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Sample records for y-family polymerases bypass

  1. Kinetic Analysis of the Bypass of a Bulky DNA Lesion Catalyzed by Human Y-family DNA Polymerases

    Science.gov (United States)

    Sherrer, Shanen M.; Sanman, Laura E.; Xia, Cynthia X.; Bolin, Eric R.; Malik, Chanchal K.; Efthimiopoulos, Georgia; Basu, Ashis K.; Suo, Zucai

    2012-01-01

    1-Nitropyrene (1-NP), a mutagen and potential carcinogen, is the most abundant nitro polyaromatic hydrocarbon in diesel exhaust, which reacts with DNA to form predominantly N-(deoxyguanosin-8-yl)-1-aminopyrene (dGAP). If not repaired, this DNA lesion is presumably bypassed in vivo by any of human Y-family DNA polymerases kappa (hPolκ), iota (hPolτ), eta (hPolη), and Rev1 (hRev1). Our running start assays demonstrated that each of these enzymes was indeed capable of traversing a site-specifically placed dGAP on a synthetic DNA template but hRev1 was stopped after lesion bypass. The time required to bypass 50% of the dGAP sites (t50bypass ) encountered by hPolη, hPolκ and hPolτ was determined to be 2.5 s, 4.1 s, and 106.5 s, respectively. The efficiency order of catalyzing translesion synthesis of dGAP (hPolη > hPolκ > hPolτ >> hRev1) is the same as the order for these human Y-family enzymes to elongate undamaged DNA. Although hPolη bypassed dGAP efficiently, replication by both hPolκ and hPolτ was strongly stalled at the lesion site and at a site immediately downstream from dGAP. By employing pre-steady state kinetic methods, a kinetic basis was established for polymerase pausing at these DNA template sites. Besides efficiency of bypass, the fidelity of those low-fidelity polymerases at these pause sites was also significantly decreased. Thus, if the translesion DNA synthesis of dGAP in vivo is catalyzed by a human Y-family DNA polymerase, e.g. hPolη, the process is certainly mutagenic. PMID:22324639

  2. Quantitative Analysis of the Mutagenic Potential of 1-Aminopyrene-DNA Adduct Bypass Catalyzed by Y-Family DNA Polymerases

    Science.gov (United States)

    Sherrer, Shanen M.; Taggart, David J.; Pack, Lindsey R.; Malik, Chanchal K.; Basu, Ashis K.; Suo, Zucai

    2012-01-01

    N- (deoxyguanosin-8-yl)-1-aminopyrene (dGAP) is the predominant nitro polyaromatic hydrocarbon product generated from the air pollutant 1-nitropyrene reacting with DNA. Previous studies have shown that dGAP induces genetic mutations in bacterial and mammalian cells. One potential source of these mutations is the error-prone bypass of dGAP lesions catalyzed by the low-fidelity Y-family DNA polymerases. To provide a comparative analysis of the mutagenic potential of the translesion DNA synthesis (TLS) of dGAP, we employed short oligonucleotide sequencing assays (SOSAs) with the model Y-family DNA polymerase from Sulfolobus solfataricus, DNA Polymerase IV (Dpo4), and the human Y-family DNA polymerases eta (hPolη), kappa (hPolκ), and iota (hPolι). Relative to undamaged DNA, all four enzymes generated far more mutations (base deletions, insertions, and substitutions) with a DNA template containing a site-specifically placed dGAP. Opposite dGAP and at an immediate downstream template position, the most frequent mutations made by the three human enzymes were base deletions and the most frequent base substitutions were dAs for all enzymes. Based on the SOSA data, Dpo4 was the least error-prone Y-family DNA polymerase among the four enzymes during the TLS of dGAP. Among the three human Y-family enzymes, hPolκ made the fewest mutations at all template positions except opposite the lesion site. hPolκ was significantly less error-prone than hPolι and hPolη during the extension of dGAP bypass products. Interestingly, the most frequent mutations created by hPolι at all template positions were base deletions. Although hRev1, the fourth human Y-family enzyme, could not extend dGAP bypass products in our standing start assays, it preferentially incorporated dCTP opposite the bulky lesion. Collectively, these mutagenic profiles suggest that hPolkk and hRev1 are the most suitable human Y-family DNA polymerases to perform TLS of dGAP in humans. PMID:22917544

  3. Structural insight into dynamic bypass of the major cisplatin-DNA adduct by Y-family polymerase Dpo4

    Energy Technology Data Exchange (ETDEWEB)

    Wong, Jimson H.Y.; Brown, Jessica A.; Suo, Zucai; Blum, Paul; Nohmi, Takehiko; Ling, Hong (OSU); (NINA-Japan); (UNL); (UWO)

    2010-08-23

    Y-family DNA polymerases bypass Pt-GG, the cisplatin-DNA double-base lesion, contributing to the cisplatin resistance in tumour cells. To reveal the mechanism, we determined three structures of the Y-family DNA polymerase, Dpo4, in complex with Pt-GG DNA. The crystallographic snapshots show three stages of lesion bypass: the nucleotide insertions opposite the 3{prime}G (first insertion) and 5{prime}G (second insertion) of Pt-GG, and the primer extension beyond the lesion site. We observed a dynamic process, in which the lesion was converted from an open and angular conformation at the first insertion to a depressed and nearly parallel conformation at the subsequent reaction stages to fit into the active site of Dpo4. The DNA translocation-coupled conformational change may account for additional inhibition on the second insertion reaction. The structures illustrate that Pt-GG disturbs the replicating base pair in the active site, which reduces the catalytic efficiency and fidelity. The in vivo relevance of Dpo4-mediated Pt-GG bypass was addressed by a dpo-4 knockout strain of Sulfolobus solfataricus, which exhibits enhanced sensitivity to cisplatin and proteomic alterations consistent with genomic stress.

  4. Mechanistic Investigation of the Bypass of a Bulky Aromatic DNA Adduct Catalyzed by a Y-family DNA Polymerase

    Science.gov (United States)

    Gadkari, Varun V.; Tokarsky, E. John; Malik, Chanchal K.; Basu, Ashis K.; Suo, Zucai

    2014-01-01

    3-Nitrobenzanthrone (3-NBA), a nitropolyaromatic hydrocarbon (NitroPAH) pollutant in diesel exhaust, is a potent mutagen and carcinogen. After metabolic activation, the primary metabolites of 3-NBA react with DNA to form dG and dA adducts. One of the three major adducts identified is N-(2’-deoxyguanosin-8-yl)-3-aminobenzanthrone (dGC8-N-ABA). This bulky adduct likely stalls replicative DNA polymerases but can be traversed by lesion bypass polymerases in vivo. Here, we employed running start assays to show that a site-specifically placed dGC8-N-ABA is bypassed in vitro by Sulfolobus solfataricus DNA polymerase IV (Dpo4), a model Y-family DNA polymerase. However, the nucleotide incorporation rate of Dpo4 was significantly reduced opposite both the lesion and the template position immediately downstream from the lesion site, leading to two strong pause sites. To investigate the kinetic effect of dGC8-N-ABA on polymerization, we utilized pre-steady-state kinetic methods to determine the kinetic parameters for individual nucleotide incorporations upstream, opposite, and downstream from the dGC8-N-ABA lesion. Relative to the replication of the corresponding undamaged DNA template, both nucleotide incorporation efficiency and fidelity of Dpo4 were considerably decreased during dGC8-N-ABA lesion bypass and the subsequent extension step. The lower nucleotide incorporation efficiency caused by the lesion is a result of a significantly reduced dNTP incorporation rate constant and modestly weaker dNTP binding affinity. At both pause sites, nucleotide incorporation followed biphasic kinetics with a fast and a slow phase and their rates varied with nucleotide concentration. In contrast, only the fast phase was observed with undamaged DNA. A kinetic mechanism was proposed for the bypass of dGC8-N-ABA bypass catalyzed by Dpo4. PMID:25048879

  5. Mechanistic Basis for the Bypass of a Bulky DNA Adduct Catalyzed by a Y-Family DNA Polymerase

    Science.gov (United States)

    Vyas, Rajan; Efthimiopoulos, Georgia; Tokarsky, E. John; Malik, Chanchal K.; Basu, Ashis K.; Suo, Zucai

    2015-01-01

    1-Nitropyrene (1-NP), an environmental pollutant, induces DNA damage in vivo and is considered to be carcinogenic. The DNA adducts formed by the 1-NP metabolites stall replicative DNA polymerases but are presumably bypassed by error-prone Y-family DNA polymerases at the expense of replication fidelity and efficiency in vivo. Our running start assays confirmed that a site-specifically placed 8-(deoxyguanosin-N2-yl)-1-aminopyrene (dG1,8), one of the DNA adducts derived from 1-NP, can be bypassed by Sulfolobus solfataricus DNA polymerase IV (Dpo4), although this representative Y-family enzyme was paused strongly by the lesion. Pre-steady-state kinetic assays were employed to determine the low nucleotide incorporation fidelity and establish a minimal kinetic mechanism for the dG1,8 bypass by Dpo4. To reveal a structural basis for dCTP incorporation opposite dG1,8, we solved the crystal structures of the complexes of Dpo4 and DNA containing a templating dG1,8 lesion in the absence or presence of dCTP. The Dpo4·DNA-dG1,8 binary structure shows that the aminopyrene moiety of the lesion stacks against the primer/template junction pair, while its dG moiety projected into the cleft between the Finger and Little Finger domains of Dpo4. In the Dpo4·DNA-dG1,8·dCTP ternary structure, the aminopyrene moiety of the dG1,8 lesion, is sandwiched between the nascent and junction base pairs, while its base is present in the major groove. Moreover, dCTP forms a Watson–Crick base pair with dG, two nucleotides upstream from the dG1,8 site, creating a complex for “-2” frameshift mutation. Mechanistically, these crystal structures provide additional insight into the aforementioned minimal kinetic mechanism. PMID:26327169

  6. Recent Insight into the Kinetic Mechanisms and Conformational Dynamics of Y-Family DNA Polymerases

    OpenAIRE

    Maxwell, Brian A.; Suo, Zucai

    2014-01-01

    The kinetic mechanisms by which DNA polymerases catalyze DNA replication and repair have long been areas of active research. Recently discovered Y-family DNA polymerases catalyze the bypass of damaged DNA bases that would otherwise block replicative DNA polymerases and stall replication forks. Unlike DNA polymerases from the five other families, the Y-family DNA polymerases have flexible, solvent-accessible active sites that are able to tolerate various types of damaged template bases and all...

  7. Global conformational dynamics of a Y-family DNA polymerase during catalysis.

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    Cuiling Xu

    2009-10-01

    Full Text Available Replicative DNA polymerases are stalled by damaged DNA while the newly discovered Y-family DNA polymerases are recruited to rescue these stalled replication forks, thereby enhancing cell survival. The Y-family DNA polymerases, characterized by low fidelity and processivity, are able to bypass different classes of DNA lesions. A variety of kinetic and structural studies have established a minimal reaction pathway common to all DNA polymerases, although the conformational intermediates are not well defined. Furthermore, the identification of the rate-limiting step of nucleotide incorporation catalyzed by any DNA polymerase has been a matter of long debate. By monitoring time-dependent fluorescence resonance energy transfer (FRET signal changes at multiple sites in each domain and DNA during catalysis, we present here a real-time picture of the global conformational transitions of a model Y-family enzyme: DNA polymerase IV (Dpo4 from Sulfolobus solfataricus. Our results provide evidence for a hypothetical DNA translocation event followed by a rapid protein conformational change prior to catalysis and a subsequent slow, post-chemistry protein conformational change. Surprisingly, the DNA translocation step was induced by the binding of a correct nucleotide. Moreover, we have determined the directions, rates, and activation energy barriers of the protein conformational transitions, which indicated that the four domains of Dpo4 moved in a synchronized manner. These results showed conclusively that a pre-chemistry conformational change associated with domain movements was too fast to be the rate-limiting step. Rather, the rearrangement of active site residues limited the rate of correct nucleotide incorporation. Collectively, the conformational dynamics of Dpo4 offer insights into how the inter-domain movements are related to enzymatic function and their concerted interactions with other proteins at the replication fork.

  8. (1)H, (13)C, and (15)N backbone resonance assignments of the full-length 40 kDa S. acidocaldarius Y-family DNA polymerase, dinB homolog.

    Science.gov (United States)

    Moro, Sean L; Cocco, Melanie J

    2015-10-01

    The dinB homolog (Dbh) is a member of the Y-family of translesion DNA polymerases, which are specialized to accurately replicate DNA across from a wide variety of lesions in living cells. Lesioned bases block the progression of high-fidelity polymerases and cause detrimental replication fork stalling; Y-family polymerases can bypass these lesions. The active site of the translesion synthesis polymerase is more open than that of a replicative polymerase; consequently Dbh polymerizes with low fidelity. Bypass polymerases also have low processivity. Short extension past the lesion allows the high-fidelity polymerase to switch back onto the site of replication. Dbh and the other Y-family polymerases have been used as structural models to investigate the mechanisms of DNA polymerization and lesion bypass. Many high-resolution crystal structures of Y-family polymerases have been reported. NMR dynamics studies can complement these structures by providing a measure of protein motions. Here we report the (15)N, (1)H, and (13)C backbone resonance assignments at two temperatures (35 and 50 °C) for Sulfolobus acidocaldarius Dbh polymerase. Backbone resonance assignments have been obtained for 86 % of the residues. The polymerase active site is assigned as well as the majority of residues in each of the four domains.

  9. Backbone assignment of the little finger domain of a Y-family DNA polymerase.

    Science.gov (United States)

    Ma, Dejian; Fowler, Jason D; Suo, Zucai

    2011-10-01

    Sulfolobus solfataricus DNA polymerase IV (Dpo4), a prototype Y-family DNA polymerase, contains a unique little finger domain besides a catalytic core. Here, we report the chemical shift assignments for the backbone nitrogens, α and β carbons, and amide protons of the little finger domain of Dpo4. This work and our published backbone assignment for the catalytic core provide the basis for investigating the conformational dynamics of Dpo4 during catalysis using solution NMR spectroscopy.

  10. Following DNA chain extension and protein conformational changes in crystals of a Y-family DNA polymerase via Raman crystallography.

    Science.gov (United States)

    Espinoza-Herrera, Shirly J; Gaur, Vineet; Suo, Zucai; Carey, Paul R

    2013-07-23

    Y-Family DNA polymerases are known to bypass DNA lesions in vitro and in vivo. Sulfolobus solfataricus DNA polymerase (Dpo4) was chosen as a model Y-family enzyme for investigating the mechanism of DNA synthesis in single crystals. Crystals of Dpo4 in complexes with DNA (the binary complex) in the presence or absence of an incoming nucleotide were analyzed by Raman microscopy. (13)C- and (15)N-labeled d*CTP, or unlabeled dCTP, were soaked into the binary crystals with G as the templating base. In the presence of the catalytic metal ions, Mg(2+) and Mn(2+), nucleotide incorporation was detected by the disappearance of the triphosphate band of dCTP and the retention of *C modes in the crystal following soaking out of noncovalently bound C(or *C)TP. The addition of the second coded base, thymine, was observed by adding cognate dTTP to the crystal following a single d*CTP addition. Adding these two bases caused visible damage to the crystal that was possibly caused by protein and/or DNA conformational change within the crystal. When d*CTP is soaked into the Dpo4 crystal in the absence of Mn(2+) or Mg(2+), the primer extension reaction did not occur; instead, a ternary protein·template·d*CTP complex was formed. In the Raman difference spectra of both binary and ternary complexes, in addition to the modes of d(*C)CTP, features caused by ring modes from the template/primer bases being perturbed and from the DNA backbone appear, as well as features from perturbed peptide and amino acid side chain modes. These effects are more pronounced in the ternary complex than in the binary complex. Using standardized Raman intensities followed as a function of time, the C(*C)TP population in the crystal was maximal at ∼20 min. These remained unchanged in the ternary complex but declined in the binary complexes as chain incorporation occurred.

  11. Mechanistic Studies with DNA Polymerases Reveal Complex Outcomes following Bypass of DNA Damage

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    Robert L. Eoff

    2010-01-01

    Full Text Available DNA is a chemically reactive molecule that is subject to many different covalent modifications from sources that are both endogenous and exogenous in origin. The inherent instability of DNA is a major obstacle to genomic maintenance and contributes in varying degrees to cellular dysfunction and disease in multi-cellular organisms. Investigations into the chemical and biological aspects of DNA damage have identified multi-tiered and overlapping cellular systems that have evolved as a means of stabilizing the genome. One of these pathways supports DNA replication events by in a sense adopting the mantra that one must “make the best of a bad situation” and tolerating covalent modification to DNA through less accurate copying of the damaged region. Part of this so-called DNA damage tolerance pathway involves the recruitment of specialized DNA polymerases to sites of stalled or collapsed replication forks. These enzymes have unique structural and functional attributes that often allow bypass of adducted template DNA and successful completion of genomic replication. What follows is a selective description of the salient structural features and bypass properties of specialized DNA polymerases with an emphasis on Y-family members.

  12. Characterization of a Y-Family DNA Polymerase eta from the Eukaryotic Thermophile Alvinella pompejana

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    Kashiwagi, Sayo; Kuraoka, Isao; Fujiwara, Yoshie; Hitomi, Kenichi; Cheng, Quen J.; Fuss, Jill O.; Shin, David S.; Masutani, Chikahide; Tainer, John A.; Hanaoka, Fumio; Iwai, Shigenori

    2010-01-01

    Human DNA polymerase η (HsPolη) plays an important role in translesion synthesis (TLS), which allows for replication past DNA damage such as UV-induced cis-syn cyclobutane pyrimidine dimers (CPDs). Here, we characterized ApPolη from the thermophilic worm Alvinella pompejana, which inhabits deep-sea hydrothermal vent chimneys. ApPolη shares sequence homology with HsPolη and contains domains for binding ubiquitin and proliferating cell nuclear antigen. Sun-induced UV does not penetrate Alvinella's environment; however, this novel DNA polymerase catalyzed efficient and accurate TLS past CPD, as well as 7,8-dihydro-8-oxoguanine and isomers of thymine glycol induced by reactive oxygen species. In addition, we found that ApPolη is more thermostable than HsPolη, as expected from its habitat temperature. Moreover, the activity of this enzyme was retained in the presence of a higher concentration of organic solvents. Therefore, ApPolη provides a robust, human-like Polη that is more active after exposure to high temperatures and organic solvents. PMID:20936172

  13. Dynamic conformational change regulates the protein-DNA recognition: an investigation on binding of a Y-family polymerase to its target DNA.

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    Xiakun Chu

    2014-09-01

    Full Text Available Protein-DNA recognition is a central biological process that governs the life of cells. A protein will often undergo a conformational transition to form the functional complex with its target DNA. The protein conformational dynamics are expected to contribute to the stability and specificity of DNA recognition and therefore may control the functional activity of the protein-DNA complex. Understanding how the conformational dynamics influences the protein-DNA recognition is still challenging. Here, we developed a two-basin structure-based model to explore functional dynamics in Sulfolobus solfataricus DNA Y-family polymerase IV (DPO4 during its binding to DNA. With explicit consideration of non-specific and specific interactions between DPO4 and DNA, we found that DPO4-DNA recognition is comprised of first 3D diffusion, then a short-range adjustment sliding on DNA and finally specific binding. Interestingly, we found that DPO4 is under a conformational equilibrium between multiple states during the binding process and the distributions of the conformations vary at different binding stages. By modulating the strength of the electrostatic interactions, the flexibility of the linker, and the conformational dynamics in DPO4, we drew a clear picture on how DPO4 dynamically regulates the DNA recognition. We argue that the unique features of flexibility and conformational dynamics in DPO4-DNA recognition have direct implications for low-fidelity translesion DNA synthesis, most of which is found to be accomplished by the Y-family DNA polymerases. Our results help complete the description of the DNA synthesis process for the Y-family polymerases. Furthermore, the methods developed here can be widely applied for future investigations on how various proteins recognize and bind specific DNA substrates.

  14. DNA polymerase eta participates in the mutagenic bypass of adducts induced by benzo[a]pyrene diol epoxide in mammalian cells.

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    Alden C Klarer

    Full Text Available Y-family DNA-polymerases have larger active sites that can accommodate bulky DNA adducts allowing them to bypass these lesions during replication. One member, polymerase eta (pol eta, is specialized for the bypass of UV-induced thymidine-thymidine dimers, correctly inserting two adenines. Loss of pol eta function is the molecular basis for xeroderma pigmentosum (XP variant where the accumulation of mutations results in a dramatic increase in UV-induced skin cancers. Less is known about the role of pol eta in the bypass of other DNA adducts. A commonly encountered DNA adduct is that caused by benzo[a]pyrene diol epoxide (BPDE, the ultimate carcinogenic metabolite of the environmental chemical benzo[a]pyrene. Here, treatment of pol eta-deficient fibroblasts from humans and mice with BPDE resulted in a significant decrease in Hprt gene mutations. These studies in mammalian cells support a number of in vitro reports that purified pol eta has error-prone activity on plasmids with site-directed BPDE adducts. Sequencing the Hprt gene from this work shows that the majority of mutations are G>T transversions. These data suggest that pol eta has error-prone activity when bypassing BPDE-adducts. Understanding the basis of environmental carcinogen-derived mutations may enable prevention strategies to reduce such mutations with the intent to reduce the number of environmentally relevant cancers.

  15. Structural and kinetic insights into binding and incorporation of L-nucleotide analogs by a Y-family DNA polymerase

    OpenAIRE

    Gaur, Vineet; Vyas, Rajan; Fowler, Jason D.; Efthimiopoulos, Georgia; Feng, Joy Y.; Suo, Zucai

    2014-01-01

    Considering that all natural nucleotides (D-dNTPs) and the building blocks (D-dNMPs) of DNA chains possess D-stereochemistry, DNA polymerases and reverse transcriptases (RTs) likely possess strongD-stereoselectivity by preferably binding and incorporating D-dNTPs over unnatural L-dNTPs during DNA synthesis. Surprisingly, a structural basis for the discrimination against L-dNTPs by DNA polymerases or RTs has not been established although L-deoxycytidine analogs (lamivudine and emtricitabine) a...

  16. How Y-Family DNA polymerase IV is more accurate than Dpo4 at dCTP insertion opposite an N2-dG adduct of benzo[a]pyrene.

    Science.gov (United States)

    Sholder, Gabriel; Creech, Amanda; Loechler, Edward L

    2015-11-01

    To bypass DNA damage, cells have Y-Family DNA polymerases (DNAPs). One Y-Family-class includes DNAP κ and DNAP IV, which accurately insert dCTP opposite N(2)-dG adducts, including from the carcinogen benzo[a]pyrene (BP). Another class includes DNAP η and DNAP V, which insert accurately opposite UV-damage, but inaccurately opposite BP-N(2)-dG. To investigate structural differences between Y-Family-classes, regions are swapped between DNAP IV (a κ/IV-class-member) and Dpo4 (a η/V-class-member); the kinetic consequences are evaluated via primer-extension studies with a BP-N(2)-dG-containing template. Four key structural elements are revealed. (1) Y-Family DNAPs have discreet non-covalent contacts between their little finger-domain (LF-Domain) and their catalytic core-domain (CC-Domain), which we call "non-covalent bridges" (NCBs). Arg37 and Arg38 in DNAP IV's CC-Domain near the active site form a non-covalent bridge (AS-NCB) by interacting with Glu251 and Asp252, respectively, in DNAP IV's LF-Domain. Without these interactions dATP/dGTP/dTTP misinsertions increase. DNAP IV's AS-NCB suppresses misinsertions better than Dpo4's equivalent AS-NCB. (2) DNAP IV also suppresses dATP/dGTP/dTTP misinsertions via a second non-covalent bridge, which is ∼8Å from the active site (Distal-NCB). Dpo4 has no Distal-NCB, rendering it inferior at dATP/dGTP/dTTP suppression. (3) dCTP insertion is facilitated by the larger minor groove opening near the active site in DNAP IV versus Dpo4, which is sensible given that Watson/Crick-like [dCTP:BP-N(2)-dG] pairing requires the BP-moiety to be in the minor groove. (4) Compared to Dpo4, DNAP IV has a smaller major groove opening, which suppresses dGTP misinsertion, implying BP-N(2)-dG bulk in the major groove during Hoogsteen syn-adduct-dG:dGTP pairing. In summary, DNAP IV has a large minor groove opening to enhance dCTP insertion, a plugged major groove opening to suppress dGTP misinsertion, and two non-covalent bridges (near and distal

  17. Identification of an Unfolding Intermediate for a DNA Lesion Bypass Polymerase

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    Sherrer, Shanen M.; Maxwell, Brian A.; Pack, Lindsey R.; Fiala, Kevin A.; Fowler, Jason D.; Zhang, Jun; Suo, Zucai

    2012-01-01

    Sulfolobus solfataricusDNA Polymerase IV (Dpo4), a prototype Y-family DNA polymerase, has been well characterized biochemically and biophysically at 37 °C or lower temperatures. However, the physiological temperature of the hyperthermophile S. solfataricus is approximately 80 °C. With such a large discrepancy in temperature, the in vivo relevance of these in vitro studies of Dpo4 has been questioned. Here, we employed circular dichroism spectroscopy and fluorescence-based thermal scanning to investigate the secondary structural changes of Dpo4 over a temperature range from 26 to 119 °C. Dpo4 was shown to display a high melting temperature characteristic of hyperthermophiles. Unexpectedly, the Little Finger domain of Dpo4, which is only found in the Y-family DNA polymerases, was shown to be more thermostable than the polymerase core. More interestingly, Dpo4 exhibited a three-state cooperative unfolding profile with an unfolding intermediate. The linker region between the Little Finger and Thumb domains of Dpo4 was found to be a source of structural instability. Through site-directed mutagenesis, the interactions between the residues in the linker region and the Palm domain were identified to play a critical role in the formation of the unfolding intermediate. Notably, the secondary structure of Dpo4 was not altered when the temperature was increased from 26 to 87.5 °C. Thus, in addition to providing structural insights into the thermal stability and an unfolding intermediate of Dpo4, our work also validated the relevance of the in vitro studies of Dpo4 performed at temperatures significantly lower than 80 °C. PMID:22667759

  18. Bypass of a psoralen DNA interstrand cross-link by DNA polymerases beta, iota, and kappa in vitro

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    Smith, Leigh A.; Makarova, Alena V.; Samson, Laura; Thiesen, Katherine E.; Dhar, Alok; Bessho, Tadayoshi

    2012-01-01

    Repair of DNA inter-strand cross-links in mammalian cells involves several biochemically distinctive processes, including the release of one of the cross-linked strands and translesion DNA synthesis (TLS). In this report, we investigated in vitro TLS activity of psoralen DNA inter-strand cross-link by three DNA repair polymerases, DNA polymerase beta, kappa and iota. DNA polymerase beta is capable of bypassing a psoralen cross-link with a low efficiency. Cell extracts prepared from DNA polymerase beta knockout mouse embryonic fibroblast showed a reduced bypass activity of the psoralen cross-link and purified DNA polymerase beta restored the bypass activity. In addition, DNA polymerase iota mis-incorporated thymine across the psoralen cross-link and DNA polymerase kappa extended these mis-paired primer ends, suggesting that DNA polymerase iota may serve as an inserter and DNA polymerase kappa may play a role as an extender in the repair of psoralen DNA inter-strand cross-links. The results demonstrated here indicate that multiple DNA polymerases could participate in TLS steps in mammalian DNA inter-strand cross-link repair. PMID:23106263

  19. An In Vitro Model for Studying Neutrophil Activation During Cardiopulmonary Bypass by Using a Polymerase Chain Reaction Thermocycler

    NARCIS (Netherlands)

    Tang, Min; Zhao, Xiao-Gang; Gu, Y. John; Chen, Chang-Zhi

    The accurate temperature control of a polymerase chain reaction (PCR) thermocycler was exploited in developing an in vitro model to study neutrophil activation during cardiopulmonary bypass. Neutrophils from 12 volunteers underwent temperature changes in a PCR thermocycler (37 degrees C for 30

  20. Conformational Dynamics of a Y-Family DNA Polymerase during Substrate Binding and Catalysis As Revealed by Interdomain F?rster Resonance Energy Transfer

    OpenAIRE

    Maxwell, Brian A.; Xu, Cuiling; Suo, Zucai

    2014-01-01

    Numerous kinetic, structural, and theoretical studies have established that DNA polymerases adjust their domain structures to enclose nucleotides in their active sites and then rearrange critical active site residues and substrates for catalysis, with the latter conformational change acting to kinetically limit the correct nucleotide incorporation rate. Additionally, structural studies have revealed a large conformational change between the apoprotein and the DNA?protein binary state for Y-fa...

  1. Viewing Human DNA Polymerase β Faithfully and Unfaithfully Bypass an Oxidative Lesion by Time-Dependent Crystallography

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    Vyas, Rajan; Reed, Andrew J.; Tokarsky, E. John; Suo, Zucai

    2015-01-01

    One common oxidative DNA lesion, 8-oxo-7,8-dihydro-2′-deoxyguanine (8-oxoG), is highly mutagenic in vivo due to its anti-conformation forming a Watson–Crick base pair with correct deoxycytidine 5′-triphosphate (dCTP) and its syn-conformation forming a Hoogsteen base pair with incorrect deoxyadenosine 5′-triphosphate (dATP). Here, we utilized time-resolved X-ray crystallography to follow 8-oxoG bypass by human DNA polymerase β (hPolβ). In the 12 solved structures, both Watson–Crick (anti-8-oxoG:anti-dCTP) and Hoogsteen (syn-8-oxoG:anti-dATP) base pairing were clearly visible and were maintained throughout the chemical reaction. Additionally, a third Mg2+ appeared during the process of phosphodiester bond formation and was located between the reacting α- and β-phosphates of the dNTP, suggesting its role in stabilizing reaction intermediates. After phosphodiester bond formation, hPolβ reopened its conformation, pyrophosphate was released, and the newly incorporated primer 3′-terminal nucleotide stacked, rather than base paired, with 8-oxoG. These structures provide the first real-time pictures, to our knowledge, of how a polymerase correctly and incorrectly bypasses a DNA lesion. PMID:25825995

  2. The beta subunit modulates bypass and termination at UV lesions during in vitro replication with DNA polymerase III holoenzyme of Escherichia coli

    International Nuclear Information System (INIS)

    Shavitt, O.; Livneh, Z.

    1989-01-01

    The cycling time of DNA polymerase III holoenzyme during replication of UV-irradiated single-stranded (ss) DNA was longer than with unirradiated DNA (8 versus 3 min, respectively), most likely due to slow dissociation from lesion-terminated nascent DNA strands. Initiation of elongation on primed ssDNA was not significantly inhibited by the presence of UV lesions as indicated by the identical distribution of replication products synthesized at early and late reaction times and by the identical duration of the initial synthesis bursts on both unirradiated and UV-irradiated DNA templates. When replication was performed with DNA polymerase III* supplemented with increasing quantities of purified beta 2 subunit, the cycling time on UV-irradiated DNA decreased from 14.8 min at 1.7 nM beta 2 down to 6 min at 170 nM beta 2, a concentration in which beta 2 was in large excess over the polymerase. In parallel to the reduction in cycling time, also the bypass frequency of cyclobutane-photodimers decreased with increasing beta 2 concentration, and at 170 nM beta 2, bypass of photodimers was essentially eliminated. It has been shown that polymerase complexes with more than one beta 2 per polymerase molecule were formed at high beta 2 concentrations. It is plausible that polymerase complexes obtained under high beta 2 concentration dissociate from lesion-terminated primers faster than polymerase complexes formed at a low beta 2 concentration. This is expected to favor termination over bypass at pyrimidine photodimers and thus decrease their bypass frequency. These results suggest that the beta 2 subunit might act as a sensor for obstacles to replication caused by DNA damage, and that it terminates elongation at these sites by promoting dissociation. The intracellular concentration of beta 2 was estimated to be 250 nM

  3. 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.

    Science.gov (United States)

    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. Copyright © 2015 Elsevier B.V. All rights reserved.

  4. A Crystallographic Study of the Role of Sequence Context in Thymine Glycol Bypass by a Replicative DNA Polymerase Serendipitously Sheds Light on the Exonuclease Complex

    Energy Technology Data Exchange (ETDEWEB)

    Aller, Pierre; Duclos, Stéphanie; Wallace, Susan S.; Doublié, Sylvie (Vermont)

    2012-06-27

    Thymine glycol (Tg) is the most common oxidation product of thymine and is known to be a strong block to replicative DNA polymerases. A previously solved structure of the bacteriophage RB69 DNA polymerase (RB69 gp43) in complex with Tg in the sequence context 5'-G-Tg-G shed light on how Tg blocks primer elongation: The protruding methyl group of the oxidized thymine displaces the adjacent 5'-G, which can no longer serve as a template for primer elongation [Aller, P., Rould, M. A., Hogg, M, Wallace, S. S. and Doublie S. (2007). A structural rationale for stalling of a replicative DNA polymerase at the most common oxidative thymine lesion, thymine glycol. Proc. Natl. Acad. Sci. USA, 104, 814-818.]. Several studies showed that in the sequence context 5'-C-Tg-purine, Tg is more likely to be bypassed by Klenow fragment, an A-family DNA polymerase. We set out to investigate the role of sequence context in Tg bypass in a B-family polymerase and to solve the crystal structures of the bacteriophage RB69 DNA polymerase in complex with Tg-containing DNA in the three remaining sequence contexts: 5'-A-Tg-G, 5'-T-Tg-G, and 5'-C-Tg-G. A combination of several factors - including the associated exonuclease activity, the nature of the 3' and 5' bases surrounding Tg, and the cis-trans interconversion of Tg - influences Tg bypass. We also visualized for the first time the structure of a well-ordered exonuclease complex, allowing us to identify and confirm the role of key residues (Phe123, Met256, and Tyr257) in strand separation and in the stabilization of the primer strand in the exonuclease site.

  5. Error-prone bypass of O6-methylguanine by DNA polymerase of Pseudomonas aeruginosa phage PaP1.

    Science.gov (United States)

    Gu, Shiling; Xiong, Jingyuan; Shi, Ying; You, Jia; Zou, Zhenyu; Liu, Xiaoying; Zhang, Huidong

    2017-09-01

    O 6 -Methylguanine (O 6 -MeG) is highly mutagenic and is commonly found in DNA exposed to methylating agents, generally leads to G:C to A:T mutagenesis. To study DNA replication encountering O 6 -MeG by the DNA polymerase (gp90) of P. aeruginosa phage PaP1, we analyzed steady-state and pre-steady-state kinetics of nucleotide incorporation opposite O 6 -MeG by gp90 exo - . O 6 -MeG partially inhibited full-length extension by gp90 exo - . O 6 -MeG greatly reduces dNTP incorporation efficiency, resulting in 67-fold preferential error-prone incorporation of dTTP than dCTP. Gp90 exo - extends beyond T:O 6 -MeG 2-fold more efficiently than C:O 6 -MeG. Incorporation of dCTP opposite G and incorporation of dCTP or dTTP opposite O 6 -MeG show fast burst phases. The pre-steady-state incorporation efficiency (k pol /K d,dNTP ) is decreased in the order of dCTP:G>dTTP:O 6 -MeG>dCTP:O 6 -MeG. The presence of O 6 -MeG at template does not affect the binding affinity of polymerase to DNA but it weakened their binding in the presence of dCTP and Mg 2+ . Misincorporation of dTTP opposite O 6 -MeG further weakens the binding affinity of polymerase to DNA. The priority of dTTP incorporation opposite O 6 -MeG is originated from the fact that dTTP can induce a faster conformational change step and a faster chemical step than dCTP. This study reveals that gp90 bypasses O 6 -MeG in an error-prone manner and provides further understanding in DNA replication encountering mutagenic alkylation DNA damage for P. aeruginosa phage PaP1. Copyright © 2017 Elsevier B.V. All rights reserved.

  6. Role of exonucleolytic processing and polymerase-DNA association in bypass of lesions during replication in vitro. Significance for SOS-targeted mutagenesis

    International Nuclear Information System (INIS)

    Shwartz, H.; Shavitt, O.; Livneh, Z.

    1988-01-01

    The role of exonuclease activity in trans-lesion DNA replication with Escherichia coli DNA polymerase III holoenzyme was investigated. RecA protein inhibited the 3'----5' exonuclease activity of the polymerase 2-fold when assayed in the absence of replication and had no effect on turnover of dNTPs into dNMPs. In contrast, single-stranded DNA-binding protein, which had no effect on the exonuclease activity in the absence of replication, showed a pronounced 7-fold suppression of the 3'----5' exonuclease activity during replication. The excision of incorporated dNMP alpha S residues from DNA by the 3'----5' exonuclease activity of DNA polymerase III holoenzyme was inhibited 10-20-fold; still no increase in bypass of pyrimidine photodimers was observed. Thus, in agreement with our previous results in which the exonuclease activity was inhibited at the protein level, inhibition at the DNA level also did not increase bypass of photodimers. Fractionation of the replication mixture after termination of DNA synthesis on a Bio-Gel A-5m column under conditions which favor polymerase-DNA binding yielded a termination complex which could perform turnover of dNTPs into dNMPs. Adding challenge-primed single-stranded DNA to the complex yielded a burst of DNA synthesis which was promoted most likely by DNA polymerase III holoenzyme molecules transferred from the termination complex to the challenge DNA thus demonstrating the instability of the polymerase-DNA association. Addition of a fresh sample of DNA polymerase III holoenzyme to purified termination products, which consist primarily of partially replicated molecules with nascent chains terminated at UV lesions, did not result in any net DNA synthesis as expected

  7. Replication of UV-irradiated single-stranded DNA by DNA polymerase III holoenzyme of Escherichia coli: evidence for bypass of pyrimidine photodimers

    International Nuclear Information System (INIS)

    Livneh, Z.

    1986-01-01

    Replication of UV-irradiated circular single-stranded phage M13 DNA by Escherichia coli RNA polymerase (EC 2.7.7.6) and DNA polymerase III holoenzyme (EC 2.7.7.7) in the presence of single-stranded DNA binding protein yielded full-length as well as partially replicated products. A similar result was obtained with phage G4 DNA primed with E. coli DNA primase, and phage phi X174 DNA primed with a synthetic oligonucleotide. The fraction of full-length DNA was several orders of magnitude higher than predicted if pyrimidine photodimers were to constitute absolute blocks to DNA replication. Recent models have suggested that pyrimidine photodimers are absolute blocks to DNA replication and that SOS-induced proteins are required to allow their bypass. Our results demonstrate that, under in vitro replication conditions, E. coli DNA polymerase III holoenzyme can insert nucleotides opposite pyrimidine dimers to a significant extent, even in the absence of SOS-induced proteins

  8. Analysis of UV-induced mutation spectra in Escherichia coli by DNA polymerase {eta} from Arabidopsis thaliana

    Energy Technology Data Exchange (ETDEWEB)

    Santiago, Maria Jesus [Departamento de Genetica, Facultad de Ciencias, Edificio Gregor Mendel, Campus Rabanales, Universidad de Cordoba (Spain); Alejandre-Duran, Encarna [Departamento de Genetica, Facultad de Ciencias, Edificio Gregor Mendel, Campus Rabanales, Universidad de Cordoba (Spain); Ruiz-Rubio, Manuel [Departamento de Genetica, Facultad de Ciencias, Edificio Gregor Mendel, Campus Rabanales, Universidad de Cordoba (Spain)]. E-mail: ge1rurum@uco.es

    2006-10-10

    DNA polymerase {eta} belongs to the Y-family of DNA polymerases, enzymes that are able to synthesize past template lesions that block replication fork progression. This polymerase accurately bypasses UV-associated cis-syn cyclobutane thymine dimers in vitro and therefore may contributes to resistance against sunlight in vivo, both ameliorating survival and decreasing the level of mutagenesis. We cloned and sequenced a cDNA from Arabidopsis thaliana which encodes a protein containing several sequence motifs characteristics of Pol{eta} homologues, including a highly conserved sequence reported to be present in the active site of the Y-family DNA polymerases. The gene, named AtPOLH, contains 14 exons and 13 introns and is expressed in different plant tissues. A strain from Saccharomyces cerevisiae, deficient in Pol{eta} activity, was transformed with a yeast expression plasmid containing the AtPOLH cDNA. The rate of survival to UV irradiation in the transformed mutant increased to similar values of the wild type yeast strain, showing that AtPOLH encodes a functional protein. In addition, when AtPOLH is expressed in Escherichia coli, a change in the mutational spectra is detected when bacteria are irradiated with UV light. This observation might indicate that AtPOLH could compete with DNA polymerase V and then bypass cyclobutane pyrimidine dimers incorporating two adenylates.

  9. Translesion Synthesis of the N2-2′-Deoxyguanosine Adduct of the Dietary Mutagen IQ in Human Cells: Error-Free Replication by DNA Polymerase κ and Mutagenic Bypass by DNA Polymerases η, ζ, and Rev1

    Science.gov (United States)

    2016-01-01

    Translesion synthesis (TLS) of the N2-2′-deoxyguanosine (dG-N2-IQ) adduct of the carcinogen 2-amino-3-methylimidazo[4,5-f]quinoline (IQ) was investigated in human embryonic kidney 293T cells by replicating plasmid constructs in which the adduct was individually placed at each guanine (G1, G2, or G3) of the NarI sequence (5′-CG1G2CG3CC-3′). TLS efficiency was 38%, 29%, and 25% for the dG-N2-IQ located at G1, G2, and G3, respectively, which suggests that dG-N2-IQ is bypassed more efficiently by one or more DNA polymerases at G1 than at either G2 or G3. TLS efficiency was decreased 8–35% in cells with knockdown of pol η, pol κ, pol ι, pol ζ, or Rev1. Up to 75% reduction in TLS occurred when pol η, pol ζ, and Rev1 were simultaneously knocked down, suggesting that these three polymerases play important roles in dG-N2-IQ bypass. Mutation frequencies (MFs) of dG-N2-IQ at G1, G2, and G3 were 23%, 17%, and 11%, respectively, exhibiting a completely reverse trend of the previously reported MF of the C8-dG adduct of IQ (dG-C8-IQ), which is most mutagenic at G3 ((2015) Nucleic Acids Res.43, 8340−835126220181). The major type of mutation induced by dG-N2-IQ was targeted G → T, as was reported for dG-C8-IQ. In each site, knockdown of pol κ resulted in an increase in MF, whereas MF was reduced when pol η, pol ι, pol ζ, or Rev1 was knocked down. The reduction in MF was most pronounced when pol η, pol ζ, and Rev1 were simultaneously knocked down and especially when the adduct was located at G3, where MF was reduced by 90%. We conclude that pol κ predominantly performs error-free TLS of the dG-N2-IQ adduct, whereas pols η, pol ζ, and Rev1 cooperatively carry out the error-prone TLS. However, in vitro experiments using yeast pol ζ and κ showed that the former was inefficient in full-length primer extension on dG-N2-IQ templates, whereas the latter was efficient in both error-free and error-prone extensions. We believe that the observed differences between

  10. Accommodation of an N-(deoxyguanosin-8-yl)-2-acetylaminofluorene adduct in the active site of human DNA polymerase iota: Hoogsteen or Watson-Crick base pairing?

    Science.gov (United States)

    Donny-Clark, Kerry; Shapiro, Robert; Broyde, Suse

    2009-01-13

    Bypass across DNA lesions by specialized polymerases is essential for maintenance of genomic stability. Human DNA polymerase iota (poliota) is a bypass polymerase of the Y family. Crystal structures of poliota suggest that Hoogsteen base pairing is employed to bypass minor groove DNA lesions, placing them on the spacious major groove side of the enzyme. Primer extension studies have shown that poliota is also capable of error-free nucleotide incorporation opposite the bulky major groove adduct N-(deoxyguanosin-8-yl)-2-acetylaminofluorene (dG-AAF). We present molecular dynamics simulations and free energy calculations suggesting that Watson-Crick base pairing could be employed in poliota for bypass of dG-AAF. In poliota with Hoogsteen-paired dG-AAF the bulky AAF moiety would reside on the cramped minor groove side of the template. The Hoogsteen-capable conformation distorts the active site, disrupting interactions necessary for error-free incorporation of dC opposite the lesion. Watson-Crick pairing places the AAF rings on the spacious major groove side, similar to the position of minor groove adducts observed with Hoogsteen pairing. Watson-Crick-paired structures show a well-ordered active site, with a near reaction-ready ternary complex. Thus our results suggest that poliota would utilize the same spacious region for lesion bypass of both major and minor groove adducts. Therefore, purine adducts with bulk on the minor groove side would use Hoogsteen pairing, while adducts with the bulky lesion on the major groove side would utilize Watson-Crick base pairing as indicated by our MD simulations for dG-AAF. This suggests the possibility of an expanded role for poliota in lesion bypass.

  11. Pre-Steady-State Kinetic Analysis of Truncated and Full-Length Saccharomyces cerevisiae DNA Polymerase Eta

    Science.gov (United States)

    Brown, Jessica A.; Zhang, Likui; Sherrer, Shanen M.; Taylor, John-Stephen; Burgers, Peter M. J.; Suo, Zucai

    2010-01-01

    Understanding polymerase fidelity is an important objective towards ascertaining the overall stability of an organism's genome. Saccharomyces cerevisiae DNA polymerase η (yPolη), a Y-family DNA polymerase, is known to efficiently bypass DNA lesions (e.g., pyrimidine dimers) in vivo. Using pre-steady-state kinetic methods, we examined both full-length and a truncated version of yPolη which contains only the polymerase domain. In the absence of yPolη's C-terminal residues 514–632, the DNA binding affinity was weakened by 2-fold and the base substitution fidelity dropped by 3-fold. Thus, the C-terminus of yPolη may interact with DNA and slightly alter the conformation of the polymerase domain during catalysis. In general, yPolη discriminated between a correct and incorrect nucleotide more during the incorporation step (50-fold on average) than the ground-state binding step (18-fold on average). Blunt-end additions of dATP or pyrene nucleotide 5′-triphosphate revealed the importance of base stacking during the binding of incorrect incoming nucleotides. PMID:20798853

  12. Pre-Steady-State Kinetic Analysis of Truncated and Full-Length Saccharomyces cerevisiae DNA Polymerase Eta

    Directory of Open Access Journals (Sweden)

    Jessica A. Brown

    2010-01-01

    Full Text Available Understanding polymerase fidelity is an important objective towards ascertaining the overall stability of an organism's genome. Saccharomyces cerevisiae DNA polymerase η (yPolη, a Y-family DNA polymerase, is known to efficiently bypass DNA lesions (e.g., pyrimidine dimers in vivo. Using pre-steady-state kinetic methods, we examined both full-length and a truncated version of yPolη which contains only the polymerase domain. In the absence of yPolη's C-terminal residues 514–632, the DNA binding affinity was weakened by 2-fold and the base substitution fidelity dropped by 3-fold. Thus, the C-terminus of yPolη may interact with DNA and slightly alter the conformation of the polymerase domain during catalysis. In general, yPolη discriminated between a correct and incorrect nucleotide more during the incorporation step (50-fold on average than the ground-state binding step (18-fold on average. Blunt-end additions of dATP or pyrene nucleotide 5′-triphosphate revealed the importance of base stacking during the binding of incorrect incoming nucleotides.

  13. Accommodation of an N-(deoxyguanosin-8-yl)-2-acetylaminofluorene adduct in the active site of human DNA polymerase ι: Hoogsteen or Watson-Crick base pairing?†

    Science.gov (United States)

    Donny-Clark, Kerry; Shapiro, Robert; Broyde, Suse

    2009-01-01

    Bypass across DNA lesions by specialized polymerases is essential for maintenance of genomic stability. Human DNA polymerase ι (polι) is a bypass polymerase of the Y family. Crystal structures of polι suggest that Hoogsteen base pairing is employed to bypass minor groove DNA lesions, placing them on the spacious major groove side of the enzyme. Primer extension studies have shown that polι is also capable of error-free nucleotide incorporation opposite the bulky major groove adduct N-(deoxyguanosin-8-yl)-2-acetyl-aminofluorene (dG-AAF). We present molecular dynamics simulations and free energy calculations suggesting that Watson-Crick base pairing could be employed in polι for bypass of dG-AAF. In polι with Hoogsteen paired dG-AAF the bulky AAF moiety would reside on the cramped minor groove side of the template. The Hoogsteen-capable conformation distorts the active site, disrupting interactions necessary for error-free incorporation of dC opposite the lesion. Watson-Crick pairing places the AAF rings on the spacious major groove side, similar to the position of minor groove adducts observed with Hoogsteen pairing. Watson-Crick paired structures show a well-ordered active site, with a near reaction-ready ternary complex. Thus our results suggest that polι would utilize the same spacious region for lesion bypass of both major and minor groove adducts. Therefore, purine adducts with bulk on the minor groove side would use Hoogsteen pairing, while adducts with the bulky lesion on the major groove side would utilize Watson-Crick base pairing as indicated by our MD simulations for dG-AAF. This suggests the possibility of an expanded role for polι in lesion bypass. PMID:19072536

  14. Lesion Orientation of O4-Alkylthymidine Influences Replication by Human DNA Polymerase η.

    Science.gov (United States)

    O'Flaherty, D K; Patra, A; Su, Y; Guengerich, F P; Egli, M; Wilds, C J

    2016-08-01

    DNA lesions that elude repair may undergo translesion synthesis catalyzed by Y-family DNA polymerases. O 4 -Alkylthymidines, persistent adducts that can result from carcinogenic agents, may be encountered by DNA polymerases. The influence of lesion orientation around the C4- O 4 bond on processing by human DNA polymerase η (hPol η ) was studied for oligonucleotides containing O 4 -methylthymidine, O 4 -ethylthymidine, and analogs restricting the O 4 -methylene group in an anti -orientation. Primer extension assays revealed that the O 4 -alkyl orientation influences hPol η bypass. Crystal structures of hPol η •DNA•dNTP ternary complexes with O 4 -methyl- or O 4 -ethylthymidine in the template strand showed the nucleobase of the former lodged near the ceiling of the active site, with the syn - O 4 -methyl group engaged in extensive hydrophobic interactions. This unique arrangement for O 4 -methylthymidine with hPol η , inaccessible for the other analogs due to steric/conformational restriction, is consistent with differences observed for nucleotide incorporation and supports the concept that lesion conformation influences extension across DNA damage. Together, these results provide mechanistic insights on the mutagenicity of O 4 MedT and O 4 EtdT when acted upon by hPol η .

  15. Heart bypass surgery

    Science.gov (United States)

    Off-pump coronary artery bypass; OPCAB; Beating heart surgery; Bypass surgery - heart; CABG; Coronary artery bypass graft; Coronary artery bypass surgery; Coronary bypass surgery; Coronary artery disease - CABG; CAD - CABG; Angina - ...

  16. The role of DNA polymerase {iota} in UV mutational spectra

    Energy Technology Data Exchange (ETDEWEB)

    Choi, Jun-Hyuk [Division of Biology, Beckman Research Institute, City of Hope, Duarte, CA 91010 (United States); Besaratinia, Ahmad [Division of Biology, Beckman Research Institute, City of Hope, Duarte, CA 91010 (United States); Lee, Dong-Hyun [Division of Biology, Beckman Research Institute, City of Hope, Duarte, CA 91010 (United States); Lee, Chong-Soon [Department of Biochemistry, College of Natural Sciences, Yeungnam University, Gyongsan 712-749 (Korea, Republic of); Pfeifer, Gerd P. [Division of Biology, Beckman Research Institute, City of Hope, Duarte, CA 91010 (United States)]. E-mail: gpfeifer@coh.org

    2006-07-25

    UVB (280-320 nm) and UVC (200-280 nm) irradiation generate predominantly cyclobutane pyrimidine dimers (CPDs) and (6-4) photoproducts in DNA. CPDs are thought to be responsible for most of the UV-induced mutations. Thymine-thymine CPDs, and probably also CPDs containing cytosine, are replicated in vivo in a largely accurate manner by a DNA polymerase {eta} (Pol {eta}) dependent process. Pol {eta} is a DNA damage-tolerant and error-prone DNA polymerase encoded by the POLH (XPV) gene in humans. Another member of the Y family of error-prone DNA polymerases is POLI encoding DNA polymerase iota (Pol {iota}). In order to clarify the specific role of Pol {iota} in UV mutagenesis, we have used an siRNA knockdown approach in combination with a supF shuttle vector which replicates in mammalian cells, similar as we have previously done for Pol {eta}. Synthetic RNA duplexes were used to efficiently inhibit Pol {iota} expression in 293T cells. The supF shuttle vector was irradiated with 254 nm UVC and replicated in 293T cells in presence of anti-Pol {iota} siRNA. Surprisingly, there was a consistent reduction of recovered plasmid from cells with Pol {iota} knockdown and this was independent of UV irradiation of the plasmid. The supF mutant frequency was unchanged in the siRNA knockdown cells relative to control cells confirming that Pol {iota} does not play an important role in UV mutagenesis. UV-induced supF mutants were sequenced from siRNA-treated cells and controls. Neither the type of mutations nor their distribution along the supF gene were significantly different between controls and siRNA knockdown cells and were predominantly C to T and CC to TT transitions at dipyrimidine sites. These results show that Pol {iota} has no significant role in UV lesion bypass and mutagenesis in vivo and provides some initial data suggesting that this polymerase may be involved in replication of extrachromosomal DNA.

  17. Interactions and Localization of Escherichia coli Error-Prone DNA Polymerase IV after DNA Damage.

    Science.gov (United States)

    Mallik, Sarita; Popodi, Ellen M; Hanson, Andrew J; Foster, Patricia L

    2015-09-01

    Escherichia coli's DNA polymerase IV (Pol IV/DinB), a member of the Y family of error-prone polymerases, is induced during the SOS response to DNA damage and is responsible for translesion bypass and adaptive (stress-induced) mutation. In this study, the localization of Pol IV after DNA damage was followed using fluorescent fusions. After exposure of E. coli to DNA-damaging agents, fluorescently tagged Pol IV localized to the nucleoid as foci. Stepwise photobleaching indicated ∼60% of the foci consisted of three Pol IV molecules, while ∼40% consisted of six Pol IV molecules. Fluorescently tagged Rep, a replication accessory DNA helicase, was recruited to the Pol IV foci after DNA damage, suggesting that the in vitro interaction between Rep and Pol IV reported previously also occurs in vivo. Fluorescently tagged RecA also formed foci after DNA damage, and Pol IV localized to them. To investigate if Pol IV localizes to double-strand breaks (DSBs), an I-SceI endonuclease-mediated DSB was introduced close to a fluorescently labeled LacO array on the chromosome. After DSB induction, Pol IV localized to the DSB site in ∼70% of SOS-induced cells. RecA also formed foci at the DSB sites, and Pol IV localized to the RecA foci. These results suggest that Pol IV interacts with RecA in vivo and is recruited to sites of DSBs to aid in the restoration of DNA replication. DNA polymerase IV (Pol IV/DinB) is an error-prone DNA polymerase capable of bypassing DNA lesions and aiding in the restart of stalled replication forks. In this work, we demonstrate in vivo localization of fluorescently tagged Pol IV to the nucleoid after DNA damage and to DNA double-strand breaks. We show colocalization of Pol IV with two proteins: Rep DNA helicase, which participates in replication, and RecA, which catalyzes recombinational repair of stalled replication forks. Time course experiments suggest that Pol IV recruits Rep and that RecA recruits Pol IV. These findings provide in vivo evidence

  18. Lesion Orientation of O4-Alkylthymidine Influences Replication by Human DNA Polymerase η

    OpenAIRE

    O’Flaherty, D. K.; Patra, A.; Su, Y.; Guengerich, F. P.; Egli, M.; Wilds, C. J.

    2016-01-01

    DNA lesions that elude repair may undergo translesion synthesis catalyzed by Y-family DNA polymerases. O4-Alkylthymidines, persistent adducts that can result from carcinogenic agents, may be encountered by DNA polymerases. The influence of lesion orientation around the C4-O4 bond on processing by human DNA polymerase η (hPol η) was studied for oligonucleotides containing O4-methylthymidine, O4-ethylthymidine, and analogs restricting the O4-methylene group in an anti-orientation. Primer extens...

  19. Roles of the active site residues and metal cofactors in noncanonical base-pairing during catalysis by human DNA polymerase iota.

    Science.gov (United States)

    Makarova, Alena V; Ignatov, Artem; Miropolskaya, Nataliya; Kulbachinskiy, Andrey

    2014-10-01

    Human DNA polymerase iota (Pol ι) is a Y-family polymerase that can bypass various DNA lesions but possesses very low fidelity of DNA synthesis in vitro. Structural analysis of Pol ι revealed a narrow active site that promotes noncanonical base-pairing during catalysis. To better understand the structure-function relationships in the active site of Pol ι we investigated substitutions of individual amino acid residues in its fingers domain that contact either the templating or the incoming nucleotide. Two of the substitutions, Y39A and Q59A, significantly decreased the catalytic activity but improved the fidelity of Pol ι. Surprisingly, in the presence of Mn(2+) ions, the wild-type and mutant Pol ι variants efficiently incorporated nucleotides opposite template purines containing modifications that disrupted either Hoogsteen or Watson-Crick base-pairing, suggesting that Pol ι may use various types of interactions during nucleotide addition. In contrast, in Mg(2+) reactions, wild-type Pol ι was dependent on Hoogsteen base-pairing, the Y39A mutant was essentially inactive, and the Q59A mutant promoted Watson-Crick interactions with template purines. The results suggest that Pol ι utilizes distinct mechanisms of nucleotide incorporation depending on the metal cofactor and reveal important roles of specific residues from the fingers domain in base-pairing and catalysis. Copyright © 2014 Elsevier B.V. All rights reserved.

  20. Role of polymerase η in mitochondrial mutagenesis of Saccharomyces cerevisiae

    Energy Technology Data Exchange (ETDEWEB)

    Chatterjee, Nimrat; Pabla, Ritu [Dept. of Cell Biology and Anatomy, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107 (United States); Siede, Wolfram, E-mail: wolfram.siede@unthsc.edu [Dept. of Cell Biology and Anatomy, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107 (United States)

    2013-02-08

    Highlights: ► DNA polymerase η is detectable in mitochondria of budding yeast. ► Pol η reduces UV-induced mitochondrial base pair substitutions and frameshifts. ► For UV-induced base pair substitutions, Pol η and Pol ζ interact epistatically. -- Abstract: DNA polymerase η mostly catalyzes an error-free bypass of the most frequent UV lesions, pyrimidine dimers of the cyclobutane-type. In addition to its nuclear localization, we show here for the first time its mitochondrial localization in budding yeast. In mitochondria, this polymerase improves bypass replication fidelity opposite UV damage as shown in base pair substitution and frameshift assays. For base pair substitutions, polymerase η appears to be related in function and epistatic to DNA polymerase ζ which, however, plays the opposite role in the nucleus.

  1. Replisome-mediated Translesion Synthesis and Leading Strand Template Lesion Skipping Are Competing Bypass Mechanisms*

    Science.gov (United States)

    Gabbai, Carolina B.; Yeeles, Joseph T. P.; Marians, Kenneth J.

    2014-01-01

    A number of different enzymatic pathways have evolved to ensure that DNA replication can proceed past template base damage. These pathways include lesion skipping by the replisome, replication fork regression followed by either correction of the damage and origin-independent replication restart or homologous recombination-mediated restart of replication downstream of the lesion, and bypass of the damage by a translesion synthesis DNA polymerase. We report here that of two translesion synthesis polymerases tested, only DNA polymerase IV, not DNA polymerase II, could engage productively with the Escherichia coli replisome to bypass leading strand template damage, despite the fact that both enzymes are shown to be interacting with the replicase. Inactivation of the 3′ → 5′ proofreading exonuclease of DNA polymerase II did not enable bypass. Bypass by DNA polymerase IV required its ability to interact with the β clamp and act as a translesion polymerase but did not require its “little finger” domain, a secondary region of interaction with the β clamp. Bypass by DNA polymerase IV came at the expense of the inherent leading strand lesion skipping activity of the replisome, indicating that they are competing reactions. PMID:25301949

  2. Integrated turbine bypass system

    Energy Technology Data Exchange (ETDEWEB)

    Johnson, L.H.; Dickenson, R.J.; Parry, W.T.; Retzlaff, K.M.

    1982-07-01

    Turbine steam-flow bypasses have been used for years in various sizes and applications. Because of differing system requirements, their use has been more predominant in Europe than in the United States. Recently, some utilities and consulting engineers have been re-evaluating their need for various types of bypass operation in fossil-fuelled power plants.

  3. Evolving a polymerase for hydrophobic base analogues.

    Science.gov (United States)

    Loakes, David; Gallego, José; Pinheiro, Vitor B; Kool, Eric T; Holliger, Philipp

    2009-10-21

    Hydrophobic base analogues (HBAs) have shown great promise for the expansion of the chemical and coding potential of nucleic acids but are generally poor polymerase substrates. While extensive synthetic efforts have yielded examples of HBAs with favorable substrate properties, their discovery has remained challenging. Here we describe a complementary strategy for improving HBA substrate properties by directed evolution of a dedicated polymerase using compartmentalized self-replication (CSR) with the archetypal HBA 5-nitroindole (d5NI) and its derivative 5-nitroindole-3-carboxamide (d5NIC) as selection substrates. Starting from a repertoire of chimeric polymerases generated by molecular breeding of DNA polymerase genes from the genus Thermus, we isolated a polymerase (5D4) with a generically enhanced ability to utilize HBAs. The selected polymerase. 5D4 was able to form and extend d5NI and d5NIC (d5NI(C)) self-pairs as well as d5NI(C) heteropairs with all four bases with efficiencies approaching, or exceeding, those of the cognate Watson-Crick pairs, despite significant distortions caused by the intercalation of the d5NI(C) heterocycles into the opposing strand base stack, as shown by nuclear magnetic resonance spectroscopy (NMR). Unlike Taq polymerase, 5D4 was also able to extend HBA pairs such as Pyrene: varphi (abasic site), d5NI: varphi, and isocarbostyril (ICS): 7-azaindole (7AI), allowed bypass of a chemically diverse spectrum of HBAs, and enabled PCR amplification with primers comprising multiple d5NI(C)-substitutions, while maintaining high levels of catalytic activity and fidelity. The selected polymerase 5D4 promises to expand the range of nucleobase analogues amenable to replication and should find numerous applications, including the synthesis and replication of nucleic acid polymers with expanded chemical and functional diversity.

  4. Gastric bypass surgery

    Science.gov (United States)

    ... your body will not get all of the calories from the food you eat. ... to a small hole in your pouch. The food you eat will now travel ... absorb fewer calories. Gastric bypass can be done in two ways. ...

  5. Cardiopulmonary bypass and hemostasis

    NARCIS (Netherlands)

    Eijsman, Leon

    1992-01-01

    In chapter 1, we recalled that intracardiac defects can only be corrected when cardiopulmonary circulation is maintained by extracorporeal criculation and ventilation. To prevent clot formation in this artificial circuit, the socalled cardiopulmonary bypass (CPB), we completely depend on the

  6. Coronary Artery Bypass Grafting

    Science.gov (United States)

    ... lung bypass machine is used during this procedure. Robot-assisted technique. This type of procedure allows for ... driving after 3 to 8 weeks. Returning to work after 6 weeks is common unless your job ...

  7. Bypass of a Nick by the Replisome of Bacteriophage T7*

    Science.gov (United States)

    Zhu, Bin; Lee, Seung-Joo; Richardson, Charles C.

    2011-01-01

    DNA polymerase and DNA helicase are essential components of DNA replication. The helicase unwinds duplex DNA to provide single-stranded templates for DNA synthesis by the DNA polymerase. In bacteriophage T7, movement of either the DNA helicase or the DNA polymerase alone terminates upon encountering a nick in duplex DNA. Using a minicircular DNA, we show that the helicase·polymerase complex can bypass a nick, albeit at reduced efficiency of 7%, on the non-template strand to continue rolling circle DNA synthesis. A gap in the non-template strand cannot be bypassed. The efficiency of bypass synthesis depends on the DNA sequence downstream of the nick. A nick on the template strand cannot be bypassed. Addition of T7 single-stranded DNA-binding protein to the complex stimulates nick bypass 2-fold. We propose that the association of helicase with the polymerase prevents dissociation of the helicase upon encountering a nick, allowing the helicase to continue unwinding of the duplex downstream of the nick. PMID:21701044

  8. Bypass of a nick by the replisome of bacteriophage T7.

    Science.gov (United States)

    Zhu, Bin; Lee, Seung-Joo; Richardson, Charles C

    2011-08-12

    DNA polymerase and DNA helicase are essential components of DNA replication. The helicase unwinds duplex DNA to provide single-stranded templates for DNA synthesis by the DNA polymerase. In bacteriophage T7, movement of either the DNA helicase or the DNA polymerase alone terminates upon encountering a nick in duplex DNA. Using a minicircular DNA, we show that the helicase · polymerase complex can bypass a nick, albeit at reduced efficiency of 7%, on the non-template strand to continue rolling circle DNA synthesis. A gap in the non-template strand cannot be bypassed. The efficiency of bypass synthesis depends on the DNA sequence downstream of the nick. A nick on the template strand cannot be bypassed. Addition of T7 single-stranded DNA-binding protein to the complex stimulates nick bypass 2-fold. We propose that the association of helicase with the polymerase prevents dissociation of the helicase upon encountering a nick, allowing the helicase to continue unwinding of the duplex downstream of the nick.

  9. Your diet after gastric bypass surgery

    Science.gov (United States)

    Gastric bypass surgery - your diet; Obesity - diet after bypass; Weight loss - diet after bypass ... You had gastric bypass surgery. This surgery made your stomach smaller by closing off most of your stomach with staples. It changed the way your ...

  10. Optimal Bypass and Cream Skimming.

    OpenAIRE

    Laffont, Jean-Jacques; Tirole, Jean

    1990-01-01

    This paper develops a normative model of regulatory policy toward bypass and cream skimming. It analyzes the effects of bypass on second-degree price discrimination, on the rent of the regulated firm, and on the welfare of low-demand customers. It shows that pricing under marginal cost may be optimal for the regulated firm, excessive cream skimming occurs if access to the bypass technology is not regulated, and the prohibition of bypass may increase or decrease the regulated firm's rent. Copy...

  11. The Best Bypass Surgery Trial

    DEFF Research Database (Denmark)

    Møller, Christian H; Jensen, Birte Østergaard; Gluud, Christian

    2007-01-01

    Recent trials suggest that off-pump coronary artery bypass grafting (OPCAB) reduces the risk of mortality and morbidity compared with conventional coronary artery bypass grafting (CCAB) using cardiopulmonary bypass. Patients with a moderate- to high-risk of complications after CCAB may have...

  12. Are There Mutator Polymerases?

    Directory of Open Access Journals (Sweden)

    Miguel Garcia-Diaz

    2003-01-01

    Full Text Available DNA polymerases are involved in different cellular events, including genome replication and DNA repair. In the last few years, a large number of novel DNA polymerases have been discovered, and the biochemical analysis of their properties has revealed a long list of intriguing features. Some of these polymerases have a very low fidelity and have been suggested to play mutator roles in different processes, like translesion synthesis or somatic hypermutation. The current view of these processes is reviewed, and the current understanding of DNA polymerases and their role as mutator enzymes is discussed.

  13. Aortic valve bypass

    DEFF Research Database (Denmark)

    Lund, Jens T; Jensen, Maiken Brit; Arendrup, Henrik

    2013-01-01

    In aortic valve bypass (AVB) a valve-containing conduit is connecting the apex of the left ventricle to the descending aorta. Candidates are patients with symptomatic aortic valve stenosis rejected for conventional aortic valve replacement (AVR) or transcatheter aortic valve implantation (TAVI). ...

  14. Inhibiting DNA Polymerases as a Therapeutic Intervention against Cancer

    Directory of Open Access Journals (Sweden)

    Anthony J. Berdis

    2017-11-01

    Full Text Available Inhibiting DNA synthesis is an important therapeutic strategy that is widely used to treat a number of hyperproliferative diseases including viral infections, autoimmune disorders, and cancer. This chapter describes two major categories of therapeutic agents used to inhibit DNA synthesis. The first category includes purine and pyrmidine nucleoside analogs that directly inhibit DNA polymerase activity. The second category includes DNA damaging agents including cisplatin and chlorambucil that modify the composition and structure of the nucleic acid substrate to indirectly inhibit DNA synthesis. Special emphasis is placed on describing the molecular mechanisms of these inhibitory effects against chromosomal and mitochondrial DNA polymerases. Discussions are also provided on the mechanisms associated with resistance to these therapeutic agents. A primary focus is toward understanding the roles of specialized DNA polymerases that by-pass DNA lesions produced by DNA damaging agents. Finally, a section is provided that describes emerging areas in developing new therapeutic strategies targeting specialized DNA polymerases.

  15. Cardiopulmonary bypass in pregnancy

    OpenAIRE

    Mukul Chandra Kapoor

    2014-01-01

    Cardiac surgery carried out on cardiopulmonary bypass (CPB) in a pregnant woman is associated with poor neonatal outcomes although maternal outcomes are similar to cardiac surgery in non-pregnant women. Most adverse maternal and fetal outcomes from cardiac surgery during pregnancy are attributed to effects of CPB. The CPB is associated with utero-placental hypoperfusion due to a number of factors, which may translate into low fetal cardiac output, hypoxia and even death. Better maternal and f...

  16. Basics of cardiopulmonary bypass

    Directory of Open Access Journals (Sweden)

    Manjula Sarkar

    2017-01-01

    Full Text Available Cardiopulmonary bypass (CPB provides a bloodless field for cardiac surgery. It incorporates an extracorporeal circuit to provide physiological support in which venous blood is drained to a reservoir, oxygenated and sent back to the body using a pump. Team effort between surgeon, perfusionist and anaesthesiologist is paramount for the successful use of CPB. However, it also has its share of complications and strategies to reduce these complications are the area of the current research.

  17. The expanding polymerase universe.

    Science.gov (United States)

    Goodman, M F; Tippin, B

    2000-11-01

    Over the past year, the number of known prokaryotic and eukaryotic DNA polymerases has exploded. Many of these newly discovered enzymes copy aberrant bases in the DNA template over which 'respectable' polymerases fear to tread. The next step is to unravel their functions, which are thought to range from error-prone copying of DNA lesions, somatic hypermutation and avoidance of skin cancer, to restarting stalled replication forks and repairing double-stranded DNA breaks.

  18. Site-specifically modified oligodeoxyribonucleotides as templates for Escherichia coli DNA polymerase I

    International Nuclear Information System (INIS)

    O'Connor, D.; Stoehrer, G.

    1985-01-01

    Oligodeoxyribonucleotides with site-specific modifications have been used as substrates for Escherichia coli DNA polymerase I holoenzyme and Klenow fragment. Modifications included the bulky guanine-8-aminofluorene adduct and a guanine oxidation product resembling the product of photosensitized DNA oxidation. By a combination of primers and nick-mers, conditions of single-strand-directed DNA synthesis and nick-translation could be created. The results show that the polymerase can bypass both types of lesions. Bypass occurs on a single-stranded template but is facilitated on a nicked, double-stranded template. Only purines, with guanine more favored than adenine, are incorporated across both lesions. The results indicate that site-specifically modified oligonucleotides can be sensitive probes for the action of polymerases on damaged templates. They also suggest a function for polymerase I, in its nick-translation capacity, during DNA repair and mutagenesis

  19. Spiritual Bypass: A Preliminary Investigation

    Science.gov (United States)

    Cashwell, Craig S.; Glosoff, Harriet L.; Hammond, Cheree

    2010-01-01

    The phenomenon of spiritual bypass has received limited attention in the transpersonal psychology and counseling literature and has not been subjected to empirical inquiry. This study examines the phenomenon of spiritual bypass by considering how spirituality, mindfulness, alexithymia (emotional restrictiveness), and narcissism work together to…

  20. Haemodynamics in axillobifemoral bypass grafts

    NARCIS (Netherlands)

    C.H. Wittens

    1992-01-01

    textabstractThis thesis is based on four publications on the subject of graft configuration and haemodynamics in axillobifemoral bypass grafts: 1. A clinical evaluation of 17 patients with axillobifemoral bypass graft operations, performed for various indications. Two important observations were

  1. Transient expression and activity of human DNA polymerase iota in loach embryos.

    Science.gov (United States)

    Makarova, Irina V; Kazakov, Andrey A; Makarova, Alena V; Khaidarova, Nella V; Kozikova, Larisa V; Nenasheva, Valentina V; Gening, Leonid V; Tarantul, Vyacheslav Z; Andreeva, Ludmila E

    2012-02-01

    Human DNA polymerase iota (Pol ι) is a Y-family DNA polymerase with unusual biochemical properties and not fully understood functions. Pol ι preferentially incorporates dGTP opposite template thymine. This property can be used to monitor Pol ι activity in the presence of other DNA polymerases, e.g. in cell extracts of tissues and tumors. We have now confirmed the specificity and sensitivity of the method of Pol ι activity detection in cell extracts using an animal model of loach Misgurnus fossilis embryos transiently expressing human Pol ι. The overexpression of Pol ι was shown to be accompanied by an increase in abnormalities in development and the frequency of pycnotic nuclei in fish embryos. Further analysis of fish embryos with constitutive or regulated Pol ι expression may provide insights into Pol ι functions in vertebrate animals.

  2. Cardiopulmonary bypass in pregnancy.

    Science.gov (United States)

    Kapoor, Mukul Chandra

    2014-01-01

    Cardiac surgery carried out on cardiopulmonary bypass (CPB) in a pregnant woman is associated with poor neonatal outcomes although maternal outcomes are similar to cardiac surgery in non-pregnant women. Most adverse maternal and fetal outcomes from cardiac surgery during pregnancy are attributed to effects of CPB. The CPB is associated with utero-placental hypoperfusion due to a number of factors, which may translate into low fetal cardiac output, hypoxia and even death. Better maternal and fetal outcomes may be achieved by early pre-operative optimization of maternal cardiovascular status, use of perioperative fetal monitoring, optimization of CPB, delivery of a viable fetus before the operation and scheduling cardiac surgery on an elective basis during the second trimester.

  3. Cardiopulmonary bypass in pregnancy

    Directory of Open Access Journals (Sweden)

    Mukul Chandra Kapoor

    2014-01-01

    Full Text Available Cardiac surgery carried out on cardiopulmonary bypass (CPB in a pregnant woman is associated with poor neonatal outcomes although maternal outcomes are similar to cardiac surgery in non-pregnant women. Most adverse maternal and fetal outcomes from cardiac surgery during pregnancy are attributed to effects of CPB. The CPB is associated with utero-placental hypoperfusion due to a number of factors, which may translate into low fetal cardiac output, hypoxia and even death. Better maternal and fetal outcomes may be achieved by early pre-operative optimization of maternal cardiovascular status, use of perioperative fetal monitoring, optimization of CPB, delivery of a viable fetus before the operation and scheduling cardiac surgery on an elective basis during the second trimester.

  4. Visual Memories Bypass Normalization.

    Science.gov (United States)

    Bloem, Ilona M; Watanabe, Yurika L; Kibbe, Melissa M; Ling, Sam

    2018-05-01

    How distinct are visual memory representations from visual perception? Although evidence suggests that briefly remembered stimuli are represented within early visual cortices, the degree to which these memory traces resemble true visual representations remains something of a mystery. Here, we tested whether both visual memory and perception succumb to a seemingly ubiquitous neural computation: normalization. Observers were asked to remember the contrast of visual stimuli, which were pitted against each other to promote normalization either in perception or in visual memory. Our results revealed robust normalization between visual representations in perception, yet no signature of normalization occurring between working memory stores-neither between representations in memory nor between memory representations and visual inputs. These results provide unique insight into the nature of visual memory representations, illustrating that visual memory representations follow a different set of computational rules, bypassing normalization, a canonical visual computation.

  5. Roles of Saccharomyces cerevisiae DNA polymerases Poleta and Polzeta in response to irradiation by simulated sunlight.

    Science.gov (United States)

    Kozmin, Stanislav G; Pavlov, Youri I; Kunkel, Thomas A; Sage, Evelyne

    2003-08-01

    Sunlight causes lesions in DNA that if unrepaired and inaccurately replicated by DNA polymerases yield mutations that result in skin cancer in humans. Two enzymes involved in translesion synthesis (TLS) of UV-induced photolesions are DNA polymerase eta (Poleta) and polymerase zeta (Polzeta), encoded by the RAD30A and REV3 genes, respectively. Previous studies have investigated the TLS roles of these polymerases in human and yeast cells irradiated with monochromatic, short wavelength UVC radiation (254 nm). However, less is known about cellular responses to solar radiation, which is of higher and mixed wavelengths (310-1100 nm) and produces a different spectrum of DNA lesions, including Dewar photoproducts and oxidative lesions. Here we report on the comparative cytotoxic and mutagenic effects of simulated sunlight (SSL) and UVC radiation on yeast wild-type, rad30Delta, rev3Delta and rev3Delta rad30Delta strains. The results with SSL support several previous interpretations on the roles of these two polymerases in TLS of photodimers and (6-4) photoproducts derived from studies with UVC. They further suggest that Poleta participates in the non-mutagenic bypass of SSL-dependent cytosine-containing Dewar photoproducts and 8-oxoguanine, while Polzeta is mainly responsible for the mutagenic bypass of all types of Dewar photoproducts. They also suggest that in the absence of Polzeta, Poleta contributes to UVC- and SSL-induced mutagenesis, possibly by the bypass of photodimers containing deaminated cytosine.

  6. Structure of human DNA polymerase iota and the mechanism of DNA synthesis.

    Science.gov (United States)

    Makarova, A V; Kulbachinskiy, A V

    2012-06-01

    Cellular DNA polymerases belong to several families and carry out different functions. Highly accurate replicative DNA polymerases play the major role in cell genome replication. A number of new specialized DNA polymerases were discovered at the turn of XX-XXI centuries and have been intensively studied during the last decade. Due to the special structure of the active site, these enzymes efficiently perform synthesis on damaged DNA but are characterized by low fidelity. Human DNA polymerase iota (Pol ι) belongs to the Y-family of specialized DNA polymerases and is one of the most error-prone enzymes involved in DNA synthesis. In contrast to other DNA polymerases, Pol ι is able to use noncanonical Hoogsteen interactions for nucleotide base pairing. This allows it to incorporate nucleotides opposite various lesions in the DNA template that impair Watson-Crick interactions. Based on the data of X-ray structural analysis of Pol ι in complexes with various DNA templates and dNTP substrates, we consider the structural peculiarities of the Pol ι active site and discuss possible mechanisms that ensure the unique behavior of the enzyme on damaged and undamaged DNA.

  7. Mechanisms of Insertion of dCTP and dTTP Opposite the DNA Lesion O6-Methyl-2′-deoxyguanosine by Human DNA Polymerase η*

    Science.gov (United States)

    Patra, Amitraj; Zhang, Qianqian; Guengerich, F. Peter; Egli, Martin

    2016-01-01

    O6-Methyl-2′-deoxyguanosine (O6-MeG) is a ubiquitous DNA lesion, formed not only by xenobiotic carcinogens but also by the endogenous methylating agent S-adenosylmethionine. It can introduce mutations during DNA replication, with different DNA polymerases displaying different ratios of correct or incorrect incorporation opposite this nucleoside. Of the “translesion” Y-family human DNA polymerases (hpols), hpol η is most efficient in incorporating equal numbers of correct and incorrect C and T bases. However, the mechanistic basis for this specific yet indiscriminate activity is not known. To explore this question, we report biochemical and structural analysis of the catalytic core of hpol η. Activity assays showed the truncated form displayed similar misincorporation properties as the full-length enzyme, incorporating C and T equally and extending from both. X-ray crystal structures of both dC and dT paired with O6-MeG were solved in both insertion and extension modes. The structures revealed a Watson-Crick-like pairing between O6-MeG and 2"-deoxythymidine-5"-[(α, β)-imido]triphosphate (approximating dT) at both the insertion and extension stages with formation of two H-bonds. Conversely, both the structures with O6- MeG opposite dCTP and dC display sheared configuration of base pairs but to different degrees, with formation of two bifurcated H-bonds and two single H-bonds in the structures trapped in the insertion and extension states, respectively. The structural data are consistent with the observed tendency of hpol η to insert both dC and dT opposite the O6-MeG lesion with similar efficiencies. Comparison of the hpol η active site configurations with either O6-MeG:dC or O6-MeG:dT bound compared with the corresponding situations in structures of complexes of Sulfolobus solfataricus Dpo4, a bypass pol that favors C relative to T by a factor of ∼4, helps rationalize the more error-prone synthesis opposite the lesion by hpol η. PMID:27694439

  8. Heart bypass surgery - minimally invasive - discharge

    Science.gov (United States)

    ... invasive direct coronary artery bypass - discharge; MIDCAB - discharge; Robot assisted coronary artery bypass - discharge; RACAB - discharge; Keyhole ... M. is also a founding member of Hi-Ethics and subscribes to the principles of the Health ...

  9. Collins' bypass for the main ring

    International Nuclear Information System (INIS)

    Ohnuma, S.

    1982-01-01

    Design of the bypass for the main ring at Fermilab is discussed. Specific design features discussed include space, path length, geometric closure, matching of betatron functions, and external dispersion. Bypass parameters are given

  10. Dynamic Cerebral Autoregulation after Cardiopulmonary Bypass

    DEFF Research Database (Denmark)

    Christiansen, Claus Behrend; Berg, Ronan M G; Plovsing, Ronni R

    2016-01-01

    Background Cerebral hemodynamic disturbances in the peri- or postoperative period may contribute to postoperative cognitive dysfunction (POCD) in patients undergoing coronary artery bypass grafting (CABG) with cardiopulmonary bypass (CPB). We therefore examined dynamic cerebral autoregulation (d...

  11. Interventions in Infrainguinal Bypass Grafts

    International Nuclear Information System (INIS)

    Mueller-Huelsbeck, S.; Order, B.-M.; Jahnke, T.

    2006-01-01

    The interventional radiologist plays an important role in the detection and prevention of infrainguinal bypass failure. Early detection and evaluation of flow-limiting lesions effectively preserve graft (venous bypass and polyester or expanded polytetrafluoroethylene bypass) patency by identifying stenoses before occlusion occurs. Delay in treatment of the at-risk graft may result in graft failure and a reduced chance of successful revascularization. For this reason, surveillance protocols form an important part of follow-up after infrainguinal bypass surgery. As well as having an understanding of the application of imaging techniques including ultrasound, MR angiography, CT angiography and digital subtraction angiography, the interventional radiologist should have detailed knowledge of the minimally invasive therapeutic options. Percutaneous transluminal angioplasty (PTA), or alternatively cutting balloon angioplasty, is the interventional treatment of choice in prevention of graft failure and occlusion. Further alternatives include metallic stent placement, fibrinolysis, and mechanical thrombectomy. Primary assisted patency rates following PTA can be up to 65% at 5 years. When the endovascular approach is unsuccessful, these therapeutic options are complemented by surgical procedures including vein patch revision, jump grafting, or placement of a new graft

  12. Heart bypass surgery - minimally invasive

    Science.gov (United States)

    ... MIDCAB; Robot-assisted coronary artery bypass; RACAB; Keyhole heart surgery; CAD - MIDCAB; Coronary artery disease - MIDCAB ... To perform this surgery: The heart surgeon will make a 3- to 5-inch (8 to 13 centimeters) surgical cut in the left part of your chest ...

  13. Gut hormones and gastric bypass

    DEFF Research Database (Denmark)

    Holst, Jens J.

    2016-01-01

    Gut hormone secretion in response to nutrient ingestion appears to depend on membrane proteins expressed by the enteroendocrine cells. These include transporters (glucose and amino acid transporters), and, in this case, hormone secretion depends on metabolic and electrophysiological events elicited...... that determines hormone responses. It follows that operations that change intestinal exposure to and absorption of nutrients, such as gastric bypass operations, also change hormone secretion. This results in exaggerated increases in the secretion of particularly the distal small intestinal hormones, GLP-1, GLP-2......, oxyntomodulin, neurotensin and peptide YY (PYY). However, some proximal hormones also show changes probably reflecting that the distribution of these hormones is not restricted to the bypassed segments of the gut. Thus, cholecystokinin responses are increased, whereas gastric inhibitory polypeptide responses...

  14. Bypass flow rate control method

    International Nuclear Information System (INIS)

    Kiyama, Yoichi.

    1997-01-01

    In a PWR type reactor, bypass flow rate is controlled by exchanging existent jetting hole plugs of a plurality of nozzles disposed to the upper end of incore structures in order to flow a portion of primary coolants as a bypass flow to the upper portion of the pressure vessel. Two kinds of exchange plugs, namely, a first plug and a second plug each having a jetting out hole of different diameter are used as exchange plugs. The first plug has the diameter as that of an existent plug and the second plug has a jetting out hole having larger diameter than that of the existent plug. Remained extent plugs are exchanged to a combination of the first and the second plugs without exchanging existent plugs having seizing with the nozzles, in which the number and the diameter of the jetting out holes of the second plugs are previously determined based on predetermined total bypass flow rate to be jetted from the entire plugs after exchange of plugs. (N.H.)

  15. Pre-Steady State Kinetic Investigation of the Incorporation of Anti-Hepatitis B Nucleotide Analogs Catalyzed by Non-Canonical Human DNA Polymerases

    Science.gov (United States)

    Brown, Jessica A.; Pack, Lindsey R.; Fowler, Jason D.; Suo, Zucai

    2011-01-01

    Antiviral nucleoside analogs have been developed to inhibit the enzymatic activities of the hepatitis B virus (HBV) polymerase, thereby preventing the replication and production of HBV. However, the usage of these analogs can be limited by drug toxicity because the 5′-triphosphates of these nucleoside analogs (nucleotide analogs) are potential substrates for human DNA polymerases to incorporate into host DNA. Although they are poor substrates for human replicative DNA polymerases, it remains to be established whether these nucleotide analogs are substrates for the recently discovered human X- and Y-family DNA polymerases. Using pre-steady state kinetic techniques, we have measured the substrate specificity values for human DNA polymerases β, λ, η, ι, κ, and Rev1 incorporating the active forms of the following anti-HBV nucleoside analogs approved for clinical use: adefovir, tenofovir, lamivudine, telbivudine, and entecavir. Compared to the incorporation of a natural nucleotide, most of the nucleotide analogs were incorporated less efficiently (2 to >122,000) by the six human DNA polymerases. In addition, the potential for entecavir and telbivudine, two drugs which possess a 3′-hydroxyl, to become embedded into human DNA was examined by primer extension and DNA ligation assays. These results suggested that telbivudine functions as a chain terminator while entecavir was efficiently extended by the six enzymes and was a substrate for human DNA ligase I. Our findings suggested that incorporation of anti-HBV nucleotide analogs catalyzed by human X- and Y-family polymerases may contribute to clinical toxicity. PMID:22132702

  16. DNA polymerase catalysis in the absence of Watson-Crick hydrogen bonds

    Science.gov (United States)

    Potapova, Olga; Chan, Chikio; DeLucia, Angela M.; Helquist, Sandra A.; Kool, Eric T.; Grindley, Nigel D. F.; Joyce, Catherine M.

    2008-01-01

    We report the first pre-steady-state kinetic studies of DNA replication in the absence of hydrogen bonds. We have used nonpolar nucleotide analogues that mimic the shape of a Watson-Crick base pair in order to investigate the kinetic consequences of a lack of hydrogen bonds in the polymerase reaction catalyzed by the Klenow fragment of DNA Polymerase I from Escherichia coli. With a thymine isostere lacking hydrogen bonding ability in the nascent pair, the efficiency (kpol/Kd) of the polymerase reaction is decreased by 30-fold, affecting ground state (Kd) and transition state (kpol) approximately equally. When both thymine and adenine analogues in the nascent pair lack hydrogen bonding ability, the efficiency of the polymerase reaction is decreased by about 1000-fold, with most the decrease attributable to the transition state. Reactions using nonpolar analogues at the primer terminal base pair demonstrated the requirement for a hydrogen bond between the polymerase and the minor groove of the primer-terminal base. The R668A mutation of Klenow fragment abolished this requirement, identifying R668 as the probable hydrogen bond donor. Detailed examination of the kinetic data suggested that Klenow fragment has an extremely low tolerance of even minor deviations of the analogue base pairs from ideal Watson-Crick geometry. Consistent with this idea, some analogue pairings were better tolerated by Klenow fragment mutants having more spacious active sites. By contrast, the Y-family polymerase Dbh was much less sensitive to changes in base pair dimensions, and more dependent on hydrogen bonding between base-paired partners. PMID:16411765

  17. 75 FR 71145 - San Joaquin River Restoration Program: Reach 4B, Eastside Bypass, and Mariposa Bypass Channel and...

    Science.gov (United States)

    2010-11-22

    ..., Eastside Bypass, and Mariposa Bypass Channel and Structural Improvements Project, Merced County, CA AGENCY... on the effects of the proposed Reach 4B, Eastside Bypass, and Mariposa Bypass Channel and Structural... Mariposa Bypass with the San Joaquin River (generally referred to as Reach 4B1). The improvements will...

  18. Coronary Artery Bypass in Octogenarians

    Directory of Open Access Journals (Sweden)

    Chen-Yen Chien

    2012-09-01

    Full Text Available Prevalence of coronary artery disease (CAD has increased with the expansion of life span among the elderly population in the world. Hence, the issue of the coronary artery bypass in octogenarians has attracted more attention. Recent literature about the topic revealed nearly the same excellent results as those in the younger population under the newly developed operative techniques and improving concept in perioperative management and postoperative care. In this article, we review the current status of the procedure that was thought to be dangerous in the earlier era, including its risk factors, result, and benefit.

  19. [Coronary artery bypass grafting without use of cardiopulmonary bypass].

    Science.gov (United States)

    Mujanović, Emir; Bergsland, Jacob; Hadziselimović, Mehdin; Softić, Muniba; Azabagic, Azur; Stanimirović-Mujanović, Sanja; Kabil, Emir

    2002-01-01

    Although it is possible to find a number of comparative studies in the world literature discussing the results of coronary artery bypass surgery (CABG) with and without cardiopulmonary bypass (CPB), until now such analysis has not been made in Bosnia and Herzegovina. The main aim of this scientific work was to compare morbidity and mortality, need for blood transfusions, length of stay in the intensive care unit and total length of hospitalisation in two groups of patients operated with these methods. One hundred and four patients with coronary artery disease operated in Cardiovascular Clinic Tuzla, from September, 1998 to September 2002 divided in two groups, were included in this study. There were 52 patients in the first group operated with CPB and 52 patients in the second group operated without CPB. The groups were matched for gender, age, ejection fraction and preoperative risk factors. The incidence of postoperative complications was lower in patients operated without CPB (5.77% vs. 21.15%). The mortality rate was reduced in patients operated without CPB (0.00% vs. 5.76%). There were reduced need for transfusion in patients operated without CPB (0.28 vs. 1.11 units of blood). The average time spent on respirators was shorter in patients operated without CPB (1.50 vs. 4.76 hours). The average time of total hospitalisation was also shorter in patients operated withouth CPB (6.53 vs. 8.13 days). In conclusion CABG without CPB has many advantages compared to the conventional method. Mortality and morbidity are reduced and there is less need for transfusion. The time spent on mechanical ventilation is reduced and less time is spent in intensive care and the total hospitalisation time is also less.

  20. In situ bypass og diabetes

    DEFF Research Database (Denmark)

    Jensen, Leif Panduro; Schroeder, T V; Lorentzen, J E

    1993-01-01

    decreased survival rate was found in diabetics (p useful in the treatment of critical ischaemia of the lower limb in diabetic patients. The overall results in diabetic patients, whether insulin-dependent or not, were equal to those in non-diabetic......From 1986 through to 1990 a total of 483 in situ bypass procedures were performed in 444 patients. Preoperative risk-factors were equally distributed among diabetic (DM) and non-diabetic (NDM) patients, except for smoking habits (DM:48%, NDM:64%, p = 0.002) and cardiac disease (DM:45%, NDM:29%, p...... = 0.005). Critical limb-ischaemia was more often present in diabetic than non-diabetic patients (DM:57%, NDM:36%, p = 0.0002). Diabetic patients had a significantly lower distal anastomosis than non-diabetic patients (p = 0.00001). There were no differences among diabetic and non-diabetic patients...

  1. N-terminal domains of human DNA polymerase lambda promote primer realignment during translesion DNA synthesis

    Science.gov (United States)

    Taggart, David J.; Dayeh, Daniel M.; Fredrickson, Saul W.; Suo, Zucai

    2014-01-01

    The X-family DNA polymerases λ (Polλ) and β (Polβ) possess similar 5′-2-deoxyribose-5-phosphatelyase (dRPase) and polymerase domains. Besides these domains, Polλ also possesses a BRCA1 C-terminal (BRCT) domain and a proline-rich domain at its N terminus. However, it is unclear how these non-enzymatic domains contribute to the unique biological functions of Polλ. Here, we used primer extension assays and a newly developed high-throughput short oligonucleotide sequencing assay (HT-SOSA) to compare the efficiency of lesion bypass and fidelity of human Polβ, Polλ and two N-terminal deletion constructs of Polλ during the bypass of either an abasic site or a 8-oxo-7,8-dihydro-2′-deoxyguanosine (8-oxodG) lesion. We demonstrate that the BRCT domain of Polλ enhances the efficiency of abasic site bypass by approximately 1.6-fold. In contrast, deletion of the N-terminal domains of Polλ did not affect the efficiency of 8-oxodG bypass relative to nucleotide incorporations opposite undamaged dG. HT-SOSA analysis demonstrated that Polλ and Polβ preferentially generated −1 or −2 frameshift mutations when bypassing an abasic site and the single or double base deletion frequency was highly sequence dependent. Interestingly, the BRCT and proline-rich domains of Polλ cooperatively promoted the generation of −2 frameshift mutations when the abasic site was situated within a sequence context that was susceptible to homology-driven primer realignment. Furthermore, both N-terminal domains of Polλ increased the generation of −1 frameshift mutations during 8-oxodG bypass and influenced the frequency of substitution mutations produced by Polλ opposite the 8-oxodG lesion. Overall, our data support a model wherein the BRCT and proline-rich domains of Polλ act cooperatively to promote primer/template realignment between DNA strands of limited sequence homology. This function of the N-terminal domains may facilitate the role of Polλ as a gap-filling polymerase

  2. Coronary Bypass Surgery in a 105-Year-Old Patient with Cardiopulmonary Bypass

    Directory of Open Access Journals (Sweden)

    Temucin Noyan Ogus

    2010-01-01

    Full Text Available Coronary artery bypass grafting is one of the routine daily surgical procedures in the current era. Parallel to the increasing life expectancy, cardiac surgery is commonly performed in octogenarians. However, literature consists of only seldom reports of coronary artery bypass grafting in patients above 90 years of age. In this report, we present our management strategy in a 105-year-old patient who underwent coronary artery bypass grafting at our institution.

  3. Advancing Polymerase Ribozymes Towards Self-Replication

    Science.gov (United States)

    Tjhung, K. F.; Joyce, G. F.

    2017-07-01

    Autocatalytic replication and evolution in vitro by (i) a cross-chiral RNA polymerase catalyzing polymerization of mononucleotides of the opposite handedness; (ii) non-covalent assembly of component fragments of an existing RNA polymerase ribozyme.

  4. A nucleotide-analogue-induced gain of function corrects the error-prone nature of human DNA polymerase iota.

    Science.gov (United States)

    Ketkar, Amit; Zafar, Maroof K; Banerjee, Surajit; Marquez, Victor E; Egli, Martin; Eoff, Robert L

    2012-06-27

    Y-family DNA polymerases participate in replication stress and DNA damage tolerance mechanisms. The properties that allow these enzymes to copy past bulky adducts or distorted template DNA can result in a greater propensity for them to make mistakes. Of the four human Y-family members, human DNA polymerase iota (hpol ι) is the most error-prone. In the current study, we elucidate the molecular basis for improving the fidelity of hpol ι through use of the fixed-conformation nucleotide North-methanocarba-2'-deoxyadenosine triphosphate (N-MC-dATP). Three crystal structures were solved of hpol ι in complex with DNA containing a template 2'-deoxythymidine (dT) paired with an incoming dNTP or modified nucleotide triphosphate. The ternary complex of hpol ι inserting N-MC-dATP opposite dT reveals that the adenine ring is stabilized in the anti orientation about the pseudo-glycosyl torsion angle, which mimics precisely the mutagenic arrangement of dGTP:dT normally preferred by hpol ι. The stabilized anti conformation occurs without notable contacts from the protein but likely results from constraints imposed by the bicyclo[3.1.0]hexane scaffold of the modified nucleotide. Unmodified dATP and South-MC-dATP each adopt syn glycosyl orientations to form Hoogsteen base pairs with dT. The Hoogsteen orientation exhibits weaker base-stacking interactions and is less catalytically favorable than anti N-MC-dATP. Thus, N-MC-dATP corrects the error-prone nature of hpol ι by preventing the Hoogsteen base-pairing mode normally observed for hpol ι-catalyzed insertion of dATP opposite dT. These results provide a previously unrecognized means of altering the efficiency and the fidelity of a human translesion DNA polymerase.

  5. A nucleotide analogue induced gain of function corrects the error-prone nature of human DNA polymerase iota

    Science.gov (United States)

    Ketkar, Amit; Zafar, Maroof K.; Banerjee, Surajit; Marquez, Victor E.; Egli, Martin; Eoff, Robert L

    2012-01-01

    Y-family DNA polymerases participate in replication stress and DNA damage tolerance mechanisms. The properties that allow these enzymes to copy past bulky adducts or distorted template DNA can result in a greater propensity for them to make mistakes. Of the four human Y-family members, human DNA polymerase iota (hpol ι) is the most error-prone. In the current study, we elucidate the molecular basis for improving the fidelity of hpol ι through use of the fixed-conformation nucleotide North-methanocarba-2′-deoxyadenosine triphosphate (N-MC-dATP). Three crystal structures were solved of hpol ι in complex with DNA containing a template 2′-deoxythymidine (dT) paired with an incoming dNTP or modified nucleotide triphosphate. The ternary complex of hpol ι inserting N-MC-dATP opposite dT reveals that the adenine ring is stabilized in the anti orientation about the pseudo-glycosyl torsion angle (χ), which mimics precisely the mutagenic arrangement of dGTP:dT normally preferred by hpol ι. The stabilized anti conformation occurs without notable contacts from the protein but likely results from constraints imposed by the bicyclo[3.1.0]hexane scaffold of the modified nucleotide. Unmodified dATP and South-MC-dATP each adopt syn glycosyl orientations to form Hoogsteen base pairs with dT. The Hoogsteen orientation exhibits weaker base stacking interactions and is less catalytically favorable than anti N-MC-dATP. Thus, N-MC-dATP corrects the error-prone nature of hpol ι by preventing the Hoogsteen base-pairing mode normally observed for hpol ι-catalyzed insertion of dATP opposite dT. These results provide a previously unrecognized means of altering the efficiency and the fidelity of a human translesion DNA polymerase. PMID:22632140

  6. Ketamine has no effect on oxygenation indices following elective coronary artery bypass grafting under cardiopulmonary bypass

    Directory of Open Access Journals (Sweden)

    Parthasarathi Gayatri

    2011-01-01

    Full Text Available Cardiopulmonary bypass is known to elicit systemic inflammatory response syndrome and organ dysfunction. This can result in pulmonary dysfunction and deterioration of oxygenation after cardiac surgery and cardiopulmonary bypass. Previous studies have reported varying results on anti-inflammatory strategies and oxygenation after cardiopulmonary bypass. Ketamine administered as a single dose at induction has been shown to reduce the pro-inflammatory serum markers in patients undergoing cardiopulmonary bypass. Therefore we investigated if ketamine can result in better oxygenation in these patients. This was a prospective randomized blinded study. Eighty consecutive adult patients undergoing elective coronary artery bypass grafting under cardiopulmonary bypass were included in the study. Patients were divided into two groups. Patients in ketamine group received 1mg/kg of ketamine intravenously at induction of anesthesia. Control group patients received an equal volume of saline. All patients received standard anesthesia, operative and postoperative care.Paired t test and independent sample t test were used to compare the inter-group and between group oxygenation indices respectively. Oxygenation index and duration of ventilation were analyzed. Deterioration of oxygenation index was noted in both the groups after cardiopulmonary bypass. However, there was no significant difference in the oxygenation index at various time points after cardiopulmonary bypass or the duration of ventilation between the two groups. This study shows that the administered as a single dose at induction does not result in better oxygenation after cardiopulmonary bypass.

  7. Monsanto may bypass NIH in microbe test.

    Science.gov (United States)

    Sun, Marjorie

    1985-01-11

    The Monsanto Company is planning to ask the Environmental Protection Agency for clearance to field test a genetically engineered microbial pesticide, bypassing the traditional approval process of the National Institutes of Health. Although only federally funded institutions are required to obtain NIH approval for genetic engineering tests, Monsanto is the first company to bypass the NIH regulatory process, which has become mired in a lawsuit brought by Jeremy Rifkin.

  8. [Simplified laparoscopic gastric bypass. Initial experience].

    Science.gov (United States)

    Hernández-Miguelena, Luis; Maldonado-Vázquez, Angélica; Cortes-Romano, Pablo; Ríos-Cruz, Daniel; Marín-Domínguez, Raúl; Castillo-González, Armando

    2014-01-01

    Obesity surgery includes various gastrointestinal procedures. Roux-en-Y gastric bypass is the prototype of mixed procedures being the most practiced worldwide. A similar and novel technique has been adopted by Dr. Almino Cardoso Ramos and Dr. Manoel Galvao called "simplified bypass," which has been accepted due to the greater ease and very similar results to the conventional technique. The aim of this study is to describe the results of the simplified gastric bypass for treatment of morbid obesity in our institution. We performed a descriptive, retrospective study of all patients undergoing simplified gastric bypass from January 2008 to July 2012 in the obesity clinic of a private hospital in Mexico City. A total of 90 patients diagnosed with morbid obesity underwent simplified gastric bypass. Complications occurred in 10% of patients; these were more frequent bleeding and internal hernia. Mortality in the study period was 0%. The average weight loss at 12 months was 72.7%. Simplified gastric bypass surgery is safe with good mid-term results and a loss of adequate weight in 71% of cases.

  9. Roles of Saccharomyces cerevisiae DNA polymerases Polη and Polζ in response to irradiation by simulated sunlight

    Science.gov (United States)

    Kozmin, Stanislav G.; Pavlov, Youri I.; Kunkel, Thomas A.; Sage, Evelyne

    2003-01-01

    Sunlight causes lesions in DNA that if unrepaired and inaccurately replicated by DNA polymerases yield mutations that result in skin cancer in humans. Two enzymes involved in translesion synthesis (TLS) of UV-induced photolesions are DNA polymerase η (Polη) and polymerase ζ (Polζ), encoded by the RAD30A and REV3 genes, respectively. Previous studies have investigated the TLS roles of these polymerases in human and yeast cells irradiated with monochromatic, short wavelength UVC radiation (254 nm). However, less is known about cellular responses to solar radiation, which is of higher and mixed wavelengths (310–1100 nm) and produces a different spectrum of DNA lesions, including Dewar photoproducts and oxidative lesions. Here we report on the comparative cytotoxic and mutagenic effects of simulated sunlight (SSL) and UVC radiation on yeast wild-type, rad30Δ, rev3Δ and rev3Δ rad30Δ strains. The results with SSL support several previous interpretations on the roles of these two polymerases in TLS of photodimers and (6–4) photoproducts derived from studies with UVC. They further suggest that Polη participates in the non-mutagenic bypass of SSL-dependent cytosine-containing Dewar photoproducts and 8-oxoguanine, while Polζ is mainly responsible for the mutagenic bypass of all types of Dewar photoproducts. They also suggest that in the absence of Polζ, Polη contributes to UVC- and SSL-induced mutagenesis, possibly by the bypass of photodimers containing deaminated cytosine. PMID:12888515

  10. DNA Polymerase κ Is a Key Cellular Factor for the Formation of Covalently Closed Circular DNA of Hepatitis B Virus.

    Directory of Open Access Journals (Sweden)

    Yonghe Qi

    2016-10-01

    Full Text Available Hepatitis B virus (HBV infection of hepatocytes begins by binding to its cellular receptor sodium taurocholate cotransporting polypeptide (NTCP, followed by the internalization of viral nucleocapsid into the cytoplasm. The viral relaxed circular (rc DNA genome in nucleocapsid is transported into the nucleus and converted into covalently closed circular (ccc DNA to serve as a viral persistence reservoir that is refractory to current antiviral therapies. Host DNA repair enzymes have been speculated to catalyze the conversion of rcDNA to cccDNA, however, the DNA polymerase(s that fills the gap in the plus strand of rcDNA remains to be determined. Here we conducted targeted genetic screening in combination with chemical inhibition to identify the cellular DNA polymerase(s responsible for cccDNA formation, and exploited recombinant HBV with capsid coding deficiency which infects HepG2-NTCP cells with similar efficiency of wild-type HBV to assure cccDNA synthesis is exclusively from de novo HBV infection. We found that DNA polymerase κ (POLK, a Y-family DNA polymerase with maximum activity in non-dividing cells, substantially contributes to cccDNA formation during de novo HBV infection. Depleting gene expression of POLK in HepG2-NTCP cells by either siRNA knockdown or CRISPR/Cas9 knockout inhibited the conversion of rcDNA into cccDNA, while the diminished cccDNA formation in, and hence the viral infection of, the knockout cells could be effectively rescued by ectopic expression of POLK. These studies revealed that POLK is a crucial host factor required for cccDNA formation during a de novo HBV infection and suggest that POLK may be a potential target for developing antivirals against HBV.

  11. Brain microvascular function during cardiopulmonary bypass

    International Nuclear Information System (INIS)

    Sorensen, H.R.; Husum, B.; Waaben, J.; Andersen, K.; Andersen, L.I.; Gefke, K.; Kaarsen, A.L.; Gjedde, A.

    1987-01-01

    Emboli in the brain microvasculature may inhibit brain activity during cardiopulmonary bypass. Such hypothetical blockade, if confirmed, may be responsible for the reduction of cerebral metabolic rate for glucose observed in animals subjected to cardiopulmonary bypass. In previous studies of cerebral blood flow during bypass, brain microcirculation was not evaluated. In the present study in animals (pigs), reduction of the number of perfused capillaries was estimated by measurements of the capillary diffusion capacity for hydrophilic tracers of low permeability. Capillary diffusion capacity, cerebral blood flow, and cerebral metabolic rate for glucose were measured simultaneously by the integral method, different tracers being used with different circulation times. In eight animals subjected to normothermic cardiopulmonary bypass, and seven subjected to hypothermic bypass, cerebral blood flow, cerebral metabolic rate for glucose, and capillary diffusion capacity decreased significantly: cerebral blood flow from 63 to 43 ml/100 gm/min in normothermia and to 34 ml/100 gm/min in hypothermia and cerebral metabolic rate for glucose from 43.0 to 23.0 mumol/100 gm/min in normothermia and to 14.1 mumol/100 gm/min in hypothermia. The capillary diffusion capacity declined markedly from 0.15 to 0.03 ml/100 gm/min in normothermia but only to 0.08 ml/100 gm/min in hypothermia. We conclude that the decrease of cerebral metabolic rate for glucose during normothermic cardiopulmonary bypass is caused by interruption of blood flow through a part of the capillary bed, possibly by microemboli, and that cerebral blood flow is an inadequate indicator of capillary blood flow. Further studies must clarify why normal microvascular function appears to be preserved during hypothermic cardiopulmonary bypass

  12. Analgesic Treatment in Laparoscopic Gastric Bypass Surgery

    DEFF Research Database (Denmark)

    Andersen, Lars P H; Werner, Mads U; Rosenberg, Jacob

    2014-01-01

    This review aimed to present an overview of the randomized controlled trials investigating analgesic regimens used in laparoscopic Roux-en-Y gastric bypass (LRYGB) surgery. Literature search was performed in PubMed and EMBASE databases in August 2013 in accordance to PRISMA guidelines. The litera......This review aimed to present an overview of the randomized controlled trials investigating analgesic regimens used in laparoscopic Roux-en-Y gastric bypass (LRYGB) surgery. Literature search was performed in PubMed and EMBASE databases in August 2013 in accordance to PRISMA guidelines...

  13. Alternative splicing at exon 2 results in the loss of the catalytic activity of mouse DNA polymerase iota in vitro.

    Science.gov (United States)

    Kazachenko, Konstantin Y; Miropolskaya, Nataliya A; Gening, Leonid V; Tarantul, Vyacheslav Z; Makarova, Alena V

    2017-02-01

    Y-family DNA polymerase iota (Pol ι) possesses both DNA polymerase and dRP lyase activities and was suggested to be involved in DNA translesion synthesis and base excision repair in mammals. The 129 strain of mice and its derivatives have a natural nonsense codon mutation in the second exon of the Pol ι gene resulting in truncation of the Pol ι protein. These mice were widely used as a Pol ι-null model for in vivo studies of the Pol ι function. However whether 129-derived strains of mice are fully deficient in the Pol ι functions was a subject of discussion since Pol ι mRNA undergoes alternative splicing at exon 2. Here we report purification of mouse Pol ι lacking the region encoded by exon 2, which includes several conserved residues involved in catalysis. We show that the deletion abrogates both the DNA polymerase and dRP lyase activities of Pol ι in the presence of either Mg 2+ or Mn 2+ ions. Thus, 129-derived strains of mice express catalytically inactive alternatively spliced Pol ι variant, whose cellular functions, if any exist, remain to be established. Copyright © 2017 Elsevier B.V. All rights reserved.

  14. 21 CFR 870.4350 - Cardiopulmonary bypass oxygenator.

    Science.gov (United States)

    2010-04-01

    ... bypass oxygenator. (a) Identification. A cardiopulmonary bypass oxygenator is a device used to exchange gases between blood and a gaseous environment to satisfy the gas exchange needs of a patient during open...

  15. Altered minor-groove hydrogen bonds in DNA block transcription elongation by T7 RNA polymerase.

    Science.gov (United States)

    Tanasova, Marina; Goeldi, Silvan; Meyer, Fabian; Hanawalt, Philip C; Spivak, Graciela; Sturla, Shana J

    2015-05-26

    DNA transcription depends upon the highly efficient and selective function of RNA polymerases (RNAPs). Modifications in the template DNA can impact the progression of RNA synthesis, and a number of DNA adducts, as well as abasic sites, arrest or stall transcription. Nonetheless, data are needed to understand why certain modifications to the structure of DNA bases stall RNA polymerases while others are efficiently bypassed. In this study, we evaluate the impact that alterations in dNTP/rNTP base-pair geometry have on transcription. T7 RNA polymerase was used to study transcription over modified purines and pyrimidines with altered H-bonding capacities. The results suggest that introducing wobble base-pairs into the DNA:RNA heteroduplex interferes with transcriptional elongation and stalls RNA polymerase. However, transcriptional stalling is not observed if mismatched base-pairs do not H-bond. Together, these studies show that RNAP is able to discriminate mismatches resulting in wobble base-pairs, and suggest that, in cases of modifications with minor steric impact, DNA:RNA heteroduplex geometry could serve as a controlling factor for initiating transcription-coupled DNA repair. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. Variable volume combustor with an air bypass system

    Science.gov (United States)

    Johnson, Thomas Edward; Ziminsky, Willy Steve; Ostebee, Heath Michael; Keener, Christopher Paul

    2017-02-07

    The present application provides a combustor for use with flow of fuel and a flow of air in a gas turbine engine. The combustor may include a number of micro-mixer fuel nozzles positioned within a liner and an air bypass system position about the liner. The air bypass system variably allows a bypass portion of the flow of air to bypass the micro-mixer fuel nozzles.

  17. Interaction of gold nanoparticles with Pfu DNA polymerase and effect on polymerase chain reaction.

    Science.gov (United States)

    Sun, L-P; Wang, S; Zhang, Z-W; Ma, Y-Y; Lai, Y-Q; Weng, J; Zhang, Q-Q

    2011-03-01

    The interaction of gold nanoparticles with Pfu DNA polymerase has been investigated by a number of biological, optical and electronic spectroscopic techniques. Polymerase chain reaction was performed to show gold nanoparticles' biological effect. Ultraviolet-visible and circular dichroism spectra analysis were applied to character the structure of Pfu DNA polymerase after conjugation with gold nanoparticles. X-ray photoelectron spectroscopy was used to investigate the bond properties of the polymerase-gold nanoparticles complex. The authors demonstrate that gold nanoparticles do not affect the amplification efficiency of polymerase chain reaction using Pfu DNA polymerase, and Pfu DNA polymerase displays no significant changes of the secondary structure upon interaction with gold nanoparticles. The adsorption of Pfu DNA polymerase to gold nanoparticles is mainly through Au-NH(2) bond and electrostatic interaction. These findings may have important implications regarding the safety issue as gold nanoparticles are widely used in biomedical applications.

  18. 21 CFR 870.4390 - Cardiopulmonary bypass pump tubing.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Cardiopulmonary bypass pump tubing. 870.4390 Section 870.4390 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES... bypass pump tubing. (a) Identification. A cardiopulmonary bypass pump tubing is polymeric tubing which is...

  19. 21 CFR 870.4240 - Cardiopulmonary bypass heat exchanger.

    Science.gov (United States)

    2010-04-01

    ... bypass heat exchanger. (a) Identification. A cardiopulmonary bypass heat exchanger is a device, consisting of a heat exchange system used in extracorporeal circulation to warm or cool the blood or... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Cardiopulmonary bypass heat exchanger. 870.4240...

  20. 21 CFR 870.4320 - Cardiopulmonary bypass pulsatile flow generator.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Cardiopulmonary bypass pulsatile flow generator... Cardiopulmonary bypass pulsatile flow generator. (a) Identification. A cardiopulmonary bypass pulsatile flow generator is an electrically and pneumatically operated device used to create pulsatile blood flow. The...

  1. 21 CFR 870.4300 - Cardiopulmonary bypass gas control unit.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Cardiopulmonary bypass gas control unit. 870.4300... bypass gas control unit. (a) Identification. A cardiopulmonary bypass gas control unit is a device used to control and measure the flow of gas into the oxygenator. The device is calibrated for a specific...

  2. Bypassing BDD Construction for Reliability Analysis

    DEFF Research Database (Denmark)

    Williams, Poul Frederick; Nikolskaia, Macha; Rauzy, Antoine

    2000-01-01

    In this note, we propose a Boolean Expression Diagram (BED)-based algorithm to compute the minimal p-cuts of boolean reliability models such as fault trees. BEDs make it possible to bypass the Binary Decision Diagram (BDD) construction, which is the main cost of fault tree assessment....

  3. Post-Bypass Extensive Ascites due to Splanchnic Bypass and the Effectiveness of Hyperalimentation Treatment

    Directory of Open Access Journals (Sweden)

    Veysel Temizkan

    2013-04-01

    Full Text Available Reperfusion edema may develop in the early periods of chronic ischemic tissue reperfusion. Reperfusion edema may be represented after the splanchnic bypass with ascites, abdominal distension, and liver and kidney function impairment. In this article, we are reporting the hyperalimentation treatment and its results for the common ascites and hepatorenal syndrome, after a coeliac and superior mesenteric artery bypass. [Arch Clin Exp Surg 2013; 2(2.000: 124-128

  4. Polymerase Gamma Disease through the Ages

    Science.gov (United States)

    Saneto, Russell P.; Naviaux, Robert K.

    2010-01-01

    The most common group of mitochondrial disease is due to mutations within the mitochondrial DNA polymerase, polymerase gamma 1 ("POLG"). This gene product is responsible for replication and repair of the small mitochondrial DNA genome. The structure-function relationship of this gene product produces a wide variety of diseases that at times, seems…

  5. DNA Polymerase Fidelity: Beyond Right and Wrong.

    Science.gov (United States)

    Washington, M Todd

    2016-11-01

    Accurate DNA replication depends on the ability of DNA polymerases to discriminate between correctly and incorrectly paired nucleotides. In this issue of Structure, Batra et al. (2016) show the structural basis for why DNA polymerases do not efficiently add correctly paired nucleotides immediately after incorporating incorrectly paired ones. Copyright © 2016 Elsevier Ltd. All rights reserved.

  6. Fluid distribution kinetics during cardiopulmonary bypass

    Directory of Open Access Journals (Sweden)

    Mattias Törnudd

    2014-08-01

    Full Text Available OBJECTIVE: The purpose of this study was to examine the isovolumetric distribution kinetics of crystalloid fluid during cardiopulmonary bypass. METHODS: Ten patients undergoing coronary artery bypass grafting participated in this prospective observational study. The blood hemoglobin and the serum albumin and sodium concentrations were measured repeatedly during the distribution of priming solution (Ringer's acetate 1470 ml and mannitol 15% 200 ml and initial cardioplegia. The rate of crystalloid fluid distribution was calculated based on 3-min Hb changes. The preoperative blood volume was extrapolated from the marked hemodilution occurring during the onset of cardiopulmonary bypass. Clinicaltrials.gov: NCT01115166. RESULTS: The distribution half-time of Ringer's acetate averaged 8 minutes, corresponding to a transcapillary escape rate of 0.38 ml/kg/min. The intravascular albumin mass increased by 5.4% according to mass balance calculations. The preoperative blood volume, as extrapolated from the drop in hemoglobin concentration by 32% (mean at the beginning of cardiopulmonary bypass, was 0.6-1.2 L less than that estimated by anthropometric methods (p<0.02. The mass balance of sodium indicated a translocation from the intracellular to the extracellular fluid space in 8 of the 10 patients, with a median volume of 236 ml. CONCLUSIONS: The distribution half-time of Ringer's solution during isovolumetric cardiopulmonary bypass was 8 minutes, which is the same as for crystalloid fluid infusions in healthy subjects. The intravascular albumin mass increased. Most patients were hypovolemic prior to the start of anesthesia. Intracellular edema did not occur.

  7. Thermally multiplexed polymerase chain reaction.

    Science.gov (United States)

    Phaneuf, Christopher R; Pak, Nikita; Saunders, D Curtis; Holst, Gregory L; Birjiniuk, Joav; Nagpal, Nikita; Culpepper, Stephen; Popler, Emily; Shane, Andi L; Jerris, Robert; Forest, Craig R

    2015-07-01

    Amplification of multiple unique genetic targets using the polymerase chain reaction (PCR) is commonly required in molecular biology laboratories. Such reactions are typically performed either serially or by multiplex PCR. Serial reactions are time consuming, and multiplex PCR, while powerful and widely used, can be prone to amplification bias, PCR drift, and primer-primer interactions. We present a new thermocycling method, termed thermal multiplexing, in which a single heat source is uniformly distributed and selectively modulated for independent temperature control of an array of PCR reactions. Thermal multiplexing allows amplification of multiple targets simultaneously-each reaction segregated and performed at optimal conditions. We demonstrate the method using a microfluidic system consisting of an infrared laser thermocycler, a polymer microchip featuring 1 μl, oil-encapsulated reactions, and closed-loop pulse-width modulation control. Heat transfer modeling is used to characterize thermal performance limitations of the system. We validate the model and perform two reactions simultaneously with widely varying annealing temperatures (48 °C and 68 °C), demonstrating excellent amplification. In addition, to demonstrate microfluidic infrared PCR using clinical specimens, we successfully amplified and detected both influenza A and B from human nasopharyngeal swabs. Thermal multiplexing is scalable and applicable to challenges such as pathogen detection where patients presenting non-specific symptoms need to be efficiently screened across a viral or bacterial panel.

  8. DNA polymerase preference determines PCR priming efficiency.

    Science.gov (United States)

    Pan, Wenjing; Byrne-Steele, Miranda; Wang, Chunlin; Lu, Stanley; Clemmons, Scott; Zahorchak, Robert J; Han, Jian

    2014-01-30

    Polymerase chain reaction (PCR) is one of the most important developments in modern biotechnology. However, PCR is known to introduce biases, especially during multiplex reactions. Recent studies have implicated the DNA polymerase as the primary source of bias, particularly initiation of polymerization on the template strand. In our study, amplification from a synthetic library containing a 12 nucleotide random portion was used to provide an in-depth characterization of DNA polymerase priming bias. The synthetic library was amplified with three commercially available DNA polymerases using an anchored primer with a random 3' hexamer end. After normalization, the next generation sequencing (NGS) results of the amplified libraries were directly compared to the unamplified synthetic library. Here, high throughput sequencing was used to systematically demonstrate and characterize DNA polymerase priming bias. We demonstrate that certain sequence motifs are preferred over others as primers where the six nucleotide sequences at the 3' end of the primer, as well as the sequences four base pairs downstream of the priming site, may influence priming efficiencies. DNA polymerases in the same family from two different commercial vendors prefer similar motifs, while another commercially available enzyme from a different DNA polymerase family prefers different motifs. Furthermore, the preferred priming motifs are GC-rich. The DNA polymerase preference for certain sequence motifs was verified by amplification from single-primer templates. We incorporated the observed DNA polymerase preference into a primer-design program that guides the placement of the primer to an optimal location on the template. DNA polymerase priming bias was characterized using a synthetic library amplification system and NGS. The characterization of DNA polymerase priming bias was then utilized to guide the primer-design process and demonstrate varying amplification efficiencies among three commercially

  9. DNA Repair Mechanisms and the Bypass of DNA Damage in Saccharomyces cerevisiae

    Science.gov (United States)

    Boiteux, Serge; Jinks-Robertson, Sue

    2013-01-01

    DNA repair mechanisms are critical for maintaining the integrity of genomic DNA, and their loss is associated with cancer predisposition syndromes. Studies in Saccharomyces cerevisiae have played a central role in elucidating the highly conserved mechanisms that promote eukaryotic genome stability. This review will focus on repair mechanisms that involve excision of a single strand from duplex DNA with the intact, complementary strand serving as a template to fill the resulting gap. These mechanisms are of two general types: those that remove damage from DNA and those that repair errors made during DNA synthesis. The major DNA-damage repair pathways are base excision repair and nucleotide excision repair, which, in the most simple terms, are distinguished by the extent of single-strand DNA removed together with the lesion. Mistakes made by DNA polymerases are corrected by the mismatch repair pathway, which also corrects mismatches generated when single strands of non-identical duplexes are exchanged during homologous recombination. In addition to the true repair pathways, the postreplication repair pathway allows lesions or structural aberrations that block replicative DNA polymerases to be tolerated. There are two bypass mechanisms: an error-free mechanism that involves a switch to an undamaged template for synthesis past the lesion and an error-prone mechanism that utilizes specialized translesion synthesis DNA polymerases to directly synthesize DNA across the lesion. A high level of functional redundancy exists among the pathways that deal with lesions, which minimizes the detrimental effects of endogenous and exogenous DNA damage. PMID:23547164

  10. Mini-cardiopulmonary bypass impact on blood conservation strategy in coronary artery bypass grafting.

    Science.gov (United States)

    Abdel Aal, Mohamed; ElNahal, Nezar; Bakir, Bakir Moustafa; Fouda, Mohamed

    2011-04-01

    Cardiopulmonary bypass (CPB) using a closed circuit system with minimal priming volume can be a solution to ameliorate adverse effects of CPB. We hypothesize that the use of mini-bypass in routine coronary artery bypass grafting (CABG) reduces homologous blood product use and postoperative bleeding. The study is designed to determine the differences in blood loss and transfusion requirements associated with a minimized CPB circuit vs. a standard bypass circuit. From February 2009 to August 2009, 80 patients were prospectively randomized to undergo elective CABG. Group A included 40 patients who had the minimized bypass circuit (Medtronic Resting Heart Circuit). Group B had an equal number of patients who had the standard CPB circuit (Stockert III, SEC.BM). Laboratory parameters for hemoglobin, hematocrit and platelet count were measured at baseline after initiation of CPB and after bypass. Blood usage was controlled by study-specific protocol (transfusion for hemoglobin platelets (1.95±2.95 units vs. 3.23±2.85), and postoperative drainage in 24 hours (531.62±220.12 ml vs. 729±294.9 ml, P<0.05). The hematocrit was 33±5% in group A, and 27±1% in group B. There was statistical differences seen in the mean hemoglobin level which was 10.19±0.65 g/dl in group A, and 9.4±0.68 g/dl in group B. There was statistical difference in the duration of ventilation, length of ICU stay. The requirement of inotropic support was lower in group A. The adoption of mini-bypass significantly reduces morbidity including donor blood usage and postoperative bleeding in routine CABG patients.

  11. Dynamics of termination during in vitro replication of ultraviolet-irradiated DNA with DNA polymerase III holoenzyme of Escherichia coli

    International Nuclear Information System (INIS)

    Shwartz, H.; Livneh, Z.

    1987-01-01

    During in vitro replication of UV-irradiated single-stranded DNA with Escherichia coli DNA polymerase III holoenzyme termination frequently occurs at pyrimidine photodimers. The termination stage is dynamic and characterized by at least three different events: repeated dissociation-reinitiation cycles of the polymerase at the blocked termini; extensive hydrolysis of ATP to ADP and inorganic phosphate; turnover of dNTPs into dNMP. The reinitiation events are nonproductive and are not followed by further elongation. The turnover of dNTPs into dNMPs is likely to result from repeated cycles of insertion of dNMP residues opposite the blocking lesions followed by their excision by the 3'----5' exonucleolytic activity of the polymerase. Although all dNTPs are turned over, there is a preference for dATP, indicating that DNA polymerase III holoenzyme has a preference for inserting a dAMP residue opposite blocking pyrimidine photodimers. We suggest that the inability of the polymerase to bypass photodimers during termination is due to the formation of defective initiation-like complexes with reduced stability at the blocked termini

  12. Gradual Hunterian ligation for infected prosthetic bypass.

    Science.gov (United States)

    Egun, A; Slade, D; McCollum, C N

    2000-04-01

    To review gradual snare occlusion for the management of complex or recurrent graft infection. Medical records of patients treated with gradual snare occlusion following graft infection were reviewed for indication for operation, type of bypass and graft material used. In addition, infecting organism, grade of infection (Szilágyi) and outcome were recorded. Four femoropopliteal, two extra-anatomic (axillofemoral) and aortobifemoral bypasses were included in this study. All had chronic infection (Szilágyi grade III) with onset of 4 to 24 months and two of which were recurrent. The causative organisms were coagulase-negative staphylococci, Staphylococcus epidermidis and methicillin-resistant Staphylococcus aureus in three patients, with no organism isolated in the remaining cases. There was no loss of limb following gradual snare occlusion but there was only one death due to aortic stump rupture 2 weeks later. Gradual snare occlusion is an alternative for the management of chronic or recurrent graft infection. Copyright 1999 Harcourt Publishers Ltd.

  13. Advanced DVI for ECC direct bypass mitigation

    International Nuclear Information System (INIS)

    Kwon, Tae-Soon; Song, Chul-Hwa; Baek, Won-Pil

    2009-01-01

    An ECC direct bypass fraction during a late reflood phase of a LBLOCA is strongly dependent on the characteristics of the cross flow and the geometrical configuration of a DVI in the downcomer of a pressurized light water reactor. The important design parameters of a DVI are the elevation, the azimuthal angle, and the separator to prevent a steam-water interaction. An ECC sub-channel to separate or to isolate an ECC water from a high-speed cross flow is one of the important design features to mitigate the ECC bypass phenomena. A dual core barrel cylinder as an ECC flow separator is located between a reactor vessel and a core barrel outer wall in the downcomer annulus. A new narrow gap between the core barrel and the additional dual core barrel plays the role of a downward ECC flow channel or an ECC flow separator in a high-speed cross flow field of the downcomer annulus. The flow zone around a broken cold leg in the downcomer annulus has the role of a high ECC direct bypass due to a strong suction force while the wake zone of a hot leg has the role of an ECC penetration. Thus, the relative azimuthal angle of the DVI nozzle from the broken cold leg is an important design parameter. A large azimuthal angle from a cold leg to a hot leg needs to avoid a high suction flow zone when an ECC water is being injected. The other enhancing mechanism of an ECC penetration is a grooved core barrel which has small rectangular-shaped grooves vertically arranged on the core barrel wall of the reactor vessel downcomer annulus. These grooves have the role for a generation of a vortex induced by a high-speed cross flow. Since the stagnant flow in a lateral direction and rotational vortex provides the pulling force of an ECC drop or film to flow down into the lower downcomer annulus by gravity, the ECC direct bypass fraction is reduced when compared to the current design of a smoothed wall. An open channel of grooves generates a stagnant vortex, while a closed channel of grooves

  14. Mechanism of replication of ultraviolet-irradiated single-stranded DNA by DNA polymerase III holoenzyme of Escherichia coli. Implications for SOS mutagenesis

    International Nuclear Information System (INIS)

    Livneh, Z.

    1986-01-01

    Replication of UV-irradiated oligodeoxynucleotide-primed single-stranded phi X174 DNA with Escherichia coli DNA polymerase III holoenzyme in the presence of single-stranded DNA-binding protein was investigated. The extent of initiation of replication on the primed single-stranded DNA was not altered by the presence of UV-induced lesions in the DNA. The elongation step exhibited similar kinetics when either unirradiated or UV-irradiated templates were used. Inhibition of the 3'----5' proofreading exonucleolytic activity of the polymerase by dGMP or by a mutD mutation did not increase bypass of pyrimidine photodimers, and neither did purified RecA protein influence the extent of photodimer bypass as judged by the fraction of full length DNA synthesized. Single-stranded DNA-binding protein stimulated bypass since in its absence the fraction of full length DNA decreased 5-fold. Termination of replication at putative pyrimidine dimers involved dissociation of the polymerase from the DNA, which could then reinitiate replication at other available primer templates. Based on these observations a model for SOS-induced UV mutagenesis is proposed

  15. A variable current bypass shunt for electromagnets

    International Nuclear Information System (INIS)

    Berndt, M.M.; Lipari, J.J.

    1992-11-01

    An IGBT is used to control the current in bypass circuits that vary the relative strength of magnets connected in series. Each circuit consists of a water cooled assembly rated for continuous operation at 70 Volts and 0--50 Amperes DC, with 1 KV insulation between control/monitoring elements and magnets. The circuit operates as a 10KHz PWM switcher that includes filters and transient protection

  16. Hypothenar hammer syndrome and basilic bypass.

    Science.gov (United States)

    Chander, R K; Phair, J; Oza, P; Patel, M; Balar, N

    2014-12-01

    We report a case of hypothenar hammer syndrome. The case presents necessary diagnostic measures and discusses the etiology of this syndrome. Additionally, the case reviews treatments, which culminated in the eventual use of ulnar artery bypass with autogenous basilica vein to treat and resolve the ischemic fingers of the patient. © The Author(s) 2013 Reprints and permissions: sagepub.co.uk/journalsPermissions.nav.

  17. Trans-Lesion DNA Polymerases May Be Involved in Yeast Meiosis

    Science.gov (United States)

    Arbel-Eden, Ayelet; Joseph-Strauss, Daphna; Masika, Hagit; Printzental, Oxana; Rachi, Eléanor; Simchen, Giora

    2013-01-01

    Trans-lesion DNA polymerases (TLSPs) enable bypass of DNA lesions during replication and are also induced under stress conditions. Being only weakly dependent on their template during replication, TLSPs introduce mutations into DNA. The low processivity of these enzymes ensures that they fall off their template after a few bases are synthesized and are then replaced by the more accurate replicative polymerase. We find that the three TLSPs of budding yeast Saccharomyces cerevisiae Rev1, PolZeta (Rev3 and Rev7), and Rad30 are induced during meiosis at a time when DNA double-strand breaks (DSBs) are formed and homologous chromosomes recombine. Strains deleted for one or any combination of the three TLSPs undergo normal meiosis. However, in the triple-deletion mutant, there is a reduction in both allelic and ectopic recombination. We suggest that trans-lesion polymerases are involved in the processing of meiotic double-strand breaks that lead to mutations. In support of this notion, we report significant yeast two-hybrid (Y2H) associations in meiosis-arrested cells between the TLSPs and DSB proteins Rev1-Spo11, Rev1-Mei4, and Rev7-Rec114, as well as between Rev1 and Rad30. We suggest that the involvement of TLSPs in processing of meiotic DSBs could be responsible for the considerably higher frequency of mutations reported during meiosis compared with that found in mitotically dividing cells, and therefore may contribute to faster evolutionary divergence than previously assumed. PMID:23550131

  18. Extra-intracranial standard bypass in the elderly

    DEFF Research Database (Denmark)

    Sandow, Nora; von Weitzel-Mudersbach, Paul; Rosenbaum, Sverre

    2013-01-01

    Patients with chronic atherosclerotic vessel occlusion and cerebrovascular hemodynamic insufficiency may benefit from extra-intracranial (EC-IC) bypass surgery. Due to demographic changes, an increasing number of elderly patients presents with cerebrovascular hemodynamic insufficiency. So far......, little data for EC-IC bypass surgery in elderly patients suffering occlusive cerebrovascular disease are available. We therefore designed a retrospective study to address the question whether EC-IC bypass is a safe and efficient treatment in a patient cohort ≥70 years....

  19. Evaluation of the patency of an extracranial-intracranial bypass using magnetic resonance angiography with selective presaturation of bypass vessels

    Energy Technology Data Exchange (ETDEWEB)

    Mabuchi, Shoji; Nakayama, Naoki; Isu, Toyohiko; Harata, Tatsuo; Nanbu, Toshikazu [Kushiro Rousai Hospital, Hokkaido (Japan)

    1994-06-01

    Three-dimensional time-of-flight magnetic resonance (MR) angiography using radiofrequency presaturation pulses was used to evaluate the patency of extracranial-intracranial (EC/IC) bypass in 11 patients. Presaturation causes signal loss in the vascular territory supplied by the presaturated EC/IC bypass graft. In all patients with a patent EC/IC bypass graft confirmed on conventional angiography, disappearance of the signal of the middle cerebral artery receiving blood flow from the bypass graft was clearly observed on MR angiograms with presaturation, indicating patency of the EC/IC bypass graft. MR angiography with presaturation pulses is a noninvasive and repeatable method for evaluation of the function of an EC/IC bypass graft. (author).

  20. Structure and function of DNA polymerase μ

    International Nuclear Information System (INIS)

    Matsumoto, Takuro; Maezawa, So

    2013-01-01

    DNA polymerases are enzymes playing the central role in DNA metabolism, including DNA replication, DNA repair and recombination. DNA polymerase μ (pol μ DNA polymerase λ (pol λ) and terminal deoxynucleotidyltransferase (TdT) in X family DNA polymerases function in non-homologous end-joining (NHEJ), which is the predonmiant repair pathway for DNA double-strand breaks (DSBs). NHEJ involves enzymes that capture both ends of the broken DNA strand, bring them together in a synaptic DNA-protein complex, and repair the DSB. Pol μ and pol λ fill in the gaps at the junction to maintain the genomic integrity. TdT synthesizes N region at the junction during V(D)J recombination and promotes diversity of immunoglobulin or T-cell receptor gene. Among these three polymerases, the regulatory mechanisms of pol μ remain rather unclear. We have approached the mechanism of pol μ from both sides of structure and cellular dynamics. Here, we propose some new insights into pol μ and the probable NHEJ model including our findings. (author)

  1. Impossible Airway Requiring Venovenous Bypass for Tracheostomy

    Directory of Open Access Journals (Sweden)

    Johnathan Gardes

    2012-01-01

    Full Text Available The elective surgical airway is the definitive management for a tracheal stenotic lesion that is not a candidate for tracheal resection, or who has failed multiple-tracheal dilations. This case report details the management of a patient who has failed an elective awake tracheostomy secondary to the inability to be intubated as well as severe scar tissue at the surgical site. A combination of regional anesthesia and venovenous bypass is used to facilitate the surgical airway management of this patient. Cerebral oximetry and a multidisciplinary team approach aid in early detection of an oxygenation issue, as well as the emergent intervention that preserved this patient’s life.

  2. Work on the Geneva motorway bypass

    CERN Multimedia

    État de Genève, DCTI, Direction du génie civil

    2006-01-01

    Work on the airport section of the Geneva motorway bypass is continuing and will require the temporary closure of two sliproads allowing traffic to make a U-turn near the airport and the Palexpo exhibition centre. The sliproads on the French and Lausanne sides will be closed until autumn 2006. U-turns will still be possible via clearly marked deviations. For further information: www.autoroute-aeroport.ch We would like to thank you in advance for your understanding. Civil Engineering Department, DCTI, State of Geneva

  3. Perforated marginal ulcers after laparoscopic gastric bypass.

    Science.gov (United States)

    Felix, Edward L; Kettelle, John; Mobley, Elijah; Swartz, Daniel

    2008-10-01

    Perforated marginal ulcer (PMU) after laparoscopic Roux-en-Y gastric bypass (LRYGB) is a serious complication, but its incidence and etiology have rarely been investigated. Therefore, a retrospective review of all patients undergoing LRYGB at the authors' center was conducted to determine the incidence of PMU and whether any causative factors were present. A prospectively kept database of all patients at the authors' bariatric center was retrospectively reviewed. The complete records of patients with a PMU were examined individually for accuracy and analyzed for treatment, outcome, and possible underlying causes of the marginal perforation. Between April 1999 and August 2007, 1% of the patients (35/3,430) undergoing laparoscopic gastric bypass experienced one or more perforated marginal ulcers 3 to 70 months (median, 18 months) after LRYGB. The patients with and without perforation were not significantly different in terms of mean age (37 vs 41 years), weight (286 vs 287 lb), body mass index (BMI) (46 vs 47), or female gender (89% vs 83%). Of the patients with perforations, 2 (6%) were taking steroids, 10 (29%) were receiving nonsteroidal antiinflammatory drugs (NSAIDs) at the time of the perforation, 18 (51%) were actively smoking, and 6 of the smokers also were taking NSAIDs. Eleven of the patients (31%) who perforated did not have at least one of these possible risk factors, but 4 (36%) of the 11 patients in this group had been treated after bypass for a marginal ulcer. Only 7 (20%) of the 35 patients who had laparoscopic bypass, or 7 (0.2%) in the entire group of 3,430 patients, perforated without any warning. There were no deaths, but three patients reperforated. The incidence of a marginal ulcer perforating after LRYGB was significant (>1%) and appeared to be related to smoking or the use of NSAIDs or steroids. Because only 0.2% of all patients acutely perforated without some risk factor or warning, long-term ulcer prophylaxis or treatment may be necessary

  4. Carotid artery bypass in acute postendarterectomy thrombosis.

    Science.gov (United States)

    Paty, P S; Darling, R C; Cordero, J A; Shah, D M; Chang, B B; Leather, R P

    1996-08-01

    Carotid endarterectomy has demonstrated excellent results over the past 2 decades with combined stroke mortality of improvement in symptoms in 79% (11 of 14) of the patients and complete resolution in 57% (8 of 14). In long-term follow up (1 to 41 months), there have been no occlusions and one restenosis requiring revision at 11 months. Carotid artery bypass can be performed safely with acceptable results. The use of autogenous venous conduits allows reconstruction with an endothelial lined conduit that may improve results in patients with acute postoperative neurologic deficit secondary to thrombosis of the endarterectomized carotid artery.

  5. Progress in Management of Sediment Bypassing at Coastal Inlets: Natural Bypassing, Weir Jetties, Jetty Spurs, and Engineering Aids in Design

    National Research Council Canada - National Science Library

    Seabergh, William C; Kraus, Nicholas C

    2003-01-01

    .... Artificial bypassing mimics or preserves the pathways of sediment in the littoral zone and harmonizes the requirement for deepening navigation channels within the context of the natural sediment...

  6. Indications and Outcomes of Prophylactic and Therapeutic Extracranial-to-intracranial Arterial Bypass for Cerebral Revascularization

    Directory of Open Access Journals (Sweden)

    Emre Gazyakan, MD, MSc

    2015-04-01

    Conclusions: The collaboration of neurosurgeons and plastic surgeons in performing EC-IC bypass can result in excellent outcomes with a high bypass patency rate and few complications, particularly for prophylactic EC-IC bypass.

  7. RNA polymerase II mediated transcription from the polymerase III promoters in short hairpin RNA expression vector

    International Nuclear Information System (INIS)

    Rumi, Mohammad; Ishihara, Shunji; Aziz, Monowar; Kazumori, Hideaki; Ishimura, Norihisa; Yuki, Takafumi; Kadota, Chikara; Kadowaki, Yasunori; Kinoshita, Yoshikazu

    2006-01-01

    RNA polymerase III promoters of human ribonuclease P RNA component H1, human U6, and mouse U6 small nuclear RNA genes are commonly used in short hairpin RNA (shRNA) expression vectors due their precise initiation and termination sites. During transient transfection of shRNA vectors, we observed that H1 or U6 promoters also express longer transcripts enough to express several reporter genes including firefly luciferase, green fluorescent protein EGFP, and red fluorescent protein JRed. Expression of such longer transcripts was augmented by upstream RNA polymerase II enhancers and completely inhibited by downstream polyA signal sequences. Moreover, the transcription of firefly luciferase from human H1 promoter was sensitive to RNA polymerase II inhibitor α-amanitin. Our findings suggest that commonly used polymerase III promoters in shRNA vectors are also prone to RNA polymerase II mediated transcription, which may have negative impacts on their targeted use

  8. Human Pol ζ purified with accessory subunits is active in translesion DNA synthesis and complements Pol η in cisplatin bypass.

    Science.gov (United States)

    Lee, Young-Sam; Gregory, Mark T; Yang, Wei

    2014-02-25

    DNA polymerase ζ (Pol ζ) is a eukaryotic B-family DNA polymerase that specializes in translesion synthesis and is essential for normal embryogenesis. At a minimum, Pol ζ consists of a catalytic subunit Rev3 and an accessory subunit Rev7. Mammalian Rev3 contains >3,000 residues and is twice as large as the yeast homolog. To date, no vertebrate Pol ζ has been purified for biochemical characterization. Here we report purification of a series of human Rev3 deletion constructs expressed in HEK293 cells and identification of a minimally catalytically active human Pol ζ variant. With a tagged form of an active Pol ζ variant, we isolated two additional accessory subunits of human Pol ζ, PolD2 and PolD3. The purified four-subunit Pol ζ4 (Rev3-Rev7-PolD2-PolD3) is much more efficient and more processive at bypassing a 1,2-intrastrand d(GpG)-cisplatin cross-link than the two-subunit Pol ζ2 (Rev3-Rev7). We show that complete bypass of cisplatin lesions requires Pol η to insert dCTP opposite the 3' guanine and Pol ζ4 to extend the primers.

  9. Towards the molecular bases of polymerase dynamics

    International Nuclear Information System (INIS)

    Chela Flores, J.

    1991-03-01

    One aspect of the strong relationship that is known to exist between the processes of DNA replication and transcription is manifest in the coupling of the rates of movement of the replication fork (r f ) and RNA polymerase (r t ). We address two issues concerning the largely unexplored area of polymerase dynamics: (i) The validity of an approximate kinematic formula linking r f and r t suggested by experiments in which transcription is initiated in some prokaryotes with the antibiotic streptolydigin, and (ii) What are the molecular bases of the kinematic formula? An analysis of the available data suggests possible molecular bases for polymerase dynamics. In particular, we are led to a hypothesis: In active chromatin r t may depend on the length (λ t ) of the transcript of the primary messenger RNA (pre-mRNA). This new effect is subject to experimental verification. We discuss possible experiments that may be performed in order to test this prediction. (author). Refs, 6 tabs

  10. Resveratrol combined with total flavones of hawthorn alleviate the endothelial cells injury after coronary bypass graft surgery.

    Science.gov (United States)

    Zhu, Ying; Feng, Bing; He, Songmin; Su, Zuqing; Zheng, Guangjuan

    2018-02-01

    To explore the preventive and therapeutic effects of Resveratrol combined with total flavones of hawthorn, compatibility of traditional Chinese medicines, on the endothelial cells injury after artery bypass graft surgery. The animal model of coronary artery bypass grafting (CABG) was prepared by transplanting a segment of autologous jugular vein onto the transected common carotid artery in rabbits. After CABG surgery, the rabbits were administrated with saline (model group), aspirin (Aspirin group), resveratrol (Res group), total flavones of hawthorn (Haw group) and resveratrol combined with total flavones of hawthorn (Res+Haw group) once a day for eight weeks, respectively. Eight weeks later, the grafting arteries from all group were obtained for the pathomorphism observation, peripheral blood was collected to detect circulating endothelial cells (CECs) by flow cytometry. And the concentration of albumen and mRNA of ICAM-1 in the serum were measured by western blot and quantitative real-time polymerase chain reaction, respectively. Compared with the model group, the level of CECs density and the expressions of albumen and mRNA of ICAM-1 were significantly decreased in the aspirin,resveratrol,total flavones of hawthorn and resveratrol combined with total flavones of hawthorn groups (P Resveratrol combined with total flavones of hawthorn could protect the endothelial cells after coronary artery bypass graft. Copyright © 2018 Elsevier GmbH. All rights reserved.

  11. 21 CFR 870.4200 - Cardiopulmonary bypass accessory equipment.

    Science.gov (United States)

    2010-04-01

    ... Cardiopulmonary bypass accessory equipment. (a) Identification. Cardiopulmonary bypass accessory equipment is a... mounting bracket or system-priming equipment. (b) Classification. (1) Class I. The device is classified as class I if it does not involve an electrical connection to the patient. The device is exempt from the...

  12. Renal tubular acidosis secondary to jejunoileal bypass for morbid obesity

    DEFF Research Database (Denmark)

    Schaffalitzky de Muckadell, O B; Ladefoged, Jens; Thorup, Jørgen Mogens

    1985-01-01

    Renal handling of acid and base was studied in patients with persistent metabolic acidosis 3-9 years after jejunoileal bypass for morbid obesity. Excretion of acid was studied before and after intravenous infusion of NH4Cl and excretion of bicarbonate after infusion of NaHCO3. Bypass patients...

  13. Concomitant coronary artery revascularization and right pneumonectomy without cardiopulmonary bypass

    NARCIS (Netherlands)

    Hensens, AG; Zeebregts, C.J.A.M.; Liem, TH; Gehlmann, H; Lacquet, LK

    Combined coronary artery bypass grafting (CABG) and pneumonectomy has a high morbidity and mortality rate, especially when the right lung has to be removed. A patient is described who underwent a CABG operation through a midline sternotomy without the use of cardiopulmonary bypass (CPB), and a right

  14. Dacron or PTFE for above-knee femoropopliteal bypass. a multicenter randomised study

    DEFF Research Database (Denmark)

    Jensen, L P; Lepäntalo, M; Fossdal, J E

    2007-01-01

    To compare polytetrafluorethylene (PTFE) and polyester grafts (Dacron) for above knee femoropopliteal bypass.......To compare polytetrafluorethylene (PTFE) and polyester grafts (Dacron) for above knee femoropopliteal bypass....

  15. Cardiopulmonary bypass: development of John Gibbon's heart-lung machine

    Directory of Open Access Journals (Sweden)

    Andréia Cristina Passaroni

    2015-04-01

    Full Text Available AbstractObjective:To provide a brief review of the development of cardiopulmonary bypass.Methods:A review of the literature on the development of extracorporeal circulation techniques, their essential role in cardiovascular surgery, and the complications associated with their use, including hemolysis and inflammation.Results:The advancement of extracorporeal circulation techniques has played an essential role in minimizing the complications of cardiopulmonary bypass, which can range from various degrees of tissue injury to multiple organ dysfunction syndrome. Investigators have long researched the ways in which cardiopulmonary bypass may insult the human body. Potential solutions arose and laid the groundwork for development of safer postoperative care strategies.Conclusion:Steady progress has been made in cardiopulmonary bypass in the decades since it was first conceived of by Gibbon. Despite the constant evolution of cardiopulmonary bypass techniques and attempts to minimize their complications, it is still essential that clinicians respect the particularities of each patient's physiological function.

  16. Insertion of the T3 DNA polymerase thioredoxin binding domain enhances the processivity and fidelity of Taq DNA polymerase

    OpenAIRE

    Davidson, John F.; Fox, Richard; Harris, Dawn D.; Lyons-Abbott, Sally; Loeb, Lawrence A.

    2003-01-01

    Insertion of the T3 DNA polymerase thioredoxin binding domain (TBD) into the distantly related thermostable Taq DNA polymerase at an analogous position in the thumb domain, converts the Taq DNA polymerase from a low processive to a highly processive enzyme. Processivity is dependent on the presence of thioredoxin. The enhancement in processivity is 20–50-fold when compared with the wild-type Taq DNA polymerase or to the recombinant polymerase in the absence of thioredoxin. The recombinant Taq...

  17. RNA Polymerase II–The Transcription Machine

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 12; Issue 3. RNA Polymerase II – The Transcription Machine - Nobel Prize in Chemistry 2006. Jiyoti Verma Aruna Naorem Anand Kumar Manimala Sen Parag Sadhale. General Article Volume 12 Issue 3 March 2007 pp 47-53 ...

  18. Determining Annealing Temperatures for Polymerase Chain Reaction

    Science.gov (United States)

    Porta, Angela R.; Enners, Edward

    2012-01-01

    The polymerase chain reaction (PCR) is a common technique used in high school and undergraduate science teaching. Students often do not fully comprehend the underlying principles of the technique and how optimization of the protocol affects the outcome and analysis. In this molecular biology laboratory, students learn the steps of PCR with an…

  19. RNA polymerase II collision interrupts convergent transcription

    DEFF Research Database (Denmark)

    Hobson, David J; Wei, Wu; Steinmetz, Lars M

    2012-01-01

    Antisense noncoding transcripts, genes-within-genes, and convergent gene pairs are prevalent among eukaryotes. The existence of such transcription units raises the question of what happens when RNA polymerase II (RNAPII) molecules collide head-to-head. Here we use a combination of biochemical...

  20. Bypass of lethality with mosaic mice generated by Cre-loxP-mediated recombination.

    Science.gov (United States)

    Betz, U A; Vosshenrich, C A; Rajewsky, K; Müller, W

    1996-10-01

    The analysis of gene function based on the generation of mutant mice by homologous recombination in embryonic stem cells is limited if gene disruption results in embryonic lethality. Mosaic mice, which contain a certain proportion of mutant cells in all organs, allow lethality to be circumvented and the potential of mutant cells to contribute to different cell lineages to be analyzed. To generate mosaic animals, we used the bacteriophage P1-derived Cre-loxP recombination system, which allows gene alteration by Cre-mediated deletion of loxP-flanked gene segments. We generated nestin-cre transgenic mouse lines, which expressed the Cre recombinase under the control of the rat nestin promoter and its second intron enhancer. In crosses to animals carrying a loxP-flanked target gene, partial deletion of the loxP-flanked allele occurred before day 10.5 post coitum and was detectable in all adult organs examined, including germ-line cells. Using this approach, we generated mosaic mice containing cells deficient in the gamma-chain of the interleukin-2 receptor (IL-2R gamma); in these animals, the IL-2R gamma-deficient cells were underrepresented in the thymus and spleen. Because mice deficient in DNA polymerase beta die perinatally, we studied the effects of DNA polymerase beta deficiency in mosaic animals. We found that some of the mosaic polymerase beta-deficient animals were viable, but were often reduced in size and weight. The fraction of DNA polymerase beta-deficient cells in mosaic embryos decreased during embryonic development, presumably because wild-type cells had a competitive advantage. The nestin-cre transgenic mice can be used to generate mosaic animals in which target genes are mutated by Cre-mediated recombination of loxP-flanked target genes. By using mosaic animals, embryonic lethality can be bypassed and cell lineages for whose development a given target gene is critical can be identified. In the case of DNA polymerase beta, deficient cells are already

  1. Emergent cardiopulmonary bypass during pectus excavatum repair

    Directory of Open Access Journals (Sweden)

    Ryan Craner

    2013-01-01

    Full Text Available Pectus excavatum is a chest wall deformity that produces significant cardiopulmonary disability and is typically seen in younger patients. Minimally invasive repair of pectus excavatum or Nuss procedure has become a widely accepted technique for adult and pediatric patients. Although it is carried out through a thoracoscopic approach, the procedure is associated with a number of potential intraoperative and post-operative complications. We present a case of cardiac perforation requiring emergent cardiopulmonary bypass in a 29-year-old male with Marfan syndrome and previous mitral valve repair undergoing a Nuss procedure for pectus excavatum. This case illustrates the importance of vigilance and preparation by the surgeons, anesthesia providers as well as the institution to be prepared with resources to handle the possible complications. This includes available cardiac surgical backup, perfusionist support and adequate blood product availability.

  2. Bypass grafting to the anterior tibial artery.

    Science.gov (United States)

    Armour, R H

    1976-01-01

    Four patients with severe ischaemia of a leg due to atherosclerotic occlusion of the tibial and peroneal arteries had reversed long saphenous vein grafts to the patent lower part of the anterior tibial artery. Two of these grafts continue to function 19 and 24 months after operation respectively. One graft failed on the fifth postoperative day and another occluded 4 months after operation. The literature on femorotibial grafting has been reviewed. The early failure rate of distal grafting is higher than in the case of femoropopliteal bypass, but a number of otherwise doomed limbs can be salvaged. Contrary to widely held views, grafting to the anterior tibial artery appears to give results comparable to those obtained when the lower anastomosis is made to the posterior tibial artery.

  3. Rumen bypass nutrients: Manipulation and implications

    International Nuclear Information System (INIS)

    Leng, R.A.; Nolan, J.V.; Preston, T.R.

    1983-01-01

    The feeds available for ruminants in developing countries are either agro-industrial by-products or specially grown forage crops. Many of these feeds are low in protein and require supplementation with non-protein N (NPN) to maintain efficient rumen function and digestibility. The principles for utilizing high energy, low protein feeds by ruminants are discussed in relation to the supply of NPN, the establishment of efficient rumen function, maximizing feed intake by means of supplements, and increasing total energy and protein intake by using supplements which bypass the rumen. To illustrate it the application of these principles to feeding systems based on molasses, chopped whole sugar cane and derinded sugar cane is discussed. The implications of the principles in increasing the feeding value of straw are also discussed. (author)

  4. PCR fidelity of pfu DNA polymerase and other thermostable DNA polymerases.

    Science.gov (United States)

    Cline, J; Braman, J C; Hogrefe, H H

    1996-09-15

    The replication fidelities of Pfu, Taq, Vent, Deep Vent and UlTma DNA polymerases were compared using a PCR-based forward mutation assay. Average error rates (mutation frequency/bp/duplication) increased as follows: Pfu (1.3 x 10(-6)) Pfu and UlTma (approximately 5 x 10(-5)). Buffer optimization experiments indicated that Pfu fidelity was highest in the presence of 2-3 mM MgSO4 and 100-300 microM each dNTP and at pH 8.5-9.1. Under these conditions, the error rate of exo- Pfu was approximately 40-fold higher (5 x 10(-5)) than the error rate of Pfu. As the reaction pH was raised from pH 8 to 9, the error rate of Pfu decreased approximately 2-fold, while the error rate of exo- Pfu increased approximately 9-fold. An increase in error rate with pH has also been noted for the exonuclease-deficient DNA polymerases Taq and exo- Klenow, suggesting that the parameters which influence replication error rates may be similar in pol l- and alpha-like polymerases. Finally, the fidelity of 'long PCR' DNA polymerase mixtures was examined. The error rates of a Taq/Pfu DNA polymerase mixture and a Klentaq/Pfu DNA polymerase mixture were found to be less than the error rate of Taq DNA polymerase, but approximately 3-4-fold higher than the error rate of Pfu DNA polymerase.

  5. Functional roles of DNA polymerases β and γ

    International Nuclear Information System (INIS)

    Huebscher, U.; Kuenzle, C.C.; Spadari, S.

    1979-01-01

    The physiological functions of DNA polymerases (deoxynucleosidetriphosphate:DNA deoxynucleotidyltransferase, EC2.7.7.7)β and γ were investigated by using neuronal nuclei and synaptosomes isolated from rat brain. uv irradiation of neuronal nuclei from 60-day-old rats resulted in a 7- to 10-fold stimulation of DNA repair synthesis attributable to DNA polymerase β which, at this developmental stage, is virtually the only DNA polymerase present in the nuclei. No repair synthesis could be elicited by treating the nuclei with N-methyl-N-nitrosourea, but this was probably due to the inability of brain tissue to excise alkylated bases from DNA. The role of DNA polymerase γ was studied in synaptosomes by using a system mimicking in vivo mitochondrial DNA synthesis. By showing that under these conditions, DNA replication occurs in miatochondria, and exploiting the fact that DNA polymerase γ is the only DNA polymerase present in mitochondria, evidence was obtained for a role of DNA polymerase γ in mitochondrial DNA replication. Based on these results and on the wealth of literature on DNA polymerase α, we conclude that DNA polymerase α is mainly responsible for DNA replication in nuclei, DNA polymerase β is involved in nuclear DNA repair, and DNA polymerase γ is the mitochondrial replicating enzyme. However, minor roles for DNA polymerase α in DNA repair or for DNA polymerase β in DNA replication cannot be excluded

  6. Complications of Laparoscopic Retroperitoneal Sutureless and Clampless Aortobifemoral Bypass

    Directory of Open Access Journals (Sweden)

    B. Segers

    Full Text Available : Introduction: This report describes our experience with early complications that occurred in two patients who underwent sutureless aortobifemoral bypass using the EndoVascular REtroperitoneoScopic Technique (EVREST. Report: Two patients who underwent EVREST for aortoiliac TASC D lesions experienced a dislocation of the proximal assembly. The first dislocation occurred four hours post-operatively and led to the death of the patient, and the second occurred during surgery and led to open conversion. Conclusion: As a result of these serious complications, we recommend the use of anchorage stitches while using an endograft connector in a sutureless aortobifemoral bypass. Keywords: Early complications, Sutureless, Clampless, Retroperitoneoscopy, Aortobifemoral bypass

  7. Intraoperative echocardiographic imaging of coronary arteries and graft anastomoses during coronary artery bypass grafting without cardiopulmonary bypass.

    Science.gov (United States)

    Suematsu, Y; Takamoto, S; Ohtsuka, T

    2001-12-01

    No accepted approach exists for the intraoperative evaluation of the quality of coronary arteries and the technical adequacy of graft anastomoses during coronary artery bypass grafting without cardiopulmonary bypass. We assessed the accuracy of high-frequency epicardial echocardiography and power Doppler imaging in evaluating coronary arteries during coronary artery bypass grafting without cardiopulmonary bypass. To validate measurements of coronary arteries and graft anastomoses by high-frequency epicardial echocardiography and power Doppler imaging, we compared luminal diameters determined by these methods with diameters determined histologically in a study of off-pump coronary artery bypass grafting in 20 dogs. Technical errors were deliberately created in 10 grafts (stenosis group). The results of these animal validation studies showed that the maximum luminal diameters of coronary arteries and graft anastomoses measured by high-frequency epicardial echocardiography (HEE) and power Doppler imaging (PDI) correlated well with the histologic measurements: HEE = 1.027 x Histologic measurements + 0.005 (P anastomoses were examined intraoperatively by high-frequency epicardial echocardiography and power Doppler imaging, and luminal diameters determined by power Doppler imaging were compared with those determined by postoperative coronary angiography. The results demonstrated that graft anastomosis by power Doppler imaging correlated well with the angiographic measurements: PDI = 1.018 x Angiographic measurements - 0.106 (P anastomoses and can detect technical errors and inadequacies during coronary artery bypass grafting without cardiopulmonary bypass.

  8. Off-pump versus on-pump coronary artery bypass grafting for ischaemic heart disease

    DEFF Research Database (Denmark)

    Møller, Christian H; Penninga, Luit; Wetterslev, Jørn

    2012-01-01

    Coronary artery bypass grafting (CABG) is performed both without and with cardiopulmonary bypass, referred to as off-pump and on-pump CABG respectively. However, the preferable technique is unclear.......Coronary artery bypass grafting (CABG) is performed both without and with cardiopulmonary bypass, referred to as off-pump and on-pump CABG respectively. However, the preferable technique is unclear....

  9. Changes in the vessels following aorto-coronary bypass operation

    International Nuclear Information System (INIS)

    Goebel, N.; Pfluger, N.; Speiser, K.; Turina, M.; Rothlin, M.; Zurich Univ.; Zurich Univ.

    1983-01-01

    In a prospective study (238 men, mean age 53 years) the changes of the native vessels were studied 3 months after a-c-bypass operation and 5 months after preop. angiography. Progression was defined as increase of stenoses of at least 20% or new total occlusion. Progression was significantly more frequent in vessels with than without bypass and was located proximally to the anastomoses in most cases, less frequently at the anastomoses and very rarely distally to the anastomoses. Proximal progression was significantly more frequent with patent than with occluded bypasses. Stenoses at the anastomoses were significantly more frequent with occluded than with patent bypasses. Stenoses of higher degrees hat a stonger tendency for progression than slighter stenoses. Regression was rare and nearly always caused by surgery. (orig.) [de

  10. Coronary Artery Bypass Surgery: MedlinePlus Health Topic

    Science.gov (United States)

    ... Living With Related Issues Specifics See, Play and Learn Images Videos and Tutorials Research Clinical Trials Journal Articles Resources ... bypass surgery - slideshow (Medical Encyclopedia) Also in ... is better to reduce postoperative stroke... Article: Blood transfusion and ...

  11. Oil Bypass Filter Technology Performance Evaluation - January 2003 Quarterly Report

    Energy Technology Data Exchange (ETDEWEB)

    Laurence R. Zirker; James E. Francfort

    2003-01-01

    This report details the initial activities to evaluate the performance of the oil bypass filter technology being tested by the Idaho National Engineering and Environmental Laboratory (INEEL) for the U.S. Department of Energy's FreedomCAR & Vehicle Technologies Program. Eight full-size, four-cycle diesel-engine buses used to transport INEEL employees on various routes have been equipped with oil bypass systems from the puraDYN Corporation. Each bus averages about 60,000 miles a year. The evaluation includes an oil analysis regime to monitor the presence of necessary additives in the oil and to detect undesirable contaminants. Very preliminary economic analysis suggests that the oil bypass system can reduce life-cycle costs. As the evaluation continues and oil avoidance costs are quantified, it is estimated that the bypass system economics may prove increasingly favorable, given the anticipated savings in operational costs and in reduced use of oil and waste oil avoidance.

  12. Oil Bypass Filter Technology Performance Evaluation - First Quarterly Report

    Energy Technology Data Exchange (ETDEWEB)

    Zirker, L.R.; Francfort, J.E.

    2003-01-31

    This report details the initial activities to evaluate the performance of the oil bypass filter technology being tested by the Idaho National Engineering and Environmental Laboratory (INEEL) for the U.S. Department of Energy's FreedomCAR & Vehicle Technologies Program. Eight full-size, four-cycle diesel-engine buses used to transport INEEL employees on various routes have been equipped with oil bypass systems from the puraDYN Corporation. Each bus averages about 60,000 miles a year. The evaluation includes an oil analysis regime to monitor the presence of necessary additives in the oil and to detect undesirable contaminants. Very preliminary economic analysis suggests that the oil bypass system can reduce life-cycle costs. As the evaluation continues and oil avoidance costs are quantified, it is estimated that the bypass system economics may prove increasingly favorable, given the anticipated savings in operational costs and in reduced use of oil and waste oil avoidance.

  13. Prolonged successful therapy for hyperinsulinaemic hypoglycaemia after gastric bypass

    DEFF Research Database (Denmark)

    Myint, K S; Greenfield, J R; Farooqi, I S

    2012-01-01

    Spontaneous hyperinsulinaemic hypoglycaemia following gastric bypass surgery (GBS) is increasingly recognised. However, its pathophysiology remains unclear. Some patients require pancreatectomy. Medical therapy with calcium channel blockers, acarbose and diazoxide has been reported to be beneficial...

  14. Protection of semiconductor converters for controlled bypass reactors

    International Nuclear Information System (INIS)

    Dolgopolov, A. G.; Akhmetzhanov, N. G.; Karmanov, V. F.

    2010-01-01

    Possible ways of protecting thyristor converters in systems for magnetizing 110 - 500 kV controlled bypass reactors during switching and automatic reclosing are examined based on experience with the development of equipment, line tests, and mathematical modelling.

  15. [Psychoprophylaxis in patients after coronary artery bypass graft operations].

    Science.gov (United States)

    Rymaszewska, Joanna; Chładzińska-Kiejna, Sylwia; Górna, Renata; Kustrzycki, Wojciech

    2004-05-01

    The paper presented problems of quality of life and psychosocial functioning of patients following coronary artery bypass grafting operations. Possibilities of psychoprophylactic effects towards these patients and its efficacy were described.

  16. Crohn’s disease after gastric bypass surgery

    OpenAIRE

    Janczewska, Izabella; Nekzada, Qayium; Kapraali, Marjo

    2011-01-01

    Bariatric surgery for the treatment of severe obesity has increased dramatically in recent years in the USA and parts of Western Europe. The most commonly used technique is the Roux-en Y gastric bypass (RYGBP). Several nutritional and gastrointestinal complications after bariatric surgery have been described during the last 10 years. The authors present two patients with diarrhoea and malnutrition; one after RYGBP and the other after jejunoileal bypass surgery. These patients were subsequentl...

  17. Transfusion requirements in elective cardiopulmonary bypass surgery patients

    DEFF Research Database (Denmark)

    Sivapalan, Praleene; Bäck, Anne Caroline; Ostrowski, Sisse Rye

    2017-01-01

    Managing haemostasis in patients undergoing cardiopulmonary bypass (CPB) surgery remains a challenge. There is no established laboratory test to predict transfusion requirements in cardiac surgery. We investigated whether preoperative Thromboelastography (TEG) with Platelet Mapping Assay (PMA......) or Multiple Electrode Aggrometry (MEA) could predict transfusion requirements in patients undergoing elective coronary artery bypass grafting (CABG) or combined CABG with aortic or mitral valve replacement. We prospectively investigated 199 patients undergoing elective CABG or combined procedures. PMA and MEA...

  18. Severe hypoglycaemia post-gastric bypass requiring partial pancreatectomy

    DEFF Research Database (Denmark)

    Patti, M E; McMahon, G; Mun, E C

    2005-01-01

    AIMS/HYPOTHESIS: Postprandial hypoglycaemia following gastric bypass for obesity is considered a late manifestation of the dumping syndrome and can usually be managed with dietary modification. We investigated three patients with severe postprandial hypoglycaemia and hyperinsulinaemia unresponsive...... was assessed in all three patients. RESULTS: All three patients had evidence of severe postprandial hyperinsulinaemia and hypoglycaemia. In one patient, reversal of gastric bypass was ineffective in reversing hypoglycaemia. All three patients ultimately required partial pancreatectomy for control...

  19. Cardiopulmonary bypass: development of John Gibbon's heart-lung machine

    OpenAIRE

    Passaroni, Andréia Cristina; Silva, Marcos Augusto de Moraes; Yoshida, Winston Bonetti

    2015-01-01

    AbstractObjective:To provide a brief review of the development of cardiopulmonary bypass.Methods:A review of the literature on the development of extracorporeal circulation techniques, their essential role in cardiovascular surgery, and the complications associated with their use, including hemolysis and inflammation.Results:The advancement of extracorporeal circulation techniques has played an essential role in minimizing the complications of cardiopulmonary bypass, which can range from vari...

  20. Prediction of Active Site and Distal Residues in E. coli DNA Polymerase III alpha Polymerase Activity.

    Science.gov (United States)

    Parasuram, Ramya; Coulther, Timothy A; Hollander, Judith M; Keston-Smith, Elise; Ondrechen, Mary Jo; Beuning, Penny J

    2018-02-20

    The process of DNA replication is carried out with high efficiency and accuracy by DNA polymerases. The replicative polymerase in E. coli is DNA Pol III, which is a complex of 10 different subunits that coordinates simultaneous replication on the leading and lagging strands. The 1160-residue Pol III alpha subunit is responsible for the polymerase activity and copies DNA accurately, making one error per 10 5 nucleotide incorporations. The goal of this research is to determine the residues that contribute to the activity of the polymerase subunit. Homology modeling and the computational methods of THEMATICS and POOL were used to predict functionally important amino acid residues through their computed chemical properties. Site-directed mutagenesis and biochemical assays were used to validate these predictions. Primer extension, steady-state single-nucleotide incorporation kinetics, and thermal denaturation assays were performed to understand the contribution of these residues to the function of the polymerase. This work shows that the top 15 residues predicted by POOL, a set that includes the three previously known catalytic aspartate residues, seven remote residues, plus five previously unexplored first-layer residues, are important for function. Six previously unidentified residues, R362, D405, K553, Y686, E688, and H760, are each essential to Pol III activity; three additional residues, Y340, R390, and K758, play important roles in activity.

  1. Cerebroprotective effect of piracetam in patients undergoing coronary bypass burgery.

    Science.gov (United States)

    Holinski, Sebastian; Claus, Benjamin; Alaaraj, Nour; Dohmen, Pascal Maria; Kirilova, Kremena; Neumann, Konrad; Uebelhack, Ralf; Konertz, Wolfgang

    2008-11-01

    Reduction of cognitive function is a possible side effect after cardiac surgery using cardiopulmonary bypass. We investigated the cerebroprotective effect of piracetam on cognitive performance in patients undergoing coronary artery bypass surgery under cardiopulmonary bypass. Patients scheduled for elective, primary and isolated coronary bypass surgery were randomised either to piracetam or placebo group. The study was performed in a double blind fashion. Patients received either 12 g piracetam or placebo at the beginning of the operation. Six neuropsychological subtests from the Syndrom Kurz Test and the Alzheimer's Disease Assessment Scale were performed preoperatively and on the third postoperative day. To assess the overall cognitive function and the degree of cognitive decline across all tests after surgery we combined the six test-scores by principal component analysis. A total number of 120 patients were enrolled into the study. Preoperative overall cognitive function were not significantly different between the groups. The postoperative combined score of the neuropsychological tests showed a deterioration of cognitive function in both groups (placebo-pre: -0.06+/-0.99 vs placebo-post: -1.38+/-1.11; ppiracetam-pre: 0.06+/-1.02 vs piracetam-post: -0.65+/-0.93; ppiracetam patients performed significantly better compared to the placebo patients after the operation and had a less decline of overall cognitive function (pPiracetam has a cerebroprotective effect in patients undergoing coronary artery bypass surgery with the use of cardiopulmonary bypass. It reduces an early postoperative substantial decline of neuropsychological abilities.

  2. Prediction of coronary artery bypass graft flow

    International Nuclear Information System (INIS)

    Tamiya, Eiji; Hada, Yoshiyuki; Asano, Ken-ichi; Iio, Masahiro.

    1991-01-01

    To predict the coronary artery bypass graft (CABG) flow based on the time density curve (TDC) obtained from the digital subtraction aortograms (DSA), we developed a pulsatile CABG model (perfusion pressure 60,130 mmHg, pulse rate 53,126/min, cardiac output 3-7 l/min, diameter of the graft 2.1∼6.0 mm). After positioning the regions of interest (ROI), we injected contrast medium(5∼40 ml/sec, 5∼40 ml) into the outlet conduit. Concerning the TDCs, we calculated appearance time (Ta), peak densities (Dp), peak time (Tp), disappearance time (Td), integral of TDC, ΔTp (difference of Tp between two ROI) and ΔTa (difference of Ta between two ROI). Perfusion pressure, graft flow and output curve were similar to those of patients with CABG. Ta, Tp, Td, and ΔTp were affected by both the injection rate and the volume of the contrast medium; while Dp and the TDC integral were only affected by the latter parameter. Under the same conditions of contrast medium injection, the TDC depended strongly on graft flow, diameter of the graft, output and pulse rate. 21.6+0.92π·d 2 /4·Δ1/ΔTp·60 provided the most accurate estimation of CABG flow (r=0.865, p<0.01). We conclude that densitometric analysis of DSA may be useful in the prediction of CABG flow. (author)

  3. Postoperative abdominal complications after cardiopulmonary bypass

    Directory of Open Access Journals (Sweden)

    Dong Guohua

    2012-10-01

    Full Text Available Abstract Background To summarize the diagnostic and therapeutic experiences on the patients who suffered abdominal complications after cardiovascular surgery with cardiopulmonary bypass(CPB. Methods A total of 2349 consecutive patients submitted to cardiovascular surgery with CPB in our hospital from Jan 2004 to Dec 2010 were involved. The clinical data of any abdominal complication, including its incidence, characters, relative risks, diagnostic measures, medical or surgical management and mortality, was retrospectively analyzed. Results Of all the patients, 33(1.4% developed abdominal complications postoperatively, including 11(33.3% cases of paralytic ileus, 9(27.3% of gastrointestinal haemorrhage, 2(6.1% of gastroduodenal ulcer perforation, 2(6.1% of acute calculus cholecystitis, 3(9.1% of acute acalculus cholecystitis, 4(12.1% of hepatic dysfunction and 2(6.1% of ischemia bowel diseases. Of the 33 patients, 26 (78.8% accepted medical treatment and 7 (21.2% underwent subsequent surgical intervention. There were 5(15.2% deaths in this series, which was significantly higher than the overall mortality (2.7%. Positive history of peptic ulcer, advanced ages, bad heart function, preoperative IABP support, prolonged CPB time, low cardiac output and prolonged mechanical ventilation are the risk factors of abdominal complications. Conclusions Abdominal complications after cardiovascular surgery with CPB have a low incidence but a higher mortality. Early detection and prompt appropriate intervention are essential for the outcome of the patients.

  4. Right atrial bypass model in the dog.

    Science.gov (United States)

    Breen, P H; Isserles, S A

    1995-02-01

    In gas exchange studies addressing the storage and transport of CO2 in dogs, a model in which cardiac output (QT) can be precisely controlled and measured would be beneficial. We identified problems with described extracorporeal circuits and implemented right atrial bypass (RAB) in dogs. In 6 anesthetized (chloralose and urethane), heparinized dogs (mean +/- SD, 24 +/- 4 kg) with open thorax, cannulas were inserted in both vena cavas to drain venous blood return to a reservoir (anaerobic bag or bubble oxygenator). A roller pump then drove blood through a heat exchanger back to the right atrial appendage. After 1.8 +/- 1.4 hour of RAB, physiologic variables remained within reference limits for dogs (QT, 1.5 +/- 0.3 L/min; blood pressure, 92 +/- 25 mm of Hg; arterial PCO2, 35 +/- 4 mm of Hg; PO2, 513 +/- 39 mm of Hg; pH, 7.39 +/- 0.08; and tissue CO2 production, 126 +/- 56 ml/min). To permit study of gas exchange, venous return (and thus, QT) and venous PCO2 and PO2 could be accurately regulated and measured over a wide range. Maintenance of native pulsatile lung perfusion and cardiogenic oscillations minimizes mismatching of pulmonary ventilation and perfusion and facilitates studies addressing pulmonary gas exchange. This RAB model is designed so that investigators can establish the preparation in a few hours.

  5. Variations in dietary intake after bypass surgery for obesity. Possible relation to development of fatty liver after jejunoileal bypass

    International Nuclear Information System (INIS)

    Rogus, J.; Blumenthal, S.A.

    1981-01-01

    Consumption of nutrients and food energy was compared, with concomitant chemical and radiologic measurements of hepatic fat content, preoperatively and postoperatively in 25 patients who underwent gastric or jejunoileal bypass for obesity. Patients in the two operative groups ingested similar quantities of food before surgery. After surgery, caloric intake from all sources decreased in both groups but to a significantly greater extent in the gastric bypass patients. During the first six months postoperatively, the 13 gastric bypass patients showed no changes in hepatic fat content, whereas substantial increases in liver fat uniformly occurred in the 12 patients who had jejunoileal bypasses. It is suggested that dietary carbohydrate may have contributed to the accretion of liver fat in these 12 patients

  6. Chemical fidelity of an RNA polymerase ribozyme

    DEFF Research Database (Denmark)

    Attwater, J.; Tagami, S.; Kimoto, M.

    2013-01-01

    for function. Here we have explored the chemical fidelity, i.e. substrate selectivity and specificity for both single and multiple catalytic steps of the Z RNA polymerase ribozyme-a modern day analogue of the primordial RNA replicase. Using a wide range of nucleotide analogues and ionic conditions, we observe......The emergence of catalytically active RNA enzymes (ribozymes) is widely believed to have been an important transition in the origin of life. In the context of a likely heterogeneous chemical environment, substrate specificity and selectivity of these primordial enzymes would have been critical...

  7. Bordetella pertussis diagnosed by polymerase chain reaction

    DEFF Research Database (Denmark)

    Birkebaek, N H; Heron, I; Skjødt, K

    1994-01-01

    The object of this work was to test the polymerase chain reaction (PCR) for demonstration of Bordetella pertussis (BP) in nasopharyngeal secretions. The method was applied to patients with recently diagnosed pertussis, as verified by BP culture. In order to test the sensitivity and specificity...... in 25 patients in whose nasopharyngeal secretions BP had been demonstrated after 4-7 days of culture. The detection limit of PCR in aqueous solution was 1-2 BP bacteria per reaction tube. PCR was 100% specific for BP, showing no response with other Bordetella species or other bacteria known to colonize...

  8. Role of damage-specific DNA polymerases in M13 phage mutagenesis induced by a major lipid peroxidation product trans-4-hydroxy-2-nonenal

    Energy Technology Data Exchange (ETDEWEB)

    Janowska, Beata [Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw (Poland); Kurpios-Piec, Dagmara [Department of Biochemistry, Medical University of Warsaw, Banacha 1, 02-097 Warsaw (Poland); Prorok, Paulina [Institute of Genetics and Biotechnology, Warsaw University, Pawinskiego 5a, 02-106 Warsaw (Poland); Szparecki, Grzegorz [Medical University of Warsaw, Zwirki i Wigury 61, 02-097 Warsaw (Poland); Komisarski, Marek [Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw (Poland); Kowalczyk, Pawel [Interdisciplinary Centre for Mathematical and Computational Modelling, Warsaw University, Pawinskiego 5a, 02-106 Warsaw (Poland); Janion, Celina [Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw (Poland); Tudek, Barbara, E-mail: tudek@ibb.waw.pl [Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw (Poland); Institute of Genetics and Biotechnology, Warsaw University, Pawinskiego 5a, 02-106 Warsaw (Poland)

    2012-01-03

    One of the major lipid peroxidation products trans-4-hydroxy-2-nonenal (HNE), forms cyclic propano- or ethenoadducts bearing six- or seven-carbon atom side chains to G > C Much-Greater-Than A > T. To specify the role of SOS DNA polymerases in HNE-induced mutations, we tested survival and mutation spectra in the lacZ{alpha} gene of M13mp18 phage, whose DNA was treated in vitro with HNE, and which was grown in uvrA{sup -}Escherichia coli strains, carrying one, two or all three SOS DNA polymerases. When Pol IV was the only DNA SOS polymerase in the bacterial host, survival of HNE-treated M13 DNA was similar to, but mutation frequency was lower than in the strain containing all SOS DNA polymerases. When only Pol II or Pol V were present in host bacteria, phage survival decreased dramatically. Simultaneously, mutation frequency was substantially increased, but exclusively in the strain carrying only Pol V, suggesting that induction of mutations by HNE is mainly dependent on Pol V. To determine the role of Pol II and Pol IV in HNE induced mutagenesis, Pol II or Pol IV were expressed together with Pol V. This resulted in decrease of mutation frequency, suggesting that both enzymes can compete with Pol V, and bypass HNE-DNA adducts in an error-free manner. However, HNE-DNA adducts were easily bypassed by Pol IV and only infrequently by Pol II. Mutation spectrum established for strains expressing only Pol V, showed that in uvrA{sup -} bacteria the frequency of base substitutions and recombination increased in relation to NER proficient strains, particularly mutations at adenine sites. Among base substitutions A:T {yields} C:G, A:T {yields} G:C, G:C {yields} A:T and G:C {yields} T:A prevailed. The results suggest that Pol V can infrequently bypass HNE-DNA adducts inducing mutations at G, C and A sites, while bypass by Pol IV and Pol II is error-free, but for Pol II infrequent.

  9. Bypass transition in compressible boundary layers

    Science.gov (United States)

    Vandervegt, J. J.

    1992-01-01

    Transition to turbulence in aerospace applications usually occurs in a strongly disturbed environment. For instance, the effects of free-stream turbulence, roughness and obstacles in the boundary layer strongly influence transition. Proper understanding of the mechanisms leading to transition is crucial in the design of aircraft wings and gas turbine blades, because lift, drag and heat transfer strongly depend on the state of the boundary layer, laminar or turbulent. Unfortunately, most of the transition research, both theoretical and experimental, has focused on natural transition. Many practical flows, however, defy any theoretical analysis and are extremely difficult to measure. Morkovin introduced in his review paper the concept of bypass transition as those forms of transition which bypass the known mechanisms of linear and non-linear transition theories and are currently not understood by experiments. In an effort to better understand the mechanisms leading to transition in a disturbed environment, experiments are conducted studying simpler cases, viz. the effects of free stream turbulence on transition on a flat plate. It turns out that these experiments are very difficult to conduct, because generation of free stream turbulence with sufficiently high fluctuation levels and reasonable homogeneity is non trivial. For a discussion see Morkovin. Serious problems also appear due to the fact that at high Reynolds numbers the boundary layers are very thin, especially in the nose region of the plate where the transition occurs, which makes the use of very small probes necessary. The effects of free-stream turbulence on transition are the subject of this research and are especially important in a gas turbine environment, where turbulence intensities are measured between 5 and 20 percent, Wang et al. Due to the fact that the Reynolds number for turbine blades is considerably lower than for aircraft wings, generally a larger portion of the blade will be in a laminar

  10. Bowel habits after gastric bypass versus the duodenal switch operation.

    Science.gov (United States)

    Wasserberg, Nir; Hamoui, Nahid; Petrone, Patrizio; Crookes, Peter F; Kaufman, Howard S

    2008-12-01

    One of the perceived disadvantages of the biliopancreatic diversion with duodenal switch operation is diarrhea. The aim of this study was to compare the bowel habits of patients after duodenal switch operation or Roux-en-Y gastric bypass. A prospective comparative case series design was used. Forty-six patients who underwent duodenal switch (n=28) or gastric bypass (n=18) were asked to complete a daily diary for 14 days after losing least 50% of their excess body weight. Data were collected on number of bowel episodes, incontinence, urgency, stool consistency, and awakening from sleep to defecate. Background variables were recorded from the medical files. The duodenal switch group was heavier (body mass index 53.5 vs 47.0 kg/m(2), p=0.03) and older (47.5 vs 41.0 years, p=NS) than the gastric bypass group. Median time to 50% excess body weight loss was 22 months in the duodenal switch group compared to 10.0 months in the gastric bypass group (p=0.001). Patients after duodenal switch surgery reported a median of 23.5 bowel episodes over the 14-day study period compared to 16.5 in the gastric bypass group (p=NS). There was no between-group differences in any of the other bowel parameters studied. Although duodenal switch is associated with more bowel episodes than gastric bypass, the difference is not statistically significant. Bowel habits are similar in patients who achieve 50% estimated body weight loss with duodenal switch surgery or gastric bypass.

  11. Annular MHD Physics for Turbojet Energy Bypass

    Science.gov (United States)

    Schneider, Steven J.

    2011-01-01

    The use of annular Hall type MHD generator/accelerator ducts for turbojet energy bypass is evaluated assuming weakly ionized flows obtained from pulsed nanosecond discharges. The equations for a 1-D, axisymmetric MHD generator/accelerator are derived and numerically integrated to determine the generator/accelerator performance characteristics. The concept offers a shockless means of interacting with high speed inlet flows and potentially offers variable inlet geometry performance without the complexity of moving parts simply by varying the generator loading parameter. The cycle analysis conducted iteratively with a spike inlet and turbojet flying at M = 7 at 30 km altitude is estimated to have a positive thrust per unit mass flow of 185 N-s/kg. The turbojet allowable combustor temperature is set at an aggressive 2200 deg K. The annular MHD Hall generator/accelerator is L = 3 m in length with a B(sub r) = 5 Tesla magnetic field and a conductivity of sigma = 5 mho/m for the generator and sigma= 1.0 mho/m for the accelerator. The calculated isentropic efficiency for the generator is eta(sub sg) = 84 percent at an enthalpy extraction ratio, eta(sub Ng) = 0.63. The calculated isentropic efficiency for the accelerator is eta(sub sa) = 81 percent at an enthalpy addition ratio, eta(sub Na) = 0.62. An assessment of the ionization fraction necessary to achieve a conductivity of sigma = 1.0 mho/m is n(sub e)/n = 1.90 X 10(exp -6), and for sigma = 5.0 mho/m is n(sub e)/n = 9.52 X 10(exp -6).

  12. RNA polymerase activity of Ustilago maydis virus

    Energy Technology Data Exchange (ETDEWEB)

    Yie, S.W.

    1986-01-01

    Ustilago maydis virus has an RNA polymerase enzyme which is associated with virion capsids. In the presence of Mg/sup 2 +/ ion and ribonucleotide triphosphate, the enzyme catalyzes the in vitro synthesis of mRNA by using dsRNA as a template. The products of the UmV RNA polymerase were both ssRNA and dsRNA. The dsRNA was determined by characteristic mobilities in gel electrophoresis, lack of sensitivity to RNase, and specific hybridization tests. The ssRNAs were identified by elution from a CF-11 column and by their RNase sensitivity. On the basis of the size of ssRNAs, it was concluded that partial transcripts were produced from H dsRNA segments, and full length transcripts were produced from M and L dsRNA segments. The following observations indicates that transcription occurs by strand displacement; (1) Only the positive strand of M2 dsRNA was labeled by the in vitro reaction. (2) The M2 dsRNA which had been labeled with /sup 32/''P-UTP in vitro could be chased from dsRNA with unlabeled UTP. The transcription products of three UmV strains were compared, and the overall pattern of transcription was very similar among them.

  13. Replicative DNA polymerase mutations in cancer☆

    Science.gov (United States)

    Heitzer, Ellen; Tomlinson, Ian

    2014-01-01

    Three DNA polymerases — Pol α, Pol δ and Pol ɛ — are essential for DNA replication. After initiation of DNA synthesis by Pol α, Pol δ or Pol ɛ take over on the lagging and leading strand respectively. Pol δ and Pol ɛ perform the bulk of replication with very high fidelity, which is ensured by Watson–Crick base pairing and 3′exonuclease (proofreading) activity. Yeast models have shown that mutations in the exonuclease domain of Pol δ and Pol ɛ homologues can cause a mutator phenotype. Recently, we identified germline exonuclease domain mutations (EDMs) in human POLD1 and POLE that predispose to ‘polymerase proofreading associated polyposis’ (PPAP), a disease characterised by multiple colorectal adenomas and carcinoma, with high penetrance and dominant inheritance. Moreover, somatic EDMs in POLE have also been found in sporadic colorectal and endometrial cancers. Tumors with EDMs are microsatellite stable and show an ‘ultramutator’ phenotype, with a dramatic increase in base substitutions. PMID:24583393

  14. Replicative DNA polymerase mutations in cancer.

    Science.gov (United States)

    Heitzer, Ellen; Tomlinson, Ian

    2014-02-01

    Three DNA polymerases - Pol α, Pol δ and Pol ɛ - are essential for DNA replication. After initiation of DNA synthesis by Pol α, Pol δ or Pol ɛ take over on the lagging and leading strand respectively. Pol δ and Pol ɛ perform the bulk of replication with very high fidelity, which is ensured by Watson-Crick base pairing and 3'exonuclease (proofreading) activity. Yeast models have shown that mutations in the exonuclease domain of Pol δ and Pol ɛ homologues can cause a mutator phenotype. Recently, we identified germline exonuclease domain mutations (EDMs) in human POLD1 and POLE that predispose to 'polymerase proofreading associated polyposis' (PPAP), a disease characterised by multiple colorectal adenomas and carcinoma, with high penetrance and dominant inheritance. Moreover, somatic EDMs in POLE have also been found in sporadic colorectal and endometrial cancers. Tumors with EDMs are microsatellite stable and show an 'ultramutator' phenotype, with a dramatic increase in base substitutions. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

  15. Solving the RNA polymerase I structural puzzle

    Energy Technology Data Exchange (ETDEWEB)

    Moreno-Morcillo, María [European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg (Germany); Taylor, Nicholas M. I. [Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid (Spain); Gruene, Tim [Georg-August-University, Tammannstrasse 4, 37077 Göttingen (Germany); Legrand, Pierre [SOLEIL Synchrotron, L’Orme de Merisiers, Saint Aubin, Gif-sur-Yvette (France); Rashid, Umar J. [European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg (Germany); Ruiz, Federico M. [Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid (Spain); Steuerwald, Ulrich; Müller, Christoph W. [European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg (Germany); Fernández-Tornero, Carlos, E-mail: cftornero@cib.csic.es [Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid (Spain); European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg (Germany)

    2014-10-01

    Details of the RNA polymerase I crystal structure determination provide a framework for solution of the structures of other multi-subunit complexes. Simple crystallographic experiments are described to extract relevant biological information such as the location of the enzyme active site. Knowing the structure of multi-subunit complexes is critical to understand basic cellular functions. However, when crystals of these complexes can be obtained they rarely diffract beyond 3 Å resolution, which complicates X-ray structure determination and refinement. The crystal structure of RNA polymerase I, an essential cellular machine that synthesizes the precursor of ribosomal RNA in the nucleolus of eukaryotic cells, has recently been solved. Here, the crucial steps that were undertaken to build the atomic model of this multi-subunit enzyme are reported, emphasizing how simple crystallographic experiments can be used to extract relevant biological information. In particular, this report discusses the combination of poor molecular replacement and experimental phases, the application of multi-crystal averaging and the use of anomalous scatterers as sequence markers to guide tracing and to locate the active site. The methods outlined here will likely serve as a reference for future structural determination of large complexes at low resolution.

  16. DNA repair synthesis in human fibroblasts requires DNA polymerase delta

    International Nuclear Information System (INIS)

    Nishida, C.; Reinhard, P.; Linn, S.

    1988-01-01

    When UV-irradiated cultured diploid human fibroblasts were permeabilized with Brij-58 then separated from soluble material by centrifugation, conservative DNA repair synthesis could be restored by a soluble factor obtained from the supernatant of similarly treated HeLa cells. Extensive purification of this factor yielded a 10.2 S, 220,000-dalton polypeptide with the DNA polymerase and 3'- to 5'-exonuclease activities reported for DNA polymerase delta II. Monoclonal antibody to KB cell DNA polymerase alpha, while binding to HeLa DNA polymerase alpha, did not bind to the HeLa DNA polymerase delta. Moreover, at micromolar concentrations N2-(p-n-butylphenyl)-2'-deoxyguanosine 5'-triphosphate (BuPdGTP) and 2-(p-n-butylanilino)-2'-deoxyadenosine 5'-triphosphate (BuAdATP) were potent inhibitors of DNA polymerase alpha, but did not inhibit the DNA polymerase delta. Neither purified DNA polymerase alpha nor beta could promote repair DNA synthesis in the permeabilized cells. Furthermore, under conditions which inhibited purified DNA polymerase alpha by greater than 90%, neither monoclonal antibodies to DNA polymerase alpha, BuPdGTP, nor BuAdATP was able to inhibit significantly the DNA repair synthesis mediated by the DNA polymerase delta. Thus, it appears that a major portion of DNA repair synthesis induced by UV irradiation might be catalyzed by DNA polymerase delta. When xeroderma pigmentosum human diploid fibroblasts were utilized, DNA repair synthesis dependent upon ultraviolet light could be restored by addition of both T4 endonuclease V and DNA polymerase delta, but not by addition of either one alone

  17. Thermal activation of dislocations in large scale obstacle bypass

    Science.gov (United States)

    Sobie, Cameron; Capolungo, Laurent; McDowell, David L.; Martinez, Enrique

    2017-08-01

    Dislocation dynamics simulations have been used extensively to predict hardening caused by dislocation-obstacle interactions, including irradiation defect hardening in the athermal case. Incorporating the role of thermal energy on these interactions is possible with a framework provided by harmonic transition state theory (HTST) enabling direct access to thermally activated reaction rates using the Arrhenius equation, including rates of dislocation-obstacle bypass processes. Moving beyond unit dislocation-defect reactions to a representative environment containing a large number of defects requires coarse-graining the activation energy barriers of a population of obstacles into an effective energy barrier that accurately represents the large scale collective process. The work presented here investigates the relationship between unit dislocation-defect bypass processes and the distribution of activation energy barriers calculated for ensemble bypass processes. A significant difference between these cases is observed, which is attributed to the inherent cooperative nature of dislocation bypass processes. In addition to the dislocation-defect interaction, the morphology of the dislocation segments pinned to the defects play an important role on the activation energies for bypass. A phenomenological model for activation energy stress dependence is shown to describe well the effect of a distribution of activation energies, and a probabilistic activation energy model incorporating the stress distribution in a material is presented.

  18. Natural Product Screening Reveals Naphthoquinone Complex I Bypass Factors.

    Directory of Open Access Journals (Sweden)

    Scott B Vafai

    Full Text Available Deficiency of mitochondrial complex I is encountered in both rare and common diseases, but we have limited therapeutic options to treat this lesion to the oxidative phosphorylation system (OXPHOS. Idebenone and menadione are redox-active molecules capable of rescuing OXPHOS activity by engaging complex I-independent pathways of entry, often referred to as "complex I bypass." In the present study, we created a cellular model of complex I deficiency by using CRISPR genome editing to knock out Ndufa9 in mouse myoblasts, and utilized this cell line to develop a high-throughput screening platform for novel complex I bypass factors. We screened a library of ~40,000 natural product extracts and performed bioassay-guided fractionation on a subset of the top scoring hits. We isolated four plant-derived 1,4-naphthoquinone complex I bypass factors with structural similarity to menadione: chimaphilin and 3-chloro-chimaphilin from Chimaphila umbellata and dehydro-α-lapachone and dehydroiso-α-lapachone from Stereospermum euphoroides. We also tested a small number of structurally related naphthoquinones from commercial sources and identified two additional compounds with complex I bypass activity: 2-methoxy-1,4-naphthoquinone and 2-methoxy-3-methyl-1,4,-naphthoquinone. The six novel complex I bypass factors reported here expand this class of molecules and will be useful as tool compounds for investigating complex I disease biology.

  19. An Experimental Design of Bypass Magneto-Rheological (MR) damper

    Science.gov (United States)

    Rashid, MM; Aziz, Mohammad Abdul; Raisuddin Khan, Md.

    2017-11-01

    The magnetorheological (MR) fluid bypass damper fluid flow through a bypass by utilizing an external channel which allows the controllability of MR fluid in the channel. The Bypass MR damper (BMRD) contains a rectangular bypass flow channel, current controlled movable piston shaft arrangement and MR fluid. The static piston coil case is winding by a coil which is used inside the piston head arrangement. The current controlled coil case provides a magnetic flux through the BMRD cylinder for controllability. The high strength of alloy steel materials are used for making piston shaft which allows magnetic flux propagation throughout the BMRD cylinder. Using the above design materials, a Bypass MR damper is designed and tested. An excitation of current is applied during the experiment which characterizes the BMRD controllability. It is shown that the BMRD with external flow channel allows a high controllable damping force using an excitation current. The experimental result of damping force-displacement characteristics with current excitation and without current excitation are compared in this research. The BMRD model is validated by the experimental result at various frequencies and applied excitation current.

  20. The influence of core bypass flow during SBLOCA

    International Nuclear Information System (INIS)

    Maselj, A.; Jurkovic, M.

    1996-01-01

    Many parameters affect the behaviour of a NPP during a Small Break Loss of Coolant Accident (SBLOCA). The bypass flow between the core side and the downcomer is one of them. Different PWRs have different values of core bypass flow. In spite of the complexity of the real situation in the primary system during SBLOCA, some fundamental details of the phenomena can be explained with simplified mathematical models, which relate on basic parameters of the primary coolant. These models define the conditions for loop seal clearance and final results are confirmed with measured values. The analysis presented in the paper refers to Bethsy Test 9.1.b SB LOCA scenario, with variation of core bypass flow. Basic RELAP5 input model calculation results show very good agreement with the experimental data. The core liquid level depression before loop seal clearance is lower in case of smaller core bypass flow. This affects the fuel clad temperature because of different heat transfer mechanisms. Time of loop seal clearance is delayed with larger core bypass flow and consequently lower differential pressure between downcomer and core. (author)

  1. Pathogen detection by the polymerase chain reaction

    Energy Technology Data Exchange (ETDEWEB)

    Chitpatima, S T; Settachan, D; Pornsilpatip, J; Visawapoka, U [Pramongkutklao College of Medicine, Bangkok (Thailand). Molecular Biology Lab.; Dvorak, D R [Amersham International Ltd., Singapore (Singapore)

    1994-05-01

    In recent years, significant advances in the knowledge of DNA and its make up have led to the development of a powerful technique called polymerase chain reaction (PCR). Since the advent of PCR, laboratories around the globe have been exploiting this technology to bridge limitations or to overcome common problems encountered in molecular biology techniques. In addition, this technology has been employed successfully in diagnostic and basic scientific research and development. The true potentials of this technology is realized in early detection of pathogens and genetic abnormalities. In this paper two PCR protocols are described. The first is for detection of HIV-1 DNA in blood, the other for detection of rabies virus RNA in brain cells. 6 refs, 3 figs, 1 tab.

  2. Polymerase chain reaction methods (PCR in agrobiotechnology

    Directory of Open Access Journals (Sweden)

    Taški-Ajduković Ksenija

    2006-01-01

    Full Text Available The agricultural biotechnology applies polymerase chain reaction (PCR technology at numerous steps throughout product development. The major uses of PCR technology during product development include gene discovery and cloning, vector construction, transformant identification, screening and characterization as well as seed quality control. Commodity and food companies as well as testing laboratories rely on PCR technology to verify the presence or absence of genetically modification (GM in a product or to quantify the amount of GM material present in the product. This article describes the fundamental elements of PCR analysis and its application to the testing of grains and highlights some of areas to which attention must be paid in order to produce reliable test results. The article also discuses issues related to the analysis of different matrixes and the effect they may have on the accuracy of the PCR analytical results.

  3. Conformational Dynamics of Thermus aquaticus DNA Polymerase I during Catalysis

    OpenAIRE

    Xu, Cuiling; Maxwell, Brian A.; Suo, Zucai

    2014-01-01

    Despite the fact that DNA polymerases have been investigated for many years and are commonly used as tools in a number of molecular biology assays, many details of the kinetic mechanism they use to catalyze DNA synthesis remain unclear. Structural and kinetic studies have characterized a rapid, pre-catalytic open-to-close conformational change of the Finger domain during nucleotide binding for many DNA polymerases including Thermus aquaticus DNA polymerase I (Taq Pol), a thermostable enzyme c...

  4. Rankine cycle load limiting through use of a recuperator bypass

    Science.gov (United States)

    Ernst, Timothy C.

    2011-08-16

    A system for converting heat from an engine into work includes a boiler coupled to a heat source for transferring heat to a working fluid, a turbine that transforms the heat into work, a condenser that transforms the working fluid into liquid, a recuperator with one flow path that routes working fluid from the turbine to the condenser, and another flow path that routes liquid working fluid from the condenser to the boiler, the recuperator being configured to transfer heat to the liquid working fluid, and a bypass valve in parallel with the second flow path. The bypass valve is movable between a closed position, permitting flow through the second flow path and an opened position, under high engine load conditions, bypassing the second flow path.

  5. RNA binding and replication by the poliovirus RNA polymerase

    International Nuclear Information System (INIS)

    Oberste, M.S.

    1988-01-01

    RNA binding and RNA synthesis by the poliovirus RNA-dependent RNA polymerase were studied in vitro using purified polymerase. Templates for binding and RNA synthesis studies were natural RNAs, homopolymeric RNAs, or subgenomic poliovirus-specific RNAs synthesized in vitro from cDNA clones using SP6 or T7 RNA polymerases. The binding of the purified polymerase to poliovirion and other RNAs was studied using a protein-RNA nitrocellulose filter binding assay. A cellular poly(A)-binding protein was found in the viral polymerase preparations, but was easily separated from the polymerase by chromatography on poly(A) Sepharose. The binding of purified polymerase to 32 P-labeled ribohomopolymeric RNAs was examined, and the order of binding observed was poly(G) >>> poly(U) > poly(C) > poly(A). The K a for polymerase binding to poliovirion RNA and to a full-length negative strand transcript was about 1 x 10 9 M -1 . The polymerase binds to a subgenomic RNAs which contain the 3' end of the genome with a K a similar to that for virion RNA, but binds less well to 18S rRNA, globin mRNA, and subgenomic RNAs which lack portions of the 3' noncoding region

  6. Exercise thallium-201 scintigraphy in evaluating aortocoronary bypass surgery

    International Nuclear Information System (INIS)

    Iskandrian, A.S.; Haaz, W.; Segal, B.L.; Kane, S.A.

    1981-01-01

    Thirty patients with recurrent symptoms after aortocoronary bypass graft surgery underwent angiography as well as exercise thallium 201 imaging. Exercise imaging has been shown to be highly specific (100 percent in our study) in evaluating patients after bypass surgery. Patients with complete revascularization have normal thallium 201 images. Similarly, exercise-induced defects are seen only in the presence of incomplete revascularization. There are patients, however, with incomplete revascularization with normal exercise images, but these generally limited to the right coronary artery or the diagonal vessels or their grafts

  7. Role of ternary fission in synthesis of bypassed nuclei

    International Nuclear Information System (INIS)

    Kramarovskij, Ya.M.; Chechev, V.P.

    1983-01-01

    A possible influence of ternary fission with escape of neutron-enriched light charged particles on the synthesis of bypassed nuclides is considered. It is shown that this concept cannot give explanation of bypassed isotope concentrations, but it can make some contribution, if the probability of ternary fission for superheavy nuclei grows sharply with Z 2 /A parameter. The account of β-delayed fission contributes to the shift of ternary fission fragments into the region of neutron-deficient isotopes. Consistent consideration of the ternary fission role in the nucleosynthesis is possible only with an important accumulation of experimental and theoretical data on this process, particularly for the nuclei with Z > 100

  8. Construct exploit constraint in crash analysis by bypassing canary

    Science.gov (United States)

    Huang, Ning; Huang, Shuguang; Huang, Hui; Chang, Chao

    2017-08-01

    Selective symbolic execution is a common program testing technology. Developed on the basis of it, some crash analysis systems are often used to test the fragility of the program by constructing exploit constraints, such as CRAX. From the study of crash analysis based on symbolic execution, this paper find that this technology cannot bypass the canary stack protection mechanisms. This paper makes the improvement uses the API hook in Linux. Experimental results show that the use of API hook can effectively solve the problem that crash analysis cannot bypass the canary protection.

  9. DNA polymerase η modulates replication fork progression and DNA damage responses in platinum-treated human cells

    Science.gov (United States)

    Sokol, Anna M.; Cruet-Hennequart, Séverine; Pasero, Philippe; Carty, Michael P.

    2013-11-01

    Human cells lacking DNA polymerase η (polη) are sensitive to platinum-based cancer chemotherapeutic agents. Using DNA combing to directly investigate the role of polη in bypass of platinum-induced DNA lesions in vivo, we demonstrate that nascent DNA strands are up to 39% shorter in human cells lacking polη than in cells expressing polη. This provides the first direct evidence that polη modulates replication fork progression in vivo following cisplatin and carboplatin treatment. Severe replication inhibition in individual platinum-treated polη-deficient cells correlates with enhanced phosphorylation of the RPA2 subunit of replication protein A on serines 4 and 8, as determined using EdU labelling and immunofluorescence, consistent with formation of DNA strand breaks at arrested forks in the absence of polη. Polη-mediated bypass of platinum-induced DNA lesions may therefore represent one mechanism by which cancer cells can tolerate platinum-based chemotherapy.

  10. Outcomes of lower extremity bypass performed for acute limb ischemia.

    Science.gov (United States)

    Baril, Donald T; Patel, Virendra I; Judelson, Dejah R; Goodney, Philip P; McPhee, James T; Hevelone, Nathanael D; Cronenwett, Jack L; Schanzer, Andres

    2013-10-01

    Acute limb ischemia remains one of the most challenging emergencies in vascular surgery. Historically, outcomes following interventions for acute limb ischemia have been associated with high rates of morbidity and mortality. The purpose of this study was to determine contemporary outcomes following lower extremity bypass performed for acute limb ischemia. All patients undergoing infrainguinal lower extremity bypass between 2003 and 2011 within hospitals comprising the Vascular Study Group of New England were identified. Patients were stratified according to whether or not the indication for lower extremity bypass was acute limb ischemia. Primary end points included bypass graft occlusion, major amputation, and mortality at 1 year postoperatively as determined by Kaplan-Meier life table analysis. Multivariable Cox proportional hazards models were constructed to evaluate independent predictors of mortality and major amputation at 1 year. Of 5712 lower extremity bypass procedures, 323 (5.7%) were performed for acute limb ischemia. Patients undergoing lower extremity bypass for acute limb ischemia were similar in age (66 vs 67; P = .084) and sex (68% male vs 69% male; P = .617) compared with chronic ischemia patients, but were less likely to be on aspirin (63% vs 75%; P < .0001) or a statin (55% vs 68%; P < .0001). Patients with acute limb ischemia were more likely to be current smokers (49% vs 39%; P < .0001), to have had a prior ipsilateral bypass (33% vs 24%; P = .004) or a prior ipsilateral percutaneous intervention (41% vs 29%; P = .001). Bypasses performed for acute limb ischemia were longer in duration (270 vs 244 minutes; P = .007), had greater blood loss (363 vs 272 mL; P < .0001), and more commonly utilized prosthetic conduits (41% vs 33%; P = .003). Acute limb ischemia patients experienced increased in-hospital major adverse events (20% vs 12%; P < .0001) including myocardial infarction, congestive heart failure exacerbation, deterioration in renal function

  11. Multi-slice CT angiography in evaluation of extracranial-intracranial bypass

    Energy Technology Data Exchange (ETDEWEB)

    Teksam, Mehmet E-mail: mehmetteksam@yahoo.com; McKinney, Alexander; Truwit, Charles L

    2004-12-01

    Multi-slice CT (MSCT) scanners provided significant improvement in vascular applications. In this study, our purpose was to determine the clinical utility of MSCTA in evaluation of extracranial-intracranial (EC-IC) bypass patency. Eleven (4 men and 7 women; mean age, 46 years; age range, 19-68 years) consecutive patients who underwent MSCTA and DSA after EC-IC bypass surgery were evaluated retrospectively. All patients underwent DSA within 3 weeks of MSCTA. The indications for EC-IC bypass were severe stenosis or occlusion of intracranial arteries in seven patients and therapeutic occlusion of intracranial artery for unclippable giant aneurysm in four patients. Ten patients underwent superficial temporal artery (STA)-middle cerebral artery (MCA) bypass and one patient underwent occipital artery-posterior cerebral artery (PCA) bypass. Eight STA-MCA bypasses in six patients were patent on MSCTA which were confirmed on DSA. Two MSCTA bypasses and one occipital artery-posterior cerebral artery (PCA) bypass were occluded in three patients on MSCTA and DSA. In one patient, minimal stenosis of the STA-MCA bypass was identified on MSCTA and DSA. In 1 patient, STA-MCA bypass was not well seen on MSCTA and suspected for occlusion. DSA identified the occlusion of bypass on this patient. MSCTA seems to be a very promising noninvasive technique in evaluation of EC-IC bypass.

  12. Multi-slice CT angiography in evaluation of extracranial-intracranial bypass

    International Nuclear Information System (INIS)

    Teksam, Mehmet; McKinney, Alexander; Truwit, Charles L.

    2004-01-01

    Multi-slice CT (MSCT) scanners provided significant improvement in vascular applications. In this study, our purpose was to determine the clinical utility of MSCTA in evaluation of extracranial-intracranial (EC-IC) bypass patency. Eleven (4 men and 7 women; mean age, 46 years; age range, 19-68 years) consecutive patients who underwent MSCTA and DSA after EC-IC bypass surgery were evaluated retrospectively. All patients underwent DSA within 3 weeks of MSCTA. The indications for EC-IC bypass were severe stenosis or occlusion of intracranial arteries in seven patients and therapeutic occlusion of intracranial artery for unclippable giant aneurysm in four patients. Ten patients underwent superficial temporal artery (STA)-middle cerebral artery (MCA) bypass and one patient underwent occipital artery-posterior cerebral artery (PCA) bypass. Eight STA-MCA bypasses in six patients were patent on MSCTA which were confirmed on DSA. Two MSCTA bypasses and one occipital artery-posterior cerebral artery (PCA) bypass were occluded in three patients on MSCTA and DSA. In one patient, minimal stenosis of the STA-MCA bypass was identified on MSCTA and DSA. In 1 patient, STA-MCA bypass was not well seen on MSCTA and suspected for occlusion. DSA identified the occlusion of bypass on this patient. MSCTA seems to be a very promising noninvasive technique in evaluation of EC-IC bypass

  13. 21 CFR 870.4360 - Nonroller-type cardiopulmonary bypass blood pump.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Nonroller-type cardiopulmonary bypass blood pump... Nonroller-type cardiopulmonary bypass blood pump. (a) Identification. A nonroller-type cardiopulmonary bypass blood pump is a device that uses a method other than revolving rollers to pump the blood through...

  14. 21 CFR 870.4370 - Roller-type cardiopulmonary bypass blood pump.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Roller-type cardiopulmonary bypass blood pump. 870... Roller-type cardiopulmonary bypass blood pump. (a) Identification. A roller-type cardiopulmonary bypass blood pump is a device that uses a revolving roller mechanism to pump the blood through the...

  15. 21 CFR 870.4260 - Cardiopulmonary bypass arterial line blood filter.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Cardiopulmonary bypass arterial line blood filter... Cardiopulmonary bypass arterial line blood filter. (a) Identification. A cardiopulmonary bypass arterial line blood filter is a device used as part of a gas exchange (oxygenator) system to filter nonbiologic...

  16. 21 CFR 870.4410 - Cardiopulmonary bypass in-line blood gas sensor.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Cardiopulmonary bypass in-line blood gas sensor... Cardiopulmonary bypass in-line blood gas sensor. (a) Identification. A cardiopulmonary bypass in-line blood gas sensor is a transducer that measures the level of gases in the blood. (b) Classification. Class II...

  17. On-pump versus off-pump coronary artery bypass surgery

    DEFF Research Database (Denmark)

    Houlind, Kim Christian

    2013-01-01

    Off pump coronary artery bypass surgery has been purported to be safer than conventional coronary artery bypass surgery performed using cardiopulmonary bypass. This theory was supported by a number of early series, but failed to be confirmed by a number of small, randomized controlled trials...

  18. Accurate Digital Polymerase Chain Reaction Quantification of Challenging Samples Applying Inhibitor-Tolerant DNA Polymerases.

    Science.gov (United States)

    Sidstedt, Maja; Romsos, Erica L; Hedell, Ronny; Ansell, Ricky; Steffen, Carolyn R; Vallone, Peter M; Rådström, Peter; Hedman, Johannes

    2017-02-07

    Digital PCR (dPCR) enables absolute quantification of nucleic acids by partitioning of the sample into hundreds or thousands of minute reactions. By assuming a Poisson distribution for the number of DNA fragments present in each chamber, the DNA concentration is determined without the need for a standard curve. However, when analyzing nucleic acids from complex matrixes such as soil and blood, the dPCR quantification can be biased due to the presence of inhibitory compounds. In this study, we evaluated the impact of varying the DNA polymerase in chamber-based dPCR for both pure and impure samples using the common PCR inhibitor humic acid (HA) as a model. We compared the TaqMan Universal PCR Master Mix with two alternative DNA polymerases: ExTaq HS and Immolase. By using Bayesian modeling, we show that there is no difference among the tested DNA polymerases in terms of accuracy of absolute quantification for pure template samples, i.e., without HA present. For samples containing HA, there were great differences in performance: the TaqMan Universal PCR Master Mix failed to correctly quantify DNA with more than 13 pg/nL HA, whereas Immolase (1 U) could handle up to 375 pg/nL HA. Furthermore, we found that BSA had a moderate positive effect for the TaqMan Universal PCR Master Mix, enabling accurate quantification for 25 pg/nL HA. Increasing the amount of DNA polymerase from 1 to 5 U had a strong effect for ExTaq HS, elevating HA-tolerance four times. We also show that the average Cq values of positive reactions may be used as a measure of inhibition effects, e.g., to determine whether or not a dPCR quantification result is reliable. The statistical models developed to objectively analyze the data may also be applied in quality control. We conclude that the choice of DNA polymerase in dPCR is crucial for the accuracy of quantification when analyzing challenging samples.

  19. Polymerase chain reaction to search for Herpes viruses in uveitic ...

    African Journals Online (AJOL)

    Objective: To analyse aqueous polymerase chain reaction (PCR) results in patients diagnosed with undifferentiated uveitis ... Cite as: Laaks D, Smit DP, Harvey J. Polymerase chain reaction to search for Herpes viruses in uveitic and healthy eyes: a South African ... may be mild and patients do not seek medical attention.

  20. A Double Polymerase Chain Reaction Method for Detecting African ...

    African Journals Online (AJOL)

    Keywords: African swine fever, Swine vesicular disease, Polymerase chain reaction, Recombinant plasmids ... included 5 μL of 10×Pfu DNA polymerase buffer,. 1 μL of Pfu DNA .... Garcia-Barreno B, Sanz A, Nogal ML, Vinuela E,. Enjuanes L.

  1. Polymerase chain reaction for the detection of Mycobacterium leprae

    NARCIS (Netherlands)

    Hartskeerl, R. A.; de Wit, M. Y.; Klatser, P. R.

    1989-01-01

    A polymerase chain reaction (PCR) using heat-stable Taq polymerase is described for the specific detection of Mycobacterium leprae, the causative agent of leprosy. A set of primers was selected on the basis of the nucleotide sequence of a gene encoding the 36 kDa antigen of M. leprae. With this set

  2. Reverse transcriptase-quantitative polymerase chain reaction (RT ...

    African Journals Online (AJOL)

    The reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) is a highly specific polymerase chain reaction (PCR) method that allows one to detect very low transcription levels of functional gene(s) in soil. RT-qPCR helps us to know the active members of the microbial community, and their activities can be ...

  3. Esophageal bypass after failed chemoradiotherapy for unresectable esophageal cancer

    International Nuclear Information System (INIS)

    Matono, Satoru; Tanaka, Toshiaki; Mori, Naoki; Nagano, Takeshi; Fujita, Hiromasa; Shirouzu, Kazuo

    2013-01-01

    Esophageal stenosis and/or fistula often occur after chemoradiotherapy (CRT) for unresectable esophageal cancer. In such patients, an esophageal stent can help achieve oral intake. However an esophageal stent cannot be inserted where there is complete stenosis or where the tumor is located. In such cases, esophageal bypass surgery may be necessary. Here, we investigated the clinical characteristics and outcomes in patients who underwent esophageal bypass surgery in our institution. We reviewed 10 cases of esophageal bypass surgery (gastric tube in 8 cases, colon in 2 cases) after CRT for unresectable esophageal cancer, between 2001 and 2009. There were 5 of stenosis-only cases, 4 fistula-only cases, and 1 case of stenosis and fistula. There were postoperative complications in 5 cases (50%), and all these were treated conservatively and healed. The median survival from surgery to peroral intake was 20 days (range 9-90 days), and the median survival after starting peroral intake was 130 days (range 48-293 days). Esophageal bypass surgery can achieve good performance status and improve peroral intake. (author)

  4. Myocardial injury and protection related to cardiopulmonary bypass

    NARCIS (Netherlands)

    de Hert, Stefan; Moerman, Anneliese

    2015-01-01

    During cardiac surgery with cardiopulmonary bypass, the heart is isolated from the circulation. This inevitably induces myocardial ischemia. In addition to this ischemic insult, an additional hit will occur upon reperfusion, which may worsen the extent of tissue damage and organ dysfunction. Over

  5. Gastrointestinal motility during cardiopulmonary bypass : A sonomicrometric study

    NARCIS (Netherlands)

    Gu, YJ; de Kroon, TL; Elstrodt, JM; Rakhorst, G

    Cardiopulmonary bypass (CPB) is known to impair the integrity of the gastrointestinal tract. However, little is known about the movement behavior of the gastrointestinal tract during CPB. This study was aimed to assess the gastrointestinal motility with sonomicrometry, a distance measurement using

  6. PREVENTION OF BLOOD ACTIVATION DURING AND COMPLICATIONS AFTER CARDIOPULMONARY BYPASS

    NARCIS (Netherlands)

    VANOEVEREN, W; WILDEVUUR, CRH

    1991-01-01

    The cardiopulmonary bypass (CPB) circuit for open heart surgery initiates a whole body inflammatory reaction (WBIR) resulting in impaired hemostasis and organ dysfunction. Impaired hemostasis appeared to be related to the activation of the contact system (factor XII), which can be inhibited by

  7. Welded tracheal stent removal in a child under cardiopulmonary bypass.

    Science.gov (United States)

    Kao, S C; Chang, W K; Pong, M W; Cheng, K W; Chan, K H; Tsai, S K

    2003-08-01

    Metallic tracheal stents have been used in the treatment of paediatric tracheomalacia for more than a decade. We describe a case in which critical airway obstruction occurred during removal of a welded tracheal stent using a rigid bronchoscope under general anaesthesia. Life-saving cardiopulmonary bypass was instituted urgently, and the welded stent was then removed successfully by directly opening the trachea.

  8. Emergency bypass post percutaneous atrial ablation: a case report.

    LENUS (Irish Health Repository)

    Hargrove, M

    2010-11-01

    A 34-year-old male undergoing percutaneous atrial ablation procedure for paroxysmal fibrillation required emergency sternotomy for cardiac tamponade. The patient had been anticoagulated and had received plavix and aspirin prior to and during the ablation procedure. Seven units of red cell concentrate had been transfused in the cardiac catherisation laboratory. On arrival in theatre, the patient was hypotensive, but was awake on induction of anaesthesia. No recordable blood pressure with non-invasive monitoring was observed. A sternotomy was immediately performed and, on evacuation of the pericardium, a bleeding site was not visible. The patient was commenced on cardiopulmonary bypass. Bleeding site was identified and the defect closed. The patient was weaned from cardiopulmonary bypass with minimal inotropic support and made an uneventful recovery. Bypass time was 38 minutes. A literature review showed a 1% incidence of post-ablation bleeding(1). The incidence of reverting to bypass for such an event has not been reported previously. During these procedures, it might be wise to have the cardiothoracic team notified while atrial ablation procedures are being performed in the cardiac catheterization laboratory.

  9. CDK9-dependent RNA polymerase II pausing controls transcription initiation.

    Science.gov (United States)

    Gressel, Saskia; Schwalb, Björn; Decker, Tim Michael; Qin, Weihua; Leonhardt, Heinrich; Eick, Dirk; Cramer, Patrick

    2017-10-10

    Gene transcription can be activated by decreasing the duration of RNA polymerase II pausing in the promoter-proximal region, but how this is achieved remains unclear. Here we use a 'multi-omics' approach to demonstrate that the duration of polymerase pausing generally limits the productive frequency of transcription initiation in human cells ('pause-initiation limit'). We further engineer a human cell line to allow for specific and rapid inhibition of the P-TEFb kinase CDK9, which is implicated in polymerase pause release. CDK9 activity decreases the pause duration but also increases the productive initiation frequency. This shows that CDK9 stimulates release of paused polymerase and activates transcription by increasing the number of transcribing polymerases and thus the amount of mRNA synthesized per time. CDK9 activity is also associated with long-range chromatin interactions, suggesting that enhancers can influence the pause-initiation limit to regulate transcription.

  10. Foxtail millet NF-Y families: genome-wide survey and evolution analyses identified two functional genes important in abiotic stresses

    Directory of Open Access Journals (Sweden)

    Zhi-Juan eFeng

    2015-12-01

    Full Text Available It was reported that Nuclear Factor Y (NF-Y genes were involved in abiotic stress in plants. Foxtail millet (Setaria italica, an elite stress tolerant crop, provided an impetus for the investigation of the NF-Y families in abiotic responses. In the present study, a total of 39 NF-Y genes were identified in foxtail millet. Synteny analyses suggested that foxtail millet NF-Y genes had experienced rapid expansion and strong purifying selection during the process of plant evolution. De novo transcriptome assembly of foxtail millet revealed 11 drought up-regulated NF-Y genes. SiNF-YA1 and SiNF-YB8 were highly activated in leaves and/or roots by drought and salt stresses. Abscisic acid (ABA and H2O2 played positive roles in the induction of SiNF-YA1 and SiNF-YB8 under stress treatments. Transient luciferase (LUC expression assays revealed that SiNF-YA1 and SiNF-YB8 could activate the LUC gene driven by the tobacco (Nicotiana tobacam NtERD10, NtLEA5, NtCAT, NtSOD or NtPOD promoter under normal or stress conditions. Overexpression of SiNF-YA1 enhanced drought and salt tolerance by activating stress-related genes NtERD10 and NtCAT1 and by maintaining relatively stable relative water content (RWC and contents of chlorophyll, superoxide dismutase (SOD, peroxidase (POD, catalase (CAT and malondialdehyde (MDA in transgenic lines under stresses. SiNF-YB8 regulated expression of NtSOD, NtPOD, NtLEA5 and NtERD10 and conferred relatively high RWC and chlorophyll contents and low MDA content, resulting in drought and osmotic tolerance in transgenic lines under stresses. Therefore, SiNF-YA1 and SiNF-YB8 could activate stress-related genes and improve physiological traits, resulting in tolerance to abiotic stresses in plants. All these results will facilitate functional characterization of foxtail millet NF-Ys in future studies.

  11. Kinetic mechanism of DNA polymerase I (Klenow)

    International Nuclear Information System (INIS)

    Kuchta, R.D.; Mizrahi, V.; Benkovic, P.A.; Johnson, K.A.; Benkovic, S.J.

    1987-01-01

    The minimal kinetic scheme for DNA polymerization catalyzed by the Klenow fragment of DNA polymerase I (KF) from Escherichia coli has been determined with short DNA oligomers of defined sequence, labeled with [ 32 P]-nucleotides. A key feature of this scheme is a minimal two-step sequence that interconverts the ternary KF-DNA/sub n/-dNTP and KF-DNA/sub n+1/-PP/sub i/ complexes. The rate is not limited by the actual polymerization but by a separate step, possibly important in ensuring fidelity. Evidence for this sequence is supplied by the observation of biphasic kinetics in single-turnover pyrophosphorolysis experiments (the microscopic reverse of polymerization). Data analysis then provides an estimate of the internal equilibrium constant. The dissociations of DNA, dNTP, and PP/sub i/ from the various binary and ternary complexes were measured by partitioning (isotope-trapping) experiments. The rate constant for DNA dissociation from KF is sequence dependent and is rate limiting during nonprocessive DNA synthesis. The combination of single-turnover (both directions) and isotope-trapping experiments provides sufficient information to permit a quantitative evaluation of the kinetic scheme for specific DNA sequences

  12. Is phonology bypassed in normal or dyslexic development?

    Science.gov (United States)

    Pennington, B F; Lefly, D L; Van Orden, G C; Bookman, M O; Smith, S D

    1987-01-01

    A pervasive assumption in most accounts of normal reading and spelling development is that phonological coding is important early in development but is subsequently superseded by faster, orthographic coding which bypasses phonology. We call this assumption, which derives from dual process theory, the developmental bypass hypothesis. The present study tests four specific predictions of the developmental bypass hypothesis by comparing dyslexics and nondyslexics from the same families in a cross-sectional design. The four predictions are: 1) That phonological coding skill develops early in normal readers and soon reaches asymptote, whereas orthographic coding skill has a protracted course of development; 2) that the correlation of adult reading or spelling performance with phonological coding skill is considerably less than the correlation with orthographic coding skill; 3) that dyslexics who are mainly deficient in phonological coding skill should be able to bypass this deficit and eventually close the gap in reading and spelling performance; and 4) that the greatest differences between dyslexics and developmental controls on measures of phonological coding skill should be observed early rather than late in development.None of the four predictions of the developmental bypass hypothesis were upheld. Phonological coding skill continued to develop in nondyslexics until adulthood. It accounted for a substantial (32-53 percent) portion of the variance in reading and spelling performance in adult nondyslexics, whereas orthographic coding skill did not account for a statistically reliable portion of this variance. The dyslexics differed little across age in phonological coding skill, but made linear progress in orthographic coding skill, surpassing spelling-age (SA) controls by adulthood. Nonetheless, they didnot close the gap in reading and spelling performance. Finally, dyslexics were significantly worse than SA (and Reading Age [RA]) controls in phonological coding skill

  13. Platelet hyperreactivity in response to on- and off-pump coronary artery bypass grafting

    DEFF Research Database (Denmark)

    Bochsen, Louise; Rosengaard, Lisbeth Bredahl; Nielsen, Allan Bybeck

    2009-01-01

    Hypercoagulability has been reported after off-pump coronary artery bypass grafting (OPCAB) compared with patients undergoing standard coronary artery bypass grafting (CABG) with cardiopulmonary bypass. The aim of this study was to evaluate the changes in platelet reactivity in response to cardiac...... and this study identified 23% of patients needing coronary bypass surgery to be at high risk for recurrent ischemic events at 1 month after surgery, based on the MA. These results suggest that a more aggressive antithrombotic treatment might be warranted for patients undergoing coronary artery bypass grafting...

  14. Sub-nuclear irradiation, in-vivo microscopy and single-molecule imaging to study a DNA Polymerase

    Energy Technology Data Exchange (ETDEWEB)

    Soria, G; Mansilla, S; Belluscio, L; Speroni, J; D' Alessio, C; Gottifredi, V [Fundacion Leloir, Buenos Aires (Argentina); Essers, J; Kanaar, R [Erasmus Medical Center, Rotterdam (Netherlands)

    2009-07-01

    When the DNA is damaged in cells progressing through S phase, replication blockage can be avoided by TLS (Translesion DNA synthesis). This is an auxiliary replication mechanism that relies on the function of specialized polymerases that accomplish DNA damage bypass. An example of a classical TLS polymerase is Pol {eta} ({eta}). The current model implies that Pol {eta} activity is circumscribed to S-phase. Here we perform a systematic characterization of Pol {eta} behaviour after DNA-damage. We show that Pol {eta} is recruited to UV-induced DNA lesions in cells outside S phase including cells permanently arrested in G1. This observation was confirmed by different sub-nuclear damage strategies including global UV irradiation, local UV irradiation and local multi-photon laser irradiation of single nuclei in living cells. By local UV irradiation and alpha particle irradiation we evaluated the potential connection between Pol h recruitment to DNA lesions outside S phase and Homologous recombination repair (HRR) or Nucleotide excision repair (NER). Finally, we employ a single-molecule imaging approach (known as DNA fiber-assay) to determine how Pol h influences the progression of the replication fork. Our data reveals that the re-localization of Pol {eta} to DNA lesions might be temporally and mechanistically uncoupled from replicative DNA synthesis and from DNA damage processing. (authors)

  15. Sub-nuclear irradiation, in-vivo microscopy and single-molecule imaging to study a DNA Polymerase

    International Nuclear Information System (INIS)

    Soria, G.; Mansilla, S.; Belluscio, L.; Speroni, J.; D'Alessio, C.; Gottifredi, V.; Essers, J.; Kanaar, R.

    2009-01-01

    When the DNA is damaged in cells progressing through S phase, replication blockage can be avoided by TLS (Translesion DNA synthesis). This is an auxiliary replication mechanism that relies on the function of specialized polymerases that accomplish DNA damage bypass. An example of a classical TLS polymerase is Pol η (eta). The current model implies that Pol η activity is circumscribed to S-phase. Here we perform a systematic characterization of Pol η behaviour after DNA-damage. We show that Pol η is recruited to UV-induced DNA lesions in cells outside S phase including cells permanently arrested in G1. This observation was confirmed by different sub-nuclear damage strategies including global UV irradiation, local UV irradiation and local multi-photon laser irradiation of single nuclei in living cells. By local UV irradiation and alpha particle irradiation we evaluated the potential connection between Pol h recruitment to DNA lesions outside S phase and Homologous recombination repair (HRR) or Nucleotide excision repair (NER). Finally, we employ a single-molecule imaging approach (known as DNA fiber-assay) to determine how Pol h influences the progression of the replication fork. Our data reveals that the re-localization of Pol η to DNA lesions might be temporally and mechanistically uncoupled from replicative DNA synthesis and from DNA damage processing. (authors)

  16. Cooperation of terminal deoxynucleotidyl transferase with DNA polymerase α in the replication of ultraviolet-irradiated DNA

    International Nuclear Information System (INIS)

    Yoshida, S.; Masaki, S.; Nakamura, H.; Morita, T.

    1981-01-01

    The amount of DNA synthesis in vitro with the ultraviolet-irradiated poly(dT).oligo(rA) template initiators catalysed by DNA polymerase α (Masaki, S. and Yoshida, S., Biochim. Biophys. Acta 521, 74-88) decreased with the dose of ultraviolet-irradiation. The ultraviolet irradiation to the template, however, did not affect the rate of incorporation of incorrect deoxynucleotides into the newly synthesized poly(dA). The addition of terminal deoxynucleotidyl transferase to this system enhanced the DNA synthesis to a level which is comparable to that of the control and it concomitantly increased the incorporation of the mismatched deoxynucleotide into the newly synthesized poly(dA) strands. On the other hand, with an unirradiated template initiator, the misincorporation was only slightly enhanced by the addition of terminal deoxynucleotidyl transferase. The sizes of newly synthesized DNA measured by the sedimentation velocities were found to be smaller with the ultraviolet-irradiated templates but they increased to the control level with the addition of terminal deoxynucleotidyl transferase to the systems. These results suggest that terminal deoxynucleotidyl transferase can help DNA polymerase α to bypass thymine dimers in vitro by the formation of mismatched regions at the positions opposite to pyrimidine dimers on the template. (Auth.)

  17. Rural health care bypass behavior: how community and spatial characteristics affect primary health care selection.

    Science.gov (United States)

    Sanders, Scott R; Erickson, Lance D; Call, Vaughn R A; McKnight, Matthew L; Hedges, Dawson W

    2015-01-01

    (1) To assess the prevalence of rural primary care physician (PCP) bypass, a behavior in which residents travel farther than necessary to obtain health care, (2) To examine the role of community and non-health-care-related characteristics on bypass behavior, and (3) To analyze spatial bypass patterns to determine which rural communities are most affected by bypass. Data came from the Montana Health Matters survey, which gathered self-reported information from Montana residents on their health care utilization, satisfaction with health care services, and community and demographic characteristics. Logistic regression and spatial analysis were used to examine the probability and spatial patterns of bypass. Overall, 39% of respondents bypass local health care. Similar to previous studies, dissatisfaction with local health care was found to increase the likelihood of bypass. Dissatisfaction with local shopping also increases the likelihood of bypass, while the number of friends in a community, and commonality with community reduce the likelihood of bypass. Other significant factors associated with bypass include age, income, health, and living in a highly rural community or one with high commuting flows. Our results suggest that outshopping theory, in which patients bundle services and shopping for added convenience, extends to primary health care selection. This implies that rural health care selection is multifaceted, and that in addition to perceived satisfaction with local health care, the quality of local shopping and levels of community attachment also influence bypass behavior. © 2014 National Rural Health Association.

  18. Discovery of cyanophage genomes which contain mitochondrial DNA polymerase.

    Science.gov (United States)

    Chan, Yi-Wah; Mohr, Remus; Millard, Andrew D; Holmes, Antony B; Larkum, Anthony W; Whitworth, Anna L; Mann, Nicholas H; Scanlan, David J; Hess, Wolfgang R; Clokie, Martha R J

    2011-08-01

    DNA polymerase γ is a family A DNA polymerase responsible for the replication of mitochondrial DNA in eukaryotes. The origins of DNA polymerase γ have remained elusive because it is not present in any known bacterium, though it has been hypothesized that mitochondria may have inherited the enzyme by phage-mediated nonorthologous displacement. Here, we present an analysis of two full-length homologues of this gene, which were found in the genomes of two bacteriophages, which infect the chlorophyll-d containing cyanobacterium Acaryochloris marina. Phylogenetic analyses of these phage DNA polymerase γ proteins show that they branch deeply within the DNA polymerase γ clade and therefore share a common origin with their eukaryotic homologues. We also found homologues of these phage polymerases in the environmental Community Cyberinfrastructure for Advanced Microbial Ecology Research and Analysis (CAMERA) database, which fell in the same clade. An analysis of the CAMERA assemblies containing the environmental homologues together with the filter fraction metadata indicated some of these assemblies may be of bacterial origin. We also show that the phage-encoded DNA polymerase γ is highly transcribed as the phage genomes are replicated. These findings provide data that may assist in reconstructing the evolution of mitochondria.

  19. EARLY POSTOPERATIVE COMPLICATIONS IN ROUX-EN-Y GASTRIC BYPASS.

    Science.gov (United States)

    Stoll, Aluisio; Rosin, Leandro; Dias, Mariana Fernandes; Marquiotti, Bruna; Gugelmin, Giovana; Stoll, Gabriela Fanezzi

    Roux-en-Y gastric bypass is one of the most common bariatric surgery and leads to considerable weight loss in the first months. To quantify the main early postoperative complications in patients submitted to the gastric bypass. Observational retrospective cohort. Data of 1051 patients with class II obesity associated with comorbidities or class III obesity submitted to the gastric bypass with 30 days of follow-up starting from the date of the surgery. The age average was 36 years with a predominance of females (81.1%). The mean preoperative body mass index was 43 kg/m². The major complication was fistula (2.3%), followed by intestinal obstruction (0.5%) and pulmonary embolism (0.5%). Death occurred in 0.6% of the cases. In the period of 30 days after surgery the overall complication rate was 3.8%; reoperation was necessary in 2.6% and death occurred in 0.6%. Fistula was the main complication and the leading cause of hospitalization in intensive care unit, reoperation and death. Bypass gástrico em Y-de-Roux é uma das operações bariátricas mais comuns e leva a perdas consideráveis de peso já nos primeiros meses. Quantificar as principais complicações pós-operatórias precoces em pacientes submetidos ao bypass gástrico. Coorte retrospectiva observacional. Amostra de 1051 pacientes portadores de obesidade grau II associada à comorbidades ou grau III submetidos ao bypass gástrico com acompanhamento de 30 dias a partir da data da operação. A idade média dos pacientes foi de 36 anos com predominância de mulheres (81,1%). O índice de massa corporal pré-operatório médio foi de 43 kg/m². A principal complicação foi fístula (2,3%), seguida de obstrução intestinal (0,5%) e tromboembolismo pulmonar (0,5%). Óbito ocorreu em 0,6% dos casos. No período de 30 dias de pós-operatório a taxa geral de complicações foi de 3,8%; a de reoperação de 2,6% e óbito em 0,6%. A fístula foi a principal complicação e a principal causa de internamento em

  20. DNA Polymerases ImuC and DinB Are Involved in DNA Alkylation Damage Tolerance in Pseudomonas aeruginosa and Pseudomonas putida.

    Science.gov (United States)

    Jatsenko, Tatjana; Sidorenko, Julia; Saumaa, Signe; Kivisaar, Maia

    2017-01-01

    Translesion DNA synthesis (TLS), facilitated by low-fidelity polymerases, is an important DNA damage tolerance mechanism. Here, we investigated the role and biological function of TLS polymerase ImuC (former DnaE2), generally present in bacteria lacking DNA polymerase V, and TLS polymerase DinB in response to DNA alkylation damage in Pseudomonas aeruginosa and P. putida. We found that TLS DNA polymerases ImuC and DinB ensured a protective role against N- and O-methylation induced by N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) in both P. aeruginosa and P. putida. DinB also appeared to be important for the survival of P. aeruginosa and rapidly growing P. putida cells in the presence of methyl methanesulfonate (MMS). The role of ImuC in protection against MMS-induced damage was uncovered under DinB-deficient conditions. Apart from this, both ImuC and DinB were critical for the survival of bacteria with impaired base excision repair (BER) functions upon alkylation damage, lacking DNA glycosylases AlkA and/or Tag. Here, the increased sensitivity of imuCdinB double deficient strains in comparison to single mutants suggested that the specificity of alkylated DNA lesion bypass of DinB and ImuC might also be different. Moreover, our results demonstrated that mutagenesis induced by MMS in pseudomonads was largely ImuC-dependent. Unexpectedly, we discovered that the growth temperature of bacteria affected the efficiency of DinB and ImuC in ensuring cell survival upon alkylation damage. Taken together, the results of our study disclosed the involvement of ImuC in DNA alkylation damage tolerance, especially at low temperatures, and its possible contribution to the adaptation of pseudomonads upon DNA alkylation damage via increased mutagenesis.

  1. Translesion DNA polymerases Pol ζ, Pol η, Pol ι, Pol κ and Rev1 are ...

    Indian Academy of Sciences (India)

    MADU

    Specialized DNA polymerases called translesion polymerases are among the major determinants of spontaneous and DNA damage-induced mutation in both prokaryotes and eukaryotes. (Livneh 2001). The classical replicative DNA polymerases can synthesize DNA with remarkable efficiency and fidelity.

  2. Management of broken instrument by file bypass technique

    Directory of Open Access Journals (Sweden)

    Sultana Parveen

    2017-02-01

    Full Text Available Different devices and techniques have been developed to retrieve fractured instruments during the endodontic procedures. This case report describes the management of a broken instrument, which was accidentally broken during cleaning and shaping of the root canal in right 2nd molar tooth. A # 25 stainless steel K-file was separated in mesiobuccal canal of the treated tooth. At first, a radiograph was taken to confirm the level of separation of the instrument. The instrument was found to be separated at the apical 3rd of the mesial canal and then file bypass technique was performed. Calcium hydroxide dressing was given for 7 days followed by obturation with guttapercha cone and zinc oxide eugenol sealer in lateral condensation technique. It can be concluded that bypass technique can be considered as simple and effective technique for the management of broken instrument into the root canal.

  3. Decrease of total antioxidant capacity during coronary artery bypass surgery.

    Science.gov (United States)

    Kunt, Alper Sami; Selek, Sahbettin; Celik, Hakim; Demir, Deniz; Erel, Ozcan; Andac, Mehmet Halit

    2006-09-01

    Cardiac surgery induces an oxidative stress, which may lead to impairment of cardiac function. In this study, we aimed to measure the changes of oxidative and antioxidative status of patients undergoing coronary artery bypass surgery (CABG). We studied 79 patients who underwent CABG with and without cardiopulmonary bypass (CPB). Of the 79 patients, 39 had CPB and 40 did not. Blood samples were drawn before, during, and after the surgery. Antioxidant status was evaluated by measuring total antioxidant capacity (TAC), and oxidative status was evaluated by measuring total peroxide (TP) levels and oxidative stress index (OSI). TP and OSI levels increased, while TAC decreased progressively after the beginning of surgery, for all patients. There were negative correlations between TAC levels and aortic cross-clamping period and anastomosis time ( r = -0.553, p antioxidant vitamins such as vitamins C and E may be beneficial for patients undergoing CABG.

  4. Aorto-aortic intrathoracic bypass in surgical treatment of aortic

    International Nuclear Information System (INIS)

    Gutierrez Perez, F.; Duran Reyes, A.; Bigalli, D.; Filgueira Berobide, J.

    1998-01-01

    The prevalence of coarctation of the aorta is 6.5 percent of all congenital heart defects, according to national and international data. There is a restenosis rate of patients after surgery. Factors that influence this evolution depends on the age at which patients underwent surgery for the first time the anatomy of the aortic arch and type of surgical technique. Several procedures can be used to correct the coarctation, which include surgery and balloon catheter dilation. We present here a case of a patient of 22 years old, with a recurrent coarctation of the aorta studied by echocardiography and magnetic resonance imaging. The patient underwent surgery a third time. We used an anterior approach (median sternotomy) and performed an aortic bypass graft, intrathoracic, under cardiopulmonary bypass. Evolved favorably and was discharged on the sixth day of post operative day (Author) [es

  5. Pharmacological Bypass of Cockayne Syndrome B Function in Neuronal Differentiation

    Directory of Open Access Journals (Sweden)

    Yuming Wang

    2016-03-01

    Full Text Available Cockayne syndrome (CS is a severe neurodevelopmental disorder characterized by growth abnormalities, premature aging, and photosensitivity. Mutation of Cockayne syndrome B (CSB affects neuronal gene expression and differentiation, so we attempted to bypass its function by expressing downstream target genes. Intriguingly, ectopic expression of Synaptotagmin 9 (SYT9, a key component of the machinery controlling neurotrophin release, bypasses the need for CSB in neuritogenesis. Importantly, brain-derived neurotrophic factor (BDNF, a neurotrophin implicated in neuronal differentiation and synaptic modulation, and pharmacological mimics such as 7,8-dihydroxyflavone and amitriptyline can compensate for CSB deficiency in cell models of neuronal differentiation as well. SYT9 and BDNF are downregulated in CS patient brain tissue, further indicating that sub-optimal neurotrophin signaling underlies neurological defects in CS. In addition to shedding light on cellular mechanisms underlying CS and pointing to future avenues for pharmacological intervention, these data suggest an important role for SYT9 in neuronal differentiation.

  6. Distinctive striatal dopamine signaling after dieting and gastric bypass.

    Science.gov (United States)

    Hankir, Mohammed K; Ashrafian, Hutan; Hesse, Swen; Horstmann, Annette; Fenske, Wiebke K

    2015-05-01

    Highly palatable and/or calorically dense foods, such as those rich in fat, engage the striatum to govern and set complex behaviors. Striatal dopamine signaling has been implicated in hedonic feeding and the development of obesity. Dieting and bariatric surgery have markedly different outcomes on weight loss, yet how these interventions affect central homeostatic and food reward processing remains poorly understood. Here, we propose that dieting and gastric bypass produce distinct changes in peripheral factors with known roles in regulating energy homeostasis, resulting in differential modulation of nigrostriatal and mesolimbic dopaminergic reward circuits. Enhancement of intestinal fat metabolism after gastric bypass may also modify striatal dopamine signaling contributing to its unique long-term effects on feeding behavior and body weight in obese individuals. Copyright © 2015 Elsevier Ltd. All rights reserved.

  7. In situ saphenous vein bypass surgery in diabetic patients

    DEFF Research Database (Denmark)

    Jensen, L P; Schroeder, T V; Lorentzen, J E

    1992-01-01

    .005). Indication for surgery was gangrene or ulceration in 57% of diabetics, as opposed to 36% in non-diabetic patients (p = 0.0002). A femoro-popliteal bypass was performed in 18% of patients, whereas 82% received an infrapopliteal procedure, of which 42% were to the distal third of the calf or foot. Diabetic......From 1986 through to 1990 a total of 483 consecutive in situ infra-inguinal vein bypass procedures were performed in 444 patients, of whom 112 (25%) were diabetics (57 insulin dependent diabetes mellitus and 55 non-insulin-dependent diabetes mellitus). Based on a prospective vascular data registry...... this material was analysed to determine the influence of diabetes on the outcome. Preoperative risk factors were equally distributed among diabetic and non-diabetic patients, except for smoking habits (diabetics: 48%; non-diabetics: 64%, p = 0.002) and cardiac disease (diabetics: 45%; non-diabetics: 29%, p = 0...

  8. Reverse transcriptase-quantitative polymerase chain reaction (RT ...

    African Journals Online (AJOL)

    zino

    2014-02-05

    Feb 5, 2014 ... ecological studies - A review ... The objective of this review is to assess the importance of RT-qPCR in soil related ... phenol extraction step with heat inactivation of the added .... Real time polymerase chain reaction (PCR).

  9. The application of polymerase chain reaction-denaturing gradient ...

    African Journals Online (AJOL)

    Jane

    2011-05-23

    May 23, 2011 ... dominance in microbial ecology if the corresponding environment samples had been provided. This ... yeast peptone dextrose; PCR, polymerase chain reaction. method, DGGE method ..... Two nuclear mutations that block.

  10. Hepatitis B virus DNA polymerase gene polymorphism based ...

    African Journals Online (AJOL)

    Hepatitis B virus DNA polymerase gene polymorphism based prediction of genotypes in chronic HBV patients from Western India. Yashwant G. Chavan, Sharad R. Pawar, Minal Wani, Amol D. Raut, Rabindra N. Misra ...

  11. Study of bypass diodes configuration on PV modules

    Energy Technology Data Exchange (ETDEWEB)

    Silvestre, S.; Boronat, A.; Chouder, A. [Electronics Engineering Department - UPC., C/Jordi Girona 1-3, Modul C4 Campus Nord UPC., 08034 Barcelona (Spain)

    2009-09-15

    A procedure of simulation and modelling solar cells and PV modules, working partially shadowed in Pspice environment, is presented. Simulation results have been contrasted with real measured data from a commercial PV module of 209 Wp from Siliken. Some cases of study are presented as application examples of this simulation methodology, showing its potential on the design of bypass diodes configuration to include in a PV module and also on the study of PV generators working in partial shading conditions. (author)

  12. Microsurgical Bypass Training Rat Model: Part 2-Anastomosis Configurations.

    Science.gov (United States)

    Tayebi Meybodi, Ali; Lawton, Michael T; Yousef, Sonia; Mokhtari, Pooneh; Gandhi, Sirin; Benet, Arnau

    2017-11-01

    Mastery of microsurgical anastomosis is key to achieving good outcomes in cerebrovascular bypass procedures. Animal models (especially rodents) provide an optimal preclinical bypass training platform. However, the existing models for practicing different anastomosis configurations have several limitations. We sought to optimize the use of the rat's abdominal aorta and common iliac arteries (CIA) for practicing the 3 main anastomosis configurations commonly used in cerebrovascular surgery. Thirteen male Sprague-Dawley rats underwent inhalant anesthesia. The abdominal aorta and the CIAs were exposed. The distances between the major branches of the aorta were measured to find the optimal location for an end-to-end anastomosis. Also, the feasibility of performing side-to-side and end-to-side anastomoses between the CIAs was assessed. All bypass configurations could be performed between the left renal artery and the CIA bifurcation. The longest segments of the aorta without major branches were 1) between the left renal and left iliolumbar arteries (16.9 mm ± 4.6), and 2) between the right iliolumbar artery and the aortic bifurcation (9.7 mm ± 4.7). The CIAs could be juxtaposed for an average length of 7.6 mm ± 1.3, for a side-to-side anastomosis. The left CIA could be successfully reimplanted on to the right CIA at an average distance of 9.1 mm ± 1.6 from the aortic bifurcation. Our results show that rat's abdominal aorta and CIAs may be effectively used for all the anastomosis configurations used in cerebral revascularization procedures. We also provide technical nuances and anatomic descriptions to plan for practicing each bypass configuration. Copyright © 2017 Elsevier Inc. All rights reserved.

  13. Constitutive modeling of coronary artery bypass graft with incorporated torsion

    Czech Academy of Sciences Publication Activity Database

    Horný, L.; Chlup, Hynek; Žitný, R.; Adámek, T.

    2009-01-01

    Roč. 49, č. 2 (2009), s. 273-277 ISSN 0543-5846 R&D Projects: GA ČR(CZ) GA106/08/0557 Institutional research plan: CEZ:AV0Z20760514 Keywords : coronary artery bypass graft * constitutive model * digital image correlation Subject RIV: BJ - Thermodynamics Impact factor: 0.439, year: 2009 http://web.tuke.sk/sjf-kamam/mmams2009/contents.pdf

  14. Disseminated intravascular and intracardiac thrombosis after cardiopulmonary bypass

    Directory of Open Access Journals (Sweden)

    Deepak K Tempe

    2017-01-01

    Full Text Available Massive intracardiac and intravascular thrombosis is a rare complication following cardiopulmonary bypass (CPB. Most of the cases of the disseminated thrombosis have been reported in patients undergoing complex cardiac surgeries and those receiving antifibrinolytic agents during CPB. We report the occurrence of disseminated intravascular and intracardiac thrombosis after CPB in a patient undergoing mitral valve replacement in which no antifibrinolytic agent was used. The possible pathophysiology and management of the patient is discussed.

  15. Evaluation of coronary artery bypass grafts with magnetic resonance imaging

    International Nuclear Information System (INIS)

    Okamura, Yoshitaka; Yamada, Yasuyuki; Mochizuki, Yoshihiko; Iida, Hiroshi; Mori, Hideaki; Sugita, You-ichi; Shimada, Kou-ichirou

    1997-01-01

    Currently, the efficacy of magnetic resonance imaging (MRI) for evaluating coronary artery disease has been reported. In this study, we have evaluated the usefulness and the problems of MRI for evaluating the patency of coronary artery bypass grafts. Thirty-five patients who received coronary artery bypass grafting (CABG) were evaluated by using MRI for determining the graft patency compared with conventional coronary angiography. There were 30 men and 5 women. The mean age was 61.2 years (range 45 to 75). The 35 patients had a total of 92 grafts (28 internal thoracic artery, 7 gastroepiploic artery and 57 saphenous vein grafts). Magnetic resonance coronary angiogram (MRCA) was performed with SIGNA HORIZON 1.5 T (GE Inc.) by using 2D-FASTCARD sequence. All patients underwent imaging in the transverse and coronal planes, most had imaging in the sagittal plane, and a few had in the oblique plane. By using MRCA, 82 of 90 grafts were diagnosed correctly as patent, and 1 of 2 grafts were diagnosed correctly as occluded. Thirty-four of 40 LAD grafts (85%), 20 of 22 RCA grafts (91%) and 29 of 30 Cx grafts (97%) were correctly evaluated. The efficacy of MRCA for evaluating the patency of coronary artery bypass grafts was recognized. But the sternal wire (stainless steel) and hemoclip interfere with the interpretation and reduce the sensitivity. Higher sensitivity may be obtained by changing the material of the sternal wires and hemoclips at coronary surgery. (author)

  16. Augmented reality-assisted bypass surgery: embracing minimal invasiveness.

    Science.gov (United States)

    Cabrilo, Ivan; Schaller, Karl; Bijlenga, Philippe

    2015-04-01

    The overlay of virtual images on the surgical field, defined as augmented reality, has been used for image guidance during various neurosurgical procedures. Although this technology could conceivably address certain inherent problems of extracranial-to-intracranial bypass procedures, this potential has not been explored to date. We evaluate the usefulness of an augmented reality-based setup, which could help in harvesting donor vessels through their precise localization in real-time, in performing tailored craniotomies, and in identifying preoperatively selected recipient vessels for the purpose of anastomosis. Our method was applied to 3 patients with Moya-Moya disease who underwent superficial temporal artery-to-middle cerebral artery anastomoses and 1 patient who underwent an occipital artery-to-posteroinferior cerebellar artery bypass because of a dissecting aneurysm of the vertebral artery. Patients' heads, skulls, and extracranial and intracranial vessels were segmented preoperatively from 3-dimensional image data sets (3-dimensional digital subtraction angiography, angio-magnetic resonance imaging, angio-computed tomography), and injected intraoperatively into the operating microscope's eyepiece for image guidance. In each case, the described setup helped in precisely localizing donor and recipient vessels and in tailoring craniotomies to the injected images. The presented system based on augmented reality can optimize the workflow of extracranial-to-intracranial bypass procedures by providing essential anatomical information, entirely integrated to the surgical field, and help to perform minimally invasive procedures. Copyright © 2015 Elsevier Inc. All rights reserved.

  17. Modulation method of scroll compressor based on suction gas bypass

    International Nuclear Information System (INIS)

    Wang Baolong; Han Linjun; Shi Wenxing; Li Xianting

    2012-01-01

    The air conditioners and heat pumps tend to work in much mild environments and part load situations rather than provide the rated full capacity under severe rated testing conditions. Both the capacity and inner compression ratio of the compressor should be regulated according to the working condition for higher energy efficiency and occupants’ comfort. A potential modulating technology of the scroll compressor, suction gas bypass, is investigated in this paper. The principle and operation method are illuminated and the adaptability is validated by experiments and simulations. As a conclusion, an appropriate suction gas bypass can reduce the inner compression loss of the scroll compressor under over compression conditions, enhance the system COP and also largely decrease the heating/cooling capacity of the refrigeration/heat pump system. - Highlights: ► Suction gas bypass (SGB) is an effective regulating method of scroll compressor. ► SGB reduces the inner compression loss under over compression conditions. ► SGB largely decreases the heating/cooling capacity of the refrigeration system.

  18. Carotid disease in diabetic patients undergoing coronary artery bypass grafting

    International Nuclear Information System (INIS)

    Shahid, M.; Abid, A.R.; Dar, M.A.; Noeman, A.; Amin, S.; Azhar, M.

    2012-01-01

    Objective: To compare the severity of carotid artery disease in diabetic and non-diabetic patients undergoing coronary artery bypass grafting. Methods: From January to June 2008, 379 patients undergoing elective coronary artery bypass surgery were preoperatively evaluated for the presence of carotid stenoses by duplex scanning. Patients were divided into two groups, Group I, 156 (41.2%) diabetic patients and Group II, 223 (58.8%) non-diabetic patients. Results: There were 314 (82.8%) males and 65 (17.2%) females with a mean age of 57.2+-9.1 years. In diabetic group there were 125 (80.1%) males and 31 (19.9%) females with a mean age of 56.3+-8.9 years. Left main stem stenosis was present in 59 (37.8%) diabetics and 45 (20.2%) non-diabetics (p 70% stenosis was present in 20 (5.3%) with 13 (8.3%) diabetics and 7 (3.1%) non-diabetics (p<0.025). Stenosis of 50-70% was observed in 30 (7.9%) of which 17 (10.9%) were diabetics and 13 (5.8%) were non-diabetics. Conclusion: Presence of diabetes mellitus is associated with diffuse coronary artery disease and significant carotid artery disease in patients undergoing coronary artery bypass grafting. (author)

  19. Ruptured peroneal aneurysm after infrapopliteal prosthetic bypass with Taylor patch

    Directory of Open Access Journals (Sweden)

    Florian Enzmann

    Full Text Available Introduction: A 45-year-old mailman underwent an implantation of a femoro-peroneal polytetrafluoroethylene (PTFE bypass with a distal Taylor patch six years prior to admission after two failed autologous reconstructions and extensive fasciotomy. The initial pathology was an acute ischemia due to popliteal entrapment with subsequent popliteal thrombectomy. Report: The patient was examined because of pain, reduction of walking distance and development of a palpable mass at the medial fasciotomy site. A 6-cm pseudoaneurysm with complete disruption of the suture line of the vein patch was discovered and resected. Arterial continuity with a vein interposition graft was established using non-reversed cephalic vein. Conclusion: The etiology of the aneurysm is not entirely clear. One may argue that the fourth revascularization could have been performed with an arm vein instead of a prosthetic graft with the probability of a better long term patency in a young patient. 15 months after the procedure the bypass is patent and the patient is without any symptoms. This complication of a Taylor patch has not been reported before. Keywords: Taylor patch, Pseudoaneurysm, Infrapopliteal bypass

  20. Simultaneous nephrectomy and coronary artery bypass grafting through extended sternotomy

    Directory of Open Access Journals (Sweden)

    Budrikis Algimantas

    2012-08-01

    Full Text Available Abstract Background The advances in surgical techniques, resuscitation and anesthesiology support over the last years have allowed simultaneous thoracic and abdominal operations to be made for cancer and concomitant severe heart vessel disease relieving the patient from several diseases simultaneously and achieving long lasting remission or cure. Clinical case A simultaneous nephrectomy and coronary artery bypass grafting procedure through extended sternotomy is reported. A 63-year-old man with severe coronary artery disease was found to have renal carcinoma. Diagnosis Postoperative pathological investigation of the tumor revealed the presence of renal cell carcinoma pT3a N0 M0, G2. Coronarography revealed advanced three-vessel coronary artery disease. Treatment We successfully performed a simultaneous curative surgery for renal carcinoma and coronary artery bypass graft surgery under cardiopulmonary bypass using a novel technique of extended sternotomy. Simultaneous surgery thus appears to be a beneficial and safe approach for the treatment of coronary artery disease and resectable renal cancer in carefully selected patients.

  1. Flow Simulation of Supersonic Inlet with Bypass Annular Duct

    Science.gov (United States)

    Kim, HyoungJin; Kumano, Takayasu; Liou, Meng-Sing; Povinelli, Louis A.; Conners, Timothy R.

    2011-01-01

    A relaxed isentropic compression supersonic inlet is a new concept that produces smaller cowl drag than a conventional inlet, but incurs lower total pressure recovery and increased flow distortion in the (radially) outer flowpath. A supersonic inlet comprising a bypass annulus to the relaxed isentropic compression inlet dumps out airflow of low quality through the bypass duct. A reliable computational fluid dynamics solution can provide considerable useful information to ascertain quantitatively relative merits of the concept, and further provide a basis for optimizing the design. For a fast and reliable performance evaluation of the inlet performance, an equivalent axisymmetric model whose area changes accounts for geometric and physical (blockage) effects resulting from the original complex three-dimensional configuration is proposed. In addition, full three-dimensional calculations are conducted for studying flow phenomena and verifying the validity of the equivalent model. The inlet-engine coupling is carried out by embedding numerical propulsion system simulation engine data into the flow solver for interactive boundary conditions at the engine fan face and exhaust plane. It was found that the blockage resulting from complex three-dimensional geometries in the bypass duct causes significant degradation of inlet performance by pushing the terminal normal shock upstream.

  2. Breast cancer biomarkers predict weight loss after gastric bypass surgery

    Directory of Open Access Journals (Sweden)

    Sauter Edward R

    2012-01-01

    Full Text Available Abstract Background Obesity has long been associated with postmenopausal breast cancer risk and more recently with premenopausal breast cancer risk. We previously observed that nipple aspirate fluid (n levels of prostate specific antigen (PSA were associated with obesity. Serum (s levels of adiponectin are lower in women with higher body mass index (BMI and with breast cancer. We conducted a prospective study of obese women who underwent gastric bypass surgery to determine: 1 change in n- and s-adiponectin and nPSA after surgery and 2 if biomarker change is related to change in BMI. Samples (30-s, 28-n and BMI were obtained from women 0, 3, 6 and 12 months after surgery. Findings There was a significant increase after surgery in pre- but not postmenopausal women at all time points in s-adiponectin and at 3 and 6 months in n-adiponectin. Low n-PSA and high s-adiponectin values were highly correlated with decrease in BMI from baseline. Conclusions Adiponectin increases locally in the breast and systemically in premenopausal women after gastric bypass. s-adiponectin in pre- and nPSA in postmenopausal women correlated with greater weight loss. This study provides preliminary evidence for biologic markers to predict weight loss after gastric bypass surgery.

  3. Ubiquitylation and degradation of elongating RNA polymerase II

    DEFF Research Database (Denmark)

    Wilson, Marcus D; Harreman, Michelle; Svejstrup, Jesper Q

    2013-01-01

    During its journey across a gene, RNA polymerase II has to contend with a number of obstacles to its progression, including nucleosomes, DNA-binding proteins, DNA damage, and sequences that are intrinsically difficult to transcribe. Not surprisingly, a large number of elongation factors have....... In this review, we describe the mechanisms and factors responsible for the last resort mechanism of transcriptional elongation. This article is part of a Special Issue entitled: RNA polymerase II Transcript Elongation....

  4. Assessing Patient bypass Behavior Using Taxi Trip Origin–Destination (OD Data

    Directory of Open Access Journals (Sweden)

    Gege Yang

    2016-09-01

    Full Text Available Many patients prefer to use the best hospitals even if there are one or more other hospitals closer to their homes; this behavior is called “hospital bypass behavior”. Because this behavior can be problematic in urban areas, it is important that it be reduced. In this paper, the taxi GPS data of Beijing and Suzhou were used to measure hospital bypass behavior. The “bypass behavior index” (BBI represents the bypass behavior for each hospital. The results indicated that the mean hospital bypass trip distance value ranges from 5.988 km to 9.754 km in Beijing and from 4.168 km to 10.283 km in Suzhou. In general, the bypass shares of both areas show a gradually increasing trend. The following hospitals exhibited significant patient bypass behavior: the 301 Hospital, Beijing Children’s Hospital, the Second Affiliated Hospital of Soochow University and the Suzhou Hospital of Traditional Chinese Medicine. The hospitals’ reputation, transport accessibility and spatial distribution were found to be the main factors affecting patient bypass behavior. Although the hospital bypass phenomena generally appeared to be more pronounced in Beijing, the bypass trip distances between hospitals were found to be more significant in Suzhou.

  5. Enhancement of DNA polymerase activity in potato tuber slices

    International Nuclear Information System (INIS)

    Watanabe, Akira; Imaseki, Hidemasa

    1977-01-01

    DNA polymerase was extracted from potato (Soleum tuberosum L.) tuber discs and the temporal correlation of its activity change to DNA synthesis in vivo was examined during aging of the discs. Most of the DNA polymerase was recovered as a bound form in the 18,000 x g precipitate. Reaction with the bound-form enzyme was dependent on the presence of four deoxynucleoside triphosphates, Mg 2+ , and a template. ''Activated'' DNA and heat-denatured DNA, but not native DNA, were utilized as templates. The polymerase activity was sensitive to SH reagents. Fresh discs, which do not synthesize DNA in vivo, contained a significant amount of DNA polymerase and its activity increased linearly with time until 48 hr after slicing and became four times that of fresh discs after 72 hr, whereas the activity of DNA synthesis in vivo increased with time and decreased after reaching a maximum at 30 hr. Cycloheximide inhibited the enhancement of polymerase activity. DNA polymerase from aged and fresh discs had identical requirements for deoxynucleotides and a template in their reactions, sensitivity to SH reagent, and affinity to thymidine triphosphate. (auth.)

  6. Graft type for femoro-popliteal bypass surgery.

    Science.gov (United States)

    Ambler, Graeme K; Twine, Christopher P

    2018-02-11

    Femoro-popliteal bypass is implemented to save limbs that might otherwise require amputation, in patients with ischaemic rest pain or tissue loss; and to improve walking distance in patients with severe life-limiting claudication. Contemporary practice involves grafts using autologous vein, polytetrafluoroethylene (PTFE) or Dacron as a bypass conduit. This is the second update of a Cochrane review first published in 1999 and last updated in 2010. To assess the effects of bypass graft type in the treatment of stenosis or occlusion of the femoro-popliteal arterial segment, for above- and below-knee femoro-popliteal bypass grafts. For this update, the Cochrane Vascular Information Specialist searched the Vascular Specialised Register (13 March 2017) and CENTRAL (2017, Issue 2). Trial registries were also searched. We included randomised trials comparing at least two different types of femoro-popliteal grafts for arterial reconstruction in patients with femoro-popliteal ischaemia. Randomised controlled trials comparing bypass grafting to angioplasty or to other interventions were not included. Both review authors (GKA and CPT) independently screened studies, extracted data, assessed trials for risk of bias and graded the quality of the evidence using GRADE criteria. We included nineteen randomised controlled trials, with a total of 3123 patients (2547 above-knee, 576 below-knee bypass surgery). In total, nine graft types were compared (autologous vein, polytetrafluoroethylene (PTFE) with and without vein cuff, human umbilical vein (HUV), polyurethane (PUR), Dacron and heparin bonded Dacron (HBD); FUSION BIOLINE and Dacron with external support). Studies differed in which graft types they compared and follow-up ranged from six months to 10 years.Above-knee bypassFor above-knee bypass, there was moderate-quality evidence that autologous vein grafts improve primary patency compared to prosthetic grafts by 60 months (Peto odds ratio (OR) 0.47, 95% confidence interval (CI

  7. PCR fidelity of pfu DNA polymerase and other thermostable DNA polymerases.

    OpenAIRE

    Cline, J; Braman, J C; Hogrefe, H H

    1996-01-01

    The replication fidelities of Pfu, Taq, Vent, Deep Vent and UlTma DNA polymerases were compared using a PCR-based forward mutation assay. Average error rates (mutation frequency/bp/duplication) increased as follows: Pfu (1.3 x 10(-6)) < Deep Vent (2.7 x 10(-6)) < Vent (2.8 x 10(-6)) < Taq (8.0 x 10(-6)) < < exo- Pfu and UlTma (approximately 5 x 10(-5)). Buffer optimization experiments indicated that Pfu fidelity was highest in the presence of 2-3 mM MgSO4 and 100-300 microM each dNTP and at p...

  8. Changes in Global Transcriptional Profiling of Women Following Obesity Surgery Bypass.

    Science.gov (United States)

    Pinhel, Marcela Augusta de Souza; Noronha, Natalia Yumi; Nicoletti, Carolina Ferreira; de Oliveira, Bruno Affonso Parente; Cortes-Oliveira, Cristiana; Pinhanelli, Vitor Caressato; Salgado Junior, Wilson; Machry, Ana Julia; da Silva Junior, Wilson Araújo; Souza, Dorotéia Rossi Silva; Marchini, Júlio Sérgio; Nonino, Carla Barbosa

    2018-01-01

    Differential gene expression in peripheral blood mononuclear cells (PBMCs) after Roux-en-Y gastric bypass (RYGB) is poorly characterized. Markers of these processes may provide a deeper understanding of the mechanisms that underlie these events. The main goal of this study was to identify changes in PBMC gene expression in women with obesity before and 6 months after RYGB-induced weight loss. The ribonucleic acid (RNA) of PBMCs from 13 obese women was analyzed before and 6 months after RYGB; the RNA of PBMCs from nine healthy women served as control. The gene expression levels were determined by microarray analysis. Significant differences in gene expression were validated by real-time quantitative polymerase chain reaction (RT-qPCR). Microarray analysis for comparison of the pre- and postoperative periods showed that 1366 genes were differentially expressed genes (DEGs). The main pathways were related to gene transcription; lipid, energy, and glycide metabolism; inflammatory and immunological response; cell differentiation; oxidative stress regulation; response to endogenous and exogenous stimuli; substrate oxidation; mTOR signaling pathway; interferon signaling; mitogen-activated protein kinases (MAPK), cAMP response element binding protein (CREB1), heat shock factor 1 (HSF1), and sterol regulatory element binding protein 1c (SREBP-1c) gene expression; adipocyte differentiation; and methylation. Six months after bariatric surgery and significant weight loss, many molecular pathways involved in obesity and metabolic diseases change. These findings are an important tool to identify potential targets for therapeutic intervention and clinical practice of nutritional genomics in obesity.

  9. Passage of downstream migrant American eels through an airlift-assisted deep bypass

    Science.gov (United States)

    Haro, Alexander J.; Watten, Barnaby J.; Noreika, John

    2016-01-01

    Traditional downstream guidance and bypass facilities for anadromous fishes (i.e., surface bypasses, surface guidance structures, and behavioral barriers) have frequently been ineffective for anguillid eels. Because eels typically spend the majority of their time near the bottom in the vicinity of intake structures, deep bypass structures with entrances near the bottom hold promise for increased effectiveness, thereby aiding in the recovery of this important species. A new design of a deep bypass system that uses airlift technology (the Conte Airlift Bypass) to induce flow in a bypass pipe was tested in a simulated intake entrance environment under controlled laboratory conditions. Water velocities of 0.9–1.5 m s−1 could be generated at the bypass entrance (opening with 0.073 m2 area), with corresponding flows through the bypass pipe of 0.07–0.11 m3 s−1. Gas saturation and hydrostatic pressure within the bypass pipe did not vary appreciably from a control (no air) condition under tested airflows. Migratory silver-phase American eels (Anguilla rostrata) tested during dark conditions readily located, entered, and passed through the bypass; initial avoidance rates (eels approaching but not entering the bypass entrance) were lower at higher entrance velocities. Eels that investigated the bypass pipe entrance tended to enter headfirst, but those that then exited the pipe upstream did so more frequently at lower entrance velocities. Eels appeared to swim against the flow while being transported downstream through the pipe; median transit times through the bypass for each test velocity ranged from 5.8 to 12.2 s, with transit time decreasing with increasing entrance velocity. Eels did not show strong avoidance of the vertical section of the pipe which contained injected air. No mortality or injury of bypassed eels was observed, and individual eels repeatedly passed through the bypass at rates of up to 40 passes per hour, suggesting that individuals do not

  10. Perioperative risk factors for prolonged mechanical ventilation and tracheostomy in women undergoing coronary artery bypass graft with cardiopulmonary bypass

    Directory of Open Access Journals (Sweden)

    Zahra S Faritous

    2011-01-01

    Full Text Available Background: Prolonged mechanical ventilation is an important recognized complication occurring during cardiovascular surgery procedures. This study was done to assess the perioperative risk factors related to postoperative pulmonary complications and tracheostomy in women undergoing coronary artery bypass graft with cardiopulmonary bypass. Methods: It was a retrospective study on 5,497 patients, including 31 patients with prolonged ventilatory support and 5,466 patients without it; from the latter group, 350 patients with normal condition (extubated in 6-8 hours without any complication were selected randomly. Possible perioperative risk factors were compared between the two groups using a binary logistic regression model. Results: Among the 5,497 women undergoing coronary artery bypass graft (CABG, 31 women needed prolonged mechanical ventilation (PMV, and 15 underwent tracheostomy. After logistic regression, 7 factors were determined as being independent perioperative risk factors for PMV. Discussion: Age ≥70 years old, left ventricular ejection fraction (LVEF ≤30%, preexisting respiratory or renal disease, emergency or re-do operation and use of preoperative inotropic agents are the main risk factors determined in this study on women undergoing CABG.

  11. MsDpo4—a DinB Homolog from Mycobacterium smegmatis—Is an Error-Prone DNA Polymerase That Can Promote G:T and T:G Mismatches

    Directory of Open Access Journals (Sweden)

    Amit Sharma

    2012-01-01

    Full Text Available Error-prone DNA synthesis in prokaryotes imparts plasticity to the genome to allow for evolution in unfavorable environmental conditions, and this phenomenon is termed adaptive mutagenesis. At a molecular level, adaptive mutagenesis is mediated by upregulating the expression of specialized error-prone DNA polymerases that generally belong to the Y-family, such as the polypeptide product of the dinB gene in case of E. coli. However, unlike E. coli, it has been seen that expression of the homologs of dinB in Mycobacterium tuberculosis are not upregulated under conditions of stress. These studies suggest that DinB homologs in Mycobacteria might not be able to promote mismatches and participate in adaptive mutagenesis. We show that a representative homolog from Mycobacterium smegmatis (MsDpo4 can carry out template-dependent nucleotide incorporation and therefore is a DNA polymerase. In addition, it is seen that MsDpo4 is also capable of misincorporation with a significant ability to promote G:T and T:G mismatches. The frequency of misincorporation for these two mismatches is similar to that exhibited by archaeal and prokaryotic homologs. Overall, our data show that MsDpo4 has the capacity to facilitate transition mutations and can potentially impart plasticity to the genome.

  12. A study on bypass flow gap distribution in a prismatic VHTR core

    International Nuclear Information System (INIS)

    Kim, M. H.; Jo, C. K.; Lim, H. S.

    2010-01-01

    Core bypass flow in VHTR is one of the key issues for core thermal margins and efficiency. The bypass flow in the prismatic core varies during core cycles due to the irradiation shrinkage and thermal expansion of the graphite blocks. A procedure to evaluate the local gap size variation between graphite blocks was developed and applied to a prismatic core VHTR. The influence of the core restraint mechanism on the bypass flow gap was evaluated. The predicted gap size is as much as 8 mm when the graphite block is exposed to its allowable limit of irradiation fluence. The analysis for the core bypass flow and hot spot was carried out based on the calculated gap distributions. The results indicate that the bypass flow and the location of core hot spots are closely related and a measure to reduce the bypass flow is necessary. (authors)

  13. Rural Bypass of Critical Access Hospitals in Iowa: Do Visiting Surgical Specialists Make a Difference?

    Science.gov (United States)

    Weigel, Paula A M; Ullrich, Fred; Ward, Marcia M

    2018-02-01

    Rural bypass for elective surgical procedures is a challenge for critical access hospitals, yet there are opportunities for rural hospitals to improve local retention of surgical candidates through alternative approaches to developing surgery lines of business. In this study we examine the effect of visiting surgical specialists on the odds of rural bypass. Discharge data from the 2011 State Inpatient Databases and State Ambulatory Surgery Databases for Iowa were linked to outreach data from the Office of Statewide Clinical Education Programs and Iowa Physician Information System to model the effect of surgeon specialist supply on rural patients' decision to bypass rural critical access hospitals. Patients in rural communities with a local general surgeon were more likely to be retained in a community than to bypass. Those in communities with visiting general surgeons were more likely to bypass, as were those in communities with visiting urologists and obstetricians. Patients in communities with visiting ophthalmologists and orthopedic surgeons were at higher odds of being retained for their elective surgeries. In addition to known patient and local hospital factors that have an influence on bypass behavior among rural patients seeking elective surgery, availability of surgeon specialists also plays an important role in whether patients bypass or not. Visiting ophthalmologists and orthopedic surgeons were associated with less bypass, as was having local general surgeons. Visiting general surgeons, urologists, and obstetricians were associated with greater odds of bypass. © 2016 National Rural Health Association.

  14. The Effects of Normothermic and Hypothermic Cardiopulmonary Bypass Upon Defibrillation Energy Requirements and Transmyocardial Impedance

    National Research Council Canada - National Science Library

    Martin, David

    1993-01-01

    .... To evaluate these questions we studied the effect of controlled hypothermia upon defibrillation energy requirements and transcardiac impedance in a canine model of cardiopulmonary bypass in which 26...

  15. Tidlige erfaringer med duplexovervågning af femoropopliteale og -krurale vene-bypass

    DEFF Research Database (Denmark)

    Nielsen, Tina G; von Jessen, Frants; Schroeder, T V

    1993-01-01

    Identification and correction of graft stenoses in femoropopliteal and -crural vein bypasses can prevent reconstruction failure. Sixty six consecutive vein bypasses entered a postoperative surveillance protocol, which implied clinical assessment, measurement of ankle blood pressure and duplex...... could not be reestablished. Of the 34 bypasses with normal duplex-scans only 2 (6%) thrombosed (p blood pressure measurement could reliably predict graft failure. This study indicates that duplex......-scanning effectively identifies grafts at risk and can be expected to improve long-term patency of infrainguinal vein bypasses....

  16. Two distinct modes of RecA action are required for DNA polymerase V-catalyzed translesion synthesis.

    Science.gov (United States)

    Pham, Phuong; Seitz, Erica M; Saveliev, Sergei; Shen, Xuan; Woodgate, Roger; Cox, Michael M; Goodman, Myron F

    2002-08-20

    SOS mutagenesis in Escherichia coli requires DNA polymerase V (pol V) and RecA protein to copy damaged DNA templates. Here we show that two distinct biochemical modes for RecA protein are necessary for pol V-catalyzed translesion synthesis. One RecA mode is characterized by a strong stimulation in nucleotide incorporation either directly opposite a lesion or at undamaged template sites, but by the absence of lesion bypass. A separate RecA mode is necessary for translesion synthesis. The RecA1730 mutant protein, which was identified on the basis of its inability to promote pol V (UmuD'(2)C)-dependent UV-mutagenesis, appears proficient for the first mode of RecA action but is deficient in the second mode. Data are presented suggesting that the two RecA modes are "nonfilamentous". That is, contrary to current models for SOS mutagenesis, formation of a RecA nucleoprotein filament may not be required for copying damaged DNA templates. Instead, SOS mutagenesis occurs when pol V interacts with two RecA molecules, first at a 3' primer end, upstream of a template lesion, where RecA mode 1 stimulates pol V activity, and subsequently at a site immediately downstream of the lesion, where RecA mode 2 cocatalyzes lesion bypass. We posit that in vivo assembly of a RecA nucleoprotein filament may be required principally to target pol V to a site of DNA damage and to stabilize the pol V-RecA interaction at the lesion. However, it is only a RecA molecule located at the 3' filament tip, proximal to a damaged template base, that is directly responsible for translesion synthesis.

  17. PCR performance of a thermostable heterodimeric archaeal DNA polymerase

    Science.gov (United States)

    Killelea, Tom; Ralec, Céline; Bossé, Audrey; Henneke, Ghislaine

    2014-01-01

    DNA polymerases are versatile tools used in numerous important molecular biological core technologies like the ubiquitous polymerase chain reaction (PCR), cDNA cloning, genome sequencing, and nucleic acid based diagnostics. Taking into account the multiple DNA amplification techniques in use, different DNA polymerases must be optimized for each type of application. One of the current tendencies is to reengineer or to discover new DNA polymerases with increased performance and broadened substrate spectra. At present, there is a great demand for such enzymes in applications, e.g., forensics or paleogenomics. Current major limitations hinge on the inability of conventional PCR enzymes, such as Taq, to amplify degraded or low amounts of template DNA. Besides, a wide range of PCR inhibitors can also impede reactions of nucleic acid amplification. Here we looked at the PCR performances of the proof-reading D-type DNA polymerase from P. abyssi, Pab-polD. Fragments, 3 kilobases in length, were specifically PCR-amplified in its optimized reaction buffer. Pab-polD showed not only a greater resistance to high denaturation temperatures than Taq during cycling, but also a superior tolerance to the presence of potential inhibitors. Proficient proof-reading Pab-polD enzyme could also extend a primer containing up to two mismatches at the 3' primer termini. Overall, we found valuable biochemical properties in Pab-polD compared to the conventional Taq, which makes the enzyme ideally suited for cutting-edge PCR-applications. PMID:24847315

  18. Repair of Clustered Damage and DNA Polymerase Iota.

    Science.gov (United States)

    Belousova, E A; Lavrik, O I

    2015-08-01

    Multiple DNA lesions occurring within one or two turns of the DNA helix known as clustered damage are a source of double-stranded DNA breaks, which represent a serious threat to the cells. Repair of clustered lesions is accomplished in several steps. If a clustered lesion contains oxidized bases, an individual DNA lesion is repaired by the base excision repair (BER) mechanism involving a specialized DNA polymerase after excising DNA damage. Here, we investigated DNA synthesis catalyzed by DNA polymerase iota using damaged DNA templates. Two types of DNA substrates were used as model DNAs: partial DNA duplexes containing breaks of different length, and DNA duplexes containing 5-formyluracil (5-foU) and uracil as a precursor of apurinic/apyrimidinic sites (AP) in opposite DNA strands. For the first time, we showed that DNA polymerase iota is able to catalyze DNA synthesis using partial DNA duplexes having breaks of different length as substrates. In addition, we found that DNA polymerase iota could catalyze DNA synthesis during repair of clustered damage via the BER system by using both undamaged and 5-foU-containing templates. We found that hPCNA (human proliferating cell nuclear antigen) increased efficacy of DNA synthesis catalyzed by DNA polymerase iota.

  19. PCR performance of a thermostable heterodimeric archaeal DNA polymerase

    Directory of Open Access Journals (Sweden)

    Tom eKillelea

    2014-05-01

    Full Text Available DNA polymerases are versatile tools used in numerous important molecular biological core technologies like the ubiquitous polymerase chain reaction (PCR, cDNA cloning, genome sequencing and nucleic acid based diagnostics. Taking into account the multiple DNA amplification techniques in use, different DNA polymerases must be optimized for each type of application. One of the current tendencies is to reengineer or to discover new DNA polymerases with increased performance and broadened substrate spectra. At present, there is a great demand for such enzymes in applications, e.g., forensics or paleogenomics. Current major limitations hinge on the inability of conventional PCR enzymes, such as Taq, to amplify degraded or low amounts of template DNA. Besides, a wide range of PCR inhibitors can also impede reactions of nucleic acid amplification. Here we looked at the PCR performances of the proof-reading D-type DNA polymerase from P. abyssi, Pab-polD. Fragments, 3 kilobases in length, were specifically PCR-amplified in its optimized reaction buffer. Pab-polD showed not only a greater resistance to high denaturation temperatures than Taq during cycling, but also a superior tolerance to the presence of potential inhibitors. Proficient proof-reading Pab-polD enzyme could also extend a primer containing up to two mismatches at the 3’ primer termini. Overall, we found valuable biochemical properties in Pab-polD compared to the conventional Taq, which makes the enzyme ideally suited for cutting-edge PCR-applications.

  20. Optimal conditions to use Pfu exo(-) DNA polymerase for highly efficient ligation-mediated polymerase chain reaction protocols.

    Science.gov (United States)

    Angers, M; Cloutier, J F; Castonguay, A; Drouin, R

    2001-08-15

    Ligation-Mediated Polymerase Chain Reaction (LMPCR) is the most sensitive sequencing technique available to map single-stranded DNA breaks at the nucleotide level of resolution using genomic DNA. LMPCR has been adapted to map DNA damage and reveal DNA-protein interactions inside living cells. However, the sequence context (GC content), the global break frequency and the current combination of DNA polymerases used in LMPCR affect the quality of the results. In this study, we developed and optimized an LMPCR protocol adapted for Pyrococcus furiosus exo(-) DNA polymerase (Pfu exo(-)). The relative efficiency of Pfu exo(-) was compared to T7-modified DNA polymerase (Sequenase 2.0) at the primer extension step and to Thermus aquaticus DNA polymerase (Taq) at the PCR amplification step of LMPCR. At all break frequencies tested, Pfu exo(-) proved to be more efficient than Sequenase 2.0. During both primer extension and PCR amplification steps, the ratio of DNA molecules per unit of DNA polymerase was the main determinant of the efficiency of Pfu exo(-), while the efficiency of Taq was less affected by this ratio. Substitution of NaCl for KCl in the PCR reaction buffer of Taq strikingly improved the efficiency of the DNA polymerase. Pfu exo(-) was clearly more efficient than Taq to specifically amplify extremely GC-rich genomic DNA sequences. Our results show that a combination of Pfu exo(-) at the primer extension step and Taq at the PCR amplification step is ideal for in vivo DNA analysis and DNA damage mapping using LMPCR.

  1. Distal anastomotic vein adjunct usage in infrainguinal prosthetic bypasses.

    Science.gov (United States)

    McPhee, James T; Goodney, Philip P; Schanzer, Andres; Shaykevich, Shimon; Belkin, Michael; Menard, Matthew T

    2013-04-01

    Single-segment saphenous vein remains the optimal conduit for infrainguinal revascularization. In its absence, prosthetic conduit may be used. Existing data regarding the significance of anastomotic distal vein adjunct (DVA) usage with prosthetic grafts are based on small series. This is a retrospective cohort analysis derived from the regional Vascular Study Group of New England as well as the Brigham and Women's hospital database. A total of 1018 infrainguinal prosthetic bypass grafts were captured in the dataset from 73 surgeons at 15 participating institutions. Propensity scoring and 3:1 matching was performed to create similar exposure groups for analysis. Outcome measures of interest included: primary patency, freedom from major adverse limb events (MALEs), and amputation free survival at 1 year as a function of vein patch utilization. Time to event data were compared with the log-rank test; multivariable Cox proportional hazard models were used to evaluate the adjusted association between vein cuff usage and the primary end points. DVA was defined as a vein patch, cuff, or boot in any configuration. Of the 1018 bypass operations, 94 (9.2%) had a DVA whereas 924 (90.8%) did not (no DVA). After propensity score matching, 88 DVAs (25%) and 264 no DVAs (75%) were analyzed. On univariate analysis of the matched cohort, the DVA and no DVA groups were similar in terms of mean age (70.0 vs 69.0; P = .55), male sex (58.0% vs 58.3%; P > .99), and preoperative characteristics such as living at home (93.2% vs 94.3%; P = .79) and independent ambulatory status (72.7% vs 75.7%; P = .64). The DVA and no DVA groups had similar rates of major comorbidities such as hypertension chronic obstructive pulmonary disease, diabetes mellitus, coronary artery disease, and dialysis dependence (P > .05 for all). Likewise, they had similar rates of distal origin grafts (13.6% vs 12.5%; P = .85), critical limb ischemia indications (P = .53), and prior arterial bypass (58% vs 47%; P = .08

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  19. File list: Pol.Lng.20.RNA_Polymerase_II.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  20. File list: Pol.Plc.20.RNA_polymerase_III.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  1. File list: Pol.Bon.20.RNA_polymerase_III.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  2. File list: Pol.Gon.50.RNA_polymerase_II.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  3. File list: Pol.Emb.05.RNA_Polymerase_III.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  4. File list: Pol.Kid.20.RNA_polymerase_II.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  5. File list: Pol.Emb.10.RNA_polymerase_III.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  6. File list: Pol.Pan.10.RNA_Polymerase_III.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  7. File list: Pol.Adl.05.RNA_Polymerase_II.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  8. File list: Pol.PSC.50.RNA_Polymerase_II.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  9. File list: Pol.Bon.05.RNA_Polymerase_III.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  10. File list: Pol.Epd.10.RNA_polymerase_II.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  11. File list: Pol.Epd.10.RNA_Polymerase_II.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  12. File list: Pol.Adp.20.RNA_polymerase_III.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  13. File list: Pol.Brs.10.RNA_Polymerase_II.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  14. File list: Pol.Spl.10.RNA_Polymerase_III.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  15. File list: Pol.Dig.20.RNA_Polymerase_II.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  16. File list: Pol.Spl.05.RNA_Polymerase_II.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  17. File list: Pol.PSC.20.RNA_Polymerase_II.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  18. File list: Pol.Pup.05.RNA_polymerase_II.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  19. File list: Pol.Unc.50.RNA_polymerase_II.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  20. File list: Pol.Plc.10.RNA_polymerase_II.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Plc.10.RNA_polymerase_II.AllCell hg19 RNA polymerase RNA polymerase II Placenta... http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.Plc.10.RNA_polymerase_II.AllCell.bed ...

  1. File list: Pol.Adp.10.RNA_polymerase_III.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Adp.10.RNA_polymerase_III.AllCell hg19 RNA polymerase RNA polymerase III Adipoc...yte http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.Adp.10.RNA_polymerase_III.AllCell.bed ...

  2. File list: Pol.Dig.20.RNA_polymerase_III.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  3. File list: Pol.Myo.10.RNA_polymerase_III.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Myo.10.RNA_polymerase_III.AllCell hg19 RNA polymerase RNA polymerase III Muscle... http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.Myo.10.RNA_polymerase_III.AllCell.bed ...

  4. File list: Pol.Epd.20.RNA_polymerase_III.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  5. File list: Pol.Unc.05.RNA_polymerase_II.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  6. File list: Pol.Plc.10.RNA_polymerase_III.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Plc.10.RNA_polymerase_III.AllCell hg19 RNA polymerase RNA polymerase III Placen...ta http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.Plc.10.RNA_polymerase_III.AllCell.bed ...

  7. File list: Pol.ALL.05.RNA_polymerase_II.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.ALL.05.RNA_polymerase_II.AllCell dm3 RNA polymerase RNA polymerase II All cell ...013077,SRX050604,SRX050605 http://dbarchive.biosciencedbc.jp/kyushu-u/dm3/assembled/Pol.ALL.05.RNA_polymerase_II.AllCell.bed ...

  8. File list: Pol.Adp.50.RNA_polymerase_II.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  9. File list: Pol.ALL.10.RNA_polymerase_II.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  10. File list: Pol.Brs.20.RNA_polymerase_III.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Brs.20.RNA_polymerase_III.AllCell hg19 RNA polymerase RNA polymerase III Breast... http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.Brs.20.RNA_polymerase_III.AllCell.bed ...

  11. File list: Pol.ALL.05.RNA_polymerase_II.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  12. File list: Pol.Emb.50.RNA_polymerase_II.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Emb.50.RNA_polymerase_II.AllCell dm3 RNA polymerase RNA polymerase II Embryo SR...7582,SRX050604,SRX050605,SRX013073 http://dbarchive.biosciencedbc.jp/kyushu-u/dm3/assembled/Pol.Emb.50.RNA_polymerase_II.AllCell.bed ...

  13. File list: Pol.Brs.05.RNA_polymerase_III.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Brs.05.RNA_polymerase_III.AllCell hg19 RNA polymerase RNA polymerase III Breast... http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.Brs.05.RNA_polymerase_III.AllCell.bed ...

  14. File list: Pol.PSC.05.RNA_polymerase_III.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  15. File list: Pol.Epd.20.RNA_polymerase_II.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Epd.20.RNA_polymerase_II.AllCell hg19 RNA polymerase RNA polymerase II Epidermi...248,SRX663247,SRX807622 http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.Epd.20.RNA_polymerase_II.AllCell.bed ...

  16. File list: Pol.Plc.05.RNA_polymerase_II.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Plc.05.RNA_polymerase_II.AllCell hg19 RNA polymerase RNA polymerase II Placenta... http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.Plc.05.RNA_polymerase_II.AllCell.bed ...

  17. File list: Pol.Unc.20.RNA_polymerase_II.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Unc.20.RNA_polymerase_II.AllCell ce10 RNA polymerase RNA polymerase II Unclassi...p://dbarchive.biosciencedbc.jp/kyushu-u/ce10/assembled/Pol.Unc.20.RNA_polymerase_II.AllCell.bed ...

  18. File list: Pol.Kid.10.RNA_polymerase_II.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  19. File list: Pol.Prs.10.RNA_polymerase_III.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Prs.10.RNA_polymerase_III.AllCell hg19 RNA polymerase RNA polymerase III Prosta...te http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.Prs.10.RNA_polymerase_III.AllCell.bed ...

  20. File list: Pol.Oth.50.RNA_polymerase_III.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Oth.50.RNA_polymerase_III.AllCell hg19 RNA polymerase RNA polymerase III Others... http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.Oth.50.RNA_polymerase_III.AllCell.bed ...

  1. File list: Pol.Utr.10.RNA_polymerase_III.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Utr.10.RNA_polymerase_III.AllCell hg19 RNA polymerase RNA polymerase III Uterus... SRX017001,SRX018606,SRX017002 http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.Utr.10.RNA_polymerase_III.AllCell.bed ...

  2. File list: Pol.Adl.50.RNA_polymerase_II.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  3. File list: Pol.CDV.05.RNA_polymerase_III.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.CDV.05.RNA_polymerase_III.AllCell hg19 RNA polymerase RNA polymerase III Cardio...vascular http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.CDV.05.RNA_polymerase_III.AllCell.bed ...

  4. File list: Pol.Prs.50.RNA_polymerase_II.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Prs.50.RNA_polymerase_II.AllCell hg19 RNA polymerase RNA polymerase II Prostate...932,SRX020922,SRX022582 http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.Prs.50.RNA_polymerase_II.AllCell.bed ...

  5. File list: Pol.PSC.20.RNA_polymerase_II.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.PSC.20.RNA_polymerase_II.AllCell hg19 RNA polymerase RNA polymerase II Pluripot...670820,SRX702057,SRX702061 http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.PSC.20.RNA_polymerase_II.AllCell.bed ...

  6. File list: Pol.Utr.50.RNA_polymerase_II.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  7. File list: Pol.Brs.10.RNA_polymerase_III.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Brs.10.RNA_polymerase_III.AllCell hg19 RNA polymerase RNA polymerase III Breast... http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.Brs.10.RNA_polymerase_III.AllCell.bed ...

  8. File list: Pol.Adl.20.RNA_polymerase_II.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  9. File list: Pol.Kid.10.RNA_polymerase_III.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  10. File list: Pol.ALL.20.RNA_polymerase_III.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  11. File list: Pol.Emb.05.RNA_polymerase_II.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Emb.05.RNA_polymerase_II.AllCell ce10 RNA polymerase RNA polymerase II Embryo S...,SRX043867 http://dbarchive.biosciencedbc.jp/kyushu-u/ce10/assembled/Pol.Emb.05.RNA_polymerase_II.AllCell.bed ...

  12. File list: Pol.Dig.05.RNA_polymerase_II.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Dig.05.RNA_polymerase_II.AllCell hg19 RNA polymerase RNA polymerase II Digestiv...//dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.Dig.05.RNA_polymerase_II.AllCell.bed ...

  13. File list: Pol.Neu.50.RNA_polymerase_II.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  14. File list: Pol.Emb.05.RNA_polymerase_II.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  15. File list: Pol.Liv.20.RNA_polymerase_II.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  16. File list: Pol.Prs.10.RNA_polymerase_II.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  17. File list: Pol.Pan.10.RNA_polymerase_II.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  18. File list: Pol.Liv.05.RNA_polymerase_III.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Liv.05.RNA_polymerase_III.AllCell hg19 RNA polymerase RNA polymerase III Liver ...http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.Liv.05.RNA_polymerase_III.AllCell.bed ...

  19. File list: Pol.Neu.05.RNA_polymerase_II.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  20. File list: Pol.Myo.05.RNA_polymerase_III.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Myo.05.RNA_polymerase_III.AllCell hg19 RNA polymerase RNA polymerase III Muscle... http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.Myo.05.RNA_polymerase_III.AllCell.bed ...

  1. File list: Pol.Lng.20.RNA_polymerase_III.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  2. File list: Pol.Kid.05.RNA_polymerase_III.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Kid.05.RNA_polymerase_III.AllCell hg19 RNA polymerase RNA polymerase III Kidney... SRX016996 http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.Kid.05.RNA_polymerase_III.AllCell.bed ...

  3. File list: Pol.ALL.05.RNA_polymerase_III.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.ALL.05.RNA_polymerase_III.AllCell hg19 RNA polymerase RNA polymerase III All ce...,SRX150396,SRX015144,SRX150101,SRX150102 http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.ALL.05.RNA_polymerase_III.AllCell.bed ...

  4. File list: Pol.Dig.50.RNA_polymerase_III.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Dig.50.RNA_polymerase_III.AllCell hg19 RNA polymerase RNA polymerase III Digest...ive tract http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.Dig.50.RNA_polymerase_III.AllCell.bed ...

  5. File list: Pol.Oth.20.RNA_polymerase_III.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Oth.20.RNA_polymerase_III.AllCell hg19 RNA polymerase RNA polymerase III Others... http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.Oth.20.RNA_polymerase_III.AllCell.bed ...

  6. File list: Pol.Lng.10.RNA_polymerase_II.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Lng.10.RNA_polymerase_II.AllCell hg19 RNA polymerase RNA polymerase II Lung SRX... http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.Lng.10.RNA_polymerase_II.AllCell.bed ...

  7. File list: Pol.Lar.10.RNA_polymerase_III.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Lar.10.RNA_polymerase_III.AllCell ce10 RNA polymerase RNA polymerase III Larvae... http://dbarchive.biosciencedbc.jp/kyushu-u/ce10/assembled/Pol.Lar.10.RNA_polymerase_III.AllCell.bed ...

  8. File list: Pol.Liv.50.RNA_polymerase_III.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Liv.50.RNA_polymerase_III.AllCell hg19 RNA polymerase RNA polymerase III Liver ...http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.Liv.50.RNA_polymerase_III.AllCell.bed ...

  9. File list: Pol.Unc.20.RNA_polymerase_II.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Unc.20.RNA_polymerase_II.AllCell hg19 RNA polymerase RNA polymerase II Unclassi...fied http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.Unc.20.RNA_polymerase_II.AllCell.bed ...

  10. File list: Pol.Unc.10.RNA_polymerase_II.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Unc.10.RNA_polymerase_II.AllCell sacCer3 RNA polymerase RNA polymerase II Uncla...ssified http://dbarchive.biosciencedbc.jp/kyushu-u/sacCer3/assembled/Pol.Unc.10.RNA_polymerase_II.AllCell.bed ...

  11. File list: Pol.Gon.10.RNA_polymerase_III.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Gon.10.RNA_polymerase_III.AllCell hg19 RNA polymerase RNA polymerase III Gonad ...http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.Gon.10.RNA_polymerase_III.AllCell.bed ...

  12. File list: Pol.Bld.50.RNA_polymerase_III.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Bld.50.RNA_polymerase_III.AllCell hg19 RNA polymerase RNA polymerase III Blood ...SRX150560,SRX018610,SRX015143,SRX017006,SRX150396,SRX015144 http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.Bld.50.RNA_polymerase_III.AllCell.bed ...

  13. File list: Pol.Lar.20.RNA_polymerase_II.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Lar.20.RNA_polymerase_II.AllCell dm3 RNA polymerase RNA polymerase II Larvae SR...SRX661503,SRX026742,SRX013070,SRX013072,SRX182775,SRX151961,SRX013082,SRX013113 http://dbarchive.biosciencedbc.jp/kyushu-u/dm3/assembled/Pol.Lar.20.RNA_polymerase_II.AllCell.bed ...

  14. File list: Pol.ALL.05.RNA_polymerase_III.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  15. File list: Pol.Prs.05.RNA_polymerase_II.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Prs.05.RNA_polymerase_II.AllCell hg19 RNA polymerase RNA polymerase II Prostate...363,SRX173198,SRX173197 http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.Prs.05.RNA_polymerase_II.AllCell.bed ...

  16. File list: Pol.Plc.05.RNA_polymerase_III.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Plc.05.RNA_polymerase_III.AllCell hg19 RNA polymerase RNA polymerase III Placen...ta http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.Plc.05.RNA_polymerase_III.AllCell.bed ...

  17. File list: Pol.Lng.50.RNA_polymerase_III.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Lng.50.RNA_polymerase_III.AllCell hg19 RNA polymerase RNA polymerase III Lung S...RX016555,SRX150101,SRX150102 http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.Lng.50.RNA_polymerase_III.AllCell.bed ...

  18. File list: Pol.Bon.20.RNA_polymerase_II.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Bon.20.RNA_polymerase_II.AllCell hg19 RNA polymerase RNA polymerase II Bone SRX...,SRX351408 http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.Bon.20.RNA_polymerase_II.AllCell.bed ...

  19. File list: Pol.Myo.50.RNA_polymerase_II.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Myo.50.RNA_polymerase_II.AllCell hg19 RNA polymerase RNA polymerase II Muscle h...ttp://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.Myo.50.RNA_polymerase_II.AllCell.bed ...

  20. File list: Pol.ALL.20.RNA_polymerase_II.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.ALL.20.RNA_polymerase_II.AllCell sacCer3 RNA polymerase RNA polymerase II All c...ell types http://dbarchive.biosciencedbc.jp/kyushu-u/sacCer3/assembled/Pol.ALL.20.RNA_polymerase_II.AllCell.bed ...

  1. File list: Pol.Oth.50.RNA_polymerase_II.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Oth.50.RNA_polymerase_II.AllCell hg19 RNA polymerase RNA polymerase II Others S...RX1027436,SRX1027435,SRX1027434,SRX1027433,SRX668218,SRX099880,SRX099879 http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.Oth.50.RNA_polymerase_II.AllCell.bed ...

  2. File list: Pol.Bld.50.RNA_polymerase_II.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Bld.50.RNA_polymerase_II.AllCell hg19 RNA polymerase RNA polymerase II Blood SR...,SRX153079,SRX017717,SRX103447,SRX386121,SRX038919,SRX038920,SRX080132 http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.Bld.50.RNA_polymerase_II.AllCell.bed ...

  3. File list: Pol.Myo.10.RNA_polymerase_II.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Myo.10.RNA_polymerase_II.AllCell hg19 RNA polymerase RNA polymerase II Muscle h...ttp://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.Myo.10.RNA_polymerase_II.AllCell.bed ...

  4. File list: Pol.Myo.05.RNA_polymerase_II.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Myo.05.RNA_polymerase_II.AllCell hg19 RNA polymerase RNA polymerase II Muscle h...ttp://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.Myo.05.RNA_polymerase_II.AllCell.bed ...

  5. File list: Pol.Emb.50.RNA_polymerase_II.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Emb.50.RNA_polymerase_II.AllCell ce10 RNA polymerase RNA polymerase II Embryo S...,SRX043866 http://dbarchive.biosciencedbc.jp/kyushu-u/ce10/assembled/Pol.Emb.50.RNA_polymerase_II.AllCell.bed ...

  6. File list: Pol.Emb.50.RNA_polymerase_III.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Emb.50.RNA_polymerase_III.AllCell ce10 RNA polymerase RNA polymerase III Embryo... http://dbarchive.biosciencedbc.jp/kyushu-u/ce10/assembled/Pol.Emb.50.RNA_polymerase_III.AllCell.bed ...

  7. File list: Pol.ALL.10.RNA_polymerase_II.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.ALL.10.RNA_polymerase_II.AllCell hg19 RNA polymerase RNA polymerase II All cell...,SRX1013886,SRX1013900 http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.ALL.10.RNA_polymerase_II.AllCell.bed ...

  8. File list: Pol.Oth.05.RNA_polymerase_III.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Oth.05.RNA_polymerase_III.AllCell hg19 RNA polymerase RNA polymerase III Others... http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.Oth.05.RNA_polymerase_III.AllCell.bed ...

  9. File list: Pol.Liv.50.RNA_polymerase_II.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Liv.50.RNA_polymerase_II.AllCell hg19 RNA polymerase RNA polymerase II Liver SR...1013886 http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.Liv.50.RNA_polymerase_II.AllCell.bed ...

  10. File list: Pol.Bon.05.RNA_polymerase_III.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Bon.05.RNA_polymerase_III.AllCell hg19 RNA polymerase RNA polymerase III Bone h...ttp://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.Bon.05.RNA_polymerase_III.AllCell.bed ...

  11. File list: Pol.Unc.20.RNA_polymerase_III.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Unc.20.RNA_polymerase_III.AllCell ce10 RNA polymerase RNA polymerase III Unclas...sified http://dbarchive.biosciencedbc.jp/kyushu-u/ce10/assembled/Pol.Unc.20.RNA_polymerase_III.AllCell.bed ...

  12. File list: Pol.Gon.20.RNA_polymerase_III.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Gon.20.RNA_polymerase_III.AllCell hg19 RNA polymerase RNA polymerase III Gonad ...http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.Gon.20.RNA_polymerase_III.AllCell.bed ...

  13. File list: Pol.Emb.05.RNA_polymerase_III.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Emb.05.RNA_polymerase_III.AllCell ce10 RNA polymerase RNA polymerase III Embryo... http://dbarchive.biosciencedbc.jp/kyushu-u/ce10/assembled/Pol.Emb.05.RNA_polymerase_III.AllCell.bed ...

  14. File list: Pol.PSC.50.RNA_polymerase_III.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.PSC.50.RNA_polymerase_III.AllCell hg19 RNA polymerase RNA polymerase III Plurip...otent stem cell http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.PSC.50.RNA_polymerase_III.AllCell.bed ...

  15. File list: Pol.Adl.10.RNA_polymerase_III.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Adl.10.RNA_polymerase_III.AllCell ce10 RNA polymerase RNA polymerase III Adult ...SRX395531,SRX331268,SRX331270,SRX395532 http://dbarchive.biosciencedbc.jp/kyushu-u/ce10/assembled/Pol.Adl.10.RNA_polymerase_III.AllCell.bed ...

  16. File list: Pol.Kid.05.RNA_polymerase_II.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Kid.05.RNA_polymerase_II.AllCell hg19 RNA polymerase RNA polymerase II Kidney S...SRX128201,SRX128200,SRX003882,SRX1206065,SRX1206066,SRX1206067,SRX367323 http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.Kid.05.RNA_polymerase_II.AllCell.bed ...

  17. File list: Pol.Myo.50.RNA_polymerase_III.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Myo.50.RNA_polymerase_III.AllCell hg19 RNA polymerase RNA polymerase III Muscle... http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.Myo.50.RNA_polymerase_III.AllCell.bed ...

  18. File list: Pol.Plc.20.RNA_polymerase_II.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Plc.20.RNA_polymerase_II.AllCell hg19 RNA polymerase RNA polymerase II Placenta... http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.Plc.20.RNA_polymerase_II.AllCell.bed ...

  19. File list: Pol.Pan.50.RNA_polymerase_II.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Pan.50.RNA_polymerase_II.AllCell hg19 RNA polymerase RNA polymerase II Pancreas... SRX190244 http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.Pan.50.RNA_polymerase_II.AllCell.bed ...

  20. File list: Pol.Bon.10.RNA_polymerase_II.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Bon.10.RNA_polymerase_II.AllCell hg19 RNA polymerase RNA polymerase II Bone SRX...,SRX351408 http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.Bon.10.RNA_polymerase_II.AllCell.bed ...

  1. File list: Pol.Bld.10.RNA_polymerase_II.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Bld.10.RNA_polymerase_II.AllCell hg19 RNA polymerase RNA polymerase II Blood SR...,SRX017986,SRX017985,SRX728781,SRX017717,SRX005163,SRX024360,SRX017718 http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.Bld.10.RNA_polymerase_II.AllCell.bed ...

  2. File list: Pol.Plc.50.RNA_polymerase_III.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Plc.50.RNA_polymerase_III.AllCell hg19 RNA polymerase RNA polymerase III Placen...ta http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.Plc.50.RNA_polymerase_III.AllCell.bed ...

  3. File list: Pol.Epd.05.RNA_polymerase_II.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Epd.05.RNA_polymerase_II.AllCell hg19 RNA polymerase RNA polymerase II Epidermi...245,SRX663247,SRX807622 http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.Epd.05.RNA_polymerase_II.AllCell.bed ...

  4. File list: Pol.Lar.05.RNA_polymerase_III.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Lar.05.RNA_polymerase_III.AllCell ce10 RNA polymerase RNA polymerase III Larvae... http://dbarchive.biosciencedbc.jp/kyushu-u/ce10/assembled/Pol.Lar.05.RNA_polymerase_III.AllCell.bed ...

  5. File list: Pol.Emb.10.RNA_polymerase_II.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Emb.10.RNA_polymerase_II.AllCell dm3 RNA polymerase RNA polymerase II Embryo SR...7582,SRX050604,SRX050605,SRX013077 http://dbarchive.biosciencedbc.jp/kyushu-u/dm3/assembled/Pol.Emb.10.RNA_polymerase_II.AllCell.bed ...

  6. File list: Pol.Myo.20.RNA_polymerase_II.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Myo.20.RNA_polymerase_II.AllCell hg19 RNA polymerase RNA polymerase II Muscle h...ttp://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.Myo.20.RNA_polymerase_II.AllCell.bed ...

  7. File list: Pol.Bon.50.RNA_polymerase_III.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Bon.50.RNA_polymerase_III.AllCell hg19 RNA polymerase RNA polymerase III Bone h...ttp://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.Bon.50.RNA_polymerase_III.AllCell.bed ...

  8. File list: Pol.Oth.10.RNA_polymerase_III.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Oth.10.RNA_polymerase_III.AllCell hg19 RNA polymerase RNA polymerase III Others... http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.Oth.10.RNA_polymerase_III.AllCell.bed ...

  9. File list: Pol.ALL.50.RNA_polymerase_II.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.ALL.50.RNA_polymerase_II.AllCell dm3 RNA polymerase RNA polymerase II All cell ...050605,SRX013073 http://dbarchive.biosciencedbc.jp/kyushu-u/dm3/assembled/Pol.ALL.50.RNA_polymerase_II.AllCell.bed ...

  10. File list: Pol.Kid.50.RNA_polymerase_III.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Kid.50.RNA_polymerase_III.AllCell hg19 RNA polymerase RNA polymerase III Kidney... SRX016996 http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.Kid.50.RNA_polymerase_III.AllCell.bed ...

  11. File list: Pol.Unc.10.RNA_polymerase_II.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Unc.10.RNA_polymerase_II.AllCell ce10 RNA polymerase RNA polymerase II Unclassi...p://dbarchive.biosciencedbc.jp/kyushu-u/ce10/assembled/Pol.Unc.10.RNA_polymerase_II.AllCell.bed ...

  12. File list: Pol.Unc.10.RNA_polymerase_II.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Unc.10.RNA_polymerase_II.AllCell hg19 RNA polymerase RNA polymerase II Unclassi...fied http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.Unc.10.RNA_polymerase_II.AllCell.bed ...

  13. File list: Pol.CDV.50.RNA_polymerase_III.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.CDV.50.RNA_polymerase_III.AllCell hg19 RNA polymerase RNA polymerase III Cardio...vascular http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.CDV.50.RNA_polymerase_III.AllCell.bed ...

  14. File list: Pol.PSC.05.RNA_polymerase_II.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.PSC.05.RNA_polymerase_II.AllCell hg19 RNA polymerase RNA polymerase II Pluripot...833412,SRX149642,SRX702059 http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.PSC.05.RNA_polymerase_II.AllCell.bed ...

  15. File list: Pol.Kid.50.RNA_polymerase_II.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Kid.50.RNA_polymerase_II.AllCell hg19 RNA polymerase RNA polymerase II Kidney S...SRX1206066,SRX1206067,SRX003882,SRX003883,SRX1206065,SRX367323,SRX326416 http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.Kid.50.RNA_polymerase_II.AllCell.bed ...

  16. File list: Pol.Unc.05.RNA_polymerase_II.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Unc.05.RNA_polymerase_II.AllCell ce10 RNA polymerase RNA polymerase II Unclassi...p://dbarchive.biosciencedbc.jp/kyushu-u/ce10/assembled/Pol.Unc.05.RNA_polymerase_II.AllCell.bed ...

  17. File list: Pol.Prs.05.RNA_polymerase_III.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Prs.05.RNA_polymerase_III.AllCell hg19 RNA polymerase RNA polymerase III Prosta...te http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.Prs.05.RNA_polymerase_III.AllCell.bed ...

  18. File list: Pol.Dig.50.RNA_polymerase_II.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Dig.50.RNA_polymerase_II.AllCell hg19 RNA polymerase RNA polymerase II Digestiv...//dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.Dig.50.RNA_polymerase_II.AllCell.bed ...

  19. File list: Pol.Bld.20.RNA_polymerase_III.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Bld.20.RNA_polymerase_III.AllCell hg19 RNA polymerase RNA polymerase III Blood ...SRX017006,SRX015143,SRX150560,SRX018610,SRX150396,SRX015144 http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.Bld.20.RNA_polymerase_III.AllCell.bed ...

  20. File list: Pol.Prs.20.RNA_polymerase_II.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Prs.20.RNA_polymerase_II.AllCell hg19 RNA polymerase RNA polymerase II Prostate...557,SRX173197,SRX173198 http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.Prs.20.RNA_polymerase_II.AllCell.bed ...

  1. File list: Pol.Emb.20.RNA_polymerase_III.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Emb.20.RNA_polymerase_III.AllCell ce10 RNA polymerase RNA polymerase III Embryo... http://dbarchive.biosciencedbc.jp/kyushu-u/ce10/assembled/Pol.Emb.20.RNA_polymerase_III.AllCell.bed ...

  2. File list: Pol.YSt.20.RNA_polymerase_II.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.YSt.20.RNA_polymerase_II.AllCell sacCer3 RNA polymerase RNA polymerase II Yeast... strain http://dbarchive.biosciencedbc.jp/kyushu-u/sacCer3/assembled/Pol.YSt.20.RNA_polymerase_II.AllCell.bed ...

  3. File list: Pol.ALL.50.RNA_polymerase_II.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.ALL.50.RNA_polymerase_II.AllCell sacCer3 RNA polymerase RNA polymerase II All c...ell types http://dbarchive.biosciencedbc.jp/kyushu-u/sacCer3/assembled/Pol.ALL.50.RNA_polymerase_II.AllCell.bed ...

  4. File list: Pol.Lng.05.RNA_polymerase_II.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Lng.05.RNA_polymerase_II.AllCell hg19 RNA polymerase RNA polymerase II Lung SRX... http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.Lng.05.RNA_polymerase_II.AllCell.bed ...

  5. File list: Pol.Epd.50.RNA_polymerase_III.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Epd.50.RNA_polymerase_III.AllCell hg19 RNA polymerase RNA polymerase III Epider...mis SRX016997 http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.Epd.50.RNA_polymerase_III.AllCell.bed ...

  6. File list: Pol.Oth.05.RNA_polymerase_II.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

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    Lifescience Database Archive (English)

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    Lifescience Database Archive (English)

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    Lifescience Database Archive (English)

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    Lifescience Database Archive (English)

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    Lifescience Database Archive (English)

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    Lifescience Database Archive (English)

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    Lifescience Database Archive (English)

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    Lifescience Database Archive (English)

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    Lifescience Database Archive (English)

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    Lifescience Database Archive (English)

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  20. File list: Pol.Gon.50.RNA_polymerase_III.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  1. Circulating and Urinary miR-210 and miR-16 Increase during Cardiac Surgery Using Cardiopulmonary Bypass - A Pilot Study.

    Science.gov (United States)

    Mazzone, Annette L; Baker, Robert A; McNicholas, Kym; Woodman, Richard J; Michael, Michael Z; Gleadle, Jonathan M

    2018-03-01

    A pilot study to measure and compare blood and urine microRNAs miR-210 and miR-16 in patients undergoing cardiac surgery with cardiopulmonary bypass (CPB) and off-pump coronary artery bypass grafting surgery. Frequent serial blood and urine samples were taken from patients undergoing cardiac surgery with CPB (n = 10) and undergoing off-pump cardiac surgery (n = 5) before, during, and after surgery. Circulating miR-210 and miR-16 levels were determined by relative quantification real-time polymerase chain reaction. Levels of plasma-free haemoglobin (fHb), troponin-T, creatine kinase, and creatinine were measured. Perioperative serum miR-210 and miR-16 were elevated significantly compared to preoperative levels in patients undergoing cardiac surgery with CPB (CPB vs. Pre Op and Rewarm vs. Pre Op; p Octopus on vs. Pre Op); however, the release was less marked when compared to cardiac surgery with CPB. A significant association was observed between both miR-16 and miR-210 and plasma fHb when CPB was used ( r = -.549, p red cell, and renal injury during cardiac surgery.

  2. Factors influencing Recombinase polymerase amplification (RPA) assay outcomes at point of care.

    Science.gov (United States)

    Lillis, Lorraine; Siverson, Joshua; Lee, Arthur; Cantera, Jason; Parker, Mathew; Piepenburg, Olaf; Lehman, Dara A; Boyle, David S

    2016-04-01

    Recombinase Polymerase Amplification (RPA) can be used to detect pathogen-specific DNA or RNA in under 20 min without the need for complex instrumentation. These properties enable its potential use in resource limited settings. However, there are concerns that deviations from the manufacturer's protocol and/or storage conditions could influence its performance in low resource settings. RPA amplification relies upon viscous crowding agents for optimal nucleic acid amplification, and thus an interval mixing step after 3-6 min of incubation is recommended to distribute amplicons and improve performance. In this study we used a HIV-1 RPA assay to evaluate the effects of this mixing step on assay performance. A lack of mixing led to a longer time to amplification and inferior detection signal, compromising the sensitivity of the assay. However lowering the assay volume from 50 μL to 5 μL showed similar sensitivity with or without mixing. We present the first peer-reviewed study that assesses long term stability of RPA reagents without a cold chain. Reagents stored at -20 °C, and 25 °C for up to 12 weeks were able to detect 10 HIV-1 DNA copies. Reagents stored at 45 °C for up to 3 weeks were able to detect 10 HIV-1 DNA copies, with reduced sensitivity only after >3 weeks at 45 °C. Together our results show that reducing reaction volumes bypassed the need for the mixing step and that RPA reagents were stable even when stored for 3 weeks at very high temperatures. Copyright © 2016 Elsevier Ltd. All rights reserved.

  3. Evaluation of aortocoronary bypass graft patency by reconstructed CT image

    International Nuclear Information System (INIS)

    Kawakita, Seizaburo; Koide, Takashi; Saito, Yoshio; Yamamoto, Tadao; Iwasaki, Tadaaki

    1982-01-01

    Ten patients were examined in the period of three months from January to March 1981. The patients were operated from 1 month to 7 years before CT. A bypass to the left anterior descending artery (LAD) was grafted in 10 cases, 2 to the right coronary artery (RCA), 4 to an obtuse marginal artery (OM), and 1 to a diagonal artery. Image reconstruction was performed in 10 cases by using an image analytical computer Evaluskop. Appropriate planes for reconstruction were selected by trial and error methods upon observation of CT images. When gained picture of a graft course coincided with surgical records or angiography, the work of building images was concluded. On cross section, grafts to LAD were visualized in all 10 cases: 9 in the entire course and 1 in a proximal part of the graft. Two to RCA, 4 to OM and 1 to a diagonal were also successfully visualized. Reconstruction of graft images succeeded in 9 grafts of 6 cases. The course of a graft could be pursued from the proximal to the distal end adjacent to the cardiac chamber. The picture of a bypass to LAD was visualized in 6 of 10 grafts. Two bypass to RCA could be depicted, and 1 to OM was also found. However 3 to OM and 1 to a diagonal failed to be visualized throughout their courses in reconstructed images. I think that the causes of faillure mainly depended upon the course of the graft. When a graft was running arc-like surrounding the heart chamber, it was very difficult to depict its entire length in reconstructed images, though the graft could be detected in cross sections. These preliminary studies indicated that reconstruction of CT images had some benefits for the pursuit of graft courses. (J.P.N.)

  4. Patient-controlled analgesia after coronary bypass: Remifentanil or sufentanil?

    Science.gov (United States)

    Alavi, Seyed Mostafa; Ghoreishi, Seyed Mohammadmehran; Chitsazan, Mitra; Ghandi, Iman; Fard, Alireza Jahangiri; Hosseini, Seyed Saeed; Mahjoobifard, Maziar; Fani, Kamal

    2014-07-01

    adequate pain control after cardiac surgery is mandatory to reduce its remarkable morbidity. In this study, we aimed to compare the efficacy of patient-controlled analgesia with remifentanil or sufentanil for pain management after coronary artery bypass grafting. 249 patients who underwent coronary artery bypass were randomly assigned to receive patient-controlled analgesia with remifentanil or sufentanil during the first 24 h postoperatively. Pain intensity during patient-controlled analgesia was assessed using 4 different pain rating scales. patients given remifentanil had lower Visual Analog Scale scores at 24 h compared to those given sufentanil (p = 0.002). The Numeric Rating Scale at 24 h was also significantly lower in patients using remifentanil (p = 0.004). The Faces Pain Scale scores at 4, 18, and 24 h were significantly lower in patients using remifentanil compared to those using sufentanil (p = 0.045, 0.036, and 0.011, respectively). No significant differences between groups were seen in the pain intensity assessed by the Behavior Rating Scale at any time point during the first 24 h postoperatively. our study showed that both remifentanil and sufentanil patient-controlled analgesia can provide acceptable analgesia after coronary artery bypass. The difference between their efficacies was inconspicuous until 24 h postoperatively. Remifentanil seems to result in better pain relief at 24 h postoperatively. © The Author(s) 2013 Reprints and permissions: sagepub.co.uk/journalsPermissions.nav.

  5. Deoxypyrimidine monophosphate bypass therapy for thymidine kinase 2 deficiency

    OpenAIRE

    Garone, Caterina; Garc??a-D??az, Beatriz; Emmanuele, Valentina; L??pez Garc??a, Luis Carlos; Tadesse, Saba; Akman, Hasan O.; Tanji, Kurenai; Quinzii, Catarina M.; Hirano, Michio

    2014-01-01

    Autosomal recessive mutations in the thymidine kinase 2 gene (TK2) cause mitochondrial DNA depletion, multiple deletions, or both due to loss of TK2 enzyme activity and ensuing unbalanced deoxynucleotide triphosphate (dNTP) pools. To bypass Tk2 deficiency, we administered deoxycytidine and deoxythymidine monophosphates (dCMP+dTMP) to the Tk2 H126N (Tk2 −/− ) knock-in mouse model from postnatal day 4, when mutant mice are phenotypically normal, but biochemically affected. Assessment of 13-day-...

  6. Sen perforation af tyndtarm efter laparoskopisk gastrisk bypass

    DEFF Research Database (Denmark)

    Spanager, Lene; Sigild, Ulf Henrik; Neuenschwander, Anders Ulrich

    2010-01-01

    We present two cases in which the patients were admitted to a local hospital with acute abdominal pain four or five months after having undergone laparoscopic gastric bypass. In both cases, operation revealed a perforation of the small bowel close to the distal anastomosis. In the first case......, a massive constipation of the small bowel was most likely a contributing factor. In the second case, the cause was a kink of the entero-entero anastomosis leading to obstruction and finally perforation of the biliary limp. Late perforations are among the rarely reported complications associated with gastric...

  7. Vacuum-assisted drainage in cardiopulmonary bypass: advantages and disadvantages.

    Science.gov (United States)

    Carvalho Filho, Elio Barreto de; Marson, Fernando Augusto de Lima; Costa, Loredana Nilkenes Gomes da; Antunes, Nilson

    2014-01-01

    Systematic review of vacuum assisted drainage in cardiopulmonary bypass, demonstrating its advantages and disadvantages, by case reports and evidence about its effects on microcirculation. We conducted a systematic search on the period 1997-2012, in the databases PubMed, Medline, Lilacs and SciELO. Of the 70 selected articles, 26 were included in the review. Although the vacuum assisted drainage has significant potential for complications and requires appropriate technology and professionalism, prevailed in literature reviewed the concept that vacuum assisted drainage contributed in reducing the rate of transfusions, hemodilutions, better operative field, no significant increase in hemolysis, reduced complications surgical, use of lower prime and of smaller diameter cannulas.

  8. Cost Benefit Analysis: Bypass of Prešov city

    Directory of Open Access Journals (Sweden)

    Margorínová Martina

    2017-01-01

    Full Text Available The paper describes decision making process based on economic evaluation, i.e. Cost Benefit Analysis for motorway bypass of the Prešov city. Three variants were evaluated by means of the Highway Development and Management Tool (HDM-4. HDM-4 is a software system for evaluating options for investing in road transport infrastructure. Vehicle operating costs and travel time costs were monetized with the use of the software. The investment opportunities were evaluated in terms of Cost Benefit Analysis results, i.e. economic indicators.

  9. Return to the workforce following coronary artery bypass grafting

    DEFF Research Database (Denmark)

    Butt, Jawad H; Rørth, Rasmus; Kragholm, Kristian

    2018-01-01

    Background Returning to the workforce after coronary artery bypass grafting (CABG) holds important socioeconomic consequences not only for patients, but the society as well. Yet data on this issue are limited. We examined return to the workforce and associated factors in patients of working age.......0%) patients had returned to the workforce, 614 (10.2%) were on paid sick leave, 267 (4.4%) received disability pension, 250 (4.1%) were on early retirement, 57 (0.9%) had died, and 16 (0.3%) had emigrated. Factors associated with return to the workforce were identified using multivariable logistic regression...

  10. Incidental invasive thymoma during coronary artery bypass surgery

    International Nuclear Information System (INIS)

    Al-Smady, Moaath M.; Hammdan, Farouq F.; Abu-Abeeleh, Mahmood M.; Massad, Islam M.

    2009-01-01

    We encountered 2 incidental cases of invasive thymomas at Jordan University Hospital, Amman, Jordan: during the routine coronary artery bypass graft surgery between 2005 and 2008 with an incidence of 0.6%. Both patients presented with angina pain. None of the 2 patients had pressure symptoms (cough, shortness of breath or superior vena cava syndrome) or Myasthenia Gravis symptoms. Total thyectomy with dissection of perithymic fat was performed on both cases. No radiotherapy was given. No recurrence of the tumor was seen in 2 years follow-up. These cases are presented to emphasize the occurrence of this tumor. (author)

  11. Reconstructive surgery after jejunoileal bypass or gastric partition operations.

    Science.gov (United States)

    Bingham, H G

    1982-05-01

    Twenty-five morbidly obese patients had plastic operations to remove redundant tissue after either jejunoileal bypass or gastric partition. The average weight loss in this group of patients was 79.9 kg (176 lb) and the average age was 32 years. Abdominoplasty was the most common operation, and, although there was no mortality, postoperative complications were common and usually related to wound healing. The average hospital stay was ten days. Most of these patients were pleased with their results and lived happier and more productive lives.

  12. Cine CT in the evaluation of coronary bypass graft patency

    International Nuclear Information System (INIS)

    Stanford, W.; Rooholamini, M.; Rumberger, J.; Marcus, M.; Hiratzka, L.

    1986-01-01

    Cine CT produces axial images over an 8-cm section of the aorta in 50 msec. This characteristic makes the technique useful for evaluating coronary bypass graft (CBG) patency. With the use of 40 ml of 67% iothalamate sodium injected via an antecubital vein, 28 patients with 68 CBGs underwent cine CT. Ten patients with 21 CBGs also underwent cardiac catheterization. In the latter group the overall accuracy of cine CT compared to cardiac catheterization was 95.2% (20/21). The sensitivity was 94.1% (16/17), and the specificity was 100% (4/4). This figure compares favorably with the 92% sensitivity achieved with conventional CT

  13. PCNA mono-ubiquitination and activation of translesion DNA polymerases by DNA polymerase {alpha}.

    Science.gov (United States)

    Suzuki, Motoshi; Niimi, Atsuko; Limsirichaikul, Siripan; Tomida, Shuta; Miao Huang, Qin; Izuta, Shunji; Usukura, Jiro; Itoh, Yasutomo; Hishida, Takashi; Akashi, Tomohiro; Nakagawa, Yoshiyuki; Kikuchi, Akihiko; Pavlov, Youri; Murate, Takashi; Takahashi, Takashi

    2009-07-01

    Translesion DNA synthesis (TLS) involves PCNA mono-ubiquitination and TLS DNA polymerases (pols). Recent evidence has shown that the mono-ubiquitination is induced not only by DNA damage but also by other factors that induce stalling of the DNA replication fork. We studied the effect of spontaneous DNA replication errors on PCNA mono-ubiquitination and TLS induction. In the pol1L868F strain, which expressed an error-prone pol alpha, PCNA was spontaneously mono-ubiquitinated. Pol alpha L868F had a rate-limiting step at the extension from mismatched primer termini. Electron microscopic observation showed the accumulation of a single-stranded region at the DNA replication fork in yeast cells. For pol alpha errors, pol zeta participated in a generation of +1 frameshifts. Furthermore, in the pol1L868F strain, UV-induced mutations were lower than in the wild-type and a pol delta mutant strain (pol3-5DV), and deletion of the RAD30 gene (pol eta) suppressed this defect. These data suggest that nucleotide misincorporation by pol alpha induces exposure of single-stranded DNA, PCNA mono-ubiquitination and activates TLS pols.

  14. Active RNA polymerases: mobile or immobile molecular machines?

    Directory of Open Access Journals (Sweden)

    Argyris Papantonis

    2010-07-01

    Full Text Available It is widely assumed that active RNA polymerases track along their templates to produce a transcript. We test this using chromosome conformation capture and human genes switched on rapidly and synchronously by tumour necrosis factor alpha (TNFalpha; one is 221 kbp SAMD4A, which a polymerase takes more than 1 h to transcribe. Ten minutes after stimulation, the SAMD4A promoter comes together with other TNFalpha-responsive promoters. Subsequently, these contacts are lost as new downstream ones appear; contacts are invariably between sequences being transcribed. Super-resolution microscopy confirms that nascent transcripts (detected by RNA fluorescence in situ hybridization co-localize at relevant times. Results are consistent with an alternative view of transcription: polymerases fixed in factories reel in their respective templates, so different parts of the templates transiently lie together.

  15. Backtracking dynamics of RNA polymerase: pausing and error correction

    Science.gov (United States)

    Sahoo, Mamata; Klumpp, Stefan

    2013-09-01

    Transcription by RNA polymerases is frequently interrupted by pauses. One mechanism of such pauses is backtracking, where the RNA polymerase translocates backward with respect to both the DNA template and the RNA transcript, without shortening the transcript. Backtracked RNA polymerases move in a diffusive fashion and can return to active transcription either by diffusive return to the position where backtracking was initiated or by cleaving the transcript. The latter process also provides a mechanism for proofreading. Here we present some exact results for a kinetic model of backtracking and analyse its impact on the speed and the accuracy of transcription. We show that proofreading through backtracking is different from the classical (Hopfield-Ninio) scheme of kinetic proofreading. Our analysis also suggests that, in addition to contributing to the accuracy of transcription, backtracking may have a second effect: it attenuates the slow down of transcription that arises as a side effect of discriminating between correct and incorrect nucleotides based on the stepping rates.

  16. MMS exposure promotes increased MtDNA mutagenesis in the presence of replication-defective disease-associated DNA polymerase γ variants.

    Science.gov (United States)

    Stumpf, Jeffrey D; Copeland, William C

    2014-10-01

    Mitochondrial DNA (mtDNA) encodes proteins essential for ATP production. Mutant variants of the mtDNA polymerase cause mutagenesis that contributes to aging, genetic diseases, and sensitivity to environmental agents. We interrogated mtDNA replication in Saccharomyces cerevisiae strains with disease-associated mutations affecting conserved regions of the mtDNA polymerase, Mip1, in the presence of the wild type Mip1. Mutant frequency arising from mtDNA base substitutions that confer erythromycin resistance and deletions between 21-nucleotide direct repeats was determined. Previously, increased mutagenesis was observed in strains encoding mutant variants that were insufficient to maintain mtDNA and that were not expected to reduce polymerase fidelity or exonuclease proofreading. Increased mutagenesis could be explained by mutant variants stalling the replication fork, thereby predisposing the template DNA to irreparable damage that is bypassed with poor fidelity. This hypothesis suggests that the exogenous base-alkylating agent, methyl methanesulfonate (MMS), would further increase mtDNA mutagenesis. Mitochondrial mutagenesis associated with MMS exposure was increased up to 30-fold in mip1 mutants containing disease-associated alterations that affect polymerase activity. Disrupting exonuclease activity of mutant variants was not associated with increased spontaneous mutagenesis compared with exonuclease-proficient alleles, suggesting that most or all of the mtDNA was replicated by wild type Mip1. A novel subset of C to G transversions was responsible for about half of the mutants arising after MMS exposure implicating error-prone bypass of methylated cytosines as the predominant mutational mechanism. Exposure to MMS does not disrupt exonuclease activity that suppresses deletions between 21-nucleotide direct repeats, suggesting the MMS-induce mutagenesis is not explained by inactivated exonuclease activity. Further, trace amounts of CdCl2 inhibit mtDNA replication but

  17. A domain of the Klenow fragment of Escherichia coli DNA polymerase I has polymerase but no exonuclease activity.

    Science.gov (United States)

    Freemont, P S; Ollis, D L; Steitz, T A; Joyce, C M

    1986-09-01

    The Klenow fragment of DNA polymerase I from Escherichia coli has two enzymatic activities: DNA polymerase and 3'-5' exonuclease. The crystal structure showed that the fragment is folded into two distinct domains. The smaller domain has a binding site for deoxynucleoside monophosphate and a divalent metal ion that is thought to identify the 3'-5' exonuclease active site. The larger C-terminal domain contains a deep cleft that is believed to bind duplex DNA. Several lines of evidence suggested that the large domain also contains the polymerase active site. To test this hypothesis, we have cloned the DNA coding for the large domain into an expression system and purified the protein product. We find that the C-terminal domain has polymerase activity (albeit at a lower specific activity than the native Klenow fragment) but no measurable 3'-5' exonuclease activity. These data are consistent with the hypothesis that each of the three enzymatic activities of DNA polymerase I from E. coli resides on a separate protein structural domain.

  18. Fuel temperature prediction using a variable bypass gap size in the prismatic VHTR

    International Nuclear Information System (INIS)

    Lee, Sung Nam; Tak, Nam-il; Kim, Min Hwan

    2016-01-01

    Highlights: • The bypass flow of the prismatic very high temperature reactor is analyzed. • The bypass gap sizes are calculated considering the effect of the neutron fluences and thermal expansion. • The fuel hot spot temperature and temperature profiles are calculated using the variable gap size. • The BOC, MOC and EOC condition at the cycle 07 and 14 are applied. - Abstract: The temperature gradient and hot spot temperatures were calculated in the prismatic very high temperature reactor as a function of the variable bypass gap size. Many previous studies have predicted the temperature of the reactor core based on a fixed bypass gap size. The graphite matrix of the assemblies in the reactor core undergoes a dimensional change during the operation due to thermal expansion and neutron fluence. The expansion and shrinkage of the bypass gaps change the coolant flow fractions into the coolant channels, the control rod holes, and the bypass gaps. Therefore, the temperature of the assemblies may differ compared to those for the fixed bypass gap case. The temperature gradient and the hot spot temperatures are important for the design of reactor structures to ensure their safety and efficiency. In the present study, the temperature variation of the PMR200 is studied at the beginning (BOC), middle (MOC), and end (EOC) of cycles 07 and 14. CORONA code which has been developed in KAERI is applied to solve the thermal-hydraulics of the reactor core of the PMR200. CORONA solves a fluid region using a one-dimensional formulation and a solid region using a three-dimensional formulation to enhance the computational speed and still obtain a reasonable accuracy. The maximum temperatures in the fuel assemblies using the variable bypass gaps did not differ much from the corresponding temperatures using the fixed bypass gaps. However, the maximum temperatures in the reflector assemblies using the variable bypass gaps differ significantly from the corresponding temperatures

  19. The yeast Saccharomyces cerevisiae DNA polymerase IV: possible involvement in double strand break DNA repair.

    OpenAIRE

    Leem, S H; Ropp, P A; Sugino, A

    1994-01-01

    We identified and purified a new DNA polymerase (DNA polymerase IV), which is similar to mammalian DNA polymerase beta, from Saccharomyces cerevisiae and suggested that it is encoded by YCR14C (POLX) on chromosome III. Here, we provided a direct evidence that the purified DNA polymerase IV is indeed encoded by POLX. Strains harboring a pol4 deletion mutation exhibit neither mitotic growth defect nor a meiosis defect, suggesting that DNA polymerase IV participates in nonessential functions in ...

  20. Results of The Comparative Study of 200 Cases: One Anastomosis Gastric Bypass vs Roux-en-Y Gastric Bypass.

    Science.gov (United States)

    Navarrete, Salvador; Leyba, José Luis; Ll, Salvador Navarrete; Borjas, Guillermo; Tapia, José León; Alcázar, Ruben

    2018-05-01

    Obesity has experienced worldwide increase and surgery has become the treatment that has achieved the best results. Several techniques have been described; the most popular are vertical gastrectomy (GV) and the Roux-en-Y gastric bypass (RYGB). However, mini-gastric bypass/one anastomosis gastric bypass (MGB/OAGB) has gained popularity due to its simplicity and good results. To comparatively evaluate the results of MGB/OAGB with those of RYGB with 1-year follow-up. The paper presents a comparative case and control study of 100 patients that underwent MGB/OAGB surgery and another 100 with RYGB surgery, operated between 2008 and 2016. Patients were not submitted to revision surgery and had the following pre-operative variables: age 40.46 ± 12.4 vs. 39.43 ± 10.33 years; sex 64 and 54 women, 36 and 46 men; BMI 44.8 ± 12.06 and 45.29 ± 8.82 kg/m 2 ; 50 and 54 cases with comorbidities, respectively, these being non-significant differences. The surgical time was 69.01 ± 4.62 (OAGB) vs. 88.98 ± 3.44 min; the time of hospitalization was 2 days, reaching a BMI of 27.7 ± 7.85 and 29 ± 4.52 kg/m 2 , with an excess weight loss 1 year after surgery of 89.4 vs. 85.9%, respectively. The morbidity rates are 9% for OAGB and 11% for the RYGB. There was a comorbidity resolution of 84.4 and 83.7% respectively, without mortality. The results show the benefits of both techniques, OAGB being the easiest to perform and with less surgical time.

  1. Perioperative outcomes in minimally invasive direct coronary artery bypass versus off-pump coronary artery bypass with sternotomy.

    Science.gov (United States)

    Tekin, Ali İhsan; Arslan, Ümit

    2017-09-01

    Surgical treatment of isolated left anterior descending coronary artery disease can be performed with either minimally invasive direct coronary artery bypass via a left anterior thoracotomy (MIDCAB) or off-pump coronary artery bypass via a median sternotomy (OPCAB). To compare the perioperative outcomes of patients undergoing MIDCAB or OPCAB surgery. Patients who underwent either MIDCAB or OPCAB for isolated left anterior descending (LAD) coronary artery disease between October 2013 and December 2015 were retrospectively evaluated. Operations were carried out by the same surgical team. Preoperative, intraoperative and postoperative data of the patients were recorded for analyses. Twenty-three patients (7 females, 16 males) underwent MIDCAB surgery, and 24 patients (4 female, 20 males) underwent OPCAB surgery. The two groups were comparable regarding preoperative patient characteristics. Duration of mechanical ventilation (5.1 ±0.7 h vs. 6.6 ±0.9 h), intensive care unit stay (19.4 ±2.5 h vs. 45.8 ±5.4 h) and hospital stay (4.3 ±0.4 days vs. 5.6 ±0.8 days) were significantly shorter in the MIDCAB group (p < 0.01). Patients in the OPCAB group required significantly more blood transfusions (1.83 ±0.38 units vs. 0.17 ±0.38 units) and fresh frozen plasma use (2.33 ±0.96 units vs. 0.69 ±0.76 units) (p < 0.01). Conversion to sternotomy was not required in the MIDCAB group. There was no mortality, conversion to cardiopulmonary bypass or serious complication in either group. We believe that the MIDCAB technique is more advantageous than the OPCAB technique in the treatment of patients with a critical LAD lesion.

  2. A new step in cement plant bypass technology; Une nouvelle avancee pour les by-pass en cimenterie

    Energy Technology Data Exchange (ETDEWEB)

    Civiel, G. [Technip, 92 - Rueil-Malmaison (France)

    2001-12-01

    The demand of valorizing more and more waste fuel in cement industry results in an increase of volatile element quantities in kiln system, particularly chlorine. In 'Ciment, Betons, Platres, Chaux' no 849 May-June 2001, we made reference to the two new approaches developed by TECHNIP CL to solve the problem of the volatile elements in clinker burning lines: the raw meal curtain and the Taiheyo by-pass. The following article is focused on the second system. (author)

  3. The impact of avoiding cardiopulmonary by-pass during coronary artery bypass surgery in elderly patients: the Danish On-pump Off-pump Randomisation Study (DOORS)

    DEFF Research Database (Denmark)

    Houlind, Kim; Kjeldsen, Bo Juul; Madsen, Susanne Nørgaard

    2009-01-01

    BACKGROUND: Coronary Artery Bypass Graft operation for ischemic heart disease provides improved quality of life and, in some patients, prolonged survival. Concern has, however, been raised about complications that may be related to the use of cardiopulmonary by-pass (CPB) and aortic cross......-clamping. It has been hypothesized that when coronary artery by-pass grafting is performed without the use of CPB, the rate of serious complications is reduced. METHODS/DESIGN: The trial is designed as an open, randomized, controlled, clinical trial with blinded assessment of end-points. Patients at or above 70...... years of age, referred for surgical myocardial revascularisation, are included and randomised to receive coronary artery by-pass grafting either with or without the use of CPB and aortic cross-clamping. Follow-up is performed by clinical, biochemical, electrocardiographic, and angiographic data...

  4. The effects of conventional extracorporeal circulation versus miniaturized extracorporeal circulation on microcirculation during cardiopulmonary bypass-assisted coronary artery bypass graft surgery

    NARCIS (Netherlands)

    Yuruk, Koray; Bezemer, Rick; Euser, Mariska; Milstein, Dan M. J.; de Geus, Hilde H. R.; Scholten, Evert W.; de Mol, Bas A. J. M.; Ince, Can

    2012-01-01

    OBJECTIVES: To reduce the complications associated with cardiopulmonary bypass (CPB) during cardiac surgery, many modifications have been made to conventional extracorporeal circulation systems. This trend has led to the development of miniaturized extracorporeal circulation systems. Cardiac surgery

  5. The problem of calcified ascending aorta during aortocoronary bypass

    Directory of Open Access Journals (Sweden)

    Nežić Duško G.

    2004-01-01

    Full Text Available Heavily calcified ascending aorta significantly increased morbidity and lethality during open-heart surgery. Cannulation and clamping (partial or total of severely atherosclerotic ascending aorta can easily cause damage and rupture of aortic wall, with consequential distal (often fatal embolization with atheromatous debris (brain, myocardium. From June 1998. until June 2000, 11 of 2 136 (0.5% patients who underwent coronary artery bypass grafting were with the severe atheromatous ascending aorta. The site of cannulation was in the aortic arch in three patients (aorta was occluded with Foley catheter in one case, and single clamp technique was used in the other two cases. The femoral artery was the cannulation site in other five cases. Profound hypothermia, ventricular fibrillation, and circulatory arrest, with no cross-clamping or cardioplegia, were used in three patients. Two patients were operated on with extracorporeal circulation, one in normothermia, on the beating heart, the other in moderate hypothermia, on fibrillating heart. In three patients myocardial revascularization was performed on the beating heart, in normothermia, without extracorporeal circulation. Postoperative course was uneventful in all 11 patients. Neither atheroembolism in the peripheral organs, nor atheroembolism of the extramities occurred. The proposed surgical approaches have the potential to reduce the prevalence of stroke and systemic embolization associated with coronary artery bypass grafting in patients with heavily calcified ascending aorta. This result was achieved due to the applied modifications of standard cardiosurgical technique.

  6. Plasma magnesium concentration in patients undergoing coronary artery bypass grafting.

    Science.gov (United States)

    Kotlinska-Hasiec, Edyta; Makara-Studzinska, Marta; Czajkowski, Marek; Rzecki, Ziemowit; Olszewski, Krzysztof; Stadnik, Adam; Pilat, Jacek; Rybojad, Beata; Dabrowski, Wojciech

    2017-05-11

    [b]Introduction[/b]. Magnesium (Mg) plays a crucial role in cell physiology and its deficiency may cause many disorders which often require intensive treatment. The aim of this study was to analyse some factors affecting preoperative plasma Mg concentration in patients undergoing coronary artery bypass grafting (CABG). [b]Materials and method[/b]. Adult patients scheduled for elective CABG with cardio-pulmonary bypass (CPB) under general anaesthesia were studied. Plasma Mg concentration was analysed before surgery in accordance with age, domicile, profession, tobacco smoking and preoperative Mg supplementation. Blood samples were obtained from the radial artery just before the administration of anaesthesia. [b]Results. [/b]150 patients were studied. Mean preoperative plasma Mg concentration was 0.93 ± 0.17 mmol/L; mean concentration in patients - 1.02 ± 0.16; preoperative Mg supplementation was significantly higher than in patients without such supplementation. Moreover, intellectual workers supplemented Mg more frequently and had higher plasma Mg concentration than physical workers. Plasma Mg concentration decreases in elderly patients. Patients living in cities, on average, had the highest plasma Mg concentration. Smokers had significantly lower plasma Mg concentration than non-smokers. [b]Conclusions. [/b]1. Preoperative magnesium supplementation increases its plasma concentration. 2. Intellectual workers frequently supplement magnesium. 3. Smoking cigarettes decreases plasma magnesium concentration.

  7. Proliferative and morphologic changes in rat colon following bypass surgery.

    Science.gov (United States)

    Barkla, D H; Tutton, P J

    1985-06-01

    In this study the proliferative and morphologic changes that occur in the colon of normal and dimethylhydrazine-treated rats following surgical bypass of the middle third of the colon are reported. Proliferative changes were measured by estimating accumulated mitotic indexes following vinblastine treatment and morphologic changes were observed with the use of light microscopy and scanning electron microscopy. Data were collected on Days 0, 7, 14, 30, and 72 after surgery. The results show that surgical bypass produces contrasting effects in the segments proximal to and distal to the suture line. In the proximal segment there was morphologic evidence of hyperplasia, although proliferative activity was unchanged except for an increase at 7 days in normal rats. In the distal segment there was a long-lived increase in the mitotic index, although morphologic changes were not seen. The results for DMH-treated rats were similar to those in normal rats. Groups of isolated dysplastic epithelial cells were often seen in the submucosa adjacent to sutures up to 72 days after surgery. Increased lymphoid infiltration was seen in segments proximal to but not distal to the suture line. It is hypothesized that the different responses of the proximal and distal segments may be related to the different embryologic origins of those segments. It is also hypothesized that the seeding of the submucosa with epithelial cells during suturing may be a factor in tumor recurrence.

  8. Impact of gender on outcome after coronary artery bypass surgery.

    Science.gov (United States)

    Ennker, Ina C; Albert, Alexander; Pietrowski, Detlef; Bauer, Kerstin; Ennker, Juergen; Florath, Ines

    2009-06-01

    Following recent studies concerning the increased risk of coronary artery bypass surgery for women, the impact of sex is still a controversial issue. Between 1996 and 2006, 9,527 men and 3,079 women underwent isolated coronary artery bypass in our institute. To adjust for dissimilarities in preoperative risk profiles, propensity score-based matching was applied. Before adjustment, clinical outcomes in terms of operative mortality, arrhythmias, intensive care unit stay, and maximum creatine kinase-MB levels were significantly different for men and women. After balancing the preoperative characteristics, including height, no significant differences in clinical outcomes were observed. However, there was decreased use of internal mammary artery, less total arterial revascularization, and increasing creatine kinase-MB levels with decreasing height. This study supports the theory that female sex per se does not increase operative risk, but shorter height, which is more common in women, affects the outcome, probably due to technical difficulties in shorter patients with smaller internal mammary arteries and coronary vessels. Thus women may especially benefit from sequential arterial grafting.

  9. Anesthesia for off-pump coronary artery bypass surgery

    Directory of Open Access Journals (Sweden)

    Thomas M Hemmerling

    2013-01-01

    Full Text Available The evolution of techniques and knowledge of beating heart surgery has led anesthesia toward the development of new procedures and innovations to promote patient safety and ensure high standards of care. Off-pump coronary artery bypass (OPCAB surgery has shown to have some advantages compared to on-pump cardiac surgery, particularly the reduction of postoperative complications including systemic inflammation, myocardial injury, and cerebral injury. Minimally invasive surgery for single vessel OPCAB through a limited thoracotomy incision can offer the advantage of further reduction of complications. The anesthesiologist has to deal with different issues, including hemodynamic instability and myocardial ischemia during aorto-coronary bypass grafting. The anesthesiologist and surgeon should collaborate and plan the best perioperative strategy to provide optimal care and ensure a rapid and complete recovery. The use of high thoracic epidural analgesia and fast-track anesthesia offers particular benefits in beating heart surgery. The excellent analgesia, the ability to reduce myocardial oxygen consumption, and the good hemodynamic stability make high thoracic epidural analgesia an interesting technique. New scenarios are entering in cardiac anesthesia: ultra-fast-track anesthesia with extubation in the operating room and awake surgery tend to be less invasive, but can only be performed on selected patients.

  10. Myocardial contractile function in survived neonatal piglets after cardiopulmonary bypass

    Directory of Open Access Journals (Sweden)

    Popov Aron-Frederik

    2010-11-01

    Full Text Available Abstract Background Hemodynamic function may be depressed in the early postoperative stages after cardiac surgery. The aim of this study was the analysis of the myocardial contractility in neonates after cardiopulmonary bypass (CPB and mild hypothermia. Methods Three indices of left ventricular myocardial contractile function (dP/dt, (dP/dt/P, and wall thickening were studied up to 6 hours after CPB in neonatal piglets (CPB group; n = 4. The contractility data were analysed and then compared to the data of newborn piglets who also underwent median thoracotomy and instrumentation for the same time intervals but without CPB (non-CPB group; n = 3. Results Left ventricular dP/dtmax and (dP/dtmax/P remained stable in CPB group, while dP/dtmax decreased in non-CPB group 5 hours postoperatively (1761 ± 205 mmHg/s at baseline vs. 1170 ± 205 mmHg/s after 5 h; p max and (dP/dtmax/P there were no statistically significant differences between the two groups. Comparably, although myocardial thickening decreased in the non-CPB group the differences between the two groups were not statistically significant. Conclusions The myocardial contractile function in survived neonatal piglets remained stable 6 hours after cardiopulmonary bypass and mild hypothermia probably due to regional hypercontractility.

  11. Surgical revascularization of posterior coronary arteries without cardiopulomonary bypass

    Directory of Open Access Journals (Sweden)

    Lobo Filho J. Glauco

    1999-01-01

    Full Text Available OBJECTIVE: To assess the results observed during the early postoperative period in patients who had the posterior coronary arteries revascularized without cardiopulmonary bypass (CPB, in regard to the following parameters: age, sex,bypass grafts types, morbidity and mortality. METHODS: From January 1995 to June 1998, 673 patients underwent myocardial revascularization (MR. Of this total, 607 (90.20% MR procedures were performed without CPB. The posterior coronary arteries (PCA were revascularized in 298 (44.27% patients, 280 (93.95% without CPB. The age of the patients ranged from 37 to 88 years (mean, 61 years. The male gender predominated, with 198 men (70.7%. The revascularization of the posterior coronary arteries had the following distribution: diagonalis artery (31 patients, 10%; marginal branches of the circumflex artery (243 patients, 78.7%; posterior ventricular artery (4 patients, 1.3%; and posterior descending artery (31 patients, 10%. RESULTS: Procedure-related complications without death occurred in 7 cases, giving a morbidity of 2.5%. There were 11 deaths in the early postoperative period (mortality of 3.9%. CONCLUSION: Similarly to the anterior coronary arteries, the posterior coronary arteries may benefit from myocardial revascularization without CPB.

  12. Evaluation of olfactory memory after coronary artery bypass grafting.

    Science.gov (United States)

    Erdem, Kemalettin; Yurttas, Veysel; Bilgi, Murat; Demırhan, Abdullah; Apuhan, Tayfun; Bugra, Onursal; Daglar, Bahadir

    2014-12-01

    This study determined whether coronary artery bypass grafting (CABG) surgery has any effect on olfactory function, employing the Brief Smell Identification Test (B-SIT). All the participants were informed preoperatively about the B-SIT test and the mode of its application. The test was performed by each patient preoperatively (d0) as well as 1 (d1) and 3 (d3) days following the surgery. C-reactive protein (CRP) levels were recorded at the same time as the smell test. This prospective study included 45 patients. The mean age was 67 ± 7.55, and the group was 29% male. The mean durations of cross clamping and cardiopulmonary bypass were 54 ± 32 min and 62.5 ± 37.0 min, respectively. Eleven different odors were tested. Significant differences were observed for several odors: leather between d0 and d3, pine between d0 and d3, onion between d0 and d1, onion between d0 and d3, and soap between d0 and d1. The postoperative CRP levels were significantly higher than the preoperative levels. The correlation analysis determined that the postoperative CRP levels were negatively correlated with the B-SIT score (r = -0.48, p = 0.001). Our findings suggest that patients after CABG are prone to develop olfactory dysfunction in the early postoperative period and that olfactory dysfunction is associated with postoperative CRP levels.

  13. Error-Prone Translesion DNA Synthesis by Escherichia coli DNA Polymerase IV (DinB on Templates Containing 1,2-dihydro-2-oxoadenine

    Directory of Open Access Journals (Sweden)

    Masaki Hori

    2010-01-01

    Full Text Available Escherichia coli DNA polymerase IV (Pol IV is involved in bypass replication of damaged bases in DNA. Reactive oxygen species (ROS are generated continuously during normal metabolism and as a result of exogenous stress such as ionizing radiation. ROS induce various kinds of base damage in DNA. It is important to examine whether Pol IV is able to bypass oxidatively damaged bases. In this study, recombinant Pol IV was incubated with oligonucleotides containing thymine glycol (dTg, 5-formyluracil (5-fodU, 5-hydroxymethyluracil (5-hmdU, 7,8-dihydro-8-oxoguanine (8-oxodG and 1,2-dihydro-2-oxoadenine (2-oxodA. Primer extension assays revealed that Pol IV preferred to insert dATP opposite 5-fodU and 5-hmdU, while it inefficiently inserted nucleotides opposite dTg. Pol IV inserted dCTP and dATP opposite 8-oxodG, while the ability was low. It inserted dCTP more effectively than dTTP opposite 2-oxodA. Pol IV's ability to bypass these lesions decreased in the order: 2-oxodA > 5-fodU~5-hmdU > 8-oxodG > dTg. The fact that Pol IV preferred to insert dCTP opposite 2-oxodA suggests the mutagenic potential of 2-oxodA leading to A:T→G:C transitions. Hydrogen peroxide caused an ~2-fold increase in A:T→G:C mutations in E. coli, while the increase was significantly greater in E. coli overexpressing Pol IV. These results indicate that Pol IV may be involved in ROS-enhanced A:T→G:C mutations.

  14. DNA polymerases κ and ζ cooperatively perform mutagenic translesion synthesis of the C8–2′-deoxyguanosine adduct of the dietary mutagen IQ in human cells

    Science.gov (United States)

    Bose, Arindam; Pande, Paritosh; Jasti, Vijay P.; Millsap, Amy D.; Hawkins, Edward K.; Rizzo, Carmelo J.; Basu, Ashis K.

    2015-01-01

    The roles of translesion synthesis (TLS) DNA polymerases in bypassing the C8–2′-deoxyguanosine adduct (dG-C8-IQ) formed by 2-amino-3-methylimidazo[4,5-f]quinoline (IQ), a highly mutagenic and carcinogenic heterocyclic amine found in cooked meats, were investigated. Three plasmid vectors containing the dG-C8-IQ adduct at the G1-, G2- or G3-positions of the NarI site (5′-G1G2CG3CC-3′) were replicated in HEK293T cells. Fifty percent of the progeny from the G3 construct were mutants, largely G→T, compared to 18% and 24% from the G1 and G2 constructs, respectively. Mutation frequency (MF) of dG-C8-IQ was reduced by 38–67% upon siRNA knockdown of pol κ, whereas it was increased by 10–24% in pol η knockdown cells. When pol κ and pol ζ were simultaneously knocked down, MF of the G1 and G3 constructs was reduced from 18% and 50%, respectively, to IQ. We conclude that pol κ and pol ζ cooperatively carry out the majority of the error-prone TLS of dG-C8-IQ, whereas pol η is involved primarily in its error-free bypass. PMID:26220181

  15. No major differences in 30-day outcomes in high-risk patients randomized to off-pump versus on-pump coronary bypass surgery: the best bypass surgery trial

    DEFF Research Database (Denmark)

    Møller, Christian H; Perko, Mario J; Lund, Jens T

    2010-01-01

    Off-pump coronary artery bypass grafting compared with coronary revascularization with cardiopulmonary bypass seems safe and results in about the same outcome in low-risk patients. Observational studies indicate that off-pump surgery may provide more benefit in high-risk patients. Our objective...... was to compare 30-day outcomes in high-risk patients randomized to coronary artery bypass grafting without or with cardiopulmonary bypass....

  16. α,β-D-constrained nucleic acids are strong terminators of thermostable DNA polymerases in polymerase chain reaction.

    Directory of Open Access Journals (Sweden)

    Olivier Martínez

    Full Text Available (S(C5', R(P α,β-D- Constrained Nucleic Acids (CNA are dinucleotide building blocks that can feature either B-type torsional angle values or non-canonical values, depending on their 5'C and P absolute stereochemistry. These CNA are modified neither on the nucleobase nor on the sugar structure and therefore represent a new class of nucleotide with specific chemical and structural characteristics. They promote marked bending in a single stranded DNA so as to preorganize it into a loop-like structure, and they have been shown to induce rigidity within oligonucleotides. Following their synthesis, studies performed on CNA have only focused on the constraints that this family of nucleotides introduced into DNA. On the assumption that bending in a DNA template may produce a terminator structure, we investigated whether CNA could be used as a new strong terminator of polymerization in PCR. We therefore assessed the efficiency of CNA as a terminator in PCR, using triethylene glycol phosphate units as a control. Analyses were performed by denaturing gel electrophoresis and several PCR products were further analysed by sequencing. The results showed that the incorporation of only one CNA was always skipped by the polymerases tested. On the other hand, two CNA units always stopped proofreading polymerases, such as Pfu DNA polymerase, as expected for a strong replication terminator. Non-proofreading enzymes, e.g. Taq DNA polymerase, did not recognize this modification as a strong terminator although it was predominantly stopped by this structure. In conclusion, this first functional use of CNA units shows that these modified nucleotides can be used as novel polymerization terminators of proofreading polymerases. Furthermore, our results lead us to propose that CNA and their derivatives could be useful tools for investigating the behaviour of different classes of polymerases.

  17. Myocardial metabolism during anaesthesia with propofol--low dose fentanyl for coronary artery bypass surgery

    NARCIS (Netherlands)

    Vermeyen, K. M.; de Hert, S. G.; Erpels, F. A.; Adriaensen, H. F.

    1991-01-01

    We have studied the haemodynamic and myocardial effects of propofol-fentanyl anaesthesia in 12 patients undergoing coronary artery bypass surgery during the pre-bypass period. The induction dose of propofol was 1.5 mg kg-1 and mean infusion rate during maintenance was 4.48 mg kg-1 h-1 (range

  18. 40 CFR 63.1569 - What are my requirements for HAP emissions from bypass lines?

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 12 2010-07-01 2010-07-01 true What are my requirements for HAP emissions from bypass lines? 63.1569 Section 63.1569 Protection of Environment ENVIRONMENTAL PROTECTION... HAP emissions from bypass lines? (a) What work practice standards must I meet? (1) You must meet each...

  19. 40 CFR 63.307 - Standards for bypass/bleeder stacks.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 9 2010-07-01 2010-07-01 false Standards for bypass/bleeder stacks. 63.307 Section 63.307 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS... Standards for Coke Oven Batteries § 63.307 Standards for bypass/bleeder stacks. (a)(1) Except as otherwise...

  20. Effective void fraction for a BWR assembly with boiling in the bypass region

    International Nuclear Information System (INIS)

    Galperin, A.; Segev, M.; Knoglinger, E.

    1991-09-01

    Average BWR assembly cross-sections for nominal conditions, namely for zero bypass void, can be utilised in the analysis of transient conditions with boiling in the bypass. A model is developed to yield an effective channel void for such conditions. The use of this void in conjunction with the 'nominal conditions' cross section library approximately preserves the assembly K-infinity corresponding to the true channel and bypass voids. The effective void is an augmentation of the actual channel void. The augment is proportional to the bypass-to-channel volume ratio, to the bypass void, and to a weight W which is introduced to quantify the fact that a water molecule in the bypass has a different assembly criticality worth than one in the channel. The formula developed is superior to the practice of choosing W=1, namely a simple, non-weighted, transfer of water from channel to bypass. The use of this approximate effective channel void reproduces actual K-infinity values of assemblies to better than 5 mk, whereas the use of a simple model sometimes misspredicts the assembly K-infinity by 40 mK. The effective void model cannot handle cases in which both channel and bypass void value are high, simply because then the effective void α ch eff becomes meaningless. A method to treat the α eff >1 domain is developed by which corrections to cross sections are provided. Such corrections are synthesised as functions of the assembly parameters. (author) figs., tabs., refs