the effect of Cdt1 on loading of Mcm4 and Rpa70 onto chromatin was examined. The results showed that Cdt1 suppressed the excessive Rpa70 binding caused by extensive, aphidicolin-induced DNA unwinding; this unwinding occurs between stalled DNA polymerases and advancing replication forks. These findings suggested that excess Cdt1 suppressed the progression of replication forks.

  15. Bed-material entrainment potential, Roaring Fork River at Basalt, Colorado

    Science.gov (United States)

    Elliott, John G.

    2002-01-01

    The Roaring Fork River at Basalt, Colorado, has a frequently mobile streambed composed of gravel, cobbles, and boulders. Recent urban and highway development on the flood plain, earlier attempts to realign and confine the channel, and flow obstructions such as bridge openings and piers have altered the hydrology, hydraulics, sediment transport, and sediment deposition areas of the Roaring Fork. Entrainment and deposition of coarse sediment on the streambed and in large alluvial bars have reduced the flood-conveying capacity of the river. Previous engineering studies have identified flood-prone areas and hazards related to inundation and high streamflow velocity, but those studies have not evaluated the potential response of the channel to discharges that entrain the coarse streambed. This study builds upon the results of earlier flood studies and identifies some potential areas of concern associated with bed-material entrainment. Cross-section surveys and simulated water-surface elevations from a previously run HEC?RAS model were used to calculate the boundary shear stress on the mean streambed, in the thalweg, and on the tops of adjacent alluvial bars for four reference streamflows. Sediment-size characteristics were determined for surficial material on the streambed, on large alluvial bars, and on a streambank. The median particle size (d50) for the streambed samples was 165 millimeters and for the alluvial bars and bank samples was 107 millimeters. Shear stresses generated by the 10-, 50-, and 100-year floods, and by a more common flow that just inundated most of the alluvial bars in the study reach were calculated at 14 of the cross sections used in the Roaring Fork River HEC?RAS model. The Shields equation was used with a Shields parameter of 0.030 to estimate the critical shear stress for entrainment of the median sediment particle size on the mean streambed, in the thalweg, and on adjacent alluvial bar surfaces at the 14 cross sections. Sediment

  16. Spatially detailed quantification of metal loading for decision making: Metal mass loading to American fork and Mary Ellen Gulch, Utah

    Science.gov (United States)

    Kimball, B.A.; Runkel, R.L.

    2009-01-01

    Effective remediation requires an understanding of the relative contributions of metals from all sources in a catchment, and that understanding must be based on a spatially detailed quantification of metal loading. A traditional approach to quantifying metal loading has been to measure discharge and chemistry at a catchment outlet. This approach can quantify annual loading and the temporal changes in load, but does not provide the needed spatial detail to evaluate specific sources, which is needed to support remediation decisions. A catchment or massloading approach provides spatial detail by combining tracer-injection and synoptic-sampling methods to quantify loading. Examples of studies in American Fork, Utah, and its tributary Mary Ellen Gulch illustrate this different approach. The mass-loading study in American Fork treated Mary Ellen Gulch as a single inflow. From that point of view, Mary Ellen Gulch was one of the greatest sources of Fe, Mn, Zn, and colloidal Pb loads to American Fork. But when Mary Ellen Gulch was evaluated in a separate catchment study, the detailed locations of metal loading were identified, and the extent of metal attenuation upstream from the mouth of Mary Ellen Gulch was quantified. The net, instantaneous load measured at the mouth of Mary Ellen Gulch for remediation planning would greatly underestimate the contributions of principal sources within the catchment. Extending the detailed sampling downstream from Mary Ellen Gulch indicated the possibility of diffuse groundwater inflow from Mary Ellen Gulch to American Fork. Comparing loads for Mary Ellen Gulch in the two studies indicates that metal loads could be substantially underestimated for planning purposes without the detailed catchment approach for the low-flow conditions in these studies. A mass-loading approach provides both the needed quantification of metal loading and the spatial detail to guide remediation decisions that would be the most effective in the catchments

  17. Environmental Assessment Addressing the Integrated Control of Nuisance Species at Grand Forks Air Force Base, North Dakota

    Science.gov (United States)

    2013-04-01

    consists of binding diquat in the gut with suspensions of activated charcoal or bentonite clay , adminis- tration of cathartics to enhance elimination...begin IMMEDIATELY. Treatment consists of binding diquat in the gut with suspensions of activated charcoal or bentonite clay , administration of...deposits. The glacial deposits are composed of silts and clays with occasional sand and gravel lenses (CBP 2008). Topography. Grand Forks AFB is

  18. Demonstration of Advanced Geophysics and Classification Methods on Munitions Response Sites - East Fork Valley Range Complex, Former Camp Hale

    Science.gov (United States)

    2016-04-01

    ESTCP to test the effectiveness of advanced geophysical sensors and physics -based data analysis tools for anomaly classification . The project purpose is...the project data. 50 10.0 REFERENCES ESTCP. 2009. “Geophysical System Verification (GSV): A Physics -Based Alternative to Geophysical Prove-Outs for...Technical Report Demonstration of Advanced Geophysics and Classification Methods on Munitions Response Sites - East Fork Valley

  19. Confirmatory Sampling and Analysis Plan for the Lower East Fork Poplar Creek Operable Unit, Oak Ridge, Tennessee

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1996-12-01

    This document describes the organization, strategy, and procedures to be used to confirm that mercury concentrations in soils in the remediated areas are statistically less than, or equal to, the cleanup standard of 400 ppm. It focuses on confirming the cleanup of the stretch of the Lower East Fork Popular Creed flowing from Lake Reality at the Y-12 Plant, through the City of Oak Ridge, to Poplar Creek on the Oak Ridge Reservation and its associated flood plain.

  20. South Fork Flathead Watershed Westslope Cutthroat Trout Conservation Program, Annual Report 2002.

    Energy Technology Data Exchange (ETDEWEB)

    Grisak, Grant; Marotz, Brian

    2003-06-01

    In 1999, Montana Fish, Wildlife & Parks (MFWP) began a program aimed at conserving the genetically pure populations of westslope cutthroat trout in the South Fork Flathead River drainage. The objective of this program is to eliminate all of the exotic and hybrid trout that threaten the genetically pure westslope cutthroat populations in the South Fork Flathead. The exotic and hybrid trout populations occur in several headwater lakes and their outflow streams. In 2001 MFWP released a draft environmental assessment, pursuant to the Montana Environmental Policy Act (MEPA), that addressed the use of motorized equipment to deliver personnel and materials to some of these lakes in the Bob Marshall and Great Bear Wildernesses (Grisak 2001). After a 30-day public comment period, MFWP determined that the complexity of issues was too great and warranted a more detailed analysis. These issues included transportation options for personnel, equipment and materials, the use of motorized equipment in wilderness, fish removal methods, fish stocking, and the status and distribution of amphibian populations in the project area. Because the program also involves the U.S. Forest Service (USFS) and Bonneville Power Administration (BPA), the environmental analysis needs to comply with the National Environmental Policy Act (NEPA). In October 2001, pursuant to NEPA, MFWP, along with the USFS and BPA initiated an environmental assessment to address these issues. In June 2002, the three agencies determined that the scope of these issues warranted an Environmental Impact Statement. This specialist report describes the logistical, technical and biological issues associated with this project and provides an analysis of options for fish removal, transportation and fish stocking. It further analyzes issues and concerns associated with amphibian populations and creating new domesticated stocks of westslope cutthroat trout. Finally, this document provides a description of each lake, the best

  1. Quarterly Progress Report - Biological Monitoring Program for East Fork Poplar Creek

    Energy Technology Data Exchange (ETDEWEB)

    Adams, S.M.; Christensen, S.W.; Greeley, M.S. jr; Hill, W.R.; McCarthy, J.F.; Peterson, M.J.; Ryon, M.G.; Smith, J.G.; Southworth, G.R.; Stewart, A.J.

    2000-07-18

    In May 1985, a National Pollutant Discharge Elimination System (NPDES) permit was issued for the Oak Ridge Y-12 Plant. As a condition of the permit, a Biological Monitoring and Abatement Program (BMAP) was developed to demonstrate that the effluent limitations established for the Y-12 Plant protect the classified uses of the receiving stream (East Fork Poplar Creek; EFPC), in particular, the growth and propagation of aquatic life (Loar et al. 1989). A second objective of the BMAP is to document the ecological effects resulting from the implementation of a water pollution control program designed to eliminate direct discharges of wastewaters to EFPC and to minimize the inadvertent release of pollutants to the environment. Because of the complex nature of the discharges to EFPC and the temporal and spatial variability in the composition of the discharges, a comprehensive, integrated approach to biological monitoring was developed. A new permit was issued to the Y-12 Plant on April 28, 1995 and became effective on July 1, 1995. Biological monitoring continues to be required under the new permit. The BMAP consists of four major tasks that reflect different but complementary approaches to evaluating the effects of the Y-12 Plant discharges on the aquatic integrity of EFPC. These tasks are (1) toxicity monitoring, (2) biological indicator studies, (3) bioaccumulation studies, and (4) ecological surveys of the periphyton, benthic macroinvertebrate, and fish communities. Monitoring is currently being conducted at five primary EFPC sites, although sites may be excluded or added depending upon the specific objectives of the various tasks. Criteria used in selecting the sites include: (1) location of sampling sites used in other studies, (2) known or suspected sources of downstream impacts, (3) proximity to U.S. Department of Energy (DOE) Oak Ridge Reservation (ORR) boundaries, (4) concentration of mercury in the adjacent floodplain, (5) appropriate habitat distribution, and

  2. Quarterly Progress Report - Biological Monitoring Program for East Fork Poplar Creek

    Energy Technology Data Exchange (ETDEWEB)

    Adams, S.M.; Christensen, S.W.; Greeley, M.S.jr; Hill, W.R.; McCarthy, J.F.; Peterson, M.J.; Ryon, M.G.; Smith, J.G.; Southworth, G.R.; Stewart, A.J.

    2000-10-18

    In May 1985, a National Pollutant Discharge Elimination System (NPDES) permit was issued for the Oak Ridge Y-12 Plant. As a condition of the permit, a Biological Monitoring and Abatement Program (BMAP) was developed to demonstrate that the effluent limitations established for the Y-12 Plant protect the classified uses of the receiving stream (East Fork Poplar Creek; EFPC), in particular, the growth and propagation of aquatic life (Loar et al. 1989). A second objective of the BMAP is to document the ecological effects resulting from the implementation of a water pollution control program designed to eliminate direct discharges of wastewaters to EFPC and to minimize the inadvertent release of pollutants to the environment. Because of the complex nature of the discharges to EFPC and the temporal and spatial variability in the composition of the discharges, a comprehensive, integrated approach to biological monitoring was developed. A new permit was issued to the Y-12 Plant on April 28, 1995 and became effective on July 1, 1995. Biological monitoring continues to be required under the new permit. The BMAP consists of four major tasks that reflect different but complementary approaches to evaluating the effects of the Y-12 Plant discharges on the aquatic integrity of EFPC. These tasks are (1) toxicity monitoring, (2) biological indicator studies, (3) bioaccumulation studies, and (4) ecological surveys of the periphyton, benthic macroinvertebrate, and fish communities. Monitoring is currently being conducted at five primary EFPC sites, although sites may be excluded or added depending upon the specific objectives of the various tasks. Criteria used in selecting the sites include: (1) location of sampling sites used in other studies, (2) known or suspected sources of downstream impacts, (3) proximity to U.S. Department of Energy (DOE) Oak Ridge Reservation (ORR) boundaries, (4) concentration of mercury in the adjacent floodplain, (5) appropriate habitat distribution, and

  3. Vibration Sensitivity Reduction of Micromachined Tuning Fork Gyroscopes through Stiffness Match Method with Negative Electrostatic Spring Effect

    Directory of Open Access Journals (Sweden)

    Yanwei Guan

    2016-07-01

    Full Text Available In this paper, a stiffness match method is proposed to reduce the vibration sensitivity of micromachined tuning fork gyroscopes. Taking advantage of the coordinate transformation method, a theoretical model is established to analyze the anti-phase vibration output caused by the stiffness mismatch due to the fabrication imperfections. The analytical solutions demonstrate that the stiffness mismatch is proportional to the output induced by the external linear vibration from the sense direction in the anti-phase mode frequency. In order to verify the proposed stiffness match method, a tuning fork gyroscope (TFG with the stiffness match electrodes is designed and implemented using the micromachining technology and the experimental study is carried out. The experimental tests illustrate that the vibration output can be reduced by 73.8% through the stiffness match method than the structure without the stiffness match. Therefore, the proposed stiffness match method is experimentally validated to be applicable to vibration sensitivity reduction in the Micro-Electro-Mechanical-Systems (MEMS tuning fork gyroscopes without sacrificing the scale factor.

  4. Vibration Sensitivity Reduction of Micromachined Tuning Fork Gyroscopes through Stiffness Match Method with Negative Electrostatic Spring Effect.

    Science.gov (United States)

    Guan, Yanwei; Gao, Shiqiao; Liu, Haipeng; Jin, Lei; Zhang, Yaping

    2016-07-22

    In this paper, a stiffness match method is proposed to reduce the vibration sensitivity of micromachined tuning fork gyroscopes. Taking advantage of the coordinate transformation method, a theoretical model is established to analyze the anti-phase vibration output caused by the stiffness mismatch due to the fabrication imperfections. The analytical solutions demonstrate that the stiffness mismatch is proportional to the output induced by the external linear vibration from the sense direction in the anti-phase mode frequency. In order to verify the proposed stiffness match method, a tuning fork gyroscope (TFG) with the stiffness match electrodes is designed and implemented using the micromachining technology and the experimental study is carried out. The experimental tests illustrate that the vibration output can be reduced by 73.8% through the stiffness match method than the structure without the stiffness match. Therefore, the proposed stiffness match method is experimentally validated to be applicable to vibration sensitivity reduction in the Micro-Electro-Mechanical-Systems (MEMS) tuning fork gyroscopes without sacrificing the scale factor.

  5. Bioaccumulation of metals by Hyalella azteca exposed to contaminated sediments from the upper Clark Fork River, Montana

    Science.gov (United States)

    Ingersoll, Christopher G.; Brumbaugh, William G.; Dwyer, F. James; Kemble, Nile E.

    1994-01-01

    Macroinvertebrates contaminated with metals in the Clark Fork River of Montana have been demonstrated to be a potentially toxic component in the diet of trout Because sediment was the suspected source of metals to these invertebrates, bioaccumulation of As, Cd, Cu, Pb, and Zn from sediment was evaluated by exposing the amphipod Hyalella azteca for 28 d in the laboratory to samples of sediment collected from depositional areas of the Clark Fork River Benthic invertebrates collected from riffles adjacent to the depositional areas were also analyzed for metals The pattern of metal accumulation between laboratory-exposed and field-collected animals was similar, however, the concentrations of metals in laboratory exposed amphipods were often 50 to 75% less than were the concentrations of metals in the field collected invertebrates These findings indicate that sediment is a significant source of metals to invertebrates in the Clark Fork River Additional studies should be conducted to determine threshold concentrations for effects of dietary metals on fish Long-term monitoring of the river should include sampling benthic invertebrates for metal accumulation.

  6. A tuning fork based wide range mechanical characterization tool with nanorobotic manipulators inside a scanning electron microscope

    Energy Technology Data Exchange (ETDEWEB)

    Acosta, Juan Camilo; Hwang, Gilgueng; Regnier, Stephane [Institut des Systemes Intelligents et de Robotique Universite Pierre et Marie Curie, CNRS UMR 7222 4 Place Jussieu, 75252 Paris Cedex (France); Polesel-Maris, Jerome [CEA, IRAMIS, Service de Physique et Chimie des Surfaces et Interfaces, F-91191 Gif-sur-Yvette (France)

    2011-03-15

    This study proposes a tuning fork probe based nanomanipulation robotic system for mechanical characterization of ultraflexible nanostructures under scanning electron microscope. The force gradient is measured via the frequency modulation of a quartz tuning fork and two nanomanipulators are used for manipulation of the nanostructures. Two techniques are proposed for attaching the nanostructure to the tip of the tuning fork probe. The first technique involves gluing the nanostructure for full range characterization whereas the second technique uses van der Waals and electrostatic forces in order to avoid destroying the nanostructure. Helical nanobelts (HNB) are proposed for the demonstration of the setup. The nonlinear stiffness behavior of HNBs during their full range tensile studies is clearly revealed for the first time. Using the first technique, this was between 0.009 N/m for rest position and 0.297 N/m before breaking of the HNB with a resolution of 0.0031 N/m. For the second experiment, this was between 0.014 N/m for rest position and 0.378 N/m before detaching of the HNB with a resolution of 0.0006 N/m. This shows the wide range sensing of the system for potential applications in mechanical property characterization of ultraflexible nanostructures.

  7. Integrated tuning fork nanocavity optomechanical transducers with high $f_{M}Q_{M}$ product and stress-engineered frequency tuning

    CERN Document Server

    Zhang, R; Davanco, M I; Ren, Y; Aksyuk, V; Liu, Y; Srinivasan, K

    2015-01-01

    Cavity optomechanical systems are being widely developed for precision force and displacement measurements. For nanomechanical transducers, there is usually a trade-off between the frequency ($f_{M}$) and quality factor ($Q_{M}$), which limits temporal resolution and sensitivity. Here, we present a monolithic cavity optomechanical transducer supporting both high $f_{M}$ and high $Q_{M}$. By replacing the common doubly-clamped, Si$_3$N$_4$ nanobeam with a tuning fork geometry, we demonstrate devices with the fundamental $f_{M}\\approx29$ MHz and $Q_{M}\\approx2.2$$\\times10^5$, corresponding to an $f_{M}Q_{M}$ product of 6.35$\\times10^{12}$ Hz, comparable to the highest values previously demonstrated for room temperature operation. This high $f_{M}Q_{M}$ product is partly achieved by engineering the stress of the tuning fork to be 3 times the residual film stress through clamp design, which results in an increase of $f_{M}$ up to 1.5 times. Simulations reveal that the tuning fork design simultaneously reduces the...

  8. Metals-contaminated benthic invertebrates in the Clark Fork River, Montana: Effects on age-0 brown trout and rainbow trout

    Science.gov (United States)

    Woodward, Daniel F.; Farag, Aïda M.; Bergman, Harold L.; Delonay, Aaron J.; Little, Edward E.; Smiths, Charlie E.; Barrows, Frederic T.

    1995-01-01

    Benthic organisms in the upper Clark Fork River have recently been implicated as a dietary source of metals that may be a chronic problem for young-of-the-year rainbow trout (Oncorhynchus mykiss). In this present study, early life stage brown trout (Salmo trutta) and rainbow trout were exposed for 88 d to simulated Clark Fork River water and a diet of benthic invertebrates collected from the river. These exposures resulted in reduced growth and elevated levels of metals in the whole body of both species. Concentrations of As, Cd, Cu, and Pb increased in whole brown trout; in rainbow trout, As and Cd increased in whole fish, and As also increased in liver. Brown trout on the metals-contaminated diets exhibited constipation, gut impaction, increased cell membrane damage (lipid peroxidation), decreased digestive enzyme production (zymogen), and a sloughing of intestinal mucosal epithelial cells. Rainbow trout fed the contaminated diets exhibited constipation and reduced feeding activity. We believe that the reduced standing crop of trout in the Clark Fork River results partly from chronic effects of metals contamination in benthic invertebrates that are important as food for young-of-the-year fish.

  9. Vibration Sensitivity Reduction of Micromachined Tuning Fork Gyroscopes through Stiffness Match Method with Negative Electrostatic Spring Effect

    Science.gov (United States)

    Guan, Yanwei; Gao, Shiqiao; Liu, Haipeng; Jin, Lei; Zhang, Yaping

    2016-01-01

    In this paper, a stiffness match method is proposed to reduce the vibration sensitivity of micromachined tuning fork gyroscopes. Taking advantage of the coordinate transformation method, a theoretical model is established to analyze the anti-phase vibration output caused by the stiffness mismatch due to the fabrication imperfections. The analytical solutions demonstrate that the stiffness mismatch is proportional to the output induced by the external linear vibration from the sense direction in the anti-phase mode frequency. In order to verify the proposed stiffness match method, a tuning fork gyroscope (TFG) with the stiffness match electrodes is designed and implemented using the micromachining technology and the experimental study is carried out. The experimental tests illustrate that the vibration output can be reduced by 73.8% through the stiffness match method than the structure without the stiffness match. Therefore, the proposed stiffness match method is experimentally validated to be applicable to vibration sensitivity reduction in the Micro-Electro-Mechanical-Systems (MEMS) tuning fork gyroscopes without sacrificing the scale factor. PMID:27455272

  10. Bloom syndrome complex promotes FANCM recruitment to stalled replication forks and facilitates both repair and traverse of DNA interstrand crosslinks.

    Science.gov (United States)

    Ling, Chen; Huang, Jing; Yan, Zhijiang; Li, Yongjiang; Ohzeki, Mioko; Ishiai, Masamichi; Xu, Dongyi; Takata, Minoru; Seidman, Michael; Wang, Weidong

    2016-01-01

    The recruitment of FANCM, a conserved DNA translocase and key component of several DNA repair protein complexes, to replication forks stalled by DNA interstrand crosslinks (ICLs) is a step upstream of the Fanconi anemia (FA) repair and replication traverse pathways of ICLs. However, detection of the FANCM recruitment has been technically challenging so that its mechanism remains exclusive. Here, we successfully observed recruitment of FANCM at stalled forks using a newly developed protocol. We report that the FANCM recruitment depends upon its intrinsic DNA translocase activity, and its DNA-binding partner FAAP24. Moreover, it is dependent on the replication checkpoint kinase, ATR; but is independent of the FA core and FANCD2-FANCI complexes, two essential components of the FA pathway, indicating that the FANCM recruitment occurs downstream of ATR but upstream of the FA pathway. Interestingly, the recruitment of FANCM requires its direct interaction with Bloom syndrome complex composed of BLM helicase, Topoisomerase 3α, RMI1 and RMI2; as well as the helicase activity of BLM. We further show that the FANCM-BLM complex interaction is critical for replication stress-induced FANCM hyperphosphorylation, for normal activation of the FA pathway in response to ICLs, and for efficient traverse of ICLs by the replication machinery. Epistasis studies demonstrate that FANCM and BLM work in the same pathway to promote replication traverse of ICLs. We conclude that FANCM and BLM complex work together at stalled forks to promote both FA repair and replication traverse pathways of ICLs.

  11. Fork-join and data-driven execution models on multi-core architectures: Case study of the FMM

    KAUST Repository

    Amer, Abdelhalim

    2013-01-01

    Extracting maximum performance of multi-core architectures is a difficult task primarily due to bandwidth limitations of the memory subsystem and its complex hierarchy. In this work, we study the implications of fork-join and data-driven execution models on this type of architecture at the level of task parallelism. For this purpose, we use a highly optimized fork-join based implementation of the FMM and extend it to a data-driven implementation using a distributed task scheduling approach. This study exposes some limitations of the conventional fork-join implementation in terms of synchronization overheads. We find that these are not negligible and their elimination by the data-driven method, with a careful data locality strategy, was beneficial. Experimental evaluation of both methods on state-of-the-art multi-socket multi-core architectures showed up to 22% speed-ups of the data-driven approach compared to the original method. We demonstrate that a data-driven execution of FMM not only improves performance by avoiding global synchronization overheads but also reduces the memory-bandwidth pressure caused by memory-intensive computations. © 2013 Springer-Verlag.

  12. Syntactic-Head-Driven Generation

    CERN Document Server

    Koenig, E

    1994-01-01

    The previously proposed semantic-head-driven generation methods run into problems if none of the daughter constituents in the syntacto-semantic rule schemata of a grammar fits the definition of a semantic head given in Shieber et al. 1990. This is the case for the semantic analysis rules of certain constraint-based semantic representations, e.g. Underspecified Discourse Representation Structures (UDRSs) (Frank/Reyle 1992). Since head-driven generation in general has its merits, we simply return to a syntactic definition of `head' and demonstrate the feasibility of syntactic-head-driven generation. In addition to its generality, a syntactic-head-driven algorithm provides a basis for a logically well-defined treatment of the movement of (syntactic) heads, for which only ad-hoc solutions existed, so far.

  13. Comparison between Measured and Calculated Sediment Transport Rates in North Fork Caspar Creek, California

    Science.gov (United States)

    Kim, T. W.; Yarnell, S. M.; Yager, E.; Leidman, S. Z.

    2015-12-01

    Caspar Creek is a gravel-bedded stream located in the Jackson Demonstration State Forest in the coast range of California. The Caspar Creek Experimental Watershed has been actively monitored and studied by the Pacific Southwest Research Station and California Department of Forestry and Fire Protection for over five decades. Although total annual sediment yield has been monitored through time, sediment transport during individual storm events is less certain. At a study site on North Fork Caspar Creek, cross-section averaged sediment flux was collected throughout two storm events in December 2014 and February 2015 to determine if two commonly used sediment transport equations—Meyer-Peter-Müller and Wilcock—approximated observed bedload transport. Cross-section averaged bedload samples were collected approximately every hour during each storm event using a Helley-Smith bedload sampler. Five-minute composite samples were collected at five equally spaced locations along a cross-section and then sieved to half-phi sizes to determine the grain size distribution. The measured sediment flux values varied widely throughout the storm hydrographs and were consistently less than two orders of magnitude in value in comparison to the calculated values. Armored bed conditions, changing hydraulic conditions during each storm and variable sediment supply may have contributed to the observed differences.

  14. Chronic toxicity of Clark Fork River invertebrates to rainbow trout when administered via the diet

    Energy Technology Data Exchange (ETDEWEB)

    Barth, A.; Cohen, A.; Stubblefield, W. [ENSR, Fort Collins, CO (United States)

    1995-12-31

    A 46-day exposure examined the effects of metals contamination in a live natural freshwater diet on rainbow trout fry. Survival, growth, and whole-body tissue metals were compared among groups of trout fed live planktonic invertebrates (primarily Daphnia pulex) collected from the Clark Fork River (CFR), Montana and trout fed live laboratory-reared D. pulex. Metals of interest in the diets were As, Cu, Cd, Pb, and Zn. In addition to dietary exposure, treatments included simultaneous exposure to a mixture of waterborne metals (Cu, Cd, Pb, and Zn) at sublethal concentrations. Trout showed no statistically significant effects on survival or growth from mean CFR invertebrate metal concentrations of 20.1 mg As/kg dwt, 60.7 mg Cu/kg dwt, 4.0 mg Cd/kg dwt, 4.9 mg Pb/kg dwt, and 249 mg Zn/kg dwt. Waterborne and dietary Cd and Pb appeared to result in increased tissue concentrations of these metals, while only dietary As resulted in increased tissue As. Neither dietary nor waterborne copper or zinc had a substantial effect on tissue levels of these metals. Results were consistent, in terms of the lack of statistically significant growth and survival effects, with those of previous in-house studies exposing rainbow trout to metals-enriched Artemia sp. (brine shrimp) diets.

  15. Research on the Sensing Performance of the Tuning Fork-Probe as a Micro Interaction Sensor

    Directory of Open Access Journals (Sweden)

    Fengli Gao

    2015-09-01

    Full Text Available The shear force position system has been widely used in scanning near-field optical microscopy (SNOM and recently extended into the force sensing area. The dynamic properties of a tuning fork (TF, the core component of this system, directly determine the sensing performance of the shear positioning system. Here, we combine experimental results and finite element method (FEM analysis to investigate the dynamic behavior of the TF probe assembled structure (TF-probe. Results from experiments under varying atmospheric pressures illustrate that the oscillation amplitude of the TF-probe is linearly related to the quality factor, suggesting that decreasing the pressure will dramatically increase the quality factor. The results from FEM analysis reveal the influences of various parameters on the resonant performance of the TF-probe. We compared numerical results of the frequency spectrum with the experimental data collected by our recently developed laser Doppler vibrometer system. Then, we investigated the parameters affecting spatial resolution of the SNOM and the dynamic response of the TF-probe under longitudinal and transverse interactions. It is found that the interactions in transverse direction is much more sensitive than that in the longitudinal direction. Finally, the TF-probe was used to measure the friction coefficient of a silica–silica interface.

  16. Remedial design work plan for Lower East Fork Poplar Creek Operable Unit, Oak Ridge, Tennessee

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1995-10-01

    The Remedial Design Work Plan (RDWP) for Lower East Fork Poplar Creek (EFPC) Operable Unit (OU) in Oak Ridge, Tennessee. This remedial action fits into the overall Oak Ridge Reservation (ORR) cleanup strategy by addressing contaminated floodplain soil. The objective of this remedial action is to minimize the risk to human health and the environment from contaminated soil in the Lower EFPC floodplain pursuant to the Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA) and the Federal Facility Agreement (FFA) (1992). In accordance with the FFA, a remedial investigation (RI) (DOE 1994a) and a feasibility study (DOE 1994b) were conducted to assess contamination of the Lower EFPC and propose remediation alternatives. The remedial investigation determined that the principal contaminant is mercury, which originated from releases during Y-12 Plant operations, primarily between 1953 and 1963. The recommended alternative by the feasibility study was to excavate and dispose of floodplain soils contaminated with mercury above the remedial goal option. Following the remedial investigation/feasibility study, and also in accordance with the FFA, a proposed plan was prepared to more fully describe the proposed remedy.

  17. Design of a compact tuning fork-shaped notched ultrawideband antenna for wireless communication application.

    Science.gov (United States)

    Shakib, M N; Moghavvemi, M; Mahadi, W N L

    2014-01-01

    A new compact planar notched ultrawideband (UWB) antenna is designed for wireless communication application. The proposed antenna has a compact size of 0.182λ × 0.228λ × 0.018λ where λ is the wavelength of the lowest operating frequency. The antenna is comprised of rectangular radiating patch, ground plane, and an arc-shaped strip in between radiating patch and feed line. By introducing a new Tuning Fork-shaped notch in the radiating plane, a stopband is obtained. The antenna is tested and measured. The measured result indicated that fabricated antenna has achieved a wide bandwidth of 4.33-13.8 GHz (at -10 dB return loss) with a rejection frequency band of 5.28-6.97 GHz (WiMAX, WLAN, and C-band). The effects of the parameters of the antenna are discussed. The experiment results demonstrate that the proposed antenna can well meet the requirement for the UWB communication in spite of its compactness and small size.

  18. A Z-axis Quartz Cross-fork Micromachined Gyroscope Based on Shear Stress Detection

    Directory of Open Access Journals (Sweden)

    Peitao Dong

    2010-03-01

    Full Text Available Here we propose a novel quartz micromachined gyroscope. The sensor has a simple cross-fork structure in the x-y plane of quartz crystal. Shear stress rather than normal stress is utilized to sense Coriolis’ force generated by the input angular rate signal. Compared to traditional quartz gyroscopes, which have two separate sense electrodes on each sidewall, there is only one electrode on each sidewall of the sense beam. As a result, the fabrication of the electrodes is simplified and the structure can be easily miniaturized. In order to increase sensitivity, a pair of proof masses is attached to the ends of the drive beam, and the sense beam has a tapered design. The structure is etched from a z-cut quartz wafer and the electrodes are realized by direct evaporation using the aperture mask method. The drive mode frequency of the prototype is 13.38 kHz, and the quality factor is approximately 1,000 in air. Therefore, the gyroscope can work properly without a vacuum package. The measurement ability of the shear stress detection design scheme is validated by the Coriolis’ force test. The performance of the sensor is characterized on a precision rate table using a specially designed readout circuit. The experimentally obtained scale factor is 1.45 mV/°/s and the nonlinearity is 3.6% in range of ±200 °/s.

  19. Quarterly Progress Report on the Biological Monitoring Program for East Fork Poplar Creek

    Energy Technology Data Exchange (ETDEWEB)

    Adams, S.M.; Ashwood, T.L.; Cicerone, D.S.; Greeley, M.S. Jr.; Hill, W.R.; Kszos, L.A.

    1996-12-30

    In May 1985, a National Pollutant Discharge Elimination System (NPDES) permit was issued for the Oak Ridge Y-12 Plant. As a condition of the permit, a Biological Monitoring and Abatement Program ( BMAP) was developed to demonstrate that the effluent limitations established for the Y-12 Plant protect the classified uses of the receiving stream (East Fork Poplar Creek; EFPC), in particular, the growth and propagation of aquatic life (Lear et al. 1989). A second objective of the BMAP is to document the ecological effects resulting from the implementation of a water pollution control program designed to eliminate direct discharges of wastewaters to EFPC and to minimize the inadvertent release of pollutants to the environment. Because of the complex nature of the discharges to EFPC and the temporal and spatial variability in the composition of the discharges, a comprehensive, integrated approach to biological monitoring was developed. A new permit was issued to the Y-12 Plant on April 28, 1995 and became effective on July 1, 1995. Biological monitoring continues to be required under the new permit. The BMAP consists of four major tasks that reflect different but complementary approaches to evaluating the effects of the Y-12 Plant discharges on the aquatic integrity of EFPC. These tasks are (1) toxicity monitoring, (2) biological indicator studies, (3) bioaccumulation studies, and (4) ecological surveys of the periphyton, benthic macroinvertebrate, and fish communities.

  20. Montana's Clark Fork River Basin Task Force: a vehicle for integrated water resources management?

    Science.gov (United States)

    Shively, David D; Mueller, Gerald

    2010-11-01

    This article examines what is generally considered to be an unattainable goal in the western United States: integrated water resources management (IWRM). Specifically, we examine an organization that is quite unique in the West, Montana's Clark Fork River Basin Task Force (Task Force), and we analyze its activities since its formation in 2001 to answer the question: are the activities and contributions of the Task Force working to promote a more strongly integrated approach to water resources management in Montana? After reviewing the concepts underlying IWRM, some of the issues that have been identified for achieving IWRM in the West, and the Montana system of water right allocation and issues it faces, we adapt Mitchell's IWRM framework and apply it to the analysis of the Task Force's activities in the context of IWRM. In evaluating the physical, interaction, and protocol/planning/policy components of IWRM, we find that the Task Force has been contributing to the evolution of Montana's water resources management towards this framework, though several factors will likely continue to prevent its complete realization. The Task Force has been successful in this regard because of its unique nature and charge, and because of the authority and power given it by successive Montana legislatures. Also critical to the success of the organization is its ability to help translate into policy the outcomes of legal and quasi-judicial decisions that have impacted the state's water resources management agency.

  1. Rock fall simulation at Timpanogos Cave National Monument, American Fork Canyon, Utah, USA

    Science.gov (United States)

    Harp, Edwin L.; Dart, Richard L.; Reichenbach, Paola

    2011-01-01

    Rock fall from limestone cliffs at Timpanogos Cave National Monument in American Fork Canyon east of Provo, Utah, is a common occurrence. The cave is located in limestone cliffs high on the southern side of the canyon. One fatality in 1933 led to the construction of rock fall shelters at the cave entrance and exit in 1976. Numerous rock fall incidents, including a near miss in 2000 in the vicinity of the trail below the cave exit, have led to a decision to extend the shelter at the cave exit to protect visitors from these ongoing rock fall events initiating from cliffs immediately above the cave exit. Three-dimensional rock fall simulations from sources at the top of these cliffs have provided data from which to assess the spatial frequencies and velocities of rock falls from the cliffs and to constrain the design of protective measures to reduce the rock fall hazard. Results from the rock fall simulations are consistent with the spatial patterns of rock fall impacts that have been observed at the cave exit site.

  2. Waste Management Plan for the Lower East Fork Poplar Creek Remedial Action Project Oak Ridge, Tennessee

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1996-08-01

    The Lower East Fork Poplar Creek (LEFPC) Remedial Action project will remove mercury-contaminated soils from the floodplain of LEFPC, dispose of these soils at the Y-12 Landfill V, and restore the affected floodplain upon completion of remediation activities. This effort will be conducted in accordance with the Record of Decision (ROD) for LEFPC as a Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA) action. The Waste Management Plan addresses management and disposition of all wastes generated during the remedial action for the LEFPC Project Most of the solid wastes will be considered to be sanitary or construction/demolition wastes and will be disposed of at existing Y-12 facilities for those types of waste. Some small amounts of hazardous waste are anticipated, and the possibility of low- level or mixed waste exists (greater than 35 pCi/g), although these are not expected. Liquid wastes will be generated which will be sanitary in nature and which will be capable of being disposed 0214 of at the Oak Ridge Sewage Treatment Plant.

  3. Oxbow Conservation Area; Middle Fork John Day River, Annual Report 2003-2004.

    Energy Technology Data Exchange (ETDEWEB)

    Cochran, Brian

    2004-02-01

    In early 2001, the Confederated Tribes of Warm Springs, through their John Day Basin Office, concluded the acquisition of the Oxbow Ranch, now know as the Oxbow Conservation Area (OCA). Under a memorandum of agreement with the Bonneville Power Administration (BPA), the Tribes are required to provided BPA an 'annual written report generally describing the real property interests in the Project, HEP analyses undertaken or in progress, and management activities undertaken or in progress'. The project during 2003 was crippled due to the aftermath of the BPA budget crisis. Some objectives were not completed during the first half of this contract because of limited funds in the 2003 fiscal year. The success of this property purchase can be seen on a daily basis. Water rights were utilized only in the early, high water season and only from diversion points with functional fish screens. After July 1, all of the OCA water rights were put instream. Riparian fences on the river, Ruby and Granite Boulder creeks continued to promote important vegetation to provide shade and bank stabilization. Hundreds of willow, dogwood, Douglas-fir, and cottonwood were planted along the Middle Fork John Day River. Livestock grazing on the property was carefully managed to ensure the protection of fish and wildlife habitat, while promoting meadow vigor and producing revenue for property taxes. Monitoring of property populations, resources, and management activities continued in 2003 to build a database for future management of this and other properties in the region.

  4. Post construction report for Lower East Fork Poplar Creek Project, Phase 1, Oak Ridge, Tennessee

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1996-11-01

    This Phase 1 Remedial Action (RA) effort was conducted in accordance with the Record of Decision (ROD) for Lower East Fork Poplar Creek (LEFPC) as a Comprehensive Environmental Response, Compensation, and Liability Act action. The LEFPC, Phase 1 RA removed approximately 5,560 yd{sup 3} of mercury-contaminated soils, {ge} 400 ppm, from selected portions of the National Oceanographic and Atmospheric Administration (NOAA) site LEFPC floodplain from July 8, 1996--September 14, 1996. During excavation activities, pockets of elevated radiologically contaminated soils (greater than 35 pCi/g) were located by the continuous monitoring of the excavation areas and contaminated soils with radiological monitoring instruments. Through characterization sampling it has been determined that {approximately} 90 yd{sup 3} are less than 35 pCi/g uranium contaminated and will be transported to the Y-12 Landfill V for disposal and the remaining {approximately}40 yd{sup 3} do not meet the WAC for radiological constituents included in the Special Waste Permit for Landfill V. The radiologically contaminated soil will be placed in 21st Century containers for storage at the K-25 site.

  5. Head first C#

    CERN Document Server

    Stellman, Andrew

    2008-01-01

    Head First C# is a complete learning experience for object-oriented programming, C#, and the Visual Studio IDE. Built for your brain, this book covers C# 3.0 and Visual Studio 2008, and teaches everything from language fundamentals to advanced topics including garbage collection, extension methods, and double-buffered animation. You'll also master C#'s hottest and newest syntax, LINQ, for querying SQL databases, .NET collections, and XML documents. By the time you're through, you'll be a proficient C# programmer, designing and coding large-scale applications. Every few chapters you will come

  6. Head first C#

    CERN Document Server

    Stellman, Andrew

    2010-01-01

    You want to learn C# programming, but you're not sure you want to suffer through another tedious technical book. You're in luck: Head First C# introduces this language in a fun, visual way. You'll quickly learn everything from creating your first program to learning sophisticated coding skills with C# 4.0, Visual Studio 2010 and .NET 4, while avoiding common errors that frustrate many students. The second edition offers several hands-on labs along the way to help you build and test programs using skills you've learned up to that point. In the final lab, you'll put everything together. From o

  7. Head First Python

    CERN Document Server

    Barry, Paul

    2010-01-01

    Ever wished you could learn Python from a book? Head First Python is a complete learning experience for Python that helps you learn the language through a unique method that goes beyond syntax and how-to manuals, helping you understand how to be a great Python programmer. You'll quickly learn the language's fundamentals, then move onto persistence, exception handling, web development, SQLite, data wrangling, and Google App Engine. You'll also learn how to write mobile apps for Android, all thanks to the power that Python gives you. We think your time is too valuable to waste struggling with

  8. Head First Web Design

    CERN Document Server

    Watrall, Ethan

    2008-01-01

    Want to know how to make your pages look beautiful, communicate your message effectively, guide visitors through your website with ease, and get everything approved by the accessibility and usability police at the same time? Head First Web Design is your ticket to mastering all of these complex topics, and understanding what's really going on in the world of web design. Whether you're building a personal blog or a corporate website, there's a lot more to web design than div's and CSS selectors, but what do you really need to know? With this book, you'll learn the secrets of designing effecti

  9. Head First Mobile Web

    CERN Document Server

    Gardner, Lyza; Grigsby, Jason

    2011-01-01

    Despite the huge number of mobile devices and apps in use today, your business still needs a website. You just need it to be mobile. Head First Mobile Web walks you through the process of making a conventional website work on a variety smartphones and tablets. Put your JavaScript, CSS media query, and HTML5 skills to work-then optimize your site to perform its best in the demanding mobile market. Along the way, you'll discover how to adapt your business strategy to target specific devices. Navigate the increasingly complex mobile landscapeTake both technical and strategic approaches to mobile

  10. A whole genome RNAi screen identifies replication stress response genes.

    Science.gov (United States)

    Kavanaugh, Gina; Ye, Fei; Mohni, Kareem N; Luzwick, Jessica W; Glick, Gloria; Cortez, David

    2015-11-01

    Proper DNA replication is critical to maintain genome stability. When the DNA replication machinery encounters obstacles to replication, replication forks stall and the replication stress response is activated. This response includes activation of cell cycle checkpoints, stabilization of the replication fork, and DNA damage repair and tolerance mechanisms. Defects in the replication stress response can result in alterations to the DNA sequence causing changes in protein function and expression, ultimately leading to disease states such as cancer. To identify additional genes that control the replication stress response, we performed a three-parameter, high content, whole genome siRNA screen measuring DNA replication before and after a challenge with replication stress as well as a marker of checkpoint kinase signalling. We identified over 200 replication stress response genes and subsequently analyzed how they influence cellular viability in response to replication stress. These data will serve as a useful resource for understanding the replication stress response.

  11. Magnetic Resonance Imaging (MRI) -- Head

    Medline Plus

    Full Text Available ... have special pediatric considerations. The teddy bear denotes child-specific content. Related Articles ... Videos related to Magnetic Resonance Imaging (MRI) - Head Sponsored ...

  12. HEADS UP: Sensorimotor control of the head-neck system

    NARCIS (Netherlands)

    Forbes, P.A.

    2014-01-01

    Head-neck stabilization is inherently challenging even when stationary, requiring constant vigilance to counter the downward pull of gravity. It involves a highly complex biomechanical system comprised of a large mass (the head) balanced on top of seven vertebrae (the neck), that are in turn connect

  13. Evolution of closely linked gene pairs in vertebrate genomes

    NARCIS (Netherlands)

    Franck, E.; Hulsen, T.; Huynen, M.A.; Jong, de W.W.; Lunsen, N.H.; Madsen, O.

    2008-01-01

    The orientation of closely linked genes in mammalian genomes is not random: there are more head-to-head (h2h) gene pairs than expected. To understand the origin of this enrichment in h2h gene pairs, we have analyzed the phylogenetic distribution of gene pairs separated by less than 600 bp of interge

  14. Bedload and river hydraulics - Inferences from the East Fork River, Wyoming

    Science.gov (United States)

    Leopold, Luna Bergere; Emmett, William W.

    1997-01-01

    During 1973-79, bedload data were collected in a sophisticated trap on a river of moderate size, the East Fork. The transport rate was measured most days through a full snowmelt season, and the rate was determined separately for eight zones across the channel width. The quantitative data are unique and unlikely to be repeated. Nor need they be, because as a result of this effort a practical bedload sampler was adequately tested against full river measurement.It was shown that bedload moves sporadically and randomly on the river bed. Therefore, transport rate is highly variable in short periods of time. There is also a wide variance from day to day. Yet, different rivers have transport rates, which are functions of discharge, depth, and sediment size, that are clearly distinct. Comparison of computed and measured transport rates indicates that a major problem remains: What grain size is representative of the bedload when there is a wide or heterogeneous particle-size distribution? Size of the bedload in motion may be very different from the size of bed material obtained from samples of the streambed.For general computation, the river channel slope may be averaged, and it may be assumed that water-surface slope does not change materially with changing discharge. Indeed, this generality is correct, in that, compared with depth, velocity, and width, slope is conservative at-a-station. However, in more detail, slope changes importantly with discharge in short reaches of channel, and those changes are very different in pool and riffle.These local changes in slope are not merely an aspect of a detailed longitudinal profile but involve cross-channel as well as down-channel components. The pool and riffle sequence involves not only undulation of bed elevation and bar formation on alternate sides of the channel, but alternation of the zone of superovulation of the water surface, and changing relation of watersurface slope to discharge. These details can be seen only in the

  15. Quarterly Progress Report - Biological Monitoring Program for East Fork Poplar Creek

    Energy Technology Data Exchange (ETDEWEB)

    Adams, S. M.; Christensen, S. W.; Greeley, M.S. jr; McCracken, M.K.; Peterson, M.J.; Ryon, M.G.; Smith, J.G.; Southworth G. R.; Stewart, A. J.

    2001-01-19

    In May 1985, a National Pollutant Discharge Elimination System (NPDES) permit was issued for the Oak Ridge Y-12 National Security Complex (formerly the Oak Ridge Y-12 Plant). As a condition of the permit, a Biological Monitoring and Abatement Program (BMAP) was developed to demonstrate that the effluent limitations established for the Y-12 Complex protect the classified uses of the receiving stream (East Fork Poplar Creek; EFPC), in particular, the growth and propagation of aquatic life (Loar et al. 1989). A second objective of the BMAP is to document the ecological effects resulting from the implementation of a water pollution control program designed to eliminate direct discharges of wastewaters to EFPC and to minimize the inadvertent release of pollutants to the environment. Because of the complex nature of the discharges to EFPC and the temporal and spatial variability in the composition of the discharges, a comprehensive, integrated approach to biological monitoring was developed. A new permit was issued to the Y-12 Complex on April 28, 1995 and became effective on July 1, 1995. Biological monitoring continues to be required under the new permit. The BMAP consists of four major tasks that reflect different but complementary approaches to evaluating the effects of the Y-12 Complex discharges on the aquatic integrity of EFPC. These tasks are (1) toxicity monitoring, (2) biological indicator studies, (3) bioaccumulation studies, and (4) ecological surveys of the periphyton, benthic macroinvertebrate, and fish communities. Monitoring is currently being conducted at five primary EFPC sites, although sites may be excluded or added depending upon the specific objectives of the various tasks. Criteria used in selecting the sites include: (1) location of sampling sites used in other studies, (2) known or suspected sources of downstream impacts, (3) proximity to U.S. Department of Energy (DOE) Oak Ridge Reservation (ORR) boundaries, (4) concentration of mercury in the

  16. Quarterly Progress Report - Biological Monitoring Program for East Fork Poplar Creek

    Energy Technology Data Exchange (ETDEWEB)

    Adams, S. M.; Christensen, S. W.; Greeley, M.S. jr; McCracken, M.K.; Peterson, M.J.; Ryon, M.G.; Smith, J.G.; Southworth G. R.; Stewart, A. J.

    2001-01-19

    In May 1985, a National Pollutant Discharge Elimination System (NPDES) permit was issued for the Oak Ridge Y-12 National Security Complex (formerly the Oak Ridge Y-12 Plant). As a condition of the permit, a Biological Monitoring and Abatement Program (BMAP) was developed to demonstrate that the effluent limitations established for the Y-12 Complex protect the classified uses of the receiving stream (East Fork Poplar Creek; EFPC), in particular, the growth and propagation of aquatic life (Loar et al. 1989). A second objective of the BMAP is to document the ecological effects resulting from the implementation of a water pollution control program designed to eliminate direct discharges of wastewaters to EFPC and to minimize the inadvertent release of pollutants to the environment. Because of the complex nature of the discharges to EFPC and the temporal and spatial variability in the composition of the discharges, a comprehensive, integrated approach to biological monitoring was developed. A new permit was issued to the Y-12 Complex on April 28, 1995 and became effective on July 1, 1995. Biological monitoring continues to be required under the new permit. The BMAP consists of four major tasks that reflect different but complementary approaches to evaluating the effects of the Y-12 Complex discharges on the aquatic integrity of EFPC. These tasks are (1) toxicity monitoring, (2) biological indicator studies, (3) bioaccumulation studies, and (4) ecological surveys of the periphyton, benthic macroinvertebrate, and fish communities. Monitoring is currently being conducted at five primary EFPC sites, although sites may be excluded or added depending upon the specific objectives of the various tasks. Criteria used in selecting the sites include: (1) location of sampling sites used in other studies, (2) known or suspected sources of downstream impacts, (3) proximity to U.S. Department of Energy (DOE) Oak Ridge Reservation (ORR) boundaries, (4) concentration of mercury in the

  17. Chryse 'Alien Head'

    Science.gov (United States)

    2005-01-01

    26 January 2004 This Mars Global Surveyor (MGS) Mars Orbiter Camera (MOC) image shows an impact crater in Chryse Planitia, not too far from the Viking 1 lander site, that to seems to resemble a bug-eyed head. The two odd depressions at the north end of the crater (the 'eyes') may have formed by wind or water erosion. This region has been modified by both processes, with water action occurring in the distant past via floods that poured across western Chryse Planitia from Maja Valles, and wind action common occurrence in more recent history. This crater is located near 22.5oN, 47.9oW. The 150 meter scale bar is about 164 yards long. Sunlight illuminates the scene from the left/lower left.

  18. NASA head sworn in

    Science.gov (United States)

    James C. Fletcher was sworn in on May 12, 1986, as administrator of the National Aeronautics and Space Administration (NASA). At a news conference after he was sworn in, Fletcher said that NASA would deal with both its technical problems and its procedural problems before the shuttle will fly again. According to press accounts, he stressed that funds should be made available to replace the Challenger orbiter, which was lost in an explosion on January 28.Fletcher, who had also headed the agency from 1971 to 1977, succeeds James M. Beggs, who was indicted in December 1985 for conspiring to defraud the federal government while serving as a senior executive at the General Dynamics Corporation.

  19. Quality control mechanisms exclude incorrect polymerases from the eukaryotic replication fork

    Science.gov (United States)

    Schauer, Grant D.; O’Donnell, Michael E.

    2017-01-01

    The eukaryotic genome is primarily replicated by two DNA polymerases, Pol ε and Pol δ, that function on the leading and lagging strands, respectively. Previous studies have established recruitment mechanisms whereby Cdc45-Mcm2-7-GINS (CMG) helicase binds Pol ε and tethers it to the leading strand, and PCNA (proliferating cell nuclear antigen) binds tightly to Pol δ and recruits it to the lagging strand. The current report identifies quality control mechanisms that exclude the improper polymerase from a particular strand. We find that the replication factor C (RFC) clamp loader specifically inhibits Pol ε on the lagging strand, and CMG protects Pol ε against RFC inhibition on the leading strand. Previous studies show that Pol δ is slow and distributive with CMG on the leading strand. However, Saccharomyces cerevisiae Pol δ–PCNA is a rapid and processive enzyme, suggesting that CMG may bind and alter Pol δ activity or position it on the lagging strand. Measurements of polymerase binding to CMG demonstrate Pol ε binds CMG with a Kd value of 12 nM, but Pol δ binding CMG is undetectable. Pol δ, like bacterial replicases, undergoes collision release upon completing replication, and we propose Pol δ–PCNA collides with the slower CMG, and in the absence of a stabilizing Pol δ–CMG interaction, the collision release process is triggered, ejecting Pol δ on the leading strand. Hence, by eviction of incorrect polymerases at the fork, the clamp machinery directs quality control on the lagging strand and CMG enforces quality control on the leading strand. PMID:28069954

  20. The poultry-associated microbiome: network analysis and farm-to-fork characterizations.

    Directory of Open Access Journals (Sweden)

    Brian B Oakley

    Full Text Available Microbial communities associated with agricultural animals are important for animal health, food safety, and public health. Here we combine high-throughput sequencing (HTS, quantitative-PCR assays, and network analysis to profile the poultry-associated microbiome and important pathogens at various stages of commercial poultry production from the farm to the consumer. Analysis of longitudinal data following two flocks from the farm through processing showed a core microbiome containing multiple sequence types most closely related to genera known to be pathogenic for animals and/or humans, including Campylobacter, Clostridium, and Shigella. After the final stage of commercial poultry processing, taxonomic richness was ca. 2-4 times lower than the richness of fecal samples from the same flocks and Campylobacter abundance was significantly reduced. Interestingly, however, carcasses sampled at 48 hr after processing harboured the greatest proportion of unique taxa (those not encountered in other samples, significantly more than expected by chance. Among these were anaerobes such as Prevotella, Veillonella, Leptrotrichia, and multiple Campylobacter sequence types. Retail products were dominated by Pseudomonas, but also contained 27 other genera, most of which were potentially metabolically active and encountered in on-farm samples. Network analysis was focused on the foodborne pathogen Campylobacter and revealed a majority of sequence types with no significant interactions with other taxa, perhaps explaining the limited efficacy of previous attempts at competitive exclusion of Campylobacter. These data represent the first use of HTS to characterize the poultry microbiome across a series of farm-to-fork samples and demonstrate the utility of HTS in monitoring the food supply chain and identifying sources of potential zoonoses and interactions among taxa in complex communities.