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Sample records for differential nucleotide excision

  1. Nucleotide excision repair in differentiated cells

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    Wees, Caroline van der [Department of Toxicogenetics, Leiden University Medical Center, Leiden (Netherlands); Department of Cardiology, Leiden University Medical Center, Leiden (Netherlands); Jansen, Jacob [Department of Toxicogenetics, Leiden University Medical Center, Leiden (Netherlands); Vrieling, Harry [Department of Toxicogenetics, Leiden University Medical Center, Leiden (Netherlands); Laarse, Arnoud van der [Department of Cardiology, Leiden University Medical Center, Leiden (Netherlands); Zeeland, Albert van [Department of Toxicogenetics, Leiden University Medical Center, Leiden (Netherlands); Mullenders, Leon [Department of Toxicogenetics, Leiden University Medical Center, Leiden (Netherlands)]. E-mail: l.mullenders@lumc.nl

    2007-01-03

    Nucleotide excision repair (NER) is the principal pathway for the removal of a wide range of DNA helix-distorting lesions and operates via two NER subpathways, i.e. global genome repair (GGR) and transcription-coupled repair (TCR). Although detailed information is available on expression and efficiency of NER in established mammalian cell lines, little is known about the expression of NER pathways in (terminally) differentiated cells. The majority of studies in differentiated cells have focused on repair of UV-induced cyclobutane pyrimidine dimers (CPD) and 6-4-photoproducts (6-4PP) because of the high frequency of photolesions at low level of toxicity and availability of sensitive technologies to determine photolesions in defined regions of the genome. The picture that emerges from these studies is blurred and rather complex. Fibroblasts and terminally differentiated myocytes of the rat heart display equally efficient GGR of 6-4PP but poor repair of CPD due to the absence of p48 expression. This repair phenotype is clearly different from human terminal differentiated neurons. Furthermore, both cell types were found to carry out TCR of CPD, thus mimicking the repair phenotype of established rodent cell lines. In contrast, in intact rat spermatogenic cells repair was very inefficient at the genome overall level and in transcriptionally active genes indicating that GGR and TCR are non-functional. Also, non-differentiated mouse embryonic stem (ES) cells exhibit low levels of NER after UV irradiation. However, the mechanisms that lead to low NER activity are clearly different: in differentiated spermatogenic cells differences in chromatin compaction and sequestering of NER proteins may underlie the lack of NER activity in pre-meiotic cells, whereas in non-differentiated ES cells NER is impaired by a strong apoptotic response.

  2. Nucleotide excision repair in yeast

    NARCIS (Netherlands)

    Eijk, Patrick van

    2012-01-01

    Nucleotide Excision Repair (NER) is a conserved DNA repair pathway capable of removing a broad spectrum of DNA damage. In human cells a defect in NER leads to the disorder Xeroderma pigmentosum (XP). The yeast Saccharomyces cerevisiae is an excellent model organism to study the mechanism of NER. The

  3. Nucleotide excision repair in the test tube.

    NARCIS (Netherlands)

    N.G.J. Jaspers (Nicolaas); J.H.J. Hoeijmakers (Jan)

    1995-01-01

    textabstractThe eukaryotic nucleotide excision-repair pathway has been reconstituted in vitro, an achievement that should hasten the full enzymological characterization of this highly complex DNA-repair pathway.

  4. Histone displacement during nucleotide excision repair

    DEFF Research Database (Denmark)

    Dinant, C.; Bartek, J.; Bekker-Jensen, S.

    2012-01-01

    Nucleotide excision repair (NER) is an important DNA repair mechanism required for cellular resistance against UV light and toxic chemicals such as those found in tobacco smoke. In living cells, NER efficiently detects and removes DNA lesions within the large nuclear macromolecular complex called...... of histone variants and histone displacement (including nucleosome sliding). Here we review current knowledge, and speculate about current unknowns, regarding those chromatin remodeling activities that physically displace histones before, during and after NER. © 2012 by the authors; licensee MDPI, Basel...

  5. Regulation of nucleotide excision repair through ubiquitination

    Institute of Scientific and Technical Information of China (English)

    Jia Li; Audesh Bhat; Wei Xiao

    2011-01-01

    Nucleotide excision repair (NER) is the most versatile DNA-repair pathway in all organisms.While bacteria require only three proteins to complete the incision step of NER,eukaryotes employ about 30 proteins to complete the same step.Here we summarize recent studies demonstrating that ubiquitination,a post-translational modification,plays critical roles in regulating the NER activity either dependent on or independent of ubiquitin-proteolysis.Several NER components have been shown as targets of ubiquitination while others are actively involved in the ubiquitination process.We argue through this analysis that ubiquitination serves to coordinate various steps of NER and meanwhile connect NER with other related pathways to achieve the efficient global DNA-damage response.

  6. Nucleotide Excision Repair in Caenorhabditis elegans

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    Hannes Lans

    2011-01-01

    Full Text Available Nucleotide excision repair (NER plays an essential role in many organisms across life domains to preserve and faithfully transmit DNA to the next generation. In humans, NER is essential to prevent DNA damage-induced mutation accumulation and cell death leading to cancer and aging. NER is a versatile DNA repair pathway that repairs many types of DNA damage which distort the DNA helix, such as those induced by solar UV light. A detailed molecular model of the NER pathway has emerged from in vitro and live cell experiments, particularly using model systems such as bacteria, yeast, and mammalian cell cultures. In recent years, the versatility of the nematode C. elegans to study DNA damage response (DDR mechanisms including NER has become increasingly clear. In particular, C. elegans seems to be a convenient tool to study NER during the UV response in vivo, to analyze this process in the context of a developing and multicellular organism, and to perform genetic screening. Here, we will discuss current knowledge gained from the use of C. elegans to study NER and the response to UV-induced DNA damage.

  7. Modulation of DNA base excision repair during neuronal differentiation

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    Sykora, Peter; Yang, Jenq-Lin; Ferrarelli, Leslie K

    2013-01-01

    Neurons are terminally differentiated cells with a high rate of metabolism and multiple biological properties distinct from their undifferentiated precursors. Previous studies showed that nucleotide excision DNA repair is downregulated in postmitotic muscle cells and neurons. Here, we characterize...... DNA damage susceptibility and base excision DNA repair (BER) capacity in undifferentiated and differentiated human neural cells. The results show that undifferentiated human SH-SY5Y neuroblastoma cells are less sensitive to oxidative damage than their differentiated counterparts, in part because...

  8. Nucleotide excision repair syndromes: molecular basis and clinical symptoms.

    NARCIS (Netherlands)

    D. Bootsma (Dirk); G. Weeda (Geert); W. Vermeulen (Wim); H. van Vuuren; C. Troelstra (Christine); J.H.J. Hoeijmakers (Jan); P.J. van der Spek (Peter)

    1995-01-01

    textabstractThe phenotypic consequences of a nucleotide excision repair (NER) defect in man are apparent from three distinct inborn diseases characterized by hypersensitivity of the skin to ultraviolet light and a remarkable clinical and genetic heterogeneity. These are the prototype repair

  9. Nucleotide excision repair of DNA: The very early history.

    Science.gov (United States)

    Friedberg, Errol C

    2011-07-15

    This article, taken largely from the book Correcting the Blueprint of Life: An Historical Account of the Discovery of DNA Repair Mechanisms, summarizes the very early history of the discovery of nucleotide excision repair. Copyright © 2011 Elsevier B.V. All rights reserved.

  10. Nucleosome positioning, nucleotide excision repair and photoreactivation in Saccharomyces cerevisiae.

    Science.gov (United States)

    Guintini, Laetitia; Charton, Romain; Peyresaubes, François; Thoma, Fritz; Conconi, Antonio

    2015-12-01

    The position of nucleosomes on DNA participates in gene regulation and DNA replication. Nucleosomes can be repressors by limiting access of factors to regulatory sequences, or activators by facilitating binding of factors to exposed DNA sequences on the surface of the core histones. The formation of UV induced DNA lesions, like cyclobutane pyrimidine dimers (CPDs), is modulated by DNA bending around the core histones. Since CPDs are removed by nucleotide excision repair (NER) and photolyase repair, it is of paramount importance to understand how DNA damage and repair are tempered by the position of nucleosomes. In vitro, nucleosomes inhibit NER and photolyase repair. In vivo, nucleosomes slow down NER and considerably obstruct photoreactivation of CPDs. However, over-expression of photolyase allows repair of nucleosomal DNA in a second time scale. It is proposed that the intrinsic abilities of nucleosomes to move and transiently unwrap could facilitate damage recognition and repair in nucleosomal DNA.

  11. Eukaryotic nucleotide excision repair: from understanding mechanisms to influencing biology

    Institute of Scientific and Technical Information of China (English)

    Sarah C Shuck; Emily A Short; John J Turchi

    2008-01-01

    Repair of bulky DNA adducts by the nucleotide excision repair (NER) pathway is one of the more versatile DNA repair pathways for the removal of DNA lesions. There are two subsets of the NER pathway, global genomic-NER (GG-NER) and transcription-coupled NER (TC-NER), which differ only in the step involving recognition of the DNA lesion. Following recognition of the damage, the sub-pathways then converge for the incision/excision steps and subsequent gap filling and ligation steps. This review will focus on the GGR sub-pathway of NER while the TCR sub-pathway will be covered in another article in this issue. The ability of the NER pathway to repair a wide array of adducts stems, in part, from the mechanisms involved in the initial recognition step of the damaged DNA and results in NER impacting an equally wide array of human physiological responses and events. In this review, the impact of NER on carcinogenesis, neurological function, sensitivity to environmental factors and sensitivity to cancer therapeutics will be discussed. The knowledge generated in our understanding of the NER pathway over the past 40 years has resulted from advances in the fields of animal model systems, mammalian genetics and in vitro biochemistry, as well as from reconstitution studies and structural analyses of the proteins and enzymes that participate in this pathway. Each of these avenues of research has contributed significantly to our understanding of how the NER pathway works and how alterations in NER activity, both positive and negative, influence human biology.

  12. Base Sequence Context Effects on Nucleotide Excision Repair

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    Yuqin Cai

    2010-01-01

    Full Text Available Nucleotide excision repair (NER plays a critical role in maintaining the integrity of the genome when damaged by bulky DNA lesions, since inefficient repair can cause mutations and human diseases notably cancer. The structural properties of DNA lesions that determine their relative susceptibilities to NER are therefore of great interest. As a model system, we have investigated the major mutagenic lesion derived from the environmental carcinogen benzo[a]pyrene (B[a]P, 10S (+-trans-anti-B[a]P-2-dG in six different sequence contexts that differ in how the lesion is positioned in relation to nearby guanine amino groups. We have obtained molecular structural data by NMR and MD simulations, bending properties from gel electrophoresis studies, and NER data obtained from human HeLa cell extracts for our six investigated sequence contexts. This model system suggests that disturbed Watson-Crick base pairing is a better recognition signal than a flexible bend, and that these can act in concert to provide an enhanced signal. Steric hinderance between the minor groove-aligned lesion and nearby guanine amino groups determines the exact nature of the disturbances. Both nearest neighbor and more distant neighbor sequence contexts have an impact. Regardless of the exact distortions, we hypothesize that they provide a local thermodynamic destabilization signal for repair.

  13. Regulation of nucleotide excision repair by nuclear lamin b1.

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    Veronika Butin-Israeli

    Full Text Available The nuclear lamins play important roles in the structural organization and function of the metazoan cell nucleus. Recent studies on B-type lamins identified a requirement for lamin B1 (LB1 in the regulation of cell proliferation in normal diploid cells. In order to further investigate the function of LB1 in proliferation, we disrupted its normal expression in U-2 OS human osteosarcoma and other tumor cell lines. Silencing LB1 expression induced G1 cell cycle arrest without significant apoptosis. The arrested cells are unable to mount a timely and effective response to DNA damage induced by UV irradiation. Several proteins involved in the detection and repair of UV damage by the nucleotide excision repair (NER pathway are down-regulated in LB1 silenced cells including DDB1, CSB and PCNA. We propose that LB1 regulates the DNA damage response to UV irradiation by modulating the expression of specific genes and activating persistent DNA damage signaling. Our findings are relevant to understanding the relationship between the loss of LB1 expression, DNA damage signaling, and replicative senescence.

  14. Implication of Posttranslational Histone Modifications in Nucleotide Excision Repair

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    Shisheng Li

    2012-09-01

    Full Text Available Histones are highly alkaline proteins that package and order the DNA into chromatin in eukaryotic cells. Nucleotide excision repair (NER is a conserved multistep reaction that removes a wide range of generally bulky and/or helix-distorting DNA lesions. Although the core biochemical mechanism of NER is relatively well known, how cells detect and repair lesions in diverse chromatin environments is still under intensive research. As with all DNA-related processes, the NER machinery must deal with the presence of organized chromatin and the physical obstacles it presents. A huge catalogue of posttranslational histone modifications has been documented. Although a comprehensive understanding of most of these modifications is still lacking, they are believed to be important regulatory elements for many biological processes, including DNA replication and repair, transcription and cell cycle control. Some of these modifications, including acetylation, methylation, phosphorylation and ubiquitination on the four core histones (H2A, H2B, H3 and H4 or the histone H2A variant H2AX, have been found to be implicated in different stages of the NER process. This review will summarize our recent understanding in this area.

  15. Nucleotide Excision Repair in Cellular Chromatin: Studies with Yeast from Nucleotide to Gene to Genome

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    Simon Reed

    2012-09-01

    Full Text Available Here we review our development of, and results with, high resolution studies on global genome nucleotide excision repair (GGNER in Saccharomyces cerevisiae. We have focused on how GGNER relates to histone acetylation for its functioning and we have identified the histone acetyl tranferase Gcn5 and acetylation at lysines 9/14 of histone H3 as a major factor in enabling efficient repair. We consider results employing primarily MFA2 as a model gene, but also those with URA3 located at subtelomeric sequences. In the latter case we also see a role for acetylation at histone H4. We then go on to outline the development of a high resolution genome-wide approach that enables one to examine correlations between histone modifications and the nucleotide excision repair (NER of UV-induced cyclobutane pyrimidine dimers throughout entire genomes. This is an approach that will enable rapid advances in understanding the complexities of how compacted chromatin in chromosomes is processed to access DNA damage and then returned to its pre-damaged status to maintain epigenetic codes.

  16. Nucleotide excision repair: ERCC1 and TFIIH complexes

    NARCIS (Netherlands)

    A.J. van Vuuren (Hanneke)

    1995-01-01

    textabstractDNA is the carrier of genetic information in living organisms. The information stored in the nucleotide sequence of DNA is transmitted to the offspring by generating identical copies of the parental DNA molecules. Damage in DNA can cause loss of genetic information. Nevertheless, the DNA

  17. The Fanconi anaemia components UBE2T and FANCM are functionally linked to nucleotide excision repair.

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    Ian R Kelsall

    Full Text Available The many proteins that function in the Fanconi anaemia (FA monoubiquitylation pathway initiate replicative DNA crosslink repair. However, it is not clear whether individual FA genes participate in DNA repair pathways other than homologous recombination and translesion bypass. Here we show that avian DT40 cell knockouts of two integral FA genes--UBE2T and FANCM are unexpectedly sensitive to UV-induced DNA damage. Comprehensive genetic dissection experiments indicate that both of these FA genes collaborate to promote nucleotide excision repair rather than translesion bypass to protect cells form UV genotoxicity. Furthermore, UBE2T deficiency impacts on the efficient removal of the UV-induced photolesion cyclobutane pyrimidine dimer. Therefore, this work reveals that the FA pathway shares two components with nucleotide excision repair, intimating not only crosstalk between the two major repair pathways, but also potentially identifying a UBE2T-mediated ubiquitin-signalling response pathway that contributes to nucleotide excision repair.

  18. Nucleotide excision repair in intact cells contrasts with high dual incision activity in vitro

    NARCIS (Netherlands)

    Jansen, J.; Olsen, A.K.; Wiger, R.; Naegeli, H.; Boer, de P.; Hoeven, van der F.; Holme, J.A.; Brunborg, G.; Mullenders, L.

    2001-01-01

    The acquisition of genotoxin-induced mutations in the mammalian germline is detrimental to the stable transfer of genomic information. In somatic cells, nucleotide excision repair (NER) is a major pathway to counteract the mutagenic effects of DNA damage. Two NER subpathways have been identified, gl

  19. Transcription-coupled nucleotide excision repair in mammalian cells: molecular mechanisms and biological effects

    Institute of Scientific and Technical Information of China (English)

    Mafia Fousteri; Leon HF Mullenders

    2008-01-01

    The encounter of elongating RNA polymerase Ⅱ (RNAPIIo) with DNA lesions has severe consequences for the cell as this event provides a strong signal for P53-dependent apoptosis and cell cycle arrest. To counteract prolonged blockage of transcription, the cell removes the RNAPllo-hlocking DNA lesions by transcription-coupled repair (TC-NER), a specialized subpathway of nucleotide excision repair (NER). Exposure of mice to UVB light or chemicals has elucidated that TC-NER is a critical survival pathway protecting against acute toxic and long-term effects (cancer) of genotoxic exposure. Deficiency in TC-NER is associated with mutations in the CSA and CSB genes giving rise to the rare hu-man disorder Cockayne syndrome (CS). Recent data suggest that CSA and CSB play differential roles in mammalian TC-NER: CSB as a repair coupling factor to attract NER proteins, chromatin remodellers and the CSA- E3-ubiquitin iigase complex to the stalled RNAPI io. CSA is dispensable for attraction of NER proteins, yet in cooperation with CSB is required to recruit XAB2, the nucleosomal binding protein HMGNl and TFIIS. The emerging picture of TC-NER is complex: repair of transcription-blocking lesions occurs without displacement of the DNA damage-stalled RNAPIIo, and requires at least two essential assembly factors (CSA and CSB), the core NER factors (except for XPC-RAD23B), and TC-NER specific factors. These and yet unidentified proteins will accomplish not only efficient repair of transcrip-tion-blocking lesions, but are also likely to contribute to DNA damage signalling events.

  20. Recombination-dependent deletion formation in mammalian cells deficient in the nucleotide excision repair gene ERCC1

    OpenAIRE

    Sargent, R. Geoffrey; Rolig, Rhonda L.; Kilburn, April E.; Adair, Gerald M.; Wilson, John H.; Nairn, Rodney S.

    1997-01-01

    Nucleotide excision repair proteins have been implicated in genetic recombination by experiments in Saccharomyces cerevisiae and Drosophila melanogaster, but their role, if any, in mammalian cells is undefined. To investigate the role of the nucleotide excision repair gene ERCC1, the hamster homologue to the S. cerevisiae RAD10 gene, we disabled the gene by targeted knockout. Partial tandem duplications of the adenine phosphoribosyltransferase (APRT) gene then were constructed at the endogeno...

  1. Early days of DNA repair: discovery of nucleotide excision repair and homology-dependent recombinational repair.

    Science.gov (United States)

    Rupp, W Dean

    2013-12-13

    The discovery of nucleotide excision repair in 1964 showed that DNA could be repaired by a mechanism that removed the damaged section of a strand and replaced it accurately by using the remaining intact strand as the template. This result showed that DNA could be actively metabolized in a process that had no precedent. In 1968, experiments describing postreplication repair, a process dependent on homologous recombination, were reported. The authors of these papers were either at Yale University or had prior Yale connections. Here we recount some of the events leading to these discoveries and consider the impact on further research at Yale and elsewhere.

  2. Nucleotide excision repair pathway assessment in DNA exposed to low-intensity red and infrared lasers.

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    Fonseca, A S; Campos, V M A; Magalhães, L A G; Paoli, F

    2015-10-01

    Low-intensity lasers are used for prevention and management of oral mucositis induced by anticancer therapy, but the effectiveness of treatment depends on the genetic characteristics of affected cells. This study evaluated the survival and induction of filamentation of Escherichia coli cells deficient in the nucleotide excision repair pathway, and the action of T4endonuclease V on plasmid DNA exposed to low-intensity red and near-infrared laser light. Cultures of wild-type (strain AB1157) E. coli and strain AB1886 (deficient in uvrA protein) were exposed to red (660 nm) and infrared (808 nm) lasers at various fluences, powers and emission modes to study bacterial survival and filamentation. Also, plasmid DNA was exposed to laser light to study DNA lesions produced in vitro by T4endonuclease V. Low-intensity lasers:i) had no effect on survival of wild-type E. coli but decreased the survival of uvrA protein-deficient cells,ii) induced bacterial filamentation, iii) did not alter the electrophoretic profile of plasmids in agarose gels, andiv) did not alter the electrophoretic profile of plasmids incubated with T4 endonuclease V. These results increase our understanding of the effects of laser light on cells with various genetic characteristics, such as xeroderma pigmentosum cells deficient in nucleotide excision pathway activity in patients with mucositis treated by low-intensity lasers.

  3. Nucleotide excision repair pathway assessment in DNA exposed to low-intensity red and infrared lasers

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    Fonseca, A.S.; Campos, V.M.A.; Magalhaes, L.A.G., E-mail: adnfonseca@ig.com.br [Instituto de Biologia Roberto Alcantara Gomes, Rio de Janeiro, RJ (Brazil). Departamento de Biofisica e Biometria. Lab. de Ciencias Radiologicas; Paoli, F. [Universidade Federal de Juiz de Fora (UFJF), Juiz de Fora, MG (Brazil). Instituto de Ciencias Biologicas. Departamento de Morfologia

    2015-10-15

    Low-intensity lasers are used for prevention and management of oral mucositis induced by anticancer therapy, but the effectiveness of treatment depends on the genetic characteristics of affected cells. This study evaluated the survival and induction of filamentation of Escherichia coli cells deficient in the nucleotide excision repair pathway, and the action of T{sub 4} endonuclease V on plasmid DNA exposed to low-intensity red and near-infrared laser light. Cultures of wild-type (strain AB1157) E. coli and strain AB1886 (deficient in uvrA protein) were exposed to red (660 nm) and infrared (808 nm) lasers at various fluences, powers and emission modes to study bacterial survival and filamentation. Also, plasmid DNA was exposed to laser light to study DNA lesions produced in vitro by T{sub 4} endonuclease V. Low-intensity lasers: i) had no effect on survival of wild-type E. coli but decreased the survival of uvrA protein-deficient cells, ii) induced bacterial filamentation, iii) did not alter the electrophoretic profile of plasmids in agarose gels, and iv) did not alter the electrophoretic profile of plasmids incubated with T{sub 4} endonuclease V. These results increase our understanding of the effects of laser light on cells with various genetic characteristics, such as xeroderma pigmentosum cells deficient in nucleotide excision pathway activity in patients with mucositis treated by low-intensity lasers. (author)

  4. Transcription-coupled nucleotide excision repair factors promote R-loop-induced genome instability.

    Science.gov (United States)

    Sollier, Julie; Stork, Caroline Townsend; García-Rubio, María L; Paulsen, Renee D; Aguilera, Andrés; Cimprich, Karlene A

    2014-12-18

    R-loops, consisting of an RNA-DNA hybrid and displaced single-stranded DNA, are physiological structures that regulate various cellular processes occurring on chromatin. Intriguingly, changes in R-loop dynamics have also been associated with DNA damage accumulation and genome instability; however, the mechanisms underlying R-loop-induced DNA damage remain unknown. Here we demonstrate in human cells that R-loops induced by the absence of diverse RNA processing factors, including the RNA/DNA helicases Aquarius (AQR) and Senataxin (SETX), or by the inhibition of topoisomerase I, are actively processed into DNA double-strand breaks (DSBs) by the nucleotide excision repair endonucleases XPF and XPG. Surprisingly, DSB formation requires the transcription-coupled nucleotide excision repair (TC-NER) factor Cockayne syndrome group B (CSB), but not the global genome repair protein XPC. These findings reveal an unexpected and potentially deleterious role for TC-NER factors in driving R-loop-induced DNA damage and genome instability.

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

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

    2015-06-15

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

  6. Transcription-coupled nucleotide excision repair factors promote R-loop-induced genome instability

    Science.gov (United States)

    Sollier, Julie; Stork, Caroline Townsend; García-Rubio, María L.; Paulsen, Renee D.; Aguilera, Andrés; Cimprich, Karlene A.

    2014-01-01

    Summary R-loops, consisting of an RNA-DNA hybrid and displaced single-stranded DNA, are physiological structures that regulate various cellular processes occurring on chromatin. Intriguingly, changes in R-loop dynamics have also been associated with DNA damage accumulation and genome instability, however the mechanisms underlying R-loop induced DNA damage remain unknown. Here we demonstrate in human cells that R-loops induced by the absence of diverse RNA processing factors, including the RNA/DNA helicases Aquarius (AQR) and Senataxin (SETX), or by the inhibition of topoisomerase I, are actively processed into DNA double-strand breaks (DSBs) by the nucleotide excision repair endonucleases XPF and XPG. Surprisingly, DSB formation requires the transcription-coupled nucleotide excision repair (TC-NER) factor Cockayne syndrome group B (CSB), but not the global genome repair protein XPC. These findings reveal an unexpected and potentially deleterious role for TC-NER factors in driving R-loop-induced DNA damage and genome instability. PMID:25435140

  7. Transcriptional and Posttranslational Regulation of Nucleotide Excision Repair: The Guardian of the Genome against Ultraviolet Radiation

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    Jeong-Min Park

    2016-11-01

    Full Text Available Ultraviolet (UV radiation from sunlight represents a constant threat to genome stability by generating modified DNA bases such as cyclobutane pyrimidine dimers (CPD and pyrimidine-pyrimidone (6-4 photoproducts (6-4PP. If unrepaired, these lesions can have deleterious effects, including skin cancer. Mammalian cells are able to neutralize UV-induced photolesions through nucleotide excision repair (NER. The NER pathway has multiple components including seven xeroderma pigmentosum (XP proteins (XPA to XPG and numerous auxiliary factors, including ataxia telangiectasia and Rad3-related (ATR protein kinase and RCC1 like domain (RLD and homologous to the E6-AP carboxyl terminus (HECT domain containing E3 ubiquitin protein ligase 2 (HERC2. In this review we highlight recent data on the transcriptional and posttranslational regulation of NER activity.

  8. Photoreactive DNA as a tool for studying topography of nucleotide excision repair complex

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    Lavrik O. I.

    2012-06-01

    Full Text Available Nucleotide excision repair (NER is one of the major DNA repair pathways in eukaryotic cells preventing genetic abnormalities caused by DNA damage. NER removes a wide set of structurally diverse lesions such as pyrimidine dimers arising upon UV irradiation and bulky chemical adducts arising upon exposure to environmental carcinogens or chemotherapeutic drugs. In view of the extraordinarily broad substrate specificity of NER, it is of interest to understand how a certain set of proteins recognizes various DNA lesions in the context of a large excess of intact DNA. This review focuses on contribution of photoaffinity labeling technique in the study of DNA damage recognition and following stages resulting in preincision complex assembly, the key and still most unclear steps of NER.

  9. Regulation of global genome nucleotide excision repair by SIRT1 through xeroderma pigmentosum C

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    Ming, Mei; Shea, Christopher R.; Guo, Xiumei; Li, Xiaoling; Soltani, Keyoumars; Han, Weinong; He, Yu-Ying

    2010-01-01

    Disruption of the nucleotide excision repair (NER) pathway by mutations can cause xeroderma pigmentosum, a syndrome predisposing affected individuals to development of skin cancer. The xeroderma pigmentosum C (XPC) protein is essential for initiating global genome NER by recognizing the DNA lesion and recruiting downstream factors. Here we show that inhibition of the deacetylase and longevity factor SIRT1 impairs global genome NER through suppressing the transcription of XPC in a SIRT1 deacetylase-dependent manner. SIRT1 enhances XPC expression by reducing AKT-dependent nuclear localization of the transcription repressor of XPC. Finally, we show that SIRT1 levels are significantly reduced in human skin tumors from Caucasian patients, a population at highest risk. These findings suggest that SIRT1 acts as a tumor suppressor through its role in DNA repair. PMID:21149730

  10. E2F1 and p53 Transcription Factors as Accessory Factors for Nucleotide Excision Repair

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    David G. Johnson

    2012-10-01

    Full Text Available Many of the biochemical details of nucleotide excision repair (NER have been established using purified proteins and DNA substrates. In cells however, DNA is tightly packaged around histones and other chromatin-associated proteins, which can be an obstacle to efficient repair. Several cooperating mechanisms enhance the efficiency of NER by altering chromatin structure. Interestingly, many of the players involved in modifying chromatin at sites of DNA damage were originally identified as regulators of transcription. These include ATP-dependent chromatin remodelers, histone modifying enzymes and several transcription factors. The p53 and E2F1 transcription factors are well known for their abilities to regulate gene expression in response to DNA damage. This review will highlight the underappreciated, transcription-independent functions of p53 and E2F1 in modifying chromatin structure in response to DNA damage to promote global NER.

  11. Structural and Functional Studies on Nucleotide Excision Repair From Recognition to Incision.

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    Caroline Kisker

    2001-01-01

    Maintenance of the correct genetic information is crucial for all living organisms because mutations are the primary cause of hereditary diseases, as well as cancer and may also be involved in aging. The importance of genomic integrity is underscored by the fact that 80 to 90% of all human cancers are ultimately due to DNA damage. Among the different repair mechanisms that have evolved to protect the genome, nucleotide excision repair (NER) is a universal pathway found in all organisms. NER removes a wide variety of bulky DNA adducts including the carcinogenic cyclobutane pyrimidine dimers induced by UV radiation, benzo(a)pyrene-guanine adducts caused by smoking and the guanine-cisplatin adducts induced by chemotherapy. The importance of this repair mechanism is reflected by three severe inherited diseases in humans, which are due to defects in NER: xeroderma pigmentosum, Cockayne's syndrome and trichothiodystrophy.

  12. Polymorphisms in nucleotide excision repair genes, smoking and intake of fruit and vegetables in relation to lung cancer

    DEFF Research Database (Denmark)

    Raaschou-Nielsen, Ole; Sørensen, Mette; Overvad, Kim

    2007-01-01

    Polymorphisms in nucleotide excision repair genes have been associated with risk for lung cancer. We examined gene-environment interactions in relation to lung cancer in 430 cases and 790 comparison persons identified within a prospective cohort of 57,053 persons. We included polymorphisms...... in the XPC, XPA and XPD genes involved in the nucleotide excision DNA repair pathway and analysed possible interactions with smoking and dietary intake of fruit and vegetables in relation to risk for lung cancer. We found that intake of fruit was associated with lower risk for lung cancer only among carriers...

  13. Genetic polymorphisms in the nucleotide excision repair pathway and lung cancer risk: A meta-analysis

    Directory of Open Access Journals (Sweden)

    Chikako Kiyohara, Kouichi Yoshimasu

    2007-01-01

    Full Text Available Various DNA alterations can be caused by exposure to environmental and endogenous carcinogens. Most of these alterations, if not repaired, can result in genetic instability, mutagenesis and cell death. DNA repair mechanisms are important for maintaining DNA integrity and preventing carcinogenesis. Recent lung cancer studies have focused on identifying the effects of single nucleotide polymorphisms (SNPs in candidate genes, among which DNA repair genes are increasingly being studied. Genetic variations in DNA repair genes are thought to modulate DNA repair capacity and are suggested to be related to lung cancer risk. We identified a sufficient number of epidemiologic studies on lung cancer to conduct a meta-analysis for genetic polymorphisms in nucleotide excision repair pathway genes, focusing on xeroderma pigmentosum group A (XPA, excision repair cross complementing group 1 (ERCC1, ERCC2/XPD, ERCC4/XPF and ERCC5/XPG. We found an increased risk of lung cancer among subjects carrying the ERCC2 751Gln/Gln genotype (odds ratio (OR = 1.30, 95% confidence interval (CI = 1.14 - 1.49. We found a protective effect of the XPA 23G/G genotype (OR = 0.75, 95% CI = 0.59 - 0.95. Considering the data available, it can be conjectured that if there is any risk association between a single SNP and lung cancer, the risk fluctuation will probably be minimal. Advances in the identification of new polymorphisms and in high-throughput genotyping techniques will facilitate the analysis of multiple genes in multiple DNA repair pathways. Therefore, it is likely that the defining feature of future epidemiologic studies will be the simultaneous analysis of large samples.

  14. Nucleotide excision repair is not induced in human embryonic lung fibroblasts treated with environmental pollutants.

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    Pavel Rossner

    Full Text Available The cellular response to genotoxic treatment depends on the cell line used. Although tumor cell lines are widely used for genotoxicity tests, the interpretation of the results may be potentially hampered by changes in cellular processes caused by malignant transformation. In our study we used normal human embryonic lung fibroblasts (HEL12469 cells and tested their response to treatment with benzo[a]pyrene (B[a]P and extractable organic matter (EOM from ambient air particles <2.5 µm (PM2.5 collected in two Czech cities differing in levels and sources of air pollution. We analyzed multiple endpoints associated with exposure to polycyclic aromatic hydrocarbons (PAHs including the levels of bulky DNA adducts and the nucleotide excision repair (NER response [expression of XPE, XPC and XPA genes on the level of mRNA and proteins, unscheduled DNA synthesis (UDS]. EOMs were collected in the winter and summer of 2011 in two Czech cities with different levels and sources of air pollution. The effects of the studied compounds were analyzed in the presence (+S9 and absence (-S9 of the rat liver microsomal S9 fraction. The levels of bulky DNA adducts were highest after treatment with B[a]P, followed by winter EOMs; their induction by summer EOMs was weak. The induction of both mRNA and protein expression was observed, with the most pronounced effects after treatment with B[a]P (-S9; the response induced by EOMs from both cities and seasons was substantially weaker. The expression of DNA repair genes was not accompanied by the induction of UDS activity. In summary, our results indicate that the tested compounds induced low levels of DNA damage and affected the expression of NER genes; however, nucleotide excision repair was not induced.

  15. True Lies: The Double Life of the Nucleotide Excision Repair Factors in Transcription and DNA Repair

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    Nicolas Le May

    2010-01-01

    Full Text Available Nucleotide excision repair (NER is a major DNA repair pathway in eukaryotic cells. NER removes structurally diverse lesions such as pyrimidine dimers, arising upon UV irradiation or bulky chemical adducts, arising upon exposure to carcinogens and some chemotherapeutic drugs. NER defects lead to three genetic disorders that result in predisposition to cancers, accelerated aging, neurological and developmental defects. During NER, more than 30 polypeptides cooperate to recognize, incise, and excise a damaged oligonucleotide from the genomic DNA. Recent papers reveal an additional and unexpected role for the NER factors. In the absence of a genotoxic attack, the promoters of RNA polymerases I- and II-dependent genes recruit XPA, XPC, XPG, and XPF to initiate gene expression. A model that includes the growth arrest and DNA damage 45α protein (Gadd45α and the NER factors, in order to maintain the promoter of active genes under a hypomethylated state, has been proposed but remains controversial. This paper focuses on the double life of the NER factors in DNA repair and transcription and describes the possible roles of these factors in the RNA synthesis process.

  16. Removal of misincorporated ribonucleotides from prokaryotic genomes: an unexpected role for nucleotide excision repair.

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    Alexandra Vaisman

    2013-11-01

    Full Text Available Stringent steric exclusion mechanisms limit the misincorporation of ribonucleotides by high-fidelity DNA polymerases into genomic DNA. In contrast, low-fidelity Escherichia coli DNA polymerase V (pol V has relatively poor sugar discrimination and frequently misincorporates ribonucleotides. Substitution of a steric gate tyrosine residue with alanine (umuC_Y11A reduces sugar selectivity further and allows pol V to readily misincorporate ribonucleotides as easily as deoxynucleotides, whilst leaving its poor base-substitution fidelity essentially unchanged. However, the mutability of cells expressing the steric gate pol V mutant is very low due to efficient repair mechanisms that are triggered by the misincorporated rNMPs. Comparison of the mutation frequency between strains expressing wild-type and mutant pol V therefore allows us to identify pathways specifically directed at ribonucleotide excision repair (RER. We previously demonstrated that rNMPs incorporated by umuC_Y11A are efficiently removed from DNA in a repair pathway initiated by RNase HII. Using the same approach, we show here that mismatch repair and base excision repair play minimal back-up roles in RER in vivo. In contrast, in the absence of functional RNase HII, umuC_Y11A-dependent mutagenesis increases significantly in ΔuvrA, uvrB5 and ΔuvrC strains, suggesting that rNMPs misincorporated into DNA are actively repaired by nucleotide excision repair (NER in vivo. Participation of NER in RER was confirmed by reconstituting ribonucleotide-dependent NER in vitro. We show that UvrABC nuclease-catalyzed incisions are readily made on DNA templates containing one, two, or five rNMPs and that the reactions are stimulated by the presence of mispaired bases. Similar to NER of DNA lesions, excision of rNMPs proceeds through dual incisions made at the 8(th phosphodiester bond 5' and 4(th-5(th phosphodiester bonds 3' of the ribonucleotide. Ribonucleotides misinserted into DNA can therefore be

  17. Localized degradation of foreign DNA strands in cells: Only excising the first nucleotide of 5' region.

    Science.gov (United States)

    Li, Hui; Shen, Wei; Lam, Michael Hon-Wah; Liang, Haojun

    2017-09-15

    Intracellular delivery of foreign DNA probes sharply increases the efficiency of various biodetection protocols. Spherical nucleic acid (SNA) conjugate is a new type of probe that consists of a dense oligonucleotide shell attached typically to a gold nanoparticle core. They are widely used as novel labels for in vitro biodetection and intracellular assay. However, the degradation of foreign DNA still remains a challenge that can cause significant signal leakage (false positive signal). Hence, the site and behavior of intracellular degradation need to be investigated. Herein, we discover a localized degradation behavior that only excises the first nucleotide of 5' terminal from a DNA strand, whereas the residual portion of this strand is unbroken in MCF-7 cell. This novel degradation action totally differs from previous opinion that foreign DNA strand would be digested into tiny fragments or even individual nucleotides in cellular environment. On the basis of these findings, we propose a simple and effective way to avoid degradation-caused false positive that one can bypass the degradable site and choose a secure region to label fluorophore along the DNA stand, when using DNA probes for intracellular biodetection. Copyright © 2017 Elsevier Inc. All rights reserved.

  18. Deletion of the nucleotide excision repair gene Ercc1 reduces immunoglobulin class switching and alters mutations near switch recombination junctions

    NARCIS (Netherlands)

    C.E. Schrader; J. Vardo; E. Linehan; M.Z. Twarog; L.J. Niedernhofer (Laura); J. Stavnezer; J.H.J. Hoeijmakers (Jan)

    2004-01-01

    textabstractThe structure-specific endonuclease ERCC1-XPF is an essential component of the nucleotide excision DNA repair pathway. ERCC1-XPF nicks double-stranded DNA immediately adjacent to 3' single-strand regions. Substrates include DNA bubbles and flaps. Furthermore, ERCC1 interacts with Msh2, a

  19. Replication factor c recruits dna polymerase δ to sites of nucleotide excision repair but is not required for PCNA recruitment

    NARCIS (Netherlands)

    R.M. Overmeer (René); A.M. Gourdin (Audrey); G. Giglia-Mari (Giuseppina); H. Kool (Hanneke); A.B. Houtsmuller (Adriaan); T. Siegal (Tali); M.I. Fousteri (Maria); L.H.F. Mullenders (Leon); W. Vermeulen (Wim)

    2010-01-01

    textabstractNucleotide excision repair (NER) operates through coordinated assembly of repair factors into pre- and postincisioncomplexes. The postincision step of NER includes gap-filling DNA synthesis and ligation. However, the exact composition of this NER-associated DNA synthesis complex in vivo

  20. XPC and human homologs of RAD23: intracellular localization and relationship to other nucleotide excision repair complexes.

    NARCIS (Netherlands)

    P.J. van der Spek (Peter); A.P.M. Eker (André); S. Rademakers (Suzanne); C.E. Visser (Cécile); K. Sugasawa (Kaoru); C. Masutani (Chikahide); F. Hanaoka (Fumio); D. Bootsma (Dirk); J.H.J. Hoeijmakers (Jan)

    1996-01-01

    textabstractThe xeroderma pigmentosum syndrome complementation group C (XP-C) is due to a defect in the global genome repair subpathway of nucleotide excision repair (NER). The XPC protein is complexed with HHR23B, one of the two human homologs of the yeast NER protein, RAD23 (Masutani at al. (1994)

  1. Cloning, comparative mapping, and RNA expression of the mouse homologues of the Saccharomyces cerevisiae nucleotide excision repair gene RAD23.

    NARCIS (Netherlands)

    P.J. van der Spek (Peter); C.E. Visser (Cécile); F. Hanaoka (Fumio); B. Smit (Bep); A. Hagemeijer (Anne); D. Bootsma (Dirk); J.H.J. Hoeijmakers (Jan)

    1996-01-01

    textabstractThe Saccharomyces cerevisiae RAD23 gene is involved in nucleotide excision repair (NER). Two human homologs of RAD23, HHR23A and HHR23B (HGMW-approved symbols RAD23A and RAD23B), were previously isolated. The HHR23B protein is complexed with the protein defective in the cancer-prone

  2. Fluorescence correlation spectroscopy of the binding of nucleotide excision repair protein XPC-hHr23B with DNA substrates

    NARCIS (Netherlands)

    Y. Roche; D. Zhang (Dan); G.M. Segers-Nolten; W. Vermeulen (Wim); C. Wyman (Claire); K. Sugasawa (Kaoru); J.H.J. Hoeijmakers (Jan); C. Otto

    2008-01-01

    textabstractThe interaction of the nucleotide excision repair (NER) protein dimeric complex XPC-hHR23B, which is implicated in the DNA damage recognition step, with three Cy3.5 labeled 90-bp double-stranded DNA substrates (unmodified, with a central unpaired region, and cholesterol modified) and a 9

  3. New design of nucleotide excision repair (NER) inhibitors for combination cancer therapy.

    Science.gov (United States)

    Gentile, Francesco; Tuszynski, Jack A; Barakat, Khaled H

    2016-04-01

    Many cancer chemotherapy agents act by targeting the DNA of cancer cells, causing substantial damage within their genome and causing them to undergo apoptosis. An effective DNA repair pathway in cancer cells can act in a reverse way by removing these drug-induced DNA lesions, allowing cancer cells to survive, grow and proliferate. In this context, DNA repair inhibitors opened a new avenue in cancer treatment, by blocking the DNA repair mechanisms from removing the chemotherapy-mediated DNA damage. In particular, the nucleotide excision repair (NER) involves more than thirty protein-protein interactions and removes DNA adducts caused by platinum-based chemotherapy. The excision repair cross-complementation group 1 (ERCC1)-xeroderma pigmentosum, complementation group A (XPA) protein (XPA-ERCC1) complex seems to be one of the most promising targets in this pathway. ERCC1 is over expressed in cancer cells and the only known cellular function so far for XPA is to recruit ERCC1 to the damaged point. Here, we build upon our recent advances in identifying inhibitors for this interaction and continue our efforts to rationally design more effective and potent regulators for the NER pathway. We employed in silico drug design techniques to: (1) identify compounds similar to the recently discovered inhibitors, but more effective at inhibiting the XPA-ERCC1 interactions, and (2) identify different scaffolds to develop novel lead compounds. Two known inhibitor structures have been used as starting points for two ligand/structure-hybrid virtual screening approaches. The findings described here form a milestone in discovering novel inhibitors for the NER pathway aiming at improving the efficacy of current platinum-based therapy, by modulating the XPA-ERCC1 interaction.

  4. Conservation of the nucleotide excision repair pathway: characterization of hydra Xeroderma Pigmentosum group F homolog.

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    Apurva Barve

    Full Text Available Hydra, one of the earliest metazoans with tissue grade organization and nervous system, is an animal with a remarkable regeneration capacity and shows no signs of organismal aging. We have for the first time identified genes of the nucleotide excision repair (NER pathway from hydra. Here we report cloning and characterization of hydra homolog of xeroderma pigmentosum group F (XPF gene that encodes a structure-specific 5' endonuclease which is a crucial component of NER. In silico analysis shows that hydra XPF amino acid sequence is very similar to its counterparts from other animals, especially vertebrates, and shows all features essential for its function. By in situ hybridization, we show that hydra XPF is expressed prominently in the multipotent stem cell niche in the central region of the body column. Ectoderm of the diploblastic hydra was shown to express higher levels of XPF as compared to the endoderm by semi-quantitative RT-PCR. Semi-quantitative RT-PCR analysis also demonstrated that interstitial cells, a multipotent and rapidly cycling stem cell lineage of hydra, express higher levels of XPF mRNA than other cell types. Our data show that XPF and by extension, the NER pathway is highly conserved during evolution. The prominent expression of an NER gene in interstitial cells may have implications for the lack of senescence in hydra.

  5. 17{alpha}-Ethinylestradiol hinders nucleotide excision repair in zebrafish liver cells

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    Notch, Emily G. [Department of Biochemistry, Microbiology and Molecular Biology, University of Maine 5735 Hitchner Hall, Orono, ME 04469 (United States); Mayer, Gregory D., E-mail: greg.mayer@ttu.edu [The Institute of Environmental and Human Health, Texas Tech University, Box 41163, Lubbock, TX 79409-1163 (United States)

    2009-12-13

    Nucleotide excision repair (NER) is the primary mechanism that removes bulky DNA adducts such as those caused by ubiquitous environmental mutagens including benzo(a)pyrene and other polycyclic aromatic hydrocarbons. Recent data suggest that exposure to environmentally relevant concentrations of estrogen decreases hepatic mRNA abundance of several key NER genes in adult zebrafish (Danio rerio). However, the impact of decreased hepatic NER expression on NER function was not investigated in the previous study. The goal of this study was to examine the effect of the potent estrogen receptor agonist 17{alpha}-ethinylestradiol (EE{sub 2}) on rate and magnitude of bulky DNA adduct repair. Here we show that exposure of zebrafish liver (ZFL) cells to physiologically relevant concentrations of EE{sub 2} resulted in reduced ability of ZFL cells to repair damaged DNA in comparison to control cells. Co-exposure to EE{sub 2} and a complete estrogen receptor antagonist (ICI 182,780) also resulted in reduced NER capacity, whereas ICI 182,780 alone did not affect the ability of ZFL cells to repair UV damage. These results indicate that estrogen exposure can decrease cellular NER capacity and that this effect can occur in the presence of an estrogen receptor antagonist, suggesting that EE{sub 2} can affect NER processes through mechanisms other than nuclear estrogen receptor activation.

  6. Transcription coupled nucleotide excision repair in the yeast Saccharomyces cerevisiae: The ambiguous role of Rad26.

    Science.gov (United States)

    Li, Shisheng

    2015-12-01

    Transcription coupled nucleotide excision repair (TC-NER) is believed to be triggered by an RNA polymerase stalled at a lesion in the transcribed strand of actively transcribed genes. Rad26, a DNA-dependent ATPase in the family of SWI2/SNF2 chromatin remodeling proteins, plays an important role in TC-NER in Saccharomyces cerevisiae. However, Rad26 is not solely responsible for TC-NER and Rpb9, a nonessential subunit of RNA polymerase II (RNAP II), is largely responsible for Rad26-independent TC-NER. The Rad26-dependent and Rpb9-dependent TC-NER have different efficiencies in genes with different transcription levels and in different regions of a gene. Rad26 becomes entirely or partially dispensable for TC-NER in the absence of Rpb4, another nonessential subunit of RNAP II, or a number of transcription elongation factors (Spt4, Spt5 and the RNAP II associated factor complex). Rad26 may not be a true transcription-repair coupling factor that recruits the repair machinery to the damaged sites where RNAP II stalls. Rather, Rad26 may facilitate TC-NER indirectly, by antagonizing the action of TC-NER repressors that normally promote transcription elongation. The underlying mechanism of how Rad26 functions in TC-NER remains to be elucidated.

  7. CBP and p300 acetylate PCNA to link its degradation with nucleotide excision repair synthesis.

    Science.gov (United States)

    Cazzalini, Ornella; Sommatis, Sabrina; Tillhon, Micol; Dutto, Ilaria; Bachi, Angela; Rapp, Alexander; Nardo, Tiziana; Scovassi, A Ivana; Necchi, Daniela; Cardoso, M Cristina; Stivala, Lucia A; Prosperi, Ennio

    2014-07-01

    The proliferating cell nuclear antigen (PCNA) protein serves as a molecular platform recruiting and coordinating the activity of factors involved in multiple deoxyribonucleic acid (DNA) transactions. To avoid dangerous genome instability, it is necessary to prevent excessive retention of PCNA on chromatin. Although PCNA functions during DNA replication appear to be regulated by different post-translational modifications, the mechanism regulating PCNA removal and degradation after nucleotide excision repair (NER) is unknown. Here we report that CREB-binding protein (CBP), and less efficiently p300, acetylated PCNA at lysine (Lys) residues Lys13,14,77 and 80, to promote removal of chromatin-bound PCNA and its degradation during NER. Mutation of these residues resulted in impaired DNA replication and repair, enhanced the sensitivity to ultraviolet radiation, and prevented proteolytic degradation of PCNA after DNA damage. Depletion of both CBP and p300, or failure to load PCNA on DNA in NER deficient cells, prevented PCNA acetylation and degradation, while proteasome inhibition resulted in accumulation of acetylated PCNA. These results define a CBP and p300-dependent mechanism for PCNA acetylation after DNA damage, linking DNA repair synthesis with removal of chromatin-bound PCNA and its degradation, to ensure genome stability.

  8. The Emerging Roles of ATP-Dependent Chromatin Remodeling Enzymes in Nucleotide Excision Repair

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    Wioletta Czaja

    2012-09-01

    Full Text Available DNA repair in eukaryotic cells takes place in the context of chromatin, where DNA, including damaged DNA, is tightly packed into nucleosomes and higher order chromatin structures. Chromatin intrinsically restricts accessibility of DNA repair proteins to the damaged DNA and impacts upon the overall rate of DNA repair. Chromatin is highly responsive to DNA damage and undergoes specific remodeling to facilitate DNA repair. How damaged DNA is accessed, repaired and restored to the original chromatin state, and how chromatin remodeling coordinates these processes in vivo, remains largely unknown. ATP-dependent chromatin remodelers (ACRs are the master regulators of chromatin structure and dynamics. Conserved from yeast to humans, ACRs utilize the energy of ATP to reorganize packing of chromatin and control DNA accessibility by sliding, ejecting or restructuring nucleosomes. Several studies have demonstrated that ATP-dependent remodeling activity of ACRs plays important roles in coordination of spatio-temporal steps of different DNA repair pathways in chromatin. This review focuses on the role of ACRs in regulation of various aspects of nucleotide excision repair (NER in the context of chromatin. We discuss current understanding of ATP-dependent chromatin remodeling by various subfamilies of remodelers and regulation of the NER pathway in vivo.

  9. The nucleotide excision repair pathway is required for UV-C-induced apoptosis in Caenorhabditis elegans.

    Science.gov (United States)

    Stergiou, L; Doukoumetzidis, K; Sendoel, A; Hengartner, M O

    2007-06-01

    Ultraviolet (UV) radiation is a mutagen of major clinical importance in humans. UV-induced damage activates multiple signaling pathways, which initiate DNA repair, cell cycle arrest and apoptosis. To better understand these pathways, we studied the responses to UV-C light (254 nm) of germ cells in Caenorhabditis elegans. We found that UV activates the same cellular responses in worms as in mammalian cells. Both UV-induced apoptosis and cell cycle arrest were completely dependent on the p53 homolog CEP-1, the checkpoint proteins HUS-1 and CLK-2, and the checkpoint kinases CHK-2 and ATL-1 (the C. elegans homolog of ataxia telangiectasia and Rad3-related); ATM-1 (ataxia telangiectasia mutated-1) was also required, but only at low irradiation doses. Importantly, mutation of genes encoding nucleotide excision repair pathway components severely disrupted both apoptosis and cell cycle arrest, suggesting that these genes not only participate in repair, but also signal the presence of damage to downstream components of the UV response pathway that we delineate here. Our study suggests that whereas DNA damage response pathways are conserved in metazoans in their general outline, there is significant evolution in the relative importance of individual checkpoint genes in the response to specific types of DNA damage.

  10. Global genome nucleotide excision repair is organized into domains that promote efficient DNA repair in chromatin

    Science.gov (United States)

    Yu, Shirong; Evans, Katie; Bennett, Mark; Webster, Richard M.; Leadbitter, Matthew; Teng, Yumin; Waters, Raymond

    2016-01-01

    The rates at which lesions are removed by DNA repair can vary widely throughout the genome, with important implications for genomic stability. To study this, we measured the distribution of nucleotide excision repair (NER) rates for UV-induced lesions throughout the budding yeast genome. By plotting these repair rates in relation to genes and their associated flanking sequences, we reveal that, in normal cells, genomic repair rates display a distinctive pattern, suggesting that DNA repair is highly organized within the genome. Furthermore, by comparing genome-wide DNA repair rates in wild-type cells and cells defective in the global genome–NER (GG-NER) subpathway, we establish how this alters the distribution of NER rates throughout the genome. We also examined the genomic locations of GG-NER factor binding to chromatin before and after UV irradiation, revealing that GG-NER is organized and initiated from specific genomic locations. At these sites, chromatin occupancy of the histone acetyl-transferase Gcn5 is controlled by the GG-NER complex, which regulates histone H3 acetylation and chromatin structure, thereby promoting efficient DNA repair of UV-induced lesions. Chromatin remodeling during the GG-NER process is therefore organized into these genomic domains. Importantly, loss of Gcn5 significantly alters the genomic distribution of NER rates; this has implications for the effects of chromatin modifiers on the distribution of mutations that arise throughout the genome. PMID:27470111

  11. The Role of Altered Nucleotide Excision Repair and UVB-Induced DNA Damage in Melanomagenesis

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    Timothy Budden

    2013-01-01

    Full Text Available UVB radiation is the most mutagenic component of the UV spectrum that reaches the earth’s surface and causes the development of DNA damage in the form of cyclobutane pyrimidine dimers and 6-4 photoproducts. UV radiation usually results in cellular death, but if left unchecked, it can affect DNA integrity, cell and tissue homeostasis and cause mutations in oncogenes and tumour-suppressor genes. These mutations, if unrepaired, can lead to abnormal cell growth, increasing the risk of cancer development. Epidemiological data strongly associates UV exposure as a major factor in melanoma development, but the exact biological mechanisms involved in this process are yet to be fully elucidated. The nucleotide excision repair (NER pathway is responsible for the repair of UV-induced lesions. Patients with the genetic disorder Xeroderma Pigmentosum have a mutation in one of eight NER genes associated with the XP complementation groups XP-A to XP-G and XP variant (XP-V. XP is characterized by diminished repair capacity, as well as a 1000-fold increase in the incidence of skin cancers, including melanoma. This has suggested a significant role for NER in melanoma development as a result of UVB exposure. This review discusses the current research surrounding UVB radiation and NER capacity and how further investigation of NER could elucidate the role of NER in avoiding UV-induced cellular death resulting in melanomagenesis.

  12. A UV-induced genetic network links the RSC complex to nucleotide excision repair and shows dose-dependent rewiring.

    Science.gov (United States)

    Srivas, Rohith; Costelloe, Thomas; Carvunis, Anne-Ruxandra; Sarkar, Sovan; Malta, Erik; Sun, Su Ming; Pool, Marijke; Licon, Katherine; van Welsem, Tibor; van Leeuwen, Fred; McHugh, Peter J; van Attikum, Haico; Ideker, Trey

    2013-12-26

    Efficient repair of UV-induced DNA damage requires the precise coordination of nucleotide excision repair (NER) with numerous other biological processes. To map this crosstalk, we generated a differential genetic interaction map centered on quantitative growth measurements of >45,000 double mutants before and after different doses of UV radiation. Integration of genetic data with physical interaction networks identified a global map of 89 UV-induced functional interactions among 62 protein complexes, including a number of links between the RSC complex and several NER factors. We show that RSC is recruited to both silenced and transcribed loci following UV damage where it facilitates efficient repair by promoting nucleosome remodeling. Finally, a comparison of the response to high versus low levels of UV shows that the degree of genetic rewiring correlates with dose of UV and reveals a network of dose-specific interactions. This study makes available a large resource of UV-induced interactions, and it illustrates a methodology for identifying dose-dependent interactions based on quantitative shifts in genetic networks.

  13. A UV-Induced Genetic Network Links the RSC Complex to Nucleotide Excision Repair and Shows Dose-Dependent Rewiring

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    Rohith Srivas

    2013-12-01

    Full Text Available Efficient repair of UV-induced DNA damage requires the precise coordination of nucleotide excision repair (NER with numerous other biological processes. To map this crosstalk, we generated a differential genetic interaction map centered on quantitative growth measurements of >45,000 double mutants before and after different doses of UV radiation. Integration of genetic data with physical interaction networks identified a global map of 89 UV-induced functional interactions among 62 protein complexes, including a number of links between the RSC complex and several NER factors. We show that RSC is recruited to both silenced and transcribed loci following UV damage where it facilitates efficient repair by promoting nucleosome remodeling. Finally, a comparison of the response to high versus low levels of UV shows that the degree of genetic rewiring correlates with dose of UV and reveals a network of dose-specific interactions. This study makes available a large resource of UV-induced interactions, and it illustrates a methodology for identifying dose-dependent interactions based on quantitative shifts in genetic networks.

  14. Deficiency in nucleotide excision repair family gene activity, especially ERCC3, is associated with non-pigmented hair fiber growth.

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    Mei Yu

    Full Text Available We conducted a microarray study to discover gene expression patterns associated with a lack of melanogenesis in non-pigmented hair follicles (HF by microarray. Pigmented and non-pigmented HFs were collected and micro-dissected into the hair bulb (HB and the upper hair sheaths (HS including the bulge region. In comparison to pigmented HS and HBs, nucleotide excision repair (NER family genes ERCC1, ERCC2, ERCC3, ERCC4, ERCC5, ERCC6, XPA, NTPBP, HCNP, DDB2 and POLH exhibited statistically significantly lower expression in non- pigmented HS and HBs. Quantitative PCR verified microarray data and identified ERCC3 as highly differentially expressed. Immunohistochemistry confirmed ERCC3 expression in HF melanocytes. A reduction in ERCC3 by siRNA interference in human melanocytes in vitro reduced their tyrosinase production ability. Our results suggest that loss of NER gene function is associated with a loss of melanin production capacity. This may be due to reduced gene transcription and/or reduced DNA repair in melanocytes which may eventually lead to cell death. These results provide novel information with regard to melanogenesis and its regulation.

  15. Defective transcription initiation causes postnatal growth failure in a mouse model of nucleotide excision repair (NER) progeria

    Science.gov (United States)

    Kamileri, Irene; Karakasilioti, Ismene; Sideri, Aria; Kosteas, Theodoros; Tatarakis, Antonis; Talianidis, Iannis; Garinis, George A.

    2012-01-01

    Nucleotide excision repair (NER) defects are associated with cancer, developmental disorders and neurodegeneration. However, with the exception of cancer, the links between defects in NER and developmental abnormalities are not well understood. Here, we show that the ERCC1-XPF NER endonuclease assembles on active promoters in vivo and facilitates chromatin modifications for transcription during mammalian development. We find that Ercc1−/− mice demonstrate striking physiological, metabolic and gene expression parallels with Taf10−/− animals carrying a liver-specific transcription factor II D (TFIID) defect in transcription initiation. Promoter occupancy studies combined with expression profiling in the liver and in vitro differentiation cell assays reveal that ERCC1-XPF interacts with TFIID and assembles with POL II and the basal transcription machinery on promoters in vivo. Whereas ERCC1-XPF is required for the initial activation of genes associated with growth, it is dispensable for ongoing transcription. Recruitment of ERCC1-XPF on promoters is accompanied by promoter-proximal DNA demethylation and histone marks associated with active hepatic transcription. Collectively, the data unveil a role of ERCC1/XPF endonuclease in transcription initiation establishing its causal contribution to NER developmental disorders. PMID:22323595

  16. Decreased nucleotide excision repair in steatotic livers associates with myeloperoxidase-immunoreactivity

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    Schults, Marten A.; Nagle, Peter W. [Department of Toxicology, NUTRIM-School for Nutrition, Toxicology and Metabolism, Maastricht University Medical Centre, PO Box 616, 6200 MD Maastricht (Netherlands); Rensen, Sander S. [Department of Surgery, NUTRIM-School for Nutrition, Toxicology and Metabolism, Maastricht University Medical Centre, PO Box 616, 6200 MD Maastricht (Netherlands); Godschalk, Roger W. [Department of Toxicology, NUTRIM-School for Nutrition, Toxicology and Metabolism, Maastricht University Medical Centre, PO Box 616, 6200 MD Maastricht (Netherlands); Munnia, Armelle; Peluso, Marco [Cancer Risk Factor Branch, ISPO Cancer Prevention and Research Institute, Via Cosimo il Vecchio 2, 50139 Florence (Italy); Claessen, Sandra M. [Department of Toxicogenomics, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, PO Box 616, 6200 MD Maastricht (Netherlands); Greve, Jan W. [Department of Surgery, NUTRIM-School for Nutrition, Toxicology and Metabolism, Maastricht University Medical Centre, PO Box 616, 6200 MD Maastricht (Netherlands); Driessen, Ann [Department of Pathology, NUTRIM-School for Nutrition, Toxicology and Metabolism, Maastricht University Medical Centre, PO Box 616, 6200 MD Maastricht (Netherlands); Verdam, Froukje J.; Buurman, Wim A. [Department of Surgery, NUTRIM-School for Nutrition, Toxicology and Metabolism, Maastricht University Medical Centre, PO Box 616, 6200 MD Maastricht (Netherlands); Schooten, Frederik J. van [Department of Toxicology, NUTRIM-School for Nutrition, Toxicology and Metabolism, Maastricht University Medical Centre, PO Box 616, 6200 MD Maastricht (Netherlands); Chiu, Roland K., E-mail: r.k.chiu@med.umcg.nl [Department of Toxicology, NUTRIM-School for Nutrition, Toxicology and Metabolism, Maastricht University Medical Centre, PO Box 616, 6200 MD Maastricht (Netherlands)

    2012-08-01

    Chronic inflammation is characterized by the influx of neutrophils and is associated with an increased production of reactive oxygen species that can damage DNA. Oxidative DNA damage is generally thought to be involved in the increased risk of cancer in inflamed tissues. We previously demonstrated that activated neutrophil mediated oxidative stress results in a reduction in nucleotide excision repair (NER) capacity, which could further enhance mutagenesis. Inflammation and oxidative stress are critical factors in the progression of nonalcoholic fatty liver disease that is linked with enhanced liver cancer risk. In this report, we therefore evaluated the role of neutrophils and the associated oxidative stress in damage recognition and DNA repair in steatotic livers of 35 severely obese subjects with either nonalcoholic steatohepatitis (NASH) (n = 17) or steatosis alone (n = 18). The neutrophilic influx in liver was assessed by myeloperoxidase (MPO) staining and the amount of oxidative DNA damage by measuring M{sub 1}dG adducts. No differences in M{sub 1}dG adduct levels were observed between patients with or without NASH and also not between individuals with high or low MPO immunoreactivity. However, we found that high expression of MPO in the liver, irrespective of disease status, reduced the damage recognition capacity as determined by staining for histone 2AX phosphorylation ({gamma}H2AX). This reduction in {gamma}H2AX formation in individuals with high MPO immunoreactivity was paralleled by a significant decrease in NER capacity as assessed by a functional repair assay, and was not related to cell proliferation. Thus, the observed reduction in NER capacity upon hepatic inflammation is associated with and may be a consequence of reduced damage recognition. These findings suggest a novel mechanism of liver cancer development in patients with nonalcoholic fatty liver disease.

  17. Exposure of Human Lung Cells to Tobacco Smoke Condensate Inhibits the Nucleotide Excision Repair Pathway.

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    Nathaniel Holcomb

    Full Text Available Exposure to tobacco smoke is the number one risk factor for lung cancer. Although the DNA damaging properties of tobacco smoke have been well documented, relatively few studies have examined its effect on DNA repair pathways. This is especially true for the nucleotide excision repair (NER pathway which recognizes and removes many structurally diverse DNA lesions, including those introduced by chemical carcinogens present in tobacco smoke. The aim of the present study was to investigate the effect of tobacco smoke on NER in human lung cells. We studied the effect of cigarette smoke condensate (CSC, a surrogate for tobacco smoke, on the NER pathway in two different human lung cell lines; IMR-90 lung fibroblasts and BEAS-2B bronchial epithelial cells. To measure NER, we employed a slot-blot assay to quantify the introduction and removal of UV light-induced 6-4 photoproducts and cyclobutane pyrimidine dimers. We find a dose-dependent inhibition of 6-4 photoproduct repair in both cell lines treated with CSC. Additionally, the impact of CSC on the abundance of various NER proteins and their respective RNAs was investigated. The abundance of XPC protein, which is required for functional NER, is significantly reduced by treatment with CSC while the abundance of XPA protein, also required for NER, is unaffected. Both XPC and XPA RNA levels are modestly reduced by CSC treatment. Finally, treatment of cells with MG-132 abrogates the reduction in the abundance of XPC protein produced by treatment with CSC, suggesting that CSC enhances proteasome-dependent turnover of the protein that is mediated by ubiquitination. Together, these findings indicate that tobacco smoke can inhibit the same DNA repair pathway that is also essential for the removal of some of the carcinogenic DNA damage introduced by smoke itself, increasing the DNA damage burden of cells exposed to tobacco smoke.

  18. Nucleotide Excision Repair and Vitamin D--Relevance for Skin Cancer Therapy.

    Science.gov (United States)

    Pawlowska, Elzbieta; Wysokinski, Daniel; Blasiak, Janusz

    2016-04-06

    Ultraviolet (UV) radiation is involved in almost all skin cancer cases, but on the other hand, it stimulates the production of pre-vitamin D3, whose active metabolite, 1,25-dihydroxyvitamin D3 (1,25VD3), plays important physiological functions on binding with its receptor (vitamin D receptor, VDR). UV-induced DNA damages in the form of cyclobutane pyrimidine dimers or (6-4)-pyrimidine-pyrimidone photoproducts are frequently found in skin cancer and its precursors. Therefore, removing these lesions is essential for the prevention of skin cancer. As UV-induced DNA damages are repaired by nucleotide excision repair (NER), the interaction of 1,25VD3 with NER components can be important for skin cancer transformation. Several studies show that 1,25VD3 protects DNA against damage induced by UV, but the exact mechanism of this protection is not completely clear. 1,25VD3 was also shown to affect cell cycle regulation and apoptosis in several signaling pathways, so it can be considered as a potential modulator of the cellular DNA damage response, which is crucial for mutagenesis and cancer transformation. 1,25VD3 was shown to affect DNA repair and potentially NER through decreasing nitrosylation of DNA repair enzymes by NO overproduction by UV, but other mechanisms of the interaction between 1,25VD3 and NER machinery also are suggested. Therefore, the array of NER gene functioning could be analyzed and an appropriate amount of 1.25VD3 could be recommended to decrease UV-induced DNA damage important for skin cancer transformation.

  19. Nucleotide Excision Repair and Vitamin D—Relevance for Skin Cancer Therapy

    Directory of Open Access Journals (Sweden)

    Elzbieta Pawlowska

    2016-04-01

    Full Text Available Ultraviolet (UV radiation is involved in almost all skin cancer cases, but on the other hand, it stimulates the production of pre-vitamin D3, whose active metabolite, 1,25-dihydroxyvitamin D3 (1,25VD3, plays important physiological functions on binding with its receptor (vitamin D receptor, VDR. UV-induced DNA damages in the form of cyclobutane pyrimidine dimers or (6-4-pyrimidine-pyrimidone photoproducts are frequently found in skin cancer and its precursors. Therefore, removing these lesions is essential for the prevention of skin cancer. As UV-induced DNA damages are repaired by nucleotide excision repair (NER, the interaction of 1,25VD3 with NER components can be important for skin cancer transformation. Several studies show that 1,25VD3 protects DNA against damage induced by UV, but the exact mechanism of this protection is not completely clear. 1,25VD3 was also shown to affect cell cycle regulation and apoptosis in several signaling pathways, so it can be considered as a potential modulator of the cellular DNA damage response, which is crucial for mutagenesis and cancer transformation. 1,25VD3 was shown to affect DNA repair and potentially NER through decreasing nitrosylation of DNA repair enzymes by NO overproduction by UV, but other mechanisms of the interaction between 1,25VD3 and NER machinery also are suggested. Therefore, the array of NER gene functioning could be analyzed and an appropriate amount of 1.25VD3 could be recommended to decrease UV-induced DNA damage important for skin cancer transformation.

  20. ROLE OF INTERACTION OF XPF WITH RPA IN NUCLEOTIDE EXCISION REPAIR

    Science.gov (United States)

    Fisher, Laura A.; Bessho, Mika; Wakasugi, Mitsuo; Matsunaga, Tsukasa; Bessho, Tadayoshi

    2011-01-01

    Nucleotide excision repair (NER) is a very important defense system against various types of DNA damage and it is necessary for maintaining genomic stability. The molecular mechanism of NER has been studied in considerable detail, and it has been shown that proper protein-protein interactions among NER factors are critical for efficient repair. A structure-specific endonuclease, XPF-ERCC1, which makes the 5’ incision in NER, was shown to interact with a single-stranded DNA binding protein, RPA. However, the biological significance of this interaction was not studied in detail. We used the yeast two-hybrid assay to determine that XPF interacts with the p70 subunit of RPA. To further examine the role of this XPF-p70 interaction, a p70-interaction deficient mutant form of XPF that contains a single amino acid substitution in the N-terminus of XPF was isolated by the reverse yeast two-hybrid assay using randomly mutagenized XPF. Biochemical properties of this RPA-interaction deficient mutant XPF-ERCC1 are very similar to wild type XPF-ERCC1 in vitro. Interestingly, expression of this mutated form of XPF in the XPF-deficient Chinese hamster ovary (CHO) cell line, UV41, only partially restores NER activity and UV resistance in vivo compared to wild type XPF. We discovered that the RPA-interaction deficient XPF is not localized in nuclei and the mislocalization of XPF-ERCC1 prevents the complex from functioning in NER. PMID:21875596

  1. The mechanism of nucleotide excision repair-mediated UV-induced mutagenesis in nonproliferating cells.

    Science.gov (United States)

    Kozmin, Stanislav G; Jinks-Robertson, Sue

    2013-03-01

    Following the irradiation of nondividing yeast cells with ultraviolet (UV) light, most induced mutations are inherited by both daughter cells, indicating that complementary changes are introduced into both strands of duplex DNA prior to replication. Early analyses demonstrated that such two-strand mutations depend on functional nucleotide excision repair (NER), but the molecular mechanism of this unique type of mutagenesis has not been further explored. In the experiments reported here, an ade2 adeX colony-color system was used to examine the genetic control of UV-induced mutagenesis in nondividing cultures of Saccharomyces cerevisiae. We confirmed a strong suppression of two-strand mutagenesis in NER-deficient backgrounds and demonstrated that neither mismatch repair nor interstrand crosslink repair affects the production of these mutations. By contrast, proteins involved in the error-prone bypass of DNA damage (Rev3, Rev1, PCNA, Rad18, Pol32, and Rad5) and in the early steps of the DNA-damage checkpoint response (Rad17, Mec3, Ddc1, Mec1, and Rad9) were required for the production of two-strand mutations. There was no involvement, however, for the Pol η translesion synthesis DNA polymerase, the Mms2-Ubc13 postreplication repair complex, downstream DNA-damage checkpoint factors (Rad53, Chk1, and Dun1), or the Exo1 exonuclease. Our data support models in which UV-induced mutagenesis in nondividing cells occurs during the Pol ζ-dependent filling of lesion-containing, NER-generated gaps. The requirement for specific DNA-damage checkpoint proteins suggests roles in recruiting and/or activating factors required to fill such gaps.

  2. Impaired nucleotide excision repair pathway as a possible factor in pathogenesis of head and neck cancer

    Energy Technology Data Exchange (ETDEWEB)

    Sliwinski, T. [Department of Molecular Genetics, University of Lodz, Lodz (Poland); Markiewicz, L. [Department of Clinical Chemistry and Biochemistry, Medical University of Lodz, Lodz (Poland); Rusin, P. [Department of Molecular Genetics, University of Lodz, Lodz (Poland); Department of Clinical Chemistry and Biochemistry, Medical University of Lodz, Lodz (Poland); Kabzinski, J. [Department of Clinical Chemistry and Biochemistry, Medical University of Lodz, Lodz (Poland); Dziki, L. [Department of General and Colorectal Surgery, Medical University of Lodz, Lodz (Poland); Milonski, J.; Olszewski, J. [Department of Otolaryngology and Oncology, Medical University of Lodz, Lodz (Poland); Blaszczyk, J. [Department of Human Physiology, Medical University of Lodz, Lodz (Poland); Szemraj, J. [Department of Medical Biochemistry, Medical University of Lodz, Lodz (Poland); Majsterek, I., E-mail: ireneusz.majsterek@umed.lodz.pl [Department of Clinical Chemistry and Biochemistry, Medical University of Lodz, Lodz (Poland)

    2011-11-01

    Tobacco smoking is one of the major risk factors in pathogenesis of head and neck squamous cell carcinomas (HNSCC). Many of the chemical compounds present in tobacco are well-known carcinogens which form adducts with DNA. Cells remove these adducts mainly by the nucleotide excision repair pathway (NER). NER also eliminates a broad spectrum of pyrimidine dimers (CPD) and photo-products (6-4PP) induced by UV-radiation or DNA cross-links after cisplatin anti-cancer treatment. In this study DNA damage and repair was examined in peripheral blood lymphocytes obtained from 20 HNSCC patients and 20 healthy controls as well as HTB-43 larynx and SSC-25 tongue cancer cell lines. DNA repair kinetics in the examined cells after cisplatin or UV-radiation treatment were investigated using alkaline comet assay during 240 min of post-treatment incubation. MTT assay was used to analyse cell viability and the Annexin V-FITC kit specific for kinase-3 was employed to determine apoptosis after treating the cells with UV-radiation at dose range from 0.5 to 60 J/m{sup 2}. NER capability was assessed in vitro with cell extracts by the use of a bacterial plasmid irradiated with UV-light as a substrate for the repair. The results show that lymphocytes from HNSCC patients and HTB-43 or SSC-25 cancer cells were more sensitive to genotoxic treatment with UV-radiation and displayed impaired DNA repair. Also evidenced was a higher rate of apoptosis induction after UV-radiation treatment of lymphocytes from the HNSCC patients and the HTB-43 cancer cells than after treatment of those from healthy donors. Finally, our results showed that there was a significant decrease in NER capacity in HTB-43 or SSC-25 cancer cells as well as in peripheral blood lymphocytes of HNSCC patients compared to controls. In conclusion, we suggest that the impaired NER pathway might be a critical factor in pathogenesis of head and neck cancer.

  3. Gastroesophageal junction adenocarcinoma displays abnormalities in homologous recombination and nucleotide excision repair

    Directory of Open Access Journals (Sweden)

    Dewalt RI

    2014-02-01

    Full Text Available Robin I Dewalt,1 Kenneth A Kesler,2 Zane T Hammoud,3 LeeAnn Baldridge,4 Eyas M Hattab,4 Shadia I Jalal1,5 1Division of Hematology/Oncology, Department of Medicine, 2Cardiothoracic Division, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, USA; 3Henry Ford Hospital, Detroit, MI, USA; 4Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA; 5Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, IN, USA Objective: Esophageal adenocarcinoma (EAC continues to be a disease associated with high mortality. Among the factors leading to poor outcomes are innate resistance to currently available therapies, advanced stage at diagnosis, and complex biology. Platinum and ionizing radiation form the backbone of treatment for the majority of patients with EAC. Of the multiple processes involved in response to platinum chemotherapy or ionizing radiation, deoxyribonucleic acid (DNA repair has been a major player in cancer sensitivity to these agents. DNA repair defects have been described in various malignancies. The purpose of this study was to determine whether alterations in DNA repair are present in EAC compared with normal gastroesophageal tissues. Methods: We analyzed the expression of genes involved in homologous recombination (HR, nonhomologous end-joining, and nucleotide excision repair (NER pathways in 12 EAC tumor samples with their matched normal counterparts. These pathways were chosen because they are the main pathways involved in the repair of platinum- or ionizing-radiation-induced damage. In addition, abnormalities in these pathways have not been well characterized in EAC. Results: We identified increased expression of at least one HR gene in eight of the EAC tumor samples. Alterations in the expression of EME1, a structure-specific endonuclease involved in HR, were the most prevalent, with messenger (mRNA overexpression in six of the EAC samples

  4. Nrf1 CNC-bZIP protein promotes cell survival and nucleotide excision repair through maintaining glutathione homeostasis.

    Science.gov (United States)

    Han, Weinong; Ming, Mei; Zhao, Rui; Pi, Jingbo; Wu, Chunli; He, Yu-Ying

    2012-05-25

    Skin cancer is the most common cancer in the United States. Its major environmental risk factor is UVB radiation in sunlight. In response to UVB damage, epidermal keratinocytes activate a specific repair pathway, i.e. nucleotide excision repair, to remove UVB-induced DNA lesions. However, the regulation of UVB response is not fully understood. Here we show that the long isoform of the nuclear factor erythroid 2-related factor 1 (Nrf1, also called NFE2L1), a cytoprotective transcription factor critical for the expression of multiple antioxidant response element-dependent genes, plays an important role in the response of keratinocytes to UVB. Nrf1 loss sensitized keratinocytes to UVB-induced apoptosis by up-regulating the expression of the proapoptotic Bcl-2 family member Bik through reducing glutathione levels. Knocking down Bik reduced UVB-induced apoptosis in Nrf1-inhibited cells. In UVB-irradiated surviving cells, however, disruption of Nrf1 impaired nucleotide excision repair through suppressing the transcription of xeroderma pigmentosum C (XPC), a factor essential for initiating the global genome nucleotide excision repair by recognizing the DNA lesion and recruiting downstream factors. Nrf1 enhanced XPC expression by increasing glutathione availability but was independent of the transcription repressor of XPC. Adding XPC or glutathione restored the DNA repair capacity in Nrf1-inhibited cells. Finally, we demonstrate that Nrf1 levels are significantly reduced by UVB radiation in mouse skin and are lower in human skin tumors than in normal skin. These results indicate a novel role of Nrf1 in UVB-induced DNA damage repair and suggest Nrf1 as a tumor suppressor in the skin.

  5. Haploinsufficiency for BRCA1 is associated with normal levels of DNA nucleotide excision repair in breast tissue and blood lymphocytes

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    Johnson Jennifer M

    2005-06-01

    Full Text Available Abstract Background Screening mammography has had a positive impact on breast cancer mortality but cannot detect all breast tumors. In a small study, we confirmed that low power magnetic resonance imaging (MRI could identify mammographically undetectable tumors by applying it to a high risk population. Tumors detected by this new technology could have unique etiologies and/or presentations, and may represent an increasing proportion of clinical practice as new screening methods are validated and applied. A very important aspect of this etiology is genomic instability, which is associated with the loss of activity of the breast cancer-predisposing genes BRCA1 and BRCA2. In sporadic breast cancer, however, there is evidence for the involvement of a different pathway of DNA repair, nucleotide excision repair (NER, which remediates lesions that cause a distortion of the DNA helix, including DNA cross-links. Case presentation We describe a breast cancer patient with a mammographically undetectable stage I tumor identified in our MRI screening study. She was originally considered to be at high risk due to the familial occurrence of breast and other types of cancer, and after diagnosis was confirmed as a carrier of a Q1200X mutation in the BRCA1 gene. In vitro analysis of her normal breast tissue showed no differences in growth rate or differentiation potential from disease-free controls. Analysis of cultured blood lymphocyte and breast epithelial cell samples with the unscheduled DNA synthesis (UDS assay revealed no deficiency in NER. Conclusion As new breast cancer screening methods become available and cost effective, patients such as this one will constitute an increasing proportion of the incident population, so it is important to determine whether they differ from current patients in any clinically important ways. Despite her status as a BRCA1 mutation carrier, and her mammographically dense breast tissue, we did not find increased cell

  6. NDR1 modulates the UV-induced DNA-damage checkpoint and nucleotide excision repair

    Energy Technology Data Exchange (ETDEWEB)

    Park, Jeong-Min; Choi, Ji Ye [Department of Biological Science, Dong-A University, Busan (Korea, Republic of); Yi, Joo Mi [Research Center, Dongnam Institute of Radiological & Medical Sciences, Busan (Korea, Republic of); Chung, Jin Woong; Leem, Sun-Hee; Koh, Sang Seok [Department of Biological Science, Dong-A University, Busan (Korea, Republic of); Kang, Tae-Hong, E-mail: thkang@dau.ac.kr [Department of Biological Science, Dong-A University, Busan (Korea, Republic of)

    2015-06-05

    Nucleotide excision repair (NER) is the sole mechanism of UV-induced DNA lesion repair in mammals. A single round of NER requires multiple components including seven core NER factors, xeroderma pigmentosum A–G (XPA–XPG), and many auxiliary effector proteins including ATR serine/threonine kinase. The XPA protein helps to verify DNA damage and thus plays a rate-limiting role in NER. Hence, the regulation of XPA is important for the entire NER kinetic. We found that NDR1, a novel XPA-interacting protein, modulates NER by modulating the UV-induced DNA-damage checkpoint. In quiescent cells, NDR1 localized mainly in the cytoplasm. After UV irradiation, NDR1 accumulated in the nucleus. The siRNA knockdown of NDR1 delayed the repair of UV-induced cyclobutane pyrimidine dimers in both normal cells and cancer cells. It did not, however, alter the expression levels or the chromatin association levels of the core NER factors following UV irradiation. Instead, the NDR1-depleted cells displayed reduced activity of ATR for some set of its substrates including CHK1 and p53, suggesting that NDR1 modulates NER indirectly via the ATR pathway. - Highlights: • NDR1 is a novel XPA-interacting protein. • NDR1 accumulates in the nucleus in response to UV irradiation. • NDR1 modulates NER (nucleotide excision repair) by modulating the UV-induced DNA-damage checkpoint response.

  7. Detoxification of olefinic epoxides and nucleotide excision repair of epoxide-mediated DNA damage: Insights from animal models examining human sensitivity to 1,3-butadiene.

    Science.gov (United States)

    Wickliffe, Jeffrey K; Herring, Stacy M; Hallberg, Lance M; Galbert, Lori A; Masters, Oscar E; Ammenheuser, Marinel M; Xie, Jingwu; Friedberg, Errol C; Lloyd, R Stephen; Abdel-Rahman, Sherif Z; Ward, Jonathan B

    2007-03-20

    1,3-Butadiene (BD) is a well-documented mutagen and carcinogen in rodents and is currently classified as a probable carcinogen in humans. Studies investigating workers exposed to BD indicate that, in some plants, there may be an increased genetic risk, and that polymorphisms in biotransformation and DNA repair proteins may modulate genetic susceptibility. To investigate the role of genetic polymorphisms in microsomal epoxide hydrolase (mEH) or nucleotide excision repair (NER) in contributing to the mutagenicity of BD, we conducted a series of experiments in which mice lacking mEH or NER activity were exposed to BD by inhalation or to the reactive epoxide metabolites of BD (epoxybutene-EB or diepoxybutane-DEB) by i.p. injection. Genetic susceptibility was measured using the Hprt cloning assay. Both deficient strains of mouse were significantly more sensitive to the mutagenic effects of BD and the injected epoxides. These studies provide support for the critical role that mEH plays in the biotransformation of BD, and the role that NER plays in maintaining genomic integrity following exposure to BD. Additional studies are needed to examine the importance of base excision repair (BER) in maintaining genomic integrity, the differential formation of DNA and protein adducts in deficient strains, and the potential for enhanced sensitivity to BD genotoxicity in mice either lacking or deficient in both biotransformation and DNA repair activity.

  8. Recombination-dependent deletion formation in mammalian cells deficient in the nucleotide excision repair gene ERCC1.

    Science.gov (United States)

    Sargent, R G; Rolig, R L; Kilburn, A E; Adair, G M; Wilson, J H; Nairn, R S

    1997-11-25

    Nucleotide excision repair proteins have been implicated in genetic recombination by experiments in Saccharomyces cerevisiae and Drosophila melanogaster, but their role, if any, in mammalian cells is undefined. To investigate the role of the nucleotide excision repair gene ERCC1, the hamster homologue to the S. cerevisiae RADIO gene, we disabled the gene by targeted knockout. Partial tandem duplications of the adenine phosphoribosyltransferase (APRT) gene then were constructed at the endogenous APRT locus in ERCC1- and ERCC1+ cells. To detect the full spectrum of gene-altering events, we used a loss-of-function assay in which the parental APRT+ tandem duplication could give rise to APRT- cells by homologous recombination, gene rearrangement, or point mutation. Measurement of rates and analysis of individual APRT- products indicated that gene rearrangements (principally deletions) were increased at least 50-fold, whereas homologous recombination was affected little. The formation of deletions is not caused by a general effect of the ERCC1 deficiency on gene stability, because ERCC1- cell lines with a single wild-type copy of the APRT gene yielded no increase in deletions. Thus, deletion formation is dependent on the tandem duplication, and presumably the process of homologous recombination. Recombination-dependent deletion formation in ERCC1- cells is supported by a significant decrease in a particular class of crossover products that are thought to arise by repair of a heteroduplex intermediate in recombination. We suggest that the ERCC1 gene product in mammalian cells is involved in the processing of heteroduplex intermediates in recombination and that the misprocessed intermediates in ERCC1- cells are repaired by illegitimate recombination.

  9. Proteins of nucleotide and base excision repair pathways interact in mitochondria to protect from loss of subcutaneous fat, a hallmark of aging

    NARCIS (Netherlands)

    Y. Kamenisch (York); M.I. Fousteri (Maria); J. Knoch (Jennifer); A.K. Von Thaler (Anna Katherina); B. Fehrenbacher (Birgit); H. Kato (Hiroki); T. Becker (Tim); M.E.T. Dollé (Martijn); R. Kuiper (Ruud); M. Majora (Marc); M. Schaller (Martin); G.T.J. van der Horst (Gijsbertus); H. van Steeg (Harry); M. Röcken (Martin); D. Rapaport (Doron); J. Krutmann (Jean); L.H.F. Mullenders (Leon); M. Berneburg (Mark)

    2010-01-01

    textabstractDefects in the DNA repair mechanism nucleotide excision repair (NER) may lead to tumors in xeroderma pigmentosum (XP) or to premature aging with loss of subcutaneous fat in Cockayne syndrome (CS). Mutations of mitochondrial (mt)DNA play a role in aging, but a link between the

  10. Sealing of chromosomal DNA nicks during nucleotide excision repair requires XRCC1 and DNA ligase III alpha in a cell-cycle-specific manner

    NARCIS (Netherlands)

    Moser, Jill; Kool, Hanneke; Giakzidis, Ioannis; Caldecott, Keith; Mullenders, Leon H. F.; Fousteri, Maria I.

    2007-01-01

    Impaired gap filling and sealing of chromosomal DNA in nucleotide excision repair (NER) leads to genome instability. XRCC1-DNA ligase III alpha (XRCC1-Lig3) plays a central role in the repair of DNA single-strand breaks but has never been implicated in NER. Here we show that XRCC1-Lig3 is indispensa

  11. The UV-damaged DNA binding protein mediates efficient targeting of the nucleotide excision repair complex to UV-induced photo lesions

    NARCIS (Netherlands)

    Moser, J; Volker, M; Kool, H; Alekseev, S; Vrieling, H; Yasui, A; van Zeeland, AA; Mullenders, LHF

    2005-01-01

    Previous studies point to the XPC-hHR23B complex as the principal initiator of global genome nucleotide excision repair (NER) pathway, responsible for the repair of UV-induced cyclobutane pyrimidine dimers (CPD) and 6-4 photoproducts (6-4PP) in human cells. However, the UV-damaged DNA binding protei

  12. Influence of nucleotide excision repair on N-hydroxy-2-acetylaminofluorene-induced mutagenesis studied in λlacZ-transgenic mice

    NARCIS (Netherlands)

    Frijhoff, A.F.W.; Krul, C.A.M.; Vries, A. de; Kelders, M.C.J.M.; Weeda, G.; Steeg, H. van; Baan, R.A.

    1998-01-01

    To study the influence of nucleotide excision repair (NER) on mutagenesis in vivo, ERCC1+/-, XPA-/-, and wild-type (ERCC1+/+ and XPA+/+, respectively) λlacZ-transgenic mice were treated i.p. with N-hydroxy-2-acetylaminofluorene (N-OH-AAF) and lacZ mutant frequencies were determined in liver. No sign

  13. First reported patient with human ERCC1 deficiency has cerebro-oculo-facio- skeletal syndrome with a mild defect in nucleotide excision repair and severe developmental failure

    NARCIS (Netherlands)

    N.G.J. Jaspers (Nicolaas); A. Raams (Anja); M.C. Silengo; N. Wijgers (Nils); L.J. Niedernhofer (Laura); A.R. Robinson (Andria Rasile); G. Giglia-Mari (Giuseppina); D. Hoogstraten (Deborah); W.J. Kleijer (Wim); J.H.J. Hoeijmakers (Jan); W. Vermeulen (Wim)

    2007-01-01

    textabstractNucleotide excision repair (NER) is a genome caretaker mechanism responsible for removing helix-distorting DNA lesions, most notably ultraviolet photodimers. Inherited defects in NER result in profound photosensitivity and the cancer-prone syndrome xeroderma pigmentosum (XP) or two

  14. First reported patient with human ERCC1 deficiency has cerebro-oculo-facio- skeletal syndrome with a mild defect in nucleotide excision repair and severe developmental failure

    NARCIS (Netherlands)

    N.G.J. Jaspers (Nicolaas); A. Raams (Anja); M.C. Silengo; N. Wijgers (Nils); L.J. Niedernhofer (Laura); A.R. Robinson (Andria Rasile); G. Giglia-Mari (Giuseppina); D. Hoogstraten (Deborah); W.J. Kleijer (Wim); J.H.J. Hoeijmakers (Jan); W. Vermeulen (Wim)

    2007-01-01

    textabstractNucleotide excision repair (NER) is a genome caretaker mechanism responsible for removing helix-distorting DNA lesions, most notably ultraviolet photodimers. Inherited defects in NER result in profound photosensitivity and the cancer-prone syndrome xeroderma pigmentosum (XP) or two proge

  15. Sealing of chromosomal DNA nicks during nucleotide excision repair requires XRCC1 and DNA ligase III alpha in a cell-cycle-specific manner

    NARCIS (Netherlands)

    Moser, Jill; Kool, Hanneke; Giakzidis, Ioannis; Caldecott, Keith; Mullenders, Leon H. F.; Fousteri, Maria I.

    2007-01-01

    Impaired gap filling and sealing of chromosomal DNA in nucleotide excision repair (NER) leads to genome instability. XRCC1-DNA ligase III alpha (XRCC1-Lig3) plays a central role in the repair of DNA single-strand breaks but has never been implicated in NER. Here we show that XRCC1-Lig3 is

  16. Transcription-induced CAG repeat contraction in human cells is mediated in part by transcription-coupled nucleotide excision repair.

    Science.gov (United States)

    Lin, Yunfu; Wilson, John H

    2007-09-01

    Expansions of CAG repeat tracts in the germ line underlie several neurological diseases. In human patients and mouse models, CAG repeat tracts display an ongoing instability in neurons, which may exacerbate disease symptoms. It is unclear how repeats are destabilized in nondividing cells, but it cannot involve DNA replication. We showed previously that transcription through CAG repeats induces their instability (Y. Lin, V. Dion, and J. H. Wilson, Nat. Struct. Mol. Biol. 13:179-180). Here, we present a genetic analysis of the link between transcription-induced repeat instability and nucleotide excision repair (NER) in human cells. We show that short interfering RNA-mediated knockdown of CSB, a component specifically required for transcription-coupled NER (TC-NER), and knockdowns of ERCC1 and XPG, which incise DNA adjacent to damage, stabilize CAG repeat tracts. These results suggest that TC-NER is involved in the pathway for transcription-induced CAG repeat instability. In contrast, knockdowns of OGG1 and APEX1, key components involved in base excision repair, did not affect repeat instability. In addition, repeats are stabilized by knockdown of transcription factor IIS, consistent with a requirement for RNA polymerase II (RNAPII) to backtrack from a transcription block. Repeats also are stabilized by knockdown of either BRCA1 or BARD1, which together function as an E3 ligase that can ubiquitinate arrested RNAPII. Treatment with the proteasome inhibitor MG132, which stabilizes repeats, confirms proteasome involvement. We integrate these observations into a tentative pathway for transcription-induced CAG repeat instability that can account for the contractions observed here and potentially for the contractions and expansions seen with human diseases.

  17. Genome-wide analysis of human global and transcription-coupled excision repair of UV damage at single-nucleotide resolution.

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    Hu, Jinchuan; Adar, Sheera; Selby, Christopher P; Lieb, Jason D; Sancar, Aziz

    2015-05-01

    We developed a method for genome-wide mapping of DNA excision repair named XR-seq (excision repair sequencing). Human nucleotide excision repair generates two incisions surrounding the site of damage, creating an ∼30-mer. In XR-seq, this fragment is isolated and subjected to high-throughput sequencing. We used XR-seq to produce stranded, nucleotide-resolution maps of repair of two UV-induced DNA damages in human cells: cyclobutane pyrimidine dimers (CPDs) and (6-4) pyrimidine-pyrimidone photoproducts [(6-4)PPs]. In wild-type cells, CPD repair was highly associated with transcription, specifically with the template strand. Experiments in cells defective in either transcription-coupled excision repair or general excision repair isolated the contribution of each pathway to the overall repair pattern and showed that transcription-coupled repair of both photoproducts occurs exclusively on the template strand. XR-seq maps capture transcription-coupled repair at sites of divergent gene promoters and bidirectional enhancer RNA (eRNA) production at enhancers. XR-seq data also uncovered the repair characteristics and novel sequence preferences of CPDs and (6-4)PPs. XR-seq and the resulting repair maps will facilitate studies of the effects of genomic location, chromatin context, transcription, and replication on DNA repair in human cells.

  18. Cross-talk between nucleotide excision and homologous recombination DNA repair pathways in the mechanism of action of antitumor trabectedin.

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    Herrero, Ana B; Martín-Castellanos, Cristina; Marco, Esther; Gago, Federico; Moreno, Sergio

    2006-08-15

    Trabectedin (Yondelis) is a potent antitumor drug that has the unique characteristic of killing cells by poisoning the DNA nucleotide excision repair (NER) machinery. The basis for the NER-dependent toxicity has not yet been elucidated but it has been proposed as the major determinant for the drug's cytotoxicity. To study the in vivo mode of action of trabectedin and to explore the role of NER in its cytotoxicity, we used the fission yeast Schizosaccharomyces pombe as a model system. Treatment of S. pombe wild-type cells with trabectedin led to cell cycle delay and activation of the DNA damage checkpoint, indicating that the drug causes DNA damage in vivo. DNA damage induced by the drug is mostly caused by the NER protein, Rad13 (the fission yeast orthologue to human XPG), and is mainly repaired by homologous recombination. By constructing different rad13 mutants, we show that the DNA damage induced by trabectedin depends on a 46-amino acid region of Rad13 that is homologous to a DNA-binding region of human nuclease FEN-1. More specifically, an arginine residue in Rad13 (Arg961), conserved in FEN1 (Arg314), was found to be crucial for the drug's cytotoxicity. These results lead us to propose a model for the action of trabectedin in eukaryotic cells in which the formation of a Rad13/DNA-trabectedin ternary complex, stabilized by Arg961, results in cell death.

  19. An interaction between teh DNA repair factor XPA and replication protein A appears essential for nucleotide excision repair

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    Li, Lei; Lu, Xiaoyan; Peterson, C.A.; Legerski, R.J. [Univ. of Texas, Houston, TX (United States)

    1995-10-01

    Replication protein A (RPA) is required for simian virus 40-directed DNA replication in vitro and for nucleotide excision repair (NER). Here we report that RPA and the human repair protein XPA specifically interact both in vitro and in vivo. Mapping of the RPA-interactive domains in XPA revealed that both of the largest subunits of RPA, RPA-70 and RPA-34, interact with XPA at distinct sites. A domain involved in mediating the interaction with RPA-70 was located between XPA residues 153 and 176. Deletion of highly conserved motifs within this region identified two mutants that were deficient in binding RPA in vitro and highly defective in NER both in vitro and in vivo. The second domain mediating the interaction with RPA-34 was identified within the first 58 residues in XPA. Deletion of this region, however, only moderately affects the complementing activity of XPA in vivo. Finally, the XPA-RPA complex is shown to have a greater affinity for damaged DNA than XPA alone. Taken together, these results indicate that the interaction between XPA and RPA is required for NER but that only the interaction with RPA-70 is essential. 52 refs., 7 figs.

  20. Nucleotide excision repair is associated with the replisome and its efficiency depends on a direct interaction between XPA and PCNA.

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    Karin M Gilljam

    Full Text Available Proliferating cell nuclear antigen (PCNA is an essential protein for DNA replication, DNA repair, cell cycle regulation, chromatin remodeling, and epigenetics. Many proteins interact with PCNA through the PCNA interacting peptide (PIP-box or the newly identified AlkB homolog 2 PCNA interacting motif (APIM. The xeroderma pigmentosum group A (XPA protein, with a central but somewhat elusive role in nucleotide excision repair (NER, contains the APIM sequence suggesting an interaction with PCNA. With an in vivo based approach, using modern techniques in live human cells, we show that APIM in XPA is a functional PCNA interacting motif and that efficient NER of UV lesions is dependent on an intact APIM sequence in XPA. We show that XPA(-/- cells complemented with XPA containing a mutated APIM sequence have increased UV sensitivity, reduced repair of cyclobutane pyrimidine dimers and (6-4 photoproducts, and are consequently more arrested in S phase as compared to XPA(-/- cells complemented with wild type XPA. Notably, XPA colocalizes with PCNA in replication foci and is loaded on newly synthesized DNA in undamaged cells. In addition, the TFIIH subunit XPD, as well as XPF are loaded on DNA together with XPA, and XPC and XPG colocalize with PCNA in replication foci. Altogether, our results suggest a presence of the NER complex in the vicinity of the replisome and a novel role of NER in post-replicative repair.

  1. Calcium-binding capacity of centrin2 is required for linear POC5 assembly but not for nucleotide excision repair.

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    Tiago J Dantas

    Full Text Available Centrosomes, the principal microtubule-organising centres in animal cells, contain centrins, small, conserved calcium-binding proteins unique to eukaryotes. Centrin2 binds to xeroderma pigmentosum group C protein (XPC, stabilising it, and its presence slightly increases nucleotide excision repair (NER activity in vitro. In previous work, we deleted all three centrin isoforms present in chicken DT40 cells and observed delayed repair of UV-induced DNA lesions, but no centrosome abnormalities. Here, we explore how centrin2 controls NER. In the centrin null cells, we expressed centrin2 mutants that cannot bind calcium or that lack sites for phosphorylation by regulatory kinases. Expression of any of these mutants restored the UV sensitivity of centrin null cells to normal as effectively as expression of wild-type centrin. However, calcium-binding-deficient and T118A mutants showed greatly compromised localisation to centrosomes. XPC recruitment to laser-induced UV-like lesions was only slightly slower in centrin-deficient cells than in controls, and levels of XPC and its partner HRAD23B were unaffected by centrin deficiency. Interestingly, we found that overexpression of the centrin interactor POC5 leads to the assembly of linear, centrin-dependent structures that recruit other centrosomal proteins such as PCM-1 and NEDD1. Together, these observations suggest that assembly of centrins into complex structures requires calcium binding capacity, but that such assembly is not required for centrin activity in NER.

  2. The nucleotide excision repair (NER system of Helicobacter pylori: Role in mutation prevention and chromosomal import patterns after natural transformation

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    Moccia Claudia

    2012-05-01

    Full Text Available Abstract Background Extensive genetic diversity and rapid allelic diversification are characteristics of the human gastric pathogen Helicobacter pylori, and are believed to contribute to its ability to cause chronic infections. Both a high mutation rate and frequent imports of short fragments of exogenous DNA during mixed infections play important roles in generating this allelic diversity. In this study, we used a genetic approach to investigate the roles of nucleotide excision repair (NER pathway components in H. pylori mutation and recombination. Results Inactivation of any of the four uvr genes strongly increased the susceptibility of H. pylori to DNA damage by ultraviolet light. Inactivation of uvrA and uvrB significantly decreased mutation frequencies whereas only the uvrA deficient mutant exhibited a significant decrease of the recombination frequency after natural transformation. A uvrC mutant did not show significant changes in mutation or recombination rates; however, inactivation of uvrC promoted the incorporation of significantly longer fragments of donor DNA (2.2-fold increase into the recipient chromosome. A deletion of uvrD induced a hyper-recombinational phenotype. Conclusions Our data suggest that the NER system has multiple functions in the genetic diversification of H. pylori, by contributing to its high mutation rate, and by controlling the incorporation of imported DNA fragments after natural transformation.

  3. RNA interference against transcription elongation factor SII does not support its role in transcription-coupled nucleotide excision repair.

    Science.gov (United States)

    Mackinnon-Roy, Christine; Stubbert, Lawton J; McKay, Bruce C

    2011-01-10

    RNA polymerase II is unable to bypass bulky DNA lesions induced by agents like ultraviolet light (UV light) and cisplatin that are located in the template strand of active genes. Arrested polymerases form a stable ternary complex at the site of DNA damage that is thought to pose an impediment to the repair of these lesions. Transcription-coupled nucleotide excision repair (TC-NER) preferentially repairs these DNA lesions through an incompletely defined mechanism. Based on elegant in vitro experiments, it was hypothesized that the transcription elongation factor IIS (TFIIS) may be required to couple transcription to repair by catalyzing the reverse translocation of the arrested polymerase, allowing access of repair proteins to the site of DNA damage. However the role of TFIIS in this repair process has not been tested in vivo. Here, silencing TFIIS using an RNA interference strategy did not affect the ability of cells to recover nascent RNA synthesis following UV exposure or the ability of cells to repair a UV-damaged reporter gene while a similar strategy to decrease the expression Cockayne syndrome group B protein (CSB) resulted in the expected repair defect. Furthermore, RNA interference against TFIIS did not increase the sensitivity of cells to UV light or cisplatin while decreased expression of CSB did. Taken together, these results indicate that TFIIS is not limiting for the repair of transcription-blocking DNA lesions and thus the present work does not support a role for TFIIS in TC-NER.

  4. A mutation-promotive role of nucleotide excision repair in cell cycle-arrested cell populations following UV irradiation.

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    Heidenreich, Erich; Eisler, Herfried; Lengheimer, Theresia; Dorninger, Petra; Steinboeck, Ferdinand

    2010-01-01

    Growing attention is paid to the concept that mutations arising in stationary, non-proliferating cell populations considerably contribute to evolution, aging, and pathogenesis. If such mutations are beneficial to the affected cell, in the sense of allowing a restart of proliferation, they are called adaptive mutations. In order to identify cellular processes responsible for adaptive mutagenesis in eukaryotes, we study frameshift mutations occurring during auxotrophy-caused cell cycle arrest in the model organism Saccharomyces cerevisiae. Previous work has shown that an exposure of cells to UV irradiation during prolonged cell cycle arrest resulted in an increased incidence of mutations. In the present work, we determined the influence of defects in the nucleotide excision repair (NER) pathway on the incidence of UV-induced adaptive mutations in stationary cells. The mutation frequency was decreased in Rad16-deficient cells and further decreased in Rad16/Rad26 double-deficient cells. A knockout of the RAD14 gene, the ortholog of the human XPA gene, even resulted in a nearly complete abolishment of UV-induced mutagenesis in cell cycle-arrested cells. Thus, the NER pathway, responsible for a normally accurate repair of UV-induced DNA damage, paradoxically is required for the generation and/or fixation of UV-induced frameshift mutations specifically in non-replicating cells.

  5. Nucleotide Excision Repair and Transcription-coupled DNA Repair Abrogate the Impact of DNA Damage on Transcription.

    Science.gov (United States)

    Nadkarni, Aditi; Burns, John A; Gandolfi, Alberto; Chowdhury, Moinuddin A; Cartularo, Laura; Berens, Christian; Geacintov, Nicholas E; Scicchitano, David A

    2016-01-01

    DNA adducts derived from carcinogenic polycyclic aromatic hydrocarbons like benzo[a]pyrene (B[a]P) and benzo[c]phenanthrene (B[c]Ph) impede replication and transcription, resulting in aberrant cell division and gene expression. Global nucleotide excision repair (NER) and transcription-coupled DNA repair (TCR) are among the DNA repair pathways that evolved to maintain genome integrity by removing DNA damage. The interplay between global NER and TCR in repairing the polycyclic aromatic hydrocarbon-derived DNA adducts (+)-trans-anti-B[a]P-N(6)-dA, which is subject to NER and blocks transcription in vitro, and (+)-trans-anti-B[c]Ph-N(6)-dA, which is a poor substrate for NER but also blocks transcription in vitro, was tested. The results show that both adducts inhibit transcription in human cells that lack both NER and TCR. The (+)-trans-anti-B[a]P-N(6)-dA lesion exhibited no detectable effect on transcription in cells proficient in NER but lacking TCR, indicating that NER can remove the lesion in the absence of TCR, which is consistent with in vitro data. In primary human cells lacking NER, (+)-trans-anti-B[a]P-N(6)-dA exhibited a deleterious effect on transcription that was less severe than in cells lacking both pathways, suggesting that TCR can repair the adduct but not as effectively as global NER. In contrast, (+)-trans-anti-B[c]Ph-N(6)-dA dramatically reduces transcript production in cells proficient in global NER but lacking TCR, indicating that TCR is necessary for the removal of this adduct, which is consistent with in vitro data showing that it is a poor substrate for NER. Hence, both global NER and TCR enhance the recovery of gene expression following DNA damage, and TCR plays an important role in removing DNA damage that is refractory to NER.

  6. Nucleotide sequence, DNA damage location and protein stoichiometry influence base excision repair outcome at CAG/CTG repeats

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    Goula, Agathi-Vasiliki; Pearson, Christopher E.; Della Maria, Julie; Trottier, Yvon; Tomkinson, Alan E.; Wilson, David M.; Merienne, Karine

    2012-01-01

    Expansion of CAG/CTG repeats is the underlying cause of >fourteen genetic disorders, including Huntington’s disease (HD) and myotonic dystrophy. The mutational process is ongoing, with increases in repeat size enhancing the toxicity of the expansion in specific tissues. In many repeat diseases the repeats exhibit high instability in the striatum, whereas instability is minimal in the cerebellum. We provide molecular insights as to how base excision repair (BER) protein stoichiometry may contribute to the tissue-selective instability of CAG/CTG repeats by using specific repair assays. Oligonucleotide substrates with an abasic site were mixed with either reconstituted BER protein stoichiometries mimicking the levels present in HD mouse striatum or cerebellum, or with protein extracts prepared from HD mouse striatum or cerebellum. In both cases, repair efficiency at CAG/CTG repeats and at control DNA sequences was markedly reduced under the striatal conditions, likely due to the lower level of APE1, FEN1 and LIG1. Damage located towards the 5’ end of the repeat tract was poorly repaired accumulating incompletely processed intermediates as compared to an AP lesion in the centre or at the 3’ end of the repeats or within a control sequences. Moreover, repair of lesions at the 5’ end of CAG or CTG repeats involved multinucleotide synthesis, particularly under the cerebellar stoichiometry, suggesting that long-patch BER processes lesions at sequences susceptible to hairpin formation. Our results show that BER stoichiometry, nucleotide sequence and DNA damage position modulate repair outcome, and suggest that a suboptimal LP-BER activity promotes CAG/CTG repeat instability. PMID:22497302

  7. Age-related neuronal degeneration: complementary roles of nucleotide excision repair and transcription-coupled repair in preventing neuropathology.

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    Dick Jaarsma

    2011-12-01

    Full Text Available Neuronal degeneration is a hallmark of many DNA repair syndromes. Yet, how DNA damage causes neuronal degeneration and whether defects in different repair systems affect the brain differently is largely unknown. Here, we performed a systematic detailed analysis of neurodegenerative changes in mouse models deficient in nucleotide excision repair (NER and transcription-coupled repair (TCR, two partially overlapping DNA repair systems that remove helix-distorting and transcription-blocking lesions, respectively, and that are associated with the UV-sensitive syndromes xeroderma pigmentosum (XP and Cockayne syndrome (CS. TCR-deficient Csa(-/- and Csb(-/- CS mice showed activated microglia cells surrounding oligodendrocytes in regions with myelinated axons throughout the nervous system. This white matter microglia activation was not observed in NER-deficient Xpa(-/- and Xpc(-/- XP mice, but also occurred in Xpd(XPCS mice carrying a point mutation (G602D in the Xpd gene that is associated with a combined XPCS disorder and causes a partial NER and TCR defect. The white matter abnormalities in TCR-deficient mice are compatible with focal dysmyelination in CS patients. Both TCR-deficient and NER-deficient mice showed no evidence for neuronal degeneration apart from p53 activation in sporadic (Csa(-/-, Csb(-/- or highly sporadic (Xpa(-/-, Xpc(-/- neurons and astrocytes. To examine to what extent overlap occurs between both repair systems, we generated TCR-deficient mice with selective inactivation of NER in postnatal neurons. These mice develop dramatic age-related cumulative neuronal loss indicating DNA damage substrate overlap and synergism between TCR and NER pathways in neurons, and they uncover the occurrence of spontaneous DNA injury that may trigger neuronal degeneration. We propose that, while Csa(-/- and Csb(-/- TCR-deficient mice represent powerful animal models to study the mechanisms underlying myelin abnormalities in CS, neuron

  8. Triple-helix formation induces recombination in mammalian cells via a nucleotide excision repair-dependent pathway.

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    Faruqi, A F; Datta, H J; Carroll, D; Seidman, M M; Glazer, P M

    2000-02-01

    The ability to stimulate recombination in a site-specific manner in mammalian cells may provide a useful tool for gene knockout and a valuable strategy for gene therapy. We previously demonstrated that psoralen adducts targeted by triple-helix-forming oligonucleotides (TFOs) could induce recombination between tandem repeats of a supF reporter gene in a simian virus 40 vector in monkey COS cells. Based on work showing that triple helices, even in the absence of associated psoralen adducts, are able to provoke DNA repair and cause mutations, we asked whether intermolecular triplexes could stimulate recombination. Here, we report that triple-helix formation itself is capable of promoting recombination and that this effect is dependent on a functional nucleotide excision repair (NER) pathway. Transfection of COS cells carrying the dual supF vector with a purine-rich TFO, AG30, designed to bind as a third strand to a region between the two mutant supF genes yielded recombinants at a frequency of 0.37%, fivefold above background, whereas a scrambled sequence control oligomer was ineffective. In human cells deficient in the NER factor XPA, the ability of AG30 to induce recombination was eliminated, but it was restored in a corrected subline expressing the XPA cDNA. In comparison, the ability of triplex-directed psoralen cross-links to induce recombination was only partially reduced in XPA-deficient cells, suggesting that NER is not the only pathway that can metabolize targeted psoralen photoadducts into recombinagenic intermediates. Interestingly, the triplex-induced recombination was unaffected in cells deficient in DNA mismatch repair, challenging our previous model of a heteroduplex intermediate and supporting a model based on end joining. This work demonstrates that oligonucleotide-mediated triplex formation can be recombinagenic, providing the basis for a potential strategy to direct genome modification by using high-affinity DNA binding ligands.

  9. Differential diagnosis and management of giant fibroadenoma: comparing excision with reduction mammoplasty incision and excision with inframammary incision.

    Science.gov (United States)

    Ugburo, Andrew O; Olajide, Thomas O; Fadeyibi, Idowu O; Mofikoya, Bolaji O; Lawal, Abdulrazzaq O; Osinowo, Adedapo O

    2012-10-01

    Giant fibroadenoma (GFA) may present with breast asymmetry and can be excised with an inframammary incision (IFI) or reduction mammoplasty incision (RMI). This study investigated the clinical presentation and compared excision with the IFI and RMI. All patients with benign breast tumours greater than 5 cm underwent core needle biopsy and a histopathological diagnosis. All confirmed GFA had their clinical details documented and randomised into two groups for excision with an IFI or RMI. Twenty-two patients were studied. The age range was 12-46 years, mean 21.18 ± 2.22 years. The patients were divided into two groups: a juvenile group (n = 16) (73%) aged 12-18 years, mean age 14.06 ± 0.42 years, and a perimenopausal group (n = 5) aged 28-46 years. The juvenile group showed cyclic increases in breast size monthly with menstruation while the perimenopausal showed an initial slow growth of 6-24 months followed by a rapid growth. Fifteen patients (68%) had excision biopsy with IMI and seven patients with RMI. Seven of the patients treated with IFI had minimal preoperative asymmetry and satisfactory aesthetic outcome. Among the patients with severe preoperative asymmetry treated with IFI (n = 8) and RMI (n = 7), those treated with IFI had persistent postoperative skin redundancy and asymmetry, which was not found in those treated with RMI. In conclusion, for patients with significant asymmetry, excision with the IFI was associated with persistent asymmetry while excision with RMI was associated with restoration of symmetry.

  10. UvrD Participation in Nucleotide Excision Repair Is Required for the Recovery of DNA Synthesis following UV-Induced Damage in Escherichia coli

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    Kelley N. Newton

    2012-01-01

    Full Text Available UvrD is a DNA helicase that participates in nucleotide excision repair and several replication-associated processes, including methyl-directed mismatch repair and recombination. UvrD is capable of displacing oligonucleotides from synthetic forked DNA structures in vitro and is essential for viability in the absence of Rep, a helicase associated with processing replication forks. These observations have led others to propose that UvrD may promote fork regression and facilitate resetting of the replication fork following arrest. However, the molecular activity of UvrD at replication forks in vivo has not been directly examined. In this study, we characterized the role UvrD has in processing and restoring replication forks following arrest by UV-induced DNA damage. We show that UvrD is required for DNA synthesis to recover. However, in the absence of UvrD, the displacement and partial degradation of the nascent DNA at the arrested fork occur normally. In addition, damage-induced replication intermediates persist and accumulate in uvrD mutants in a manner that is similar to that observed in other nucleotide excision repair mutants. These data indicate that, following arrest by DNA damage, UvrD is not required to catalyze fork regression in vivo and suggest that the failure of uvrD mutants to restore DNA synthesis following UV-induced arrest relates to its role in nucleotide excision repair.

  11. Up-regulation of nucleotide excision repair in mouse lung and liver following chronic exposure to aflatoxin B{sub 1} and its dependence on p53 genotype

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    Mulder, Jeanne E. [Pharmacology and Toxicology Graduate Program, Department of Biomedical and Molecular Sciences, Queen' s University Kingston, Ontario K7L 3N6 (Canada); Bondy, Genevieve S.; Mehta, Rekha [Toxicology Research Division, 2202D, Bureau of Chemical Safety, Food Directorate, Health Products and Food Branch, Health Canada, Ottawa, Ontario K1A 0K9 (Canada); Massey, Thomas E., E-mail: masseyt@queensu.ca [Pharmacology and Toxicology Graduate Program, Department of Biomedical and Molecular Sciences, Queen' s University Kingston, Ontario K7L 3N6 (Canada)

    2014-03-01

    Aflatoxin B{sub 1} (AFB{sub 1}) is biotransformed in vivo into an epoxide metabolite that forms DNA adducts that may induce cancer if not repaired. p53 is a tumor suppressor gene implicated in the regulation of global nucleotide excision repair (NER). Male heterozygous p53 knockout (B6.129-Trp53{sup tm1Brd}N5, Taconic) and wild-type mice were exposed to 0, 0.2 or 1.0 ppm AFB{sub 1} for 26 weeks. NER activity was assessed with an in vitro assay, using AFB{sub 1}-epoxide adducted plasmid DNA as a substrate. For wild-type mice, repair of AFB{sub 1}–N7-Gua adducts was 124% and 96% greater in lung extracts from mice exposed to 0.2 ppm and 1.0 ppm AFB{sub 1} respectively, and 224% greater in liver extracts from mice exposed to 0.2 ppm AFB{sub 1} (p < 0.05). In heterozygous p53 knockout mice, repair of AFB{sub 1}–N7-Gua was only 45% greater in lung extracts from mice exposed to 0.2 ppm AFB{sub 1} (p < 0.05), and no effect was observed in lung extracts from mice treated with 1.0 ppm AFB{sub 1} or in liver extracts from mice treated with either AFB{sub 1} concentration. p53 genotype did not affect basal levels of repair. AFB{sub 1} exposure did not alter repair of AFB{sub 1}-derived formamidopyrimidine adducts in lung or liver extracts of either mouse genotype nor did it affect XPA or XPB protein levels. In summary, chronic exposure to AFB{sub 1} increased NER activity in wild-type mice, and this response was diminished in heterozygous p53 knockout mice, indicating that loss of one allele of p53 limits the ability of NER to be up-regulated in response to DNA damage. - Highlights: • Mice are chronically exposed to low doses of the mycotoxin aflatoxin B{sub 1} (AFB{sub 1}). • The effects of AFB{sub 1} and p53 status on nucleotide excision repair are investigated. • AFB{sub 1} increases nucleotide excision repair in wild type mouse lung and liver. • This increase is attenuated in p53 heterozygous mouse lung and liver. • Results portray the role of p53 in

  12. Important role for Mycobacterium tuberculosis UvrD1 in pathogenesis and persistence apart from its function in nucleotide excision repair.

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    Houghton, Joanna; Townsend, Carolin; Williams, Alan R; Rodgers, Angela; Rand, Lucinda; Walker, K Barry; Böttger, Erik C; Springer, Burkhard; Davis, Elaine O

    2012-06-01

    Mycobacterium tuberculosis survives and replicates in macrophages, where it is exposed to reactive oxygen and nitrogen species that damage DNA. In this study, we investigated the roles of UvrA and UvrD1, thought to be parts of the nucleotide excision repair pathway of M. tuberculosis. Strains in which uvrD1 was inactivated either alone or in conjunction with uvrA were constructed. Inactivation of uvrD1 resulted in a small colony phenotype, although growth in liquid culture was not significantly affected. The sensitivity of the mutant strains to UV irradiation and to mitomycin C highlighted the importance of the targeted genes for nucleotide excision repair. The mutant strains all exhibited heightened susceptibility to representatives of reactive oxygen intermediates (ROI) and reactive nitrogen intermediates (RNI). The uvrD1 and the uvrA uvrD1 mutants showed decreased intracellular multiplication following infection of macrophages. Most importantly, the uvrA uvrD1 mutant was markedly attenuated following infection of mice by either the aerosol or the intravenous route.

  13. Modeling nucleotide excision repair and its impact on UV-induced mutagenesis during SOS-response in bacterial cells.

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    Bugay, Aleksandr N; Krasavin, Evgeny A; Parkhomenko, Aleksandr Yu; Vasilyeva, Maria A

    2015-01-01

    A model of the UV-induced mutation process in Escherichia coli bacteria has been developed taking into account the whole sequence of molecular events starting from initial photo-damage and finishing with the fixation of point mutations. The wild-type phenotype bacterial cells are compared with UV-sensitive repair-deficient mutant cells. Attention is mainly paid to excision repair system functioning as regards induced mutagenesis.

  14. Bypass of a 5',8-cyclopurine-2'-deoxynucleoside by DNA polymerase β during DNA replication and base excision repair leads to nucleotide misinsertions and DNA strand breaks.

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    Jiang, Zhongliang; Xu, Meng; Lai, Yanhao; Laverde, Eduardo E; Terzidis, Michael A; Masi, Annalisa; Chatgilialoglu, Chryssostomos; Liu, Yuan

    2015-09-01

    5',8-Cyclopurine-2'-deoxynucleosides including 5',8-cyclo-dA (cdA) and 5',8-cyclo-dG (cdG) are induced by hydroxyl radicals resulting from oxidative stress such as ionizing radiation. 5',8-cyclopurine-2'-deoxynucleoside lesions are repaired by nucleotide excision repair with low efficiency, thereby leading to their accumulation in the human genome and lesion bypass by DNA polymerases during DNA replication and base excision repair (BER). In this study, for the first time, we discovered that DNA polymerase β (pol β) efficiently bypassed a 5'R-cdA, but inefficiently bypassed a 5'S-cdA during DNA replication and BER. We found that cell extracts from pol β wild-type mouse embryonic fibroblasts exhibited significant DNA synthesis activity in bypassing a cdA lesion located in replication and BER intermediates. However, pol β knock-out cell extracts exhibited little DNA synthesis to bypass the lesion. This indicates that pol β plays an important role in bypassing a cdA lesion during DNA replication and BER. Furthermore, we demonstrated that pol β inserted both a correct and incorrect nucleotide to bypass a cdA at a low concentration. Nucleotide misinsertion was significantly stimulated by a high concentration of pol β, indicating a mutagenic effect induced by pol β lesion bypass synthesis of a 5',8-cyclopurine-2'-deoxynucleoside. Moreover, we found that bypass of a 5'S-cdA by pol β generated an intermediate that failed to be extended by pol β, resulting in accumulation of single-strand DNA breaks. Our study provides the first evidence that pol β plays an important role in bypassing a 5',8-cyclo-dA during DNA replication and repair, as well as new insight into mutagenic effects and genome instability resulting from pol β bypassing of a cdA lesion.

  15. New insights in the removal of the hydantoins, oxidation product of pyrimidines, via the base excision and nucleotide incision repair pathways.

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    Redrejo-Rodríguez, Modesto; Saint-Pierre, Christine; Couve, Sophie; Mazouzi, Abdelghani; Ishchenko, Alexander A; Gasparutto, Didier; Saparbaev, Murat

    2011-01-01

    Oxidative damage to DNA, if not repaired, can be both miscoding and blocking. These genetic alterations can lead to mutations and/or cell death, which in turn cause cancer and aging. Oxidized DNA bases are substrates for two overlapping repair pathways: base excision (BER) and nucleotide incision repair (NIR). Hydantoin derivatives such as 5-hydroxyhydantoin (5OH-Hyd) and 5-methyl-5-hydroxyhydantoin (5OH-5Me-Hyd), major products of cytosine and thymine oxidative degradation pathways, respectively, have been detected in cancer cells and ancient DNA. Hydantoins are blocking lesions for DNA polymerases and excised by bacterial and yeast DNA glycosylases in the BER pathway. However little is known about repair of pyrimidine-derived hydantoins in human cells. Here, using both denaturing PAGE and MALDI-TOF MS analyses we report that the bacterial, yeast and human AP endonucleases can incise duplex DNA 5' next to 5OH-Hyd and 5OH-5Me-Hyd thus initiating the NIR pathway. We have fully reconstituted the NIR pathway for these lesions in vitro using purified human proteins. Depletion of Nfo in E. coli and APE1 in HeLa cells abolishes the NIR activity in cell-free extracts. Importantly, a number of redundant DNA glycosylase activities can excise hydantoin residues, including human NTH1, NEIL1 and NEIL2 and the former protein being a major DNA glycosylase activity in HeLa cells extracts. This study demonstrates that both BER and NIR pathways can compete and/or back-up each other to remove hydantoin DNA lesions in vivo.

  16. New insights in the removal of the hydantoins, oxidation product of pyrimidines, via the base excision and nucleotide incision repair pathways.

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    Modesto Redrejo-Rodríguez

    Full Text Available BACKGROUND: Oxidative damage to DNA, if not repaired, can be both miscoding and blocking. These genetic alterations can lead to mutations and/or cell death, which in turn cause cancer and aging. Oxidized DNA bases are substrates for two overlapping repair pathways: base excision (BER and nucleotide incision repair (NIR. Hydantoin derivatives such as 5-hydroxyhydantoin (5OH-Hyd and 5-methyl-5-hydroxyhydantoin (5OH-5Me-Hyd, major products of cytosine and thymine oxidative degradation pathways, respectively, have been detected in cancer cells and ancient DNA. Hydantoins are blocking lesions for DNA polymerases and excised by bacterial and yeast DNA glycosylases in the BER pathway. However little is known about repair of pyrimidine-derived hydantoins in human cells. METHODOLOGY/PRINCIPAL FINDINGS: Here, using both denaturing PAGE and MALDI-TOF MS analyses we report that the bacterial, yeast and human AP endonucleases can incise duplex DNA 5' next to 5OH-Hyd and 5OH-5Me-Hyd thus initiating the NIR pathway. We have fully reconstituted the NIR pathway for these lesions in vitro using purified human proteins. Depletion of Nfo in E. coli and APE1 in HeLa cells abolishes the NIR activity in cell-free extracts. Importantly, a number of redundant DNA glycosylase activities can excise hydantoin residues, including human NTH1, NEIL1 and NEIL2 and the former protein being a major DNA glycosylase activity in HeLa cells extracts. CONCLUSIONS/SIGNIFICANCE: This study demonstrates that both BER and NIR pathways can compete and/or back-up each other to remove hydantoin DNA lesions in vivo.

  17. Expression of domains for protein-protein interaction of nucleotide excision repair proteins modifies cancer cell sensitivity to platinum derivatives and genomic stability.

    Science.gov (United States)

    Jordheim, Lars Petter; Cros-Perrial, Emeline; Matera, Eva-Laure; Bouledrak, Karima; Dumontet, Charles

    2014-10-01

    Nucleotide excision repair (NER) is involved in the repair of DNA damage caused by platinum derivatives and has been shown to decrease the cytotoxic activity of these drugs. Because protein-protein interactions are essential for NER activity, we transfected human cancer cell lines (A549 and HCT116) with plasmids coding the amino acid sequences corresponding to the interacting domains between excision repair cross-complementation group 1 (ERCC1) and xeroderma pigmentosum, complementation group A (XPA), as well as ERCC1 and xeroderma pigmentosum, complementation group F (XPF), all NER proteins. Using the 3-(4,5-dimethyl-2 thiazoyl)-2,5-diphenyl-2H-tetrazolium bromide (MTT) assay and annexin V staining, we showed that transfected A549 cells were sensitized 1.2-2.2-fold to carboplatin and that transfected HCT116 cells were sensitized 1.4-5.4-fold to oxaliplatin in vitro. In addition, transfected cells exhibited modified in vivo sensitivity to the same drugs. Finally, in particular cell models of the interaction between ERCC1 and XPF, DNA repair was decreased, as evidenced by increased phosphorylation of the histone 2AX after exposure to mitomycin C, and genomic instability was increased, as determined by comparative genomic hybridization studies. The results indicate that the interacting peptides act as dominant negatives and decrease NER activity through inhibition of protein-protein interactions.

  18. Monte carlo simulation of base and nucleotide excision repair of clustered DNA damage sites. II. Comparisons of model predictions to measured data.

    Science.gov (United States)

    Semenenko, V A; Stewart, R D

    2005-08-01

    Clustered damage sites other than double-strand breaks (DSBs) have the potential to contribute to deleterious effects of ionizing radiation, such as cell killing and mutagenesis. In the companion article (Semenenko et al., Radiat. Res. 164, 180-193, 2005), a general Monte Carlo framework to simulate key steps in the base and nucleotide excision repair of DNA damage other than DSBs is proposed. In this article, model predictions are compared to measured data for selected low-and high-LET radiations. The Monte Carlo model reproduces experimental observations for the formation of enzymatic DSBs in Escherichia coli and cells of two Chinese hamster cell lines (V79 and xrs5). Comparisons of model predictions with experimental values for low-LET radiation suggest that an inhibition of DNA backbone incision at the sites of base damage by opposing strand breaks is active over longer distances between the damaged base and the strand break in hamster cells (8 bp) compared to E. coli (3 bp). Model estimates for the induction of point mutations in the human hypoxanthine guanine phosphoribosyl transferase (HPRT) gene by ionizing radiation are of the same order of magnitude as the measured mutation frequencies. Trends in the mutation frequency for low- and high-LET radiation are predicted correctly by the model. The agreement between selected experimental data sets and simulation results provides some confidence in postulated mechanisms for excision repair of DNA damage other than DSBs and suggests that the proposed Monte Carlo scheme is useful for predicting repair outcomes.

  19. Variation in PAH-related DNA adduct levels among non-smokers: the role of multiple genetic polymorphisms and nucleotide excision repair phenotype.

    Science.gov (United States)

    Etemadi, Arash; Islami, Farhad; Phillips, David H; Godschalk, Roger; Golozar, Asieh; Kamangar, Farin; Malekshah, Akbar Fazel-Tabar; Pourshams, Akram; Elahi, Seerat; Ghojaghi, Farhad; Strickland, Paul T; Taylor, Philip R; Boffetta, Paolo; Abnet, Christian C; Dawsey, Sanford M; Malekzadeh, Reza; van Schooten, Frederik J

    2013-06-15

    Polycyclic aromatic hydrocarbons (PAHs) likely play a role in many cancers even in never-smokers. We tried to find a model to explain the relationship between variation in PAH-related DNA adduct levels among people with similar exposures, multiple genetic polymorphisms in genes related to metabolic and repair pathways, and nucleotide excision repair (NER) capacity. In 111 randomly selected female never-smokers from the Golestan Cohort Study in Iran, we evaluated 21 SNPs in 14 genes related to xenobiotic metabolism and 12 SNPs in eight DNA repair genes. NER capacity was evaluated by a modified comet assay, and aromatic DNA adduct levels were measured in blood by32P-postlabeling. Multivariable regression models were compared by Akaike's information criterion (AIC). Aromatic DNA adduct levels ranged between 1.7 and 18.6 per 10(8) nucleotides (mean: 5.8 ± 3.1). DNA adduct level was significantly lower in homozygotes for NAT2 slow alleles and ERCC5 non-risk-allele genotype, and was higher in the MPO homozygote risk-allele genotype. The sum of risk alleles in these genes significantly correlated with the log-adduct level (r = 0.4, p adduct levels. NER capacity was affected by polymorphisms in the MTHFR and ERCC1 genes. Female non-smokers in this population had PAH-related DNA adduct levels three to four times higher than smokers and occupationally-exposed groups in previous studies, with large inter-individual variation which could best be explained by a combination of Phase I genes and NER capacity.

  20. Site-specific analysis of UV-induced cyclobutane pyrimidine dimers in nucleotide excision repair-proficient and -deficient hamster cells: Lack of correlation with mutational spectra

    Energy Technology Data Exchange (ETDEWEB)

    Vreeswijk, Maaike P.G., E-mail: vreeswijk@lumc.nl [Department of Toxicogenetics, Leiden University Medical Center, Einthovenweg 20, P.O. Box 9600, Postzone S4-P, 2300 RC Leiden (Netherlands); Department of Human Genetics, Center for Human and Clinical Genetics, Leiden University Medical Center, Building 2, Postzone S-04, P.O. Box 9600, 2300 RC Leiden (Netherlands); Meijers, Caro M.; Giphart-Gassler, Micheline; Vrieling, Harry; Zeeland, Albert A. van; Mullenders, Leon H.F.; Loenen, Wil A.M. [Department of Toxicogenetics, Leiden University Medical Center, Einthovenweg 20, P.O. Box 9600, Postzone S4-P, 2300 RC Leiden (Netherlands)

    2009-04-26

    Irradiation of cells with UVC light induces two types of mutagenic DNA photoproducts, i.e. cyclobutane pyrimidine dimers (CPD) and pyrimidine (6-4) pyrimidone photoproducts (6-4PP). To investigate the relationship between the frequency of UV-induced photolesions at specific sites and their ability to induce mutations, we quantified CPD formation at the nucleotide level along exons 3 and 8 of the hprt gene using ligation-mediated PCR, and determined the mutational spectrum of 132 UV-induced hprt mutants in the AA8 hamster cell line and of 165 mutants in its nucleotide excision repair-defective derivative UV5. In AA8 cells, transversions predominated with a strong strand bias towards thymine-containing photolesions in the non-transcribed strand. As hamster AA8 cells are proficient in global genome repair of 6-4PP but selectively repair CPD from the transcribed strand of active genes, most mutations probably resulted from erroneous bypass of CPD in the non-transcribed strand. However, the relative incidence of CPD and the positions where mutations most frequently arose do not correlate. In fact some major damage sites hardly gave rise to the formation of mutations. In the repair-defective UV5 cells, mutations were almost exclusively C > T transitions caused by photoproducts at PyC sites in the transcribed strand. Even though CPD were formed at high frequencies at some TT sites in UV5, these photoproducts did not contribute to mutation induction at all. We conclude that, even in the absence of repair, large variations in the level of induction of CPD at different sites throughout the two exons do not correspond to frequencies of mutation induction.

  1. Site-specific analysis of UV-induced cyclobutane pyrimidine dimers in nucleotide excision repair-proficient and -deficient hamster cells: Lack of correlation with mutational spectra.

    Science.gov (United States)

    Vreeswijk, Maaike P G; Meijers, Caro M; Giphart-Gassler, Micheline; Vrieling, Harry; van Zeeland, Albert A; Mullenders, Leon H F; Loenen, Wil A M

    2009-04-26

    Irradiation of cells with UVC light induces two types of mutagenic DNA photoproducts, i.e. cyclobutane pyrimidine dimers (CPD) and pyrimidine (6-4) pyrimidone photoproducts (6-4 PP). To investigate the relationship between the frequency of UV-induced photolesions at specific sites and their ability to induce mutations, we quantified CPD formation at the nucleotide level along exons 3 and 8 of the hprt gene using ligation-mediated PCR, and determined the mutational spectrum of 132 UV-induced hprt mutants in the AA8 hamster cell line and of 165 mutants in its nucleotide excision repair-defective derivative UV5. In AA8 cells, transversions predominated with a strong strand bias towards thymine-containing photolesions in the non-transcribed strand. As hamster AA8 cells are proficient in global genome repair of 6-4 PP but selectively repair CPD from the transcribed strand of active genes, most mutations probably resulted from erroneous bypass of CPD in the non-transcribed strand. However, the relative incidence of CPD and the positions where mutations most frequently arose do not correlate. In fact some major damage sites hardly gave rise to the formation of mutations. In the repair-defective UV5 cells, mutations were almost exclusively C>T transitions caused by photoproducts at PyC sites in the transcribed strand. Even though CPD were formed at high frequencies at some TT sites in UV5, these photoproducts did not contribute to mutation induction at all. We conclude that, even in the absence of repair, large variations in the level of induction of CPD at different sites throughout the two exons do not correspond to frequencies of mutation induction.

  2. Mitotic regulator Nlp interacts with XPA/ERCC1 complexes and regulates nucleotide excision repair (NER) in response to UV radiation.

    Science.gov (United States)

    Ma, Xiao-Juan; Shang, Li; Zhang, Wei-Min; Wang, Ming-Rong; Zhan, Qi-Min

    2016-04-10

    Cellular response to DNA damage, including ionizing radiation (IR) and UV radiation, is critical for the maintenance of genomic fidelity. Defects of DNA repair often result in genomic instability and malignant cell transformation. Centrosomal protein Nlp (ninein-like protein) has been characterized as an important cell cycle regulator that is required for proper mitotic progression. In this study, we demonstrate that Nlp is able to improve nucleotide excision repair (NER) activity and protects cells against UV radiation. Upon exposure of cells to UVC, Nlp is translocated into the nucleus. The C-terminus (1030-1382) of Nlp is necessary and sufficient for its nuclear import. Upon UVC radiation, Nlp interacts with XPA and ERCC1, and enhances their association. Interestingly, down-regulated expression of Nlp is found to be associated with human skin cancers, indicating that dysregulated Nlp might be related to the development of human skin cancers. Taken together, this study identifies mitotic protein Nlp as a new and important member of NER pathway and thus provides novel insights into understanding of regulatory machinery involved in NER.

  3. Measurement of DNA base and nucleotide excision repair activities in mammalian cells and tissues using the comet assay--a methodological overview.

    Science.gov (United States)

    Azqueta, Amaya; Langie, Sabine A S; Slyskova, Jana; Collins, Andrew R

    2013-11-01

    There is an increasing demand for phenotyping assays in the field of human functional genetics. DNA repair activity is representative of this functional approach, being seen as a valuable biomarker related to cancer risk. Repair activity is evaluated by incubating a cell extract with a DNA substrate containing lesions specific for the DNA repair pathway of interest. Enzymic incision at the lesion sites can be measured by means of the comet assay (single cell gel electrophoresis). The assay is particularly applicable for evaluation of base and nucleotide excision repair pathways (BER and NER). Substrate DNA containing oxidised purines gives a measure of BER, while UV-induced photolesions are the substrate for NER. While applications of comet-based DNA repair assays continue to increase, there are no commonly accepted standard protocols, which complicates inter-laboratory comparisons of results. Here we provide a comprehensive summary of protocols for the comet-based BER- and NER-specific in vitro DNA repair assays that can be applied to a wide spectrum of biological material--cultured cell lines, blood cells, animal tissue samples and human biopsies. Our intention is to provide a detailed and user-friendly account of the assays, including practical tips and recommendations to help in setting them up. By proposing standard protocols, we hope to facilitate comparison of results obtained in different laboratories.

  4. Cockayne syndrome: varied requirement of transcription-coupled nucleotide excision repair for the removal of three structurally different adducts from transcribed DNA.

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    Nataliya Kitsera

    Full Text Available Hereditary defects in the transcription-coupled nucleotide excision repair (TC-NER pathway of damaged DNA cause severe neurodegenerative disease Cockayne syndrome (CS, however the origin and chemical nature of the underlying DNA damage had remained unknown. To find out, to which degree the structural properties of DNA lesions determine the extent of transcription arrest in human CS cells, we performed quantitative host cell reactivation analyses of expression vectors containing various synthetic adducts. We found that a single 3-(deoxyguanosin-N2-yl-2-acetylaminofluorene adduct (dG(N2-AAF constitutes an unsurmountable obstacle to transcription in both CS-A and CS-B cells and is removed exclusively by the CSA- and CSB-dependent pathway. In contrast, contribution of the CS proteins to the removal of two other transcription-blocking DNA lesions - N-(deoxyguanosin-8-yl-2-acetylaminofluorene (dG(C8-AAF and cyclobutane thymine-thymine (TT dimer - is only minor (TT dimer or none (dG(C8-AAF. The unique properties of dG(N2-AAF identify this adduct as a prototype for a new class of DNA lesions that escape the alternative global genome repair and could be critical for the CS pathogenesis.

  5. Down-regulation of the Nucleotide Excision Repair gene XPG as a new mechanism of drug resistance in human and murine cancer cells

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    Geroni Cristina

    2010-09-01

    Full Text Available Abstract Background Drug resistance is one of the major obstacles limiting the activity of anticancer agents. Activation of DNA repair mechanism often accounts for increase resistance to cancer chemotherapy. Results We present evidence that nemorubicin, a doxorubicin derivative currently in clinical evaluation, acts through a mechanism of action different from classical anthracyclines, requiring an intact nucleotide excision repair (NER system to exert its activity. Cells made resistant to nemorubicin show increased sensitivity to UV damage. We have analysed the mechanism of resistance and discovered a previously unknown mechanism resulting from methylation-dependent silencing of the XPG gene. Restoration of NER activity through XPG gene transfer or treatment with demethylating agents restored sensitivity to nemorubicin. Furthermore, we found that a significant proportion of ovarian tumors present methylation of the XPG promoter. Conclusions Methylation of a NER gene, as described here, is a completely new mechanism of drug resistance and this is the first evidence that XPG gene expression can be influenced by an epigenetic mechanism. The reported methylation of XPG gene could be an important determinant of the response to platinum based therapy. In addition, the mechanism of resistance reported opens up the possibility of reverting the resistant phenotype using combinations with demethylating agents, molecules already employed in the clinical setting.

  6. H. pylori-Induced DNA Strand Breaks Are Introduced by Nucleotide Excision Repair Endonucleases and Promote NF-κB Target Gene Expression

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    Mara L. Hartung

    2015-10-01

    Full Text Available The human bacterial pathogen Helicobacter pylori exhibits genotoxic properties that promote gastric carcinogenesis. H. pylori introduces DNA double strand breaks (DSBs in epithelial cells that trigger host cell DNA repair efforts. Here, we show that H. pylori-induced DSBs are repaired via error-prone, potentially mutagenic non-homologous end-joining. A genome-wide screen for factors contributing to DSB induction revealed a critical role for the H. pylori type IV secretion system (T4SS. Inhibition of transcription, as well as NF-κB/RelA-specific RNAi, abrogates DSB formation. DSB induction further requires β1-integrin signaling. DSBs are introduced by the nucleotide excision repair endonucleases XPF and XPG, which, together with RelA, are recruited to chromatin in a highly coordinated, T4SS-dependent manner. Interestingly, XPF/XPG-mediated DNA DSBs promote NF-κB target gene transactivation and host cell survival. In summary, H. pylori induces XPF/XPG-mediated DNA damage through activation of the T4SS/β1-integrin signaling axis, which promotes NF-κB target gene expression and host cell survival.

  7. Nucleotide excision repair genes are expressed at low levels and are not detectably inducible in Caenorhabditis elegans somatic tissues, but their function is required for normal adult life after UVC exposure

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    Boyd, Windy A. [Biomolecular Screening Branch, National Toxicology Program, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC (United States); Crocker, Tracey L. [Nicholas School of the Environment, Duke University, Durham, NC 27708 (United States); Rodriguez, Ana M. [Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC (United States); Leung, Maxwell C.K. [Nicholas School of the Environment, Duke University, Durham, NC 27708 (United States); Wade Lehmann, D. [Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC (United States); Freedman, Jonathan H. [Laboratory of Molecular Toxicology, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC (United States); Van Houten, Ben [Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC (United States); Meyer, Joel N., E-mail: joel.meyer@duke.edu [Nicholas School of the Environment, Duke University, Durham, NC 27708 (United States)

    2010-01-05

    We performed experiments to characterize the inducibility of nucleotide excision repair (NER) in Caenorhabditis elegans, and to examine global gene expression in NER-deficient and -proficient strains as well as germline vs. somatic tissues, with and without genotoxic stress. We also carried out experiments to elucidate the importance of NER in the adult life of C. elegans under genotoxin-stressed and control conditions. Adult lifespan was not detectably different between wild-type and NER-deficient xpa-1 nematodes under control conditions. However, exposure to 6 J/m{sup 2}/day of ultraviolet C radiation (UVC) decreased lifespan in xpa-1 nematodes more than a dose of 100 J/m{sup 2}/day in wild-type. Similar differential sensitivities were observed for adult size and feeding. Remarkably, global gene expression was nearly identical in young adult wild-type and xpa-1 nematodes, both in control conditions and 3 h after exposure to 50 J/m{sup 2} UVC. Neither NER genes nor repair activity were detectably inducible in young adults that lacked germ cells and developing embryos (glp-1 strain). However, expression levels of dozens of NER and other DNA damage response genes were much (5-30-fold) lower in adults lacking germ cells and developing embryos, suggesting that somatic and post-mitotic cells have a much lower DNA repair ability. Finally, we describe a refinement of our DNA damage assay that allows damage measurement in single nematodes.

  8. Inter-individual variation in nucleotide excision repair pathway is modulated by non-synonymous polymorphisms in ERCC4 and MBD4 genes

    Energy Technology Data Exchange (ETDEWEB)

    Allione, Alessandra, E-mail: alessandra.allione@hugef-torino.org [Human Genetics Foundation (HuGeF), Via Nizza 52, 10126 Turin (Italy); Guarrera, Simonetta; Russo, Alessia [Human Genetics Foundation (HuGeF), Via Nizza 52, 10126 Turin (Italy); Ricceri, Fulvio [Human Genetics Foundation (HuGeF), Via Nizza 52, 10126 Turin (Italy); Department of Medical Sciences, University of Turin, Via Santena 19, 10126 Turin (Italy); Purohit, Rituraj [Human Genetics Foundation (HuGeF), Via Nizza 52, 10126 Turin (Italy); Bioinformatics Division, School of Bio Sciences and Technology, Vellore Institute of Technology University, Vellore 632014, Tamil Nadu (India); Pagnani, Andrea; Rosa, Fabio; Polidoro, Silvia; Voglino, Floriana [Human Genetics Foundation (HuGeF), Via Nizza 52, 10126 Turin (Italy); Matullo, Giuseppe [Human Genetics Foundation (HuGeF), Via Nizza 52, 10126 Turin (Italy); Department of Medical Sciences, University of Turin, Via Santena 19, 10126 Turin (Italy)

    2013-11-15

    Highlights: • We reported a large inter-individual variability of NER capacity. • ERCC4 rs1800124 and MBD4 rs10342 nsSNP variants were associated with DNA repair capacity. • DNA–protein interaction analyses showed alteration of binding for ERCC4 and MBD4 variants. • A new possible cross-talk between NER and BER pathways has been reported. - Abstract: Inter-individual differences in DNA repair capacity (DRC) may lead to genome instability and, consequently, modulate individual cancer risk. Among the different DNA repair pathways, nucleotide excision repair (NER) is one of the most versatile, as it can eliminate a wide range of helix-distorting DNA lesions caused by ultraviolet light irradiation and chemical mutagens. We performed a genotype–phenotype correlation study in 122 healthy subjects in order to assess if any associations exist between phenotypic profiles of NER and DNA repair gene single nucleotide polymorphisms (SNPs). Individuals were genotyped for 768 SNPs with a custom Illumina Golden Gate Assay, and peripheral blood mononuclear cells (PBMCs) of the same subjects were tested for a NER comet assay to measure DRC after challenging cells by benzo(a)pyrene diolepoxide (BPDE). We observed a large inter-individual variability of NER capacity, with women showing a statistically significant lower DRC (mean ± SD: 6.68 ± 4.76; p = 0.004) than men (mean ± SD: 8.89 ± 5.20). Moreover, DRC was significantly lower in individuals carrying a variant allele for the ERCC4 rs1800124 non-synonymous SNP (nsSNP) (p = 0.006) and significantly higher in subjects with the variant allele of MBD4 rs2005618 SNP (p = 0.008), in linkage disequilibrium (r{sup 2} = 0.908) with rs10342 nsSNP. Traditional in silico docking approaches on protein–DNA and protein–protein interaction showed that Gly875 variant in ERCC4 (rs1800124) decreases the DNA–protein interaction and that Ser273 and Thr273 variants in MBD4 (rs10342) indicate complete loss of protein

  9. Checkpoint Kinase ATR Promotes Nucleotide Excision Repair of UV-induced DNA Damage via Physical Interaction with Xeroderma Pigmentosum Group A*

    Science.gov (United States)

    Shell, Steven M.; Li, Zhengke; Shkriabai, Nikolozi; Kvaratskhelia, Mamuka; Brosey, Chris; Serrano, Moises A.; Chazin, Walter J.; Musich, Phillip R.; Zou, Yue

    2009-01-01

    In response to DNA damage, eukaryotic cells activate a series of DNA damage-dependent pathways that serve to arrest cell cycle progression and remove DNA damage. Coordination of cell cycle arrest and damage repair is critical for maintenance of genomic stability. However, this process is still poorly understood. Nucleotide excision repair (NER) and the ATR-dependent cell cycle checkpoint are the major pathways responsible for repair of UV-induced DNA damage. Here we show that ATR physically interacts with the NER factor Xeroderma pigmentosum group A (XPA). Using a mass spectrometry-based protein footprinting method, we found that ATR interacts with a helix-turn-helix motif in the minimal DNA-binding domain of XPA where an ATR phosphorylation site (serine 196) is located. XPA-deficient cells complemented with XPA containing a point mutation of S196A displayed a reduced repair efficiency of cyclobutane pyrimidine dimers as compared with cells complemented with wild-type XPA, although no effect was observed for repair of (6-4) photoproducts. This suggests that the ATR-dependent phosphorylation of XPA may promote NER repair of persistent DNA damage. In addition, a K188A point mutation of XPA that disrupts the ATR-XPA interaction inhibits the nuclear import of XPA after UV irradiation and, thus, significantly reduced DNA repair efficiency. By contrast, the S196A mutation has no effect on XPA nuclear translocation. Taken together, our results suggest that the ATR-XPA interaction mediated by the helix-turn-helix motif of XPA plays an important role in DNA-damage responses to promote cell survival and genomic stability after UV irradiation. PMID:19586908

  10. Nucleotide excision repair deficiency increases levels of acrolein-derived cyclic DNA adduct and sensitizes cells to apoptosis induced by docosahexaenoic acid and acrolein.

    Science.gov (United States)

    Pan, Jishen; Sinclair, Elizabeth; Xuan, Zhuoli; Dyba, Marcin; Fu, Ying; Sen, Supti; Berry, Deborah; Creswell, Karen; Hu, Jiaxi; Roy, Rabindra; Chung, Fung-Lung

    2016-07-01

    The acrolein derived cyclic 1,N(2)-propanodeoxyguanosine adduct (Acr-dG), formed primarily from ω-3 polyunsaturated fatty acids such as docosahexaenoic acid (DHA) under oxidative conditions, while proven to be mutagenic, is potentially involved in DHA-induced apoptosis. The latter may contribute to the chemopreventive effects of DHA. Previous studies have shown that the levels of Acr-dG are correlated with apoptosis induction in HT29 cells treated with DHA. Because Acr-dG is shown to be repaired by the nucleotide excision repair (NER) pathway, to further investigate the role of Acr-dG in apoptosis, in this study, NER-deficient XPA and its isogenic NER-proficient XAN1 cells were treated with DHA. The Acr-dG levels and apoptosis were sharply increased in XPA cells, but not in XAN1 cells when treated with 125μM of DHA. Because DHA can induce formation of various DNA damage, to specifically investigate the role of Acr-dG in apoptosis induction, we treated XPA knockdown HCT116+ch3 cells with acrolein. The levels of both Acr-dG and apoptosis induction increased significantly in the XPA knockdown cells. These results clearly demonstrate that NER deficiency induces higher levels of Acr-dG in cells treated with DHA or acrolein and sensitizes cells to undergo apoptosis in a correlative manner. Collectively, these results support that Acr-dG, a ubiquitously formed mutagenic oxidative DNA adduct, plays a role in DHA-induced apoptosis and suggest that it could serve as a biomarker for the cancer preventive effects of DHA.

  11. Loss of genes related to Nucleotide Excision Repair (NER) and implications for reductive genome evolution in symbionts of deep-sea vesicomyid clams

    Science.gov (United States)

    Shimamura, Shigeru; Kaneko, Takashi; Ozawa, Genki; Matsumoto, Mamiko Nishino; Koshiishi, Takeru; Takaki, Yoshihiro; Kato, Chiaki; Takai, Ken; Yoshida, Takao; Fujikura, Katsunori; Barry, James P.

    2017-01-01

    Intracellular thioautotrophic symbionts of deep-sea vesicomyid clams lack some DNA repair genes and are thought to be undergoing reductive genome evolution (RGE). In this study, we addressed two questions, 1) how these symbionts lost their DNA repair genes and 2) how such losses affect RGE. For the first question, we examined genes associated with nucleotide excision repair (NER; uvrA, uvrB, uvrC, uvrD, uvrD paralog [uvrDp] and mfd) in 12 symbionts of vesicomyid clams belonging to two clades (5 clade I and 7 clade II symbionts). While uvrA, uvrDp and mfd were conserved in all symbionts, uvrB and uvrC were degraded in all clade I symbionts but were apparently intact in clade II symbionts. UvrD was disrupted in two clade II symbionts. Among the intact genes in Ca. Vesicomyosocius okutanii (clade I), expressions of uvrD and mfd were detected by reverse transcription-polymerase chain reaction (RT-PCR), but those of uvrA and uvrDp were not. In contrast, all intact genes were expressed in the symbiont of Calyptogena pacifica (clade II). To assess how gene losses affect RGE (question 2), genetic distances of the examined genes in symbionts from Bathymodiolus septemdierum were shown to be larger in clade I than clade II symbionts. In addition, these genes had lower guanine+cytosine (GC) content and higher repeat sequence densities in clade I than measured in clade II. Our results suggest that NER genes are currently being lost from the extant lineages of vesicomyid clam symbionts. The loss of NER genes and mutY in these symbionts is likely to promote increases in genetic distance and repeat sequence density as well as reduced GC content in genomic genes, and may have facilitated reductive evolution of the genome. PMID:28199404

  12. Nucleotide excision repair and recombination are engaged in repair of trans-4-hydroxy-2-nonenal adducts to DNA bases in Escherichia coli

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    Beata Janowska, Marek Komisarski, Paulina Prorok, Beata Sokołowska, Jarosław Kuśmierek, Celina Janion, Barbara Tudek

    2009-01-01

    Full Text Available One of the major products of lipid peroxidation is trans-4-hydroxy-2-nonenal (HNE. HNE forms highly mutagenic and genotoxic adducts to all DNA bases. Using M13 phage lacZ system, we studied the mutagenesis and repair of HNE treated phage DNA in E. coli wild-type or uvrA, recA, and mutL mutants. These studies revealed that: (i nucleotide excision and recombination, but not mismatch repair, are engaged in repair of HNE adducts when present in phage DNA replicating in E. coli strains; (ii in the single uvrA mutant, phage survival was drastically decreased while mutation frequency increased, and recombination events constituted 48 % of all mutations; (iii in the single recA mutant, the survival and mutation frequency of HNE-modified M13 phage was slightly elevated in comparison to that in the wild-type bacteria. The majority of mutations in recA- strain were G:C → T:A transversions, occurring within the sequence which in recA+ strains underwent RecA-mediated recombination, and the entire sequence was deleted; (iv in the double uvrA recA mutant, phage survival was the same as in the wild-type although the mutation frequency was higher than in the wild-type and recA single mutant, but lower than in the single uvrA mutant. The majority of mutations found in the latter strain were base substitutions, with G:C → A:T transitions prevailing. These transitions could have resulted from high reactivity of HNE with G and C, and induction of SOS-independent mutations.

  13. Influence of XPB helicase on recruitment and redistribution of nucleotide excision repair proteins at sites of UV-induced DNA damage.

    Science.gov (United States)

    Oh, Kyu-Seon; Imoto, Kyoko; Boyle, Jennifer; Khan, Sikandar G; Kraemer, Kenneth H

    2007-09-01

    The XPB DNA helicase, a subunit of the basal transcription factor TFIIH, is also involved in nucleotide excision repair (NER). We examined recruitment of NER proteins in XP-B cells from patients with mild or severe xeroderma pigmentosum (XP) having different XPB mutations using local UV-irradiation through filters with 5 microm pores combined with fluorescent antibody labeling. XPC was rapidly recruited to UV damage sites containing DNA photoproducts (cyclobutane pyrimidine dimers, CPD) in all the XP-B and normal cells, thus reflecting its role in damage recognition prior to the function of XPB. Cells from the mild XP-B patients, with a missense mutation, showed delayed recruitment of all NER proteins except XPC to UV damage sites, demonstrating that this mutation impaired localization of these proteins. Surprisingly, in cells from severely affected patients, with a C-terminal XPB mutation, XPG and XPA proteins were normally recruited to UV damage sites demonstrating that this mutation permits recruitment of XPG and XPA. In marked contrast, in all the XP-B cells recruitment of XPF was absent immediately after UV and was delayed by 0.5 and 3 h in cells from the mild and severely affected XP patients, respectively. Redistribution of NER proteins was nearly complete in normal cells by 3 h but by 24 h redistribution was only partially present in cells from mild patients and virtually absent in cells from the severely affected patients. Ineffectual repair of UV-induced photoproducts resulting from delayed recruitment and impaired redistribution of NER proteins may contribute to the markedly increased frequency of skin cancer in XP patients.

  14. Trabectedin and its C subunit modified analogue PM01183 attenuate nucleotide excision repair and show activity toward platinum-resistant cells.

    Science.gov (United States)

    Soares, Daniele G; Machado, Miriana S; Rocca, Céline J; Poindessous, Virginie; Ouaret, Djamila; Sarasin, Alain; Galmarini, Carlos M; Henriques, João A P; Escargueil, Alexandre E; Larsen, Annette K

    2011-08-01

    PM01183 is a novel marine-derived covalent DNA binder in clinical development. PM01183 is structurally similar to trabectedin (yondelis, ecteinascidin-743) except for the C subunit, and this modification is accompanied by different pharmacokinetics in cancer patients. We here characterize the interaction of PM01183 with the nucleotide excision repair (NER) pathway in comparison with trabectedin. Our results show for the first time that although neither PM01183 nor trabectedin is repaired by NER, both compounds are able to interfere with the NER machinery thereby attenuating the repair of specific NER substrates. We further show that the NER activity is increased in 3 of 4 cellular models with acquired resistance to cisplatin or oxaliplatin, confirming the involvement of NER in the resistance to platinum derivatives. Importantly, both PM01183 and trabectedin show unchanged or even enhanced activity toward all 4 cisplatin- and oxaliplatin-resistant cell lines. We finally show that combinations of PM01183 and cisplatin were mostly synergistic toward both parental and cisplatin-resistant ovarian carcinoma cells as indicated by Chou and Talalay analysis. These data show that the C subunit of trabectedin can be subjected to at least some structural modifications without loss of activity or NER interaction. While PM01183 and trabectedin appear functionally similar in cellular models, it is likely that the differences in pharmacokinetics may allow different dosing and scheduling of PM01183 in the clinic that could lead to novel and/or increased antitumor activity. Taken together, our results provide a mechanistic basis to support clinical trials of PM01183 alone or in combination with cisplatin.

  15. Potential risk of esophageal squamous cell carcinoma due to nucleotide excision repair XPA and XPC gene variants and their interaction among themselves and with environmental factors.

    Science.gov (United States)

    Rafiq, Rumaisa; Bhat, Gulzar Ahmad; Lone, Mohd Maqbool; Masood, Akbar; Dar, Nazir Ahmad

    2016-08-01

    The association of nucleotide excision repair (NER) gene polymorphisms with esophageal squamous cell carcinoma (ESCC) is inconclusive. The aim of the current study was to assess the association of repair gene xeroderma pigmentosum A (XPA) (rs-1800975) and xeroderma pigmentosum C (XPC) (rs-2228000) polymorphisms with ESCC risk as well as modifying effects of environmental factors. The genotyping was done in 450 confirmed ESCC cases and equal number of individually matched controls by the polymerase chain reaction and restriction fragment length polymorphism (PCR-RFLP) and direct sequencing methods. Conditional logistic regression models were used to assess the genotypic associations and interactions. A high ESCC risk was found in subjects who carried the homozygous minor allele of XPA (odds ratio (OR) = 3.57; 95 % confidence interval (CI) = 1.76-7.23), and the risk was higher when analysis was limited to participants who were ever smokers (OR = 4.22; 95 % CI = 2.01-8.88), lived in adobe houses (OR = 8.42; 95 % CI = 3.74-18.95), consumed large volumes of salt tea (OR = 7.42; 95 % CI = 3.30-16.69), or had a positive family history of cancer (FHC) (OR = 9.47; 95 % CI = 4.67-19.20). In case of XPC, a homozygous minor allele also showed strong association with ESCC risk (OR = 4.43; 95 % CI = 2.41-8.16). We again observed a very strong effect of the above environmental factors in elevating the risk of ESCC. Further, the variant genotypes of both genes in combination showed an increased risk towards ESCC (OR = 7.01; 95 % CI = 3.14-15.64) and such association was synergistically significant. Salt tea consumption showed an interaction with genotypes of XPA and XPC. However, an interaction with FHC was significant in the case of XPA genotype only. XPA and XPC genotypes are associated with an increased risk of ESCC, and such association was reasonably modulated by different exposures.

  16. Retraction: 'Dose-dependent dual effect of HTLV-1 tax oncoprotein on p53-dependent nucleotide excision repair in human T-cells' by Yana Schavinsky-Khrapunsky, Esther Priel and Mordechai Aboud.

    Science.gov (United States)

    2017-06-15

    The above article, published online on 4 October 2007 in Wiley Online Library (wileyonlinelibrary.com), and in Volume 122, pp. 305-316, has been retracted by agreement between the journal Editor in Chief, Professor Peter Lichter, and John Wiley & Sons Ltd. The retraction has been agreed as the bands in Figs 1, 2, 5 and 6 appear to have been manipulated. Schavinsky-Khrapunsky, Y., Priel, E. and Aboud, M. (2008), Dose-dependent dual effect of HTLV-1 tax oncoprotein on p53-dependent nucleotide excision repair in human T-cells. Int. J. Cancer, 122: 305-316. doi:10.1002/ijc.23091. © 2017 UICC.

  17. Differentiation of drug and non-drug Cannabis using a single nucleotide polymorphism (SNP) assay.

    Science.gov (United States)

    Rotherham, D; Harbison, S A

    2011-04-15

    Cannabis sativa is both an illegal drug and a legitimate crop. The differentiation of illegal drug Cannabis from non-drug forms of Cannabis is relevant in the context of the growth of fibre and seed oil varieties of Cannabis for commercial purposes. This differentiation is currently determined based on the levels of tetrahydrocannabinol (THC) in adult plants. DNA based methods have the potential to assay Cannabis material unsuitable for analysis using conventional means including seeds, pollen and severely degraded material. The purpose of this research was to develop a single nucleotide polymorphism (SNP) assay for the differentiation of "drug" and "non-drug"Cannabis plants. An assay was developed based on four polymorphisms within a 399 bp fragment of the tetrahydrocannabinolic acid (THCA) synthase gene, utilising the snapshot multiplex kit. This SNP assay was tested on 94 Cannabis plants, which included 10 blind samples, and was able to differentiate between "drug" and "non-drug"Cannabis in all cases, while also differentiating between Cannabis and other species. Non-drug plants were found to be homozygous at the four sites assayed while drug Cannabis plants were either homozygous or heterozygous.

  18. A multilocus assay reveals high nucleotide diversity and limited differentiation among Scandinavian willow grouse (Lagopus lagopus

    Directory of Open Access Journals (Sweden)

    Quintela Maria

    2008-12-01

    Full Text Available Abstract Background There is so far very little data on autosomal nucleotide diversity in birds, except for data from the domesticated chicken and some passerines species. Estimates of nucleotide diversity reported so far in birds have been high (~10-3 and a likely explanation for this is the generally higher effective population sizes compared to mammals. In this study, the level of nucleotide diversity has been examined in the willow grouse, a non-domesticated bird species from the order Galliformes, which also holds the chicken. The willow grouse (Lagopus lagopus has an almost circumpolar distribution but is absent from Greenland and the north Atlantic islands. It primarily inhabits tundra, forest edge habitats and sub-alpine vegetation. Willow grouse are hunted throughout its range, and regionally it is a game bird of great cultural and economical importance. Results We sequenced 18 autosomal protein coding loci from approximately 15–18 individuals per population. We found a total of 127 SNP's, which corresponds to 1 SNP every 51 bp. 26 SNP's were amino acid replacement substitutions. Total nucleotide diversity (πt was between 1.30 × 10-4 and 7.66 × 10-3 (average πt = 2.72 × 10-3 ± 2.06 × 10-3 and silent nucleotide diversity varied between 4.20 × 10-4and 2.76 × 10-2 (average πS = 9.22 × 10-3 ± 7.43 × 10-4. The synonymous diversity is approximately 20 times higher than in humans and two times higher than in chicken. Non-synonymous diversity was on average 18 times lower than the synonymous diversity and varied between 0 and 4.90 × 10-3 (average πa = 5.08 × 10-4 ± 7.43 × 103, which suggest that purifying selection is strong in these genes. FST values based on synonymous SNP's varied between -5.60 × 10-4 and 0.20 among loci and revealed low levels of differentiation among the four localities, with an overall value of FST = 0.03 (95% CI: 0.006 – 0.057 over 60 unlinked loci. Non-synonymous SNP's gave similar results. Low

  19. Low-intensity red and infrared lasers affect mRNA expression of DNA nucleotide excision repair in skin and muscle tissue.

    Science.gov (United States)

    Sergio, Luiz Philippe S; Campos, Vera Maria A; Vicentini, Solange C; Mencalha, Andre Luiz; de Paoli, Flavia; Fonseca, Adenilson S

    2016-04-01

    Lasers emit light beams with specific characteristics, in which wavelength, frequency, power, fluence, and emission mode properties determine the photophysical, photochemical, and photobiological responses. Low-intensity lasers could induce free radical generation in biological tissues and cause alterations in macromolecules, such as DNA. Thus, the aim of this work was to evaluate excision repair cross-complementing group 1 (ERCC1) and excision repair cross-complementing group 2 (ERCC2) messenger RNA (mRNA) expression in biological tissues exposed to low-intensity lasers. Wistar rat (n = 28, 4 for each group) skin and muscle were exposed to low-intensity red (660 nm) and near-infrared (880 nm) lasers at different fluences (25, 50, and 100 J/cm(2)), and samples of these tissues were withdrawn for RNA extraction, cDNA synthesis, and gene expression evaluation by quantitative polymerase chain reaction. Laser exposure was in continuous wave and power of 100 mW. Data show that ERCC1 and ERCC2 mRNA expressions decrease in skin (p laser, but increase in muscle tissue (p  0.05), but ERCC2 mRNA expression decreases in skin (p laser. Our results show that ERCC1 and ERCC2 mRNA expression is differently altered in skin and muscle tissue exposed to low-intensity lasers depending on wavelengths and fluences used in therapeutic protocols.

  20. UV-induced endonuclease III-sensitive sites at the mating type loci in Saccharomyces cerevisiae are repaired by nucleotide excision repair: RAD7 and RAD16 are not required for their removal from HML alpha.

    Science.gov (United States)

    Reed, S H; Boiteux, S; Waters, R

    1996-03-01

    Ultraviolet irradiation of DNA induces cyclobutane pyrimidine dimers (CPDs) 6-4'-(pyrimidine 2'-one) pyrimidines and pyrimidine hydrates. The dimer is the major photoproduct, and is specifically recognized by endonuclease V of phage T4. Pyrimidine hydrates represent a small fraction of the total photoproducts, and are substrates for endonuclease III of Escherichia coli. We used these enzymes to follow the fate of their substrates in the mating type loci of Saccharomyces cerevisiae. In a RAD strain, CPSs in the transcriptionally active MAT alpha locus are preferentially repaired relative to the inactive HML alpha locus, whilst repair of endonuclease III-sensitive sites is not preferential. The rad1, 2, 3 and 4 mutants, which lack factors that are essential for the incision step of nucleotide excision repair (NER), repair neither CPDs nor endonuclease III-sensitive sites, clearly showing that these lesions are repaired by by NER pathway. Previously it had been shown that the products of the RAD7 and RAD16 genes are required for the NER of CPDs from the HML alpha locus. We show that, in the same locus, these gene products are not needed for removal of endonuclease III-sensitive sites by the same mechanism. This indicates that the components required for NER differ depending on either the type of lesion encountered or on the specific location of the lesion within the genome.

  1. Inducible nucleotide excision repair (NER) of UV-induced cyclobutane pyrimidine dimers in the cell cycle of the budding yeast Saccharomyces cerevisiae: evidence that inducible NER is confined to the G1 phase of the mitotic cell cycle.

    Science.gov (United States)

    Scott, A D; Waters, R

    1997-03-18

    We previously reported on an inducible component of nucleotide excision repair in Saccharomyces cerevisiae that is controlled by the RAD16 gene. Here we describe a study of this event at the MAT alpha and HML alpha mating-type loci and on the transcribed (TS) and nontranscribed (NTS) strands of the RAD16 gene. Events were examined at various stages of the mitotic cycle in cells synchronised by centrifugal elutriation. Repair of cyclobutane pyrimidine dimers (CPDs) following a single UV dose does not vary significantly in different stages of the mitotic cell cycle. CPDs are removed more rapidly from the transcriptionally active MAT alpha locus than from the silent HML alpha locus, and the TS of RAD16 is repaired faster than the NTS in all stages of the cycle following a single UV irradiation. Enhanced excision of CPDs at MAT alpha and HML alpha can be induced only in the G1 and early S stages of the cell cycle. Here prior irradiation of cells with 25 J/m2 enhances the removal of CPDs following a second UV dose of 70 J/m2. The level of enhancement of repair does not differ significantly between MAT alpha and HML alpha in G1. Enhanced removal of CPDs is absent when cells receive the inducing dose in late S or G2/M. Repair of CPDs in both strands of RAD16 is similarly enhanced only if cells receive the initial irradiation in G1 and early S. The level of enhanced removal of CPDs is not significantly different in the TS and NTS of RAD16 either in asynchronous cells or in cells preirradiated in G1 and early S. It has been shown by others that UV-induced expression of RAD16 remains at high levels if cells are held in G1 by treatment with alpha factor. Therefore the increase in RAD16 transcript levels in G1 may be responsible for the ability to enhance NER solely in this stage of the cell cycle.

  2. A few nucleotide polymorphisms are sufficient to recruit nuclear factors differentially to the intron 1 of HPV-16 intratypic variants.

    Science.gov (United States)

    López-Urrutia, Eduardo; Valdés, Jesús; Bonilla-Moreno, Raúl; Martínez-Salazar, Martha; Martínez-Garcia, Martha; Berumen, Jaime; Villegas-Sepúlveda, Nicolás

    2012-06-01

    The HPV-16 E6/E7 genes, which contain intron 1, are processed by alternative splicing and its transcripts are detected with a heterogeneous profile in tumours cells. Frequently, the HPV-16 positive carcinoma cells bear viral variants that contain single nucleotide polymorphisms into its DNA sequence. We were interested in analysing the contribution of this polymorphism to the heterogeneity in the pattern of the E6/E7 spliced transcripts. Using the E6/E7 sequences from three closely related HPV-16 variants, we have shown that a few nucleotide changes are sufficient to produce heterogeneity in the splicing profile. Furthermore, using mutants that contained a single SNP, we also showed that one nucleotide change was sufficient to reproduce the heterogeneous splicing profile. Additionally, a difference of two or three SNPs among these viral sequences was sufficient to recruit differentially several splicing factors to the polymorphic E6/E7 transcripts. Moreover, only one SNP was sufficient to alter the binding site of at least one splicing factor, changing the ability of splicing factors to bind the transcript. Finally, the factors that were differentially bound to the short form of intron 1 of one of these E6/E7 variants were identified as TIA1 and/or TIAR and U1-70k, while U2AF65, U5-52k and PTB were preferentially bound to the transcript of the other variants.

  3. Differentiation of Erwinia amylovora and Erwinia pyrifoliae strains with single nucleotide polymorphisms and by synthesis of dihydrophenylalanine.

    Science.gov (United States)

    Gehring, I; Geider, K

    2012-07-01

    Fire blight has spread from North America to New Zealand, Europe, and the Mediterranean region. We were able to differentiate strains from various origins with a novel PCR method. Three Single Nucleotide Polymorphisms (SNPs) in the Erwinia amylovora genome were characteristic of isolates from North America and could distinguish them from isolates from other parts of the world. They were derived from the galE, acrB, and hrpA genes of strains Ea273 and Ea1/79. These genes were analyzed by conventional PCR (cPCR) and quantitative PCR (qPCR) with differential primer annealing temperatures. North-American E. amylovora strains were further differentiated according to their production of L: -2,5-dihydrophenylalanine (DHP) as tested by growth inhibition of the yeast Rhodotorula glutinis. E. amylovora fruit tree (Maloideae) and raspberry (rubus) strains were also differentiated by Single Strand Conformational Polymorphism analysis. Strains from the related species Erwinia pyrifoliae isolated in Korea and Japan were all DHP positive, but were differentiated from each other by SNPs in the galE gene. Differential PCR is a rapid and simple method to distinguish E. amylovora as well as E. pyrifoliae strains according to their geographical origin.

  4. Binding of the human nucleotide excision repair proteins XPA and XPC/HR23B to the 5R-thymine glycol lesion and structure of the cis-(5R,6S) thymine glycol epimer in the 5′-GTgG-3′ sequence: destabilization of two base pairs at the lesion site

    OpenAIRE

    Brown, Kyle L.; Roginskaya, Marina; Zou, Yue; Altamirano, Alvin; Basu, Ashis K.; Stone, Michael P.

    2009-01-01

    The 5R thymine glycol (5R-Tg) DNA lesion exists as a mixture of cis-(5R,6S) and trans-(5R,6R) epimers; these modulate base excision repair. We examine the 7:3 cis-(5R,6S):trans-(5R,6R) mixture of epimers paired opposite adenine in the 5′-GTgG-3′ sequence with regard to nucleotide excision repair. Human XPA recognizes the lesion comparably to the C8-dG acetylaminoflourene (AAF) adduct, whereas XPC/HR23B recognition of Tg is superior. 5R-Tg is processed by the Escherichia coli UvrA and UvrABC p...

  5. Molecular cloning, nucleotide sequence, and expression of the gene encoding human eosinophil differentiation factor (interleukin 5)

    Energy Technology Data Exchange (ETDEWEB)

    Campbell, H.D.; Tucker, W.Q.J.; Hort, Y.; Martinson, M.E.; Mayo, G.; Clutterbuck, E.J.; Sanderson, C.J.; Young, I.G.

    1987-10-01

    The human eosinophil differentiation factor (EDF) gene was cloned from a genomic library in lambda phage EMBL3A by using a murine EDF cDNA clone as a probe. The DNA sequence of a 3.2-kilobase BamHI fragment spanning the gene was determined. The gene contains three introns. The predicted amino acid sequence of 134 amino acids is identical with that recently reported for human interleukin 5 but shows no significant homology with other known hemopoietic growth regulators. The amino acid sequence shows strong homology (approx. 70% identity) with that of murine EDF. Recombinant human EDF, expressed from the human EDF gene after transfection into monkey COS cells, stimulated the production of eosinophils and eosinophil colonies from normal human bone marrow but had no effect on the production of neutrophils or mononuclear cells (monocytes and lymphoid cells). The apparent specificity of human EDF for the eosinophil lineage in myeloid hemopoiesis contrasts with the properties of human interleukin 3 and granulocyte/macrophage and granulocyte colony-stimulating factors but is directly analogous to the biological properties of murine EDF. Human EDF therefore represents a distinct hemopoietic growth factor that could play a central role in the regulation of eosinophilia.

  6. Hyperpolarization-activated cyclic nucleotide-gated cation channel subtypes differentially modulate the excitability of murine small intestinal afferents

    Institute of Scientific and Technical Information of China (English)

    Ying-Ping Wang; Bi-Ying Sun; Qian Li; Li Dong; Guo-Hua Zhang; David Grundy; Wei-Fang Rong

    2012-01-01

    AIM: To assess the role of hyperpolarization-activated cyclic nucleotide-gated cation (HCN) channels in regulating the excitability of vagal and spinal gut afferents.METHODS: The mechanosensory response of mesen-teric afferent activity was measured in an ex vivo murine jejunum preparation. HCN channel activity was recorded through voltage and current clamp in acutely dissociated dorsal root ganglia (DRG) and nodose ganglia (NG) neurons retrogradely labeled from the small intestine through injection of a fluorescent marker (DiI). The isoforms of HCN channels expressed in DRG and NG neurons were examined by immunohistochemistry.RESULTS: Ramp distension of the small intestine evoked biphasic increases in the afferent nerve activity, reflecting the activation of low- and high-threshold fibers.HCN blocker CsCl (5 mmol/L) preferentially inhibited the responses of low-threshold fibers to distension and showed no significant effects on the high-threshold responses. The effect of CsCl was mimicked by the more selective HCN blocker ZD7288 (10 ?mol/L). In 71.4% of DiI labeled DRG neurons (n = 20) and 90.9% of DiI labeled NG neurons (n = 10), an inward current (Ih current) was evoked by hyperpolarization pulses which was fully eliminated by extracellular CsCl. In neurons expressing Ih current, a typical "sag" was observed upon injection of hyperpolarizing current pulses in current-clamp recordings. CsCl abolished the sag entirely. In some DiI labeled DRG neurons, the Ih current was potentiated by 8-Br-cAMP, which had no effect on the Ih current of DiI labeled NG neurons. Immunohistochemistry revealed differential expression of HCN isoforms in vagal and spinal afferents, and HCN2 and HCN3 seemed to be the dominant isoform in DRG and NG, respectively.CONCLUSION: HCNs differentially regulate the excitability of vagal and spinal afferent of murine small intestine.

  7. Hemangioma excision (image)

    Science.gov (United States)

    A hemangioma is a non-cancerous (benign) growth of blood vessels. They are the most common benign blood vessel ( ... time and occasionally with medication. Large or disfiguring hemangiomas may require surgical excision.

  8. Hemangioma excision - slideshow

    Science.gov (United States)

    ... this page: //medlineplus.gov/ency/presentations/100114.htm Hemangioma excision - series—Indications To use the sharing features ... Go to slide 3 out of 3 Overview Hemangiomas are the most common type of benign blood- ...

  9. Functional specialization in nucleotide sugar transporters occurred through differentiation of the gene cluster EamA (DUF6 before the radiation of Viridiplantae

    Directory of Open Access Journals (Sweden)

    Fredriksson Robert

    2011-05-01

    Full Text Available Abstract Background The drug/metabolite transporter superfamily comprises a diversity of protein domain families with multiple functions including transport of nucleotide sugars. Drug/metabolite transporter domains are contained in both solute carrier families 30, 35 and 39 proteins as well as in acyl-malonyl condensing enzyme proteins. In this paper, we present an evolutionary analysis of nucleotide sugar transporters in relation to the entire superfamily of drug/metabolite transporters that considers crucial intra-protein duplication events that have shaped the transporters. We use a method that combines the strengths of hidden Markov models and maximum likelihood to find relationships between drug/metabolite transporter families, and branches within families. Results We present evidence that the triose-phosphate transporters, domain unknown function 914, uracil-diphosphate glucose-N-acetylglucosamine, and nucleotide sugar transporter families have evolved from a domain duplication event before the radiation of Viridiplantae in the EamA family (previously called domain unknown function 6. We identify previously unknown branches in the solute carrier 30, 35 and 39 protein families that emerged simultaneously as key physiological developments after the radiation of Viridiplantae, including the "35C/E" branch of EamA, which formed in the lineage of T. adhaerens (Animalia. We identify a second cluster of DMTs, called the domain unknown function 1632 cluster, which has non-cytosolic N- and C-termini, and thus appears to have been formed from a different domain duplication event. We identify a previously uncharacterized motif, G-X(6-G, which is overrepresented in the fifth transmembrane helix of C-terminal domains. We present evidence that the family called fatty acid elongases are homologous to transporters, not enzymes as had previously been thought. Conclusions The nucleotide sugar transporters families were formed through differentiation of the

  10. Nucleotide Metabolism

    DEFF Research Database (Denmark)

    Martinussen, Jan; Willemoës, M.; Kilstrup, Mogens

    2011-01-01

    Metabolic pathways are connected through their utilization of nucleotides as supplier of energy, allosteric effectors, and their role in activation of intermediates. Therefore, any attempt to exploit a given living organism in a biotechnological process will have an impact on nucleotide metabolism....... The aim of this article is to provide knowledge of nucleotide metabolism and its regulation to facilitate interpretation of data arising from genetics, proteomics, and transcriptomics in connection with biotechnological processes and beyond....

  11. Nucleotide Metabolism

    DEFF Research Database (Denmark)

    Martinussen, Jan; Willemoës, M.; Kilstrup, Mogens

    2011-01-01

    Metabolic pathways are connected through their utilization of nucleotides as supplier of energy, allosteric effectors, and their role in activation of intermediates. Therefore, any attempt to exploit a given living organism in a biotechnological process will have an impact on nucleotide metabolism....... The aim of this article is to provide knowledge of nucleotide metabolism and its regulation to facilitate interpretation of data arising from genetics, proteomics, and transcriptomics in connection with biotechnological processes and beyond....

  12. Changes in the expression of epidermal differentiation markers at sites where cultured epithelial autografts were transplanted onto wounds from burn scar excision.

    Science.gov (United States)

    Kadoya, Kuniko; Amano, Satoshi; Nishiyama, Toshio; Inomata, Shinji; Tsunenaga, Makoto; Kumagai, Norio; Matsuzaki, Kyoichi

    2016-06-01

    This study investigated the recovery process during which grafted cultured epithelium formed normal epidermis. The subjects were 18 patients whose burn scars were excised at a depth not exposing the fat layer and who subsequently received cultured epithelial autografts. A total of 24 samples were obtained from the grafted sites: 6 samples within 6 weeks (stage 1), 5 samples after 6 weeks and within 6 months (stage 2), 6 samples after 6 months and within 18 months (stage 3) and 7 samples beyond 18 months (stage 4) after transplantation. These samples were stained for monoclonal antibodies against filaggrin, transglutaminase (TG), cytokeratin 6 and involucrin. Their expressions were examined in the epidermis. The expression patterns were classified using a six-grade scale. The grades of filaggrin and TG were significantly higher at stage 3 and 4 compared with stage 1. There was a marginally significant increase in the grade of cytokeratin 6 at stage 3 and it was significantly higher at stage 4 compared with stage 1. These results showed that wound healing continued at a molecular level until the end of stage 3. The recovery of involucrin was delayed compared with that of other markers. TG and involucrin are thought to be regulated independently at the grafted sites.

  13. Cap-proximal nucleotides via differential eIF4E binding and alternative promoter usage mediate translational response to energy stress

    Science.gov (United States)

    Tamarkin-Ben-Harush, Ana; Vasseur, Jean-Jacques; Debart, Françoise; Ulitsky, Igor; Dikstein, Rivka

    2017-01-01

    Transcription start-site (TSS) selection and alternative promoter (AP) usage contribute to gene expression complexity but little is known about their impact on translation. Here we performed TSS mapping of the translatome following energy stress. Assessing the contribution of cap-proximal TSS nucleotides, we found dramatic effect on translation only upon stress. As eIF4E levels were reduced, we determined its binding to capped-RNAs with different initiating nucleotides and found the lowest affinity to 5'cytidine in correlation with the translational stress-response. In addition, the number of differentially translated APs was elevated following stress. These include novel glucose starvation-induced downstream transcripts for the translation regulators eIF4A and Pabp, which are also translationally-induced despite general translational inhibition. The resultant eIF4A protein is N-terminally truncated and acts as eIF4A inhibitor. The induced Pabp isoform has shorter 5'UTR removing an auto-inhibitory element. Our findings uncovered several levels of coordination of transcription and translation responses to energy stress. DOI: http://dx.doi.org/10.7554/eLife.21907.001 PMID:28177284

  14. Targeting single-nucleotide polymorphisms in the 16S rRNA gene to detect and differentiate Legionella pneumophila and non-Legionella pneumophila species.

    Science.gov (United States)

    Zhan, Xiao-Yong; Hu, Chao-Hui; Zhu, Qing-Yi

    2016-08-01

    A PCR-based method targeting single-nucleotide polymorphisms (SNPs) in the 16S rRNA gene was developed for differential identification of Legionella pneumophila and non-Legionella pneumophila. Based on the bioinformatics analysis for 176 Legionella 16S rRNA gene fragments of 56 different Legionella species, a set of SNPs, A(628)C(629) was found to be highly specific to L. pneumophila strains. A multiplex assay was designed that was able to distinguish sites with limited sequence heterogeneity between L. pneumophila and non-L. pneumophila in the targeted 16S rRNA gene. The assay amplified a 261-bp amplicon for Legionella spp. and a set of 203- and 97-bp amplicons only specific to L. pneumophila species. Among 49 ATCC strains and 284 Legionella isolates from environmental water and clinical samples, 100 % of L. pneumophila and non-L. pneumophila strains were correctly identified and differentiated by this assay. The assay presents a more rapid, sensitive and alternative method to the currently available PCR-sequencing detection and differentiation method.

  15. Genetic Variation in Base Excision Repair Pathway Genes, Pesticide Exposure, and Prostate Cancer Risk

    National Research Council Canada - National Science Library

    Kathryn Hughes Barry; Stella Koutros; Sonja I. Berndt; Gabriella Andreotti; Jane A. Hoppin; Dale P. Sandler; Laurie A. Burdette; Meredith Yeager; Laura E. Beane Freeman; Jay H. Lubin; Xiaomei Ma; Tongzhang Zheng; Michael C. R. Alavanja

    2011-01-01

    .... OBJECTIVES: Because base excision repair (BER) is the predominant pathway involved in repairing oxidative damage, we evaluated interactions between 39 pesticides and 394 tag single-nucleotide polymorphisms (SNPs...

  16. Molecular cloning of the human excision repair gene ERCC-6.

    NARCIS (Netherlands)

    C. Troelstra (Christine); H. Odijk (Hanny); J. de Wit (Jan); A. Westerveld (Andries); L.H. Thompson; D. Bootsma (Dirk); J.H.J. Hoeijmakers (Jan)

    1990-01-01

    textabstractThe UV-sensitive, nucleotide excision repair-deficient Chinese hamster mutant cell line UV61 was used to identify and clone a correcting human gene, ERCC-6. UV61, belonging to rodent complementation group 6, is only moderately UV sensitive in comparison with mutant lines in groups 1 to 5

  17. Nucleotide Excision Repair Protein Levels vis-à -vis Anticancer Drug Resistance in 60 Human Tumor Cell Lines%人肿瘤细胞核苷酸切除修复蛋白表达与抗癌药耐药的相关性

    Institute of Scientific and Technical Information of China (English)

    陈忠平; AretiMALAPETSA

    2002-01-01

    Background & Objective: Nucleotide excision repair (NER) is a multi-enzyme DNA repair system in eukaryotes. Several NER genes in this system including XPA, XPB, ERCC1, and ERCC2 (XPD) have been implicated in anticancer drug resistance in human tumor cells. This study was designed to investigate the relationship between the expression of NER protein and the drug-resistance of human tumor cell lines. Methods: In this study, The authors assessed the levels of the above mentioned proteins, by utilizing Western blot analysis, in the USA National Cancer Institute (NCI) panel of 60 human tumor cell lines and correlated to the cytotoxicity patterns of 170 compounds that constitute the standard agent (SA) database. Results: The ERCC1, XPB, and XPD protein expression patterns yielded significant negative Pearson correlations with 13, 17, and 32 out of the 170 compounds, respectively (P < 0.05). XPA produced a random assortment of negative and positive correlations and did not appear to confer an overall resistance or sensitivity to these drugs. Protein expression was also compared with a pre-defined categorisation of the standard agents into six mechanism-of-action (MOA) groups resulting in an inverse association between XPD and alkylating agent sensitivity. Conclusion: Our present data demonstrate that XPD protein levels correlate with resistance to alkylating agents in human tumor cell lines, suggesting that XPD plays an important role in the development of this resistance.%背景与目的:核苷酸切除修复(Nucleotide excision repair,NER)是真核细胞中的DNA修复多酶系统,它可能与人肿瘤细胞对抗癌药的耐药有关.本实验将探讨NER蛋白(XPA,XPB,XPD和ERCC1)的表达与人肿瘤细胞耐药的关系.方法:采用western blot检测美国国家癌症研究所(National Cancer Institute,NCI)用于抗癌药筛选的60株人肿瘤细胞的ERCC1,XPA,XPB XPD表达,并与170种抗癌药物的细胞毒试验结果进行相关性分析.结果:ERCC1,XPB

  18. Premature aging and cancer in nucleotide excision repair-disorders

    NARCIS (Netherlands)

    K.E.M. Diderich (Karin); M. Alanazi; J.H.J. Hoeijmakers (Jan)

    2011-01-01

    textabstractDuring the past decades, the major impact of DNA damage on cancer as 'disease of the genes' has become abundantly apparent. In addition to cancer, recent years have also uncovered a very strong association of DNA damage with many features of (premature) aging. The notion that DNA repair

  19. Genomic single-nucleotide polymorphisms confirm that Gunnison and Greater sage-grouse are genetically well differentiated and that the Bi-State population is distinct

    Science.gov (United States)

    Oyler-McCance, Sara J.; Cornman, Robert S.; Jones, Kenneth L.; Fike, Jennifer

    2015-01-01

    Sage-grouse are iconic, declining inhabitants of sagebrush habitats in western North America, and their management depends on an understanding of genetic variation across the landscape. Two distinct species of sage-grouse have been recognized, Greater (Centrocercus urophasianus) and Gunnison sage-grouse (C. minimus), based on morphology, behavior, and variation at neutral genetic markers. A parapatric group of Greater Sage-Grouse along the border of California and Nevada ("Bi-State") is also genetically distinct at the same neutral genetic markers, yet not different in behavior or morphology. Because delineating taxonomic boundaries and defining conservation units is often difficult in recently diverged taxa and can be further complicated by highly skewed mating systems, we took advantage of new genomic methods that improve our ability to characterize genetic variation at a much finer resolution. We identified thousands of single-nucleotide polymorphisms (SNPs) among Gunnison, Greater, and Bi-State sage-grouse and used them to comprehensively examine levels of genetic diversity and differentiation among these groups. The pairwise multilocus fixation index (FST) was high (0.49) between Gunnison and Greater sage-grouse, and both principal coordinates analysis and model-based clustering grouped samples unequivocally by species. Standing genetic variation was lower within the Gunnison Sage-Grouse. The Bi-State population was also significantly differentiated from Greater Sage-Grouse, albeit more weakly (FST = 0.09), and genetic clustering results were consistent with reduced gene flow with Greater Sage-Grouse. No comparable genetic divisions were found within the Greater Sage-Grouse sample, which spanned the southern half of the range. Thus, we provide much stronger genetic evidence supporting the recognition of Gunnison Sage-Grouse as a distinct species with low genetic diversity. Further, our work confirms that the Bi-State population is differentiated from other

  20. The single nucleotide variant rs12722489 determines differential estrogen receptor binding and enhancer properties of an IL2RA intronic region

    Science.gov (United States)

    Putlyaeva, Lidia V.; Demin, Denis E.; Kulakovskiy, Ivan V.; Vorontsov, Ilya E.; Fridman, Marina V.; Makeev, Vsevolod J.; Kuprash, Dmitry V.; Schwartz, Anton M.

    2017-01-01

    We studied functional effect of rs12722489 single nucleotide polymorphism located in the first intron of human IL2RA gene on transcriptional regulation. This polymorphism is associated with multiple autoimmune conditions (rheumatoid arthritis, multiple sclerosis, Crohn's disease, and ulcerative colitis). Analysis in silico suggested significant difference in the affinity of estrogen receptor (ER) binding site between alternative allelic variants, with stronger predicted affinity for the risk (G) allele. Electrophoretic mobility shift assay showed that purified human ERα bound only G variant of a 32-bp genomic sequence containing rs12722489. Chromatin immunoprecipitation demonstrated that endogenous human ERα interacted with rs12722489 genomic region in vivo and DNA pull-down assay confirmed differential allelic binding of amplified 189-bp genomic fragments containing rs12722489 with endogenous human ERα. In a luciferase reporter assay, a kilobase-long genomic segment containing G but not A allele of rs12722489 demonstrated enhancer properties in MT-2 cell line, an HTLV-1 transformed human cell line with a regulatory T cell phenotype. PMID:28234966

  1. Association of a single nucleotide polymorphism in growth differentiate factor 5 with congenital dysplasia of the hip: a case-control study.

    Science.gov (United States)

    Dai, Jin; Shi, Dongquan; Zhu, Pengsheng; Qin, Jianghui; Ni, Haijian; Xu, Yong; Yao, Chen; Zhu, Lunqing; Zhu, Hongtao; Zhao, Baocheng; Wei, Jia; Liu, Baorui; Ikegawa, Shiro; Jiang, Qing; Ding, Yitao

    2008-01-01

    Congenital dysplasia of the hip is an abnormal seating of the femoral head in the acetabulum, mainly caused by shallow acetabulum and lax joint capsule. Genetic factors play a considerable role in the pathogenesis of congenital dysplasia of the hip. The gene growth differentiate factor 5 (GDF5) has been implicated in skeletal development and joint morphogenesis in humans and mice. A functional single nucleotide polymorphism (SNP) in the 5'-untranslated region of GDF5 (rs143383) was reported to be associated with osteoarthritis susceptibility. As a key regulator in morphogenesis of skeletal components and soft tissues in and around the joints, GDF5 may be involved in the aetiology and pathogenesis of congenital dysplasia of the hip. Our objective is to evaluate if the GDF5 SNP is associated with congenital dysplasia of the hip in people of Han Chinese origin. The GDF5 SNP was genotyped in 338 children with congenital dysplasia of the hip and 622 control subjects. The SNP was significantly associated with congenital dysplasia of the hip (p = 0.0037; odds ration (OR) = 1.40; 95% confidence interval (CI) = 1.11 to 1.75). A significant difference was detected in female samples when stratified by gender (p = 0.0053; OR = 1.46; 95% CI = 1.21 to 1.91), and in hip dislocation when stratified by severity (p = 0.0078; OR = 1.43; 95% CI = 1.11 to 1.85). Our results indicate that GDF5 is important in the aetiology of congenital dysplasia of the hip. To the authors' knowledge this is the first time that a definite association with the congenital dysplasia of the hip susceptibility has been detected.

  2. Association of a single nucleotide polymorphism in growth differentiate factor 5 with congenital dysplasia of the hip: a case-control study

    Science.gov (United States)

    Dai, Jin; Shi, Dongquan; Zhu, Pengsheng; Qin, Jianghui; Ni, Haijian; Xu, Yong; Yao, Chen; Zhu, Lunqing; Zhu, Hongtao; Zhao, Baocheng; Wei, Jia; Liu, Baorui; Ikegawa, Shiro; Jiang, Qing; Ding, Yitao

    2008-01-01

    Introduction Congenital dysplasia of the hip is an abnormal seating of the femoral head in the acetabulum, mainly caused by shallow acetabulum and lax joint capsule. Genetic factors play a considerable role in the pathogenesis of congenital dysplasia of the hip. The gene growth differentiate factor 5 (GDF5) has been implicated in skeletal development and joint morphogenesis in humans and mice. A functional single nucleotide polymorphism (SNP) in the 5'-untranslated region of GDF5 (rs143383) was reported to be associated with osteoarthritis susceptibility. As a key regulator in morphogenesis of skeletal components and soft tissues in and around the joints, GDF5 may be involved in the aetiology and pathogenesis of congenital dysplasia of the hip. Our objective is to evaluate if the GDF5 SNP is associated with congenital dysplasia of the hip in people of Han Chinese origin. Methods The GDF5 SNP was genotyped in 338 children with congenital dysplasia of the hip and 622 control subjects. Results The SNP was significantly associated with congenital dysplasia of the hip (p = 0.0037; odds ration (OR) = 1.40; 95% confidence interval (CI) = 1.11 to 1.75). A significant difference was detected in female samples when stratified by gender (p = 0.0053; OR = 1.46; 95% CI = 1.21 to 1.91), and in hip dislocation when stratified by severity (p = 0.0078; OR = 1.43; 95% CI = 1.11 to 1.85). Conclusions Our results indicate that GDF5 is important in the aetiology of congenital dysplasia of the hip. To the authors' knowledge this is the first time that a definite association with the congenital dysplasia of the hip susceptibility has been detected. PMID:18947434

  3. A Review of Recent Experiments on Step-to-Step “Hand-off” of the DNA Intermediates in Mammalian Base Excision Repair Pathways1

    OpenAIRE

    Prasad, R.; Beard, W A; Batra, V. K.; Liu, Y.; Shock, D. D.; Wilson, S H

    2011-01-01

    The current “working model” for mammalian base excision repair involves two sub-pathways termed single-nucleotide base excision repair and long patch base excision repair that are distinguished by their repair patch sizes and the enzymes/co-factors involved. These base excision repair sub-pathways are designed to sequester the various DNA intermediates, passing them along from one step to the next without allowing these toxic molecules to trigger cell cycle arrest, necrotic cell death, or apo...

  4. Nuclear translocation contributes to regulation of DNA excision repair activities

    DEFF Research Database (Denmark)

    Knudsen, Nina Østergaard; Andersen, Sofie Dabros; Lützen, Anne;

    2009-01-01

    , it is evident that proteins from the different DNA repair pathways interact [Y. Wang, D. Cortez, P. Yazdi, N. Neff, S.J. Elledge, J. Qin, BASC, a super complex of BRCA1-associated proteins involved in the recognition and repair of aberrant DNA structures, Genes Dev. 14 (2000) 927-939; M. Christmann, M......DNA mutations are circumvented by dedicated specialized excision repair systems, such as the base excision repair (BER), nucleotide excision repair (NER), and mismatch repair (MMR) pathways. Although the individual repair pathways have distinct roles in suppressing changes in the nuclear DNA.......T. Tomicic, W.P. Roos, B. Kaina, Mechanisms of human DNA repair: an update, Toxicology 193 (2003) 3-34; N.B. Larsen, M. Rasmussen, L.J. Rasmussen, Nuclear and mitochondrial DNA repair: similar pathways? Mitochondrion 5 (2005) 89-108]. Protein interactions are not only important for function, but also...

  5. Resolving discrepancy between nucleotides and amino acids in deep-level arthropod phylogenomics: differentiating serine codons in 21-amino-acid models.

    Directory of Open Access Journals (Sweden)

    Andreas Zwick

    Full Text Available BACKGROUND: In a previous study of higher-level arthropod phylogeny, analyses of nucleotide sequences from 62 protein-coding nuclear genes for 80 panarthopod species yielded significantly higher bootstrap support for selected nodes than did amino acids. This study investigates the cause of that discrepancy. METHODOLOGY/PRINCIPAL FINDINGS: The hypothesis is tested that failure to distinguish the serine residues encoded by two disjunct clusters of codons (TCN, AGY in amino acid analyses leads to this discrepancy. In one test, the two clusters of serine codons (Ser1, Ser2 are conceptually translated as separate amino acids. Analysis of the resulting 21-amino-acid data matrix shows striking increases in bootstrap support, in some cases matching that in nucleotide analyses. In a second approach, nucleotide and 20-amino-acid data sets are artificially altered through targeted deletions, modifications, and replacements, revealing the pivotal contributions of distinct Ser1 and Ser2 codons. We confirm that previous methods of coding nonsynonymous nucleotide change are robust and computationally efficient by introducing two new degeneracy coding methods. We demonstrate for degeneracy coding that neither compositional heterogeneity at the level of nucleotides nor codon usage bias between Ser1 and Ser2 clusters of codons (or their separately coded amino acids is a major source of non-phylogenetic signal. CONCLUSIONS: The incongruity in support between amino-acid and nucleotide analyses of the forementioned arthropod data set is resolved by showing that "standard" 20-amino-acid analyses yield lower node support specifically when serine provides crucial signal. Separate coding of Ser1 and Ser2 residues yields support commensurate with that found by degenerated nucleotides, without introducing phylogenetic artifacts. While exclusion of all serine data leads to reduced support for serine-sensitive nodes, these nodes are still recovered in the ML topology

  6. [Local excision of giant rectal polypoid neoplasms].

    Science.gov (United States)

    Cimitan, Andrea; Burza, Antonio; Basile, Ursula; Saputo, Serena; Mingazzini, Pietro; Stipa, Francesco

    2008-01-01

    Local excision is the best therapeutic option for giant adenomas of the rectum. Parks technique for lower rectal lesions and the T.E.M. technique for lesions localised in the middle and upper rectum offer exceptionally good exposure, allowing radical excision in the case of early low-risk T1 adenocarcinomas (well or moderately differentiated [G1/2] without lymphovascular invasion [L0]). From July 1987 to March 2006, 224 patients were treated by local excision for rectal lesions in our department. In 48 patients (21.4%) a large sessile benign lesion was diagnosed preoperatively. In 3 patients with a preoperative diagnosis of severe dysplasia (Tis) final pathology showed adenoma and for this reason they were included in our study group. A total of 51 patients with giant preoperative benign lesions were treated by local excision (Parks technique, T.E.M. or both). Twenty-five (49%) patients had a definitive diagnosis of adenocarcinoma: in situ (pTis) in 22 patients (88%), pT1 in 2 patients (8%) and pT2 in 1 patient (4%). In 26 patients (51%) the diagnosis was adenoma. The overall local recurrence rate was 9.8% (5/51); the recurrence rate was 7.6% (2/26) for adenomas and 12% (3/25) for carcinomas. The median hospital stay was 7 days (range 3-39). There was no operative mortality. Giant sessile polypoid lesions localized in the middle and upper rectum are best treated with T.E.M., while Parks technique is a good option in lower rectal tumours. These techniques, if correctly indicated and well performed, offer great advantages in terms of safety and radicality. In our experience the operative mortality was nil and the morbidity and recurrence rates were low.

  7. [Retarded excision of pyrimidine dimers in human unstimulated lymphocytes].

    Science.gov (United States)

    Snopov, S A; Roza, L; de Gruijl, F R

    2006-01-01

    Using immuno-labelling of cyclobutane pyrimidine dimers (CPDs) in nuclei of peripheral lymphocytes after their UVC-irradiation and cultivation, we have found that within the first four hours of cultivation the CPD-specific fluorescent signal from cell nuclei increased. Earlier, a similar increase in binding of antibody specific for pyrimidine (6-4) pyrimidone photoproducts to undenatured DNA isolated from UV-irradiated Chinese hamster ovary cells was reported (Mitchell et al., 1986). Our experiments showed that nucleotide excision repair enzyme might induce such of DNA modification in lymphocyte nuclei that increased specific antibody binding to DNA fragments with lesions. We suggest that enzymatic formation of open structures in DNA predominated qualitatively over dual-incision and excision of these fragments, and resulted in the enhanced exposure of the pyrimidine dimers in nuclei to specific antibodies. The results evidence that nucleotid excision repair in unstimualted human lymphocytes being deficient in dual incision and removal of UV-induced DNA lesions appear to be capable of performing chromatin relaxation and pre-incision uncoiling of DNA fragments with lesions.

  8. Biomolecular Simulation of Base Excision Repair and Protein Signaling

    Energy Technology Data Exchange (ETDEWEB)

    Straatsma, TP; McCammon, J A; Miller, John H; Smith, Paul E; Vorpagel, Erich R; Wong, Chung F; Zacharias, Martin W

    2006-03-03

    The goal of the Biomolecular Simulation of Base Excision Repair and Protein Signaling project is to enhance our understanding of the mechanism of human polymerase-β, one of the key enzymes in base excision repair (BER) and the cell-signaling enzymes cyclic-AMP-dependent protein kinase. This work used molecular modeling and simulation studies to specifically focus on the • dynamics of DNA and damaged DNA • dynamics and energetics of base flipping in DNA • mechanism and fidelity of nucleotide insertion by BER enzyme human polymerase-β • mechanism and inhibitor design for cyclic-AMP-dependent protein kinase. Molecular dynamics simulations and electronic structure calculations have been performed using the computer resources at the Molecular Science Computing Facility at the Environmental Molecular Sciences Laboratory.

  9. The mitochondrial transcription factor A functions in mitochondrial base excision repair

    DEFF Research Database (Denmark)

    Canugovi, Chandrika; Maynard, Scott; Bayne, Anne-Cécile V

    2010-01-01

    Mitochondrial transcription factor A (TFAM) is an essential component of mitochondrial nucleoids. TFAM plays an important role in mitochondrial transcription and replication. TFAM has been previously reported to inhibit nucleotide excision repair (NER) in vitro but NER has not yet been detected i...

  10. Lumbar disc excision through fenestration

    Directory of Open Access Journals (Sweden)

    Sangwan S

    2006-01-01

    Full Text Available Background : Lumbar disc herniation often causes sciatica. Many different techniques have been advocated with the aim of least possible damage to other structures while dealing with prolapsed disc surgically in the properly selected and indicated cases. Methods : Twenty six patients with clinical symptoms and signs of prolapsed lumbar intervertebral disc having radiological correlation by MRI study were subjected to disc excision by interlaminar fenestration method. Results : The assessment at follow-up showed excellent results in 17 patients, good in 6 patients, fair in 2 patients and poor in 1 patient. The mean preoperative and postoperative Visual Analogue Scores were 9.34 ±0.84 and 2.19 ±0.84 on scale of 0-10 respectively. These were statistically significant (p value< 0.001, paired t test. No significant complications were recorded. Conclusion : Procedures of interlaminar fenestration and open disc excision under direct vision offers sufficient adequate exposure for lumbar disc excision with a smaller incision, lesser morbidity, shorter convalescence, early return to work and comparable overall results in the centers where recent laser and endoscopy facilities are not available.

  11. Secreted protein gene derived-single nucleotide polymorphisms (SP-SNPs) reveal population diversity and differentiation of Puccinia striiformis f. sp. tritici in the United States

    Science.gov (United States)

    In population genetic studies, growing awareness has been raised on non-neutral markers which can provide more estimates of evolutionary differentiation caused by different selections among populations, even though neutral genetic markers have provided unbiased estimates of divergence time and the a...

  12. Association study of single nucleotide polymorphisms in JAK2 and STAT5B genes and their differential mRNA expression with mastitis susceptibility in Chinese Holstein cattle.

    Science.gov (United States)

    Usman, T; Wang, Y; Liu, C; Wang, X; Zhang, Y; Yu, Y

    2015-08-01

    The JAK-STAT pathway plays a key role in mediating immune responses. The genetic effects of single nucleotide polymorphisms (SNPs) in JAK2 and STAT5B were investigated for serum cytokines, mastitis indicators and productions traits in a population of 468 Chinese Holstein cattle. Pooled DNA sequencing revealed one SNP (BTA8:g.39645396A>G) in JAK2 and two SNPs (BTA19:g.43673888A>G and BTA19:g.43660093T>C) in STAT5B. A fixed effect model considering the effects of SNPs, parity, herd, season and year of calving was used by way of the general linear model procedure of sas. Genotype frequencies of these SNPs in the population were in Hardy-Weinberg equilibrium (P > 0.05). A novel SNP (g.39645396A>G) in JAK2 was predicted to change the amino acid from lysine to asparagine and was significantly associated with the somatic cell count (SCC) and somatic cell score (SCS), whereas g.43673888A>G in STAT5B was significantly associated with SCC, SCS and interleukin-4 (IL-4) (P G in JAK2 was significant for SCS, and its additive effect was significant for SCC, whereas the dominant effect of g.43673888A>G in STAT5B was significant for SCS and IL-4 (P G in JAK2 and g.43673888A>G in STAT5B showed a significant effect on SCC, SCS, IL-4 and TNF-α (P G and GG genotype g.43673888A>G indicated higher mRNA expression level and were significantly different from other genotypes (P cattle against mastitis development.

  13. Direct inhibition of excision/synthesis DNA repair activities by cadmium: Analysis on dedicated biochips

    Energy Technology Data Exchange (ETDEWEB)

    Candeias, S., E-mail: serge.candeias@cea.fr [CEA, INAC, SCIB, UJF and CNRS, LCIB (UMR-E 3 CEA-UJF and FRE 3200), Laboratoire Lesions des Acides Nucleiques, 17 Rue des Martyrs, F-38054 Grenoble Cedex 9 (France); CEA, DSV, iRTSV, LBBSI, UMR 5092 CNRS, F-38054 Grenoble Cedex 9 (France); Pons, B.; Viau, M.; Caillat, S.; Sauvaigo, S. [CEA, INAC, SCIB, UJF and CNRS, LCIB (UMR-E 3 CEA-UJF and FRE 3200), Laboratoire Lesions des Acides Nucleiques, 17 Rue des Martyrs, F-38054 Grenoble Cedex 9 (France)

    2010-12-10

    The well established toxicity of cadmium and cadmium compounds results from their additive effects on several key cellular processes, including DNA repair. Mammalian cells have evolved several biochemical pathways to repair DNA lesions and maintain genomic integrity. By interfering with the homeostasis of redox metals and antioxidant systems, cadmium promotes the development of an intracellular environment that results in oxidative DNA damage which can be mutagenic if unrepaired. Small base lesions are recognised by specialized glycosylases and excised from the DNA molecule. The resulting abasic sites are incised, and the correct sequences restored by DNA polymerases using the opposite strands as template. Bulky lesions are recognised by a different set of proteins and excised from DNA as part of an oligonucleotide. As in base repair, the resulting gaps are filled by DNA polymerases using the opposite strands as template. Thus, these two repair pathways consist in excision of the lesion followed by DNA synthesis. In this study, we analysed in vitro the direct effects of cadmium exposure on the functionality of base and nucleotide DNA repair pathways. To this end, we used recently described dedicated microarrays that allow the parallel monitoring in cell extracts of the repair activities directed against several model base and/or nucleotide lesions. Both base and nucleotide excision/repair pathways are inhibited by CdCl{sub 2}, with different sensitivities. The inhibitory effects of cadmium affect mainly the recognition and excision stages of these processes. Furthermore, our data indicate that the repair activities directed against different damaged bases also exhibit distinct sensitivities, and the direct comparison of cadmium effects on the excision of uracile in different sequences even allows us to propose a hierarchy of cadmium sensibility within the glycosylases removing U from DNA. These results indicate that, in our experimental conditions, cadmium is a

  14. Endoscopic excision of cheek lipomas.

    Science.gov (United States)

    Pyon, Jai-Kyong; Park, Bum-Jin; Mun, Goo-Hyun; Cha, Myung-Kyu; Lim, So-Young; Bang, Sa-Ik; Oh, Kap-Sung

    2008-10-01

    Although the removal of forehead and brow benign tumors using an endoscopic technique has proven to be valuable, the efficacy of an endoscopic excision for cheek masses is unclear. A retrospective review was performed on 8 patients with a lipoma (7) and a foreign body granuloma (1) located at the cheek region. There were 7 men and 1 woman with a mean age of 34.8 years (range, 22-54 years). All the excisional procedures were performed with an endoscope through 2 small incisions, one on the hair-bearing sideburns and the other behind the earlobe. The masses varied from 0.7 x 0.7 cm to 4.0 x 3.0 cm in size. There were no intraoperative or postoperative complications, and no recurrence was detected after a 5- to 61-month follow-up. An endoscopically assisted excision of cheek lipomas is an effective procedure and might be a good alternative to the more conventional procedures.

  15. Nucleotide divergence vs. gene expression differentiation: comparative transcriptome sequencing in natural isolates from the carrion crow and its hybrid zone with the hooded crow.

    Science.gov (United States)

    Wolf, Jochen B W; Bayer, Till; Haubold, Bernhard; Schilhabel, Markus; Rosenstiel, Philip; Tautz, Diethard

    2010-03-01

    Recent advances in sequencing technology promise to provide new strategies for studying population differentiation and speciation phenomena in their earliest phases. We focus here on the black carrion crow (Corvus [corone] corone), which forms a zone of hybridization and overlap with the grey coated hooded crow (Corvus [corone] cornix). However, although these semispecies are taxonomically distinct, previous analyses based on several types of genetic markers did not reveal significant molecular differentiation between them. We here corroborate this result with sequence data obtained from a set of 25 nuclear intronic loci. Thus, the system represents a case of a very early phase of species divergence that requires new molecular approaches for its description. We have therefore generated RNAseq expression profiles using barcoded massively parallel pyrosequencing of brain mRNA from six individuals of the carrion crow and five individuals from a hybrid zone with the hooded crow. We obtained 856 675 reads from two runs, with average read length of 270 nt and coverage of 8.44. Reads were assembled de novo into 19 552 contigs, 70% of which could be assigned to annotated genes in chicken and zebra finch. This resulted in a total of 7637 orthologous genes and a core set of 1301 genes that could be compared across all individuals. We find a clear clustering of expression profiles for the pure carrion crow animals and disperse profiles for the animals from the hybrid zone. These results suggest that gene expression differences may indeed be a sensitive indicator of initial species divergence.

  16. A child with xeroderma pigmentosum for excision of basal cell carcinoma

    Directory of Open Access Journals (Sweden)

    Sridevi M Mulimani

    2013-01-01

    Full Text Available Xeroderma pigmentosum (XP is characterized by hypersensitivity to sunlight, ocular involvement, and progressive neurological complications. These manifestations are due to a cellular hypersensitivity to ultraviolet radiation leading to a defect in repair of DNA by the process of nucleotide excision repair. Basal cell carcinoma which is rare in children can occur with XP. Though the XP induced changes are predominately dermatologic, pose several challenges in anaesthetic management. Hence, we are reporting a 9-year-old child with XP scheduled for excision of basal cell carcinoma under general anaesthesia.

  17. 顺势疗法药物山金车30C通过上调核苷酸切除修复基因的表达减少紫外线照射后大肠杆菌的DNA损伤%Potential of the homeopathic remedy, Arnica Montana 30C,to reduce DNA damage in Escherichia coli exposed to ultraviolet irradiation through up-regulation of nucleotide excision repair genes

    Institute of Scientific and Technical Information of China (English)

    Sreemanti Das; Santu Kumar Saha; Arnab De; Durba Das; Anisur Rahman Khuda-Bukhs

    2012-01-01

    目的:检测高度稀释的顺势疗法药物山金车30C是否能够调节暴露于紫外线照射下的大肠杆菌的核苷酸切除修复基因的表达.方法:大肠杆菌在标准培养基中培养至对数阶段,然后接受亚致死剂量的紫外线照射(25和50 J/m2分别照射22.5和45 s).接受不同剂量紫外线照射的大肠杆菌分别与山金车30C及安慰剂30C共同培养,90 min后检测其DNA损伤情况及氧化应激状态.采用多种方法及指标如彗星实验、梯度凝胶电泳、细胞内活性氧生成及测量其他生物活性指标如过氧化物歧化酶、过氧化氢酶及谷胱甘肽衡量DNA损伤情况及细胞氧化应激状态.逆转录聚合酶链反应检测大肠杆菌细胞紫外线损伤修复基因uvrA、B、C(核苷酸切除修复基因)mRNA的表达情况.结果:接受照射后的大肠杆菌出现了DNA损伤及氧化应激反应,表现为细胞内活性氧生成增加及过氧化物歧化酶、过氧化氢酶和谷胱甘肽活性降低.与安慰剂组相比,山金车30C降低了大肠杆菌的DNA损伤及氧化应激反应,表现为细胞内活性氧生成减少及过氧化物歧化酶、过氧化氢酶和谷胱甘肽活性增强.与对照组相比,山金车30C上调了大肠杆菌细胞紫外线损伤修复基因的表达.结论:山金车30C能够通过上调紫外线损伤修复基因的表达修复紫外线引起的大肠杆菌细胞的DNA损伤,并通过减少细胞内活性氧的生成及调节抗氧化酶活性降低细胞的氧化应激反应.%OBJECTIVE:To examine to what degree an ultra-highly diluted homeopathic remedy,Arnica Montana 30C (AM-30C),used in the treatment of shock and injury,can modulate the expression of nucleotide excision repair genes in Escherichia coii exposed to ultraviolet (UV) irradiation.METHODS:E.coli were cultured to their log phase in a standard Luria-Bertani medium and then exposed to sublethal doses of UV irradiation at 25 and 50 J/m2 for 22.5 and 45 s,respectively.The UV

  18. Excise tax avoidance: the case of state cigarette taxes.

    Science.gov (United States)

    DeCicca, Philip; Kenkel, Donald; Liu, Feng

    2013-12-01

    We conduct an applied welfare economics analysis of cigarette tax avoidance. We develop an extension of the standard formula for the optimal Pigouvian corrective tax to incorporate the possibility that consumers avoid the tax by making purchases in nearby lower tax jurisdictions. To provide a key parameter for our formula, we estimate a structural endogenous switching regression model of border-crossing and cigarette prices. In illustrative calculations, we find that for many states, after taking into account tax avoidance the optimal tax is at least 20% smaller than the standard Pigouvian tax that simply internalizes external costs. Our empirical estimate that tax avoidance strongly responds to the price differential is the main reason for this result. We also use our results to examine the benefits of replacing avoidable state excise taxes with a harder-to-avoid federal excise tax on cigarettes.

  19. Base excision repair in sugarcane

    Directory of Open Access Journals (Sweden)

    Agnez-Lima Lucymara F.

    2001-01-01

    Full Text Available DNA damage can be induced by a large number of physical and chemical agents from the environment as well as compounds produced by cellular metabolism. This type of damage can interfere with cellular processes such as replication and transcription, resulting in cell death and/or mutations. The low frequency of mutagenesis in cells is due to the presence of enzymatic pathways which repair damaged DNA. Several DNA repair genes (mainly from bacteria, yeasts and mammals have been cloned and their products characterized. The high conservation, especially in eukaryotes, of the majority of genes related to DNA repair argues for their importance in the maintenance of life on earth. In plants, our understanding of DNA repair pathways is still very poor, the first plant repair genes having only been cloned in 1997 and the mechanisms of their products have not yet been characterized. The objective of our data mining work was to identify genes related to the base excision repair (BER pathway, which are present in the database of the Sugarcane Expressed Sequence Tag (SUCEST Project. This search was performed by tblastn program. We identified sugarcane clusters homologous to the majority of BER proteins used in the analysis and a high degree of conservation was observed. The best results were obtained with BER proteins from Arabidopsis thaliana. For some sugarcane BER genes, the presence of more than one form of mRNA is possible, as shown by the occurrence of more than one homologous EST cluster.

  20. Main: Nucleotide Analysis [KOME

    Lifescience Database Archive (English)

    Full Text Available -acting regulatory DNA elements Database kome_place_search_result.zip kome_place_search_result ... ...Nucleotide Analysis PLACE search result Result of signal search against PLACE : cis

  1. Main: Nucleotide Analysis [KOME

    Lifescience Database Archive (English)

    Full Text Available Nucleotide Analysis Japonica genome blast search result Result of blastn search against japon...ica genome sequence kome_japonica_genome_blast_search_result.zip kome_japonica_genome_blast_search_result ...

  2. Giant rhinophyma: Excision with coblation assisted surgery

    Directory of Open Access Journals (Sweden)

    Caner Sahin

    2014-01-01

    Full Text Available An 83-year-old man presented with an unusually severe case of rhinophyma. Giant rhinopyhma is very rare in literature. The giant lesion was widely excised using sharp surgical incision and coblation assisted surgery. Using direct coblation to the nasal dorsum may cause edema in the surrounding tissue. There was minimal edema in surrounding tissue using this technique. A full thickness-skin graft was applied after excision. Cosmetic and functional postoperative results were satisfactory.

  3. Giant rhinophyma: Excision with coblation assisted surgery.

    Science.gov (United States)

    Sahin, Caner; Turker, Mesut; Celasun, Bulent

    2014-01-01

    An 83-year-old man presented with an unusually severe case of rhinophyma. Giant rhinopyhma is very rare in literature. The giant lesion was widely excised using sharp surgical incision and coblation assisted surgery. Using direct coblation to the nasal dorsum may cause edema in the surrounding tissue. There was minimal edema in surrounding tissue using this technique. A full thickness-skin graft was applied after excision. Cosmetic and functional postoperative results were satisfactory.

  4. Single Nucleotide Polymorphism

    DEFF Research Database (Denmark)

    Børsting, Claus; Pereira, Vania; Andersen, Jeppe Dyrberg

    2014-01-01

    Single nucleotide polymorphisms (SNPs) are the most frequent DNA sequence variations in the genome. They have been studied extensively in the last decade with various purposes in mind. In this chapter, we will discuss the advantages and disadvantages of using SNPs for human identification and bri...

  5. Proximal clavicle excision: an analysis of results.

    Science.gov (United States)

    Acus, R W; Bell, R H; Fisher, D L

    1995-01-01

    Medial clavicle excision has been reported by several authors, but few cases are documented, and long-term follow-up information is lacking. The purpose of this study was to examine the long-term results of medial clavicle excision in regard to function, pain, cosmesis, and complications. Fifteen patients ranging in age from 18 to 64 years (average 43 years) were evaluated an average of 4.6 years (range 1 to 14 years) after proximal clavicle excision. The indications for excision were unstable anterior subluxation/dislocation of the sternoclavicular joint (four cases), unstable posterior dislocation (one case), sternoclavicular osteoarthritis (nine cases), and proximal clavicle osteomyelitis (one case). An average of 2.9 cm of the medial clavicle was excised (range 1 to 4 cm). Fourteen of the 15 patients received significant relief of pain. On a strict grading scale four patients had an excellent result, five a good result, four a fair result, and two a poor result. Regeneration of the clavicle appeared to contribute to a poor result. No operative complications occurred. These findings aid our understanding of surgical options and outcome in the treatment of sternoclavicular joint disease.

  6. Control of Staphylococcus aureus pathogenicity island excision.

    Science.gov (United States)

    Mir-Sanchis, Ignacio; Martínez-Rubio, Roser; Martí, Miguel; Chen, John; Lasa, Íñigo; Novick, Richard P; Tormo-Más, María Ángeles; Penadés, José R

    2012-09-01

    Staphylococcus aureus pathogenicity islands (SaPIs) are a group of related 15-17 kb mobile genetic elements that commonly carry genes for superantigen toxins and other virulence factors. The key feature of their mobility is the induction of SaPI excision and replication by certain phages and their efficient encapsidation into specific small-headed phage-like infectious particles. Previous work demonstrated that chromosomal integration depends on the SaPI-encoded recombinase, Int. However, although involved in the process, Int alone was not sufficient to mediate efficient SaPI excision from chromosomal sites, and we expected that SaPI excision would involve an Xis function, which could be encoded by a helper phage or by the SaPI, itself. Here we report that the latter is the case. In vivo recombination assays with plasmids in Escherichia coli demonstrate that SaPI-coded Xis is absolutely required for recombination between the SaPI att(L) and att(R) sites, and that both sites, as well as their flanking SaPI sequences, are required for SaPI excision. Mutational analysis reveals that Xis is essential for efficient horizontal SaPI transfer to a recipient strain. Finally, we show that the master regulator of the SaPI life cycle, Stl, blocks expression of int and xis by binding to inverted repeats present in the promoter region, thus controlling SaPI excision.

  7. Intraoral excision of large submental dermoid

    Directory of Open Access Journals (Sweden)

    Ankur Bhatnagar

    2013-01-01

    Full Text Available Sublingual dermoids are the rarest forms of craniofacial dermoids mostly seen in young individuals. Excision of large and deep submental dermoid is generally done via extraoral approach scarring the most prominent part of the face, which can lead to post operative scar hypertrophy and hyperpigmentation especially in non-Caucasian races. Presence of such scars leads to adverse psychological effects in young individuals. Excision via intraoral route, although technically demanding, can be simplified using basic principles of plastic surgery leading to optimal aesthetic outcome with least downtime. We excised a large sublingual dermoid extending deep to the mylohyoid muscle through intraoral approach with excellent cosmetic results. Clinicians dealing with such lesions should keep these principals in their armamentarium when dealing with this rare subset of cases.

  8. Decreased nucleotide excision repair in steatotic livers associates with myeloperoxidase-immunoreactivity

    NARCIS (Netherlands)

    Schults, Marten A.; Nagle, Peter W.; Rensen, Sander S.; Godschalk, Roger W.; Munnia, Armelle; Peluso, Marco; Claessen, Sandra M.; Greve, Jan W.; Driessen, Ann; Verdam, Froukje J.; Buurman, Wim A.; van Schooten, Frederik J.; Chiu, Roland K.

    2012-01-01

    Chronic inflammation is characterized by the influx of neutrophils and is associated with an increased production of reactive oxygen species that can damage DNA. Oxidative DNA damage is generally thought to be involved in the increased risk of cancer in inflamed tissues. We previously demonstrated t

  9. Loss of Nucleotide Excision Repair as a Source of Genomic Instability in Breast Cancer

    Science.gov (United States)

    2006-06-01

    should arrange for someone to give you a ride. The procedure will begin with cleansing two areas close to the nipple on each breast with alcohol...grapefruit juice per day, as this has been shown to cause liver problems when people are also taking lovastatin. Drinking less than this amount (for

  10. p53 modulation of TFIIH-associated nucleotide excision repair activity

    NARCIS (Netherlands)

    X.W. Wang (Xin Wei); H. Yeh; L. Schaeffer; R. Roy (R.); V. Moncollin; J-M. Egly (Jean-Marc); Z. Wang (Z.); E.C. Friedberg (Errol); M.K. Evans; B.G. Taffe; V.A. Bohr; G. Weeda (Geert); J.H.J. Hoeijmakers (Jan); K. Forrester; C.C. Harris

    1995-01-01

    textabstractp53 has pleiotropic functions including control of genomic plasticity and integrity. Here we report that p53 can bind to several transcription factor IIH−associated factors, including transcription−repair factors, XPD (Rad3) and XPB, as well as CSB involved in strand−specific DNA repair,

  11. Loss of Nucleotide Excision Repair as a Source of Genomic Instability in Breast Cancer

    Science.gov (United States)

    2005-06-01

    on artificial levels by p53, and possibly the proteasome [(34) and unpub- substrates in vitro (22,23). A study by Jackson et al. (43) lished data...pill use, modulator, hormone replacement therapy or oral contracep- parity, breastfeeding , or prior bilateral salpingo-oophorectomy tive pill use...parity, breastfeeding , menopausal status, or prior were noted between patients who could and could not be bilateral salpingo-oophorectomy were noted

  12. Uracil Excision for Assembly of Complex Pathways

    DEFF Research Database (Denmark)

    Cavaleiro, Mafalda; Nielsen, Morten Thrane; Kim, Se Hyeuk

    2015-01-01

    Despite decreasing prices on synthetic DNA constructs, higher-order assembly of PCR-generated DNA continues to be an important exercise in molecular and synthetic biology. Simplicity and robustness are attractive features met by the uracil excision DNA assembly method, which is one of the most in...

  13. Exon sequence requirements for excision in vivo of the bacterial group II intron RmInt1

    Directory of Open Access Journals (Sweden)

    Toro Nicolás

    2011-05-01

    Full Text Available Abstract Background Group II intron splicing proceeds through two sequential transesterification reactions in which the 5' and 3'-exons are joined together and the lariat intron is released. The intron-encoded protein (IEP assists the splicing of the intron in vivo and remains bound to the excised intron lariat RNA in a ribonucleoprotein particle (RNP that promotes intron mobility. Exon recognition occurs through base-pairing interactions between two guide sequences on the ribozyme domain dI known as EBS1 and EBS2 and two stretches of sequence known as IBS1 and IBS2 on the 5' exon, whereas the 3' exon is recognized through interaction with the sequence immediately upstream from EBS1 [(δ-δ' interaction (subgroup IIA] or with a nucleotide [(EBS3-IBS3 interaction (subgroup IIB and IIC] located in the coordination-loop of dI. The δ nucleotide is involved in base pairing with another intron residue (δ' in subgroup IIB introns and this interaction facilitates base pairing between the 5' exon and the intron. Results In this study, we investigated nucleotide requirements in the distal 5'- and 3' exon regions, EBS-IBS interactions and δ-δ' pairing for excision of the group IIB intron RmInt1 in vivo. We found that the EBS1-IBS1 interaction was required and sufficient for RmInt1 excision. In addition, we provide evidence for the occurrence of canonical δ-δ' pairing and its importance for the intron excision in vivo. Conclusions The excision in vivo of the RmInt1 intron is a favored process, with very few constraints for sequence recognition in both the 5' and 3'-exons. Our results contribute to understand how group II introns spread in nature, and might facilitate the use of RmInt1 in gene targeting.

  14. Loop electrosurgical excision procedure for the treatment of cervical intraepithelial neoplasia: how much excision is enough?

    Science.gov (United States)

    Le, T; El-Sugi, R; Hicks-Boucher, W; Weberpals, J; Faught, W

    2013-08-01

    This is a retrospective observational study to compare outcomes in patients with cervical intraepithelial neoplasia (CIN) treated with loop electrosurgical excision procedure (LEEP) using combined ectocervical/endocervical resection vs ectocervical resection alone. We demonstrated that additional endocervical resection during loop electrosurgical excision procedure did not significantly lower the risk of subsequent recurrence compared with ectocervical resection alone, in the treatment of CIN. With current published data supporting subsequent increased adverse effects of LEEP on future obstetrical outcomes, endocervical excision should be applied selectively. We recommend that additional endocervical excision should be reserved only for patients with a strong suspicion of underlying endocervical canal involvement based on colposcopic assessment or in patients with unsatisfactory colposcopy, where it is essential to evaluate the endocervical canal.

  15. Brown recluse spider bites. A comparison of early surgical excision versus dapsone and delayed surgical excision.

    Science.gov (United States)

    Rees, R S; Altenbern, D P; Lynch, J B; King, L E

    1985-01-01

    In a prospective study, 31 patients with brown recluse spider bites were treated by either immediate surgical excision or with the leukocyte inhibitor, dapsone, followed by delayed surgical excision. Patients were matched for age, gender, and lesion size and were excluded if the typical history and physical findings were not present. In patients treated with immediate surgical excision (N = 14), delayed wound healing (N = 5) and objectional scarring (N = 7) were common complications. However, pretreatment treatment with dapsone reduced the incidence of wound complications (N = 1) and objectional scarring (N = 1) (p less than 0.05), while reducing the need for surgical excision (N = 1). There were no severe drug reactions due to dapsone, although one patient had persistent G.I. upset. Pretreatment with dapsone not only reduced surgical complications but also improved the outcome of patients bitten by the brown recluse spider. PMID:4051613

  16. DNA glycosylases involved in base excision repair may be associated with cancer risk in BRCA1 and BRCA2 mutation carriers

    DEFF Research Database (Denmark)

    Osorio, Ana; Milne, Roger L; Kuchenbaecker, Karoline

    2014-01-01

    Single Nucleotide Polymorphisms (SNPs) in genes involved in the DNA Base Excision Repair (BER) pathway could be associated with cancer risk in carriers of mutations in the high-penetrance susceptibility genes BRCA1 and BRCA2, given the relation of synthetic lethality that exists between one of th...

  17. DNA Glycosylases Involved in Base Excision Repair May Be Associated with Cancer Risk in BRCA1 and BRCA2 Mutation Carriers

    NARCIS (Netherlands)

    Osorio, Ana; Milne, Roger L.; Kuchenbaecker, Karoline; Vaclova, Tereza; Pita, Guillermo; Alonso, Rosario; Peterlongo, Paolo; Blanco, Ignacio; de la Hoya, Miguel; Duran, Mercedes; Diez, Orland; Ramon y Cajal, Teresa; Konstantopoulou, Irene; Martinez-Bouzas, Cristina; Conejero, Raquel Andres; Soucy, Penny; McGuffog, Lesley; Barrowdale, Daniel; Lee, Andrew; Arver, Brita; Rantala, Johanna; Loman, Niklas; Ehrencrona, Hans; Olopade, Olufunmilayo I.; Beattie, Mary S.; Domchek, Susan M.; Nathanson, Katherine; Rebbeck, Timothy R.; Arun, Banu K.; Karlan, Beth Y.; Walsh, Christine; Lester, Jenny; John, Esther M.; Whittemore, Alice S.; Daly, Mary B.; Southey, Melissa; Hopper, John; Terry, Mary B.; Buys, Saundra S.; Janavicius, Ramunas; Dorfling, Cecilia M.; van Rensburg, Elizabeth J.; Steele, Linda; Neuhausen, Susan L.; Ding, Yuan Chun; Hansen, Thomas V. O.; Jonson, Lars; Ejlertsen, Bent; Gerdes, Anne-Marie; Infante, Mar; Herraez, Belen; Moreno, Leticia Thais; Weitzel, Jeffrey N.; Herzog, Josef; Weeman, Kisa; Manoukian, Siranoush; Peissel, Bernard; Zaffaroni, Daniela; Scuvera, Giulietta; Bonanni, Bernardo; Mariette, Frederique; Volorio, Sara; Viel, Alessandra; Varesco, Liliana; Papi, Laura; Ottini, Laura; Tibiletti, Maria Grazia; Radice, Paolo; Yannoukakos, Drakoulis; Garber, Judy; Ellis, Steve; Frost, Debra; Platte, Radka; Fineberg, Elena; Evans, Gareth; Lalloo, Fiona; Izatt, Louise; Eeles, Ros; Adlard, Julian; Davidson, Rosemarie; Cole, Trevor; Eccles, Diana; Cook, Jackie; Hodgson, Shirley; Brewer, Carole; Tischkowitz, Marc; Douglas, Fiona; Porteous, Mary; Side, Lucy; Walker, Lisa; Morrison, Patrick; Donaldson, Alan; Kennedy, John; Foo, Claire; Godwin, Andrew K.; Schmutzler, Rita Katharina; Wappenschmidt, Barbara; Rhiem, Kerstin; Engel, Christoph; Meindl, Alfons; Ditsch, Nina; Arnold, Norbert; Plendl, Hans Joerg; Niederacher, Dieter; Sutter, Christian; Wang-Gohrke, Shan; Steinemann, Doris; Preisler-Adams, Sabine; Kast, Karin; Varon-Mateeva, Raymonda; Gehrig, Andrea; Stoppa-Lyonnet, Dominique; Sinilnikova, Olga M.; Mazoyer, Sylvie; Damiola, Francesca; Poppe, Bruce; Claes, Kathleen; Piedmonte, Marion; Tucker, Kathy; Backes, Floor; Rodriguez, Gustavo; Brewster, Wendy; Wakeley, Katie; Rutherford, Thomas; Caldes, Trinidad; Nevanlinna, Heli; Aittomaki, Kristiina; Rookus, Matti A.; van Os, Theo A. M.; van der Kolk, Lizet; de Lange, J. L.; Meijers-Heijboer, Hanne E. J.; van der Hout, A. H.; van Asperen, Christi J.; Gomez Garcia, Encarna B.; Hoogerbrugge, Nicoline; Collee, J. Margriet; van Deurzen, Carolien H. M.; van der Luijt, Rob B.; Devilee, Peter; Olah, Edith; Lazaro, Conxi; Teule, Alex; Menendez, Mireia; Jakubowska, Anna; Cybulski, Cezary; Gronwald, Jacek; Lubinski, Jan; Durda, Katarzyna; Jaworska-Bieniek, Katarzyna; Johannsson, Oskar Th; Maugard, Christine; Montagna, Marco; Tognazzo, Silvia; Teixeira, Manuel R.; Healey, Sue; Olswold, Curtis; Guidugli, Lucia; Lindor, Noralane; Slager, Susan; Szabo, Csilla I.; Vijai, Joseph; Robson, Mark; Kauff, Noah; Zhang, Liying; Rau-Murthy, Rohini; Fink-Retter, Anneliese; Singer, Christian F.; Rappaport, Christine; Kaulich, Daphne Geschwantler; Pfeiler, Georg; Tea, Muy-Kheng; Berger, Andreas; Phelan, Catherine M.; Greene, Mark H.; Mai, Phuong L.; Lejbkowicz, Flavio; Andrulis, Irene; Mulligan, Anna Marie; Glendon, Gord; Toland, Amanda Ewart; Bojesen, Anders; Pedersen, Inge Sokilde; Sunde, Lone; Thomassen, Mads; Kruse, Torben A.; Jensen, Uffe Birk; Friedman, Eitan; Laitman, Yael; Shimon, Shani Paluch; Simard, Jacques; Easton, Douglas F.; Offit, Kenneth; Couch, Fergus J.; Chenevix-Trench, Georgia; Antoniou, Antonis C.; Benitez, Javier

    2014-01-01

    Single Nucleotide Polymorphisms (SNPs) in genes involved in the DNA Base Excision Repair (BER) pathway could be associated with cancer risk in carriers of mutations in the high-penetrance susceptibility genes BRCA1 and BRCA2, given the relation of synthetic lethality that exists between one of the c

  18. DNA Glycosylases Involved in Base Excision Repair May Be Associated with Cancer Risk in BRCA1 and BRCA2 Mutation Carriers

    NARCIS (Netherlands)

    Osorio, Ana; Milne, Roger L.; Kuchenbaecker, Karoline; Vaclova, Tereza; Pita, Guillermo; Alonso, Rosario; Peterlongo, Paolo; Blanco, Ignacio; de la Hoya, Miguel; Duran, Mercedes; Diez, Orland; Ramon y Cajal, Teresa; Konstantopoulou, Irene; Martinez-Bouzas, Cristina; Conejero, Raquel Andres; Soucy, Penny; McGuffog, Lesley; Barrowdale, Daniel; Lee, Andrew; Arver, Brita; Rantala, Johanna; Loman, Niklas; Ehrencrona, Hans; Olopade, Olufunmilayo I.; Beattie, Mary S.; Domchek, Susan M.; Nathanson, Katherine; Rebbeck, Timothy R.; Arun, Banu K.; Karlan, Beth Y.; Walsh, Christine; Lester, Jenny; John, Esther M.; Whittemore, Alice S.; Daly, Mary B.; Southey, Melissa; Hopper, John; Terry, Mary B.; Buys, Saundra S.; Janavicius, Ramunas; Dorfling, Cecilia M.; van Rensburg, Elizabeth J.; Steele, Linda; Neuhausen, Susan L.; Ding, Yuan Chun; Hansen, Thomas V. O.; Jonson, Lars; Ejlertsen, Bent; Gerdes, Anne-Marie; Infante, Mar; Herraez, Belen; Moreno, Leticia Thais; Weitzel, Jeffrey N.; Herzog, Josef; Weeman, Kisa; Manoukian, Siranoush; Peissel, Bernard; Zaffaroni, Daniela; Scuvera, Giulietta; Bonanni, Bernardo; Mariette, Frederique; Volorio, Sara; Viel, Alessandra; Varesco, Liliana; Papi, Laura; Ottini, Laura; Tibiletti, Maria Grazia; Radice, Paolo; Yannoukakos, Drakoulis; Garber, Judy; Ellis, Steve; Frost, Debra; Platte, Radka; Fineberg, Elena; Evans, Gareth; Lalloo, Fiona; Izatt, Louise; Eeles, Ros; Adlard, Julian; Davidson, Rosemarie; Cole, Trevor; Eccles, Diana; Cook, Jackie; Hodgson, Shirley; Brewer, Carole; Tischkowitz, Marc; Douglas, Fiona; Porteous, Mary; Side, Lucy; Walker, Lisa; Morrison, Patrick; Donaldson, Alan; Kennedy, John; Foo, Claire; Godwin, Andrew K.; Schmutzler, Rita Katharina; Wappenschmidt, Barbara; Rhiem, Kerstin; Engel, Christoph; Meindl, Alfons; Ditsch, Nina; Arnold, Norbert; Plendl, Hans Joerg; Niederacher, Dieter; Sutter, Christian; Wang-Gohrke, Shan; Steinemann, Doris; Preisler-Adams, Sabine; Kast, Karin; Varon-Mateeva, Raymonda; Gehrig, Andrea; Stoppa-Lyonnet, Dominique; Sinilnikova, Olga M.; Mazoyer, Sylvie; Damiola, Francesca; Poppe, Bruce; Claes, Kathleen; Piedmonte, Marion; Tucker, Kathy; Backes, Floor; Rodriguez, Gustavo; Brewster, Wendy; Wakeley, Katie; Rutherford, Thomas; Caldes, Trinidad; Nevanlinna, Heli; Aittomaki, Kristiina; Rookus, Matti A.; van Os, Theo A. M.; van der Kolk, Lizet; de Lange, J. L.; Meijers-Heijboer, Hanne E. J.; van der Hout, A. H.; van Asperen, Christi J.; Gomez Garcia, Encarna B.; Hoogerbrugge, Nicoline; Collee, J. Margriet; van Deurzen, Carolien H. M.; van der Luijt, Rob B.; Devilee, Peter; Olah, Edith; Lazaro, Conxi; Teule, Alex; Menendez, Mireia; Jakubowska, Anna; Cybulski, Cezary; Gronwald, Jacek; Lubinski, Jan; Durda, Katarzyna; Jaworska-Bieniek, Katarzyna; Johannsson, Oskar Th; Maugard, Christine; Montagna, Marco; Tognazzo, Silvia; Teixeira, Manuel R.; Healey, Sue; Olswold, Curtis; Guidugli, Lucia; Lindor, Noralane; Slager, Susan; Szabo, Csilla I.; Vijai, Joseph; Robson, Mark; Kauff, Noah; Zhang, Liying; Rau-Murthy, Rohini; Fink-Retter, Anneliese; Singer, Christian F.; Rappaport, Christine; Kaulich, Daphne Geschwantler; Pfeiler, Georg; Tea, Muy-Kheng; Berger, Andreas; Phelan, Catherine M.; Greene, Mark H.; Mai, Phuong L.; Lejbkowicz, Flavio; Andrulis, Irene; Mulligan, Anna Marie; Glendon, Gord; Toland, Amanda Ewart; Bojesen, Anders; Pedersen, Inge Sokilde; Sunde, Lone; Thomassen, Mads; Kruse, Torben A.; Jensen, Uffe Birk; Friedman, Eitan; Laitman, Yael; Shimon, Shani Paluch; Simard, Jacques; Easton, Douglas F.; Offit, Kenneth; Couch, Fergus J.; Chenevix-Trench, Georgia; Antoniou, Antonis C.; Benitez, Javier

    2014-01-01

    Single Nucleotide Polymorphisms (SNPs) in genes involved in the DNA Base Excision Repair (BER) pathway could be associated with cancer risk in carriers of mutations in the high-penetrance susceptibility genes BRCA1 and BRCA2, given the relation of synthetic lethality that exists between one of the c

  19. Autocatalytic cyclization of an excised intervening sequence RNA is a cleavage-ligation reaction.

    Science.gov (United States)

    Zaug, A J; Grabowski, P J; Cech, T R

    The intervening sequence (IVS) of the Tetrahymena ribosomal RNA precursor is excised as a linear RNA molecule which subsequently cyclizes itself in a protein-independent reaction. Cyclization involves cleavage of the linear IVS RNA 15 nucleotides from its 5' end and formation of a phosphodiester bond between the new 5' phosphate and the original 3'-hydroxyl terminus of the IVS. This recombination mechanism is analogous to that by which splicing of the precursor RNA is achieved. The circular molecules appear to have no direct function in RNA splicing, and we propose the cyclization serves to prevent unwanted RNA from driving the splicing reactions backwards.

  20. 75 FR 9359 - Drawback of Internal Revenue Excise Tax

    Science.gov (United States)

    2010-03-02

    ... Parts 113 and 191 RIN 1505-AC18 Drawback of Internal Revenue Excise Tax AGENCY: Customs and Border... Regulations to: preclude the filing of a substitution drawback claim for internal revenue excise tax paid on imported merchandise in situations where no excise tax was paid upon the substituted merchandise or...

  1. Uracil Excision for Assembly of Complex Pathways

    DEFF Research Database (Denmark)

    Cavaleiro, Mafalda; Nielsen, Morten Thrane; Kim, Se Hyeuk

    2015-01-01

    inexpensive technologies available. Here, we describe four different protocols for uracil excision-based DNA editing: one for simple manipulations such as site-directed mutagenesis, one for plasmid-based multigene assembly in Escherichia coli, one for one-step assembly and integration of single or multiple...... genes into the genome, and a standardized assembly pipeline using benchmarked oligonucleotides for pathway assembly and multigene expression optimization....

  2. Nucleotide pools dictate the identity and frequency of ribonucleotide incorporation in mitochondrial DNA

    Science.gov (United States)

    Hoberg, Emily; Szilagyi, Zsolt; Taylor, Robert W.; Gustafsson, Claes M.; Falkenberg, Maria

    2017-01-01

    Previous work has demonstrated the presence of ribonucleotides in human mitochondrial DNA (mtDNA) and in the present study we use a genome-wide approach to precisely map the location of these. We find that ribonucleotides are distributed evenly between the heavy- and light-strand of mtDNA. The relative levels of incorporated ribonucleotides reflect that DNA polymerase γ discriminates the four ribonucleotides differentially during DNA synthesis. The observed pattern is also dependent on the mitochondrial deoxyribonucleotide (dNTP) pools and disease-causing mutations that change these pools alter both the absolute and relative levels of incorporated ribonucleotides. Our analyses strongly suggest that DNA polymerase γ-dependent incorporation is the main source of ribonucleotides in mtDNA and argues against the existence of a mitochondrial ribonucleotide excision repair pathway in human cells. Furthermore, we clearly demonstrate that when dNTP pools are limiting, ribonucleotides serve as a source of building blocks to maintain DNA replication. Increased levels of embedded ribonucleotides in patient cells with disturbed nucleotide pools may contribute to a pathogenic mechanism that affects mtDNA stability and impair new rounds of mtDNA replication. PMID:28207748

  3. Multidirectional Vector Excision Leads to Better Outcomes than Traditional Elliptical Excision of Facial Congenital Melanocytic Nevus

    Directory of Open Access Journals (Sweden)

    Seung Il Oh

    2013-09-01

    Full Text Available Background The elliptical excision is the standard method of removing benign skin lesions,such as congenital melanocytic nevi. This technique allows for primary closure, with little to nodog-ear deformity, but may sacrifice normal tissue adjacent to the lesion, resulting in scarswhich are unnecessarily long. This study was designed to compare the predicted results ofelliptical excision with those resulting from our excision technique.Methods Eighty-two patients with congenital melanocytic nevus on the face were prospectivelystudied. Each lesion was examined and an optimal ellipse was designed and marked onthe skin. After an incision on one side of the nevus margin, subcutaneous undermining wasperformed in the appropriate direction. The skin flap was pulled up and approximated alongseveral vectors to minimize the occurrence of dog-ear deformity.Results Overall, the final wound length was 21.1% shorter than that achieved by ellipticalexcision. Only 8.5% of the patients required dog-ear repair. There was no significant distortionof critical facial structures. All of the scars were deemed aesthetically acceptable based ontheir Patient and Observer Scar Assessment Scale scores.Conclusions When compared to elliptical excision, our technique appears to minimize dogeardeformity and decrease the final wound length. This technique should be considered analternative method for excision of facial nevi.

  4. FACT Assists Base Excision Repair by Boosting the Remodeling Activity of RSC.

    Science.gov (United States)

    Charles Richard, John Lalith; Shukla, Manu Shubhdarshan; Menoni, Hervé; Ouararhni, Khalid; Lone, Imtiaz Nisar; Roulland, Yohan; Papin, Christophe; Ben Simon, Elsa; Kundu, Tapas; Hamiche, Ali; Angelov, Dimitar; Dimitrov, Stefan

    2016-07-01

    FACT, in addition to its role in transcription, is likely implicated in both transcription-coupled nucleotide excision repair and DNA double strand break repair. Here, we present evidence that FACT could be directly involved in Base Excision Repair and elucidate the chromatin remodeling mechanisms of FACT during BER. We found that, upon oxidative stress, FACT is released from transcription related protein complexes to get associated with repair proteins and chromatin remodelers from the SWI/SNF family. We also showed the rapid recruitment of FACT to the site of damage, coincident with the glycosylase OGG1, upon the local generation of oxidized DNA. Interestingly, FACT facilitates uracil-DNA glycosylase in the removal of uracil from nucleosomal DNA thanks to an enhancement in the remodeling activity of RSC. This discloses a novel property of FACT wherein it has a co-remodeling activity and strongly enhances the remodeling capacity of the chromatin remodelers. Altogether, our data suggest that FACT may acts in concert with RSC to facilitate excision of DNA lesions during the initial step of BER.

  5. AP endonucleases process 5-methylcytosine excision intermediates during active DNA demethylation in Arabidopsis.

    Science.gov (United States)

    Lee, Jiyoon; Jang, Hosung; Shin, Hosub; Choi, Woo Lee; Mok, Young Geun; Huh, Jin Hoe

    2014-10-01

    DNA methylation is a primary epigenetic modification regulating gene expression and chromatin structure in many eukaryotes. Plants have a unique DNA demethylation system in that 5-methylcytosine (5mC) is directly removed by DNA demethylases, such as DME/ROS1 family proteins, but little is known about the downstream events. During 5mC excision, DME produces 3'-phosphor-α, β-unsaturated aldehyde and 3'-phosphate by successive β- and δ-eliminations, respectively. The kinetic studies revealed that these 3'-blocking lesions persist for a significant amount of time and at least two different enzyme activities are required to immediately process them. We demonstrate that Arabidopsis AP endonucleases APE1L, APE2 and ARP have distinct functions to process such harmful lesions to allow nucleotide extension. DME expression is toxic to E. coli due to excessive 5mC excision, but expression of APE1L or ARP significantly reduces DME-induced cytotoxicity. Finally, we propose a model of base excision repair and DNA demethylation pathway unique to plants. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  6. The arabidopsis cyclic nucleotide interactome

    KAUST Repository

    Donaldson, Lara

    2016-05-11

    Background Cyclic nucleotides have been shown to play important signaling roles in many physiological processes in plants including photosynthesis and defence. Despite this, little is known about cyclic nucleotide-dependent signaling mechanisms in plants since the downstream target proteins remain unknown. This is largely due to the fact that bioinformatics searches fail to identify plant homologs of protein kinases and phosphodiesterases that are the main targets of cyclic nucleotides in animals. Methods An affinity purification technique was used to identify cyclic nucleotide binding proteins in Arabidopsis thaliana. The identified proteins were subjected to a computational analysis that included a sequence, transcriptional co-expression and functional annotation analysis in order to assess their potential role in plant cyclic nucleotide signaling. Results A total of twelve cyclic nucleotide binding proteins were identified experimentally including key enzymes in the Calvin cycle and photorespiration pathway. Importantly, eight of the twelve proteins were shown to contain putative cyclic nucleotide binding domains. Moreover, the identified proteins are post-translationally modified by nitric oxide, transcriptionally co-expressed and annotated to function in hydrogen peroxide signaling and the defence response. The activity of one of these proteins, GLYGOLATE OXIDASE 1, a photorespiratory enzyme that produces hydrogen peroxide in response to Pseudomonas, was shown to be repressed by a combination of cGMP and nitric oxide treatment. Conclusions We propose that the identified proteins function together as points of cross-talk between cyclic nucleotide, nitric oxide and reactive oxygen species signaling during the defence response.

  7. Dermatofibrosarcoma protuberans: Role of wide local excision

    Directory of Open Access Journals (Sweden)

    Raashid Hamid

    2013-01-01

    Full Text Available Objectives: The main objective of the present study was to study the outcome of surgical treatment of dermatofibrosarcoma protuberans. Materials and Methods: This study included 45 patients both retrospective and prospective from December 1995 to December 2010. Results: Out of 45 patients, 30 were males and 15 females with the male to female ratio of 2:1. Mean age of presentation was 38.4 + 13.2 years. Commonest mode of presentation was raised firm multinodular lesion with fixity to overlying skin. Site distribution was 42.22% trunk, 57.88% extremities and head and neck. None of the patients had lymph node involvement All patients underwent wide local excision. On histological examination, 8 patients had positive margins. Overall recurrence rate was 22.22%. (please clarify what is the difference between the rate of recurrence following surgery and the overall recurrence rate Only 2 patients developed metastasis to lungs in the course of their follow-up. Out of 45 patients, 35 remained recurrence free over a varying period of 5 months to 13 years (mean 68 months. Ten patients developed one or more local recurrences. Average time from initial treatment to recurrence was 32 months. All patients with recurrent tumors were subjected to salvage treatment, i.e., re-excision. Average recurrence-free period was 36 + 44 months within a mean follow-up of 68 months. Conclusion: Because of the potential of local recurrence, therapy for DFSP should be directed toward adequate local excision of the primary lesion. Minimal resection should include a surrounding margin, comprising 3-cm margin of normal skin and removal of underlying deep fascia. Compromising on margins invites higher chances of local recurrence.

  8. Incidence of Incomplete Excision in Surgically Treated Cutaneous Squamous Cell Carcinoma and Identification of the Related Risk Factors

    Directory of Open Access Journals (Sweden)

    Sara Sabouri Rad

    2011-12-01

    Full Text Available Squamous cell carcinoma (SCC is the second most common type of skin cancer with potential risks for metastasis and recurrence if left untreated or incompletely excised. This case series study was designed to determine the frequency of incompletely excised SCCs and the related risk factors. A total of 273 SCCs (253 patients excised in Razi dermatology hospital of Tehran from 2006-2008, were evaluated and were analyzed by Chi-square or t-test. The incidence of incomplete excision was 17.58 % and deep margin involvement was observed in 73% of lesions. Risk factors associated with incomplete excision of SCCs were being female, location of the tumors (in particular the lesions on lateral canthus, upper lip, foot, forehead, cheek, neck, nose and ear, large lesions and grafting method of repair. There was no statistically significant difference for the age, degree of histological differentiation, childhood history of radiotherapy for tinea capitis and the type of anesthesia. More care should be taken for high risk SCCs as complete excision avoids potential risk of recurrence and metastasis.

  9. Endoscopic-assisted excision of esthesioneuroblastoma.

    Science.gov (United States)

    Prasad, Kishore Chandra; Kumar, Ashwini; Prasad, Sampath Chandra; Jain, Disha

    2007-09-01

    The purpose of this article is to report a case of esthesioneuroblastoma involving the bilateral paranasal sinuses, which was excised using an endoscopic-assisted transfacial approach. A patient presented with nasal swelling and left-sided nasal obstruction, epistaxis, and diplopia. Examination revealed broadening of the nasal dorsum with a fleshy pink mass in both nasal cavities. Computed tomographic scan showed a mass involving the nasal cavity and paranasal sinuses on both sides. The tumor was diagnosed as group C esthesioneuroblastoma. The mass was excised by bilateral medial maxillectomy and bilateral frontoethmoidectomy. Using a 0 degrees endoscope, the attachment of the tumor to the cribriform plate was identified and resected using a motordrill. On Waroff staining, Hispathology slides suggested esthesioneuroblastoma. The patient was asymptomatic for 1 year, following which he developed infection of the nasal cavity for which he had no form of treatment. He subsequently developed maggots in the nasal cavity after which he died. An endoscopic resection of the cribriform plate from the nasal cavity without a formal craniofacial resection can be safely performed with oncologic safety.

  10. Thoracoscopic excision of mediastinal cysts in children

    Directory of Open Access Journals (Sweden)

    Jain Prashant

    2007-01-01

    Full Text Available Aim: Thoracoscopy offers great advantages when compared with open surgery in terms of postoperative pain and pulmonary complications. Considering the benign nature of most of the mediastinal cysts, thoracoscopy is safe and feasible with minimal morbidity. The purpose of this article is to review our experience with four cases of mediastinal cysts resected successfully within a period of one year by thoracoscopy. Materials and Methods:The cases of mediastinal cysts operated by thoracoscopic excision in K.E.M. Hospital, Mumbai from November 2005 to December 2006 were reviewed. The age varied from six months to 10 years. The patients presented with respiratory distress or recurrent lower respiratory tract infection. All patients underwent Chest X-ray and CT scan thorax to delineate the location of the cyst and its relationship with adjacent vital structures. Two patients had anterior and two had posterior mediastinal cyst. The ports were placed depending on the location of the cyst on the CT scan, following the principles of triangularization. The cysts were excised mainly by blunt dissection. Results: All the patients were successfully managed by thoracoscopic surgery. None of them had intraoperative complications. Dissection in patient with history of recurrent respiratory tract infection was difficult because of adhesions. Intercostal drain was removed within 48hrs and the patients were discharged on the fourth postoperative day. Conclusions: Thoracoscopy in mediastinal cysts is a safe and effective procedure with low morbidity and a shorter hospital stay.

  11. Staged excisions of moderate-sized burns compared with total excision with immediate autograft: an evaluation of two strategies

    Science.gov (United States)

    Elmasry, Moustafa; Steinvall, Ingrid; Thorfinn, Johan; Abdelrahman, Islam; Olofsson, Pia; Sjoberg, Folke

    2017-01-01

    Background: Different surgical techniques have evolved since excision and autografting became the treatment of choice for deep burns in the 1970s. The treatment plan at the Burn Center, Linköping University Hospital, Sweden, has shifted from single-stage excision and immediate autografting to staged excisions and temporary cover with xenografts before autografting. The aim of this study was to find out if the change in policy resulted in extended duration of hospital stay/total body surface area burned (LOS/TBSA%). Methods: Retrospective clinical cohort including surgically-managed patients with burns of 15%-60% TBSA% within each treatment group. The first had early full excisions of deep dermal and full thickness burns and immediate autografts (1997-98), excision and immediate autograft group) and the second had staged excisions before final autografts using xenografts for temporary cover (2010-11, staged excision group). Results: The study included 57 patients with deep dermal and full-thickness burns, 28 of whom had excision and immediate autografting, and 29 of whom had staged excisions with xenografting before final autografting. Adjusted (LOS/TBSA%) was close to 1, and did not differ between groups. Mean operating time for the staged excision group was shorter and the excised area/operation was smaller. The total operating time/TBSA% did not differ between groups. Conclusion: Staged excisions with temporary cover did not affect adjusted LOS/TBSA% or total operating time. Staged excisions may be thought to be more expensive because of the cost of covering the wound between stages, but this needs to be further investigated as do the factors that predict long term outcome. PMID:28123862

  12. Precise excision of transposons and point mutations induced by chemicals.

    Science.gov (United States)

    Rusina OYu; Mirskaya, E E; Andreeva, I V; Skavronskaya, A G

    1992-11-01

    The ability of 23 chemicals (carcinogens and non-carcinogens) to induce precise excision of Tn10 and point mutations was studied in experiments with a single strain. The mutation assay was shown to detect a wider spectrum of genotoxic agents than the assay of Tn10 precise excision. The latter was induced only by potent SOS mutagens, which is in accordance with data on the SOS dependence of the induction of precise excision of Tn10. The precise excision assay as an additional test contributing to the knowledge of particular features of the action of a tested mutagen is discussed. The induction of precise excision of Tn10 by pyrene (and its failure to induce point mutations in this strain) demonstrates the value of using the transposon excision assay in cases of 'problem' mutagens.

  13. Surgical Excision of Multiple Penile Syringomas With Scrotal Flap Reconstruction

    OpenAIRE

    2014-01-01

    Objective: Penile syringomas are rare lesions usually occurring in isolation. We report the excision and reconstruction of multiple synchronous penile shaft syringomas with local scrotal flaps. Methods: We report a rare case of excision of multiple penile syringomas and reconstruction with scrotal flaps in a 29-year-old man. Results: Penile syringomas were excised and reconstructed with scrotal flaps in a single-stage procedure. Conclusions: In addition to providing wound coverage, this recon...

  14. [Nucleotide receptors and renal function].

    Science.gov (United States)

    Jankowski, Maciej

    2014-01-01

    Kidney plays a key role in homeostasis of human body. It has heterogenic structure and is characterized by complicated vascular beds and numbers of sympathetic nerves endings. Nucleotides receptors are involved in the regulation of blood flow, a fundamental process for renal function. Plasma is filtrated in renal glomerulus and activity of nucleotides receptors located on cells of glomerular filter modifies the physi- cochemical properties of filter and affects the filtration process. Electrolytes, water and low molecular weight molecules are reabsorbed from tubular fluid or secreted into fluid in proximal and distal tubules. Glomerular filtration rate and activity of tubular processes are regulated via nucleotides receptors by glomerulotubularbalance and tubuloglomerular feedback. Nucleotides receptors are involved in systemic regulation of blood pressure and carbohydrate metabolism.

  15. Conjunctival spheroid degeneration. Recurrence after excision.

    Science.gov (United States)

    Norn, M S

    1982-06-01

    After excision of part of the conjunctiva in 15 eyes (14 subjects) due to spheroid degeneration, the author noticed only fairly small, varying numbers of autofluorescent and colourless spheroids-after an observation period of 18 months, only 6% of autofluorescent and 13% of colourless bodies were observed compared to the number before biopsy. Around the biopsy site only a few spheroids were seen, with a non-significant tendency to increase in number of the colourless bodies. In the cornea the band-shaped keratopathy had aggravated, with the formation of a small number of large, autofluorescent spheroids. A pinguecula recurred in a mild degree only in 3 out of 13 cases within 18 months.

  16. Mitochondrial DNA analysis reveals a low nucleotide diversity of ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-06-17

    Jun 17, 2009 ... 3Technical Center for Inspection and Quarantine, Beijing Entry-Exit Inspection ... differentiation related to geographical distribution in C. japonica ... gene sequences of C. japonica in China to assess nucleotide ... Map of China with locations from which Caligula japonica was sampled indicated a black dot.

  17. The Bacillus anthracis chromosome contains four conserved, excision-proficient, putative prophages

    Directory of Open Access Journals (Sweden)

    Sozhamannan Shanmuga

    2006-04-01

    Full Text Available Abstract Background Bacillus anthracis is considered to be a recently emerged clone within the Bacillus cereus sensu lato group. The B. anthracis genome sequence contains four putative lambdoid prophages. We undertook this study in order to understand whether the four prophages are unique to B. anthracis and whether they produce active phages. Results More than 300 geographically and temporally divergent isolates of B. anthracis and its near neighbors were screened by PCR for the presence of specific DNA sequences from each prophage region. Every isolate of B. anthracis screened by PCR was found to produce all four phage-specific amplicons whereas none of the non-B. anthracis isolates, produced more than one phage-specific amplicon. Excision of prophages could be detected by a PCR based assay for attP sites on extra-chromosomal phage circles and for attB sites on phage-excised chromosomes. SYBR-green real-time PCR assays indicated that prophage excision occurs at very low frequencies (2 × 10-5 - 8 × 10-8/cell. Induction with mitomycin C increased the frequency of excision of one of the prophages by approximately 250 fold. All four prophages appear to be defective since, mitomycin C induced culture did not release any viable phage particle or lyse the cells or reveal any phage particle under electron microscopic examination. Conclusion The retention of all four putative prophage regions across all tested strains of B. anthracis is further evidence of the very recent emergence of this lineage and the prophage regions may be useful for differentiating the B. anthracis chromosome from that of its neighbors. All four prophages can excise at low frequencies, but are apparently defective in phage production.

  18. A comparison of key aspects of gene regulation in Streptomyces coelicolor and Escherichia coli using nucleotide-resolution transcription maps produced in parallel by global and differential RNA sequencing.

    Science.gov (United States)

    Romero, David A; Hasan, Ayad H; Lin, Yu-Fei; Kime, Louise; Ruiz-Larrabeiti, Olatz; Urem, Mia; Bucca, Giselda; Mamanova, Lira; Laing, Emma E; van Wezel, Gilles P; Smith, Colin P; Kaberdin, Vladimir R; McDowall, Kenneth J

    2014-09-30

    Streptomyces coelicolor is a model for studying bacteria renowned as the foremost source of natural products used clinically. Post-genomic studies have revealed complex patterns of gene expression and links to growth, morphological development and individual genes. However, the underlying regulation remains largely obscure, but undoubtedly involves steps after transcription initiation. Here we identify sites involved in RNA processing and degradation as well as transcription within a nucleotide-resolution map of the transcriptional landscape. This was achieved by combining RNA-sequencing approaches suited to the analysis of GC-rich organisms. Escherichia coli was analysed in parallel to validate the methodology and allow comparison. Previously, sites of RNA processing and degradation had not been mapped on a transcriptome-wide scale for E. coli. Through examples, we show the value of our approach and data sets. This includes the identification of new layers of transcriptional complexity associated with several key regulators of secondary metabolism and morphological development in S. coelicolor and the identification of host-encoded leaderless mRNA and rRNA processing associated with the generation of specialized ribosomes in E. coli. New regulatory small RNAs were identified for both organisms. Overall the results illustrate the diversity in mechanisms used by different bacterial groups to facilitate and regulate gene expression. © 2014 The Authors. Molecular Microbiology published by John Wiley & Sons Ltd.

  19. Human microRNA-155 on Chromosome 21 Differentially Interacts with Its Polymorphic Target in the AGTR1 3′ Untranslated Region: A Mechanism for Functional Single-Nucleotide Polymorphisms Related to Phenotypes

    Science.gov (United States)

    Sethupathy, Praveen ; Borel, Christelle ; Gagnebin, Maryline ; Grant, Gregory R. ; Deutsch, Samuel ; Elton, Terry S. ; Hatzigeorgiou, Artemis G. ; Antonarakis, Stylianos E. 

    2007-01-01

    Animal microRNAs (miRNAs) regulate gene expression through base pairing to their targets within the 3′ untranslated region (UTR) of protein-coding genes. Single-nucleotide polymorphisms (SNPs) located within such target sites can affect miRNA regulation. We mapped annotated SNPs onto a collection of experimentally supported human miRNA targets. Of the 143 experimentally supported human target sites, 9 contain 12 SNPs. We further experimentally investigated one of these target sites for hsa-miR-155, within the 3′ UTR of the human AGTR1 gene that contains SNP rs5186. Using reporter silencing assays, we show that hsa-miR-155 down-regulates the expression of only the 1166A, and not the 1166C, allele of rs5186. Remarkably, the 1166C allele has been associated with hypertension in many studies. Thus, the 1166C allele may be functionally associated with hypertension by abrogating regulation by hsa-miR-155, thereby elevating AGTR1 levels. Since hsa-miR-155 is on chromosome 21, we hypothesize that the observed lower blood pressure in trisomy 21 is partially caused by the overexpression of hsa-miR-155 leading to allele-specific underexpression of AGTR1. Indeed, we have shown in fibroblasts from monozygotic twins discordant for trisomy 21 that levels of AGTR1 protein are lower in trisomy 21. PMID:17668390

  20. Human microRNA-155 on chromosome 21 differentially interacts with its polymorphic target in the AGTR1 3' untranslated region: a mechanism for functional single-nucleotide polymorphisms related to phenotypes.

    Science.gov (United States)

    Sethupathy, Praveen; Borel, Christelle; Gagnebin, Maryline; Grant, Gregory R; Deutsch, Samuel; Elton, Terry S; Hatzigeorgiou, Artemis G; Antonarakis, Stylianos E

    2007-08-01

    Animal microRNAs (miRNAs) regulate gene expression through base pairing to their targets within the 3' untranslated region (UTR) of protein-coding genes. Single-nucleotide polymorphisms (SNPs) located within such target sites can affect miRNA regulation. We mapped annotated SNPs onto a collection of experimentally supported human miRNA targets. Of the 143 experimentally supported human target sites, 9 contain 12 SNPs. We further experimentally investigated one of these target sites for hsa-miR-155, within the 3' UTR of the human AGTR1 gene that contains SNP rs5186. Using reporter silencing assays, we show that hsa-miR-155 down-regulates the expression of only the 1166A, and not the 1166C, allele of rs5186. Remarkably, the 1166C allele has been associated with hypertension in many studies. Thus, the 1166C allele may be functionally associated with hypertension by abrogating regulation by hsa-miR-155, thereby elevating AGTR1 levels. Since hsa-miR-155 is on chromosome 21, we hypothesize that the observed lower blood pressure in trisomy 21 is partially caused by the overexpression of hsa-miR-155 leading to allele-specific underexpression of AGTR1. Indeed, we have shown in fibroblasts from monozygotic twins discordant for trisomy 21 that levels of AGTR1 protein are lower in trisomy 21.

  1. New patterns of bulk DNA repair in ultraviolet irradiated mouse embryo carcinoma cells following differentiation

    Energy Technology Data Exchange (ETDEWEB)

    Rasko, I.; Georgieva, M.; Farkas, G.; Santhan, M.; Burg, K. (Genetics Institute, Szeged (Hungary)); Coates, J.; Johnson, R.T. (Univ. of Cambridge (United Kingdom)); Mitchell, D.L. (M.D. Anderson Cancer Center, Smithville, TX (United States))

    1993-05-01

    Mouse embryocarcinoma stem cells differentiate in culture, given the appropriate induction. The authors examined whether these cells could provide information about the regulation of nucleotide excision repair in relation to differentiation by measuring the rate-limiting incision step, the removal of cyclobutane dimers and (6-4) photoproducts from the genome as a whole and the effect of the bacteriophage T4 endonuclease (denV) gene on repair in differentiated cells. It was found that differentiation is accompanied by a marked decline in the early incision ability after UV irradiation (sixfold for P19, fourfold for PCC7 and twofold for F9), and the authors measured, in parallel, the loss of two common UV photoproducts [cyclobutane dimers and (6-4) photoproducts] from P19 cells. After differentiation, the excellent overall cyclobutane dimer repair capacity of proliferating cells (84% removal in 24 h) is lost (no removal in 24 h), while removal of (6-4) photoproducts, although normal at 24 h (94%), is much slower than in undifferentiated P19 at 3 h (no removal versus 64%). The presence of the denV gene greatly stimulates the repair of cyclobutane dimers in undifferentiated P19 cells (94% removal at 3 h vs. no removal) and also in differentiated cells (50% removal at 24 h vs. no removal). The denV gene also stimulates the early repair of (6-4) photoproducts in both differentiated and undifferentiated cells.

  2. P element excision in drosophila melanogaster and related drosophilids

    Science.gov (United States)

    The frequency of P element excision and the structure of the resulting excision products were determined in three drosophilid species, Drosophila melanogaster, D. virilis, and Chymomyza procnemis. A transient P element mobility assay was conducted in the cells of developing insect embryos, but unlik...

  3. Effects of burn wound excision on bacterial colonization and invasion

    NARCIS (Netherlands)

    Barret, JP; Herndon, DN

    2003-01-01

    Rates of survival after thermal injury have improved in the past two decades, and rates of wound infections and sepsis have decreased during the same period. Early excision has been advocated as one of the major factors, but its safety and efficacy and the exact timing of burn excision are still und

  4. Adaptive Signal Processing Testbed signal excision software: User's manual

    Science.gov (United States)

    Parliament, Hugh A.

    1992-05-01

    The Adaptive Signal Processing Testbed (ASPT) signal excision software is a set of programs that provide real-time processing functions for the excision of interfering tones from a live spread-spectrum signal as well as off-line functions for the analysis of the effectiveness of the excision technique. The processing functions provided by the ASPT signal excision software are real-time adaptive filtering of live data, storage to disk, and file sorting and conversion. The main off-line analysis function is bit error determination. The purpose of the software is to measure the effectiveness of an adaptive filtering algorithm to suppress interfering or jamming signals in a spread spectrum signal environment. A user manual for the software is provided, containing information on the different software components available to perform signal excision experiments: the real-time excision software, excision host program, file processing utilities, and despreading and bit error rate determination software. In addition, information is presented describing the excision algorithm implemented, the real-time processing framework, the steps required to add algorithms to the system, the processing functions used in despreading, and description of command sequences for post-run analysis of the data.

  5. Laparoscopic vs open total mesorectal excision for rectal cancer

    NARCIS (Netherlands)

    Breukink, SO; Grond, AJK; Pierie, JPE; Hoff, C; Wiggers, T; Meijerink, WJHJ

    Background: Next to surgical margins, yield of lymph nodes, and length of bowel resected, macroscopic completeness of mesorectal excision may serve as another quality control of total mesorectal excision (TME). In this study, the macroscopic completeness of laparoscopic TME was evaluated. Methods: A

  6. Osteoid osteoma (OO of the coracoid: a case report of arthroscopic excision and review of literature

    Directory of Open Access Journals (Sweden)

    Goyal Saumitra

    2015-01-01

    Full Text Available Osteoid osteoma (OO of the coracoid is a rare entity that may present with variable symptoms from shoulder leading to delay in diagnosis and treatment. We present the clinical and radiological findings and management of one such case along with a review of similar cases reported in the literature. There was a delay of 2 years in diagnosis, which was later confirmed by computed tomography in addition to magnetic resonance imaging (MRI. The lesion was accessed arthroscopically and excised by unroofing and curettage. “OO” should be included in the differential diagnosis of shoulder pain in young patients not responding to long-term conservative treatment. Arthroscopic excision and curettage provide a good choice for management, with low morbidity and rapid recovery.

  7. The Versajet water dissector: a new tool for tangential excision.

    Science.gov (United States)

    Klein, Matthew B; Hunter, Sue; Heimbach, David M; Engrav, Loren H; Honari, Shari; Gallery, Ellen; Kiriluk, Diane-Marie; Gibran, Nicole S

    2005-01-01

    Goulian and Watson knives work well for tangential burn excision on large flat areas. They do not work well in small areas and in areas with a three-dimensional structure. The Versajet Hydrosurgery System (Smith and Nephew, Key Largo, FL) is a new waterjet-powered surgical tool designed for wound excision. The small size of the cutting nozzle and the ability to easily maneuver the water dissector into small spaces makes it a potentially useful tool for excision of burns of the eyelids, digits and web spaces. The Versajet Hydrosurgery System contains a power console that propels saline through a handheld cutting device. This stream of pressurized saline functions as a knife. We have used the Versajet for burn excision in 44 patients. Although there is a learning curve for both surgeons using and operating room staff setting up the device, the Versajet provides a relatively facile method for excision of challenging aesthetic and functional areas.

  8. Alar base reduction: the boomerang-shaped excision.

    Science.gov (United States)

    Foda, Hossam M T

    2011-04-01

    A boomerang-shaped alar base excision is described to narrow the nasal base and correct the excessive alar flare. The boomerang excision combined the external alar wedge resection with an internal vestibular floor excision. The internal excision was inclined 30 to 45 degrees laterally to form the inner limb of the boomerang. The study included 46 patients presenting with wide nasal base and excessive alar flaring. All cases were followed for a mean period of 18 months (range, 8 to 36 months). The laterally oriented vestibular floor excision allowed for maximum preservation of the natural curvature of the alar rim where it meets the nostril floor and upon its closure resulted in a considerable medialization of alar lobule, which significantly reduced the amount of alar flare and the amount of external alar excision needed. This external alar excision measured, on average, 3.8 mm (range, 2 to 8 mm), which is significantly less than that needed when a standard vertical internal excision was used ( P < 0.0001). Such conservative external excisions eliminated the risk of obliterating the natural alar-facial crease, which did not occur in any of our cases. No cases of postoperative bleeding, infection, or vestibular stenosis were encountered. Keloid or hypertrophic scar formation was not encountered; however, dermabrasion of the scars was needed in three (6.5%) cases to eliminate apparent suture track marks. The boomerang alar base excision proved to be a safe and effective technique for narrowing the nasal base and elimination of the excessive flaring and resulted in a natural, well-proportioned nasal base with no obvious scarring. © Thieme Medical Publishers.

  9. Lingual Thyroid Excision with Transoral Robotic Surgery

    Directory of Open Access Journals (Sweden)

    Elif Ersoy Callıoglu

    2015-01-01

    Full Text Available Ectopic thyroid gland may be detected at any place between foramen caecaum and normal thyroid localization due to inadequacy of the embryological migration of the thyroid gland. It has a prevalence varying between 1/10.000 and 1/100000 in the community. Usually follow-up without treatment is preferred except for obstructive symptoms, bleeding, and suspicion of malignity. Main symptoms are dysphagia, dysphonia, bleeding, dyspnea, and obstructive sleep apnea. In symptomatic cases, the first described method in surgical treatment is open approach since it is a region difficult to have access to. However, this approach has an increased risk of morbidity and postoperative complications. Transoral robotic surgery, which is a minimally invasive surgical procedure, has advantages such as larger three-dimensional point of view and ease of manipulation due to robotic instruments. In this report, a case at the age of 49 who presented to our clinic with obstructive symptoms increasing within the last year and was found to have lingual thyroid and underwent excision of ectopic thyroid tissue by da Vinci surgical system is presented.

  10. Complete mesocolic excision: Techniques and outcomes

    Institute of Scientific and Technical Information of China (English)

    Nikoletta; Dimitriou; John; Griniatsos

    2015-01-01

    Complete mesocolic excision(CME) for the treatment of colon cancer was first introduced in the West in 2008. The first aim of this procedure is to remove the afflicted colon and its accessory lymphovascular supply by resecting the colon and mesocolon in an intact envelope of visceral peritoneum, which holds potentiallyinvolved lymph nodes. The second component of CME is a central vascular tie to remove completely all lymph nodes in the central(vertical) direction. In its original iteration, CME was performed via laparotomy, although many centers preferentially perform laparoscopic surgery, with its associated benefits and similar oncolo-gical outcomes, as the standard treatment for colonic cancer. Here, we present the surgical techniques for CME in open and laparoscopic surgery, as well as the surgical, pathological and oncological outcomes of the procedure that are available to date. Because there are no randomized control trials comparing CME to "standard" colon surgery, the principles underlying CME seem anatomical and logical, and the results published from the Far East, reporting an 80% 5-year survival rate for Stage III cancer, should guide us.

  11. The role of DNA base excision repair in brain homeostasis and disease

    DEFF Research Database (Denmark)

    Akbari, Mansour; Morevati, Marya; Croteau, Deborah;

    2015-01-01

    Chemical modification and spontaneous loss of nucleotide bases from DNA are estimated to occur at the rate of thousands per human cell per day. DNA base excision repair (BER) is a critical mechanism for repairing such lesions in nuclear and mitochondrial DNA. Defective expression or function...... of proteins required for BER or proteins that regulate BER have been consistently associated with neurological dysfunction and disease in humans. Recent studies suggest that DNA lesions in the nuclear and mitochondrial compartments and the cellular response to those lesions have a profound effect on cellular...... energy homeostasis, mitochondrial function and cellular bioenergetics, with especially strong influence on neurological function. Further studies in this area could lead to novel approaches to prevent and treat human neurodegenerative disease....

  12. The Strategy of Excise Taxation of Tobacco Products in Ukraine

    Directory of Open Access Journals (Sweden)

    Pasichnyi Mykola D.

    2017-06-01

    Full Text Available The article is aimed at disclosing and improving approaches to the development of a strategy of excise tax policy in Ukraine, taking into account the foreign experience of harmonizing tax legislation in this sphere. An analysis of the implementation of the EU directives on the regulation of the minimum excise tax liability for the payment of excise taxes on tobacco products in the countries with transformational economies has been carried out. It has been found that, in cases of excessive tax pressure, the equilibrium of the market is disrupted, its shadow component is growing, and the overall economic efficiency level decreases. It has been determined that for the period of 2007-2016 the availability index for cigarettes in Ukraine decreased 2,3 times, which in some way demotivated their consumption. However, the change in the approach of calculation of ad valorem rate for the excise tax and introduction of the excise tax on the sub-excise goods sold by the retailers led to manipulative actions by the major actors in the market concerning the price of cigarettes, which impacted both the increase in the availability of cigarettes in 2016 and the decline in budget revenues. Regulation of the minimum excise duty is the most effective instrument of fiscal policy to achieve goals in the area of limitation of smoking.

  13. Wound Complications and Perineal Pain After Extralevator Versus Standard Abdominoperineal Excision

    DEFF Research Database (Denmark)

    Colov, Emilie Palmgren; Klein, Mads; Gögenur, Ismail

    2016-01-01

    BACKGROUND: Extralevator abdominoperineal excision was introduced as an alternative to conventional abdominoperineal excision for low rectal cancers. The perineal dissection is more extensive with extralevator abdominoperineal excision and leaves a greater defect. OBJECTIVE: The aim of this study...

  14. 77 FR 43157 - Disregarded Entities and the Indoor Tanning Services Excise Tax; Correction

    Science.gov (United States)

    2012-07-24

    ... Excise Tax; Correction AGENCY: Internal Revenue Service (IRS), Treasury. ACTION: Correcting amendment... qualified subchapter S subsidiaries) and the indoor tanning services excise tax. DATES: This correction is... Employment taxes, Estate taxes, Excise taxes, Gift taxes, Income taxes, Penalties, Reporting...

  15. 77 FR 37806 - Disregarded Entities and the Indoor Tanning Services Excise Tax

    Science.gov (United States)

    2012-06-25

    ... Services Excise Tax AGENCY: Internal Revenue Service (IRS), Treasury. ACTION: Final and temporary... (including qualified subchapter S subsidiaries) and the indoor tanning services excise tax. These regulations affect disregarded entities responsible for collecting the indoor tanning services excise tax and...

  16. Nasal base narrowing: the combined alar base excision technique.

    Science.gov (United States)

    Foda, Hossam M T

    2007-01-01

    To evaluate the role of the combined alar base excision technique in narrowing the nasal base and correcting excessive alar flare. The study included 60 cases presenting with a wide nasal base and excessive alar flaring. The surgical procedure combined an external alar wedge resection with an internal vestibular floor excision. All cases were followed up for a mean of 32 (range, 12-144) months. Nasal tip modification and correction of any preexisting caudal septal deformities were always completed before the nasal base narrowing. The mean width of the external alar wedge excised was 7.2 (range, 4-11) mm, whereas the mean width of the sill excision was 3.1 (range, 2-7) mm. Completing the internal excision first resulted in a more conservative external resection, thus avoiding any blunting of the alar-facial crease. No cases of postoperative bleeding, infection, or keloid formation were encountered, and the external alar wedge excision healed with an inconspicuous scar that was well hidden in the depth of the alar-facial crease. Finally, the risk of notching of the alar rim, which can occur at the junction of the external and internal excisions, was significantly reduced by adopting a 2-layered closure of the vestibular floor (P = .01). The combined alar base excision resulted in effective narrowing of the nasal base with elimination of excessive alar flare. Commonly feared complications, such as blunting of the alar-facial crease or notching of the alar rim, were avoided by using simple modifications in the technique of excision and closure.

  17. Early Steps in the DNA Base Excision Repair Pathway of a Fission Yeast Schizosaccharomyces pombe

    Directory of Open Access Journals (Sweden)

    Kyoichiro Kanamitsu

    2010-01-01

    Full Text Available DNA base excision repair (BER accounts for maintaining genomic integrity by removing damaged bases that are generated endogenously or induced by genotoxic agents. In this paper, we describe the roles of enzymes functioning in the early steps of BER in fission yeast. Although BER is an evolutionarily conserved process, some unique features of the yeast repair pathway were revealed by genetic and biochemical approaches. AP sites generated by monofunctional DNA glycosylases are incised mainly by AP lyase activity of Nth1p, a sole bifunctional glycosylase in yeast, to leave a blocked 3′ end. The major AP endonuclease Apn2p functions predominantly in removing the 3′ block. Finally, a DNA polymerase fills the gap, and a DNA ligase seals the nick (Nth1p-dependent or short patch BER. Apn1p backs up Apn2p. In long patch BER, Rad2p endonuclease removes flap DNA containing a lesion after DNA synthesis. A UV-specific endonuclease Uve1p engages in an alternative pathway by nicking DNA on the 5′ side of oxidative damage. Nucleotide excision repair and homologous recombination are involved in repair of BER intermediates including the AP site and single-strand break with the 3′ block. Other enzymes working in 3′ end processing are also discussed.

  18. Inhibition of Nucleotide Synthesis Targets Brain Tumor Stem Cells in a Subset of Glioblastoma.

    Science.gov (United States)

    Laks, Dan R; Ta, Lisa; Crisman, Thomas J; Gao, Fuying; Coppola, Giovanni; Radu, Caius G; Nathanson, David A; Kornblum, Harley I

    2016-06-01

    Inhibition of both the de novo (DNP) and salvage (NSP) pathways of nucleoside synthesis has been demonstrated to impair leukemia cells. We endeavored to determine whether this approach would be efficacious in glioblastoma. To diminish nucleoside biosynthesis, we utilized compound DI-39, which selectively targets NSP, in combination with thymidine (dT), which selectively targets DNP. We employed in vitro and ex vivo models to determine the effects of pretreatment with dT + DI-39 on brain tumor stem cells (BTSC). Here, we demonstrate that this combinatorial therapy elicits a differential response across a spectrum of human patient-derived glioblastoma cultures. As determined by apoptotic markers, most cultures were relatively resistant to treatment, although a subset was highly sensitive. Sensitivity was unrelated to S-phase delay and to DNA damage induced by treatment. Bioinformatics analysis indicated that response across cultures was associated with the transcription factor PAX3 (associated with resistance) and with canonical pathways, including the nucleotide excision repair pathway, PTEN (associated with resistance), PI3K/AKT (associated with sensitivity), and ErbB2-ErbB3. Our in vitro assays demonstrated that, in sensitive cultures, clonal sphere formation was reduced upon removal from pretreatment. In contrast, in a resistant culture, clonal sphere formation was slightly increased upon removal from pretreatment. Moreover, in an intracranial xenograft model, pretreatment of a sensitive culture caused significantly smaller and fewer tumors. In a resistant culture, tumors were equivalent irrespective of pretreatment. These results indicate that, in the subset of sensitive glioblastoma, BTSCs are targeted by inhibition of pyrimidine synthesis. Mol Cancer Ther; 15(6); 1271-8. ©2016 AACR. ©2016 American Association for Cancer Research.

  19. Quantitative extraction of nucleotides from frozen muscle samples of Atlantic salmon ( Salmo salar ) and rainbow trout ( Oncorhynchus mykiss ) : Effects of time taken to sample and extraction method

    DEFF Research Database (Denmark)

    Thomas, P.M.; Bremner, Allan; Pankhurst, N.W.

    2000-01-01

    Muscle excised from the dorsal flank of Atlantic salmon and rainbow trout at death and up to 120 min postmortem (P.M.) was frozen in liquid N-2 and stored at -80C. Following acid extraction, on ice (method I), or dry ice (method 2) samples were analyzed for cyclic nucleotides to determine...

  20. Relativistic MHD and excision: formulation and initial tests

    Energy Technology Data Exchange (ETDEWEB)

    Neilsen, David; Hirschmann, Eric W; Millward, R Steven [Department of Physics and Astronomy, Brigham Young University, Provo, UT 84602 (United States)

    2006-08-21

    A new algorithm for solving the general relativistic MHD equations is described in this paper. We design our scheme to incorporate black hole excision with smooth boundaries, and to simplify solving the combined Einstein and MHD equations with AMR. The fluid equations are solved using a finite difference convex ENO method. Excision is implemented using overlapping grids. Elliptic and hyperbolic divergence cleaning techniques allow for maximum flexibility in choosing coordinate systems, and we compare both methods for a standard problem. Numerical results of standard test problems are presented in two-dimensional flat space using excision, overlapping grids and elliptic and hyperbolic divergence cleaning.

  1. Relativistic MHD and black hole excision: Formulation and initial tests

    CERN Document Server

    Neilsen, D; Millward, R S; Hirschmann, Eric W; Neilsen, David

    2006-01-01

    A new algorithm for solving the general relativistic MHD equations is described in this paper. We design our scheme to incorporate black hole excision with smooth boundaries, and to simplify solving the combined Einstein and MHD equations with AMR. The fluid equations are solved using a finite difference Convex ENO method. Excision is implemented using overlapping grids. Elliptic and hyperbolic divergence cleaning techniques allow for maximum flexibility in choosing coordinate systems, and we compare both methods for a standard problem. Numerical results of standard test problems are presented in two-dimensional flat space using excision, overlapping grids, and elliptic and hyperbolic divergence cleaning.

  2. Laparoscopic choledochal cyst excision and Roux-en-Y hepaticojejunostomy.

    Science.gov (United States)

    Kayaalp, Cüneyt; Soyer, Vural; Ersan, Veysel; Aydın, Cemalettin; Karagül, Servet

    2016-01-01

    Congenital choledochal cysts are rare in adults. Due to the risk of developing cholangiocarcinoma, the current standard of care is complete excision of the cyst and reconstruction with hepaticojejunostomy. So far, more than 200 laparoscopic resections have been reported in adults, the majority being from Far Eastern countries over the last five years. Herein, the technique of laparoscopic type I choledochal cyst excision and hepaticojejunostomy is presented in a 37-year-old male with an accompanying video. The advantages of laparoscopic surgery are applicable for choledochal cyst excision as well. We believe that teamwork, expertise on intracorporeal suturing and hepatobiliary surgery are central issues for this operation.

  3. Surgical excision of acne keloidalis nuchae with secondary intention healing.

    Science.gov (United States)

    Bajaj, V; Langtry, J A A

    2008-01-01

    Acne keloidalis nuchae (AKN) is a chronic scarring folliculitis that presents clinically as follicular papules and pustules. These can coalesce into firm hypertrophic plaques and nodules on the nape of the neck, most commonly affecting young adult men. Treatment includes topical steroids/antibiotics and oral antibiotics, but often has disappointing results. Surgical approaches include excision with primary closure or skin grafting, and hair-removal lasers. Another surgical approach is excision with secondary intention healing. This can result in good cosmesis with little or no recurrence. We report two men with AKN where treatment by excision with secondary intention was successful.

  4. Mucocele-like lesions in the breast diagnosed with percutaneous biopsy: is surgical excision necessary?

    Science.gov (United States)

    Ha, Daon; Dialani, Vandana; Mehta, Tejas S; Keefe, Whitney; Iuanow, Elaine; Slanetz, Priscilla J

    2015-01-01

    The purpose of this study was to determine the frequencies of atypia and cancer at excisional biopsy of lesions with a diagnosis of mucocele-like lesion (MLL) at percutaneous breast biopsy. Retrospective review of 9286 lesions subjected to percutaneous imaging-guided biopsy identified MLLs in 35 (0.38%) patients. Medical records, imaging studies, and histologic results were reviewed. Of the 35 patients with core biopsy findings of MLL, 27 underwent stereotactic core needle biopsy (19 with microcalcifications, five with calcifications with an associated mass, and three with only a mass), and eight underwent ultrasound-guided core needle biopsy (four with a solid mass, three with a complex cystic mass). At core biopsy, 12 of 35 (34%) MLLs were associated with atypia (10 cases of atypical ductal hyperplasia, two of flat epithelial atypia), and 23 of 35 (66%) were benign MLL only. All 12 MLLs associated with atypia and 12 of 23 benign MLLs were surgically excised. Eleven patients did not undergo surgery, five of whom were lost to follow-up. One of the 12 (3% of the 35) MLLs associated with atypia was upgraded to DCIS. None were upgraded to invasive cancer. None of the benign MLLs were upgraded to malignancy, and findings at excision of four of the 23 (17%) benign MLLs led to a change in diagnosis to a high-risk lesion (three atypical ductal hyperplasia, one atypical lobular hyperplasia). MLL is a rare diagnosis but is encountered in large-volume breast practices. The findings are nonspecific with a range of imaging appearances. No imaging test is reliable for differentiating MLL from other suspicious lesions or lesions with associated atypia. Surgery is clearly warranted for MLL associated with atypia at core needle biopsy because it may be upgraded to malignancy upon excision. However, if the presence of atypia at excision of benign MLL will change clinical management, then benign MLL at core needle biopsy warrants surgical excision in some cases. In patients whose

  5. Excise Tax Rates On Packs Of Cigarettes PDF Slides

    Data.gov (United States)

    U.S. Department of Health & Human Services — Download the current excise tax rates on packs of cigarettes slides. These slides are available in PDF and PowerPoint formats. The PowerPoint version can be found...

  6. Circumareolar Incision‑subdermal Tunneling Dissection for Excision ...

    African Journals Online (AJOL)

    2017 Nigerian Journal of Surgery | Published by Wolters Kluwer - Medknow. Excision of ... superficial fascia with circumareolar incision, subdermal cone‑wise dissection was made to ..... Technical advances in skin sparing mastectomy. Int.

  7. Technical points of total laparoscopic choledochal cyst excision

    Institute of Scientific and Technical Information of China (English)

    L(U) Shao-cheng; SHI Xian-jie; WANG Hong-guang; LU Fang; LIANG Yu-rong; LUO Ying; JI Wen-bin

    2013-01-01

    Background Choledochal cyst excision and biliary enteric reconstruction constitute the best therapy for choledochal cyst.And laparoscopy is currently used to cure this disease now.Methods We retrospectively analyzed the clinical data of 34 cases of total laparoscopic choledochal cyst excision between January 2007 and August 2011.All patients underwent in vitro Roux-en-Y hepatoenterostomy.Results All 34 patients underwent successful total laparoscopic choledochal cyst excision.The operation time was 200-360 minutes.The duration of hospital stay was 3-7 days.Follow-up observations lasted 1-56 months.One patient developed an anastomotic stoma stricture,but no other cases had postoperative complications.No patients died.Conclusion Total laparoscopic choledochal cyst excision is safe and feasible.

  8. Desmoplastic fibroma of ulna: Excision and reconstruction of olecranon with a fibular graft

    Directory of Open Access Journals (Sweden)

    Tarun Goyal

    2013-01-01

    Full Text Available Desmoplastic fibroma is a rare, well differentiated, locally aggressive fibrous tumor usually arising from soft tissues, and rarely from bones. Involvement of forearm bones is extremely unusual. We present a large desmoplastic fibroma of right ulna in a 15-year-old male. The tumor was excised with a wide margin, and the bony defect was reconstructed with nonvascular autologous fibular graft. Reconstruction of the olecranon process was attempted using the fibular head and the remaining olecranon. At 2-years followup, there was no recurrence, flexion extension arc of the elbow joint was 40°-130° and there was no restriction of activities of daily living.

  9. Life cycle and mating behavior of Zygotylenchus guevarai (Nematoda: Pratylenchidae) on excised Petroselinum crispum roots.

    Science.gov (United States)

    Karakaş, Mehmet

    2007-11-15

    The life cycle and mating behavior of Zygotylenchus guevarai were observed in vitro on excised roots of Petroselinum crispum in gnotobiotic culture. Eggs hatched into juveniles whose appearance and structure were similar to those of the adults. Juveniles grew in size and each juvenile stage was terminated by a molt. Z. guevarai had four juvenile stages with the first molt occurred outside the egg shortly after hatching. After the final molt the juveniles differentiated into adult males and females. Mating was required for reproduction. After mating, fertilized females began to lay eggs. The life cycle from second stage juvenile to second stage juvenile was completed in 43 days.

  10. Dysplastic lesions of the cervix evolution after conservative excision

    OpenAIRE

    G. Costăchescu; Alina Melinte-Popescu

    2012-01-01

    This study analyzes the evolution of dysplastic lesions after conservative excision treatment (Large Loop Excision Transformation Zone – LLETZ and conization). METHODS: We performed an observational study on a group of 332 patients, diagnosed and treated for cervical dysplasia at „Cuza Vodă” Obstetrics and Gynecology Clinic Hospital Suceava between 2006 and 2011. RESULTS: High grade cervical squamous intraepithelial lesion (HSIL) accounted for 88 patients (26.5%), low grade cervical squamous ...

  11. Excision of Mucocele Using Diode Laser in Lower Lip

    Science.gov (United States)

    Ramkumar, Subramaniam; Ramkumar, Lakshmi; Malathi, Narasimhan

    2016-01-01

    Mucoceles are nonneoplastic cystic lesions of major and minor salivary glands which result from the accumulation of mucus. These lesions are most commonly seen in children. Though usually these lesions can be treated by local surgical excision, in our case, to avoid intraoperative surgical complications like bleeding and edema and to enable better healing, excision was done using a diode laser in the wavelength of 940 nm. PMID:28097026

  12. ASPT software source code: ASPT signal excision software package

    Science.gov (United States)

    Parliament, Hugh

    1992-08-01

    The source code for the ASPT Signal Excision Software Package which is part of the Adaptive Signal Processing Testbed (ASPT) is presented. The source code covers the programs 'excision', 'ab.out', 'd0.out', 'bd1.out', 'develop', 'despread', 'sorting', and 'convert'. These programs are concerned with collecting data, filtering out interference from a spread spectrum signal, analyzing the results, and developing and testing new filtering algorithms.

  13. Genomic island excisions in Bordetella petrii

    Directory of Open Access Journals (Sweden)

    Levillain Erwan

    2009-07-01

    Full Text Available Abstract Background Among the members of the genus Bordetella B. petrii is unique, since it is the only species isolated from the environment, while the pathogenic Bordetellae are obligately associated with host organisms. Another feature distinguishing B. petrii from the other sequenced Bordetellae is the presence of a large number of mobile genetic elements including several large genomic regions with typical characteristics of genomic islands collectively known as integrative and conjugative elements (ICEs. These elements mainly encode accessory metabolic factors enabling this bacterium to grow on a large repertoire of aromatic compounds. Results During in vitro culture of Bordetella petrii colony variants appear frequently. We show that this variability can be attributed to the presence of a large number of metastable mobile genetic elements on its chromosome. In fact, the genome sequence of B. petrii revealed the presence of at least seven large genomic islands mostly encoding accessory metabolic functions involved in the degradation of aromatic compounds and detoxification of heavy metals. Four of these islands (termed GI1 to GI3 and GI6 are highly related to ICEclc of Pseudomonas knackmussii sp. strain B13. Here we present first data about the molecular characterization of these islands. We defined the exact borders of each island and we show that during standard culture of the bacteria these islands get excised from the chromosome. For all but one of these islands (GI5 we could detect circular intermediates. For the clc-like elements GI1 to GI3 of B. petrii we provide evidence that tandem insertion of these islands which all encode highly related integrases and attachment sites may also lead to incorporation of genomic DNA which originally was not part of the island and to the formation of huge composite islands. By integration of a tetracycline resistance cassette into GI3 we found this island to be rather unstable and to be lost from

  14. Core needle biopsies and surgical excision biopsies in the diagnosis of lymphoma-experience at the Lymph Node Registry Kiel.

    Science.gov (United States)

    Johl, Alice; Lengfelder, Eva; Hiddemann, Wolfgang; Klapper, Wolfram

    2016-08-01

    Current guidelines of the European Society of Medical Oncology recommend surgical excision biopsies of lymph nodes for the diagnosis of lymphoma whenever possible. However, core needle biopsies are increasingly used. We aimed to understand the common practice to choose the method of biopsy in Germany. Furthermore, we wanted to understand performance of surgical excision and core needle biopsies of lymph nodes in the diagnosis of lymphoma. The files of 1510 unselected, consecutive lymph node specimens from a consultation center for lymphoma diagnosis were analyzed. Core needle biopsies were obtained frequently from lymph nodes localized in mediastinal, abdominal, retroperitoneal, or thoracic regions. Patients undergoing core needle biopsies were significantly older and suffered significantly more often from lymphoma than patients undergoing surgical excision biopsies. Although more immunohistochemical tests were ordered by the pathologist for core needle biopsies specimens than for surgical excision biopsies specimens, core needle biopsies did not yield a definite diagnosis in 8.3 % of cases, compared to 2.8 % for SEB (p = 0.0003). Restricting the analysis to cases with a final diagnosis of follicular lymphoma or diffuse large B-cell lymphoma, core needle biopsies identified a simultaneous low- and high-grade lymphoma (transformation) in 3.3 % of cases, compared to 7.6 % for surgical excision biopsies (p = 0.2317). In Germany, core needle biopsies are preferentially used in elderly patients with a high likelihood of suffering from lymphoma. Core needle appeared inferior to surgical excision biopsies at providing a definite diagnosis and at identifying multiple lymphoma differentiations and transformation.

  15. The Integration and Excision of CTnDOT.

    Science.gov (United States)

    Wood, Margaret M; Gardner, Jeffrey F

    2015-04-01

    Bacteroides species are one of the most prevalent groups of bacteria present in the human colon. Many strains carry large, integrated elements including integrative and conjugative elements (ICEs). One such ICE is CTnDOT, which is 65 kb in size and encodes resistances to tetracycline and erythromycin. CTnDOT has been increasing in prevalence in Bacteroides spp., and is now found in greater than 80% of natural isolates. In recent years, CTnDOT has been implicated in the spread of antibiotic resistance among gut microbiota. Interestingly, the excision and transfer of CTnDOT is stimulated in the presence of tetracycline. The tyrosine recombinase IntDOT catalyzes the integration and excision reactions of CTnDOT. Unlike the well-characterized lambda Int, IntDOT tolerates heterology in the overlap region between the sites of cleavage and strand exchange. IntDOT also appears to have a different arrangement of active site catalytic residues. It is missing one of the arginine residues that is conserved in other tyrosine recombinases. The excision reaction of CTnDOT is complex, involving excision proteins Xis2c, Xis2d, and Exc, as well as IntDOT and a Bacteroides host factor. Xis2c and Xis2d are small, basic proteins like other recombination directionality factors (RDFs). Exc is a topoisomerase; however, the topoisomerase function is not required for the excision reaction. Exc has been shown to stimulate excision frequencies when there are mismatches in the overlap regions, suggesting that it may play a role in resolving Holliday junctions (HJs) containing heterology. Work is currently under way to elucidate the complex interactions involved with the formation of the CTnDOT excisive intasomes.

  16. 29 CFR 779.262 - Excise taxes at the retail level.

    Science.gov (United States)

    2010-07-01

    ... 29 Labor 3 2010-07-01 2010-07-01 false Excise taxes at the retail level. 779.262 Section 779.262... Coverage Excise Taxes § 779.262 Excise taxes at the retail level. (a) Federal excise taxes are imposed at the retail level on highway vehicle fuels other than gasoline under the provisions of 26 U.S.C....

  17. Monte Carlo simulation of base and nucleotide excision repair of clustered DNA damage sites. I. Model properties and predicted trends

    Energy Technology Data Exchange (ETDEWEB)

    Semenenko, Vladimir; Stewart, Robert D.; Ackerman, Eric J.

    2005-12-31

    Single-cell irradiators and new experimental assays are rapidly expanding our ability to quantify the molecular mechanisms responsible for phenomena such as toxicant-induced adaptations in DNA repair and signal-mediated changes to the genome stability of cells not directly damaged by radiation (i.e., bystander cells). To advance our understanding of, and ability to predict and mitigate, the potentially harmful effects of radiological agents, effective strategies must be devised to incorporate information from molecular and cellular studies into mechanism-based, hierarchical models. A key advantage of the hierarchical modeling approach is that information from DNA repair and other in vitro assays can be systematically integrated into higher-level cell transformation and, eventually, carcinogenesis models. This presentation will outline the hierarchical modeling strategy used to integrate information from in vitro studies into the Virtual Cell (VC) radiobiology software (see Endnote). A new multi-path genomic instability model will be introduced and used to link biochemical processing of double strand breaks (DSBs) to neoplastic cell transformation. Bystander and directly damaged cells are treated explicitly in the model using a microdosimetric approach, although many of the details of the bystander response model are of a necessarily preliminary nature. The new model will be tested against several published radiobiological datasets. Results illustrating how hypothesized bystander mechanisms affect the shape of dose-response curves for neoplastic transformation as a function of Linear Energy Transfer (LET) will be presented. EndNote: R.D. Stewart, Virtual Cell (VC) Radiobiology Software. PNNL-13579, July 2001. Available at http://www.pnl.gov/berc/kbem/vc/ The DNA repair model used in the VC computer program is based on the Two-Lesion Kinetic (TLK) model [Radiat. Res. 156(4), 365-378 October 2001].

  18. DNA Repair Gene Polymorphisms in the Nucleotide Excision Repair Pathway and Lung Cancer Risk: A Meta-analysis

    Institute of Scientific and Technical Information of China (English)

    Chao-rong Mei; Meng Luo; Hong-mei Li; Wen-jun Deng; Qing-hua Zhou

    2011-01-01

    Objective: A number of studies have reported the association of “XPA”, “XPC”, “XPD/ERCC2” gene polymorphisms with lung cancer risk. However, the results were conflict. To clarify the impact of polymorphisms of “XPA”, “XPC”; “XPD/ERCC2”, on lung cancer risk, a meta-analysis was performed in this study. Methods: The electronic databases PubMed and Embase were retrieved for studies included in this meta-analysis by “XPA”; “XPC”, “XPD/ERCC2”, “lung”, “cancer/neoplasm/tumor/carcinoma”, “polymorphism” (An upper date limit of October, 31, 2009). A meta-analysis was performed to evaluate the relationship among XPA, XPC and XPD polymorphism and lung cancer risks. Results: A total of 31 publications retrieved from Pubmed and Embase included in this study. XPC A939C CC genotype increased lung cancer risk in total population (recessive genetic model: OR=1.23, 95% Cl:1.05-1.44;homozygote comparison: OR=1.21,95%Cl:1.02-1.43and CC vs. CA contrast: OR=1.25,95%Cl:1.06-1.48), except in Asians. XPD A751C, 751C allele and CC genotype also increased lung cancer risk in total population and in Caucasians (recessive genetic model: Total population: OR=1.20, 95%Cl:1.07-1.35). No significant correlation was found between XPD A751C and lung cancer risk in Asians and African Americans. XPD G312A AA genotype increased lung cancer risk in total population, in Asians and Caucasians(recessive genetic model: Total population: OR=1.20, 95%Cl:1.06-1.36). No significant association was found between XPA G23A, XPC C499T, XPD C156A and lung cancer risk. Conclusion: Our results suggest that the polymorphisms in XPC and XPD involve in lung cancer risks. XPA polymorphisms is less related to lung cancer risk.

  19. The diagnostic capability of laser induced fluorescence in the characterization of excised breast tissues

    Science.gov (United States)

    Galmed, A. H.; Elshemey, Wael M.

    2017-08-01

    Differentiating between normal, benign and malignant excised breast tissues is one of the major worldwide challenges that need a quantitative, fast and reliable technique in order to avoid personal errors in diagnosis. Laser induced fluorescence (LIF) is a promising technique that has been applied for the characterization of biological tissues including breast tissue. Unfortunately, only few studies have adopted a quantitative approach that can be directly applied for breast tissue characterization. This work provides a quantitative means for such characterization via introduction of several LIF characterization parameters and determining the diagnostic accuracy of each parameter in the differentiation between normal, benign and malignant excised breast tissues. Extensive analysis on 41 lyophilized breast samples using scatter diagrams, cut-off values, diagnostic indices and receiver operating characteristic (ROC) curves, shows that some spectral parameters (peak height and area under the peak) are superior for characterization of normal, benign and malignant breast tissues with high sensitivity (up to 0.91), specificity (up to 0.91) and accuracy ranking (highly accurate).

  20. European Nucleotide Archive in 2016

    Science.gov (United States)

    Toribio, Ana Luisa; Alako, Blaise; Amid, Clara; Cerdeño-Tarrága, Ana; Clarke, Laura; Cleland, Iain; Fairley, Susan; Gibson, Richard; Goodgame, Neil; ten Hoopen, Petra; Jayathilaka, Suran; Kay, Simon; Leinonen, Rasko; Liu, Xin; Martínez-Villacorta, Josué; Pakseresht, Nima; Rajan, Jeena; Reddy, Kethi; Rosello, Marc; Silvester, Nicole; Smirnov, Dmitriy; Vaughan, Daniel; Zalunin, Vadim; Cochrane, Guy

    2017-01-01

    The European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena) offers a rich platform for data sharing, publishing and archiving and a globally comprehensive data set for onward use by the scientific community. With a broad scope spanning raw sequencing reads, genome assemblies and functional annotation, the resource provides extensive data submission, search and download facilities across web and programmatic interfaces. Here, we outline ENA content and major access modalities, highlight major developments in 2016 and outline a number of examples of data reuse from ENA. PMID:27899630

  1. Developmentally programmed excision of internal DNA sequences in Paramecium aurelia.

    Science.gov (United States)

    Gratias, A; Bétermier, M

    2001-01-01

    The development of a new somatic nucleus (macronucleus) during sexual reproduction of the ciliate Paramecium aurelia involves reproducible chromosomal rearrangements that affect the entire germline genome. Macronuclear development can be induced experimentally, which makes P. aurelia an attractive model for the study of the mechanism and the regulation of DNA rearrangements. Two major types of rearrangements have been identified: the fragmentation of the germline chromosomes, followed by the formation of the new macronuclear chromosome ends in association with imprecise DNA elimination, and the precise excision of internal eliminated sequences (IESs). All IESs identified so far are short, A/T rich and non-coding elements. They are flanked by a direct repeat of a 5'-TA-3' dinucleotide, a single copy of which remains at the macronuclear junction after excision. The number of these single-copy sequences has been estimated to be around 60,000 per haploid genome. This review focuses on the current knowledge about the genetic and epigenetic determinants of IES elimination in P. aurelia, the analysis of excision products, and the tightly regulated timing of excision throughout macronuclear development. Several models for the molecular mechanism of IES excision will be discussed in relation to those proposed for DNA elimination in other ciliates.

  2. Nucleotide Metabolism and DNA Replication.

    Science.gov (United States)

    Warner, Digby F; Evans, Joanna C; Mizrahi, Valerie

    2014-10-01

    The development and application of a highly versatile suite of tools for mycobacterial genetics, coupled with widespread use of "omics" approaches to elucidate the structure, function, and regulation of mycobacterial proteins, has led to spectacular advances in our understanding of the metabolism and physiology of mycobacteria. In this article, we provide an update on nucleotide metabolism and DNA replication in mycobacteria, highlighting key findings from the past 10 to 15 years. In the first section, we focus on nucleotide metabolism, ranging from the biosynthesis, salvage, and interconversion of purine and pyrimidine ribonucleotides to the formation of deoxyribonucleotides. The second part of the article is devoted to DNA replication, with a focus on replication initiation and elongation, as well as DNA unwinding. We provide an overview of replication fidelity and mutation rates in mycobacteria and summarize evidence suggesting that DNA replication occurs during states of low metabolic activity, and conclude by suggesting directions for future research to address key outstanding questions. Although this article focuses primarily on observations from Mycobacterium tuberculosis, it is interspersed, where appropriate, with insights from, and comparisons with, other mycobacterial species as well as better characterized bacterial models such as Escherichia coli. Finally, a common theme underlying almost all studies of mycobacterial metabolism is the potential to identify and validate functions or pathways that can be exploited for tuberculosis drug discovery. In this context, we have specifically highlighted those processes in mycobacterial DNA replication that might satisfy this critical requirement.

  3. RAD1 and RAD10, but not other excision repair genes, are required for double-strand break-induced recombination in Saccharomyces cerevisiae.

    Science.gov (United States)

    Ivanov, E L; Haber, J E

    1995-04-01

    HO endonuclease-induced double-strand breaks (DSBs) in the yeast Saccharomyces cerevisiae can be repaired by the process of gap repair or, alternatively, by single-strand annealing if the site of the break is flanked by directly repeated homologous sequences. We have shown previously (J. Fishman-Lobell and J. E. Haber, Science 258:480-484, 1992) that during the repair of an HO-induced DSB, the excision repair gene RAD1 is needed to remove regions of nonhomology from the DSB ends. In this report, we present evidence that among nine genes involved in nucleotide excision repair, only RAD1 and RAD10 are required for removal of nonhomologous sequences from the DSB ends. rad1 delta and rad10 delta mutants displayed a 20-fold reduction in the ability to execute both gap repair and single-strand annealing pathways of HO-induced recombination. Mutations in RAD2, RAD3, and RAD14 reduced HO-induced recombination by about twofold. We also show that RAD7 and RAD16, which are required to remove UV photodamage from the silent HML, locus, are not required for MAT switching with HML or HMR as a donor. Our results provide a molecular basis for understanding the role of yeast nucleotide excision repair gene and their human homologs in DSB-induced recombination and repair.

  4. Flexor Tendon Ruptures After Distal Scaphoid Excision for Scaphotrapeziotrapezoid Osteoarthritis.

    Science.gov (United States)

    Deren, Matthew E; Mitchell, Charles H; Weiss, Arnold-Peter C

    2017-09-01

    Distal scaphoid excision is one treatment option for osteoarthritis of the scaphotrapeziotrapezoid (STT) joint following failure of conservative measures. Potential complications of this procedure include injury to the carpal ligaments, cartilage, and radial artery. A single case was identified by the senior author, and the medical record was reviewed for surgical notes, progress notes, and radiographs. A 68-year-old male sustained ruptures of the flexor digitorum superficialis (FDS) and flexor digitorum profundus to the index finger 3 years following a distal scaphoid excision for symptomatic STT osteoarthritis. He required a flexor tendon reconstruction using the remaining FDS tendon for graft incorporated with a Pulvertaft weave. His midcarpal pain continued after recovery of his index finger function, eventually requiring a 4-corner fusion of the wrist. Flexor tendon rupture is a previously unreported complication of distal scaphoid excision for STT arthritis.

  5. Management of Recurrent Stricture Formation after Transverse Vaginal Septum Excision

    Directory of Open Access Journals (Sweden)

    Ridhima Gupta

    2015-01-01

    Full Text Available Background. A transverse vaginal septum (TVS is a rare obstructing anomaly, caused due to improper fusion of Müllerian ducts and urogenital sinus during embryogenesis. Case. A 15-year-old girl presented with primary amenorrhea. She had multiple congenital anomalies. Initial examination and imaging investigation revealed the presence of a unicornuate uterus and a TVS. The TVS was excised; however the patient was unable to perform vaginal dilation postoperatively leading to recurrent stricture formation. She underwent multiple surgeries for excision of the stricture. The patient was eventually evaluated every day in the clinic until she was able to demonstrate successful vaginal dilatation in the presence of a clinician. Summary and Conclusion. Properly guided regular and intensive vaginal dilation after TVS excision may decrease the need of reoperations due to recurrent stricture formation.

  6. Management of Recurrent Stricture Formation after Transverse Vaginal Septum Excision.

    Science.gov (United States)

    Gupta, Ridhima; Bozzay, Joseph D; Williams, David L; DePond, Robert T; Gantt, Pickens A

    2015-01-01

    Background. A transverse vaginal septum (TVS) is a rare obstructing anomaly, caused due to improper fusion of Müllerian ducts and urogenital sinus during embryogenesis. Case. A 15-year-old girl presented with primary amenorrhea. She had multiple congenital anomalies. Initial examination and imaging investigation revealed the presence of a unicornuate uterus and a TVS. The TVS was excised; however the patient was unable to perform vaginal dilation postoperatively leading to recurrent stricture formation. She underwent multiple surgeries for excision of the stricture. The patient was eventually evaluated every day in the clinic until she was able to demonstrate successful vaginal dilatation in the presence of a clinician. Summary and Conclusion. Properly guided regular and intensive vaginal dilation after TVS excision may decrease the need of reoperations due to recurrent stricture formation.

  7. Twelve single nucleotide polymorphisms on chromosome 19q13.2-13.3

    DEFF Research Database (Denmark)

    Yin, Jiaoyang; Vogel, Ulla; Gerdes, Lars Ulrik;

    2003-01-01

    The genetic susceptibility to basal cell carcinoma (BCC) among Danish psoriatic patients was investigated in association studies with 12 single nucleotide polymorphisms on chromosome 19q13.2-3. The results show a significant association between BCC and the A-allele of a polymorphism in ERCCI exon4...... (Odds ratio 12;95% Confidence Interval 1.17-124; p(chi2, two-side) = 0.019) and to a lesser extent with XPD exon6 (p = 0.06). This is in accordance with recent studies of a different group of BCC cases (Rockenbauer et al. (in press) Carcinogenesis; Yin et al. (manuscript submitted for publication...... in nucleotide excision repair is of importance for the development of BCC....

  8. AUXIN AND GROWTH OF EXCISED ROOTS OF Bryophyllum calycinum.

    Science.gov (United States)

    Robbins, W J; Hervey, A

    1969-10-01

    Exogenous auxin (alpha-naphthalene acetic acid, indole acetic acid, or 2,4-dichlorophenoxyacetic acid) was essential for the growth of single excised root tips of Bryophyllum calycinum in 50 ml of a mineral salt-sucrose medium supplemented with vitamins. Large inocula with a dry weight of 2.0 mg or more grew with no auxin added to the medium. Evidence for the synthesis of auxin by the excised roots grown from the larger inocula is presented. Leaching of auxin from single root tips cultivated in 15 or 50 ml of basal medium is considered to account for their failure to grow.

  9. Local Excision for the Treatment of Penile Verrucous Carcinoma.

    Science.gov (United States)

    Jo, Dong In; Choi, Sang Kyu; Kim, Soon Heum; Kim, Cheol Keun; Chung, Hong; Kim, Hong Sup

    2017-07-01

    Penile verrucous carcinoma is known for its favorable biologic behavior and lack of metastatic potential. For preservation of function, treatment has been focused on partial penectomy. Despite partial penectomy for preservation of minimal functional and aesthetic aspects, patients have experienced psychosexual problems. A 73-year-old man had a cauliflower-like verrucous carcinoma on the penile glans and coronary sulcus diagnosed by using excisional biopsy. He underwent degloving excision to save the penile shaft and glans penis. Surgical margin was 3 mm. He had been tumor-free at the 2-year follow-up. For maximum preservation of the functional and aesthetic aspects, we recommend degloving excision.

  10. Local Excision for the Treatment of Penile Verrucous Carcinoma

    Directory of Open Access Journals (Sweden)

    Dong In Jo

    2017-07-01

    Full Text Available Penile verrucous carcinoma is known for its favorable biologic behavior and lack of metastatic potential. For preservation of function, treatment has been focused on partial penectomy. Despite partial penectomy for preservation of minimal functional and aesthetic aspects, patients have experienced psychosexual problems. A 73-year-old man had a cauliflower-like verrucous carcinoma on the penile glans and coronary sulcus diagnosed by using excisional biopsy. He underwent degloving excision to save the penile shaft and glans penis. Surgical margin was 3 mm. He had been tumor-free at the 2-year follow-up. For maximum preservation of the functional and aesthetic aspects, we recommend degloving excision.

  11. Cyclic nucleotide specific phosphodiesterases of Leishmania major

    Directory of Open Access Journals (Sweden)

    Linder Markus

    2006-03-01

    Full Text Available Abstract Background Leishmania represent a complex of important human pathogens that belong to the systematic order of the kinetoplastida. They are transmitted between their human and mammalian hosts by different bloodsucking sandfly vectors. In their hosts, the Leishmania undergo several differentiation steps, and their coordination and optimization crucially depend on numerous interactions between the parasites and the physiological environment presented by the fly and human hosts. Little is still known about the signalling networks involved in these functions. In an attempt to better understand the role of cyclic nucleotide signalling in Leishmania differentiation and host-parasite interaction, we here present an initial study on the cyclic nucleotide-specific phosphodiesterases of Leishmania major. Results This paper presents the identification of three class I cyclic-nucleotide-specific phosphodiesterases (PDEs from L. major, PDEs whose catalytic domains exhibit considerable sequence conservation with, among other, all eleven human PDE families. In contrast to other protozoa such as Dictyostelium, or fungi such as Saccharomyces cerevisiae, Candida ssp or Neurospora, no genes for class II PDEs were found in the Leishmania genomes. LmjPDEA contains a class I catalytic domain at the C-terminus of the polypeptide, with no other discernible functional domains elsewhere. LmjPDEB1 and LmjPDEB2 are coded for by closely related, tandemly linked genes on chromosome 15. Both PDEs contain two GAF domains in their N-terminal region, and their almost identical catalytic domains are located at the C-terminus of the polypeptide. LmjPDEA, LmjPDEB1 and LmjPDEB2 were further characterized by functional complementation in a PDE-deficient S. cerevisiae strain. All three enzymes conferred complementation, demonstrating that all three can hydrolyze cAMP. Recombinant LmjPDEB1 and LmjPDEB2 were shown to be cAMP-specific, with Km values in the low micromolar range

  12. "The lobbying strategy is to keep excise as low as possible" - tobacco industry excise taxation policy in Ukraine

    Directory of Open Access Journals (Sweden)

    Krasovsky Konstantin S

    2010-08-01

    Full Text Available Abstract Background Tobacco taxes are one of the most effective ways to reduce tobacco use. Transnational tobacco companies (TTCs claim they wish to develop and secure excise systems that benefit both governments and the profitability of the companies themselves. The objective of the paper is to use the case of Ukraine, with its inconsistent history of excise tax changes in 1992-2008, to explore tobacco industry taxation strategies and tactics, and their implications for governmental revenues. Methods Details of tobacco industry policy on tobacco taxation in Ukraine were obtained by searching tobacco industry internal documents and various published reports. Results Even before entering the market in Ukraine, TTCs had made efforts to change the excise system in the country. In 1993-1994, TTCs lobbied the Ukrainian Government, and succeeded in achieving a lowering in tobacco tax. This, however, did not produce revenue increase they promised the Government. In 1996-1998, Ukrainian authorities increased excise several times, ignoring the wishes of TTCs, caused significant growth in revenue. Due to TTCs lobbying activities in 1999-2007 the tax increases were very moderate and it resulted in increased tobacco consumption in Ukraine. In 2008, despite the TTCs position, excise rates were increased twice and it was very beneficial for revenues. Conclusions The Framework Convention on Tobacco Control includes provisions both on tobacco taxation policy and on protection of public health policy from vested interests of tobacco industry. This paper provides arguments why tobacco taxation policy should also be protected from vested interests of tobacco industry. TTCs taxation strategy appears to be consistent: keep excise as low as possible. Apparent conflicts between TTCs concerning tax structures often hide their real aim to change tax structures for competing interests without increasing total tax incidence. Governments, that aim to reduce levels of

  13. "The lobbying strategy is to keep excise as low as possible" - tobacco industry excise taxation policy in Ukraine.

    Science.gov (United States)

    Krasovsky, Konstantin S

    2010-08-31

    Tobacco taxes are one of the most effective ways to reduce tobacco use. Transnational tobacco companies (TTCs) claim they wish to develop and secure excise systems that benefit both governments and the profitability of the companies themselves. The objective of the paper is to use the case of Ukraine, with its inconsistent history of excise tax changes in 1992-2008, to explore tobacco industry taxation strategies and tactics, and their implications for governmental revenues. Details of tobacco industry policy on tobacco taxation in Ukraine were obtained by searching tobacco industry internal documents and various published reports. Even before entering the market in Ukraine, TTCs had made efforts to change the excise system in the country. In 1993-1994, TTCs lobbied the Ukrainian Government, and succeeded in achieving a lowering in tobacco tax. This, however, did not produce revenue increase they promised the Government. In 1996-1998, Ukrainian authorities increased excise several times, ignoring the wishes of TTCs, caused significant growth in revenue. Due to TTCs lobbying activities in 1999-2007 the tax increases were very moderate and it resulted in increased tobacco consumption in Ukraine. In 2008, despite the TTCs position, excise rates were increased twice and it was very beneficial for revenues. The Framework Convention on Tobacco Control includes provisions both on tobacco taxation policy and on protection of public health policy from vested interests of tobacco industry. This paper provides arguments why tobacco taxation policy should also be protected from vested interests of tobacco industry. TTCs taxation strategy appears to be consistent: keep excise as low as possible. Apparent conflicts between TTCs concerning tax structures often hide their real aim to change tax structures for competing interests without increasing total tax incidence. Governments, that aim to reduce levels of tobacco use, should not allow tobacco companies to influence the

  14. Changes of cytokinin nucleotides in an anise cell culture (Pimpinella anisum L.) during growth and embryogenesis.

    Science.gov (United States)

    Ernst, D; Oesterhelt, D

    1985-05-01

    Endogenous levels of cytokinin nucleotides in an anise cell culture were determined during proembryonal, as well as embryonal development. In both cultures the maximum level of isopentenyladenine nucleotides was found during the first four days of incubation which correlated with the beginning of logarithmic growth (embryonal: 8 ng g(-1) tresh weight; proembryonal: 17.4 ng g(-1) fresh weight). The concentration of zeatin nucleotides remained constant at a very low level. The present data and those of Ernst et al. (1984) and Ernst and Oesterhelt (1984) are concerned in ascribing a major role to cytokinins in cell division, but not in embryo differentiation.

  15. Structural basis of HIV-1 resistance to AZT by excision

    Energy Technology Data Exchange (ETDEWEB)

    Tu, Xiongying; Das, Kalyan; Han, Qianwei; Bauman, Joseph D.; Clark, Jr., Arthur D.; Hou, Xiaorong; Frenkel, Yulia V.; Gaffney, Barbara L.; Jones, Roger A.; Boyer, Paul L.; Hughes, Stephen H.; Sarafianos, Stefan G.; Arnold, Eddy (Rutgers); (Clark); (NCI)

    2011-11-23

    Human immunodeficiency virus (HIV-1) develops resistance to 3'-azido-2',3'-deoxythymidine (AZT, zidovudine) by acquiring mutations in reverse transcriptase that enhance the ATP-mediated excision of AZT monophosphate from the 3' end of the primer. The excision reaction occurs at the dNTP-binding site, uses ATP as a pyrophosphate donor, unblocks the primer terminus and allows reverse transcriptase to continue viral DNA synthesis. The excision product is AZT adenosine dinucleoside tetraphosphate (AZTppppA). We determined five crystal structures: wild-type reverse transcriptase-double-stranded DNA (RT-dsDNA)-AZTppppA; AZT-resistant (AZTr; M41L D67N K70R T215Y K219Q) RT-dsDNA-AZTppppA; AZTr RT-dsDNA terminated with AZT at dNTP- and primer-binding sites; and AZTr apo reverse transcriptase. The AMP part of AZTppppA bound differently to wild-type and AZTr reverse transcriptases, whereas the AZT triphosphate part bound the two enzymes similarly. Thus, the resistance mutations create a high-affinity ATP-binding site. The structure of the site provides an opportunity to design inhibitors of AZT-monophosphate excision.

  16. Base excision repair of 8-oxoG in dinucleosomes

    NARCIS (Netherlands)

    H. Menoni (Hervé); M.S. Shukla (Manu Shubhdarshan); V. Gerson (Véronique); S. Dimitrov (Stefan); D. Angelov (Dimitar)

    2012-01-01

    textabstractIn this work we have studied the effect of chromatin structure on the base excision repair (BER) efficiency of 8-oxoG. As a model system we have used precisely positioned dinucleosomes assembled with linker histone H1. A single 8-oxoG was inserted either in the linker or the core particl

  17. Elbow joint kinematics after excision of the radial head

    DEFF Research Database (Denmark)

    Jensen, Steen Lund; Olsen, Bo Sanderhoff; Søjbjerg, Jens Ole

    1999-01-01

    The contribution of the radial head to elbow joint kinematics was studied in 7 osteoligamentous elbow preparations. During unloaded flexion and extension, radial head excision induced a maximum varus displacement of 1.6 degrees with 20 degrees of joint flexion and a maximum external rotation of 3...

  18. 76 FR 46677 - Indoor Tanning Services; Cosmetic Services Excise Taxes

    Science.gov (United States)

    2011-08-03

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF THE TREASURY Internal Revenue Service 26 CFR Parts 40 and 49 RIN 1545-BJ40 Indoor Tanning Services; Cosmetic Services Excise Taxes AGENCY: Internal Revenue Service (IRS), Treasury. ACTION: Notice of public hearing...

  19. Targeting base excision repair as a sensitization strategy in radiotherapy.

    NARCIS (Netherlands)

    Vens, C.; Begg, A.C.

    2010-01-01

    Cellular DNA repair determines survival after ionizing radiation. Human tumors commonly exhibit aberrant DNA repair since they drive mutagenesis and chromosomal instability. Recent reports have shown alterations in the base excision repair (BER) and single strand break repair (SSBR) pathways in huma

  20. A Rat Excised Larynx Model of Vocal Fold Scar

    Science.gov (United States)

    Welham, Nathan V.; Montequin, Douglas W.; Tateya, Ichiro; Tateya, Tomoko; Choi, Seong Hee; Bless, Diane M.

    2009-01-01

    Purpose: To develop and evaluate a rat excised larynx model for the measurement of acoustic, aerodynamic, and vocal fold vibratory changes resulting from vocal fold scar. Method: Twenty-four 4-month-old male Sprague-Dawley rats were assigned to 1 of 4 experimental groups: chronic vocal fold scar, chronic vocal fold scar treated with 100-ng basic…

  1. Excise Taxes and the Price Elasticity of Demand.

    Science.gov (United States)

    Gamble, Ralph C., Jr.

    1989-01-01

    Points out that, although the analysis of the imposition of an excise tax is widely used in economics courses, the consequences of a change in the tax rate are different and ignored. This article presents an effective way to teach about such a change. (GG)

  2. Excise Taxes and the Price Elasticity of Demand.

    Science.gov (United States)

    Gamble, Ralph C., Jr.

    1989-01-01

    Points out that, although the analysis of the imposition of an excise tax is widely used in economics courses, the consequences of a change in the tax rate are different and ignored. This article presents an effective way to teach about such a change. (GG)

  3. The effect of phosphours and water deficit on phosphatase activity and proline accumulation in seedling cotyledons and roots of oilseed rape as compared to that of excised cotyledons and roots

    Directory of Open Access Journals (Sweden)

    Stanisław Flasiński

    2014-01-01

    Full Text Available Oilseed rape seedlings and excised cotyledons and roots were exposed to phosphorus and osmotic stress (-1 MPa: NaCl or PEG. The stress factors limited the growth of the seedlings and inhibited the growth of the excised roots and cotyledons. The phosphorus content in the cotyledons and roots depended on its level in the media and on the stress factors used. Phosphorus deficiency differentiated total phosphatase activity in seedling cotyledons and increased the activity in the excised cotyledons. In the excised and seedling roots, the lack of phosphorus, its deficiency and stress imposed by the addition of NaCl, caused an increase in total and specific phosphatase activity. Osmotic stress caused proline accumulation in both the seedling and excised cotyledons, but the effect of phosphorus stress was much smaller. Proline increase in seedling roots followed only after the osmotic stress caused by NaCl. The proline content in the excised roots was low. Stress factors lowered the protein content in the seedling and excised cotyledons. In both seedling and excised roots, the lowering of the protein content occurred mainly in response to osmotic stress. Kinetin modified metabolic responses in seedling cotyledons and roots. The use of in vitro culture allowed the elucidation of the tested responses. In excised cotyledons grown under stress conditions, kinetin increased the phosphorus and protein contents and lowered proline accumulation, suggesting that kinetin had the ability to overcome phosphorus and osmotic stress. The excised oilseed rape roots responded only slightly to kinetin (Drozdowska and Rogozińska 1984 and its effect was much smaller.

  4. The optimal time for early excision in major burn injury.

    Science.gov (United States)

    Muangman, Pornprom; Sullivan, Stephen R; Honari, Shari; Engrav, Lorenz H; Heimbach, David M; Gibran, Nicole S

    2006-01-01

    Early excision and grafting (E&G) drastically changed burn care in America by reducing morbidity, mortality and hospital length of stay (LOS). The present study was intended to determine whether an optimal time window exists between resuscitation and wound sepsis for the first E&G in a patient with a large burn. The authors conducted a retrospective study of patients admitted between January 1994 and December 2000 with > or = 40% TBSA burns and at least 1 E&G procedure. Patients were grouped according to the day of their first operation. Patients allowed to heal indeterminate burns prior to excision and grafting of deep partial or full thickness burns were grouped as > or = d7 and were excluded from the present study. The authors correlated the time of first excision with infection, mortality and LOS. Seventy-five patients were identified and 12 patients allowed to heal indeterminate burn prior to excision and grafting of deep partial or full thickness burns were excluded. Sixty-three remaining patients included 51 males and 12 females. Mean burn size was 49% of total body surface area (TBSA) (44% deep partial or full thickness) and the mean age was 36 years. There were 61 flame (2 combined with electrical injuries), 1 scald and 1 chemical burn. Twelve died (19%) and 52 patients developed 121 infections. Whereas there was no statistical difference in mortality for patients operated on different days (p > 0.2), 60% of patients operated within the first 48 hours after injury died; this was not significant due to a small patient number The present data suggest that patients who undergo early excision and grafting within seven days following a major burn > or = 40% TBSA have equivalent infection or mortality rates regardless of when the first operation occurs between post burn day(PBD) 2 and PBD 7 (p > 0.2).

  5. Structure of fructans from excised leaves of New Zealand flax.

    Science.gov (United States)

    Sims, I M; Cairns, A J; Furneaux, R H

    2001-07-01

    The accumulation of total water-soluble carbohydrate, and specifically sucrose and fructan, by excised leaves of Phormium tenax and P. cookianum (family Phormiaceae J. G. Agardh, order Asparagales) was investigated. Total water-soluble carbohydrate content of excised leaves of P. tenax and P. cookianum increased during 48 h of continuous illumination at an average rate of 1.3 and 0.9 mg g(-1) fresh weight leaf per hour, respectively. The sucrose content of excised leaves increased throughout the experimental period. The fructan content of excised leaves of P. tenax increased slightly throughout the experimental period, whilst that of P. cookianum was variable and showed no overall change. Chemical and spectroscopic analysis of the fructans obtained from the two Phormium species showed that they were similar to each other and contained mostly 1-linked and terminal fructofuranosyl (Fruf) residues, together with smaller amounts of 6-linked Fruf, 1,6-branched Fruf, terminal and 6-linked glucopyranosyl residues. Separation of the fructans by thin-layer and high-performance anion-exchange chromatography revealed the presence of a complex mixture of fructo-oligosaccharides and higher molecular weight fructan. The branched structure of the fructans isolated from excised leaves of Phormium resembles that of fructans and fructo-oligosaccharides isolated from some related species within the order Asparagales (Agave vera cruz, Cordyline australis and Urginea maritima), but is distinct from the linear structure of fructans from others (Allium cepa and Asparagus officinalis). The structural heterogeniety of fructans within both the order Asparagales and superorder Liliiflorae may be a useful chemotaxonomic aid.

  6. Cellular Blue Nevus Diagnosed following Excision of Melanoma: A Challenge in Diagnosis

    Directory of Open Access Journals (Sweden)

    Nives Jonjić

    2016-01-01

    Full Text Available A case of a 41-year-old woman with a history of nodular melanoma (NM, associated with an indurated dome-shaped blue-black nodule with a diameter of 1.2 cm in the gluteal region, is presented. Clinical diagnosis of the lesion, present from birth, was blue nevus. Recently, the nodule has been showing a mild enlargement and thus complete resection was performed. Histological analysis revealed a pigmented lesion with an expansive pattern of extension into the dermis and the subcutaneous adipose tissue. The lesion displayed an alveolar pattern as well as a pigmented dendritic cell pattern. The histology was consistent with cellular blue nevus (CBN; however, the history of NM which was excised one year earlier, as well as the clinical information about the slow growing lesion, included a differential diagnosis of CBN, borderline melanocytic tumor, and malignant blue nevus. Additional immunohistochemical (HMB-45, p16, and Ki-67 and molecular (BRAF V600E mutation analyses were performed on both lesions: the CBN-like and the previously excised NM. Along with lesion history and histological analyses, p16 staining and BRAF were useful diagnostic tools for confirming the benign nature of CBN in this case.

  7. Spinal cord herniation following cervical meningioma excision: a rare clinical entity and review of literature.

    Science.gov (United States)

    Aiyer, Siddharth N; Shetty, Ajoy Prasad; Kanna, Rishi; Maheswaran, Anupama; Rajasekaran, S

    2016-05-01

    Spinal cord herniation following surgery is an extremely uncommon clinical condition with very few reports in published literature. This condition usually occurs as a spontaneous idiopathic phenomenon often in the thoracic spine or following a scenario of post traumatic spinal cord/nerve root injury. Rarely has it been reported following spinal cord tumor surgery. To document a case of cervical spinal cord herniation as a late onset complication following spinal cord tumor surgery with an atypical presentation of monoparesis. Case report. We describe the clinical presentation, operative procedure, post operative outcome and review of literature of this rare clinical condition. A 57-year-old man presented with right upper limb monoparesis due to a spinal cord herniation 6 years after a cervical intradural meningioma excision. The patients underwent surgery to reduce the herniation and duroplasty with subsequent complete resolution of symptoms. Spinal cord herniation must be considered as differential diagnosis in scenarios of spinal cord tumor excision presenting with late onset neurological deficit. These cases may present as paraparesis, Brown-sequard syndrome and rarely as in our case as monoparesis.

  8. Benefits of immediate dermoglandular preserving reconstruction following giant fibroadenoma excision in two patients.

    Science.gov (United States)

    Chepla, K J; Armijo, B S; Ponsky, T A; Soltanian, H T

    2011-09-01

    Giant fibroadenoma is a rare, benign stromal tumor that typically occurs in adolescent women. This rapidly-growing tumor can result in a significant aesthetic and psychosocial morbidity due to gross asymmetry changes in the overlying skin envelope and concerns about malignancy. On initial work-up this lesion must be differentiated from other rare primary breast tumors, including phyllodes tumor, or metastatic disease. Appropriate treatment of giant fibroadenoma requires surgical excision; however, many surgeons are reluctant to perform a concomitant mastopexy or reconstruction at the time of tumor extirpation. This conservative approach results in a loose, ptotic, aesthetically displeasing breast postoperatively. While some degree of skin retraction is expected, patients may have to wait for up to a year to see final results, and further surgical correction may still be required. It is unknown whether these surgeons are not familiar with these techniques or hesitate to increase the amount of scarring on the breast mound of a young female. Using an immediate dermoglandular preserving mastopexy after giant fibroadenoma excision, we have decreased postoperative breast ptosis, removed much of the lax, poor-quality skin and achieved stable, long-term results in two patients. This technique improves the immediate aesthetic outcome, reduces the psychosocial comorbidity associated with waiting for skin retraction and decreases the likelihood of a second surgery.

  9. 76 FR 52862 - Time for Payment of Certain Excise Taxes, and Quarterly Excise Tax Payments for Small Alcohol...

    Science.gov (United States)

    2011-08-24

    ..., Surety bonds, Virgin Islands, Warehouses. 27 CFR Part 40 Cigars and cigarettes, Claims, Electronic fund... excise tax on distilled spirits, wine, beer, tobacco products, and cigarette papers and tubes, and... products, and cigarette papers and tubes. TTB's responsibilities include promulgating regulations...

  10. 76 FR 3502 - Time for Payment of Certain Excise Taxes, and Quarterly Excise Tax Payments for Small Alcohol...

    Science.gov (United States)

    2011-01-20

    ..., wine, beer, tobacco products, and cigarette papers and tubes, and also reissues temporary regulations... of distilled spirits, wine, beer, tobacco products, and cigarette papers and tubes. TTB's... method for payment of the applicable excise taxes. See 26 U.S.C. 5061 pertaining to distilled...

  11. Nucleotide Selectivity in Abiotic RNA Polymerization Reactions

    Science.gov (United States)

    Coari, Kristin M.; Martin, Rebecca C.; Jain, Kopal; McGown, Linda B.

    2017-09-01

    In order to establish an RNA world on early Earth, the nucleotides must form polymers through chemical rather than biochemical reactions. The polymerization products must be long enough to perform catalytic functions, including self-replication, and to preserve genetic information. These functions depend not only on the length of the polymers, but also on their sequences. To date, studies of abiotic RNA polymerization generally have focused on routes to polymerization of a single nucleotide and lengths of the homopolymer products. Less work has been done the selectivity of the reaction toward incorporation of some nucleotides over others in nucleotide mixtures. Such information is an essential step toward understanding the chemical evolution of RNA. To address this question, in the present work RNA polymerization reactions were performed in the presence of montmorillonite clay catalyst. The nucleotides included the monophosphates of adenosine, cytosine, guanosine, uridine and inosine. Experiments included reactions of mixtures of an imidazole-activated nucleotide (ImpX) with one or more unactivated nucleotides (XMP), of two or more ImpX, and of XMP that were activated in situ in the polymerization reaction itself. The reaction products were analyzed using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to identify the lengths and nucleotide compositions of the polymerization products. The results show that the extent of polymerization, the degree of heteropolymerization vs. homopolymerization, and the composition of the polymeric products all vary among the different nucleotides and depend upon which nucleotides and how many different nucleotides are present in the mixture.

  12. Nucleotide Selectivity in Abiotic RNA Polymerization Reactions

    Science.gov (United States)

    Coari, Kristin M.; Martin, Rebecca C.; Jain, Kopal; McGown, Linda B.

    2017-02-01

    In order to establish an RNA world on early Earth, the nucleotides must form polymers through chemical rather than biochemical reactions. The polymerization products must be long enough to perform catalytic functions, including self-replication, and to preserve genetic information. These functions depend not only on the length of the polymers, but also on their sequences. To date, studies of abiotic RNA polymerization generally have focused on routes to polymerization of a single nucleotide and lengths of the homopolymer products. Less work has been done the selectivity of the reaction toward incorporation of some nucleotides over others in nucleotide mixtures. Such information is an essential step toward understanding the chemical evolution of RNA. To address this question, in the present work RNA polymerization reactions were performed in the presence of montmorillonite clay catalyst. The nucleotides included the monophosphates of adenosine, cytosine, guanosine, uridine and inosine. Experiments included reactions of mixtures of an imidazole-activated nucleotide (ImpX) with one or more unactivated nucleotides (XMP), of two or more ImpX, and of XMP that were activated in situ in the polymerization reaction itself. The reaction products were analyzed using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to identify the lengths and nucleotide compositions of the polymerization products. The results show that the extent of polymerization, the degree of heteropolymerization vs. homopolymerization, and the composition of the polymeric products all vary among the different nucleotides and depend upon which nucleotides and how many different nucleotides are present in the mixture.

  13. PID comes full circle: Applications of V(DJ recombination excision circles in research, diagnostics and newborn screening of primary immunodeficiency disorders

    Directory of Open Access Journals (Sweden)

    Menno C. Van Zelm

    2011-05-01

    Full Text Available The vast majority of patients suffering from a primary immunodeficiency (PID have defects in their T- and/or B-cell compartments. Despite advances in molecular diagnostics, in many patients no underlying genetic defect has been identified. B- and T-lymphocytes are unique in their ability to create a receptor by genomic rearrangement of their antigen receptor genes via V(DJ recombination. During this process, stable circular excision products are formed that do not replicate when the cell proliferates. Excision circles can be reliably quantified using real-time quantitative (RQ-PCR techniques. Frequently occurring δREC–ψJα T-cell receptor excision circles (TRECs have been used to assess thymic output and intronRSS–Kde recombination excision circles (KREC to quantify B-cell replication history. In this perspective, we describe how TRECs and KRECs are formed during precursor- T and B cell differentiation, respectively. Furthermore, we discuss new insights obtained with TRECs and KRECs and specifically how these excision circles can be applied to support therapy monitoring, patient classification and newborn screening of PID.

  14. Robotic transanal total mesorectal excision for rectal cancer: experience with a first case

    NARCIS (Netherlands)

    Verheijen, P.M.; Consten, E.C.J.; Broeders, I.A.M.J.

    2014-01-01

    Background: A transanal approach for total mesorectal excision (TME) using a single incision port is feasible. The disadvantages are technical difficulties associated with limited manoeuvrability. Methods: We present our first experience with robotic-assisted transanal total mesorectal excision.

  15. Sublingual nucleotides and immune response to exercise

    Directory of Open Access Journals (Sweden)

    Ostojic Sergej M

    2012-07-01

    Full Text Available Abstract Evidence exists regarding the potential role of exogenous nucleotides as regulators of the immune function in physically active humans, yet the potential use of nucleotides has been hindered by their low bioavailability after oral administration. We conducted a double-blind, placebo-controlled, randomized trial to assess the effect of sublingual nucleotides (50 mg/day on salivary and serum immunity indicators as compared to placebo, both administered to healthy males aged 20 to 25 years for 14 days. Sublingual administration of nucleotides for 14 days increased serum immunoglobulin A, natural killer cells count and cytotoxic activity, and offset the post-exercise drop of salivary immunoglobulins and lactoferrin (P  0.05. It seems that sublingual administration of nucleotides for two weeks considerably affected immune function in healthy males.

  16. Overexpression of DNA ligase III in mitochondria protects cells against oxidative stress and improves mitochondrial DNA base excision repair

    DEFF Research Database (Denmark)

    Akbari, Mansour; Keijzers, Guido; Maynard, Scott

    2014-01-01

    slower than the preceding mitochondrial BER steps. Overexpression of DNA ligase III in mitochondria improved the rate of overall BER, increased cell survival after menadione induced oxidative stress and reduced autophagy following the inhibition of the mitochondrial electron transport chain complex I...... by rotenone. Our results suggest that the amount of DNA ligase III in mitochondria may be critical for cell survival following prolonged oxidative stress, and demonstrate a functional link between mitochondrial DNA damage and repair, cell survival upon oxidative stress, and removal of dysfunctional......Base excision repair (BER) is the most prominent DNA repair pathway in human mitochondria. BER also results in a temporary generation of AP-sites, single-strand breaks and nucleotide gaps. Thus, incomplete BER can result in the generation of DNA repair intermediates that can disrupt mitochondrial...

  17. An unprecedented nucleic acid capture mechanism for excision of DNA damage

    Energy Technology Data Exchange (ETDEWEB)

    Rubinson, Emily H.; Prakasha Gowda, A.S.; Spratt, Thomas E.; Gold, Barry; Eichmanbrand, Brandt F. (Pitt); (Vanderbilt); (Penn)

    2010-11-18

    DNA glycosylases that remove alkylated and deaminated purine nucleobases are essential DNA repair enzymes that protect the genome, and at the same time confound cancer alkylation therapy, by excising cytotoxic N3-methyladenine bases formed by DNA-targeting anticancer compounds. The basis for glycosylase specificity towards N3- and N7-alkylpurines is believed to result from intrinsic instability of the modified bases and not from direct enzyme functional group chemistry. Here we present crystal structures of the recently discovered Bacillus cereus AlkD glycosylase in complex with DNAs containing alkylated, mismatched and abasic nucleotides. Unlike other glycosylases, AlkD captures the extrahelical lesion in a solvent-exposed orientation, providing an illustration for how hydrolysis of N3- and N7-alkylated bases may be facilitated by increased lifetime out of the DNA helix. The structures and supporting biochemical analysis of base flipping and catalysis reveal how the HEAT repeats of AlkD distort the DNA backbone to detect non-Watson-Crick base pairs without duplex intercalation.

  18. Mammalian Base Excision Repair: Functional Partnership between PARP-1 and APE1 in AP-Site Repair.

    Directory of Open Access Journals (Sweden)

    Rajendra Prasad

    Full Text Available The apurinic/apyrimidinic- (AP- site in genomic DNA arises through spontaneous base loss and base removal by DNA glycosylases and is considered an abundant DNA lesion in mammalian cells. The base excision repair (BER pathway repairs the AP-site lesion by excising and replacing the site with a normal nucleotide via template directed gap-filling DNA synthesis. The BER pathway is mediated by a specialized group of proteins, some of which can be found in multiprotein complexes in cultured mouse fibroblasts. Using a DNA polymerase (pol β immunoaffinity-capture technique to isolate such a complex, we identified five tightly associated and abundant BER factors in the complex: PARP-1, XRCC1, DNA ligase III, PNKP, and Tdp1. AP endonuclease 1 (APE1, however, was not present. Nevertheless, the complex was capable of BER activity, since repair was initiated by PARP-1's AP lyase strand incision activity. Addition of purified APE1 increased the BER activity of the pol β complex. Surprisingly, the pol β complex stimulated the strand incision activity of APE1. Our results suggested that PARP-1 was responsible for this effect, whereas other proteins in the complex had no effect on APE1 strand incision activity. Studies of purified PARP-1 and APE1 revealed that PARP-1 was able to stimulate APE1 strand incision activity. These results illustrate roles of PARP-1 in BER including a functional partnership with APE1.

  19. Endoscopic excision of intraventricular neurocysticercosis blocking foramen of Monro bilaterally

    Science.gov (United States)

    Shah, Harshil Chimanlal; Jain, Kapil; Shah, Jaimin Kiran

    2016-01-01

    Neurocysticercosis (NCC) is a parasitic infestation of the central nervous system. NCC parasitic infestation can be misdiagnosed as hydatid cyst or intraventricular epidermoid cyst that can cause a diagnostic dilemma. A 23-year-old male patient presented with headache and vomiting for 3–4 days and giddiness for 4–5 days. Magnetic resonance imaging with contrast was suggestive of a rim-enhancing lesion at the level of the foramen of Monro. Endoscopic excision of the lesion was done, and the patient had relief of a headache and vomiting immediately after the procedure. He is being followed up regularly. Intraventricular NCC occluding both foramen of Monro is a rare entity. Complete endoscopic surgical excision followed by appropriate drug therapy should be given to achieve a cure. PMID:27057236

  20. T1a glottic cancers may be removed by "cold steel" excision biopsies

    DEFF Research Database (Denmark)

    Melchiors, Jacob; Tvedskov, Jesper; Kristensen, Claus Andrup

    2013-01-01

    Phonosurgical excision biopsies are gradually replacing traditional punch biopsies during direct lar-yngoscopy. As excision aims at removing all pathologic tissue, some malignant lesions may be completely removed. We present our experience with phonosurgical excision biopsies of T1a glottic cance...

  1. 77 FR 37838 - Disregarded Entities and the Indoor Tanning Services Excise Tax

    Science.gov (United States)

    2012-06-25

    ... Services Excise Tax AGENCY: Internal Revenue Service (IRS), Treasury. ACTION: Notice of proposed rulemaking... (including qualified subchapter S subsidiaries) and the indoor tanning services excise tax. These regulations affect disregarded entities responsible for collecting the indoor tanning services excise tax and...

  2. Successful treatment of recurrent epididymo-orchitis: Laparoscopic excision of the prostatic utricle

    Directory of Open Access Journals (Sweden)

    Jiwane Ashish

    2009-01-01

    Full Text Available Prostatic utricle presenting with recurrent epididymo-orchitis is not uncommon. Excision of prostatic utricle is the treatment of choice. The various techniques described in literature suffer from the disadvantages of incomplete excision due to poor view. We report the successful laparoscopic excision of prostatic utricle in childhood.

  3. 29 CFR 779.263 - Excise taxes not at the retail level.

    Science.gov (United States)

    2010-07-01

    ... 29 Labor 3 2010-07-01 2010-07-01 false Excise taxes not at the retail level. 779.263 Section 779... Coverage Excise Taxes § 779.263 Excise taxes not at the retail level. There are also a wide variety of taxes levied at the manufacturer's or distributor's level and not at the retail level. It should...

  4. Envisioning the molecular choreography of DNA base excision repair.

    Science.gov (United States)

    Parikh, S S; Mol, C D; Hosfield, D J; Tainer, J A

    1999-02-01

    Recent breakthroughs integrate individual DNA repair enzyme structures, biochemistry and biology to outline the structural cell biology of the DNA base excision repair pathways that are essential to genome integrity. Thus, we are starting to envision how the actions, movements, steps, partners and timing of DNA repair enzymes, which together define their molecular choreography, are elegantly controlled by both the nature of the DNA damage and the structural chemistry of the participating enzymes and the DNA double helix.

  5. Targeted gene deletions in C. elegans using transposon excision

    Science.gov (United States)

    Frøkjær-Jensen, Christian; Davis, M. Wayne; Hollopeter, Gunther; Taylor, Jon; Harris, Todd; Nix, Paola; Lofgren, Rachel; Prestgard-Duke, Michael; Bastiani, Michael; Moerman, Donald G.; Jorgensen, Erik M.

    2010-01-01

    We have developed a method, MosDel, to generate targeted knock-outs of genes in C. elegans. We make use of the Mos1 transposase to excise a Mos1 transposon adjacent to the region to be deleted. The double-strand break is repaired using injected DNA as a template. Repair can delete up to 25 kb of DNA and simultaneously insert a positive selection marker. PMID:20418868

  6. Excise Tax Overshifting in the Hungarian Beer Market

    OpenAIRE

    Bakó, Barna; Berezvai, Zombor

    2013-01-01

    We conduct this paper on excise tax shifting in the Hungarian beer market. Using a regression model we show that tax overshifting occurs in this market. We present a model with oligopolistic competition to explain how tax overshifting can occur because of the separated vertical structure. Our results suggests that Hungarian beer producers compete in Bertrand fashion and the hypothesis of collusion between beer producers can be rejected.

  7. Nucleic acids and survival of excised anthers in vitro.

    Science.gov (United States)

    VASIL, I K

    1959-05-29

    Excised anthers of Allium cepa and Rhoeo discolor have been successfully cultured in modified White's medium supplemented with various concentrations of ribonucleic acid and deoxyribonucleic acid. Ribonucleic acid proved to be much more useful than deoxyribonucleic acid and reduced the time required for the completion of meiosis from 48 hours to 24 hours. The role of nucleic acids in the control of nuclear divisions has been indicated.

  8. Do alcohol excise taxes affect traffic accidents? Evidence from Estonia.

    Science.gov (United States)

    Saar, Indrek

    2015-01-01

    This article examines the association between alcohol excise tax rates and alcohol-related traffic accidents in Estonia. Monthly time series of traffic accidents involving drunken motor vehicle drivers from 1998 through 2013 were regressed on real average alcohol excise tax rates while controlling for changes in economic conditions and the traffic environment. Specifically, regression models with autoregressive integrated moving average (ARIMA) errors were estimated in order to deal with serial correlation in residuals. Counterfactual models were also estimated in order to check the robustness of the results, using the level of non-alcohol-related traffic accidents as a dependent variable. A statistically significant (P traffic accidents was disclosed under alternative model specifications. For instance, the regression model with ARIMA (0, 1, 1)(0, 1, 1) errors revealed that a 1-unit increase in the tax rate is associated with a 1.6% decrease in the level of accidents per 100,000 population involving drunk motor vehicle drivers. No similar association was found in the cases of counterfactual models for non-alcohol-related traffic accidents. This article indicates that the level of alcohol-related traffic accidents in Estonia has been affected by changes in real average alcohol excise taxes during the period 1998-2013. Therefore, in addition to other measures, the use of alcohol taxation is warranted as a policy instrument in tackling alcohol-related traffic accidents.

  9. Nucleotide Salvage Deficiencies, DNA Damage and Neurodegeneration

    Directory of Open Access Journals (Sweden)

    Michael Fasullo

    2015-04-01

    Full Text Available Nucleotide balance is critically important not only in replicating cells but also in quiescent cells. This is especially true in the nervous system, where there is a high demand for adenosine triphosphate (ATP produced from mitochondria. Mitochondria are particularly prone to oxidative stress-associated DNA damage because nucleotide imbalance can lead to mitochondrial depletion due to low replication fidelity. Failure to maintain nucleotide balance due to genetic defects can result in infantile death; however there is great variability in clinical presentation for particular diseases. This review compares genetic diseases that result from defects in specific nucleotide salvage enzymes and a signaling kinase that activates nucleotide salvage after DNA damage exposure. These diseases include Lesch-Nyhan syndrome, mitochondrial depletion syndromes, and ataxia telangiectasia. Although treatment options are available to palliate symptoms of these diseases, there is no cure. The conclusions drawn from this review include the critical role of guanine nucleotides in preventing neurodegeneration, the limitations of animals as disease models, and the need to further understand nucleotide imbalances in treatment regimens. Such knowledge will hopefully guide future studies into clinical therapies for genetic diseases.

  10. Nucleotides and inorganic phosphates as potential antioxidants.

    Science.gov (United States)

    Richter, Yael; Fischer, Bilha

    2006-11-01

    Highly reactive OH radicals, formed in an iron-ion catalyzed Fenton reaction, are implicated in many pathological conditions. The quest for Fenton reaction inhibitors, either radical scavenger or metal-ion chelator antioxidants, spans the previous decades. Purine nucleotides were previously studied as natural modulators of the Fenton reaction; however, the modulatory role of purine nucleotides remained in dispute. Here, we have resolved this long-standing dispute and demonstrated a concentration-dependent biphasic modulation of the Fenton reaction by nucleotides. By electron spin resonance measurements with 0.1 mM Fe(II), we observed an increase of *OH production at low purine nucleotide concentrations (up to 0.15 mM), while at higher nucleotide concentrations, an exponential decay of *OH concentration was observed. We found that the phosphate moiety, not the nucleoside, determines the pro/antioxidant properties of a nucleotide, suggesting a chelation-based modulation. Furthermore, the biphasic modulation mode is probably due to diverse nucleotide-Fe(II) complexes formed in a concentration-dependent manner. At ATP concentrations much greater than Fe(II) concentrations, multiligand chelates are formed which inhibit the Fenton reaction owing to a full Fe(II) coordination sphere. In addition to natural nucleotides, we investigated a series of base- or phosphate-modified nucleotides, dinucleotides, and inorganic phosphates, as potential biocompatible antioxidants. Ap5A, inorganic thiophosphate and ATP-gamma-S proved highly potent antioxidants with IC50 values of 40, 30, and 10 microM, respectively. ATP-gamma-S proved 100 and 20 times more active than ATP and the potent antioxidant Trolox, respectively. In the presence of 30 microM ATP-gamma-S no *OH was detected after 5 min in the Fenton reaction mixture. The most potent antioxidants identified inhibit the Fenton reaction by forming full coordination sphere chelates.

  11. Excision of an 11-kilobase-pair DNA element from within the nifD gene in anabaena variabilis heterocysts.

    Science.gov (United States)

    Brusca, J S; Hale, M A; Carrasco, C D; Golden, J W

    1989-01-01

    The 3' region of the Anabaena variabilis nifD gene contains an 11-kilobase-pair element which is excised from the chromosome during heterocyst differentiation. We have sequenced the recombination sites which border the element in vegetative cells and the rearranged heterocyst sequences. In vegetative cells, the element was flanked by 11-base-pair direct repeats which were identical to the repeats present at the ends of the nifD element in Anabaena sp. strain PCC 7120 (Anabaena strain 7120). Although Anabaena strain 7120 and A. variabilis are quite distinct in many ways, the overall sequence similarity between the two strains for the regions sequenced was 96%. Like the Anabaena strain 7120 element, the A. variabilis element was excised in heterocysts to produce a functional nifD gene and a free circularized element which was neither amplified nor degraded. The Anabaena strain 7120 xisA gene is located at the nifK-proximal end of the nifD element and is required for excision of the element in heterocysts. The A. variabilis element also contained an xisA gene which could complement a defective Anabaena strain 7120 xisA gene. A. variabilis did not contain the equivalent of the Anabaena strain 7120 fdxN 55-kilobase-pair element. Images PMID:2502534

  12. Efficient fidelity control by stepwise nucleotide selection in polymerase elongation

    CERN Document Server

    Yu, Jin

    2014-01-01

    Polymerases select nucleotides before incorporating them for chemical synthesis during gene replication or transcription. How the selection proceeds stepwise efficiently to achieve sufficiently high fidelity and speed is essential for polymerase function. We examined step-by-step selections that have conformational transition rates tuned one at time in the polymerase elongation cycle, with a controlled differentiation free energy at each checkpoint. The elongation is sustained at non-equilibrium steady state with constant free energy input and heat dissipation. It is found that error reduction capability does not improve for selection checkpoints down the reaction path. Hence, it is essential to select early to achieve an efficient fidelity control. In particular, for two consecutive selections that reject the wrong substrate back and inhibit it forward from a same kinetic state, the same error rates are obtained at the same free energy differentiation. The initial screening is indispensible for maintaining t...

  13. Effects of nucleotides and nucleosides on coagulation

    DEFF Research Database (Denmark)

    Bune, Laurids; Thaning, Pia; Johansson, Pär I;

    2010-01-01

    Nucleotides, including ADP, ATP and uridine triphosphate (UTP), are discharged profusely in the circulation during many pathological conditions including sepsis. Sepsis can cause hypotension and systemic activation of the coagulation and fibrinolytic systems in humans, which may cause disseminated...... intravascular coagulation. We investigated whether nucleotide-induced cardiovascular collapse as provoked by systemic infusion of adenosine, ADP, ATP, UTP and nitric oxide affected the haemostatic system as assessed by whole blood thromboelastography (TEG) analysis. Ten pigs received a randomized infusion...

  14. Estimating the effect of human base excision repair protein variants on the repair of oxidative DNA base damage.

    Science.gov (United States)

    Sokhansanj, Bahrad A; Wilson, David M

    2006-05-01

    Epidemiologic studies have revealed a complex association between human genetic variance and cancer risk. Quantitative biological modeling based on experimental data can play a critical role in interpreting the effect of genetic variation on biochemical pathways relevant to cancer development and progression. Defects in human DNA base excision repair (BER) proteins can reduce cellular tolerance to oxidative DNA base damage caused by endogenous and exogenous sources, such as exposure to toxins and ionizing radiation. If not repaired, DNA base damage leads to cell dysfunction and mutagenesis, consequently leading to cancer, disease, and aging. Population screens have identified numerous single-nucleotide polymorphism variants in many BER proteins and some have been purified and found to exhibit mild kinetic defects. Epidemiologic studies have led to conflicting conclusions on the association between single-nucleotide polymorphism variants in BER proteins and cancer risk. Using experimental data for cellular concentration and the kinetics of normal and variant BER proteins, we apply a previously developed and tested human BER pathway model to (i) estimate the effect of mild variants on BER of abasic sites and 8-oxoguanine, a prominent oxidative DNA base modification, (ii) identify ranges of variation associated with substantial BER capacity loss, and (iii) reveal nonintuitive consequences of multiple simultaneous variants. Our findings support previous work suggesting that mild BER variants have a minimal effect on pathway capacity whereas more severe defects and simultaneous variation in several BER proteins can lead to inefficient repair and potentially deleterious consequences of cellular damage.

  15. Russian decree on excise duty on petroleum extraction, ukase on excise tax on mineral users and decree on improving free trade in Russia. Export trade information

    Energy Technology Data Exchange (ETDEWEB)

    1992-09-01

    The decree defines the rates for an excise duty included in the price for petroleum and gas condensate in Russia; how the excise duty is to be paid to the Russian Federation budget when petroleum and gas condensate are sold; and maximum levels of profitability in the production of all types of petroleum products.

  16. Female urogenital dysfunction following total mesorectal excision for rectal cancer

    Directory of Open Access Journals (Sweden)

    Raja Ashraf

    2006-01-01

    Full Text Available Abstract Background The effect of Total Mesorectal Excision (TME on sexual function in the male is well documented. However, there is little literature in female patients. The aim of this study was to review the pelvic autonomic nervous anatomy in the female and to perform a retrospective audit of urinary and sexual function in women following surgery for rectal cancer where TME had been performed. Urogenital dysfunction was assessed through interview and questionnaire. Method Twenty-three questionnaires, eighteen returned, were sent to women with a mean age 65.5 yrs (range 34–86. All had undergone total mesorectal excision for rectal cancer between 1998–2001. Mean follow-up was 18.8 months (range 3–35. Results Preoperatively 5/18 (28% were sexually active, 3/18 (17% of patients described urinary frequency and nocturia and 7/18 (39% described symptoms of stress incontinence prior to surgery. Postoperatively all sexually active patients remained active although all described some discomfort with penetration. Two of the patients sexually active described reduced libido secondary to the stoma. Postoperative urinary symptoms developed with 59% reporting the development of nocturia, 18% developed stress incontinence and one patient required a permanent catheter. Of those with symptoms, 80% persisted longer than three months from surgery. Symptoms were predominant in those patients with low rectal cancers, particularly those undergoing abdomino-perineal excision and in those who had previously undergone abdominal hysterectomy. Conclusion The treatment of rectal cancer involves surgery to the pelvic floor. Despite nerve preservation this is associated with the development of worsening nocturia and stress incontinence. This is most marked in those patients who had previously undergone a hysterectomy. Further studies are warranted to assess the interaction with previous gynaecological surgery.

  17. Excised Abdominoplasty Material as a Systematic Plastic Surgical Training Model

    Directory of Open Access Journals (Sweden)

    M. Erol Demirseren

    2012-01-01

    Full Text Available Achieving a level of technical skill and confidence in surgical operations is the main goal of plastic surgical training. Operating rooms were accepted as the practical teaching venues of the traditional apprenticeship model. However, increased patient population, time, and ethical and legal considerations made preoperation room practical work a must for plastic surgical training. There are several plastic surgical teaching models and simulators which are very useful in preoperation room practical training and the evaluation of plastic surgery residents. The full thickness skin with its vascular network excised in abdominoplasty procedures is an easily obtainable real human tissue which could be used as a training model in plastic surgery.

  18. [Alternative therapeutic excision of intraepithelial conjunctival carcinoma with corneal extension].

    Science.gov (United States)

    Zemba, M; Stamate, Alina-Cristina; Avram, Corina Ioana; Sîrbu, Laura Nicoleta Urucu; Camburu, Raluca Lăcrămioara; Ochinciuc, Uliana; Burcea, M

    2013-01-01

    Surgical treatment for conjunctival neoplasms, with wide local excision, with or without supplemental cryotherapy to the surgical margins represents the treatment of choice for this pathology. In some cases, these neoplasms can be diffuse or multifocal, with borders that are difficult to detect clinically, such that topical therapies offer a more efficient method for treating the entire ocular surface, delivering high drug concentrations at this level, with negligible systemic side effects. Beginning from the clinical case of a patient diagnosed with conjunctival intraepithelial neoplasia, we try to present other therapeutical alternatives, although in this case the therapeutical approach was the classic one.

  19. Successful surgical excision of primary right atrial angiosarcoma

    Directory of Open Access Journals (Sweden)

    van der Horst Iwan CC

    2011-04-01

    Full Text Available Abstract Primary cardiac angiosarcoma is a rare and aggressive tumor with a high incidence of metastatic spread (up to 89% at the time of diagnosis, which restricts the indication for surgical resection to a small number of patients. We report the case of a 50-year old Caucasian woman with non-metastatic primary right atrial angiosarcoma, who underwent successful surgical excision of the tumor (with curative intent and reconstruction of the right atrium with a porcine pericardial patch. However, after a symptom-free survival of five months the patient presented with bone and liver metastases without evidence of local tumor recurrence.

  20. Transanal vs laparoscopic total mesorectal excision for rectal cancer

    DEFF Research Database (Denmark)

    Perdawood, Sharaf; Al Khefagie, Ghalib Ali Abod

    2016-01-01

    BACKGROUND: Laparoscopic total mesorectal excision (LaTME) has improved short-term outcomes of rectal cancer surgery with comparable oncological results to open approach. LaTME can be difficult in the lower most part of the rectum, leading potentially to higher rates of complications, conversion...... to open surgery and probably suboptimal oncological quality. Transanal TME (TaTME) can potentially solve these problems. The aim of this study was to compare the short-term results after TaTME with those after LaTME. METHODS: A prospectively collected database of consecutive patients who underwent Ta...

  1. Robot assisted laparoscopic excision of a paraganglioma: new therapeutic approach

    Directory of Open Access Journals (Sweden)

    G. Cochetti

    2014-04-01

    Full Text Available The Paraganglioma is the most common extra-adrenal pheochromocytoma arising from neural crest (1 (It will better to write: The paraganglioma is an extra-adrenal pheocromocytoma arising from the neural crest. 10% of pheocromocytomas are extra-adrenal and can arise form chromaffin tissue derived from primitive neuroectoderm. Minimally invasive techniques allow surgeons to perform the procedure without wide exposure and mobilization of intra abdominal organs. To our knowledge we present the third case of robotic excision of a retroperitoneal paraganglioma (2,3.

  2. Excision arthroplasty for management of coxofemoral luxation in pet birds.

    Science.gov (United States)

    MacCoy, D M

    1989-01-01

    Coxofemoral luxation, although not a common injury, can cause considerable pelvic limb dysfunction in pet birds. Luxation usually is craniodorsal, as it is in dogs. Previously recommended treatments have not always been effective in managing the injury. Sequelae can include dorsolateral deviation of the pelvic limb, with loss of function and bumblefoot in the nonluxated limb, owing to abnormal weight-bearing. Excision arthroplasty combined with a muscular sling constructed from a segment of the iliofibularis muscle was used to treat coxofemoral luxation in a hyacinth macaw, a moluccan cockatoo, and an African gray parrot. The outcome was excellent in 2 of the 3 birds.

  3. Cytokinin and growth of excised roots of Bryophyllum calycinum.

    Science.gov (United States)

    Robbins, W J; Hervey, A

    1971-02-01

    Excised roots of Bryophyllum calycinum require for growth both auxin and cytokinin. This is demonstrated by the poor growth of 2-mm root tips in a basal medium of mineral salts, sucrose, and vitamins supplemented with either an auxin or a cytokinin, and much better growth when the basal medium is supplemented with both auxin and cytokinin. However, both substances are synthesized by the root, as is demonstrated by the growth of large inocula (dry wt 6-7 mg) through many successive passages in a medium limited to mineral salts, sugar, and vitamins.

  4. Arthroscopic excision of spinoglenoid notch cyst through two different approaches

    Institute of Scientific and Technical Information of China (English)

    WANG Yong-jian; CUI Guo-qing

    2010-01-01

    @@ With the advent of shoulder magnetic resonance imaging (MRI), ganglion cysts adjacent to the superior labrum have been increasinglyrecognized.1-3The spinoglenoid notch cyst (SGNC) which causes suprascapular nerve compression has been well documented,3-16 and the association of superior labral anterior-posterior (SLAP) lesions with spinoglenoid cysts has gained more attention.2.5-16 Mostly, the SGNC is approached through7 the labral tear within the glenohumeral joint. Because this approach can not provide enough space to operate, normally the SGNC can only be decompressed. So we try to find approaches to expose and excise the SGNC exactly.

  5. 26 CFR 55.4981-2 - Imposition of excise tax with respect to certain undistributed income of real estate investment...

    Science.gov (United States)

    2010-04-01

    ... certain undistributed income of real estate investment trusts; calendar years beginning after December 31... (CONTINUED) MISCELLANEOUS EXCISE TAXES (CONTINUED) EXCISE TAX ON REAL ESTATE INVESTMENT TRUSTS AND REGULATED INVESTMENT COMPANIES Excise Tax on Real Estate Investment Trusts § 55.4981-2 Imposition of excise tax with...

  6. FISCAL FEATURES SPECIFIC TO INTRA-COMMUNITY TRANSACTIONS OF NEW MEANS OF TRANSPORTATION AND EXCISABLE PRODUCTS

    Directory of Open Access Journals (Sweden)

    PALIU - POPA LUCIA

    2012-06-01

    Full Text Available With a view to our country's accession to the Community space, the Romanian legislation has undergone many changes, and we should point out among others those in the tax system, that primarily aims to ensure the functioning of the national economy in the globalization of the economic and social activities worldwide. Although at first sight the new procedures have a positive impact on the development of intra-Community commercial businesses, due to the elimination of customs formalities and hence of the fees paid to customs officials, however there are costs generated by the application of EU law, which should not be neglected. Considering the many situations that arise in carrying out intra-Community commercial transactions, that are aimed at the differentiated tax procedures from the value added tax perspective, we considered appropriate, to address below the tax features related to intra-Community acquisitions and supplies of new means of transport and excisable products, because these are two important categories of goods that generate differential tax treatments, so that after the tax analysis we should be able to draw some relevant conclusions.

  7. Framing the policy debate over spirits excise tax in Poland.

    Science.gov (United States)

    Zatoński, Mateusz; Hawkins, Benjamin; McKee, Martin

    2016-12-23

    Industry lobbying remains an obstacle to effective health-oriented alcohol policy. In 2013, an increase in excise tax on spirits was announced by the Polish government. This article presents a qualitative analysis of the public debate that ensued on the potential economic, health and social effects of the policy. It focuses on how competing groups, including industry actors, framed their position and sought to dominate the debate. Online archives of five Polish national newspapers, two spirits trade associations, and parliamentary and ministerial archives were searched. A thematic content analysis of the identified sources was conducted. The overall findings were compared with existing research on the framing of the Minimum Unit Pricing (MUP) debate in the UK. A total of 155 sources were analysed. Two main frames were identified: health, and economic The spirits industry successfully promoted the economic frame in their own publications and in the media. The debate was dominated by arguments about potential growth of the grey market and losses in tax revenue that might result from the excise tax increase. The framing of the debate in Poland differed from the framing of the MUP debate in the United Kingdom. The Polish public health community was unsuccessful in making health considerations a significant element of the alcohol policy debate. The strategies pursued by UK health advocates offer lessons for how to make a more substantial impact on media coverage and promote health-oriented legislation.

  8. Simultaneous laparoscopic excision for rectal carcinoma and synchronous hepatic metastasis

    Institute of Scientific and Technical Information of China (English)

    CHEN Kai-yun; XIANG Guo-an; WANG Han-ning; XIAO Fang-lian

    2011-01-01

    Background Rectal carcinoma patients are often accompanied by hepatic metastasis. The aim of this study was to evaluate the therapeutic efficacy of simultaneous laparoscopic excision for rectal carcinoma with synchronous hepatic metastasis.Methods A total of 41 patients with rectal carcinoma and synchronous hepatic metastasis detected by CT scan were included in this study. Among them, 23 patients underwent laparoscopic surgery and 18 patients underwent traditional open surgery to simultaneously remove the rectal tumor and hepatic metastasis lesions. All patients received postoperative adjuvant chemotherapy. All the patients were followed up from 36 to 72 months (mean 45.3 months).Results All the operations were performed successfully and no patient was turned to open surgery in laparoscopic group. The mean blood loss, the mean postoperative hospital stay, the mean blood transfusion and the mean intestinal functional recovery time showed a significant difference between the two groups (P<0.05). The 1-, 3- and 5-year survival rates were 82.6%, 43.5% and 8.6% in the laparoscopic group, without significant difference compared with the open group (77.8%, 38.9% and 0) (P>0.05).Conclusions Simultaneous laparoscopic excision for rectal carcinoma and synchronous hepatic metastasis is safe and effective with similar survival achieved by the traditional open abdominal surgery.

  9. A review of wide surgical excision of hidradenitis suppurativa

    Directory of Open Access Journals (Sweden)

    Alharbi Ziyad

    2012-06-01

    Full Text Available Abstract Background Hidradenitis suppurativa (HS is a chronic inflammatory cutaneous disorder that involves the infundibular terminal follicles in areas rich of apocrine glands. It can be associated with fistulating sinus, scarring and abscesses formation. Hidradenitis suppurativa is a challenging aspect and requires a proper treatment plan which may involve different specialties. We present herein the option of surgical treatment involving wide surgical excision and methods of reconstruction as well as the rate of recurrence. Furthermore, review of the literature regarding surgical treatment of hidradenitis suppurativa is provided. Methods A retrospective analysis reviewed 50 operative procedures for 32 patients in 5 anatomical sites. These anatomical sites have been divided to 23 sites involving the axilla, 17 sites involving the inguinal region and 8 sites involving the perianal/perineal area, 1 site involving the gluteal region and 1 site involving the trunk region. Results Twenty six patients (81, 25 % showed no recurrence after surgery and the average time of hospital stay period was 5 days. Recurrence was observed only in 6 patients (18, 75 %. Conclusion Elimination of the acute inflammatory process should occur in advance, including the use of antibiotics and minor surgeries such as abscess drainage with proper irrigations. After stabilizing the acute phase, wide surgical excision is recommended. Herein, planning of surgical reconstruction should be initiated to achieve the best outcome and consequently decreasing the risk of recurrence and complications after surgery.

  10. Expression of the Anabaena sp. strain PCC 7120 xisA gene from a heterologous promoter results in excision of the nifD element.

    Science.gov (United States)

    Brusca, J S; Chastain, C J; Golden, J W

    1990-01-01

    An 11-kilobase-pair element interrupts the nifD gene in vegetative cells of Anabaena sp. strain PCC 7120. The nifD element normally excises only from the chromosomes of cells that differentiate into nitrogen-fixing heterocysts. The xisA gene contained within the element is required for the excision. Shuttle vectors containing the Escherichia coli tac consensus promoter fused to various 5' deletions of the xisA gene were constructed and conjugated into Anabaena sp. strain PCC 7120 cells. Some of the expression plasmids resulted in excision of the nifD element in a high proportion of vegetative cells. Excision of the element required deletion of an xisA 5' regulatory region which presumably blocks expression in Anabaena sp. strain PCC 7120 vegetative cells but not in E. coli. Strains lacking the nifD element grew normally in medium containing a source of combined nitrogen and showed normal growth and heterocyst development in medium lacking combined nitrogen. The xisA gene was shown to be the only Anabaena gene required for the proper rearrangement in E. coli of a plasmid containing the borders of the nifD element. Images PMID:2113913

  11. Design and synthesis of ATP-based nucleotide analogues and profiling of nucleotide-binding proteins

    NARCIS (Netherlands)

    Wolters, Justina. C.; Roelfes, Gerard; Poolman, Bert

    2011-01-01

    Two nucleotide-based probes were designed and synthesized in order to enrich samples for specific classes of proteins by affinity-based protein profiling. We focused on the profiling of adenine nucleotide-binding proteins. Two properties were considered in the design of the probes: the bait needs to

  12. Design and synthesis of ATP-based nucleotide analogues and profiling of nucleotide-binding proteins

    NARCIS (Netherlands)

    Wolters, Justina. C.; Roelfes, Gerard; Poolman, Bert

    Two nucleotide-based probes were designed and synthesized in order to enrich samples for specific classes of proteins by affinity-based protein profiling. We focused on the profiling of adenine nucleotide-binding proteins. Two properties were considered in the design of the probes: the bait needs to

  13. The International Nucleotide Sequence Database Collaboration

    Science.gov (United States)

    Cochrane, Guy; Karsch-Mizrachi, Ilene; Takagi, Toshihisa; Sequence Database Collaboration, International Nucleotide

    2016-01-01

    The International Nucleotide Sequence Database Collaboration (INSDC; http://www.insdc.org) comprises three global partners committed to capturing, preserving and providing comprehensive public-domain nucleotide sequence information. The INSDC establishes standards, formats and protocols for data and metadata to make it easier for individuals and organisations to submit their nucleotide data reliably to public archives. This work enables the continuous, global exchange of information about living things. Here we present an update of the INSDC in 2015, including data growth and diversification, new standards and requirements by publishers for authors to submit their data to the public archives. The INSDC serves as a model for data sharing in the life sciences. PMID:26657633

  14. EXCISE TAX AS EXTERNAL VARIABLE (ON TABACCO PRODUCTS AT STATE AND LOCAL COMMUNITIES IN BIH

    Directory of Open Access Journals (Sweden)

    Dinko Primorac

    2012-01-01

    Full Text Available The subject of this paper is themovement and accounting for excise tax as aseparate subsystem of sales tax, with an emphasison tobacco products. Since the excise tax ontobacco products is a specific category of excisableproducts, it is possible to fully distance it fromother products. Unlike other excise goods, excisetaxes on tobacco products can not be distinguishedby the criterion of luxury and by the criterion ofharm to health. This paper explains the reasons,effects and the basic characteristics of excise taxes,and full adjustment of the special tax. The aim ofthe research paper is to present and analyze thesystem of excise tax revenue in Bosnia andHerzegovina, with special reference to the excisetax on tobacco products. Furthermore the aim is toexplore how the excise tax system in Bosnia andHerzegovina functions and how the funds fromexcise taxes are collected, and where exactly theyare expended.

  15. Lambda Excision Revisited: Testing a Model for Synapsis of Prophage Ends

    Science.gov (United States)

    Pato, Martin L.

    2001-01-01

    Excision of lambda prophage was reexamined to test a model for prophage end synapsis. The model proposes that, during in situ prophage replication, following induction, the diverging replication forks are held together. Consequently, prophage DNA is spooled through the replication machinery, drawing the prophage ends together and facilitating synapsis. The model predicts that excision will be slowed if in situ lambda replication is inhibited, and the predicted low rate of excision of a nonreplicating prophage was observed after thermoinduction. However, excision was rapid if additional Int protein was supplied or if the temperature was reduced after induction, showing that (i) Int is partially thermosensitive for excision at 42°C and (ii) in situ replication is not required for rapid excision, a finding that is inconsistent with the model. PMID:11489876

  16. Polymorphisms in base excision repair genes: Breast cancer risk and individual radiosensitivity

    Science.gov (United States)

    Patrono, Clarice; Sterpone, Silvia; Testa, Antonella; Cozzi, Renata

    2014-01-01

    Breast cancer (BC) is the most common cancer among women worldwide. The aetiology and carcinogenesis of BC are not clearly defined, although genetic, hormonal, lifestyle and environmental risk factors have been established. The most common treatment for BC includes breast-conserving surgery followed by a standard radiotherapy (RT) regimen. However, radiation hypersensitivity and the occurrence of RT-induced toxicity in normal tissue may affect patients’ treatment. The role of DNA repair in cancer has been extensively investigated, and an impaired DNA damage response may increase the risk of BC and individual radiosensitivity. Single nucleotide polymorphisms (SNPs) in DNA repair genes may alter protein function and modulate DNA repair efficiency, influencing the development of various cancers, including BC. SNPs in DNA repair genes have also been studied as potential predictive factors for the risk of RT-induced side effects. Here, we review the literature on the association between SNPs in base excision repair (BER) genes and BC risk. We focused on X-ray repair cross complementing group 1 (XRCC1), which plays a key role in BER, and on 8-oxoguanine DNA glycosylase 1, apurinic/apyrimidinic endonuclease 1 and poly (ADP-ribose) polymerase-1, which encode three important BER enzymes that interact with XRCC1. Although no association between SNPs and radiation toxicity has been validated thus far, we also report published studies on XRCC1 SNPs and variants in other BER genes and RT-induced side effects in BC patients, emphasising that large well-designed studies are needed to determine the genetic components of individual radiosensitivity. PMID:25493225

  17. NUCLEOTIDE COMPARISON OF GDF9 GENE IN INDIAN YAK AND GADDI GOAT: HIGH ALTITUDE LIVESTOCK ANIMALS

    Directory of Open Access Journals (Sweden)

    Lakshya Veer Singh

    2013-06-01

    Full Text Available The present study was undertaken to characterize exon 1 and exon 2 sequence of one of fecundity genes: GDF9 (Growth differentiation factor 9, in high altitude livestock animal (Yak and Gaddi goat. Six nucleotide differences were identified between sheep (AF078545 and goats (EF446168 in exon 1 and exon 2. Sequencing revealed nine novel single nucleotide mutations in exon 1 and exon 2 of Indian yak that compared with Bos taurus (GQ922451. These results preliminarily showed that the GDF9 gene might be a major gene that influences prolificacy of Gaddi goats and Indian yak.

  18. The formation of catalytically competent enzyme-substrate complex is not a bottleneck in lesion excision by human alkyladenine DNA glycosylase.

    Science.gov (United States)

    Kuznetsov, N A; Kiryutin, A S; Kuznetsova, A A; Panov, M S; Barsukova, M O; Yurkovskaya, A V; Fedorova, O S

    2017-04-01

    Human alkyladenine DNA glycosylase (AAG) protects DNA from alkylated and deaminated purine lesions. AAG flips out the damaged nucleotide from the double helix of DNA and catalyzes the hydrolysis of the N-glycosidic bond to release the damaged base. To understand better, how the step of nucleotide eversion influences the overall catalytic process, we performed a pre-steady-state kinetic analysis of AAG interaction with specific DNA-substrates, 13-base pair duplexes containing in the 7th position 1-N6-ethenoadenine (εA), hypoxanthine (Hx), and the stable product analogue tetrahydrofuran (F). The combination of the fluorescence of tryptophan, 2-aminopurine, and 1-N6-ethenoadenine was used to record conformational changes of the enzyme and DNA during the processes of DNA lesion recognition, damaged base eversion, excision of the N-glycosidic bond, and product release. The thermal stability of the duplexes characterized by the temperature of melting, Tm, and the rates of spontaneous opening of individual nucleotide base pairs were determined by NMR spectroscopy. The data show that the relative thermal stability of duplexes containing a particular base pair in position 7, (Tm(F/T) < Tm(εA/T) < Tm(Hx/T) < Tm(A/T)) correlates with the rate of reversible spontaneous opening of the base pair. However, in contrast to that, the catalytic lesion excision rate is two orders of magnitude higher for Hx-containing substrates than for substrates containing εA, proving that catalytic activity is not correlated with the stability of the damaged base pair. Our study reveals that the formation of the catalytically competent enzyme-substrate complex is not the bottleneck controlling the catalytic activity of AAG.

  19. Does the Type of Initial Biopsy Method Determine Re-Excision Rate of Cutaneous Melanoma?

    OpenAIRE

    Ramya Vangipuram; Mary Ramirez; Subhasis Misra; Yasir Al Abboodi

    2015-01-01

    Background: Various biopsy types are used to diagnose melanoma, after which wide local excision (WLE) is the gold standard for treatment. Depending on the final pathology report, further re-excision may be necessary despite an initial, presumably adequate, WLE. In this study, we analyzed the impact of initial biopsy type (shave, punch, or excision) on the management of melanoma. Methods: A retrospective chart review of 243 patients with clinically node-negative melanoma was completed. Eva...

  20. Effects of nucleotides and nucleosides on coagulation

    DEFF Research Database (Denmark)

    Bune, Laurids; Thaning, Pia; Johansson, Pär I;

    2010-01-01

    intravascular coagulation. We investigated whether nucleotide-induced cardiovascular collapse as provoked by systemic infusion of adenosine, ADP, ATP, UTP and nitric oxide affected the haemostatic system as assessed by whole blood thromboelastography (TEG) analysis. Ten pigs received a randomized infusion......Nucleotides, including ADP, ATP and uridine triphosphate (UTP), are discharged profusely in the circulation during many pathological conditions including sepsis. Sepsis can cause hypotension and systemic activation of the coagulation and fibrinolytic systems in humans, which may cause disseminated.......7 ng/ml; P blood was evaluated by TEG. Circulating ADP induces hypocoagulation without signs of increased fibrinolysis as evaluated by TEG. The potential...

  1. Phyllodes tumor diagnosed after ultrasound-guided vacuum-assisted excision: should it be followed by surgical excision?

    Science.gov (United States)

    Youk, Ji Hyun; Kim, Hana; Kim, Eun-Kyung; Son, Eun Ju; Kim, Min Jung; Kim, Jeong-Ah

    2015-03-01

    Our aim was to retrospectively evaluate the results of ultrasound (US)-guided vacuum-assisted excision (US-VAE) of phyllodes tumors (PTs). A total of 41 PTs diagnosed at US-VAE followed by surgery (n = 27) or at least 2 y of US monitoring (n = 14) were included. By comparison of US-VAE pathology with surgical histology or follow-up US results, cases were divided into upgraded (malignant) and non-upgraded (benign) groups. These two groups were compared with respect to clinical, procedural and US features. Among 27 surgical cases, 2 (8.7%) of 23 benign PTs were upgraded to malignant PTs. The Breast Imaging Reporting and Data System category was retrospectively assigned as 4a (50%) or 4b (50%) in the upgraded group (n = 2) and 3 (64%) or 4a (36%) in the non-upgraded group (n = 39) (p = 0.018). Residual tumor was observed at the site of US-VAE in 15 of 27 surgical cases and 0 of 14 US follow-up cases (36.6%, 15/41). Given the rates of upgrade to malignancy (8.7%) and residual tumor (36.6%), PTs diagnosed after US-VAE should be surgically excised.

  2. [Surgical treatment of the accessory navicular syndrome with simple excision].

    Science.gov (United States)

    Chi, Lei-Ting; Li, Cheng; Zhang, Dong; Li, Zhi; Huang, Bo; Zhang, Ting-Jiu; Yu, Ming; Wang, Ping-Xi

    2009-12-01

    To observe and evaluate the clinical effects of surgical treatment for the accessory navicular syndrome with simple excision. From November 2006 to December 2008, 23 patients (twenty-five feet) with accessory navicular syndrome received simple excision of the accessory navicular bone. The chief complains were intermittent pain of feet after running or walking. Physical examination showed local tenderness on palpation in the region of the navicular bone. X-ray or CT showed there was an accessory navicular bone. The present history ranged from 6 months to 12 years. There were 14 males and 9 females. The mean age was 14.6 years, ranging from 8 to 35 years. About 2 cm long incision was made at the tip of the medial prominence of the navicular bone. After partial dissection of the posterior tibial tendon, the accesssory navicular bone was exposed and excisied. The prominence of the tuberosity of the navicular bone was cut and shaved. The posterior tibial tenden was repaired before closing the wound. The foot was immobilized with cast or brace in inversion position and no weight-bearing for 2 weeks. Strenuous jumping or dancing must be avoided in 3 months after surgery. The patients with residual symptoms and signs received physical therapy and an arch support for shoes without flatfoot deformity. The average clinical follow-up during was 12 month (ranged, 3 to 18 months). The excellent results in 21 feet and good in 4 feet (3 feet with mild flat deformity and 1 foot with old sprain injury). The average hospital stay was 5 days and no wound infection occurred. All patients resumed the normal life and study after operation. Surgical treatment of the accessory navicular syndrome with simple excision has the advantages of less invasive to the posterior tibial tenden and the medial longitudinal arch of the foot, shorter time of immobilization of the foot and stay in hospital, small incision and good clinical results. This procedure is one of the best selective treatments for

  3. Running out of time: the decline of channel activity and nucleotide activation in adenosine triphosphate-sensitive K-channels

    Science.gov (United States)

    Proks, Peter; Puljung, Michael C.; Vedovato, Natascia; Sachse, Gregor; Mulvaney, Rachel; Ashcroft, Frances M.

    2016-01-01

    KATP channels act as key regulators of electrical excitability by coupling metabolic cues—mainly intracellular adenine nucleotide concentrations—to cellular potassium ion efflux. However, their study has been hindered by their rapid loss of activity in excised membrane patches (rundown), and by a second phenomenon, the decline of activation by Mg-nucleotides (DAMN). Degradation of PI(4,5)P2 and other phosphoinositides is the strongest candidate for the molecular cause of rundown. Broad evidence indicates that most other determinants of rundown (e.g. phosphorylation, intracellular calcium, channel mutations that affect rundown) also act by influencing KATP channel regulation by phosphoinositides. Unfortunately, experimental conditions that reproducibly prevent rundown have remained elusive, necessitating post hoc data compensation. Rundown is clearly distinct from DAMN. While the former is associated with pore-forming Kir6.2 subunits, DAMN is generally a slower process involving the regulatory sulfonylurea receptor (SUR) subunits. We speculate that it arises when SUR subunits enter non-physiological conformational states associated with the loss of SUR nucleotide-binding domain dimerization following prolonged exposure to nucleotide-free conditions. This review presents new information on both rundown and DAMN, summarizes our current understanding of these processes and considers their physiological roles. This article is part of the themed issue ‘Evolution brings Ca2+ and ATP together to control life and death’. PMID:27377720

  4. Cyclic Nucleotide Monophosphates and Their Cyclases in Plant Signaling

    KAUST Repository

    Gehring, Christoph A.

    2017-10-04

    The cyclic nucleotide monophosphates (cNMPs), and notably 3′,5′-cyclic guanosine monophosphate (cGMP) and 3′,5′-cyclic adenosine monophosphate (cAMP) are now accepted as key signaling molecules in many processes in plants including growth and differentiation, photosynthesis, and biotic and abiotic defense. At the single molecule level, we are now beginning to understand how cNMPs modify specific target molecules such as cyclic nucleotide-gated channels, while at the systems level, a recent study of the Arabidopsis cNMP interactome has identified novel target molecules with specific cNMP-binding domains. A major advance came with the discovery and characterization of a steadily increasing number of guanylate cyclases (GCs) and adenylate cyclases (ACs). Several of the GCs are receptor kinases and include the brassinosteroid receptor, the phytosulfokine receptor, the Pep receptor, the plant natriuretic peptide receptor as well as a nitric oxide sensor. We foresee that in the near future many more molecular mechanisms and biological roles of GCs and ACs and their catalytic products will be discovered and further establish cNMPs as a key component of plant responses to the environment.

  5. Terahertz pulsed imaging of freshly excised human colonic tissues

    Energy Technology Data Exchange (ETDEWEB)

    Reid, Caroline B; Gibson, Adam P [Department of Medical Physics and Bioengineering, University College London, London, WC1E 6BT (United Kingdom); Fitzgerald, Anthony; Wallace, Vincent P [School of Physics, University of Western Australia, Crawley 6009 (Australia); Reese, George; Tekkis, Paris [Division of Surgery, Chelsea and Westminster Campus, Imperial College London, London (United Kingdom); Goldin, Robert [Centre for Pathology, Imperial College London, St Mary' s Campus, London (United Kingdom); O' Kelly, P S [TeraView Ltd, Platinum Building, St John' s Innovation Park, Cowley Road, Cambridge, CB4 0WS (United Kingdom); Pickwell-MacPherson, Emma, E-mail: c.reid@medphys.ucl.ac.uk [Department of Electronic Engineering, Chinese University of Hong Kong, Shatin, NT (Hong Kong)

    2011-07-21

    We present the results from a feasibility study which measures properties in the terahertz frequency range of excised cancerous, dysplastic and healthy colonic tissues from 30 patients. We compare their absorption and refractive index spectra to identify trends which may enable different tissue types to be distinguished. In addition, we present statistical models based on variations between up to 17 parameters calculated from the reflected time and frequency domain signals of all the measured tissues. These models produce a sensitivity of 82% and a specificity of 77% in distinguishing between healthy and all diseased tissues and a sensitivity of 89% and a specificity of 71% in distinguishing between dysplastic and healthy tissues. The contrast between the tissue types was supported by histological staining studies which showed an increased vascularity in regions of increased terahertz absorption.

  6. DNA base excision repair nanosystem engineering: model development.

    Science.gov (United States)

    Sokhansanj, B A

    2005-01-01

    DNA base damage results from a combination of endogenous sources, (normal metabolism, increased metabolism due to obesity, stress from diseases such as arthritis and diabetes, and ischemia) and the environment (ingested toxins, ionizing radiation, etc.). If unrepaired DNA base damage can lead to diminished cell function, and potentially diseases and eventually mutations that lead to cancer. Sophisticated DNA repair mechanisms have evolved in all living cells to preserve the integrity of inherited genetic information and transcriptional control. Understanding a system like DNA repair is greatly enhanced by using engineering methods, in particular modeling interactions and using predictive simulation to analyze the impact of perturbations. We describe the use of such a "nanosystem engineering" approach to analyze the DNA base excision repair pathway in human cells, and use simulation to predict the impact of varying enzyme concentration on DNA repair capacity.

  7. Management of Ocular Surface Tumors: Excision vs. Topical Treatment

    Directory of Open Access Journals (Sweden)

    Sotiria Palioura

    2014-10-01

    Full Text Available Ocular surface squamous neoplasia (OSSN encompasses a range of corneal and conjunctival lesions from intraepithelial dysplasia to invasive squamous cell carcinoma. The mainstay of treatment for OSSN has traditionally been surgical excision with wide margins and cryotherapy. Increasing evidence on the efficacy and safety of medical therapy and the avoidance of surgical complications has made topical chemotherapy increasingly popular among corneal specialists. The most common topical agents used for the treatment of OSSN include mitomycin C, 5-fluorouracil, and interferon a 2b. Herein, we review recent advances in the surgical and medical management of OSSN and discuss advantages and disadvantages of each approach. The role of ultra highresolution optical coherence tomography in the diagnosis and treatment of primary and recurrent OSSN lesions is also discussed.

  8. Limb salvage surgery in the excision of a massive fibromatosis.

    Science.gov (United States)

    Redmond, Karen C; Kuppusamy, Madhankumar; Nicholson, Andrew G; Searle, Adam; Thomas, Meirion; Goldstraw, Peter

    2011-09-01

    Fibromatosis is a rare fibroproliferative disorder with a tendency for local infiltrative and destructive growth. Local recurrence is frequent, despite apparent complete resection after radical excision. We present a case of a 22-year-old woman with massive recurrent thoracic fibromatosis extending into the neck and impairing the function of her right upper limb. This required a multidisciplinary approach to surgery to salvage the limb. The case highlights the fact that while every attempt should be made to achieve negative histologic margins, local recurrence is not uncommon. Therefore, if fibromatosis occurs adjacent to or involves vital structures, these should not be sacrificed to achieve negative margins. Function and structure preserving procedures are important as the primary goal, if not even more important. Copyright © 2011 The Society of Thoracic Surgeons. Published by Elsevier Inc. All rights reserved.

  9. Laser excision of a mucocele: A case report

    Directory of Open Access Journals (Sweden)

    Rajashree Ganguly

    2015-01-01

    Full Text Available A mucous cyst (mucocele, mucous retention cyst, ranula, and epulis is usually a painless, thin sac on the inner surface of the lips. It contains clear fluid. It is painless but can be bothersome. The cyst is thought to be caused due to sucking of the lip membranes between the teeth. A mucous cyst is common and harmless. However, if left untreated, it can organize and form a permanent bump on the inner surface of the lip. A mucous cyst is called ranula when it occurs on the floor of the mouth and epulis when it occurs on the gums. The sac may also be formed around the jewellery (piercings that has been inserted into the lips or the tongue. This article highlights the use of lasers in the treatment of the excision of mucocele.

  10. Excising a boosted rotating black hole with overlapping grids

    CERN Document Server

    Calabrese, G; Calabrese, Gioel; Neilsen, David

    2004-01-01

    We use the overlapping grids method to construct a fourth order accurate discretization of a first order reduction of the Klein-Gordon scalar field equation on a boosted spinning black hole blackground in axisymmetry. This method allows us to use a spherical outer boundary and excise the singularity from the domain with a spheroidal inner boundary which is moving with respect to the main grid. We discuss the use of higher order accurate energy conserving schemes to handle the axis of symmetry and compare it with a simpler technique based on regularity conditions. We also compare the single grid long term stability property of this formulation of the wave equation with that of a different first order reduction.

  11. Quantifying Long-term Retention of Excised Fat Grafts

    DEFF Research Database (Denmark)

    bxg165, bxg165; Ørholt, Mathias; Glovinski, Peter V.

    2017-01-01

    Background: Predicting the degree of fat graft retention is essential whenplanning reconstruction or augmentation with free fat grafting. Most surgeonsobserve volume loss over time after fat grafting; however, the portion lost toresorption after surgery is still poorly defined, and the time...... to reach steadystate is unknown. Methods: The authors compiled a retrospective, longitudinal cohort of patientswith vestibular schwannoma who had undergone ablative surgery and reconstructionwith excised fat between the years 2006 and 2015. Fat volume retentionwas quantified by computed tomography....... The average baseline graft volumewas 18.1 ± 4.8 ml. The average time to reach steady state was 806 days aftertransplantation. By this time, the average fat graft retention was 50.6 percent(95 percent CI, 46.4 to 54.7 percent). No statistically significant association wasfound between baseline graft volume...

  12. Endoscopic Excision of Symptomatic Simple Bone Cyst at Skull Base

    Science.gov (United States)

    Gunawat, Prashant; Karmarkar, Vikram; Deopujari, Chandrashekhar; Shah, Nishit

    2016-01-01

    Seizure is a classical feature of intra axial brain parenchymal lesion. Simple bone cyst is an unusual bony pathology at skull base presenting with unexpected symptoms of complex partial seizures. Skull base neuro-endoscopy has managed such lesions more effectively with reduced post-operative morbidity as compared to transcranial approach. This case report discusses a 20-year-old male who presented with 3 episodes of seizure over a time period of 10 months. MRI brain revealed T1 hypo and T2 hyper intense cystic lesion in middle cranial fossa with no enhancement on contrast administration. CT scan showed cystic lesion involving greater wing and pterygoid plate of sphenoid on left side. CT cisternographic evaluation showed CSF outpouching in the sphenoid air sinus. Excision of the cystic lesion was carried out through endoscopic transmaxillary transpterygoid approach. Histopathological examination showed the lesion to be a simple bone cyst. PMID:27891396

  13. Transanal total mesorectal excision: dissection tips using 'O's and 'triangles'.

    Science.gov (United States)

    Bernardi, M-P; Bloemendaal, A L A; Albert, M; Whiteford, M; Stevenson, A R L; Hompes, R

    2016-11-01

    Transanal total mesorectal excision (taTME) requires specific technical expertise, as it is often difficult to ascertain the correct dissection plane. Consequently, one can easily enter an incorrect plane, potentially resulting in bleeding (sidewall or presacral vessels), autonomic nerve injury and urethral injury. We aim to demonstrate specific visual features, which may be encountered during surgery and can guide the surgeon to perform the dissection in the correct plane. Specific features of dissection in the correct and incorrect planes are demonstrated in the accompanying video. The 'triangles' created using appropriate traction can aid in performing a precise dissection in the correct plane. Recognition of features described as 'O's can alert surgeons that they are entering a new fascial plane and can avoid incursion into an incorrect plane. Understanding and recognizing the described features which can be encountered in taTME surgery, a safe and accurate TME dissection can be facilitated.

  14. Accurate Evolutions of Orbiting Black-Hole Binaries Without Excision

    CERN Document Server

    Campanelli, M; Marronetti, P; Zlochower, Y

    2006-01-01

    We present a new algorithm for evolving orbiting black-hole binaries that does not require excision or a corotating shift. Our algorithm is based on a novel technique to handle the singular puncture conformal factor. This system, based on the BSSN formulation of Einstein's equations, when used with a `pre-collapsed' initial lapse, is non-singular at the start of the evolution, and remains non-singular and stable provided that a good choice is made for the gauge. As a test case, we use this technique to fully evolve orbiting black-hole binaries from near the Innermost Stable Circular Orbit (ISCO) regime. We show fourth order convergence of waveforms and compute the radiated gravitational energy and angular momentum from the plunge. These results are in good agreement with those predicted by the Lazarus approach.

  15. [Sublicons containing amino acids and nucleotides].

    Science.gov (United States)

    Kaĭmakov, E A

    1979-01-01

    Sublicons have been obtained. Sublicons are threadlike structures appearing during sublimation of frozen solutions of small concentrations, containing racemate mixture of amino acids and nucleotides. It is suggested that close location of chains and their zonal distribution by the section of helix spire forming sublicon wall, should provide the formation of stereohomogenous and complementary successions of biomonomers of different clases.

  16. Impact of cigarette taxation policy on excise revenues and cigarette consumption in Uzbekistan

    Directory of Open Access Journals (Sweden)

    Konstantin S. Krasovsky

    2013-05-01

    Full Text Available BACKGROUND: In 2012, Uzbekistan ratified the Framework Convention on Tobacco Control, which states that price and tax measures are an effective means of reducing tobacco consumption. We aimed to explore the effect of taxation policies on revenues and cigarette consumption. METHODS: Data on tax rates, revenues, cigarette sales were taken from national reports. To forecast potential revenues, a scenario analysis was performed. RESULTS: In 1991-2004, ad valorem excise system was in place in Uzbekistan, which was later replaced by the specific excise system. In 1997-2011, the nominal average excise has increased by a factor of twenty, but in real terms, after a sharp increase in 1999, average excise declined annually and increased only in 2010-2011. Annual cigarette sales per capita of adult population in 1999-2007 constituted 17-25 cigarette packs, while in 2008-2011 it increased to 30-37 packs. Four scenarios of excise tax increases in 2012 were developed: one actual scenario based on the rates effective in Uzbekistan in 2012, and three hypothetical ones anticipating excise rates increase by 1.5, 2 and 3-fold. With actual excise increase in 2012, the inflation-adjusted budget revenues would grow by 5%, and with three hypothetical - by 17%, 35% and 66% respectively, despite the decline of tax-paid cigarette sales. CONCLUSION: Stabilization or reduction in cigarette excises in Uzbekistan in 2002-2008 led to a decline in real excise revenues and the growth of cigarette sales. In 1999 and 2010-2011, excises were significantly increased and the real revenues have risen, despite the decline in cigarette sales. As cigarette prices are low, the illegal outflow of cigarettes from Uzbekistan apparently exceeds the illegal inflow. A significant increase in cigarette excise (1.5-3 fold can both increase budget revenues and reduce cigarette consumption, with greater increase yielding more benefits.

  17. Early excision and late excision of heterotopic ossification after traumatic brain injury are equivalent: a systematic review of the literature.

    Science.gov (United States)

    Chalidis, Byron; Stengel, Dirk; Giannoudis, Peter V

    2007-11-01

    Heterotopic ossification (HO) is a common complication in patients with coma after brain injury. As the optimal timing of surgical resection is still controversial and unclear, a review of the literature was performed in order to determine the impact of early operation on recurrence rate and joint mobility. We identified all types of studies dealing with surgical excision of HO in patients after head injury in major medical and publishers' databases. Publication bias and statistical heterogeneity were assessed by funnel-plot asymmetry and Galbraith regression. We abstracted demographic and outcome information from manuscripts that tabulated individual patient data (IPD) to build univariate logistic and linear regression models. Means and proportions for random-effects meta-regression analysis were also obtained. Of 318 studies originally identified, 16 observational studies enrolling 255 patients (212 men, 329 affected joints, mean age of 30.6 [+/-SEM of 1.4] years) were included in the analysis. The reported overall recurrence rate in eleven studies was 38/192 (19.8%). Both IPD and meta-regression analysis failed to show a marked impact of the interval to resection on the probability of recurrence (odds ratio 1.00, 95% CI 0.98-1.03). The predicted probability of recurrence after 13, 21, and 30 months of waiting was 9%, 14%, and 19%, respectively. The length of coma period and patient's neurologic deficit were statistically significant negative predictors for both recurrence rate and functional outcome. Although no conclusive inferences can be drawn from the identified studies, the available data do not support the concept that early excision triggers later recurrence.

  18. 76 FR 77053 - Proposed Collection; Income, Excise, and Estate and Gift Taxes Effective Dates, etc.

    Science.gov (United States)

    2011-12-09

    ... Internal Revenue Service Proposed Collection; Income, Excise, and Estate and Gift Taxes Effective Dates... information collection requirements related to income, excise, and estate and gift taxes; effective dates and other issues arising under the employee benefit provisions of the tax reform act of 1984. DATES: Written...

  19. Recent trends in tobacco sales, excise revenues, and affordability in the former USSR countries

    Directory of Open Access Journals (Sweden)

    Konstantin Krasovsky

    2017-05-01

    Cigarette sales in the region decreased in 2008-2015 and the key factor for the decline was the reduction of tobacco affordability. Only the substantial increase in excise rates can guarantee both revenue growth and the reduction of tobacco consumption. To reduce tobacco consumption, excise rates should be increased annually taking into account inflation and income growth.

  20. Acorns containing deeper plumule survive better: how white oaks counter embryo excision by rodents.

    Science.gov (United States)

    Zhang, Mingming; Dong, Zhong; Yi, Xianfeng; Bartlow, Andrew W

    2014-01-01

    Several squirrel species excise the embryo of acorns of most white oak species to arrest germination for long-term storage. However, it is not clear how these acorns counter embryo excision and survive in the arms race of coevolution. In this study, we simulated the embryo excision behavior of squirrels by removing 4 mm of cotyledon from the apical end of white oak acorns differing in embryo depths to investigate the effects of embryo excision on acorn germination and seedling performance of white oak species. The embryo depth in the cotyledons was significantly different among white oak acorns, with Quercus mongolica containing the embryo most deeply in the acorns. We found that artificial embryo excision significantly decreased acorn germination rates of Quercus variabilis, Quercus acutissima, Quercus aliena, Quercus aliena var. acutiserrata, Quercus serrata. var. brevipetiolata but not Q. mongolica. Artificial embryo excision exerted significant negative impacts on seedling performance of all oak species except Quercus aliena. Our study demonstrates the role of embryo depth of acorns in countering embryo excision by squirrels and may explain the fact that squirrels do not perform embryo excision in acorns of Q. mongolica with deeper embryos. This apparent adaptation of acorns sheds light on the coevolutionary dynamics between oaks and their seed predators.

  1. Periodontal plastic procedure for the management of the residual gingival defect after excision of an epulis

    Directory of Open Access Journals (Sweden)

    Varun Choudhary

    2015-01-01

    Full Text Available Dentinal hypersensitivity and unesthetic appearance are common findings after excision of an epulis due to exposure of root and underlying bone. The simultaneous placement of subepithelial connective tissue grafting after excision of the lesion seems to be viable surgical option in such cases. Furthermore, this will avoid second surgical procedure for the management of the residual gingival defect.

  2. Oesophageal pseudodiverticulum after foregut duplication cyst excision: Case report and literature review

    Directory of Open Access Journals (Sweden)

    Iuliana D Bobanga

    2016-01-01

    Full Text Available Oesophageal pseudodiverticula rarely occur after excision of benign oesophageal neoplasms. While management and outcomes have been reported in the adult leiomyoma literature, sparse data exist on the occurrence and management of pseudodiverticula after foregut duplication cyst excision. We discuss our experience with a paediatric patient and review relevant literature regarding operative techniques and surgical outcomes.

  3. 78 FR 6189 - Federal Acquisition Regulation; Unallowability of Costs Associated With Foreign Contractor Excise...

    Science.gov (United States)

    2013-01-29

    ... 9000-AM13 Federal Acquisition Regulation; Unallowability of Costs Associated With Foreign Contractor... excise tax on certain Federal procurement payments to foreign persons. The rule disallows the cost associated with the 2 percent excise tax on certain foreign procurements. DATES: Effective Date: February 28...

  4. On the role of a coumarin derivative for sensing applications: Nucleotide identification using a micellar system.

    Science.gov (United States)

    Bettoschi, Alexandre; Ceglie, Andrea; Lopez, Francesco; Meli, Valeria; Murgia, Sergio; Tamburro, Manuela; Caltagirone, Claudia; Cuomo, Francesca

    2016-09-01

    The recognition of nucleotides is of crucial importance because they are the basic constituents of nucleic acids. The present study is focused on the selective interaction between a novel amphiphilic fluorophore containing coumarin and imidazole, CI (1-methyl-3-(12-((2-oxo-2H-chromen-7-yl)oxy)dodecyl)-1H-imidazol-3-ium bromide), and different nucleotide-monophosphates (NMPs). It was supposed that the solubilization of the low water soluble CI in a micelle system of hexadecyltrimethylammonium chloride (CTAC) would make the coumarin moiety of CI available to the interaction with the water-soluble NMPs. Changes in CTAC critical micelle concentration suggested that CI strongly interacted with the host cationic surfactant, thus forming a positively charged interface enriched with coumarin able to interact with the anionic NMPs. Steady-state fluorescence quenching revealed that CI/CTAC system was capable of distinguish between purine- and pyrimidine-based nucleotides. A modified Stern-Volmer equation permitted the use of a quenching model that accounted for the possible interactions between the micelles and the nucleotides. The data analysis allowed calculating selective parameters that differentiated according to the type of nucleotide either at 25 or 50°C. Our results established the utility of the novel coumarin derivative fluorophore, supported by the simple and suitable micellar systems, as a tool for DNA sensing applications.

  5. Enhanced excision repair and lack of PSII activity contribute to higher UV survival of Chlamydomonas reinhardtii cells in dark.

    Science.gov (United States)

    Chaudhari, Vishalsingh R; Vyawahare, Aniket; Bhattacharjee, Swapan K; Rao, Basuthkar J

    2015-03-01

    Plant cells are known to differentiate their responses to stress depending up on the light conditions. We observed that UVC sensitive phenotype of light grown asynchronous Chlamydomonas reinhardtii culture (Light culture: LC) can be converted to relatively resistant form by transfer to dark condition (Dark culture: DC) before UVC exposure. The absence of photosystem II (PSII) function, by either atrazine treatment in wild type or in D1 (psbA) null mutant, conferred UV protection even in LC. We provide an indirect support for involvement of reactive oxygen species (ROS) signalling by showing higher UV survival on exposures to mild dose of H2O2 or Methyl Viologen. Circadian trained culture also showed a rhythmic variation in UV sensitivity in response to alternating light-dark (12 h:12 h) entrainment, with maximum UV survival at the end of 12 h dark and minimum at the end of 12 h light. This rhythm failed to maintain in "free running" conditions, making it a non-circadian phenotype. Moreover, atrazine strongly inhibited rhythmic UV sensitivity and conferred a constitutively high resistance, without affecting internal circadian rhythm marker expression. Dampening of UV sensitivity rhythm in Thymine-dimer excision repair mutant (cc-888) suggested the involvement of DNA repair in this phenomenon. DNA excision repair (ER) assays in cell-free extracts revealed that dark incubated cells exhibit higher ER compared to those growing in light, underscoring the role of ER in conferring differential UV sensitivity in dark versus light incubation. We suggest that multiple factors such as ROS changes triggered by differences in PSII activity, concomitant with differential ER efficiency collectively contribute to light-dark (12 h: 12 h) rhythmicity in C. reinhardtii UV sensitivity.

  6. CORNEAL STROMAL THINNING: A RARE CORNEAL COMPLICATION AFTER BARE SCL ERA PTERYG I UM EXCISION TECHNIQUE

    Directory of Open Access Journals (Sweden)

    Sulaiman Abdul

    2015-06-01

    Full Text Available INTRODUCTION : Bare sclera technique without using any anti - mitotic drugs are commonly employed in rural population. Corneal dellen formation and recurrence of pterygium are more common in these cases. But the corneal complication like stromal thinning, necrosis of corne a and sclera are not common. The corneal epithelium is a highly differentiated cell type that is self - renewing. Also corneal epithelium is important for the stromal replacement in the situations like chemical, thermal burns, ocular surgery like pterygium s urgery. Interference with status of stem cell replacement and as a consequent to it, stromal thinning is occurring in the pterygium surgery. P atient 1: A 68 yr s. old male patient underwent pterygium surgery ( B aresclera excision technique. After 30 days he developed corneal thinning with the punched out partial stromal loss without perforation or descmetocele or scleral thinning. Patient 2: A 60yr s. old male patient underwent pterygium surgery 2months back, he developed same type of corneal thinning. Both P atients were treated with tear drops and improved. CONCLUSION : The stromal thinning in these two cases is may be due to chemical factors like collagenase which might have been released from the traumatised conjunctival epithelial cells causing thinning wit hout replacement of stroma by limbal stem cells.

  7. Radiation and thermal stabilities of adenine nucleotides.

    Science.gov (United States)

    Demidov, V V; Potaman, V N; Solyanina, I P; Trofimov, V I

    1995-03-01

    We have investigated in detail radiation and thermal stabilities and transformations of adenosine mono- and triphosphates in liquid and frozen solid aqueous solutions within a wide range of absorbed radiation dose (up to 75 kGy) and temperature (up to 160 degrees C). Dephosphorylation is the main pathway of high temperature hydrolysis of adenine nucleotides. Basic thermodynamic and kinetic parameters of this process have been determined. Radiolysis of investigated compounds at room temperature results in scission of N-glycosidic bond with a radiation yield about of 1 mol/100 eV. Solution freezing significantly enhances radiation stability of nucleotides as well as other biomolecules. This circumstance is essential in the discussion of panspermia concepts.

  8. Nucleotide sequence of papaya mosaic virus RNA.

    Science.gov (United States)

    Sit, T L; Abouhaidar, M G; Holy, S

    1989-09-01

    The RNA genome of papaya mosaic virus is 6656 nucleotides long [excluding the poly(A) tail] with six open reading frames (ORFs) more than 200 nucleotides long. The four nearest the 5' end each overlap with adjacent ORFs and could code for proteins with Mr 176307, 26248, 11949 and 7224 (ORFs 1 to 4). The fifth ORF produces the capsid protein of Mr 23043 and the sixth ORF, located completely within ORF1, could code for a protein with Mr 14113. The translation products of ORFs 1 to 3 show strong similarity with those of other potexviruses but the ORF 4 protein has only limited similarity with the other potexvirus ORF 4 proteins of 7K to 11K.

  9. Nucleotide Manipulatives to Illustrate the Central Dogma

    Directory of Open Access Journals (Sweden)

    Sonja B. Yung

    2015-08-01

    Full Text Available The central dogma is a core concept that is critical for introductory biology and microbiology students to master. However, students often struggle to conceptualize the processes involved, and fail to move beyond simply memorizing the basic facts. To encourage critical thinking, we have designed a set of magnetic nucleotide manipulatives that allow students to model DNA structure, along with the processes of replication, transcription, and translation.

  10. Visualization of cyclic nucleotide dynamics in neurons

    Directory of Open Access Journals (Sweden)

    Kirill eGorshkov

    2014-12-01

    Full Text Available The second messengers cAMP and cGMP transduce many neuromodulatory signals from hormones and neurotransmitters into specific functional outputs. Their production, degradation and signaling are spatiotemporally regulated to achieve high specificity in signal transduction. The development of genetically encodable fluorescent biosensors has provided researchers with useful tools to study these versatile second messengers and their downstream effectors with unparalleled spatial and temporal resolution in cultured cells and living animals. In this review, we introduce the general design of these fluorescent biosensors and describe several of them in more detail. Then we discuss a few examples of using cyclic nucleotide fluorescent biosensors to study regulation of neuronal function and finish with a discussion of advances in the field. Although there has been significant progress made in understanding how the specific signaling of cyclic nucleotide second messengers is achieved, the mechanistic details in complex cell types like neurons are only just beginning to surface. Current and future fluorescent protein reporters will be essential to elucidate the role of cyclic nucleotide signaling dynamics in the functions of individual neurons and their networks.

  11. Nucleotide-Dependent Bioautocatalytic Timer Reaction.

    Science.gov (United States)

    Chen, Ting-Ru; Hsu, Ching-Fong; Chen, Chih-Lin; Witek, Henryk A; Urban, Pawel L

    2016-09-16

    We describe a biochemical timer composed of three biocatalytic reactions involving three types of adenylate nucleotides: adenosine triphosphate (ATP), adenosine diphosphate (ADP), and adenosine monophosphate (AMP). The timer is triggered by a small amount of ATP or ADP. An abrupt increase in the ATP concentration (following numerous amplification cycles) leads to a sudden increase of luminescence from the reaction mixture. The time point when the luminescence appears is found to be a function of the initial concentration of the triggering nucleotide (5.0 × 10(-8)-1.0 × 10(-6) M), even in the presence of a complex biological matrix. The mechanism of the observed dependence of the time of luminescence increase on the concentration has been confirmed with simple kinetic models. Due to the biocompatibility of the proposed trienzymatic reaction scheme (sensitivity to common nucleotides and occurrence in a neutral pH aqueous environment), the scheme can be used in bioengineered systems that require modulation of the response time (light emission) by concentration.

  12. Multiphasic interactions between nucleotides and target proteins

    CERN Document Server

    Nissen, Per

    2016-01-01

    The nucleotides guanosine tetraphosphate (ppGpp) and guanosine pentaphosphate (pppGpp) bind to target proteins to promote bacterial survival (Corrigan et al. 2016). Thus, the binding of the nucleotides to RsgA, a GTPase, inhibits the hydrolysis of GTP. The dose response, taken to be curvilinear with respect to the logarithm of the inhibitor concentration, is instead much better (P<0.001 when the 6 experiments are combined) represented as multiphasic, with high to exceedingly high absolute r values for the straight lines, and with transitions in the form of non-contiguities (jumps). Profiles for the binding of radiolabeled nucleotides to HprT and Gmk, GTP synthesis enzymes, were, similarly, taken to be curvilinear with respect to the logarithm of the protein concentration. However, the profiles are again much better represented as multiphasic than as curvilinear (the P values range from 0.047 to <0.001 for each of the 8 experiments for binding of ppGpp and pppGpp to HprT). The binding of GTP to HprT and ...

  13. Vacuum ultraviolet photoionization of carbohydrates and nucleotides

    Energy Technology Data Exchange (ETDEWEB)

    Shin, Joong-Won, E-mail: jshin@govst.edu [Division of Science, Governors State University, University Park, Illinois 60484-0975 (United States); Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523-1872 (United States); Bernstein, Elliot R., E-mail: erb@lamar.colostate.edu [Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523-1872 (United States)

    2014-01-28

    Carbohydrates (2-deoxyribose, ribose, and xylose) and nucleotides (adenosine-, cytidine-, guanosine-, and uridine-5{sup ′}-monophosphate) are generated in the gas phase, and ionized with vacuum ultraviolet photons (VUV, 118.2 nm). The observed time of flight mass spectra of the carbohydrate fragmentation are similar to those observed [J.-W. Shin, F. Dong, M. Grisham, J. J. Rocca, and E. R. Bernstein, Chem. Phys. Lett. 506, 161 (2011)] for 46.9 nm photon ionization, but with more intensity in higher mass fragment ions. The tendency of carbohydrate ions to fragment extensively following ionization seemingly suggests that nucleic acids might undergo radiation damage as a result of carbohydrate, rather than nucleobase fragmentation. VUV photoionization of nucleotides (monophosphate-carbohydrate-nucleobase), however, shows that the carbohydrate-nucleobase bond is the primary fragmentation site for these species. Density functional theory (DFT) calculations indicate that the removed carbohydrate electrons by the 118.2 nm photons are associated with endocyclic C–C and C–O ring centered orbitals: loss of electron density in the ring bonds of the nascent ion can thus account for the observed fragmentation patterns following carbohydrate ionization. DFT calculations also indicate that electrons removed from nucleotides under these same conditions are associated with orbitals involved with the nucleobase-saccharide linkage electron density. The calculations give a general mechanism and explanation of the experimental results.

  14. A CLINICAL STUDY ON ENDOSCOPIC ASSISTED TRANSORAL EXCISION OF PARAPHARYNGEAL TUMORS

    Directory of Open Access Journals (Sweden)

    Madhusudhan Reddy

    2015-05-01

    Full Text Available INTRODUCTION : Parapharyngeal space tumors are rare , but are reported all over the world with an incidence of 0.5% of Head and Neck tumors. Parapharyngeal space is a potential space lateral to the upper part of pharynx extending from base of the s kull to the Hyoid bone. It contains important and vital structures connecting the Head and thorax. The importance of the tumors of this space lies in the fact that its approach from outside (Trans cervical is a surgical challenge and from within (Transora l does not give a good vascular control. Improved visibility and monitored dissection is reported with the use of endoscopes to assist Transoral approach to parapharyngeal tumors excision is reported from all over the world. A retrospective study of sinus endoscopes assisted excision of parapharyngeal tumors was conducted at the Government Hospital attached to Kakatiya Medical College , Thiruvananthapuram , Telangana between August 2012 and July 2013. MATERIALS AND METHODS : 19 patients were operated for Para - pharyngeal tumors. All the tumors were benign in nature. They included 9 tumors of mixed salivary gland type , 6 were neurogenic , 2 were Schwanomas and 2 were lipomas. Operative notes and video films of the surgical procedure undertaken by different su rgeons are the source of the present study. OBSERVATIONS : The diagnosis of all the tumors was based on HRCT of the neck. Pre - operative arteriogram was not undertaken in any of the patients. HRCT helped to determine the size and extent of the tumor and to d ifferentiate tumors of parotid and extra - parotid origin and to demonstrate degree of tumor vascularity. Sensitivity to differentiate between benign and malignant tumors with HRCT was found to be 97%. The tumor resectability was judged by the presence of fa t at the periphery of the tumor which gives low density marking. Sinus endoscope (Zero degree and thirty degree was found to be useful to magnify , observe the cleavage of dissection

  15. Quantitative imaging of excised osteoarthritic cartilage using spectral CT

    Energy Technology Data Exchange (ETDEWEB)

    Rajendran, Kishore; Bateman, Christopher J.; Younis, Raja Aamir; De Ruiter, Niels J.A.; Ramyar, Mohsen; Anderson, Nigel G. [University of Otago - Christchurch, Department of Radiology, Christchurch (New Zealand); Loebker, Caroline [University of Otago, Christchurch Regenerative Medicine and Tissue Engineering Group, Department of Orthopaedic Surgery and Musculoskeletal Medicine, Christchurch (New Zealand); University of Twente, Department of Developmental BioEngineering, Enschede (Netherlands); Schon, Benjamin S.; Hooper, Gary J.; Woodfield, Tim B.F. [University of Otago, Christchurch Regenerative Medicine and Tissue Engineering Group, Department of Orthopaedic Surgery and Musculoskeletal Medicine, Christchurch (New Zealand); Chernoglazov, Alex I. [University of Canterbury, Human Interface Technology Laboratory New Zealand, Christchurch (New Zealand); Butler, Anthony P.H. [University of Otago - Christchurch, Department of Radiology, Christchurch (New Zealand); European Organisation for Nuclear Research (CERN), Geneva (Switzerland); MARS Bioimaging, Christchurch (New Zealand)

    2017-01-15

    To quantify iodine uptake in articular cartilage as a marker of glycosaminoglycan (GAG) content using multi-energy spectral CT. We incubated a 25-mm strip of excised osteoarthritic human tibial plateau in 50 % ionic iodine contrast and imaged it using a small-animal spectral scanner with a cadmium telluride photon-processing detector to quantify the iodine through the thickness of the articular cartilage. We imaged both spectroscopic phantoms and osteoarthritic tibial plateau samples. The iodine distribution as an inverse marker of GAG content was presented in the form of 2D and 3D images after applying a basis material decomposition technique to separate iodine in cartilage from bone. We compared this result with a histological section stained for GAG. The iodine in cartilage could be distinguished from subchondral bone and quantified using multi-energy CT. The articular cartilage showed variation in iodine concentration throughout its thickness which appeared to be inversely related to GAG distribution observed in histological sections. Multi-energy CT can quantify ionic iodine contrast (as a marker of GAG content) within articular cartilage and distinguish it from bone by exploiting the energy-specific attenuation profiles of the associated materials. (orig.)

  16. Technical note on complete excision of choledochal cysts

    Institute of Scientific and Technical Information of China (English)

    2013-01-01

    BACKGROUND: Choledochal  cysts  are  congenital  cystic dilatations  of  the  extrahepatic  or  intrahepatic  portion  of  the biliary tree. Complete excision of choledochal cysts is currently regarded  as  the  gold  standard  treatment,  while  less  extensive procedures  including  cystoduodenostomy  have  become obsolete  due  to  the  potential  for  malignant  change  in  the remnant cyst. For type-1 choledochal cysts, which sometimes extend to the main pancreatic duct closely, some surgeons may adopt a less aggressive approach in order to avoid damage to the main pancreatic duct as such damage can lead to serious consequences.  However,  incomplete  excision  of  choledochal cysts may also cause problems. METHOD: Here we report on a reoperation treating incomplete excision of a choledochal cyst with focus on the technical aspect. RESULTS: In the reoperation, meticulous dissection of the liver hilum which had been previously operated on was performed. The hepaticojejunostomy was left intact. With the assistance of intraoperative cholangiography, the residual pancreatic portion of the choledochal cyst was completely excised. The pancreatic opening  and  the  lower  end  of  the  common  bile  duct  were reconstructed. Whipple operation was avoided. CONCLUSION: Careful  planning  with  the  aid  of  precise imaging before and during the operation largely enhanced the accuracy of the excision of the choledochal cyst.

  17. Post-Loop Electrosurgical Excision Procedure Complications in Srinagarind Hospital.

    Science.gov (United States)

    Maleerat, Pimjai; Chumworathayi, Bandit; Kietpeerakool, Chumnan; Luanratanakorn, Sanguanchoke; Temtanakitpaisan, Amornrat

    2016-01-01

    The purpose of this study was to evaluate the prevalence and predictors of post-Loop Electrosurgical Excision Procedure (LEEP) complications in Srinagarind Hospital, Khon Kaen, Thailand. Retrospective chart review was performed for 200 patients undergoing LEEP during January 2012 to February 2013. Their mean age was 45 years-old. Fifty-three (26.5%) were menopausal. The three most common preceding abnormal cervical cytology were high-grade squamous intraepithelial lesion (HSIL; 50%), atypical squamous cell cannot exclude HSIL (ASC-H; 10.5%), and low-grade squamous intraepithelial lesion (LSIL; 10%). The overall complications prevalence rate was 16.5% (95%CI, 11.4-21.6). Complications included bleeding (11%; 95%CI, 6.66-15.3), offensive discharge (4%; 95%CI, 1.28-6.72), and pelvic inflammatory disease (1.5%; 95%CI, 0.18-3.18). Only mode of delivery was an independent predictor of post-LEEP complications. Women with previous caesarean sections carried an increased risk of complications by 3.9 times (95%CI, 1.21-12.56) compared with vaginal delivery. In conclusion, LEEP is generally safe with an acceptable complication rate. Previous caesarean section was the only independent predictor for post-LEEP complications. However, this predictor still needs prudent evaluation as no clear cause-effect relationship was identified.

  18. A retrospective study of surgically excised phaeochromocytomas in Newfoundland, Canada

    Directory of Open Access Journals (Sweden)

    Joanna Holland

    2014-01-01

    Full Text Available Objective: A retrospective study detailing the circumstances surrounding diagnosis and treatment of pheochromocytomas with the associated genetic disorders. Materials and Methods: All patients with surgically excised pheochromocytomas in the Health Sciences Center, St. John′s, Newfoundland, Canada between January 2001 and December 2010 were retrospectively analyzed to determine associated familial syndromes, age, tumor size, symptomatology, and percentage of paragangliomas and bilateral pheochromocytomas. Pathology specimen reports, adrenalectomy lists and Meditech (electronic medical record diagnostic codes provided a comprehensive database for this study. Results: Twenty-four patients were studied; familial disorder patients comprised 42% (10/24. Average age at diagnosis was 57 among the sporadic and 34 in familial disorder groups (P = 0.006. Average tumor size was 4.5 cm in the sporadic group and 3 cm in the familial disorder group (P = 0.19. All atypical cases including bilateral or extra-adrenal tumors and malignancy occurred in familial disorder patients. Conclusions: The proportion of familial disorder patients (42% was higher in this study than would be expected, likely a result of the relatively high incidence of hereditary autosomal dominant disorders within Newfoundland. Among familial disorder patients, the average younger age at diagnosis and the smaller tumor size suggest syndromic pheochromocytomas may develop earlier, however they are more likely to be diagnosed sooner due to biochemical surveillance testing in known genetic disorder patients. We also demonstrate a relatively high incidence of surgically resected pheochromocytomas of 4.679/million/year in Newfoundland.

  19. Total Humeral Endoprosthetic Replacement following Excision of Malignant Bone Tumors

    Directory of Open Access Journals (Sweden)

    Suhel Kotwal

    2016-01-01

    Full Text Available Humerus is a common site for malignant tumors. Advances in adjuvant therapies and reconstructive methods provide salvage of the upper limb with improved outcomes. Reports of limb salvage with total humeral replacement in extensive humeral tumors are sparse. We undertook a retrospective study of 20 patients who underwent total humeral endoprosthetic replacement as limb salvage following excision of extensile malignant tumor from 1990 to 2011. With an average followup of 42.9, functional and oncological outcomes were analyzed. Ten patients were still alive at the time of review. Mean estimated blood loss was 1131 mL and duration of surgery was 314 minutes. Deep infection was encountered in one patient requiring debridement while mechanical loosening of ulnar component was identified in one patient. Subluxation of prosthetic humeral head was noted in 3 patients. Mean active shoulder abduction was 12.5° and active flexion was 15°. Incompetence of abduction mechanism was the major determinant of poor active functional outcome. Mean elbow flexion was 103.5° with 30.5° flexion contracture in 10 patients with good and useful hand function. Average MSTS score was 71.5%. Total humeral replacement is a reliable treatment option in restoring mechanical stability and reasonable functional results without compromising patient survival, with low complication rate.

  20. Pulsatile airflow during phonation: an excised larynx model.

    Science.gov (United States)

    Alipour, F; Scherer, R C

    1995-02-01

    Pulsatile airflow in the excised larynx was investigated with simultaneous recordings of air velocity, subglottal pressure, volume flow, and the electroglottograph signal for various conditions of the larynx. Canine larynges were mounted on a bench with sutures attached to cartilages to mimic the function of laryngeal muscles. Sustained oscillations were established and maintained with the flow of heated and humidified air through the trachea. The instantaneous air velocity above the glottis, which is the summation of a periodic velocity and the turbulent component, was measured with a constant temperature hot-wire probe at various locations. The phase-averaged velocity was used to construct the patterns of jet flow at selected time frames of the oscillation cycle. Results suggest that supraglottal air velocity is highly spatially and temporally dependent. Cycles of local air velocity with double peaks were not uncommon and a case is provided. For one phase-averaged phonatory cycle, a 9 x 13 velocity measurement grid demonstrated strongly nonuniform velocity surfaces for eight phases of the cycle, with greater velocities located anteriorly.

  1. A retrospective study of surgically excised phaeochromocytomas in Newfoundland, Canada.

    Science.gov (United States)

    Holland, Joanna; Chandurkar, Vikram

    2014-07-01

    A retrospective study detailing the circumstances surrounding diagnosis and treatment of pheochromocytomas with the associated genetic disorders. All patients with surgically excised pheochromocytomas in the Health Sciences Center, St. John's, Newfoundland, Canada between January 2001 and December 2010 were retrospectively analyzed to determine associated familial syndromes, age, tumor size, symptomatology, and percentage of paragangliomas and bilateral pheochromocytomas. Pathology specimen reports, adrenalectomy lists and Meditech (electronic medical record) diagnostic codes provided a comprehensive database for this study. Twenty-four patients were studied; familial disorder patients comprised 42% (10/24). Average age at diagnosis was 57 among the sporadic and 34 in familial disorder groups (P = 0.006). Average tumor size was 4.5 cm in the sporadic group and 3 cm in the familial disorder group (P = 0.19). All atypical cases including bilateral or extra-adrenal tumors and malignancy occurred in familial disorder patients. The proportion of familial disorder patients (42%) was higher in this study than would be expected, likely a result of the relatively high incidence of hereditary autosomal dominant disorders within Newfoundland. Among familial disorder patients, the average younger age at diagnosis and the smaller tumor size suggest syndromic pheochromocytomas may develop earlier, however they are more likely to be diagnosed sooner due to biochemical surveillance testing in known genetic disorder patients. We also demonstrate a relatively high incidence of surgically resected pheochromocytomas of 4.679/million/year in Newfoundland.

  2. Single nucleotide polymorphism in Egyptian cattle insulin-like growth factor binding protein-3 gene

    Directory of Open Access Journals (Sweden)

    Othman E. Othman

    2014-12-01

    It is concluded that the IGFBP-3/HaeIII polymorphism may be utilized as a good marker for genetic differentiation between cattle animals for different body functions such as growth, metabolism, reproduction, immunity and energy balance. The nucleotide sequences of Egyptian cattle IGFBP-3 A and C alleles were submitted to GenBank with the accession numbers KF899893 and KF899894, respectively.

  3. Remarkable similarity in genome nucleotide sequences between the Schwarz FF-8 and AIK-C measles virus vaccine strains and apparent nucleotide differences in the phosphoprotein gene.

    Science.gov (United States)

    Ito, Chie; Ohgimoto, Shinji; Kato, Seiichi; Sharma, Luna Bhatta; Ayata, Minoru; Komase, Katsuhiro; Takeuchi, Kaoru; Ihara, Toshiaki; Ogura, Hisashi

    2011-07-01

    The Schwarz FF-8 (FF-8) and AIK-C measles virus vaccine strains are currently used for vaccination in Japan. Here, the complete genome nucleotide sequence of the FF-8 strain has been determined and its genome sequence found to be remarkably similar to that of the AIK-C strain. These two strains are differentiated only by two nucleotide differences in the phosphoprotein gene. Since the FF-8 strain does not possess the amino acid substitutions in the phospho- and fusion proteins which are responsible for the temperature-sensitivity and small syncytium formation phenotypes of the AIK-C strain, respectively, other unidentified common mechanisms likely attenuate both the FF-8 and AIK-C strains.

  4. Overexpression of DNA ligase III in mitochondria protects cells against oxidative stress and improves mitochondrial DNA base excision repair.

    Science.gov (United States)

    Akbari, Mansour; Keijzers, Guido; Maynard, Scott; Scheibye-Knudsen, Morten; Desler, Claus; Hickson, Ian D; Bohr, Vilhelm A

    2014-04-01

    Base excision repair (BER) is the most prominent DNA repair pathway in human mitochondria. BER also results in a temporary generation of AP-sites, single-strand breaks and nucleotide gaps. Thus, incomplete BER can result in the generation of DNA repair intermediates that can disrupt mitochondrial DNA replication and transcription and generate mutations. We carried out BER analysis in highly purified mitochondrial extracts from human cell lines U2OS and HeLa, and mouse brain using a circular DNA substrate containing a lesion at a specific position. We found that DNA ligation is significantly slower than the preceding mitochondrial BER steps. Overexpression of DNA ligase III in mitochondria improved the rate of overall BER, increased cell survival after menadione induced oxidative stress and reduced autophagy following the inhibition of the mitochondrial electron transport chain complex I by rotenone. Our results suggest that the amount of DNA ligase III in mitochondria may be critical for cell survival following prolonged oxidative stress, and demonstrate a functional link between mitochondrial DNA damage and repair, cell survival upon oxidative stress, and removal of dysfunctional mitochondria by autophagy.

  5. DNA polymerases beta and lambda mediate overlapping and independent roles in base excision repair in mouse embryonic fibroblasts.

    Directory of Open Access Journals (Sweden)

    Elena K Braithwaite

    Full Text Available Base excision repair (BER is a DNA repair pathway designed to correct small base lesions in genomic DNA. While DNA polymerase beta (pol beta is known to be the main polymerase in the BER pathway, various studies have implicated other DNA polymerases in back-up roles. One such polymerase, DNA polymerase lambda (pol lambda, was shown to be important in BER of oxidative DNA damage. To further explore roles of the X-family DNA polymerases lambda and beta in BER, we prepared a mouse embryonic fibroblast cell line with deletions in the genes for both pol beta and pol lambda. Neutral red viability assays demonstrated that pol lambda and pol beta double null cells were hypersensitive to alkylating and oxidizing DNA damaging agents. In vitro BER assays revealed a modest contribution of pol lambda to single-nucleotide BER of base lesions. Additionally, using co-immunoprecipitation experiments with purified enzymes and whole cell extracts, we found that both pol lambda and pol beta interact with the upstream DNA glycosylases for repair of alkylated and oxidized DNA bases. Such interactions could be important in coordinating roles of these polymerases during BER.

  6. The role of the PHP domain associated with DNA polymerase X from Thermus thermophilus HB8 in base excision repair.

    Science.gov (United States)

    Nakane, Shuhei; Nakagawa, Noriko; Kuramitsu, Seiki; Masui, Ryoji

    2012-11-01

    Base excision repair (BER) is one of the most commonly used DNA repair pathways involved in genome stability. X-family DNA polymerases (PolXs) play critical roles in BER, especially in filling single-nucleotide gaps. In addition to a polymerase core domain, bacterial PolXs have a polymerase and histidinol phosphatase (PHP) domain with phosphoesterase activity which is also required for BER. However, the role of the PHP domain of PolX in bacterial BER remains unresolved. We found that the PHP domain of Thermus thermophilus HB8 PolX (ttPolX) functions as two types of phosphoesterase in BER, including a 3'-phosphatase and an apurinic/apyrimidinic (AP) endonuclease. Experiments using T. thermophilus HB8 cell lysates revealed that the majority of the 3'-phosphatase and AP endonuclease activities are attributable to the another phosphoesterase in T. thermophilus HB8, endonuclease IV (ttEndoIV). However, ttPolX possesses significant 3'-phosphatase activity in ΔttendoIV cell lysate, indicating possible complementation. Our experiments also reveal that there are only two enzymes that display the 3'-phosphatase activity in the T. thermophilus HB8 cell, ttPolX and ttEndoIV. Furthermore, phenotypic analysis of ΔttpolX, ΔttendoIV, and ΔttpolX/ΔttendoIV using hydrogen peroxide and sodium nitrite supports the hypothesis that ttPolX functions as a backup for ttEndoIV in BER.

  7. A recurrence of benign multicystic peritoneal mesothelioma treated through laparoscopic excision: a case report and review of the literature.

    Science.gov (United States)

    Witek, Tadeusz D; Marchese, Joseph W; Farrell, Timothy J

    2014-04-01

    Benign multicystic peritoneal mesothelioma is a rare cystic tumor with approximately 140 cases reported to date. It is found mainly in women of reproductive age and is commonly attached to the serosal surface of pelvic viscera. The pathogenesis is uncertain and debate regarding its neoplastic or reactive nature exists. The presenting symptoms are often nonspecific and most commonly include vague lower abdominal pain and fullness. Imaging studies are used to identify the lesion, but histologic studies with the aid of immunohistochemical techniques are needed for definitive diagnosis as the differential diagnosis is quite extensive. Surgical resection is the primary form of treatment, and follow-up is important due to the high rate of recurrence and the rare possibility of malignant transformation. Here, we present a case of a 50-year-old female with a recurrence of benign multicystic peritoneal mesothelioma treated through laparoscopic excision and also a review of the literature.

  8. Lumpectomy cavity shaved margins do not impact re-excision rates in breast cancer patients.

    Science.gov (United States)

    Coopey, Suzanne B; Buckley, Julliette M; Smith, Barbara L; Hughes, Kevin S; Gadd, Michele A; Specht, Michelle C

    2011-10-01

    The benefits of taking shaved cavity margins (SCM) at the time of lumpectomy are unclear. We sought to determine if taking SCM decreases re-excision rates by increasing the total breast tissue volume excised. We undertook a retrospective review of breast cancer patients who underwent lumpectomy from 2004 to 2006. Patients were divided into three groups. Group 1 had lumpectomy alone, group 2 had lumpectomy plus select (1-3) SCM, and group 3 had lumpectomy plus complete (≥4) SCM. Pathologic findings and surgical outcomes were compared between groups. 773 cancers treated by lumpectomy were included in this study; 197 were in group 1, 130 were in group 2, and 446 were in group 3. The mean total volume of breast tissue excised in group 1 (106.6 cm(3)) was significantly larger than the volume excised in groups 2 (79.3 cm(3)) and 3 (76.3 cm(3)). Rates of re-excision and successful breast-conservation therapy (BCT) were not significantly different between groups. Despite a lower total volume of breast tissue excised in groups 2 and 3, there was no significant increase in locoregional recurrence rates (LRR) at median follow-up of 54 months. Taking additional SCM during lumpectomy resulted in a significantly lower overall volume of breast tissue excised, with no increase in LRR. Contrary to prior studies, we found that SCM did not decrease re-excision rates or impact the success of BCT. Therefore, the main advantage of taking SCM appears to be that less breast tissue is excised, which could potentially improve cosmetic outcomes.

  9. Editor's Highlight: Base Excision Repair Variants and Pesticide Exposure Increase Parkinson's Disease Risk.

    Science.gov (United States)

    Sanders, Laurie H; Paul, Kimberly C; Howlett, Evan H; Lawal, Hakeem; Boppana, Sridhar; Bronstein, Jeff M; Ritz, Beate; Greenamyre, J Timothy

    2017-07-01

    Exposure to certain pesticides induces oxidative stress and increases Parkinson's disease (PD) risk. Mitochondrial DNA (mtDNA) damage is found in dopaminergic neurons in idiopathic PD and following pesticide exposure in experimental models thereof. Base excision repair (BER) is the major pathway responsible for repairing oxidative DNA damage in cells. Whether single nucleotide polymorphisms (SNPs) in BER genes alone or in combination with pesticide exposure influence PD risk is unknown. We investigated the contributions of functional SNPs in 2 BER genes (APEX1 and OGG1) and mitochondrial dysfunction- or oxidative stress-related pesticide exposure, including paraquat, to PD risk. We also studied the effect of paraquat on levels of mtDNA damage and mitochondrial bioenergetics. 619 PD patients and 854 population-based controls were analyzed for the 2 SNPs, APEX1 rs1130409 and OGG1 rs1052133. Ambient pesticide exposures were assessed with a geographic information system. Individually, or in combination, the BER SNPs did not influence PD risk. Mitochondrial-inhibiting (OR = 1.79, 95% CI [1.32, 2.42]), oxidative stress-inducing pesticides (OR = 1.61, 95% CI [1.22, 2.11]), and paraquat (OR = 1.54, 95% CI [1.23, 1.93]) were associated with PD. Statistical interactions were detected, including for a genetic risk score based on rs1130409 and rs1052133 and oxidative stress inducing pesticides, where highly exposed carriers of both risk genotypes were at the highest risk of PD (OR = 2.21, 95% CI [1.25, 3.86]); similar interactions were estimated for mitochondrial-inhibiting pesticides and paraquat alone. Additionally, paraquat exposure was found to impair mitochondrial respiration and increase mtDNA damage in in vivo and in vitro systems. Our findings provide insight into possible mechanisms involved in increased PD risk due to pesticide exposure in the context of BER genotype variants. © The Author 2017. Published by Oxford University Press on behalf of the

  10. ENGINES: exploring single nucleotide variation in entire human genomes

    Directory of Open Access Journals (Sweden)

    Salas Antonio

    2011-04-01

    Full Text Available Abstract Background Next generation ultra-sequencing technologies are starting to produce extensive quantities of data from entire human genome or exome sequences, and therefore new software is needed to present and analyse this vast amount of information. The 1000 Genomes project has recently released raw data for 629 complete genomes representing several human populations through their Phase I interim analysis and, although there are certain public tools available that allow exploration of these genomes, to date there is no tool that permits comprehensive population analysis of the variation catalogued by such data. Description We have developed a genetic variant site explorer able to retrieve data for Single Nucleotide Variation (SNVs, population by population, from entire genomes without compromising future scalability and agility. ENGINES (ENtire Genome INterface for Exploring SNVs uses data from the 1000 Genomes Phase I to demonstrate its capacity to handle large amounts of genetic variation (>7.3 billion genotypes and 28 million SNVs, as well as deriving summary statistics of interest for medical and population genetics applications. The whole dataset is pre-processed and summarized into a data mart accessible through a web interface. The query system allows the combination and comparison of each available population sample, while searching by rs-number list, chromosome region, or genes of interest. Frequency and FST filters are available to further refine queries, while results can be visually compared with other large-scale Single Nucleotide Polymorphism (SNP repositories such as HapMap or Perlegen. Conclusions ENGINES is capable of accessing large-scale variation data repositories in a fast and comprehensive manner. It allows quick browsing of whole genome variation, while providing statistical information for each variant site such as allele frequency, heterozygosity or FST values for genetic differentiation. Access to the data mart

  11. Induction of the Tn10 Precise Excision in E. coli Cells after Accelerated Heavy Ions Irradiation

    CERN Document Server

    Zhuravel, D V

    2003-01-01

    The influence of the irradiation of different kinds on the indication of the structural mutations in the bacteria Escherichia coli is considered. The regularities of the Tn10 precise excision after accelerated ^{4}He and ^{12}C ions irradiations with different linear energy transfer (LET) were investigated. Dose dependences of the survival and relative frequency of the Tn10 precise excision were obtained. It was shown, that the relative frequency of the Tn10 precise excision is the exponential function from the irradiation dose. Relative biological efficiency (RBE), and relative genetic efficiency (RGE) were calculated, and were treated as the function of the LET.

  12. Periprosthetic soft tissue recurrence of chondroblastoma after attempted en bloc excision from the proximal humerus

    Energy Technology Data Exchange (ETDEWEB)

    Hammond, G.W.; Tehranzadeh, J.; Hoang, B.H. [University of California, Irvine, Department of Orthopaedic Surgery, Orange (United States); Gu, M. [University of California, Irvine, Department of Pathology, Orange (United States)

    2006-01-01

    A case of soft tissue recurrence of chondroblastoma after attempted en bloc excision and endoprosthetic replacement is described. This tumor in the proximal humerus recurred after initial curettage and was subsequently treated by attempted en bloc excision with positive microscopic margins. The patient then presented with a large soft tissue recurrence surrounding the endoprosthesis. This periprosthetic recurrence necessitated re-excision and revision of the endoprosthesis. Recurrence is not uncommon following curettage of chondroblastoma. However, less is known about soft tissue recurrence after en bloc resection of this tumor with positive margins. A subset of chondroblastoma may exist with more locally aggressive behavior. (orig.)

  13. Copper-Controllable, Site-Specific DNA Excision in Transgenic Plants

    Institute of Scientific and Technical Information of China (English)

    PENG Xiang-lei; LIANG Bin; CHEN Ming; HU Yuan-lei; LIN Zhong-ping

    2003-01-01

    A copper-inducible, Cre-loxP recombination-mediated DNA excision system has been developed in transgenic tobacco plants. The copper inducible system derived from yeast was used for the control of the expression of the Cre recombinase. Upon copper induction, the GUS reporter gene expression unit flanked by two direct lox sites was excised from the transgenic tobacco genome. Quantitative fluorometric GUS assays,Northern blot and PCR analyses showed a high-efficient, copper-dependent and Cre-loxP mediated DNA recombination in all the tested transgenic lines. The copper inducible foreign gene excision might be of great potential in genetic control of transgenic crops.

  14. Alcohol excise duties in the European Union. Alkoholi maksustamine Euroopa Liidus

    Directory of Open Access Journals (Sweden)

    Viktor Trasberg

    2015-12-01

    Full Text Available Alcohol taxation plays an important role in the alcohol policies of countries in the European Union. Alcohol excise duties are not a very significant part of government budgets; however, they form consumer behaviour, limit access to alcohol products and correct market externalities. The paper analyses the level and structure of alcohol excise duties in European countries. In the EU, the levels of alcohol excise duties are harmonized across the member states. Nevertheless, there is significant variety in the alcohol tax rates. The paper highlights the correlations between alcohol tax rates and interprets alcohol tax rate design across EU countries

  15. Divergent mechanisms for enzymatic excision of 5-formylcytosine and 5-carboxylcytosine from DNA

    OpenAIRE

    Maiti, Atanu; Michelson, Anna Zhachkina; Armwood, Cherece J; Lee, Jeehiun K.; Drohat, Alexander C.

    2013-01-01

    5-methylcytosine (mC) is an epigenetic mark that impacts transcription, development, and genome stability, and aberrant DNA methylation contributes to aging and cancer. Active DNA demethylation involves stepwise oxidation of mC to 5-hydroxymethylcytosine, 5-formylcytosine (fC), and potentially 5-carboxylcytosine (caC), excision of fC or caC by thymine DNA glycosylase (TDG), and restoration of cytosine via follow-on base excision repair. Here, we investigate the mechanism for TDG excision of f...

  16. Different characteristics and nucleotide binding properties of inosine monophosphate dehydrogenase (IMPDH isoforms.

    Directory of Open Access Journals (Sweden)

    Elaine C Thomas

    Full Text Available We recently reported that Inosine Monophosphate Dehydrogenase (IMPDH, a rate-limiting enzyme in de novo guanine nucleotide biosynthesis, clustered into macrostructures in response to decreased nucleotide levels and that there were differences between the IMPDH isoforms, IMPDH1 and IMPDH2. We hypothesised that the Bateman domains, which are present in both isoforms and serve as energy-sensing/allosteric modules in unrelated proteins, would contribute to isoform-specific differences and that mutations situated in and around this domain in IMPDH1 which give rise to retinitis pigmentosa (RP would compromise regulation. We employed immuno-electron microscopy to investigate the ultrastructure of IMPDH macrostructures and live-cell imaging to follow clustering of an IMPDH2-GFP chimera in real-time. Using a series of IMPDH1/IMPDH2 chimera we demonstrated that the propensity to cluster was conferred by the N-terminal 244 amino acids, which includes the Bateman domain. A protease protection assay suggested isoform-specific purine nucleotide binding characteristics, with ATP protecting IMPDH1 and AMP protecting IMPDH2, via a mechanism involving conformational changes upon nucleotide binding to the Bateman domain without affecting IMPDH catalytic activity. ATP binding to IMPDH1 was confirmed in a nucleotide binding assay. The RP-causing mutation, R224P, abolished ATP binding and nucleotide protection and this correlated with an altered propensity to cluster. Collectively these data demonstrate that (i the isoforms are differentially regulated by AMP and ATP by a mechanism involving the Bateman domain, (ii communication occurs between the Bateman and catalytic domains and (iii the RP-causing mutations compromise such regulation. These findings support the idea that the IMPDH isoforms are subject to distinct regulation and that regulatory defects contribute to human disease.

  17. Excision Arthroplasty for First CMC Joint Tuberculous Osteomyelitis

    Science.gov (United States)

    Vora, Harshil J.; Patil, Sanjay; latkar, Chintamani; Sawant, Sarvesh

    2015-01-01

    Introduction: Tuberculous involvement of metacarpals and phalanges is a rare presentation of extrapulmonary tuberculosis in adult. Tuberculous infection of the metacarpals, metatarsal and phalanges of hands and feet is known as tubercular dactylitis. Case Report: A 65 years old female with history of pain and swelling at 1st metacarpal of left hand, since 3 months which gradual in onset and progressive in nature associated with multiple cervical swellings. While radiographs showed a pathological fracture of the 1st carpo-metacarpal joint (CMCJ) with soft tissue swelling, MRI revealed a large heterogenous lesion at the carpo-metacarpal joint of the thumb with bony erosions of the trapezium and 1st metacarpal base on T2W-STIR images. The lesion was extending upto the palmar aspect of the hand and displacing flexor pollicis longus tendon medially. During surgery, there was caseous material seen which was debrided and the fractured fragment was excised and sent for biopsy. The CMCJ was found to be unstable and a kirschner wire was used to stabilize the 1st CMCJ and immobilized in a POP splint. The biopsy of the fragment revealed tuberculous osteomyeltis. On follow-up the K-wire had backed out partially at the end of 5 weeks which was then removed and range of motion was started. At end of 1 year follow up the patient had little restriction of movement as compared to the opposite hand with no pain and hindrance in daily activity. Conclusion: The swelling subsided once Anti-Tubercular Treatment was started. The cervical lymphadenopathy also resolved over a period of 1 month. PMID:27299036

  18. Ku80-deleted cells are defective at base excision repair

    Energy Technology Data Exchange (ETDEWEB)

    Li, Han [The University of Texas Health Science Center at San Antonio, The Institute of Biotechnology, The Department of Molecular Medicine, 15355 Lambda Drive, San Antonio, TX 78245-3207 (United States); Tumor Suppression Group, Spanish National Cancer Research Centre (CNIO), Madrid 28029 (Spain); Marple, Teresa [The University of Texas Health Science Center at San Antonio, The Institute of Biotechnology, The Department of Molecular Medicine, 15355 Lambda Drive, San Antonio, TX 78245-3207 (United States); Hasty, Paul, E-mail: hastye@uthscsa.edu [The University of Texas Health Science Center at San Antonio, The Institute of Biotechnology, The Department of Molecular Medicine, 15355 Lambda Drive, San Antonio, TX 78245-3207 (United States); Tumor Suppression Group, Spanish National Cancer Research Centre (CNIO), Madrid 28029 (Spain)

    2013-05-15

    Graphical abstract: - Highlights: • Ku80-deleted cells are hypersensitive to ROS and alkylating agents. • Cells deleted for Ku80, but not Ku70 or Lig4, have reduced BER capacity. • OGG1 rescues hypersensitivity to H{sub 2}O{sub 2} and paraquat in Ku80-mutant cells. • Cells deleted for Ku80, but not Lig4, are defective at repairing AP sites. • Cells deleted for Ku80, but not Lig4 or Brca2 exon 27, exhibit increased PAR. - Abstract: Ku80 forms a heterodimer with Ku70, called Ku, that repairs DNA double-strand breaks (DSBs) via the nonhomologous end joining (NHEJ) pathway. As a consequence of deleting NHEJ, Ku80-mutant cells are hypersensitive to agents that cause DNA DSBs like ionizing radiation. Here we show that Ku80 deletion also decreased resistance to ROS and alkylating agents that typically cause base lesions and single-strand breaks (SSBs). This is unusual since base excision repair (BER), not NHEJ, typically repairs these types of lesions. However, we show that deletion of another NHEJ protein, DNA ligase IV (Lig4), did not cause hypersensitivity to these agents. In addition, the ROS and alkylating agents did not induce γ-H2AX foci that are diagnostic of DSBs. Furthermore, deletion of Ku80, but not Lig4 or Ku70, reduced BER capacity. Ku80 deletion also impaired BER at the initial lesion recognition/strand scission step; thus, involvement of a DSB is unlikely. Therefore, our data suggests that Ku80 deletion impairs BER via a mechanism that does not repair DSBs.

  19. Robotic complete mesocolic excision for right-sided colon cancer.

    Science.gov (United States)

    Ozben, Volkan; Baca, Bilgi; Atasoy, Deniz; Bayraktar, Onur; Aghayeva, Afag; Cengiz, Turgut Bora; Erguner, Ilknur; Karahasanoglu, Tayfun; Hamzaoglu, Ismail

    2016-10-01

    Complete mesocolic excision (CME) with central vascular ligation for right-sided colon cancer has been proven to provide superior oncologic outcomes and survival advantage when compared to standard lymphadenectomy [1]. A number of studies comparing conventional laparoscopic versus open CME have shown feasibility and safety of the laparoscopic approach with acceptable oncological profile and postoperative outcomes [2, 3]. The introduction of robotic systems with its technical advantages, including improved vision, better ergonomics and precise dissection, has further revolutionized minimally invasive approach in colorectal surgery. However, there seems to be a relatively slow adoption of robotic approach in the CME technique for right-sided colon cancer. This video demonstrates our detailed operative technique and feasibility for performing right-sided CME robotically. The surgical procedure is performed with a medial-to-lateral approach through four 8-mm robotic and one assistant ports. First, the ileocolic vessels are isolated, clipped and transected near their origins. Cephalad dissection continues along the ventral aspect of the superior mesenteric vein. Staying in the embryological planes between the mesocolon and retroperitoneal structures, mesenteric dissection is extended up to the root of the right colic vessels, if present, and the middle colic vessels, which are clipped and divided individually near their origins. After the terminal ileum is transected using an endolinear staple, the colon is mobilized fully from gastrocolic tissue and then from its lateral attachments. The transverse colon is transected under the guidance of near-infrared fluorescence imaging. Creation of an intracorporeal side-to-side ileotransversostomy anastomosis and extraction of the specimen complete the operation. We consider robotic CME to be feasible, safe and oncologically adequate for the treatment of right-sided colon cancer. Its technical advantages may lead to further

  20. Polymorphism of the DNA Base Excision Repair Genes in Keratoconus

    Directory of Open Access Journals (Sweden)

    Katarzyna A. Wojcik

    2014-10-01

    Full Text Available Keratoconus (KC is a degenerative corneal disorder for which the exact pathogenesis is not yet known. Oxidative stress is reported to be associated with this disease. The stress may damage corneal biomolecules, including DNA, and such damage is primarily removed by base excision repair (BER. Variation in genes encoding BER components may influence the effectiveness of corneal cells to cope with oxidative stress. In the present work we genotyped 5 polymorphisms of 4 BER genes in 284 patients and 353 controls. The A/A genotype of the c.–1370T>A polymorphism of the DNA polymerase γ (POLG gene was associated with increased occurrence of KC, while the A/T genotype was associated with decreased occurrence of KC. The A/G genotype and the A allele of the c.1196A>G polymorphism of the X-ray repair cross-complementing group 1 (XRCC1 were associated with increased, and the G/G genotype and the G allele, with decreased KC occurrence. Also, the C/T and T as well as C/C genotypes and alleles of the c.580C>T polymorphism of the same gene displayed relationship with KC occurrence. Neither the g.46438521G>C polymorphism of the Nei endonuclease VIII-like 1 (NEIL1 nor the c.2285T>C polymorphism of the poly(ADP-ribose polymerase-1 (PARP-1 was associated with KC. In conclusion, the variability of the XRCC1 and POLG genes may play a role in KC pathogenesis and determine the risk of this disease.

  1. Iontophoretic delivery of 5-fluorouracil through excised human stratum corneum.

    Science.gov (United States)

    Singh, B N; Jayaswal, S B

    2008-04-01

    The objective of this study was to determine the effects of ionization, current density and penetration enhancers on the iontophoretic delivery of 5-fluorouracil (5-FU) through excised human stratum corneum (HSC). The iontophoretic (cathodal) transport of 5-FU was assessed in vitro at three physiologically relevant pH values of 5.0, 7.4 and 8.0, at various levels of current density ranging between 0.15 to 0.98 mA/cm2, and in the presence of suitable penetration enhancers, namely Azone(®) (AZ), lauryl alcohol (LA), and isopropyl myristate (IPM). The steady-state flux at constant current density (0.47 mA/cm(2)) was increased by approximately 19, 10 and 27 fold at pH 5, 7.4 and 8.0, respectively. The effect of current density at pH 7.4 exhibited a linear correlation between current density and steady-state flux (r = 0.98, p = 0.002), which indicates the potential of iontophoresis for controlled transdermal delivery of 5-FU. The combination of cathodal iontophoresis with IPM produced an additive enhancement which may be attributed to aggravated skin perturbation effect and increased skin conductivity. Other enhancers such as AZ and LA produced negative or no further enhancement respectively, when used in conjunction with cathodal iontophoresis. It may be therefore concluded that pH and current density play critical role during iontophoretic delivery of 5-FU, and combination of a chemical penetration enhancer and iontophoresis can not be always viewed as a synergistic strategy which should be evaluated on a case-by-case basis for each drug candidate/enhancer combination.

  2. Single-nucleotide polymorphisms in the Toll-like receptor pathway increase susceptibility to infections in severely injured trauma patients

    NARCIS (Netherlands)

    M.W.G.A. Bronkhorst (Maarten); N.D.A. Boyé (Nicole); M.A.Z. Lomax (Miranda); R. Vossen (Rolf); J.F. Bakker (Jurriaan); P. Patka (Peter); E.M.M. van Lieshout (Esther)

    2013-01-01

    textabstractBackground: Sepsis and subsequent multiple-organ failure are the predominant causes of late mortality in trauma patients. Susceptibility and response to infection is, in part, heritable. Single-nucleotide polymorphisms (SNPs) in Toll-like receptor (TLR) and cluster of differentiation 14

  3. Dbl family guanine nucleotide exchange factors.

    Science.gov (United States)

    Zheng, Y

    2001-12-01

    The Dbl family of guanine nucleotide exchange factors are multifunctional molecules that transduce diverse intracellular signals leading to the activation of Rho GTPases. The tandem Dbl-homology and pleckstrin-homology domains shared by all members of this family represent the structural module responsible for catalyzing the GDP-GTP exchange reaction of Rho proteins. Recent progress in genomic, genetic, structural and biochemical studies has implicated Dbl family members in diverse biological processes, including growth and development, skeletal muscle formation, neuronal axon guidance and tissue organization. The detailed pictures of their autoregulation, agonist-controlled activation and mechanism of interaction with Rho GTPase substrates, have begun to emerge.

  4. In Vitro Selection Using Modified or Unnatural Nucleotides

    Science.gov (United States)

    Stovall, Gwendolyn M.; Bedenbaugh, Robert S.; Singh, Shruti; Meyer, Adam J.; Hatala, Paul J.; Ellington, Andrew D.; Hall, Bradley

    2014-01-01

    Incorporation of modified nucleotides into in vitro RNA or DNA selections offer many potential advantages, such as the increased stability of selected nucleic acids against nuclease degradation, improved affinities, expanded chemical functionality, and increased library diversity. This unit provides useful information and protocols for in vitro selection using modified nucleotides. It includes a discussion of when to use modified nucleotides; protocols for evaluating and optimizing transcription reactions, as well as confirming the incorporation of the modified nucleotides; protocols for evaluating modified nucleotide transcripts as template in reverse transcription reactions; protocols for the evaluation of the fidelity of modified nucleotides in the replication and the regeneration of the pool; and a protocol to compare modified nucleotide pools and selection conditions. PMID:25606981

  5. [Identification of single nucleotide polymorphisms in centenarians].

    Science.gov (United States)

    Gambini, Juan; Gimeno-Mallench, Lucía; Inglés, Marta; Olaso, Gloria; Abdelaziz, Kheira Mohamed; Avellana, Juan Antonio; Belenguer, Ángel; Cruz, Raquel; Mas-Bargues, Cristina; Borras, Consuelo; Viña, José

    2016-01-01

    Longevity is determined by genetic and external factors, such as nutritional, environmental, social, etc. Nevertheless, when living conditions are optimal, longevity is determined by genetic variations between individuals. In a same population, with relative genotypic homogeneity, subtle changes in the DNA sequence affecting a single nucleotide can be observed. These changes, called single nucleotide polymorphisms (SNP) are present in 1-5% of the population. A total of 92 subjects were recruited, including 28 centenarians and 64 controls, in order to find SNP that maybe implicated in the extreme longevity, as in the centenarians. Blood samples were collected to isolate and amplify the DNA in order to perform the analysis of SPN by Axiom™ Genotyping of Affymetrix technology. Statistical analyses were performed using the Plink program and libraries SNPassoc and skatMeta. Our results show 12 mutations with a p<.001, where 5 of these (DACH1, LOC91948, BTB16, NFIL3 y HDAC4) have regulatory functions of the expressions of others genes. Therefore, these results suggest that the genetic variation between centenarians and controls occurs in five genes that are involved in the regulation of gene expression to adapt to environmental changes better than controls. Copyright © 2015 SEGG. Published by Elsevier Espana. All rights reserved.

  6. Estimation of evolutionary distances between nucleotide sequences.

    Science.gov (United States)

    Zharkikh, A

    1994-09-01

    A formal mathematical analysis of the substitution process in nucleotide sequence evolution was done in terms of the Markov process. By using matrix algebra theory, the theoretical foundation of Barry and Hartigan's (Stat. Sci. 2:191-210, 1987) and Lanave et al.'s (J. Mol. Evol. 20:86-93, 1984) methods was provided. Extensive computer simulation was used to compare the accuracy and effectiveness of various methods for estimating the evolutionary distance between two nucleotide sequences. It was shown that the multiparameter methods of Lanave et al.'s (J. Mol. Evol. 20:86-93, 1984), Gojobori et al.'s (J. Mol. Evol. 18:414-422, 1982), and Barry and Hartigan's (Stat. Sci. 2:191-210, 1987) are preferable to others for the purpose of phylogenetic analysis when the sequences are long. However, when sequences are short and the evolutionary distance is large, Tajima and Nei's (Mol. Biol. Evol. 1:269-285, 1984) method is superior to others.

  7. Classifying Coding DNA with Nucleotide Statistics

    Directory of Open Access Journals (Sweden)

    Nicolas Carels

    2009-10-01

    Full Text Available In this report, we compared the success rate of classification of coding sequences (CDS vs. introns by Codon Structure Factor (CSF and by a method that we called Universal Feature Method (UFM. UFM is based on the scoring of purine bias (Rrr and stop codon frequency. We show that the success rate of CDS/intron classification by UFM is higher than by CSF. UFM classifies ORFs as coding or non-coding through a score based on (i the stop codon distribution, (ii the product of purine probabilities in the three positions of nucleotide triplets, (iii the product of Cytosine (C, Guanine (G, and Adenine (A probabilities in the 1st, 2nd, and 3rd positions of triplets, respectively, (iv the probabilities of G in 1st and 2nd position of triplets and (v the distance of their GC3 vs. GC2 levels to the regression line of the universal correlation. More than 80% of CDSs (true positives of Homo sapiens (>250 bp, Drosophila melanogaster (>250 bp and Arabidopsis thaliana (>200 bp are successfully classified with a false positive rate lower or equal to 5%. The method releases coding sequences in their coding strand and coding frame, which allows their automatic translation into protein sequences with 95% confidence. The method is a natural consequence of the compositional bias of nucleotides in coding sequences.

  8. Surgical Excision of Non–Melanoma Skin Cancer in an Elderly Veteran’s Affairs Population

    Directory of Open Access Journals (Sweden)

    C. Malcolm M. Stewart, BS

    2014-12-01

    Conclusions: Although reduction of residual tumor at reexcision is noted with both BCC and even more so with SCC, the rate at which this occurs is not sufficient that a general recommendation to forgo surgical excision can be made.

  9. Excise Tax Rates On Packs Of Cigarettes PowerPoint Slides

    Data.gov (United States)

    U.S. Department of Health & Human Services — Download the current cigarette excise tax rates on packs of cigarettes slides. These slides are available in PDF and PowerPoint formats. The PDF version can be found...

  10. Excision of the urachal remnant using the abdominal wall-lift laparoscopy: A case report

    Directory of Open Access Journals (Sweden)

    Kosuke Kobayashi

    2016-01-01

    Discussion and conclusion: Urachal sinus excision using the abdominal wall-lift laparoscopy seems to surpass the previously reported methods in term of safety, cosmetics, and adequacy of surgical procedures.

  11. Evaluation of endoscopic laser excision of polypropylene mesh/sutures following anti-incontinence procedures.

    LENUS (Irish Health Repository)

    Davis, N F

    2012-11-01

    We reviewed our experience with and outcome of the largest series to our knowledge of patients who underwent endoscopic laser excision of eroded polypropylene mesh or sutures as a complication of previous anti-incontinence procedures.

  12. Surgical Excision of Benign Papillomas Diagnosed with Core Biopsy: A Community Hospital Approach

    Directory of Open Access Journals (Sweden)

    Eka Rozentsvayg

    2011-01-01

    Full Text Available Our goal was to assess the value of surgical excision of benign papillomas of the breast diagnosed on percutaneous core biopsy by determining the frequency of upgrade to malignancies and high risk lesions on a final surgical pathology. We reviewed 67 patients who had biopsies yielding benign papilloma and underwent subsequent surgical excision. Surgical pathology of the excised lesions was compared with initial core biopsy pathology results. 54 patients had concordant benign core and excisional pathology. Cancer (ductal carcinoma in situ and invasive ductal carcinoma was diagnosed in five (7% patients. Surgery revealed high-risk lesions in 8 (12% patients, including atypical ductal hyperplasia, atypical lobular hyperplasia, and lobular carcinoma in situ. Cancer and high risk lesions accounted for 13 (19% upstaging events from benign papilloma diagnosis. Our data suggests that surgical excision is warranted with core pathology of benign papilloma.

  13. Natural orifice total mesorectal excision using transanal port and laparoscopic assistance

    OpenAIRE

    Tuech, Jean-Jacques; Bridoux, Valérie; Kianifard, Babak; Schwarz, Lilian; Tsilividis, Basile; Huet, Emmanuel; Michot, Francis

    2011-01-01

    Abstract Natural Orifice Transluminal Endoscopic Surgery (NOTES) is an emerging concept which has been recently applied to the field of rectal excision. The authors describe a case of total mesorectal excision using a transanal port and laparoscopic assistance We described a procedure performed in a A 45-year-old for a rectal adenocarcinoma (1cm wide, T1sm3) 3cm above the dentate line. The procedure is described in the text and in a didactic video. ...

  14. Effect of Topical Application of Silymarin (Silybum marianum) on Excision Wound Healing in Albino Rats

    OpenAIRE

    Naghmeh Ghannadian; Mahboobeh Mehrabani Natanzi; Maliheh Paknejad; Seyed Mohammad Tavangar; Ahmad Reza Dehpour; Mohammad Kamalinejad; Hossein Rastegar (PhD); Roya Sharifi; Minoo Akbari; Parvin Pasalar

    2012-01-01

    Silymarin, an extract from Silybum marianum, has been shown to have antioxidant properties. However, there is no scientific report on wound healing activity of the silymarin. The purpose of this study was to evaluate the effect of topical administration of silymarin on excision wound healing in rats. Excision wounds were made on the back of rats. Rats were divided into three groups, as control, vehicle, and treatment. Vehicle and treatment groups received polyethylene glycol and silymarin dis...

  15. Nucleotide diversity patterns of local adaptation at drought-related candidate genes in wild tomatoes.

    Science.gov (United States)

    Xia, Hui; Camus-Kulandaivelu, Létizia; Stephan, Wolfgang; Tellier, Aurélien; Zhang, Zhenwen

    2010-10-01

    We surveyed nucleotide diversity at two candidate genes LeNCED1 and pLC30-15, involved in an ABA (abscisic acid) signalling pathway, in two closely related tomato species Solanum peruvianum and Solanum chilense. Our six population samples (three for each species) cover a range of mesic to very dry habitats. The ABA pathway plays an important role in the plants' response to drought stress. LeNCED1 is an upstream gene involved in ABA biosynthesis, and pLC30-15 is a dehydrin gene positioned downstream in the pathway. The two genes show very different patterns of nucleotide variation. LeNCED1 exhibits very low nucleotide diversity relative to the eight neutral reference loci that were previously surveyed in these populations. This suggests that strong purifying selection has been acting on this gene. In contrast, pLC30-15 exhibits higher levels of nucleotide diversity and, in particular in S. chilense, higher genetic differentiation between populations than the reference loci, which is indicative of local adaptation. In the more drought-tolerant species S. chilense, one population (from Quicacha) shows a significant haplotype structure, which appears to be the result of positive (diversifying) selection.

  16. Rasp21 sequences opposite the nucleotide binding pocket are required for GRF-mediated nucleotide release

    DEFF Research Database (Denmark)

    Leonardsen, L; DeClue, J E; Lybaek, H;

    1996-01-01

    , the sensitivity of H-Ras to GRF was abolished when residues 130-139 were replaced by proline-aspartic acid-glutamine, whereas substitution of the entire loop 8 (residues 123-130 replaced by leucine-isoleucine-arginine) had no effect on the stimulation of guanine nucleotide release by GRF. Substrate activity...

  17. Neurological manifestations following partial excision in spinal meningioma: case report.

    Science.gov (United States)

    Okoth, P A

    2007-01-01

    Presented here is a 16-year-old girl who was referred on 30th January 1996 with diagnosis of cord compression with spastic paraplegia with sensory level at T7/T8. CT scan myelogam confirmed soft tissue density mass displacing cord to the left with no dye being seen beyond T3. Thoracic spine decompressive laminectomy was performed on 1st January 1996 at Nairobi West Hospital extending from T3 to T6 level, which revealed a fibrous haemorrhagic tumour. Histology showed meningioma (mixed fibrous type and meningoepitheliomatous type) with many psammoma bodies. She had a stormy post-operative period, with infection and wound dehiscence. This was treated with appropriate antibiotics and wound care. She was eventually rehabilitated and was able to walk with the aid of a walking frame because of persistent spasticity of right leg. She was seen once as an outpatient by author on 6th July 1996, she was able to use the walking frame, but the right leg was still held in flexion deformity at the knee. She was thus referred to an orthopaedic surgeon for possible tenotomy. She was able to resume her studies at the University ambulating using a wheel chair and walking frame. She presented with worsening of symptoms in 2001 (five years after her first surgery). MRI scan thoracic spine revealed a left anterolateral intradural lesion extending from T3 to T5 vertebral body level compressing and displacing the spinal cord. She had a repeat surgery on 6th March 2001 at Kenyatta National Hospital; spastic paraparesis and urinary incontinenece persisted. She also developed bed sores and recurrent urinary tract infections. She was followed up by the author and other medical personnel in Mwea Mission Hospital where she eventually succumbed in 2005, nine years after her first surgery. This case is presented as a case of incompletely excised spinal meningioma to highlight some of the problems of managing spinal meningiomas when operating microscope and embolisation of tumours are not readily

  18. Effects of methylene-blue staining on the extent of pilonidal sinus excision.

    Science.gov (United States)

    Ardelt, M; Kocijan, R; Dittmar, Y; Fahrner, R; Rauchfuss, F; Scheuerlein, H; Settmacher, U

    2016-06-01

    We aimed to examine the effects of methylene-blue staining (MBS) on the volume of specimens after excision of pilonidal sinuses. This was a retrospective analysis of 135 excised specimens after pilonidal sinus (PS) surgery. All patients underwent procedures at the Department of Surgery of University Hospital Jena between 2000 and 2010. All specimens were measured in three dimensions. To calculate the volumes of excised specimens, we used a model of a hemi-ellipsoid. Demographic information (age, height, weight, body mass index, smoking status) were also obtained for all patients. Excised specimens with MBS had significantly larger volumes (pmethylene blue (MB). In addition, the volume was larger in subjects with a recurrent PS (p=0.021), which was predominantly the case in female subjects (p=0.025). These data suggest that excised specimens with MBS had significantly larger volumes of the excised specimen compared with specimens that were not stained with MB. MBS of a fistula system could enable such a system to be marked sufficiently, thereby facilitating complete resection of a PS.

  19. Apoplastic superoxide production and peroxidase activity by intact and excised axenically grown seedling roots of sunflower.

    Science.gov (United States)

    Garrido, Inmaculada; Espinosa, Francisco; Alvarez-Tinaut, M Carmen

    2012-10-01

    Excised and cold-preincubated sunflower seedling roots were compared with intact non-preincubated roots to test the effect of the injury stress and cold preincubation on the oxidative burst measured as apoplastic superoxide (O (2) (.-) ) generation and exocellular peroxidase (ECPOX) activity. Preincubated excised or intact roots released into the medium apoplastic proteins with peroxidase activity. Intact and excised roots responded to methyl jasmonate by an immediate oxidative burst that could not be induced by salicylic acid; both phytohormones also induced a slight and slow O (2)(.-) generation and ECPOX activity on excised roots, when added to the cold preincubation medium. The results with cyanide, azide, SHAM (ECPOX inhibitors) and diphenylene iodonium (inhibitor of trans-plasma membrane NAD(P)H-oxidases (NOX)-respiratory burst oxidase homologue in plants (RBOH), the trans-plasmamembrane nicotinamide adenine dinucleotide phosphate oxidase) are consistent with the hypothesis that different systems may be the origin of O (2) (.-) in intact and excised roots; ECPOX was an important component of them in both, together with NOX-RBOH in intact roots, but in excised roots the last one was replaced by an oxidase sensitive to the same inhibitors as the alternative mitochondrial oxidase. According to our hypothesis, these results could be explained if the electron flux would be deviated to different interconnected plasma membrane-redox systems, with different terminal oxidases, activated by different effectors or stresses.

  20. Mutations of PKA cyclic nucleotide-binding domains reveal novel aspects of cyclic nucleotide selectivity.

    Science.gov (United States)

    Lorenz, Robin; Moon, Eui-Whan; Kim, Jeong Joo; Schmidt, Sven H; Sankaran, Banumathi; Pavlidis, Ioannis V; Kim, Choel; Herberg, Friedrich W

    2017-07-06

    Cyclic AMP and cyclic GMP are ubiquitous second messengers that regulate the activity of effector proteins in all forms of life. The main effector proteins, the 3',5'-cyclic adenosine monophosphate (cAMP)-dependent protein kinase (PKA) and the 3',5'-cyclic guanosine monophosphate (cGMP)-dependent protein kinase (PKG), are preferentially activated by cAMP and cGMP, respectively. However, the molecular basis of this cyclic nucleotide selectivity is still not fully understood. Analysis of isolated cyclic nucleotide-binding (CNB) domains of PKA regulatory subunit type Iα (RIα) reveals that the C-terminal CNB-B has a higher cAMP affinity and selectivity than the N-terminal CNB-A. Here, we show that introducing cGMP-specific residues using site-directed mutagenesis reduces the selectivity of CNB-B, while the combination of two mutations (G316R/A336T) results in a cGMP-selective binding domain. Furthermore, introducing the corresponding mutations (T192R/A212T) into the PKA RIα CNB-A turns this domain into a highly cGMP-selective domain, underlining the importance of these contacts for achieving cGMP specificity. Binding data with the generic purine nucleotide 3',5'-cyclic inosine monophosphate (cIMP) reveal that introduced arginine residues interact with the position 6 oxygen of the nucleobase. Co-crystal structures of an isolated CNB-B G316R/A336T double mutant with either cAMP or cGMP reveal that the introduced threonine and arginine residues maintain their conserved contacts as seen in PKG I CNB-B. These results improve our understanding of cyclic nucleotide binding and the molecular basis of cyclic nucleotide specificity. © 2017 The Author(s); published by Portland Press Limited on behalf of the Biochemical Society.

  1. Interaction of p21CDKN1A with PCNA regulates the histone acetyltransferase activity of p300 in nucleotide excision repair

    Science.gov (United States)

    Cazzalini, Ornella; Perucca, Paola; Savio, Monica; Necchi, Daniela; Bianchi, Livia; Stivala, Lucia A.; Ducommun, Bernard; Scovassi, A. Ivana; Prosperi, Ennio

    2008-01-01

    The cell-cycle inhibitor p21CDKN1A has been suggested to directly participate in DNA repair, thanks to the interaction with PCNA. Yet, its role has remained unclear. Among proteins interacting with both p21 and PCNA, the histone acetyltransferase (HAT) p300 has been shown to participate in DNA repair. Here we report evidence indicating that p21 protein localizes and interacts with both p300 and PCNA at UV-induced DNA damage sites. The interaction between p300 and PCNA is regulated in vivo by p21. Indeed, loss of p21, or its inability to bind PCNA, results in a prolonged binding to chromatin and an increased association of p300 with PCNA, in UV-irradiated cells. Concomitantly, HAT activity of p300 is reduced after DNA damage. In vitro experiments show that inhibition of p300 HAT activity induced by PCNA is relieved by p21, which disrupts the association between recombinant p300 and PCNA. These results indicate that p21 is required during DNA repair to regulate p300 HAT activity by disrupting its interaction with PCNA. PMID:18263614

  2. Reconstruction of the Auricular Defect After Excision of Verrucous Carcinoma.

    Science.gov (United States)

    Oh, Jeong-Hoon; Lee, Ho Seok; Hwang, Jae Hyung; Park, Kyung-Ho

    2016-01-01

    Verrucous carcinoma is a highly differentiated variant of squamous cell carcinoma with a high local recurrence rate. Few studies of primary verrucous carcinoma of the auricle have reported on the surgical outcome. The authors present herein a case in which a verrucous carcinoma of the auricle was successfully removed and reconstructed using a retroauricular pull-through island flap, and the authors briefly review the relevant literature.

  3. [Nucleotide receptors--structure and function, history and perspectives].

    Science.gov (United States)

    Barańska, Jolanta

    2014-01-01

    First nucleotide receptors were discovered by Geoffrey Burnstock in 70ties of the last century, as a purinoreceptors activated by ATP. It was further found that they may be activated both by purine and pyrimidine nucleotides and their name was changed to nucleotide receptors. They are divided into two fsamilies: P1, activated by adenosine and P2, activated by nucleotides which are further divided into P2X and P2Y subfamilies. P2X are ionotropic receptors activated by ATP, P2Y (as the P1) are metabotropic receptors coupled with protein G. P2Y receptors are activated by ATP, ADP, UTP, UDP and UDP-sugar derivatives. This review describes early history of extracellular nucleotide signaling studies and presents current knowledge of the particular nucleotide receptors subtypes. The article also describes the structure and functional roles of these receptors and speculates about future research and therapeutic directions in this field.

  4. Unique nucleotide polymorphism of ankyrin gene cluster in Arabidopsis

    Indian Academy of Sciences (India)

    Jianchang Du; Xingna Wang; Mingsheng Zhang; Dacheng Tian; Yong-Hua Yang

    2007-01-01

    The ankyrin (ANK) gene cluster is a part of a multigene family encoding ANK transmembrane proteins in Arabidopsis thaliana, and plays an important role in protein–protein interactions and in signal pathways. In contrast to other regions of a genome, the ANK gene cluster exhibits an extremely high level of DNA polymorphism in an ∼5-kb region, without apparent decay. Phylogenetic analysis detects two clear, deeply differentiated haplotypes (dimorphism). The divergence between haplotypes of accession Col-0 and Ler-0 (Hap-C and Hap-L) is estimated to be 10.7%, approximately equal to the 10.5% average divergence between A. thaliana and A. lyrata. Sequence comparisons for the ANK gene cluster homologues in Col-0 indicate that the members evolve independently, and that the similarity among paralogues is lower than between alleles. Very little intralocus recombination or gene conversion is detected in ANK regions. All these characteristics of the ANK gene cluster are consistent with a tandem gene duplication and birth-and-death process. The possible mechanisms for and implications of this elevated nucleotide variation are also discussed, including the suggestion of balancing selection.

  5. Assessment of single nucleotide polymorphisms in screening 52 DNA repair and cell cycle control genes in Fanconi anemia patients

    Directory of Open Access Journals (Sweden)

    Petrović Sandra

    2015-01-01

    Full Text Available Fanconi anemia (FA is a rare genetically heterogeneous disorder associated with bone marrow failure, birth defects and cancer susceptibility. Apart from the disease- causing mutations in FANC genes, the identification of specific DNA variations, such as single nucleotide polymorphisms (SNPs, in other candidate genes may lead to a better clinical description of this condition enabling individualized treatment with improvement of the prognosis. In this study, we have assessed 95 SNPs located in 52 key genes involved in base excision repair (BER, nucleotide excision repair (NER, mismatch repair (MMR, double strand break (DSB repair and cell cycle control using a DNA repair chip (Asper Biotech, Estonia which includes most of the common variants for the candidate genes. The SNP genotyping was performed in five FA-D2 patients and in one FA-A patient. The polymorphisms studied were synonymous (n=10, nonsynonymous (missense (n=52 and in non-coding regions of the genome (introns and 5 ‘and 3’ untranslated regions (UTR (n=33. Polymorphisms found at the homozygous state are selected for further analysis. Our results have shown a significant inter-individual variability among patients in the type and the frequency of SNPs and also elucidate the need for further studies of polymorphisms located in ATM, APEX APE 1, XRCC1, ERCC2, MSH3, PARP4, NBS1, BARD1, CDKN1B, TP53 and TP53BP1 which may be of great importance for better clinical description of FA. In addition, the present report recommends the use of SNPs as predictive and prognostic genetic markers to individualize therapy of FA patients. [Projekat Ministarstva nauke Republike Srbije, br. 173046

  6. Association between single nucleotide polymorphisms in ERCC4 and risk of squamous cell carcinoma of the head and neck.

    Directory of Open Access Journals (Sweden)

    Hongping Yu

    Full Text Available BACKGROUND: Excision repair cross-complementation group 4 gene (ERCC4/XPF plays an important role in nucleotide excision repair and participates in removal of DNA interstrand cross-links and DNA double-strand breaks. Single nucleotide polymorphisms (SNPs in ERCC4 may impact repair capacity and affect cancer susceptibility. METHODOLOGY/PRINCIPAL FINDINGS: In this case-control study, we evaluated associations of four selected potentially functional SNPs in ERCC4 with risk of squamous cell carcinoma of the head and neck (SCCHN in 1,040 non-Hispanic white patients with SCCHN and 1,046 cancer-free matched controls. We found that the variant GG genotype of rs2276466 was significantly associated with a decreased risk of SCCHN (OR = 0.69, 95% CI 0.50-0.96, and that the variant TT genotype of rs3136038 showed a borderline significant decreased risk with SCCHN (OR = 0.76, 95% CI: 0.58-1.01 in the recessive model. Such protective effects were more evident in oropharyngeal cancer (OR = 0.61, 95% CI: 0.40-0.92 for rs2276466; OR = 0.69, 95% CI: 0.48-0.98 for rs3136038. No significant associations were found for the other two SNPs (rs1800067 and rs1799798. In addition, individuals with the rs2276466 GG or with the rs3136038 TT genotypes had higher levels of ERCC4 mRNA expression than those with the corresponding wild-type genotypes in 90 Epstein-Barr virus-transformed lymphoblastoid cell lines derived from Caucasians. CONCLUSIONS: These results suggest that these two SNPs (rs2276466 and rs3136038 in ERCC4 may be functional and contribute to SCCHN susceptibility. However, our findings need to be replicated in further large epidemiological and functional studies.

  7. Structural basis for dual nucleotide selectivity of aminoglycoside 2''-phosphotransferase IVa provides insight on determinants of nucleotide specificity of aminoglycoside kinases.

    Science.gov (United States)

    Shi, Kun; Berghuis, Albert M

    2012-04-13

    Enzymatic phosphorylation through a family of enzymes called aminoglycoside O-phosphotransferases (APHs) is a major mechanism by which bacteria confer resistance to aminoglycoside antibiotics. Members of the APH(2″) subfamily are of particular clinical interest because of their prevalence in pathogenic strains and their broad substrate spectra. APH(2″) enzymes display differential preferences between ATP or GTP as the phosphate donor, with aminoglycoside 2″-phosphotransferase IVa (APH(2″)-IVa) being a member that utilizes both nucleotides at comparable efficiencies. We report here four crystal structures of APH(2″)-IVa, two of the wild type enzyme and two of single amino acid mutants, each in complex with either adenosine or guanosine. Together, these structures afford a detailed look at the nucleoside-binding site architecture for this enzyme and reveal key elements that confer dual nucleotide specificity, including a solvent network in the interior of the nucleoside-binding pocket and the conformation of an interdomain linker loop. Steady state kinetic studies, as well as sequence and structural comparisons with members of the APH(2″) subfamily and other aminoglycoside kinases, rationalize the different substrate preferences for these enzymes. Finally, despite poor overall sequence similarity and structural homology, analysis of the nucleoside-binding pocket of APH(2″)-IVa shows a striking resemblance to that of eukaryotic casein kinase 2 (CK2), which also exhibits dual nucleotide specificity. These results, in complement with the multitude of existing inhibitors against CK2, can serve as a structural basis for the design of nucleotide-competitive inhibitors against clinically relevant APH enzymes.

  8. Structural Basis for Dual Nucleotide Selectivity of Aminoglycoside 2″-Phosphotransferase IVa Provides Insight on Determinants of Nucleotide Specificity of Aminoglycoside Kinases*♦

    Science.gov (United States)

    Shi, Kun; Berghuis, Albert M.

    2012-01-01

    Enzymatic phosphorylation through a family of enzymes called aminoglycoside O-phosphotransferases (APHs) is a major mechanism by which bacteria confer resistance to aminoglycoside antibiotics. Members of the APH(2″) subfamily are of particular clinical interest because of their prevalence in pathogenic strains and their broad substrate spectra. APH(2″) enzymes display differential preferences between ATP or GTP as the phosphate donor, with aminoglycoside 2″-phosphotransferase IVa (APH(2″)-IVa) being a member that utilizes both nucleotides at comparable efficiencies. We report here four crystal structures of APH(2″)-IVa, two of the wild type enzyme and two of single amino acid mutants, each in complex with either adenosine or guanosine. Together, these structures afford a detailed look at the nucleoside-binding site architecture for this enzyme and reveal key elements that confer dual nucleotide specificity, including a solvent network in the interior of the nucleoside-binding pocket and the conformation of an interdomain linker loop. Steady state kinetic studies, as well as sequence and structural comparisons with members of the APH(2″) subfamily and other aminoglycoside kinases, rationalize the different substrate preferences for these enzymes. Finally, despite poor overall sequence similarity and structural homology, analysis of the nucleoside-binding pocket of APH(2″)-IVa shows a striking resemblance to that of eukaryotic casein kinase 2 (CK2), which also exhibits dual nucleotide specificity. These results, in complement with the multitude of existing inhibitors against CK2, can serve as a structural basis for the design of nucleotide-competitive inhibitors against clinically relevant APH enzymes. PMID:22371504

  9. Anorectal and sexual functions after preoperative radiotherapy and full-thickness local excision of rectal cancer.

    Science.gov (United States)

    Gornicki, A; Richter, P; Polkowski, W; Szczepkowski, M; Pietrzak, L; Kepka, L; Rutkowski, A; Bujko, K

    2014-06-01

    Local excision with preoperative radiotherapy may be considered as alternative management to abdominal surgery alone for small cT2-3N0 tumours. However, little is known about anorectal and sexual functions after local excision with preoperative radiotherapy. Evaluation of this issue was a secondary aim of our previously published prospective multicentre study. Functional evaluation was based on a questionnaire completed by 44 of 64 eligible disease-free patients treated with preoperative radiotherapy and local excision. Additionally, ex post, these results were confronted with those recorded retrospectively in the control group treated with anterior resection alone (N = 38). In the preoperative radiotherapy and local excision group, the median number of bowel movements was two per day, incontinence of flatus occurred in 51% of patients, incontinence of loose stool in 46%, clustering of stools in 59%, and urgency in 49%; these symptoms occurred often or very often in 11%-21% of patients. Thirty-eight per cent of patients claimed that their quality of life was affected by anorectal dysfunction. Nineteen per cent of men and 20% of women claimed that the treatment negatively influenced their sexual life. The anorectal functions in the preoperative radiotherapy and local excision group were not much different from that observed in the anterior resection alone group. Our study suggests that anorectal functions after preoperative radiotherapy and local excision may be worse than expected and not much different from that recorded after anterior resection alone. It is possible that radiotherapy compromises the functional effects achieved by local excision. Copyright © 2013 Elsevier Ltd. All rights reserved.

  10. Frequency and Correlation of Nearest Neighboring Nucleotides in Human Genome

    Science.gov (United States)

    Jin, Neng-zhi; Liu, Zi-xian; Qiu, Wen-yuan

    2009-02-01

    Zipf's approach in linguistics is utilized to analyze the statistical features of frequency and correlation of 16 nearest neighboring nucleotides (AA, AC, AG, ..., TT) in 12 human chromosomes (Y, 22, 21, 20, 19, 18, 17, 16, 15, 14, 13, and 12). It is found that these statistical features of nearest neighboring nucleotides in human genome: (i) the frequency distribution is a linear function, and (ii) the correlation distribution is an inverse function. The coefficients of the linear function and inverse function depend on the GC content. It proposes the correlation distribution of nearest neighboring nucleotides for the first time and extends the descriptor about nearest neighboring nucleotides.

  11. Fluoride ion promoted deprotection and transesterification in nucleotide triesters.

    Science.gov (United States)

    Ogilvie, K K; Beaucage, S L

    1979-10-10

    Tetrabutylammonium fluoride will remove phenyl, trichloroethyl and cyanoethyl groups from nucleotides. In addition to the desired nucleotide products other results including chain cleavage, phosphofluoridates and cyanoethylated thymidine units may be obtained depending on the conditions used. Fluoride ion has been used to successfully exchange phenyl and trichloroethyl groups for methyl, ethyl and butyl groups in nucleotide triesters. This represents a rapid high yield route to a variety of phosphate esters. The synthesis of a novel nucleotide analogue in which two chains are bridged through their phosphates is described.

  12. Correlated Evolution of Nucleotide Positions within Splice Sites in Mammals.

    Science.gov (United States)

    Denisov, Stepan; Bazykin, Georgii; Favorov, Alexander; Mironov, Andrey; Gelfand, Mikhail

    2015-01-01

    Splice sites (SSs)--short nucleotide sequences flanking introns--are under selection for spliceosome binding, and adhere to consensus sequences. However, non-consensus nucleotides, many of which probably reduce SS performance, are frequent. Little is known about the mechanisms maintaining such apparently suboptimal SSs. Here, we study the correlations between strengths of nucleotides occupying different positions of the same SS. Such correlations may arise due to epistatic interactions between positions (i.e., a situation when the fitness effect of a nucleotide in one position depends on the nucleotide in another position), their evolutionary history, or to other reasons. Within both the intronic and the exonic parts of donor SSs, nucleotides that increase (decrease) SS strength tend to co-occur with other nucleotides increasing (respectively, decreasing) it, consistent with positive epistasis. Between the intronic and exonic parts of donor SSs, the correlations of nucleotide strengths tend to be negative, consistent with negative epistasis. In the course of evolution, substitutions at a donor SS tend to decrease the strength of its exonic part, and either increase or do not change the strength of its intronic part. In acceptor SSs, the situation is more complicated; the correlations between adjacent positions appear to be driven mainly by avoidance of the AG dinucleotide which may cause aberrant splicing. In summary, both the content and the evolution of SSs is shaped by a complex network of interdependences between adjacent nucleotides that respond to a range of sometimes conflicting selective constraints.

  13. An affinity pull-down approach to identify the plant cyclic nucleotide interactome

    KAUST Repository

    Donaldson, Lara Elizabeth

    2013-09-03

    Cyclic nucleotides (CNs) are intracellular second messengers that play an important role in mediating physiological responses to environmental and developmental signals, in species ranging from bacteria to humans. In response to these signals, CNs are synthesized by nucleotidyl cyclases and then act by binding to and altering the activity of downstream target proteins known as cyclic nucleotide-binding proteins (CNBPs). A number of CNBPs have been identified across kingdoms including transcription factors, protein kinases, phosphodiesterases, and channels, all of which harbor conserved CN-binding domains. In plants however, few CNBPs have been identified as homology searches fail to return plant sequences with significant matches to known CNBPs. Recently, affinity pull-down techniques have been successfully used to identify CNBPs in animals and have provided new insights into CN signaling. The application of these techniques to plants has not yet been extensively explored and offers an alternative approach toward the unbiased discovery of novel CNBP candidates in plants. Here, an affinity pull-down technique for the identification of the plant CN interactome is presented. In summary, the method involves an extraction of plant proteins which is incubated with a CN-bait, followed by a series of increasingly stringent elutions that eliminates proteins in a sequential manner according to their affinity to the bait. The eluted and bait-bound proteins are separated by one-dimensional gel electrophoresis, excised, and digested with trypsin after which the resultant peptides are identified by mass spectrometry - techniques that are commonplace in proteomics experiments. The discovery of plant CNBPs promises to provide valuable insight into the mechanism of CN signal transduction in plants. © Springer Science+Business Media New York 2013.

  14. Nucleotide variability and linkage disequilibrium patterns in the porcine MUC4 gene

    Directory of Open Access Journals (Sweden)

    Yang Ming

    2012-07-01

    Full Text Available Abstract Background MUC4 is a type of membrane anchored glycoprotein and serves as the major constituent of mucus that covers epithelial surfaces of many tissues such as trachea, colon and cervix. MUC4 plays important roles in the lubrication and protection of the surface epithelium, cell proliferation and differentiation, immune response, cell adhesion and cancer development. To gain insights into the evolution of the porcine MUC4 gene, we surveyed the nucleotide variability and linkage disequilibrium (LD within this gene in Chinese indigenous breeds and Western commercial breeds. Results A total of 53 SNPs covering the MUC4 gene were genotyped on 5 wild boars and 307 domestic pigs representing 11 Chinese breeds and 3 Western breeds. The nucleotide variability, haplotype phylogeny and LD extent of MUC4 were analyzed in these breeds. Both Chinese and Western breeds had considerable nucleotide diversity at the MUC4 locus. Western pig breeds like Duroc and Large White have comparable nucleotide diversity as many of Chinese breeds, thus artificial selection for lean pork production have not reduced the genetic variability of MUC4 in Western commercial breeds. Haplotype phylogeny analyses indicated that MUC4 had evolved divergently in Chinese and Western pigs. The dendrogram of genetic differentiation between breeds generally reflected demographic history and geographical distribution of these breeds. LD patterns were unexpectedly similar between Chinese and Western breeds, in which LD usually extended less than 20 kb. This is different from the presumed high LD extent (more than 100 kb in Western commercial breeds. The significant positive Tajima’D, and Fu and Li’s D statistics in a few Chinese and Western breeds implied that MUC4 might undergo balancing selection in domestic breeds. Nevertheless, we cautioned that the significant statistics could be upward biased by SNP ascertainment process. Conclusions Chinese and Western breeds have

  15. The Saccharomyces cerevisiae RAD7 and RAD16 genes are required for inducible excision of endonuclease III sensitive-sites, yet are not needed for the repair of these lesions following a single UV dose.

    Science.gov (United States)

    Scott, A D; Waters, R

    1997-01-31

    The RAD7 and RAD16 genes of Saccharomyces cerevisiae have roles in the repair of UV induced CPDs in nontranscribed genes [1], and in the repair of CPDs in the nontranscribed strand of transcribed genes [2]. Previously, we identified an inducible component to nucleotide excision repair (NER), which is absent in a rad16 delta strain [3]. We have examined the repair of UV induced endonuclease III sensitive-sites (EIIISS), and have shown repair of these lesions to proceed by NER but their removal from nontranscribed regions is independent of RAD7 and RAD16. Furthermore, EIIISS are repaired with equal efficiency from both transcribed and nontranscribed genes [4]. In order to dissect the roles of RAD7 and RAD16 in the above processes we examined the repair of EIIISS in the MAT alpha and HML alpha loci, which are, respectively, transcriptionally active and inactive in alpha haploid cells. These loci have elevated levels of these lesions after UV (in genomic DNA EIIISS constitute about 10% of total lesions, whereas CPDs are about 70% of total lesions). We have shown that excision of UV induced EIIISS is enhanced following a prior UV irradiation. No enhancement of repair was detected in either the rad7 delta or the rad16 delta mutant. The fact that RAD7 and RAD16 are not required for the repair of EIIISS per se yet are required for the enhanced excision of these lesions from MAT alpha and HML alpha suggests two possibilities. These genes have two roles in NER, namely in the repair of CPDs from nontranscribed sequences, and in enhancing NER itself regardless of whether these genes' products are required for the excision of the specific lesion being repaired. In the latter case, the induction of RAD7 and RAD16 may increase the turnover of complexes stalled in nontranscribed DNA so as to increase the availability of NER proteins for the repair of CPDs and EIIISS in all regions of the genome.

  16. The Relationship between Tax Rate, Penalty Rate, Tax Fairness and Excise Duty Non-compliance.

    Directory of Open Access Journals (Sweden)

    Sinnasamy Perabavathi

    2017-01-01

    Full Text Available The rise of indirect tax non-compliance by taxpayers became the main concern of most of the tax authorities around the globe. In Malaysia, non complaince such as smuggling and illegal trade activities by importers involving cigarettes, liquor and imported vehicles bound under Excise Act 1976 have caused revenue losses in monetary and non-monetary aspects. Therefore, the objective of this study is to examine the relationship of tax rate, penalty rate and tax fairness of excise duty non-compliance. This study uses the Deterrence Theory as a basis theory to investigate the phenomenon of excise duty non complaince. A total of 500 excise duty offenders throughout Malaysia responded to the survey. The model was empirically tested by using Partial Least Squares (PLS with disproportionate stratified random sampling technique. The results indicated that the perception of tax rate and penalty rate are positively related while tax fairness is negatively related to excise duty non-compliance among importers.

  17. Circumareolar incision-subdermal tunneling dissection for excision of multiple breast fibroadenomata

    Directory of Open Access Journals (Sweden)

    S O Agodirin

    2017-01-01

    Full Text Available Excision of multiple fibroadenomas (MF in separate breast quadrants presents difficulties of number and location of incision(s and extent of tissue dissection and may be associated with more complications and poorer cosmetic outcome. This is a report of excision of MF in multiple quadrants of the breast using a modification of subcutaneous dissection technique dubbed the circumareolar incision and subdermal tunneling (CAST dissection. After exposure of the superficial fascia with circumareolar incision, subdermal cone-wise dissection was made to allow mobilization of the segment bearing the lump(s. The lump(s were enucleated and removed. MF were removed from four breasts in three young unmarried females. The first patient had multiple adenomas removed from three quadrants of both breasts: 14 on the right and six on the left. The second patient had excision of three lumps in three separate quadrants, and the third patient had excision of two lumps in two separate quadrants. All patients had edema and bruising. One breast had wound infection and dehiscence. There were no skin necrosis, no nipple loss, and no breast distortion. All ensuing scars were camouflaged. CAST dissection was used for excision of MF in multiple quadrants of the breast with preservation of excellent cosmetic outcome of a single circumareolar incision.

  18. Nucleotide sequence analysis of Adh genes estimates the time of geographic isolation of the Bogota population of Drosophila pseudoobscura.

    Science.gov (United States)

    Schaeffer, S W; Miller, E L

    1991-01-01

    The population of Drosophila pseudoobscura at Bogota, Columbia, is geographically and partially reproductively isolated from populations in the main body of the species in North America. The degree of genetic differentiation and time of divergence between populations at Bogota and Apple Hill, CA, were estimated by comparison of 3388 nucleotides in the alcohol dehydrogenase region (Adh and Adh-Dup genes) of 18 strains. Of the 146 polymorphic nucleotide sites detected, 68 and 31 were unique to the Apple Hill and Bogota samples, respectively, and 53 were shared. On the basis of an observed net divergence per nucleotide site of 0.264% between the two samples, the Bogota and North American populations were estimated to have been separated for at least 155,000 years. This divergence time suggests that D. pseudoobscura extended its range from North America to South America in a period of Pleistocene glaciation, when habitat suitable for the species presumably existed in lowland Central America. PMID:2068088

  19. Human molecular cytogenetics: From cells to nucleotides.

    Science.gov (United States)

    Riegel, Mariluce

    2014-03-01

    The field of cytogenetics has focused on studying the number, structure, function and origin of chromosomal abnormalities and the evolution of chromosomes. The development of fluorescent molecules that either directly or via an intermediate molecule bind to DNA has led to the development of fluorescent in situ hybridization (FISH), a technology linking cytogenetics to molecular genetics. This technique has a wide range of applications that increased the dimension of chromosome analysis. The field of cytogenetics is particularly important for medical diagnostics and research as well as for gene ordering and mapping. Furthermore, the increased application of molecular biology techniques, such as array-based technologies, has led to improved resolution, extending the recognized range of microdeletion/microduplication syndromes and genomic disorders. In adopting these newly expanded methods, cytogeneticists have used a range of technologies to study the association between visible chromosome rearrangements and defects at the single nucleotide level. Overall, molecular cytogenetic techniques offer a remarkable number of potential applications, ranging from physical mapping to clinical and evolutionary studies, making a powerful and informative complement to other molecular and genomic approaches. This manuscript does not present a detailed history of the development of molecular cytogenetics; however, references to historical reviews and experiments have been provided whenever possible. Herein, the basic principles of molecular cytogenetics, the technologies used to identify chromosomal rearrangements and copy number changes, and the applications for cytogenetics in biomedical diagnosis and research are presented and discussed.

  20. Human molecular cytogenetics: from cells to nucleotides

    Directory of Open Access Journals (Sweden)

    Mariluce Riegel

    2014-01-01

    Full Text Available The field of cytogenetics has focused on studying the number, structure, function and origin of chromosomal abnormalities and the evolution of chromosomes. The development of fluorescent molecules that either directly or via an intermediate molecule bind to DNA has led to the development of fluorescent in situ hybridization (FISH, a technology linking cytogenetics to molecular genetics. This technique has a wide range of applications that increased the dimension of chromosome analysis. The field of cytogenetics is particularly important for medical diagnostics and research as well as for gene ordering and mapping. Furthermore, the increased application of molecular biology techniques, such as array-based technologies, has led to improved resolution, extending the recognized range of microdeletion/microduplication syndromes and genomic disorders. In adopting these newly expanded methods, cytogeneticists have used a range of technologies to study the association between visible chromosome rearrangements and defects at the single nucleotide level. Overall, molecular cytogenetic techniques offer a remarkable number of potential applications, ranging from physical mapping to clinical and evolutionary studies, making a powerful and informative complement to other molecular and genomic approaches. This manuscript does not present a detailed history of the development of molecular cytogenetics; however, references to historical reviews and experiments have been provided whenever possible. Herein, the basic principles of molecular cytogenetics, the technologies used to identify chromosomal rearrangements and copy number changes, and the applications for cytogenetics in biomedical diagnosis and research are presented and discussed.

  1. Adenine nucleotides of the stria vascularis.

    Science.gov (United States)

    Thalmann, I; Marcus, N Y; Thalmann, R

    1979-01-01

    The levels of the adenine nucleotides ATP, ADP, and AMP in the stria vascularis were measured under normal conditions, and following various durations of ischemia. The concentrations of these compounds were used for the calculation of the adenylate energy charge, the energy status and the phosphorylation state of the stria. Following 10 min of ischemia the adenylate energy charge had decreased three fold, the energy status seven fold and the phosphorylation state 14 fold. To study the potential for recovery of strial function following various brief and prolonged ischemic intervals, a method for the perfusion of the ear via the anterior inferior cerebellar artery was developed. For various reasons it was found advantageous to use "artifical blood" as perfusate, relying upon fluorocarbons as oxygen carriers. The endolymphatic potential was used as electrical indicator of strial function. Recovery of the endolymphatic potential following brief periods of ischemia was paralleled by a corresponding increase of the ATP levels and a drastic decrease of the AMP levels of the stria vascularis. Preliminary results on the effects of substrate-free perfusion are presented.

  2. Genetic Evidence for Genotoxic Effect of Entecavir, an Anti-Hepatitis B Virus Nucleotide Analog.

    Directory of Open Access Journals (Sweden)

    Lei Jiang

    Full Text Available Nucleoside analogues (NAs have been the most frequently used treatment option for chronic hepatitis B patients. However, they may have genotoxic potentials due to their interference with nucleic acid metabolism. Entecavir, a deoxyguanosine analog, is one of the most widely used oral antiviral NAs against hepatitis B virus. It has reported that entecavir gave positive responses in both genotoxicity and carcinogenicity assays. However the genotoxic mechanism of entecavir remains elusive. To evaluate the genotoxic mechanisms, we analyzed the effect of entecavir on a panel of chicken DT40 B-lymphocyte isogenic mutant cell line deficient in DNA repair and damage tolerance pathways. Our results showed that Parp1-/- mutant cells defective in single-strand break (SSB repair were the most sensitive to entecavir. Brca1-/-, Ubc13-/- and translesion-DNA-synthesis deficient cells including Rad18-/- and Rev3-/- were hypersensitive to entecavir. XPA-/- mutant deficient in nucleotide excision repair was also slightly sensitive to entecavir. γ-H2AX foci forming assay confirmed the existence of DNA damage by entecavir in Parp1-/-, Rad18-/- and Brca1-/- mutants. Karyotype assay further showed entecavir-induced chromosomal aberrations, especially the chromosome gaps in Parp1-/-, Brca1-/-, Rad18-/- and Rev3-/- cells when compared with wild-type cells. These genetic comprehensive studies clearly identified the genotoxic potentials of entecavir and suggested that SSB and postreplication repair pathways may suppress entecavir-induced genotoxicity.

  3. Nucleotide insertion initiated by van der Waals interaction during polymerase beta DNA replication

    CERN Document Server

    Arulsamy, Andrew Das

    2011-01-01

    Immortality will remain a fantasy for as long as aging is determined by the erroneous biochemical reactions during a particular DNA replication. The replication and base excision repair mechanism, associated to eukaryotic DNA polymerase-beta enzyme are central to maintaining a healthy cell. Here, we give a series of unambiguous theoretical analyses and prove that the exclusive biochemical reaction involved in a single nucleotide insertion into the DNA primer can be efficiently tracked using the renormalized van der Waals interaction of the stronger type, and the Hermansson blue-shifting hydrogen bond effect. We found that there are two biochemical steps involved to complete the insertion of a single dCTP into the 3' end of a DNA primer. First, the O3' (from a DNA primer) initiates the nucleophilic attack on P_alpha?(from an incoming dCTP), in response, O3_alpha (bonded to P_alpha) retaliates by interacting with H' (bonded to O3'). These interactions are shown to be strongly interdependent and require the form...

  4. Condensing the information in DNA with double-headed nucleotides

    DEFF Research Database (Denmark)

    Hornum, Mick; Sharma, Pawan K; Reslow-Jacobsen, Charlotte

    2017-01-01

    A normal duplex holds as many Watson-Crick base pairs as the number of nucleotides in its constituent strands. Here we establish that single nucleotides can be designed to functionally imitate dinucleotides without compromising binding affinity. This effectively allows sequence information to be ...

  5. Supplementary Material for: The arabidopsis cyclic nucleotide interactome

    KAUST Repository

    Donaldson, Lara

    2016-01-01

    Abstract Background Cyclic nucleotides have been shown to play important signaling roles in many physiological processes in plants including photosynthesis and defence. Despite this, little is known about cyclic nucleotide-dependent signaling mechanisms in plants since the downstream target proteins remain unknown. This is largely due to the fact that bioinformatics searches fail to identify plant homologs of protein kinases and phosphodiesterases that are the main targets of cyclic nucleotides in animals. Methods An affinity purification technique was used to identify cyclic nucleotide binding proteins in Arabidopsis thaliana. The identified proteins were subjected to a computational analysis that included a sequence, transcriptional co-expression and functional annotation analysis in order to assess their potential role in plant cyclic nucleotide signaling. Results A total of twelve cyclic nucleotide binding proteins were identified experimentally including key enzymes in the Calvin cycle and photorespiration pathway. Importantly, eight of the twelve proteins were shown to contain putative cyclic nucleotide binding domains. Moreover, the identified proteins are post-translationally modified by nitric oxide, transcriptionally co-expressed and annotated to function in hydrogen peroxide signaling and the defence response. The activity of one of these proteins, GLYGOLATE OXIDASE 1, a photorespiratory enzyme that produces hydrogen peroxide in response to Pseudomonas, was shown to be repressed by a combination of cGMP and nitric oxide treatment. Conclusions We propose that the identified proteins function together as points of cross-talk between cyclic nucleotide, nitric oxide and reactive oxygen species signaling during the defence response.

  6. Prebiotic nucleotide synthesis demonstration of a geologically plausible pathway

    NARCIS (Netherlands)

    Schwartz, A.W.; Veen, van der M.; Bisseling, T.; Chittenden, G.J.

    1975-01-01

    Mineral phosphate (apatite) is activated for the synthesis of nucleotides when dilute solutions containing nucleoside and ammonium oxalate are evaporated in its presence. A natural, igneous fluorapatite was found to be even more effective in nucleotide synthesis than the more soluble hydroxylapatite

  7. Removal of the bloom syndrome DNA helicase extends the utility of imprecise transposon excision for making null mutations in Drosophila.

    Science.gov (United States)

    Witsell, Alice; Kane, Daniel P; Rubin, Sarah; McVey, Mitch

    2009-11-01

    Transposable elements are frequently used in Drosophila melanogaster for imprecise excision screens to delete genes of interest. However, these screens are highly variable in the number and size of deletions that are recovered. Here, we show that conducting excision screens in mus309 mutant flies that lack DmBlm, the Drosophila ortholog of the Bloom syndrome protein, increases the percentage and overall size of flanking deletions recovered after excision of either P or Minos elements.

  8. Effects of hypobaric hypoxia on adenine nucleotide pools, adenine nucleotide transporter activity and protein expression in rat liver

    Institute of Scientific and Technical Information of China (English)

    Cong-Yang Li; Jun-Ze Liu; Li-Ping Wu; Bing Li; Li-Fen Chen

    2006-01-01

    AIM: To explore the effect of hypobaric hypoxia on mitochondrial energy metabolism in rat liver.METHODS: Adult male Wistar rats were exposed to a hypobaric chamber simulating 5000 m high altitude for 23 h every day for 0 (HO), 1 (H1), 5 (HS), 15 (H15) and 30 d (H30) respectively. Rats were sacrificed by decapitation and liver was removed. Liver mitochondria were isolated by differential centrifugation program. The size of adenine nucleotide pool (ATP, ADP, and AMP) in tissue and mitochondria was separated and measured by high performance liquid chromatography (HPLC). The adenine nucleotide transporter (ANT) activity was determined by isotopic technique. The ANT total protein level was determined by Western blot. RESULTS: Compared with HO group, intra-mitochondrial ATP content decreased in all hypoxia groups. However,the H5 group reached the lowest point (70.6%) (P< 0.01)when compared to the control group. Intra-mitochondrial ADP and AMP level showed similar change in all hypoxia groups and were significantly lower than that in HO group. In addition, extra-mitochondrial ATP and ADP content decreased significantly in all hypoxia groups.Furthermore, extra-mitochondrial AMP in groups H5, H15and H30 was significantly lower than that in HO group,whereas H1 group had no marked change compared to the control situation. The activity of ANT in hypoxia groups decreased significantly, which was the lowest in H5 group (55.7%) (P<0.01) when compared to HO group. ANT activity in H30 group was higher than in H15 group, but still lower than that in HO group. ANT protein level in H5, H15, H30 groups, compared with HO group decreased significantly, which in H5 group was the lowest, being 27.1% of that in HO group (P<0.01). ANT protein level in H30 group was higher than in H15 group,but still lower than in HO group.CONCLUSION: Hypobaric hypoxia decreases the mitochondrial ATP content in rat liver, while mitochondrial ATP level recovers during long-term hypoxia exposure.The lower

  9. Role of cyclic nucleotide-gated channels in the modulation of mouse hippocampal neurogenesis.

    Directory of Open Access Journals (Sweden)

    Maria Vittoria Podda

    Full Text Available Neural stem cells generate neurons in the hippocampal dentate gyrus in mammals, including humans, throughout adulthood. Adult hippocampal neurogenesis has been the focus of many studies due to its relevance in processes such as learning and memory and its documented impairment in some neurodegenerative diseases. However, we are still far from having a complete picture of the mechanism regulating this process. Our study focused on the possible role of cyclic nucleotide-gated (CNG channels. These voltage-independent channels activated by cyclic nucleotides, first described in retinal and olfactory receptors, have been receiving increasing attention for their involvement in several brain functions. Here we show that the rod-type, CNGA1, and olfactory-type, CNGA2, subunits are expressed in hippocampal neural stem cells in culture and in situ in the hippocampal neurogenic niche of adult mice. Pharmacological blockade of CNG channels did not affect cultured neural stem cell proliferation but reduced their differentiation towards the neuronal phenotype. The membrane permeant cGMP analogue, 8-Br-cGMP, enhanced neural stem cell differentiation to neurons and this effect was prevented by CNG channel blockade. In addition, patch-clamp recording from neuron-like differentiating neural stem cells revealed cGMP-activated currents attributable to ion flow through CNG channels. The current work provides novel insights into the role of CNG channels in promoting hippocampal neurogenesis, which may prove to be relevant for stem cell-based treatment of cognitive impairment and brain damage.

  10. Long-term results of lunocapitate arthrodesis with scaphoid excision for SLAC and SNAC wrists.

    Science.gov (United States)

    Ferreres, A; Garcia-Elias, M; Plaza, R

    2009-10-01

    When treating the degenerative arthritis that follows scapholunate instability or scaphoid pseudarthrosis, excision of the scaphoid must be combined with a stabilisation of the midcarpal joint. Two alternatives have been proposed for that purpose: fusing the lunate, triquetrum, capitate and hamate (four corner fusion), 4CF; or limiting the arthrodesis to the lunate and capitate, preserving or excising the triquetrum. Previous reports have attributed a high level of complications to lunocapitate arthrodesis, mainly in respect of nonunion. We have reviewed 17 patients who had been treated with a lunocapitate fusion, after an 8 to 12-year follow-up period, and found similar results compared with 4CF, even with a major degree of motion in ulnar-radial deviation. Recent work on the innervation of the radiotriquetral ligaments has given relevance to the preservation of lunotriquetral motion in maintaining proprioception. Also if the triquetrum is excised to gain more motion, the proprioceptive role of the radiotriquetral ligaments is compromised.

  11. S-Shaped Wide Excision with Primary Closure for Extensive Chronic Pilonidal Sinus Disease

    Directory of Open Access Journals (Sweden)

    Kerem Karaman

    2014-01-01

    Full Text Available Background. The management of complex pilonidal sinus disease (PSD with multiple pits on and beside the natal cleft is variable, contentious, and problematic. Wide excision of the sinus and reconstruction of the defect using different flap techniques have become more popular in recent years. Case Report. We report a case with a complex chronic PSD to which we applied primary closure after S-shaped wide excision. The patient’s postoperative course was uneventful, and at the end of one-year followup he is now disease-free and comes for routine checkups. Conclusion. The simplicity of the technique and the promising results support the applicability of the S-shaped wide excision in chronic bilaterally extended large PSDs. Further studies entailing large patient populations are needed to reach a definite conclusion.

  12. Modulated Lapped Biorthogonal Transform for Non-orthogonal Narrowband Interference Excision in Spread Spectrum Communications

    Institute of Scientific and Technical Information of China (English)

    朱丽平; 胡光锐; 赵海波; 朱义胜

    2005-01-01

    Traditional lapped transform domain excision techniques obtain good performance at the expense of increased processing delay. Extension of transform domain filtering techniques to the lapped biorthogonal transform domain can help solve the problem. By incorporating biorthogonality into the lapped transforms, more flexibility is obtained in the design of windows. Thus transform bases with better stopband attenuation can be generated by designing windows, but not by increasing the overlapping factor. In this paper, a new modulated lapped biorthogonal transform (MLBT) with optimized windows is introduced for efficient compression of multi-tone interfering signal energy. The bit error rate (BER) performance of the receiver employing the proposed MLBT excision technique is analyzed and compared with that of the lapped transform domain excision-based receivers. Simulation results demonstrate the improved performance and increased robustness of the proposed technique.

  13. Green and non-green callus induction from excised rice (Oryza sativa) embryos: effects of exogenous plant growth regulators

    Science.gov (United States)

    Kim, D.; Brock, T. G.; Kaufman, P. B.

    1992-01-01

    Calli were induced either from excised rice embryos or from whole seeds in the presence of 1 to 5 mg l-1 NAA. After 12 days of culture, calli were induced only from excised rice embryos. We found that excised embryos accumulated NAA up to 6 times higher concentration than did whole seeds. In the presence of 1 to 5 mg l-1 NAA and 2 to 10 mg l-1 kinetin, chlorophyllous calli were induced from excised rice embryos. Chlorophyll contents in the callus tissue increased with increasing kinetin concentration while percent callus induction decreased. The total chlorophyll content was linearly correlated with the ratio of kinetin to NAA in the medium.

  14. Immediate tangential excision accelerates wound closure but does not reduce scarring of mid-dermal porcine burns

    OpenAIRE

    Macri, L.K..; Singer, A J; McClain, S.A.; Crawford, L; Prasad, A.; Kohn, J; Clark, R.A.F.

    2016-01-01

    Current evidence supports the use of excision to remove eschar from deep dermal and full-thickness burns. However, the role of excision of mid-dermal burns remains unclear. This study aimed to develop a porcine model that could produce reproducible middermal thermal burns that undergo tangential excision; and investigate the effects of immediate tangential excision (30 minutes postburn) on healing and scarring. An aluminum bar preheated in hot water (70°C) was applied for 20 or 30 s to produc...

  15. 2-cm versus 4-cm surgical excision margins for primary cutaneous melanoma thicker than 2 mm: a randomised, multicentre trial

    DEFF Research Database (Denmark)

    Gillgren, Peter; Drzewiecki, Krzysztof T; Niin, Marianne;

    2011-01-01

    Optimum surgical resection margins for patients with clinical stage IIA-C cutaneous melanoma thicker than 2 mm are controversial. The aim of the study was to test whether survival was different for a wide local excision margin of 2 cm compared with a 4-cm excision margin.......Optimum surgical resection margins for patients with clinical stage IIA-C cutaneous melanoma thicker than 2 mm are controversial. The aim of the study was to test whether survival was different for a wide local excision margin of 2 cm compared with a 4-cm excision margin....

  16. Excision of periocular basal cell carcinoma guided by en face frozen section.

    Science.gov (United States)

    Tullett, Mark; Sagili, Suresh; Barrett, Andrew; Malhotra, Raman

    2013-09-01

    We describe a technique for monitoring excision margins in periocular basal cell carcinoma (BCC) using en face frozen sections and report outcomes. We excised periocular BCC with 3mm margins. An outer 1mm sliver of the perimeter of the specimen was mapped and sent for evaluation by en face frozen section. The central tumour mass was processed using routine paraffin sections. A further 3mm level was excised at the site of any affected margin and the outer 1mm sliver was again evaluated by frozen section. We identified 78 patients from November 2003 to July 2009; 67 had primary tumours and 11 (14%) had recurrent BCC of which 52 (66%) were located on the lower eyelid. Growth patterns were nodular (n=34, 43%), infiltrative (n=25, 32%), micronodular (n=12, 16%), and superficial (n=7, 9%). A third of BCC with a clinically nodular appearance showed additional histological patterns including infiltrative and micronodular growth patterns. Of 30 clinically nodular carcinomas, 29 were excised completely with one level, and one required 2 levels of excision for clearance after evaluation by frozen section. Mean follow-up was 23 months (range 2-60). There was one recurrence (1%). Excision of margins guided by en face frozen section is justified by the low rates of recurrence, and it can easily be taught or imported into hospital practice. Clinically nodular BCC have subclinical extensions that can be missed on bread loaf sectioning, which makes the sampling of margins a standard for periocular BCC. Copyright © 2012 The British Association of Oral and Maxillofacial Surgeons. Published by Elsevier Ltd. All rights reserved.

  17. Long-term outcome of benign fibroadenomas treated by ultrasound-guided percutaneous excision.

    Science.gov (United States)

    Grady, Ian; Gorsuch, Heidi; Wilburn-Bailey, Shelly

    2008-01-01

    Surgical as well as conservative treatment has been described for fibroadenomas. Both have disadvantages. A minimally invasive treatment, ultrasound-guided, vacuum-assisted percutaneous excision has been shown to facilitate the removal of all imaged evidence of benign breast lesions, including fibroadenomas up to 3 cm in diameter. This study is performed to assess the long-term outcome of ultrasound-guided percutaneous excision as a minimally invasive treatment for fibroadenomas. A retrospective review of 69 consecutive fibroadenomas treated with ultrasound-guided percutaneous excision between May, 2001 and December, 2005 was carried out. All these lesions underwent percutaneous excision of all imaged lesion evidence. Clinical and sonographic follow-up was recommended for all patients every 6 months. Initial size, location, and patient age were recorded for each treated lesion. Of 69 lesions treated, 52 were available for follow-up. The median follow-up period was 22 months, with a range of 7 to 59 months. At 6 months, there were no fibroadenoma recurrences. Follow-up sonography demonstrated recurrences in 13 lesions distributed across eight patients. The overall recurrence rate was 15% (8/52) with an actuarial recurrence rate of 33% at 59 months. All of the recurrences were in lesions which were larger than 2 cm in size at initial presentation. Our data suggest that the mechanism of recurrence is the regrowth of retained lesion fragments too small to be detected by ultrasound--not the incomplete excision of all imaged lesion evidence. Despite successful percutaneous excision, fibroadenomas do recur. Lesions smaller than 2 cm in size, so treated, do not need additional therapy or surveillance. Fibroadenomas larger than 2 cm are prone to recurrence and require additional treatment.

  18. Treatment failure following excision therapy of CIN: the impact of direct colposcopic vision during procedure.

    Science.gov (United States)

    Heineman, Mellie; Mancini, Julien; Villeret, Julia; Agostini, Aubert; Houvenaeghel, Gilles; Boubli, Léon; Carcopino, Xavier

    2016-04-01

    To assess whether the use of direct colposcopic vision during excision therapy of cervical intraepithelial neoplasia (CIN) has an impact on the risk of treatment failure. Data from 285 patients who had had excision therapy with proven CIN at specimen histological analysis were reviewed. Primary endpoint was the occurrence of post-treatment failure defined by the histological diagnosis of CIN 2-3 during follow-up. Data were analysed according to the use of colposcopy at the time of initial therapy of CIN. The use of direct colposcopic vision (DCV) resulted in a significant reduction in the mean height (p = 0.008) and diameter (p treatment failure. Compared to excisions performed without any use of colposcopy, DCV was not found to have any significant impact on the risk of treatment failure (HR: 0.58; 95 % CI 0.16-2.13, p = 0.412), neither when compared to excisions performed immediately after colposcopy (HR: 0.91; 95 % CI 0.47-1.79; p = 0.794). The only factors found to have a significant impact on the risk of treatment failure was the identification of clear margins (HR: 0.36; 95 %CI 0.19-0.69; p = 0.002) and the diameter of the surgical specimen (HR: 0.94; 95 %CI 0.89-0.99; p = 0.040). Although the use of DCV during excision therapy of CIN was associated with a significant reduction in the dimensions of the excised cervical specimen, it did not result in a significant change in the risk of treatment failure.

  19. Abscisic Acid accumulates at positive turgor potential in excised soybean seedling growing zones.

    Science.gov (United States)

    Creelman, R A; Mullet, J E

    1991-04-01

    Abscisic acid (ABA) accumulated in soybean (Glycine max [L.] Merr. cv Williams) hypocotyl elongating regions when seedlings were transferred to low water potential vermiculite (Psi = -0.3 megapascals) even though positive turgor is retained in this tissue. Accumulation of ABA in growing zones could occur from de novo biosynthesis within this tissue or transport from adjacent nongrowing zones. Both growing and nongrowing hypocotyl and root tissues accumulated significant levels of ABA when excised and dehydrated to reduce turgor. Surprisingly, excised growing zones (which experienced no water loss) also accumulated ABA when incubated in darkness for 4 hours at 100% relative humidity and 29 degrees C. Induction of ABA accumulation in the excised elongating region of the hypocotyl was not caused by disruption of root pressure or wounding. While excision of hypocotyl elongating regions induced ABA accumulation, no change in either extensin or p33 mRNA levels was observed. Accumulation of extensin or p33 mRNA required more severe wounding. This suggests that ABA is not involved in the response of these genes in wounded tissue and that wound signals are not causing ABA accumulation in excised tissue. Accumulation of ABA in excised elongating regions was correlated with growth inhibition and a decline in turgor to the yield threshold (Psi;(p) = 0.37 megapascals; R Matyssek, S Maruyama, JS Boyer [1988] Plant Physiol 86: 1163-1167). Inhibiting hypocotyl growth by transferring seedlings to lower temperatures or light did not cause ABA accumulation. We conclude that induction of ABA accumulation in growing zones is more sensitive to changes in turgor than the induction which occurs in mature tissues.

  20. Transposase-Mediated Excision, Conjugative Transfer, and Diversity of ICE6013 Elements in Staphylococcus aureus.

    Science.gov (United States)

    Sansevere, Emily A; Luo, Xiao; Park, Joo Youn; Yoon, Sunghyun; Seo, Keun Seok; Robinson, D Ashley

    2017-04-15

    ICE6013 represents one of two families of integrative conjugative elements (ICEs) identified in the pan-genome of the human and animal pathogen Staphylococcus aureus Here we investigated the excision and conjugation functions of ICE6013 and further characterized the diversity of this element. ICE6013 excision was not significantly affected by growth, temperature, pH, or UV exposure and did not depend on recA The IS30-like DDE transposase (Tpase; encoded by orf1 and orf2) of ICE6013 must be uninterrupted for excision to occur, whereas disrupting three of the other open reading frames (ORFs) on the element significantly affects the level of excision. We demonstrate that ICE6013 conjugatively transfers to different S. aureus backgrounds at frequencies approaching that of the conjugative plasmid pGO1. We found that excision is required for conjugation, that not all S. aureus backgrounds are successful recipients, and that transconjugants acquire the ability to transfer ICE6013 Sequencing of chromosomal integration sites in serially passaged transconjugants revealed a significant integration site preference for a 15-bp AT-rich palindromic consensus sequence, which surrounds the 3-bp target site that is duplicated upon integration. A sequence analysis of ICE6013 from different host strains of S. aureus and from eight other species of staphylococci identified seven divergent subfamilies of ICE6013 that include sequences previously classified as a transposon, a plasmid, and various ICEs. In summary, these results indicate that the IS30-like Tpase functions as the ICE6013 recombinase and that ICE6013 represents a diverse family of mobile genetic elements that mediate conjugation in staphylococci.IMPORTANCE Integrative conjugative elements (ICEs) encode the abilities to integrate into and excise from bacterial chromosomes and plasmids and mediate conjugation between bacteria. As agents of horizontal gene transfer, ICEs may affect bacterial evolution. ICE6013 represents one

  1. Arthroscopic T-capsulotomy for excision of pigmented villonodular synovitis in the hip.

    Science.gov (United States)

    McCormick, Frank; Alpaugh, Kyle; Haughom, Bryan; Nho, Shane

    2015-04-01

    Pigmented villonodular synovitis (PVNS) is a benign synovial tumor of unknown etiology with a predilection for the large joints of the appendicular skeleton. The poor prognosis for patients with hip disease is partially imparted by current surgical techniques. Recent advances in hip arthroscopy technique and instrumentation may enable arthroscopic treatment for PVNS in the hip. The authors report the first case where hip arthroscopy was used to surgically excise a biopsy-confirmed local PVNS lesion in the hip. Using selected capsular releases and accessory portals, the authors achieved adequate visualization and instrument mobilization to successfully excise the entire PVNS tumor with no identifiable complications. Copyright 2015, SLACK Incorporated.

  2. Accurate DNA assembly and genome engineering with optimized uracil excision cloning

    DEFF Research Database (Denmark)

    Cavaleiro, Mafalda; Kim, Se Hyeuk; Seppala, Susanna

    2015-01-01

    Simple and reliable DNA editing by uracil excision (a.k.a. USER cloning) has been described by several research groups, but the optimal design of cohesive DNA ends for multigene assembly remains elusive. Here, we use two model constructs based on expression of gfp and a four-gene pathway that pro......Simple and reliable DNA editing by uracil excision (a.k.a. USER cloning) has been described by several research groups, but the optimal design of cohesive DNA ends for multigene assembly remains elusive. Here, we use two model constructs based on expression of gfp and a four-gene pathway...

  3. Asymptotic Excisions of Metric Spaces and Ideals of Asymptotic Coarse Roe Algebras

    Institute of Scientific and Technical Information of China (English)

    LI Jin-xiu; WANG Qin

    2006-01-01

    We introduce in this note the notions of asymptotic excision of proper metric spaces and asymptotic equivalence relation for subspaces of metric spaces, which are relevant in characterizing spatial ideals of the asymptotic coarse Roe algebras. We show that the lattice of the asymptotic equivalence classes of the subspaces of a proper metric space is isomorphic to the lattice of the spatial ideals of the asymptotic Roe algebra. For asymptotic excisions of the metric space, we also establish a Mayer-Vietoris sequence in K-theory of the asymptotic coarse Roe algebras.

  4. Arthroscopic Excision of an Intraarticular Osteoid Osteoma in the Distal Femur

    Science.gov (United States)

    Kang, Suk; Kim, Young Sung; Lee, Ho Min; Lee, Min Young

    2016-01-01

    An intraarticular osteoid osteoma of the knee is uncommon, and its treatment is challenging. The authors present a case of arthroscopic excision of an intraarticular osteoid osteoma in the distal femur, which was accessible through the knee joint. After confirming the nidus of the osteoid osteoma by computed tomography, the lesion was completely removed arthroscopically. The patient reported complete pain relief immediately after surgery. This case demonstrates that intraarticular osteoid osteomas in the knee joint can be treated by arthroscopic excision and that good results can be obtained. PMID:27904732

  5. Insights into the biological functions of Dock family guanine nucleotide exchange factors.

    Science.gov (United States)

    Laurin, Mélanie; Côté, Jean-François

    2014-03-15

    Rho GTPases play key regulatory roles in many aspects of embryonic development, regulating processes such as differentiation, proliferation, morphogenesis, and migration. Two families of guanine nucleotide exchange factors (GEFs) found in metazoans, Dbl and Dock, are responsible for the spatiotemporal activation of Rac and Cdc42 proteins and their downstream signaling pathways. This review focuses on the emerging roles of the mammalian DOCK family in development and disease. We also discuss, when possible, how recent discoveries concerning the biological functions of these GEFs might be exploited for the development of novel therapeutic strategies.

  6. Empirical Bayes analysis of single nucleotide polymorphisms

    Directory of Open Access Journals (Sweden)

    Ickstadt Katja

    2008-03-01

    Full Text Available Abstract Background An important goal of whole-genome studies concerned with single nucleotide polymorphisms (SNPs is the identification of SNPs associated with a covariate of interest such as the case-control status or the type of cancer. Since these studies often comprise the genotypes of hundreds of thousands of SNPs, methods are required that can cope with the corresponding multiple testing problem. For the analysis of gene expression data, approaches such as the empirical Bayes analysis of microarrays have been developed particularly for the detection of genes associated with the response. However, the empirical Bayes analysis of microarrays has only been suggested for binary responses when considering expression values, i.e. continuous predictors. Results In this paper, we propose a modification of this empirical Bayes analysis that can be used to analyze high-dimensional categorical SNP data. This approach along with a generalized version of the original empirical Bayes method are available in the R package siggenes version 1.10.0 and later that can be downloaded from http://www.bioconductor.org. Conclusion As applications to two subsets of the HapMap data show, the empirical Bayes analysis of microarrays cannot only be used to analyze continuous gene expression data, but also be applied to categorical SNP data, where the response is not restricted to be binary. In association studies in which typically several ten to a few hundred SNPs are considered, our approach can furthermore be employed to test interactions of SNPs. Moreover, the posterior probabilities resulting from the empirical Bayes analysis of (prespecified interactions/genotypes can also be used to quantify the importance of these interactions.

  7. Predictors of Pathologic Complete Response in Rectal Cancer Patients Undergoing Total Mesorectal Excision After Preoperative Chemoradiation.

    Science.gov (United States)

    Han, Yoon Dae; Kim, Woo Ram; Park, Seung Wan; Cho, Min Soo; Hur, Hyuk; Min, Byung Soh; Baik, Seung Hyuk; Lee, Kang Young; Kim, Nam Kyu

    2015-11-01

    Preoperative chemoradiotherapy (CRT) is the standard of care for patients with stage II and III rectal cancer. This strategy leads to pathologic complete response (pCR) in a significant number of patients. Factors predictive of pCR are currently being extensively investigated. The aim of this study was to analyze clinical factors that might be predictive of pCR.This study was a retrospective analysis of rectal cancer patients from January 2004 through December 2012. A total of 332 stage II and III patients with middle and low rectal cancer (≤10 cm) who received CRT and underwent curative total mesorectal excision were eligible. The median radiation dose was 50.4 Gy, and 72.6% of patients received infusional 5-fluorouracil with leucovorin, whereas 19.6% of patients received TS-1 with irinotecan, and 7.8% of patients received xeloda only. Pathologic complete response was confirmed by using pathologic specimens and analyzed based on predictive clinical factors.Among the 332 patients, 27.4% (n = 91) achieved pCR. Age, sex, body mass index, clinical T and N stages, tumor differentiation, the chemotherapy agent for CRT, and the time interval between CRT and surgery did not differ between the pCR and non-pCR groups. Carcinoembryogenic antigen (CEA) levels before CRT were 4.61 ± 7.38 ng/mL in the pCR group and 10.49 ± 23.83 ng/mL in the non-pCR group (P = 0.035). Post-CRT CEA levels were 1.4 ± 1.07 ng/mL in the pCR group and 2.16 ± 2.8 ng/mL in the non-pCR group (P = 0.014), and the proportion of middle rectal cancer patients was higher in pCR group (54.9%, P = 0.028). The results from multivariate logistic regression analysis indicated that higher tumor location (odds ratio 2.151; P = 0.003) and low post-CRT CEA level (odds ratio 0.789; P = 0.04) were independent predictive factors for pCR.Tumor location and post-CRT CEA level were predictive factors in pCR for rectal cancer patients. Therefore, these factors may

  8. Decreased Nucleotide and Expression Diversity and Modified Coexpression Patterns Characterize Domestication in the Common Bean.

    Science.gov (United States)

    Bellucci, Elisa; Bitocchi, Elena; Ferrarini, Alberto; Benazzo, Andrea; Biagetti, Eleonora; Klie, Sebastian; Minio, Andrea; Rau, Domenico; Rodriguez, Monica; Panziera, Alex; Venturini, Luca; Attene, Giovanna; Albertini, Emidio; Jackson, Scott A; Nanni, Laura; Fernie, Alisdair R; Nikoloski, Zoran; Bertorelle, Giorgio; Delledonne, Massimo; Papa, Roberto

    2014-05-21

    Using RNA sequencing technology and de novo transcriptome assembly, we compared representative sets of wild and domesticated accessions of common bean (Phaseolus vulgaris) from Mesoamerica. RNA was extracted at the first true-leaf stage, and de novo assembly was used to develop a reference transcriptome; the final data set consists of ∼190,000 single nucleotide polymorphisms from 27,243 contigs in expressed genomic regions. A drastic reduction in nucleotide diversity (∼60%) is evident for the domesticated form, compared with the wild form, and almost 50% of the contigs that are polymorphic were brought to fixation by domestication. In parallel, the effects of domestication decreased the diversity of gene expression (18%). While the coexpression networks for the wild and domesticated accessions demonstrate similar seminal network properties, they show distinct community structures that are enriched for different molecular functions. After simulating the demographic dynamics during domestication, we found that 9% of the genes were actively selected during domestication. We also show that selection induced a further reduction in the diversity of gene expression (26%) and was associated with 5-fold enrichment of differentially expressed genes. While there is substantial evidence of positive selection associated with domestication, in a few cases, this selection has increased the nucleotide diversity in the domesticated pool at target loci associated with abiotic stress responses, flowering time, and morphology.

  9. Regulatory single nucleotide polymorphisms at the beginning of intron 2 of the human gene

    Indian Academy of Sciences (India)

    Elena V Antontseva; Marina Yu Matveeva; Natalia P Bondar; Elena V Kashina; Elena Yu Leberfarb; Leonid O Bryzgalov; Polina A Gervas; Anastasia A Ponomareva; Nadezhda V Cherdyntseva; Yury L Orlov; Tatiana I Merkulova

    2015-12-01

    There are two regulatory single nucleotide polymorphisms (rSNPs) at the beginning of the second intron of the mouse - gene that are strongly associated with lung cancer susceptibility. We performed functional analysis of three SNPs (rs12228277: T>A, rs12226937: G>A, and rs61761074: T>G) located in the same region of human . We found that rs12228277 and rs61761074 result in differential binding patterns of lung nuclear proteins to oligonucleotide probes corresponding two alternative alleles; in both cases, the transcription factor NF-Y is involved. G>A substitution (rs12226937) had no effect on the binding of lung nuclear proteins. However, all the nucleotide substitutions under study showed functional effects in a luciferase reporter assay. Among them, rs61761074 demonstrated a significant correlation with allele frequency in non-small-cell lung cancer (NSCLC). Taken together, the results of our study suggest that a T>G substitution at nucleotide position 615 in the second intron of the KRAS gene (rs61761074) may represent a promising genetic marker of NSCLC.

  10. Identifying 2'-O-methylationation sites by integrating nucleotide chemical properties and nucleotide compositions.

    Science.gov (United States)

    Chen, Wei; Feng, Pengmian; Tang, Hua; Ding, Hui; Lin, Hao

    2016-06-01

    2'-O-methylationation is an important post-transcriptional modification and plays important roles in many biological processes. Although experimental technologies have been proposed to detect 2'-O-methylationation sites, they are cost-ineffective. As complements to experimental techniques, computational methods will facilitate the identification of 2'-O-methylationation sites. In the present study, we proposed a support vector machine-based method to identify 2'-O-methylationation sites. In this method, RNA sequences were formulated by nucleotide chemical properties and nucleotide compositions. In the jackknife cross-validation test, the proposed method obtained an accuracy of 95.58% for identifying 2'-O-methylationation sites in the human genome. Moreover, the model was also validated by identifying 2'-O-methylation sites in the Mus musculus and Saccharomyces cerevisiae genomes, and the obtained accuracies are also satisfactory. These results indicate that the proposed method will become a useful tool for the research on 2'-O-methylation.

  11. Differential characters

    CERN Document Server

    Bär, Christian

    2014-01-01

    Providing a systematic introduction to differential characters as introduced by Cheeger and Simons, this text describes important concepts such as fiber integration, higher dimensional holonomy, transgression, and the product structure in a geometric manner. Differential characters form a model of what is nowadays called differential cohomology, which is the mathematical structure behind the higher gauge theories in physics.  

  12. Frequency and Correlation of Nearest Neighboring Nucleotides in Human Genome

    Institute of Scientific and Technical Information of China (English)

    Neng-zhi Jin; Zi-xian Liu; Wen-yuan Qiu

    2009-01-01

    Zipf's approach in linguistics is utilized to analyze the statistical features of frequency and mosomes (Y, 22, 21, 20, 19, 18, 17, 16, 15, 14, 13, and 12). It is found that these statistical features of nearest neighboring nucleotides in human genome: (ⅰ) the frequency distribution is a linear function, and (ⅱ) the correlation distribution is an inverse function. The coeffi-cients of the linear function and inverse function depend on the GC content. It proposes the correlation distribution of nearest neighboring nucleotides for the first time and extends the descriptor about nearest neighboring nucleotides.

  13. Building phylogenetic trees by using gene Nucleotide Genomic Signals.

    Science.gov (United States)

    Cristea, Paul Dan

    2012-01-01

    Nucleotide genomic signal (NuGS) methodology allows a molecular level approach to determine distances between homologous genes or between conserved equivalent non-coding genome regions in various species or individuals of the same species. Therefore, distances between the genes of species or individuals can be computed and phylogenetic trees can be built. The paper illustrates the use of the nucleotide imbalance (N) and nucleotide pair imbalance (P) signals to determine the distances between the genes of several Hominidae. The results are in accordance with those of other genetic or phylogenetic approaches to establish distances between Hominidae species.

  14. Male sexual function and lower urinary tract symptoms after laparoscopic total mesorectal excision

    NARCIS (Netherlands)

    Breukink, S. O.; Driel, M. F. van; Pierie, J. P. E. N.; Dobbins, C.; Wiggers, T.; Meijerink, W. J. H. J.

    2008-01-01

    The aim of this study was to investigate sexual function and the presence of lower urinary tract symptoms (LUTS) in male patients with rectal cancer following short-term radiotherapy and laparoscopic total mesorectal excision (LTME) by physical and psychological measurements. Sexual function and LUT

  15. Keratoacanthoma centrifugum marginatum: unresponsive to oral retinoid and successfully treated with wide local excision.

    Directory of Open Access Journals (Sweden)

    Kapildev Das

    2010-01-01

    Full Text Available We describe a case of a 65-year-old male presenting with a large plaque with a rolled-out interrupted margin, atrophic center, and island of normal skin over the left arm. It grew peripherally with central healing, and there was a history of recurrence after inadequate excision. Investigations ruled out other clin­ical mimickers; namely, squamous cell carcinoma, lupus vulgaris, botryomycosis, and blastomycosis-like pyoderma. Histopathological sections showed irregularly shaped craters filled with keratin and epithelial pearl but no evidence of granuloma or cellular atypia. Clinico­pathological correlation proved the lesion to be keratoacanthoma centrifugum marginatum (KCM, a rare variant of keratoacanthoma, which spreads centrifugally, attains a huge size, and never involutes spontaneously. Treatment of KCM has been a problem always and, in our case, systemic retinoid (acitretin for three months proved ineffective. The patient also had a history of recurrence following surgical intervention previously, necessitating wide excision to achieve complete clearance of tumor cells. Hence, after failure of retinoid therapy, the decision of excision with a 1-centimeter margin was taken and the large defect was closed by a split thickness skin graft. The graft uptake was satisfactory, and the patient is being followed-up presently and shows no signs of recurrence after six months, highlighting wide local excision as a useful treatment option.

  16. Base excision repair deficient mice lacking the Aag alkyladenine DNA glycosylase.

    NARCIS (Netherlands)

    B.P. Engelward (Bevin); G. Weeda (Geert); M.D. Wyatt; J.L.M. Broekhof (Jose'); J. de Wit (Jan); I. Donker (Ingrid); J.M. Allan (James); B. Gold (Bert); J.H.J. Hoeijmakers (Jan); L.D. Samson (Leona)

    1997-01-01

    textabstract3-methyladenine (3MeA) DNA glycosylases remove 3MeAs from alkylated DNA to initiate the base excision repair pathway. Here we report the generation of mice deficient in the 3MeA DNA glycosylase encoded by the Aag (Mpg) gene. Alkyladenine DNA glycosylase turns out to be the major DNA glyc

  17. Combined Liposuction and Excision of Lipomas: Long-Term Evaluation of a Large Sample of Patients

    Directory of Open Access Journals (Sweden)

    Libby R. Copeland-Halperin

    2015-01-01

    Full Text Available Background. Lipomas are benign tumors of mature fat cells. They can be removed by liposuction, yet this technique is seldom employed because of concerns that removal may be incomplete and recurrence may be more frequent than after conventional excision. Objectives. We assessed the short- and long-term clinical outcomes and recurrence of combined liposuction and limited surgical excision of subcutaneous lipomas. Methods. From 2003 to 2012, 25 patients with 48 lipomas were treated with liposuction followed by direct excision through the same incision to remove residual lipomatous tissue. Initial postoperative follow-up ranged from 1 week to 3 months, and long-term outcomes, complications, and recurrence were surveyed 1 to 10 years postoperatively. Results. Lipomas on the head, neck, trunk, and extremities ranged from 1 to 15 cm in diameter. Early postoperative hematoma and seromas were managed by aspiration. Among 23 survey respondents (92%, patients were uniformly pleased with the cosmetic results; none reported recurrent lipoma. Conclusions. The combination of liposuction and excision is a safe alternative for lipoma removal; malignancy and recurrence are uncommon. Liposuction performed through a small incision provides satisfactory aesthetic results in most cases. Once reduced in size, residual lipomatous and capsular tissue can be removed without expanding the incision. These favorable outcomes support wider application of this technique in appropriate cases.

  18. Robot-assisted excision of seminal vesicle cyst associated with ipsilateral renal agenesis

    Directory of Open Access Journals (Sweden)

    Marcello Scarcia

    2016-01-01

    Full Text Available Seminal vesicle cysts (SVCs associated with other genitourologic abnormalities are rare. Often associated with ipsilateral renal agenesis in a symptomatic patient. In symptomatic patients open surgical excision is the treatment of choice. The laparoscopic approach is a less invasive option. Recently robot-assisted management has gained a primary role for the treatment of this condition.

  19. Lateral parascapular extrapleural approach for single-stage excision of dumb-bell neurofibroma.

    Science.gov (United States)

    O'Reilly, G; Jackowski, A; Weiner, G; Thomas, D

    1994-01-01

    An excision of a T1 dumb-bell neurofibroma via a single-stage lateral parascapular extrapleural approach is described. The different surgical approaches that can be used to approach dumb-bell tumours are reviewed, together with the relevant literature.

  20. Management of fluoroscopy-induced radiation ulcer: One-stage radical excision and immediate reconstruction

    Science.gov (United States)

    Wei, Kai-Che; Yang, Kuo-Chung; Chen, Lee-Wei; Liu, Wen-Chung; Chen, Wen-Chieh; Chiou, Wen-Yen; Lai, Ping-Chin

    2016-01-01

    With increasing use of cardiac fluoroscopic intervention, the incidence of fluoroscopy-induced radiation ulcer is increasing. Radiation ulcer is difficult to manage and currently there are no treatment guidelines. To identify the optimal treatment approaches for managing cardiac fluoroscopy-induced radiation ulcers, we retrospectively reviewed medical records of 13 patients with fluoroscopy-induced radiation ulcers receiving surgical interventions and following up in our hospital from 2012 to 2015. Conventional wound care and hyperbaric oxygen therapy were of little therapeutic benefit. Twelve patients received reconstruction with advancement flap or split thick skin graft. One-stage radical excision of radiation damaged area in eight cases with immediate reconstruction led to better outcomes than conservative excisions in four cases. Radical surgical excision to remove all the radiation damaged tissues in combination with immediate reconstruction appears to offer the optimal treatment results for cardiac fluoroscopy-induced radiation ulcers. Adequate excision of the damaged areas in both vertical (to the muscular fascia) and horizontal (beyond the sclerotic areas) dimension is pivotal to achieve good treatment outcomes. PMID:27767187

  1. Definition of total mesorectal excision, including the perineal phase : Technical considerations

    NARCIS (Netherlands)

    Havenga, Klaas; Grossmann, Irene; DeRuiter, Marco; Wiggers, Theo

    2007-01-01

    Background: Total mesorectal excision (TME) has contributed to a decline in local recurrence. The operation is difficult because of the complicated anatomy of the pelvis and the narrow spaces in the pelvis. We review the anatomy related to TME and we present our surgical technique. Anatomy: The pelv

  2. Teenage Patients with Ingrown Toenails: Treatment with Partial Matrix Excision or Segmental Phenolization

    Science.gov (United States)

    Korkmaz, Murat; Çölgeçen, Emine; Erdoğan, Yalçın; Bal, Ahmet; Özyurt, Kemal

    2013-01-01

    Background: Ingrown toenails (IT) is a very common problem leading to significant associated morbidity. The articles related to phenolization for matrix removal in teenagers with IT are not enough in the foot surgery literature. Aims: To compare the postoperative recovery periods, complication rate, and tolerability of partial matrix excision and segmental phenolization in teenagers with IT. Materials and Methods: Thirty-nine patients (13-17 years) with 48 IT were randomly divided into two groups and were treated with partial matrix excision (Group I) and segmental phenolization (Group II). We assessed the recurrence rates, postoperative complications, duration of analgesic usage, and time to return to daily activities. Results: There was no significant difference between the demographic and clinical data of the two groups. Three patients in Group I and two patients in Group II experienced moderate pain postoperatively. These patients used analgesics for 3 days. The rates of postoperative complications and recurrences between the two groups showed no statistically significant difference (P = 0.688). The time to return to normal daily activities was significantly shorter in Group II patients than in Group I patients (P < 0.05). Conclusions: Partial matrix excision is a very safe model of therapy in the surgical treatment of teenagers with IT. It has low recurrence rate and minimal postoperative morbidity. We concluded that segmental phenolization is also as safe as partial matrix excision in the treatment of IT and patients return to their daily activities in less time with this treatment modality. PMID:23919026

  3. Teenage patients with ingrown toenails: Treatment with partial matrix excision or segmental phenolization

    Directory of Open Access Journals (Sweden)

    Murat Korkmaz

    2013-01-01

    Full Text Available Background: Ingrown toenails (IT is a very common problem leading to significant associated morbidity. The articles related to phenolization for matrix removal in teenagers with IT are not enough in the foot surgery literature. Aims: To compare the postoperative recovery periods, complication rate, and tolerability of partial matrix excision and segmental phenolization in teenagers with IT. Materials and Methods: Thirty-nine patients (13-17 years with 48 IT were randomly divided into two groups and were treated with partial matrix excision (Group I and segmental phenolization (Group II. We assessed the recurrence rates, postoperative complications, duration of analgesic usage, and time to return to daily activities. Results: There was no significant difference between the demographic and clinical data of the two groups. Three patients in Group I and two patients in Group II experienced moderate pain postoperatively. These patients used analgesics for 3 days. The rates of postoperative complications and recurrences between the two groups showed no statistically significant difference ( P = 0.688. The time to return to normal daily activities was significantly shorter in Group II patients than in Group I patients ( P < 0.05. Conclusions: Partial matrix excision is a very safe model of therapy in the surgical treatment of teenagers with IT. It has low recurrence rate and minimal postoperative morbidity. We concluded that segmental phenolization is also as safe as partial matrix excision in the treatment of IT and patients return to their daily activities in less time with this treatment modality.

  4. Risk factors for anastomotic failure after total mesorectal excision of rectal cancer

    NARCIS (Netherlands)

    Peeters, KCMJ; Tollenaar, RAEM; Marijnen, CAM; Kranenbarg, EK; Steup, WH; Wiggers, T; Rutten, HJ; van de Velde, CJH

    2005-01-01

    Background: Anastomotic leakage is a major complication of rectal cancer surgery. The aim of this study was to investigate risk factors associated with symptomatic anastomotic leakage after total mesorectal excision (TME). Methods: Between 1996 and 1999, patients with operable rectal cancer were ran

  5. An HPLC-tandem mass spectrometry method for simultaneous detection of alkylated base excision repair products.

    Science.gov (United States)

    Mullins, Elwood A; Rubinson, Emily H; Pereira, Kevin N; Calcutt, M Wade; Christov, Plamen P; Eichman, Brandt F

    2013-11-01

    DNA glycosylases excise a broad spectrum of alkylated, oxidized, and deaminated nucleobases from DNA as the initial step in base excision repair. Substrate specificity and base excision activity are typically characterized by monitoring the release of modified nucleobases either from a genomic DNA substrate that has been treated with a modifying agent or from a synthetic oligonucleotide containing a defined lesion of interest. Detection of nucleobases from genomic DNA has traditionally involved HPLC separation and scintillation detection of radiolabeled nucleobases, which in the case of alkylation adducts can be laborious and costly. Here, we describe a mass spectrometry method to simultaneously detect and quantify multiple alkylpurine adducts released from genomic DNA that has been treated with N-methyl-N-nitrosourea (MNU). We illustrate the utility of this method by monitoring the excision of N3-methyladenine (3 mA) and N7-methylguanine (7 mG) by a panel of previously characterized prokaryotic and eukaryotic alkylpurine DNA glycosylases, enabling a comparison of substrate specificity and enzyme activity by various methods. Detailed protocols for these methods, along with preparation of genomic and oligonucleotide alkyl-DNA substrates, are also described.

  6. Iatrogenic displacement of tumor cells to the sentinel node after surgical excision in primary breast cancer

    DEFF Research Database (Denmark)

    Tvedskov, Tove F; Jensen, Maj-Britt; Kroman, Niels;

    2012-01-01

    Isolated tumor cells (ITC) are more common in the sentinel node (SN) after needle biopsy of a breast cancer, indicating iatrogenic displacement of tumor cells. We here investigate whether similar iatrogenic displacement occurs after surgical excision of a breast tumor. We compared the incidence...

  7. Similar long-term overall and disease-free survival after conventional and extralevator abdominoperineal excision

    DEFF Research Database (Denmark)

    Klein, Mads; Colov, Emilie Palmgren; Gögenur, Ismail

    2016-01-01

    PURPOSE: The purpose of the present study was to assess, compare, and identify factors of importance for long-term overall (OS) and disease-free (DFS) survival after conventional (cAPE) and extralevator abdominoperineal excision (ELAPE) on a nationwide basis. METHODS: This was a database study ba...

  8. Base excision repair deficient mice lacking the Aag alkyladenine DNA glycosylase.

    NARCIS (Netherlands)

    B.P. Engelward (Bevin); G. Weeda (Geert); M.D. Wyatt; J.L.M. Broekhof (Jose'); J. de Wit (Jan); I. Donker (Ingrid); J.M. Allan (James); B. Gold (Bert); J.H.J. Hoeijmakers (Jan); L.D. Samson (Leona)

    1997-01-01

    textabstract3-methyladenine (3MeA) DNA glycosylases remove 3MeAs from alkylated DNA to initiate the base excision repair pathway. Here we report the generation of mice deficient in the 3MeA DNA glycosylase encoded by the Aag (Mpg) gene. Alkyladenine DNA glycosylase turns out to be the major DNA glyc

  9. A high excision potential of TALENs for integrated DNA of HIV-based lentiviral vector.

    Science.gov (United States)

    Ebina, Hirotaka; Kanemura, Yuka; Misawa, Naoko; Sakuma, Tetsushi; Kobayashi, Tomoko; Yamamoto, Takashi; Koyanagi, Yoshio

    2015-01-01

    DNA-editing technology has made it possible to rewrite genetic information in living cells. Human immunodeficiency virus (HIV) provirus, an integrated form of viral complementary DNA in host chromosomes, could be a potential target for this technology. We recently reported that HIV proviral DNA could be excised from the chromosomal DNA of HIV-based lentiviral DNA-transduced T cells after multiple introductions of a clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 endonuclease system targeting HIV long terminal repeats (LTR). Here, we generated a more efficient strategy that enables the excision of HIV proviral DNA using customized transcription activator-like effector nucleases (TALENs) targeting the same HIV LTR site. A single transfection of TALEN-encoding mRNA, prepared from in vitro transcription, resulted in more than 80% of lentiviral vector DNA being successfully removed from the T cell lines. Furthermore, we developed a lentiviral vector system that takes advantage of the efficient proviral excision with TALENs and permits the simple selection of gene-transduced and excised cells in T cell lines.

  10. A high excision potential of TALENs for integrated DNA of HIV-based lentiviral vector.

    Directory of Open Access Journals (Sweden)

    Hirotaka Ebina

    Full Text Available DNA-editing technology has made it possible to rewrite genetic information in living cells. Human immunodeficiency virus (HIV provirus, an integrated form of viral complementary DNA in host chromosomes, could be a potential target for this technology. We recently reported that HIV proviral DNA could be excised from the chromosomal DNA of HIV-based lentiviral DNA-transduced T cells after multiple introductions of a clustered regularly interspaced short palindromic repeat (CRISPR/Cas9 endonuclease system targeting HIV long terminal repeats (LTR. Here, we generated a more efficient strategy that enables the excision of HIV proviral DNA using customized transcription activator-like effector nucleases (TALENs targeting the same HIV LTR site. A single transfection of TALEN-encoding mRNA, prepared from in vitro transcription, resulted in more than 80% of lentiviral vector DNA being successfully removed from the T cell lines. Furthermore, we developed a lentiviral vector system that takes advantage of the efficient proviral excision with TALENs and permits the simple selection of gene-transduced and excised cells in T cell lines.

  11. Evolution and mutagenesis of the mammalian excision repair gene ERCC-1

    NARCIS (Netherlands)

    M. van Duin (Mark); J. van den Tol; P. Warmerdam (Peter); H. Odijk (Hanny); D.N. Meijer (Dies); A. Westerveld (Andries); D. Bootsma (Dirk); J.H.J. Hoeijmakers (Jan)

    1988-01-01

    textabstractThe human DNA excision repair protein ERCC-1 exhibits homology to the yeast RADIO repair protein and its longer C-terminus displays similarity to parts of the E.coli repair proteins uvrA and uvrC. To study the evolution of this 'mosaic' ERCC-1 gene we have isolated the mouse homologue.

  12. Long-term outcome of surgical excision of leukoplakia in a screening intervention trial, Kerala, India

    Directory of Open Access Journals (Sweden)

    Gigi Thomas

    2012-01-01

    There were four (5 7% cases of malignant transformation during the mean follow-up period of 8-1 years. The superiority of surgical excision over other modalities of management of leukoplakia could not be established in the present study.

  13. Cloning and characterization of the human DNA-excision repair gene ERCC-1

    NARCIS (Netherlands)

    M. van Duin (Michel)

    1988-01-01

    textabstractIt is the aim of the work described in this thesis to isolate and characterize human genes involved DNA excision repair. This will facilitate the understanding of the mechanism of this repair process whereas it also provides an important step to better understand the relationship

  14. Studies on percutaneous penetration of chemicals - Impact of storage conditions for excised human skin.

    Science.gov (United States)

    Dennerlein, Kathrin; Schneider, Désirée; Göen, Thomas; Schaller, Karl Heinz; Drexler, Hans; Korinth, Gintautas

    2013-03-01

    According to international guidelines skin penetration experiments can be carried out using freshly excised or frozen stored skin. However, this recommendation refers to data obtained in experiments with human cadaver skin. In our study, the percutaneous penetration of the occupationally relevant chemicals anisole, cyclohexanone and 1,4-dioxane was investigated for freshly excised as well as for 4 and 30 days at -20°C stored human skin using the diffusion cell technique. As indicator for the impairment of skin barrier by freezing cholesterol dissolution was determined in the solvents in exposure chambers of diffusion cells. Considering the percutaneously penetrated amounts, the following ranking was determined: 1,4-dioxane>anisole>cyclohexanone (decline to a factor of 5.9). The differences of fluxes between freshly excised and frozen stored skin (4 and 30 days) were not significant (p>0.05). Cholesterol dissolved from the skin indicates no significant differences between freshly excised and frozen stored skin. This study shows that freezing of human skin for up to 30 days does not alter the skin barrier function and the permeability of chemicals.

  15. Clinical analysis of risk factors contributing to recurrence of pterygium after excision and graft surgery

    Institute of Scientific and Technical Information of China (English)

    Sang; Won; Ha; Joon; Ho; Park; Im; Hee; Shin; Hong; Kyun; Kim

    2015-01-01

    AIM: To find the risk factors related to the reproliferation of the pterygial tissue after excision and graft surgery.METHODS: Charts of 130 eyes of 130 patients who had pterygial excision from March 2006 to April 2011 were reviewed. Preoperative pterygium morphology, surgical methods, and adjunctive treatments were statistically analyzed for their relationship with recurrence.RESULTS: During the follow-up period, recurrence was observed in 20 eyes(15.4%). None of the preoperative morphologic features were affected the rate of the recurrence. However, an age <40y [P =0.085, odds ratio(OR) 3.609, 95% confidence interval(CI) 0.838-15.540]and amniotic membrane graft instead of conjunctival autograft(P =0.002, OR 9.093, 95% CI 2.316-35.698) were statistically significant risk factors for recurrence.Multivariate analysis revealed that intraoperative mitomycin C(MMC)(P =0.072, OR 0.298, 95% CI 0.080-1.115)decreased the rate of recurrence. CONCLUSION: Younger age is a risk factor for reproliferation of pterygial tissue after excision and amniotic membrane transplantation(AMT) are less effective in preventing recurrence of pterygium after excision based on the comparison between conjunctival autograft and AMT. Intraoperative MMC application and conjunctival autograft reduce recurrence.

  16. Randomized clinical trial of symptom control after stapled anopexy or diathermy excision for haemorrhoid prolapse

    DEFF Research Database (Denmark)

    Nyström, P-O; Qvist, N; Raahave, D;

    2010-01-01

    BACKGROUND: : This multicentre randomized clinical trial studied how symptoms improved after either stapled anopexy or diathermy excision of haemorrhoids. METHODS: : The study involved 18 hospitals in Sweden, Denmark and the UK. Some 207 patients were randomized to either anopexy or Milligan-Morg...

  17. Excision Hemorrhoidectomy: New Methods to Improve the Outcomes of an Old Technique

    Directory of Open Access Journals (Sweden)

    Heng

    2016-02-01

    Full Text Available Context Hemorrhoidal disease is the most common anorectal disorder that requires surgical intervention. Hemorrhoids require treatment when they result in symptoms such as bleeding or prolapse. Surgical intervention is indicated for significant prolapse, and a number of accepted and viable methods are available for treating prolapsing hemorrhoids that do not reduce spontaneously (Grade III and IV. Excision hemorrhoidectomy remains the gold standard treatment for Grade III and IV hemorrhoids despite great interest in alternative procedures such as stapled hemorrhoidopexy and Doppler-guided hemorrhoidal artery ligation with mucopexy. A large body of evidence demonstrates that excision hemorrhoidectomy is an effective, safe, and affordable procedure. Nevertheless, the main drawback of excision hemorrhoidectomy remains its notorious association with significant postoperative pain. Evidence Acquisition A comprehensive literature search was conducted through MEDLINE and the Cochrane database of systematic reviews. Only prospective case-controlled studies, review articles, and meta-analyses were considered. Results Many strategies have been put forward in the literature to address the issue of pain after excision hemorrhoidectomy. These strategies can be broadly categorized into surgical techniques (e.g., LigaSure hemorrhoidectomy and pharmacological adjuncts (e.g., intradermal methylene blue and chemical sphincterotomy with glyceryl trinitrate ointment. In recent years, meta-analyses and randomized controlled trials have been performed to evaluate their effects. Conclusions This article evaluates the evidence behind these strategies and outlines the new methods available to improve the outcomes of an old technique.

  18. Cloning and characterization of the human DNA-excision repair gene ERCC-1

    NARCIS (Netherlands)

    M. van Duin (Michel)

    1988-01-01

    textabstractIt is the aim of the work described in this thesis to isolate and characterize human genes involved DNA excision repair. This will facilitate the understanding of the mechanism of this repair process whereas it also provides an important step to better understand the relationship between

  19. In situ carcinoma of the conjunctiva: surgical excision associated with cryotherapy

    Directory of Open Access Journals (Sweden)

    Crim N

    2013-09-01

    Full Text Available Nicolás Crim, María Elena Forniés-Paz, Rodolfo Monti, Evangelina Espósito, Juan Pablo Maccio, Julio A Urrets-Zavalía Department of Ophthalmology, University Clinic Reina Fabiola, Universidad Católica de Córdoba, Argentina Background: Although frequently underdiagnosed, squamous cell carcinoma is the most commonly observed malignancy of the conjunctiva. Multiple different treatments have been proposed to date. The purpose of this paper is to report our experience in the treatment of In situ carcinoma of the conjunctiva by surgical excision associated with cryotherapy. Methods: Four eyes in four consecutive patients (two men and two women of average age 53.2 (range 39–71 years at the time of diagnosis of ocular surface squamous neoplasia were treated by simple surgical excision and cryotherapy of the resulting surgical bed margins. In all cases, the diagnosis of in situ carcinoma was confirmed histopathologically. Results: On histopathology, the edges of the surgical specimens were free of malignant cells in three of four patients. All patients showed excellent evolution without recurrence. Mean follow-up was 6.5 (range 2–14 years. Conclusion: In situ carcinoma of the conjunctiva may be simply and successfully treated with surgical excision and cryotherapy. Keywords: conjunctival squamous cell carcinoma, surgical excision, cryotherapy

  20. Surgical excision of lung metastases from squamous carcinoma of the cervix. A report of 2 cases

    Energy Technology Data Exchange (ETDEWEB)

    De Moor, N.G.; Berry, A.V.; Nissenbaum, M.M. (University of the Witwatersrand, Johannesburg (South Africa))

    1983-01-01

    These 2 case reports serve to emphasize two important points concerning carcinoma of the cervix: (i) blood-borne metastases are now frequently encountered in this disease; and (ii) in selected cases surgical excision of a secondary deposit in the lung is the treatment of choice and may even result in cure.

  1. Surgical excision of lung metastases from squamous carcinoma of the cervix. A report of 2 cases.

    Science.gov (United States)

    de Moor, N G; Berry, A V; Nissenbaum, M M

    1983-01-01

    These 2 case reports serve to emphasize two important points concerning carcinoma of the cervix: (i) blood-borne metastases are now frequently encountered in this disease; and (ii) in selected cases surgical excision of a secondary deposit in the lung is the treatment of choice and may even result in cure.

  2. Prospective evaluation of quality of life and sexual functioning after laparoscopic total mesorectal excision

    NARCIS (Netherlands)

    Breukink, S. O.; van der Zaag-Loonen, H. J.; Bouma, E. M. C.; Pierie, J. P. E. N.; Hoff, C.; Wiggers, T.; Meijerink, W. J. H. J.

    PURPOSE: This study was designed to investigate how the quality of life of patients with rectal cancer changes with time after laparoscopic total mesorectal excision. METHODS: Patients completed the Medical Outcomes Study Short Form 36 and the European Organisation for Research and Treatment of

  3. Male sexual function and lower urinary tract symptoms after laparoscopic total mesorectal excision

    NARCIS (Netherlands)

    Breukink, S. O.; Driel, M. F. van; Pierie, J. P. E. N.; Dobbins, C.; Wiggers, T.; Meijerink, W. J. H. J.

    2008-01-01

    The aim of this study was to investigate sexual function and the presence of lower urinary tract symptoms (LUTS) in male patients with rectal cancer following short-term radiotherapy and laparoscopic total mesorectal excision (LTME) by physical and psychological measurements. Sexual function and

  4. Sponge and skin excision sampling for recovery of Salmonella and Campylobacter from defeathered broiler carcasses

    Science.gov (United States)

    Introduction: Salmonella and Campylobacter contamination of broiler carcass skin increases during feather removal. There are several methods for sampling carcasses including sponging or swabbing of skin surface and skin excision. It is unclear whether sponge sampling is adequate to remove bacteria f...

  5. Interference Excision in Spread Spectrum Communications Using Adaptive Positive Time-Frequency Analysis

    Directory of Open Access Journals (Sweden)

    Krishnan Sridhar

    2007-01-01

    Full Text Available This paper introduces a novel algorithm to excise single and multicomponent chirp-like interferences in direct sequence spread spectrum (DSSS communications. The excision algorithm consists of two stages: adaptive signal decomposition stage and directional element detection stage based on the Hough-Radon transform (HRT. Initially, the received spread spectrum signal is decomposed into its time-frequency (TF functions using an adaptive signal decomposition algorithm, and the resulting TF functions are mapped onto the TF plane. We then use a line detection algorithm based on the HRT that operates on the image of the TF plane and detects energy varying directional elements that satisfy a parametric constraint. Interference is modeled by reconstructing the corresponding TF functions detected by the HRT, and subtracted from the received signal. The proposed technique has two main advantages: (i it localizes the interferences on the TF plane with no cross-terms, thus facilitating simple filtering techniques based on thresholding of the TF functions, and is an efficient way to excise the interference; (ii it can be used for the detection of any directional interferences that can be parameterized. Simulation results with synthetic models have shown successful performance with linear and quadratic chirp interferences for single and multicomponent interference cases. The proposed method excises the interference even under very low SNR conditions of  dB, and the technique could be easily extended to any interferences that could be represented by a parametric equation in the TF plane.

  6. [Preliminary influence of 2015 cigarette excise tax up-regulation on cigarette retail price].

    Science.gov (United States)

    Feng, G Z; Wang, C X; Yang, J Q; Jiang, Y

    2016-10-10

    Objective: To evaluate the impact of cigarette excise tax up-regulation on the retail price of cigarettes in 2015. Methods: Nominal and real price of selected cigarette varieties were calculated with data from Tobacco Retail Price Monitoring Project, which was conducted in 10 cities of China from 2013 to 2015. The trend of the cigarette prices changing was analyzed with annual data. Results: A total of 352 varieties of cigarettes were surveyed during the three years. The nominal price of these cigarettes did not change significantly from 2013 to 2014. Compared with nominal price of 2014, the price of 286 varieties increased and the price of 10 most popular varieties increased from 0.6% to 7.4% after cigarette excise tax increased, but the actual prices had both rise and fall compared with 2013. Conclusions: Cigarette excise tax raise in 2015 had influence on the retail price of cigarettes. But the increase in retail price was very limited, if factors including inflation and purchasing power are taken into consideration. Therefore, the influence of 2015 cigarette excise tax raise on tobacco control needs further evaluation.

  7. Anterograde excision of a sublingual gland: new surgical technique for the treatment of ranulas.

    Science.gov (United States)

    Liu, Zhigang; Wang, Bin

    2016-02-01

    Wharton's duct is dissected in a retrograde direction from the orifice of the duct to the hilum of the submandibular gland when the gland is being excised conventionally. Here we describe an anterograde technique, in which Wharton's duct is dissected in an anterograde direction from the hilum of the submandibular gland to the orifice of the duct. This prospective clinical study included 50 consecutive patients with ranulas who had anterograde excision of the sublingual gland between May 2012 and January 2015. The intraoral incision was similar to that for conventional excision. Wharton's duct and other important anatomical structures located in the space behind the sublingual gland were all identified at the beginning of the procedure, followed by anterograde dissection of Wharton's duct. After the glandular tissue lateral to the duct had been incised completely, the duct was exposed and the gland cut into two parts. Finally, the two parts were removed, and the ranula ruptured. The patients were followed up from 6 months-2 years. There were no complications. Anterograde excision of the sublingual gland is based on the anatomy, and this reduces the risk of complications after removal of a ranula.

  8. X-ray repair cross complementing protein 1 in base excision repair

    DEFF Research Database (Denmark)

    Hanssen-Bauer, Audun; Solvang-Garten, Karin; Akbari, Mansour;

    2012-01-01

    X-ray Repair Cross Complementing protein 1 (XRCC1) acts as a scaffolding protein in the converging base excision repair (BER) and single strand break repair (SSBR) pathways. XRCC1 also interacts with itself and rapidly accumulates at sites of DNA damage. XRCC1 can thus mediate the assembly of large...

  9. Recommendations for excision following core needle biopsy of the breast: a contemporary evaluation of the literature.

    Science.gov (United States)

    Calhoun, Benjamin C; Collins, Laura C

    2016-01-01

    Pathologists frequently encounter non-malignant histological findings in percutaneous core needle biopsies (CNBs). Standards for the management of patients with lesions such as atypical ductal hyperplasia, atypical lobular hyperplasia, and lobular carcinoma in situ, as well as other benign lesions, are not well defined, and recommendations for surgical biopsy or continued clinical and radiological follow-up are inconsistent. The frequency with which these lesions are 'upgraded' to carcinoma in excision specimens is widely variable in the literature. Many CNB studies lack careful radiological-pathological correlation, clear criteria for excision, and clinical follow-up for patients on whom excision was not performed. This review of the recent literature emphasizes studies with radiological-pathological correlation, with the goal of developing a contemporary, evidence-based approach to the management of non-malignant lesions of the breast diagnosed on CNB. The data supporting an emerging consensus on which lesions may not require excision are highlighted. The management of non-malignant lesions diagnosed on magnetic resonance imaging-guided CNB is also discussed.

  10. [The radicality of surgical resection in rectal cancer. Analysis of factors associated with incomplete mesorectal excision].

    Science.gov (United States)

    Ferko, A; Orhalmi, J; Nikolov, D H; Hovorková, E; Chobola, M; Vošmik, M; Cermáková, E

    2013-06-01

    Circumferential resection margin (pCRM) and the completeness of mesorectal excision (ME) are two independent prognostic factors significantly associated with the radicality of surgical treatment. Positive pCRM and incomplete mesorectal excision are associated with a significantly higher incidence of local recurrence and worse patient prognosis. The aim of this article is to analyze the risk factors associated with incomplete mesorectal excision. Patients operated on at the Department of Surgery, University Hospital Hradec Kralove between January 2011 and February 2013 were included in the study. The patients data were prospectively collected and entered in the Dg C20 registry. The following factors were analyzed: sex, age, BMI, cN, pT, clinical stage, the involved segment of the rectum, neoadjuvant therapy, circumferential tumour location, the type of surgical approach and the type of surgery. 168 patients were operated on during the above period. 9 (5.3%) palliative stomas and 159 (94.6%) resection procedures were performed in this group of 168 patients. 7 (4.4%) patients were excluded because the quality of excision was not assessed in them. 114 (75%) resections, including 5 intersphincteric resections, were performed in the group of the remaining 152 patients. 10 (7%) were Hartmanns procedures a 28 (18%) were amputation procedures. Out of 152 procedures, 69 (45%) were performed laparoscopically. Positive (y)pCRO was recorded in 26 (17%) patients, predominantly after abdominoperineal resection (APR) - 11 out of 27 (41%), and Hartmanns operation - 6 out of 10 (60%). Incomplete ME was observed in 45 patients (30%), complete ME in 81 patients (53%) and partially complete in 26 patients (17%). Univariate analysis confirmed statistically significant factors associated with incomplete mesorectal excision: (y)pT (P = 0.00027), type of surgery (P = 0.00001) and tumour location (P = 0.00001). Multivariate analysis then confirmed two independent prognostic factors

  11. 2-cm versus 4-cm surgical excision margins for primary cutaneous melanoma thicker than 2 mm: a randomised, multicentre trial

    DEFF Research Database (Denmark)

    Gillgren, Peter; Drzewiecki, Krzysztof T; Niin, Marianne;

    2011-01-01

    Optimum surgical resection margins for patients with clinical stage IIA-C cutaneous melanoma thicker than 2 mm are controversial. The aim of the study was to test whether survival was different for a wide local excision margin of 2 cm compared with a 4-cm excision margin....

  12. Verapamil is Less Effective than Triamcinolone for Prevention of Keloid Scar Recurrence After Excision in a Randomized Controlled Trial

    DEFF Research Database (Denmark)

    Danielsen, Patricia L; Rea, Suzanne M; Wood, Fiona M;

    2016-01-01

    A double-blind randomized controlled trial with a paired split-scar design compared verapamil, an L-type Ca2+ channel antagonist, and triamcinolone for prevention of keloid recurrence after excision. Ca2+ channel blocking activity of verapamil in keloid cells was explored. One keloid was excised...

  13. Classification of pseudo pairs between nucleotide bases and amino acids by analysis of nucleotide-protein complexes.

    Science.gov (United States)

    Kondo, Jiro; Westhof, Eric

    2011-10-01

    Nucleotide bases are recognized by amino acid residues in a variety of DNA/RNA binding and nucleotide binding proteins. In this study, a total of 446 crystal structures of nucleotide-protein complexes are analyzed manually and pseudo pairs together with single and bifurcated hydrogen bonds observed between bases and amino acids are classified and annotated. Only 5 of the 20 usual amino acid residues, Asn, Gln, Asp, Glu and Arg, are able to orient in a coplanar fashion in order to form pseudo pairs with nucleotide bases through two hydrogen bonds. The peptide backbone can also form pseudo pairs with nucleotide bases and presents a strong bias for binding to the adenine base. The Watson-Crick side of the nucleotide bases is the major interaction edge participating in such pseudo pairs. Pseudo pairs between the Watson-Crick edge of guanine and Asp are frequently observed. The Hoogsteen edge of the purine bases is a good discriminatory element in recognition of nucleotide bases by protein side chains through the pseudo pairing: the Hoogsteen edge of adenine is recognized by various amino acids while the Hoogsteen edge of guanine is only recognized by Arg. The sugar edge is rarely recognized by either the side-chain or peptide backbone of amino acid residues.

  14. Cre/lox-mediated marker gene excision in transgenic maize (Zea mays L.) plants.

    Science.gov (United States)

    Zhang, W; Subbarao, S; Addae, P; Shen, A; Armstrong, C; Peschke, V; Gilbertson, L

    2003-11-01

    After the initial transformation and tissue culture process is complete, selectable marker genes, which are used in virtually all transformation approaches, are not required for the expression of the gene of interest in the transgenic plants. There are several advantages to removing the selectable marker gene after it is no longer needed, such as enabling the reuse of selectable markers and simplifying transgene arrays. We have tested the Cre/ lox system from bacteriophage P1 for its ability to precisely excise stably integrated marker genes from chromosomes in transgenic maize plants. Two strategies, crossing and autoexcision, have been tested and demonstrated. In the crossing strategy, plants expressing the Cre recombinase are crossed with plants bearing a transgene construct in which the selectable marker gene is flanked by directly repeated lox sites. Unlike previous reports in which incomplete somatic and germline excision were common, in our experiments complete somatic and germline marker gene excision occurred in the F(1) plants from most crosses with multiple independent Cre and lox lines. In the autoexcision strategy, the cre gene, under the control of a heat shock-inducible promoter, is excised along with the nptII marker gene. Our results show that a transient heat shock treatment of primary transgenic callus is sufficient for inducing cre and excising the cre and nptII genes. Genetic segregation and molecular analysis confirmed that marker gene removal is precise, complete and stable. The autoexcision strategy provides a way of removing the selectable marker gene from callus or other tissues such as embryos and kernels.

  15. Single nucleotide polymorphisms and inherited risk of chronic lymphocytic leukemia among African Americans

    Science.gov (United States)

    Coombs, Catherine C.; Rassenti, Laura Z.; Falchi, Lorenzo; Slager, Susan L.; Strom, Sara S.; Ferrajoli, Alessandra; Weinberg, J. Brice; Kipps, Thomas J.

    2012-01-01

    The incidence of chronic lymphocytic leukemia (CLL) is significantly lower in African Americans than whites, but overall survival is inferior. The biologic basis for these observations remains unexplored. We hypothesized that germline genetic predispositions differ between African Americans and whites with CLL and yield inferior clinical outcomes among African Americans. We examined a discovery cohort of 42 African American CLL patients ascertained at Duke University and found that the risk allele frequency of most single nucleotide polymorphisms known to confer risk of development for CLL is significantly lower among African Americans than whites. We then confirmed our results in a distinct cohort of 68 African American patients ascertained by the CLL Research Consortium. These results provide the first evidence supporting differential genetic risk for CLL between African Americans compared with whites. A fuller understanding of differential genetic risk may improve prognostication and therapeutic decision making for all CLL patients. PMID:22745306

  16. T Cell Receptor Excision Circle (TREC) Monitoring after Allogeneic Stem Cell Transplantation; a Predictive Marker for Complications and Clinical Outcome

    Science.gov (United States)

    Gaballa, Ahmed; Sundin, Mikael; Stikvoort, Arwen; Abumaree, Muhamed; Uzunel, Mehmet; Sairafi, Darius; Uhlin, Michael

    2016-01-01

    Allogeneic hematopoietic stem cell transplantation (HSCT) is a well-established treatment modality for a variety of malignant diseases as well as for inborn errors of the metabolism or immune system. Regardless of disease origin, good clinical effects are dependent on proper immune reconstitution. T cells are responsible for both the beneficial graft-versus-leukemia (GVL) effect against malignant cells and protection against infections. The immune recovery of T cells relies initially on peripheral expansion of mature cells from the graft and later on the differentiation and maturation from donor-derived hematopoietic stem cells. The formation of new T cells occurs in the thymus and as a byproduct, T cell receptor excision circles (TRECs) are released upon rearrangement of the T cell receptor. Detection of TRECs by PCR is a reliable method for estimating the amount of newly formed T cells in the circulation and, indirectly, for estimating thymic function. Here, we discuss the role of TREC analysis in the prediction of clinical outcome after allogeneic HSCT. Due to the pivotal role of T cell reconstitution we propose that TREC analysis should be included as a key indicator in the post-HSCT follow-up. PMID:27727179

  17. Overview of the application of nucleotide in aquaculture

    Directory of Open Access Journals (Sweden)

    Hoang Do Huu

    2016-10-01

    Full Text Available Although long history application in infant formula, dietary nucleotide supplementation has been used only recently in the evaluation of growth performance, stress and pathogen resistance in aquaculture species. This paper addresses the present knowledge of the use of nucleotide supplemented in the diet for culture species. Research reveals that dietary nucleotide may have significant impact and is recommended to add to the feed of aquatic species to get better performance. However, more studies should also be conducted to have better understandings on dose requirement, duration of application, impact on different life stage and under different environmental stress and pathogens. Further study should also examine the effects of dietary nucleotide supplementation of intestinal microbiota and gut morphology, and immune response of aquaculture species.

  18. Nucleotide Metabolism and its Control in Lactic Acid Bacteria

    DEFF Research Database (Denmark)

    Kilstrup, Mogens; Hammer, Karin; Jensen, Peter Ruhdal

    2005-01-01

    Most metabolic reactions are connected through either their utilization of nucleotides or their utilization of nucleotides or their regulation by these metabolites. In this review the biosynthetic pathways for pyrimidine and purine metabolism in lactic acid bacteria are described including...... the interconversion pathways, the formation of deoxyribonucleotides and the salvage pathways for use of exogenous precursors. The data for the enzymatic and the genetic regulation of these pathways are reviewed, as well as the gene organizations in different lactic acid bacteria. Mutant phenotypes and methods...... for manipulation of nucleotide pools are also discussed. Our aim is to provide an overview of the physiology and genetics of nucleotide metabolism and its regulation that will facilitate the interpretation of data arising from genetics, metabolomics, proteomics, and transcriptomics in lactic acid bacteria....

  19. Overview of the application of nucleotide in aquaculture

    Institute of Scientific and Technical Information of China (English)

    Hoang Do Huu

    2016-01-01

    Although long history application in infant formula, dietary nucleotide supplementation has been used only recently in the evaluation of growth performance, stress and pathogen resistance in aquaculture species. This paper addresses the present knowledge of the use of nucleotide supplemented in the diet for culture species. Research reveals that dietary nucleotide may have significant impact and is recommended to add to the feed of aquatic species to get better performance. However, more studies should also be conducted to have better understandings on dose requirement, duration of application, impact on different life stage and under different environmental stress and pathogens. Further study should also examine the effects of dietary nucleotide supplementation of intestinal microbiota and gut morphology, and immune response of aquaculture species.

  20. Association study of nonsynonymous single nucleotide polymorphisms in schizophrenia

    DEFF Research Database (Denmark)

    Carrera, Noa; Arrojo, Manuel; Sanjuán, Julio

    2012-01-01

    Genome-wide association studies using several hundred thousand anonymous markers present limited statistical power. Alternatively, association studies restricted to common nonsynonymous single nucleotide polymorphisms (nsSNPs) have the advantage of strongly reducing the multiple testing problem, ...